Craig H. Bassing, PhD

Professor of Pathology and Laboratory Medicine
Perelman School of Medicine at the University of Pennsylvania

Contact InformationChildren’s Hospital of Philadelphia
Colket Translational Research Building, Rm. 4054
3501 Civic Center Boulevard
Philadelphia, PA 19104
Tel: 267-426-0311

Specialty Division

CHOP Cancer Pathobiology

Research Expertise

Research Interests: Elucidate genetic, epigenetic, and signal transduction mechanisms that govern the differentiation and function of lymphocytes to establish effective immunity and suppress autoimmunity and genomic aberrations that cause leukemia or lymphoma.

Key Words: Genome topology, transcriptional control, chromatin biology, genomic stability, antigen receptor gene diversification, lymphocyte development and selection, DNA damage response signaling, immunodeficiency, autoimmunity, and lymphoid cancers

Research Overview: My laboratory studies how developing B and T cells alter their genome topology, chromatin, and gene expression to create de novo the vast antigen receptor gene diversity necessary to protect host organisms from a broad range of external pathogens and damaged host cells. We also aim to determine ubiquitous, cell type-specific, and chromatin-location specific mechanisms through which developing B and T cells orchestrate and exploit DNA breakage, respectively, to suppress oncogenic translocations and regulate gene expression changes that govern the selection of lymphocytes based on antigen receptor specificity. Our goal is to identify participating factors and pathways and leverage this information to engineer better molecular and cellular therapeutics for immunodeficiency, autoimmunity, lymphoid cancers, and chronic inflammatory diseases.

Mentoring Overview: A major focus and the most important and rewarding aspect of my professional career is mentoring and training others to develop skills instrumental for their own unique career path. I pursue this through my many active roles in the Cell and Molecular Biology and Immunology graduate groups, and most intensely by my role as thesis advisor for PhD students in these and other programs. I have had the pleasure of mentoring 14 PhD students, including two Saul Winegrad Award winners for an outstanding thesis in their program (Bu Yin for CAMB, Glendon Wu for Immunology). I also actively mentor and train postdoctoral fellows, clinical fellows, undergraduates, and technicians. My laboratory members and I are committed to maintaining a safe, open, and diverse environment where everyone helps each other and everyone's opinions and input are valued.

Current Projects:
1. Elucidating how changes in genome topology and chromatin structure regulate antigen receptor gene expression and recombination - Mechanisms that control genome topology and chromatin structure are of much interest as they regulate gene expression and genome replication, segregation, recombination, and repair, and their dysfunction causes ~25% of human diseases. We study these mechanisms focusing on the mouse T cell receptor beta (Tcrb) locus in vivo because the proper recombination and expression of genes in this multigenic locus are essential for adaptive immunity and dysregulation of these molecular processes cause immunodeficiency, autoimmunity, and lymphoid cancers. Our findings from molecular and cellular analyses of normal and genetically modified mice imply that phase separation of chromatin domains, point-to-point chromosome looping, and how loops form all cooperate to establish individual cell-specific genomic architectures and gene transcription programs that ensures each T cell creates and expresses a unique Tcrb protein. We also have discovered long non-coding RNAs (lncRNAs) within the locus with expression patterns that imply important roles in lineage- and developmental stage-specific regulation of Tcrb locus topology, transcription, and recombination. We are continuing this new line of research by generating mice with additional gene-targeted Tcrb locus modifications, developing novel next-generation sequencing and computational methodologies, and incorporating single cell genomics and live cell imaging over time. This integrated approach should allow us unprecedented insights into mechanisms that operate in four-dimensions to control gene expression, recombination, and DNA repair.

