The 2026 Immcantation Users Group Meeting will take place on January 22nd, 2026.

Note that all times shown here use ET.

Start End Speaker Affiliation Title
10:00 am 10:10 am Kleinstein lab Yale University (US) Welcome
10:10 am 10:30 am Mr. Titas Grabauskas The Jackson Laboratory for Genomic Medicine (US) Latent CMV is Associated with Putative CMV-specific Clonal Expansion in Th1 and GZMK⁺ CD8 T Cells
10:30 am 10:50 am Mr. Kevin Sung Fred Hutch Cancer Center (US) Nucleotide Context Models Outperform Protein Language Models For Predicting Antibody Affinity Maturation
10:50 am 11:10 am Dr. Seyedmojtaba Seyedraoufi University of Oslo (NO) GATHeR: Graph-based Accurate Tool for immunoglobulin HEavy- and light-chain Reconstruction
11:10 am 11:30 am Prof. Nadia Tahiri University of Sherbrooke (CA) New Generalized Metric Based on Branch Length Distance to Compare B Cell Lineage Trees
11:30 am 11:50 am Mr. Vishal Rao Icahn School of Medicine at Mount Sinai (US) Clonotype-specificity reveals differential roles of somatic hypermutation in epitope targeting
11:50 am 12:10 pm Break Break
12:10 pm 12:30 pm Dr. Patrick Madden La Jolla Institute for Immunology (US) Germline-targeting vaccination elicits HIV broadly neutralizing antibodies in nonhuman primates
12:30 pm 12:50 pm Mr. Eric Zhang Columbia University Irving Medical Center (US) Tissue-directed maintenance of vaccine-specific human B-cell memory
12:50 pm 1:10 pm Dr. Kristen Wells University of Colorado Anschutz Medical Campus (US) Activated Polyreactive B Cells Are Clonally Expanded in Autoantibody-positive and Patients with New-Onset Type 1 Diabetes
1:10 pm 1:30 pm Dr. Money Gupta University of New South Wales (AU) Early emergence of signatures associated with HCV infection outcome
1:30 pm Kleinstein lab Yale University (US) Wrap up

Abstracts

Latent CMV is Associated with Putative CMV-specific Clonal Expansion in Th1 and GZMK⁺ CD8⁺ T Cells

Titas Grabauskas1,2,‡, Luke Trinity1,‡, Chris P. Verschoor3,4, Radu Marches1, Asa Thibodeau1, Djamel Nehar-Belaid1, Giray Eryilmaz1, Avinash S. Mahajan1,2, Sathya Baarathi1, Emilie Picard3, Chia-Ling Kuo2, Kenneth E. Schmader5, Cathleen Colon-Emeric5, Heather E. Whitson5, Silke Paust1, Adolfo García-Sastre6-11, Gur Yaari12, Jacques Banchereau1,13,*, George A. Kuchel2,14,*, and Duygu Ucar1,15,*

1The Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA; 2University of Connecticut School of Medicine, Farmington, CT 06030, USA; 3Health Sciences North Research Institute, NOSM University, Sudbury, ON P3E 2H3, Canada; 4Department of Medicine, McMaster University, Hamilton, ON L8S 4L8 Canada; 5Department of Medicine and Duke Center for the Study of Aging and Human Development (Aging Center), and GRECC, Durham VA Health Care System, Durham, NC 27705, USA; 6Department of Microbiology, Icahn School of Medicine at Mount Sinai; New York, NY 10029, USA; 7Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; 8Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; 9The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; 10Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; 11The Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; 12Department of Pathology, Yale School of Medicine, New Haven, CT 06510-3222, USA; 13Immunoledge LLC; Montclair, NJ 07042, USA; 14UConn Center on Aging, University of Connecticut School of Medicine, Farmington, CT 06032, USA.; 15Institute for Systems Genomics, University of Connecticut Health Center, Farmington, CT 06032, USA.

‡These authors contributed equally to this work.

