T-Cell Receptor Repertoire Sequencing and Its Applications: Focus on Infectious Diseases and Cancer

Article Biochemical Research Methods

TCRpower: quantifying the detection power of T-cell receptor sequencing with a novel computational pipeline calibrated by spike-in sequences

Shiva Dahal-Koirala et al.

Summary: The development of a novel computational pipeline called TCRpower allows for quantifying the statistical detection power of TCR sequencing methods, enabling reliable detection of disease-relevant TCRs for diagnostic applications.

BRIEFINGS IN BIOINFORMATICS (2022)

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Article Pathology

The role of next-generation sequencing in detecting gene fusions with known and unknown partners: a single-center experience with methodologies' integration

Andrea Ambrosini-Spaltro et al.

Summary: This study evaluated the reliability of next-generation sequencing (NGS) in detecting gene fusions with known and unknown partners. The results showed that NGS is a reliable method for detecting gene fusions with known partners, but less accurate for identifying gene fusions with unknown partners.

HUMAN PATHOLOGY (2022)

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Review Immunology

Genetics of rheumatoid arthritis

Leonid Padyukov

Summary: Rheumatoid arthritis is an inflammatory autoimmune disease with significant genetic associations and variations. Current research focuses on immune receptor binding, T cell activation, and cell signaling mechanisms. More than 150 candidate loci have been identified, with further discoveries expected in the future.

SEMINARS IN IMMUNOPATHOLOGY (2022)

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Review Immunology

TCR-sequencing in cancer and autoimmunity: barcodes and beyond

Kristen E. Pauken et al.

Summary: The T cell receptor serves as a molecular barcode tracking T cell functions and immune responses. Recent technological advances allow for single-cell TCR sequencing on an unprecedented scale.

TRENDS IN IMMUNOLOGY (2022)

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Review Immunology

Single-Cell RNA Sequencing in Lung Cancer: Revealing Phenotype Shaping of Stromal Cells in the Microenvironment

Jianhong Zhang et al.

Summary: The stromal components in the lung tumor microenvironment play a crucial role in the progression and treatment of lung cancer. Single-cell RNA sequencing technology allows us to gain a deeper understanding of gene expression profiles, revealing the correlations among heterogeneity, signaling pathways, drug resistance, and microenvironment molding in lung cancer, which is essential for effective treatment.

FRONTIERS IN IMMUNOLOGY (2022)

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Review Immunology

Revealing Clonal Responses of Tumor-Reactive T-Cells Through T Cell Receptor Repertoire Analysis

Hiroyasu Aoki et al.

Summary: CD8(+) T cells are crucial for the antitumor immune response. TCR repertoire analysis allows for a better understanding of the response of tumor-specific T cells in the tumor microenvironment.

FRONTIERS IN IMMUNOLOGY (2022)

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Article Cell Biology

Analysis of TCR Repertoire by High-Throughput Sequencing Indicates the Feature of T Cell Immune Response after SARS-CoV-2 Infection

Yifan Wang et al.

Summary: This study analyzed the T cell receptor (TCR) repertoire of COVID-19 patients after recovery using advanced sequencing technology. The results showed that specific TCR clones underwent clonal expansion after infection, and CD4(+) and CD8(+) T cells in patients at different stages of recovery exhibited preferential gene recombination usage. Furthermore, certain TCR clones were shared between CD4(+) and CD8(+) T cells of different patients.

CELLS (2022)

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Review Oncology

TCR-T Immunotherapy: The Challenges and Solutions

Yating Liu et al.

Summary: TCR-T cell therapy is a potential cellular immunotherapy for cancer treatment. However, its efficacy in solid tumors is lower compared to hematological malignancies. This article discusses the barriers and strategies affecting the efficacy of TCR-T cell immunotherapy in solid tumors.

FRONTIERS IN ONCOLOGY (2022)

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Article Immunology

Characterization of the TCR β Chain Repertoire in Peripheral Blood from Hepatitis B Vaccine Responders and Non-Responders

Jiezuan Yang et al.

