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Dimitriadis S, Dova L, Kotsianidis I, Hatzimichael E, Kapsali E, Markopoulos GS. Imaging Flow Cytometry: Development, Present Applications, and Future Challenges. Methods Protoc 2024; 7:28. [PMID: 38668136 PMCID: PMC11054958 DOI: 10.3390/mps7020028] [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: 01/29/2024] [Revised: 03/13/2024] [Accepted: 03/21/2024] [Indexed: 04/29/2024] Open
Abstract
Imaging flow cytometry (ImFC) represents a significant technological advancement in the field of cytometry, effectively merging the high-throughput capabilities of flow analysis with the detailed imaging characteristics of microscopy. In our comprehensive review, we adopt a historical perspective to chart the development of ImFC, highlighting its origins and current state of the art and forecasting potential future advancements. The genesis of ImFC stemmed from merging the hydraulic system of a flow cytometer with advanced camera technology. This synergistic coupling facilitates the morphological analysis of cell populations at a high-throughput scale, effectively evolving the landscape of cytometry. Nevertheless, ImFC's implementation has encountered hurdles, particularly in developing software capable of managing its sophisticated data acquisition and analysis needs. The scale and complexity of the data generated by ImFC necessitate the creation of novel analytical tools that can effectively manage and interpret these data, thus allowing us to unlock the full potential of ImFC. Notably, artificial intelligence (AI) algorithms have begun to be applied to ImFC, offering promise for enhancing its analytical capabilities. The adaptability and learning capacity of AI may prove to be essential in knowledge mining from the high-dimensional data produced by ImFC, potentially enabling more accurate analyses. Looking forward, we project that ImFC may become an indispensable tool, not only in research laboratories, but also in clinical settings. Given the unique combination of high-throughput cytometry and detailed imaging offered by ImFC, we foresee a critical role for this technology in the next generation of scientific research and diagnostics. As such, we encourage both current and future scientists to consider the integration of ImFC as an addition to their research toolkit and clinical diagnostic routine.
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Affiliation(s)
- Savvas Dimitriadis
- Hematology Laboratory, Unit of Molecular Biology and Translational Flow Cytometry, University Hospital of Ioannina, 45100 Ioannina, Greece; (S.D.); (L.D.)
| | - Lefkothea Dova
- Hematology Laboratory, Unit of Molecular Biology and Translational Flow Cytometry, University Hospital of Ioannina, 45100 Ioannina, Greece; (S.D.); (L.D.)
| | - Ioannis Kotsianidis
- Department of Hematology, University Hospital of Alexandroupolis, Democritus University of Thrace, 69100 Alexandroupolis, Greece;
| | - Eleftheria Hatzimichael
- Department of Hematology, Faculty of Medicine, University of Ioannina, 45110 Ioannina, Greece; (E.H.); (E.K.)
| | - Eleni Kapsali
- Department of Hematology, Faculty of Medicine, University of Ioannina, 45110 Ioannina, Greece; (E.H.); (E.K.)
| | - Georgios S. Markopoulos
- Hematology Laboratory, Unit of Molecular Biology and Translational Flow Cytometry, University Hospital of Ioannina, 45100 Ioannina, Greece; (S.D.); (L.D.)
- Department of Surgery, Faculty of Medicine, University of Ioannina, 45110 Ioannina, Greece
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Chen L, Tong F, Peng L, Huang Y, Yin P, Feng Y, Cheng S, Wang J, Dong X. Efficacy and safety of recombinant human endostatin combined with whole-brain radiation therapy in patients with brain metastases from non-small cell lung cancer. Radiother Oncol 2022; 174:44-51. [PMID: 35788355 DOI: 10.1016/j.radonc.2022.06.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 06/11/2022] [Accepted: 06/24/2022] [Indexed: 11/29/2022]
Abstract
BACKGROUND AND PURPOSE Brain metastasis (BM) is the leading cause of poor prognosis in non-small cell lung cancer (NSCLC) patients. To date, whole-brain radiation therapy (WBRT) is a standard treatment for patients with multiple BMs, while its effectiveness is currently unsatisfactory. This study aimed to investigate the effects of Rh-endostatin combined with WBRT on NSCLC patients with BMs. MATERIALS AND METHODS A total of 43 patients with BM were randomly divided into two groups. The Rh-endostatin combination group (n=19) received Rh-endostatin combined with WBRT, and the radiation group (n=24) received WBRT only. The primary endpoint of the study was progression-free survival (PFS), and the secondary endpoints were intracranial progression free survival (iPFS), overall survival (OS), objective response rate (ORR), and changes in the cerebral blood volume (CBV) and cerebral blood flow (CBF). RESULTS Median PFS (mPFS) was 8.1 months in the Rh-endostatin combination group and 4.9 months in the radiation group (95%CI 0.2612-0.9583, p=0·0428). Besides, the median iPFS was 11.6 months in the Rh-endostatin combination group and 4.8 months in the radiation group (95%CI 0.2530-0.9504, p=0·0437). OS was 14.2 months in the Rh-endostatin combination group and 6.4 months in the radiation group (95%CI 0.2508-1.026, p=0·0688). CBV and CBF in the Rh-endostatin combination group were better improved than that in the radiation group, which indicated that Rh-endostatin might improve local blood supply and microcirculation. CONCLUSION Rh-endostatin showed better survival and improved cerebral perfusion parameters, which may provide further insights into the application of Rh-endostatin for NSCLC patients with BMs.
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Affiliation(s)
- Lingjuan Chen
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China.
| | - Fang Tong
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China.
| | - Ling Peng
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China.
| | - Yu Huang
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Ping Yin
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China
| | - Yue Feng
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China
| | - Shishi Cheng
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Jing Wang
- Department of Radiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Hubei Province Key Laboratory of Molecular Imaging, Wuhan, China.
| | - Xiaorong Dong
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China.
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Rophina M, Pandhare K, Jadhao S, Nagaraj SH, Scaria V. BGvar: A comprehensive resource for blood group immunogenetics. Transfus Med 2021; 32:229-236. [PMID: 34897852 DOI: 10.1111/tme.12844] [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: 09/24/2021] [Revised: 11/11/2021] [Accepted: 12/01/2021] [Indexed: 11/29/2022]
Abstract
BACKGROUND Blood groups form the basis of effective and safe blood transfusion. There are about 43 well-recognised human blood group systems presently known. Blood groups are molecularly determined by the presence of specific antigens on the red blood cells and are genetically determined and inherited following Mendelian principles. The lack of a comprehensive, relevant, manually compiled and genome-ready dataset of red cell antigens limited the widespread application of genomic technologies to characterise and interpret the blood group complement of an individual from genomic datasets. MATERIALS AND METHODS A range of public datasets was used to systematically annotate the variation compendium for its functionality and allele frequencies across global populations. Details on phenotype or relevant clinical importance were collated from reported literature evidence. RESULTS We have compiled the Blood Group Associated Genomic Variant Resource (BGvar), a manually curated online resource comprising all known human blood group related allelic variants including a total of 1700 International Society of Blood Transfusion approved alleles and 1706 alleles predicted and curated from literature reports. This repository includes 1682 single nucleotide variations (SNVs), 310 Insertions, Deletions (InDels) and Duplications (Copy Number Variations) and about 1360 combination mutations corresponding to 43 human blood group systems and 2 transcription factors. This compendium also encompasses gene fusion and rearrangement events occurring in human blood group genes. CONCLUSION To the best of our knowledge, BGvar is a comprehensive and a user-friendly resource with most relevant collation of blood group alleles in humans. BGvar is accessible online at URL: http://clingen.igib.res.in/bgvar/.
