Andrew D. Wells, Ph.D.

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Associate Professor of Pathology and Laboratory Medicine
Member, The Children's Hospital of Philadelphia Research Institute
Co-Director, Center for Spatial and Functional Genomics, The Children's Hospital of Philadelphia Research Institute
Co-Director, Spatial and Functional Genomics Research Affinity Group, The Children's Hospital of Philadelphia
Program Leader, Institute for Immunology, Perelman School of Medicine at the University of Pennsylvania
Department: Pathology and Laboratory Medicine
Graduate Group Affiliations

Contact information
916D Abramson Research Center
3516 Civic Center Boulevard
Philadelphia, PA 19104
Office: (215) 590-8710
B.A. (Microbiology)
Miami University , 1991.
Ph.D. (Medical Microbiology and Immunology)
University of Wisconsin-Madison, 1996.
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Description of Research Expertise

My laboratory studies how T lymphocyte activation, differentiation, and tolerance are regulated by components of the cyclin-dependent kinase (CDK) cascade like CDK2 and p27KIP1, and by transcription factors like FOXP3 and IKAROS in cooperation with epigenetic factors like DNMT3A. We have over 15 years of experience in cellular immunology, cell biology, and molecular biology research, including mouse models, in vivo and in vitro lymphocyte function, biochemistry, transcriptional biology and epigenetics. More recently, we have incorporated ‘next generation’ approaches like ATAC-seq, ChIP-seq and methyl-DIP-seq to study transcription factor binding, chromatin remodeling, and DNA methylation genome-wide, and three-dimensional chromosome conformation capture (3C)-based techniques like 4C-seq and Capture C to study long-range interactions between enhancers and promoters. We also use CRISPR/CAS9 genome editing technology to mutate gene regulatory elements in mice and in human cells. Two of the most current projects in the lab are outlined below:

A regulatory T cell-intrinsic role for CDK2 and p27kip1 in acquired immune tolerance:

We previously found that the cyclin-dependent kinase CDK2 phosphorylates the Treg transcription factor Foxp3, targeting it for proteolytic degradation. Treg with defective CDK2 activity express more Foxp3 and are better able to mediate cardiac allograft tolerance in response to costimulatory blockade. We now report that normal Treg development in the thymus and TGFB-mediated iTreg differentiation is associated with marked induction of p27kip1, the natural inhibitor of CDK2. This suggests that effective Treg development or function may require tight control of CDK activity. Indeed, conventional CD4+ T cells genetically deficient for p27kip1 exhibited defective induction of Foxp3 in response to TGFB in vitro, which was associated with CDK2-mediated phosphorylation of Foxp3 as measured by a novel phospho-specific Ab. To determine whether p27kip1 is required for Treg function in vivo, we used p27kip1-fl/fl-Foxp3-YFP-Cre mice in which p27kip1 is specifically deleted in the Treg lineage as recipients of cardiac allografts treated with CD28-CD40 costimulatory blockade. While this treatment led to long-term acceptance of cardiac allografts in p27kip1-sufficient control recipients, recipients with Treg-specific deletion of p27kip1 rejected their allografts. These studies establish a Treg-intrinsic role for p27kip1 in Treg stability and function, and point to the cyclin-dependent kinase pathway as a potential new therapeutic target for promoting transplantation tolerance.

Discovery of new disease-associated regulatory elements controlling inflammatory gene expression in T cells:

