Review
Immunology
Guangyao Tian, Mingqian Li, Guoyue Lv
Summary: This article reviews the recent advances in TCR sequencing techniques and computational tools, as well as the recent discovery in overall TCR profile and antigen-specific T cells tracking in transplantation. The challenges and potential of using TCR sequencing-based assays to profile alloreactive TCR repertoire as the fingerprint for immune monitoring and prediction of rejection and tolerance are further discussed.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Microbiology
Hu-Qin Yang, Yi-Shan Wang, Kan Zhai, Zhao-Hui Tong
Summary: This study found that mice infected with Pneumocystis demonstrated reduced TCR diversity in CD4(+) T cells and increased diversity in CD8(+) T cells. Th17 cells were mainly composed of CD4(+) T cells and exhibited the phenotype of tissue-resident memory-like Th17 cells. Additionally, Pneumocystis-infected mice showed biased usage of TCR beta VDJ genes.
FRONTIERS IN MICROBIOLOGY
(2021)
Review
Immunology
Ksenia V. Zornikova, Saveliy A. Sheetikov, Alexander Yu Rusinov, Rustam N. Iskhakov, Apollinariya V. Bogolyubova
Summary: The T cell response is crucial for controlling and clearing SARS-CoV-2 infection. However, there are still important questions regarding the role of cellular immunity in COVID-19, such as the characteristics of disease-specific T cell repertoires in convalescent patients and vaccinated individuals, and how T cell responses to other pathogens, particularly common cold coronaviruses, affect susceptibility to SARS-CoV-2 infection and disease progression. This review focuses on the shaping of T cell receptor (TCR) repertoires by natural infection and vaccination, cross-reactive T cell responses, and the implications of TCR repertoire diversity and cross-reactivity for the development of vaccines that can provide broad protection against SARS-CoV-2 variants.
FRONTIERS IN IMMUNOLOGY
(2023)
Review
Biochemical Research Methods
Kerui Peng, Theodore S. Nowicki, Katie Campbell, Mohammad Vahed, Dandan Peng, Yiting Meng, Anish Nagareddy, Yu-Ning Huang, Aaron Karlsberg, Zachary Miller, Jaqueline Brito, Brian Nadel, Victoria M. Pak, Malak S. Abedalthagafi, Amanda M. Burkhardt, Houda Alachkar, Antoni Ribas, Serghei Mangul
Summary: Researchers have evaluated the ability of RNA-Seq-based methods to detect T-cell receptor (TCR) sequences by analyzing 19 cancer cohorts. The results show that RNA-Seq-based methods can effectively capture clonotypes and estimate the diversity of TCR repertoires, particularly in T-cell-rich tissues and low-diversity tissues. However, the ability of RNA-Seq methods is limited in T-cell-poor tissues, especially in highly diverse repertoires. Therefore, incorporating RNA-Seq into immune repertoire screening of cancer patients provides broader transcriptomic knowledge beyond the limited information of TCR-Seq.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Medicine, Research & Experimental
Hongmei Liu, Wenjing Pan, Congli Tang, Yujie Tang, Haijing Wu, Akihiko Yoshimura, Yan Deng, Nongyue He, Song Li
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.
Article
Immunology
Maria Eschke, Peter F. Moore, Haiyang Chang, Gottfried Alber, Stefan M. Keller
Summary: In this study, a detailed atlas of peripheral blood TCR alpha beta(+) T cell populations in healthy dogs was generated using single-cell RNA sequencing and immune repertoire sequencing. The researchers identified 22 T cell clusters, classified into CD4-dominant, CD8A-dominant, and CD4/CD8A-mixed groups. They also discovered several T cell populations not previously described in dogs, including mucosa-associated invariant T cell (MAIT)-like cells. This study provides important reference data for future research and has implications for T cell-specific therapies.
FRONTIERS IN IMMUNOLOGY
(2023)
Review
Immunology
Jianing Fu, Mohsen Khosravi-Maharlooei, Megan Sykes
Summary: Recent advances in high throughput sequencing and transcriptomic analysis, particularly at the single cell level, have provided new insights into human immunology and immune-related diseases. The use of HTS of TCRs has allowed assessment of the human alloresponse development, magnitude, and nature at a new level, and has provided a tool for tracking the fate of pre-transplant-defined TCRs. Studies combining high throughput TCR sequencing with single cell transcriptional analyses have shed light on human allograft rejection and tolerance.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Plant Sciences
Bin Luo, Panpan Wang, Jianhui Tian, Xiaoge Chu, Xinyi Lu, Yun Yang, Yiyang Zhou, Yan Li, Zujun Que
Summary: The study aimed to explore the effect of Jinfukang (JFK) in inhibiting lung cancer metastasis by regulating T-cell receptors (TCRs). The results showed that JFK could reduce the number of pulmonary metastatic nodules and the burden of lung tumor metastasis. Additionally, JFK could increase the proportion of CD4+ T, CD8+ T, and NKT cells in peripheral blood and reverse the TCR changes caused by tumor metastasis.