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Affiliation(s)
- Mercy Rophina
- Genome Informatics and Big Data, CSIR Institute of Genomics and Integrative Biology, Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Kavita Pandhare
- Genome Informatics and Big Data, CSIR Institute of Genomics and Integrative Biology, Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Sudhir Jadhao
- Institute of Health and Biomedical Innovation and School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia.,Translational Research Institute, Brisbane, Australia
| | - Shivashankar H Nagaraj
- Institute of Health and Biomedical Innovation and School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia.,Translational Research Institute, Brisbane, Australia
| | - Vinod Scaria
- Genome Informatics and Big Data, CSIR Institute of Genomics and Integrative Biology, Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
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Sulen A, Islam S, Wolff ASB, Oftedal BE. The prospects of single-cell analysis in autoimmunity. Scand J Immunol 2020; 92:e12964. [PMID: 32869859 DOI: 10.1111/sji.12964] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 07/18/2020] [Accepted: 08/21/2020] [Indexed: 12/29/2022]
Abstract
In the last decade, there has been a tremendous development of technologies focused on analysing various molecular attributes in single cells, with an ever-increasing number of parameters becoming available at the DNA, RNA and protein levels. Much of this progress has involved cells in suspension, but also in situ analysis of tissues has taken great leaps. Paralleling the development in the laboratory, and because of increasing complexity, the analysis of single-cell data is also constantly being updated with new algorithms and analysis platforms. Our immune system shares this complexity, and immunologists have therefore been in the forefront of this technological development. These technologies clearly open new avenues for immunology research, maybe particularly within autoimmunity where the interaction between the faulty immune system and the thymus or the target organ is important. However, the technologies currently available can seem overwhelming and daunting. The aim of this review is to remedy this by giving a balanced overview of the prospects of using single-cell analysis in basal and clinical autoimmunity research, with an emphasis on endocrine autoimmunity.
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Affiliation(s)
- André Sulen
- KG Jebsen Center for Autoimmune Disorders, University of Bergen, Bergen, Norway.,Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Shahinul Islam
- KG Jebsen Center for Autoimmune Disorders, University of Bergen, Bergen, Norway.,Department of Clinical Science, University of Bergen, Bergen, Norway.,Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Anette S B Wolff
- KG Jebsen Center for Autoimmune Disorders, University of Bergen, Bergen, Norway.,Department of Clinical Science, University of Bergen, Bergen, Norway.,Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Bergithe E Oftedal
- KG Jebsen Center for Autoimmune Disorders, University of Bergen, Bergen, Norway.,Department of Clinical Science, University of Bergen, Bergen, Norway
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Baek DW, Lee JM, Kim JH, Cho HJ, Ham JY, Suh JS, Sohn SK, Moon JH. Favorable long-term survival using consolidation chemotherapy without allogeneic hematopoietic cell transplantation for acute myeloid leukemia with wild-type NPM1 without FLT3-ITD. Blood Res 2019; 54:189-197. [PMID: 31730679 PMCID: PMC6779939 DOI: 10.5045/br.2019.54.3.189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 06/09/2019] [Accepted: 06/20/2019] [Indexed: 11/17/2022] Open
Abstract
Background The role of allogeneic hematopoietic cell transplantation (allo-HCT) compared with consolidation chemotherapy alone in intermediate-risk acute myeloid leukemia (AML) patients with wild-type nucleophosmin/negative or a low level of Fms related tyrosine kinase 3 internal tandem duplication (NPM1 wt/FLT3-ITDneg/low) has not yet been elucidated. Methods In this study, we retrospectively investigated 88 patients newly diagnosed with AML who received intensive induction chemotherapy at Kyungpook National University Hospital from March 2015 to July 2017. The selection criteria included the presence of results on genetic abnormalities including NPM1 and FLT3-ITD. Results According to the European LeukemiaNet (ELN) risk classification, 25 patients (28%) were categorized as favorable, 44 (50%) as intermediate, and 19 (22%) as adverse risk. Among the intermediate-risk patients, 40 were identified as NPM1 wt/FLT3-ITDneg/low. Among the patients with NPM1 wt/FLT3-ITDneg/low, complete remission (CR) was achieved in 26 patients out of 40 (65%). One-year overall survival (OS) rate was 100% in the favorable-risk group and 87.9% in the NPM1 wt/FLT3-ITDneg/low group (P=0.233). Among the intermediate-risk NPM1 wt/FLT3-ITDneg/low patients, there was no survival benefit with allo-HCT (N=19) compared to consolidation chemotherapy (N=21; P=0.372). In the multivariate analysis, the ELN risk group [hazard ratio (HR), 6.36; P=0.019] and the achievement of CR (HR, 2.95; P=0.017) were both identified as factors affecting OS of patients with newly diagnosed AML. Conclusion Among the AML patients, intermediate-risk NPM1 wt/FLT3-ITDneg/low patients and favorable-risk patients showed similar OS rates. Our results suggested that allo-HCT might have limited clinical benefit for the intermediate-risk NPM1 wt/FLT3-ITDneg/low patients. Well controlled studies are needed to confirm the current results.
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Affiliation(s)
- Dong Won Baek
- Department of Hematology/Oncology, Kyungpook National University Hospital, School of Medicine, Kyungpook National University, Daegu, Korea
| | - Jung Min Lee
- Department of Hematology/Oncology, Kyungpook National University Hospital, School of Medicine, Kyungpook National University, Daegu, Korea
| | - Ju-Hyung Kim
- Department of Hematology/Oncology, Kyungpook National University Hospital, School of Medicine, Kyungpook National University, Daegu, Korea
| | - Hee Jeong Cho
- Department of Hematology/Oncology, Kyungpook National University Hospital, School of Medicine, Kyungpook National University, Daegu, Korea
| | - Ji-Yeon Ham
- Department of Laboratory Medicine, Kyungpook National University Hospital, School of Medicine, Kyungpook National University, Daegu, Korea
| | - Jang-Soo Suh
- Department of Laboratory Medicine, Kyungpook National University Hospital, School of Medicine, Kyungpook National University, Daegu, Korea
| | - Sang-Kyun Sohn
- Department of Hematology/Oncology, Kyungpook National University Hospital, School of Medicine, Kyungpook National University, Daegu, Korea
| | - Joon Ho Moon
- Department of Hematology/Oncology, Kyungpook National University Hospital, School of Medicine, Kyungpook National University, Daegu, Korea
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Luo J, Hu S, Wei T, Sun J, Liu N, Wang J. TGF-beta 1 levels are associated with lymphocyte percentages in patients with lung cancer treated with radiation therapy. Onco Targets Ther 2018; 11:8349-8355. [PMID: 30568457 PMCID: PMC6267770 DOI: 10.2147/ott.s175956] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Purpose Plasma TGF-β1 protein levels reportedly may predict the treatment outcomes of lung cancer. We hypothesized that in patients with lung cancer treated with radiation therapy (RT), TGF-β1 levels may correlate with the percentages of CD4+ T cells, CD8+ T cells, and the CD4+/CD8+ T cell ratio in peripheral blood. Patients and methods Eighty-two lung cancer patients satisfied the inclusion criteria. Platelet-poor plasma was obtained before RT, at the second and fourth weeks during RT, and at the end of RT (pre-, during-, and post-RT, respectively). TGF-β1 was measured via ELISA, while recording the percentages of lymphocyte subsets in peripheral blood. Short-term efficacy was categorized as complete response, partial response, stable disease, or progressive disease. Results Patients who had significantly lower TGF-β1 protein levels after RT than pre-RT seemed to have a better short-term effect (P<0.05) than those who had higher TGF-β1 levels. There was a significant association between the TGF-β1 levels and percentages of CD4+ T cells, CD8+ T cells, or CD4+/CD8+ T cell ratio during and at the end of RT. Changes in CD3+ T cells, B cells, or natural killer cells were not statistically related to the changes in TGF-β1 levels. Conclusion Lung cancer patients with TGF-β1 levels in plasma after RT that are below pre-RT levels may experience better short-term efficacy. The underlying mechanism may be related to the influence of TGF-β1 on antitumor immunity.
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Affiliation(s)
- Jing Luo
- Department of Radiation Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, .,Key Laboratory of Cancer Prevention and Therapy, .,Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China,
| | - Sainan Hu
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing 210000, China
| | - Tingting Wei
- Department of Radiation Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, .,Key Laboratory of Cancer Prevention and Therapy, .,Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China,
| | - Jifeng Sun
- Department of Radiation Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, .,Key Laboratory of Cancer Prevention and Therapy, .,Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China,
| | - Ningbo Liu
- Department of Radiation Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, .,Key Laboratory of Cancer Prevention and Therapy, .,Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China,
| | - Jun Wang
- Department of Radiation Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, .,Key Laboratory of Cancer Prevention and Therapy, .,Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China,
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Spooner W, McLaren W, Slidel T, Finch DK, Butler R, Campbell J, Eghobamien L, Rider D, Kiefer CM, Robinson MJ, Hardman C, Cunningham F, Vaughan T, Flicek P, Huntington CC. Haplosaurus computes protein haplotypes for use in precision drug design. Nat Commun 2018; 9:4128. [PMID: 30297836 PMCID: PMC6175845 DOI: 10.1038/s41467-018-06542-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 09/07/2018] [Indexed: 01/08/2023] Open
Abstract
Selecting the most appropriate protein sequences is critical for precision drug design. Here we describe Haplosaurus, a bioinformatic tool for computation of protein haplotypes. Haplosaurus computes protein haplotypes from pre-existing chromosomally-phased genomic variation data. Integration into the Ensembl resource provides rapid and detailed protein haplotypes retrieval. Using Haplosaurus, we build a database of unique protein haplotypes from the 1000 Genomes dataset reflecting real-world protein sequence variability and their prevalence. For one in seven genes, their most common protein haplotype differs from the reference sequence and a similar number differs on their most common haplotype between human populations. Three case studies show how knowledge of the range of commonly encountered protein forms predicted in populations leads to insights into therapeutic efficacy. Haplosaurus and its associated database is expected to find broad applications in many disciplines using protein sequences and particularly impactful for therapeutics design.
