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High-throughput sequencing of the B-cell receptor in African Burkitt lymphoma reveals clues to pathogenesis

Lombardo et al.
Blood
Papers
March 2017
Authors and Affiliates
Katharine A. Lombardo,1,2 David G. Coffey,1,3 Alicia J. Morales,1 Christopher S. Carlson,4 Andrea M. H. Towlerton,1 Sarah E. Gerdts,5 Francis K. Nkrumah,6 Janet Neequaye,7 Robert J. Biggar,8 Jackson Orem,9 Corey Casper,1,3-5,10,11 Sam M. Mbulaiteye,12 Kishor G. Bhatia,12 and Edus H. Warren1,3 1Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA; 2Molecular and Cellular Biology Program and 3Department of Medicine, School of Medicine, University of Washington, Seattle, WA; 4Division of Public Health Sciences and 5Division of Vaccine and Infectious Diseases, Fred Hutchinson Cancer Research Center, Seattle, WA; 6Noguchi Institute for Medical Research and 7Department of Child Health, Medical School, University of Ghana, Accra, Ghana; 8Institute of Health and Biotechnical Innovation, Queensland University of Technology, Brisbane, QLD, Australia; 9Uganda Cancer Institute, Kampala, Uganda; 10Department of Global Health, School of Medicine, and 11Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA; and 12Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD

Antigen presentation profiling reveals recognition of lymphoma immunoglobulin neoantigens

Khodadoust et al.
Nature
Papers
March 2017
Authors and Affiliates
Michael S. Khodadoust1, Niclas Olsson2, Lisa E. Wagar3, Ole A. W. Haabeth1, Binbin Chen1,4, Kavya Swaminathan2, Keith Rawson2, Chih Long Liu1, David Steiner5, Peder Lund3, Samhita Rao2, Lichao Zhang2, Caleb Marceau3, Henning Stehr1, Aaron M. Newman1,6, Debra K. Czerwinski1, Victoria E. H. Carlton7, Martin Moorhead7, Malek Faham7, Holbrook E. Kohrt1, Jan Carette3, Michael R. Green1, Mark M. Davis3,8, Ronald Levy1, Joshua E. Elias2 & Ash A. Alizadeh1,6,9 1Department of Medicine, Division of Oncology, Stanford University, Stanford, California 94305, USA. 2Department of Chemical & Systems Biology, Stanford University, Stanford, California 94305, USA. 3Department of Microbiology & Immunology, Stanford University, Stanford, California 94305, USA. 4Department of Genetics, Stanford University, Stanford, California 94305, USA. 5Department of Pathology, Stanford University, Stanford, California 94305, USA. 6Center for Cancer Systems Biology, Stanford University, Stanford, California 94305, USA. 7Adaptive Biotechnologies, South San Francisco, California 94080, USA. 8Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA. 9Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, California 94305, USA.

PD-L1 on tumor cells is sufficient for immune evasion in immunogenic tumors and inhibits CD8 T cell cytotoxicity

Juneja et al.
Journal of Experimental Medicine
Papers
March 2017
Authors and Affiliates
Vikram R. Juneja,1,2,5 Kathleen A. McGuire,2,5 Robert T. Manguso,3,6 Martin W. LaFleur,2,5,6 Natalie Collins,4,6,8 W. Nicholas Haining,4,6,8 Gordon J. Freeman,7 and Arlene H. Sharpe2,5 1Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA 02139, 2Department of Microbiology and Immunobiology, 3Division of Medical Sciences, and 4Division of Hematology/Oncology, Children's Hospital, Harvard Medical School, Boston, MA 02115, 5Evergrande Center for Immunological Diseases, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA 02115, 6Department of Pediatric Oncology and 7Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, 8Broad Institute of MIT and Harvard, Cambridge, MA 02142

T-cell infiltration and clonality correlate with programmed cell death protein 1 and programmed death-ligand 1 expression in patients with soft tissue sarcomas

