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Cellular Origins and Genetic Landscape of Cutaneous Gamma Delta T Cell Lymphomas

Daniels et al.
Nature Communications
April 2020
Authors and Affiliates
Jay Daniels 1 2, Peter G Doukas 1, Maria E Martinez Escala 1, Kimberly G Ringbloom 1, David J H Shih 3, Jingyi Yang 1, Kyle Tegtmeyer 1, Joonhee Park 1, Jane J Thomas 1, Mehmet E Selli 1, Can Altunbulakli 1, Ragul Gowthaman 4 5, Samuel H Mo 6, Balaji Jothishankar 7, David R Pease 1, Barbara Pro 8, Farah R Abdulla 9, Christopher Shea 7, Nidhi Sahni 3 10 11 12, Alejandro A Gru 13 14, Brian G Pierce 4 5, Abner Louissaint Jr 15, Joan Guitart 16, Jaehyuk Choi 17 18 19 20; 1Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA. 2Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA. 3Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. 4University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, USA. 5Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA. 6University of Illinois College of Medicine, Chicago, IL, USA. 7Department of Medicine, Section of Dermatology, University of Chicago Pritzker School of Medicine, Chicago, IL, USA. 8Division of Hematology/Oncology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA. 9Division of Dermatology, City of Hope Comprehensive Cancer Center, Duarte, CA, USA. 10Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, USA. 11Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. 12Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, USA. 13Department of Pathology, University of Virginia Health System, Charlottesville, VA, USA. 14Department of Dermatology, University of Virginia Health System, Charlottesville, VA, USA. 15Department of Pathology, Massachusetts General Hospital, Boston, MA, USA. alouissaint@partners.org. 16Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA. JGUITART@nm.org. 17Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA. jaehyuk.choi@northwestern.edu. 18Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA. jaehyuk.choi@northwestern.edu. 19Center for Genetic Medicine, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA. jaehyuk.choi@northwestern.edu. 20Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA. jaehyuk.choi@northwestern.edu.

Cathepsin S Regulates Antigen Processing and T Cell Activity in Non-Hodgkin Lymphoma

Dheilly et al.
Cancer Cell
April 2020
Authors and Affiliates
Dheilly E1, Battistello E2, Katanayeva N1, Sungalee S1, Michaux J3, Duns G4, Wehrle S5, Sordet-Dessimoz J6, Mina M7, Racle J8, Farinha P4, Coukos G3, Gfeller D8, Mottok A9, Kridel R10, Correia BE11, Steidl C4, Bassani-Sternberg M3, Ciriello G7, Zoete V12, Oricchio E13.; 1 Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, EPFL, Lausanne, 1015 Switzerland; Swiss Cancer Center Leman (SCCL), Lausanne, 1015 Switzerland. 2 Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, EPFL, Lausanne, 1015 Switzerland; Swiss Cancer Center Leman (SCCL), Lausanne, 1015 Switzerland; Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics (SIB), Lausanne 1015, Switzerland. 3 Swiss Cancer Center Leman (SCCL), Lausanne, 1015 Switzerland; Ludwig Institute for Cancer Research and Department of Oncology, University of Lausanne, Lausanne, Switzerland; Department of Oncology, University Hospital of Lausanne, Lausanne, Switzerland. 4 Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, BC, Canada. 5 Institute of Bioengineering, EPFL, 1015 Lausanne, Switzerland. 6 Histology Core Facility, EPFL, 1015 Lausanne, Switzerland. 7 Swiss Cancer Center Leman (SCCL), Lausanne, 1015 Switzerland; Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics (SIB), Lausanne 1015, Switzerland. 8 Swiss Cancer Center Leman (SCCL), Lausanne, 1015 Switzerland; Swiss Institute of Bioinformatics (SIB), Lausanne 1015, Switzerland; Ludwig Institute for Cancer Research and Department of Oncology, University of Lausanne, Lausanne, Switzerland; Department of Oncology, University Hospital of Lausanne, Lausanne, Switzerland. 9 Institute of Human Genetics, Ulm University and Ulm University Medical Center, Germany. 10 Princess Margaret Cancer Center, Toronto, Canada. 11 Swiss Institute of Bioinformatics (SIB), Lausanne 1015, Switzerland; Institute of Bioengineering, EPFL, 1015 Lausanne, Switzerland. 12 Swiss Cancer Center Leman (SCCL), Lausanne, 1015 Switzerland; Swiss Institute of Bioinformatics (SIB), Lausanne 1015, Switzerland; Ludwig Institute for Cancer Research and Department of Oncology, University of Lausanne, Lausanne, Switzerland; Molecular Modeling Group, SIB, Lausanne, Switzerland. 13 Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, EPFL, Lausanne, 1015 Switzerland; Swiss Cancer Center Leman (SCCL), Lausanne, 1015 Switzerland. Electronic address: elisa.oricchio@epfl.ch.