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Affiliation(s)
- William Spooner
- Eagle Genomics Ltd., Biodata Innovation Centre, Wellcome Genome Campus, Hinxton, Cambridge, CB10 3DR UK
- Genomics England, QMUL Dawson Hall, London, EC1M 6BQ UK
| | - William McLaren
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | | | | | - Robin Butler
- MedImmune Ltd., Granta Park, Cambridge, CB21 4QR UK
| | | | | | - David Rider
- MedImmune Ltd., Granta Park, Cambridge, CB21 4QR UK
| | | | | | | | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | | | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
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Shires K, Van Wyk T. The role of Cancer/Testis Antigens in Multiple Myeloma pathogenesis and their application in disease monitoring and therapy. Crit Rev Oncol Hematol 2018; 132:17-26. [PMID: 30447924 DOI: 10.1016/j.critrevonc.2018.09.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 08/22/2018] [Accepted: 09/12/2018] [Indexed: 12/17/2022] Open
Abstract
A unique group of genes, encoding tumour associated antigens, known as the Cancer/Testis Antigens (CTAs), have been explored as novel markers of disease progression and as targets of immunotherapy in several cancers, including the haematological malignancy Multiple Myeloma (MM). This review aims to update the knowledge of CTA involvement in MM pathogenesis and how their potential as biomarkers for disease monitoring and targets of immunotherapy has been explored in the MM disease arena. Despite the initial promise of these antigens, their use as immunotherapy targets has not been successful, yet with a greater understanding of their role in disease pathogenesis they may still have a significant role to play as biomarkers of disease and therapeutic targets.
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Affiliation(s)
- Karen Shires
- Division of Haematology, Department of Pathology, University of Cape Town and National Health Laboratory Service/Groote Schuur Hospital, Cape Town, South Africa.
| | - Teagan Van Wyk
- Department of Medicine, University of Cape Town, South Africa
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Heather JM, Ismail M, Oakes T, Chain B. High-throughput sequencing of the T-cell receptor repertoire: pitfalls and opportunities. Brief Bioinform 2018; 19:554-565. [PMID: 28077404 PMCID: PMC6054146 DOI: 10.1093/bib/bbw138] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 11/21/2016] [Indexed: 02/06/2023] Open
Abstract
T-cell specificity is determined by the T-cell receptor, a heterodimeric protein coded for by an extremely diverse set of genes produced by imprecise somatic gene recombination. Massively parallel high-throughput sequencing allows millions of different T-cell receptor genes to be characterized from a single sample of blood or tissue. However, the extraordinary heterogeneity of the immune repertoire poses significant challenges for subsequent analysis of the data. We outline the major steps in processing of repertoire data, considering low-level processing of raw sequence files and high-level algorithms, which seek to extract biological or pathological information. The latest generation of bioinformatics tools allows millions of DNA sequences to be accurately and rapidly assigned to their respective variable V and J gene segments, and to reconstruct an almost error-free representation of the non-templated additions and deletions that occur. High-level processing can measure the diversity of the repertoire in different samples, quantify V and J usage and identify private and public T-cell receptors. Finally, we discuss the major challenge of linking T-cell receptor sequence to function, and specifically to antigen recognition. Sophisticated machine learning algorithms are being developed that can combine the paradoxical degeneracy and cross-reactivity of individual T-cell receptors with the specificity of the overall T-cell immune response. Computational analysis will provide the key to unlock the potential of the T-cell receptor repertoire to give insight into the fundamental biology of the adaptive immune system and to provide powerful biomarkers of disease.
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Affiliation(s)
| | | | | | - Benny Chain
- Division of Infection and Immunity, University College of London, Bloomsbury, UK
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10
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Liu S, Zhu Y, Lin LW, Ding SK, Lin XC, Zhong KL, Pan K, Dai Y. The composition and variation of the BCR CDR3s in gastric cancer. Oncol Lett 2018; 16:239-246. [PMID: 29928407 PMCID: PMC6006485 DOI: 10.3892/ol.2018.8677] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 04/26/2018] [Indexed: 12/25/2022] Open
Abstract
Gastric cancer (GC) is the fourth most common type of cancer and the second most common cause of cancer-associated mortality worldwide. B cell-associated autoantibodies against tumor-associated antigens are attractive biomarkers for the development of noninvasive serological tests for the early detection of cancer. This is due to their specificity and stability in the sera. In the present study multiplex polymerase chain reaction and Illumina high-throughput sequencing (HTS) was used to study the composition and variation of the B cell receptor (BCR) complimentary-determining region 3 (CDR3) in GC. The peripheral blood, cancer tissues and peri-cancer tissues were included from 7 patients with GC. On average there was a total of 403,959 CDR3 sequences, with 72,367 unique CDR3 nt sequences and 61,709 unique CDR3 aa sequences per sample identified, which are critical for further understanding the BCR repertoire in GC. The details of GC CDR3s may accelerate the screening process for possible new autoantigens and may provide additional information necessary for generating effective B cell targeted diagnosis and therapeutic strategies.
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Affiliation(s)
- Song Liu
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, P.R. China
| | - Ying Zhu
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, P.R. China
| | - Lie-Wen Lin
- Department of Gastrointestinal Surgery, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, P.R. China
| | - Shun-Kai Ding
- Department of Gastrointestinal Surgery, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, P.R. China
| | - Xiao-Cong Lin
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, P.R. China
| | - Ke-Li Zhong
- Department of Gastrointestinal Surgery, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, P.R. China
| | - Kai Pan
- Department of Gastrointestinal Surgery, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, P.R. China
| | - Yong Dai
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, P.R. China
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5-Hydroxymethylcytosine correlates with epigenetic regulatory mutations, but may not have prognostic value in predicting survival in normal karyotype acute myeloid leukemia. Oncotarget 2018; 8:8305-8314. [PMID: 28039446 PMCID: PMC5352402 DOI: 10.18632/oncotarget.14171] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 11/24/2016] [Indexed: 12/18/2022] Open
Abstract
Stem cells display remarkably high levels of 5-hydroxymethylcytosine (5hmC). Both TET2 and IDH1/2 mutations can impair the production of 5hmC, thus decreasing 5hmC levels. TET2 or IDH1/2 mutations are commonly observed in acute myeloid leukemia (AML). However, the implications of 5hmC on survival in normal karyotype AML patients have not been fully evaluated. The 5hmC levels were analyzed in 375 patients using ELISA. The levels of 5hmC in DNA samples were converted to a log scale for the analysis and correlations with TET2 and/or IDH1/2 mutations were evaluated. The median 5hmC level was 0.065% (range 0.001–0.999). Mutation rates were 13.1% for TET2mut, 6.7% for IDH1mut, and 13.9% for IDH2mut. The prevalence of TET2 and/or IDH1/2 was 33.1% (124/375). TET2 and IDH1/2 mutated patients had significantly lower levels of log(5hmC) compared with patients without TET2 or IDH1/2 mutations (p<0.001). With a median follow-up of 55.5 months (range, 0.7–179.8), there was no significant difference in overall survival, event-free survival, and relapse risk according to TET2mut or IDH1/2mut (all, p>0.05). To identify its prognostic value, we sub-classified the levels of 5hmC into tertiles for 5hmC values. However, there was no significant association between the categories of 5hmC levels and survival or relapse risk (all p>0.05). Patients with TET2 or IDH1/2 mutations had lower levels of 5hmC. The 5hmC levels may not be predictive of survival in patients with normal karyotype AML.
