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Levi R, Dvorkin S, Louzoun Y. Shared bias in H chain V-J pairing in naive and memory B cells. Front Immunol 2023; 14:1166116. [PMID: 37790930 PMCID: PMC10543446 DOI: 10.3389/fimmu.2023.1166116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 08/23/2023] [Indexed: 10/05/2023] Open
Abstract
Introduction H chain rearrangement in B cells is a two-step process where first DH binds JH, and only then VH is joined to the complex. As such, there is no direct rearrangement between VH and JH. Results Nevertheless, we here show that the VHJH combinations frequency in humans deviates from the one expected based on each gene usage frequency. This bias is observed mainly in functional rearrangements, and much less in out-of-frame rearrangements. The bias cannot be explained by preferred binding for DH genes or a preferred reading frame. Preferred VH JH combinations are shared between donors. Discussion These results suggest a common structural mechanism for these biases. Through development, thepreferred VH JH combinations evolve during peripheral selection to become stronger, but less shared. We propose that peripheral Heavy chain VH JH usage is initially shaped by a structural selection before the naive B cellstate, followed by pathogen-induced selection for host specific VH-JH pairs.
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Affiliation(s)
| | | | - Yoram Louzoun
- Department of Mathematics, Bar Ilan University, Ramat Gan, Israel
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2
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Garg AD. The dynamic interface of genetics and immunity: toward future horizons in health & disease. Genes Immun 2023; 24:155-158. [PMID: 37464025 DOI: 10.1038/s41435-023-00213-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Affiliation(s)
- Abhishek D Garg
- Cell Stress & Immunity (CSI) Lab, Department for Cellular & Molecular Medicine (CMM), KU Leuven, Leuven, Belgium.
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Akerman O, Isakov H, Levi R, Psevkin V, Louzoun Y. Counting is almost all you need. Front Immunol 2023; 13:1031011. [PMID: 36741395 PMCID: PMC9896581 DOI: 10.3389/fimmu.2022.1031011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 12/27/2022] [Indexed: 01/21/2023] Open
Abstract
The immune memory repertoire encodes the history of present and past infections and immunological attributes of the individual. As such, multiple methods were proposed to use T-cell receptor (TCR) repertoires to detect disease history. We here show that the counting method outperforms two leading algorithms. We then show that the counting can be further improved using a novel attention model to weigh the different TCRs. The attention model is based on the projection of TCRs using a Variational AutoEncoder (VAE). Both counting and attention algorithms predict better than current leading algorithms whether the host had CMV and its HLA alleles. As an intermediate solution between the complex attention model and the very simple counting model, we propose a new Graph Convolutional Network approach that obtains the accuracy of the attention model and the simplicity of the counting model. The code for the models used in the paper is provided at: https://github.com/louzounlab/CountingIsAlmostAllYouNeed.
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Affiliation(s)
- Ofek Akerman
- Department of Mathematics, Bar-Ilan University, Ramat Gan, Israel
- Department of Computer Science, Bar-Ilan University, Ramat Gan, Israel
| | - Haim Isakov
- Department of Mathematics, Bar-Ilan University, Ramat Gan, Israel
| | - Reut Levi
- Department of Mathematics, Bar-Ilan University, Ramat Gan, Israel
| | - Vladimir Psevkin
- Department of Mathematics, Bar-Ilan University, Ramat Gan, Israel
| | - Yoram Louzoun
- Department of Mathematics, Bar-Ilan University, Ramat Gan, Israel
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4
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Levi R, Louzoun Y. Two Step Selection for Bias in β Chain V-J Pairing. Front Immunol 2022; 13:906217. [PMID: 35911711 PMCID: PMC9330483 DOI: 10.3389/fimmu.2022.906217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
The β chain rearrangement in T cells is a two-step process where first Dβ and Jβ bind, and only then Vβ is joined to the complex. We here show that the frequency of human and mouse Vβ
Jβ combinations deviates from the one expected based on each gene usage frequency. This bias is observed mainly in functional (F) rearrangements, but also slightly in non-functional (NF) rearrangements. Preferred Vβ
Jβ combinations in F clones are shared between donors and samples, suggesting a common structural mechanism for these biases in addition to any host-specific antigen-induced peripheral selection. The sharing holds even in clones with Jβ1 that share the same Dβ1 gene. Vβ
Jβ usage is correlated with the Molecular Weight and Isoelectric Point in F clones. The pairing is also observed in the Double Positive cells in mice thymocytes, suggesting that the selection leading to such a pairing occurs before thymic selection. These results suggest an additional structural checkpoint in the beta chain development prior to thymic selection during the T cell receptor expression. Understanding this structural selection is important for the distinction between normal and aberrant T cell development, and crucial for the design of engineered TCRs.
