When the Human Genome Project successfully sequenced the last of the more than 3 billion nucleotides that make up the human genome in 2003, it was hailed as the operating manual for the approximately 20,000 genes that determine all of the shared and unique characteristics that determine a human being. Little did we know that it was just the beginning.
Today, we know that roughly 90% of the genetic variations within the human genome that are responsible for unique traits and, possibly, enhanced disease risk are not found in those ~ 20,000 genes, but are instead in regions of non-coding DNA; regions once coined “junk DNA”. We also know that many of these non-coding genetic variations are located in regulatory regions that control gene expression. The unique characteristics of an individual, as well as the risk for developing complex heritable diseases, are the result of thousands of inherited non-coding genetic variations that collectively modify gene expression.
I have dedicated my research career to identifying which non-coding genetic variations are associated with the debilitating autoimmune disease, systemic lupus erythematosus (lupus), and how those genetic variations function to disrupt the immune system, leading to inflammation, organ failure, and, in some cases, premature death. By improving our understanding of the complex regulatory mechanisms embedded within the human genome, we hope to advance early detection strategies and the development of more effective treatments for lupus.
My primary research focus is to decipher the complex genetic landscape of lupus and other autoimmune diseases. Like other autoimmune diseases, lupus is characterized by a production of autoantibodies that attack a wide variety of tissues and organs resulting in systemic inflammation and organ failure.
Our work has contributed significantly over the last decade to establish a strong genetic basis for lupus, and to provide important information about how genetic variations influence immune cell function to drive lupus development and progression. We use state-of-the-art high throughput sequencing technologies coupled with bioinformatics and functional analyses to systematically evaluate how genetic variations associated with lupus alter the genetic landscape and subsequent gene expression. Our overall objective is to develop a comprehensive view of the genetic landscape of lupus that can then be used to develop new or improved predictive and monitoring tools for patients with lupus.
B.S., Saint John’s University, Collegeville, MN, 1983
M.D., University of Minnesota, Minneapolis, MN, 1991
Honors and Awards
Midwest Trainee Investigator Award, American Federation for Clinical Research, 1996
Molecular Genetics Fellowship, University of Minnesota, 1997
Participant, Genetic-Epidemiological Studies of Complex Diseases, Cold Spring Harbor Laboratory, 1998
NIH NIAMS Clinical Investigator Award, 1999
Young Investigator Award, Department of Medicine, University of Minnesota, 2000
Cancer and Leukemia Group B Junior Faculty Research Award, 2005
Faculty Career Development Award, Department of Medicine, University of Minnesota, 2006
The Merrick Award for Outstanding Research, Merrick Foundation, 2008, 2011
Edward L. and Thelma Gaylord Prize for Scientific Achievement, Oklahoma Medical Research Foundation, 2013
J.G. Puterbaugh Chair in Medical Research, Oklahoma Medical Research Foundation, 2013-present
Member, Scientific Advisory Committee, SLE Biomarkers Working Group, 2004-present
Member, Scientific Advisory Committee, DeCide Clinical Trial, University of Chicago Medical School, 2005-present
Member, SLEGEN Consortium Data Analysis Committee, 2006-present
Adjunct Associate Professor, University of Oklahoma Health Sciences Center, 2008-present
OUHSC MD/PhD Program Steering Committee, 2010-present
JoVE Editorial Board Member, Clinical and Translational Medicine, 2014-present
Member, Scientific Advisory Panel, The International Foundation for Autoimmune Arthritis (IFAA), 2014-present
Co-Chair, American College of Rheumatology Abstract Selection Committee, Genetics, Genomics and Proteomics category, 2014-present
Member, External Advisory Committee, The Medical University of South Caroline Clinical Resource Center (MUSC CRC), 2016-present
Associate Director, OUHSC MD/PHD Program, 2016-present
OMRF Scientific Promotions Committee, 2017-present
Occupational Health Physician, OMRF IACUC, 2022-present
Member, OMRF Scientific Computing Committee, 2009-present
American Society of Human Genetics
American College of Rheumatology
Henry Kunkel Society
Joined OMRF scientific staff in 2007
Jiang K, Fu Y, Kelly JA, Gaffney PM, Holmes LC, Jarvis JN. Comparison of the three-dimensional chromatin structures of adolescent and adult peripheral blood B cells: implications for the study of pediatric autoimmune diseases. bioRxiv, 2023 September, PMID: 37745336, PMCID: PMC10515843
Fu Y, Kelly JA, Gopalakrishnan J, Pelikan RC, Tessneer KL, Pasula S, Grundahl K, Murphy DA, Gaffney PM. Massively Parallel Reporter Assay Confirms Regulatory Potential of hQTLs and Reveals Important Variants in Lupus and Other Autoimmune Diseases. bioRxiv, 2023 August, PMID: 37645944, PMCID: PMC10462090
Joachims ML, Khatri B, Li C, Tessneer KL, Ice JA, Stolarczyk AM, Means N, Grundahl KM, Glenn SB, Kelly JA, Lewis DM, Radfar L, Stone DU, Guthridge JM, James JA, Scofield RH, Wiley GB, Wren JD, Gaffney PM, Montgomery CG, Sivils KL, Rasmussen A, Farris AD, Adrianto I, Lessard CJ. Dysregulated long non-coding RNA in Sjögren's disease impacts both interferon and adaptive immune responses. RMD Open 8, 2022 November, PMID: 36456101, PMCID: PMC9717416
Gopalakrishnan J, Tessneer KL, Fu Y, Pasula S, Pelikan RC, Kelly JA, Wiley GB, Gaffney PM. Variants on the UBE2L3/YDJC Autoimmune Disease Risk Haplotype Increase UBE2L3 Expression by Modulating CCCTC-Binding Factor and YY1 Binding. Arthritis Rheumatol. 2022 Jan;74(1):163-173. doi: 10.1002/art.41925. Epub 2021 Dec 13. PMID: 34279042, PMCID: PMC8712360.
