Systemic Sclerosis-Associated Class II HLA Alleles Restrict the Diversity of the CDR3 and the T Cell Receptor Repertoire in African American Patients

Urvashi Kaundal¹, Chloe Borden¹, Cihan Oguz², Jinghua Lu², Emilee Stenson¹, Ami Shah³, Maureen Mayes⁴, Ayo Doumatey⁵, Amy Bentley⁵, Daniel Shriner⁵, Robyn Domsic⁶, Thomas Medsger⁷, Paula Ramos⁸, Richard Silver⁸, Virginia Steen⁹, John Varga¹⁰, Vivien Hsu¹¹, Lesley Ann Saketkoo¹², Elena Schiopu¹³, Dinesh Khanna¹⁴, Jessica Gordon¹⁵, Lindsey Criswell¹⁶, Heather Gladue¹⁷, Chris Derk¹⁸, Elana Bernstein¹⁹, S. Louis Bridges, Jr.¹⁵, Victoria Shanmugam²⁰, Lorinda Chung²¹, Suzanne Kafaja²², Reem Jan²³, Marcin Trojanowski²⁴, Avram Goldberg²⁵, Benjamin Korman²⁶, Settara Chandrasekharappa⁵, Faiza Naz²⁷, Stefania Dell'Orso¹, Adebowale Adeyemo⁵, Charles Rotimi⁵, Elaine Remmers⁵, Francesco Boin²⁸, Fredrick Wigley²⁹, Peter Sun², Daniel Kastner⁵ and Pravitt Gourh³⁰, ¹National Institutes of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health (NIH), Bethesda, MD, ²National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, ³Johns Hopkins Rheumatology, Baltimore, MD, ⁴Division of Rheumatology and Clinical Immunogenetics, University of Texas McGovern Medical School, Houston, TX, ⁵National Human Genome Research Institute, Bethesda, MD, ⁶University of Pittsburgh, Pittsburgh, PA, ⁷University of Pittsburgh School of Medicine, Pittsburgh, PA, ⁸Medical University of South Carolina, Charleston, SC, ⁹Georgetown University School of Medicine, Washington, DC, ¹⁰University of Michigan, Ann Arbor, MI, ¹¹Rutgers-RWJ Medical School, South Plainfield, NJ, ¹²University Medical Center - Comprehensive Pulmonary Hypertension Center and ILD Clinic Programs // New Orleans Scleroderma and Sarcoidosis Patient Care & Research Centeris, New Orleans, LA, ¹³Michigan Medicine, Ann Arbor, MI, ¹⁴Division of Rheumatology, Department of Internal Medicine, Scleroderma Program, University of Michigan, Ann Arbor, MI, ¹⁵Hospital for Special Surgery, New York, NY, ¹⁶National Human Genome Research Institute, NIH, Bethesda, MD, ¹⁷Arthritis & Osteoporosis Consultants of the Carolinas, Charlotte, NC, ¹⁸University of Pennsylvania, Philadelphia, PA, ¹⁹Columbia University, New York, NY, ²⁰George Washington University, Great Falls, VA, ²¹Stanford University, Stanford, CA, ²²UCLA Department of Medicine, Division of Rheumatology, Los Angeles, CA, ²³University of Chicago, Chicago, IL, ²⁴Boston University School of Medicine, Boston, MA, ²⁵NYU Langone Medical Center - NYU Hospital for Joint Diseases, Lake Success, NY, ²⁶University of Rochester, Rochester, NY, ²⁷National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, MD, ²⁸Cedars-Sinai Medical Center, Los Angeles, CA, ²⁹Johns Hopkins University, Baltimore, MD, ³⁰National Institutes of Health, Bethesda, MD

Meeting: ACR Convergence 2022

Keywords: Disparities, genomics, Systemic sclerosis, T Cell

Session Information

Date: Monday, November 14, 2022

Title: T Cell Biology and Targets in Autoimmune and Inflammatory Disease Poster

Session Type: Poster Session D

Session Time: 1:00PM-3:00PM

Background/Purpose: Systemic sclerosis (SSc) is an autoimmune, fibrotic disorder that disproportionately affects African Americans (AA). Previous work from our lab and others has suggested a pivotal role of HLA-II genes in SSc pathogenesis. HLA-II alleles encode for variations in antigen binding grooves of HLA proteins that present antigens to T-cell receptors (TCRs) and can contribute to antigen-specific immune responses. The TCR repertoire is HLA-restricted, antigen-specific, and recognizes antigens presented by HLA proteins. In this study, we explored the diversity of the hypervariable complementarity determining region 3 (CDR3) and TCR repertoire in SSc patients. We also examined the role of HLA-II alleles, especially HLA-DPB1*13:01, in the selection of the specific sequence and amino acid composition of the TCR in SSc patients.

Methods: Genomic DNA from 132 AA SSc patients from the GRASP consortium along with 50 AA healthy control samples were extracted and the TCRβ chain was deep sequenced using the immunoSEQ assay (Adaptive Biotechnologies, USA). Data was analyzed using Immunarch to identify differences in unique clones, CDR3 length, V gene usage, J gene usage, and amino acid usage in the FG-Loop of the TCRβ chain between the two SSc groups. Benjamini Hochberg FDR was used to correct for multiple testing.