Summary: T cell response characteristics can differentiate responders and non-responders to Hepatitis B vaccination, providing new targets for optimizing vaccine efficacy.

JOURNAL OF INFLAMMATION RESEARCH (2022)

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Article Biotechnology & Applied Microbiology

A versatile 5′ RACE-Seq methodology for the accurate identification of the 5′ termini of mRNAs

Panagiotis G. Adamopoulos et al.

Summary: In this study, a 5' RACE-seq method was developed to accurately reveal the 5' termini of mRNA targets through the optimization of template-switching and 5' RACE assays. The results showed that the optimized method significantly increased the efficiency of downstream 5' RACE, supporting the existence of two distinct 5' termini for BCL2L12 and identifying multiple annotated and novel 5' UTRs for the KLK gene family members.

BMC GENOMICS (2022)

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Article Immunology

CD8+ T-Cell Exhaustion Phenotype in Chronic Hepatitis C Virus Infection Is Associated With Epitope Sequence Variation

Sylwia Osuch et al.

Summary: This study aimed to investigate the relationship between T-cell exhaustion phenotype and NS3 viral immunodominant epitopes in chronic HCV infection. The results showed an interplay between viral epitope sequences and exhaustion phenotype of CD8(+) T-cells. The expression of PD-1/Tim-3 receptors was largely determined by viral epitope sequence, indicating the importance of evaluating autologous viral epitope sequences in the investigation of CD8(+) T-cell exhaustion in HCV infection.

FRONTIERS IN IMMUNOLOGY (2022)

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Review Immunology

Emerging Strategies in TCR-Engineered T Cells

Fang Wei et al.

Summary: Immunotherapy of cancer, especially TCR-T, has shown remarkable progress in recent years. This review summarizes the challenges and opportunities of TCR-T and proposes a strategy of combining different treatments to target solid tumors effectively.

FRONTIERS IN IMMUNOLOGY (2022)

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Article Cell Biology

Rapid screening of TCR-pMHC interactions by the YAMTAD system

Lihui Wang et al.

Summary: In this study, a system called YAMTAD was designed for rapid screening of TCR-pMHC interactions. The system showed high sensitivity and specificity in identifying antigens for a given TCR and recognizing TCRs for a given pMHC. Additionally, the system demonstrated the enrichment of high-affinity TCR-pMHC interactions through library-on-library screening.

CELL DISCOVERY (2022)

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Review Medicine, General & Internal

Utility of Bulk T-Cell Receptor Repertoire Sequencing Analysis in Understanding Immune Responses to COVID-19

Hannah Kockelbergh et al.

Summary: This article discusses the utility and importance of bulk TCR repertoire sequencing for evaluating immunity to SARS-CoV-2 and explores the analysis methods and findings of sequencing data. The study found that SARS-CoV-2-specific clonotypes undergo early expansion and contraction during active infection. Maintaining TCR repertoire diversity is beneficial for anti-SARS-CoV-2 responses, while TCR repertoire narrowing is associated with severe COVID-19. Additionally, the study found that SARS-CoV-2 may have a superantigen-like activity, which could be the basis for multisystem inflammatory syndrome and cytokine storms in COVID-19.

DIAGNOSTICS (2022)

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Article

Concurrence of Rheumatoid Arthritis and Ankylosing Spondylitis: Analysis of Seven Cases and Literature Review

Bryan-Josué Flores-Robles et al.

Case Reports in Rheumatology (2022)

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Article Immunology

Process Development for Adoptive Cell Therapy in Academia: A Pipeline for Clinical-Scale Manufacturing of Multiple TCR-T Cell Products

Daniela Nascimento Silva et al.

Summary: Researchers provide a pipeline for the process development and clinical-scale manufacturing of TCR-T cells in academia, addressing the need for cancer and chronic viral infection treatments. They successfully reproduced the functional characteristics of specific TCRs and demonstrated the similarity and efficient production of TCR-T cell products.

FRONTIERS IN IMMUNOLOGY (2022)

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Review Cell Biology

The human T-cell receptor repertoire in health and disease and potential for omics integration

Thomas S. Watkins et al.

