Obesity

New image-based cellular profiling tool peers deeply into metabolic biology

makenziekohler — Fri, 30 Jun 2023 14:30:09 +0000

New image-based cellular profiling tool peers deeply into metabolic biology

By Makenzie Kohler June 30, 2023

New image-based cellular profiling tool peers deeply into metabolic biology

LipocyteProfiler captures disease-relevant phenotypes in an inexpensive microscopy assay

By Makenzie Kohler

June 30, 2023

Credit: Phil Kubitz, Claussnitzer lab

Fat cells, or adipocytes, with stains highlighting nuclei (blue); mitochondria (red); lipid droplets (green); and the actin cytoskeleton, plasma membrane, and Golgi apparatus (yellow).

The field of microscopy has advanced immensely over the last fifty years in its ability to extract both quantitative and qualitative data from microscopy images. In a paper published in Cell Genomics, researchers at the ӳ��ý, Harvard Medical School, Massachusetts General Hospital, Technical School of Munich (TUM), and the University of Oxford have presented LipocyteProfiler, a new, high-throughput quantitative bioimaging tool to help bridge the gap between morphological observation and functional profiling.

LipocyteProfiler is a powerful imaging technique that generates comprehensive microscopy-based profiles of cells using multiple fluorescent dyes chosen specifically for studies of cardiometabolic biology. Image analysis software captures information about more than 3,000 cellular features, providing a deep view into the impacts of genetic variants, small molecule or genetic perturbations, and more on cellular shape, structure, and function.

“It moves the community from a very targeted, hypothesis-driven, unidimensional cell-based assay framework to one that allows us to survey biological processes in a cell and assign function to genes and genetic variations in an unbiased manner,” said Melina Claussnitzer, who is a ӳ��ý institute member, associate director of the institute's Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, faculty of the Center for Genomic Medicine at Mass General, and the senior researcher of the study.

Common genetic variants associated with cardiometabolic disease can produce phenotype changes of such small effect that they can be difficult to characterize. The current proof-of-concept study showcases how the use of a set of dyes chosen with a disease or trait in mind can illuminate cellular and subcellular behaviors at unprecedented depth and scale.

LipocyteProfiler builds on the concept of image-based profiling that was first introduced in the context of morphology mapping by Cell Painting, a high-content imaging assay developed by ӳ��ý institute scientist and Imaging Platform senior director Anne Carpenter. Whereas Cell Painting labels eight general organelles or components of the cell, LipocyteProfiler uses six fluorescent dyes that together illuminate the morphology and activity of nine cellular compartments: the nucleus, nucleoli, mitochondria, endoplasmic reticulum (ER), Golgi apparatus, cytoplasmic RNA, f-actin cytoskeleton, and plasma membrane, and lipid droplets (fat-storing organelles that regulate lipids within every type of cell and which are particularly common in adipocytes). It then extracts features from images of stained cells and creates cellular profiles, categorizing cells based on patterns (often imperceptible to the human eye) that they share with other cells, which directly inform disease biology.

Fat cells stained yellow to show the actin cytoskeleton, plasma membrane, and Golgi apparatus. Credit: Phil Kubitz, Claussnitzer lab

Fat cells stained blue to show nuclei. Credit: Phil Kubitz, Claussnitzer lab

Fat cells stained red to show mitochondria. Credit: Phil Kubitz, Claussnitzer lab

Fat cells stained green to show lipid droplets. Credit: Phil Kubitz, Claussnitzer lab

A merged image showing all of the stained cellular components together. Credit: Phil Kubitz, Claussnitzer lab.

To assess LipocyteProfiler, the researchers analyzed white and brown fat cells and liver cells, focusing on traits such as the size, the number, and the location of lipid droplets in a cell. When comparing cells with a particular genetic variant to those without, the team found that the LipocyteProfiler protocol detects morphological and mechanistic differences between the cells, allowing for linkage of genetic variation to phenotypic traits. LipocyteProfiler also highlighted discrete cellular mechanisms and pathways when used to analyze metabolic traits associated with high polygenic risk scores.

