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Home - Science - Scientist Directory - Gaffney, Patrick M.

Patrick M. Gaffney, M.D.

Member and Program Chair
Genes & Human Disease Research Program

J.G. Puterbaugh Chair in Medical Research

Co-director, MD/PhD Training Program, University of Oklahoma Health Sciences Center

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My 101

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.

Research

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.

Brief CV

Education
B.S., Saint John’s University, Collegeville, MN, 1983
M.D., University of Minnesota, Minneapolis, MN, 1991

Honors and Awards
1996 Midwest Trainee Investigator Award, American Federation for Clinical Research
1997 Molecular Genetics Fellowship, University of Minnesota
1998 Participant, Genetic-Epidemiological Studies of Complex Diseases, Cold Spring Harbor Laboratory
1999 NIH NIAMS Clinical Investigator Award
2000 Young Investigator Award, Department of Medicine, University of Minnesota
2005 Cancer and Leukemia Group B Junior Faculty Research Award
2006 Faculty Career Development Award, Department of Medicine, University of Minnesota
2008, 2011 The Merrick Award for Outstanding Research, Merrick Foundation, Oklahoma City, OK
2013 Edward L. and Thelma Gaylord Prize for Scientific Achievement, Oklahoma City, OK
2013 J.G. Puterbaugh Chair in Medical Research, Oklahoma Medical Research Foundation, Oklahoma City, OK
OMRF Scientific Promotions Committee (2017-present)
OUHSC MD/PhD Program Steering Committee (2010-present)
OMRF Post-Doctoral Training Committee (2017-present)

Other Activities
Member, Scientific Advisory Committee, SLE Biomarkers Working Group (2004 to present)
Member, Scientific Advisory Committee, DeCide Clinical Trial, University of Chicago Medical School (2005 to present)
Member, SLEGEN Consortium Data Analysis Committee (2006 to present)
Adjunct Associate Professor, University of Oklahoma Health Sciences Center (2008 to present)
JoVE Editorial Board Member, Clinical and Translational Medicine (2014-present)
Member, Scientific Advisory Panel, The International Foundation for Autoimmune Arthritis (IFAA) (2014 to present)
Co-Chair, American College of Rheumatology Abstract Selection Committee, Genetics, Genomics and Proteomics category (2014 to present)
Standing Member, NIH Hypersensitivity, Autoimmune and Immune-mediated (HAI) Disease NIH Study Section (2015 to 2019)
Member, External Advisory Committee, The Medical University of South Caroline Clinical Resource Center (MUSC CRC) (2016 to present)

Memberships
American Society of Hematology
American Society of Clinical Oncology
American Society of Human Genetics
American Association for Cancer Research
American College of Rheumatology
Henry Kunkel Society

Joined OMRF Scientific Staff in 2007

Publications

View more publications

Recent Publications

Tarbell E, Jiang K, Hennon TR, Holmes L, Williams S, Fu Y, Gaffney PM, Liu T, Jarvis JN. CD4  T cells from children with active juvenile idiopathic arthritis show altered chromatin features associated with transcriptional abnormalities. Sci Rep 11:4011, 2021 February, PMID: 33597588, PMCID: PMC7889855

Shi C, Ray-Jones H, Ding J, Duffus K, Fu Y, Gaddi VP, Gough O, Hankinson J, Martin P, McGovern A, Yarwood A, Gaffney P, Eyre S, Rattray M, Warren RB, Orozco G. Chromatin looping links target genes with genetic risk loci for dermatological traits. J Invest Dermatol, 2021 February, PMID: 33607115

Chai G, Webb A, Li C, Antaki D, Lee S, Breuss MW, Lang N, Stanley V, Anzenberg P, Yang X, Marshall T, Gaffney P, Wierenga KJ, Chung BH, Tsang MH, Pais LS, Lovgren AK, VanNoy GE, Rehm HL, Mirzaa G, Leon E, Diaz J, Neumann A, Kalverda AP, Manfield IW, Parry DA, Logan CV, Johnson CA, Bonthron DT, Valleley EMA, Issa MY, Abdel-Ghafar SF, Abdel-Hamid MS, Jennings P, Zaki MS, Sheridan E, Gleeson JG. Mutations in Spliceosomal Genes PPIL1 and PRP17 Cause Neurodegenerative Pontocerebellar Hypoplasia with Microcephaly. Neuron, 2020 November, PMID: 33220177

Selected Publications
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: PMC30046115

