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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.

A critical insulin TCR contact residue selects high affinity and pathogenic insulin specific T cells

Bettini et al.
Diabetes
December 2019
Authors and Affiliates
Maria Bettini,1,2,7 Marissa A. Scavuzzo,4,6 Baoyu Liu,5 Elizabeth Kolawole,5 Lin Guo,1 Brian D. Evavold,5 Malgorzata Borowiak2,3,4 and Matthew L. Bettini1,2,7 1Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030 2 USA. 3 4 5Division of Microbiology and Immunology, Department of Pathology, University of Utah, Salt Lake City, UT 84112 6 Present address: Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH, 44106 USA 7Present address: Division of Microbiology and Immunology, Department of Pathology, University of Utah, Salt Lake City, UT 84112

Epigenetic and transcriptional analysis supports human regulatory T cell commitment at the CD4+CD8+ thymocyte stage

Vanhanen et al.
Cellular Immunology
December 2019
Authors and Affiliates
Vanhanen R1, Leskinen K2, Mattila IP3, Saavalainen P2, Arstila TP4; 1 Translational Immunology Research Program, University of Helsinki, 00014 Helsinki, Finland. Electronic address: reetta.vanhanen@helsinki.fi. 2 Translational Immunology Research Program, University of Helsinki, 00014 Helsinki, Finland. 3 Department of Pediatric Cardiac and Transplantation Surgery, Hospital for Children and Adolescents, Helsinki University Central Hospital, 00290 Helsinki, Finland. 4 Translational Immunology Research Program, University of Helsinki, 00014 Helsinki, Finland; Medicum, University of Helsinki, 00014 Helsinki, Finland.

An intra-tumoral niche maintains and differentiates stem-like CD8 T cells

Jansen et al.
Nature
December 2019
Authors and Affiliates
Caroline S. Jansen1, Nataliya Prokhnevska1, Viraj A. Master1,2, Martin G. Sanda1,2, Jennifer W. Carlisle2,3, Mehmet Asim Bilen2,3, Maria Cardenas1, Scott Wilkinson4, Ross Lake4, Adam G. Sowalsky4, Rajesh M. Valanparambil5,6, William H. Hudson5,6, Donald McGuire5,6, Kevin Melnick1, Amir I. Khan1, Kyu Kim1, Yun Min Chang5, Alice Kim1, Christopher P. Filson1,2, Mehrdad Alemozaffar1,2, Adeboye O. Osunkoya1,2,7, Patrick Mullane7, Carla Ellis7, Rama Akondy5,6, Se Jin Im5,6, Alice O. Kamphorst8, Adriana Reyes1, Yuan Liu2,9 & Haydn Kissick1,2,5,6* 1Department of Urology, Emory University School of Medicine, Atlanta, GA, USA. 2Winship Cancer Institute of Emory University, Atlanta, GA, USA. 3Department of Hematology and Oncology, Emory University School of Medicine, Atlanta, GA, USA. 4Laboratory of Genitourinary Cancer Pathogenesis, National Cancer Institute, Bethesda, MD, USA. 5Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA. 6Emory Vaccine Centre, Emory University School of Medicine, Atlanta, GA, USA. 7Department of Pathology, Emory University School of Medicine, Atlanta, GA, USA. 8Department of Oncological Sciences, Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York City, NY, USA. 9Rollins School of Public Health, Emory University, Atlanta, GA, USA. *e-mail: haydn.kissick@emory.edu

B cell clonal expansion within immune infiltrates in human cardiac allograft vasculopathy

Moore et al.
American Journal of Transplantation
December 2019
Authors and Affiliates
Moore C1,2,3, Gao B1,4, Roskin KM2,3,5, Vasilescu EM6, Addonizio L7, Givertz MM8, Madsen JC1,9, Zorn E1,10. 1 Center for Transplantation Science, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA. 2 Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA. 3 Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA. 4 Transplant Center, The First Hospital of Jilin University, Changchun, China. 5 Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, Ohio, USA. 6 Department of Pathology & Cell Biology, Columbia University Medical Center, New York, New York, USA. 7 Division of Cardiothoracic Surgery, Department of Surgery, Columbia University Medical Center, New York, New York, USA. 8 Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA. 9 Division of Cardiac Surgery, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA. 10 Columbia Center for Translational Immunology, Columbia University Medical Center, New York, New York, USA.
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