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Article ; Online: Immunosequencing: applications of immune repertoire deep sequencing.

Robins, Harlan

2013 Volume 25, Issue 5, Page(s) 646–652

Abstract: Advances in high-throughput sequencing have enabled the development of a powerful new technology for probing the adaptive immune system. Millions of B or T cell receptor sequences can be read in parallel from a single sample. The dynamics of an adaptive ... ...

Abstract	Advances in high-throughput sequencing have enabled the development of a powerful new technology for probing the adaptive immune system. Millions of B or T cell receptor sequences can be read in parallel from a single sample. The dynamics of an adaptive immune response, which is based on clonal expansion and contraction, can be monitored in real time at high sensitivity and the global properties of the adaptive immune repertoires can be studied. A large set of clinical applications for this technology are presently under study, with a few diagnostic applications for hematological malignancies already available. A review of this new field termed immunosequencing is presented.
MeSH term(s)	DNA/analysis ; DNA/genetics ; Genomics ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Lymphocytes/immunology ; RNA, Messenger/analysis ; RNA, Messenger/genetics ; Somatic Hypermutation, Immunoglobulin
Chemical Substances	RNA, Messenger ; DNA (9007-49-2)
Language	English
Publishing date	2013-10
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	1035767-1
ISSN	1879-0372 ; 0952-7915
ISSN (online)	1879-0372
ISSN	0952-7915
DOI	10.1016/j.coi.2013.09.017
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Detecting and monitoring lymphoma with high-throughput sequencing.

Robins, Harlan

Oncotarget

2011 Volume 2, Issue 4, Page(s) 287–288

MeSH term(s)	Clinical Laboratory Techniques/trends ; Genes, Neoplasm/genetics ; High-Throughput Nucleotide Sequencing/methods ; High-Throughput Nucleotide Sequencing/statistics & numerical data ; Humans ; Lymphoma/diagnosis ; Lymphoma/genetics ; Medical Oncology/methods ; Monitoring, Physiologic/methods ; Neoplasm, Residual
Language	English
Publishing date	2011-04-30
Publishing country	United States
Document type	Journal Article ; Comment
ZDB-ID	2560162-3
ISSN	1949-2553 ; 1949-2553
ISSN (online)	1949-2553
ISSN	1949-2553
DOI	10.18632/oncotarget.270
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Article: Immunosequencing: applications of immune repertoire deep sequencing

Robins, Harlan

Current Opinion in Immunology. 2013 Oct., v. 25, no. 5

2013

Abstract	Advances in high-throughput sequencing have enabled the development of a powerful new technology for probing the adaptive immune system. Millions of B or T cell receptor sequences can be read in parallel from a single sample. The dynamics of an adaptive immune response, which is based on clonal expansion and contraction, can be monitored in real time at high sensitivity and the global properties of the adaptive immune repertoires can be studied. A large set of clinical applications for this technology are presently under study, with a few diagnostic applications for hematological malignancies already available. A review of this new field termed immunosequencing is presented.
Keywords	T-lymphocytes ; adaptive immunity ; high-throughput nucleotide sequencing ; technology
Language	English
Dates of publication	2013-10
Size	p. 646-652.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	1035767-1
ISSN	1879-0372 ; 0952-7915
ISSN (online)	1879-0372
ISSN	0952-7915
DOI	10.1016/j.coi.2013.09.017
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Self-Reported Use of COVID-19 Immunologic Test Results to Inform Decisions About Daily Activities and COVID-19 Vaccination

Jiang, Miao / Akers, Nicholas K. / Gill, Darcy B. / Eckhert, Benjamin / Svejnoha, Emily / Robins, Harlan

medRxiv

Abstract: Importance: Despite widespread use of clinical diagnostic tests to assess prior exposure to SARS-CoV-2, limited evidence exists regarding how test results affect patient behaviors and decision-making. Objective: To understand the rationale behind ... ...

