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A Pan-Cancer Census of Dominant Tumor Immune Archetypes

99 Pages Posted: 23 Apr 2021 Publication Status: Published

See all articles by Alexis J. Combes

Alexis J. Combes

University of California, San Francisco (UCSF) - UCSF CoLabs

Bushra Samad

University of California, San Francisco (UCSF) - Department of Pathology

Jessica Tsui

University of California, San Francisco (UCSF) - Department of Pathology

Nayvin W. Chew

University of California, San Francisco (UCSF) - Department of Pathology

Peter Yan

University of California, San Francisco (UCSF) - Department of Pathology

Gabriella C. Reeder

University of California, San Francisco (UCSF) - Department of Pathology

Divyashree Kushnoor

University of California, San Francisco (UCSF) - Department of Pathology

Alan Shen

University of California, San Francisco (UCSF) - Department of Pathology

Brittany Davidson

University of California, San Francisco (UCSF) - ImmunoX Initiative

Andrea J. Barczak

University of California, San Francisco (UCSF) - UCSF CoLabs

Michael Adkisson

University of California, San Francisco (UCSF) - UCSF CoLabs

Austin Edwards

University of California, San Francisco (UCSF) - Department of Pathology

Mohammad Naser

University of California, San Francisco (UCSF) - Department of Pathology

Kevin C. Barry

Fred Hutchinson Cancer Research Center - Translational Research Program

Tristan Courau

University of California, San Francisco (UCSF) - Department of Pathology

Taymour Hammoudi

University of California, San Francisco (UCSF) - Department of Pathology

Rafael Arguello

Aix-Marseille University - Centre d'Immunologie de Marseille-Luminy

Arjun Arkal Rao

University of California, San Francisco (UCSF) - UCSF CoLabs

Adam B. Olshen

University of California, San Francisco (UCSF) - Helen Diller Family Comprehensive Cancer Center

The Immunoprofiler Consortium

Independent

Cathy Cai

University of California, San Francisco (UCSF) - Department of Pathology

Jenny Zhan

University of California, San Francisco (UCSF) - Department of Pathology

Katelyn C. Davis

University of California, San Francisco (UCSF) - Department of Pathology

Robin K. Kelley

University of California, San Francisco (UCSF) - Helen Diller Family Comprehensive Cancer Center

Jocelyn S. Chapman

University of California, San Francisco (UCSF) - Department of Obstetrics, Gynecology and Reproductive Sciences

Chloe E. Attreya

University of California, San Francisco (UCSF) - Helen Diller Family Comprehensive Cancer Center

Amar Patel

University of California, San Francisco (UCSF) - Division of Hematology and Oncology

Adil Daud

University of California, San Francisco (UCSF) - Department of Medicine; University of California, San Francisco (UCSF) - Department of Dermatology

Patrick Ha

University of California, San Francisco (UCSF) - Department of Otolaryngology

Aaron A. Diaz

University of California, San Francisco (UCSF) - Department of Neurological Surgery

Johannes R. Kratz

University of California, San Francisco (UCSF) - ImmunoX Initiative

Eric A. Collisson

University of California, San Francisco (UCSF) - Helen Diller Family Comprehensive Cancer Center

Gabriela K. Fragiadakis

University of California, San Francisco (UCSF) - UCSF CoLabs

David J. Erle

University of California, San Francisco (UCSF) - UCSF CoLabs

Alexandre Boissonnas

Sorbonne University - Centre d'Immunologie et des Maladies Infectieuses

Saurabh Asthana

University of California, San Francisco (UCSF) - Department of Epidemiology and Biostatistics

Vincent Chan

University of California, San Francisco (UCSF) - Department of Microbiology and Immunology

Matthew F. Krummel

University of California, San Francisco (UCSF) - Department of Pathology; University of California, San Francisco (UCSF) - Department of Anatomy

