ArticleCommunications biology2022
A multi-omic analysis of MCF10A cells provides a resource for integrative assessment of ligand-mediated molecular and phenotypic responses.
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Article in Communications biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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21citing papers in PubMed
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21 citing papers in PubMed.
- Oncogenic cell fate decision in breast epithelial cells I: growth factors and mechanisms.Research square · 2026Article
- Single-cell morphodynamical trajectories enable prediction of gene expression accompanying cell state change.Cell systems · 2026Article
- QSAR Modeling for Predicting ICInternational journal of molecular sciences · 2025Article
- SIRT1/DNMT3B-mediated epigenetic gene silencing in response to phytoestrogens in mammary epithelial cells.Epigenetics · 2025Article
- Oncostatin M orchestrates collective epithelial migration via HIF1A activation.bioRxiv : the preprint server for biology · 2025Article
- Microenvironmental signals combine to induce non-additive molecular and phenotypic responses in mammary epithelial cells.iScience · 2025Article
- Article
- Nucleosome dynamics render heterochromatin accessible in living human cells.Nature communications · 2025Article
- Novel determinants of NOTCH1 trafficking and signaling in breast epithelial cells.Life science alliance · 2025Article
- TNBC response to paclitaxel phenocopies interferon response which reveals cell cycle-associated resistance mechanisms.Scientific reports · 2025Article
- The structure is the message: Preserving experimental context through tensor decomposition.Cell systems · 2024Review
- Multiomics2Targets identifies targets from cancer cohorts profiled with transcriptomics, proteomics, and phosphoproteomics.Cell reports methods · 2024Article
- TNBC response to paclitaxel phenocopies interferon response which reveals cell cycle-associated resistance mechanisms.bioRxiv : the preprint server for biology · 2024Article
- Low-frequency ERK and Akt activity dynamics are predictive of stochastic cell division events.NPJ systems biology and applications · 2024Article
- Outlook and opportunities for engineered environments of breast cancer dormancy.Science advances · 2024Review
- Article
- MOBILE pipeline enables identification of context-specific networks and regulatory mechanisms.Nature communications · 2023Article
- Morphodynamical cell state description via live-cell imaging trajectory embedding.Communications biology · 2023Article
- MEMMAL: A tool for expanding large-scale mechanistic models with machine learned associations and big datasets.Frontiers in systems biology · 2023Article
- Application of perturbation gene expression profiles in drug discovery-From mechanism of action to quantitative modelling.Frontiers in systems biology · 2023Review
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Authors and funding
50 authors.
Sean M GrossDepartment of Biomedical Engineering, OHSU, Portland, OR, USA.
Mark A DaneDepartment of Biomedical Engineering, OHSU, Portland, OR, USA.ORCID 0000-0003-3742-9866
Rebecca L SmithDepartment of Biomedical Engineering, OHSU, Portland, OR, USA.
Kaylyn L DevlinDepartment of Biomedical Engineering, OHSU, Portland, OR, USA.
Ian C McLeanDepartment of Biomedical Engineering, OHSU, Portland, OR, USA.ORCID 0000-0003-2741-7941
Daniel S DerrickDepartment of Biomedical Engineering, OHSU, Portland, OR, USA.
Caitlin E MillsLaboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA, USA.ORCID 0000-0002-2608-4084
Kartik SubramanianLaboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA, USA.
Alexandra B LondonDepartment of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
Denis TorreDepartment of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
John Erol EvangelistaDepartment of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
Daniel J B ClarkeDepartment of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
Zhuorui XieDepartment of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
Cemal ErdemDepartment of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC, USA.ORCID 0000-0003-3663-3646
Nicholas LyonsBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Ted NatoliBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Sarah PessaBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Xiaodong LuBroad Institute of MIT and Harvard, Cambridge, MA, USA.
James MullahooBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Jonathan LiDepartment of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
Miriam AdamDepartment of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
Brook WassieDepartment of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
Moqing LiuDepartment of Biomedical Engineering, OHSU, Portland, OR, USA.
David F KilburnDepartment of Biomedical Engineering, OHSU, Portland, OR, USA.
Tiera A LibyDepartment of Biomedical Engineering, OHSU, Portland, OR, USA.
Elmar BucherDepartment of Biomedical Engineering, OHSU, Portland, OR, USA.ORCID 0000-0002-2929-2460
Crystal Sanchez-AguilaDepartment of Biomedical Engineering, OHSU, Portland, OR, USA.
Kenneth DailySage Bionetworks, Seattle, WA, USA.
Larsson OmbergSage Bionetworks, Seattle, WA, USA.
Yunguan WangLaboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA, USA.
Connor JacobsonLaboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA, USA.
Clarence YappLaboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA, USA.
Mirra ChungLaboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA, USA.
Dusica VidovicSylvester Comprehensive Cancer Center, University of Miami, Miami, FL, 33136, USA.
Yiling LuDepartment of Genomic Medicine, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
Stephan SchurerSylvester Comprehensive Cancer Center, University of Miami, Miami, FL, 33136, USA.ORCID 0000-0001-7180-0978
Albert LeeHeart, Lung, and Blood Institute, National Institutes of Health, Bethesda, USA.
Ajay PillaiHuman Genome Research Institute, National Institutes of Health, Bethesda, USA.