Neutrophil Expansion Defines an Immunoinhibitory Peripheral and Intratumoral Inflammatory Milieu in Resected Non-Small Cell Lung Cancer: A Descriptive Analysis of a Prospectively Immunoprofiled Cohort

Mitchell et al.
Journal for ImmunoTherapy of Cancer
April 2020
Authors and Affiliates
Kyle G Mitchell 1, Lixia Diao 2, Tatiana Karpinets 3, Marcelo V Negrao 4, Hai T Tran 4, Edwin R Parra 5, Erin M Corsini 1, Alexandre Reuben 4, Lorenzo Federico 6, Chantale Bernatchez 6, Hitoshi Dejima 5, Alejandro Francisco-Cruz 5, Jing Wang 2, Mara B Antonoff 1, Ara A Vaporciyan 1, Stephen G Swisher 1, Tina Cascone 4, Ignacio I Wistuba 4 5, John V Heymach 4, Don L Gibbons 4 7, Jianjun Zhang 4, Cara L Haymaker # 8, Boris Sepesi # 9 1Thoracic and Cardiovascular Surgery, University of Texas MD Anderson Cancer Center, Houston, Texas, USA. 2Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA. 3Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, USA. 4Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA. 5Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA. 6Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA. 7Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA. 8Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA CHaymaker@mdanderson.org BSepesi@MDAnderson.org. 9Thoracic and Cardiovascular Surgery, University of Texas MD Anderson Cancer Center, Houston, Texas, USA CHaymaker@mdanderson.org BSepesi@MDAnderson.org. #Contributed equally.

A T Cell Receptor Sequencing-Based Assay Identifies Cross-Reactive Recall CD8 + T Cell Clonotypes Against Autologous HIV-1 Epitope Variants

Chan et al.
Frontiers in Immunology
April 2020
Authors and Affiliates
Hok Yee Chan 1 2, Jiajia Zhang 1 2, Caroline C Garliss 3, Abena K Kwaa 3, Joel N Blankson 3 4, Kellie N Smith 1 2; 1Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, United States. 2Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, United States. 3Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, United States. 4Department of Molecular and Comparative Pathobiology, Johns Hopkins School of Medicine, Baltimore, MD, United States.

Neoadjuvant Immunotherapy Leads to Pathological Responses in MMR-proficient and MMR-deficient Early-Stage Colon Cancers

