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SSRN 2022年

作者： Lees, William D. Christley, Scott Peres, Ayelet Kos, Justin T. Corrie, Brian Ralph, Duncan Breden, Felix Cowell, Lindsay G. Yaari, Gur Corcoran, Martin Karlsson Hedestam, Gunilla B. Ohlin, Mats Collins, Andrew M. Watson, Corey T. Busse, Christian E. Institute of Structural and Molecular Biology Birkbeck College London United Kingdom Human-Centered Computing and Information Science Institute for Systems and Computer Engineering Technology and Science Porto Portugal Peter O’Donnell Jr School of Public Health Department of Immunology UT Southwestern Medical Center Texas United States Bioengineering Program Faculty of Engineering Bar-Ilan University Ramat Gan Israel Department of Biochemistry and Molecular Genetics School of Medicine University of Louisville Kentucky United States Department of Biological Sciences Simon Fraser University BurnabyBC Canada Fred Hutchinson Cancer Research Center SeattleWA United States Department of Microbiology Tumor and Cell Biology Karolinska Institute Stockholm Sweden Department of Immunotechnology Lund University Lund Sweden School of Biotechnology and Biomolecular Sciences University of New South Wales SydneyNSW Australia Division of B Cell Immunology German Cancer Research Center Heidelberg Germany

Analysis of an individual’s immunoglobulin or T cell receptor gene repertoire can provide important insights into immune function. High-quality analysis of adaptive immune receptor repertoire sequencing data depends upon accurate and relatively complete germline sets, but current sets are known to be incomplete. Established processes for the review and systematic naming of receptor germline genes and alleles require specific evidence and data types, but the discovery landscape is rapidly changing. To exploit the potential of emerging data, and to provide the field with improved state-of-the-art germline sets, an intermediate approach is needed that will allow the rapid publication of consolidated sets derived from these emerging sources. These sets must use a consistent naming scheme and allow refinement and consolidation into genes as new information emerges. Name changes should be minimised, but, where changes occur, the naming history of a sequence must be traceable. Here we outline the current issues and opportunities for the curation of germline IG/TR genes and present a forward-looking data model for building out more robust germline sets that can dovetail with current established processes and provides transparency based on principles of findability, accessibility, interoperability, and reusability. We describe results obtained by applying the data model and associated principles within the AIRR Community, including supporting software and databases. © 2022, The Authors. All rights reserved.

关键词： Genes

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Author Correction: T cell-encoded CD80 and 4-1BBL induce auto- and transcostimulation, resulting in potent tumor rejection

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Nature medicine 2024年第6期30卷 1788页

作者： Matthias T Stephan Vladimir Ponomarev Renier J Brentjens Alex H Chang Konstantin V Dobrenkov Glenn Heller Michel Sadelain Center for Cell Engineering Molecular Pharmacology and Chemistry Program Memorial Sloan-Kettering Cancer Center (MSKCC) New York 10021 New York USA. Immunology Graduate Program Weill Graduate School of Medical Sciences Cornell University New York 10021 New York USA. Department of Radiology MSKCC New York 10021 New York USA. Department of Medicine MSKCC New York 10021 New York USA. Department of Epidemiology and Biostatistics MSKCC New York 10021 New York USA. Center for Cell Engineering Molecular Pharmacology and Chemistry Program Memorial Sloan-Kettering Cancer Center (MSKCC) New York 10021 New York USA. m-sadelain@***. Immunology Graduate Program Weill Graduate School of Medical Sciences Cornell University New York 10021 New York USA. m-sadelain@***. Department of Medicine MSKCC New York 10021 New York USA. m-sadelain@***.