Summary: The TCR system, believed to be one of the most complex in science, evolved over 600 million years and has been fine-tuned by generations of our ancestors. Recent discoveries have challenged old dogmas in the field, shedding new light on TCR biology. Standardizing TCR sequencing data is crucial for big data bioinformatics and predictive analysis, while TCR NGS has the potential to uncover new signatures and phenomena in health and disease.

IMMUNOLOGY AND CELL BIOLOGY (2021)

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Article Gastroenterology & Hepatology

Clinical and genomic characterisation of mismatch repair deficient pancreatic adenocarcinoma

Robert C. Grant et al.

Summary: Patients with MMRD pancreatic cancer exhibit longer overall survival, distinct histopathological and genomic features, and may benefit from targeted therapies based on their unique genomic drivers.

GUT (2021)

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Article Biotechnology & Applied Microbiology

Benchmarking of T cell receptor repertoire profiling methods reveals large systematic biases

Pierre Barennes et al.

Summary: This study systematically compared the results of nine different TCR sequencing methods on the same T cell sample, revealing significant differences in accuracy and reproducibility, with most methods showing a lower ability to capture TRA diversity and low RNA input affecting representativeness. Despite better clonotype quantification accuracy, some methods were found to be more sensitive in detecting rare clonotypes.

NATURE BIOTECHNOLOGY (2021)

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Review Genetics & Heredity

Integrating genetic and non-genetic determinants of cancer evolution by single-cell multi-omics

Anna S. Nam et al.

Summary: Cancer is an evolutionary process involving genetic and non-genetic factors, with intratumoural heterogeneity playing a key role in cancer evolution. Single-cell multi-omics technologies are essential for capturing and integrating the different layers of heritable information to study cancer evolution effectively.

NATURE REVIEWS GENETICS (2021)

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Review Biochemistry & Molecular Biology

Role of CD4+T Cells in the Control of Viral Infections: Recent Advances and Open Questions

Jerome Kervevan et al.

Summary: CD4+ T cells play a crucial role in adaptive immune responses by recruiting and providing help to other immune effectors, as well as exerting direct effector functions. High-affinity T cell receptor (TCR) clonotypes are important in mediating antiviral CD4+ T cell responses.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2021)

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Article Oncology

Applying high-dimensional single-cell technologies to the analysis of cancer immunotherapy

Satyen H. Gohil et al.

Summary: Advances in single-cell analysis technologies have enabled the study of tumor heterogeneity, interactions between immune cells and tumor cells, and the evolutionary trajectory of each tumor. Multidimensional biomarker signatures will be crucial for guiding clinical decision-making for cancer patients.

NATURE REVIEWS CLINICAL ONCOLOGY (2021)

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Review Oncology

The head and neck cancer genome in the era of immunotherapy

N. Ari Wijetunga et al.

Summary: Recent advances in sequencing technologies have helped unravel the complex interactions between HPV virus, tumor, host factors, and tumor microenvironment (TME) in head and neck squamous cell carcinoma (HNSCC), shedding light on the interaction of the immune system with these malignancies.

ORAL ONCOLOGY (2021)

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Review Immunology

T Cells: Warriors of SARS-CoV-2 Infection

Paola de Candia et al.

Summary: Severe infection with SARS-CoV-2 is characterized by massive cytokine release and T cell loss. The exaggerated host immune response, possibly dependent on T cell immunological memory, may significantly contribute to immunopathology and massive collateral damage in COVID-19 patients, especially in adults compared with children.

TRENDS IN IMMUNOLOGY (2021)

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Article Cell Biology

Tumour microenvironment-based molecular profiling reveals ideal candidates for high-grade serous ovarian cancer immunotherapy

Xiaofan Lu et al.

Summary: The study identified two immune subtypes of high-grade serous ovarian cancer (HGSOC), one of which showed more positive response to immunotherapy, particularly to anti-PD1 antibody therapy. These findings provide new insights for immunotherapy in HGSOC.

