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Extensive intrathecal T cell renewal following hematopoietic transplantation for multiple sclerosis

Harris et al.
JCI Insight
January 2020
Authors and Affiliates
Kristina M. Harris1, Noha Lim1, Paul Lindau2, Harlan Robins2,3, Linda M. Griffith4, Richard A. Nash5, Laurence A. Turka1,6, and Paolo A. Muraro7 1Immune Tolerance Network (ITN), Bethesda, Maryland, USA 2Fred Hutchinson Cancer Research Center, Seattle, Washington, USA 3Adaptive Biotechnologies, Seattle, Washington, USA 4 Division of Allergy, Immunology and Transplantation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA 5Colorado Blood Cancer Institute at Presbyterian / St. Luke’s, Denver, Colorado, USA 6Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts, USA 7Department of Brain Sciences, Department of Medicine, Imperial College London, London, United Kingdom

Comprehensive T cell repertoire characterization of non-small cell lung cancer

Reuben et al.
Nature Communications
January 2020
Authors and Affiliates
Alexandre Reuben,#1,2 Jiexin Zhang,#3 Shin-Heng Chiou,#4 Rachel M. Gittelman,#5 Jun Li,6 Won-Chul Lee,6 Junya Fujimoto,7 Carmen Behrens,1,7 Xiaoke Liu,1 Feng Wang,6 Kelly Quek,1 Chunlin Wang,8 Farrah Kheradmand,9 Runzhe Chen,1 Chi-Wan Chow,7 Heather Lin,3 Chantale Bernatchez,10 Ali Jalali,11 Xin Hu,6 Chang-Jiun Wu,6 Agda Karina Eterovic,12 Edwin Roger Parra,7 Erik Yusko,5 Ryan Emerson,5 Sharon Benzeno,5 Marissa Vignali,5 Xifeng Wu,13 Yuanqing Ye,13 Latasha D. Little,6 Curtis Gumbs,6 Xizeng Mao,10 Xingzhi Song,6 Samantha Tippen,6 Rebecca L. Thornton,6 Tina Cascone,1 Alexandra Snyder,5 Jennifer A. Wargo,2,6 Roy Herbst,14 Stephen Swisher,15 Humam Kadara,7 Cesar Moran,16 Neda Kalhor,16 Jianhua Zhang,6 Paul Scheet,13 Ara A. Vaporciyan,15 Boris Sepesi,15 Don L. Gibbons,1 Harlan Robins,5,17 Patrick Hwu,10 John V. Heymach,1 Padmanee Sharma,18,19 James P. Allison,19 Veera Baladandayuthapani,20 Jack J. Lee,20 Mark M. Davis,corresponding author21 Ignacio I. Wistuba,corresponding author1,7 P. Andrew Futreal,corresponding author6 and Jianjun Zhangcorresponding author1,6; 1Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030 USA 2Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030 USA 3Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030 USA 4Institute for Immunity, Transplantation, and Infection Operations, Howard Hughes Medical Institute, 450 Serra Mall, Stanford, CA 94305 USA 5Adaptive Biotechnologies, 1551 Eastlake Ave East, Seattle, WA 98102 USA 6Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030 USA 7Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030 USA 8iRepertoire, Inc., 800 Hudson Way, Suite 2304, Huntsville, AL 35806 USA 9Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030 USA 10Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030 USA 11Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030 USA 12Department of Systems Biology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030 USA 13Department of Epidemiology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030 USA 14Department of Medical Oncology, 333 Cedar Street, Yale Cancer Center, New Haven, CT 06510 USA 15Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030 USA 16Department of Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030 USA 17Computational Biology Program, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave North, Seattle, WA 98109 USA 18Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030 USA 19Department of Immunology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030 USA 20Department of Biostatistics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030 USA 21Department of Microbiology and Immunology, Howard Hughes Medical Institute, Stanford, 450 Serra Mall, Stanford, CA 94305 USA

Molecular analysis of primary melanoma T cells identifies patients at risk for metastatic recurrence

Pruessmann et al.
Nature Cancer
January 2020
Authors and Affiliates
Wiebke Pruessmann 1,8,10, Julie Rytlewski 2,10, James Wilmott 3,10, Martin C. Mihm Jr1, Grace H. Attrill3, Beatrice Dyring-Andersen1,9, Paul Fields 2, Qian Zhan1, Andrew J. Colebatch3,4, Peter M. Ferguson3,4, John F. Thompson 3,5, Klaus Kallenbach6, Erik Yusko2, Rachael A. Clark1, Harlan Robins2,7, Richard A. Scolyer 3,4,10 and Thomas S. Kupper 1,10*; 1Department of Dermatology and Harvard Medical School, Brigham and Women’s Hospital, Boston, MA, USA. 2Adaptive Biotechnologies, Seattle, WA, USA. 3Melanoma Institute Australia, University of Sydney, Sydney, New South Wales, Australia. 4Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia. 5Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia. 6Department of Surgical Pathology, Zealand University Hospital, Roskilde, Denmark. 7Fred Hutchinson Cancer Research Center, Seattle, WA, USA. 8Present address: Department of Dermatology, University of Luebeck, Luebeck, Germany. 9Present address: Novo Nordisk Foundation Centre for Protein Research, University of Copenhagen, Copenhagen, Denmark. 10These authors contributed equally: Wiebke Pruessmann, Julie Rytlewski, James Wilmott, Richard A. Scolyer, Thomas S. Kupper.