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Microbiota imbalance induced by dietary sugar disrupts immune-mediated protection from metabolic syndrome

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四川生理科学杂志 2022年第8期44卷 1455-1455页

作者： Yoshinaga Kawano Department of Microbiology and Immunology Vagelos College of Physicians and Surgeons Columbia University New York NY 10032 USA Integrated Program in Cellular Molecular and Biomedical Studies Columbia University New York NY 10032 USA Department of Systems Biology Vagelos College of Physicians and Surgeons Columbia University New York NY 10032 USA Department of Pathology and Cell Biology Vagelos College of Physicians and Surgeons Columbia University New York NY 10032 USA Department of Pediatrics Vagelos College of Physicians and Surgeons Columbia University New York NY 10032 USA Laboratory of Mucosal Immunology The Rockefeller University New York NY 10065 USA Howard Hughes Medical Institute The Rockefeller University New York NY 10065 USA Department of Microbiology and Immunology Keio University School of Medicine Tokyo Japan RIKEN Center for Integrative Medical Sciences Yokohama Japan Division of Biology and Biological Engineering California Institute of Technology Pasadena CA 91125 USA

How intestinal microbes regulate metabolic syndrome is incompletely *** show that intestinal microbiota protects against development of obesity,metabolic syndrome,and pre-diabetic phenotypes by inducing commensal-specific Th17 ***-fat,high-sugar diet promoted metabolic disease by depleting Th17-inducing microbes,and recovery of commensal Th17 cells restored ***-induced Th17 cells afforded protection by regulating lipid absorption across intestinal epithelium in an IL-17-dependent ***-induced loss of protective Th17 cells was mediated by the presence of sugar.

关键词： Th17 protective sugar

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The regulation of cancer-associated thrombosis by podoplanin

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Thrombosis Update 2024年 15卷 100174-100174页

作者： Gupta, Neha Saifi, Mohd Faiz Wilson, Kiesha Hisada, Yohei Evans, Colin E. Department of Biosciences Faculty of Natural Sciences Jamia Millia Islamia New Delhi India Department of Gastroenterology and Human Nutrition Unit All India Institute of Medical Sciences New Delhi India Department of Pathology Microbiology and Immunology University of South Carolina School of Medicine Columbia SC United States Division of Hematology Department of Medicine University of North Carolina at Chapel Hill Chapel Hill NC United States UNC Blood Research Center University of North Carolina at Chapel Hill Chapel Hill NC United States Department of Cell Biology and Anatomy University of South Carolina School of Medicine Columbia SC United States Cardiovascular Translational Research Center University of South Carolina Columbia SC United States Institute on Cardiovascular Disease Research University of South Carolina Columbia United States Biomedical Engineering Program College of Engineering and Computing University of South Carolina Columbia SC United States

The incidence of venous thromboembolism (VTE) in cancer patients is 4–9 fold higher compared with the general population. The mortality rate of patients with cancer and VTE is more than 2-fold greater versus cancer patients without VTE. Given that the pathophysiology of thrombosis in cancer is multi-faceted, investigations of the mechanisms that regulate cancer-associated thrombosis (CAT) could improve the understanding and treatment of CAT. These mechanisms include activation of the coagulation and fibrinolytic systems. Tumor cells activate coagulation by expressing procoagulant molecules, releasing pro-inflammatory and pro-angiogenic cytokines, and adhering to vascular and blood cells. Tumor-secreted and tissue factor-positive extracellular vesicles are another major driver of CAT, while emerging studies have discovered a role for podoplanin (PDPN) in intratumoral thrombosis, hyper-coagulation, and enhanced VTE risk. In this article, we will review studies of PDPN in CAT, which together suggest that PDPN contributes not only to cancer progression and metastasis, but also to CAT. PDPN may therefore represent an attractive putative target for therapies that aim to simultaneously reduce cancer progression and associated VTE. © 2024 The Authors

关键词： Cancer-associated thrombosis Podoplanin Thrombosis

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Gmr Biosensing with Magnetic Nanowires as Labels for the Detection of Osteosarcoma cells

SSRN

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SSRN 2022年

作者： Su, Diqing Um, Joseph Moreno, Julian Nemati, Zohreh Srinivasan, Karthik Chen, Junyang Kouhpanji, M. Reza Zamani Shore, Daniel Wu, Kai Kosel, Jürgen Modiano, Jaime F. Franklin, Rhonda Wang, Jian-Ping Stadler, Bethanie Department of Chemical Engineering and Materials Science University of Minnesota MinneapolisMN55455 United States Department of Electrical and Computer Engineering University of Minnesota MinneapolisMN55455 United States Electrical Engineering Department King Abdullah University of Science and Technology Thuwal 23955 Saudi Arabia Animal Cancer Care and Research Program University of Minnesota St. PaulMN55108 United States Department of Veterinary Clinical Sciences College of Veterinary Medicine University of Minnesota St. PaulMN55108 United States Masonic Cancer Center University of Minnesota MinneapolisMN55455 United States Center for Immunology University of Minnesota MinneapolisMN55455 United States Stem Cell Institute University of Minnesota MinneapolisMN55455 United States Institute for Engineering in Medicine University of Minnesota MinneapolisMN55455 United States

