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Deep learning identifies antigenic determinants of severe SARS-CoV-2 infection within T-cell repertoires

Sidhom JW and Baras AS
Scientific Reports
July 2021
Authors and Affiliates
John-William Sidhom 1,2,3, Alexander S Baras 4,5,6; 1 Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA. jsidhom1@jhmi.edu. 2 The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA. jsidhom1@jhmi.edu. 3 Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA. jsidhom1@jhmi.edu. 4 Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA. 5 The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA. 6 Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.

Evaluating T-cell cross-reactivity between tumors and immune-related adverse events with TCR sequencing: pitfalls in interpretations of functional relevance

Cottrell T, et al.
July 2021
Authors and Affiliates
Tricia Cottrell #,1,2,3, Jiajia Zhang #,2,4,5, Boyang Zhang 6, Genevieve J Kaunitz 7, Poromendro Burman 2,4,5, Hok-Yee Chan 2,4,5, Franco Verde 8, Jody E Hooper 1, Hans Hammers 4,9, Mohamad E Allaf 2,4, Hongkai Ji 6, Janis Taube 1,2,4,10, Kellie N Smith 11,4,5,10; 1 Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA. 2 Bloomberg~Kimmel Institute for Cancer Immunotherapy, Baltimore, MD, USA. 3 Queen's Cancer Research Institute at Queens University, Kingston, Ontario, Canada. 4 Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland, USA. 5 Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA. 6 Department of Biostatistics, Johns Hopkins University, Baltimore, Maryland, USA. 7 Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA. 8 Department of Radiology, Johns Hopkins School of Medicine, Baltimore, MD, USA. 9 Harold C. Simmons Comprehensive Cancer Center, Dallas, TX, USA. 10 The Mark Foundation Center for Advanced Genomics and Imaging, Baltimore, MD, USA. 11 Bloomberg~Kimmel Institute for Cancer Immunotherapy, Baltimore, MD, USA ksmit228@jhmi.edu. # Contributed equally.

Humans with inherited T cell CD28 deficiency are susceptible to skin papillomaviruses but are otherwise healthy