*Corresponding authors: , ,

Abstract:

Cytomegalovirus (CMV) is a common herpesvirus that establishes lifelong latency and becomes increasingly prevalent with age. While CMV-associated effects on CD4+/CD8+ TEMRA and NK cells are well established, the impact on other immune populations and T cell clonal expansion remain poorly defined. Here, we used single-cell RNA-sequencing and flow cytometry to profile peripheral blood mononuclear cells from healthy older adults (median age: 73), stratified by CMV serostatus with comparable age, sex, BMI, and frailty. Systems-level characterization identified novel CMV-associated changes in cell frequencies: increase in GZMK⁺ CD8⁺ T and atypical B cells, and reduction in CD56dim NK cells. We also validated these observations in an independent younger adult cohort. To infer CMV serostatus in single-cell datasets lacking serological data, we developed CMVerify, a machine learning model that predicts CMV serostatus with 97% accuracy (97% sensitivity; 98% specificity). Applying CMVerify and Immcantation’s Alakazam to a public single-cell dataset with TCR sequencing (and no CMV serology data) revealed reduced TCR clonal diversity in CMV-seropositive individuals across CD4+/CD8+ TEMRAs, GZMK⁺ CD8⁺ T, and Th1 cells. Importantly, we show that putatively expanded CMV-specific clones within these subsets drive the reduction in TCR clonal diversity. Our results establish CMV as a key driver of immune heterogeneity in both younger and older adults, describe novel associations, and present a tool to effectively infer CMV serostatus from single-cell data.

Associated publications:

Funding:

This study was made possible by generous financial support of the National Institutes of Health (NIH) grants under award number:

  • UH2 AG056925 (to G.K, CCE, J.B., D.U.)
  • U01 AI165452 (to D.U., G.K.)
  • P30AG067988 Older Americans Independence Pepper Center (to G.A.K., R.M., D.U.)
  • P30AG028716 Duke Older Americans Independence Center (to K.E.S, C.C.E, H.E.W)
  • NIH grant U19 AI168631 (to A.G.-S.)
  • CRIPT (Center for Research on Influenza Pathogenesis and Transmission), a as NIAID-funded Center of Excellence for Influenza Research and Response (CEIRR, contract # 75N93021C00014) (to A.G.S.)
  • 1T32AG062409-01A1 (to L.T.)

Other partial sources of funding include:

  • JAX Cancer Center (P30 CA034196)
  • American Heart Association Predoctoral Fellowship (24PRE1186316) (to T.G.)

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Nucleotide Context Models Outperform Protein Language Models For Predicting Antibody Affinity Maturation

Mackenzie M. Johnson1, Kevin Sung1, Hugh K. Haddox1, Ashni A. Vora2, Tatsuya Araki2, Gabriel Victora2, Yun S. Song4,5, Julia Fukuyama6, Frederick A. Matsen IV1,3,7,8,*

1Computational Biology Program, Fred Hutch Cancer Center; 2Laboratory of Lymphocyte Dynamics, The Rockefeller University; 3Howard Hughes Medical Instititute; 4Computer Science Division, University of California, Berkeley; 5Department of Statistics, University of California, Berkeley; 6Department of Statistics, Indiana University, Bloomington; 7Department of Genome Sciences, University of Washington; 8Department of Statistics, University of Washington

*Corresponding author

Abstract:

Antibodies play a crucial role in adaptive immunity. They develop as B cell receptors (BCRs) that are expressed on the surfaces of B cells. BCRs are refined through affinity maturation, a process of somatic hypermutation (SHM) and natural selection, to improve binding to an antigen. Computational models of affinity maturation have developed from two main perspectives: molecular evolution and language modeling. The molecular evolution perspective focuses on nucleotide sequence context to describe mutation and selection; the language modeling perspective involves learning patterns from large data sets of protein sequences. We compared models from both perspectives on their ability to predict the course of antibody affinity maturation along phylogenetic trees of BCR sequences. This included models of SHM – such as the S5F model, models of SHM combined with an estimate of selection, and protein language models AbLang2 and ESM-1v. We evaluated models on large human BCR repertoire data sets, as well as an antigen-specific mouse experiment with a pre-rearranged cognate naive antibody. We demonstrated that precise modeling of SHM, which requires the nucleotide context, provides a substantial amount of predictive power for predicting the course of affinity maturation. Notably, a simple nucleotide-based convolutional neural network modeling SHM outperformed state-of-the-art protein language models, including one trained exclusively on antibody sequences. Furthermore, incorporating estimates of selection based on a custom deep mutational scanning experiment brought only modest improvement in predictive power. To support further research, we introduce EPAM (Evaluating Predictions of Affinity Maturation), a benchmarking framework to integrate evolutionary principles with advances in language modeling.

