An Omic and Multidimensional Spatial Atlas from Serial Biopsies of an Evolving Metastatic Breast Cancer

Mechanisms of therapeutic resistance manifest in metastatic cancers as tumor cell intrinsic alterations and extrinsic microenvironmental influences that can change during treatment. To support the development of methods for the identification of these mechanisms in individual patients, we present he...

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Hauptverfasser: Johnson, Brett E., Creason, Allison L., Stommel, Jayne M., Keck, Jamie M., Parmar, Swapnil, Betts, Courtney B., Blucher, Aurora, Boniface, Christopher, Bucher, Elmar, Burlingame, Erik, Camp, Todd, Chin, Koei, Eng, Jennifer, Estabrook, Joseph, Feiler, Heidi S., Hu, Zhi, Kolodzie, Annette, Kong, Ben L., Labrie, Marilyne, Lee, Jinho, Leyshock, Patrick, Mitri, Souraya, Patterson, Janice, Riesterer, Jessica L., Sivagnanam, Shamilene, Somers, Julia, Sudar, Damir, Thibault, Guillaume, Zheng, Christina, Nan, Xiaolin, Heiser, Laura M., Spellman, Paul T., Thomas, George, Demir, Emek, Chang, Young Hwan, Coussens, Lisa M., Guimaraes, Alexander R., Corless, Christopher, Goecks, Jeremy, Bergan, Raymond, Mitri, Zahi, Mills, Gordon B., Gray, Joe W.
Format: Paper
Sprache:Englisch
Veröffentlicht: Cold Spring Harbor Laboratory 16.07.2021
Ausgabe:1.2
Schlagworte:
Cancer Biology
precision oncology
human tumor atlas
metastatic breast cancer
personalized medicine
ISSN:2692-8205
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Abstract Mechanisms of therapeutic resistance manifest in metastatic cancers as tumor cell intrinsic alterations and extrinsic microenvironmental influences that can change during treatment. To support the development of methods for the identification of these mechanisms in individual patients, we present here an Omic and Multidimensional Spatial (OMS) Atlas generated from four serial biopsies of a metastatic breast cancer patient during 3.5 years of therapy. This resource links detailed, longitudinal clinical metadata including treatment times and doses, anatomic imaging, and blood-based response measurements to exploratory analytics including comprehensive DNA, RNA, and protein profiles, images of multiplexed immunostaining, and 2- and 3-dimensional scanning electron micrographs. These data reveal aspects of therapy-associated heterogeneity and evolution of the cancer’s genome, signaling pathways, immune microenvironment, cellular composition and organization, and ultrastructure. We present illustrative examples showing how integrative analyses of these data provide insights into potential mechanisms of response and resistance, and suggest novel therapeutic vulnerabilities.
AbstractList Mechanisms of therapeutic resistance manifest in metastatic cancers as tumor cell intrinsic alterations and extrinsic microenvironmental influences that can change during treatment. To support the development of methods for the identification of these mechanisms in individual patients, we present here an Omic and Multidimensional Spatial (OMS) Atlas generated from four serial biopsies of a metastatic breast cancer patient during 3.5 years of therapy. This resource links detailed, longitudinal clinical metadata including treatment times and doses, anatomic imaging, and blood-based response measurements to exploratory analytics including comprehensive DNA, RNA, and protein profiles, images of multiplexed immunostaining, and 2- and 3-dimensional scanning electron micrographs. These data reveal aspects of therapy-associated heterogeneity and evolution of the cancer’s genome, signaling pathways, immune microenvironment, cellular composition and organization, and ultrastructure. We present illustrative examples showing how integrative analyses of these data provide insights into potential mechanisms of response and resistance, and suggest novel therapeutic vulnerabilities.
Author Kong, Ben L.
Demir, Emek
Stommel, Jayne M.
Lee, Jinho
Coussens, Lisa M.
Thibault, Guillaume
Sivagnanam, Shamilene
Thomas, George
Keck, Jamie M.
Mitri, Zahi
Labrie, Marilyne
Zheng, Christina
Chin, Koei
Corless, Christopher
Blucher, Aurora
Creason, Allison L.
Heiser, Laura M.
Chang, Young Hwan
Boniface, Christopher
Riesterer, Jessica L.
Burlingame, Erik
Mills, Gordon B.
Eng, Jennifer
Leyshock, Patrick
Somers, Julia
Spellman, Paul T.
Guimaraes, Alexander R.
Patterson, Janice
Sudar, Damir
Mitri, Souraya
Johnson, Brett E.
Goecks, Jeremy
Bergan, Raymond
Bucher, Elmar
Parmar, Swapnil
Camp, Todd
Feiler, Heidi S.
Nan, Xiaolin
Hu, Zhi
Kolodzie, Annette
Estabrook, Joseph
Gray, Joe W.
Betts, Courtney B.
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Cites_doi 10.3791/53154
10.1080/15548627.2021.1919969
10.1016/j.patter.2021.100257
ContentType Paper
Copyright 2021, Posted by Cold Spring Harbor Laboratory
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DOI 10.1101/2020.12.03.408500
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Keywords precision oncology
human tumor atlas
metastatic breast cancer
personalized medicine
Language English
License This pre-print is available under a Creative Commons License (Attribution 4.0 International), CC BY 4.0, as described at http://creativecommons.org/licenses/by/4.0
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Notes Competing Interest Statement: D.S. is employed by Quantitative Imaging Systems, which sells image analysis software. L.M.C. is a paid consultant for Cell Signaling Technologies, Shasqi Inc., and AbbVie Inc.; received reagent and/or research support from Plexxikon Inc., Pharmacyclics Inc., Acerta Pharma, LLC, Deciphera Pharmaceuticals, LLC, Genentech Inc., Roche Glycart AG, Syndax Pharmaceuticals Inc., Innate Pharma, and NanoString Technologies; and is a member of the Scientific Advisory Boards of Syndax Pharmaceuticals, Carisma Therapeutics, Zymeworks Inc., Verseau Therapeutics, Cytomix Therapeutics Inc., and Kineta Inc. G.B.M. has licensed technologies to Myriad Genetics and Nanostring; is on the SAB or is a consultant to Amphista, AstraZeneca, Chrysallis Biotechnology, GSK, ImmunoMET, Ionis, Lilly, PDX Pharmaceuticals, Signalchem Lifesciences, Symphogen, Tarveda, Turbine, and Zentalis Pharmaceuticals; and has stock/options/financial interests in Catena Pharmaceuticals, ImmunoMet, SignalChem, and Tarveda. J.W.G. has licensed technologies to Abbott Diagnostics; has ownership positions in Convergent Genomics, Health Technology Innovations, Zorro Bio, and PDX Pharmaceuticals; serves as a paid consultant to New Leaf Ventures; has received research support from Thermo Fisher Scientific (formerly FEI), Zeiss, Miltenyi Biotech, Quantitative Imaging, Health Technology Innovations, and Micron Technologies; and owns stock in Abbott Diagnostics, AbbVie, Alphabet, Amazon, Amgen, Apple, General Electric, Gilead, Intel, Microsoft, Nvidia, and Zimmer Biomet.
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Publisher Cold Spring Harbor Laboratory
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Snippet Mechanisms of therapeutic resistance manifest in metastatic cancers as tumor cell intrinsic alterations and extrinsic microenvironmental influences that can...
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SubjectTerms Cancer Biology
Title An Omic and Multidimensional Spatial Atlas from Serial Biopsies of an Evolving Metastatic Breast Cancer
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