Abstract	Importance: Despite widespread use of clinical diagnostic tests to assess prior exposure to SARS-CoV-2, limited evidence exists regarding how test results affect patient behaviors and decision-making. Objective: To understand the rationale behind ordering diagnostic T-cell receptor (TCR) immunosequencing for assessment of prior SARS-CoV-2 infection and evaluate how test results affect patient behaviors, including day-to-day activities and decisions about vaccination. Design: Mandatory demographic information and clinical characteristics were collected for all individuals ordering T-DetectTM COVID. Study participants completed a one-time survey that included additional questions about demographics and clinical characteristics, relevant interactions with healthcare providers, reasons for ordering diagnostic TCR immunosequencing, and the utility of test results. Setting: US participants ordering T-Detect COVID between February 2021 and March 2022. Participants: Of the 806 individuals who underwent diagnostic TCR immunosequencing, provided informed consent, and were sent the email survey, 718 completed the survey (response rate, 89.1%). At the time of receiving the test report, 25.5% of participants had been vaccinated against COVID-19, 29.7% reported a previous COVID-19 infection, and 25.6% were immunocompromised. Main Outcome(s) and Measure(s): Patient demographics and clinical characteristics were reported using descriptive statistics. Additional analyses explored trends in reported data over time and evaluated reasons for ordering diagnostic TCR immunosequencing and behaviors among participant subgroups (vaccinated or unvaccinated individuals and those with positive or negative test results). Logistic regression analysis evaluated factors that increased the likelihood of post-test vaccination. Results: Study participants ordered diagnostic TCR immunosequencing to understand their health status (55.0%) and to inform decision-making about daily activities (43.6%) and vaccination (38.3%). Most participants (92.1%) ordered diagnostic TCR immunosequencing for themselves without consulting their physician. Testing negative for prior SARS-CoV-2 infection was associated with increased likelihood of subsequent COVID-19 vaccination (31.0% vs 6.9%; median time to vaccination, 17.0 days vs 47.5 days), which was confirmed by logistic regression analysis. Conclusions and Relevance: This report presents patient-reported clinical utility of a commercial COVID-19 assay based on an immune response readout. Our findings suggest that participants used diagnostic TCR immunosequencing results to inform decisions about daily activities and COVID-19 vaccination. Trial Registration: Not applicable.
Keywords	covid19
Language	English
Publishing date	2022-07-02
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2022.07.01.22277108
Database	COVID19

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Article ; Online: Impact of HLA type, age and chronic viral infection on peripheral T-cell receptor sharing between unrelated individuals.

Johnson, Sarah A / Seale, Spencer L / Gittelman, Rachel M / Rytlewski, Julie A / Robins, Harlan S / Fields, Paul A

PloS one

2021 Volume 16, Issue 8, Page(s) e0249484

Abstract: The human adaptive immune system must generate extraordinary diversity to be able to respond to all possible pathogens. The T-cell repertoire derives this high diversity through somatic recombination of the T-cell receptor (TCR) locus, a random process ... ...

Abstract	The human adaptive immune system must generate extraordinary diversity to be able to respond to all possible pathogens. The T-cell repertoire derives this high diversity through somatic recombination of the T-cell receptor (TCR) locus, a random process that results in repertoires that are largely private to each individual. However, factors such as thymic selection and T-cell proliferation upon antigen exposure can affect TCR sharing among individuals. By immunosequencing the TCRβ variable region of 426 healthy individuals, we find that, on average, fewer than 1% of TCRβ clones are shared between individuals, consistent with largely private TCRβ repertoires. However, we detect a significant correlation between increased HLA allele sharing and increased number of shared TCRβ clones, with each additional shared HLA allele contributing to an increase in ~0.01% of the total shared TCRβ clones, supporting a key role for HLA type in shaping the immune repertoire. Surprisingly, we find that shared antigen exposure to CMV leads to fewer shared TCRβ clones, even after controlling for HLA, indicative of a largely private response to major viral antigenic exposure. Consistent with this hypothesis, we find that increased age is correlated with decreased overall TCRβ clone sharing, indicating that the pattern of private TCRβ clonal expansion is a general feature of the T-cell response to other infectious antigens as well. However, increased age also correlates with increased sharing among the lowest frequency clones, consistent with decreased repertoire diversity in older individuals. Together, all of these factors contribute to shaping the TCRβ repertoire, and understanding their interplay has important implications for the use of T cells for therapeutics and diagnostics.
MeSH term(s)	Adult ; Age Factors ; Chronic Disease ; Cytomegalovirus Infections/immunology ; HLA Antigens/immunology ; Histocompatibility Testing/methods ; Humans ; Receptors, Antigen, T-Cell/immunology ; Virus Diseases/immunology
Chemical Substances	HLA Antigens ; Receptors, Antigen, T-Cell
Language	English
Publishing date	2021-08-30
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0249484
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Impact of HLA type, age and chronic viral infection on peripheral T-cell receptor sharing between unrelated individuals.

