Cell Receptor Repertoire In Patients Research Articles

Characterisation of T and B cell receptor repertoire in patients with systemic lupus erythematosus.

Systemic lupus erythematosus (SLE) is an autoimmune disease with extreme heterogeneity, marked clinically by multi-systemic inflammatory involvement. However, the molecular mechanism of breakdown of self-tolerance is still unclear. T cell/B cell-mediated immune disorders may play a vital role in the pathogenesis of SLE. In this context, we used a combination of multiplex-PCR, Illumina sequencing and IMGT/HighV-QUEST for a standardised analysis of the T cell receptor β-chain (TCRβ) and B cell receptor H-chain (BCR-H) repertoire of peripheral blood mononuclear cells in SLE patients compared with healthy volunteers. The results showed that there was an obvious reduction in BCR-H repertoire diversity and BCR-H CDR3 length in SLE patients. Notably, the pre-selection BCR-H CDR3s in SLE patients also displayed abnormal shortening, which suggests that early events in bone marrow B cell development and repertoire generation were abnormal in SLE patients. However, there was no obvious change of T cell repertoire in SLE patients, including repertoire diversity and CDR3 length. In addition, there was skewed usage of V genes and CDR3 sequences in SLE patients, which might be the result of physiological responses to environmental antigens or pathogens. In conclusion, our data revealed the specific changes of the TCR and BCR repertoires in SLE patients, which may provide new ideas for its prevention and treatment.

Comprehensive analysis of B and T cell receptor repertoire in patients after kidney transplantation by high-throughput sequencing

PurposeThe dynamic immunity of kidney transplant patients has not been fully elucidated. In this study, we explored the repertoire features of B/T cell receptor (BCR/TCR) of kidney transplant patients. MethodsUsing combined multiplex PCR amplification and high-throughput sequencing technique, we analyzed the uremic patients' BCR H chain and TCR beta chain repertoire which obtained 1 day before kidney transplantation (PRE-1), 1 day and 7 day after kidney transplantation (POST-1 and POST-7). ResultsOur analysis results showed the diversity of TCRβ CDR3 in POST-7 group was highest. In addition, there were specific skewed usage of TRBV gene subfamilies, and V-J combinations in different time points during kidney transplantation. Moreover, the overlap degrees of BCR-H (TCR-β) CDR3 repertoire among each group were identified. Notably, the abundance of some TCR-β CDR3 sequences changed regularly in the time point of kidney transplantation. ConclusionsThe BCR-H (TCR-β) CDR3 repertoire of kidney transplant patients changed dynamically.

Comprehensive analysis of T cell receptor repertoire in patients with KRAS mutant non-small cell lung cancer.

BackgroundKirsten rat sarcoma viral oncogene homolog (KRAS) is one of the most frequently mutated oncogenes in non-small cell lung cancer (NSCLC). The administration of immunotherapy has demonstrated significant efficacy in prolonging the overall survival of patients with KRAS mutation in recent years. However, the efficacy of immunotherapy in KRAS mutant NSCLC is variable. Analysis of T cell receptor (TCR) repertoire may contribute to a better understanding of the mechanisms behind such differential outcomes.MethodsA total of 47 patients with KRAS mutant NSCLC were enrolled in this study. Deep sequencing of the TCR β chain complementarity-determining regions in tumor tissue and paired peripheral blood specimens was conducted. Comprehensive analysis of TCR repertoire metrics was performed with different KRAS mutation subtypes and concomitant mutations. Moreover, the associations between TCR repertoire metrics and tumor mutation burden (TMB), as well as programmed death-ligand 1 were explored, respectively.ResultsTCR repertoire metrics, including Shannon index, Clonality, and Morisita index (MOI), showed no significant differences among different KRAS mutation subtypes. The similar results were observed between patients with tumor protein p53 (TP53) mutation and those with wild-type TP53. In contrast, although no significant differences were found in Shannon index and Clonality, patients with KRAS/serine/threonine kinase 11 (STK11) comutation showed a significantly higher MOI compared to their STK11 wild-type counterparts (P=0.012). In addition, TCR repertoire metrics were neither associated with TMB nor programmed death-ligand 1 expression in KRAS mutant NSCLC.ConclusionsThis retrospective study comprehensively described the TCR repertoire in KRAS mutant NSCLC. A higher MOI represented more overlap of the TCR repertoire between tumor tissue and paired peripheral blood, indicating distinctive immunological features in NSCLC with KRAS/STK11 comutation.

