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A hotspot mutation in transcription factor IKZF3 drives B cell neoplasia via transcriptional dysregulation

Lazarian G., et al.
Cancer Cell
March 2021
Authors and Affiliates
Gregory Lazarian 1, Shanye Yin 2, Elisa Ten Hacken 2, Tomasz Sewastianik 3, Mohamed Uduman 4, Alba Font-Tello 5, Satyen H Gohil 6, Shuqiang Li 7, Ekaterina Kim 8, Heather Joyal 9, Leah Billington 9, Elizabeth Witten 9, Mei Zheng 10, Teddy Huang 11, Mariano Severgnini 12, Valerie Lefebvre 13, Laura Z Rassenti 14, Catherine Gutierrez 2, Katia Georgopoulos 15, Christopher J Ott 16, Lili Wang 17, Thomas J Kipps 18, Jan A Burger 8, Kenneth J Livak 19, Donna S Neuberg 20, Fanny Baran-Marszak 21, Florence Cymbalista 21, Ruben D Carrasco 22, Catherine J Wu 23; 1 Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; INSERM, U978, Université Paris 13, Bobigny, France; Laboratoire d'Hématologie, APHP Hôpital Avicenne, Bobigny, France. 2 Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA. 3 Harvard Medical School, Boston, MA, USA; Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Experimental Hematology, Institute of Hematology and Transfusion Medicine, Warsaw, Poland. 4 Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA. 5 Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA. 6 Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Academic Haematology, University College London, London, UK. 7 Broad Institute of MIT and Harvard, Cambridge, MA, USA; Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA. 8 Department of Leukemia, the University of Texas MD Anderson Cancer Center, Houston, TX, USA. 9 Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA. 10 Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA. 11 Broad Institute of MIT and Harvard, Cambridge, MA, USA. 12 Center for Immuno-Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA. 13 Laboratoire d'Hématologie, APHP Hôpital Avicenne, Bobigny, France. 14 Moores Cancer Center, University of California, San Diego, USA. 15 Cutaneous Biology Research Center, Massachusetts General Hospital, Charlestown, MA, USA. 16 Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA. 17 Department of Systems Biology, Beckman Research Institute, City of Hope National Comprehensive Cancer Center, Monrovia, CA, USA. 18 Division of Hematology-Oncology, Department of Medicine, Moores Cancer Center, University of California, San Diego, USA. 19 Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA. 20 Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA. 21 INSERM, U978, Université Paris 13, Bobigny, France; Laboratoire d'Hématologie, APHP Hôpital Avicenne, Bobigny, France. 22 Harvard Medical School, Boston, MA, USA; Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA. 23 Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA. Electronic address: cwu@partners.org.

Global analysis of shared T cell specificities in human non-small cell lung cancer enables HLA inference and antigen discovery

