Tag Archives: #transcriptomics

Obesity Changes Cell Response to Glucose, Uses Slower Metabolic Path in Mouse Liver (Medicine)

Healthy cells and cells with type 2 diabetes use completely different pathways to manage blood sugar levels, according to results from a study in mice. Researchers used a trans-omic approach, combining data from genes (transcriptomics) and metabolites (metabolomics) to identify and connect the many separate processes involved in responding to glucose.

The trans-omic network includes regulatory pathways that are specific to obese mice and those specific to healthy mice. Color coding highlights pathways that respond to glucose only in normal-weight mice (WT, blue), only obese mice (ob/ob, red), pathways in common (green), and pathways that react in opposite ways in obese and normal-weight mice (pink). Credit: Toshiya Kokaji, CC-BY, first published in Science Signaling, DOI: 10.1126/scisignal.aaz1236

“Many regulatory pathways for diabetes are already well known. What we have done is map the total landscape of diabetes regulation,” said Professor Shinya Kuroda, leader of the Systems Biology Lab at the University of Tokyo. Kuroda’s team previously mapped the different cell signaling pathways activated in response to high or low concentrations of insulin.

“We expected only small differences between the healthy and diabetes regulatory network, but we found they were totally different,” said Kuroda.

Obese mice lack most of the rapid response to glucose found in healthy metabolism, instead relying on much slower methods like changing gene expression.

Building a trans-omic network of glucose response

After eating a meal or sugary drink, insulin triggers cells to allow glucose molecules to move from the blood into cells, where glucose is broken down and converted into energy. In type 2 diabetes, cells become insensitive to insulin, so glucose remains in the blood causing prolonged high blood sugar levels known as hyperglycemia.

Decades of diabetes research have revealed that many signaling pathways become active when glucose is inside the cell. Many of those paths involve enzymes and small molecules called metabolites, which are themselves products of metabolic pathways.

Kuroda’s team studied healthy mice and a strain of mouse with a genetic mutation that causes the mice to overeat and develop diabetes in adulthood. All mice drank sugary water and then researchers waited between 20 minutes to four hours before taking blood samples and dissecting their liver. The liver is a major site of glucose metabolism in both mice and humans.

Researchers used a wide range of experiments to identify molecules that changed in response to glucose.

After collecting the data, researchers searched scientific databases for information about any glucose-responsive molecule they had identified in their measurements. Knowledge in the databases allowed researchers to connect these individual molecules to networks of intercellular signaling pathways.

Trans-omics allows researchers to turn a long list of discrete measurements into a wide web of knowledge about how cells reacted to glucose.

The analysis was complicated by the fact that scientific databases are highly specialized, with different databases dedicated to individual types of molecules. For example, a database about genes is not connected to a database about enzymes.

Project Research Associate Toshiya Kokaji, first author of the research publication, estimates that it took four years to complete the data analysis and construct the trans-omic network.

“Now that the pipeline is defined, we can complete the data analysis and trans-omic network construction in one to two years,” said Kokaji.

Researchers built a five-layered trans-omic map with information about insulin signaling, transcription factors (types of proteins that regulate gene activity), enzymes, metabolic reactions and metabolites.

Mapping cells’ different glucose responses

Color-coding the glucose-responsive molecules that were measured in healthy or obese mice revealed the vastly different signaling paths they use.

Healthy mice rapidly respond to glucose using enzymes and metabolites produced as byproducts of glucose metabolism, returning to normal blood sugar levels in about one hour.

Obese mice lack most of this rapid response, instead changing the expression of some genes over several hours and producing different molecules to cope with the glucose.

This slower and very different approach in obese mice fits the typical understanding of diabetes as the global impairment of metabolic control. Additionally, the approach used in obese mice requires cells to expend more energy compared to the specific and specialized paths activated in healthy cells.

Researchers hope that the data contained in the trans-omic network will allow the research community to find new cell signaling pathways to explore, both generally and for glucose-specific metabolism.

The research team plans to continue their trans-omic analysis of glucose response by adding additional layers of information to the network and studying glucose response in other cell types that consume large amounts of glucose, such as muscle cells.