Mutation-derived Neoantigen-specific T-cell Responses in Multiple Myeloma

Perumal et al.
Clinical Cancer Research
January 2020
Authors and Affiliates
Perumal D1,2, Imai N1,2, Laganà A3,4, Finnigan J1,2,5, Melnekoff D3,4, Leshchenko VV1,2, Solovyov A5,6,7, Madduri D1,2, Chari A1,2, Cho HJ1,2, Dudley JT3,4, Brody JD1,2,5, Jagannath S1,2, Greenbaum B5,6,7, Gnjatic S2,5, Bhardwaj N1,2,5, Parekh S8,2. Author information 1 Department of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, New York. 2 Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York. 3 Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York. 4 Institute for Next Generation Healthcare, Icahn School of Medicine at Mount Sinai, New York, New York. 5 Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York. 6 Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York. 7 Center for Computational Immunology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York. 8 Department of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, New York. samir.parekh@mssm.edu.

Intratumoral heterogeneity and clonal evolution in liver cancer

Losic et al.
Nature Communications
January 2020
Authors and Affiliates
Losic B1,2,3, Craig AJ4, Villacorta-Martin C4, Martins-Filho SN4,5, Akers N1,6, Chen X1, Ahsen ME1, von Felden J4,7, Labgaa I4,8, DʹAvola D4,9, Allette K1,2, Lira SA10, Furtado GC10, Garcia-Lezana T4, Restrepo P1, Stueck A11, Ward SC12, Fiel MI12, Hiotis SP13, Gunasekaran G13, Sia D4, Schadt EE2,14, Sebra R1,2,14, Schwartz M13, Llovet JM4,15,16, Thung S12, Stolovitzky G1,17, Villanueva A18,19; 1 Department of Genetics and Genomic Sciences, Cancer Immunology Program, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA. 2 Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA. 3 Diabetes, Obesity and Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA. 4 Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA. 5 Department of Pathology, University of Sao Paulo School of Medicine, Sao Paulo, Brazil. 6 Adaptive Biotechnologies, Seattle, WA, USA. 7 I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany. 8 Department of Visceral Surgery, Lausanne University Hospital CHUV, Lausanne, Switzerland. 9 Liver Unit and Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Clínica Universidad de Navarra, Pamplona, Spain. 10 Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA. 11 Department of Pathology, Dalhousie University, Halifax, NS, Canada. 12 Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA. 13 Department of Surgery, Icahn School of Medicine at Mount Sinai, New York, NY, USA. 14 Sema4, a Mount Sinai venture, Stamford, CT, USA. 15 Liver Cancer Translational Research Laboratory, BCLC Group, IDIBAPS, Hospital Clinic, Universitat de Barcelona, Barcelona, Catalonia, Spain. 16 Institució Catalana de Recerca i Estudis Avançats, Barcelona, Catalonia, Spain. 17 IBM T. J. Watson Research Center, Yorktown Heights, New York, NY, USA. 18 Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA. augusto.villanueva@mssm.edu. 19 Division of Hematology and Medical Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA. augusto.villanueva@mssm.edu.

Predominance of central memory T cells with high T-cell receptor repertoire diversity is associated with response to PD-1/PD-L1 inhibition in Merkel cell carcinoma

Spassova et al.
Clinical Cancer Research
January 2020
Authors and Affiliates
Ivelina Spassova1*, Selma Ugurel2*, Patrick Terheyden3, Antje Sucker2, Jessica Hassel4, Cathrin Ritter1, Linda Kubat1, Daniel Habermann5, Farnoush Farahpour5, Mohammadkarim Saeedghalati5, Lukas Peiffer1,6, Rajiv Kumar6,7, David Schrama8, Daniel Hoffmann5, Dirk Schadendorf2, Jürgen C. Becker1,2,6* 1Translational Skin Cancer Research, German Consortium for Translational Cancer Research (Deutsches Konsortium für Translationale Krebsforschung; DKTK), Essen, Germany. 2Department of Dermatology, University Hospital of Essen, Essen, Germany. 3Department of Dermatology, University Hospital of Lübeck, Lübeck, Germany. 4Department of Dermatology, University Hospital of Heidelberg, Germany. 5Bioinformatics and Computational Biophysics, University of Duisburg-Essen, Essen, Germany. 6German Cancer Research Center (Deutsches Krebsforschungs Zentrum, DKFZ), Heidelberg, Germany 7Division of Molecular Genetic Epidemiology, Heidelberg, Germany. 8Department of Dermatology, University Hospital of Würzburg, Germany. *equal contribution