Chiou S., et al.
Immunity
March 2021
Authors and Affiliates
Shin-Heng Chiou 1, Diane Tseng 2, Alexandre Reuben 3, Vamsee Mallajosyula 1, Irene S Molina 1, Stephanie Conley 4, Julie Wilhelmy 5, Alana M McSween 1, Xinbo Yang 6, Daisuke Nishimiya 6, Rahul Sinha 4, Barzin Y Nabet 7, Chunlin Wang 1, Joseph B Shrager 8, Mark F Berry 9, Leah Backhus 8, Natalie S Lui 8, Heather A Wakelee 10, Joel W Neal 10, Sukhmani K Padda 2, Gerald J Berry 11, Alberto Delaidelli 12, Poul H Sorensen 12, Elena Sotillo 13, Patrick Tran 13, Jalen A Benson 9, Rebecca Richards 14, Louai Labanieh 15, Dorota D Klysz 13, David M Louis 1, Steven A Feldman 13, Maximilian Diehn 16, Irving L Weissman 4, Jianjun Zhang 17, Ignacio I Wistuba 18, P Andrew Futreal 19, John V Heymach 3, K Christopher Garcia 20, Crystal L Mackall 21, Mark M Davis 22; 1 Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA. 2 Department of Medicine, Division of Oncology, Stanford University, Stanford, CA 94305, USA. 3 Department of Thoracic Head and Neck Medical Oncology, Division of Cancer Medicine, MD Anderson Cancer Center, Houston, TX 77030, USA. 4 Institute for Stem Cell Biology and Regenerative Medicine Institute, Stanford University, Stanford, CA 94305, USA. 5 Stanford Genome Technology Center, Stanford University, Stanford, CA 94305, USA. 6 Department of Molecular and Cellular Physiology and Structural Biology, Stanford University, Stanford, CA 94305, USA. 7 Department of Radiation Oncology, Stanford University, Stanford, CA 94305, USA. 8 Department of Cardiothoracic Surgery - Thoracic Surgery, Stanford University, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford, CA 94305, USA. 9 Department of Cardiothoracic Surgery - Thoracic Surgery, Stanford University, Stanford, CA 94305, USA. 10 Department of Medicine, Division of Oncology, Stanford University, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford, CA 94305, USA. 11 Department of Pathology, Stanford University, Stanford, CA 94305, USA. 12 Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada. 13 Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA. 14 Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA; Department of Pediatrics, Stanford University, Stanford, CA 94305, USA. 15 Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA. 16 Institute for Stem Cell Biology and Regenerative Medicine Institute, Stanford University, Stanford, CA 94305, USA; Department of Radiation Oncology, Stanford University, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford, CA 94305, USA. 17 Department of Thoracic Head and Neck Medical Oncology, Division of Cancer Medicine, MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genomic Medicine, Division of Cancer Medicine, MD Anderson Cancer Center, Houston, TX 77030, USA. 18 Department of Translational Molecular Pathology, Division of Pathology and Laboratory Medicine, MD Anderson Cancer Center, Houston, TX 77030, USA. 19 Department of Genomic Medicine, Division of Cancer Medicine, MD Anderson Cancer Center, Houston, TX 77030, USA. 20 Department of Molecular and Cellular Physiology and Structural Biology, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA. 21 Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA; Department of Pediatrics, Stanford University, Stanford, CA 94305, USA; Department of Medicine, Stanford University, Stanford, CA 94305, USA. 22 Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA. Electronic address: mmdavis@stanford.edu.

Molecular correlates of response to nivolumab at baseline and on treatment in patients with RCC

Ross-Macdonald P., et al.
Journal for ImmunoTherapy of Cancer
March 2021
Authors and Affiliates
Petra Ross-Macdonald 1, Alice M Walsh 1, Scott D Chasalow 1, Ron Ammar 1, Simon Papillon-Cavanagh 1, Peter M Szabo 1, Toni K Choueiri 2, Mario Sznol 3, Megan Wind-Rotolo 4; 1 Translational Medicine, Bristol Myers Squibb, Princeton, New Jersey, USA. 2 Department of Genitourinary Oncology, The Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, and Harvard Medical School, Boston, Massachusetts, USA. 3 Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut, USA. 4 Translational Medicine, Bristol Myers Squibb, Princeton, New Jersey, USA megan.windrotolo@bms.com.

Gene Editing Rescues In vitro T Cell Development of RAG2-Deficient Induced Pluripotent Stem Cells in an Artificial Thymic Organoid System

Gardner CL, et al.,
Journal of Clinical Immunology
March 2021
Authors and Affiliates
Cameron L Gardner 1,2, Mara Pavel-Dinu 3, Kerry Dobbs 1, Marita Bosticardo 1, Paul K Reardon 2, Justin Lack 4,5, Suk See DeRavin 1, Kent Le 1, Ezekiel Bello 1, Francesca Pala 1, Ottavia M Delmonte 1, Harry Malech 1, Amelie Montel-Hagan 6, Gay Crooks 6, Oreste Acuto 7, Matthew H Porteus 8, Luigi D Notarangelo 9; 1 Immune Deficiency Genetics Section, Laboratory of Clinical Immunology and Microbiology, DIR, NIAID, NIH, 10 Center Drive, Bldg. 10 CRC, Room 5-3950, Bethesda, MD, 20892-1456, USA. 2 Sir William Dunn School of Pathology, University of Oxford, Oxford, OX14RE, UK. 3 Division of Stem Cell Transplantation and Regenerative Medicine, Department of Pediatrics, Stanford School of Medicine, Stanford University, Stanford, CA, USA. 4 NIAID Collaborative Bioinformatics Resource, NIAID, NIH, Bethesda, MD, USA. 5 Advanced Biomedical Computational Science (ABCS), Frederick National Laboratory for Cancer Research, Frederick, MD, USA. 6 Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA. 7 Sir William Dunn School of Pathology, University of Oxford, Oxford, OX14RE, UK. oreste.acuto@path.ox.ac.uk. 8 Division of Stem Cell Transplantation and Regenerative Medicine, Department of Pediatrics, Stanford School of Medicine, Stanford University, Stanford, CA, USA. mporteus@stanford.edu. 9 Immune Deficiency Genetics Section, Laboratory of Clinical Immunology and Microbiology, DIR, NIAID, NIH, 10 Center Drive, Bldg. 10 CRC, Room 5-3950, Bethesda, MD, 20892-1456, USA. luigi.notarangelo2@nih.gov.