Magnetic nanowires (MNWs) were explored as potential magnetic tags for cell detection with giant magnetoresistance (GMR) biosensors based on a handheld system. Due to size, shape anisotropy and higher moment materials, the signal detected from a single MNW was 2500 times larger than that from a single magnetic iron oxide nanobead, which is important for ultra-low concentration cell detection. A model was used to determine how the MNW orientation with respect to the GMR sensor impacts detection performance, and the results aligned well with the experimental results. As a proof of concept OSCA-8 cells tagged with Ni MNWs were also detected using the same handheld system. The limit of detection (LOD) in aqueous solution appeared to be 133 cells, and single-cell detection can be realized if the cell is in direct contact with the sensor surface. Since MNWs are already employed in magnetic separation of cells, directly using MNWs as tags in cell detection eliminates the need of additional functionalization with other labels. This largely simplifies the detection process and reduces the risk of contamination during sample preparation. © 2022, The Authors. All rights reserved.

关键词： Biosensors

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Miniaturized Microarray-Format Digital ELISA Enabled by Lithographic Protein Patterning

SSRN

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SSRN 2023年

作者： Stephens, Andrew D. Song, Yujing McClellan, Brandon L. Su, Shiuan-Haur Xu, Sonnet Chen, Kevin Castro, Maria G. Singer, Benjamin H. Kurabayashi, Katsuo Department of Mechanical Engineering University of Michigan Ann ArborMI48109 United States Department of Neurosurgery University of Michigan Medical School Ann ArborMI48109 United States Department of Cell and Developmental Biology University of Michigan Medical School Ann ArborMI48109 United States Graduate Program in Immunology University of Michigan Medical School Ann ArborMI48109 United States Department of Biomedical Engineering University of Michigan Ann ArborMI48109 United States Rogel Cancer Center University of Michigan Ann ArborMI48109 United States Department of Internal Medicine Division of Pulmonary and Critical Care Medicine University of Michigan Ann ArborMI48109 United States Department of Electrical Engineering and Computer Science University of Michigan Ann ArborMI48109 United States Weil Institute for Critical Care Research and Innovation University of Michigan Ann ArborMI48109 United States

The search for reliable protein biomarker candidates is critical for early disease detection and treatment. However, current immunoassay technologies are failing to meet increasing demands for sensitivity and multiplexing. Here, the authors have created a highly sensitive protein microarray using the principle of single-molecule counting for signal amplification, capable of simultaneously detecting a panel of cancer biomarkers at sub-pg/mL levels. To enable this amplification strategy, the authors introduce a novel method of protein patterning using photolithography to subdivide addressable arrays of capture antibody spots into hundreds of thousands of individual microwells. This allows for the total sensor area to be miniaturized, increasing the total possible multiplex capacity. With the immunoassay realized on a standard 75x25 mm form factor glass substrate, sample volume consumption is minimized to © 2023, The Authors. All rights reserved.

关键词： Biomarkers

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The IBEX Imaging Knowledge-Base: A Community Resource Enabling Adoption and Development of Immunofluoresence Imaging Methods