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12
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He L, Wang J, Chang D, Lv D, Li H, Zhang H. Clinical value of Pro-GRP and T lymphocyte subpopulation for the assessment of immune functions of lung cancer patients after DC-CIK biological therapy. Exp Ther Med 2018; 15:1580-1585. [PMID: 29399130 DOI: 10.3892/etm.2017.5520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 07/11/2017] [Indexed: 11/05/2022] Open
Abstract
The present study investigated the aptness of assessing the levels of progastrin-releasing peptide (Pro-GRP) in addition to the T lymphocyte subpopulation in lung cancer patients prior to and after therapy for determining immune function. A total of 45 patients with lung cancer were recruited and stratified in to a non-small cell lung cancer (NSCLC) and an SCLC group. Prior to and after treatment by combined biological therapy comprising chemotherapy or chemoradiotherapy followed by three cycles of retransformation of autologous dendritic cells-cytokine-induced killer cells (DC-CIK), the peripheral blood was assessed for populations of CD3+, CD4+, CD8+ and regulatory T cells (Treg) by flow cytometry, and for the levels of pro-GRP, carcinoembryonic antigen, neuron-specific enolase and Cyfra 21-1. The results revealed that in NSCLC patients, CD8+ T lymphocytes and Treg populations were decreased, and that CD3+ and CD4+ T lymphocytes as well as the CD4+/CD8+ ratio were increased after therapy; in SCLC patients, CD3+, CD4+ and CD8+ T lymphocytes were increased, while Treg cells were decreased after treatment compared with those at baseline. In each group, Pro-GRP was decreased compared with that prior to treatment, and in the SCLC group only, an obvious negative correlation was identified between Pro-GRP and the T lymphocyte subpopulation. Furthermore, a significant correlation between Pro-GRP and Tregs was identified in each group. In conclusion, the present study revealed that the immune function of the patients was improved after biological therapy. The results suggested a significant correlation between Pro-GRP and the T lymphocyte subpopulation in SCLC patients. Detection of Pro-GRP may assist the early clinical diagnosis of SCLC and may also be used to assess the immune regulatory function of patients along with the T lymphocyte subpopulation. Biological therapy with retransformed autologous DC-CIK was indicated to enhance the specific elimination of tumor cells and improve the immune surveillance function in cancer patients, and also restrained the immune evasion of the tumor, leading to decreased Pro-GRP levels.
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Affiliation(s)
- Lijie He
- Department of T Lymphocyte Subpopulation, Tianjin Fifth Central Hospital, Tianjin 300450, P.R. China
| | - Jing Wang
- Department of Immunologic Function, Tianjin Fifth Central Hospital, Tianjin 300450, P.R. China
| | - Dandan Chang
- Department of Immunologic Function, Tianjin Fifth Central Hospital, Tianjin 300450, P.R. China
| | - Dandan Lv
- Department of Biological Therapy, Tianjin Fifth Central Hospital, Tianjin 300450, P.R. China
| | - Haina Li
- Department of Biological Therapy, Tianjin Fifth Central Hospital, Tianjin 300450, P.R. China
| | - Heping Zhang
- Department of Biological Therapy, Tianjin Fifth Central Hospital, Tianjin 300450, P.R. China
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13
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Maniangou B, Retière C, Gagne K. Next-generation sequencing technology a new tool for killer cell immunoglobulin-like receptor allele typing in hematopoietic stem cell transplantation. Transfus Clin Biol 2018; 25:87-89. [DOI: 10.1016/j.tracli.2017.07.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 07/20/2017] [Indexed: 12/26/2022]
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14
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Shin SY, Lee ST, Kim HJ, Cho EH, Kim JW, Park S, Jung CW, Kim SH. Mutation profiling of 19 candidate genes in acute myeloid leukemia suggests significance of DNMT3A mutations. Oncotarget 2018; 7:54825-54837. [PMID: 27359055 PMCID: PMC5342384 DOI: 10.18632/oncotarget.10240] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 05/13/2016] [Indexed: 11/25/2022] Open
Abstract
We selected 19 significantly-mutated genes in AMLs, including FLT3, DNMT3A, NPM1, TET2, RUNX1, CEBPA, WT1, IDH1, IDH2, NRAS, ASXL1, SETD2, PTPN11, TP53, KIT, JAK2, KRAS, BRAF and CBL, and performed massively parallel sequencing for 114 patients with acute myeloid leukemias, mainly including those with normal karyotypes (CN-AML). More than 80% of patients had at least one mutation in the genes tested. DNMT3A mutation was significantly associated with adverse outcome in addition to conventional risk stratification such as the European LeukemiaNet (ELN) classification. We observed clinical usefulness of mutation testing on multiple target genes and the association with disease subgroups, clinical features and prognosis in AMLs.
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Affiliation(s)
- Sang-Yong Shin
- Department of Laboratory Medicine, Center for Diagnostic Oncology, Hospital and Research Institute, National Cancer Center, Goyang, Korea
| | - Seung-Tae Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Hee-Jin Kim
- Department of Laboratory Medicine & Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | | | - Jong-Won Kim
- Department of Laboratory Medicine & Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Silvia Park
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Chul Won Jung
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Sun-Hee Kim
- Department of Laboratory Medicine & Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
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15
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Li Q, Zhou J, Cao X, Liu Q, Li Q, Li W, Wang X. Clonal Characteristics of T-Cell Receptor Repertoires in Violent and Non-violent Patients With Schizophrenia. Front Psychiatry 2018; 9:403. [PMID: 30233426 PMCID: PMC6127418 DOI: 10.3389/fpsyt.2018.00403] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 08/09/2018] [Indexed: 01/28/2023] Open
Abstract
Background: Activated or impaired T-cell function in inflammatory and degenerative process can contribute to the risk and progression of schizophrenia. This study used immune repertoire sequencing to investigate the T-cell receptor beta variable chain (TRBV) presence in blood mononuclear cells in the violent or non-violent schizophrenic patients. Methods: Ten violent and 10 non-violent schizophrenic patients and 8 matched healthy controls were enrolled. The Brief Psychiatric Rating Scale (BPRS) was used to evaluate patients' psychiatric symptoms. The level of aggression was assessed using the Modified Overt Aggression Scale (MOAS). The complementarity-determining region 3 (CDR3) of TRBV was detected using multiplex-PCR and high-throughput sequencing. Results: The TCR repertoire diversity were no significant differences in the Shannon-Wiener or inverse Simpson diversity index between three groups. Principal component analysis (PCA) of TRBV composition and abundance showed that principal component 1 and principal component 2 can explain 28.88 and 13.24% of total variation, respectively. Schizophrenic patients (violent and non-violent) had significantly different V gene distribution compared to healthy controls. In particular, TRBV2 occurred at a significantly higher frequency in the violent schizophrenia group than in the non-violent schizophrenia and healthy control groups, and TRBV7-2 occurred at a significantly higher frequency in the non-violent schizophrenia group than in the violent schizophrenia and healthy control groups. Conclusions: The results suggest that violent and non-violent schizophrenic patients carry abnormal T-cell receptor repertoires, and these data provide a useful clue to explore the etiology of violent behavior in schizophrenia.
