/ en /news/new-dna-sequencing-technique-preserves-cells%E2%80%99-locations-within-tissues <span class="field field--name-title field--type-string field--label-hidden"><h1>New DNA sequencing technique preserves cells’ locations within tissues</h1> </span> <span class="field field--name-uid field--type-entity-reference field--label-hidden"> <span>By Tom Ulrich</span> </span> <span class="field field--name-created field--type-created field--label-hidden"><time datetime="2021-12-15T11:05:12-05:00" class="datetime">December 15, 2021</time> </span> <div class="hero-section container"> <div class="hero-section__row row"> <div class="hero-section__content hero-section__content_left col-6"> <div class="hero-section__breadcrumbs"> <div class="block block-layout-builder block-extra-field-blocknodenewsbreadcrumbs"> <nav class="breadcrumb" role="navigation" aria-labelledby="system-breadcrumb"> <h2 id="system-breadcrumb" class="visually-hidden">Breadcrumb</h2> <ol> <li> <a href="/">Home</a> </li> <li> <a href="/news">News</a> </li> </ol> </nav> </div> </div> <div class="hero-section__title"> <div class="block block-layout-builder block-field-blocknodenewstitle"> <span class="field field--name-title field--type-string field--label-hidden"><h1>New DNA sequencing technique preserves cells’ locations within tissues</h1> </span> </div> </div> <div class="hero-section__description"> <div class="block block-layout-builder block-field-blocknodenewsbody"> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><div class="summary-only"> <p> Slide-DNA-seq helps researchers better understand spatial differences and patterns in complex tissues such as tumors.</p> </div> </div> </div> </div> <div class="hero-section__author"> <div class="block block-layout-builder block-extra-field-blocknodenewsextra-field-author-custom"> By Jessica Lau, Harvard Department of Stem Cell and Regenerative Biology </div> </div> <div class="hero-section__date"> <div class="block block-layout-builder block-field-blocknodenewscreated"> <span class="field field--name-created field--type-created field--label-hidden"><time datetime="2021-12-15T11:05:12-05:00" class="datetime">December 15, 2021</time> </span> </div> </div> </div> <div class="hero-section__right col-6"> <div class="hero-section__image"> <div class="block block-layout-builder block-field-blocknodenewsfield-image"> <div class="field field--name-field-image field--type-entity-reference field--label-hidden field__item"> <article class="media media--type-image media--view-mode-multiple-content-types-header"> <div class="field field--name-field-media-image field--type-image field--label-hidden field__item"> <picture> <source srcset="/files/styles/multiple_ct_header_desktop_xl/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=Mj-O2mVa 1x" media="all and (min-width: 1921px)" type="image/png" width="754" height="503"> <source srcset="/files/styles/multiple_ct_header_desktop_xl/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=Mj-O2mVa 1x" media="all and (min-width: 1601px) and (max-width: 1920px)" type="image/png" width="754" height="503"> <source srcset="/files/styles/multiple_ct_header_desktop/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=ZBfVHHl3 1x" media="all and (min-width: 1340px) and (max-width: 1600px)" type="image/png" width="736" height="520"> <source srcset="/files/styles/multiple_ct_header_laptop/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=NQXuPw1V 1x" media="all and (min-width: 800px) and (max-width: 1339px)" type="image/png" width="641" height="451"> <source srcset="/files/styles/multiple_ct_header_tablet/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=vEqZYhdy 1x" media="all and (min-width: 540px) and (max-width: 799px)" type="image/png" width="706" height="417"> <source srcset="/files/styles/multiple_ct_header_phone/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=raZa4Wiq 1x" media="all and (max-width: 539px)" type="image/png" width="499" height="294"> <img loading="eager" width="499" height="294" src="/files/styles/multiple_ct_header_phone/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=raZa4Wiq" alt="An image of how slide-DNA-seq &quot;sees&quot; cells' organization within a tumor." title="An image of how slide-DNA-seq &quot;sees&quot; cells' organization within a tumor." typeof="foaf:Image"> </picture> </div> <div class="media-caption"> <div class="media-caption__credit"> Credit: <a href="https://www.nature.com/articles/s41586-021-04217-4" target="_blank">Zhao T, Chiang Z, et al. <em>Nature</em>, 2021</a> </div> <div class="media-caption__description"> An image of how slide-DNA-seq "sees" cells' organization within a tumor. </div> </div> </article> </div> </div> </div> </div> </div> </div> <div class="content-section content-section_with-sidebars container"> <div class="row"> <div class="content-section__left col-2"> <div class="block block-better-social-sharing-buttons block-social-sharing-buttons-block"> <div style="display: none"><link rel="preload" href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg" as="image" type="image/svg+xml" crossorigin="anonymous"></div> <div class="social-sharing-buttons"> <a href="https://www.facebook.com/sharer/sharer.php?u=/taxonomy/term/592/feed&amp;title=" target="_blank" title="Share to Facebook" aria-label="Share to Facebook" class="social-sharing-buttons-button share-facebook" rel="noopener"> <svg aria-hidden="true" width="32px" height="32px" style="border-radius:100%;"> <use href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg#facebook" /> </svg> </a> <a href="https://twitter.com/intent/tweet?text=+/taxonomy/term/592/feed" target="_blank" title="Share to X" aria-label="Share to X" class="social-sharing-buttons-button share-x" rel="noopener"> <svg aria-hidden="true" width="32px" height="32px" style="border-radius:100%;"> <use href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg#x" /> </svg> </a> <a href="mailto:?subject=&amp;body=/taxonomy/term/592/feed" title="Share to Email" aria-label="Share to Email" class="social-sharing-buttons-button share-email" target="_blank" rel="noopener"> <svg aria-hidden="true" width="32px" height="32px" style="border-radius:100%;"> <use href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg#email" /> </svg> </a> </div> </div> </div> <div class="content-section__main col-8"> <div class="block block-layout-builder block-field-blocknodenewsbody"> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><p> Within complex tissues such as cancer tumors, individual cells can vary widely from each other. Internally, cancer cells can develop unique DNA mutations and genomic changes, potentially leading to drug resistance, metastasis, or relapse. Externally, the cells’ specific locations within the tissue also matter, since the local structure of a tumor and its surrounding tissues can affect cell state and drug permeability.</p> <p> To measure both genetic and local factors at the same time, researchers from Harvard University’s Department of Stem Cell and Regenerative Biology (HSCRB) and the Ó³»­´«Ã½ of MIT and Harvard developed a new technique of spatially-resolved DNA sequencing, called slide-DNA-seq. When further combined with spatially-resolved gene expression analysis, the technology gives researchers a better understanding of cancer progression and potential treatment.</p> <p> The researchers’ findings are published in the journal <a href="https://www.nature.com/articles/s41586-021-04217-4" target="_blank"><em>Nature</em></a>.</p> <p> Slide-DNA-seq analyzes slices of intact tissue, in which each cell remains in its original location — as opposed to conventional sequencing techniques, where cells are dissociated before DNA extraction. The researchers used microbeads, each tagged with a unique spatial barcode and bound to specially-prepared glass slides, to capture DNA from the tissue.&nbsp;</p> <p> "Each bead is about the size of a cell," said co-corresponding author&nbsp;<a href="/node/113836">Fei Chen</a>, who is an assistant professor in HSCRB and a core institute member at the Ó³»­´«Ã½. "Together, they are like individual pixels on a camera which takes snapshots of genomic alterations within each cell in the tissue."</p> <p> After measuring genomic changes, the researchers applied a related&nbsp;<a href="/node/488166">RNA-based Slide-seq method</a>&nbsp;Chen and collaborators developed in 2019, which used gene expression profiles to identify and map the locations of cell types and subtypes within a tissue slice.&nbsp;&nbsp;</p> <p> "We can use the same barcoded beads to capture the transcriptome from each cell, and combine these two measurements into a multi-modal image," Chen said.&nbsp;In other words, the researchers can see changes in both the cells’ DNA and gene expression within the context of tissues.</p> <p> The researchers applied the technique to a mouse model of metastatic cancer, as well as a primary tumor sample from a patient with colorectal cancer. In each tissue, the researchers were able to identify subpopulations of cancer cells in distinct regions, corresponding with unique genomic evolutionary paths and gene expression states.</p> <p> "We applied this to DNA sequencing and cancer, which are hugely important areas of medical research,"&nbsp;said co-corresponding author <a href="/node/113841">Jason Buenrostro</a>, who is a HSCRB assistant professor, an associate member of the Ó³»­´«Ã½, and co-director of the Ó³»­´«Ã½'s <a href="/node/768556">Gene Regulation Observatory</a>. "However, the technology also opens the door to more broadly measuring DNA molecules within tissues. As such, we imagine future approaches will use this work as a foundation to build tools that measure modifications to DNA as well, such as the epigenome."</p> <p> <em>This study received funding from the Allen Institute Distinguished Investigator Award, the National Institutes of Health, a National Human Genome Research Institute training grant, the Burroughs Wellcome Fund, and the Harvard Quantitative Biology Initiative.</em></p> <p> <em>Adapted from <a href="https://hscrb.harvard.edu/news/genomic-sequencing-that-preserves-cells-locations-within-tissues/" target="_blank">a story originally published by the Harvard University Department of Stem Cell and Regenerative Biology</a>.</em></p> </div> </div> <div class="block block-layout-builder block-field-blocknodenewsfield-news-pappers"> <h2>Paper(s) cited</h2> <div class="clearfix text-formatted field field--name-field-news-pappers field--type-text-long field--label-hidden field__item"><p> Zhao T, Chiang ZD, et al.&nbsp;<a href="https://www.nature.com/articles/s41586-021-04217-4" target="_blank">Spatial genomics enables multi-modal study of clonal heterogeneity in tissues</a>. <em>Nature</em>. DOI: 10.1038/s41586-021-04217-4.</p> </div> </div> <div class="block-node-broad-tags block block-layout-builder block-field-blocknodenewsfield-broad-tags"> <div class="block-node-broad-tags__row"> <div class="block-node-broad-tags__title">Tags:</div> <div class="field field--name-field-broad-tags field--type-entity-reference field--label-hidden field__items"> <div class="field__item"><a href="/broad-tags/genome-regulation-cellular-circuitry-and-epigenomics" hreflang="en">Genome Regulation, Cellular Circuitry and Epigenomics</a></div> <div class="field__item"><a href="/broad-tags/genome-regulation-cell-circuitry-and-epigenomics" hreflang="en">Genome regulation, cell circuitry, and epigenomics</a></div> </div> </div> </div> </div> <div class="content-section__right col-2"> <div class="block block-ctools block-entity-viewnode"> <article about="/news/new-dna-sequencing-technique-preserves-cells%E2%80%99-locations-within-tissues" class="node node--type-news node--promoted node--view-mode-sidebar"> <div class="node__content"> <div class="sidebar-group"> <div class="sidebar-group__content"> <div class="block block-layout-builder block-field-blocknodenewsfield-news-extra-info"> <div class="clearfix text-formatted field field--name-field-news-extra-info field--type-text-long field--label-hidden field__item"><h2> Related People</h2> <p> <a href="/node/113841">Jason Buenrostro</a></p> <p> <a href="/node/113836">Fei Chen</a><br> &nbsp;</p> <h2> Related Programs</h2> <p> <a href="/node/768556">Gene Regulation Observatory</a><br> &nbsp;</p> <h2> Related News</h2> <p> <a href="/node/488166"><img alt src="/files/styles/blog__557x415_/public/news/images/2019/Projections_of_Composite_MainStoryPage_1.gif?itok=UafnfWmI" style="width: 212px; height: 158px;"></a></p> <p> <a href="/node/488166">New tool uses RNA sequencing to chart rich maps of cellular and tissue function</a><br> &nbsp;</p> </div> </div> </div> </div> </div> </article> </div> </div> </div> </div> Wed, 15 Dec 2021 16:05:12 +0000 tulrich@broadinstitute.org 1126886 at /news/epigenomic-map-reveals-circuitry-30000-human-disease-regions <span class="field field--name-title field--type-string field--label-hidden"><h1>New DNA sequencing technique preserves cells’ locations within tissues</h1> </span> <span class="field field--name-uid field--type-entity-reference field--label-hidden"> <span>By Tom Ulrich</span> </span> <span class="field field--name-created field--type-created field--label-hidden"><time datetime="2021-12-15T11:05:12-05:00" class="datetime">December 15, 2021</time> </span> <div class="hero-section container"> <div class="hero-section__row row"> <div class="hero-section__content hero-section__content_left col-6"> <div class="hero-section__breadcrumbs"> <div class="block block-layout-builder block-extra-field-blocknodenewsbreadcrumbs"> <nav class="breadcrumb" role="navigation" aria-labelledby="system-breadcrumb"> <h2 id="system-breadcrumb" class="visually-hidden">Breadcrumb</h2> <ol> <li> <a href="/">Home</a> </li> <li> <a href="/news">News</a> </li> </ol> </nav> </div> </div> <div class="hero-section__title"> <div class="block block-layout-builder block-field-blocknodenewstitle"> <span class="field field--name-title field--type-string field--label-hidden"><h1>New DNA sequencing technique preserves cells’ locations within tissues</h1> </span> </div> </div> <div class="hero-section__description"> <div class="block block-layout-builder block-field-blocknodenewsbody"> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><div class="summary-only"> <p> Slide-DNA-seq helps researchers better understand spatial differences and patterns in complex tissues such as tumors.