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)
Review
Genetics & Heredity
Yiran Shen, Alexandria Voigt, Xuebing Leng, Amy A. Rodriguez, Cuong Q. Nguyen
Summary: T cell receptors (TCR) play a vital role in immune response to foreign antigens, and understanding specific TCR involvement in autoimmunity can provide insights into autoimmune diseases. RNA-seq is a valuable tool for studying TCR repertoires and can provide information on antigen prediction. This review discusses the application and development of bulk RNA-seq and single-cell (SC) RNA-seq in examining TCR repertoires, as well as bioinformatic tools for studying peptide/TCR/MHC structure and predicting antigenic epitopes using artificial intelligence.
FRONTIERS IN GENETICS
(2023)
Article
Medicine, General & Internal
Danielle E. Madden, Jessica R. Webb, Eike J. Steinig, Bart J. Currie, Erin P. Price, Derek S. Sarovich
Summary: This study compared the performance of different antimicrobial resistance software in Burkholderia pseudomallei and found existing tools have limitations in detecting all resistance determinants, leading to the development of a new software ARDaP which successfully identified all resistance determinants and predicted resistance in mixed strain data.
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.
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
Immunology
He Li, Yuehan Gao, Lihui Xie, Rong Wang, Runping Duan, Zhaohuai Li, Binyao Chen, Lei Zhu, Xianggui Wang, Wenru Su
Summary: Single-cell transcriptional immune cell atlas based on prednisone-treated or untreated experimental autoimmune uveitis (EAU) mice revealed that prednisone partially reversed the globally activated immune cells in terms of cell composition, gene expression, transcription factor regulation, and cell-cell communication, with significant rescue effects on T and B cells.
FRONTIERS IN IMMUNOLOGY
(2021)
Review
Immunology
Siting Li, Guang Song, Yina Bai, Ning Song, Jiuliang Zhao, Jian Liu, Chaojun Hu
Summary: Dysregulated autoantibodies and cytokines are important indicators for potential diseases, such as various cancers and autoimmune diseases. Protein microarray technology provides a versatile and robust platform for easily profiling dysregulated autoantibodies and cytokines associated with autoimmune diseases, mainly using serum samples.
FRONTIERS IN IMMUNOLOGY
(2021)
Review
Cell Biology
Daniel Schreyer, John P. Neoptolemos, Simon T. Barry, Peter Bailey
Summary: Comprehensive molecular landscaping studies offer hope for PDAC patients and reveal advancements in techniques such as minimally invasive liquid biopsies and integrated genomics, enabling early disease detection and personalized treatment.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Immunology
Mao-Jan Lin, Yu-Chun Lin, Nae-Chyun Chen, Allen Chilun Luo, Sheng-Kai Lai, Chia-Lang Hsu, Jacob Shujui Hsu, Chien-Yu Chen, Wei-Shiung Yang, Pei-Lung Chen
Summary: The study of adaptive immune receptor repertoire (AIRR) is crucial for understanding adaptive immune responses. The authors developed the gAIRR Suite, which includes three modules: gAIRR-seq, gAIRR-call, and gAIRR-annotate. Using this suite, they were able to accurately profile and annotate the germline genes encoding AIRR, leading to the discovery of new alleles and comparison of gene differences across genomes.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Oncology
John W. Rutland, Corey M. Gill, Joshua Loewenstern, Hanane Arib, Margaret Pain, Melissa Umphlett, Yayoi Kinoshita, Russell B. McBride, Joshua Bederson, Michael Donovan, Robert Sebra, Raj K. Shrivastava, Mary Fowkes
Summary: The study evaluated 145 meningiomas and found lymphocytes distributed in both scattered and aggregated forms. Meningiomas with scattered lymphocytes had higher tumor mutational burden, while density of aggregated lymphocytes and macrophages was associated with higher tumor grade. NF2 mutational status was linked to increased scattered lymphocyte density in meningiomas, suggesting a potential biomarker for tumor mutational burden in meningiomas.