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Affiliation(s)
- Qiguang Li
- Department of Psychiatry and Mental Health Institute of the Second Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center on Mental Disorders and National Technology Institute on Mental Disorders, Hunan Key Laboratory of Psychiatry and Mental Health, Changsha, China
| | - Jiansong Zhou
- Department of Psychiatry and Mental Health Institute of the Second Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center on Mental Disorders and National Technology Institute on Mental Disorders, Hunan Key Laboratory of Psychiatry and Mental Health, Changsha, China
| | - Xia Cao
- Department of Health Management Center, Third Xiangya Hospital, Central South University, Changsha, China
| | - Qiang Liu
- Department of Surgery, Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, China
| | - Qi Li
- Department of Psychiatry, State Key Laboratory for Cognitive and Brain Sciences, HKU-SIRI, University of Hong Kong, Hong Kong, China
| | - Wen Li
- Department of Psychiatry and Mental Health Institute of the Second Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center on Mental Disorders and National Technology Institute on Mental Disorders, Hunan Key Laboratory of Psychiatry and Mental Health, Changsha, China
| | - Xiaoping Wang
- Department of Psychiatry and Mental Health Institute of the Second Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center on Mental Disorders and National Technology Institute on Mental Disorders, Hunan Key Laboratory of Psychiatry and Mental Health, Changsha, China
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16
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Oftedal BE, Ardesjö Lundgren B, Hamm D, Gan PY, Holdsworth SR, Hahn CN, Schreiber AW, Scott HS. T cell receptor assessment in autoimmune disease requires access to the most adjacent immunologically active organ. J Autoimmun 2017; 81:24-33. [DOI: 10.1016/j.jaut.2017.03.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 02/28/2017] [Accepted: 03/06/2017] [Indexed: 01/22/2023]
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17
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Maniangou B, Legrand N, Alizadeh M, Guyet U, Willem C, David G, Charpentier E, Walencik A, Retière C, Gagne K. Killer Immunoglobulin-Like Receptor Allele Determination Using Next-Generation Sequencing Technology. Front Immunol 2017; 8:547. [PMID: 28579987 PMCID: PMC5437120 DOI: 10.3389/fimmu.2017.00547] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 04/24/2017] [Indexed: 02/05/2023] Open
Abstract
The impact of natural killer (NK) cell alloreactivity on hematopoietic stem cell transplantation (HSCT) outcome is still debated due to the complexity of graft parameters, HLA class I environment, the nature of killer cell immunoglobulin-like receptor (KIR)/KIR ligand genetic combinations studied, and KIR+ NK cell repertoire size. KIR genes are known to be polymorphic in terms of gene content, copy number variation, and number of alleles. These allelic polymorphisms may impact both the phenotype and function of KIR+ NK cells. We, therefore, speculate that polymorphisms may alter donor KIR+ NK cell phenotype/function thus modulating post-HSCT KIR+ NK cell alloreactivity. To investigate KIR allele polymorphisms of all KIR genes, we developed a next-generation sequencing (NGS) technology on a MiSeq platform. To ensure the reliability and specificity of our method, genomic DNA from well-characterized cell lines were used; high-resolution KIR typing results obtained were then compared to those previously reported. Two different bioinformatic pipelines were used allowing the attribution of sequencing reads to specific KIR genes and the assignment of KIR alleles for each KIR gene. Our results demonstrated successful long-range KIR gene amplifications of all reference samples using intergenic KIR primers. The alignment of reads to the human genome reference (hg19) using BiRD pipeline or visualization of data using Profiler software demonstrated that all KIR genes were completely sequenced with a sufficient read depth (mean 317× for all loci) and a high percentage of mapping (mean 93% for all loci). Comparison of high-resolution KIR typing obtained to those published data using exome capture resulted in a reported concordance rate of 95% for centromeric and telomeric KIR genes. Overall, our results suggest that NGS can be used to investigate the broad KIR allelic polymorphism. Hence, these data improve our knowledge, not only on KIR+ NK cell alloreactivity in HSCT but also on the role of KIR+ NK cell populations in control of viral infections and diseases.
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Affiliation(s)
- Bercelin Maniangou
- Etablissement Français du Sang Pays de la Loire, Nantes, France.,CRCINA, INSERM U1232 CNRS, Université d'Angers, Université de Nantes, Nantes, France
| | - Nolwenn Legrand
- Etablissement Français du Sang Pays de la Loire, Nantes, France.,CRCINA, INSERM U1232 CNRS, Université d'Angers, Université de Nantes, Nantes, France
| | - Mehdi Alizadeh
- Laboratoire de Recherche et Développement, EFS Rennes, Rennes, France
| | - Ulysse Guyet
- L'institut du thorax, INSERM, CNRS, UNIV Nantes, Nantes, France
| | - Catherine Willem
- Etablissement Français du Sang Pays de la Loire, Nantes, France.,CRCINA, INSERM U1232 CNRS, Université d'Angers, Université de Nantes, Nantes, France
| | - Gaëlle David
- Etablissement Français du Sang Pays de la Loire, Nantes, France.,CRCINA, INSERM U1232 CNRS, Université d'Angers, Université de Nantes, Nantes, France
| | | | | | - Christelle Retière
- Etablissement Français du Sang Pays de la Loire, Nantes, France.,CRCINA, INSERM U1232 CNRS, Université d'Angers, Université de Nantes, Nantes, France
| | - Katia Gagne
- Etablissement Français du Sang Pays de la Loire, Nantes, France.,CRCINA, INSERM U1232 CNRS, Université d'Angers, Université de Nantes, Nantes, France.,Laboratoire d'Histocompatibilité, EFS Nantes, Nantes, France.,LabeX Transplantex, Université de Strasbourg, Strasbourg, France
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18
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Lubin IM, Aziz N, Babb LJ, Ballinger D, Bisht H, Church DM, Cordes S, Eilbeck K, Hyland F, Kalman L, Landrum M, Lockhart ER, Maglott D, Marth G, Pfeifer JD, Rehm HL, Roy S, Tezak Z, Truty R, Ullman-Cullere M, Voelkerding KV, Worthey EA, Zaranek AW, Zook JM. Principles and Recommendations for Standardizing the Use of the Next-Generation Sequencing Variant File in Clinical Settings. J Mol Diagn 2017; 19:417-426. [PMID: 28315672 DOI: 10.1016/j.jmoldx.2016.12.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 12/05/2016] [Accepted: 12/23/2016] [Indexed: 11/30/2022] Open
Abstract
A national workgroup convened by the Centers for Disease Control and Prevention identified principles and made recommendations for standardizing the description of sequence data contained within the variant file generated during the course of clinical next-generation sequence analysis for diagnosing human heritable conditions. The specifications for variant files were initially developed to be flexible with regard to content representation to support a variety of research applications. This flexibility permits variation with regard to how sequence findings are described and this depends, in part, on the conventions used. For clinical laboratory testing, this poses a problem because these differences can compromise the capability to compare sequence findings among laboratories to confirm results and to query databases to identify clinically relevant variants. To provide for a more consistent representation of sequence findings described within variant files, the workgroup made several recommendations that considered alignment to a common reference sequence, variant caller settings, use of genomic coordinates, and gene and variant naming conventions. These recommendations were considered with regard to the existing variant file specifications presently used in the clinical setting. Adoption of these recommendations is anticipated to reduce the potential for ambiguity in describing sequence findings and facilitate the sharing of genomic data among clinical laboratories and other entities.
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Affiliation(s)
- Ira M Lubin
- Division of Laboratory Systems, Centers for Disease Control and Prevention, Atlanta, Georgia.
| | - Nazneen Aziz
- College of American Pathologists, Chicago, Illinois; Kaiser Permanente Research Bank, Oakland, California
| | - Lawrence J Babb
- Partners Healthcare Personalized Medicine, Cambridge, Massachusetts; GeneInsight, a Sunquest Company, Boston, Massachusetts
| | | | - Himani Bisht
- Center for Devices and Radiological Health, US Food and Drug Administration, Silver Spring, Maryland
| | - Deanna M Church
- Personalis, Menlo Park, California; National Center for Biotechnology Information, NIH, Bethesda, Maryland; 10× Genomics, Pleasanton, California
| | | | - Karen Eilbeck
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah
| | | | - Lisa Kalman
- Division of Laboratory Systems, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Melissa Landrum
- National Center for Biotechnology Information, NIH, Bethesda, Maryland
| | - Edward R Lockhart
- Division of Laboratory Systems, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Donna Maglott
- National Center for Biotechnology Information, NIH, Bethesda, Maryland
| | - Gabor Marth
- Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, Utah; Boston College, Chestnut Hill, Massachusetts
| | - John D Pfeifer
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
| | - Heidi L Rehm
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Somak Roy
- Division of Molecular and Genomic Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Zivana Tezak
- Center for Devices and Radiological Health, US Food and Drug Administration, Silver Spring, Maryland
| | - Rebecca Truty
- Complete Genomics, Mountain View, California; Invitae Corporation, San Francisco, California
| | | | - Karl V Voelkerding
- Department of Pathology, University of Utah and the Institute for Clinical and Experimental Pathology, Associated Regional and University Pathologists Laboratories, Salt Lake City, Utah
| | - Elizabeth A Worthey
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Alexander W Zaranek
- Personal Genome Project, Harvard Medical School, Boston, Massachusetts; Curoverse, Inc., Somerville, Massachusetts
| | - Justin M Zook
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland
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19
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A preliminary evaluation of next-generation sequencing as a screening tool for targeted genotyping of erythrocyte and platelet antigens in blood donors. BLOOD TRANSFUSION = TRASFUSIONE DEL SANGUE 2017; 16:285-292. [PMID: 28287381 DOI: 10.2450/2017.0253-16] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 11/16/2016] [Indexed: 01/11/2023]
Abstract
BACKGROUND Matching the compatibility of donor blood with the recipient's antigens prevents alloimmunisation. Next-generation sequencing (NGS) technology is a promising method for extensive blood group and platelet antigen genotyping of blood donors. It circumvents the limitations of detecting known alleles based on predefined polymorphisms and enables targeted sequencing on a massive scale. The aim of this study was to evaluate the NGS AmpliSeq application on the Ion Torrent platform as a screening tool for genotyping blood donors' erythrocyte/platelet antigens. MATERIALS AND METHODS Primers for regions encoding antigens RhD (exons 5, 7), Rhc, RhE/e, Fya/b, Jka/b, M/N, S/s, HPA-1, 2, 3, 5, 15 were designed with Ion AmpliSeq Designer with manual inclusion of RHCE*C primers. DNA libraries of 57 regular blood donors with determined phenotype/genotype (prepared using the Ion AmpliSeq Library Kit and 14 primer pairs) were sequenced on the Ion Torrent PGM using 316v2 chips and 200 bp chemistry. RESULTS Sequencing was successful in all but the MN and HPA-5 regions. Mean sequencing coverage in one experiment was 4,606 reads, except for the RHCE*C region (mean 568 reads). NGS results agreed with the known phenotype/genotype of donors except in one phenotypically Fy(a+b-) case in whom FY*A/FY*B alleles were found. Reading rates for homozygotes were 97-100%, while they were around 50% for heterozygotes. NGS of RHD regions led to identification of mutations in two RhD negative donors. DISCUSSION NGS can be performed as a screening test to determine erythrocyte/platelet antigens in blood donors. This method allowed testing of 48 donors for 14 features (200 bp long) with the depth of a few thousand reads simultaneously, and the estimation of natural chimerism or hemi/homozygotic status. NGS screening can be adjusted to the genetic background of a given tested population.