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Abstract

Cancers display significant heterogeneity with respect to tissue of origin, driver mutations and other features of the surrounding tissue. It is likely that persistent tumors differentially engage inherent patterns–here ‘Archetypes’–of the immune system, to both benefit from a tumor immune microenvironment (TIME) and to disengage tumor-targeting. To discover dominant immune system archetypes, the Immunoprofiler Initiative (IPI) processed 364 individual tumors across 12 cancer types using standardized protocols. Computational clustering of flow cytometry and transcriptomic data obtained from cell sub compartments uncovered archetypes that exist across indications. These Immune composition-based archetypes differentiate tumors based upon unique immune and tumor gene-expression patterns. Archetypes discovered this way also tie closely to well-established classifications of tumor biology. The IPI resource provides a template for understanding cancer immunity as a collection of dominant patterns of immune infiltration and provides a rational path forward to learn how to modulate these patterns to improve therapy.

Suggested Citation

Combes, Alexis J. and Samad, Bushra and Tsui, Jessica and Chew, Nayvin W. and Yan, Peter and Reeder, Gabriella C. and Kushnoor, Divyashree and Shen, Alan and Davidson, Brittany and Barczak, Andrea J. and Adkisson, Michael and Edwards, Austin and Naser, Mohammad and Barry, Kevin C. and Courau, Tristan and Hammoudi, Taymour and Arguello, Rafael and Rao, Arjun Arkal and Olshen, Adam B. and Consortium, The Immunoprofiler and Cai, Cathy and Zhan, Jenny and Davis, Katelyn C. and Kelley, Robin K. and Chapman, Jocelyn S. and Attreya, Chloe E. and Patel, Amar and Daud, Adil and Ha, Patrick and Diaz, Aaron A. and Kratz, Johannes R. and Collisson, Eric A. and Fragiadakis, Gabriela K. and Erle, David J. and Boissonnas, Alexandre and Asthana, Saurabh and Chan, Vincent and Krummel, Matthew F., A Pan-Cancer Census of Dominant Tumor Immune Archetypes. Available at SSRN: https://ssrn.com/abstract=3833003 or http://dx.doi.org/10.2139/ssrn.3833003
This version of the paper has not been formally peer reviewed.

Alexis J. Combes

University of California, San Francisco (UCSF) - UCSF CoLabs ( email )

San Francisco, CA
United States

Bushra Samad

University of California, San Francisco (UCSF) - Department of Pathology ( email )

San Francisco, CA 94143
United States

Jessica Tsui

University of California, San Francisco (UCSF) - Department of Pathology ( email )

San Francisco, CA 94143
United States

Nayvin W. Chew

University of California, San Francisco (UCSF) - Department of Pathology ( email )

San Francisco, CA 94143
United States

Peter Yan

University of California, San Francisco (UCSF) - Department of Pathology ( email )

San Francisco, CA 94143
United States

Gabriella C. Reeder

University of California, San Francisco (UCSF) - Department of Pathology ( email )

San Francisco, CA 94143
United States

Divyashree Kushnoor

University of California, San Francisco (UCSF) - Department of Pathology ( email )

San Francisco, CA 94143
United States

Alan Shen

University of California, San Francisco (UCSF) - Department of Pathology

San Francisco, CA 94143
United States

Brittany Davidson

University of California, San Francisco (UCSF) - ImmunoX Initiative

Third Avenue and Parnassus
San Francisco, CA CA 94143
United States

Andrea J. Barczak

University of California, San Francisco (UCSF) - UCSF CoLabs ( email )

Third Avenue and Parnassus
San Francisco, CA CA 94143
United States

Michael Adkisson

University of California, San Francisco (UCSF) - UCSF CoLabs ( email )

Third Avenue and Parnassus
San Francisco, CA CA 94143
United States

Austin Edwards

University of California, San Francisco (UCSF) - Department of Pathology ( email )

San Francisco, CA 94143
United States

Mohammad Naser

University of California, San Francisco (UCSF) - Department of Pathology

San Francisco, CA 94143
United States

Kevin C. Barry

Fred Hutchinson Cancer Research Center - Translational Research Program ( email )