CANCER IMMUNOLOGY IMMUNOTHERAPY
(2021)
Review
Oncology
Wenjing Qian, Mingfang Zhao, Ruoyu Wang, Heming Li
Summary: Immune checkpoint therapy has achieved significant efficacy in certain tumor types by blocking inhibitory pathways to release T lymphocytes' function using anti-PD-1/PD-L1 monoclonal antibodies. However, limited efficacy, toxic side effects, and lack of accurate biomarkers pose challenges. Further research is needed to identify more representative predictive and target molecules for improving immune checkpoint therapy outcomes.
JOURNAL OF HEMATOLOGY & ONCOLOGY
(2021)
Review
Immunology
Meiyu Wu, Ming Zhao, Haijing Wu, Qianjin Lu
Summary: The diversity of the immune repertoire allows the immune system to differentiate a wide range of antigens encountered throughout life, but can also contribute to autoimmune disease pathogenesis. High-throughput sequencing technology aids in monitoring immune responses and identifying disease-specific immune repertoires, providing potential targets for diagnosis and treatment.
Article
Multidisciplinary Sciences
Akshay J. Patel, Zena N. Willsmore, Naeem Khan, Alex Richter, Babu Naidu, Mark T. Drayson, Sophie Papa, Andrew Cope, Sophia N. Karagiannis, Esperanza Perucha, Gary W. Middleton
Summary: Checkpoint blockade with Pembrolizumab has proven effective in treating advanced non-small cell lung cancer. However, some patients experience high-grade immune related adverse events (irAEs) during treatment. This study reveals that a deficient Breg checkpoint fails to control self-reactive T cell activity and auto-antibody formation in these patients, leading to severe auto-inflammatory sequelae. Pre-therapy B cell profiling may help identify patients at high risk of developing severe irAEs.
NATURE COMMUNICATIONS
(2022)
Article
Immunology
Yang Liu, Yankang Wu, Bing Liu, Youpeng Zhang, Dan San, Yu Chen, Yu Zhou, Long Yu, Haihong Zeng, Yun Zhou, Fuxiang Zhou, Heng Yang, Lei Yin, Yafei Huang
Summary: This study investigated the dynamic changes of the host immune response to SARS-CoV-2 infection, identifying biomarkers associated with COVID-19 development and revealing distinct features of immune response. Abnormally high levels of B-cell response in acute infection and sustained T-cell response in the convalescent phase may play key roles in the pathogenesis and prevention of reinfection, respectively.
FRONTIERS IN IMMUNOLOGY
(2021)
Review
Immunology
Svenja Foth, Sara Voelkel, Daniel Bauersachs, Michael Zemlin, Chrysanthi Skevaki
Summary: A newborn must develop cellular immunity to defend against pathogens, with dysregulation leading to severe disorders. This review discusses the role of T cell immunity in antigen detection, characteristics of mature TCR repertoire, and assessments methods. Various early childhood disorders and changes in the TCR repertoire are outlined, along with the latest findings and research gaps.