T-cell CX3CR1 expression as a dynamic blood-based biomarker of response to immune checkpoint inhibitors

Yamauchi T., et al.,
Nature Communications
March 2021
Authors and Affiliates
Takayoshi Yamauchi 1, Toshifumi Hoki 1,2, Takaaki Oba 1, Vaibhav Jain 1, Hongbin Chen 3,4, Kristopher Attwood 5, Sebastiano Battaglia 1,6, Saby George 3,4, Gurkamal Chatta 3, Igor Puzanov 3, Carl Morrison 7, Kunle Odunsi 1,8,9,10, Brahm H Segal 3,4,9, Grace K Dy 3, Marc S Ernstoff 3,4,11, Fumito Ito 12,13,14,15; 1 Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA. 2 Merck Sharp & Dohme, Tokyo, Japan. 3 Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA. 4 Department of Medicine, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, The State University of New York, Buffalo, NY, USA. 5 Department of Biostatistics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA. 6 Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA. 7 Department of Pathology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA. 8 Department of Gynecologic Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA. 9 Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA. 10 University of Chicago Comprehensive Cancer Center, Chicago, IL, USA. 11 Division of Cancer Treatment and Diagnosis, Developmental Therapeutics Program, National Cancer Institute, Bethesda, MD, USA. 12 Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA. fumito.ito@roswellpark.org. 13 Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA. fumito.ito@roswellpark.org. 14 Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA. fumito.ito@roswellpark.org. 15 Department of Surgery, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, The State University of New York, Buffalo, NY, USA. fumito.ito@roswellpark.org.

Tumor immune infiltration estimated from gene expression profiles predicts colorectal cancer relapse

Kamal Y, et al.,
OncoImmunology
March 2021
Authors and Affiliates
Yasmin Kamal 1, Dennis Dwan 1, Hannah J. Hoehn 2, Rebeca Sanz-Pamplona 3,4, M. Henar Alonso 3,4,5, Victor Moreno 3,4,5, Chao Cheng 6,7,8, Michael J. Schell 9, Youngchul Kim 9, Seth I. Felder 10, Hedy S. Rennert 11,12, Marilena Melas 13, 14, Charalampos Lazaris 13,15,16, Joseph D. Bonner 17, Erin M. Siegel 18, David Shibata 19, Gad Rennert 11,12, Stephen B. Gruber 7, H. Robert Frost 1, Christopher I. Amos 1,7,8, and Stephanie L. Schmit 2,10; 1 Department of Biomedical Data Sciences, Geisel School of Medicine at Dartmouth, Hanover, NH, USA 2 Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA 3 Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain 4 Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain 5 Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain 6 Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA 7 Department of Medicine, Baylor College of Medicine, Houston, TX, USA 8 Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA 9 Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Columbus, OH, USA 10 Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center and Research Institute, Columbus, OH, USA 11 Department of Community Medicine & Epidemiology, Lady Davis Carmel Medical Center, Ruth & Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel 12 Steve and Cindy Rasmussen Institute for Genomic Medicine, Lady Davis Carmel Medical Center and Technion Faculty of Medicine, Clalit National Cancer Control Center, Haifa, Israel 13 Department of Medical Oncology and Therapeutics Research, Center for Precision Medicine, City of Hope National Medical Center, Duarte, CA, USA 14 Nationwide Children’s Hospital, Columbus, OH, USA 15 Whitehead Institute for Biomedical Research, Cambridge, MA, USA 16 Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA 17 Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA 18 Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Columbus, OH, USA 19 Department of Surgery, University of Tennessee Health Science Center, Memphis, TN, USA

