1
|
Combes AJ, Samad B, Tsui J, Chew NW, Yan P, Reeder GC, Kushnoor D, Shen A, Davidson B, Barczak AJ, Adkisson M, Edwards A, Naser M, Barry KC, Courau T, Hammoudi T, Argüello RJ, Rao AA, Olshen AB, Cai C, Zhan J, Davis KC, Kelley RK, Chapman JS, Atreya CE, Patel A, Daud AI, Ha P, Diaz AA, Kratz JR, Collisson EA, Fragiadakis GK, Erle DJ, Boissonnas A, Asthana S, Chan V, Krummel MF, Fong L, Nelson A, Kumar R, Lee J, Burra A, Hsu J, Hackett C, Tolentino K, Sjarif J, Johnson P, Shao E, Abrau D, Lupin L, Shaw C, Collins Z, Lea T, Corvera C, Nakakura E, Carnevale J, Alvarado M, Loo K, Chen L, Chow M, Grandis J, Ryan W, El-Sayed I, Jablons D, Woodard G, Meng MW, Porten SP, Okada H, Tempero M, Ko A, Kirkwood K, Vandenberg S, Guevarra D, Oropeza E, Cyr C, Glenn P, Bolen J, Morton A, Eckalbar W. Discovering dominant tumor immune archetypes in a pan-cancer census. Cell 2022; 185:184-203.e19. [PMID: 34963056 PMCID: PMC8862608 DOI: 10.1016/j.cell.2021.12.004] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 08/25/2021] [Accepted: 12/03/2021] [Indexed: 01/09/2023]
Abstract
Cancers display significant heterogeneity with respect to tissue of origin, driver mutations, and other features of the surrounding tissue. It is likely that individual tumors engage common patterns of the immune system-here "archetypes"-creating prototypical non-destructive tumor immune microenvironments (TMEs) and modulating tumor-targeting. To discover the dominant immune system archetypes, the University of California, San Francisco (UCSF) 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 dominant patterns of immune composition across cancers. These archetypes were profound insofar as they also differentiated tumors based upon unique immune and tumor gene-expression patterns. They also partitioned well-established classifications of tumor biology. The IPI resource provides a template for understanding cancer immunity as a collection of dominant patterns of immune organization and provides a rational path forward to learn how to modulate these to improve therapy.
Collapse
Affiliation(s)
- Alexis J. Combes
- Department of Pathology, University of California San Francisco, San Francisco, CA 94143, USA,ImmunoX Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF CoLabs, University of California San Francisco, San Francisco, CA 94143, USA,Correspondence: and
| | - Bushra Samad
- Department of Pathology, University of California San Francisco, San Francisco, CA 94143, USA,ImmunoX Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF CoLabs, University of California San Francisco, San Francisco, CA 94143, USA
| | - Jessica Tsui
- Department of Pathology, University of California San Francisco, San Francisco, CA 94143, USA,ImmunoX Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF CoLabs, University of California San Francisco, San Francisco, CA 94143, USA
| | - Nayvin W. Chew
- Department of Pathology, University of California San Francisco, San Francisco, CA 94143, USA,ImmunoX Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF CoLabs, University of California San Francisco, San Francisco, CA 94143, USA
| | - Peter Yan
- Department of Pathology, University of California San Francisco, San Francisco, CA 94143, USA,ImmunoX Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF CoLabs, University of California San Francisco, San Francisco, CA 94143, USA
| | - Gabriella C. Reeder
- Department of Pathology, University of California San Francisco, San Francisco, CA 94143, USA,ImmunoX Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF CoLabs, University of California San Francisco, San Francisco, CA 94143, USA
| | - Divyashree Kushnoor
- Department of Pathology, University of California San Francisco, San Francisco, CA 94143, USA,ImmunoX Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF CoLabs, University of California San Francisco, San Francisco, CA 94143, USA
| | - Alan Shen
- Department of Pathology, University of California San Francisco, San Francisco, CA 94143, USA,ImmunoX Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF CoLabs, University of California San Francisco, San Francisco, CA 94143, USA
| | - Brittany Davidson
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF CoLabs, University of California San Francisco, San Francisco, CA 94143, USA
| | - Andrea J. Barczak
- UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF CoLabs, University of California San Francisco, San Francisco, CA 94143, USA
| | - Michael Adkisson
- UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF CoLabs, University of California San Francisco, San Francisco, CA 94143, USA