CELL PROLIFERATION (2021)

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Article Biotechnology & Applied Microbiology

Comprehensive analysis of TCR repertoire in COVID-19 using single cell sequencing

Pingping Wang et al.

Summary: This study analyzed the TCR repertoire in COVID-19 patients using single-cell V(D)J sequencing and found distinct T cell clonal expansion as well as significant changes in VJ gene combinations. Moreover, preferential usage of V and J gene segments was observed in samples infected by different viruses, providing novel insights on the immune response in COVID-19.

GENOMICS (2021)

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Article Immunology

High-throughput and high-dimensional single-cell analysis of antigen-specific CD8+ T cells

Ke-Yue Ma et al.

Summary: The study introduces a new high-throughput method for simultaneous profiling of TCR sequences, cognate antigen specificities, gene expression, and surface-protein expression from tens of thousands of single cells, providing valuable insights into T cell responses.

NATURE IMMUNOLOGY (2021)

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Review Oncology

The Current Lung Cancer Neoantigen Landscape and Implications for Therapy

Linda Ye et al.

Summary: Neoantigens are unique mutant peptides in tumors that can elicit T-cell-mediated immune responses and are potential targets for personalized cancer therapies. Immunotherapy based on neoantigens in lung cancer shows promising prospects and opportunities for clinical applications.

JOURNAL OF THORACIC ONCOLOGY (2021)

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Article Virology

In Chronic Infection, HIV Gag-Specific CD4+ T Cell Receptor Diversity Is Higher than CD8+ T Cell Receptor Diversity and Is Associated with Less HIV Quasispecies Diversity

Mark A. Pilkinton et al.

Summary: Cellular immune responses to Gag are associated with improved HIV control, with CD8(+) T cell response dominated by a few unique TCRs and CD4(+) T cell response displaying a more diverse TCR repertoire. Greater TCR diversity in CD4(+) T cells may limit HIV genetic diversity during chronic infection.

JOURNAL OF VIROLOGY (2021)

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Article Biochemistry & Molecular Biology

TCR-engineered T cells targeting E7 for patients with metastatic HPV-associated epithelial cancers

Nisha B. Nagarsheth et al.

Summary: In a first-in-human phase 1 trial, T cells targeting HPV-16 E7 showed promising results in treating metastatic epithelial cancers, with objective clinical responses observed in 6 out of 12 patients. This suggests that genetically engineered T cell therapy may be effective in treating common carcinomas, but further studies are needed to understand the resistance mechanisms in advanced epithelial cancer.

NATURE MEDICINE (2021)

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Article Oncology

An Empirical Antigen Selection Method Identifies Neoantigens That Either Elicit Broad Antitumor T-cell Responses or Drive Tumor Growth

Hubert Lam et al.

Summary: The ATLAS bioassay is developed to identify neoantigens empirically by expressing patient-specific tumor mutations individually, revealing both stimulatory and inhibitory responses. Therapeutic immunization with stimulatory neoantigens protected animals, while immunization with inhibitory responses resulted in accelerated tumor growth. Empirical testing shows that T-cell responses to neoantigens are more nuanced than straightforward MHC antigen recognition and could impact cancer immunotherapy design.

CANCER DISCOVERY (2021)

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Article Immunology

TCRMatch: Predicting T-Cell Receptor Specificity Based on Sequence Similarity to Previously Characterized Receptors

William D. Chronister et al.

Summary: The study introduces a new tool called TCR Match, which aims to identify epitope specificity of T cell receptors by comparing sequence similarities, providing new insights for the development of strategies for monitoring and treating infectious, allergic, autoimmune diseases, and cancer.

FRONTIERS IN IMMUNOLOGY (2021)

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Article Immunology

Contribution of resident and circulating precursors to tumor-infiltrating CD8(+) T cell populations in lung cancer

Paul Gueguen et al.

Summary: Tumor-infiltrating lymphocytes, especially CD8(+) TILs, serve as a favorable prognostic factor in non-small cell lung cancer. The study used single-cell RNA and TCR sequencing to investigate the functional organization of TIL populations in primary NSCLC, identifying two CD8(+) TIL subpopulations expressing memory-like gene modules and showing their differentiation pathways in the tumor microenvironment.

