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Huang J, Mao L, Lei Q, Guo AY. Bioinformatics tools and resources for cancer and application. Chin Med J (Engl) 2024; 137:2052-2064. [PMID: 39075637 PMCID: PMC11374212 DOI: 10.1097/cm9.0000000000003254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Indexed: 07/31/2024] Open
Abstract
ABSTRACT Tumor bioinformatics plays an important role in cancer research and precision medicine. The primary focus of traditional cancer research has been molecular and clinical studies of a number of fundamental pathways and genes. In recent years, driven by breakthroughs in high-throughput technologies, large-scale cancer omics data have accumulated rapidly. How to effectively utilize and share these data is particularly important. To address this crucial task, many computational tools and databases have been developed over the past few years. To help researchers quickly learn and understand the functions of these tools, in this review, we summarize publicly available bioinformatics tools and resources for pan-cancer multi-omics analysis, regulatory analysis of tumorigenesis, tumor treatment and prognosis, immune infiltration analysis, immune repertoire analysis, cancer driver gene and driver mutation analysis, and cancer single-cell analysis, which may further help researchers find more suitable tools for their research.
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Affiliation(s)
- Jin Huang
- Department of Thoracic Surgery, West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Lingzi Mao
- Hubei Bioinformatics & Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Qian Lei
- Department of Thoracic Surgery, West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - An-Yuan Guo
- Department of Thoracic Surgery, West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
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Mullan KA, Zhang JB, Jones CM, Goh SJ, Revote J, Illing PT, Purcell AW, La Gruta NL, Li C, Mifsud NA. TCR_Explore: A novel webtool for T cell receptor repertoire analysis. Comput Struct Biotechnol J 2023; 21:1272-1282. [PMID: 36814721 PMCID: PMC9939424 DOI: 10.1016/j.csbj.2023.01.046] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 01/31/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
T cells expressing either alpha-beta or gamma-delta T cell receptors (TCR) are critical sentinels of the adaptive immune system, with receptor diversity being essential for protective immunity against a broad array of pathogens and agents. Programs available to profile TCR clonotypic signatures can be limiting for users with no coding expertise. Current analytical pipelines can be inefficient due to manual processing steps, open to data entry errors and have multiple analytical tools with unique inputs that require coding expertise. Here we present a bespoke webtool designed for users irrespective of coding expertise, coined 'TCR_Explore', enabling analysis either derived via Sanger sequencing or next generation sequencing (NGS) platforms. Further, TCR_Explore incorporates automated quality control steps for Sanger sequencing. The creation of flexible and publication ready figures are enabled for different sequencing platforms following universal conversion to the TCR_Explore file format. TCR_Explore will enhance a user's capacity to undertake in-depth TCR repertoire analysis of both new and pre-existing datasets for identification of T cell clonotypes associated with health and disease. The web application is located at https://tcr-explore.erc.monash.edu for users to interactively explore TCR repertoire datasets.
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Affiliation(s)
- Kerry A. Mullan
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia,Corresponding authors.
| | - Justin B. Zhang
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
| | - Claerwen M. Jones
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
| | - Shawn J.R. Goh
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
| | - Jerico Revote
- Monash eResearch Centre, Monash University, Melbourne, VIC 3800, Australia
| | - Patricia T. Illing
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
| | - Anthony W. Purcell
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
| | - Nicole L. La Gruta
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
| | - Chen Li
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
| | - Nicole A. Mifsud
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia,Corresponding authors.
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Peng K, Moore J, Vahed M, Brito J, Kao G, Burkhardt AM, Alachkar H, Mangul S. pyTCR: A comprehensive and scalable solution for TCR-Seq data analysis to facilitate reproducibility and rigor of immunogenomics research. Front Immunol 2022; 13:954078. [PMID: 36451811 PMCID: PMC9704496 DOI: 10.3389/fimmu.2022.954078] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 10/05/2022] [Indexed: 01/29/2023] Open
Abstract
T cell receptor (TCR) studies have grown substantially with the advancement in the sequencing techniques of T cell receptor repertoire sequencing (TCR-Seq). The analysis of the TCR-Seq data requires computational skills to run the computational analysis of TCR repertoire tools. However biomedical researchers with limited computational backgrounds face numerous obstacles to properly and efficiently utilizing bioinformatics tools for analyzing TCR-Seq data. Here we report pyTCR, a computational notebook-based solution for comprehensive and scalable TCR-Seq data analysis. Computational notebooks, which combine code, calculations, and visualization, are able to provide users with a high level of flexibility and transparency for the analysis. Additionally, computational notebooks are demonstrated to be user-friendly and suitable for researchers with limited computational skills. Our tool has a rich set of functionalities including various TCR metrics, statistical analysis, and customizable visualizations. The application of pyTCR on large and diverse TCR-Seq datasets will enable the effective analysis of large-scale TCR-Seq data with flexibility, and eventually facilitate new discoveries.