</p> </div> </div> </div> </div> <div class="hero-section__author"> <div class="block block-layout-builder block-extra-field-blocknodenewsextra-field-author-custom"> By Jessica Lau, Harvard Department of Stem Cell and Regenerative Biology </div> </div> <div class="hero-section__date"> <div class="block block-layout-builder block-field-blocknodenewscreated"> <span class="field field--name-created field--type-created field--label-hidden"><time datetime="2021-12-15T11:05:12-05:00" class="datetime">December 15, 2021</time> </span> </div> </div> </div> <div class="hero-section__right col-6"> <div class="hero-section__image"> <div class="block block-layout-builder block-field-blocknodenewsfield-image"> <div class="field field--name-field-image field--type-entity-reference field--label-hidden field__item"> <article class="media media--type-image media--view-mode-multiple-content-types-header"> <div class="field field--name-field-media-image field--type-image field--label-hidden field__item"> <picture> <source srcset="/files/styles/multiple_ct_header_desktop_xl/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=Mj-O2mVa 1x" media="all and (min-width: 1921px)" type="image/png" width="754" height="503"> <source srcset="/files/styles/multiple_ct_header_desktop_xl/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=Mj-O2mVa 1x" media="all and (min-width: 1601px) and (max-width: 1920px)" type="image/png" width="754" height="503"> <source srcset="/files/styles/multiple_ct_header_desktop/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=ZBfVHHl3 1x" media="all and (min-width: 1340px) and (max-width: 1600px)" type="image/png" width="736" height="520"> <source srcset="/files/styles/multiple_ct_header_laptop/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=NQXuPw1V 1x" media="all and (min-width: 800px) and (max-width: 1339px)" type="image/png" width="641" height="451"> <source srcset="/files/styles/multiple_ct_header_tablet/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=vEqZYhdy 1x" media="all and (min-width: 540px) and (max-width: 799px)" type="image/png" width="706" height="417"> <source srcset="/files/styles/multiple_ct_header_phone/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=raZa4Wiq 1x" media="all and (max-width: 539px)" type="image/png" width="499" height="294"> <img loading="eager" width="499" height="294" src="/files/styles/multiple_ct_header_phone/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=raZa4Wiq" alt="An image of how slide-DNA-seq &quot;sees&quot; cells' organization within a tumor." title="An image of how slide-DNA-seq &quot;sees&quot; cells' organization within a tumor." typeof="foaf:Image"> </picture> </div> <div class="media-caption"> <div class="media-caption__credit"> Credit: <a href="https://www.nature.com/articles/s41586-021-04217-4" target="_blank">Zhao T, Chiang Z, et al. <em>Nature</em>, 2021</a> </div> <div class="media-caption__description"> An image of how slide-DNA-seq "sees" cells' organization within a tumor. </div> </div> </article> </div> </div> </div> </div> </div> </div> <div class="content-section content-section_with-sidebars container"> <div class="row"> <div class="content-section__left col-2"> <div class="block block-better-social-sharing-buttons block-social-sharing-buttons-block"> <div style="display: none"><link rel="preload" href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg" as="image" type="image/svg+xml" crossorigin="anonymous"></div> <div class="social-sharing-buttons"> <a href="https://www.facebook.com/sharer/sharer.php?u=/taxonomy/term/592/feed&amp;title=" target="_blank" title="Share to Facebook" aria-label="Share to Facebook" class="social-sharing-buttons-button share-facebook" rel="noopener"> <svg aria-hidden="true" width="32px" height="32px" style="border-radius:100%;"> <use href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg#facebook" /> </svg> </a> <a href="https://twitter.com/intent/tweet?text=+/taxonomy/term/592/feed" target="_blank" title="Share to X" aria-label="Share to X" class="social-sharing-buttons-button share-x" rel="noopener"> <svg aria-hidden="true" width="32px" height="32px" style="border-radius:100%;"> <use href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg#x" /> </svg> </a> <a href="mailto:?subject=&amp;body=/taxonomy/term/592/feed" title="Share to Email" aria-label="Share to Email" class="social-sharing-buttons-button share-email" target="_blank" rel="noopener"> <svg aria-hidden="true" width="32px" height="32px" style="border-radius:100%;"> <use href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg#email" /> </svg> </a> </div> </div> </div> <div class="content-section__main col-8"> <div class="block block-layout-builder block-field-blocknodenewsbody"> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><p> Within complex tissues such as cancer tumors, individual cells can vary widely from each other. Internally, cancer cells can develop unique DNA mutations and genomic changes, potentially leading to drug resistance, metastasis, or relapse. Externally, the cells’ specific locations within the tissue also matter, since the local structure of a tumor and its surrounding tissues can affect cell state and drug permeability.</p> <p> To measure both genetic and local factors at the same time, researchers from Harvard University’s Department of Stem Cell and Regenerative Biology (HSCRB) and the Ó³»­´«Ã½ of MIT and Harvard developed a new technique of spatially-resolved DNA sequencing, called slide-DNA-seq. When further combined with spatially-resolved gene expression analysis, the technology gives researchers a better understanding of cancer progression and potential treatment.</p> <p> The researchers’ findings are published in the journal <a href="https://www.nature.com/articles/s41586-021-04217-4" target="_blank"><em>Nature</em></a>.</p> <p> Slide-DNA-seq analyzes slices of intact tissue, in which each cell remains in its original location — as opposed to conventional sequencing techniques, where cells are dissociated before DNA extraction. The researchers used microbeads, each tagged with a unique spatial barcode and bound to specially-prepared glass slides, to capture DNA from the tissue.&nbsp;</p> <p> "Each bead is about the size of a cell," said co-corresponding author&nbsp;<a href="/node/113836">Fei Chen</a>, who is an assistant professor in HSCRB and a core institute member at the Ó³»­´«Ã½. "Together, they are like individual pixels on a camera which takes snapshots of genomic alterations within each cell in the tissue."</p> <p> After measuring genomic changes, the researchers applied a related&nbsp;<a href="/node/488166">RNA-based Slide-seq method</a>&nbsp;Chen and collaborators developed in 2019, which used gene expression profiles to identify and map the locations of cell types and subtypes within a tissue slice.&nbsp;&nbsp;</p> <p> "We can use the same barcoded beads to capture the transcriptome from each cell, and combine these two measurements into a multi-modal image," Chen said.&nbsp;In other words, the researchers can see changes in both the cells’ DNA and gene expression within the context of tissues.</p> <p> The researchers applied the technique to a mouse model of metastatic cancer, as well as a primary tumor sample from a patient with colorectal cancer. In each tissue, the researchers were able to identify subpopulations of cancer cells in distinct regions, corresponding with unique genomic evolutionary paths and gene expression states.</p> <p> "We applied this to DNA sequencing and cancer, which are hugely important areas of medical research,"&nbsp;said co-corresponding author <a href="/node/113841">Jason Buenrostro</a>, who is a HSCRB assistant professor, an associate member of the Ó³»­´«Ã½, and co-director of the Ó³»­´«Ã½'s <a href="/node/768556">Gene Regulation Observatory</a>. "However, the technology also opens the door to more broadly measuring DNA molecules within tissues. As such, we imagine future approaches will use this work as a foundation to build tools that measure modifications to DNA as well, such as the epigenome."</p> <p> <em>This study received funding from the Allen Institute Distinguished Investigator Award, the National Institutes of Health, a National Human Genome Research Institute training grant, the Burroughs Wellcome Fund, and the Harvard Quantitative Biology Initiative.</em></p> <p> <em>Adapted from <a href="https://hscrb.harvard.edu/news/genomic-sequencing-that-preserves-cells-locations-within-tissues/" target="_blank">a story originally published by the Harvard University Department of Stem Cell and Regenerative Biology</a>.</em></p> </div> </div> <div class="block block-layout-builder block-field-blocknodenewsfield-news-pappers"> <h2>Paper(s) cited</h2> <div class="clearfix text-formatted field field--name-field-news-pappers field--type-text-long field--label-hidden field__item"><p> Zhao T, Chiang ZD, et al.&nbsp;<a href="https://www.nature.com/articles/s41586-021-04217-4" target="_blank">Spatial genomics enables multi-modal study of clonal heterogeneity in tissues</a>. <em>Nature</em>. DOI: 10.1038/s41586-021-04217-4.</p> </div> </div> <div class="block-node-broad-tags block block-layout-builder block-field-blocknodenewsfield-broad-tags"> <div class="block-node-broad-tags__row"> <div class="block-node-broad-tags__title">Tags:</div> <div class="field field--name-field-broad-tags field--type-entity-reference field--label-hidden field__items"> <div class="field__item"><a href="/broad-tags/genome-regulation-cellular-circuitry-and-epigenomics" hreflang="en">Genome Regulation, Cellular Circuitry and Epigenomics</a></div> <div class="field__item"><a href="/broad-tags/genome-regulation-cell-circuitry-and-epigenomics" hreflang="en">Genome regulation, cell circuitry, and epigenomics</a></div> </div> </div> </div> </div> <div class="content-section__right col-2"> <div class="block block-ctools block-entity-viewnode"> <article about="/news/new-dna-sequencing-technique-preserves-cells%E2%80%99-locations-within-tissues" class="node node--type-news node--promoted node--view-mode-sidebar"> <div class="node__content"> <div class="sidebar-group"> <div class="sidebar-group__content"> <div class="block block-layout-builder block-field-blocknodenewsfield-news-extra-info"> <div class="clearfix text-formatted field field--name-field-news-extra-info field--type-text-long field--label-hidden field__item"><h2> Related People</h2> <p> <a href="/node/113841">Jason Buenrostro</a></p> <p> <a href="/node/113836">Fei Chen</a><br> &nbsp;</p> <h2> Related Programs</h2> <p> <a href="/node/768556">Gene Regulation Observatory</a><br> &nbsp;</p> <h2> Related News</h2> <p> <a href="/node/488166"><img alt src="/files/styles/blog__557x415_/public/news/images/2019/Projections_of_Composite_MainStoryPage_1.gif?itok=UafnfWmI" style="width: 212px; height: 158px;"></a></p> <p> <a href="/node/488166">New tool uses RNA sequencing to chart rich maps of cellular and tissue function</a><br> &nbsp;</p> </div> </div> </div> </div> </div> </article> </div> </div> </div> </div> Mon, 08 Feb 2021 16:56:59 +0000 tulrich@broadinstitute.org 758811 at /news/research-roundup-july-31-2020 <span class="field field--name-title field--type-string field--label-hidden"><h1>New DNA sequencing technique preserves cells’ locations within tissues</h1> </span> <span class="field field--name-uid field--type-entity-reference field--label-hidden"> <span>By Tom Ulrich</span> </span> <span class="field field--name-created field--type-created field--label-hidden"><time datetime="2021-12-15T11:05:12-05:00" class="datetime">December 15, 2021</time> </span> <div class="hero-section container"> <div class="hero-section__row row"> <div class="hero-section__content hero-section__content_left col-6"> <div class="hero-section__breadcrumbs"> <div class="block block-layout-builder block-extra-field-blocknodenewsbreadcrumbs"> <nav class="breadcrumb" role="navigation" aria-labelledby="system-breadcrumb"> <h2 id="system-breadcrumb" class="visually-hidden">Breadcrumb</h2> <ol> <li> <a href="/">Home</a> </li> <li> <a href="/news">News</a> </li> </ol> </nav> </div> </div> <div class="hero-section__title"> <div class="block block-layout-builder block-field-blocknodenewstitle"> <span class="field field--name-title field--type-string field--label-hidden"><h1>New DNA sequencing technique preserves cells’ locations within tissues</h1> </span> </div> </div> <div class="hero-section__description"> <div class="block block-layout-builder block-field-blocknodenewsbody"> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><div class="summary-only"> <p> Slide-DNA-seq helps researchers better understand spatial differences and patterns in complex tissues such as tumors.</p> </div> </div> </div> </div> <div class="hero-section__author"> <div class="block block-layout-builder block-extra-field-blocknodenewsextra-field-author-custom"> By Jessica Lau, Harvard Department of Stem Cell and Regenerative Biology </div> </div> <div class="hero-section__date"> <div class="block block-layout-builder block-field-blocknodenewscreated"> <span class="field field--name-created field--type-created field--label-hidden"><time datetime="2021-12-15T11:05:12-05:00" class="datetime">December 15, 2021</time> </span> </div> </div> </div> <div class="hero-section__right col-6"> <div class="hero-section__image"> <div class="block block-layout-builder block-field-blocknodenewsfield-image"> <div class="field field--name-field-image field--type-entity-reference field--label-hidden field__item"> <article class="media media--type-image media--view-mode-multiple-content-types-header"> <div class="field field--name-field-media-image field--type-image field--label-hidden field__item"> <picture> <source srcset="/files/styles/multiple_ct_header_desktop_xl/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=Mj-O2mVa 1x" media="all and (min-width: 1921px)" type="image/png" width="754" height="503"> <source srcset="/files/styles/multiple_ct_header_desktop_xl/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=Mj-O2mVa 1x" media="all and (min-width: 1601px) and (max-width: 1920px)" type="image/png" width="754" height="503"> <source srcset="/files/styles/multiple_ct_header_desktop/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=ZBfVHHl3 1x" media="all and (min-width: 1340px) and (max-width: 1600px)" type="image/png" width="736" height="520"> <source srcset="/files/styles/multiple_ct_header_laptop/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=NQXuPw1V 1x" media="all and (min-width: 800px) and (max-width: 1339px)" type="image/png" width="641" height="451"> <source srcset="/files/styles/multiple_ct_header_tablet/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=vEqZYhdy 1x" media="all and (min-width: 540px) and (max-width: 799px)" type="image/png" width="706" height="417"> <source srcset="/files/styles/multiple_ct_header_phone/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=raZa4Wiq 1x" media="all and (max-width: 539px)" type="image/png" width="499" height="294"> <img loading="eager" width="499" height="294" src="/files/styles/multiple_ct_header_phone/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=raZa4Wiq" alt="An image of how slide-DNA-seq &quot;sees&quot; cells' organization within a tumor." title="An image of how slide-DNA-seq &quot;sees&quot; cells' organization within a tumor." typeof="foaf:Image"> </picture> </div> <div class="media-caption"> <div class="media-caption__credit"> Credit: <a href="https://www.nature.com/articles/s41586-021-04217-4" target="_blank">Zhao T, Chiang Z, et al. <em>Nature</em>, 2021</a> </div> <div class="media-caption__description"> An image of how slide-DNA-seq "sees" cells' organization within a tumor. </div> </div> </article> </div> </div> </div> </div> </div> </div> <div class="content-section content-section_with-sidebars container"> <div class="row"> <div class="content-section__left col-2"> <div class="block block-better-social-sharing-buttons block-social-sharing-buttons-block"> <div style="display: none"><link rel="preload" href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg" as="image" type="image/svg+xml" crossorigin="anonymous"></div> <div class="social-sharing-buttons"> <a href="https://www.facebook.com/sharer/sharer.php?u=/taxonomy/term/592/feed&amp;title=" target="_blank" title="Share to Facebook" aria-label="Share to Facebook" class="social-sharing-buttons-button share-facebook" rel="noopener"> <svg aria-hidden="true" width="32px" height="32px" style="border-radius:100%;"> <use href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg#facebook" /> </svg> </a> <a href="https://twitter.com/intent/tweet?text=+/taxonomy/term/592/feed" target="_blank" title="Share to X" aria-label="Share to X" class="social-sharing-buttons-button share-x" rel="noopener"> <svg aria-hidden="true" width="32px" height="32px" style="border-radius:100%;"> <use href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg#x" /> </svg> </a> <a href="mailto:?subject=&amp;body=/taxonomy/term/592/feed" title="Share to Email" aria-label="Share to Email" class="social-sharing-buttons-button share-email" target="_blank" rel="noopener"> <svg aria-hidden="true" width="32px" height="32px" style="border-radius:100%;"> <use href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg#email" /> </svg> </a> </div> </div> </div> <div class="content-section__main col-8"> <div class="block block-layout-builder block-field-blocknodenewsbody"> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><p> Within complex tissues such as cancer tumors, individual cells can vary widely from each other. Internally, cancer cells can develop unique DNA mutations and genomic changes, potentially leading to drug resistance, metastasis, or relapse. Externally, the cells’ specific locations within the tissue also matter, since the local structure of a tumor and its surrounding tissues can affect cell state and drug permeability.