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Rettig TA, Tan JC, Nishiyama NC, Chapes SK, Pecaut MJ. An Analysis of the Effects of Spaceflight and Vaccination on Antibody Repertoire Diversity. Immunohorizons 2021; 5:675-686. [PMID: 34433623 PMCID: PMC10996920 DOI: 10.4049/immunohorizons.2100056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 07/26/2021] [Indexed: 11/19/2022] Open
Abstract
Ab repertoire diversity plays a critical role in the host's ability to fight pathogens. CDR3 is partially responsible for Ab-Ag binding and is a significant source of diversity in the repertoire. CDR3 diversity is generated during VDJ rearrangement because of gene segment selection, gene segment trimming and splicing, and the addition of nucleotides. We analyzed the Ab repertoire diversity across multiple experiments examining the effects of spaceflight on the Ab repertoire after vaccination. Five datasets from four experiments were analyzed using rank-abundance curves and Shannon indices as measures of diversity. We discovered a trend toward lower diversity as a result of spaceflight but did not find the same decrease in our physiological model of microgravity in either the spleen or bone marrow. However, the bone marrow repertoire showed a reduction in diversity after vaccination. We also detected differences in Shannon indices between experiments and tissues. We did not detect a pattern of CDR3 usage across the experiments. Overall, we were able to find differences in the Ab repertoire diversity across experimental groups and tissues.
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Affiliation(s)
- Trisha A Rettig
- Division of Biomedical Engineering Sciences, Department of Basic Sciences, Loma Linda University, Loma Linda, CA
- Division of Biology, Kansas State University, Manhattan, KS
| | - John C Tan
- Division of Biomedical Engineering Sciences, Department of Basic Sciences, Loma Linda University, Loma Linda, CA
| | - Nina C Nishiyama
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC; and
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | - Michael J Pecaut
- Division of Biomedical Engineering Sciences, Department of Basic Sciences, Loma Linda University, Loma Linda, CA;
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6
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Dvorkin S, Levi R, Louzoun Y. Autoencoder based local T cell repertoire density can be used to classify samples and T cell receptors. PLoS Comput Biol 2021; 17:e1009225. [PMID: 34310600 PMCID: PMC8341707 DOI: 10.1371/journal.pcbi.1009225] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 08/05/2021] [Accepted: 06/28/2021] [Indexed: 11/18/2022] Open
Abstract
Recent advances in T cell repertoire (TCR) sequencing allow for the characterization of repertoire properties, as well as the frequency and sharing of specific TCR. However, there is no efficient measure for the local density of a given TCR. TCRs are often described either through their Complementary Determining region 3 (CDR3) sequences, or theirV/J usage, or their clone size. We here show that the local repertoire density can be estimated using a combined representation of these components through distance conserving autoencoders and Kernel Density Estimates (KDE). We present ELATE-an Encoder-based LocAl Tcr dEnsity and show that the resulting density of a sample can be used as a novel measure to study repertoire properties. The cross-density between two samples can be used as a similarity matrix to fully characterize samples from the same host. Finally, the same projection in combination with machine learning algorithms can be used to predict TCR-peptide binding through the local density of known TCRs binding a specific target.
