GTEx findings reveal new insights into how DNA differences influence gene activity, disease susceptibility
Researchers funded by the National Institutes of Health Genotype-Tissue Expression (GTEx) project, including scientists from the Broad Institute of MIT and Harvard, have created a new and much-anticipated data resource to help establish how differences in an individual’s genomic make-up can affect gene activity and contribute to disease. The new resource will enable scientists to examine the underlying genomics of many different human tissues and cells at the same time, and promises to open new avenues to the study and understanding of human biology.
GTEx investigators reported initial findings from a two-year pilot study in several papers appearing online May 7, 2015, in Science and other journals. These efforts provide new insights into how genomic variants – inherited spelling differences in the DNA code – control how, when, and how much genes are turned on and off in different tissues, and can predispose people to diseases such as cancer, heart disease, and diabetes.
“GTEx was designed to sample as many tissues as possible from a large number of individuals in order to understand the causal effects of genes and variants, and which tissues contribute to predisposition to disease,” said Emmanouil Dermitzakis, Ph.D., professor of genetics at the University of Geneva Faculty of Medicine, Switzerland, and a corresponding author on the main Science paper. “The number of tissues examined in GTEx provides an unprecedented depth of genomic variation. It gives us unique insights into how people differ in gene expression in tissues and organs.”
NIH launched the GTEx Project in 2010 to create a data resource and tissue bank for scientists to study how genomic variants may affect gene activity and disease susceptibility. Investigators are collecting more than 30 tissue types from autopsy and organ donations in addition to tissue transplant programs. The DNA and RNA from those samples are then analyzed using cutting-edge genomic methods. The project will eventually include tissue samples from about 900 deceased donors. GTEx is supported by the NIH Common Fund and administered by the National Human Genome Research Institute (NHGRI), the National Institute of Mental Health (NIMH), and the National Cancer Institute (NCI), all part of NIH.
“GTEx will be a great resource for understanding human biological function, and will have many practical applications in areas such as drug development,” said NHGRI Program Director Simona Volpi, Pharm.D., Ph.D. “Scientists studying asthma or kidney cancer, for example, will be interested in understanding how specific variants influence the biological function of the lung, kidney, and other organs.”
In the main Science paper, researchers analyzed the gene activity readouts of more than 1,600 tissue samples collected from 175 individuals and 43 different tissue types. One way that researchers evaluate gene activity is to measure RNA, which is the readout from the genome’s DNA instructions. Investigators focused much of their analyses on samples from the nine most available tissue types: fat, heart, lung, skeletal muscle, skin, thyroid, blood, and tibial artery and nerve.
The genomic blueprint of every cell is the same, but what makes a kidney cell different from a liver cell is the set of genes that are turned on (expressed) and off over time and the level at which those genes are expressed. GTEx investigators used a methodology – expression quantitative trait locus (eQTL) analysis – to gauge how variants affect gene expression activity. An eQTL is an association between a variant at a specific genomic location and the level of activity of a gene in a particular tissue. One of the goals of GTEx is to identify eQTLs for all genes and assess whether or not their effects are shared among multiple tissues.
Investigators discovered a set of variants with common activity among the different tissue types. In fact, about half of the eQTLs for protein-coding genes were active in all nine tissues. They identified approximately 900 to 2,200 eQTL genes – genes linked to nearby genomic variants – for each of the nine tissues studied, and 6,486 eQTL genes across all the tissues. “We didn’t know how specific this regulation would be in different tissues,” said co-corresponding author Kristin Ardlie, Ph.D., who directs the GTEx Laboratory Data Analysis and Coordination Center at the Broad Institute of MIT and Harvard. “The analysis showed a large number of variants whose effects are common across tissues, and at the same time, there are subsets of variants whose effects are tissue-specific.”
Comparing tissue-specific eQTLs with genetic disease associations might help provide insights into which tissues are the most relevant to a disease. The researchers also found a great deal of eQTL sharing among tissues, which can help explain how genomic variants affect the different tissues in which they are active.
Even when active in multiple tissues, the same variant can sometimes have a different effect in different tissues. GTEx researchers found, for example, that a variant that affects the activity of two genes associated with blood pressure had a stronger effect on gene expression relevant to blood pressure in the tibial artery – even though there was greater overall gene activity in other tissues. They also noted that the same gene activity profiles characterizing tissues from living donors were seen in the GTEx samples from deceased donors.
Two companion studies in Science used GTEx data to examine other aspects of gene activity in different tissues. One study characterized the effects of protein-truncating variants (PTVs) on gene activity. PTVs shorten the protein-coding sequence of genes, and affect their function. Some rare PTVs can lead to diseases, such as Duchenne muscular dystrophy. Each person’s genome carries about 100 PTVs, though most have little or no effect (and in some cases can even protect against disease).