References: (1) Toshiya Kokaji, Atsushi Hatano, Yuki Ito, Katsuyuki Yugi, Miki Eto, Keigo Morita, Satoshi Ohno, Masashi Fujii, Ken-ichi Hironaka, Riku Egami, Akira Terakawa, Takaho Tsuchiya, Haruka Ozaki, Hiroshi Inoue, Shinsuke Uda, Hiroyuki Kubota, Yutaka Suzuki, Kazutaka Ikeda, Makoto Arita, Masaki Matsumoto, Keiichi I. Nakayama, Akiyoshi Hirayama, Tomoyoshi Soga, Shinya Kuroda, “Trans-omic analysis reveals allosteric and gene regulation-axes for altered glucose-responsive liver metabolism associated with obesity”, Science Signaling, Vol. 13, Issue 660, eaaz1236 2020. DOI: 10.1126/scisignal.aaz1236 https://stke.sciencemag.org/content/13/660/eaaz1236 (2) Kawata K, Hatano A,i Yugi K, Kubota H, Sano T, Fujii M, Tomizawa Y, Kokaji T, Tanaka KY, Uda S, Suzuki Y, Matsumoto M, Nakayama KI, Kaori Saitoh K, Kato K, Ueno A, Ohishi M, Hirayama A, Soga T, and Kuroda S. 11 September 2018. Trans-omic analysis reveals selective responses to induced and basal insulin across signaling, transcriptional, and metabolic networks. iScience. 10.1016/j.isci.2018.07.022

Provided by University of Tokyo

Fruit Flies Reveal New Insights Into Space Travel’s Effect on the Heart (Planetary Science)

Scientists at Sanford Burnham Prebys Medical Discovery Institute have shown that fruit flies that spent several weeks on the International Space Station (ISS)–about half of their lives–experienced profound structural and biochemical changes to their hearts. The study, published today in Cell Reports, suggests that astronauts who spend a lengthy amount of time in space–which would be required for formation of a moon colony or travel to distant Mars–could suffer similar effects and may benefit from protective measures to keep their hearts healthy. The research also revealed new insights that could one day help people on Earth who are on long-term bed rest or living with heart disease.

©Stanley walls

“For the first time, we can see the cellular and molecular changes that may underlie the heart conditions seen in astronaut studies,” says Karen Ocorr, Ph.D., assistant professor in the Development, Aging and Regeneration Program at Sanford Burnham Prebys and co-senior author of the study. “We initiated this study to understand the effects of microgravity on the heart, and now we have a roadmap we can use to start to develop strategies to keep astronaut hearts strong and healthy.”

Past studies have shown that under microgravity conditions, the human heart shifts from an oval to a more spherical shape. Space flight also causes the heart muscle to weaken (atrophy), reducing its ability to pump blood throughout the body. However, until now, human heart studies–completed using ultrasounds performed on the ISS–have been limited to a relatively small number of astronauts. While important, these studies didn’t reveal the cellular and molecular changes that drive these transformations–information needed to develop countermeasures that will keep astronauts safe on prolonged flights.

“As we continue our work to establish a colony on the moon and send the first astronauts to Mars, understanding the effects of extended time in microgravity on the human body is imperative,” says Sharmila Bhattacharya, Ph.D., senior scientist at NASA and a study author. “Today’s results show that microgravity can have dramatic effects on the heart, suggesting that medical intervention may be needed for long-duration space travel, and point to several directions for therapeutic development.”

Fruit flies are surprisingly good models for studying the human heart. The insects share nearly 75% of disease-causing genes found in humans, and their tube-shaped hearts mirror an early version of ours–which begins as a tube when we’re in the womb and later folds into the four chambers with which we’re familiar. Fortunately, fruit flies are also largely self-sustaining. All the food the flies needed for the duration of the trip were contained in special boxes designed for this study–allowing busy astronauts to focus on other tasks.