Associated publications:

Funding Information:

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GATHeR: Graph-based Accurate Tool for immunoglobulin HEavy- and light-chain Reconstruction

Seyedmojtaba Seyedraoufi1, Mari Bergstøl Gornitzka1, Andreas Lossius1,*

1Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway

*Corresponding author

Abstract:

Recovering full-length, paired B cell receptor (BCR) sequences from scRNA-seq reads remains difficult, especially in naive and memory B cells with sparse immunoglobulin transcripts. Current methods provide incomplete constant-region coverage, limiting isoform, subclass, and allele resolution. We present GATHeR, an open-source tool that assembles and annotates paired heavy- and light-chain BCR sequences and extends assembled sequences into constant regions. This enables confident subclass and allele assignment and recovery of the membrane isoform, including the transmembrane segment and cytoplasmic tail, thereby distinguishing surface BCRs from secreted antibodies. GATHeR supports Smart-Seq and 10x Genomics libraries and outperforms existing methods across benchmarks, with the largest gains in naive and memory B cells. Notably, in these populations the constant-region extension also revealed splice variation, including heavy-chain intron retention. By delivering high-fidelity receptor, isoform, and clonal lineage information, GATHeR broadens the analytical reach of scRNA-seq for B cell immunology.

Associated publications:

Immcantation Tools Used:

Immcantation tools used in the postprocessing steps (integrated in the code). Change-O used in the clonality analysis part, and Dowser for phylogenetic analysis.

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New Generalized Metric Based on Branch Length Distance to Compare B Cell Lineage Trees

Mahsa Farnia1, Nadia Tahiri1,*

1Department of Computer Science, University of Sherbrooke, 2500, boulevard de l’Université, Sherbrooke, QC, J1K 2R1, Canada

*Corresponding author

Abstract:

Tracking the progression of naïve B cells and monitoring their differentiation leads to the construction of lineage trees, representing adaptive processes within a single species. These trees provide structured representations of B cell maturation from hematopoietic stem cells to antibody-producing cells. Building upon prior computational evaluation of lineage trees (Farnia and Tahiri, 2024), this study introduces a systematic framework for clustering B cell lineage trees with increased granularity. Our approach incorporates structural and numerical features, including tree topology, branch lengths, node out-degree, tree height, and clonal family size. Feature weighting is adjustable to accommodate specific experimental or clinical objectives. To perform lineage reconstruction and B cell repertoire analysis, we employed the Immcantation framework, including Dowser for tree building and visualization, and Alakazam for clonal lineage diversity analysis. Extracted tree features were then analyzed using the DBSCAN (Density-Based Spatial Clustering of Applications with Noise) algorithm, chosen for its ability to detect clusters in low-dimensional feature spaces while identifying atypical or outlier structures. This framework allows systematic comparison of B cell lineage trees, providing insights into affinity maturation, class switching, and memory B cell diversification. By integrating detailed structural features with density-based clustering, the study offers an analytical basis for understanding B cell adaptive dynamics and evaluating immune responses under different physiological or pathological conditions.

Associated Publications:

Funding:

This research was funded by the Natural Sciences and Engineering Research Council of Canada - Discovery Grants and Fonds de Recherche du Québec - Nature and Technologies.

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Clonotype-specificity reveals differential roles of somatic hypermutation in epitope targeting

Vishal N. Rao1,2,3, Iden A. Sapse1,3, Hallie Cohn1,2, Duck-Kyun Yoo4, Pei Tong4, Jordan J. Clark1,2, Bailey Bozarth1,2, Yuexing Chen1,2, Komal Srivastava1,2, Gagandeep Singh1,2, Florian Krammer1,2,5,6, Viviana Simon1,2,4,7,8, Ali H Ellebedy9, Duane R. Wesemann4,10,11,12,13,*, Goran Bajic1,*, Camila H. Coelho1,2,14,*

1Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; 2Center for Vaccine Research and Pandemic Preparedness, Icahn School of Medicine at Mount Sinai, New York, NY, USA; 3Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; 4Department of Medicine, Division of Allergy and Clinical Immunology, Division of Genetics, Brigham and Women’s Hospital, Boston, MA, USA; 5Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA; 6Ignaz Semmelweis Institute, Interuniversity Institute for Infection Research, Medical University of Vienna, Vienna, Austria; 7The Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; 8Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA; 9Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO, USA; 10Harvard Medical School, Boston, MA, USA; 11The Broad Institute of MIT and Harvard, Cambridge, MA, USA; 12The Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA; 13Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA; 14Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.