SCIENCE IMMUNOLOGY (2021)

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Article Hematology

TCR gene-engineered cell therapy for solid tumors

Elaine Tan et al.

Summary: TCR-based cellular therapy has shown promise in targeting solid tumors by recognizing intracellular tumor antigens and inducing cytotoxic responses. Despite various challenges, multiple clinical trials are currently underway to address these limitations.

BEST PRACTICE & RESEARCH CLINICAL HAEMATOLOGY (2021)

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Review Biochemical Research Methods

High-throughput and single-cell T cell receptor sequencing technologies

Joy A. Pai et al.

Summary: This Review discusses methodological advances in high-throughput analysis of the TCR repertoire, particularly at single-cell resolution. Recent studies have developed high-throughput sequencing technologies to identify TCR sequences and analyze their antigen specificities, providing important insights into T cell-mediated immune responses.

NATURE METHODS (2021)

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Review Gastroenterology & Hepatology

Human immune repertoire in hepatitis B virus infection

Qiao Zhan et al.

Summary: This review summarizes the methodology and application of immune repertoire sequencing (IRS) in studying the human immune system, focusing on its role in predicting the progression, treatment, and vaccination of Hepatitis B virus (HBV) infection.

WORLD JOURNAL OF GASTROENTEROLOGY (2021)

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Article Multidisciplinary Sciences

The T cell receptor repertoire of tumor infiltrating T cells is predictive and prognostic for cancer survival

Sara Valpione et al.

Summary: High baseline T cell receptor diversity is predictive of favorable prognosis in multiple cancer types, while monoclonal expansion of T cells pre-treatment correlates with good response to immune checkpoint blockade therapy in metastatic melanoma patients.

NATURE COMMUNICATIONS (2021)

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Review Biology

Biological controls for standardization and interpretation of adaptive immune receptor repertoire profiling

Johannes Truck et al.

Summary: The use of adaptive immune receptor repertoire sequencing (AIRR-seq) has provided new insights into the immune system but also comes with challenges. The AIRR Community's Biological Resources Working Group conducted a survey to understand the need for standards and controls in generating and annotating AIRR-seq data, and offered recommendations for developing AIRR-seq standards and controls based on the survey results.

ELIFE (2021)

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Review Genetics & Heredity

Mechanisms Underlying the Suppression of Chromosome Rearrangements by Ataxia-Telangiectasia Mutated

Motohiro Yamauchi

Summary: Chromosome rearrangements are structural variations in chromosomes and are associated with a variety of human diseases. Ataxia-telangiectasia (A-T) is an autosomal recessive disorder characterized by chromosome rearrangements at the cellular level, particularly in T lymphocytes. The defective gene in A-T is ataxia-telangiectasia mutated (ATM), which plays a central role in cellular response to DNA damage, including suppressing chromosome rearrangements.

GENES (2021)

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Review Immunology

Promising New Tools for Targeting p53 Mutant Cancers: Humoral and Cell-Based Immunotherapies

Vitaly Chasov et al.

Summary: Mutations in the p53 protein result in loss of transcriptional functions, leading to deactivation of tumor suppressive responses and acquisition of pro-oncogenic properties. Hotspot mutations of p53 are often immunogenic, eliciting T cell responses to mutant p53 neoantigens.

FRONTIERS IN IMMUNOLOGY (2021)

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Review Immunology

Applications of Single-Cell Omics in Tumor Immunology

Junwei Liu et al.

Summary: The tumor microenvironment (TME) is a complex ecosystem involving various cell types, and understanding the interactions between cancer cells and immune cells within the TME is crucial for cancer biology and tumor immunology. The rapid development of single-cell techniques provides powerful tools to profile the omics status of the TME at single-cell resolution, shedding light on cancer pathogenic mechanisms and dysfunctions of tumor immunity. Advanced techniques that can characterize multi-omics and spatial information at the single-cell level are also being developed to reveal disease-specific cell populations comprehensively and improve clinical diagnosis and prognosis.