JOURNAL OF ETHNOPHARMACOLOGY
(2024)
Article
Immunology
Sung Noh Hong, Joo-Young Park, So-Yun Yang, Chansu Lee, Young-Ho Kim, Je-Gun Joung
Summary: This study found that the diversity of the TCR repertoire is reduced in inflamed mucosa of CD patients, which may be associated with intestinal inflammation.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Immunology
Yizhe Li, Jian Hu, Yongsi Wang, Dongdong Liu, Yaling Shi, Jiaqi Zhang, Yuntao Liu, Dongzi Lin, Jing Lin, Wei Hu, Haolan He, Wei Wang, Wentao Fan, Linlin Li, Dawei Wang, Kejian Wang, Jianhua Xu
Summary: By analyzing the peripheral T-cell receptor repertoire of 54 COVID-19 patients, a set of characteristic gene combinations were identified to distinguish asymptomatic and symptomatic patients, and predict the risk of recurrence in re-detectable positive cases. These findings have the potential to strengthen clinical surveillance and the development of immunotherapy for COVID-19.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Immunology
Mikiya Tsunoda, Hiroyasu Aoki, Haruka Shimizu, Shigeyuki Shichino, Kouji Matsushima, Satoshi Ueha
Summary: Temporal analysis of T cell receptor (TCR) repertoire is important for monitoring changes in antigen-specific T cells in cancer patients. However, lack of experimental models for temporal analysis within a homogeneous population limits understanding of the relationship between TCR repertoire changes and antitumor responses. Bilateral tumor model showed highly similar T-cell clones in bilateral tumors and different patterns in draining lymph nodes, suggesting independent induction of tumor-reactive T cell clones in each lymph node.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Immunology
Sabrina Pollastro, Marie de Bourayne, Giulia Balzaretti, Aldo Jongejan, Barbera D. C. van Schaik, Ilse T. G. Niewold, Antoine H. C. van Kampen, Bernard Maillere, Niek de Vries
Summary: The study demonstrated a new method to identify and characterize antigen-responsive T cell clones using high-throughput T-cell receptor repertoire sequencing. By combining datasets and a novel analysis protocol, the researchers successfully explored the dynamics of T cell clonal expansion and antigen response characteristics.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Immunology
Hai Yang, Jason Cham, Brian Patrick Neal, Zenghua Fan, Tao He, Li Zhang
Summary: T cells are important for adaptive immunity and play a role in anti-tumoral immunity and defense against infections, including respiratory viruses like SARS-CoV-2. A customized pipeline for Network Analysis of Immune Repertoire (NAIR) was developed to analyze T-cell receptor (TCR) sequences. Network analysis and statistical methods were used to characterize the repertoire and correlate it with clinical outcomes. Disease-specific/associated clusters and shared clusters were identified, and a new metric incorporating clonal generation probability and clonal abundance was used to identify disease-specific TCRs. The proposed approach revealed potential disease-specific TCRs responsible for the immune response to COVID-19.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Microbiology
Ming-Ming Shao, Feng-Shuang Yi, Zhong-Yin Huang, Peng Peng, Feng-Yao Wu, Huan-Zhong Shi, Kan Zhai
Summary: Characterization of T cell receptor repertoires in tuberculous patients revealed differences in TCR sequences, hydrophobicity, and usage patterns between CD4(+) and CD8(+) T cells. A new subset of polyfunctional CD4(+) T cells with protective immunity against Mtb was identified.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Immunology
Tara K. Sigdel, Paul A. Fields, Juliane Liberto, Izabella Damm, Maggie Kerwin, Jill Hood, Parhom Towfighi, Marina Sirota, Harlan S. Robins, Minnie M. Sarwal
Summary: In this study, researchers analyzed the T-cell repertoire in kidney transplant recipients and found that changes in the repertoire are associated with post-transplant rejection episodes. T-cell receptor sequencing may serve as a valuable tool for predicting rejection risk after transplantation.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Oncology
Hiromi Sugiyama, Munechika Misumi, Alina Brenner, Eric J. Grant, Ritsu Sakata, Atsuko Sadakane, Mai Utada, Dale L. Preston, Kiyohiko Mabuchi, Kotaro Ozasa
INTERNATIONAL JOURNAL OF CANCER
(2020)
Article
Biology
Norio Takahashi, Munechika Misumi, Yasuharu Niwa, Hideko Murakami, Waka Ohishi, Toshiya Inaba, Akiko Nagamachi, Satoshi Tanaka, Ignacia Braga Tanaka, Gen Suzuki
RADIATION RESEARCH
(2020)
Article
Biology
Jan Christian Kaiser, Munechika Misumi, Kyoji Furukawa
Summary: This study focused on the radiation risk of PTC, proposing the use of the CLIP2 gene as a molecular biomarker to distinguish radiogenic from sporadic PTC and developing a biologically-based risk model. By demonstrating the portability of the model concept across different cohorts and improving the determination of radiation-induced cancer probability through the two-path concept, the study confirmed and improved the understanding of radiation-induced PTC.