Chalabi et al.
Nature Medicine
April 2020
Authors and Affiliates
Myriam Chalabi 1 2 3, Lorenzo F Fanchi 4 5, Krijn K Dijkstra 4 5, José G Van den Berg 6, Arend G Aalbers 7, Karolina Sikorska 8, Marta Lopez-Yurda 8 9, Cecile Grootscholten 10, Geerard L Beets 7 11, Petur Snaebjornsson 6, Monique Maas 12, Marjolijn Mertz 13, Vivien Veninga 4 5, Gergana Bounova 5 14, Annegien Broeks 15, Regina G Beets-Tan 11 12, Thomas R de Wijkerslooth 10, Anja U van Lent 16, Hendrik A Marsman 17, Elvira Nuijten 8, Niels F Kok 7, Maria Kuiper 10, Wieke H Verbeek 10, Marleen Kok 18 19, Monique E Van Leerdam 10, Ton N Schumacher 4 5, Emile E Voest 20 21 22, John B Haanen 4 18; 1Gastrointestinal Oncology, Netherlands Cancer Institute, Amsterdam, the Netherlands. m.chalabi@nki.nl. 2Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, the Netherlands. m.chalabi@nki.nl. 3Medical Oncology, Netherlands Cancer Institute, Amsterdam, the Netherlands. m.chalabi@nki.nl. 4Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, the Netherlands. 5Oncode Institute, Utrecht, the Netherlands. 6Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands. 7Surgical Oncology, Netherlands Cancer Institute, Amsterdam, the Netherlands. 8Biometrics, Netherlands Cancer Institute, Amsterdam, the Netherlands. 9Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands. 10Gastrointestinal Oncology, Netherlands Cancer Institute, Amsterdam, the Netherlands. 11GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, the Netherlands. 12Radiology, Netherlands Cancer Institute, Amsterdam, the Netherlands. 13Bioimaging Facility, Netherlands Cancer Institute, Amsterdam, the Netherlands. 14Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, the Netherlands. 15Core Facility Molecular Pathology & Biobanking, Netherlands Cancer Institute, Amsterdam, the Netherlands. 16Gastroenterology & Hepatology, Onze Lieve Vrouwe Gasthuis, Amsterdam, the Netherlands. 17Surgery, Onze Lieve Vrouwe Gasthuis, Amsterdam, the Netherlands. 18Medical Oncology, Netherlands Cancer Institute, Amsterdam, the Netherlands. 19Tumor Biology & Immunology, Netherlands Cancer Institute, Amsterdam, the Netherlands. 20Gastrointestinal Oncology, Netherlands Cancer Institute, Amsterdam, the Netherlands. e.voest@nki.nl. 21Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, the Netherlands. e.voest@nki.nl. 22Oncode Institute, Utrecht, the Netherlands. e.voest@nki.nl.

Outcomes of Observation vs Stereotactic Ablative Radiation for Oligometastatic Prostate Cancer

Phillips et al.
JAMA Oncology
March 2020
Authors and Affiliates
Ryan Phillips, MD, PhD1; William Yue Shi, BS2; Matthew Deek, MD1; Noura Radwan, MD1; Su Jin Lim, ScM3; Emmanuel S. Antonarakis, MD3; Steven P. Rowe, MD, PhD4,5; Ashley E. Ross, MD, PhD5; Michael A. Gorin, MD4,5; Curtiland Deville, MD1; Stephen C. Greco, MD1; Hailun Wang, PhD1; Samuel R. Denmeade, MD3; Channing J. Paller, MD3; Shirl Dipasquale, MS, RN1; Theodore L. DeWeese, MD1,3,5; Daniel Y. Song, MD1,3,5; Hao Wang, PhD3; Michael A. Carducci, MD3; Kenneth J. Pienta, MD3,5; Martin G. Pomper, MD, PhD4,5; Adam P. Dicker, MD, PhD6; Mario A. Eisenberger, MD3; Ash A. Alizadeh, MD, PhD7; Maximilian Diehn, MD, PhD2; Phuoc T. Tran, MD, PhD1,3,5 Author Affiliations Article Information 1Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 2Stanford Cancer Institute, Department of Radiation Oncology, School of Medicine, Stanford University, Stanford, California 3Department of Medical Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 4The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, Maryland 5The James Buchanan Brady Urological Institute and Department of Urology, Johns Hopkins University School of Medicine, Baltimore, Maryland 6Sidney Kimmel Cancer Center, Department of Radiation Oncology, Thomas Jefferson University, Philadelphia, Pennsylvania 7Stanford Cancer Institute, Division of Oncology, Department of Medicine, School of Medicine, Stanford University, Stanford, California

Epstein-Barr Virus Epitope-Major Histocompatibility Complex Interaction Combined with Convergent Recombination Drives Selection of Diverse T Cell Receptor α and β Repertoires

Gil et al.
mBio
March 2020
Authors and Affiliates
Gil A#1, Kamga L#2, Chirravuri-Venkata R3, Aslan N1, Clark F1, Ghersi D3, Luzuriaga K#4, Selin LK#5; 1 Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts, USA. 2 Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA. 3 School of Interdisciplinary Informatics, University of Nebraska at Omaha, Omaha, Nebraska, USA. 4 Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA katherine.luzuriaga@umassmed.edu liisa.selin@umassmed.edu. 5 Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts, USA katherine.luzuriaga@umassmed.edu liisa.selin@umassmed.edu. # Contributed equally

