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Recipient-specific T-cell repertoire reconstitution in the gut following murine hematopoietic cell transplant. Blood Adv 2021; 4:4232-4243. [PMID: 32898248 DOI: 10.1182/bloodadvances.2019000977] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 06/27/2020] [Indexed: 01/12/2023] Open
Abstract
Graft-versus-host disease (GVHD) is a complication of hematopoietic cell transplantation (HCT) caused by alloreactive T cells. Murine models of HCT are used to understand GVHD and T-cell reconstitution in GVHD target organs, most notably the gastrointestinal (GI) tract where the disease contributes most to patient mortality. T-cell receptor (TCR) repertoire sequencing was used to measure T-cell reconstitution from the same donor graft (C57BL/6 H-2b) in the GI tract of different recipients across a spectrum of matching, from syngeneic (C57BL/6), to minor histocompatibility (MHC) antigen mismatch BALB.B (H-2b), to major MHC mismatched B10.BR (H-2k) and BALB/c (H-2d). Although the donor T-cell pools had highly similar TCR, the TCR repertoire after HCT was very specific to recipients in each experiment independent of geography. A single invariant natural killer T clone was identifiable in every recipient group and was enriched in syngeneic recipients according to clonal count and confirmatory flow cytometry. Using a novel cluster analysis of the TCR repertoire, we could classify recipient groups based only on their CDR3 size distribution or TCR repertoire relatedness. Using a method for evaluating the contribution of common TCR motifs to relatedness, we found that reproducible sets of clones were associated with specific recipient groups within each experiment and that relatedness did not necessarily depend on the most common clones in allogeneic recipients. This finding suggests that TCR reconstitution is highly stochastic and likely does not depend on the evaluation of the most expanded TCR clones in any individual recipient but instead depends on a complex polyclonal architecture.
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Correia RP, Puga RD, Muto NH, Lee MLDM, Torres DC, Hassan R, Bacal NS, Hamerschlak N, Campregher PV. High-throughput sequencing of immunoglobulin heavy chain for minimal residual disease detection in B-lymphoblastic leukemia. Int J Lab Hematol 2021; 43:724-731. [PMID: 33393719 DOI: 10.1111/ijlh.13453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 11/24/2020] [Accepted: 12/17/2020] [Indexed: 11/30/2022]
Abstract
INTRODUCTION Minimal residual disease (MRD) is a cornerstone for stratification of upfront B-lymphoblastic leukemia (B-ALL) treatment protocols to decrease relapse risk. Although its detection by flow cytometry (FC) and real-time quantitative polymerase has clinical usefulness, evidence suggests that methods with increased sensitivity could lead to improved outcomes. The aim of this study was to develop an amplicon-based assay followed by high-throughput sequencing of the immunoglobulin heavy chain variable region for MRD detection in B-ALL. METHODS We analyzed 84 samples, 27 from diagnosis, 5 from relapse, 40 from post-treatment samples, and 12 from healthy controls. RESULTS Our assay was able to identify more neoplastic clones at diagnosis than Sanger sequencing including incomplete DJ rearrangements. From the 40 MRD samples evaluated 21 were positive by our new approach on high-throughput sequencing assay, but only 15 of these were positive by FC. The remaining 19 were negative by the two techniques. CONCLUSION We have developed a novel approach on high-sensitive assay for MRD detection in B-ALL, which could add clinical value in the management of patients, especially in cases negative for MRD by FC.