*Corresponding authors

Abstract:

The human antibody repertoire uses a wide range of V genes against diverse pathogenic threats. While some V genes show pathogen-specific biases, others are repeatedly used across different infections. This raises the question of whether somatic hypermutations (SHMs) in these shared V genes evolve toward recognition of specific epitopes. We investigated this using the public antibody M15, which targets the S2 domain of sarbecoviruses and is elicited upon SARS-CoV-2 infection/vaccination. From two cohorts of mRNA vaccinees and public databases (CoV-AbDAb, Observed Antibody Space), we identified 147 M15-like sequences based on VJ gene identity (assigned using the ‘changeo’ package in Immcantation) and >70% CDR3 similarity. Using these, we identified convergent SHMs in the light chain, enriched within the M15 clonotype compared with antibodies using the same V gene against unrelated antigens. Reverting these clonotype-enriched SHMs to their germline residues reduced M15 binding affinity 12-fold, equivalent to the reconstructed germline antibody, underscoring their role in affinity maturation. Cryo-EM structure of M15 bound to S2 showed that these SHMs enable interactions with a hydrophobic cleft in a novel central interface epitope, occluded in prefusion spike. Serum antibodies targeting this site increase with repeated SARS-CoV-2 vaccinations. In contrast, among SARS-CoV-2 mRNA vaccinated individuals, we show that SHMs shared across spike-specific germinal center B cell clonotypes, are commonly acquired and exhibit similar functional roles in antibodies interacting with other viral antigens. Overall, our results reveal two layers of SHM function: common, pan-antigenic SHMs, and rare clonotype-enriched SHMs that enable affinity maturation toward atypical epitopes.

Associated Publications:

Funding:

This project was funded by the Icahn School of Medicine at Mount Sinai and partially funded by the National Institutes of Health (NIH FIRST U54CA267776 to C.H.C.; AI165072 and AI170715 to D.R.W.). We acknowledge support from the NIH R01 AI168178 and the Irma T. Hirschl/Monique Weill-Caulier Trust to G.B. Some of this work was performed at the National Center for CryoEM Access and Training (NCCAT) and the Simons Electron Microscopy Center located at the New York Structural Biology Center, supported by the NIH Common Fund Transformative High Resolution Cryo-Electron Microscopy program (U24 GM129539) and by grants from the Simons Foundation (SF349247) and the NY State Assembly. This work was supported in part through the computational and data resources and staff expertise provided by Scientific Computing and Data at the Icahn School of Medicine at Mount Sinai and supported by the Clinical and Translational Science Awards (CTSA) grant UL1TR004419 from the National Center for Advancing Translational Sciences. Research reported in this publication was also supported by the Office of Research Infrastructure of the National Institutes of Health under award nos. S10OD026880 and S10OD030463. We thank the Flow Cytometry Core Facility and staff at the Icahn School of Medicine at Mount Sinai for their assistance. The BSL-3 facility used in this project for work with SARS-CoV-2 virus stocks is an NIH BSL-3/ABSL-3 facility, part of the BSL-3 Biocontainment CoRE. This core is supported by funding from the ISMMS Dean’s Office and investigator contributions through a cost recovery mechanism. The facility use reported in this publication was supported by the National Institute of Allergy and Infectious Diseases of the National Institutes of Health under award no. G20AI174733 (R.A. Albrecht).

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Germline-targeting vaccination elicits HIV broadly neutralizing antibodies in nonhuman primates

Patrick J Madden1,2,‡, Jon Steichen2,3,‡, Monolina Shil1,2, Alessia Liguori2,3,4, Parham Ramezani-Rad1,2, Ivy Phung1,2, Claudia Flynn2,4, Diane G Carnathan5, JH Lee2,4, Guido Silvestri5, William R Schief2,3,4,6,*, Shane Crotty1,2,7,*

1Center for Vaccine Innovation, La Jolla Institute for Immunology; 2Consortium for HIV/AIDS Vaccine Development; 3Department of Immunology and Microbiology, The Scripps Research Institute; 4IAVI Neutralizing Antibody Center, The Scripps Research Institute; 5Emory National Primate Research Center and Emory Vaccine Center, Emory University School of Medicine; 6Moderna, Inc.; 7Department of Medicine, Division of Infectious Disease and Global Public Health, University of California, San Diego

‡These authors contributed equally to this work.