Béziat V, et al.
Cell
July 2021
Authors and Affiliates
Vivien Béziat 1, Franck Rapaport 2, Jiafen Hu 3, Matthias Titeux 4, Mathilde Bonnet des Claustres 4, Mathieu Bourgey 5, Heather Griffin 6, Élise Bandet 4, Cindy S Ma 7, Roya Sherkat 8, Hassan Rokni-Zadeh 9, David M Louis 10, Majid Changi-Ashtiani 11, Ottavia M Delmonte 12, Toshiaki Fukushima 13, Tanwir Habib 14, Andrea Guennoun 14, Taushif Khan 14, Noemi Bender 15, Mahbuba Rahman 14, Frédégonde About 4, Rui Yang 2, Geetha Rao 7, Claire Rouzaud 16, Jingwei Li 3, Debra Shearer 3, Karla Balogh 3, Fatima Al Ali 14, Manar Ata 14, Soroosh Dabiri 17, Mana Momenilandi 18, Justine Nammour 4, Marie-Alexandra Alyanakian 19, Marianne Leruez-Ville 19, David Guenat 20, Marie Materna 4, Léa Marcot 4, Natasha Vladikine 4, Christine Soret 20, Hassan Vahidnezhad 21, Leila Youssefian 21, Amir Hossein Saeidian 21, Jouni Uitto 21, Émilie Catherinot 22, Shadi Sadat Navabi 23, Mohammed Zarhrate 4, David T Woodley 24, Mohamed Jeljeli 25, Thomas Abraham 3, Serkan Belkaya 2, Lazaro Lorenzo 4, Jérémie Rosain 16, Mousa Bayat 17, Fanny Lanternier 16, Olivier Lortholary 16, Faramarz Zakavi 26, Philippe Gros 27, Gérard Orth 28, Laurent Abel 29, Jean-Luc Prétet 20, Sylvie Fraitag 19, Emmanuelle Jouanguy 29, Mark M Davis 30, Stuart G Tangye 7, Luigi D Notarangelo 12, Nico Marr 14, Tim Waterboer 15, David Langlais 27, John Doorbar 6, Alain Hovnanian 16, Neil Christensen 3, Xavier Bossuyt 18, Mohammad Shahrooei 31, Jean-Laurent Casanova 32; 1 University of Paris, Imagine Institute, INSERM U1163, 75015 Paris, France; The Rockefeller University, New York, NY 10065, USA. Electronic address: vivien.beziat@inserm.fr. 2 The Rockefeller University, New York, NY 10065, USA. 3 Pennsylvania State University College of Medicine, Hershey, PA 17033, USA. 4 University of Paris, Imagine Institute, INSERM U1163, 75015 Paris, France. 5 McGill University, Montreal, QC H3A 0G1, Canada. 6 University of Cambridge, Cambridge CB2 1QP, UK. 7 Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; St. Vincent's Clinical School, UNSW Sydney, Sydney, NSW 2052, Australia. 8 Isfahan University of Medical Sciences, AIRC, Isfahan 81746-73461, Iran. 9 Zanjan University of Medical Sciences, Zanjan 45139-56184, Iran. 10 Stanford University Medical School, Stanford, CA 94305, USA. 11 Institute for Research in Fundamental Sciences (IPM), Tehran 19395-5746, Iran. 12 National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA. 13 Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8501, Japan. 14 Sidra Medicine, Doha, Qatar. 15 German Cancer Research Center, 69120 Heidelberg, Germany. 16 University of Paris, Imagine Institute, INSERM U1163, 75015 Paris, France; Necker Hospital for Sick Children, AP-HP, 75015 Paris, France. 17 Zahedan University of Medical Sciences, 054 Zahedan, Iran. 18 University of Leuven, 3000 Leuven, Belgium. 19 Necker Hospital for Sick Children, AP-HP, 75015 Paris, France. 20 Papillomavirus National Reference Center, Besançon Hospital, 25030 Besançon, France. 21 Thomas Jefferson University, Philadelphia, PA 19107, USA. 22 Foch Hospital, 92150 Suresnes, France. 23 Dr. Shahrooei Lab, Ahvaz, Iran. 24 University of Southern California, Los Angeles, CA 90033, USA. 25 Cochin University Hospital, AP-HP, 75014 Paris, France. 26 Ahvaz Jundishapur University of Medical Sciences, 061 Ahvaz, Iran. 27 McGill University, Montreal, QC H3A 0G1, Canada; McGill Research Centre on Complex Traits, Montreal, QC H3G 0B1, Canada. 28 Pasteur Institute, 75015 Paris, France. 29 University of Paris, Imagine Institute, INSERM U1163, 75015 Paris, France; The Rockefeller University, New York, NY 10065, USA. 30 HHMI, Stanford University Medical School, Stanford, CA 94305, USA. 31 University of Leuven, 3000 Leuven, Belgium; Dr. Shahrooei Lab, Ahvaz, Iran. 32 University of Paris, Imagine Institute, INSERM U1163, 75015 Paris, France; The Rockefeller University, New York, NY 10065, USA; HHMI, New York, NY 10065, USA. Electronic address: casanova@rockefeller.edu.