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Affiliation(s)
- Rodolfo P Correia
- Departments of Clinical Pathology Laboratory, Hematology and Hemotherapy, Research Institute, Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Renato D Puga
- Departments of Clinical Pathology Laboratory, Hematology and Hemotherapy, Research Institute, Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Nair H Muto
- Departments of Clinical Pathology Laboratory, Hematology and Hemotherapy, Research Institute, Hospital Israelita Albert Einstein, São Paulo, Brazil
| | | | - Davi C Torres
- Bone Marrow Transplantation Center, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Rocio Hassan
- Bone Marrow Transplantation Center, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Nydia S Bacal
- Departments of Clinical Pathology Laboratory, Hematology and Hemotherapy, Research Institute, Hospital Israelita Albert Einstein, São Paulo, Brazil.,Centro de Hematologia de São Paulo, São Paulo, Brazil
| | - Nelson Hamerschlak
- Departments of Clinical Pathology Laboratory, Hematology and Hemotherapy, Research Institute, Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Paulo V Campregher
- Departments of Clinical Pathology Laboratory, Hematology and Hemotherapy, Research Institute, Hospital Israelita Albert Einstein, São Paulo, Brazil
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Shah O, Tamaresis JS, Kenyon LJ, Xu L, Zheng P, Gupta P, Rangarajan K, Lee S, Spellman S, Nikiforow S, Zehnder J, Meyer EH. Analysis of the Whole CDR3 T Cell Receptor Repertoire after Hematopoietic Stem Cell Transplantation in 2 Clinical Cohorts. Biol Blood Marrow Transplant 2020; 26:1050-1070. [PMID: 32081787 DOI: 10.1016/j.bbmt.2020.01.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 01/12/2020] [Accepted: 01/27/2020] [Indexed: 01/19/2023]
Abstract
A major cause of morbidity and mortality for patients who undergo hematologic stem cell transplantation (HSCT) is acute graft-versus-host disease (aGVHD), a mostly T cell-mediated disease. Examination of the T cell receptor (TCR) repertoire of HSCT recipients and the use of next-generation nucleotide sequencing have raised the question of whether features of TCR repertoire reconstitution might reproducibly associate with aGVHD. We hypothesized that the peripheral blood TCR repertoire of patients with steroid-nonresponsive aGVHD would be less diverse. We also hypothesized that patients with GVHD who shared HLA might also share common clones at the time of GVHD diagnosis, thereby potentially providing potential clinical indicators for treatment stratification. We further hypothesized that HSCT recipients with the same HLA mismatch might share a more similar TCR repertoire based on a potentially shared focus of alloreactive responses. We studied 2 separate patient cohorts and 2 separate platforms for measuring TCR repertoire. The first cohort of patients was from a multicenter Phase III randomized double-blinded clinical trial of patients who developed aGVHD (NCT01002742). The second cohort comprised samples from biobanks from 2 transplantation centers and the Center for International Blood and Marrow Transplant Research of patients who underwent mismatched HSCT. There were no statistically significant differences in the TCR diversity of steroid responders and nonresponders among patients with aGVHD on the day of diagnosis. Most clones in the repertoire were unique to each patient, but a small number of clones were found to be both exclusive to and shared among aGVHD nonresponders. We were also able to show a strong correlation between the presence of Vβ20 and Vβ29 and steroid responsiveness. Using the Bhattacharya coefficient, those patients who shared the same HLA mismatch were shown to be no more similar to one another than to those who had a completely different mismatch. Using 2 separate clinical cohorts and 2 separate platforms for analyzing the TCR repertoire, we have shown that the sampled human TCR repertoire is largely unique to each patient but contains glimmers of common clones of subsets of clones based on responsiveness to steroids in aGVHD on the day of diagnosis. These studies are informative for future strategies to assess for reproducible TCR responses in human alloreactivity and possible markers of GVHD responsiveness to therapy.
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Affiliation(s)
- Omid Shah
- Division of Blood and Marrow Transplantation, Stanford University School of Medicine, Stanford, California
| | - John S Tamaresis
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, California
| | - Laura Jean Kenyon
- Division of Blood and Marrow Transplantation, Stanford University School of Medicine, Stanford, California
| | - Liwen Xu
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Pingping Zheng
- Division of Blood and Marrow Transplantation, Stanford University School of Medicine, Stanford, California
| | - Puja Gupta
- Division of Blood and Marrow Transplantation, Stanford University School of Medicine, Stanford, California
| | - Krish Rangarajan
- Division of Blood and Marrow Transplantation, Stanford University School of Medicine, Stanford, California
| | - Stephanie Lee
- Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Stephen Spellman
- National Marrow Donor Program/C Center for International Blood and Marrow Transplant Research, Minneapolis, Minnesota
| | | | - James Zehnder
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Everett H Meyer
- Division of Blood and Marrow Transplantation, Stanford University School of Medicine, Stanford, California.
