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Angius A, Scanu AM, Arru C, Muroni MR, Carru C, Porcu A, Cossu-Rocca P, De Miglio MR. A Portrait of Intratumoral Genomic and Transcriptomic Heterogeneity at Single-Cell Level in Colorectal Cancer. MEDICINA (KAUNAS, LITHUANIA) 2021; 57:1257. [PMID: 34833475 PMCID: PMC8624593 DOI: 10.3390/medicina57111257] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/14/2021] [Accepted: 11/15/2021] [Indexed: 12/24/2022]
Abstract
In the study of cancer, omics technologies are supporting the transition from traditional clinical approaches to precision medicine. Intra-tumoral heterogeneity (ITH) is detectable within a single tumor in which cancer cell subpopulations with different genome features coexist in a patient in different tumor areas or may evolve/differ over time. Colorectal carcinoma (CRC) is characterized by heterogeneous features involving genomic, epigenomic, and transcriptomic alterations. The study of ITH is a promising new frontier to lay the foundation towards successful CRC diagnosis and treatment. Genome and transcriptome sequencing together with editing technologies are revolutionizing biomedical research, representing the most promising tools for overcoming unmet clinical and research challenges. Rapid advances in both bulk and single-cell next-generation sequencing (NGS) are identifying primary and metastatic intratumoral genomic and transcriptional heterogeneity. They provide critical insight in the origin and spatiotemporal evolution of genomic clones responsible for early and late therapeutic resistance and relapse. Single-cell technologies can be used to define subpopulations within a known cell type by searching for differential gene expression within the cell population of interest and/or effectively isolating signal from rare cell populations that would not be detectable by other methods. Each single-cell sequencing analysis is driven by clustering of cells based on their differentially expressed genes. Genes that drive clustering can be used as unique markers for a specific cell population. In this review we analyzed, starting from published data, the possible achievement of a transition from clinical CRC research to precision medicine with an emphasis on new single-cell based techniques; at the same time, we focused on all approaches and issues related to this promising technology. This transition might enable noninvasive screening for early diagnosis, individualized prediction of therapeutic response, and discovery of additional novel drug targets.
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Affiliation(s)
- Andrea Angius
- Istituto di Ricerca Genetica e Biomedica (IRGB), CNR, Cittadella Universitaria di Cagliari, 09042 Monserrato, Italy
| | - Antonio Mario Scanu
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, Via P. Manzella, 4, 07100 Sassari, Italy; (A.M.S.); (M.R.M.); (A.P.); (P.C.-R.)
| | - Caterina Arru
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (C.A.); (C.C.)
| | - Maria Rosaria Muroni
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, Via P. Manzella, 4, 07100 Sassari, Italy; (A.M.S.); (M.R.M.); (A.P.); (P.C.-R.)
| | - Ciriaco Carru
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (C.A.); (C.C.)
| | - Alberto Porcu
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, Via P. Manzella, 4, 07100 Sassari, Italy; (A.M.S.); (M.R.M.); (A.P.); (P.C.-R.)
| | - Paolo Cossu-Rocca
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, Via P. Manzella, 4, 07100 Sassari, Italy; (A.M.S.); (M.R.M.); (A.P.); (P.C.-R.)
| | - Maria Rosaria De Miglio
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, Via P. Manzella, 4, 07100 Sassari, Italy; (A.M.S.); (M.R.M.); (A.P.); (P.C.-R.)