Manuel Rivas, a Ph.D. candidate at the University of Oxford, and his colleagues used GTEx data and information from a large European project to examine the gene readouts from more than 600 individuals. The team found PTVs that affect protein production either through the degradation of gene transcripts or by disrupting a process called splicing. In both cases, the researchers were able to use the GTEx data to measure these effects across individuals and tissue types. The group is now developing better methods for predicting the impact of PTVs identified in patients with diseases.
In another companion study in Science, Roderic Guigo, Ph.D., coordinator for the Bioinformatics and Genomics Program at the Centre for Genomic Regulation in Barcelona, Spain, and his colleagues examined patterns in gene readouts across nearly 1,500 GTEx tissue samples. The researchers found that gene activity differed substantially more across tissues than across individuals.
Investigators discovered just under 2,000 genes that vary with age, including genes related to neurodegenerative diseases such as Parkinson’s disease and Alzheimer’s disease. They also found more than 750 genes with differences in activity between men and women. Some genes are related to diseases with differences in prevalence between men and women, including five related to heart disease.
Three other studies analyzing GTEx data also appear May 8 in the journals Bioinformatics, PLoS Computational Biology, and Genome Research.
This work was supported by the NIH Common Fund and the following NIH grants: R01 DA006227-17, R01 MH090941, R01 MH090951, R01 MH090937, R01 MH090936, R01 MH090948, R01 GM104371, R01 AG046170, R01 CA163772 and U01AI111598-01. Additional funding was provided by the European Research Council, the Swiss National Science Foundation and Louis-Jeantet Foundation, the Wellcome Trust, the Clarendon Scholarship, the NDM Studentship and the Green Templeton College Award.
About the Broad Institute of MIT and Harvard
The Eli and Edythe L. Broad Institute of MIT and Harvard was launched in 2004 to empower this generation of creative scientists to transform medicine. The Broad Institute seeks to describe all the molecular components of life and their connections; discover the molecular basis of major human diseases; develop effective new approaches to diagnostics and therapeutics; and disseminate discoveries, tools, methods and data openly to the entire scientific community.
Founded by MIT, Harvard and its affiliated hospitals, and the visionary Los Angeles philanthropists Eli and Edythe L. Broad, the Broad Institute includes faculty, professional staff and students from throughout the MIT and Harvard biomedical research communities and beyond, with collaborations spanning over a hundred private and public institutions in more than 40 countries worldwide. For further information about the Broad Institute, go to broadinstitute.org.
About the National Institutes of Health (NIH)
NIH, the nation's medical research agency, includes 27 institutes and centers and is a component of the U.S. Department of Health and Human Services. NIH is the primary federal agency conducting and supporting basic, clinical, and translational medical research, and is investigating the causes, treatments, and cures for both common and rare diseases. For more information about NIH and its programs, visit http://www.nih.gov.
About the National Human Genome Research Institute (NHGRI)
NHGRI is one of the 27 institutes and centers at the National Institutes of Health. The NHGRI Extramural Research Program supports grants for research and training and career development at sites nationwide. Additional information about NHGRI can be found at http://www.genome.gov.
About the National Cancer Institute (NCI)
NCI leads the National Cancer Program and the NIH effort to dramatically reduce the burden of cancer and improve the lives of cancer patients and their families, through research into prevention and cancer biology, the development of new interventions, and the training and mentoring of new researchers. For more information about cancer, please visit the NCI website at http://www.cancer.gov or call NCI's Cancer Information Service at 1-800-4-CANCER (1-800-422-6237).
About the National Institute of Mental Health (NIMH)
The mission of the NIMH is to transform the understanding and treatment of mental illnesses through basic and clinical research, paving the way for prevention, recovery and cure. For more information, visit www.nimh.nih.gov.
About the NIH Common Fund
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The GTEx Consortium. The Genotype-Tissue Expression (GTEx) pilot analysis: multi-tissue gene regulation in humans. Science. Online May 7, 2015. DOI: 10.1126/science.1262110
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Melé, M. et al. The human transcriptome across tissues and individuals. Science. Online May 7, 2015. DOI: 10.1126/science.aaa0355
Pierson, E. et al. Sharing and specificity of co-expression networks across 35 human tissues. PLoS Computational Biology. Online May 7, 2015. DOI: 10.1371/journal.pcbi.1004220
Pirinen, M. et al. Assessing allele-specific expression across multiple tissues from RNA-seq read data. Bioinformatics. Online March 27, 2015. DOI: 10.1093/bioinformatics/btv074
Rivas, M. et al. Effect of predicted protein-truncating genetic variants on the human transcriptome. Science. Online May 7, 2015. DOI: 10.1126/science.1261877