Results: The CDR3 length was similar between SSc patients and controls (Figure 1A, B). The TCRβ repertoire was clonally expanded in HLA-DPB1*13:01+ SSc patients as compared to patients who did not carry this allele (Figure 1C). The proportion of small and hyperexpanded TCRβ clonotypes was increased in HLA-DPB1*13:01+ SSc patients (Figure 1D). Analysis of V gene and J gene usage identified statistically significantly increased usage of TRBV5-1, TRBV7-3, TRBJ2-1, and TRBJ2-2 genes and a decreased usage of TRBV6-1, TRBV6-4, TRBV6-5, TRBV25-1, and TRBJ1-5 genes in SSc patients compared to controls and the differences were statistically significant (Figure 2A, B). Overall amino acid usage of the FG loop of the TCRβ chain (antigen binding region) identified increased usage of hydrophobic amino acids, leucine and valine, and reduced usage of negatively charged glutamine in the FG loop of SSc patients compared to controls. Positional amino acid usage analysis of the FG loop of the TCRβ chain revealed increased usage of leucine at position 108 with decreased usage of tyrosine, glutamine, and aspartate.

Conclusion: This is the first study to report an association between HLA-II alleles and specific CDR3 composition in SSc patients. We examined the TCRβ repertoire of a large number of AA SSc patients and identified differential V and J gene and FG-loop amino acid usage that correlated with the presence of a specific HLA-II allele. Hydrophobic amino acid usage in the FG loop of the TCRβ chain has been reported to increase the avidity of TCR-MHC interaction and increased autoreactivity. Based on our findings, we can hypothesize that the TCRβ sequences favored by the SSc-associated HLA-II alleles are involved in autoantigen recognition and autoimmunity. These results highlight the important role of HLA-II alleles and T cells in SSc pathogenesis.

Figure 1. A. CDR3 length distribution in SSc patients (SSc) and controls; B. CDR3 length distribution in control, HLA-DPB1*1301- , HLA-DPB1*1301+ group; C. Number of unique clones in control, HLA-DPB1*1301- , HLA-DPB1*1301+ group; D. Proportion of TCR clonotype groups within frequency ranges: rare (0 to 10-5); small- (10-5 to 10_4); medium (10_4 to 10_3); large (10_3 to 10_2); and hyperexpanded (10_2 to 1).

Figure 2. TCR A. V-gene usage; B. J-gene usage

Disclosures: U. Kaundal, None; C. Borden, None; C. Oguz, None; J. Lu, None; E. Stenson, None; A. Shah, Arena Pharmaceuticals, Medpace/Eicos, Kadmon Corporation; M. Mayes, Actelion Pharma, Mitsubishi-Tanabe, Boehringer Ingelheim, EICOS, Horizon Pharma, Prometheus, Corbus, Medtelligence; A. Doumatey, None; A. Bentley, None; D. Shriner, None; R. Domsic, None; T. Medsger, None; P. Ramos, None; R. Silver, None; V. Steen, None; J. Varga, Boehringer-Ingelheim; V. Hsu, None; L. Saketkoo, None; E. Schiopu, None; D. Khanna, Boehringer Ingelheim, Genentech, Prometheus, Horizon, Chemomab, Talaris, Gesynta, Amgen, Acceleron, Actelion, Bayer, CSL Behring, Paracrine Cell Therapy, Mitsubishi Tanabe, Theraly, Eicos Sciences; J. Gordon, None; L. Criswell, None; H. Gladue, GlaxoSmithKlein(GSK), AstraZeneca; C. Derk, None; E. Bernstein, Boehringer-Ingelheim, Kadmon, Pfizer; S. Bridges, Jr., Bristol Myers Squibb; V. Shanmugam, None; L. Chung, Kyverna, Mitsubishi Tanabe, Eicos, Boehringer-Ingelheim, Jasper, Genentech; S. Kafaja, None; R. Jan, None; M. Trojanowski, None; A. Goldberg, None; B. Korman, None; S. Chandrasekharappa, None; F. Naz, None; S. Dell'Orso, None; A. Adeyemo, None; C. Rotimi, None; E. Remmers, None; F. Boin, None; F. Wigley, None; P. Sun, None; D. Kastner, None; P. Gourh, None.

To cite this abstract in AMA style:

Kaundal U, Borden C, Oguz C, Lu J, Stenson E, Shah A, Mayes M, Doumatey A, Bentley A, Shriner D, Domsic R, Medsger T, Ramos P, Silver R, Steen V, Varga J, Hsu V, Saketkoo L, Schiopu E, Khanna D, Gordon J, Criswell L, Gladue H, Derk C, Bernstein E, Bridges, Jr. S, Shanmugam V, Chung L, Kafaja S, Jan R, Trojanowski M, Goldberg A, Korman B, Chandrasekharappa S, Naz F, Dell'Orso S, Adeyemo A, Rotimi C, Remmers E, Boin F, Wigley F, Sun P, Kastner D, Gourh P. Systemic Sclerosis-Associated Class II HLA Alleles Restrict the Diversity of the CDR3 and the T Cell Receptor Repertoire in African American Patients [abstract]. Arthritis Rheumatol. 2022; 74 (suppl 9). https://acrabstracts.org/abstract/systemic-sclerosis-associated-class-ii-hla-alleles-restrict-the-diversity-of-the-cdr3-and-the-t-cell-receptor-repertoire-in-african-american-patients/. Accessed .

« Back to ACR Convergence 2022

ACR Meeting Abstracts - https://acrabstracts.org/abstract/systemic-sclerosis-associated-class-ii-hla-alleles-restrict-the-diversity-of-the-cdr3-and-the-t-cell-receptor-repertoire-in-african-american-patients/