INTERNATIONAL JOURNAL OF RADIATION BIOLOGY
(2021)
Article
Biology
Norio Takahashi, Munechika Misumi, Hideko Murakami, Yasuharu Niwa, Waka Ohishi, Toshiya Inaba, Akiko Nagamachi, Gen Suzuki
JOURNAL OF RADIATION RESEARCH
(2020)
Article
Biology
Mark P. Little, David Pawel, Munechika Misumi, Nobuyuki Hamada, Harry M. Cullings, Richard Wakeford, Kotaro Ozasa
RADIATION RESEARCH
(2020)
Article
Endocrinology & Metabolism
Sakurako Kira, Chikako Ito, Rumi Fujikawa, Munechika Misumi
BMJ OPEN DIABETES RESEARCH & CARE
(2020)
Article
Hematology
Kengo Yoshida, Munechika Misumi, Yoichiro Kusunoki, Michiko Yamada
Summary: The study found that red blood cell distribution width (RDW) increases with age and is positively correlated with radiation dose, and elevated RDW is also associated with higher all-cause mortality. Further research is needed to explore the biological mechanisms behind these associations.
BRITISH JOURNAL OF HAEMATOLOGY
(2021)
Article
Public, Environmental & Occupational Health
Hiromi Sugiyama, Munechika Misumi, Ritsu Sakata, Alina V. Brenner, Mai Utada, Kotaro Ozasa
Summary: The study found that antenatal radiation exposure is a consistent risk factor for increased solid cancer mortality among females, but not among males. The effect of exposure to atomic bomb radiation on noncancer disease and external cause mortality among individuals exposed in utero was mediated through small head size, low birth weight, and parental loss.
EUROPEAN JOURNAL OF EPIDEMIOLOGY
(2021)
Article
Public, Environmental & Occupational Health
Tomoki Nakamizo, John Cologne, Kismet Cordova, Michiko Yamada, Tetsuya Takahashi, Munechika Misumi, Saeko Fujiwara, Masayasu Matsumoto, Yasuki Kihara, Ayumi Hida, Waka Ohishi
Summary: This study investigated the association between radiation exposure and atherosclerosis in Japanese atomic bomb survivors. It found a small but significant linear association of radiation with calcification and plaque, equivalent to about 2 years of aging per Gy of radiation exposure. The model with latent factors representing underlying atherosclerotic pathologies fitted better and had narrower confidence intervals compared to separate ordinary regression models.
EUROPEAN JOURNAL OF EPIDEMIOLOGY
(2021)
Article
Biology
John Cologne, Hiromi Sugiyama, Kanya Hamasaki, Yoshimi Tatsukawa, Benjamin French, Ritsu Sakata, Munechika Misumi
Summary: A study on atomic-bomb survivors exposed in utero suggests an increase in translocations at low doses. Factors such as smoking behavior, medical irradiation, sex, mother's age, and trimester do not significantly influence the number of translocations.
RADIATION AND ENVIRONMENTAL BIOPHYSICS
(2022)
Article
Biology
Kayoko Ishihara, Naohiro Kato, Munechika Misumi, Hiroko Kitamura, Ayumi Hida, Michiko Yamada
Summary: This study aimed to investigate the impact of atomic bomb radiation exposure on late-life neurocognitive function in children. The results showed that age, sex, and education level were related to neurocognitive function, while radiation dose did not appear to significantly affect neurocognitive function.
RADIATION RESEARCH
(2022)
Article
Biology
Tomoki Nakamizo, Munechika Misumi, Tetsuya Takahashi, Satoshi Kurisu, Masayasu Matsumoto, Akira Tsujino
Summary: The female sex in patients with atrial fibrillation (AF) is a paradoxical risk factor for stroke, as it increases the risk among older women of certain ethnicities but contradicts the male predominance in cardiovascular diseases. Through simulations, it was found that this sex difference may be generated non-causally through left truncation due to competing risks (CR) such as coronary artery diseases. The study demonstrated that left truncation can identify spurious risk factors, and that female sex in patients with AF may be a paradoxical risk factor for stroke.
Article
Public, Environmental & Occupational Health
Hisashi Noma, Munechika Misumi, Shiro Tanaka
Summary: Ordinary logistic regression analyses are widely used in case-cohort studies, but their odds ratio estimates cannot be interpreted as relative risk measures unless the event rate is low. This study introduces pseudo-Poisson and pseudo-normal linear regression methods that can estimate risk ratios and risk differences. By using weighting and auxiliary variable information, these estimators provide accurate and precise results. These alternative approaches are recommended for case-cohort studies, especially when the event rate is not low.
JOURNAL OF EPIDEMIOLOGY
(2023)