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MESH Headings
- Algorithms
- Amino Acid Sequence
- Complementarity Determining Regions/classification
- Complementarity Determining Regions/genetics
- Computational Biology
- Databases, Genetic
- Gene Rearrangement, alpha-Chain T-Cell Antigen Receptor
- Gene Rearrangement, beta-Chain T-Cell Antigen Receptor
- Humans
- Immunoglobulin Variable Region/genetics
- Machine Learning
- Receptors, Antigen, T-Cell/classification
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell, alpha-beta/classification
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Software
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Affiliation(s)
- Shirit Dvorkin
- Department of Mathematics, Bar Ilan University, Ramat Gan, Israel
| | - Reut Levi
- Department of Mathematics, Bar Ilan University, Ramat Gan, Israel
| | - Yoram Louzoun
- Department of Mathematics, Bar Ilan University, Ramat Gan, Israel
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Breden F, Watson CT. Using High-Throughput Sequencing to Characterize the Development of the Antibody Repertoire During Infections: A Case Study of HIV-1. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1053:245-263. [PMID: 29549643 DOI: 10.1007/978-3-319-72077-7_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
High throughput sequencing (HTS) approaches have only recently been applied to describing the antibody/B-cell repertoire in fine detail, but these data sets have already become critical to the design of vaccines and therapeutics, and monitoring of cancer immunotherapy. As a case study, we describe the potential and present limitations of HTS studies of the Ab repertoire during infection with HIV-1. Most of the present studies restrict their analyses to lineages of specific bnAbs. We discuss future initiatives to expand this type of analysis to more complete repertoires and to improve comparing and sharing of these Ab repertoire data across studies and institutions.
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Affiliation(s)
- Felix Breden
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC, Canada.
| | - Corey T Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
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Toledano A, Elhanati Y, Benichou JIC, Walczak AM, Mora T, Louzoun Y. Evidence for Shaping of Light Chain Repertoire by Structural Selection. Front Immunol 2018; 9:1307. [PMID: 29988361 PMCID: PMC6023962 DOI: 10.3389/fimmu.2018.01307] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Accepted: 05/25/2018] [Indexed: 11/13/2022] Open
Abstract
The naïve immunoglobulin (IG) repertoire in the blood differs from the direct output of the rearrangement process. These differences stem from selection that affects the germline gene usage and the junctional nucleotides. A major complication obscuring the details of the selection mechanism in the heavy chain is the failure to properly identify the D germline and determine the nucleotide addition and deletion in the junction region. The selection affecting junctional diversity can, however, be studied in the light chain that has no D gene. We use probabilistic and deterministic models to infer and disentangle generation and selection of the light chain, using large samples of light chains sequenced from healthy donors and transgenic mice. We have previously used similar models for the beta chain of T-cell receptors and the heavy chain of IGs. Selection is observed mainly in the CDR3. The CDR3 length and mass distributions are narrower after selection than before, indicating stabilizing selection for mid-range values. Within the CDR3, proline and cysteine undergo negative selection, while glycine undergoes positive selection. The results presented here suggest structural selection maintaining the size of the CDR3 within a limited range, and preventing turns in the CDR3 region.
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Affiliation(s)
- Adar Toledano
- Department of Mathematics, Gonda Brain Research Center, Bar Ilan University, Ramat Gan, Israel
| | - Yuval Elhanati
- Joseph Henry Laboratories, Princeton University, Princeton, NJ, United States
| | - Jennifer I C Benichou
- Department of Mathematics, Gonda Brain Research Center, Bar Ilan University, Ramat Gan, Israel
| | - Aleksandra M Walczak
- Laboratoire de Physique Théorique, UMR8549, CNRS and Ecole Normale Supérieure, Paris, France
| | - Thierry Mora
- Laboratoire de physique statistique, UMR8550, CNRS, UPMC and Ecole normale supérieure, Paris, France
| | - Yoram Louzoun
- Department of Mathematics, Gonda Brain Research Center, Bar Ilan University, Ramat Gan, Israel
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