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2
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Song R, Jia X, Zhao J, Du P, Zhang JA. T cell receptor revision and immune repertoire changes in autoimmune diseases. Int Rev Immunol 2021; 41:517-533. [PMID: 34243694 DOI: 10.1080/08830185.2021.1929954] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Autoimmune disease (AID) is a condition in which the immune system breaks down and starts to attack the body. Some common AIDs include systemic lupus erythematosus, rheumatoid arthritis, type 1 diabetes mellitus and so forth. The changes in T-cell receptor (TCR) repertoire have been found in several autoimmune diseases, and may be responsible for the breakdown of peripheral immune tolerance. In this review, we discussed the processes of TCR revision in peripheral immune environment, the changes in TCR repertoire that occurred in various AIDs, and the specifically expanded T cell clones. We hope our discussion can provide insights for the future studies, helping with the discovery of disease biomarkers and expanding the strategies of immune-targeted therapy. HighlightsRestricted TCR repertoire and biased TCR-usage are found in a variety of AIDs.TCR repertoire shows tissue specificity in a variety of AID diseases.The relationship between TCR repertoire diversity and disease activity is still controversial in AIDs.Dominant TCR clonotypes may help to discover new disease biomarkers and expand the strategies of immune-targeted therapy.
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Affiliation(s)
- Ronghua Song
- Department of Endocrinology, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai, China
| | - Xi Jia
- Department of Endocrinology, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai, China
| | - Jing Zhao
- Department of Endocrinology, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai, China
| | - Peng Du
- Department of Endocrinology, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai, China
| | - Jin-An Zhang
- Department of Endocrinology, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai, China
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3
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Dispen-Seq: a single-microparticle dispenser based strategy towards flexible cell barcoding for single-cell RNA sequencing. Sci China Chem 2021. [DOI: 10.1007/s11426-020-9925-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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4
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Yamawaki TM, Lu DR, Ellwanger DC, Bhatt D, Manzanillo P, Arias V, Zhou H, Yoon OK, Homann O, Wang S, Li CM. Systematic comparison of high-throughput single-cell RNA-seq methods for immune cell profiling. BMC Genomics 2021; 22:66. [PMID: 33472597 PMCID: PMC7818754 DOI: 10.1186/s12864-020-07358-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 12/27/2020] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Elucidation of immune populations with single-cell RNA-seq has greatly benefited the field of immunology by deepening the characterization of immune heterogeneity and leading to the discovery of new subtypes. However, single-cell methods inherently suffer from limitations in the recovery of complete transcriptomes due to the prevalence of cellular and transcriptional dropout events. This issue is often compounded by limited sample availability and limited prior knowledge of heterogeneity, which can confound data interpretation. RESULTS Here, we systematically benchmarked seven high-throughput single-cell RNA-seq methods. We prepared 21 libraries under identical conditions of a defined mixture of two human and two murine lymphocyte cell lines, simulating heterogeneity across immune-cell types and cell sizes. We evaluated methods by their cell recovery rate, library efficiency, sensitivity, and ability to recover expression signatures for each cell type. We observed higher mRNA detection sensitivity with the 10x Genomics 5' v1 and 3' v3 methods. We demonstrate that these methods have fewer dropout events, which facilitates the identification of differentially-expressed genes and improves the concordance of single-cell profiles to immune bulk RNA-seq signatures. CONCLUSION Overall, our characterization of immune cell mixtures provides useful metrics, which can guide selection of a high-throughput single-cell RNA-seq method for profiling more complex immune-cell heterogeneity usually found in vivo.
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Affiliation(s)
- Tracy M Yamawaki
- Genome Analysis Unit, Amgen Research, 1120 Veterans Blvd, South San Francisco, CA, 94080, USA
| | - Daniel R Lu
- Genome Analysis Unit, Amgen Research, 1120 Veterans Blvd, South San Francisco, CA, 94080, USA
| | - Daniel C Ellwanger
- Genome Analysis Unit, Amgen Research, 1120 Veterans Blvd, South San Francisco, CA, 94080, USA
| | - Dev Bhatt
- Oncology/Inflammation, Amgen Research, 1120 Veterans Blvd, South San Francisco, CA, United States
| | - Paolo Manzanillo
- Oncology/Inflammation, Amgen Research, 1120 Veterans Blvd, South San Francisco, CA, United States
| | - Vanessa Arias
- Genome Analysis Unit, Amgen Research, 1120 Veterans Blvd, South San Francisco, CA, 94080, USA
| | - Hong Zhou
- Genome Analysis Unit, Amgen Research, 1120 Veterans Blvd, South San Francisco, CA, 94080, USA
| | - Oh Kyu Yoon
- Genome Analysis Unit, Amgen Research, 1120 Veterans Blvd, South San Francisco, CA, 94080, USA
| | - Oliver Homann
- Genome Analysis Unit, Amgen Research, 1120 Veterans Blvd, South San Francisco, CA, 94080, USA
| | - Songli Wang
- Genome Analysis Unit, Amgen Research, 1120 Veterans Blvd, South San Francisco, CA, 94080, USA
| | - Chi-Ming Li
- Genome Analysis Unit, Amgen Research, 1120 Veterans Blvd, South San Francisco, CA, 94080, USA.