“We could identify and examine more than 700 features just related to lipid accumulation,” said Sophie Strobel, a lead author on the paper who is now at TUM. “That teaches us far more than looking for just a single informative data point.”

The researchers also looked at the tool’s ability to detect changes in cellular phenotypes after exposure to drugs and small molecule compounds. Typically, studying drug therapies is an expensive and time-consuming undertaking. With high-resolution, cell-based profiling techniques, extracting a large amount of data can be done cheaply and efficiently.

“I think drug screens are an obvious next step for using the platform because image-based screens tend to be pretty inexpensive, and they can be scaled up so that you can assess and evaluate hundreds of thousands of compounds and see which ones impact the phenotypes that are associated with disease,” said Cell Painting creator Carpenter, who collaborated on the LipocyteProfiler project.

LipocyteProfiler is already being used experimentally to look at relationships between genetic variants and their functions. Claussnitzer and the University of Chicago's Marcelo Nobrega recently used LipocyteProfiler to reveal a mechanism connecting the gene COBLL1 and a diabetes-related metabolic phenotype called metabolically obese normal weight. By using the tool, Clausnnitzer and others saw how a variant that reduces COBLL1 expression interferes with lipid droplets' growth within a cell.

Claussnitzer's lab is now working to expand the machine-learning aspect of LipocyteProfiler, with an eye towards tracking information flow within single cells from transcription to phenotypes. Experimentally, the lab continues to use LipocyteProfiler to assess the relationships between genetic variants and cellular programs, to understand highly granular processes of disease biology.

Claussnitzer notes that LipocyteProfiler is a powerful addition to the -omics tool box, one that looks beyond epigenomics, transcriptomics, and proteomics to allow systematic, unbiased, image-based profiling of cellular phenotypes. And while the technology is the first to adapt the Cell Painting protocol, researchers at the ӳ��ý and beyond are already working to create assays like LipocyteProfiler for their own respective fields.

“Just as we applied stains related to lipid biology and metabolism,” Strobel said, “one could instead swap in stains for something related to, say, lymphocyte biology, depending on the question you want to answer and what disease you are looking at.”

Carpenter notes that she is satisfied seeing people expand on her work on Cell Painting, saying “in the end, none of the work matters if biologists aren't adapting it in their labs for the myriad of disease areas that people work on.”

Funding

Support for this work was provided by Novo Nordisk Foundation, the Foundation for the National Institutes of Health, the National Institute of Diabetes and Digestive and Kidney Diseases, the National Human Genome Research Institute, the American Diabetes Association, the Gates Foundation, the Doris Duke Charitable Foundation, the ӳ��ý, and other sources.

Papers cited

Laber S, Strobel SM, et al. Discovering cellular programs of intrinsic and extrinsic drivers of metabolic traits using LipocyteProfiler. Cell Genomics. Online June 20, 2023. DOI: 10.1016/j.xgen.2023.100346

Tags:

Imaging Platform

Metabolism Program

Connecting variants to functions

Cardiovascular disease

Diabetes

Obesity

Heart Disease

Image-Based Profiling

Cells can use uridine, a component of RNA, as a source of energy

adicorat — Wed, 17 May 2023 15:00:00 +0000

Cells can use uridine, a component of RNA, as a source of energy

By Allessandra DiCorato May 17, 2023

Cells can use uridine, a component of RNA, as a source of energy

Researchers have discovered a new biochemical pathway in cells that could contribute to the immune response as well as some cancers and metabolic disorders.

By Allessandra DiCorato

May 17, 2023

Credit: Sonja Vasiljeva, ӳ��ý Communications

Our bodies burn carbohydrates, proteins, and fat for fuel, and now, researchers at the ӳ��ý of MIT and Harvard and the University of Lausanne have discovered another important energy source for cells: uridine, the chemical building block unique to RNA.