2. Determining mechanisms that mediate monogenic and monoallelic expression of antigen receptor genes - The monogenic and monoallelic expression of genes is pervasive throughout biology, including X-chromosome inactivation, autosomal gene imprinting, and immune genes. These processes are vital for normal biology and thought to be regulated at least in part through similar epigenetic mechanisms. However, additional mechanisms most likely control mono-genic and mono-allelic antigen receptor gene expression, referred to as allelic exclusion, due to the obligate assembly of these genes through regulated DNA recombination. In this context, the field hypothesizes that allelic exclusion occurs by mechanisms that: i) orchestrate initiation of recombination on only one allele and at a single gene on the allele, ii) signals triggered by the recombination process that transiently halt further recombination, and iii) signals from resulting proteins that permanently silence additional recombination. Our lab elucidated that the DNA elements that direct recombination ensure monogenic and monoallelic initiation of Tcrb locus recombination to ensure that individual T cells express a single unique type of Tcrb protein. We are using gene targeted replacement of these DNA elements to tailor the naïve Tcrb repertoire in mice to understand how Tcrb gene diversity provides immunity and perhaps develop new stem cell engineering therapeutics for human lymphoid cancers. We also have demonstrated that DNA breaks induced during Tcrb gene recombination on one allele activate transient signals that inhibit initiation of recombination on the other allele. This response correlates with transcriptional repression of the lymphocyte-specific recombinase and Tcrb locus lncRNAs and upregulated transcription of sense Tcrb locus transcripts. Notably, a subset of these responses depends on the ubiquitous Ataxia Telangiectasia-mutated (ATM) kinase that orchestrates the conserved cellular DNA damage response to suppress oncogenic genomic lesions. We are continuing this line of research by elucidating ATM-dependent and ATM-independent signaling pathways that mediate these responses and investigating roles of these transcriptional changes in modulating genome topology to inhibit antigen receptor gene rearrangements and suppress oncogenic translocations.

3. Ascertaining physiological roles of antigen receptor gene allelic exclusion - Since the 1960s, the field has hypothesized that antigen receptor allelic exclusion suppresses autoimmunity and ensures highly specific robust immune responses by ensuring that individual B and T cells express antigen receptors of uniform specificity. However, there is little evidence to support these models because allelic exclusion mechanisms have not been elucidated to extents permitting experimental disruption of monogenic and monoallelic antigen receptor expression in model organisms. Our recent advances have empowered us to engineer mice that create and express up to four distinct Tcrb proteins on a major fraction of T cells. We are studying these mice to determine if monogenic and monoallelic Tcrb protein expression: i) inhibits autoimmunity by facilitating negative selection of self-reactive conventional T cells and development of immunosuppressive regulatory T cells, and/or ii) ensures highly specific and robust immune responses through increasing the number and density of clonally disrupted antigen-specific receptors on individual T cells. We have introduced the innovative hypothesis that allelic exclusion mechanisms are important to prevent generation of oncogenic antigen receptor locus translocations and resulting lymphoid cancers by inhibiting further DNA breaks while protein from a gene assembled on one allele is driving cells to proliferate. Our recent finding that our mice that recombine multiple Tcrb genes within most developing T cells exhibit rapid onset of T lineage lymphomas supports our novel model and provides a tractable experimental platform for further mechanistic interrogation.

4. Investigate roles of antigen receptor gene rearrangements in signaling gene expression changes that facilitate differentiation and function of lymphocytes - DNA breaks introduced by antigen receptor gene rearrangements within lymphoid progenitor and precursor cells signal transient and permanent changes in expression of genes known to regulate antigen receptor signaling, antigen presentation, and cellular fitness. Genetic mutations that impair these gene expression changes, but also diminish antigen receptor gene assembly and DNA damage responses, impair differentiation of lymphocytes both through antigen receptor specificity quality control checkpoints and into specialized lineages that function in adaptive or innate immunity. We are developing new mouse models to elucidate how DNA breaks signal these gene expression changes to abrogate them without impairing antigen receptor gene assembly or DNA damage responses. The knowledge and reagents acquired from these studies should allow us to investigate roles of antigen receptor gene rearrangements beyond generating antigen receptor diversity.