FRONTIERS IN IMMUNOLOGY (2021)

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Review Immunology

Single-Cell TCR and Transcriptome Analysis: An Indispensable Tool for Studying T-Cell Biology and Cancer Immunotherapy

Anna Pasetto et al.

Summary: T cells are essential in immune responses and cancer immunotherapy. Single-cell sequencing techniques have enabled scientists to study T cells at a deeper level, including T-cell receptor and transcriptome analysis. These techniques also aid in the identification of T-cell neoantigens, advancing T-cell mediated cancer therapy.

FRONTIERS IN IMMUNOLOGY (2021)

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Review Oncology

CART-Cell Therapy: Recent Advances and New Evidence in Multiple Myeloma

Massimo Martino et al.

Summary: Anti-BCMA CART-cell therapy has shown efficacy and manageable toxicity in heavily pretreated R/R MM patients. However, key issues such as patient relapse and safety concerns remain. Strategies to prevent relapse include dual-targeting CAR T-cells and upregulation of BCMA expression. The adverse effects of the therapy, such as CRS and neurologic toxicity, along with the extended manufacturing timeline and limited access to treatment, are important considerations for further development and optimization of BCMA-targeted CAR T-cell therapy.

CANCERS (2021)

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Review Cell Biology

Evolution of CD8+ T Cell Receptor (TCR) Engineered Therapies for the Treatment of Cancer

Yimo Sun et al.

Summary: Engineered TCR-T cell therapy has revolutionized the treatment of human cancer by targeting tumor antigen-specific adaptable cellular products. However, challenges such as low TCR avidity, off-target toxicities, and target antigen loss have limited the efficacy of TCR-T therapy for solid tumors. Further research is needed to address these limitations and improve the safety and efficacy of TCR-T therapies.

CELLS (2021)

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Article Genetics & Heredity

Genetic polymorphism of HLA-G gene (G01:03, G01:04, and G*01:05N) in Iraqi patients with inflammatory bowel disease (ulcerative colitis and Crohn's disease)

Sarah S. Abdul-Hussein et al.

Summary: This study indicated that HLA-G*01:04 and HLA-G*01:05N alleles may influence susceptibility to UC and CD in Iraqi patients.

EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS (2021)

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Article Cell Biology

Single-cell analysis shows that adipose tissue of persons with both HIV and diabetes is enriched for clonal, cytotoxic, and CMV-specific CD4+ T cells

Celestine N. Wanjalla et al.

Summary: Individuals with HIV are at higher risk for diabetes compared to those without HIV, and T cells in adipose tissue play an important role in regulating glucose and lipid metabolism in both groups. The different subsets of T cells in adipose tissue of HIV and diabetes patients may have distinct characteristics and functions, with potential implications for future research on viral antigens and immune responses.

CELL REPORTS MEDICINE (2021)

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Article Medicine, General & Internal

Tumor Mutation Burden, Immune Cell Infiltration, and Construction of Immune-Related Genes Prognostic Model in Head and Neck Cancer

Ai-Min Jiang et al.

Summary: High TMB is associated with poor prognosis in HNSCC patients, and the IRGs prognostic model constructed based on TMB and immune cell infiltration may have potential prognostic value for these individuals. Further validation in large-scale and prospective studies is needed.

INTERNATIONAL JOURNAL OF MEDICAL SCIENCES (2021)

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Article Medicine, Research & Experimental

The methods and advances of adaptive immune receptors repertoire sequencing

Hongmei Liu et al.

Summary: The adaptive immune response recognizes and neutralizes threats through T or B lymphatic receptors. High-throughput sequencing and bioinformatics offer research opportunities. Analyzing immune repertoire data reveals biological information and aids in improving experimental and computational methods.

THERANOSTICS (2021)

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Article Medicine, General & Internal

Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study

Nanshan Chen et al.

LANCET (2020)

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Article Medicine, General & Internal

Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China

Chaolin Huang et al.