1100 Fairview Avenue North
M2-C206
Seattle, WA 98109-1024
United States

Tristan Courau

University of California, San Francisco (UCSF) - Department of Pathology ( email )

San Francisco, CA 94143
United States

Taymour Hammoudi

University of California, San Francisco (UCSF) - Department of Pathology ( email )

San Francisco, CA 94143
United States

Rafael Arguello

Aix-Marseille University - Centre d'Immunologie de Marseille-Luminy ( email )

France

Arjun Arkal Rao

University of California, San Francisco (UCSF) - UCSF CoLabs ( email )

San Francisco, CA
United States

Adam B. Olshen

University of California, San Francisco (UCSF) - Helen Diller Family Comprehensive Cancer Center ( email )

Box 0981, UCSF
San Francisco, CA 94143-0981
United States

Cathy Cai

University of California, San Francisco (UCSF) - Department of Pathology

San Francisco, CA 94143
United States

Jenny Zhan

University of California, San Francisco (UCSF) - Department of Pathology

San Francisco, CA 94143
United States

Katelyn C. Davis

University of California, San Francisco (UCSF) - Department of Pathology ( email )

San Francisco, CA 94143
United States

Robin K. Kelley

University of California, San Francisco (UCSF) - Helen Diller Family Comprehensive Cancer Center ( email )

Box 0981, UCSF
San Francisco, CA 94143-0981
United States

Jocelyn S. Chapman

University of California, San Francisco (UCSF) - Department of Obstetrics, Gynecology and Reproductive Sciences ( email )

San Francisco, CA 94143
United States

Chloe E. Attreya

University of California, San Francisco (UCSF) - Helen Diller Family Comprehensive Cancer Center ( email )

Box 0981, UCSF
San Francisco, CA 94143-0981
United States

Amar Patel

University of California, San Francisco (UCSF) - Division of Hematology and Oncology

Third Avenue and Parnassus
San Francisco, CA CA 94143
United States

Adil Daud

University of California, San Francisco (UCSF) - Department of Medicine ( email )

San Francisco, CA
United States

University of California, San Francisco (UCSF) - Department of Dermatology ( email )

Third Avenue and Parnassus
San Francisco, CA 94143
United States

Patrick Ha

University of California, San Francisco (UCSF) - Department of Otolaryngology ( email )

CA
United States

Aaron A. Diaz

University of California, San Francisco (UCSF) - Department of Neurological Surgery ( email )

United States

Johannes R. Kratz

University of California, San Francisco (UCSF) - ImmunoX Initiative ( email )

San Francisco, CA
United States

Eric A. Collisson

University of California, San Francisco (UCSF) - Helen Diller Family Comprehensive Cancer Center ( email )

Box 0981, UCSF
San Francisco, CA 94143-0981
United States

Gabriela K. Fragiadakis

University of California, San Francisco (UCSF) - UCSF CoLabs ( email )

San Francisco, CA
United States

David J. Erle

University of California, San Francisco (UCSF) - UCSF CoLabs ( email )

San Francisco, CA
United States

Alexandre Boissonnas

Sorbonne University - Centre d'Immunologie et des Maladies Infectieuses ( email )

France

Saurabh Asthana

University of California, San Francisco (UCSF) - Department of Epidemiology and Biostatistics ( email )

Third Avenue and Parnassus
San Francisco, CA CA 94143
United States

Vincent Chan

University of California, San Francisco (UCSF) - Department of Microbiology and Immunology

Third Avenue and Parnassus
San Francisco, CA CA 94143
United States

Matthew F. Krummel (Contact Author)

University of California, San Francisco (UCSF) - Department of Pathology ( email )

San Francisco, CA 94143
United States

University of California, San Francisco (UCSF) - Department of Anatomy ( email )

San Francisco, CA 94143
United States

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