arXiv

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arXiv 2024年

作者： Yaniv, Ziv Anidi, Ifeanyichukwu U. Arakkal, Leanne Arroyo-Mejías, Armando J. Beuschel, Rebecca T. Börner, Katy Chu, Colin J. Clark, Beatrice Clatworthy, Menna R. Colautti, Jake Coscia, Fabian Croteau, Joshua Denha, Saven Dever, Rose Dutra, Walderez O. Fritzsche, Sonja Fullam, Spencer Gerner, Michael Y. Gola, Anita Gollob, Kenneth J. Hernandez, Jonathan M. Hor, Jyh Liang Ichise, Hiroshi Jing, Zhixin Jonigk, Danny Kandov, Evelyn Kastenmüller, Wolfgang Koenig, Joshua F.E. Kothurkar, Aanandita Kortekaas, Rosa K. Kreins, Alexandra Y. Lamborn, Ian T. Lin, Yuri Morais, Katia Luciano Pereira Lunich, Aleksandra Luz, Jean C.S. MacDonald, Ryan B. Makranz, Chen Maltez, Vivien I. McDonough, John E. Moriarty, Ryan V. Ocampo-Godinez, Juan M. Olyntho, Vitoria M. Oxenius, Annette Padhan, Kartika Remmert, Kirsten Richoz, Nathan Schrom, Edward C. Shang, Wanjing Shi, Lihong Shih, Rochelle M. Speranza, Emily Stierli, Salome Teichmann, Sarah A. Veres, Tibor Z. Vierhout, Megan Wachter, Brianna T. Williams, Margaret Zangger, Nathan Germain, Ronald N. Radtke, Andrea J. Bioinformatics and Computational Bioscience Branch National Institute of Allergy and Infectious Diseases National Institutes of Health BethesdaMD United States Critical Care Medicine and Pulmonary Branch National Heart Lung and Blood Institute National Institutes of Health BethesdaMD United States Lymphocyte Biology Section Laboratory of Immune System Biology NIAID NIH BethesdaMD United States Department of Intelligent Systems Engineering Indiana University BloomingtonIN United States UCL Institute of Ophthalmology NIHR Moorfields Biomedical Research Centre London United Kingdom Cambridge Institute for Therapeutic Immunology and Infectious Diseases University of Cambridge Department of Medicine Molecular Immunity Unit Laboratory of Molecular Biology Cambridge United Kingdom McMaster Immunology Research Centre Schroeder Allergy and Immunology Research Institute Department of Medicine Faculty of Health Sciences McMaster University HamiltonON Canada Spatial Proteomics Group Berlin Germany Department of Business Development BioLegend Inc. San DiegoCA United States Functional Immunogenomics Unit National Institute of Arthritis and Musculoskeletal and Skin Diseases National Institutes of Health BethesdaMD United States Laboratory of Cell-Cell Interactions Department of Morphology Institute of Biological Sciences Universidade Federal de Minas Gerais MG Belo Horizonte Brazil Division of Rheumatology Rush University Medical Center ChicagoIL United States Department of Immunology University of Washington School of Medicine SeattleWA United States Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development The Rockefeller University New YorkNY United States Hospital Israelita Albert Einstein SP Sao Paulo Brazil Surgical Oncology Program National Cancer Institute National Institutes of Health BethesdaMD United States Institute of Pathology Aachen Medical University RWTH Aachen Aachen Germany Hannover Germany Würzburg Institute

The iterative bleaching extends multiplexity (IBEX) Knowledge-Base is a central portal for researchers adopting IBEX and related 2D and 3D immunofluorescence imaging methods. The design of the Knowledge-Base is modeled after efforts in the open-source software community and includes three facets: a development platform (GitHub), static website, and service for data archiving. The Knowledge-Base facilitates the practice of open science throughout the research life cycle by providing validation data for recommended and non-recommended reagents, e.g., primary and secondary antibodies. In addition to reporting negative data, the Knowledge-Base empowers method adoption and evolution by providing a venue for sharing protocols, videos, datasets, software, and publications. A dedicated discussion forum fosters a sense of community among researchers while addressing questions not covered in published manuscripts. Together, scientists from around the world are advancing scientific discovery at a faster pace, reducing wasted time and effort, and instilling greater confidence in the resulting data. © 2024, CC BY.