Current Lab Members:
Becca Glynn – CHOP Postdoctoral Fellow
Kymberle Shields – CHOP Research Technician
Agustin Velasco – CHOP Research Technician
Brittney Allyn – Penn IGG Student
Katharina Hayer – CHOP Bioinformatics Scientist II & Drexel Computational PhD Student

Former Lab Trainees:        
Dr. Rahul Arya  CHOP Postdoctoral Fellow        Brenna Brady Penn IGG PhD Student
Dr. Lori Ehrlich CHOP Clinical Fellow   Andrea Carpenter Penn IGG PhD Student
Dr. Angella Fusello CHOP Postdoctoral Fellow            Megan Fisher Penn IGG PhD Student
Dr. Charline Miot CHOP Postdoctoral Fellow   Julie Horowitz Penn IGG PhD Student
Erica Culberson CHOP Research Technician   Marta Rowh Penn IGG PhD Student
Kyutae Lee CHOP Research Technician   Natalie Steinel Penn IGG PhD Student
Becca Glynn Penn CAMB PhD Student   Glendon Wu Penn IGG PhD Student
Amy DeMicco Penn CAMB/CB PhD Student   Rawan Shraim Drexel Masters Student
Bu Yin Penn CAMB/CB PhD Student   Linda Chao Harvard Undergrad Student
Velibor Savic Penn CAMB/G&E PhD Student   Jocelyn Proferes Northeastern Undergrad Student Intern
Levi Rupp Penn CAMB/CTV PhD Student   Tyler Riech Penn Undergrad Student


Graduate Groups

Cell and Molecular Biology


BA (Biology), The Johns Hopkins University, 1992
PhD (Biology), Duke University, 1997

Specialty Certification

Postgraduate Training

Research Fellow, Genetics, Harvard Medical School, 1997-2002
Research Fellow, Molecular Immunology, Irvington Institute for Immunological Research, 1997-2000
Research Fellow, Medicine, Boston Children's Hospital, 1997-2002
Research Fellow, Molecular Immunology, CBR Institute for Biomedical Research, 1997-2000
Research Associate, Molecular Immunology, Howard Hughes Medical Institute, 2000-03
Research Fellow, Cancer Genetics, Lymphoma Research Foundation, 2003-05

Awards and Honors

Alpha Epsilon Delta Honor Society, The Johns Hopkins University Chapter, 1990
Summer Fellow, Howard Hughes Medical Institute, 1991
Phi Beta Kappa Honor Society, The Johns Hopkins University Chapter, 1991
Golden Key Honor Society, The Johns Hopkins University Chapter, 1992
Pre-Doctoral Fellow Award, National Science Foundation, 1992-95
Departmental Honors (Biology), The Johns Hopkins University, 1992
University Honors, The Johns Hopkins University, 1992
Fellow Award, Irvington Institute for Immunological Research, 1997-2000
Fellow Award, Lymphoma Research Foundation, 2003-05
Foerderer-Murray Award, 2005-06
Pew Scholar in the Biomedical Sciences, 2005-09
American Cancer Society Institutional Research Award, 2005-08
W.W. Smith Charitable Trust Award, 2005-07
Lassin Family Cancer Research Award at the Abramson Cancer Center of the University of Pennsylvania School of Medicine, 2008-09
Michael S. Brown New Investigator Research Award, University of Pennsylvania School of Medicine, 2009
Pathology and Laboratory Medicine Chair Award of Children's Hospital of Philadelphia, 2010
Leukemia and Lymphoma Society Scholar Award, 2010-15
Simon Flexner Award (for teaching and mentoring), Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, 2017