Pollack et al.
Cancer
Papers
March 2017
Authors and Affiliates
Seth M. Pollack, MD1,2; Qianchuan He, PhD1,3; Jennifer H. Yearley, PhD4; Ryan Emerson, PhD5; Marissa Vignali, PhD5; Yuzheng Zhang, MA1,3; Mary W. Redman, PhD1; Kelsey K. Baker, MA1; Sara Cooper, MS1; Bailey Donahue, BS1; Elizabeth T. Loggers, MD, PhD1,2; Lee D. Cranmer, MD, PhD1,2; Matthew B. Spraker, MD, PhD6; Y. David Seo, MD7; Venu G. Pillarisetty, MD7; Robert W. Ricciotti, MD8; Benjamin L. Hoch, MD8; Terrill K. McClanahan, PhD4; Erin Murphy, BS4; Wendy M. Blumenschein, BA4; Steven M. Townson, PhD4; Sharon Benzeno, PhD5; Stanley R. Riddell, MD, PhD1,2,9; and Robin L. Jones, MD1,2,10 1Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; 2Department of Medicine, University of Washington, Seattle, Washington; 3Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; 4Merck & Co., Inc. Kenilworth New Jersey; 5Adaptive Biotechnologies Corporation, Seattle, Washington; 6Department of Radiation Oncology, University of Washington, Seattle, Washington; 7Department of Surgery, University of Washington, Seattle, Washington; 8Department of Pathology, University of Washington, Seattle, Washington; 9Institute for Advanced Study, Technical University of Munich, Munich, Germany; 10Royal Marsden Hospital and Institute of Cancer Research, London.

Neutrophils dominate the immune cell composition in non-small cell lung cancer

Kargl et al.
Nature Communications
Papers
February 2017
Authors and Affiliates
Julia Kargl1,2, Stephanie E. Busch1, Grace H.Y. Yang1, Kyoung-Hee Kim1, Mark L. Hanke1, Heather E. Metz1, Jesse J. Hubbard1, Sylvia M. Lee1, David K. Madtes1,3, Martin W. McIntosh4 & A. McGarry Houghton1,3,5 1Clinical Research Division, Seattle, Washington 98109, USA. 2Institute of Experimental and Clinical Pharmacology, Medical University of Graz, Universitaetsplatz 4, Graz 8010, Austria. 3Division of Pulmonary and Critical Care Medicine, University of Washington, Campus Box 356522, Seattle, Washington 98195-6522, USA. 4Public Health Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N, Seattle, Washington 98109, USA. 5Human Biology Division, Seattle, Washington 98109, USA

Selective expansion of high functional avidity memory CD8 T cell clonotypes during hepatitis C virus reinfection and clearance

Abdel-Hakeem et al.
Papers
PLOS Pathogens
February 2017
Authors and Affiliates
Mohamed S. Abdel-Hakeem1,2,3, Maude Boisvert1, Julie Bruneau1,4, Hugo Soudeyns3,5, Naglaa H. Shoukry1,6 1Centre de Recherche du Centre Hospitalier de l’Universite de Montreal (CRCHUM), Montreal, Quebec, Canada, 2Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt, 3Departement de microbiologie, infectiologie et immunologie, Universite de Montreal, Montreal, Quebec, Canada, 4Departement de me decine familiale et de medecine d’urgence, Universite de Montreal, Montreal, Quebec,Canada, 5Centre hospitalier universitaire Sainte-Justine, Montreal, Quebec, Canada, 6Departement de medecine, Universite de Montreal, Montreal, Quebec, Canada

Identification of patient-specific and tumor-shared T cell receptor sequences in renal cell carcinoma patients