Aravind SubramanianBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Malvina PapanastasiouBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0003-3378-6612
Ernest FraenkelBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0001-9249-8181
Heidi S FeilerDepartment of Biomedical Engineering, OHSU, Portland, OR, USA.ORCID 0000-0002-6580-3547
Gordon B MillsKnight Cancer Institute, OHSU, Portland, OR, USA.
Jake D JaffeBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0001-9845-1210
Avi Ma'ayanDepartment of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
Marc R BirtwistleDepartment of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC, USA.
Peter K SorgerLaboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA, USA.ORCID 0000-0002-3364-1838
James E KorkolaDepartment of Biomedical Engineering, OHSU, Portland, OR, USA.
Joe W GrayDepartment of Biomedical Engineering, OHSU, Portland, OR, USA.
Laura M HeiserDepartment of Biomedical Engineering, OHSU, Portland, OR, USA. heiserl@ohsu.edu.ORCID 0000-0003-3330-0950
Funding
Tumor Evolution and Metastasis ProgramP30CA016672 · NCI · UNIVERSITY OF TX MD ANDERSON CAN CTR · PI Fabien Delerue · 1985 to 2026
$290.8MUnderstanding the origins of rapid recurrence of pancreatic cancer after resectionP30CA069533 · NCI · OREGON HEALTH & SCIENCE UNIVERSITY · PI Grace B Gill · 1997 to 2026
$60.5MData Coordination and Integration Center for LINCS-BD2KU54HL127624 · NHLBI · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI MA'AYAN, AVI, SCHURER, STEPHAN C · 2014 to 2019
$23.5MDiscovering existing medicines that abrogate cellular responses to SARS CoV-2 infectionU54HL127366 · NHLBI · BROAD INSTITUTE, INC. · PI GOLUB, TODD R. · 2014 to 2020
$14.3MPharmaco Response Signatures and Disease MechanismU54HL127365 · NHLBI · HARVARD MEDICAL SCHOOL · PI SORGER, PETER KARL · 2014 to 2019
$13.1MDrug Combination Signatures for Prediction and Mitigation of ToxicityU54HG008098 · NHGRI · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI BIRTWISTLE, MARC R., BIRTWISTLE, MARC R. · 2014 to 2019
$11.8MNeuron and Glial Cellular Signatures from Normal and Diseased iPS Cells-SupplementU54NS091046 · NINDS · UNIVERSITY OF CALIFORNIA-IRVINE · PI FINKBEINER, STEVEN M, FRAENKEL, ERNEST · 2014 to 2020
$11.7MOutreachU54HG008100 · NHGRI · OREGON HEALTH & SCIENCE UNIVERSITY · PI GRAY, JOE W., HEISER, LAURA MADELINE · 2014 to 2019
$10.5MThere and Back Again: Epigenetic Reinforcement of Cellular Signaling States - OverallU54HG008097 · NHGRI · BROAD INSTITUTE, INC. · PI JAFFE, JACOB DAVID · 2014 to 2019
$9.3MGraduate Training in Computational and Systems BiologyT32GM087237 · NIGMS · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI BURGE, CHRISTOPHER B · 2009 to 2023
$4.6MPredicting the Heterogeneity of Cell-Fate DecisionsR01GM104184 · NIGMS · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI BIRTWISTLE, MARC R. · 2014 to 2018
$1.8MNCI NIH HHS P30 CA016672NCI NIH HHS P30 CA069533NHGRI NIH HHS U54 HG008097NHGRI NIH HHS U54 HG008098NHGRI NIH HHS U54 HG008100NHLBI NIH HHS U54 HL127365NHLBI NIH HHS U54 HL127366NHLBI NIH HHS U54 HL127624NIGMS NIH HHS R01 GM104184NIGMS NIH HHS T32 GM087237NINDS NIH HHS U54 NS091046U.S. Department of Health & Human Services | National Institutes of Health (NIH) U54-HG008097U.S. Department of Health & Human Services | National Institutes of Health (NIH) U54-HG008100U.S. Department of Health & Human Services | National Institutes of Health (NIH) U54HL127366U.S. Department of Health & Human Services | National Institutes of Health (NIH) U54HL127624U.S. Department of Health & Human Services | National Institutes of Health (NIH) U54NS091046
Abstract
The phenotype of a cell and its underlying molecular state is strongly influenced by extracellular signals, including growth factors, hormones, and extracellular matrix proteins. While these signals are normally tightly controlled, their dysregulation leads to phenotypic and molecular states associated with diverse diseases. To develop a detailed understanding of the linkage between molecular and phenotypic changes, we generated a comprehensive dataset that catalogs the transcriptional, proteomic, epigenomic and phenotypic responses of MCF10A mammary epithelial cells after exposure to the ligands EGF, HGF, OSM, IFNG, TGFB and BMP2. Systematic assessment of the molecular and cellular phenotypes induced by these ligands comprise the LINCS Microenvironment (ME) perturbation dataset, which has been curated and made publicly available for community-wide analysis and development of novel computational methods ( synapse.org/LINCS_MCF10A ). In illustrative analyses, we demonstrate how this dataset can be used to discover functionally related molecular features linked to specific cellular phenotypes. Beyond these analyses, this dataset will serve as a resource for the broader scientific community to mine for biological insights, to compare signals carried across distinct molecular modalities, and to develop new computational methods for integrative data analysis.
Indexed as
Epidermal Growth FactorProteomicsExtracellular Matrix ProteinsLigandsPhenotypeEpidermal Growth FactorExtracellular Matrix ProteinsLigands
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