</p> <p> To measure both genetic and local factors at the same time, researchers from Harvard University’s Department of Stem Cell and Regenerative Biology (HSCRB) and the Ó³»­´«Ã½ of MIT and Harvard developed a new technique of spatially-resolved DNA sequencing, called slide-DNA-seq. When further combined with spatially-resolved gene expression analysis, the technology gives researchers a better understanding of cancer progression and potential treatment.</p> <p> The researchers’ findings are published in the journal <a href="https://www.nature.com/articles/s41586-021-04217-4" target="_blank"><em>Nature</em></a>.</p> <p> Slide-DNA-seq analyzes slices of intact tissue, in which each cell remains in its original location — as opposed to conventional sequencing techniques, where cells are dissociated before DNA extraction. The researchers used microbeads, each tagged with a unique spatial barcode and bound to specially-prepared glass slides, to capture DNA from the tissue.&nbsp;</p> <p> "Each bead is about the size of a cell," said co-corresponding author&nbsp;<a href="/node/113836">Fei Chen</a>, who is an assistant professor in HSCRB and a core institute member at the Ó³»­´«Ã½. "Together, they are like individual pixels on a camera which takes snapshots of genomic alterations within each cell in the tissue."</p> <p> After measuring genomic changes, the researchers applied a related&nbsp;<a href="/node/488166">RNA-based Slide-seq method</a>&nbsp;Chen and collaborators developed in 2019, which used gene expression profiles to identify and map the locations of cell types and subtypes within a tissue slice.&nbsp;&nbsp;</p> <p> "We can use the same barcoded beads to capture the transcriptome from each cell, and combine these two measurements into a multi-modal image," Chen said.&nbsp;In other words, the researchers can see changes in both the cells’ DNA and gene expression within the context of tissues.</p> <p> The researchers applied the technique to a mouse model of metastatic cancer, as well as a primary tumor sample from a patient with colorectal cancer. In each tissue, the researchers were able to identify subpopulations of cancer cells in distinct regions, corresponding with unique genomic evolutionary paths and gene expression states.</p> <p> "We applied this to DNA sequencing and cancer, which are hugely important areas of medical research,"&nbsp;said co-corresponding author <a href="/node/113841">Jason Buenrostro</a>, who is a HSCRB assistant professor, an associate member of the Ó³»­´«Ã½, and co-director of the Ó³»­´«Ã½'s <a href="/node/768556">Gene Regulation Observatory</a>. "However, the technology also opens the door to more broadly measuring DNA molecules within tissues. As such, we imagine future approaches will use this work as a foundation to build tools that measure modifications to DNA as well, such as the epigenome."</p> <p> <em>This study received funding from the Allen Institute Distinguished Investigator Award, the National Institutes of Health, a National Human Genome Research Institute training grant, the Burroughs Wellcome Fund, and the Harvard Quantitative Biology Initiative.</em></p> <p> <em>Adapted from <a href="https://hscrb.harvard.edu/news/genomic-sequencing-that-preserves-cells-locations-within-tissues/" target="_blank">a story originally published by the Harvard University Department of Stem Cell and Regenerative Biology</a>.</em></p> </div> </div> <div class="block block-layout-builder block-field-blocknodenewsfield-news-pappers"> <h2>Paper(s) cited</h2> <div class="clearfix text-formatted field field--name-field-news-pappers field--type-text-long field--label-hidden field__item"><p> Zhao T, Chiang ZD, et al.&nbsp;<a href="https://www.nature.com/articles/s41586-021-04217-4" target="_blank">Spatial genomics enables multi-modal study of clonal heterogeneity in tissues</a>. <em>Nature</em>. DOI: 10.1038/s41586-021-04217-4.</p> </div> </div> <div class="block-node-broad-tags block block-layout-builder block-field-blocknodenewsfield-broad-tags"> <div class="block-node-broad-tags__row"> <div class="block-node-broad-tags__title">Tags:</div> <div class="field field--name-field-broad-tags field--type-entity-reference field--label-hidden field__items"> <div class="field__item"><a href="/broad-tags/genome-regulation-cellular-circuitry-and-epigenomics" hreflang="en">Genome Regulation, Cellular Circuitry and Epigenomics</a></div> <div class="field__item"><a href="/broad-tags/genome-regulation-cell-circuitry-and-epigenomics" hreflang="en">Genome regulation, cell circuitry, and epigenomics</a></div> </div> </div> </div> </div> <div class="content-section__right col-2"> <div class="block block-ctools block-entity-viewnode"> <article about="/news/new-dna-sequencing-technique-preserves-cells%E2%80%99-locations-within-tissues" class="node node--type-news node--promoted node--view-mode-sidebar"> <div class="node__content"> <div class="sidebar-group"> <div class="sidebar-group__content"> <div class="block block-layout-builder block-field-blocknodenewsfield-news-extra-info"> <div class="clearfix text-formatted field field--name-field-news-extra-info field--type-text-long field--label-hidden field__item"><h2> Related People</h2> <p> <a href="/node/113841">Jason Buenrostro</a></p> <p> <a href="/node/113836">Fei Chen</a><br> &nbsp;</p> <h2> Related Programs</h2> <p> <a href="/node/768556">Gene Regulation Observatory</a><br> &nbsp;</p> <h2> Related News</h2> <p> <a href="/node/488166"><img alt src="/files/styles/blog__557x415_/public/news/images/2019/Projections_of_Composite_MainStoryPage_1.gif?itok=UafnfWmI" style="width: 212px; height: 158px;"></a></p> <p> <a href="/node/488166">New tool uses RNA sequencing to chart rich maps of cellular and tissue function</a><br> &nbsp;</p> </div> </div> </div> </div> </div> </article> </div> </div> </div> </div> Fri, 31 Jul 2020 15:36:28 +0000 Namrata Sengupta 635586 at /news/study-hints-why-aggressive-form-brain-cancer-hard-treat <span class="field field--name-title field--type-string field--label-hidden"><h1>New DNA sequencing technique preserves cells’ locations within tissues</h1> </span> <span class="field field--name-uid field--type-entity-reference field--label-hidden"> <span>By Tom Ulrich</span> </span> <span class="field field--name-created field--type-created field--label-hidden"><time datetime="2021-12-15T11:05:12-05:00" class="datetime">December 15, 2021</time> </span> <div class="hero-section container"> <div class="hero-section__row row"> <div class="hero-section__content hero-section__content_left col-6"> <div class="hero-section__breadcrumbs"> <div class="block block-layout-builder block-extra-field-blocknodenewsbreadcrumbs"> <nav class="breadcrumb" role="navigation" aria-labelledby="system-breadcrumb"> <h2 id="system-breadcrumb" class="visually-hidden">Breadcrumb</h2> <ol> <li> <a href="/">Home</a> </li> <li> <a href="/news">News</a> </li> </ol> </nav> </div> </div> <div class="hero-section__title"> <div class="block block-layout-builder block-field-blocknodenewstitle"> <span class="field field--name-title field--type-string field--label-hidden"><h1>New DNA sequencing technique preserves cells’ locations within tissues</h1> </span> </div> </div> <div class="hero-section__description"> <div class="block block-layout-builder block-field-blocknodenewsbody"> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><div class="summary-only"> <p> Slide-DNA-seq helps researchers better understand spatial differences and patterns in complex tissues such as tumors.</p> </div> </div> </div> </div> <div class="hero-section__author"> <div class="block block-layout-builder block-extra-field-blocknodenewsextra-field-author-custom"> By Jessica Lau, Harvard Department of Stem Cell and Regenerative Biology </div> </div> <div class="hero-section__date"> <div class="block block-layout-builder block-field-blocknodenewscreated"> <span class="field field--name-created field--type-created field--label-hidden"><time datetime="2021-12-15T11:05:12-05:00" class="datetime">December 15, 2021</time> </span> </div> </div> </div> <div class="hero-section__right col-6"> <div class="hero-section__image"> <div class="block block-layout-builder block-field-blocknodenewsfield-image"> <div class="field field--name-field-image field--type-entity-reference field--label-hidden field__item"> <article class="media media--type-image media--view-mode-multiple-content-types-header"> <div class="field field--name-field-media-image field--type-image field--label-hidden field__item"> <picture> <source srcset="/files/styles/multiple_ct_header_desktop_xl/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=Mj-O2mVa 1x" media="all and (min-width: 1921px)" type="image/png" width="754" height="503"> <source srcset="/files/styles/multiple_ct_header_desktop_xl/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=Mj-O2mVa 1x" media="all and (min-width: 1601px) and (max-width: 1920px)" type="image/png" width="754" height="503"> <source srcset="/files/styles/multiple_ct_header_desktop/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=ZBfVHHl3 1x" media="all and (min-width: 1340px) and (max-width: 1600px)" type="image/png" width="736" height="520"> <source srcset="/files/styles/multiple_ct_header_laptop/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=NQXuPw1V 1x" media="all and (min-width: 800px) and (max-width: 1339px)" type="image/png" width="641" height="451"> <source srcset="/files/styles/multiple_ct_header_tablet/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=vEqZYhdy 1x" media="all and (min-width: 540px) and (max-width: 799px)" type="image/png" width="706" height="417"> <source srcset="/files/styles/multiple_ct_header_phone/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=raZa4Wiq 1x" media="all and (max-width: 539px)" type="image/png" width="499" height="294"> <img loading="eager" width="499" height="294" src="/files/styles/multiple_ct_header_phone/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=raZa4Wiq" alt="An image of how slide-DNA-seq &quot;sees&quot; cells' organization within a tumor." title="An image of how slide-DNA-seq &quot;sees&quot; cells' organization within a tumor." typeof="foaf:Image"> </picture> </div> <div class="media-caption"> <div class="media-caption__credit"> Credit: <a href="https://www.nature.com/articles/s41586-021-04217-4" target="_blank">Zhao T, Chiang Z, et al. <em>Nature</em>, 2021</a> </div> <div class="media-caption__description"> An image of how slide-DNA-seq "sees" cells' organization within a tumor. </div> </div> </article> </div> </div> </div> </div> </div> </div> <div class="content-section content-section_with-sidebars container"> <div class="row"> <div class="content-section__left col-2"> <div class="block block-better-social-sharing-buttons block-social-sharing-buttons-block"> <div style="display: none"><link rel="preload" href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg" as="image" type="image/svg+xml" crossorigin="anonymous"></div> <div class="social-sharing-buttons"> <a href="https://www.facebook.com/sharer/sharer.php?u=/taxonomy/term/592/feed&amp;title=" target="_blank" title="Share to Facebook" aria-label="Share to Facebook" class="social-sharing-buttons-button share-facebook" rel="noopener"> <svg aria-hidden="true" width="32px" height="32px" style="border-radius:100%;"> <use href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg#facebook" /> </svg> </a> <a href="https://twitter.com/intent/tweet?text=+/taxonomy/term/592/feed" target="_blank" title="Share to X" aria-label="Share to X" class="social-sharing-buttons-button share-x" rel="noopener"> <svg aria-hidden="true" width="32px" height="32px" style="border-radius:100%;"> <use href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg#x" /> </svg> </a> <a href="mailto:?subject=&amp;body=/taxonomy/term/592/feed" title="Share to Email" aria-label="Share to Email" class="social-sharing-buttons-button share-email" target="_blank" rel="noopener"> <svg aria-hidden="true" width="32px" height="32px" style="border-radius:100%;"> <use href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg#email" /> </svg> </a> </div> </div> </div> <div class="content-section__main col-8"> <div class="block block-layout-builder block-field-blocknodenewsbody"> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><p> Within complex tissues such as cancer tumors, individual cells can vary widely from each other. Internally, cancer cells can develop unique DNA mutations and genomic changes, potentially leading to drug resistance, metastasis, or relapse. Externally, the cells’ specific locations within the tissue also matter, since the local structure of a tumor and its surrounding tissues can affect cell state and drug permeability.</p> <p> To measure both genetic and local factors at the same time, researchers from Harvard University’s Department of Stem Cell and Regenerative Biology (HSCRB) and the Ó³»­´«Ã½ of MIT and Harvard developed a new technique of spatially-resolved DNA sequencing, called slide-DNA-seq. When further combined with spatially-resolved gene expression analysis, the technology gives researchers a better understanding of cancer progression and potential treatment.</p> <p> The researchers’ findings are published in the journal <a href="https://www.nature.com/articles/s41586-021-04217-4" target="_blank"><em>Nature</em></a>.</p> <p> Slide-DNA-seq analyzes slices of intact tissue, in which each cell remains in its original location — as opposed to conventional sequencing techniques, where cells are dissociated before DNA extraction. The researchers used microbeads, each tagged with a unique spatial barcode and bound to specially-prepared glass slides, to capture DNA from the tissue.&nbsp;</p> <p> "Each bead is about the size of a cell," said co-corresponding author&nbsp;<a href="/node/113836">Fei Chen</a>, who is an assistant professor in HSCRB and a core institute member at the Ó³»­´«Ã½. "Together, they are like individual pixels on a camera which takes snapshots of genomic alterations within each cell in the tissue."</p> <p> After measuring genomic changes, the researchers applied a related&nbsp;<a href="/node/488166">RNA-based Slide-seq method</a>&nbsp;Chen and collaborators developed in 2019, which used gene expression profiles to identify and map the locations of cell types and subtypes within a tissue slice.&nbsp;&nbsp;</p> <p> "We can use the same barcoded beads to capture the transcriptome from each cell, and combine these two measurements into a multi-modal image," Chen said.&nbsp;In other words, the researchers can see changes in both the cells’ DNA and gene expression within the context of tissues.</p> <p> The researchers applied the technique to a mouse model of metastatic cancer, as well as a primary tumor sample from a patient with colorectal cancer. In each tissue, the researchers were able to identify subpopulations of cancer cells in distinct regions, corresponding with unique genomic evolutionary paths and gene expression states.</p> <p> "We applied this to DNA sequencing and cancer, which are hugely important areas of medical research,"&nbsp;said co-corresponding author <a href="/node/113841">Jason Buenrostro</a>, who is a HSCRB assistant professor, an associate member of the Ó³»­´«Ã½, and co-director of the Ó³»­´«Ã½'s <a href="/node/768556">Gene Regulation Observatory</a>. "However, the technology also opens the door to more broadly measuring DNA molecules within tissues. As such, we imagine future approaches will use this work as a foundation to build tools that measure modifications to DNA as well, such as the epigenome."