Massa et al.
Oncotarget
Papers
February 2017
Authors and Affiliates
Chiara Massa1, Harlan Robins2, Cindy Desmarais2, Dagmar Riemann1, Corinna Fahldieck1, Paolo Fornara3, Barbara Seliger1 1Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, 06112 Halle (Saale), Germany 2Adaptive Biotechnologies Corp, 98102 Seattle (WA), USA 3Clinic of Urology, Martin Luther University Halle-Wittenberg, 06112 Halle (Saale), Germany

Class I-restricted T-cell responses to a polymorphic peptide in a gene therapy clinical trial for α-1-antitrypsin deficiency

Calcedoa et al.
Papers
Proceedings of the National Academy of Sciences
February 2017
Authors and Affiliates
Roberto Calcedoa, Suryanarayan Somanathana, Qiuyue Qina, Michael R. Bettsb, Andrew J. Rechc, Robert H. Vonderheidec, Christian Muellerd, Terence R. Flotted, and James M. Wilsona aGene Therapy Program, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104; bDepartment of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104; cAbramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104; dDepartment of Pediatrics, University of Massachusetts Medical School, Worcester, MA 01655

CD49a Expression Defines Tissue-Resident CD8+ T Cells Poised for Cytotoxic Function in Human Skin

Cheuk et al.
Immunity
Papers
February 2017
Authors and Affiliates
Stanley Cheuk,1 Heinrich Schlums,2 Irene Gallais Serezal,1,3 Elisa Martini,1 Samuel C. Chiang,2 Nicole Marquardt,3 Anna Gibbs,1 Ebba Detlofsson,1 Andrea Introini,1 Marianne Forkel,3 Charlotte Hoog,4 Annelie Tjernlund,1 Jakob Michaelsson,3 Lasse Folkersen,5 Jenny Mjosberg,3 Lennart Blomqvist,6 Marcus Ehrstrom,7 Mona Stahle,1,3 Yenan T. Bryceson,2,8 and Liv Eidsmo1,3 1Department of Medicine Solna, Karolinska Institutet, Stockholm 171 77, Sweden, 2Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm 171 77, Sweden, 3Dermatology Department, Karolinska University Hospital, Stockholm 141 86, Sweden, 4Unit for Inflammation, Gastroenterology and Rheumatology, Department of Medicine, Huddinge, Karolinska Institutet, Stockholm 171 77, Sweden, 5Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Building 208, DK-2800 Kongens Lyngby 2800, Denmark, 6Unit for Endocrinology and Diabetes, Department of Medicine, Huddinge, Karolinska Institutet, Stockholm 171 77, Sweden, 7Department of Reconstructive Plastic Surgery, Karolinska University Hospital Solna, Stockholm 171 76, Sweden, 8Broegelmann Research Laboratory, Department of Clinical Science, University of Bergen, Bergen 5021, Norway

3D: diversity, dynamics, differential testing – a proposed pipeline for analysis of next-generation sequencing T cell repertoire data

Zhang et al.
BMC Bioinformatics
Papers
February 2017
Authors and Affiliates
Li Zhang1,3, Jason Cham2, Alan Paciorek3, James Trager4, Nadeem Sheikh5, and Lawrence Fong2 1Division of Hematology and Oncology, Department of Medicine, UCSF Helen Diller Family Comprehensive Cancer Center, 550 16th Street, 6th Floor, UCSF Box 0981, San Francisco, CA 94158, USA. 2Division of Hematology and Oncology, Department of Medicine, University of California, Room HSE301, UCSF Box 1270, 513 Parnassus Ave, San Francisco, CA 94143-1270, USA. 3Department of Epidemiology and Biostatistics, University of California, San Francisco, 550 16th Street, 6th Floor, UCSF Box 0981, San Francisco, CA 94158, USA. 4Research and Development, Nkarta, Inc, 329 Oyster Point Blvd, South San Francisco, CA 94080, USA. 5Department of Research - Translational Biology, Dendreon Pharmaceuticals Inc, 1208 Eastlake Ave E, Seattle, WA 98102, USA.
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