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20
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Liu S, Hou XL, Sui WG, Lu QJ, Hu YL, Dai Y. Direct measurement of B-cell receptor repertoire's composition and variation in systemic lupus erythematosus. Genes Immun 2017; 18:22-27. [PMID: 28053320 DOI: 10.1038/gene.2016.45] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 10/30/2016] [Accepted: 11/01/2016] [Indexed: 01/11/2023]
Abstract
Systemic lupus erythematosus (SLE) is a systemic autoimmune disease that is known to be associated with polyclonal B-cell hyper-reactivity. B-cell receptor (BCR) has a central role in B-cell development, activation, survival and apoptosis, and thus is a critical component of the regulation of both protective and autoreactive B cells. In this study, we applied multiplex PCR and Illumina high-throughput sequencing to study the composition and variation of the BCRs in peripheral blood mononuclear cells from SLE patients and healthy donors (NC). We found that SLE group displayed significantly shorter CDR3 average length (14.86±0.76aa vs 15.70±0.43aa), more arginine percentage of CDR3 amino acids (7.57±0.20% vs 7.32±0.19%) and poorer immunological diversity than the healthy ones. CDR3 sequence YGMDV present in all SLE samples may provide more information in generating more effective B-cell targeted diagnosis/therapies strategies.
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Affiliation(s)
- S Liu
- Department of Clinical Medical Research, The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Shenzhen, China
| | - X L Hou
- Nephrology Department of Guilin 181st Hospital, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin, China
| | - W G Sui
- Nephrology Department of Guilin 181st Hospital, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin, China
| | - Q J Lu
- Department of Dermatology, Second Xiangya Hospital, Central South University, Hunan Key Laboratory of Medical Epigenomics, Changsha, China
| | - Y L Hu
- Department of Cancer Research, Shenzhen University, Shenzhen, China.,Department of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Y Dai
- Department of Clinical Medical Research, The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Shenzhen, China
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21
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Xu L, You X, Zheng P, Zhang BM, Gupta PK, Lavori P, Meyer E, Zehnder JL. Methodologic Considerations in the Application of Next-Generation Sequencing of Human TRB Repertoires for Clinical Use. J Mol Diagn 2016; 19:72-83. [PMID: 27815002 DOI: 10.1016/j.jmoldx.2016.07.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 06/24/2016] [Accepted: 07/28/2016] [Indexed: 01/08/2023] Open
Abstract
Next-generation sequencing (NGS) of immune receptors has become a standard tool to assess minimal residual disease (MRD) in patients treated for lymphoid malignancy, and it is being used to study the T-cell repertoire in many clinical settings. To better understanding the potential clinical utility and limitations of this application outside of MRD, we developed a BIOMED-2 primer-based NGS method and characterized its performance in controls and patients with graft-versus-host disease (GVHD) after allogeneic hematopoietic transplant. For controls and patients with GVHD, replicate sequencing of the same T-cell receptor β (TRB) libraries was highly reproducible. Higher variability was observed in sequencing of different TRB libraries made from the same DNA stock. Variability was increased in patients with GVHD compared with controls; patients with GVHD also had lower diversity than controls. In the T-cell repertoire of a healthy person, approximately 99.6% of the CDR3 clones were in low abundance, with frequency <10-3. A single library could identify >93% of the clones with frequency ≥10-3 in the repertoire. Sequencing in duplicate increased the average detection rate to >97%. This work demonstrates that NGS reliably and robustly characterizes TRB populations in healthy individuals and patients with GVHD with frequency ≥10-3 and provides a methodologic framework for applying NGS immune repertoire methods to clinical testing applications beyond MRD.
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Affiliation(s)
- Liwen Xu
- Department of Pathology, Stanford School of Medicine, Stanford University, Stanford, California
| | - Xiaoqing You
- Department of Pathology, Stanford School of Medicine, Stanford University, Stanford, California
| | - PingPing Zheng
- Division of Blood and Marrow Transplantation, Department of Medicine, Stanford School of Medicine, Stanford University, Stanford, California
| | - Bing M Zhang
- Department of Pathology, Stanford School of Medicine, Stanford University, Stanford, California
| | - Puja K Gupta
- Division of Blood and Marrow Transplantation, Department of Medicine, Stanford School of Medicine, Stanford University, Stanford, California
| | - Philip Lavori
- Department of Biomedical Data Science, Stanford School of Medicine, Stanford University, Stanford, California
| | - Everett Meyer
- Division of Blood and Marrow Transplantation, Department of Medicine, Stanford School of Medicine, Stanford University, Stanford, California
| | - James L Zehnder
- Department of Pathology, Stanford School of Medicine, Stanford University, Stanford, California.
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22
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Han Y, Li H, Guan Y, Huang J. Immune repertoire: A potential biomarker and therapeutic for hepatocellular carcinoma. Cancer Lett 2016; 379:206-12. [DOI: 10.1016/j.canlet.2015.06.022] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 06/29/2015] [Accepted: 06/30/2015] [Indexed: 12/27/2022]
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23
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Kohrt HE, Tumeh PC, Benson D, Bhardwaj N, Brody J, Formenti S, Fox BA, Galon J, June CH, Kalos M, Kirsch I, Kleen T, Kroemer G, Lanier L, Levy R, Lyerly HK, Maecker H, Marabelle A, Melenhorst J, Miller J, Melero I, Odunsi K, Palucka K, Peoples G, Ribas A, Robins H, Robinson W, Serafini T, Sondel P, Vivier E, Weber J, Wolchok J, Zitvogel L, Disis ML, Cheever MA. Immunodynamics: a cancer immunotherapy trials network review of immune monitoring in immuno-oncology clinical trials. J Immunother Cancer 2016; 4:15. [PMID: 26981245 PMCID: PMC4791805 DOI: 10.1186/s40425-016-0118-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 02/15/2016] [Indexed: 12/26/2022] Open
Abstract
The efficacy of PD-1/PD-L1 targeted therapies in addition to anti-CTLA-4 solidifies immunotherapy as a modality to add to the anticancer arsenal. Despite raising the bar of clinical efficacy, immunologically targeted agents raise new challenges to conventional drug development paradigms by highlighting the limited relevance of assessing standard pharmacokinetics (PK) and pharmacodynamics (PD). Specifically, systemic and intratumoral immune effects have not consistently correlated with standard relationships between systemic dose, toxicity, and efficacy for cytotoxic therapies. Hence, PK and PD paradigms remain inadequate to guide the selection of doses and schedules, both starting and recommended Phase 2 for immunotherapies. The promise of harnessing the immune response against cancer must also be considered in light of unique and potentially serious toxicities. Refining immune endpoints to better inform clinical trial design represents a high priority challenge. The Cancer Immunotherapy Trials Network investigators review the immunodynamic effects of specific classes of immunotherapeutic agents to focus immune assessment modalities and sites, both systemic and importantly intratumoral, which are critical to the success of the rapidly growing field of immuno-oncology.