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Author Correction: Senolytic CAR T cells reverse senescence-associated pathologies

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Nature 2024年第8004期627卷 E9页

作者： Corina Amor Judith Feucht Josef Leibold Yu-Jui Ho Changyu Zhu Direna Alonso-Curbelo Jorge Mansilla-Soto Jacob A Boyer Xiang Li Theodoros Giavridis Amanda Kulick Shauna Houlihan Ellinor Peerschke Scott L Friedman Vladimir Ponomarev Alessandra Piersigilli Michel Sadelain Scott W Lowe Louis V. Gerstner Jr Graduate School of Biomedical Sciences Memorial Sloan Kettering Cancer Center New York NY USA. Department of Cancer Biology and Genetics Sloan Kettering Institute Memorial Sloan Kettering Cancer Center New York NY USA. Center for Cell Engineering Memorial Sloan Kettering Cancer Center New York NY USA. Immunology Program Sloan Kettering Institute Memorial Sloan Kettering Cancer Center New York NY USA. Molecular Pharmacology and Chemistry Program Memorial Sloan Kettering Cancer Center New York NY USA. Weill Cornell Graduate School of Medical Sciences New York NY USA. Department of Laboratory Medicine Memorial Sloan Kettering Cancer Center New York NY USA. Division of Liver Diseases Icahn School of Medicine at Mount Sinai New York NY USA. Department of Radiology Memorial Sloan Kettering Cancer Center New York NY USA. Laboratory of Comparative Pathology Rockefeller University Weill Cornell Medicine and Memorial Sloan Kettering Cancer Center New York NY USA. Center for Cell Engineering Memorial Sloan Kettering Cancer Center New York NY USA. m-sadelain@***. Immunology Program Sloan Kettering Institute Memorial Sloan Kettering Cancer Center New York NY USA. m-sadelain@***. Department of Cancer Biology and Genetics Sloan Kettering Institute Memorial Sloan Kettering Cancer Center New York NY USA. lowes@***. Howard Hughes Medical Institute Chevy Chase MD USA. lowes@***.

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The IBEX Knowledge-Base: Achieving more together with open science

arXiv

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arXiv 2024年

作者： Radtke, Andrea J. Anidi, Ifeanyichukwu Arakkal, Leanne Arroyo-Mejias, Armando Beuschel, Rebecca T. Börner, Katy Chu, Colin J. Clark, Beatrice Clatworthy, Menna R. Colautti, Jake Croteau, Joshua Denha, Saven Dever, Rose Dutra, Walderez O. Fritzsche, Sonja Fullam, Spencer Gerner, Michael Y. Gola, Anita Gollob, Kenneth J. Hernandez, Jonathan M. Hor, Jyh Liang Ichise, Hiroshi Jing, Zhixin Jonigk, Danny Kandov, Evelyn Kastenmüller, Wolfgang Koenig, Joshua F.E. Kothurkar, Aanandita Kreins, Alexandra Y. Lamborn, Ian Lin, Yuri Morais, Katia Luciano Pereira Lunich, Aleksandra Luz, Jean C.S. MacDonald, Ryan B. Makranz, Chen Maltez, Vivien I. Moriaty, Ryan V. Ocampo-Godinez, Juan M. Olyntho, Vitoria M. Padhan, Kartika Remmert, Kirsten Richoz, Nathan Schrom, Edward C. Shang, Wanjing Shi, Lihong Shih, Rochelle M. Speranza, Emily Stierli, Salome Teichmann, Sarah A. Veres, Tibor Z. Vierhout, Megan Wachter, Brianna T. Wade-Vallance, Adam K. Williams, Margaret Zangger, Nathan Germain, Ronald N. Yaniv, Ziv Lymphocyte Biology Section Center for Advanced Tissue Imaging Laboratory of Immune System Biology National Institute of Allergy and Infectious Diseases National Institutes of Health BethesdaMD United States Critical Care Medicine and Pulmonary Branch National Heart Lung and Blood Institute National Institutes of Health BethesdaMD United States Lymphocyte Biology Section Laboratory of Immune System Biology National Institute of Allergy and Infectious Diseases National Institutes of Health BethesdaMD United States Department of Intelligent Systems Engineering Indiana University BloomingtonIN United States UCL Institute of Ophthalmology NIHR Moorfields Biomedical Research Centre London United Kingdom Cambridge Institute for Therapeutic Immunology and Infectious Diseases University of Cambridge Department of Medicine Molecular Immunity Unit Laboratory of Molecular Biology Cambridge United Kingdom McMaster Immunology Research Centre Schroeder Allergy and Immunology Research Institute Department of Medicine Faculty of Health Sciences McMaster University HamiltonON Canada Department of Business Development BioLegend Inc. San DiegoCA United States Functional Immunogenomics Unit National Institute of Arthritis and Musculoskeletal and Skin Diseases National Institutes of Health BethesdaMD United States Laboratory of Cell-Cell Interactions Department of Morphology Institute of Biological Sciences Universidade Federal de Minas Gerais MG Belo Horizonte Brazil Spatial Proteomics Group Berlin Germany Division of Rheumatology Rush University Medical Center ChicagoIL United States Department of Immunology University of Washington School of Medicine SeattleWA United States Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development The Rockefeller University New YorkNY United States Hospital Israelita Albert Einstein SP Sao Paulo Brazil Surgical Oncology Program National Cancer Institute National Institutes of Health BethesdaMD United St

