Matthew J. Berberich

Corrigendum to “Comprehensive Proteomics Metadata and Integrative Web Portals Facilitate Sharing and Integration of LINCS Multiomics Data”

D. Vidović, Behrouz Shamsaei, Stephan C. Schürer, Phillip Kogan et autres

Comprehensive Proteomics Metadata and Integrative Web Portals Facilitate Sharing and Integration of LINCS Multiomics Data

D. Vidović, Behrouz Shamsaei, Stephan C. Schürer, Phillip Kogan et autres

The Library of Integrated Network-based Cellular Signatures (LINCS), an NIH Common Fund program, has cataloged and analyzed cellular function and molecular activity profiles in response to >80,000 perturbing agents that are potentially disruptive to cells. Because of the importance of proteins and …

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Proteomic profiling across breast cancer cell lines and models

Marian Kalocsay, Matthew J. Berberich, Robert A. Everley, Maulik K. Nariya et autres

We performed quantitative proteomics on 60 human-derived breast cancer cell line models to a depth of ~13,000 proteins. The resulting high-throughput datasets were assessed for quality and reproducibility. We used the datasets to identify and characterize the subtypes of breast cancer and …

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Catalytic Degraders Effectively Address Kinase Site Mutations in EML4-ALK Oncogenic Fusions

Yang Gao, Baishan Jiang, Hellen Kim, Matthew J. Berberich et autres

Heterobifunctional degraders, known as proteolysis targeting chimeras (PROTACs), theoretically possess a catalytic mode-of-action, yet few studies have either confirmed or exploited this potential advantage of event-driven pharmacology. Degraders of oncogenic EML4-ALK fusions were developed by conjugating ALK inhibitors to cereblon ligands. Simultaneous …

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Abstract 5333: Combining chemoproteomics with machine learning identifies functionally active covalent fragments for hard-to-drug cancer drivers

Johannes C. Hermann, Robert A. Everley, Laura J. Marholz, Matthew J. Berberich et autres

Abstract a) Many cancer drivers are considered “undruggable” and without targeted treatments because they lack binding sites for conventional small molecules. Here, we introduce The FRONTIER™ Platform applying machine learning (ML), chemoproteomics and covalent chemistry to identify binding sites and cell-active covalent …

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Time‐series transcriptomics and proteomics reveal alternative modes to decode p53 oscillations

Alba Jiménez, Dan Lü, Marian Kalocsay, Matthew J. Berberich et autres

The cell stress-responsive transcription factor p53 influences the expression of its target genes and subsequent cellular responses based in part on its dynamics (changes in level over time). The mechanisms decoding p53 dynamics into subsequent target mRNA and protein dynamics remain unclear. …

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Discovery and resistance mechanism of a selective CDK12 degrader

Baishan Jiang, Yang Gao, Jianwei Che, Wenchao Lu et autres

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Data Descriptor: Proteomic profiling across breast cancer cell lines and models

Marian Kalocsay, Matthew J. Berberich, Robert A. Everley, Maulik K. Nariya et autres

Abstract We performed quantitative proteomics on 61 human-derived breast cancer cell lines to a depth of ~13,000 proteins. The resulting high-throughput datasets were assessed for quality and reproducibility. We used the datasets to identify and characterize the subtypes of breast cancer and …

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Targeting immunosuppressive macrophages overcomes PARP inhibitor resistance in BRCA1-associated triple-negative breast cancer

Anita Kuldeep Mehta, Emily M. Cheney, Christina Hartl, Constantia Pantelidou et autres

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860 Targeting immunosuppressive macrophages overcomes PARP-inhibitor resistance in BRCA1-associated triple-negative breast cancer

Anita Kuldeep Mehta, Emily M. Cheney, Christina Hartl, Constantia Pantelidou et autres

Background Despite objective responses to PARP inhibition and improvements in progression-free survival compared to standard chemotherapy in patients with BRCA-associated triple-negative breast cancer (TNBC), benefits are transitory. Methods Using high dimensional single-cell profiling of human TNBC, here we demonstrate that macrophages are …

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Impact of Zika virus on the human type I interferon osteoimmune response

Arnaud C. Drouin, Nicholas J. Wallbillich, Marc Theberge, Sharon Liu et autres

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Abstract P5-04-01: PARP inhibition modulates the infiltration, phenotype and function of tumor-associated macrophages (TAMs) in BRCA-associated breast cancer and can be augmented by harnessing the anti-tumor potential of TAMs

Jennifer L. Guerriero, Anita Kuldeep Mehta, Emily M. Cheney, Jessica A. Castrillon et autres

Abstract Patients with BRCA-associated triple negative breast cancer (TNBC) have few effective treatment options. PARP inhibitors are promising, and we recently showed they induce an influx of white blood cells, including CD8+ T-cells and macrophages into the tumor. The influx of CD8+ …

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