Research Expertise

My research addresses the fundamental question of how a healthy immune system is able to tolerate self-tissues and beneficial microbes or antigens, and how this process breaks down in autoimmunity and organ transplant rejection. Our early established that immune tolerance is imprinted epigenetically, but like all studies at the time, were limited by incomplete knowledge of the genome and technologies not powered to explore these processes at genome-scale. A significant challenge to understanding gene regulation is the remarkable vastness of the genome, which consists of 3 billion nucleotides or 2 meters of DNA packed so tightly into chromatin that it fits into the 10-micron nucleus of a cell. The Human Genome Project revealed that only 3% of the genome is comprised of genes, while the other 97% enigmatically encodes the instructions for how genes are expressed. Advances in genomics led to copious genome-wide association studies (GWAS) of autoimmune disease risk, offering the potential to understand the genetics of human immune tolerance, but 90% of disease-associated polymorphisms are located in remote regions of the genome with no clear hint of how they might regulate which genes. Genes can therefore be controlled by elements that are incredibly far away in linear sequence, but are very close in 3D, so without a spatial map of genome structure in a given cell type it is impossible to know a gene’s full cis-regulatory architecture and how genetic variants contribute to its expression.

My laboratory has tackled these challenges by adopting powerful new methods for mapping the 3D structure of the genome (3C, capture-C, HiC). When combined with innovative techniques for measuring genome accessibility (ATAC-seq), transcription factor occupancy (ChIP-seq), disease-associated genetic variation (GWAS), and gene expression (RNA-seq), these maps can capture active genetic elements in the act of looping over large distances to physically contact and regulate their target genes in cells. Incorporating the genetics of immune tolerance into our research means that the laboratory uses an array of systems, including mouse models, human cellular assays, and lymphoid organoid platforms. As the co-director of the Center for Spatial and Functional Genomics at The Children’s Hospital of Philadelphia, I collaborate with multidisciplinary teams of human geneticists, bioinformatic scientists, and clinicians to access critical patient samples, generate and analyze multi-omic datasets, and conduct GWAS to position our data in the context of human disease. Below are a few examples of ongoing projects:

Long-range control of Interleukin-2 gene expression by a novel, distal enhancer
Interleukin-2 (IL-2) is an immune hormone with crucial roles in immune tolerance, and for decades a ~350 bp upstream regulatory region (URR) was considered necessary and sufficient for tissue-specific, inducible expression of IL2. However, work from our group and others began to suggest that genomic elements in addition to the URR might contribute to regulation of this gene. For example, genetic studies in humans and mice have implicated IL2 in autoimmune disease susceptibility, but the associated variants do not localize to the URR. To search for additional cis-regulatory mechanisms for IL2, my laboratory surveyed the ~100 kb intergenic space between IL2 and its distant neighbor IL21 and identified a 400 bp element located 83 kb upstream of IL2 that exhibits increased accessibility, active histone modifications, and long-range looping to physically interact with the URR in a manner directly associated with transcription of IL2 mRNA (1). This element is evolutionarily conserved between mice and humans, contains a single-nucleotide polymorphism (SNP) associated with multiple autoimmune disorders, and can potently enhance IL2 transcription in recombinant reporter assays. This study was the first to demonstrate that the regulatory paradigm of IL2, a gene whose transcriptional control has been studied extensively since 1986, was incomplete, and suggested a novel molecular basis for the genetic association of IL2 polymorphism with autoimmune disease.