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5
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Nucleic acid extraction: Fundamentals of sample preparation methodologies, current advancements, and future endeavors. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2020.115985] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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6
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Jia X, Wang B, Zhai T, Yao Q, Li Q, Zhang JA. WITHDRAWN: T cell receptor revision and immune repertoire changes in autoimmune diseases. Clin Immunol 2018:S1521-6616(18)30724-1. [PMID: 30543918 DOI: 10.1016/j.clim.2018.12.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
This article has been withdrawn at the request of the author(s) and/or editor. The Publisher apologizes for any inconvenience this may cause. The full Elsevier Policy on Article Withdrawal can be found at https://www.elsevier.com/about/our-business/policies/article-withdrawal.
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Affiliation(s)
- Xi Jia
- Department of Endocrinology, Jinshan Hospital of Fudan University, Shanghai 201508, China
| | - Bing Wang
- Department of Endocrinology, Jinshan Hospital of Fudan University, Shanghai 201508, China
| | - Tianyu Zhai
- Department of Endocrinology, Zhongshan Hospital of Fudan University, Shanghai 201508, China
| | - Qiuming Yao
- Department of Endocrinology, Jinshan Hospital of Fudan University, Shanghai 201508, China
| | - Qian Li
- Department of Endocrinology, Jinshan Hospital of Fudan University, Shanghai 201508, China
| | - Jin-An Zhang
- Department of Endocrinology, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai 201318, China.
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AlJanahi AA, Danielsen M, Dunbar CE. An Introduction to the Analysis of Single-Cell RNA-Sequencing Data. Mol Ther Methods Clin Dev 2018; 10:189-196. [PMID: 30094294 PMCID: PMC6072887 DOI: 10.1016/j.omtm.2018.07.003] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The recent development of single-cell RNA sequencing has deepened our understanding of the cell as a functional unit, providing new insights based on gene expression profiles of hundreds to hundreds of thousands of individual cells, and revealing new populations of cells with distinct gene expression profiles previously hidden within analyses of gene expression performed on bulk cell populations. However, appropriate analysis and utilization of the massive amounts of data generated from single-cell RNA sequencing experiments are challenging and require an understanding of the experimental and computational pathways taken between preparation of input cells and output of interpretable data. In this review, we will discuss the basic principles of these new technologies, focusing on concepts important in the analysis of single-cell RNA-sequencing data. Specifically, we summarize approaches to quality-control measures for determination of which single cells to include for further examination, methods of data normalization and scaling to overcome the relatively inefficient capture rate of mRNA from each cell, and clustering and visualization algorithms used for dimensional reduction of the data to a two-dimensional plot.