Inherited PD-1 deficiency underlies tuberculosis and autoimmunity in a child

Ogishi M, et al.
July 2021
Authors and Affiliates
Masato Ogishi 1,2, Rui Yang 3, Caner Aytekin 4, David Langlais 5, Mathieu Bourgey 6, Taushif Khan 7, Fatima Al Ali 7, Mahbuba Rahman 7, Ottavia M Delmonte 8, Maya Chrabieh 9,10, Peng Zhang 3, Conor Gruber 11,12,13,14, Simon J Pelham 3, András N Spaan 3, Jérémie Rosain 9,10, Wei-Te Lei 3, Scott Drutman 3, Matthew D Hellmann 15,16, Margaret K Callahan 15,16, Matthew Adamow 17,18, Phillip Wong 17, Jedd D Wolchok 15,16,18,19, Geetha Rao 20, Cindy S Ma 20,21, Yuka Nakajima 22, Tomonori Yaguchi 22, Kenji Chamoto 22, Samuel C Williams 23,24, Jean-Francois Emile 25, Flore Rozenberg 26, Michael S Glickman 27, Franck Rapaport 3, Gaspard Kerner 9,10, Garrett Allington 28,29,30, Ilhan Tezcan 31, Deniz Cagdas 31, Ferda O Hosnut 32, Figen Dogu 33, Aydan Ikinciogullari 33, V Koneti Rao 34, Leena Kainulainen 35, Vivien Béziat 3,9,10, Jacinta Bustamante 3,9,10,36, Silvia Vilarinho #,28,29,30, Richard P Lifton #,28,37, Bertrand Boisson #,3,9,10, Laurent Abel #,3,9,10, Dusan Bogunovic #,11,12,13,14, Nico Marr #,7,38, Luigi D Notarangelo #,8, Stuart G Tangye #,20,21, Tasuku Honjo #,22, Philippe Gros #,39,40, Stéphanie Boisson-Dupuis #,41,42,43, Jean-Laurent Casanova #,44,45,46,47; 1 St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA. mogishi@rockefeller.edu. 2 The David Rockefeller Graduate Program, Rockefeller University, New York, NY, USA. 3 St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA. 4 Department of Pediatric Immunology, Dr. Sami Ulus Maternity and Children's Health and Diseases Training and Research Hospital, Ankara, Turkey. 5 Department of Human Genetics, McGill University, Montreal, Quebec, Canada. 6 McGill University Genome Center, Montreal, Quebec, Canada. 7 Department of Immunology, Research Branch, Sidra Medicine, Doha, Qatar. 8 Immune Deficiency Genetics Section, Laboratory of Host Defenses, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA. 9 Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France. 10 University of Paris, Imagine Institute, Paris, France. 11 Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA. 12 Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA. 13 The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA. 14 Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA. 15 Department of Medicine, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA. 16 Weill Cornell Medicine, New York, NY, USA. 17 Immune Monitoring Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA. 18 Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA. 19 Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA. 20 Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia. 21 St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Darlinghurst, New South Wales, Australia. 22 Department of Immunology and Genomic Medicine, Center for Cancer Immunotherapy and Immunobiology, Kyoto University Graduate School of Medicine, Kyoto, Japan. 23 Laboratory of Investigative Dermatology, Rockefeller University, New York, NY, USA. 24 Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY, USA. 25 Department of Pathology, Assistance Publique-Hôpitaux de Paris, Ambroise Paré Hospital, Boulogne-Billancourt, France. 26 Department of Virology, Cochin Hospital, University of Paris, Paris, France. 27 Immunology Program, Sloan Kettering Institute, New York, NY, USA. 28 Department of Genetics, Yale University School of Medicine, New Haven, CT, USA. 29 Section of Digestive Diseases, Departments of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA. 30 Department of Pathology, Yale University School of Medicine, New Haven, CT, USA. 31 Department of Pediatric Immunology, Hacettepe University Medical Faculty, Ankara, Turkey. 32 Department of Pediatric Gastroenterology, Dr. Sami Ulus Maternity and Children's Health and Diseases Training and Research Hospital, Ankara, Turkey. 33 Department of Pediatric Immunology and Allergy, Ankara University School of Medicine, Ankara, Turkey. 34 Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA. 35 Department of Pediatrics and Department of Medicine, Turku University Hospital, Turku, Finland. 36 Study Center of Immunodeficiencies, Necker Hospital for Sick Children, Paris, France. 37 Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY, USA. 38 College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar. 39 McGill Research Centre on Complex Traits, Montreal, Quebec, Canada. 40 Department of Biochemistry, McGill University, Montreal, Quebec, Canada. 41 St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA. stbo603@rockefeller.edu. 42 Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France. stbo603@rockefeller.edu. 43 University of Paris, Imagine Institute, Paris, France. stbo603@rockefeller.edu. 44 St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA. casanova@rockefeller.edu. 45 Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France. casanova@rockefeller.edu. 46 University of Paris, Imagine Institute, Paris, France. casanova@rockefeller.edu. 47 Howard Hughes Medical Institute, New York, NY, USA. casanova@rockefeller.edu. # Contributed equally.