Immune tolerance depends on cooperativity between the transcription factors Ikaros and Foxp3
Regulatory T cells (Treg) are a subset of immune cells that suppress conventional T cell activity and are required for immune tolerance. Nearly two decades ago, my laboratory established that the Treg lineage transcription factor Foxp3 binds to and remodels the chromatin at Treg hallmark genes to reprogram conventional T cells into Treg. Following my promotion, we continued to reveal novel mechanisms by which Foxp3 regulates gene expression, and by which Foxp3 activity is modulated by post-translational modifications. In a study co-led by myself and Lin Chen at USC, we determined the crystal structure of Foxp3 bound to DNA, showed that Foxp3 forms a stable domain-swapped dimer to bridge DNA, and used chromosome conformation capture (4C-seq) to show that the activity of Foxp3 in T cells is sufficient to re-organize long-range genomic contacts at Foxp3-bound genetic loci (2). These results showed that, in addition to remodeling local chromatin at cis-regulatory elements, Foxp3 orchestrates large-scale chromosomal architecture as part of its gene regulatory activity in regulatory T cells. My laboratory also established a crucial role for the transcription factor Ikaros as a central regulator of T cell tolerance. In a series of papers published since my promotion, we showed that Ikaros binds to and silences inflammatory genes in CD4+ and CD8+ T cells, and that T cells lacking Ikaros are able to escape tolerance, avoid Treg-mediated suppression, and drive inappropriate inflammatory responses. Because Foxp3 and Ikaros regulate many of the same genes, we hypothesized that Ikaros and Foxp3 cooperate to regulate gene expression in Treg. Indeed, we found that Ikaros binds to and cooperates with Foxp3 at the level of DNA binding and chromatin remodeling to establish a large portion of the Treg epigenome and transcriptome (3). Ikaros-deficient Treg exhibit abnormal expression of pro-inflammatory genes, and mice lacking Ikaros in the Treg lineage are unable to control T cell-mediated immune pathology in models of IBD and organ transplantation. Our work on toleragenic reprogramming of T cells by Foxp3 in cooperation with Ikaros not only has significantly forwarded the field’s understanding of core mechanisms of immune tolerance, but has been influential in the development of cellular therapy efforts by others in the biotech/pharma space that are based on Foxp3-reprogrammed cells for the treatment of autoimmune diseases like rheumatoid arthritis and type 1 diabetes. In addition, our work suggests that Ikaros antagonists could be used to oppose Treg suppressive activity to improve immune responses to vaccines or cancer.

How human genetic variation contributes to autoimmune disease susceptibility
A major challenge to understanding how common genetic variation influences immunity and inflammatory disease is that GWAS does not identify causal variants, causal genes, or target tissues. Our 3D maps of gene regulatory architectures in human cells provide a solution to each of these problems. By placing regulatory variant maps into the 3-dimensional context of our HiC maps in the same cells, we can physically connect disease variants to the genes they likely regulate. We have applied this variant-to-gene (V2G) mapping approach to over 30 genetic diseases, including COVID-19, but here I highlight two particularly impactful autoimmune studies from my laboratory. Systemic lupus erythematosus (SLE) is an autoimmune disorder resulting from dysregulated humoral immunity. We generated high-resolution spatial maps of SLE variant accessibility and gene connectivity in human follicular helper T cells (TFH), a cell type required for the pathogenic autoantibodies characteristic of SLE (4). Of the ~400 potential regulatory variants identified, 90% exhibit spatial proximity to genes distant in the 1D genome sequence, including variants that contact and regulate the canonical TFH genes BCL6 and CXCR5. SLE V2G maps also implicate genes with no known role in TFH/SLE disease biology, including the kinases HIPK1 and MINK1. Targeting these kinases in TFH inhibited production of IL-21, a cytokine crucial for class-switched B cell antibodies. In a separate study, our 3D epigenomic approach localized risk variants from 15 autoimmune GWAS to regulatory elements active during activation of naïve human CD4+ T cells (5). We identified ~1,200 protein-coding genes physically connected to accessible disease variants at 423 GWAS loci, one-third of which are dynamically regulated by activation. These maps predicted five evolutionarily conserved elements ~150 kb upstream of the IL2 gene that we validated by recombinant reporter assays and CRISPR/CAS9 genome editing as bona fide enhancers whose activity is influenced by autoimmune-associated genetic variation and is required for normal IL2 gene expression in both human and mouse. This set of variant-implicated genes included many with no previously established role in T cell/autoimmune biology. To test the predictive power of our approach, we selected a subset of novel, readily ‘druggable’ targets and were able to pharmacologically validate 80% of these as novel regulators of T cell activation. These studies clearly demonstrate to the field that 3D chromatin-based V2G provides mechanistic insight into the gene regulatory architecture of human immune tolerance and identifies novel therapeutic targets for immunomodulation.

1: Long-range transcriptional control of the Il2 gene by an intergenic enhancer. Mehra P. and Wells A.D. Mol. Cell Biol. 2015 35:3880-91.
2: DNA binding by Foxp3 domain-swapped dimer suggests mechanisms of long-range chromosomal interactions. Chen Y., Chen C., Zhang Z., Liu C.C., Johnson M.E., Espinoza C.A., Edsall L.E., Ren B., Zhou X.J., Grant S.F.A., Wells A.D., Chen L. Nucleic Acids Res. 2015 43:1268-82.
3: Foxp3 depends on Ikaros for control of regulatory T cell gene expression and function. Thomas, R.M., Pahl, M.C., Wang, L., Grant, S.F.A, Hancock, W.W., Wells A.D. eLife 2023 In Press https://doi.org/10.7554/eLife.91392.1
4: Mapping effector genes at lupus GWAS loci using promoter Capture-C in follicular helper T cells. Su C., Johnson M.E., Torres A., Thomas R.M., Manduchi E., Sharma P., Mehra P., Le Coz C., Leonard M.E., Lu S., Hodge K.M., Chesi A., Pippin J., Romberg N., Grant S.F.A., Wells A.D. Nat Commun. 2020 11:3294.
5: Dynamic chromatin architecture identifies new autoimmune-associated enhancers for IL2 and novel genes regulating CD4+ T cell activation. Pahl, M.C., Sharma, P., Thomas, R.M., Thompson, Z., Mount, Z., Pippin, J, Morawski, P.A., Sun, P., Su, C., Campbell, D.J., Grant, S.F.A., Wells A.D. eLife 2024, In Press https://www.biorxiv.org/content/10.1101/2023.04.05.535731v2.full.pdf