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Affiliation(s)
- Aisha A. AlJanahi
- Translational Stem Cell Biology Branch, NHLBI, NIH, Bethesda, MD, USA
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC, USA
| | - Mark Danielsen
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC, USA
| | - Cynthia E. Dunbar
- Translational Stem Cell Biology Branch, NHLBI, NIH, Bethesda, MD, USA
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Hutchison S, Pritchard AL. Identifying neoantigens for use in immunotherapy. Mamm Genome 2018; 29:714-730. [PMID: 30167844 PMCID: PMC6267674 DOI: 10.1007/s00335-018-9771-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 08/08/2018] [Indexed: 12/14/2022]
Abstract
This review focuses on the types of cancer antigens that can be recognised by the immune system and form due to alterations in the cancer genome, including cancer testis, overexpressed and neoantigens. Specifically, neoantigens can form when cancer cell-specific mutations occur that result in alterations of the protein from ‘self’. This type of antigen can result in an immune response sufficient to clear tumour cells when activated. Furthermore, studies have reported that the likelihood of successful immunotherapeutic targeting of cancer by many different methods was reliant on immune response to neoantigens. The recent resurgence of interest in the immune response to tumour cells, in conjunction with technological advances, has resulted in a large increase in the predicted, identified and functionally confirmed neoantigens. This growth in identified neoantigen sequences has increased the contents of training sets for algorithms, which in turn improves the prediction of which genetic mutations may form neoantigens. Additionally, algorithms predicting how proteins will be processed into peptide epitopes by the proteasome and which peptides bind to the transporter complex are also improving with this research. Now that large screens of all the tumour-specific protein altering mutations are possible, the emerging data from assessment of the immunogenicity of neoantigens suggest that only a minority of variants will form targetable epitopes. The potential for immunotherapeutic targeting of neoantigens will therefore be greater in cancers with a higher frequency of protein altering somatic variants. There is considerable potential in the use of neoantigens to treat patients, either alone or in combination with other immunotherapies and with continued advancements, these potentials will be realised.
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Affiliation(s)
- Sharon Hutchison
- Genetics and Immunology Research Group, University of the Highlands and Islands, An Lòchran, 10 Inverness Campus, Inverness, IV2 5NA, Scotland, UK
| | - Antonia L Pritchard
- Genetics and Immunology Research Group, University of the Highlands and Islands, An Lòchran, 10 Inverness Campus, Inverness, IV2 5NA, Scotland, UK.
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9
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Ellipilli S, Phillips JD, Heemstra JM. Synthesis of comb-shaped DNA using a non-nucleosidic branching phosphoramidite. Org Biomol Chem 2018; 16:4659-4664. [PMID: 29881861 DOI: 10.1039/c8ob00626a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Branched DNAs (bDNAs) having comb-like structures have found wide utility in molecular diagnostics and DNA nanotechnology. bDNAs can be generated either by designing and assembling linear DNA molecules into rigid non-covalent structures or by using an orthogonally protected branching unit to synthesize covalently linked structures. Despite the advantages of the covalently linked structures, use of this motif has been hampered by the challenging synthesis of appropriately protected branching monomers. We report the facile synthesis of a branching monomer having orthogonal DMT and Lev protecting groups using readily available δ-velarolactone and 1,3-diaminopropan-2-ol. Using this branching monomer, a comb-shaped bDNA was synthesized having three different DNA arms. The synthesis and hybridization capability of the bDNA was assessed by fluorescence microscopy using fluorescently labeled complementary and mismatched DNA probes. Convenient access to an orthogonally protected branching monomer is anticipated to accelerate applications of bDNAs in applications including diagnostics, biosensing, gene-profiling, DNA computing, multicolor imaging, and nanotechnology.
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Affiliation(s)
- Satheesh Ellipilli
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, USA.
| | - John D Phillips
- Department of Internal Medicine, University of Utah, Salt Lake City, Utah 84112, USA
| | - Jennifer M Heemstra
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, USA.