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Walia R, Yeung CCS. An Update on Molecular Biology of Cutaneous T Cell Lymphoma. Front Oncol 2020; 9:1558. [PMID: 32039026 PMCID: PMC6987372 DOI: 10.3389/fonc.2019.01558] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 12/23/2019] [Indexed: 12/21/2022] Open
Abstract
Cutaneous T cell lymphomas represent a heterogenous group of lymphoproliferative disorders defined by clonal proliferation of T cells present in the skin. The latest WHO classification in 2016 and WHO-EORTC classification in 2018 has updated the classification of these entities based on the molecular profile. Research in the field of molecular genetics of CTCL has allowed a better understanding of the biology of these tumors and has helped to identify potential targets for therapy that can be tailored to individual patients. In this review, we discuss the latest developments in the molecular profile of CTCLs including biomarkers for diagnosis, prognosis, and potential therapeutic targets. We have also touched upon the utility of various molecular diagnostic modalities. For the purpose of this review, we researched papers in PubMed indexed journals in English literature published in the past 20 years using keywords CTCL, mycosis fungoides, molecular profile, molecular diagnosis, whole genome profile, genomic landscape, TCR clonality.
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Affiliation(s)
- Ritika Walia
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Cecilia C S Yeung
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States.,Department of Pathology, University of Washington, Seattle, WA, United States
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Miyasaka A, Yoshida Y, Wang T, Takikawa Y. Next-generation sequencing analysis of the human T-cell and B-cell receptor repertoire diversity before and after hepatitis B vaccination. Hum Vaccin Immunother 2019; 15:2738-2753. [PMID: 30945971 PMCID: PMC6930056 DOI: 10.1080/21645515.2019.1600987] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The hepatitis B (HB) vaccine effectively prevents the incidence of hepatitis B virus (HBV) infection. However, vaccine failure occurs in 5-10% of the recipients. The precise mechanisms leading to responsiveness to the HB vaccine are poorly understood. High-throughput sequencing (HTS) may help clarify the immune response to the HB vaccine, so we applied this method to investigate whether the HB vaccine induced a specific change in the T-cell receptor (TCR) and B-cell receptor (BCR) repertoires. We conducted HTS of the TCR β chain and BCR IgG heavy (H) chain complementary determining region 3 (CDR3) repertoires in five volunteers before and after the second and third immunizations with the HB vaccine. The HB surface antibody (HBsAb) levels were >10 mIU/ml after the third vaccination in all five participants. The TCR β chain CDR3 repertoire diversity significantly increased, while the BCR IgG H chain CDR3 repertoire diversity significantly decreased after the second vaccination. Although there was no marked inter-individual variation in terms of the numbers of unique reads, it is possible that the TCR β chain and BCR IgG H chain CDR3 repertoires may have changed within the same numbers of unique reads. Our data failed to identify the specific dominant clones that responded to the HB vaccine. In summary, the TCR β chain CDR3 repertoire diversity significantly increased, while the BCR IgG H chain CDR3 repertoire diversity significantly decreased, after the second HB vaccination. These diversity changes might be associated with a better response to the HB vaccine.