Their new findings reveal that cells ranging from healthy immune cells to cancer cells can process uridine from RNA like they do with sugar to sustain growth when glucose is limited. Previous research has shown that a diet rich in uridine leads to obesity and pre-diabetes in mice, but scientists didn’t know if or how cells convert RNA into ATP, the molecule cells burn for energy.

In a study published today in Nature Metabolism, the research team pinpointed a biochemical pathway that cells use to break down uridine-derived sugar that they then burn for energy. The researchers say that targeting this pathway could potentially help treat cancers and metabolic disorders such as diabetes, and could help tune the immune response.

The findings are from a team including co-senior authors Alexis Jourdain, an assistant professor at the University of Lausanne in Switzerland; and Vamsi Mootha, an institute member at the ӳ��ý, a professor of systems biology and medicine at Harvard Medical School, and a professor of molecular biology at Massachusetts General Hospital; as well as co-first authors Owen Skinner, a postdoctoral fellow in Mootha’s lab, and Joan Blanco-Fernández, a PhD student in Jourdain’s lab.

“Living organisms are packed with RNA, generally in the form of ribosomes, and therefore uridine,” said Jourdain, who was a postdoctoral fellow in Mootha’s lab when the study began. “You can eat a low-carb diet, but as long as there is RNA in your food, your body is able to convert that RNA into sugar.”

Uridine as food

As a researcher in Mootha’s lab, Jourdain wanted to know which genes and pathways cells might use to stay alive when nutrients are limited. Using a genetic screen, Jourdain and his colleagues found that the expression of two genes, UPP1 and UPP2, dramatically increases the growth of cells in media without glucose. These genes encode enzymes that help break down uridine, and cells expressing UPP1 and UPP2 grew when uridine was their only food source.

Jourdain wondered if cells could also derive uridine from RNA, so he added RNA to a dish of cancer cells in sugar-free media. To his surprise, the cells grew, suggesting they were able to process uridine even when it’s part of RNA.

“I remember telling my friends that I did a crazy experiment where I tried to feed cells with RNA,” Jourdain remembers. “I did not think this was going to work — I was very surprised to see the cells grow.”

To further probe how common the pathway is across cancer types, the team used PRISM, a technology at the ӳ��ý that allows for high throughput screening of hundreds of human cancer cell lines. Together with David Fisher’s team at Harvard Medical School, they found that glycolysis from uridine is especially prominent in melanoma, but also occurs in other cancers.

The scientists also showed that this process occurs in immune cells, where uridine may help sustain the immune response by providing energy to cells. Gene expression patterns documented by other researchers suggest the pathway likely occurs in blood cells, the lungs, brain, and kidneys.

Though glycolysis from RNA and uridine is widespread, it is not regulated by the cell, which could have important implications in metabolic diseases. This lack of regulation means that cells continue to burn RNA or uridine even when they don’t need energy, and could help explain why diets high in uridine are associated with obesity, fatty liver disease, and pre-diabetes in mice.

Harnessing glycolysis from uridine

Jourdain sees a range of ways to exploit this pathway for therapeutic purposes. Scientists could inhibit the pathway in cancers to starve them, or dial back the activity of overactive immune cells in autoimmune disorders. Conversely, they could promote the pathway to boost immune cells that fight pathogens.

Jourdain’s lab is now working to find inhibitors of the pathway and their physiology in animal models. Ultimately, they’d also like to study the effects of RNA-rich foods on obesity in humans.

“We’ve been underestimating how much energy we can get from eating nucleotides,” Jourdain said. “This is really a new player in the field of metabolism and nutrition.”

Funding:

This work was supported in part by the National Institutes of Health; the Dr. Miriam and Sheldon Adelson Medical Research Foundation; the Hungarian Academy of Sciences; the National Research, Development and Innovation Office of Hungary; the Swiss National Science Foundation; the Foundation Pierre Mercier pour la Science; and the Howard Hughes Medical Institute.