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Affiliation(s)
- Kerui Peng
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA, United States
| | - Jaden Moore
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA, United States,Computer Science Department, Orange Coast College, Costa Mesa, CA, United States
| | - Mohammad Vahed
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA, United States
| | - Jaqueline Brito
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA, United States
| | - Guoyun Kao
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, United States
| | - Amanda M. Burkhardt
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA, United States
| | - Houda Alachkar
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA, United States
| | - Serghei Mangul
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA, United States,*Correspondence: Serghei Mangul,
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Kockelbergh H, Evans S, Deng T, Clyne E, Kyriakidou A, Economou A, Luu Hoang KN, Woodmansey S, Foers A, Fowler A, Soilleux EJ. Utility of Bulk T-Cell Receptor Repertoire Sequencing Analysis in Understanding Immune Responses to COVID-19. Diagnostics (Basel) 2022; 12:1222. [PMID: 35626377 PMCID: PMC9140453 DOI: 10.3390/diagnostics12051222] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/09/2022] [Accepted: 05/10/2022] [Indexed: 01/27/2023] Open
Abstract
Measuring immunity to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 19 (COVID-19), can rely on antibodies, reactive T cells and other factors, with T-cell-mediated responses appearing to have greater sensitivity and longevity. Because each T cell carries an essentially unique nucleic acid sequence for its T-cell receptor (TCR), we can interrogate sequence data derived from DNA or RNA to assess aspects of the immune response. This review deals with the utility of bulk, rather than single-cell, sequencing of TCR repertoires, considering the importance of study design, in terms of cohort selection, laboratory methods and analysis. The advances in understanding SARS-CoV-2 immunity that have resulted from bulk TCR repertoire sequencing are also be discussed. The complexity of sequencing data obtained by bulk repertoire sequencing makes analysis challenging, but simple descriptive analyses, clonal analysis, searches for specific sequences associated with immune responses to SARS-CoV-2, motif-based analyses, and machine learning approaches have all been applied. TCR repertoire sequencing has demonstrated early expansion followed by contraction of SARS-CoV-2-specific clonotypes, during active infection. Maintenance of TCR repertoire diversity, including the maintenance of diversity of anti-SARS-CoV-2 response, predicts a favourable outcome. TCR repertoire narrowing in severe COVID-19 is most likely a consequence of COVID-19-associated lymphopenia. It has been possible to follow clonotypic sequences longitudinally, which has been particularly valuable for clonotypes known to be associated with SARS-CoV-2 peptide/MHC tetramer binding or with SARS-CoV-2 peptide-induced cytokine responses. Closely related clonotypes to these previously identified sequences have been shown to respond with similar kinetics during infection. A possible superantigen-like effect of the SARS-CoV-2 spike protein has been identified, by means of observing V-segment skewing in patients with severe COVID-19, together with structural modelling. Such a superantigen-like activity, which is apparently absent from other coronaviruses, may be the basis of multisystem inflammatory syndrome and cytokine storms in COVID-19. Bulk TCR repertoire sequencing has proven to be a useful and cost-effective approach to understanding interactions between SARS-CoV-2 and the human host, with the potential to inform the design of therapeutics and vaccines, as well as to provide invaluable pathogenetic and epidemiological insights.
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Affiliation(s)
- Hannah Kockelbergh
- Department of Health Data Science, Institute of Population Health, University of Liverpool, Liverpool L69 3GF, UK;
| | - Shelley Evans
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK; (S.E.); (T.D.); (E.C.); (K.N.L.H.); (S.W.)
| | - Tong Deng
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK; (S.E.); (T.D.); (E.C.); (K.N.L.H.); (S.W.)
| | - Ella Clyne
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK; (S.E.); (T.D.); (E.C.); (K.N.L.H.); (S.W.)
| | - Anna Kyriakidou
- School of Clinical Medicine, University of Cambridge, Cambridge CB2 1QP, UK; (A.K.); (A.E.)
| | - Andreas Economou
- School of Clinical Medicine, University of Cambridge, Cambridge CB2 1QP, UK; (A.K.); (A.E.)
| | - Kim Ngan Luu Hoang
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK; (S.E.); (T.D.); (E.C.); (K.N.L.H.); (S.W.)
| | - Stephen Woodmansey
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK; (S.E.); (T.D.); (E.C.); (K.N.L.H.); (S.W.)