Memberships and Professional Organizations

American Association for the Advancement of Science, 1992-present
Immunology Graduate Group (IGG), University of Pennsylvania, 2004-present
--- IGG Admissions Committee, 2005-14
--- IGG Student Affairs Committee: Member, 2005-08; Ad Hoc Member, 2009-13
--- IGG Curriculum Committee, 2010-14
--- IGG Executive Committee, 2010-14
--- IGG Curriculum Review Panel, 2011
Cell and Molecular Biology (CAMB) Graduate Group, University of Pennsylvania, 2004-present
--- CAMB Events Committee, 2005-06
--- Cancer Biology Program:
---------- Curriculum Committee, 2007-08
---------- Executive Committee, 2008
---------- Chair of Executive Committee, 2014-18
---------- Preliminary Exams Committee, 2009
---------- Advising Committee 2009-14 (Chair, 2012-14)
---------- Program Chair, 2014-18
--- Executive Committee, Cell and Molecular Biology Training Grant, 2012-present
--- CAMB Executive Committee, 2014-present
--- CAMB Curriculum Committee, 2018-present
--- Vice Chair, 2018-present
Abramson Cancer Center, Penn Medicine, 2005-present
--- Tumor Biology, 2005-10
--- Review Committee for American Cancer Society Pilot & Institutional Grants, 2009-17
--- Pediatric Oncology Research, 2010-present
Abramson Family Cancer Research Institute, 2005-present
--- Assistant Investigator, 2005-11
--- Associate Investigator, 2011-present
American Association of Immunologists, 2005-present
Cerimon Pharmaceuticals, Inc., Scientific Advisory Board, 2006-08
Irvington Institute for Immunological Research, Fundraising and Selection Committee for the
Frederick W. Alt Award, 2006
National Cancer Institute, Avon-NCI Progress for Patients Grants Program Reviewer, 2006
CHOP Institutional Animal Care and Use Committee, 2007-16 (Chair, 2011-13)
CHOP Institutional Core Advisory Committee, 2007-16
American Association for Cancer Research, 2008-present
CHOP Rodent Users Committee, Chair, 2008
UK Cancer Research Project, Project Program Reviewer, 2008
Wellcome Trust, Reviewer for the Research Career Development Fellowship Program, 2008
Children's Hospital of Philadelphia Research Institute, Center for Childhood Cancer Research, 2009-present
--- Biobank Scientific Review Council, 2012-present
National Institutes of Health:
--- Cellular and Molecular Immunology B Study Section, Section of Scientific Review
---------- Ad Hoc Reviewer, 2009, 2016
---------- Standing Member, 2018-present
--- Special Emphasis Panel/Scientific Review Group 2009/10 ZRG1 OBT-A (58) R Meeting, 2009
--- Study Section ZRG1 IMM-D (02) M - Member Conflict: Myeloid cell Development and Immunoglobulin Repertoire, 2010
--- National Institute of Arthritis and Musculoskeletal and Skin Diseases, Division of Intramural Research, Board of Scientific Counselors, 2014, 2021
--- Special Emphasis Panel/Scientific Review Group 2014/05 ZRG1 IMM-M (80) S Meeting, 2014
New York Academy of Sciences, 2009-present
Austrian Academy of Sciences, Austrian Programme for Advanced Research and Technology, Reviewer of Postdoctoral Fellowships, 2010
The Henry Kunkel Society, 2010-12
Institute for Immunology, Perelman School of Medicine at the University of Pennsylvania, 2010-present
--- Pilot Grant Program Review Panel, 2010, 2014
Israel Science Foundation Grant Program Reviewer, 2010
Michael S. Brown New Investigator Research Award Selection Committee, Perelman School of Medicine at the University of Pennsylvania, 2010-15
H1 Connect (fka Faculty Opinions, Faculty of 1000), Immunology Experts, Leukocyte Development Section, 2012-present
Penn Biomedical Advisory Committee, 2014-present
Radiation Safety Committee of the University of Pennsylvania, 2014-present
Biomedical Graduate Studies (BGS) at the University of Pennsylvania, Curriculum Committee, 2018-present
CHOP Department of Veterinary Resources, Vice Chair of Faculty Advisory Committee, 2022-24

Web Links

Selected Publications

The RAG1 Ubiquitin Ligase Domain Stimulates Recombination of TCRβ and TCRα Genes and Influences Development of αβ T Cell Lineages

Burn TN, Miot C, Gordon SM, Culberson EJ, Diamond T, Kreiger PA, Hayer KE, Bhattacharyya A, Jones JM, Bassing CH, Behrens EM. J Immunol 209(5):938-949, Sep 2022. doi: 10.4049/jimmunol.2001441. Epub 2022 Aug 10. PMID: 35948399; PMCID: PMC9492648.