Sarah A Johnson / Spencer L Seale / Rachel M Gittelman / Julie A Rytlewski / Harlan S Robins / Paul A Fields

PLoS ONE, Vol 16, Iss 8, p e

2021 Volume 0249484

Abstract	The human adaptive immune system must generate extraordinary diversity to be able to respond to all possible pathogens. The T-cell repertoire derives this high diversity through somatic recombination of the T-cell receptor (TCR) locus, a random process that results in repertoires that are largely private to each individual. However, factors such as thymic selection and T-cell proliferation upon antigen exposure can affect TCR sharing among individuals. By immunosequencing the TCRβ variable region of 426 healthy individuals, we find that, on average, fewer than 1% of TCRβ clones are shared between individuals, consistent with largely private TCRβ repertoires. However, we detect a significant correlation between increased HLA allele sharing and increased number of shared TCRβ clones, with each additional shared HLA allele contributing to an increase in ~0.01% of the total shared TCRβ clones, supporting a key role for HLA type in shaping the immune repertoire. Surprisingly, we find that shared antigen exposure to CMV leads to fewer shared TCRβ clones, even after controlling for HLA, indicative of a largely private response to major viral antigenic exposure. Consistent with this hypothesis, we find that increased age is correlated with decreased overall TCRβ clone sharing, indicating that the pattern of private TCRβ clonal expansion is a general feature of the T-cell response to other infectious antigens as well. However, increased age also correlates with increased sharing among the lowest frequency clones, consistent with decreased repertoire diversity in older individuals. Together, all of these factors contribute to shaping the TCRβ repertoire, and understanding their interplay has important implications for the use of T cells for therapeutics and diagnostics.
Keywords	Medicine ; R ; Science ; Q
Subject code	570
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Identifying immune signatures of common exposures through co-occurrence of T-cell receptors in tens of thousands of donors

May, Damon H. / Woodhouse, Steven / Zahid, H. Jabran / Elyanow, Rebecca / Doroschak, Kathryn / Noakes, Matthew T. / Taniguchi, Ruth / Yang, Zheng / Grino, John R. / Byron, Rachel / Oaks, Jamie / Sherwood, Anna / Greissl, Julia / Chen-Harris, Haiyin / Howie, Bryan / Robins, Harlan S.

bioRxiv

Abstract: Memory T cells are records of clonal expansion from prior immune exposures, such as infections, vaccines and chronic diseases like cancer. A subset of the receptors of these expanded T cells in a typical immune repertoire are highly public, i.e., present ...