- Department of Respiratory Medicine, University Hospitals of Morecambe Bay, Kendal LA9 7RG, UK
| | - Andrew Foers
- Kennedy Institute of Rheumatology, University of Oxford, Oxford OX3 7YF, UK;
| | - Anna Fowler
- Department of Health Data Science, Institute of Population Health, University of Liverpool, Liverpool L69 3GF, UK;
| | - Elizabeth J. Soilleux
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK; (S.E.); (T.D.); (E.C.); (K.N.L.H.); (S.W.)
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Ysebaert L, Quillet-Mary A, Tosolini M, Pont F, Laurent C, Fournié JJ. Lymphoma Heterogeneity Unraveled by Single-Cell Transcriptomics. Front Immunol 2021; 12:597651. [PMID: 33732232 PMCID: PMC7959738 DOI: 10.3389/fimmu.2021.597651] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 01/18/2021] [Indexed: 12/12/2022] Open
Abstract
High-definition transcriptomic studies through single-cell RNA sequencing (scRNA-Seq) have revealed the heterogeneity and functionality of the various microenvironments across numerous solid tumors. Those pioneer studies have highlighted different cellular signatures correlated with clinical response to immune checkpoint inhibitors. scRNA-Seq offers also a unique opportunity to unravel the intimate heterogeneity of the ecosystems across different lymphoma entities. In this review, we will first cover the basics and future developments of the technology, and we will discuss its input in the field of translational lymphoma research, from determination of cell-of-origin and functional diversity, to monitoring of anti-cancer targeted drugs response and toxicities, and how new improvements in both data collection and interpretation will further foster precision medicine in the upcoming years.
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Affiliation(s)
- Loic Ysebaert
- Centre de Recherches en Cancérologie de Toulouse, INSERM UMR1037, Toulouse, France.,Toulouse University, Toulouse, France.,ERL 5294 CNRS, Toulouse, France.,Institut Universitaire du Cancer-Oncopole, Toulouse, France.,Laboratoire d'Excellence 'TOUCAN', Toulouse, France.,Institut Carnot Lymphome CALYM, Lyon, France.,Service d'Hématologie, CHU Toulouse, Toulouse, France
| | - Anne Quillet-Mary
- Centre de Recherches en Cancérologie de Toulouse, INSERM UMR1037, Toulouse, France.,Toulouse University, Toulouse, France.,ERL 5294 CNRS, Toulouse, France.,Institut Universitaire du Cancer-Oncopole, Toulouse, France.,Laboratoire d'Excellence 'TOUCAN', Toulouse, France.,Institut Carnot Lymphome CALYM, Lyon, France
| | - Marie Tosolini
- Centre de Recherches en Cancérologie de Toulouse, INSERM UMR1037, Toulouse, France.,Toulouse University, Toulouse, France.,ERL 5294 CNRS, Toulouse, France.,Institut Universitaire du Cancer-Oncopole, Toulouse, France.,Laboratoire d'Excellence 'TOUCAN', Toulouse, France.,Institut Carnot Lymphome CALYM, Lyon, France
| | - Frederic Pont
- Centre de Recherches en Cancérologie de Toulouse, INSERM UMR1037, Toulouse, France.,Institut Carnot Lymphome CALYM, Lyon, France
| | - Camille Laurent
- Centre de Recherches en Cancérologie de Toulouse, INSERM UMR1037, Toulouse, France.,Toulouse University, Toulouse, France.,ERL 5294 CNRS, Toulouse, France.,Institut Universitaire du Cancer-Oncopole, Toulouse, France.,Laboratoire d'Excellence 'TOUCAN', Toulouse, France.,Institut Carnot Lymphome CALYM, Lyon, France.,Laboratoire d'anatomo-pathologie, CHU Toulouse, Toulouse, France
| | - Jean-Jacques Fournié
- Centre de Recherches en Cancérologie de Toulouse, INSERM UMR1037, Toulouse, France.,Toulouse University, Toulouse, France.,ERL 5294 CNRS, Toulouse, France.,Institut Universitaire du Cancer-Oncopole, Toulouse, France.,Laboratoire d'Excellence 'TOUCAN', Toulouse, France.,Institut Carnot Lymphome CALYM, Lyon, France
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