ArticleCell reports. Medicine2022
An omic and multidimensional spatial atlas from serial biopsies of an evolving metastatic breast cancer.
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Article in Cell reports. Medicine, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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34citing papers in PubMed
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34 citing papers in PubMed, 51 citations in OpenAlex.
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- Three-dimensional analysis of mitochondria in a patient-derived xenograft model of triple negative breast cancer reveals mitochondrial network remodeling following chemotherapy treatments.bioRxiv : the preprint server for biology · 2024Article
- Spatial molecular profiling of mixed invasive ductal and lobular breast cancers reveals heterogeneity in intrinsic molecular subtypes, oncogenic signatures, and mutations.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
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Authors and funding
46 authors at 2 institutions in 1 country.
Brett E JohnsonKnight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA.
Allison L CreasonKnight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA.
Jayne M StommelKnight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA.
Jamie M KeckKnight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA.
Swapnil ParmarKnight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA.
Courtney B BettsKnight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA.
Aurora BlucherKnight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA.
Christopher BonifaceDepartment of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA.
Elmar BucherDepartment of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA.
Erik BurlingameDepartment of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA.
Todd CampKnight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA.
Koei ChinKnight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA.
Jennifer EngDepartment of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA.
Joseph EstabrookKnight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA.
Heidi S FeilerKnight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA.
Michael B HeskettDepartment of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA.
Zhi HuKnight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA.
Annette KolodzieKnight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA.
Ben L KongKnight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA.
Marilyne LabrieKnight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA.
Jinho LeeKnight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA.
Patrick LeyshockKnight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA.
Souraya MitriKnight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA.
Janice PattersonKnight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA.
Jessica L RiestererDepartment of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA.
Shamilene SivagnanamKnight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA.
Julia SomersKnight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA.
Damir SudarQuantitative Imaging Systems LLC, Portland, OR 97239, USA.
Guillaume ThibaultDepartment of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA.
Benjamin R WeederDepartment of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA.
Christina ZhengKnight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA.
Xiaolin NanDepartment of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA.
Reid F ThompsonDepartment of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA.
Laura M HeiserKnight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA.
Paul T SpellmanDepartment of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA.
George ThomasKnight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA.
Emek DemirKnight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA.
Young Hwan ChangDepartment of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA.
Lisa M CoussensKnight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA.
Alexander R GuimaraesKnight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA.
Christopher CorlessDepartment of Pharmacy Services, Oregon Health & Science University, Portland, OR 97239, USA.
Jeremy GoecksKnight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA.
Raymond BerganFred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA.
Zahi MitriDivision of Hematology & Medical Oncology, Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA.
Gordon B MillsKnight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA.
Joe W GrayKnight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA.
Oregon Health & Science University · USUniversity of Nebraska Medical Center · US
Funding
Understanding the origins of rapid recurrence of pancreatic cancer after resectionP30CA069533 · NCI · OREGON HEALTH & SCIENCE UNIVERSITY · PI Grace B Gill · 1997 to 2026
$60.5MUnderstanding the Impact of Microscale and Nanoscale Heterogeneity and ResistanceU54CA209988 · NCI · OREGON HEALTH & SCIENCE UNIVERSITY · PI DEMIR, EMEK, HEISER, LAURA MADELINE · 2017 to 2021
$10.3MOmic and Multidimensional Spatial Atlas of Metastatic Breast CancerU2CCA233280 · NCI · OREGON HEALTH & SCIENCE UNIVERSITY · PI DEMIR, EMEK, MILLS, GORDON B. · 2018 to 2023
$9.7MA Federated Galaxy for user-friendly large-scale cancer genomics researchU24CA231877 · NCI · OREGON HEALTH & SCIENCE UNIVERSITY · PI GOECKS, JEREMY, SCHATZ, MICHAEL · 2018 to 2022
$3.9MIntegrative bioinformatics and functional characterization of oncogenic driver aberrations in cancerU01CA217842 · NCI · UNIVERSITY OF TX MD ANDERSON CAN CTR · PI DENEEN, BENJAMIN, MILLS, GORDON B. · 2017 to 2021
$3.6MComparative analysis between patient-derived models of pancreatic ductal adenocarcinomas and matched tumor specimensU01CA224012 · NCI · OREGON HEALTH & SCIENCE UNIVERSITY · PI BRODY, JONATHAN, COUSSENS, LISA M. · 2019 to 2023
$2.9MUltra-High Content Analysis (UHCA) of Single Cells in Tissue: 60+ channel immunofluorescence labeling kits and companion imaging software for everyoneR44CA224994 · NCI · QUANTITATIVE IMAGING SYSTEMS, LLC · PI NEDERLOF, MICHEL · 2017 to 2019
$1.7MDefining mechanisms of Ras clustering and signaling in membrane nanodomains with multiplexed superresolution and correlative microscopiesR01GM132322 · NIGMS · OREGON HEALTH & SCIENCE UNIVERSITY · PI NAN, XIAOLIN · 2020 to 2023
$1.4MNCI NIH HHS P30 CA069533NCI NIH HHS R44 CA224994NCI NIH HHS U01 CA217842NCI NIH HHS U01 CA224012NCI NIH HHS U2C CA233280NCI NIH HHS U54 CA209988
Abstract
Mechanisms of therapeutic resistance and vulnerability evolve in metastatic cancers as tumor cells and extrinsic microenvironmental influences change during treatment. To support the development of methods for identifying these mechanisms in individual people, here we present an omic and multidimensional spatial (OMS) atlas generated from four serial biopsies of an individual with metastatic breast cancer during 3.5 years of therapy. This resource links detailed, longitudinal clinical metadata that includes treatment times and doses, anatomic imaging, and blood-based response measurements to clinical and exploratory analyses, which includes comprehensive DNA, RNA, and protein profiles; images of multiplexed immunostaining; and 2- and 3-dimensional scanning electron micrographs. These data report aspects of heterogeneity and evolution of the cancer genome, signaling pathways, immune microenvironment, cellular composition and organization, and ultrastructure. We present illustrative examples of how integrative analyses of these data reveal potential mechanisms of response and resistance and suggest novel therapeutic vulnerabilities.
Indexed as
Breast NeoplasmsBiopsyFemaleHumansTumor Microenvironmenthuman tumor atlasmetastatic breast cancerpersonalized medicineprecision oncology
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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.