Paper cited:

Skinner O S, Blanco-Fernández J, et al. Salvage of ribose from uridine or RNA supports glycolysis in nutrient-limited conditions. Nature Metabolism. Online May 17, 2023. DOI:10.1038/s42255-023-00774-2

Tags:

Metabolism Program

Obesity

Systematic study of free fatty acids reveals new roles in metabolic diseases

Corie Lok — Tue, 18 Apr 2023 15:00:14 +0000

Cells can use uridine, a component of RNA, as a source of energy

By Allessandra DiCorato May 17, 2023

Cells can use uridine, a component of RNA, as a source of energy

Researchers have discovered a new biochemical pathway in cells that could contribute to the immune response as well as some cancers and metabolic disorders.

By Allessandra DiCorato

May 17, 2023

Credit: Sonja Vasiljeva, ӳ��ý Communications

Uridine as food

Harnessing glycolysis from uridine

Jourdain’s lab is now working to find inhibitors of the pathway and their physiology in animal models. Ultimately, they’d also like to study the effects of RNA-rich foods on obesity in humans.

“We’ve been underestimating how much energy we can get from eating nucleotides,” Jourdain said. “This is really a new player in the field of metabolism and nutrition.”

Funding:

Paper cited:

Tags:

Metabolism Program

Obesity

Researchers catalog white fat cell types present in mice and in humans

tulrich@broadinstitute.org — Wed, 16 Mar 2022 16:10:06 +0000

Cells can use uridine, a component of RNA, as a source of energy

By Allessandra DiCorato May 17, 2023

Cells can use uridine, a component of RNA, as a source of energy

Researchers have discovered a new biochemical pathway in cells that could contribute to the immune response as well as some cancers and metabolic disorders.

By Allessandra DiCorato

May 17, 2023

Credit: Sonja Vasiljeva, ӳ��ý Communications

Uridine as food

Harnessing glycolysis from uridine

Jourdain’s lab is now working to find inhibitors of the pathway and their physiology in animal models. Ultimately, they’d also like to study the effects of RNA-rich foods on obesity in humans.

“We’ve been underestimating how much energy we can get from eating nucleotides,” Jourdain said. “This is really a new player in the field of metabolism and nutrition.”

Funding:

Paper cited:

Tags:

Metabolism Program

Obesity

Calculating genetic risk for obesity

kzusi@broadinstitute.org — Thu, 18 Apr 2019 14:48:11 +0000

Cells can use uridine, a component of RNA, as a source of energy

By Allessandra DiCorato May 17, 2023

Cells can use uridine, a component of RNA, as a source of energy

Researchers have discovered a new biochemical pathway in cells that could contribute to the immune response as well as some cancers and metabolic disorders.

By Allessandra DiCorato

May 17, 2023

Credit: Sonja Vasiljeva, ӳ��ý Communications

Uridine as food

Harnessing glycolysis from uridine

Jourdain’s lab is now working to find inhibitors of the pathway and their physiology in animal models. Ultimately, they’d also like to study the effects of RNA-rich foods on obesity in humans.

“We’ve been underestimating how much energy we can get from eating nucleotides,” Jourdain said. “This is really a new player in the field of metabolism and nutrition.”

Funding:

Paper cited:

Tags:

Metabolism Program

Obesity

Research Roundup: August 3, 2018

tulrich@broadinstitute.org — Fri, 03 Aug 2018 14:00:53 +0000

Cells can use uridine, a component of RNA, as a source of energy

By Allessandra DiCorato May 17, 2023

Cells can use uridine, a component of RNA, as a source of energy

Researchers have discovered a new biochemical pathway in cells that could contribute to the immune response as well as some cancers and metabolic disorders.

By Allessandra DiCorato

May 17, 2023

Credit: Sonja Vasiljeva, ӳ��ý Communications

Uridine as food

Harnessing glycolysis from uridine

Jourdain’s lab is now working to find inhibitors of the pathway and their physiology in animal models. Ultimately, they’d also like to study the effects of RNA-rich foods on obesity in humans.

“We’ve been underestimating how much energy we can get from eating nucleotides,” Jourdain said. “This is really a new player in the field of metabolism and nutrition.”