Abstract	Memory T cells are records of clonal expansion from prior immune exposures, such as infections, vaccines and chronic diseases like cancer. A subset of the receptors of these expanded T cells in a typical immune repertoire are highly public, i.e., present in many individuals exposed to the same exposure. For the most part, the exposures associated with these public T cells are unknown. To identify public T-cell receptor signatures of immune exposures, we mined the immunosequencing repertoires of tens of thousands of donors to define clusters of co-occurring T cells. We first built co-occurrence clusters of T cells responding to antigens presented by the same Human Leukocyte Antigen (HLA) and then combined those clusters across HLAs. Each cross-HLA cluster putatively represents the public T-cell signature of a single prevalent exposure. Using repertoires from donors with known serological status for 7 prevalent exposures (HSV-1, HSV-2, EBV, Parvovirus, Toxoplasma gondii, Cytomegalovirus and SARS CoV-2), we identified a single T-cell cluster strongly associated with each exposure and used it to construct a highly sensitive and specific diagnostic model for the exposure. These T-cell clusters constitute the public immune responses to prevalent exposures, 7 known and many others unknown. By learning the exposure associations for more T cell clusters, this approach could be used to derive a ledger of a person9s past and present immune exposures.
Keywords	covid19
Language	English
Publishing date	2024-03-27
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2024.03.26.583354
Database	COVID19

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Article ; Online: Perturbations of the T-cell immune repertoire in kidney transplant rejection.

Sigdel, Tara K / Fields, Paul A / Liberto, Juliane / Damm, Izabella / Kerwin, Maggie / Hood, Jill / Towfighi, Parhom / Sirota, Marina / Robins, Harlan S / Sarwal, Minnie M

Frontiers in immunology

2022 Volume 13, Page(s) 1012042

Abstract: In this cross-sectional and longitudinal analysis of mapping the T-cell repertoire in kidney transplant recipients, we have investigated and validated T-cell clonality, immune repertoire chronology at rejection, and contemporaneous allograft biopsy ... ...

Abstract	In this cross-sectional and longitudinal analysis of mapping the T-cell repertoire in kidney transplant recipients, we have investigated and validated T-cell clonality, immune repertoire chronology at rejection, and contemporaneous allograft biopsy quantitative tissue injury, to better understand the pathobiology of acute T-cell fraction, T-cell repertoire and antibody-mediated kidney transplant rejection. To follow the dynamic evolution of T-cell repertoire changes before and after engraftment and during biopsy-confirmed acute rejection, we sequenced 323 peripheral blood samples from 200 unique kidney transplant recipients, with (n=100) and without (n=100) biopsy-confirmed acute rejection. We report that patients who develop acute allograft rejection, have lower (p=0.01) T-cell fraction even before transplantation, followed by its rise after transplantation and at the time of acute rejection accompanied by high TCR repertoire turnover (p=0.004). Acute rejection episodes occurring after the first 6 months post-transplantation, and those with a component of antibody-mediated rejection, had the highest turnover; p=0.0016) of their T-cell repertoire. In conclusion, we validated that detecting repertoire changes in kidney transplantation correlates with post-transplant rejection episodes suggesting that T-cell receptor sequencing may provide recipient pre-transplant and post-transplant predictors of rejection risk.
MeSH term(s)	Humans ; T-Lymphocytes ; Kidney Transplantation/adverse effects ; Cross-Sectional Studies ; Postoperative Complications ; Biopsy ; Antibodies
Chemical Substances	Antibodies
Language	English
Publishing date	2022-11-16
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2606827-8
ISSN	1664-3224 ; 1664-3224
ISSN (online)	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2022.1012042
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Article ; Online: Model to improve specificity for identification of clinically-relevant expanded T cells in peripheral blood.

Julie Rytlewski / Shibing Deng / Tao Xie / Craig Davis / Harlan Robins / Erik Yusko / Jadwiga Bienkowska

PLoS ONE, Vol 14, Iss 3, p e

2019 Volume 0213684

Abstract: Current methods to quantify T-cell clonal expansion only account for variance due to random sampling from a highly diverse repertoire space. We propose a beta-binomial model to incorporate time-dependent variance into the assessment of differentially ... ...