*Corresponding authors

Abstract:

Germline-targeting and shepherding is an HIV vaccine strategy that relies on multiple phases, priming of rare precursor B cells followed by maturation of those B cells into broadly-neutralizing antibodies (bnAbs) through sequential immunizations and, finally, conversion of those bnAb-expressing B cells into long-lived responses. We recently demonstrated that the priming immunogen N332-GT5 can reproducible prime BG18 type I precursor B cells in rhesus macaques. BG18 is an HIV bnAb that targets the N332 glycan supersite on the Envelope protein and is dependent on a long CDRH3 which makes the precursors incredibly rare in the naïve repertoire (1 in 53 million in humans and estimated 8-fold lower in NHPs). To extend these findings we initiated a study using sequential immunization of progressively more native like trimer immunogens after N332-GT5 ED priming to mature the BG18 type I responses. After a series of seven booster immunizations, >50% of immunized animals developed BG18 type I like bnAb responses and demonstrated broad-neutralization in the serum. Through the use of the Immcantation framework, individual BG18 type I B cell lineages were traced throughout the study. Dowser was used to construct phylogenetic trees and trace the mutation history and development of neutralization potency and breadth in individual clonal families of up to 6000 cells, highlighting the importance of robust bioinformatic packages such as Dowser to aid in the analysis of germline-targeting vaccine regimens. Overall, these results show that germline-targeting can successfully induce bnAbs and serves as proof-of-concept that germline-targeting is a feasible vaccination strategy against HIV.

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Tissue-directed maintenance of vaccine-specific human B-cell memory

Eric Zhang1,2, Alex B. George1,2, Matteo Porotto3,4,5,9, Peter A. Sims6,7,9, Donna L. Farber1,8,9,*

1Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA; 2Medical Scientist Training Program, Columbia University Irving Medical Center, New York, NY 10032, USA; 3Center for Host-Pathogen Interaction, Columbia University Irving Medical Center, New York, NY 10032, USA; 4Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA; 5Department of Experimental Medicine, University of Campania “Luigi Vanvitelli,” 81100 Caserta, Italy; 6Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA; 7Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY 10032, USA; 8Department of Surgery, Columbia University Irving Medical Center, New York, NY 10032, USA; 9Senior author

*Corresponding author

Abstract:

The formation and maintenance of memory B cells (MBCs) after vaccination and infection is essential for lifelong immunity. A minority of MBCs circulate; instead, most reside in lymphoid reservoirs such as the spleen, lymph nodes, and bone marrow. In humans, it remains unclear whether these compartments maintain distinct MBC subsets and if such subsets contribute to vaccine immunity. To address this, we performed paired single-cell RNA and B-cell receptor (BCR) sequencing of four ubiquitous antigen-specific MBC populations—measles and tetanus (childhood-primed) and SARS-CoV-2 and H1N1 influenza (recently primed/boosted)—across spleen, lymph nodes, and bone marrow. We identified three major subsets enriched in distinct tissues: classical MBCs in lymph nodes, marginal zone–like MBCs in spleen, and atypical MBCs in bone marrow. All three subsets were present in each antigen-specific population, but their relative proportions were shaped by both tissue and antigen. Using the Immcantation framework, we found that antigen-specific MBCs were variably clonally expanded, with individual clones spanning all three subsets in a tissue-guided manner. Additionally, each subset was represented amongst class-switched and non-class-switched BCRs. Mutational inference and phylogenetic analysis revealed that MBCs sharing identical BCRs often adopted different subset identities, indicating that MBC cellular identity is highly dynamic and uncoupled from lineage. Together, these findings demonstrate substantial phenotypic and functional heterogeneity in the tissue reservoirs of human memory B cells, with implications for future vaccine design and delivery.