Funding:

Paper cited:

Tags:

Metabolism Program

Obesity

High hopes for understanding height and obesity

tulrich@broadinstitute.org — Fri, 06 Apr 2018 19:10:27 +0000

Cells can use uridine, a component of RNA, as a source of energy

By Allessandra DiCorato May 17, 2023

Cells can use uridine, a component of RNA, as a source of energy

Researchers have discovered a new biochemical pathway in cells that could contribute to the immune response as well as some cancers and metabolic disorders.

By Allessandra DiCorato

May 17, 2023

Credit: Sonja Vasiljeva, ӳ��ý Communications

Uridine as food

Harnessing glycolysis from uridine

Jourdain’s lab is now working to find inhibitors of the pathway and their physiology in animal models. Ultimately, they’d also like to study the effects of RNA-rich foods on obesity in humans.

“We’ve been underestimating how much energy we can get from eating nucleotides,” Jourdain said. “This is really a new player in the field of metabolism and nutrition.”

Funding:

Paper cited:

Tags:

Metabolism Program

Obesity

After a decade of genome-wide association studies, a new phase of discovery pushes on

leah@broadinstitute.org — Mon, 14 Aug 2017 17:00:00 +0000

Cells can use uridine, a component of RNA, as a source of energy

By Allessandra DiCorato May 17, 2023

Cells can use uridine, a component of RNA, as a source of energy

Researchers have discovered a new biochemical pathway in cells that could contribute to the immune response as well as some cancers and metabolic disorders.

By Allessandra DiCorato

May 17, 2023

Credit: Sonja Vasiljeva, ӳ��ý Communications

Uridine as food

Harnessing glycolysis from uridine

Jourdain’s lab is now working to find inhibitors of the pathway and their physiology in animal models. Ultimately, they’d also like to study the effects of RNA-rich foods on obesity in humans.

“We’ve been underestimating how much energy we can get from eating nucleotides,” Jourdain said. “This is really a new player in the field of metabolism and nutrition.”

Funding:

Paper cited:

Tags:

Metabolism Program

Obesity

New findings on β-cell proliferation points to regenerative medicine approach to diabetes

veronica@broadinstitute.org — Sat, 28 May 2016 15:00:00 +0000

Cells can use uridine, a component of RNA, as a source of energy

By Allessandra DiCorato May 17, 2023

Cells can use uridine, a component of RNA, as a source of energy

Researchers have discovered a new biochemical pathway in cells that could contribute to the immune response as well as some cancers and metabolic disorders.

By Allessandra DiCorato

May 17, 2023

Credit: Sonja Vasiljeva, ӳ��ý Communications

Uridine as food

Harnessing glycolysis from uridine

Jourdain’s lab is now working to find inhibitors of the pathway and their physiology in animal models. Ultimately, they’d also like to study the effects of RNA-rich foods on obesity in humans.

“We’ve been underestimating how much energy we can get from eating nucleotides,” Jourdain said. “This is really a new player in the field of metabolism and nutrition.”

Funding:

Paper cited:

Tags:

Metabolism Program

Obesity

What our gut tells us about the ‘hygiene hypothesis’

veronica@broadinstitute.org — Wed, 27 Apr 2016 15:43:44 +0000

Cells can use uridine, a component of RNA, as a source of energy

By Allessandra DiCorato May 17, 2023

Cells can use uridine, a component of RNA, as a source of energy

Researchers have discovered a new biochemical pathway in cells that could contribute to the immune response as well as some cancers and metabolic disorders.

By Allessandra DiCorato

May 17, 2023

Credit: Sonja Vasiljeva, ӳ��ý Communications

Uridine as food

Harnessing glycolysis from uridine

Jourdain’s lab is now working to find inhibitors of the pathway and their physiology in animal models. Ultimately, they’d also like to study the effects of RNA-rich foods on obesity in humans.

“We’ve been underestimating how much energy we can get from eating nucleotides,” Jourdain said. “This is really a new player in the field of metabolism and nutrition.”

Funding:

Paper cited:

Tags:

Metabolism Program

Obesity