Broader Epstein–Barr virus–specific T cell receptor repertoire in patients with multiple sclerosis

Epstein-Barr virus (EBV) infection precedes multiple sclerosis (MS) pathology and cross-reactive antibodies might link EBV infection to CNS autoimmunity. As an altered anti-EBV T cell reaction was suggested in MS, we queried peripheral blood T cell receptor β chain (TCRβ) repertoires of 1,395 MS patients, 887 controls, and 35 monozygotic, MS-discordant twin pairs for multimer-confirmed, viral antigen-specific TCRβ sequences. We detected more MHC-I-restricted EBV-specific TCRβ sequences in MS patients. Differences in genetics or upbringing could be excluded by validation in monozygotic twin pairs discordant for MS. Anti-VLA-4 treatment amplified this observation, while interferon β- or anti-CD20 treatment did not modulate EBV-specific T cell occurrence. In healthy individuals, EBV-specific CD8+ T cells were of an effector-memory phenotype in peripheral blood and cerebrospinal fluid. In MS patients, cerebrospinal fluid also contained EBV-specific central-memory CD8+ T cells, suggesting recent priming. Therefore, MS is not only preceded by EBV infection, but also associated with broader EBV-specific TCR repertoires, consistent with an ongoing anti-EBV immune reaction in MS.

Clonal diversity of the B cell receptor repertoire in patients with coronary in-stent restenosis and type 2 diabetes.

Type 2 diabetes mellitus (T2DM) is known as a risk factor for coronary in-stent restenosis (ISR) in patients with coronary artery disease (CAD). Evidence suggests that B cells play a functional role in the progression of atherosclerotic lesions. However, the B cell receptor (BCR) repertoire in patients with ISR remains unclear. This study aims to profile the BCR repertoire in patients with coronary ISR/T2DM. A total of 21 CAD patients with or without ISR/T2DM were enrolled. PBMCs were isolated and examined for BCR repertoire profiles using DNA-seq. Our results showed that the diversity of amino acid sequences in ISR DM patients was higher than that in ISR −DM patients. The frequencies of 21 V/J paired genes differed between ISR DM and −ISR DM patients, while frequencies of 5 V/J paired genes differed between ISR DM and ISR −DM. The −ISR −DM group presented the highest clonotype overlap rate, while ISR DM patients presented the lowest overlap rate. Our study presented the BCR repertoires in patients with ISR/T2DM. The data suggested different BCR signatures between patients with ISR and T2DM. Further analysis of BCR profiles would enhance understanding of ISR.

An analysis of abnormalities in the B cell receptor repertoire in patients with systemic sclerosis using high-throughput sequencing.

Systemic sclerosis is a chronic multisystem autoimmune disease that is associated with polyclonal B cell hyperreactivity. The CDR3 of BCRs is the major site of antigen recognition. Therefore, we analyzed the BCR repertoire of patients with SSc. The BCR repertoires in 12 subjects including eight SSc patients and four healthy controls were characterized by high-throughput sequencing, and bioinformatics analysis were studied. The average CDR3 length in the SSc group was significantly shorter. The SSc patient displayed more diverse BCR. Moreover, SSc patients with mild skin sclerosis, anti-Scl70, interstitial lung disease or female sex were more diversified. B cells from the SSc patients showed a differential V and J gene usage. SSc patients had distinct BCR repertoires.These findings reflected the differences of BCR repertoires between SSc patients and controls. The higher-usage genes for the BCR sequence might be potential biomarkers of B cell-targeted therapies or diagnosis for SSc.

