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Landscape of tumor-infiltrating T cell repertoire of human cancers

Li et al.
Nature Genetics
Papers
February 2017
Authors and Affiliates
Bo Li1,2, Taiwen Li1,3, Jean-Christophe Pignon4, Binbin Wang5, Jinzeng Wang5, Sachet Shukla6, Ruoxu Dou7, Qianming Chen3, F. Stephen Hodi8, Toni K. Choueiri9, Catherine Wu6, Nir Hacohen10, Sabina Signoretti4, Jun S. Liu2, and X. Shirley Liu1,2 1Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute, Boston, MA, USA, 2Department of Statistics, Harvard University, Boston, MA, USA, 3State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China, 4Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA, 5School of Life Science and Technology, Tongji University, China, Shanghai, China, 6Medical Oncology, Dana Farber Cancer Institute, Boston, MA, USA, 7Department of Colorectal Surgery, Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China, 8Center for ImmunoOncology, Harvard Medical School, Boston, MA, USA, 9Kidney Cancer Center, Dana Farber Cancer Institute, Boston, MA, USA, 10Center for Cancer Immunotherapy, Massachusetts General Hospital, Boston, MA, USA

Tumor-Infiltrating Merkel Cell Polyomavirus-Specific T Cells Are Diverse and Associated with Improved Patient Survival

Miller et al.
Cancer Immunology Research
Papers
February 2017
Authors and Affiliates
Natalie J. Miller1, Candice D. Church1, Lichun Dong2, David Crispin3, Matthew P. Fitzgibbon3, Kristina Lachance1, Lichen Jing2, Michi Shinohara1, Ioannis Gavvovidis4,5, Gerald Willimsky5,6, Martin McIntosh3, Thomas Blankenstein4,5,7, David M. Koelle2,8,9, and Paul Nghiem1 1Dermatology/Medicine/Pathology, University of Washington, Seattle, Washington. 2Department of Medicine/Laboratory Medicine/Global Health, University of Washington, Seattle, Washington. 3Fred Hutchinson, Public Health Sciences Division, Seattle, Washington. 4Molecular Immunology and Gene Therapy, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany. 5Institute of Immunology, Charit e, Berlin, Germany. 6German Cancer Research Center (DKFZ), Heidelberg, Germany. 7Berlin Institute of Health, Berlin, Germany. 8Fred Hutchinson, Vaccine and Infectious Disease Division, Seattle, Washington. 9Benaroya Research Institute, Seattle, Washington.

Ibrutinib Therapy Increases T Cell Repertoire Diversity in Patients with Chronic Lymphocytic Leukemia

Yin et al.
Journal of Immunology
Papers
January 2017
Authors and Affiliates
Qingsong Yin,*,†,1 Mariela Sivina,*,1 Harlan Robins,‡,x Erik Yusko,‡ Marissa Vignali,‡ Susan O’Brien,* Michael J. Keating,* Alessandra Ferrajoli,* Zeev Estrov,* Nitin Jain,* William G. Wierda,* and Jan A. Burger* *Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77230; †Department of Leukemia, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Henan Institute of Hematology, Zhengzhou, Henan 450009, China; ‡Adaptive Biotechnologies, Seattle, WA 98102; and xFred Hutchinson Cancer Research Center, Seattle, WA 98109

Evolution of Neoantigen Landscape During Immune Checkpoint Blockade in Non-Small Cell Lung Cancer

Anagnostou et al.
Cancer Discovery
Papers
January 2017
Authors and Affiliates
Valsamo Anagnostou1,2*, Kellie N. Smith1,2, Patrick M. Forde1,2, Noushin Niknafs3, Rohit Bhattacharya3, James White1, Theresa Zhang4, Vilmos Adleff1, Jillian Phallen1, Neha Wali1, Carolyn Hruban1, Violeta B. Guthrie3, Kristen Rodgers5, Jarushka Naidoo1,2, Hyunseok Kang1, William Sharfman1, Christos Georgiades6, Franco Verde7, Peter Illei1,8, Qing Kay Li8, Edward Gabrielson1,8, Malcolm V. Brock1,5, Cynthia A. Zahnow1, Stephen B. Baylin1, Rob Scharpf1, Julie R. Brahmer1,2, Rachel Karchin3, Drew M. Pardoll1,2 and Victor E. Velculescu1,2,3,8 1The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA, 2The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA 3Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland 21204, USA, 4Personal Genome Diagnostics, Baltimore, MD 21224, USA, 5Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA, 6Department of Radiology and Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA, 7Department of Radiology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA, 8Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA

BRILIA: Integrated Tool for High-Throughput Annotation and Lineage Tree Assembly of B-Cell Repertoires

Lee et al.
Frontiers in Immunology
Papers
January 2017
Authors and Affiliates
Donald W. Lee1, Ilja V. Khavrutskii1, Anders Wallqvist1, Sina Bavari2, Christopher L. Cooper2, and Sidhartha Chaudhury1 1Biotechnology HPC Software Applications Institute (BHSAI), Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, MD, USA, 2Molecular and Translational Sciences, U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA

Tissue distribution and clonal diversity of the T and B cell repertoire in type 1 diabetes

Seay et al
JCI Insight
Papers
December 2016
Authors and Affiliates
Howard R. Seay,1 Erik Yusko,2 Stephanie J. Rothweiler,1 Lin Zhang,1 Amanda L. Posgai,1 Martha Campbell-Thompson,1 Marissa Vignali,2 Ryan O. Emerson,2 John S. Kaddis,3 Dave Ko,3 Maki Nakayama,4 Mia J. Smith,5 John C. Cambier,5 Alberto Pugliese,6 Mark A. Atkinson,1 Harlan S. Robins,2,7 and Todd M. Brusko1 1Department of Pathology, Immunology and Laboratory Medicine, University of Florida Diabetes Institute, Gainesville, Florida, USA. 2Adaptive Biotechnologies Corporation, Seattle, Washington, USA. 3Department of Information Sciences, City of Hope National Medical Center, Duarte, California, USA. 4Barbara Davis Center for Childhood Diabetes and 5Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA. 6Diabetes Research Institute and Departments of Medicine, Microbiology, and Immunology, University of Miami Miller School of Medicine, Miami, Florida, USA. 7Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.

T-Cell Transfer Therapy Targeting Mutant KRAS in Cancer

Tran et al.
New England Journal of Medicine
Papers
December 2016
Authors and Affiliates
Eric Tran, Ph.D., Paul F. Robbins, Ph.D., Yong‐Chen Lu, Ph.D., Todd D. Prickett, Ph.D., Jared J. Gartner, M.Sc., Li Jia, M.Sc., Anna Pasetto, Ph.D., Zhili Zheng, Ph.D., Satyajit Ray, Ph.D., Eric M. Groh, M.D., Isaac R. Kriley, M.D., and Steven A. Rosenberg, M.D., Ph.D. Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD

Long-term maintenance of human naïve T cells through in situ homeostasis in lymphoid tissue sites

Thome et al
Papers
Science Immunology
December 2016
Authors and Affiliates
Joseph J. C. Thome,1,2* Boris Grinshpun,3* Brahma V. Kumar,1 Masaru Kubota,1,4 Yoshiaki Ohmura,1,4 Harvey Lerner,5 Gregory D. Sempowski,6 Yufeng Shen,3 Donna L. Farber1,2,4† 1 Columbia Center for Translational Immunology, Columbia University Medical Center, New York, NY 10032, USA. 2 Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA. 3 Department of Systems Biology, Columbia University Medical Center, New York, NY 10032, USA. 4 Department of Surgery, Columbia University Medical Center, New York, NY 10032, USA. 5 LiveOnNY, New York, NY 10001, USA. 6 Human Vaccine Institute, Duke University, Durham, NC 27710, USA.

Discovery of T-Cell Receptor Beta Motifs Specific to HLA-B27+ Ankylosing Spondylitis by Deep Repertoire Sequence Analysis

Faham et al
Arthritis & Rheumatology
Papers
December 2016
Authors and Affiliates
Malek Faham, MD, PhD1*, Victoria Carlton, PhD1, Martin Moorhead, PhD1, Jianbiao Zheng, PhD1, Mark Klinger, PhD1, Francois Pepin, PhD1, Thomas Asbury, PhD1, Marissa Vignali, PhD1, Ryan O. Emerson, PhD1, Harlan S. Robins, PhD 1,2, James Ireland, MSc3, Emily Baechler-Gillespie, PhD4, and Robert D. Inman, MD5 1Adaptive Biotechnologies Corp., South San Francisco, CA and Seattle, WA; 2Fred Hutchinson Cancer Research Center, Seattle WA, 3Alternate Allele Consulting, Orinda, CA; 4University of Minnesota, Minneapolis, MN; 5Toronto Western Hospital, University of Toronto, Toronto, ON
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