</p> <p> <em>This study received funding from the Allen Institute Distinguished Investigator Award, the National Institutes of Health, a National Human Genome Research Institute training grant, the Burroughs Wellcome Fund, and the Harvard Quantitative Biology Initiative.</em></p> <p> <em>Adapted from <a href="https://hscrb.harvard.edu/news/genomic-sequencing-that-preserves-cells-locations-within-tissues/" target="_blank">a story originally published by the Harvard University Department of Stem Cell and Regenerative Biology</a>.</em></p> </div> </div> <div class="block block-layout-builder block-field-blocknodenewsfield-news-pappers"> <h2>Paper(s) cited</h2> <div class="clearfix text-formatted field field--name-field-news-pappers field--type-text-long field--label-hidden field__item"><p> Zhao T, Chiang ZD, et al.&nbsp;<a href="https://www.nature.com/articles/s41586-021-04217-4" target="_blank">Spatial genomics enables multi-modal study of clonal heterogeneity in tissues</a>. <em>Nature</em>. DOI: 10.1038/s41586-021-04217-4.</p> </div> </div> <div class="block-node-broad-tags block block-layout-builder block-field-blocknodenewsfield-broad-tags"> <div class="block-node-broad-tags__row"> <div class="block-node-broad-tags__title">Tags:</div> <div class="field field--name-field-broad-tags field--type-entity-reference field--label-hidden field__items"> <div class="field__item"><a href="/broad-tags/genome-regulation-cellular-circuitry-and-epigenomics" hreflang="en">Genome Regulation, Cellular Circuitry and Epigenomics</a></div> <div class="field__item"><a href="/broad-tags/genome-regulation-cell-circuitry-and-epigenomics" hreflang="en">Genome regulation, cell circuitry, and epigenomics</a></div> </div> </div> </div> </div> <div class="content-section__right col-2"> <div class="block block-ctools block-entity-viewnode"> <article about="/news/new-dna-sequencing-technique-preserves-cells%E2%80%99-locations-within-tissues" class="node node--type-news node--promoted node--view-mode-sidebar"> <div class="node__content"> <div class="sidebar-group"> <div class="sidebar-group__content"> <div class="block block-layout-builder block-field-blocknodenewsfield-news-extra-info"> <div class="clearfix text-formatted field field--name-field-news-extra-info field--type-text-long field--label-hidden field__item"><h2> Related People</h2> <p> <a href="/node/113841">Jason Buenrostro</a></p> <p> <a href="/node/113836">Fei Chen</a><br> &nbsp;</p> <h2> Related Programs</h2> <p> <a href="/node/768556">Gene Regulation Observatory</a><br> &nbsp;</p> <h2> Related News</h2> <p> <a href="/node/488166"><img alt src="/files/styles/blog__557x415_/public/news/images/2019/Projections_of_Composite_MainStoryPage_1.gif?itok=UafnfWmI" style="width: 212px; height: 158px;"></a></p> <p> <a href="/node/488166">New tool uses RNA sequencing to chart rich maps of cellular and tissue function</a><br> &nbsp;</p> </div> </div> </div> </div> </div> </article> </div> </div> </div> </div> Thu, 18 Jul 2019 15:00:00 +0000 Abbey Bigler 568186 at /news/research-roundup-march-1-2019 <span class="field field--name-title field--type-string field--label-hidden"><h1>New DNA sequencing technique preserves cells’ locations within tissues</h1> </span> <span class="field field--name-uid field--type-entity-reference field--label-hidden"> <span>By Tom Ulrich</span> </span> <span class="field field--name-created field--type-created field--label-hidden"><time datetime="2021-12-15T11:05:12-05:00" class="datetime">December 15, 2021</time> </span> <div class="hero-section container"> <div class="hero-section__row row"> <div class="hero-section__content hero-section__content_left col-6"> <div class="hero-section__breadcrumbs"> <div class="block block-layout-builder block-extra-field-blocknodenewsbreadcrumbs"> <nav class="breadcrumb" role="navigation" aria-labelledby="system-breadcrumb"> <h2 id="system-breadcrumb" class="visually-hidden">Breadcrumb</h2> <ol> <li> <a href="/">Home</a> </li> <li> <a href="/news">News</a> </li> </ol> </nav> </div> </div> <div class="hero-section__title"> <div class="block block-layout-builder block-field-blocknodenewstitle"> <span class="field field--name-title field--type-string field--label-hidden"><h1>New DNA sequencing technique preserves cells’ locations within tissues</h1> </span> </div> </div> <div class="hero-section__description"> <div class="block block-layout-builder block-field-blocknodenewsbody"> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><div class="summary-only"> <p> Slide-DNA-seq helps researchers better understand spatial differences and patterns in complex tissues such as tumors.</p> </div> </div> </div> </div> <div class="hero-section__author"> <div class="block block-layout-builder block-extra-field-blocknodenewsextra-field-author-custom"> By Jessica Lau, Harvard Department of Stem Cell and Regenerative Biology </div> </div> <div class="hero-section__date"> <div class="block block-layout-builder block-field-blocknodenewscreated"> <span class="field field--name-created field--type-created field--label-hidden"><time datetime="2021-12-15T11:05:12-05:00" class="datetime">December 15, 2021</time> </span> </div> </div> </div> <div class="hero-section__right col-6"> <div class="hero-section__image"> <div class="block block-layout-builder block-field-blocknodenewsfield-image"> <div class="field field--name-field-image field--type-entity-reference field--label-hidden field__item"> <article class="media media--type-image media--view-mode-multiple-content-types-header"> <div class="field field--name-field-media-image field--type-image field--label-hidden field__item"> <picture> <source srcset="/files/styles/multiple_ct_header_desktop_xl/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=Mj-O2mVa 1x" media="all and (min-width: 1921px)" type="image/png" width="754" height="503"> <source srcset="/files/styles/multiple_ct_header_desktop_xl/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=Mj-O2mVa 1x" media="all and (min-width: 1601px) and (max-width: 1920px)" type="image/png" width="754" height="503"> <source srcset="/files/styles/multiple_ct_header_desktop/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=ZBfVHHl3 1x" media="all and (min-width: 1340px) and (max-width: 1600px)" type="image/png" width="736" height="520"> <source srcset="/files/styles/multiple_ct_header_laptop/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=NQXuPw1V 1x" media="all and (min-width: 800px) and (max-width: 1339px)" type="image/png" width="641" height="451"> <source srcset="/files/styles/multiple_ct_header_tablet/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=vEqZYhdy 1x" media="all and (min-width: 540px) and (max-width: 799px)" type="image/png" width="706" height="417"> <source srcset="/files/styles/multiple_ct_header_phone/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=raZa4Wiq 1x" media="all and (max-width: 539px)" type="image/png" width="499" height="294"> <img loading="eager" width="499" height="294" src="/files/styles/multiple_ct_header_phone/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=raZa4Wiq" alt="An image of how slide-DNA-seq &quot;sees&quot; cells' organization within a tumor." title="An image of how slide-DNA-seq &quot;sees&quot; cells' organization within a tumor." typeof="foaf:Image"> </picture> </div> <div class="media-caption"> <div class="media-caption__credit"> Credit: <a href="https://www.nature.com/articles/s41586-021-04217-4" target="_blank">Zhao T, Chiang Z, et al. <em>Nature</em>, 2021</a> </div> <div class="media-caption__description"> An image of how slide-DNA-seq "sees" cells' organization within a tumor. </div> </div> </article> </div> </div> </div> </div> </div> </div> <div class="content-section content-section_with-sidebars container"> <div class="row"> <div class="content-section__left col-2"> <div class="block block-better-social-sharing-buttons block-social-sharing-buttons-block"> <div style="display: none"><link rel="preload" href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg" as="image" type="image/svg+xml" crossorigin="anonymous"></div> <div class="social-sharing-buttons"> <a href="https://www.facebook.com/sharer/sharer.php?u=/taxonomy/term/592/feed&amp;title=" target="_blank" title="Share to Facebook" aria-label="Share to Facebook" class="social-sharing-buttons-button share-facebook" rel="noopener"> <svg aria-hidden="true" width="32px" height="32px" style="border-radius:100%;"> <use href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg#facebook" /> </svg> </a> <a href="https://twitter.com/intent/tweet?text=+/taxonomy/term/592/feed" target="_blank" title="Share to X" aria-label="Share to X" class="social-sharing-buttons-button share-x" rel="noopener"> <svg aria-hidden="true" width="32px" height="32px" style="border-radius:100%;"> <use href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg#x" /> </svg> </a> <a href="mailto:?subject=&amp;body=/taxonomy/term/592/feed" title="Share to Email" aria-label="Share to Email" class="social-sharing-buttons-button share-email" target="_blank" rel="noopener"> <svg aria-hidden="true" width="32px" height="32px" style="border-radius:100%;"> <use href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg#email" /> </svg> </a> </div> </div> </div> <div class="content-section__main col-8"> <div class="block block-layout-builder block-field-blocknodenewsbody"> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><p> Within complex tissues such as cancer tumors, individual cells can vary widely from each other. Internally, cancer cells can develop unique DNA mutations and genomic changes, potentially leading to drug resistance, metastasis, or relapse. Externally, the cells’ specific locations within the tissue also matter, since the local structure of a tumor and its surrounding tissues can affect cell state and drug permeability.</p> <p> To measure both genetic and local factors at the same time, researchers from Harvard University’s Department of Stem Cell and Regenerative Biology (HSCRB) and the Ó³»­´«Ã½ of MIT and Harvard developed a new technique of spatially-resolved DNA sequencing, called slide-DNA-seq. When further combined with spatially-resolved gene expression analysis, the technology gives researchers a better understanding of cancer progression and potential treatment.</p> <p> The researchers’ findings are published in the journal <a href="https://www.nature.com/articles/s41586-021-04217-4" target="_blank"><em>Nature</em></a>.</p> <p> Slide-DNA-seq analyzes slices of intact tissue, in which each cell remains in its original location — as opposed to conventional sequencing techniques, where cells are dissociated before DNA extraction. The researchers used microbeads, each tagged with a unique spatial barcode and bound to specially-prepared glass slides, to capture DNA from the tissue.&nbsp;</p> <p> "Each bead is about the size of a cell," said co-corresponding author&nbsp;<a href="/node/113836">Fei Chen</a>, who is an assistant professor in HSCRB and a core institute member at the Ó³»­´«Ã½. "Together, they are like individual pixels on a camera which takes snapshots of genomic alterations within each cell in the tissue."</p> <p> After measuring genomic changes, the researchers applied a related&nbsp;<a href="/node/488166">RNA-based Slide-seq method</a>&nbsp;Chen and collaborators developed in 2019, which used gene expression profiles to identify and map the locations of cell types and subtypes within a tissue slice.&nbsp;&nbsp;</p> <p> "We can use the same barcoded beads to capture the transcriptome from each cell, and combine these two measurements into a multi-modal image," Chen said.&nbsp;In other words, the researchers can see changes in both the cells’ DNA and gene expression within the context of tissues.</p> <p> The researchers applied the technique to a mouse model of metastatic cancer, as well as a primary tumor sample from a patient with colorectal cancer. In each tissue, the researchers were able to identify subpopulations of cancer cells in distinct regions, corresponding with unique genomic evolutionary paths and gene expression states.</p> <p> "We applied this to DNA sequencing and cancer, which are hugely important areas of medical research,"&nbsp;said co-corresponding author <a href="/node/113841">Jason Buenrostro</a>, who is a HSCRB assistant professor, an associate member of the Ó³»­´«Ã½, and co-director of the Ó³»­´«Ã½'s <a href="/node/768556">Gene Regulation Observatory</a>. "However, the technology also opens the door to more broadly measuring DNA molecules within tissues. As such, we imagine future approaches will use this work as a foundation to build tools that measure modifications to DNA as well, such as the epigenome."</p> <p> <em>This study received funding from the Allen Institute Distinguished Investigator Award, the National Institutes of Health, a National Human Genome Research Institute training grant, the Burroughs Wellcome Fund, and the Harvard Quantitative Biology Initiative.</em></p> <p> <em>Adapted from <a href="https://hscrb.harvard.edu/news/genomic-sequencing-that-preserves-cells-locations-within-tissues/" target="_blank">a story originally published by the Harvard University Department of Stem Cell and Regenerative Biology</a>.</em></p> </div> </div> <div class="block block-layout-builder block-field-blocknodenewsfield-news-pappers"> <h2>Paper(s) cited</h2> <div class="clearfix text-formatted field field--name-field-news-pappers field--type-text-long field--label-hidden field__item"><p> Zhao T, Chiang ZD, et al.&nbsp;<a href="https://www.nature.com/articles/s41586-021-04217-4" target="_blank">Spatial genomics enables multi-modal study of clonal heterogeneity in tissues</a>. <em>Nature</em>. DOI: 10.1038/s41586-021-04217-4.</p> </div> </div> <div class="block-node-broad-tags block block-layout-builder block-field-blocknodenewsfield-broad-tags"> <div class="block-node-broad-tags__row"> <div class="block-node-broad-tags__title">Tags:</div> <div class="field field--name-field-broad-tags field--type-entity-reference field--label-hidden field__items"> <div class="field__item"><a href="/broad-tags/genome-regulation-cellular-circuitry-and-epigenomics" hreflang="en">Genome Regulation, Cellular Circuitry and Epigenomics</a></div> <div class="field__item"><a href="/broad-tags/genome-regulation-cell-circuitry-and-epigenomics" hreflang="en">Genome regulation, cell circuitry, and epigenomics</a></div> </div> </div> </div> </div> <div class="content-section__right col-2"> <div class="block block-ctools block-entity-viewnode"> <article about="/news/new-dna-sequencing-technique-preserves-cells%E2%80%99-locations-within-tissues" class="node node--type-news node--promoted node--view-mode-sidebar"> <div class="node__content"> <div class="sidebar-group"> <div class="sidebar-group__content"> <div class="block block-layout-builder block-field-blocknodenewsfield-news-extra-info"> <div class="clearfix text-formatted field field--name-field-news-extra-info field--type-text-long field--label-hidden field__item"><h2> Related People</h2> <p> <a href="/node/113841">Jason Buenrostro</a></p> <p> <a href="/node/113836">Fei Chen</a><br> &nbsp;</p> <h2> Related Programs</h2> <p> <a href="/node/768556">Gene Regulation Observatory</a><br> &nbsp;</p> <h2> Related News</h2> <p> <a href="/node/488166"><img alt src="/files/styles/blog__557x415_/public/news/images/2019/Projections_of_Composite_MainStoryPage_1.gif?itok=UafnfWmI" style="width: 212px; height: 158px;"></a></p> <p> <a href="/node/488166">New tool uses RNA sequencing to chart rich maps of cellular and tissue function</a><br> &nbsp;</p> </div> </div> </div> </div> </div> </article> </div> </div> </div> </div> Fri, 01 Mar 2019 15:10:11 +0000 Namrata Sengupta 471461 at /news/researchers-map-new-cellular-atlas-acute-myeloid-leukemia <span class="field field--name-title field--type-string field--label-hidden"><h1>New DNA sequencing technique preserves cells’ locations within tissues</h1> </span> <span class="field field--name-uid field--type-entity-reference field--label-hidden"> <span>By Tom Ulrich</span> </span> <span class="field field--name-created field--type-created field--label-hidden"><time datetime="2021-12-15T11:05:12-05:00" class="datetime">December 15, 2021</time> </span> <div class="hero-section container"> <div class="hero-section__row row"> <div class="hero-section__content hero-section__content_left col-6"> <div class="hero-section__breadcrumbs"> <div class="block block-layout-builder block-extra-field-blocknodenewsbreadcrumbs"> <nav class="breadcrumb" role="navigation" aria-labelledby="system-breadcrumb"> <h2 id="system-breadcrumb" class="visually-hidden">Breadcrumb</h2> <ol> <li> <a href="/">Home</a> </li> <li> <a href="/news">News</a> </li> </ol> </nav> </div> </div> <div class="hero-section__title"> <div class="block block-layout-builder block-field-blocknodenewstitle"> <span class="field field--name-title field--type-string field--label-hidden"><h1>New DNA sequencing technique preserves cells’ locations within tissues</h1> </span> </div> </div> <div class="hero-section__description"> <div class="block block-layout-builder block-field-blocknodenewsbody"> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><div class="summary-only"> <p> Slide-DNA-seq helps researchers better understand spatial differences and patterns in complex tissues such as tumors.