Craig H. Bassing, Ph.D.

faculty photo
Professor of Pathology and Laboratory Medicine
Department: Pathology and Laboratory Medicine
Graduate Group Affiliations

Contact information
Children's Hospital of Philadelphia
4054 Colket Translational Research Building
3501 Civic Center Blvd.
Philadelphia, PA 19104
Office: 267-426-0311
Fax: 267-426-2791
B.A. (Biology)
The Johns Hopkins University, 1992.
Ph.D. (Biology)
Duke University, 1997.
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Description of Research Expertise

Research Interests: Elucidating 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
Brittney Allyn - Penn IGG PhD Student
Katharina Hayer – CHOP Bioinformatics Scientist II & Drexel Computational PhD Student
Kymberle Shields - CHOP Research Technician
Agustin Velasco - CHOP Research Technician

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

Selected Publications

Glynn, R.A. and Bassing, C.H.: ATM-Dependent Phosphorylation of Nemo SQ Motifs is Dispensable for Nemo-Mediated Gene Expression Changes in Response to DNA Double Strand Breaks. The Journal of Immunology In Revision, 2024.

Allyn, B.M., Hayer, K.E., Oyeniran, C., Nganga, V., Lee, K., Mishra, B., Sacan, A., Oltz, E.M., and Bassing, C.H.: Locus Folding Mechanisms Determine Modes of Antigen Receptor Gene Assembly. The Journal of Experimental Medicine 221, 2024.

Culberson, E.J., Shields, K.C., Glynn, R.A., Allyn, B.M., Hayer, K.E., and Bassing, C.H.: The Cyclin D3 Protein Enforces Monogenic TCRb Expression by Mediating TCRb Protein Signaled Feedback Inhibition of Vb Recombination The Journal of Immunology 212, 2024.

Culberson, E.J. and Bassing, C.H.: Monogenic TCRb Assembly and Expression is Paramount for Uniform Antigen Receptor Specificity of Individual ab T Lymphocytes. The Journal of Immunology 209, 2022.

Glynn, R.A. and Bassing, C.H.: Nemo-dependent, ATM-mediated signals from RAG DNA breaks at Igk feedback inhibit Vk recombination to enforce Igκ allelic exclusion. The Journal of Immunology 208: 371-383, 2022.

Burn, T.N., Miot, C., Gordon, S.M., Culberson, E.J., Diamond, T., Kreiger, P.A., Hayer, K.E., Bhattacharyya, A., Jones, J.M., Bassing, C.H.*, and Behrens, E.M.* *Co-corresponding authors: The RAG1 Ubiquitin Ligase Domain Stimulates Recombination of TCRb and a Genes and Influences Development of ab T Cell Lineages. The Journal of Immunology 209, 2022.

Wu, G., Culberson, E.J., Allyn, B.M., and Bassing, C.H.: Poor-Quality Vb Recombination Signal Sequences and the DNA Damage Response ATM Kinase Collaborate to Establish TCRb Gene Repertoire and Allelic Exclusion. The Journal of Immunology doi: 10.4049/jimmunol.2100489, 2022.

Beilinson, H.A., Glynn, R.A., Yadavailli, A.D., Xiao, J., Corbett, E., Saribasak, H., Arya, R., Miot, C., Bhattacharyya, A., Jones, J.M., Pongubala, J., Bassing, C.H., and Schatz, D.G. : The RAG1 N-terminal region regulates the efficiency and pathways of synapsis for V(D)J recombination. Journal of Experimental Medicine. Oct 4;218(10):e20210250. doi: 10.1084/jem.20210250. (eds.). 218(10): :e20210250, 2021.

Dauphers, D.J., Wu, G.S., Bassing, C.H., and Krangel, M.S.: Molecular Analysis of Mouse T Cell Receptor α and β Gene Rearrangements Methods in Molecular Biology In Press, 2021.

Wu, G.S. and Bassing, C.H.: Inefficient V(D)J Recombination Underlies Monogenic T Cell Receptor β Expression. Proceedings of the National Academy of Sciences, USA 117: 18172-18174, 2020.

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Last updated: 04/20/2024
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