LANCET (2020)

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Article Multidisciplinary Sciences

Clonal kinetics and single-cell transcriptional profiling of CAR-T cells in patients undergoing CD19 CAR-T immunotherapy

Alyssa Sheih et al.

NATURE COMMUNICATIONS (2020)

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Article Biochemical Research Methods

immuneSIM: tunable multi-feature simulation of B- and T-cell receptor repertoires for immunoinformatics benchmarking

Cedric R. Weber et al.

BIOINFORMATICS (2020)

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Article Microbiology

A Dynamic Immune Response Shapes COVID-19 Progression

Eugenia Ziying Ong et al.

CELL HOST & MICROBE (2020)

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Article Immunology

Downregulated Gene Expression Spectrum and Immune Responses Changed During the Disease Progression in Patients With COVID-19

Yabo Ouyang et al.

CLINICAL INFECTIOUS DISEASES (2020)

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Review Biochemistry & Molecular Biology

Molecular T-Cell Repertoire Analysis as Source of Prognostic and Predictive Biomarkers for Checkpoint Blockade Immunotherapy

Ilenia Aversa et al.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2020)

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Article Cell Biology

Immune cell profiling of COVID-19 patients in the recovery stage by single-cell sequencing

Wen Wen et al.

CELL DISCOVERY (2020)

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Article Biochemistry & Molecular Biology

Single-cell landscape of bronchoalveolar immune cells in patients with COVID-19

Mingfeng Liao et al.

NATURE MEDICINE (2020)

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Review Infectious Diseases

Lymphopenia is associated with severe coronavirus disease 2019 (COVID-19) infections: A systemic review and meta-analysis

Qianwen Zhao et al.

INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES (2020)

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Review Immunology

Immune Response, Inflammation, and the Clinical Spectrum of COVID-19

Luis F. Garcia

FRONTIERS IN IMMUNOLOGY (2020)

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Review Oncology

T-cell receptor repertoire analysis for the diagnosis and treatment of solid tumor: A methodology and clinical applications

Na Li et al.

CANCER COMMUNICATIONS (2020)

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Article Biochemistry & Molecular Biology

Robust T Cell Immunity in Convalescent Individuals with Asymptomatic or Mild COVID-19

Takuya Sekine et al.

CELL (2020)

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Article Multidisciplinary Sciences

SARS-CoV-2-reactive T cells in healthy donors and patients with COVID-19

Julian Braun et al.

NATURE (2020)

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Article Biotechnology & Applied Microbiology

COVID-19 severity correlates with airway epithelium-immune cell interactions identified by single-cell analysis

Robert Lorenz Chua et al.

NATURE BIOTECHNOLOGY (2020)

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Article Biochemistry & Molecular Biology

A single-cell atlas of the peripheral immune response in patients with severe COVID-19

Aaron J. Wilk et al.

NATURE MEDICINE (2020)

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Review Biochemical Research Methods

T-cell repertoire analysis and metrics of diversity and clonality

Johanna Chiffelle et al.

CURRENT OPINION IN BIOTECHNOLOGY (2020)

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Review Pharmacology & Pharmacy

Deciphering the TCR Repertoire to Solve the COVID-19 Mystery

Lucas Gutierrez et al.

TRENDS IN PHARMACOLOGICAL SCIENCES (2020)

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Article Multidisciplinary Sciences

Single-cell TCR sequencing reveals phenotypically diverse clonally expanded cells harboring inducible HIV proviruses during ART

Pierre Gantner et al.

NATURE COMMUNICATIONS (2020)

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Article Immunology

Longitudinal Analysis of T and B Cell Receptor Repertoire Transcripts Reveal Dynamic Immune Response in COVID-19 Patients

Xuefeng Niu et al.

FRONTIERS IN IMMUNOLOGY (2020)

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Article Immunology

SARS-CoV-2 Epitopes Are Recognized by a Public and Diverse Repertoire of Human T Cell Receptors

Alina S. Shomuradova et al.