</p> </div> </div> </div> </div> <div class="hero-section__author"> <div class="block block-layout-builder block-extra-field-blocknodenewsextra-field-author-custom"> By Jessica Lau, Harvard Department of Stem Cell and Regenerative Biology </div> </div> <div class="hero-section__date"> <div class="block block-layout-builder block-field-blocknodenewscreated"> <span class="field field--name-created field--type-created field--label-hidden"><time datetime="2021-12-15T11:05:12-05:00" class="datetime">December 15, 2021</time> </span> </div> </div> </div> <div class="hero-section__right col-6"> <div class="hero-section__image"> <div class="block block-layout-builder block-field-blocknodenewsfield-image"> <div class="field field--name-field-image field--type-entity-reference field--label-hidden field__item"> <article class="media media--type-image media--view-mode-multiple-content-types-header"> <div class="field field--name-field-media-image field--type-image field--label-hidden field__item"> <picture> <source srcset="/files/styles/multiple_ct_header_desktop_xl/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=Mj-O2mVa 1x" media="all and (min-width: 1921px)" type="image/png" width="754" height="503"> <source srcset="/files/styles/multiple_ct_header_desktop_xl/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=Mj-O2mVa 1x" media="all and (min-width: 1601px) and (max-width: 1920px)" type="image/png" width="754" height="503"> <source srcset="/files/styles/multiple_ct_header_desktop/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=ZBfVHHl3 1x" media="all and (min-width: 1340px) and (max-width: 1600px)" type="image/png" width="736" height="520"> <source srcset="/files/styles/multiple_ct_header_laptop/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=NQXuPw1V 1x" media="all and (min-width: 800px) and (max-width: 1339px)" type="image/png" width="641" height="451"> <source srcset="/files/styles/multiple_ct_header_tablet/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=vEqZYhdy 1x" media="all and (min-width: 540px) and (max-width: 799px)" type="image/png" width="706" height="417"> <source srcset="/files/styles/multiple_ct_header_phone/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=raZa4Wiq 1x" media="all and (max-width: 539px)" type="image/png" width="499" height="294"> <img loading="eager" width="499" height="294" src="/files/styles/multiple_ct_header_phone/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=raZa4Wiq" alt="An image of how slide-DNA-seq &quot;sees&quot; cells' organization within a tumor." title="An image of how slide-DNA-seq &quot;sees&quot; cells' organization within a tumor." typeof="foaf:Image"> </picture> </div> <div class="media-caption"> <div class="media-caption__credit"> Credit: <a href="https://www.nature.com/articles/s41586-021-04217-4" target="_blank">Zhao T, Chiang Z, et al. <em>Nature</em>, 2021</a> </div> <div class="media-caption__description"> An image of how slide-DNA-seq "sees" cells' organization within a tumor. </div> </div> </article> </div> </div> </div> </div> </div> </div> <div class="content-section content-section_with-sidebars container"> <div class="row"> <div class="content-section__left col-2"> <div class="block block-better-social-sharing-buttons block-social-sharing-buttons-block"> <div style="display: none"><link rel="preload" href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg" as="image" type="image/svg+xml" crossorigin="anonymous"></div> <div class="social-sharing-buttons"> <a href="https://www.facebook.com/sharer/sharer.php?u=/taxonomy/term/592/feed&amp;title=" target="_blank" title="Share to Facebook" aria-label="Share to Facebook" class="social-sharing-buttons-button share-facebook" rel="noopener"> <svg aria-hidden="true" width="32px" height="32px" style="border-radius:100%;"> <use href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg#facebook" /> </svg> </a> <a href="https://twitter.com/intent/tweet?text=+/taxonomy/term/592/feed" target="_blank" title="Share to X" aria-label="Share to X" class="social-sharing-buttons-button share-x" rel="noopener"> <svg aria-hidden="true" width="32px" height="32px" style="border-radius:100%;"> <use href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg#x" /> </svg> </a> <a href="mailto:?subject=&amp;body=/taxonomy/term/592/feed" title="Share to Email" aria-label="Share to Email" class="social-sharing-buttons-button share-email" target="_blank" rel="noopener"> <svg aria-hidden="true" width="32px" height="32px" style="border-radius:100%;"> <use href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg#email" /> </svg> </a> </div> </div> </div> <div class="content-section__main col-8"> <div class="block block-layout-builder block-field-blocknodenewsbody"> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><p> Within complex tissues such as cancer tumors, individual cells can vary widely from each other. Internally, cancer cells can develop unique DNA mutations and genomic changes, potentially leading to drug resistance, metastasis, or relapse. Externally, the cells’ specific locations within the tissue also matter, since the local structure of a tumor and its surrounding tissues can affect cell state and drug permeability.</p> <p> To measure both genetic and local factors at the same time, researchers from Harvard University’s Department of Stem Cell and Regenerative Biology (HSCRB) and the Ó³»­´«Ã½ of MIT and Harvard developed a new technique of spatially-resolved DNA sequencing, called slide-DNA-seq. When further combined with spatially-resolved gene expression analysis, the technology gives researchers a better understanding of cancer progression and potential treatment.</p> <p> The researchers’ findings are published in the journal <a href="https://www.nature.com/articles/s41586-021-04217-4" target="_blank"><em>Nature</em></a>.</p> <p> Slide-DNA-seq analyzes slices of intact tissue, in which each cell remains in its original location — as opposed to conventional sequencing techniques, where cells are dissociated before DNA extraction. The researchers used microbeads, each tagged with a unique spatial barcode and bound to specially-prepared glass slides, to capture DNA from the tissue.&nbsp;</p> <p> "Each bead is about the size of a cell," said co-corresponding author&nbsp;<a href="/node/113836">Fei Chen</a>, who is an assistant professor in HSCRB and a core institute member at the Ó³»­´«Ã½. "Together, they are like individual pixels on a camera which takes snapshots of genomic alterations within each cell in the tissue."</p> <p> After measuring genomic changes, the researchers applied a related&nbsp;<a href="/node/488166">RNA-based Slide-seq method</a>&nbsp;Chen and collaborators developed in 2019, which used gene expression profiles to identify and map the locations of cell types and subtypes within a tissue slice.&nbsp;&nbsp;</p> <p> "We can use the same barcoded beads to capture the transcriptome from each cell, and combine these two measurements into a multi-modal image," Chen said.&nbsp;In other words, the researchers can see changes in both the cells’ DNA and gene expression within the context of tissues.</p> <p> The researchers applied the technique to a mouse model of metastatic cancer, as well as a primary tumor sample from a patient with colorectal cancer. In each tissue, the researchers were able to identify subpopulations of cancer cells in distinct regions, corresponding with unique genomic evolutionary paths and gene expression states.</p> <p> "We applied this to DNA sequencing and cancer, which are hugely important areas of medical research,"&nbsp;said co-corresponding author <a href="/node/113841">Jason Buenrostro</a>, who is a HSCRB assistant professor, an associate member of the Ó³»­´«Ã½, and co-director of the Ó³»­´«Ã½'s <a href="/node/768556">Gene Regulation Observatory</a>. "However, the technology also opens the door to more broadly measuring DNA molecules within tissues. As such, we imagine future approaches will use this work as a foundation to build tools that measure modifications to DNA as well, such as the epigenome."</p> <p> <em>This study received funding from the Allen Institute Distinguished Investigator Award, the National Institutes of Health, a National Human Genome Research Institute training grant, the Burroughs Wellcome Fund, and the Harvard Quantitative Biology Initiative.</em></p> <p> <em>Adapted from <a href="https://hscrb.harvard.edu/news/genomic-sequencing-that-preserves-cells-locations-within-tissues/" target="_blank">a story originally published by the Harvard University Department of Stem Cell and Regenerative Biology</a>.</em></p> </div> </div> <div class="block block-layout-builder block-field-blocknodenewsfield-news-pappers"> <h2>Paper(s) cited</h2> <div class="clearfix text-formatted field field--name-field-news-pappers field--type-text-long field--label-hidden field__item"><p> Zhao T, Chiang ZD, et al.&nbsp;<a href="https://www.nature.com/articles/s41586-021-04217-4" target="_blank">Spatial genomics enables multi-modal study of clonal heterogeneity in tissues</a>. <em>Nature</em>. DOI: 10.1038/s41586-021-04217-4.</p> </div> </div> <div class="block-node-broad-tags block block-layout-builder block-field-blocknodenewsfield-broad-tags"> <div class="block-node-broad-tags__row"> <div class="block-node-broad-tags__title">Tags:</div> <div class="field field--name-field-broad-tags field--type-entity-reference field--label-hidden field__items"> <div class="field__item"><a href="/broad-tags/genome-regulation-cellular-circuitry-and-epigenomics" hreflang="en">Genome Regulation, Cellular Circuitry and Epigenomics</a></div> <div class="field__item"><a href="/broad-tags/genome-regulation-cell-circuitry-and-epigenomics" hreflang="en">Genome regulation, cell circuitry, and epigenomics</a></div> </div> </div> </div> </div> <div class="content-section__right col-2"> <div class="block block-ctools block-entity-viewnode"> <article about="/news/new-dna-sequencing-technique-preserves-cells%E2%80%99-locations-within-tissues" class="node node--type-news node--promoted node--view-mode-sidebar"> <div class="node__content"> <div class="sidebar-group"> <div class="sidebar-group__content"> <div class="block block-layout-builder block-field-blocknodenewsfield-news-extra-info"> <div class="clearfix text-formatted field field--name-field-news-extra-info field--type-text-long field--label-hidden field__item"><h2> Related People</h2> <p> <a href="/node/113841">Jason Buenrostro</a></p> <p> <a href="/node/113836">Fei Chen</a><br> &nbsp;</p> <h2> Related Programs</h2> <p> <a href="/node/768556">Gene Regulation Observatory</a><br> &nbsp;</p> <h2> Related News</h2> <p> <a href="/node/488166"><img alt src="/files/styles/blog__557x415_/public/news/images/2019/Projections_of_Composite_MainStoryPage_1.gif?itok=UafnfWmI" style="width: 212px; height: 158px;"></a></p> <p> <a href="/node/488166">New tool uses RNA sequencing to chart rich maps of cellular and tissue function</a><br> &nbsp;</p> </div> </div> </div> </div> </div> </article> </div> </div> </div> </div> Thu, 28 Feb 2019 16:05:46 +0000 tulrich@broadinstitute.org 470061 at /news/new-type-map-connects-dots-cellular-reprogramming <span class="field field--name-title field--type-string field--label-hidden"><h1>New DNA sequencing technique preserves cells’ locations within tissues</h1> </span> <span class="field field--name-uid field--type-entity-reference field--label-hidden"> <span>By Tom Ulrich</span> </span> <span class="field field--name-created field--type-created field--label-hidden"><time datetime="2021-12-15T11:05:12-05:00" class="datetime">December 15, 2021</time> </span> <div class="hero-section container"> <div class="hero-section__row row"> <div class="hero-section__content hero-section__content_left col-6"> <div class="hero-section__breadcrumbs"> <div class="block block-layout-builder block-extra-field-blocknodenewsbreadcrumbs"> <nav class="breadcrumb" role="navigation" aria-labelledby="system-breadcrumb"> <h2 id="system-breadcrumb" class="visually-hidden">Breadcrumb</h2> <ol> <li> <a href="/">Home</a> </li> <li> <a href="/news">News</a> </li> </ol> </nav> </div> </div> <div class="hero-section__title"> <div class="block block-layout-builder block-field-blocknodenewstitle"> <span class="field field--name-title field--type-string field--label-hidden"><h1>New DNA sequencing technique preserves cells’ locations within tissues</h1> </span> </div> </div> <div class="hero-section__description"> <div class="block block-layout-builder block-field-blocknodenewsbody"> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><div class="summary-only"> <p> Slide-DNA-seq helps researchers better understand spatial differences and patterns in complex tissues such as tumors.