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Monogenic TCRβ Assembly and Expression Are Paramount for Uniform Antigen Receptor Specificity of Individual αβ T Lymphocytes

Culberson EJ, Bassing CH. J Immunol 209(1):93-98, July 2022. doi: 10.4049/jimmunol.2200176. Epub 2022 Jun 13. PMID: 35697383; PMCID: PMC9246964.

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Poor-Quality Vβ Recombination Signal Sequences and the DNA Damage Response ATM Kinase Collaborate to Establish TCRb Gene Repertoire and Allelic Exclusion

Wu GS, Culberson EJ, Allyn BM, Bassing CHJ Immunol 208(11):2583-2592, Jun 2022. doi: 10.4049/jimmunol.2100489. Epub 2022 May 9. PMID: 35534211; PMCID: PMC9133172.

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Nemo-Dependent, ATM-Mediated Signals from RAG DNA Breaks at Igk Feedback Inhibit Vκ Recombination to Enforce Igκ Allelic Exclusion

Glynn RA, Bassing CHJ Immunol 208(2):371-383, Jan 2022. doi: 10.4049/jimmunol.2100696. Epub 2021 Dec 29. PMID: 34965965; PMCID: PMC8756740.

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The RAG1 N-terminal region regulates the efficiency and pathways of synapsis for V(D)J recombination

Beilinson HA, Glynn RA, Yadavalli AD, Xiao J, Corbett E, Saribasak H, Arya R, Miot C, Bhattacharyya A, Jones JM, Pongubala JMR, Bassing CH, Schatz DG. J Exp Med 218(10):e20210250, Oct 2021. doi: 10.1084/jem.20210250. Epub 2021 Aug 17. PMID: 34402853; PMCID: PMC8374863.

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Molecular Analysis of Mouse T Cell Receptor α and β Gene Rearrangements

Rupp LJ, Chen L, Krangel MS, Bassing CH. Methods Mol Biol 1323:179-202. doi: 10.1007/978-1-4939-2809-5_16. PMID: 26294409.

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Inefficient V(D)J Recombination Underlies Monogenic T Cell Receptor β Expression

Wu GS and Bassing CH. Proc Natl Acad Sci U S A 117(31):18172-18174,  Aug 2020. doi: 10.1073/pnas.2010077117. Epub 2020 Jul 20. PMID: 32690689; PMCID: PMC7414081.

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Genome Topology Control of Antigen Receptor Gene Assembly

Allyn BM, Lee KD, Bassing CH. J Immunol 204(10):2617-2626, May 2020. doi: 10.4049/jimmunol.1901356. PMID: 32366683; PMCID: PMC7440635.

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 A Spontaneous RAG1 Nonsense Mutation Unveils Naturally Occurring N-Terminal Truncated RAG1 Isoforms

Burn TN, Lee KD, Dawany N, Robertson TF, Fisher MR, Bassing CH, Behrens EM. Immunohorizons 4(3):119-128, Mar 2020. doi: 10.4049/immunohorizons.2000001. PMID: 32144186.

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Two Successive Inversional Vβ Rearrangements on a Single Tcrb Allele Can Contribute to the TCRβ Repertoire

Lee KD, Bassing CHJ Immunol 204(1):78-86, Jan 2020. doi: 10.4049/jimmunol.1901105. Epub 2019 Nov 18. PMID: 31740488; PMCID: PMC6920540.

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