Iterative Bleaching Extends multipleXity (IBEX) is a versatile method for highly multiplexed imaging of diverse tissues. Based on open science principles, we created the IBEX Knowledge-Base, a resource for reagents, p... 详细信息

关键词： Cleaning

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Serotonin transporter inhibits antitumor immunity through regulating the intratumoral serotonin axis

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cell 2025年

作者： Li, Bo Elsten-Brown, James Li, Miao Zhu, Enbo Li, Zhe Chen, Yuning Kang, Elliot Ma, Feiyang Chiang, Jennifer Li, Yan-Ruide Zhu, Yichen Huang, Jie Fung, Audrey Scarborough, Quentin Cadd, Robin Zhou, Jin J. Chin, Arnold I. Pellegrini, Matteo Yang, Lili Department of Microbiology Immunology and Molecular Genetics University of California Los Angeles Los Angeles 90095 CA United States Department of Materials Science and Engineering University of California Los Angeles Los Angeles 90095 CA United States Department of Molecular Cell and Developmental Biology University of California Los Angeles Los Angeles 90095 CA United States Department of Biostatistics Fielding School of Public Health University of California Los Angeles Los Angeles CA United States Department of Urology University of California Los Angeles Los Angeles 90095 CA United States Eli & Edythe Broad Center of Regenerative Medicine and Stem Cell Research University of California Los Angeles Los Angeles 90095 CA United States Jonsson Comprehensive Cancer Center David Geffen School of Medicine University of California Los Angeles Los Angeles 90095 CA United States Bioinformatics Interdepartmental Program University of California Los Angeles Los Angeles 90095 CA United States Institute for Quantitative and Computational Biosciences-The Collaboratory University of California Los Angeles Los Angeles 90095 CA United States Department of Bioengineering University of California Los Angeles Los Angeles 90095 CA United States Goodman-Luskin Microbiome Center University of California Los Angeles Los Angeles 90095 CA United States Molecular Biology Institute University of California Los Angeles Los Angeles 90095 CA United States Parker Institute for Cancer Immunotherapy University of California Los Angeles Los Angeles 90095 CA United States

Identifying additional immune checkpoints hindering antitumor T cell responses is key to the development of next-generation cancer immunotherapies. Here, we report the induction of serotonin transporter (SERT), a regulator of serotonin levels and physiological functions in the brain and peripheral tissues, in tumor-infiltrating CD8 T cells. Inhibition of SERT using selective serotonin reuptake inhibitors (SSRIs), the most widely prescribed antidepressants, significantly suppressed tumor growth and enhanced T cell antitumor immunity in various mouse syngeneic and human xenograft tumor models. Importantly, SSRI treatment exhibited significant therapeutic synergy with programmed cell death protein 1 (PD-1) blockade, and clinical data correlation studies negatively associated intratumoral SERT expression with patient survival in a range of cancers. Mechanistically, SERT functions as a negative-feedback regulator inhibiting CD8 T cell reactivities by depleting intratumoral T cell-autocrine serotonin. These findings highlight the significance of the intratumoral serotonin axis and identify SERT as an immune checkpoint, positioning SSRIs as promising candidates for cancer immunotherapy. © 2025 The Authors

关键词： antidepressants cancer immunotherapy immune checkpoint intratumoral serotonin axis PD-1 blockade serotonin serotonin transporter SSRIs T cell antitumor immunity tumor microenvironment

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