</p> </div> </div> </div> </div> <div class="hero-section__author"> <div class="block block-layout-builder block-extra-field-blocknodenewsextra-field-author-custom"> By Jessica Lau, Harvard Department of Stem Cell and Regenerative Biology </div> </div> <div class="hero-section__date"> <div class="block block-layout-builder block-field-blocknodenewscreated"> <span class="field field--name-created field--type-created field--label-hidden"><time datetime="2021-12-15T11:05:12-05:00" class="datetime">December 15, 2021</time> </span> </div> </div> </div> <div class="hero-section__right col-6"> <div class="hero-section__image"> <div class="block block-layout-builder block-field-blocknodenewsfield-image"> <div class="field field--name-field-image field--type-entity-reference field--label-hidden field__item"> <article class="media media--type-image media--view-mode-multiple-content-types-header"> <div class="field field--name-field-media-image field--type-image field--label-hidden field__item"> <picture> <source srcset="/files/styles/multiple_ct_header_desktop_xl/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=Mj-O2mVa 1x" media="all and (min-width: 1921px)" type="image/png" width="754" height="503"> <source srcset="/files/styles/multiple_ct_header_desktop_xl/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=Mj-O2mVa 1x" media="all and (min-width: 1601px) and (max-width: 1920px)" type="image/png" width="754" height="503"> <source srcset="/files/styles/multiple_ct_header_desktop/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=ZBfVHHl3 1x" media="all and (min-width: 1340px) and (max-width: 1600px)" type="image/png" width="736" height="520"> <source srcset="/files/styles/multiple_ct_header_laptop/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=NQXuPw1V 1x" media="all and (min-width: 800px) and (max-width: 1339px)" type="image/png" width="641" height="451"> <source srcset="/files/styles/multiple_ct_header_tablet/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=vEqZYhdy 1x" media="all and (min-width: 540px) and (max-width: 799px)" type="image/png" width="706" height="417"> <source srcset="/files/styles/multiple_ct_header_phone/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=raZa4Wiq 1x" media="all and (max-width: 539px)" type="image/png" width="499" height="294"> <img loading="eager" width="499" height="294" src="/files/styles/multiple_ct_header_phone/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=raZa4Wiq" alt="An image of how slide-DNA-seq &quot;sees&quot; cells' organization within a tumor." title="An image of how slide-DNA-seq &quot;sees&quot; cells' organization within a tumor." typeof="foaf:Image"> </picture> </div> <div class="media-caption"> <div class="media-caption__credit"> Credit: <a href="https://www.nature.com/articles/s41586-021-04217-4" target="_blank">Zhao T, Chiang Z, et al. <em>Nature</em>, 2021</a> </div> <div class="media-caption__description"> An image of how slide-DNA-seq "sees" cells' organization within a tumor. </div> </div> </article> </div> </div> </div> </div> </div> </div> <div class="content-section content-section_with-sidebars container"> <div class="row"> <div class="content-section__left col-2"> <div class="block block-better-social-sharing-buttons block-social-sharing-buttons-block"> <div style="display: none"><link rel="preload" href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg" as="image" type="image/svg+xml" crossorigin="anonymous"></div> <div class="social-sharing-buttons"> <a href="https://www.facebook.com/sharer/sharer.php?u=/taxonomy/term/592/feed&amp;title=" target="_blank" title="Share to Facebook" aria-label="Share to Facebook" class="social-sharing-buttons-button share-facebook" rel="noopener"> <svg aria-hidden="true" width="32px" height="32px" style="border-radius:100%;"> <use href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg#facebook" /> </svg> </a> <a href="https://twitter.com/intent/tweet?text=+/taxonomy/term/592/feed" target="_blank" title="Share to X" aria-label="Share to X" class="social-sharing-buttons-button share-x" rel="noopener"> <svg aria-hidden="true" width="32px" height="32px" style="border-radius:100%;"> <use href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg#x" /> </svg> </a> <a href="mailto:?subject=&amp;body=/taxonomy/term/592/feed" title="Share to Email" aria-label="Share to Email" class="social-sharing-buttons-button share-email" target="_blank" rel="noopener"> <svg aria-hidden="true" width="32px" height="32px" style="border-radius:100%;"> <use href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg#email" /> </svg> </a> </div> </div> </div> <div class="content-section__main col-8"> <div class="block block-layout-builder block-field-blocknodenewsbody"> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><p> Within complex tissues such as cancer tumors, individual cells can vary widely from each other. Internally, cancer cells can develop unique DNA mutations and genomic changes, potentially leading to drug resistance, metastasis, or relapse. Externally, the cells’ specific locations within the tissue also matter, since the local structure of a tumor and its surrounding tissues can affect cell state and drug permeability.</p> <p> To measure both genetic and local factors at the same time, researchers from Harvard University’s Department of Stem Cell and Regenerative Biology (HSCRB) and the Ó³»­´«Ã½ of MIT and Harvard developed a new technique of spatially-resolved DNA sequencing, called slide-DNA-seq. When further combined with spatially-resolved gene expression analysis, the technology gives researchers a better understanding of cancer progression and potential treatment.</p> <p> The researchers’ findings are published in the journal <a href="https://www.nature.com/articles/s41586-021-04217-4" target="_blank"><em>Nature</em></a>.</p> <p> Slide-DNA-seq analyzes slices of intact tissue, in which each cell remains in its original location — as opposed to conventional sequencing techniques, where cells are dissociated before DNA extraction. The researchers used microbeads, each tagged with a unique spatial barcode and bound to specially-prepared glass slides, to capture DNA from the tissue.&nbsp;</p> <p> "Each bead is about the size of a cell," said co-corresponding author&nbsp;<a href="/node/113836">Fei Chen</a>, who is an assistant professor in HSCRB and a core institute member at the Ó³»­´«Ã½. "Together, they are like individual pixels on a camera which takes snapshots of genomic alterations within each cell in the tissue."</p> <p> After measuring genomic changes, the researchers applied a related&nbsp;<a href="/node/488166">RNA-based Slide-seq method</a>&nbsp;Chen and collaborators developed in 2019, which used gene expression profiles to identify and map the locations of cell types and subtypes within a tissue slice.&nbsp;&nbsp;</p> <p> "We can use the same barcoded beads to capture the transcriptome from each cell, and combine these two measurements into a multi-modal image," Chen said.&nbsp;In other words, the researchers can see changes in both the cells’ DNA and gene expression within the context of tissues.</p> <p> The researchers applied the technique to a mouse model of metastatic cancer, as well as a primary tumor sample from a patient with colorectal cancer. In each tissue, the researchers were able to identify subpopulations of cancer cells in distinct regions, corresponding with unique genomic evolutionary paths and gene expression states.</p> <p> "We applied this to DNA sequencing and cancer, which are hugely important areas of medical research,"&nbsp;said co-corresponding author <a href="/node/113841">Jason Buenrostro</a>, who is a HSCRB assistant professor, an associate member of the Ó³»­´«Ã½, and co-director of the Ó³»­´«Ã½'s <a href="/node/768556">Gene Regulation Observatory</a>. "However, the technology also opens the door to more broadly measuring DNA molecules within tissues. As such, we imagine future approaches will use this work as a foundation to build tools that measure modifications to DNA as well, such as the epigenome."</p> <p> <em>This study received funding from the Allen Institute Distinguished Investigator Award, the National Institutes of Health, a National Human Genome Research Institute training grant, the Burroughs Wellcome Fund, and the Harvard Quantitative Biology Initiative.</em></p> <p> <em>Adapted from <a href="https://hscrb.harvard.edu/news/genomic-sequencing-that-preserves-cells-locations-within-tissues/" target="_blank">a story originally published by the Harvard University Department of Stem Cell and Regenerative Biology</a>.</em></p> </div> </div> <div class="block block-layout-builder block-field-blocknodenewsfield-news-pappers"> <h2>Paper(s) cited</h2> <div class="clearfix text-formatted field field--name-field-news-pappers field--type-text-long field--label-hidden field__item"><p> Zhao T, Chiang ZD, et al.&nbsp;<a href="https://www.nature.com/articles/s41586-021-04217-4" target="_blank">Spatial genomics enables multi-modal study of clonal heterogeneity in tissues</a>. <em>Nature</em>. DOI: 10.1038/s41586-021-04217-4.</p> </div> </div> <div class="block-node-broad-tags block block-layout-builder block-field-blocknodenewsfield-broad-tags"> <div class="block-node-broad-tags__row"> <div class="block-node-broad-tags__title">Tags:</div> <div class="field field--name-field-broad-tags field--type-entity-reference field--label-hidden field__items"> <div class="field__item"><a href="/broad-tags/genome-regulation-cellular-circuitry-and-epigenomics" hreflang="en">Genome Regulation, Cellular Circuitry and Epigenomics</a></div> <div class="field__item"><a href="/broad-tags/genome-regulation-cell-circuitry-and-epigenomics" hreflang="en">Genome regulation, cell circuitry, and epigenomics</a></div> </div> </div> </div> </div> <div class="content-section__right col-2"> <div class="block block-ctools block-entity-viewnode"> <article about="/news/new-dna-sequencing-technique-preserves-cells%E2%80%99-locations-within-tissues" class="node node--type-news node--promoted node--view-mode-sidebar"> <div class="node__content"> <div class="sidebar-group"> <div class="sidebar-group__content"> <div class="block block-layout-builder block-field-blocknodenewsfield-news-extra-info"> <div class="clearfix text-formatted field field--name-field-news-extra-info field--type-text-long field--label-hidden field__item"><h2> Related People</h2> <p> <a href="/node/113841">Jason Buenrostro</a></p> <p> <a href="/node/113836">Fei Chen</a><br> &nbsp;</p> <h2> Related Programs</h2> <p> <a href="/node/768556">Gene Regulation Observatory</a><br> &nbsp;</p> <h2> Related News</h2> <p> <a href="/node/488166"><img alt src="/files/styles/blog__557x415_/public/news/images/2019/Projections_of_Composite_MainStoryPage_1.gif?itok=UafnfWmI" style="width: 212px; height: 158px;"></a></p> <p> <a href="/node/488166">New tool uses RNA sequencing to chart rich maps of cellular and tissue function</a><br> &nbsp;</p> </div> </div> </div> </div> </div> </article> </div> </div> </div> </div> Thu, 31 Jan 2019 16:01:46 +0000 tulrich@broadinstitute.org 449611 at /news/new-multi-pronged-method-probes-how-noncoding-dna-affects-gene-expression <span class="field field--name-title field--type-string field--label-hidden"><h1>New DNA sequencing technique preserves cells’ locations within tissues</h1> </span> <span class="field field--name-uid field--type-entity-reference field--label-hidden"> <span>By Tom Ulrich</span> </span> <span class="field field--name-created field--type-created field--label-hidden"><time datetime="2021-12-15T11:05:12-05:00" class="datetime">December 15, 2021</time> </span> <div class="hero-section container"> <div class="hero-section__row row"> <div class="hero-section__content hero-section__content_left col-6"> <div class="hero-section__breadcrumbs"> <div class="block block-layout-builder block-extra-field-blocknodenewsbreadcrumbs"> <nav class="breadcrumb" role="navigation" aria-labelledby="system-breadcrumb"> <h2 id="system-breadcrumb" class="visually-hidden">Breadcrumb</h2> <ol> <li> <a href="/">Home</a> </li> <li> <a href="/news">News</a> </li> </ol> </nav> </div> </div> <div class="hero-section__title"> <div class="block block-layout-builder block-field-blocknodenewstitle"> <span class="field field--name-title field--type-string field--label-hidden"><h1>New DNA sequencing technique preserves cells’ locations within tissues</h1> </span> </div> </div> <div class="hero-section__description"> <div class="block block-layout-builder block-field-blocknodenewsbody"> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><div class="summary-only"> <p> Slide-DNA-seq helps researchers better understand spatial differences and patterns in complex tissues such as tumors.</p> </div> </div> </div> </div> <div class="hero-section__author"> <div class="block block-layout-builder block-extra-field-blocknodenewsextra-field-author-custom"> By Jessica Lau, Harvard Department of Stem Cell and Regenerative Biology </div> </div> <div class="hero-section__date"> <div class="block block-layout-builder block-field-blocknodenewscreated"> <span class="field field--name-created field--type-created field--label-hidden"><time datetime="2021-12-15T11:05:12-05:00" class="datetime">December 15, 2021</time> </span> </div> </div> </div> <div class="hero-section__right col-6"> <div class="hero-section__image"> <div class="block block-layout-builder block-field-blocknodenewsfield-image"> <div class="field field--name-field-image field--type-entity-reference field--label-hidden field__item"> <article class="media media--type-image media--view-mode-multiple-content-types-header"> <div class="field field--name-field-media-image field--type-image field--label-hidden field__item"> <picture> <source srcset="/files/styles/multiple_ct_header_desktop_xl/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=Mj-O2mVa 1x" media="all and (min-width: 1921px)" type="image/png" width="754" height="503"> <source srcset="/files/styles/multiple_ct_header_desktop_xl/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=Mj-O2mVa 1x" media="all and (min-width: 1601px) and (max-width: 1920px)" type="image/png" width="754" height="503"> <source srcset="/files/styles/multiple_ct_header_desktop/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=ZBfVHHl3 1x" media="all and (min-width: 1340px) and (max-width: 1600px)" type="image/png" width="736" height="520"> <source srcset="/files/styles/multiple_ct_header_laptop/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=NQXuPw1V 1x" media="all and (min-width: 800px) and (max-width: 1339px)" type="image/png" width="641" height="451"> <source srcset="/files/styles/multiple_ct_header_tablet/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=vEqZYhdy 1x" media="all and (min-width: 540px) and (max-width: 799px)" type="image/png" width="706" height="417"> <source srcset="/files/styles/multiple_ct_header_phone/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=raZa4Wiq 1x" media="all and (max-width: 539px)" type="image/png" width="499" height="294"> <img loading="eager" width="499" height="294" src="/files/styles/multiple_ct_header_phone/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=raZa4Wiq" alt="An image of how slide-DNA-seq &quot;sees&quot; cells' organization within a tumor." title="An image of how slide-DNA-seq &quot;sees&quot; cells' organization within a tumor." typeof="foaf:Image"> </picture> </div> <div class="media-caption"> <div class="media-caption__credit"> Credit: <a href="https://www.nature.com/articles/s41586-021-04217-4" target="_blank">Zhao T, Chiang Z, et al. <em>Nature</em>, 2021</a> </div> <div class="media-caption__description"> An image of how slide-DNA-seq "sees" cells' organization within a tumor. </div> </div> </article> </div> </div> </div> </div> </div> </div> <div class="content-section content-section_with-sidebars container"> <div class="row"> <div class="content-section__left col-2"> <div class="block block-better-social-sharing-buttons block-social-sharing-buttons-block"> <div style="display: none"><link rel="preload" href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg" as="image" type="image/svg+xml" crossorigin="anonymous"></div> <div class="social-sharing-buttons"> <a href="https://www.facebook.com/sharer/sharer.php?u=/taxonomy/term/592/feed&amp;title=" target="_blank" title="Share to Facebook" aria-label="Share to Facebook" class="social-sharing-buttons-button share-facebook" rel="noopener"> <svg aria-hidden="true" width="32px" height="32px" style="border-radius:100%;"> <use href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg#facebook" /> </svg> </a> <a href="https://twitter.com/intent/tweet?text=+/taxonomy/term/592/feed" target="_blank" title="Share to X" aria-label="Share to X" class="social-sharing-buttons-button share-x" rel="noopener"> <svg aria-hidden="true" width="32px" height="32px" style="border-radius:100%;"> <use href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg#x" /> </svg> </a> <a href="mailto:?subject=&amp;body=/taxonomy/term/592/feed" title="Share to Email" aria-label="Share to Email" class="social-sharing-buttons-button share-email" target="_blank" rel="noopener"> <svg aria-hidden="true" width="32px" height="32px" style="border-radius:100%;"> <use href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg#email" /> </svg> </a> </div> </div> </div> <div class="content-section__main col-8"> <div class="block block-layout-builder block-field-blocknodenewsbody"> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><p> Within complex tissues such as cancer tumors, individual cells can vary widely from each other. Internally, cancer cells can develop unique DNA mutations and genomic changes, potentially leading to drug resistance, metastasis, or relapse. Externally, the cells’ specific locations within the tissue also matter, since the local structure of a tumor and its surrounding tissues can affect cell state and drug permeability.