Pasula S, Tessneer KL, Fu Y, Gopalakrishnan J, Pelikan RC, Kelly JA, Wiley GB, Wiley MM, Gaffney PM. Role of systemic lupus erythematous risk variants with opposing functional effects as a driver of hypomorphic expression of TNIP1 and other genes within a three-dimensional chromatin network. Arthritis Rheumatol. 2020 May; 72(5): 780-790. PMID: 31804013, PMICD: PMC7188567
Kondo Y, Fu J, Wang H, Hoover C, McDaniel JM, Street R, Patra D, Song J, Pollard L, Cathey S, Yago T, Wiley G, Macwana S, Guthridge J, McGee S, Li S, Griffin C, Furukawa K, James JA, Ruan C, McEver R, Wierenga KJ, Gaffney PM*, Xia L (*Co-senior author). Site-1 protease deficiency causes human skeletal dysplasia due to defective inter-organelle protein trafficking. JCI Insight. 2018 Jul 26;3(14):121596.PMID: 30046013, PMCID: PMC6124414
Pelikan RC, Kelly JA, Fu Y, Lareau CA, Tessneer KL, Wiley GB, Wiley MB, Glenn SB, Harley JB, Guthridge JM, James JA, Aryee MJ, Montgomery C, Gaffney PM. Enhancer histone-QTLs are enriched on autoimmune risk haplotypes and influence gene expression within chromatin networks. Nat Commun. 2018 Jul 25;9(1):2905. PMID: 30046115, PMCID: PMC6060153
Langefeld CD, et al. (Gaffney PM – author #107 of 108; corresponding author). Transancestral mapping and genetic load in systemic lupus erythematosus. Nat Commun. 2017 Jul 17; 8:16021. PMID: 28714469, PMCID: PMC5520018
Gaffney PM, Kearns GM, Shark KB, Ortmann WA, Selby SA, Malmgren ML, Rohlf KE, Ockenden TC, Messner RP, King RA, Rich SS, Behrens TW. A genome-wide search for susceptibility genes in human systemic lupus erythematosus sib-pair families. Proc Natl Acad Sci USA. 1998 Dec 8;95(25):14875-9. PMID: 9843983, PMCID: PMC24543
Satish Pasula, Ph.D.
Yao Fu, Ph.D.
Assistant Staff Scientist
Richard Pelikan, Ph.D.
Senior Bioinformatics Scientist
Senior Manager of Laboratory
David Murphy, Ph.D.
Research Project Director
Kandice Tessneer, Ph.D.
Science Writer Specialist
Susan "Suzy" Collins
Project Coordinator II
News from the Gaffney lab
The National Institutes of Health awarded grants worth more than $4 million to two OMRF scientists. Patrick Gaffney, M.D., and Courtney Griffin, Ph.D., were each awarded five-year R01 grants to research genes related to lupus and vascular development, respectively. After identifying two genes associated with lupus—a chronic autoimmune disease that affects an estimated 2 million […]
The National Institutes of Health has awarded 17 grants worth a total of $14.7 million to OMRF. The grants are part of the $10 billion in economic stimulus funds that will be provided for medical research through the American Recovery and Reinvestment Act of 2009. The grants will fund OMRF research on a wide array […]
OMRF has received a $10 million grant from the National Institutes of Health to study the autoimmune disease lupus. The five-year award comes from the National Institute of Allergy and Infectious Diseases at the NIH. The grant will support research on the genetic origins of lupus, which affects up to an estimated 2 million Americans […]
Four Oklahomans joined the Oklahoma Medical Research Foundation’s Board of Directors at OMRF’s semiannual board meeting Wednesday. Also at the meeting, three OMRF scientists were honored. Joining the board are Dave Bialis, Ramsey Drake and Cliff Hudson of Oklahoma City and Harold Hamm of Enid. Bialis is president of Cox Oklahoma. His civic involvement includes […]
An international consortium of scientists led by OMRF investigator John B. Harley, M.D., Ph.D., has identified multiple genes linked to lupus, a devastating autoimmune disease that affects as many as 2 million Americans and 15 million people worldwide. The group’s findings appear online in two related articles in the Feb. edition of the journal Nature […]
The Oklahoma Medical Research Foundation today announced the addition of four scientists to the faculty of its Arthritis & Immunology Research Program. The four new faculty members are Patrick Gaffney, M.D., Kathy Moser, Ph.D., Jonathan Wren, Ph.D., and Igor Dozmorov, Ph.D. “Their recruitment gives us a depth of scientific commitment and expertise that is unparalleled […]