| | - Austin Edwards
- Department of Pathology, University of California San Francisco, San Francisco, CA 94143, USA,ImmunoX Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF CoLabs, University of California San Francisco, San Francisco, CA 94143, USA
| | - Mohammad Naser
- Department of Pathology, University of California San Francisco, San Francisco, CA 94143, USA,ImmunoX Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF CoLabs, University of California San Francisco, San Francisco, CA 94143, USA
| | - Kevin C. Barry
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Tristan Courau
- Department of Pathology, University of California San Francisco, San Francisco, CA 94143, USA,ImmunoX Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF CoLabs, University of California San Francisco, San Francisco, CA 94143, USA
| | - Taymour Hammoudi
- Department of Pathology, University of California San Francisco, San Francisco, CA 94143, USA,ImmunoX Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF CoLabs, University of California San Francisco, San Francisco, CA 94143, USA
| | - Rafael J Argüello
- Aix Marseille University, CNRS, INSERM, CIML, Centre d’Immunologie de Marseille-Luminy, Marseille, FRANCE
| | - Arjun Arkal Rao
- Department of Pathology, University of California San Francisco, San Francisco, CA 94143, USA,ImmunoX Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF CoLabs, University of California San Francisco, San Francisco, CA 94143, USA
| | - Adam B. Olshen
- UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA 94143, USA,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143, USA,Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94143, USA
| | | | - Cathy Cai
- Department of Pathology, University of California San Francisco, San Francisco, CA 94143, USA,ImmunoX Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF CoLabs, University of California San Francisco, San Francisco, CA 94143, USA
| | - Jenny Zhan
- Department of Pathology, University of California San Francisco, San Francisco, CA 94143, USA,ImmunoX Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF CoLabs, University of California San Francisco, San Francisco, CA 94143, USA
| | - Katelyn C. Davis
- Department of Pathology, University of California San Francisco, San Francisco, CA 94143, USA,ImmunoX Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF CoLabs, University of California San Francisco, San Francisco, CA 94143, USA
| | - Robin K. Kelley
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143, USA
| | - Jocelyn S. Chapman
- UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA 94143, USA,Departments of Obstetrics, Gynecology, and Reproductive Sciences, Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Chloe E. Atreya
- UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA 94143, USA,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143, USA,Department of Medicine, Division of Hematology and Oncology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Amar Patel
- UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA 94143, USA,Department of Medicine, Division of Hematology and Oncology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Adil I. Daud
- Department of Medicine, Division of Hematology and Oncology, University of California San Francisco, San Francisco, CA 94143, USA,Department of Dermatology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Patrick Ha
- Department of Otolaryngology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Aaron A. Diaz
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA 94143, USA
| | - Johannes R. Kratz
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA 94143, USA,Department of Surgery, University of California San Francisco, San Francisco, CA 94143, USA
| | - Eric A. Collisson
- UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA 94143, USA,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143, USA,Department of Medicine, Division of Hematology and Oncology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Gabriela K Fragiadakis
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF CoLabs, University of California San Francisco, San Francisco, CA 94143, USA,Department of Medicine Division of Rheumatology, University of California San Francisco, San Francisco, CA 94143, USA
| | - David J. Erle
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF CoLabs, University of California San Francisco, San Francisco, CA 94143, USA,Lung Biology Center, Department of Medicine and the Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA 94143, USA