</p> <p> To measure both genetic and local factors at the same time, researchers from Harvard University’s Department of Stem Cell and Regenerative Biology (HSCRB) and the Ó³»­´«Ã½ of MIT and Harvard developed a new technique of spatially-resolved DNA sequencing, called slide-DNA-seq. When further combined with spatially-resolved gene expression analysis, the technology gives researchers a better understanding of cancer progression and potential treatment.</p> <p> The researchers’ findings are published in the journal <a href="https://www.nature.com/articles/s41586-021-04217-4" target="_blank"><em>Nature</em></a>.</p> <p> Slide-DNA-seq analyzes slices of intact tissue, in which each cell remains in its original location — as opposed to conventional sequencing techniques, where cells are dissociated before DNA extraction. The researchers used microbeads, each tagged with a unique spatial barcode and bound to specially-prepared glass slides, to capture DNA from the tissue.&nbsp;</p> <p> "Each bead is about the size of a cell," said co-corresponding author&nbsp;<a href="/node/113836">Fei Chen</a>, who is an assistant professor in HSCRB and a core institute member at the Ó³»­´«Ã½. "Together, they are like individual pixels on a camera which takes snapshots of genomic alterations within each cell in the tissue."</p> <p> After measuring genomic changes, the researchers applied a related&nbsp;<a href="/node/488166">RNA-based Slide-seq method</a>&nbsp;Chen and collaborators developed in 2019, which used gene expression profiles to identify and map the locations of cell types and subtypes within a tissue slice.&nbsp;&nbsp;</p> <p> "We can use the same barcoded beads to capture the transcriptome from each cell, and combine these two measurements into a multi-modal image," Chen said.&nbsp;In other words, the researchers can see changes in both the cells’ DNA and gene expression within the context of tissues.</p> <p> The researchers applied the technique to a mouse model of metastatic cancer, as well as a primary tumor sample from a patient with colorectal cancer. In each tissue, the researchers were able to identify subpopulations of cancer cells in distinct regions, corresponding with unique genomic evolutionary paths and gene expression states.</p> <p> "We applied this to DNA sequencing and cancer, which are hugely important areas of medical research,"&nbsp;said co-corresponding author <a href="/node/113841">Jason Buenrostro</a>, who is a HSCRB assistant professor, an associate member of the Ó³»­´«Ã½, and co-director of the Ó³»­´«Ã½'s <a href="/node/768556">Gene Regulation Observatory</a>. "However, the technology also opens the door to more broadly measuring DNA molecules within tissues. As such, we imagine future approaches will use this work as a foundation to build tools that measure modifications to DNA as well, such as the epigenome."</p> <p> <em>This study received funding from the Allen Institute Distinguished Investigator Award, the National Institutes of Health, a National Human Genome Research Institute training grant, the Burroughs Wellcome Fund, and the Harvard Quantitative Biology Initiative.</em></p> <p> <em>Adapted from <a href="https://hscrb.harvard.edu/news/genomic-sequencing-that-preserves-cells-locations-within-tissues/" target="_blank">a story originally published by the Harvard University Department of Stem Cell and Regenerative Biology</a>.</em></p> </div> </div> <div class="block block-layout-builder block-field-blocknodenewsfield-news-pappers"> <h2>Paper(s) cited</h2> <div class="clearfix text-formatted field field--name-field-news-pappers field--type-text-long field--label-hidden field__item"><p> Zhao T, Chiang ZD, et al.&nbsp;<a href="https://www.nature.com/articles/s41586-021-04217-4" target="_blank">Spatial genomics enables multi-modal study of clonal heterogeneity in tissues</a>. <em>Nature</em>. DOI: 10.1038/s41586-021-04217-4.</p> </div> </div> <div class="block-node-broad-tags block block-layout-builder block-field-blocknodenewsfield-broad-tags"> <div class="block-node-broad-tags__row"> <div class="block-node-broad-tags__title">Tags:</div> <div class="field field--name-field-broad-tags field--type-entity-reference field--label-hidden field__items"> <div class="field__item"><a href="/broad-tags/genome-regulation-cellular-circuitry-and-epigenomics" hreflang="en">Genome Regulation, Cellular Circuitry and Epigenomics</a></div> <div class="field__item"><a href="/broad-tags/genome-regulation-cell-circuitry-and-epigenomics" hreflang="en">Genome regulation, cell circuitry, and epigenomics</a></div> </div> </div> </div> </div> <div class="content-section__right col-2"> <div class="block block-ctools block-entity-viewnode"> <article about="/news/new-dna-sequencing-technique-preserves-cells%E2%80%99-locations-within-tissues" class="node node--type-news node--promoted node--view-mode-sidebar"> <div class="node__content"> <div class="sidebar-group"> <div class="sidebar-group__content"> <div class="block block-layout-builder block-field-blocknodenewsfield-news-extra-info"> <div class="clearfix text-formatted field field--name-field-news-extra-info field--type-text-long field--label-hidden field__item"><h2> Related People</h2> <p> <a href="/node/113841">Jason Buenrostro</a></p> <p> <a href="/node/113836">Fei Chen</a><br> &nbsp;</p> <h2> Related Programs</h2> <p> <a href="/node/768556">Gene Regulation Observatory</a><br> &nbsp;</p> <h2> Related News</h2> <p> <a href="/node/488166"><img alt src="/files/styles/blog__557x415_/public/news/images/2019/Projections_of_Composite_MainStoryPage_1.gif?itok=UafnfWmI" style="width: 212px; height: 158px;"></a></p> <p> <a href="/node/488166">New tool uses RNA sequencing to chart rich maps of cellular and tissue function</a><br> &nbsp;</p> </div> </div> </div> </div> </div> </article> </div> </div> </div> </div> Fri, 21 Dec 2018 14:41:08 +0000 tulrich@broadinstitute.org 421636 at /news/crosstalk-between-immune-and-intestinal-stem-cells-may-help-maintain-healthy-gut <span class="field field--name-title field--type-string field--label-hidden"><h1>New DNA sequencing technique preserves cells’ locations within tissues</h1> </span> <span class="field field--name-uid field--type-entity-reference field--label-hidden"> <span>By Tom Ulrich</span> </span> <span class="field field--name-created field--type-created field--label-hidden"><time datetime="2021-12-15T11:05:12-05:00" class="datetime">December 15, 2021</time> </span> <div class="hero-section container"> <div class="hero-section__row row"> <div class="hero-section__content hero-section__content_left col-6"> <div class="hero-section__breadcrumbs"> <div class="block block-layout-builder block-extra-field-blocknodenewsbreadcrumbs"> <nav class="breadcrumb" role="navigation" aria-labelledby="system-breadcrumb"> <h2 id="system-breadcrumb" class="visually-hidden">Breadcrumb</h2> <ol> <li> <a href="/">Home</a> </li> <li> <a href="/news">News</a> </li> </ol> </nav> </div> </div> <div class="hero-section__title"> <div class="block block-layout-builder block-field-blocknodenewstitle"> <span class="field field--name-title field--type-string field--label-hidden"><h1>New DNA sequencing technique preserves cells’ locations within tissues</h1> </span> </div> </div> <div class="hero-section__description"> <div class="block block-layout-builder block-field-blocknodenewsbody"> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><div class="summary-only"> <p> Slide-DNA-seq helps researchers better understand spatial differences and patterns in complex tissues such as tumors.</p> </div> </div> </div> </div> <div class="hero-section__author"> <div class="block block-layout-builder block-extra-field-blocknodenewsextra-field-author-custom"> By Jessica Lau, Harvard Department of Stem Cell and Regenerative Biology </div> </div> <div class="hero-section__date"> <div class="block block-layout-builder block-field-blocknodenewscreated"> <span class="field field--name-created field--type-created field--label-hidden"><time datetime="2021-12-15T11:05:12-05:00" class="datetime">December 15, 2021</time> </span> </div> </div> </div> <div class="hero-section__right col-6"> <div class="hero-section__image"> <div class="block block-layout-builder block-field-blocknodenewsfield-image"> <div class="field field--name-field-image field--type-entity-reference field--label-hidden field__item"> <article class="media media--type-image media--view-mode-multiple-content-types-header"> <div class="field field--name-field-media-image field--type-image field--label-hidden field__item"> <picture> <source srcset="/files/styles/multiple_ct_header_desktop_xl/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=Mj-O2mVa 1x" media="all and (min-width: 1921px)" type="image/png" width="754" height="503"> <source srcset="/files/styles/multiple_ct_header_desktop_xl/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=Mj-O2mVa 1x" media="all and (min-width: 1601px) and (max-width: 1920px)" type="image/png" width="754" height="503"> <source srcset="/files/styles/multiple_ct_header_desktop/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=ZBfVHHl3 1x" media="all and (min-width: 1340px) and (max-width: 1600px)" type="image/png" width="736" height="520"> <source srcset="/files/styles/multiple_ct_header_laptop/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=NQXuPw1V 1x" media="all and (min-width: 800px) and (max-width: 1339px)" type="image/png" width="641" height="451"> <source srcset="/files/styles/multiple_ct_header_tablet/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=vEqZYhdy 1x" media="all and (min-width: 540px) and (max-width: 799px)" type="image/png" width="706" height="417"> <source srcset="/files/styles/multiple_ct_header_phone/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=raZa4Wiq 1x" media="all and (max-width: 539px)" type="image/png" width="499" height="294"> <img loading="eager" width="499" height="294" src="/files/styles/multiple_ct_header_phone/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=raZa4Wiq" alt="An image of how slide-DNA-seq &quot;sees&quot; cells' organization within a tumor." title="An image of how slide-DNA-seq &quot;sees&quot; cells' organization within a tumor." typeof="foaf:Image"> </picture> </div> <div class="media-caption"> <div class="media-caption__credit"> Credit: <a href="https://www.nature.com/articles/s41586-021-04217-4" target="_blank">Zhao T, Chiang Z, et al. <em>Nature</em>, 2021</a> </div> <div class="media-caption__description"> An image of how slide-DNA-seq "sees" cells' organization within a tumor. </div> </div> </article> </div> </div> </div> </div> </div> </div> <div class="content-section content-section_with-sidebars container"> <div class="row"> <div class="content-section__left col-2"> <div class="block block-better-social-sharing-buttons block-social-sharing-buttons-block"> <div style="display: none"><link rel="preload" href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg" as="image" type="image/svg+xml" crossorigin="anonymous"></div> <div class="social-sharing-buttons"> <a href="https://www.facebook.com/sharer/sharer.php?u=/taxonomy/term/592/feed&amp;title=" target="_blank" title="Share to Facebook" aria-label="Share to Facebook" class="social-sharing-buttons-button share-facebook" rel="noopener"> <svg aria-hidden="true" width="32px" height="32px" style="border-radius:100%;"> <use href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg#facebook" /> </svg> </a> <a href="https://twitter.com/intent/tweet?text=+/taxonomy/term/592/feed" target="_blank" title="Share to X" aria-label="Share to X" class="social-sharing-buttons-button share-x" rel="noopener"> <svg aria-hidden="true" width="32px" height="32px" style="border-radius:100%;"> <use href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg#x" /> </svg> </a> <a href="mailto:?subject=&amp;body=/taxonomy/term/592/feed" title="Share to Email" aria-label="Share to Email" class="social-sharing-buttons-button share-email" target="_blank" rel="noopener"> <svg aria-hidden="true" width="32px" height="32px" style="border-radius:100%;"> <use href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg#email" /> </svg> </a> </div> </div> </div> <div class="content-section__main col-8"> <div class="block block-layout-builder block-field-blocknodenewsbody"> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><p> Within complex tissues such as cancer tumors, individual cells can vary widely from each other. Internally, cancer cells can develop unique DNA mutations and genomic changes, potentially leading to drug resistance, metastasis, or relapse. Externally, the cells’ specific locations within the tissue also matter, since the local structure of a tumor and its surrounding tissues can affect cell state and drug permeability.</p> <p> To measure both genetic and local factors at the same time, researchers from Harvard University’s Department of Stem Cell and Regenerative Biology (HSCRB) and the Ó³»­´«Ã½ of MIT and Harvard developed a new technique of spatially-resolved DNA sequencing, called slide-DNA-seq. When further combined with spatially-resolved gene expression analysis, the technology gives researchers a better understanding of cancer progression and potential treatment.</p> <p> The researchers’ findings are published in the journal <a href="https://www.nature.com/articles/s41586-021-04217-4" target="_blank"><em>Nature</em></a>.</p> <p> Slide-DNA-seq analyzes slices of intact tissue, in which each cell remains in its original location — as opposed to conventional sequencing techniques, where cells are dissociated before DNA extraction. The researchers used microbeads, each tagged with a unique spatial barcode and bound to specially-prepared glass slides, to capture DNA from the tissue.&nbsp;</p> <p> "Each bead is about the size of a cell," said co-corresponding author&nbsp;<a href="/node/113836">Fei Chen</a>, who is an assistant professor in HSCRB and a core institute member at the Ó³»­´«Ã½. "Together, they are like individual pixels on a camera which takes snapshots of genomic alterations within each cell in the tissue."</p> <p> After measuring genomic changes, the researchers applied a related&nbsp;<a href="/node/488166">RNA-based Slide-seq method</a>&nbsp;Chen and collaborators developed in 2019, which used gene expression profiles to identify and map the locations of cell types and subtypes within a tissue slice.&nbsp;&nbsp;</p> <p> "We can use the same barcoded beads to capture the transcriptome from each cell, and combine these two measurements into a multi-modal image," Chen said.&nbsp;In other words, the researchers can see changes in both the cells’ DNA and gene expression within the context of tissues.</p> <p> The researchers applied the technique to a mouse model of metastatic cancer, as well as a primary tumor sample from a patient with colorectal cancer. In each tissue, the researchers were able to identify subpopulations of cancer cells in distinct regions, corresponding with unique genomic evolutionary paths and gene expression states.</p> <p> "We applied this to DNA sequencing and cancer, which are hugely important areas of medical research,"&nbsp;said co-corresponding author <a href="/node/113841">Jason Buenrostro</a>, who is a HSCRB assistant professor, an associate member of the Ó³»­´«Ã½, and co-director of the Ó³»­´«Ã½'s <a href="/node/768556">Gene Regulation Observatory</a>. "However, the technology also opens the door to more broadly measuring DNA molecules within tissues. As such, we imagine future approaches will use this work as a foundation to build tools that measure modifications to DNA as well, such as the epigenome."