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10
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Legut M, Dolton G, Mian AA, Ottmann OG, Sewell AK. CRISPR-mediated TCR replacement generates superior anticancer transgenic T cells. Blood 2018; 131:311-322. [PMID: 29122757 PMCID: PMC5774207 DOI: 10.1182/blood-2017-05-787598] [Citation(s) in RCA: 149] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 11/04/2017] [Indexed: 12/20/2022] Open
Abstract
Adoptive transfer of T cells genetically modified to express a cancer-specific T-cell receptor (TCR) has shown significant therapeutic potential for both hematological and solid tumors. However, a major issue of transducing T cells with a transgenic TCR is the preexisting expression of TCRs in the recipient cells. These endogenous TCRs compete with the transgenic TCR for surface expression and allow mixed dimer formation. Mixed dimers, formed by mispairing between the endogenous and transgenic TCRs, may harbor autoreactive specificities. To circumvent these problems, we designed a system where the endogenous TCR-β is knocked out from the recipient cells using clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein-9 (Cas9) technology, simultaneously with transduction with a cancer-reactive receptor of choice. This TCR replacement strategy resulted in markedly increased surface expression of transgenic αβ and γδ TCRs, which in turn translated to a stronger, and more polyfunctional, response of engineered T cells to their target cancer cell lines. Additionally, the TCR-plus-CRISPR-modified T cells were up to a thousandfold more sensitive to antigen than standard TCR-transduced T cells or conventional model proxy systems used for studying TCR activity. Finally, transduction with a pan-cancer-reactive γδ TCR used in conjunction with CRISPR/Cas9 knockout of the endogenous αβ TCR resulted in more efficient redirection of CD4+ and CD8+ T cells against a panel of established blood cancers and primary, patient-derived B-cell acute lymphoblastic leukemia blasts compared with standard TCR transfer. Our results suggest that TCR transfer combined with genome editing could lead to new, improved generations of cancer immunotherapies.
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Affiliation(s)
- Mateusz Legut
- Division of Infection and Immunity, School of Medicine
- Systems Immunity Research Institute, and
| | - Garry Dolton
- Division of Infection and Immunity, School of Medicine
- Systems Immunity Research Institute, and
| | - Afsar Ali Mian
- Haematology, Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Oliver G Ottmann
- Haematology, Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Andrew K Sewell
- Division of Infection and Immunity, School of Medicine
- Systems Immunity Research Institute, and
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11
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Bethune MT, Joglekar AV. Personalized T cell-mediated cancer immunotherapy: progress and challenges. Curr Opin Biotechnol 2017; 48:142-152. [DOI: 10.1016/j.copbio.2017.03.024] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 03/15/2017] [Accepted: 03/19/2017] [Indexed: 12/26/2022]
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12
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Wu W, Lin Z, Zhu C, Chen P, Li J, Jiang H. Transition-Metal-Free [3+2] Cycloaddition of Dehydroaminophosphonates and N-Tosylhydrazones: Access to Aminocyclopropanephosphonates with Adjacent Quaternary-Tetrasubstituted Carbon Centers. J Org Chem 2017; 82:12746-12756. [DOI: 10.1021/acs.joc.7b01862] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Wanqing Wu
- Key Laboratory of Functional
Molecular Engineering of Guangdong Province, School of Chemistry and
Chemical Engineering, South China University of Technology, Guangzhou 510640, China
| | - Zhiming Lin
- Key Laboratory of Functional
Molecular Engineering of Guangdong Province, School of Chemistry and
Chemical Engineering, South China University of Technology, Guangzhou 510640, China
| | - Chuanle Zhu
- Key Laboratory of Functional
Molecular Engineering of Guangdong Province, School of Chemistry and
Chemical Engineering, South China University of Technology, Guangzhou 510640, China
| | - Pengquan Chen
- Key Laboratory of Functional
Molecular Engineering of Guangdong Province, School of Chemistry and
Chemical Engineering, South China University of Technology, Guangzhou 510640, China