Abstract	Current methods to quantify T-cell clonal expansion only account for variance due to random sampling from a highly diverse repertoire space. We propose a beta-binomial model to incorporate time-dependent variance into the assessment of differentially abundant T-cell clones, identified by unique T Cell Receptor (TCR) β-chain rearrangements, and show that this model improves specificity for detecting clinically relevant clonal expansion. Using blood samples from ten healthy donors, we modeled the variance of T-cell clones within each subject over time and calibrated the dispersion parameters of the beta distribution to fit this variance. As a validation, we compared pre- versus post-treatment blood samples from urothelial cancer patients treated with atezolizumab, where clonal expansion (quantified by the earlier binomial model) was previously reported to correlate with benefit. The beta-binomial model significantly reduced the false-positive rate for detecting differentially abundant clones over time compared to the earlier binomial method. In the urothelial cancer cohort, the beta-binomial model enriched for tumor infiltrating lymphocytes among the clones detected as expanding in the peripheral blood in response to therapy compared to the binomial model and improved the overall correlation with clinical benefit. Incorporating time-dependent variance into the statistical framework for measuring differentially abundant T-cell clones improves the model's specificity for T-cells that correlate more strongly with the disease and treatment setting of-interest. Reducing background-level clonal expansion, therefore, improves the quality of clonal expansion as a biomarker for assessing the T cell immune response and correlations with clinical measures.
Keywords	Medicine ; R ; Science ; Q
Subject code	310
Language	English
Publishing date	2019-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Model to improve specificity for identification of clinically-relevant expanded T cells in peripheral blood.

Rytlewski, Julie / Deng, Shibing / Xie, Tao / Davis, Craig / Robins, Harlan / Yusko, Erik / Bienkowska, Jadwiga

PloS one

2019 Volume 14, Issue 3, Page(s) e0213684

Abstract	Current methods to quantify T-cell clonal expansion only account for variance due to random sampling from a highly diverse repertoire space. We propose a beta-binomial model to incorporate time-dependent variance into the assessment of differentially abundant T-cell clones, identified by unique T Cell Receptor (TCR) β-chain rearrangements, and show that this model improves specificity for detecting clinically relevant clonal expansion. Using blood samples from ten healthy donors, we modeled the variance of T-cell clones within each subject over time and calibrated the dispersion parameters of the beta distribution to fit this variance. As a validation, we compared pre- versus post-treatment blood samples from urothelial cancer patients treated with atezolizumab, where clonal expansion (quantified by the earlier binomial model) was previously reported to correlate with benefit. The beta-binomial model significantly reduced the false-positive rate for detecting differentially abundant clones over time compared to the earlier binomial method. In the urothelial cancer cohort, the beta-binomial model enriched for tumor infiltrating lymphocytes among the clones detected as expanding in the peripheral blood in response to therapy compared to the binomial model and improved the overall correlation with clinical benefit. Incorporating time-dependent variance into the statistical framework for measuring differentially abundant T-cell clones improves the model's specificity for T-cells that correlate more strongly with the disease and treatment setting of-interest. Reducing background-level clonal expansion, therefore, improves the quality of clonal expansion as a biomarker for assessing the T cell immune response and correlations with clinical measures.
MeSH term(s)	Adult ; Antibodies, Monoclonal, Humanized/therapeutic use ; Biomarkers, Tumor ; False Positive Reactions ; Female ; Humans ; Lymphocytes, Tumor-Infiltrating/cytology ; Male ; Middle Aged ; Receptors, Antigen, T-Cell, alpha-beta/genetics ; Reproducibility of Results ; T-Lymphocytes/cytology ; Treatment Outcome ; Urinary Bladder Neoplasms/drug therapy ; Urinary Bladder Neoplasms/immunology ; Urothelium/pathology
Chemical Substances	Antibodies, Monoclonal, Humanized ; Biomarkers, Tumor ; Receptors, Antigen, T-Cell, alpha-beta ; atezolizumab (52CMI0WC3Y)
Language	English
Publishing date	2019-03-14
Publishing country	United States
Document type	Journal Article
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0213684
Database	MEDical Literature Analysis and Retrieval System OnLINE

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