| | - Alexandre Boissonnas
- Sorbonne Université, INSERM, CNRS, Centre d’Immunologie et des Maladies Infectieuses - CIMI, Paris, France
| | - Saurabh Asthana
- UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA 94143, USA,Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94143, USA
| | - Vincent Chan
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA 94143, USA,Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Matthew F. Krummel
- Department of Pathology, University of California San Francisco, San Francisco, CA 94143, USA,ImmunoX Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA 94143, USA,Correspondence: and
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
2
|
Scott-Sheldon LAJ, Hedges LV, Cyr C, Young-Hyman D, Khan LK, Magnus M, King H, Arteaga S, Cawley J, Economos CD, Haire-Joshu D, Hunter CM, Lee BY, Kumanyika SK, Ritchie LD, Robinson TN, Schwartz MB. Childhood Obesity Evidence Base Project: A Systematic Review and Meta-Analysis of a New Taxonomy of Intervention Components to Improve Weight Status in Children 2-5 Years of Age, 2005-2019. Child Obes 2020; 16:S221-S248. [PMID: 32936038 PMCID: PMC7482126 DOI: 10.1089/chi.2020.0139] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Objective: To evaluate the efficacy of childhood obesity interventions and conduct a taxonomy of intervention components that are most effective in changing obesity-related health outcomes in children 2-5 years of age. Methods: Comprehensive searches located 51 studies from 18,335 unique records. Eligible studies: (1) assessed children aged 2-5, living in the United States; (2) evaluated an intervention to improve weight status; (3) identified a same-aged comparison group; (4) measured BMI; and (5) were available between January 2005 and August 2019. Coders extracted study, sample, and intervention characteristics. Effect sizes [ESs; and 95% confidence intervals (CIs)] were calculated by using random-effects models. Meta-regression was used to determine which intervention components explain variability in ESs. Results: Included were 51 studies evaluating 58 interventions (N = 29,085; mean age = 4 years; 50% girls). Relative to controls, children receiving an intervention had a lower BMI at the end of the intervention (g = 0.10, 95% CI = 0.02-0.18; k = 55) and at the last follow-up (g = 0.17, 95% CI = 0.04-0.30; k = 14; range = 18-143 weeks). Three intervention components moderated efficacy: engage caregivers in praise/encouragement for positive health-related behavior; provide education about the importance of screen time reduction to caregivers; and engage pediatricians/health care providers. Conclusions: Early childhood obesity interventions are effective in reducing BMI in preschool children. Our findings suggest that facilitating caregiver education about the importance of screen time reduction may be an important strategy in reducing early childhood obesity.
Collapse
Affiliation(s)
- Lori A J Scott-Sheldon
- Centers for Behavioral and Preventive Medicine, The Miriam Hospital, Providence, RI, USA
- Department of Psychiatry and Human Behavior, Alpert School of Medicine, Brown University, Providence, RI, USA
| | - Larry V Hedges
- Department of Statistics, Northwestern University, Evanston, IL, USA
| | - Chris Cyr
- Impact Genome Project, Mission Measurement, Chicago, IL, USA
| | - Deborah Young-Hyman
- Office of Behavioral and Social Sciences, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Laura Kettel Khan
- Division of Nutrition, Physical Activity, and Obesity, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Heather King
- Impact Genome Project, Mission Measurement, Chicago, IL, USA
| | - Sonia Arteaga
- Office of the Director, National Institutes of Health, National Institutes of Health, Bethesda, MD, USA
| | - John Cawley
- Department of Policy Analysis and Management, Cornell University, Ithaca, NY, USA
- Department of Economics, Cornell University, Ithaca, NY, USA
| | - Christina D Economos
- Division of Nutrition Interventions, Communication, and Behavior Change, Friedman School of Nutrition Science and Policy, Tufts University, Boston, MA, USA
| | - Debra Haire-Joshu
- Center for Obesity Prevention and Policy Research, Brown School, Washington University, Saint Louis, MO, USA
| | - Christine M Hunter
- Office of Behavioral and Social Sciences, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Bruce Y Lee
- CUNY Graduate School of Public Health and Policy, New York, NY, USA