| | - Jiawei Li
- Key Laboratory of Functional
Molecular Engineering of Guangdong Province, School of Chemistry and
Chemical Engineering, South China University of Technology, Guangzhou 510640, China
| | - Huanfeng Jiang
- Key Laboratory of Functional
Molecular Engineering of Guangdong Province, School of Chemistry and
Chemical Engineering, South China University of Technology, Guangzhou 510640, China
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13
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Giudicelli V, Duroux P, Kossida S, Lefranc MP. IG and TR single chain fragment variable (scFv) sequence analysis: a new advanced functionality of IMGT/V-QUEST and IMGT/HighV-QUEST. BMC Immunol 2017; 18:35. [PMID: 28651553 PMCID: PMC5485737 DOI: 10.1186/s12865-017-0218-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 06/16/2017] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND IMGT®, the international ImMunoGeneTics information system® ( http://www.imgt.org ), was created in 1989 in Montpellier, France (CNRS and Montpellier University) to manage the huge and complex diversity of the antigen receptors, and is at the origin of immunoinformatics, a science at the interface between immunogenetics and bioinformatics. Immunoglobulins (IG) or antibodies and T cell receptors (TR) are managed and described in the IMGT® databases and tools at the level of receptor, chain and domain. The analysis of the IG and TR variable (V) domain rearranged nucleotide sequences is performed by IMGT/V-QUEST (online since 1997, 50 sequences per batch) and, for next generation sequencing (NGS), by IMGT/HighV-QUEST, the high throughput version of IMGT/V-QUEST (portal begun in 2010, 500,000 sequences per batch). In vitro combinatorial libraries of engineered antibody single chain Fragment variable (scFv) which mimic the in vivo natural diversity of the immune adaptive responses are extensively screened for the discovery of novel antigen binding specificities. However the analysis of NGS full length scFv (~850 bp) represents a challenge as they contain two V domains connected by a linker and there is no tool for the analysis of two V domains in a single chain. METHODS The functionality "Analyis of single chain Fragment variable (scFv)" has been implemented in IMGT/V-QUEST and, for NGS, in IMGT/HighV-QUEST for the analysis of the two V domains of IG and TR scFv. It proceeds in five steps: search for a first closest V-REGION, full characterization of the first V-(D)-J-REGION, then search for a second V-REGION and full characterization of the second V-(D)-J-REGION, and finally linker delimitation. RESULTS For each sequence or NGS read, positions of the 5'V-DOMAIN, linker and 3'V-DOMAIN in the scFv are provided in the 'V-orientated' sense. Each V-DOMAIN is fully characterized (gene identification, sequence description, junction analysis, characterization of mutations and amino changes). The functionality is generic and can analyse any IG or TR single chain nucleotide sequence containing two V domains, provided that the corresponding species IMGT reference directory is available. CONCLUSION The "Analysis of single chain Fragment variable (scFv)" implemented in IMGT/V-QUEST and, for NGS, in IMGT/HighV-QUEST provides the identification and full characterization of the two V domains of full-length scFv (~850 bp) nucleotide sequences from combinatorial libraries. The analysis can also be performed on concatenated paired chains of expressed antigen receptor IG or TR repertoires.
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Affiliation(s)
- Véronique Giudicelli
- IMGT®, the international ImMunoGeneTics information system®, Laboratoire d'ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine IGH, UMR 9002, CNRS, Montpellier University, Montpellier, France.
| | - Patrice Duroux
- IMGT®, the international ImMunoGeneTics information system®, Laboratoire d'ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine IGH, UMR 9002, CNRS, Montpellier University, Montpellier, France.
| | - Sofia Kossida
- IMGT®, the international ImMunoGeneTics information system®, Laboratoire d'ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine IGH, UMR 9002, CNRS, Montpellier University, Montpellier, France.
| | - Marie-Paule Lefranc
- IMGT®, the international ImMunoGeneTics information system®, Laboratoire d'ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine IGH, UMR 9002, CNRS, Montpellier University, Montpellier, France.