Journey to space

In the study, the scientists sent the special “vented fly boxes” containing vials filled with a few female and male fruit flies to the ISS for a one-month-long orbit. While in space, these flies produced hundreds of babies that experienced three weeks of microgravity–the human equivalent of three decades. The fruit flies that were born in space returned to Earth via a splashdown off the coast of Baja California. A member of the scientific team retrieved the flies from the Port of Long Beach and–very carefully–drove the specimens to Sanford Burnham Prebys’ campus in La Jolla, California.

Once the flies arrived at the lab, the scientists sprang into action. Tests of heart function had to be taken within 24 hours of the return to Earth so gravity wouldn’t interfere with the results. The researchers worked around the clock to measure the flies’

ability to climb up a test tube; to capture videos of the beating hearts to measure contractility and heart rate; and to preserve tissue for future genetic and biochemical assays, including mapping gene expression changes that occurred in the heart.

Extensive tissue remodeling

This work revealed that the space flies had smaller hearts that were less contractile–reducing their ability to pump blood and mirroring symptoms seen in astronauts. The heart tissue also underwent extensive remodeling. For example, the normally parallel muscle fibers became misaligned and lost contact with the surrounding fibrous structures that permit the heart to generate force–resulting in impaired pumping.

“In the normal fly heart, the muscle fibers work like your fingers when they squeeze a tube of toothpaste. In the space flies, the contraction was like trying to get toothpaste out by pressing down instead of squeezing,” explains Ocorr. “For humans, this could become a big problem.”

To the scientists’ surprise, the fibrous extracellular matrix (ECM) surrounding the heart of the space flies was significantly reduced. After a heart injury such as a heart attack, this supportive tissue is often overproduced and interferes with heart function. For this reason, the interplay between the ECM and the heart is an active area of research for heart scientists.

“We were very excited to find several ECM-interacting proteins that were dysregulated in the space flies,” says Rolf Bodmer, Ph.D., director and professor in the Development, Aging and Regeneration Program at Sanford Burnham Prebys and co-senior author of the study. “These proteins weren’t previously on the radar of heart researchers, so this could accelerate the development of therapies that improve heart function by reducing fibrosis.”

The tip of the iceberg

Ocorr and Bodmer are still busy analyzing genetic and molecular data from this study and believe these insights are the “tip of the iceberg” for this type of research. Vision problems are common in astronauts, so the scientists are also analyzing eye tissue from the space flies. Another area of interest relates to the babies of the flies that were born in space, which would help reveal any inherited effects of space flight. While astronaut health is the primary goal, people on Earth may ultimately be the greatest beneficiaries of this pioneering work.

“I am confident that heart disease research is going to benefit from the insights we’re gaining from these flights,” says Ocorr. “Understanding how the heart functions in space is also going to teach us more about how the heart works and can break on Earth.”

References: Stanley Walls, Soda Diop et al., “Prolonged Exposure to Microgravity Reduces Cardiac Contractility and Initiates Remodeling in Drosophila”, Cell Reports, 2020. https://www.cell.com/cell-reports/fulltext/S2211-1247(20)31434-0?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS2211124720314340%3Fshowall%3Dtrue DOI: https://doi.org/10.1016/j.celrep.2020.108445

Provided by Sanford Burnham Prebys Medical Discovery Institute

Space Worms Experiment Reveals Gravity Affects Genes (Planetary Science)

Living at low gravity affects cells at the genetic level, according to a study of worms in space.

Genetic analysis of Caenorhabditis elegans worms on the International Space Station showed “subtle changes” in about 1,000 genes.

©Willis et al.

Stronger effects were found in some genes, especially among neurons (nervous system cells).

The study, by the University of Exeter and the NASA GeneLab, aids our understanding of why living organisms – including humans – suffer physical decline in space.

“We looked at levels of every gene in the worms’ genome and identified a clear pattern of genetic change,” said Dr Timothy Etheridge, of the University of Exeter.

“These changes might help explain why the body reacts badly to space flight.

“It also gives us some therapy targets in terms of reducing these health effects, which are currently a major barrier to deep-space exploration.”

The study exposed worms to low gravity on the International Space Station, and to high gravity in centrifuges.