| | - Shiriki K Kumanyika
- Department of Community Health and Prevention, Dornsife School of Public Health, Drexel University, Philadelphia, PA, USA
| | - Lorrene D Ritchie
- Nutrition Policy Institute, University of California, Division of Agriculture and Natural Resources, Berkeley, CA, USA
| | - Thomas N Robinson
- Departments of Pediatrics and Medicine, Stanford Solutions Science Lab, Stanford University, Stanford, CA, USA
| | - Marlene B Schwartz
- Department of Human Development and Family Studies, University of Connecticut, Hartford, CT, USA
| |
Collapse
|
3
|
King H, Magnus M, Hedges LV, Cyr C, Young-Hyman D, Kettel Khan L, Scott-Sheldon LAJ, Saul JA, Arteaga S, Cawley J, Economos CD, Haire-Joshu D, Hunter CM, Lee BY, Kumanyika SK, Ritchie LD, Robinson TN, Schwartz MB. Childhood Obesity Evidence Base Project: Methods for Taxonomy Development for Application in Taxonomic Meta-Analysis. Child Obes 2020; 16:S27-S220. [PMID: 32936039 PMCID: PMC7482109 DOI: 10.1089/chi.2020.0138] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Meta-analysis has been used to examine the effectiveness of childhood obesity prevention efforts, yet traditional conventional meta-analytic methods restrict the kinds of studies included, and either narrowly define mechanisms and agents of change, or examine the effectiveness of whole interventions as opposed to the specific actions that comprise interventions. Taxonomic meta-analytic methods widen the aperture of what can be included in a meta-analysis data set, allowing for inclusion of many types of interventions and study designs. The National Collaborative on Childhood Obesity Research Childhood Obesity Evidence Base (COEB) project focuses on interventions intended to prevent childhood obesity in children 2-5 years old who have an outcome measure of BMI. The COEB created taxonomies, anchored in the Social Ecological Model, which catalog specific outcomes, intervention components, intended recipients, and contexts of policies, initiatives, and interventions conducted at the individual, interpersonal, organizational, community, and societal level. Taxonomies were created by discovery from the literature itself using grounded theory. This article describes the process used for a novel taxonomic meta-analysis of childhood obesity prevention studies between the years 2010 and 2019. This method can be applied to other areas of research, including obesity prevention in additional populations.
Collapse
Affiliation(s)
- Heather King
- Impact Genome Project, Mission Measurement, Chicago, IL, USA
| | | | - Larry V Hedges
- Department of Statistics, Northwestern University, Evanston, IL, USA
| | - Chris Cyr
- Impact Genome Project, Mission Measurement, Chicago, IL, USA
| | - Deborah Young-Hyman
- Office of Behavioral and Social Sciences, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Laura Kettel Khan
- Division of Nutrition, Physical Activity, and Obesity, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Lori A J Scott-Sheldon
- Centers for Behavioral and Preventive Medicine, The Miriam Hospital, Providence, RI, USA
- Department of Psychiatry and Human Behavior, Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Jason A Saul
- Center for Impact Sciences, Harris School of Public Policy, University of Chicago, Chicago, IL, USA
| | - Sonia Arteaga
- Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - John Cawley
- Department of Policy Analysis and Management and Cornell University, Ithaca, NY, USA
- Department of Economics, Cornell University, Ithaca, NY, USA
| | - Christina D Economos
- Friedman School of Nutrition Science and Policy, Tufts University, Boston, MA, USA
| | - Debra Haire-Joshu
- Center for Obesity Prevention and Policy Research, Brown School Washington University, Saint Louis, MO, USA
| | - Christine M Hunter
- Office of Behavioral and Social Sciences, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Bruce Y Lee
- CUNY Graduate School of Public Health and Policy, New York, NY, USA
| | - Shiriki K Kumanyika
- Department of Community Health and Prevention, Dornsife School of Public Health, Drexel University, Philadelphia, PA, USA
| | - Lorrene D Ritchie
- Nutrition Policy Institute, University of California Agriculture and Natural Resources, Berkeley, CA, USA
| | - Thomas N Robinson
- Stanford Solutions Science Lab, Stanford University, Stanford, CA, USA
| | - Marlene B Schwartz
- Department of Human Development and Family Studies, University of Connecticut, Hartford, CT, USA
| |
Collapse
|