FRONTIERS IN IMMUNOLOGY
(2021)
Review
Obstetrics & Gynecology
Aolin Wang, Amy Padula, Marina Sirota, Tracey J. Woodruff
FERTILITY AND STERILITY
(2016)
Article
Computer Science, Information Systems
Yen S. Low, Aaron C. Daugherty, Elizabeth A. Schroeder, William Chen, Tina Seto, Susan Weber, Michael Lim, Trevor Hastie, Maya Mathur, Manisha Desai, Carl Farrington, Andrew A. Radin, Marina Sirota, Pragati Kenkare, Caroline A. Thompson, Peter P. Yu, Scarlett L. Gomez, GeorgeW Sledge, Allison W. Kurian, Nigam H. Shah
JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION
(2017)
Article
Medicine, General & Internal
Ari J. Green, Jeffrey M. Gelfand, Bruce A. Cree, Carolyn Bevan, W. John Boscardin, Feng Mei, Justin Inman, Sam Arnow, Michael Devereux, Aya Abounasr, Hiroko Nobuta, Alyssa Zhu, Matt Friessen, Roy Gerona, Hans Christian von Budingen, Roland G. Henry, Stephen L. Hauser, Jonah R. Chan
Article
Medicine, Research & Experimental
Thomas Van Blarcom, Kevin Lindquist, Zea Melton, Wai Ling Cheung, Chris Wagstrom, Dan McDonough, Cendy Valle Oseguera, Sheng Ding, Andrea Rossi, Shobha Potluri, Purnima Sundar, Steven Pitts, Marina Sirota, Meri Galindo Casas, Yu Yan, Jeffrey Jones, Zygy Roe-Zurz, Surabhi Srivatsa Srinivasan, Wenwu Zhai, Jaume Pons, Arvind Rajpal, Javier Chaparro-Riggers
Article
Medicine, General & Internal
Gabriela Schmajuk, Chris Tonner, Laura Trupin, Jing Li, Urmimala Sarkar, Dana Ludwig, Stephen Shiboski, Marina Sirota, R. Adams Dudley, Sara Murray, Jinoos Yazdany
Article
Rheumatology
Milena A. Gianfrancesco, Gabriela Schmajuk, Sarah Haserodt, Laura Trupin, Zara Izadi, Kashif Jafri, Stephen Shiboski, Marina Sirota, R. Adams Dudley, Jinoos Yazdany
RHEUMATOLOGY INTERNATIONAL
(2017)
Review
Immunology
Marina Sirota, Minnie M. Sarwal
Article
Multidisciplinary Sciences
Bin Chen, Li Ma, Hyojung Paik, Marina Sirota, Wei Wei, Mei-Sze Chua, Samuel So, Atul J. Butte
NATURE COMMUNICATIONS
(2017)
Article
Multidisciplinary Sciences
Dvir Aran, Roman Camarda, Justin Odegaard, Hyojung Paik, Boris Oskotsky, Gregor Krings, Andrei Goga, Marina Sirota, Atul J. Butte
NATURE COMMUNICATIONS
(2017)
Article
Multidisciplinary Sciences
Dexter Hadley, James Pan, Osama El-Sayed, Jihad Aljabban, Imad Aljabban, Tej D. Azad, Mohamad O. Hadied, Shuaib Raza, Benjamin Abhishek Rayikanti, Bin Chen, Hyojung Paik, Dvir Aran, Jordan Spatz, Daniel Himmelstein, Maryam Panahiazar, Sanchita Bhattacharya, Marina Sirota, Mark A. Musen, Atul J. Butte
Article
Medicine, Research & Experimental
Amar N. Mirza, Micah A. Fry, Nicole M. Urman, Scott X. Atwood, Jon Roffey, Gregory R. Ott, Bin Chen, Alex Lee, Alexander S. Brown, Sumaira Z. Aasi, Tyler Hollmig, Mark A. Ator, Bruce D. Dorsey, Bruce R. Ruggeri, Craig A. Zificsak, Marina Sirota, Jean Y. Tang, Atul Butte, Ervin Epstein, Kavita Y. Sarin, Anthony E. Oro
Article
Medicine, Research & Experimental
Erica L. Eggers, Brady A. Michel, Hao Wu, Sheng-zhi Wang, Carolyn J. Bevan, Aya Abounasr, Natalie S. Pierson, Antje Bischof, Max Kazer, Elizabeth Leitner, Ariele L. Greenfield, Stanislas Demuth, Michael R. Wilson, Roland G. Henry, Bruce A. C. Cree, Stephen L. Hauser, H. -Christian von Budingen
Article
Medicine, Research & Experimental
Klaus Lehmann-Horn, Sheng-zhi Wang, Sharon A. Sagan, Scott S. Zamvil, H. -Christian von Budingen