Interleukin-2 is a potent T cell growth factor with crucial roles in both immunity and tolerance. Genetic studies in humans and mice demonstrate a role for IL2 in autoimmune disease susceptibility, and for decades the proximal IL2 upstream regulatory region has served as a paradigm of tissue-specific, inducible gene regulation. We have used a combination of ChIP-seq, ATAC-seq and 4C-seq analyses of of chromatin and chromosome remodeling to identify a novel, long-range enhancer of the IL2 gene located 83 kb upstream of the transcription start site. This element can potently enhance IL2 transcription in recombinant reporter assays in vitro, and the native region loops to physically interact with the IL2 gene in vivo in a CD28-dependent manner. We have now edited this ~500 bp element out of the mouse genome using CRISPR/CAS9 in fertilized eggs, and CD4+ T cells from animals homozygous for deletion of the IL2-83 enhancer exhibit a ~80% reduction in IL-2 secretion in vitro. Preliminary analysis of young IL2-83 enhancer-deficient animals suggests largely normal hematopoiesis, but accumulation of activated phenotype CD4+ T cells in the peripheral lymphoid tissues. This cis regulatory element is evolutionarily conserved, and contains human SNPs associated with multiple autoimmune disorders. These results indicate that the regulatory architecture of the IL2 locus is more complex than previously appreciated, and suggest a novel molecular basis for the genetic association of IL2 polymorphism with autoimmune disease. This IL2-83 enhancer knock-out mouse represents a valuable model to study graded effects of this cytokine on activation-induced cell death, CD4 T cell differentiation, CD8 T cell memory, and regulatory T cell homeostasis in vivo.

Selected Publications

Gerriets VA, Kishton RJ, Johnson MO, Cohen S, Siska PJ, Nichols AG, Warmoes MO, de Cubas AA, MacIver NJ, Locasale JW, Turka LA, Wells AD, Rathmell JC: Foxp3 and Toll-like receptor signaling balance Treg cell anabolic metabolism for suppression. Nature Immunology 17: 1459, December 2016.

Parul Mehra and Andrew D. Wells: Long-Range Transcriptional Control of the Il2 Gene by an Intergenic Enhancer. Molecular and Cellular Biology 35(22): 3880, November 2015.

Chen Y, Chen C, Zhang Z, Liu CC, Johnson ME, Espinoza CA, Edsall LE, Ren B, Zhou XJ, Grant SF, Wells AD, Chen L.: DNA binding by FOXP3 domain-swapped dimer suggests mechanisms of long-range chromosomal interactions. Nucleic Acids Research 43(2): 1268, January 2015.

O'Brien S, Thomas RM, Wertheim GB, Zhang F, Shen H, Wells AD: Ikaros imposes a barrier to CD8+ T cell differentiation by restricting autocrine IL-2 production. The Journal of Immunology 192(11): 5118, June 2014.

Shin DS, Jordan A, Basu S, Thomas RM, Bandyopadhyay S, de Zoeten EF, Wells AD, Macian F.: Regulatory T cells suppress CD4+ T cells through NFAT-dependent transcriptional mechanisms. EMBO Reports 15(9): 991, September 2014.

Peter A. Morawski, Parul Mehra, Chunxia Chen, Tricia Bhatti, and Andrew D. Wells: Foxp3 Protein Stability Is Regulated by Cyclin-dependent Kinase 2. The Journal of Biological Chemistry 288: 24494, August 2013.

Neelanjana Chunder, Emily A. Rowell, Liqing Wang, Wayne W. Hancock, and Andrew D. Wells: Cyclin-dependent kinase 2 promotes alloimmune T cell activation and allograft rejection. The Journal of Immunology 189(12): 5659, December 2012.

Rajan M. Thomas, Hong Sai and Andrew D. Wells: Conserved Intergenic Elements and DNA Methylation Cooperate to Regulate Transcription at the il17 Locus. The Journal of Biological Chemistry 287(30): 25049, July 2012.

Northrop, John K., Wells, Andrew D. and Shen, Hao: Chromatin remodeling as a molecular basis for the enhanced functionality of memory CD8+ T cells. The Journal of Immunology 181: 865, 2008.

Chen, Chunxia, Rowell, Emily, A., Thomas, Rajan, Hancock, Wayne, W. and Wells, Andrew D.: Transcriptional regulation by Foxp3 is associated with direct promoter occupancy and modulation of histone acetylation. The Journal of Biological Chemistry 281: 36828, 2006.

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Last updated: 08/16/2023
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