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Affiliation(s)
- Akio Miyasaka
- Division of Hepatology, Department of Internal Medicine, Iwate Medical University School of Medicine, Morioka, Japan
| | - Yuichi Yoshida
- Division of Hepatology, Department of Internal Medicine, Iwate Medical University School of Medicine, Morioka, Japan
| | - Ting Wang
- Division of Hepatology, Department of Internal Medicine, Iwate Medical University School of Medicine, Morioka, Japan
| | - Yasuhiro Takikawa
- Division of Hepatology, Department of Internal Medicine, Iwate Medical University School of Medicine, Morioka, Japan
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Zhang H, Zhang BM, Guo X, Xu L, You X, West RB, Bussel JB, Zehnder JL. Blood transcriptome and clonal T-cell correlates of response and non-response to eltrombopag therapy in a cohort of patients with chronic immune thrombocytopenia. Haematologica 2019; 105:e129-e132. [PMID: 31296576 DOI: 10.3324/haematol.2019.226688] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- Haiyu Zhang
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Bing M Zhang
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Xiangqian Guo
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA.,Department of Preventive Medicine, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Liwen Xu
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Xiaoqing You
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Robert B West
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - James B Bussel
- Platelet Disorders Center, Department of Pediatrics, Weill-Cornell Medicine, New York, NY, USA
| | - James L Zehnder
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
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Tang W, Zhou T, Zhong Z, Zhong H. Meta-analysis of associations of vascular endothelial growth factor protein levels and -634G/C polymorphism with systemic lupus erythematosus susceptibility. BMC MEDICAL GENETICS 2019; 20:46. [PMID: 30902069 PMCID: PMC6431013 DOI: 10.1186/s12881-019-0783-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 03/12/2019] [Indexed: 02/06/2023]
Abstract
BACKGROUND The purpose of this study was to detect the effects of vascular endothelial growth factor (VEGF) on systemic lupus erythematosus (SLE) risk. METHODS Associated studies were extracted from the China Biological Medicine Database (CBM), and PubMed on June 10, 2018, and applicable investigations were pooled and analyzed by meta-analysis using RevMan 5.3. RESULTS VEGF levels was associated with SLE risk (mean differences (MD) =196.02, 95% CI: 135.29-256.75, P < 0.00001), and VEGF levels was associated with active SLE risk (MD =77.51, 95% CI: 10.98-144.05, P = 0.02). We also found that VEGF levels was associated with SLE developing into lupus nephritis (LN) risk (MD =223.16, 95% CI: 144.38-301.93, P < 0.00001). However, VEGF -634G/C gene polymorphism (rs2010963) was not associated with SLE risk. CONCLUSIONS VEGF levels was associated with SLE risk, active SLE risk and SLE developing into LN risk. However, there was no an association between VEGF -634G/C gene polymorphism and SLE risk.
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Affiliation(s)
- Wenzhuang Tang
- Department of Blood Purification, the First Affiliated Hospital of Hainan Medical College, Haikou, China
| | - Tianbiao Zhou
- Department of Nephrology, the Second Affiliated Hospital, Shantou University Medical College, No. 69 Dongsha Road, Shantou, 515041 China
| | - Zhiqing Zhong
- Department of Nephrology, the Second Affiliated Hospital, Shantou University Medical College, No. 69 Dongsha Road, Shantou, 515041 China
| | - Hongzhen Zhong
- Department of Nephrology, the Second Affiliated Hospital, Shantou University Medical College, No. 69 Dongsha Road, Shantou, 515041 China
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Clinical utility of recently identified diagnostic, prognostic, and predictive molecular biomarkers in mature B-cell neoplasms. Mod Pathol 2017; 30:1338-1366. [PMID: 28664939 DOI: 10.1038/modpathol.2017.58] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 04/25/2017] [Accepted: 04/26/2017] [Indexed: 12/18/2022]
Abstract
Genomic profiling studies have provided new insights into the pathogenesis of mature B-cell neoplasms and have identified markers with prognostic impact. Recurrent mutations in tumor-suppressor genes (TP53, BIRC3, ATM), and common signaling pathways, such as the B-cell receptor (CD79A, CD79B, CARD11, TCF3, ID3), Toll-like receptor (MYD88), NOTCH (NOTCH1/2), nuclear factor-κB, and mitogen activated kinase signaling, have been identified in B-cell neoplasms. Chronic lymphocytic leukemia/small lymphocytic lymphoma, diffuse large B-cell lymphoma, follicular lymphoma, mantle cell lymphoma, Burkitt lymphoma, Waldenström macroglobulinemia, hairy cell leukemia, and marginal zone lymphomas of splenic, nodal, and extranodal types represent examples of B-cell neoplasms in which novel molecular biomarkers have been discovered in recent years. In addition, ongoing retrospective correlative and prospective outcome studies have resulted in an enhanced understanding of the clinical utility of novel biomarkers. This progress is reflected in the 2016 update of the World Health Organization classification of lymphoid neoplasms, which lists as many as 41 mature B-cell neoplasms (including provisional categories). Consequently, molecular genetic studies are increasingly being applied for the clinical workup of many of these neoplasms. In this review, we focus on the diagnostic, prognostic, and/or therapeutic utility of molecular biomarkers in mature B-cell neoplasms.
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