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

Sheih et al.
Nature Communications
January 2020
Authors and Affiliates
Sheih A1, Voillet V2, Hanafi LA1, DeBerg HA3, Yajima M4, Hawkins R1, Gersuk V3, Riddell SR1,5,6, Maloney DG1,5,6, Wohlfahrt ME1, Pande D1, Enstrom MR1, Kiem HP1,5,7, Adair JE1,5,6, Gottardo R2,5,6, Linsley PS3, Turtle CJ8,9,10; 1 Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, USA. 2 Vaccine and Infectious Disease Division and Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, USA. 3 Benaroya Research Institute at Virginia Mason, Seattle, Washington, 98101, USA. 4 Department of Mathematics and Statistics, Boston University, Boston, Massachusetts, 02215, USA. 5 Department of Medicine, University of Washington, Seattle, Washington, USA. 6 Integrated Immunotherapy Research Center, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, USA. 7 Department of Pathology, University of Washington, Seattle, Washington, USA. 8 Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, USA. cturtle@fredhutch.org. 9 Department of Medicine, University of Washington, Seattle, Washington, USA. cturtle@fredhutch.org. 10 Integrated Immunotherapy Research Center, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, USA. cturtle@fredhutch.org

Identification of human CD4+ T cell populations with distinct antitumor activity

Nelson et al.
bioRxiv
January 2020
Authors and Affiliates
Michelle H. Nelson†1,2, Hannah M. Knochelmann†1,2, Stefanie R. Bailey1,2, Logan W. Huff1,2, 4 Jacob S. Bowers1,2, Kinga Majchrzak1,2, Megan M. Wyatt1,2, Mark P. Rubinstein1,3, Shikhar 5 Mehrotra1,3, Michael I. Nishimura4, Kent E. Armeson5, Paul G. Giresi6, Michael J. Zilliox7, Hal 6 E. Broxmeyer8, Chrystal M. Paulos1,2*; †Contributed equally to this work *Corresponding author; Affiliations: 1Department of Microbiology & Immunology, Medical University of South Carolina, Charleston, SC, USA. 2Department of Dermatology & Dermatologic Surgery, Medical University of South Carolina, SC, USA. 3Department of Surgery, Medical University of South Carolina, Charleston, SC, USA. 4Department of Surgery, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA. 5Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC, USA. 6Epinomics, Menlo Park, CA, USA. 7Department of Public Health Sciences, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA. 8Department of Microbiology & Immunology, Indiana University School of Medicine, Indianapolis, IN, USA.

Identifying the inheritable component of human thymic T cell repertoire generation in monozygous twins

Heikkilä et al.
European Journal of Immunology
December 2019
Authors and Affiliates
Heikkilä N1,2, Vanhanen R1,2, Yohannes DA1,3, Saavalainen P1,3, Meri S1,2, Jokiranta TS2, Jarva H2, Mattila IP4, Hamm D5, Sormunen S6, Saramäki J6, Arstila TP1,2; 1 Research Programs Unit, Translational Immunology, University of Helsinki, Helsinki, Finland. 2 Medicum, Department of Bacteriology and Immunology, University of Helsinki, Helsinki, Finland. 3 Medicum, Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland. 4 Department of Pediatric Cardiac and Transplantation Surgery, Hospital for Children and Adolescents, Helsinki University Central Hospital, Helsinki, Finland. 5 Adaptive Biotechnologies, Seattle, Washington. 6 Department of Computer Science, Aalto University, Finland.

Somatic mutations and T-cell clonality in patients with immunodeficiency

Savola et al.
Haematologica
December 2019
Authors and Affiliates
Savola P1, Martelius T2, Kankainen M3, Huuhtanen J1, Lundgren S1, Koski Y1, Eldfors S3, Kelkka T1, Keränen MAI1, Ellonen P3, Kovanen PE4, Kytölä S5, Saarela J3, Lähdesmäki H6, Seppänen MRJ7, Mustjoki S8; 1 Hematology Research Unit Helsinki, University of Helsinki, HUS, Helsinki, Finland. 2 Adult Immunodeficiency Unit, Infectious Diseases, HUS Helsinki University Hospital, Finland. 3 Institute for Molecular Medicine Finland (FIMM), HILIFE, University of Helsinki, Finland. 4 Dept. of Pathology, University of Helsinki and HUSLAB, HUS Helsinki University Hospital, Finland. 5 Laboratory of Genetics, HUSLAB, HUS Helsinki University Hospital, Finland. 6 Department of Computer Science, Aalto University School of Science, Finland. 7 Rare Diseases Center & Pediatric Research Center, HUS Helsinki University Hospital, Finland. 8 Hematology Research Unit Helsinki, University of Helsinki, HUS, Helsinki, Finland; satu.mustjoki@helsinki.fi.
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