Abstract LB-019: Anti-CD4 monoclonal antibody immunotherapy exerts an antitumor effect by replacing the T cell receptor repertoire in patients with gastrointestinal cancer

Abstract Background: Depletion of CD4+ immunosuppressive cells using an anti-CD4 monoclonal antibody (mAb) results in a strong antitumor effect by expanding a broad variety of tumor-reactive CD8+ T cells in mice. However, the impact of CD4+ cell depletion on the immune response in cancer patients is not known. Here, we analyzed changes in the T cell receptor (TCR) repertoire of blood and tumor biopsy samples following depletion of CD4+ cells by IT1208, a defucosylated humanized anti-CD4 mAb, in a first-in-human clinical trial. Methods: Patients with advanced gastrointestinal tumors were treated with 0.1 or 1.0 mg/kg IT1208. The count and immunophenotype of peripheral blood T cells were analyzed by flow cytometry. Libraries for TCR sequencing were prepared from purified blood CD4+ and CD8+ T cells, and unfractionated tumor biopsies, collected before and after IT1208 treatment. TCR sequencing was performed using Ion Proton and Ion S5 sequencers, then changes in the repertoire, and temporal and inter-organ overlap after IT1208 treatment, were analyzed. Results: Among 11 patients enrolled in the trial, one achieved a durable partial response and two achieved stable disease lasting at least 3 months. The blood CD4+ T cell count decreased rapidly after IT1208 treatment and remained low during the observation period. In contrast, the blood CD8+ T cell count increased from day 29 after treatment compared to baseline in most patients, resulting in a remarkably decreased CD4/8 ratio. Immunohistological analysis showed a decrease of CD4+ T cells in the tumor after IT1208 treatment. In the TCR repertoire analysis, a decrease in similarity and increase in clonality were observed in blood CD4+ and CD8+ T cells after IT1208 treatment, particularly in patients receiving 1.0 mg/kg IT1208. These changes persisted to at least day 60 after treatment in some cases. Temporal tracking of the blood TCR repertoire revealed that the number of expanded CD4+ T cell clones increased in a dose-dependent manner. In addition, the number of contracted CD8+ T cell clones showed a strong correlation with the increased CD8+ T cell count and CD45RAhi CCR7- effector population among CD8+ T cells in the blood. We also analyzed blood-tumor overlapping CD8+ T cell clones to investigate changes in potential tumor-associated clones. The frequency of overlapping CD8+ T cell clones in the blood tended to increase after treatment. Interestingly, an increased frequency of these overlapping clones in the blood was associated with maximum shrinkage in the tumor diameter. Conclusion: IT1208 treatment depleted CD4+ T cells from the blood and tumor. This depletion promoted the replacement of CD4+ and CD8+ T cell repertoire systemically. The IT1208 treatment-induced increase of tumor-associated CD8+ T cell clones may be associated with its anti-tumor effect in cancer patients. Citation Format: Hiroyasu Aoki, SATOSHI UEHA, Shigeyuki Shichino, Haru Ogiwara, Kohei Shitara, Tetsuya Nakatsura, Toshihiro Suzuki, Manami Shimomura, Toshiaki Yoshikawa, Kayoko Shoda, Shigehisa Kitano, Makiko Yamashita, Takayuki Nakayama, Akihiro Sato, Sakiko Kuroda, Masashi Wakabayashi, Shogo Nomura, Shoji Yokochi, Satoru Ito, Toshihiko Doi, Kouji Matsushima. Anti-CD4 monoclonal antibody immunotherapy exerts an antitumor effect by replacing the T cell receptor repertoire in patients with gastrointestinal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-019.