IMMUNITY (2020)

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Article Immunology

Identification of Mutated Peptides in Bladder Cancer From Exomic Sequencing Data Reveals Negative Correlation Between Mutation-Specific Immunoreactivity and Inflammation

Chen Wang et al.

FRONTIERS IN IMMUNOLOGY (2020)

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Review Biochemistry & Molecular Biology

The updated landscape of tumor microenvironment and drug repurposing

Ming-Zhu Jin et al.

SIGNAL TRANSDUCTION AND TARGETED THERAPY (2020)

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Letter Biochemistry & Molecular Biology

Lymphopenia predicts disease severity of COVID-19: a descriptive and predictive study

Li Tan et al.

SIGNAL TRANSDUCTION AND TARGETED THERAPY (2020)

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Software Review Biochemical Research Methods

Evaluation of tools for highly variable gene discovery from single-cell RNA-seq data

Shun H. Yip et al.

BRIEFINGS IN BIOINFORMATICS (2019)

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Article Medicine, Research & Experimental

Neoantigen screening identifies broad TP53 mutant immunogenicity in patients with epithelial cancers

Parisa Malekzadeh et al.

JOURNAL OF CLINICAL INVESTIGATION (2019)

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Review Genetics & Heredity

Integrative single-cell analysis

Tim Stuart et al.

NATURE REVIEWS GENETICS (2019)

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Article Biochemical Research Methods

Genesis of the T-cell receptor

Thomas Dupic et al.

PLOS COMPUTATIONAL BIOLOGY (2019)

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Article Oncology

Immunologic Recognition of a Shared p53 Mutated Neoantigen in a Patient with Metastatic Colorectal Cancer

Winifred Lo et al.

CANCER IMMUNOLOGY RESEARCH (2019)

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Review Genetics & Heredity

Single-Cell RNA-Seq Technologies and Related Computational Data Analysis

Geng Chen et al.

FRONTIERS IN GENETICS (2019)

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Article Oncology

Unique Neoantigens Arise from Somatic Mutations in Patients with Gastrointestinal Cancers

Maria R. Parkhurst et al.

CANCER DISCOVERY (2019)

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Article Immunology

Detection of a Low Level and Heterogeneous B Cell Immune Response in Peripheral Blood of Acute Borreliosis Patients With High Throughput Sequencing

Josiane Kirpach et al.

FRONTIERS IN IMMUNOLOGY (2019)

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Article Oncology

Efficient identification of neoantigen-specific T-cell responses in advanced human ovarian cancer

Song Liu et al.

JOURNAL FOR IMMUNOTHERAPY OF CANCER (2019)

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Article Cell Biology

Combination PD-1 and PD-L1 Blockade Promotes Durable Neoantigen-Specific T Cell-Mediated Immunity in Pancreatic Ductal Adenocarcinoma

Adam L. Burrack et al.

CELL REPORTS (2019)

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Article Biochemistry & Molecular Biology

Non-templated addition and template switching by Moloney murine leukemia virus (MMLV)-based reverse transcriptases co-occur and compete with each other

Madalee G. Wulf et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2019)

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Article Medicine, Research & Experimental

Recognition of human gastrointestinal cancer neoantigens by circulating PD-1+ lymphocytes

Alena Gros et al.

JOURNAL OF CLINICAL INVESTIGATION (2019)

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Article Multidisciplinary Sciences

Commonality despite exceptional diversity in the baseline human antibody repertoire

Bryan Briney et al.

NATURE (2019)

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Article Medicine, Research & Experimental

Clones of infected cells arise early in HIV-infected individuals

John M. Coffin et al.

JCI INSIGHT (2019)

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Article Biochemical Research Methods

Droplet-based single cell RNAseq tools: a practical guide

Robert Salomon et al.

LAB ON A CHIP (2019)

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Article Infectious Diseases

Dolutegravir reshapes the genetic diversity of HIV-1 reservoirs

Pierre Gantner et al.

JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY (2018)

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Article Multidisciplinary Sciences

Patient HLA class I genotype influences cancer response to checkpoint blockade immunotherapy

Diego Chowell et al.

SCIENCE (2018)

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Article Oncology

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