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

Graham RR, Cotsapas C, Davies L, Hackett R, Lessard CJ, Leon JM, Burtt NP, Guiducci C, Parkin M, Gates C, Plenge RM, Behrens TW, Wither JE, Rioux JD, Fortin PR, Graham DC, Wong AK, Vyse TJ, Daly MJ, Altshuler D, Moser KL, Gaffney PM. Genetic variants near TNFAIP3 on 6q23 are associated with systemic lupus erythematosus. Nat Genet. 2008 Sep;40(9):1059-61. PMID: 19165918 PMCID: PMC2772171

International Consortium for Systemic Lupus Erythematosus Genetics (SLEGEN), et al. (Gaffney PM – author #28 of 42). Genome-wide association scan in women with systemic lupus erythematosus identifies susceptibility variants in ITGAM, PXK, KIAA1542 and other loci. Nat Genet. 2008 Feb;40(2):204-10. PMID: 18204446 PMCID: PMC3712260

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

 

Contact

Genes & Human Disease Research Program, MS 57
Oklahoma Medical Research Foundation
825 N.E. 13th Street
Oklahoma City, OK 73104

Phone: (405) 271-2572
Fax: (405) 271-3045
E-mail: Patrick-Gaffney@omrf.org

Lab Staff

Satish Pasula, Ph.D.
Associate Staff Scientist

Yao Fu, Ph.D.
Assistant Staff Scientist

Richard Pelikan, Ph.D.
Senior Bioinformatics Scientist

David Murphy, Ph.D.
Postdoctoral Fellow

Jennifer Kelly
Research Project Director

Stuart Glenn
Assistant Director of Infrastructure & Research Computing

Kandice Tessneer, Ph.D.
Science Writer Specialist

Kiely Grundahl
Senior Laboratory Manager

Jaanam Gopalakrishnan
Graduate Student

Suzy Collins
Project Coordinator II

Leslie Masse
Administrative Assistant II

News from the Gaffney lab

Dr. Gaffney in the Media

News from the Gaffney lab

This St. Patrick’s Day, eat like the Irish
March 16, 2021

Elements of a traditional shamrock-centric meal have surprising nutritional advantages.

OMRF scientists transform ice storm wreckage into art
November 23, 2020

This silver lining will take time. Like science, woodworking has its roots in patience.

OMRF researchers receive lupus grants
July 16, 2020

OMRF has received a pair of grants totaling almost $600,000 from the Lupus Research Alliance.

Oklahoma teen lives with unique skeletal disorder
December 3, 2019

Sydney Rutz is one in five billion.

Are we too clean for our own good?
June 25, 2019

Mounting research suggests our quest to be clean might make children sicker, not healthier.

OMRF receives grant to study underlying causes of lupus
June 20, 2019

OMRF scientist Patrick Gaffney has received a five-year, $3.1 million grant to investigate the underlying mechanisms that lead to lupus onset.

Four OMRF scientists receive promotions
June 5, 2019

OMRF has announced the promotion of four of its principal scientists.

Shell game: New strategy for avoiding peanut allergies
April 16, 2019

Pediatricians are recommending a surprising way for parents to approach the peanut problem.

OMRF launches new genetics research program
April 1, 2019

The new Genes and Human Disease Research Program will broaden OMRF’s investigation into genetic mechanisms in various diseases.

On Christmas – and in life – OMRF researcher balances science and faith
December 24, 2018

OMRF’s Pat Gaffney, a lifelong Catholic, says science and faith need not be at war.

Oklahoma researchers solve a genetic mystery—and save a teen’s life
May 9, 2018

For more than a decade, doctors could not pinpoint Xander’s symptoms. Then DNA sequencing helped researchers save his life.

OMRF Genomics Center earns CAP accreditation
September 13, 2017

OMRF’s Clinical Genomics Center will now be able to offer services to clinicians.

Findings yield new clues to puzzling autoimmune disease
August 3, 2017

Sjögren’s syndrome may affect as many as 4 million Americans.

International study reveals 24 new genes associated with lupus
July 19, 2017

These findings will help scientists understand how to better diagnose and treat the disease.

Researchers identify gene associated with lupus
May 18, 2017

The gene, NCF1, was known by researchers, but it had not previously been linked to lupus

Think you’re Irish? Your genes may say otherwise
March 14, 2017

So what does it mean to be Irish?

Eisai, OMRF enter autoimmune disease research collaboration
October 27, 2016

The project is focused on lupus, which affects up to 1.5 million Americans.

Oklahoma researchers find clues to the origins of lupus
March 24, 2016

These new findings could play a key role in tailoring individual lupus treatments.