7O - Deciphering the intra-tumoural T cell receptor repertoire in patients with NSCLC within the lung TRACERx study

7O - Deciphering the intra-tumoural T cell receptor repertoire in patients with NSCLC within the lung TRACERx study

Longitudinal monitoring of circulating tumor DNA and peripheral T cell repertoire in patients with small cell lung cancer.

8571 Background: Advances in the treatment of small cell lung cancer (SCLC), an aggressive disease with poor prognosis, will require the development of diagnostic methods during treatment that are more sensitive and descriptive than are currently available. The emergence of “liquid biopsy” technologies coupled with comprehensive genomic information about common mutations in SCLC prompted us to implement a blood-based assay for simultaneous sequencing of circulating, cell-free tumor DNA (cfDNA) and determination of the peripheral a and b T cell receptor repertoire in patients with SCLC. Methods: Our SCLC assay uses targeted hybrid capture and next generation sequencing of cfDNA extracted from patient plasma to detect somatic mutations in 14 frequently mutated genes in SCLC. We also sequenced rearranged T cell receptor α and β genes, each with 5000 unique α and β CDR3 open reading frames per microgram of gDNA. Over 26 months we followed 27 patients with SCLC (16 with extensive stage and 11 with limited stage disease) and examined cfDNA from 141 plasma samples and T cell repertoire from 41 samples. Results: We detected somatic, disease-associated mutations in 85% of patient samples (23/27) with allele frequencies of cfDNA ranging from ≤0.5% to ≥85%. The most commonly mutated genes were TP53 (17/27 patients) and RB1 (10/27 patients) . We detected 87 unique genomic alterations in 12 different genes (in addition to TP53 and RB1 these included PTEN, NOTCH1-4, MYC, MYCL1, PIK3CA, KIT, and BRAF). The observed mutant allele frequencies in longitudinal samples tracked with treatment response, including cases in which cfDNA allele frequencies increased before clinical evidence of relapse. Longitudinal monitoring of T cell repertoire demonstrated both variability between patients and sequential changes during therapy, including one case of decreased T cell numbers accompanying disease relapse. Conclusions: As the field of immuno-oncology matures, we anticipate that coupled determination of T cell repertoire together with cfDNA monitoring will merge into a clinically useful “molecular image” of each patient’s disease status and real-time host immune response.

[T cell receptor repertoire in patients with HBV-related hepatocellular carcinoma].

[T cell receptor repertoire in patients with HBV-related hepatocellular carcinoma].

P1202 : Definition and comparative analysis of the T cell receptor repertoire in patients with primary sclerosing cholangitis

P1202 DEFINITION AND COMPARATIVE ANALYSIS OF THE T CELL RECEPTOR REPERTOIRE IN PATIENTS WITH PRIMARY SCLEROSING CHOLANGITIS E. Liaskou, E.K. Klemsdal Henriksen, K. Holm, D. Hamm, J. Fear, M.K. Viken, J. Roksund Hov, E. Melum, H. Robins, J. Olweus, T.H. Karlsen, G.M. Hirschfield. NIHR Biomedical Research Unit and Centre for Liver Research, Institution of Biomedical Research 5th Floor, University of Birmingham, Birmingham, United Kingdom; Norwegian PSC Research Center, Department of Transplantation Medicine, Research Institute of Internal Medicine, Division of Cancer, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, K.G. Jebsen Inflammation Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Adaptive Biotechnologies Corp, Seattle, WA, United States; Institute of Immunology, Oslo University Hospital Rikshospitalet, Oslo, Norway; Fred Hutchinson Cancer Research Center, Seattle, WA, United States; Department of Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, K.G. Jebsen Center for Cancer Immunotherapy, Institute of Clinical Medicine, University of Oslo, Section of Gastroenterology, Department of Transplantation Medicine, Division of Cancer, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway E-mail: e.liaskou@bham.ac.uk

908 The effect of specific immunotherapy on T cell receptor repertoire in patients with allergy to house dust mite

908 The effect of specific immunotherapy on T cell receptor repertoire in patients with allergy to house dust mite