Prevalent and diverse intratumoral oncoprotein-specific CD8+ T cells within polyoma virus-driven Merkel cell carcinomas

Jing et al.
Cancer Immunology Research
March 2020
Authors and Affiliates
Lichen Jing 1, Mariliis Ott 1, Candice D. Church 2, Rima M. Kulikauskas 2, Dafina Ibrani 2, Jayasri G. Iyer 2, Olga K. Afanasiev 2, Aric Colunga 2, Maclean M. Cook 2, Hong Xie 6, Alexander L. Greninger 6, Kelly G. Paulson 8,3, Aude G. Chapuis 8,3, Shailender Bhatia 8,3, Paul Nghiem 2,3, David M. Koelle 1,4,5,6,7,9 1 Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA, USA 2 Division of Dermatology, Department of Medicine, University of Washington, Seattle, WA, USA 3 Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA 4 Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA 5 Department of Global Health, University of Washington, Seattle, WA, USA 6 Department of Laboratory Medicine, University of Washington, Seattle, WA, USA 7 Benaroya Research Institute, Seattle, WA, USA 8 Division of Medical Oncology, Department of Medicine, University of Washington, Seattle, WA, USA 9 Correspondence at: 750 Republican Street, Room E651, Seattle, WA, 98109, USA; tel 206 616 1940; fax 206 616 4898, email dkoelle@medicine.washington.edu

Peripheral T cell expansion predicts tumour infiltration and clinical response

Wu et al.
Nature
February 2020
Authors and Affiliates
Wu TD1, Madireddi S2, de Almeida PE2, Banchereau R3, Chen YJ4, Chitre AS2, Chiang EY2, Iftikhar H2, O'Gorman WE5, Au-Yeung A5, Takahashi C5, Goldstein LD6, Poon C7, Keerthivasan S2, de Almeida Nagata DE2, Du X2, Lee HM2, Banta KL2, Mariathasan S3, Das Thakur M8, Huseni MA8, Ballinger M8, Estay I8, Caplazi P9, Modrusan Z4, Delamarre L2, Mellman I2, Bourgon R6, Grogan JL10; 1 Department of Bioinformatics and Computational Biology, Genentech, Inc., South San Francisco, CA, USA. twu@gene.com. 2 Department of Cancer Immunology, Genentech, Inc., South San Francisco, CA, USA. 3 Department of Oncology Biomarker Development, Genentech, Inc., South San Francisco, CA, USA. 4 Department of Microchemistry, Proteomics, Lipidomics and Next Generation Sequencing, Genentech, Inc., South San Francisco, CA, USA. 5 Department of OMNI Biomarker Development, Genentech, Inc., South San Francisco, CA, USA. 6 Department of Bioinformatics and Computational Biology, Genentech, Inc., South San Francisco, CA, USA. 7 Department of Research Biology, Genentech, Inc., South San Francisco, CA, USA. 8 Department of Development Sciences, Genentech, Inc., South San Francisco, CA, USA. 9 Department of Pathology, Genentech, Inc., South San Francisco, CA, USA. 10 ArsenalBio, South San Francisco, CA, USA. jane@arsenalbio.com.

Immuno-genomic landscape of osteosarcoma

Wu et al.
Nature Communications
February 2020
Authors and Affiliates
Wu CC1, Beird HC1, Andrew Livingston J2,3, Advani S3, Mitra A1, Cao S4, Reuben A5, Ingram D6, Wang WL6, Ju Z4, Hong Leung C7, Lin H7, Zheng Y1, Roszik J1, Wang W4, Patel S2, Benjamin RS2, Somaiah N2, Conley AP2, Mills GB8, Hwu P2, Gorlick R3, Lazar A6, Daw NC3, Lewis V9, Futreal PA10; 1 Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. 2 Department of Sarcoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. 3 Department of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. 4 Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. 5 Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. 6 Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. 7 Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. 8 Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. 9 Department of Orthopedic Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. 10 Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. afutreal@mdanderson.org.
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