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Activated Polyreactive B Cells Are Clonally Expanded in Autoantibody-positive and Patients with New-Onset Type 1 Diabetes

Kristen Wells1,2,*, Mia Smith1,2,*, Catherine Nicholas1,2

1Barbara Davis Center for Diabetes; 2University of Colorado Anschutz Medical Campus

*Corresponding author

Abstract:

Autoreactive B cells play an important but ill-defined role in autoimmune type 1 diabetes (T1D). We isolated pancreatic islet antigen-reactive B cells from the peripheral blood of non-diabetic autoantibody-negative first-degree relatives, autoantibody-positive, and recent-onset T1D donors. Single-cell RNA sequencing analysis revealed that islet antigen-reactive B cells from autoantibody-positive and T1D donors had altered gene expression in pathways associated with B cell signaling and inflammation. Using Immcantation to align BCR sequences and identify clonally related cells, we found a similar shift in islet antigen-reactive B cell repertoires among autoantibody-positive and T1D donors where greater clonal expansion was also observed. Notably, a substantial fraction of islet antigen-reactive B cells in autoantibody-positive and T1D donors appeared to be polyreactive, which was corroborated by analysis of recombinant monoclonal antibodies. These results expand our understanding of autoreactive B cell phenotypes during T1D and identify unique BCR repertoire changes that may serve as biomarkers for increased disease risk.

Associated Publications:

Funding:

This work was funded by the National Institutes of Health (F31DK134095 [C.A.N.], T32GM136444 [C.A.N.], K01OD028759 [M.J.S.], P30DK116073 [Lori Sussel], P30CA046934 [Cancer Center Grant], and the Leona M. & Harry B. Helmsley Charitable Trust, Project #2305-06031 (M.J.S.).

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Early emergence of signatures associated with HCV infection outcome

Money Gupta1,2,‡, Arunasingam Abayasingam1,2,‡, Bing-Ru Wu1,2,‡, Alexander P. Underwood1,2,3, Clara Young4,5, Melanie R. Walker1,2, David Agapiou1, Auda A. Eltahla1,2, Hui Li1, Elizabeth Keoshkerian1, Sarah Su1,2, Nicholas Brasher1,2, Arnold Reynaldi1, Miles P. Davenport1, Fabio Luciani2, Nicodemus Tedla2, Lisa Maher1, Andrew R. Lloyd1, Rowena A. Bull1,2,*

1The Kirby Institute, Faculty of Health and Medicine, UNSW, Sydney, NSW, Australia; 2School of Biomedical Science, Faculty of Health and Medicine, UNSW, Sydney, NSW, Australia; 3Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; 4Immunology Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia; 5St Vincent’s Clinical School, Faculty of Medicine, University of New South Wales, Darlinghurst, NSW, Australia

‡These authors contributed equally to this work.

*Corresponding authors: ,

Abstract:

Previous studies have demonstrated a delayed emergence of neutralising antibodies (nAbs) as a biomarker of failure to clear hepatitis C virus (HCV) infection, but why this happened remains unclear. Here in this study we examined whether the B cell repertoire of the HCV Transmission Founder (TF) virus was associated with this delay in the nAb development in a unique cohort of acute primary HCV infected individuals that were followed over time. TF variants from subjects that developed clearance had early formation of memory B cells and were more resistant to broadly neutralising antibodies (BnAbs). NAbs that appeared in subjects that did not clear the infection, we observed higher utilization of Vh1-69, Vh1-18 genes and somatic hypermutation (SHM) in chronics, and longer complementarity-determining region 3 (CDR3) regions in the B cell heavy chain suggesting additional rounds of maturation might be required to achieve strong binding against chronic TF variants. We used Change-O implemented in Immcantation for identification of clones and SHM in B cell repertoire, and no clonal differences were found across the outcome. This study observed a negative correlation of SHM with CDR3 whereas, an increase in the binding affinity with the increase in SHM. Transcriptomic analysis of the E2-specific memory B cells showed a distinct population within memory B cells that can be found in other infections well, and no pathway differences were found across the outcome. Finally, this work showed the relevance of identifying antibodies that can be effective vaccine targets to B cell germlines and can drive early differences in nAb development, and possibly enhance antigen valency for the development of HCV vaccines.

Funding:

UNSW Scientia PhD Scholarship

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