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Affiliation(s)
- Thomas S Watkins
- Centre for Biodiscovery and Molecular Development of Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Queensland, Australia.,School of Medicine, The University of Queensland, Brisbane, Queensland, Australia.,QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - John J Miles
- Centre for Biodiscovery and Molecular Development of Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Queensland, Australia.,School of Medicine, The University of Queensland, Brisbane, Queensland, Australia.,QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
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15
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Wong GK, Heather JM, Barmettler S, Cobbold M. Immune dysregulation in immunodeficiency disorders: The role of T-cell receptor sequencing. J Autoimmun 2017; 80:1-9. [PMID: 28400082 DOI: 10.1016/j.jaut.2017.04.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 04/01/2017] [Accepted: 04/03/2017] [Indexed: 11/28/2022]
Abstract
Immune dysregulation is a prominent feature of primary immunodeficiency disorders, which commonly manifested as autoimmunity, cytopenias and inflammatory bowel disease. In partial T-cell immunodeficiency disorders, it has been proposed that the imbalance between effector and regulatory T-cells drives the breakdown of peripheral tolerance. While there is no robust test for immune dysregulation, the T-cell receptor repertoire is used as a surrogate marker, and has been shown to be perturbed in a number of immunodeficiency disorders featuring immune dysregulation including Omenn's Syndrome, Wiskott-Aldrich Syndrome, and common variable immunodeficiency. This review discusses how recent advances in TCR next-generation sequencing and bioinformatics have led to the in-depth characterization of CDR3 sequences and an exponential growth in examinable parameters. Specifically, we highlight the use of junctional diversity as a means to differentiate intrinsic T-cell defects from secondary causes of repertoire perturbation in primary immunodeficiency disorders. However, key questions, such as the identity of antigenic targets for large, expanded T-cell clonotypes, remain unanswered despite the fact that such clones are likely to play a pathogenic role in driving immune dysregulation and autoimmunity. Finally, we discuss a number of emerging technologies such as in silico reconstruction, high-throughput pairwise αβ sequencing and single-cell RNAseq that offer the potential to define the antigenic epitope and function of a given T-cell, thereby enhancing our understanding in this field.
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Affiliation(s)
- Gabriel K Wong
- Institute of Immunology and Immunontherapy, Medical School, University of Birmingham, Edgbaston, B15 2TT, UK; UCB Pharma, Slough, Berkshire, SL1 3WE, UK
| | - James M Heather
- Massachusetts General Hospital Cancer Center and Department of Medicine Harvard Medical School, 13th Street, Charlestown, MA, 02129, USA
| | - Sara Barmettler
- Massachusetts General Hospital Cancer Center and Department of Medicine Harvard Medical School, 13th Street, Charlestown, MA, 02129, USA
| | - Mark Cobbold
- Massachusetts General Hospital Cancer Center and Department of Medicine Harvard Medical School, 13th Street, Charlestown, MA, 02129, USA.
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Lindau P, Robins HS. Advances and applications of immune receptor sequencing in systems immunology. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.coisb.2016.12.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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T cell receptor repertoire usage in cancer as a surrogate marker for immune responses. Semin Immunopathol 2017; 39:255-268. [PMID: 28074285 DOI: 10.1007/s00281-016-0614-9] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 12/15/2016] [Indexed: 12/21/2022]
Abstract
Characterizing the interaction of cancer cells with the host adaptive immune system is critical for understanding tumor immunology and the modus operandi of immunotherapeutic interventions to treat cancer. As the key cellular effectors of adaptive immunity, T cells are endowed with specialized receptors (the T cell receptor; TCR), to recognize and to eliminate cancer cells. The diversity of the TCR repertoire results from specialized genetic diversification mechanisms that generate an incredible variability allowing recognizing extensive collections of antigens. Based on the attainment and function of the TCR, the TCR repertoire is a mirror of the human immune response, and the dynamic changes of its usage can be assumed as a promising biomarker to monitor immunomodulatory therapies. Recent advances in multiplexed PCR amplification and massive parallel sequencing technologies have facilitated the characterization of TCR repertoires at high resolution even when only biomaterial of limited quantity and quality, such as formalin-fixed paraffin-embedded (FFPE) archived tissues, is available. Here, we review the concept framework and current experimental approaches to characterize the TCR repertoire usage in cancer including inherent technical and biological challenges.
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Antigen-receptor sequences captured from single T cells. Nat Methods 2016. [DOI: 10.1038/nmeth.4012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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