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Affiliation(s)
- Holbrook E Kohrt
- Division of Oncology, Stanford Cancer Institute, Stanford University Medical Center, 269 Campus Drive, CCSR 1105, Stanford, CA 94305-5151 USA
| | - Paul C Tumeh
- Division of Dermatology, Department of Medicine, University of California Los Angeles, Los Angeles, CA USA
| | - Don Benson
- Division of Hematology/Oncology, Ohio State University, Columbus, OH USA
| | - Nina Bhardwaj
- Medicine, Hematology and Medical Oncology, Mount Sinai Hospital, New York, NY USA
| | - Joshua Brody
- Medicine, Hematology and Medical Oncology, Mount Sinai Hospital, Ruttenberg Treatment Center, New York, NY USA
| | - Silvia Formenti
- Department of Radiation Oncology, New York Weill Cornell Medical Center, New York, NY USA
| | - Bernard A Fox
- SOM-Molecular Microbiology & Immunology Department, Laboratory of Molecular and Tumor Immunology, OHSU Cancer Institute, Portland, OR USA
| | - Jerome Galon
- INSERM, Integrative Cancer Immunology Team, Cordeliers Research Center, Paris, France
| | - Carl H June
- Perelman School of Medicine, University of Pennsylvania, Pathology and Laboratory Medicine, Philadelphia, PA USA
| | - Michael Kalos
- Cancer Immunobiology, Eli Lilly & Company, New York, NY USA
| | - Ilan Kirsch
- Translational Medicine, Adaptive Biotechnologies Corp, Seattle, WA USA
| | - Thomas Kleen
- Immune Monitoring, Epiontis GmbH, Berlin, Germany
| | - Guido Kroemer
- Faculty of Medicine, University of Paris Descartes, Paris, France
| | - Lewis Lanier
- Department of Microbiology and Immunology, University of California, San Francisco, CA USA
| | - Ron Levy
- Division of Oncology, Stanford School of Medicine, Stanford, CA USA
| | - H Kim Lyerly
- Duke University School of Medicine, Durham, NC USA
| | - Holden Maecker
- Human Immune Monitoring Center Shared Resource, Stanford Cancer Institute, Stanford, CA USA
| | | | - Jos Melenhorst
- Product Development and Correlative Sciences, Smilow Center for Translational Research, Philadelphia, PA USA
| | - Jeffrey Miller
- Division of Hematology, Experimental Therapeutics, University of Minnesota, Oncology and Transplantation, Minneapolis, MN USA
| | - Ignacio Melero
- Centro de Investigacion Medica Aplicada, Universidad de Navarra, Avda. Pamplona, Spain
| | - Kunle Odunsi
- Center for Immunotherapy, Roswell Park Cancer Institute, Buffalo, NY USA
| | | | - George Peoples
- Cancer Vaccine Development Program, Brooke Army Medical Center, Houston, TX USA
| | - Antoni Ribas
- Tumor Immunology Program Area, Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA USA
| | | | - William Robinson
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA USA
| | | | - Paul Sondel
- Cellular & Molecular Pathology Graduate Program, University of Wisconsin-Madison, Madison, WI USA
| | - Eric Vivier
- Centre d'Immunologie de Marseille-Luminy, Marseille, France
| | | | - Jedd Wolchok
- Immunology Program, Memorial Sloan-Kettering Cancer Center, New York, NY USA
| | - Laurence Zitvogel
- Institut National de la Santé et Recherche Médicale, Institut GrustaveRoussy, Villejuif, France
| | - Mary L Disis
- Tumor Vaccine Group, University of Washington, Seattle, WA USA
| | - Martin A Cheever
- Fred Hutchinson Cancer Research Center, 1100 Eastlake Ave N., E3-300, PO Box 19024, Seattle, WA 98109-1023 USA
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Ahn JS, Kim HJ, Kim YK, Lee SS, Jung SH, Yang DH, Lee JJ, Kim NY, Choi SH, Jung CW, Jang JH, Kim HJ, Moon JH, Sohn SK, Won JH, Kim SH, Kim DDH. DNMT3A R882 Mutation with FLT3-ITD Positivity Is an Extremely Poor Prognostic Factor in Patients with Normal-Karyotype Acute Myeloid Leukemia after Allogeneic Hematopoietic Cell Transplantation. Biol Blood Marrow Transplant 2016; 22:61-70. [DOI: 10.1016/j.bbmt.2015.07.030] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 07/28/2015] [Indexed: 12/17/2022]
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Wang J, Li T, Zhou M, Hu Z, Zhou X, Zhou S, Wang N, Huang L, Zhao L, Cao Y, Xiao M, Ma D, Zhou P, Shang Z, Zhou J. TALENs-mediated gene disruption of FLT3 in leukemia cells: Using genome-editing approach for exploring the molecular basis of gene abnormality. Sci Rep 2015; 5:18454. [PMID: 26669855 PMCID: PMC4680874 DOI: 10.1038/srep18454] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 11/17/2015] [Indexed: 12/11/2022] Open
Abstract
Novel analytic tools are needed to elucidate the molecular basis of leukemia-relevant gene mutations in the post-genome era. We generated isogenic leukemia cell clones in which the FLT3 gene was disrupted in a single allele using TALENs. Isogenic clones with mono-allelic disrupted FLT3 were compared to an isogenic wild-type control clone and parental leukemia cells for transcriptional expression, downstream FLT3 signaling and proliferation capacity. The global gene expression profiles of mutant K562 clones and corresponding wild-type controls were compared using RNA-seq. The transcriptional levels and the ligand-dependent autophosphorylation of FLT3 were decreased in the mutant clones. TALENs-mediated FLT3 haplo-insufficiency impaired cell proliferation and colony formation in vitro. These inhibitory effects were maintained in vivo, improving the survival of NOD/SCID mice transplanted with mutant K562 clones. Cluster analysis revealed that the gene expression pattern of isogenic clones was determined by the FLT3 mutant status rather than the deviation among individual isogenic clones. Differentially expressed genes between the mutant and wild-type clones revealed an activation of nonsense-mediated decay pathway in mutant K562 clones as well as an inhibited FLT3 signaling. Our data support that this genome-editing approach is a robust and generally applicable platform to explore the molecular bases of gene mutations.
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Affiliation(s)
- Jue Wang
- Department of hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Tongjuan Li
- Department of hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Mi Zhou
- Department of hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Zheng Hu
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xiaoxi Zhou
- Department of hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Shiqiu Zhou
- Department of hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Na Wang
- Department of hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Liang Huang
- Department of hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Lei Zhao
- Department of hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yang Cao
- Department of hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Min Xiao
- Department of hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Ding Ma
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Pengfei Zhou
- Wuhan YZY Bio-Pharma Co., Ltd., Wuhan, Hubei, China
| | - Zhen Shang
- Department of hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jianfeng Zhou
- Department of hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
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26
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Alexander T, Bondanza A, Muraro PA, Greco R, Saccardi R, Daikeler T, Kazmi M, Hawkey C, Simoes BP, Leblanc K, Fibbe WE, Moore J, Snarski E, Martin T, Hiepe F, Velardi A, Toubert A, Snowden JA, Farge D. SCT for severe autoimmune diseases: consensus guidelines of the European Society for Blood and Marrow Transplantation for immune monitoring and biobanking. Bone Marrow Transplant 2014; 50:173-80. [PMID: 25387090 PMCID: PMC4317973 DOI: 10.1038/bmt.2014.251] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 09/01/2014] [Indexed: 12/19/2022]
Abstract
Over the past 15 years, SCT has emerged as a promising treatment option for patients with severe autoimmune diseases (ADs). Mechanistic studies recently provided the proof-of-concept that restoration of immunological tolerance can be achieved by haematopoietic SCT in chronic autoimmunity through eradication of the pathologic, immunologic memory and profound reconfiguration of the immune system, that is, immune ‘resetting'. Nevertheless, a number of areas remain unresolved and warrant further investigation to refine our understanding of the underlying mechanisms of action and to optimize clinical SCT protocols. Due to the low number of patients transplanted in each centre, it is essential to adequately collect and analyse biological samples in a larger cohort of patients under standardized conditions. The European society for blood and marrow transplantation Autoimmune Diseases and Immunobiology Working Parties have, therefore, undertaken a joint initiative to develop and implement guidelines for ‘good laboratory practice' in relation to procurement, processing, storage and analysis of biological specimens for immune reconstitution studies in AD patients before, during and after SCT. The aim of this document is to provide practical recommendations for biobanking of samples and laboratory immune monitoring in patients with ADs undergoing SCT, both for routine supportive care purposes and investigational studies.