Graduate Groups

Cell and Molecular Biology
Immunology

Education

B.A. (Microbiology), Miami University , 1991
Ph.D. (Medical Microbiology and Immunology), University of Wisconsin-Madison, 1996

Postgraduate Training

Post-Doctoral Fellowship in Microbiology, University of Pennsylvania, 1996-1999
Research Associate, University of Pennsylvania, 1999-2001

Awards and Honors

National Institutes of Health Fellowship in Immunobiology of Normal and Neoplastic Lymphocytes - NIH/NCI-sponsored post-doctoral traineeship awarded at the University of Pennsylvania, 1996-1999
UpJohn Young Investigator Award - awarded for the best paper presented by a young investigator at the American Society of Transplant Physicians Symposium, Chicago, Illinois, 1998-1998
President’s Young Investigator Award - awarded for outstanding paper presentation by a young investigator at the American Society of Transplantation Symposium, Chicago, Illinois, 1999-1999
Best Platform Presentation - Great Lakes International Imaging and Flow Cytometry Association, 2000-2000
NIH/NIDDK K01 Mentored Research Scientist Development Award. A three-year grant awarded for the project entitled ‘T cell Division, Survival and Memory in Transplantation’, 2000-2000
Department of Pathology and Laboratory Medicine Nominee for the Pew Scholars Award, 2003-2003
Basic Science Investigator Award, American Society of Transplantation, 2012-2012
Keynote Speaker, Annual Immunology Research Retreat, McGill University, 2013-2013
Keynote Speaker, Morton Klein Memorial Conference, Temple University, 2015-2015

Memberships and Professional Organizations

American Society of Transplantation, 1999 - present
American Association of Immunologists, 1999 - present
The Wellcome Trust, 2007 - 2009
American Society for Biochemistry and Molecular Biology, 2007 - present
Dutch Arthritis Foundation, 2007 - 2007
Tolerance, Transplantation, and Tumor Immunology (TTT) study section, NIAID, NIH, 2009 - 2016
University of Missouri Research Board, 2009 - 2009
Canadian Institutes of Health Research Immunology and Transplantation Peer Review Committee, 2010 - 2011
Austrian Science Fund, 2010 - 2010
NIH ZAI1 BDP-I (M2) Special Emphasis Panel, 2015 - 2015
American Society for Microbiology, 2015 - 2019
NIH ZRG1 IMM-K 90 S Special Emphasis Panel, 2016 - 2017
NIH ZAI1-GEB-I-M1 Special Emphasis Panel, 2017 - 2017
NIH ZAI1-NVM-I (S1) R24 P01 Review Panel, 2017 - 2017
NIH ZHL1 CSR-S (F2) Special Emphasis Panel, 2017 - 2017
American Society of Human Genetics, 2017 - present
NIH ZRG1 IMM-J (03) M Special Emphasis Panel, 2018 - 2018
NIH ZRG1 IMM-F 02M Special Emphasis Panel, 2018 - 2018
NIH/NIDCR Board of Scientific Counselors Review Panel, 2018 - 2018
NIH ZAI1-DR-E-M1 Special Emphasis Panel, 2019 - 2019
Tolerance, Transplantation, and Tumor Immunology (TTT) study section, 2019 - 2019
Federation of Clinical Immunology Societies (FOCIS), 2020 - present
Hypersensitivity, Autoimmune, and Immune-mediated Diseases Study Section (HAI) study section, 2021 - 2021
NIH ZRG1 IDIB-J (02) M Special Emphasis Panel, 2021 - 2021
NIH 2022-05 ZRG1 F08-M 20 L Fellowship Review Panel, 2022 - 2022
Cellular and Molecular Immunology B (CMIB) study section, 2023 - 2023
Hypersensitivity autoimmunity and immune mediated disease (HAI) special emphasis panel 2024-10 ZRG1 IIDB-R (02) M, 2024 - 2024

Web Links

Selected Publications

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