</p> <p> <em>This study received funding from the Allen Institute Distinguished Investigator Award, the National Institutes of Health, a National Human Genome Research Institute training grant, the Burroughs Wellcome Fund, and the Harvard Quantitative Biology Initiative.</em></p> <p> <em>Adapted from <a href="https://hscrb.harvard.edu/news/genomic-sequencing-that-preserves-cells-locations-within-tissues/" target="_blank">a story originally published by the Harvard University Department of Stem Cell and Regenerative Biology</a>.</em></p> </div> </div> <div class="block block-layout-builder block-field-blocknodenewsfield-news-pappers"> <h2>Paper(s) cited</h2> <div class="clearfix text-formatted field field--name-field-news-pappers field--type-text-long field--label-hidden field__item"><p> Zhao T, Chiang ZD, et al.&nbsp;<a href="https://www.nature.com/articles/s41586-021-04217-4" target="_blank">Spatial genomics enables multi-modal study of clonal heterogeneity in tissues</a>. <em>Nature</em>. DOI: 10.1038/s41586-021-04217-4.</p> </div> </div> <div class="block-node-broad-tags block block-layout-builder block-field-blocknodenewsfield-broad-tags"> <div class="block-node-broad-tags__row"> <div class="block-node-broad-tags__title">Tags:</div> <div class="field field--name-field-broad-tags field--type-entity-reference field--label-hidden field__items"> <div class="field__item"><a href="/broad-tags/genome-regulation-cellular-circuitry-and-epigenomics" hreflang="en">Genome Regulation, Cellular Circuitry and Epigenomics</a></div> <div class="field__item"><a href="/broad-tags/genome-regulation-cell-circuitry-and-epigenomics" hreflang="en">Genome regulation, cell circuitry, and epigenomics</a></div> </div> </div> </div> </div> <div class="content-section__right col-2"> <div class="block block-ctools block-entity-viewnode"> <article about="/news/new-dna-sequencing-technique-preserves-cells%E2%80%99-locations-within-tissues" class="node node--type-news node--promoted node--view-mode-sidebar"> <div class="node__content"> <div class="sidebar-group"> <div class="sidebar-group__content"> <div class="block block-layout-builder block-field-blocknodenewsfield-news-extra-info"> <div class="clearfix text-formatted field field--name-field-news-extra-info field--type-text-long field--label-hidden field__item"><h2> Related People</h2> <p> <a href="/node/113841">Jason Buenrostro</a></p> <p> <a href="/node/113836">Fei Chen</a><br> &nbsp;</p> <h2> Related Programs</h2> <p> <a href="/node/768556">Gene Regulation Observatory</a><br> &nbsp;</p> <h2> Related News</h2> <p> <a href="/node/488166"><img alt src="/files/styles/blog__557x415_/public/news/images/2019/Projections_of_Composite_MainStoryPage_1.gif?itok=UafnfWmI" style="width: 212px; height: 158px;"></a></p> <p> <a href="/node/488166">New tool uses RNA sequencing to chart rich maps of cellular and tissue function</a><br> &nbsp;</p> </div> </div> </div> </div> </div> </article> </div> </div> </div> </div> Thu, 01 Nov 2018 15:30:02 +0000 tulrich@broadinstitute.org 386381 at /news/research-roundup-august-3-2018 <span class="field field--name-title field--type-string field--label-hidden"><h1>New DNA sequencing technique preserves cells’ locations within tissues</h1> </span> <span class="field field--name-uid field--type-entity-reference field--label-hidden"> <span>By Tom Ulrich</span> </span> <span class="field field--name-created field--type-created field--label-hidden"><time datetime="2021-12-15T11:05:12-05:00" class="datetime">December 15, 2021</time> </span> <div class="hero-section container"> <div class="hero-section__row row"> <div class="hero-section__content hero-section__content_left col-6"> <div class="hero-section__breadcrumbs"> <div class="block block-layout-builder block-extra-field-blocknodenewsbreadcrumbs"> <nav class="breadcrumb" role="navigation" aria-labelledby="system-breadcrumb"> <h2 id="system-breadcrumb" class="visually-hidden">Breadcrumb</h2> <ol> <li> <a href="/">Home</a> </li> <li> <a href="/news">News</a> </li> </ol> </nav> </div> </div> <div class="hero-section__title"> <div class="block block-layout-builder block-field-blocknodenewstitle"> <span class="field field--name-title field--type-string field--label-hidden"><h1>New DNA sequencing technique preserves cells’ locations within tissues</h1> </span> </div> </div> <div class="hero-section__description"> <div class="block block-layout-builder block-field-blocknodenewsbody"> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><div class="summary-only"> <p> Slide-DNA-seq helps researchers better understand spatial differences and patterns in complex tissues such as tumors.</p> </div> </div> </div> </div> <div class="hero-section__author"> <div class="block block-layout-builder block-extra-field-blocknodenewsextra-field-author-custom"> By Jessica Lau, Harvard Department of Stem Cell and Regenerative Biology </div> </div> <div class="hero-section__date"> <div class="block block-layout-builder block-field-blocknodenewscreated"> <span class="field field--name-created field--type-created field--label-hidden"><time datetime="2021-12-15T11:05:12-05:00" class="datetime">December 15, 2021</time> </span> </div> </div> </div> <div class="hero-section__right col-6"> <div class="hero-section__image"> <div class="block block-layout-builder block-field-blocknodenewsfield-image"> <div class="field field--name-field-image field--type-entity-reference field--label-hidden field__item"> <article class="media media--type-image media--view-mode-multiple-content-types-header"> <div class="field field--name-field-media-image field--type-image field--label-hidden field__item"> <picture> <source srcset="/files/styles/multiple_ct_header_desktop_xl/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=Mj-O2mVa 1x" media="all and (min-width: 1921px)" type="image/png" width="754" height="503"> <source srcset="/files/styles/multiple_ct_header_desktop_xl/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=Mj-O2mVa 1x" media="all and (min-width: 1601px) and (max-width: 1920px)" type="image/png" width="754" height="503"> <source srcset="/files/styles/multiple_ct_header_desktop/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=ZBfVHHl3 1x" media="all and (min-width: 1340px) and (max-width: 1600px)" type="image/png" width="736" height="520"> <source srcset="/files/styles/multiple_ct_header_laptop/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=NQXuPw1V 1x" media="all and (min-width: 800px) and (max-width: 1339px)" type="image/png" width="641" height="451"> <source srcset="/files/styles/multiple_ct_header_tablet/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=vEqZYhdy 1x" media="all and (min-width: 540px) and (max-width: 799px)" type="image/png" width="706" height="417"> <source srcset="/files/styles/multiple_ct_header_phone/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=raZa4Wiq 1x" media="all and (max-width: 539px)" type="image/png" width="499" height="294"> <img loading="eager" width="499" height="294" src="/files/styles/multiple_ct_header_phone/public/news/images/2021/fig2b_for_web.png?h=d3e04ee7&amp;itok=raZa4Wiq" alt="An image of how slide-DNA-seq &quot;sees&quot; cells' organization within a tumor." title="An image of how slide-DNA-seq &quot;sees&quot; cells' organization within a tumor." typeof="foaf:Image"> </picture> </div> <div class="media-caption"> <div class="media-caption__credit"> Credit: <a href="https://www.nature.com/articles/s41586-021-04217-4" target="_blank">Zhao T, Chiang Z, et al. <em>Nature</em>, 2021</a> </div> <div class="media-caption__description"> An image of how slide-DNA-seq "sees" cells' organization within a tumor. </div> </div> </article> </div> </div> </div> </div> </div> </div> <div class="content-section content-section_with-sidebars container"> <div class="row"> <div class="content-section__left col-2"> <div class="block block-better-social-sharing-buttons block-social-sharing-buttons-block"> <div style="display: none"><link rel="preload" href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg" as="image" type="image/svg+xml" crossorigin="anonymous"></div> <div class="social-sharing-buttons"> <a href="https://www.facebook.com/sharer/sharer.php?u=/taxonomy/term/592/feed&amp;title=" target="_blank" title="Share to Facebook" aria-label="Share to Facebook" class="social-sharing-buttons-button share-facebook" rel="noopener"> <svg aria-hidden="true" width="32px" height="32px" style="border-radius:100%;"> <use href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg#facebook" /> </svg> </a> <a href="https://twitter.com/intent/tweet?text=+/taxonomy/term/592/feed" target="_blank" title="Share to X" aria-label="Share to X" class="social-sharing-buttons-button share-x" rel="noopener"> <svg aria-hidden="true" width="32px" height="32px" style="border-radius:100%;"> <use href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg#x" /> </svg> </a> <a href="mailto:?subject=&amp;body=/taxonomy/term/592/feed" title="Share to Email" aria-label="Share to Email" class="social-sharing-buttons-button share-email" target="_blank" rel="noopener"> <svg aria-hidden="true" width="32px" height="32px" style="border-radius:100%;"> <use href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg#email" /> </svg> </a> </div> </div> </div> <div class="content-section__main col-8"> <div class="block block-layout-builder block-field-blocknodenewsbody"> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><p> Within complex tissues such as cancer tumors, individual cells can vary widely from each other. Internally, cancer cells can develop unique DNA mutations and genomic changes, potentially leading to drug resistance, metastasis, or relapse. Externally, the cells’ specific locations within the tissue also matter, since the local structure of a tumor and its surrounding tissues can affect cell state and drug permeability.</p> <p> To measure both genetic and local factors at the same time, researchers from Harvard University’s Department of Stem Cell and Regenerative Biology (HSCRB) and the Ó³»­´«Ã½ of MIT and Harvard developed a new technique of spatially-resolved DNA sequencing, called slide-DNA-seq. When further combined with spatially-resolved gene expression analysis, the technology gives researchers a better understanding of cancer progression and potential treatment.</p> <p> The researchers’ findings are published in the journal <a href="https://www.nature.com/articles/s41586-021-04217-4" target="_blank"><em>Nature</em></a>.</p> <p> Slide-DNA-seq analyzes slices of intact tissue, in which each cell remains in its original location — as opposed to conventional sequencing techniques, where cells are dissociated before DNA extraction. The researchers used microbeads, each tagged with a unique spatial barcode and bound to specially-prepared glass slides, to capture DNA from the tissue.&nbsp;</p> <p> "Each bead is about the size of a cell," said co-corresponding author&nbsp;<a href="/node/113836">Fei Chen</a>, who is an assistant professor in HSCRB and a core institute member at the Ó³»­´«Ã½. "Together, they are like individual pixels on a camera which takes snapshots of genomic alterations within each cell in the tissue."</p> <p> After measuring genomic changes, the researchers applied a related&nbsp;<a href="/node/488166">RNA-based Slide-seq method</a>&nbsp;Chen and collaborators developed in 2019, which used gene expression profiles to identify and map the locations of cell types and subtypes within a tissue slice.&nbsp;&nbsp;</p> <p> "We can use the same barcoded beads to capture the transcriptome from each cell, and combine these two measurements into a multi-modal image," Chen said.&nbsp;In other words, the researchers can see changes in both the cells’ DNA and gene expression within the context of tissues.</p> <p> The researchers applied the technique to a mouse model of metastatic cancer, as well as a primary tumor sample from a patient with colorectal cancer. In each tissue, the researchers were able to identify subpopulations of cancer cells in distinct regions, corresponding with unique genomic evolutionary paths and gene expression states.</p> <p> "We applied this to DNA sequencing and cancer, which are hugely important areas of medical research,"&nbsp;said co-corresponding author <a href="/node/113841">Jason Buenrostro</a>, who is a HSCRB assistant professor, an associate member of the Ó³»­´«Ã½, and co-director of the Ó³»­´«Ã½'s <a href="/node/768556">Gene Regulation Observatory</a>. "However, the technology also opens the door to more broadly measuring DNA molecules within tissues. As such, we imagine future approaches will use this work as a foundation to build tools that measure modifications to DNA as well, such as the epigenome."</p> <p> <em>This study received funding from the Allen Institute Distinguished Investigator Award, the National Institutes of Health, a National Human Genome Research Institute training grant, the Burroughs Wellcome Fund, and the Harvard Quantitative Biology Initiative.</em></p> <p> <em>Adapted from <a href="https://hscrb.harvard.edu/news/genomic-sequencing-that-preserves-cells-locations-within-tissues/" target="_blank">a story originally published by the Harvard University Department of Stem Cell and Regenerative Biology</a>.</em></p> </div> </div> <div class="block block-layout-builder block-field-blocknodenewsfield-news-pappers"> <h2>Paper(s) cited</h2> <div class="clearfix text-formatted field field--name-field-news-pappers field--type-text-long field--label-hidden field__item"><p> Zhao T, Chiang ZD, et al.&nbsp;<a href="https://www.nature.com/articles/s41586-021-04217-4" target="_blank">Spatial genomics enables multi-modal study of clonal heterogeneity in tissues</a>. <em>Nature</em>. DOI: 10.1038/s41586-021-04217-4.</p> </div> </div> <div class="block-node-broad-tags block block-layout-builder block-field-blocknodenewsfield-broad-tags"> <div class="block-node-broad-tags__row"> <div class="block-node-broad-tags__title">Tags:</div> <div class="field field--name-field-broad-tags field--type-entity-reference field--label-hidden field__items"> <div class="field__item"><a href="/broad-tags/genome-regulation-cellular-circuitry-and-epigenomics" hreflang="en">Genome Regulation, Cellular Circuitry and Epigenomics</a></div> <div class="field__item"><a href="/broad-tags/genome-regulation-cell-circuitry-and-epigenomics" hreflang="en">Genome regulation, cell circuitry, and epigenomics</a></div> </div> </div> </div> </div> <div class="content-section__right col-2"> <div class="block block-ctools block-entity-viewnode"> <article about="/news/new-dna-sequencing-technique-preserves-cells%E2%80%99-locations-within-tissues" class="node node--type-news node--promoted node--view-mode-sidebar"> <div class="node__content"> <div class="sidebar-group"> <div class="sidebar-group__content"> <div class="block block-layout-builder block-field-blocknodenewsfield-news-extra-info"> <div class="clearfix text-formatted field field--name-field-news-extra-info field--type-text-long field--label-hidden field__item"><h2> Related People</h2> <p> <a href="/node/113841">Jason Buenrostro</a></p> <p> <a href="/node/113836">Fei Chen</a><br> &nbsp;</p> <h2> Related Programs</h2> <p> <a href="/node/768556">Gene Regulation Observatory</a><br> &nbsp;</p> <h2> Related News</h2> <p> <a href="/node/488166"><img alt src="/files/styles/blog__557x415_/public/news/images/2019/Projections_of_Composite_MainStoryPage_1.gif?itok=UafnfWmI" style="width: 212px; height: 158px;"></a></p> <p> <a href="/node/488166">New tool uses RNA sequencing to chart rich maps of cellular and tissue function</a><br> &nbsp;</p> </div> </div> </div> </div> </div> </article> </div> </div> </div> </div> Fri, 03 Aug 2018 14:00:53 +0000 tulrich@broadinstitute.org 323591 at