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Affiliation(s)
- T Alexander
- Department of Rheumatology and Clinical Immunology, Charité-University Medicine Berlin, Berlin, Germany
| | - A Bondanza
- Hematology and Bone Marrow Transplantation Unit, San Raffaele Scientific Institute, Milano, Italy
| | - P A Muraro
- Division of Brain Sciences, Department of Medicine, Imperial College London, London, UK
| | - R Greco
- Hematology and Bone Marrow Transplantation Unit, San Raffaele Scientific Institute, Milano, Italy
| | - R Saccardi
- Cord Blood Bank, Haematology department, Careggi University Hospital, Florence, Italy
| | - T Daikeler
- Department of Rheumatology, University Hospital Basel, Basel, Switzerland
| | - M Kazmi
- Department of Haematology, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - C Hawkey
- Nottingham Digestive Diseases Centre, Nottingham, UK
| | - B P Simoes
- Department of Clinical Medicine, School of Medicine, University of Sao Paulo, Ribeirao Preto, Brazil
| | - K Leblanc
- Department of Hematology, Karolinska University Hospital, Stockholm, Sweden
| | - W E Fibbe
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Centre, Leiden, The Netherlands
| | - J Moore
- Department of Haematology, St Vincent's Hospital, Darlinghurst, Sydney, Australia
| | - E Snarski
- Department of Hematology, Oncology and Internal Diseases, Medical University of Warsaw, Warsaw, Poland
| | - T Martin
- Strasbourg University Hospital, Strasbourg, France
| | - F Hiepe
- Department of Rheumatology and Clinical Immunology, Charité-University Medicine Berlin, Berlin, Germany
| | - A Velardi
- Department of Medicine, Division of Haematology, University of Perugia, Perugia, Italy
| | - A Toubert
- Inserm U1160, Université Paris Diderot, Sorbonne Paris Cité, AP-HP, Hôpital Saint-Louis, Laboratoire d'Immunologie, Paris, France
| | - J A Snowden
- Department of Haematology, Sheffield Teaching Hospitals NHS Foundation Trust & University of Sheffield, Sheffield, UK
| | - D Farge
- Saint Louis Hospital, Unité de Médecine interne et Pathologie Vasculaire, Assistance Publique des Hôpitaux de Paris, Paris 7 University, INSERM U1160, Paris, France
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Liu Z, Liu M, Mercado T, Illoh O, Davey R. Extended blood group molecular typing and next-generation sequencing. Transfus Med Rev 2014; 28:177-86. [PMID: 25280589 DOI: 10.1016/j.tmrv.2014.08.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 08/11/2014] [Accepted: 08/25/2014] [Indexed: 02/09/2023]
Abstract
Several high-throughput multiplex blood group molecular typing platforms have been developed to predict blood group antigen phenotypes. These molecular systems support extended donor/patient matching by detecting commonly encountered blood group polymorphisms as well as rare alleles that determine the expression of blood group antigens. Extended molecular typing of a large number of blood donors by high-throughput platforms can increase the likelihood of identifying donor red blood cells that match those of recipients. This is especially important in the management of multiply-transfused patients who may have developed several alloantibodies. Nevertheless, current molecular techniques have limitations. For example, they detect only predefined genetic variants. In contrast, target enrichment next-generation sequencing (NGS) is an emerging technology that provides comprehensive sequence information, focusing on specified genomic regions. Target enrichment NGS is able to assess genetic variations that cannot be achieved by traditional Sanger sequencing or other genotyping platforms. Target enrichment NGS has been used to detect both known and de novo genetic polymorphisms, including single-nucleotide polymorphisms, indels (insertions/deletions), and structural variations. This review discusses the methodology, advantages, and limitations of the current blood group genotyping techniques and describes various target enrichment NGS approaches that can be used to develop an extended blood group genotyping assay system.
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Affiliation(s)
- Zhugong Liu
- Division of Blood Components and Devices, Office of Blood Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD.
| | - Meihong Liu
- Division of Blood Components and Devices, Office of Blood Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD
| | - Teresita Mercado
- Division of Blood Components and Devices, Office of Blood Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD
| | - Orieji Illoh
- Division of Blood Components and Devices, Office of Blood Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD
| | - Richard Davey
- Division of Blood Components and Devices, Office of Blood Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD
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28
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Engel-Nitz NM, Eckert B, Song R, Koka P, Hulbert EM, McPheeters J, Teitelbaum A. Diagnostic testing managed by hematopathology specialty and other laboratories: costs and patient diagnostic outcomes. BMC Clin Pathol 2014; 14:17. [PMID: 24817828 PMCID: PMC4016629 DOI: 10.1186/1472-6890-14-17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Accepted: 04/17/2014] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Successful management of patients with hematologic malignancies depends upon accurate and timely diagnosis, which frequently requires integration and interpretation of multiple tests. Our retrospective analysis compared diagnostic uncertainty, resource utilization, and costs for patients with diagnostic bone marrow (BM) tests managed by commercial laboratories. METHODS Patients with BM biopsies and suspected hematologic cancer/condition were identified from claims (2005-2011) within a large US health plan (coverage ≥6 pre- and ≥3-months post-biopsy). Cohorts defined by laboratories performing BM morphologic assessment/directing testing sequence: Genoptix (GX, specialty hematology-testing laboratory), large commercial laboratories (LL), other laboratories (OL). One-year post-biopsy changes in diagnosis or treatments, tests performed, and diagnostic/treatment medical costs (measured as per-patient-per-month [PPPM]) were examined. RESULTS The study population included 1,387 GX, 4,162 LL, and 19,115 OL patients with suspected hematologic malignancy/disease and BM morphology assessment. GX had lower diagnostic uncertainty measured between 2 time periods by diagnostic stability (no conditions the same; 6.16% GX, 8.04% LL, 9.73% OL; p < 0.001) and changes (≥1 condition different; 7.88% GX, 11.19% LL, and 14.08% OL; p < 0.001), fewer repeat BM biopsies, and fewer chemotherapy changes (30-days and 60-days post-initiation). One-year PPPM costs adjusted for patient characteristics differences were $8,202 GX, $7,711 LL, and $10,302 OL (p < 0.05); adjusted PPPM costs (excluding testing period) were $6,019 GX, $6,649 LL, and $7,801 OL (p < 0.05). CONCLUSIONS Our data suggests that a hematopathology specialty laboratory may result in earlier final diagnosis, fewer subsequent diagnosis changes, reduced need for follow-on testing requiring repeat biopsy procedures, and may result in lower downstream healthcare costs. Further evaluations using medical chart abstractions or registries will be valuable.
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Affiliation(s)
- Nicole M Engel-Nitz
- Optum, Eden Prairie, MN, USA
- Health Economics and Outcomes Research, Optum, 12125 Technology Drive, Eden Prairie, MN 53344, USA
| | - Benjamin Eckert
- Novartis Molecular Diagnostics, Cambridge, MA, USA
- Present address Metamark Genetics, Cambridge, MA, USA
| | | | | | | | | | - April Teitelbaum
- Optum, Eden Prairie, MN, USA
- Present address Heme Onc Associates, Carlsbad, CA, USA
- AHT BioPharma Advisory Services, Carlsbad, CA, USA
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29
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Mardis ER. The translation of cancer genomics: time for a revolution in clinical cancer care. Genome Med 2014; 6:22. [PMID: 25031616 PMCID: PMC4062062 DOI: 10.1186/gm539] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The introduction of next-generation sequencing technologies has dramatically impacted the life sciences, perhaps most profoundly in the area of cancer genomics. Clinical applications of next-generation sequencing and associated methods are emerging from ongoing large-scale discovery projects that have catalogued hundreds of genes as having a role in cancer susceptibility, onset and progression. For example, discovery cancer genomics has confirmed that many of the same genes are altered by mutation, copy number gain or loss, or structural variation across multiple tumor types, resulting in a gain or loss of function that likely contributes to cancer development in these tissues. Beyond these frequently mutated genes, we now know there is a 'long tail' of less frequently mutated, but probably important, genes that play roles in cancer onset or progression. Here, I discuss some of the remaining barriers to clinical translation, and look forward to new applications of these technologies in cancer care.
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Affiliation(s)
- Elaine R Mardis
- The Genome Institute, Washington University School of Medicine, 4444 Forest Park Blvd, St Louis, MO 63108, USA
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