Evidence map›Paper›PMID 35027560›Full record

ArticleNPJ breast cancer2022

The breast pre-cancer atlas illustrates the molecular and micro-environmental diversity of ductal carcinoma in situ.

Daniela Nachmanson, Adam Officer, Hidetoshi Mori, Jonathan Gordon, Mark F Evans, Joseph Steward, Huazhen Yao, Thomas O'Keefe, Farnaz Hasteh, Gary S Stein and 8 more

Abstract read
In one paragraph

Article in NPJ breast cancer, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.

0numbers the graph read from it
0cells of the map it votes in
13citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

13 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. Article
  5. Review
  6. Article
  7. Review
  8. Clinical Implications of APOBEC3-Mediated Mutagenesis in Breast Cancer.Clinical cancer research : an official journal of the American Association for Cancer Research · 2023
    Review
  9. Article
  10. Article
  11. Article
  12. Review
  13. Cell reports methods · 2021
    Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

18 authors.

Daniela NachmansonBioinformatics and Systems Biology Graduate Program, University of California San Diego, 9500 Gilman Drive, San Diego, CA, 92093, USA.
Adam OfficerBioinformatics and Systems Biology Graduate Program, University of California San Diego, 9500 Gilman Drive, San Diego, CA, 92093, USA.
Hidetoshi MoriDepartment of Pathology and Laboratory Medicine, Center for Immunology and Infectious Diseases, School of Medicine, University of California Davis, 2315 Stockton Blvd, Sacramento, CA, 95817, USA.
Jonathan GordonUniversity of Vermont Cancer Center, 111 Colchester Avenue Main Campus, Main Pavillion, Level, 2, Burlington, VT, 05401, USA.
Mark F EvansUniversity of Vermont Cancer Center, 111 Colchester Avenue Main Campus, Main Pavillion, Level, 2, Burlington, VT, 05401, USA.
Joseph StewardMoores Cancer Center, University of California San Diego, 3855 Health Science Drive, San Diego, CA, 92093, USA.
Huazhen YaoInstitute for Genomic Medicine, University of California San Diego, 9500 Gilman Drive, San Diego, CA, 92093, USA.
Thomas O'KeefeDepartment of Surgery, University of California San Diego, 9500 Gilman Drive, San Diego, CA, 92093, USA.
Farnaz HastehMoores Cancer Center, University of California San Diego, 3855 Health Science Drive, San Diego, CA, 92093, USA.
Gary S SteinUniversity of Vermont Cancer Center, 111 Colchester Avenue Main Campus, Main Pavillion, Level, 2, Burlington, VT, 05401, USA.
Kristen JepsenInstitute for Genomic Medicine, University of California San Diego, 9500 Gilman Drive, San Diego, CA, 92093, USA.
Donald L WeaverUniversity of Vermont Cancer Center, 111 Colchester Avenue Main Campus, Main Pavillion, Level, 2, Burlington, VT, 05401, USA.
Gillian L HirstHelen Diller Family Comprehensive Cancer Center, University of California San Francisco, 1450 3rd St, San Francisco, CA, 94158, USA.ORCID http://orcid.org/0000-0002-4502-0035
Brian L SpragueUniversity of Vermont Cancer Center, 111 Colchester Avenue Main Campus, Main Pavillion, Level, 2, Burlington, VT, 05401, USA.
Laura J EssermanHelen Diller Family Comprehensive Cancer Center, University of California San Francisco, 1450 3rd St, San Francisco, CA, 94158, USA.ORCID http://orcid.org/0000-0001-9202-4568
Alexander D BorowskyDepartment of Pathology and Laboratory Medicine, Center for Immunology and Infectious Diseases, School of Medicine, University of California Davis, 2315 Stockton Blvd, Sacramento, CA, 95817, USA.ORCID http://orcid.org/0000-0003-3117-9202
Janet L SteinUniversity of Vermont Cancer Center, 111 Colchester Avenue Main Campus, Main Pavillion, Level, 2, Burlington, VT, 05401, USA.ORCID http://orcid.org/0000-0002-2474-6822
Olivier HarismendyDivision of Biomedical Informatics, Department of Medicine, University of California San Diego, 9500 Gilman Drive, San Diego, CA, 92093, USA. oharismendy@ucsd.edu.ORCID http://orcid.org/0000-0002-8098-9888

Funding

VIRAL MALIGNANCYP30CA023100 · NCI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI DIANE M SIMEONE · 1985 to 2026
$124.9M
Understanding Factors Influencing COVID-19 Testing and Vaccination in Immigrant Low-income and Homeless Populations and Testing Targeted InterventionsU54GM115516 · NIGMS · MAINEHEALTH · PI Robert A Koza · 2017 to 2026
$51.6M
San Diego Biomedical Informatics Education & Research (SABER)T15LM011271 · NLM · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI SHAMIM NEMATI · 2012 to 2026
$9.7M
GRADUATE TRAINING PROGRAM IN BIONFORMATICST32GM008806 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI BAFNA, VINEET, REN, BING · 2001 to 2020
$6.2M
Elucidating the molecular and contextual basis for IDLE ultralow risk lesions and the tumor immune microenvironment of high risk in situ and invasive breast cancersU01CA196406 · NCI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI BOROWSKY, ALEXANDER D, ESSERMAN, LAURA J · 2015 to 2020
$5.8M
Vermont Breast Cancer Molecular Characterization LaboratoryU01CA196383 · NCI · UNIVERSITY OF VERMONT & ST AGRIC COLLEGE · PI SPRAGUE, BRIAN L, STEIN, JANET L · 2015 to 2020
$5.4M
Targeting Signaling Vulnerabilities for Oral Cancer PreventionR01DE026644 · NIDCR · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Jorge Silvio Gutkind, SCOTT M LIPPMAN · 2017 to 2026
$4.7M
NCI NIH HHS P30 CA023100NCI NIH HHS U01 CA196383NCI NIH HHS U01 CA196406NIDCR NIH HHS R01 DE026644NIGMS NIH HHS T32 GM008806NIGMS NIH HHS U54 GM115516NLM NIH HHS T15 LM011271Tobacco-Related Disease Research Program (TRDRP) 28DT-0011U.S. Department of Health & Human Services | National Institutes of Health (NIH) T15LM011271U.S. Department of Health & Human Services | National Institutes of Health (NIH) U01CA196383U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI) U01CA196406
6 · The paper itself

Abstract

Microenvironmental and molecular factors mediating the progression of Breast Ductal Carcinoma In Situ (DCIS) are not well understood, impeding the development of prevention strategies and the safe testing of treatment de-escalation. We addressed methodological barriers and characterized the mutational, transcriptional, histological, and microenvironmental landscape across 85 multiple microdissected regions from 39 cases. Most somatic alterations, including whole-genome duplications, were clonal, but genetic divergence increased with physical distance. Phenotypic and subtype heterogeneity was frequently associated with underlying genetic heterogeneity and regions with low-risk features preceded those with high-risk features according to the inferred phylogeny. B- and T-lymphocytes spatial analysis identified three immune states, including an epithelial excluded state located preferentially at DCIS regions, and characterized by histological and molecular features of immune escape, independently from molecular subtypes. Such breast pre-cancer atlas with uniquely integrated observations will help scope future expansion studies and build finer models of outcomes and progression risk.

Identifiers

PMID35027560
PMCPMC8758681

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.