Notch signaling and efficacy of PD-1/PD-L1 blockade in relapsed small cell lung cancer

Roper N, et al.
Nature Communications
July 2021
Authors and Affiliates
Nitin Roper 1, Moises J Velez 2, Alberto Chiappori 3, Yoo Sun Kim 1, Jun S Wei 4, Sivasish Sindiri 4, Nobuyuki Takahashi 1, Deborah Mulford 2, Suresh Kumar 1, Kris Ylaya 5, Christopher Trindade 5, Irena Manukyan 5, Anna-Leigh Brown 6, Jane B Trepel 1, Jung-Min Lee 7, Stephen Hewitt 5, Javed Khan 4, Anish Thomas 8; 1 Developmental Therapeutics Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD, USA. 2 Department of Pathology and Internal Medicine, University of Rochester, Rochester, NY, USA. 3 Moffitt Cancer Center, Tampa, FL, USA. 4 Genetics Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD, USA. 5 Laboratory of Pathology, Center for Cancer Research, NCI, NIH, Bethesda, MD, USA. 6 National Center for Biotechnology Information, NIH, NLM, Bethesda, MD, USA. 7 Women's Malignancies Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD, USA. 8 Developmental Therapeutics Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD, USA

Rejection of benign melanocytic nevi by nevus-resident CD4+ T cells

Schiferle EB, et al.
Science Advances
July 2021
Authors and Affiliates
Erik B Schiferle 1, Se Yun Cheon 1, Seokjin Ham 2, Heehwa G Son 1, Jonathan L Messerschmidt 1, Donald P Lawrence 3, Justine V Cohen 3, Keith T Flaherty 3, James J Moon 4, Christine G Lian 5, Ryan J Sullivan 3, Shadmehr Demehri 6; 1 Center for Cancer Immunology and Cutaneous Biology Research Center, Department of Dermatology, Center for Cancer Research, Massachusetts General Hospital Cancer Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA. 2 Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Yuseong Gu, Daejeon, South Korea. 3 Division of Hematology and Oncology, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA. 4 Center for Immunology and Inflammatory Diseases and Division of Pulmonary and Critical Care Medicine, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA. 5 Program in Dermatopathology, Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA. 6 Center for Cancer Immunology and Cutaneous Biology Research Center, Department of Dermatology, Center for Cancer Research, Massachusetts General Hospital Cancer Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.

Distinct populations of antigen specific tissue resident CD8 T cells in human cervix mucosa

Peng T, et al.
July 2021
Authors and Affiliates
Tao Peng 1, Khamsone Phasouk 2, Emily Bossard 2, Alexis Klock 3, Lei Jin 2, Kerry J Laing 3, Christine Johnston 3, Noel A Williams 2, Julie L Czartoski 2, Dana Varon 3, Annalyssa N Long 4, Jason H Bielas 5, Thomas M Snyder 6, Harlan Robins 6, David M Koelle 7, M Juliana McElrath 2, Anna Wald 7, Lawrence Corey 5, Jia Zhu 7; 1 Department of Medicine and Pathology, University of Washington, Seattle, United States of America. 2 Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seatlle, United States of America. 3 Department of Medicine, University of Washington, Seattle, United States of America. 4 Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States of America. 5 Fred Hutchinson Cancer Research Center, Seattle, United States of America. 6 Research, Adaptive Biotechnologies, Seattle, United States of America. 7 Department of Laboratory Medicine, and Pathology, University of Washington, Seattle, United States of America.