The high-gravity tests gave the researchers more data on gravity’s genetic impacts, and allowed them to look for possible treatments using high gravity in space.

“A crucial step towards overcoming any physiological condition is first understanding its underlying molecular mechanism,” said lead author Craig Willis, of the University of Exeter.

“We have identified genes with roles in neuronal function and cellular metabolism that are affected by gravitational changes.

“These worms display molecular signatures and physiological features that closely mirror those observed in humans, so our findings should provide foundations for a better understanding of spaceflight-induced health decline in mammals and, eventually, humans.”

Dr Etheridge added: “This study highlights the ongoing role of scientists from Europe and the UK in space flight life sciences research.”

References: Craig Willis et al., “Comparative Transcriptomics Identifies Neuronal and Metabolic Adaptations to Hypergravity and Microgravity in Caenorhabditis elegans”, IScience, 2020. DOI:https://doi.org/10.1016/j.isci.2020.101734 https://linkinghub.elsevier.com/retrieve/pii/S2589004220309317

Provided by University of Exeter

Scientists Uncover New Layer Of Complexity In How Our Bodies Respond To Drug Treatments (Medicine)

Scientists from the University of Glasgow have played an important role in understanding why some patients respond better to drug treatments than others.

©University of Glasgow

The study – published today in Nature and involving the University of Glasgow and a number of international partners – uncovers a new layer of complexity in how the body responds to medical treatments by using the power of data analysis on GPCRs.

GPCRs – or G protein-coupled receptors – are a family of proteins in the body and the molecular targets for many effective medicines (approximately 34% of approved drugs). However, there are individual responses to GPCR signalling in each of us, which could explain differences in receptor function and drug response.

These important drug target receptors exist in multiple structurally and functionally distinct versions distributed in a tissue-specific manner around our bodies.

By looking in detail at different isoform variants being produced from a single gene, the scientists in this study – led by Prof Madan Babu, St. Jude Children’s Research Hospital, Tennessee – have illustrated how this knowledge may be developed for the benefit of patients.

Scientists based at the Medical Research Council-funded Laboratory of Molecular Biology in Cambridge defined the expression patterns of sequence variant isoforms of all GPCRs in different tissues, and even single cell types of the human body. This gave the team a detailed understanding, on a tissue-by-tissue basis, of natural receptor activation and drug effects.

Analysis of the functional responses of such GPCR isoforms to medicines, conducted at University of Glasgow, as well as at the Universities of Cambridge and Michigan, illustrated how to take advantage of the glut of data available to understand these questions.

For the study, the collaborators integrated and analysed genomics, transcriptomics, proteomics, structural, and pharmacological data for more than 300 receptors in 30 different tissues from individual donors. This investigation created a vast amount of data that was used to generate a new resource in the GPCR database maintained at the University of Copenhagen. This resource will allow experts interested in particular GPCRs to determine if their receptor of interest can exist in one or multiple isoforms and get detailed information of receptor isoform structural and functional data on a tissue-by-tissue basis.

Professor Andrew Tobin, from the University of Glasgow’s Institute of Molecular, Cell and Systems Biology, said: “This research shines a light on why some patients respond well to medicines and others do not. If we can understand key genetic differences that determine why some patients respond better to drug treatment than others then we will be able to tailor medicines to the specific needs of patients – this will be of benefit to patients and save time and money for the health service.”

Professor Graeme Milligan, of the College of Medical, Veterinary and Life Sciences at University of Glasgow said: “Multidisciplinary approaches than link experimental laboratory studies to the analysis of large data sets offer fantastic opportunities to develop novel medicines with reduced side effects. The studies we have been part of provide an excellent example of how data and experimental scientists can and must collaborate to improve human health.”

The work was funded by UKRI MRC, Wolfson College, FEBS, Marie Skłodowska-Curie actions, Swiss National Science Foundation, NIH, NIDA Core Center of Excellence in Omics, Systems Genetics, and the Addictome, NSF, UKRI BBSRC, AstraZeneca, Lundbeck Foundation, Novo Nordisk Foundation, Lister Institute, ERC, and ALSAC.

Provided by University of Glasgow