Generation of self-reactive, shared T-cell receptor α chains in the human thymus

Heikkilä N., et al.
Journal of Autoimmunity
March 2021
Authors and Affiliates
Nelli Heikkilä 1, Silja Sormunen 2, Joonatan Mattila 3, Taina Härkönen 4, Mikael Knip 5, Emmi-Leena Ihantola 6, Tuure Kinnunen 7, Ilkka P Mattila 8, Jari Saramäki 2, T Petteri Arstila 3; 1 Research Programs Unit, Translational Immunology, and Medicum, University of Helsinki, Haartmaninkatu 3, 00290, Helsinki, Finland. Electronic address: nelli.heikkila@helsinki.fi. 2 Department of Computer Science, Aalto University, Konemiehenkatu 2, 02150, Espoo, Finland. 3 Research Programs Unit, Translational Immunology, and Medicum, University of Helsinki, Haartmaninkatu 3, 00290, Helsinki, Finland. 4 Pediatric Research Center, Children's Hospital, University of Helsinki and Helsinki University Hospital, Stenbäckinkatu 9, 00290, Helsinki, Finland. 5 Pediatric Research Center, Children's Hospital, University of Helsinki and Helsinki University Hospital, Stenbäckinkatu 9, 00290, Helsinki, Finland; Research Program for Clinical and Molecular Metabolism, University of Helsinki, Haartmaninkatu 8, 00290, Helsinki, Finland; Folkhälsan Research Center, Topeliuksenkatu 25, 00250, Helsinki, Finland; Department of Pediatrics, Tampere University Hospital, Elämänaukio 2, 33520, Tampere, Finland. 6 Department of Clinical Microbiology, Institute of Clinical Medicine, University of Eastern Finland, Puijonlaaksontie 2, 70210, Kuopio, Finland. 7 Department of Clinical Microbiology, Institute of Clinical Medicine, University of Eastern Finland, Puijonlaaksontie 2, 70210, Kuopio, Finland; Eastern Finland Laboratory Centre (ISLAB), Puijonlaaksontie 2, 70210, Kuopio, Finland. 8 Department of Pediatric Cardiac and Transplantation Surgery, Hospital for Children and Adolescents, Helsinki University Central Hospital, Stenbäckinkatu 9, 00290, Helsinki, Finland.

CD52/GPI-negative T-cells are enriched for alloreactive specificity and predict acute GvHD after stem cell transplantation.

Kinsella FA., et al.
March 2021
Authors and Affiliates
Francesca A. Kinsella 1,2, Charlotte. F. Inman 1, Wayne Croft 1, Jianmin Zuo 1, Hayden Pearce 1, Sara Barbieri 2, Charles Craddock 2, Ram Malladi 2, Paul Moss 1,2; 1 Institute of Immunology and Immunotherapy, College of Medical and Dental Studies, University of Birmingham and Birmingham Health Partners, Birmingham, UK 2 Centre for Clinical Haematology, Queen Elizabeth NHS Foundation Trust and Birmingham Health Partners, Birmingham, UK

Lymphohematopoietic graft-versus-host responses promote mixed chimerism in patients receiving intestinal transplantation

Fu J., et al.
Journal of Clinical Investigation
March 2021
Authors and Affiliates
Jianing Fu 1, Julien Zuber 1, Brittany Shonts 1, Aleksandar Obradovic 1, Zicheng Wang 2, Kristjana Frangaj 1, Wenzhao Meng 3, Aaron M Rosenfeld 3, Elizabeth E Waffarn 1, Peter Liou 4, Sai-Ping Lau 1, Thomas M Savage 1, Suxiao Yang 1, Kortney Rogers 1, Nichole M Danzl 1, Shilpa Ravella 5, Prakash Satwani 6, Alina Iuga 7, Siu-Hong Ho 1, Adam Griesemer 4, Yufeng Shen 2, Eline T Luning Prak 3, Mercedes Martinez 6, Tomoaki Kato 4, Megan Sykes 1; 1 Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, United States of America. 2 Center for Computational Biology and Bioinformatics, Department of Systems , Columbia University, New York, United States of America. 3 Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, United States of America. 4 Department of Surgery, Columbia University, New York, United States of America. 5 Division of Digestive and Liver Diseases, Department of Medicine, Columbia University, New York, United States of America. 6 Department of Pediatrics, Columbia University, New York, United States of America. 7 Department of Pathology and Cell Biology, Columbia University, New York, United States of America.
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