Researchers identify genes associated with lupus in Koreans
February 24, 2016

The study looked at genetic samples of nearly 8,000 Koreans.

Puterbaugh gift establishes new laboratory at OMRF
April 17, 2015

Lab focuses on the study of genetics in autoimmune diseases

Grant renewals bring $14.2 million to OMRF programs
September 15, 2014

Awards will fund research in cancer, heart disease, lupus and other areas

OMRF named an Autoimmunity Center of Excellence
June 25, 2014

As an ACE, OMRF will collaborate with scientists at other top institutions.

Research team discovers lupus gene’s role
April 23, 2014

BLK controls autoantibody creation in the immune system.

Could bacteria in the gut trigger lupus?
January 30, 2014

A pilot project will examine the organisms living in lupus patients’ digestive system.

Gaffney named to J.G. Puterbaugh Chair in Medical Research
October 15, 2013

The endowment has already shown results in rare disease research.

International coalition finds six new Sjögren’s syndrome genes
October 7, 2013

Researchers have exponentially increased their understanding of Sjögren’s genetics.

Four researchers receive commendations
April 19, 2013

OMRF honored four investigators for outstanding contributions to science.

OMRF, OUHSC scientists find gene at the root of rare disease
August 13, 2012

Exome sequencing helps pinpoint previously unknown genetic links

Lupus and vascular development research bring $4 million to OMRF
July 30, 2012

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 […]

OMRF receives $4.4 million grant to study immune disease
April 10, 2012

Scientists hope to find the genetic roots of sarcoidosis

OMRF discovers three new lupus genes
March 29, 2012

The international study turns up new targets for lupus research

New OMRF patent could help predict disease
September 21, 2011

A patented discovery might be key to diagnosing lupus patients.

OMRF completes African-American lupus genetics study
September 14, 2011

A study from OMRF finds five genes linked to lupus.

Robots play vital role in advancing research at OMRF
June 22, 2011

Robots are a common sight in OMRF labs, aiding the progress of research.

OMRF honors scientists, welcomes new directors
May 17, 2011

Two OMRF scientists are awarded for their lupus research contributions.

OMRF raises awareness with Lupus State Advocacy Day
May 4, 2011

Scientists emphasize the need for lupus funding and awareness.

OMRF links mutations to lupus
March 28, 2011

Altered proteins in a gene could “cuts the brakes” on the immune system.

OMRF leads international team of scientists
January 11, 2011

Nearly 50 scientists at 33 institutions collaborate to pinpoint lupus genes

Experts offer tips for beating the heat
June 24, 2010

OMRF experts offer tips for keeping your cool when the temperature soars.

OMRF researchers receive $14.7 million in federal stimulus grant funding
October 5, 2009

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 wins $10 million grant to study lupus
August 13, 2009

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 […]

New lupus treatment shows promise
July 27, 2009

Researcher calls new drug “greatest thing in 50 years”

OMRF welcomes new board members, honors scientists
November 19, 2008

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 […]

Reckless Driving: OMRF discovers gene variant that “cuts the brakes” on immune system in lupus patients
August 1, 2008

Your immune system may have more in common with a Corvette than you thought. When a virus or bacteria enters a human body, the immune system revs up to fight and expel the invader. Once the invader is gone, the body puts on the brakes to stop the immune response. But a new study by […]

It’s in the genes: OMRF leads international effort that unmasks potential genetic roots of lupus
January 21, 2008

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 […]

OMRF adds four faculty members
June 14, 2007

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 […]

Dr. Gaffney in the Media

Are we too clean for our own good?
Oklahoman.com

Foundation investigates lupus
WoodwardNews.net

Health Notes: OMRF launches genetics program
Oklahoman.com

A little dirt could be good for the immune system
MuskogeePhoenix.com

OMRF receives grant to study lupus causes
JournalRecord.com

OMRF scientist receives grant to study underlying cause of lupus
OKNursingTimes.com

OMRF scientist receives $3.1 million to study cause of lupus
KFOR.com

Business people: OMRF announces promotions
Oklahoman.com

There’s a new strategy for avoiding peanut allergies
NewsOk.com

Feeding babies peanut butter may prevent allergies
MuskogeePhoenix.com

Shell game: New way to avoid peanut allergies
OKNursingTimes.com

On Christmas–and in life–scientist balances science and faith
NewsOK.com

"Life Changing Discovery": Oklahoma researchers solve a genetic mystery, help save teen
The Oklahoman

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