Clonally Focused Public and Private T Cells in Resected Brain Tissue From Surgeries to Treat Children With Intractable Seizures

Chang JW, et al.
Frontiers in Immunology
July 2021
Authors and Affiliates
Julia W Chang 1, Samuel D Reyes 1, Emmanuelle Faure-Kumar 2, Sandi K Lam 3, Michael W Lawlor 4, Richard J Leventer 5, Sean M Lew 6, Paul J Lockhart 5, Kathryn Pope 5, Howard L Weiner 7, Noriko Salamon 8, Harry V Vinters 9, Gary W Mathern 1, Aria Fallah 1,10, Geoffrey C Owens 1; 1 Department of Neurosurgery, David Geffen School of Medicine at the University of California, Los Angeles, CA, United States. 2 Department of Medicine: Division of Digestive Diseases, David Geffen School of Medicine at the University of California, Los Angeles, CA, United States. 3 Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Ann & Robert H. Lurie Children's Hospital, Chicago, IL, United States. 4 Department of Pathology, Medical College of Wisconsin, Children's Hospital of Wisconsin, Milwaukee, WI, United States. 5 Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia. 6 Department of Neurosurgery, Medical College of Wisconsin, Children's Hospital of Wisconsin, Milwaukee, WI, United States. 7 Department of Pediatric Neurosurgery, Baylor College of Medicine, Texas Children's Hospital, Houston, TX, United States. 8 Department of Radiological Sciences, David Geffen School of Medicine at the University of California, Los Angeles, CA, United States. 9 Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at the University of California, Los Angeles, CA, United States. 10 Mattel Children's Hospital, David Geffen School of Medicine at the University of California, Los Angeles, CA, United States.

Pre-Transplant T-Cell Clonality: An Observational Study of a Biomarker for Prediction of Sepsis in Liver Transplant Recipients

Jones SL, et al.
June 2021
Authors and Affiliates
Jones, Stephen L 1, Moore, Linda W. 2,3, Li, Xian C. 3,4, Mobley, Constance M. 2, Fields, Paul A. 4, Graviss, Edward A. 5, Nguyen, Duc T. 5, V Nolte Fong, Joy 2, Saharia, Ashish 2, Hobeika, Mark J. 2, McMillan, Robert R. 2, Victor, David W. III 6, Minze, Laurie J. 3, Gaber, A. Osama 2, Ghobrial, R. Mark 2; 1 Center for Outcomes Research, Houston Methodist, Houston, TX 2 Department of Surgery, Houston Methodist, Houston, TX 3 Transplant Immunobiology, Houston Methodist, Houston, TX 4 Adaptive Biotechnologies, Seattle, WA 5 Pathology and Genomic Medicine, Houston Methodist, Houston, TX 6 Department of Medicine, Houston Methodist, Houston, TX.

CD8 + T cell immunity blocks the metastasis of carcinogen-exposed breast cancer

Li K, et al.
Science Advances
June 2021
Authors and Affiliates
Kaiwen Li 1 2, Tiancheng Li 1, Zhaoyi Feng 1, Mei Huang 1, Lei Wei 3, Zhiyu Yan 1, Mark Long 3, Qiang Hu 3, Jianmin Wang 3, Song Liu 3, Dennis C Sgroi 4, Shadmehr Demehri 5; 1 Center for Cancer Immunology and Cutaneous Biology Research Center, Department of Dermatology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA. 2 Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China. 3 Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA. 4 Molecular Pathology Unit, Department of Pathology, Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA. 5 Center for Cancer Immunology and Cutaneous Biology Research Center, Department of Dermatology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA. sdemehri1@mgh.harvard.edu.
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