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Article
Open AccessMYC Deregulation and PTEN Loss Model Tumor and Stromal Heterogeneity of Aggressive Triple-Negative Breast Cancer
Triple-negative breast cancer (TNBC) patients have a poor prognosis and few treatment options. Mouse models of TNBC are important for development of new therapies, however, few mouse models represent the compl...
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Article
Open AccessA multiplex implantable microdevice assay identifies synergistic combinations of cancer immunotherapies and conventional drugs
Systematically identifying synergistic combinations of targeted agents and immunotherapies for cancer treatments remains difficult. In this study, we integrated high-throughput and high-content techniques—an i...
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Article
Open AccessA multi-omic analysis of MCF10A cells provides a resource for integrative assessment of ligand-mediated molecular and phenotypic responses
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 normal...
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Article
Open AccessDevelopment of a nanoparticle-based immunotherapy targeting PD-L1 and PLK1 for lung cancer treatment
Immune checkpoint inhibitors (ICIs) targeting PD-L1 and PD-1 have improved survival in a subset of patients with advanced non-small cell lung cancer (NSCLC). However, only a minority of NSCLC patients respond ...
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Article
Open AccessA framework for multiplex imaging optimization and reproducible analysis
Multiplex imaging technologies are increasingly used for single-cell phenoty** and spatial characterization of tissues; however, transparent methods are needed for comparing the performance of platforms, pro...
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Article
Open AccessOligonucleotide conjugated antibody strategies for cyclic immunostaining
A number of highly multiplexed immunostaining and imaging methods have advanced spatial proteomics of cancer for improved treatment strategies. While a variety of methods have been developed, the most widely u...
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Article
Open AccessMultiomics analysis of serial PARP inhibitor treated metastatic TNBC inform on rational combination therapies
In a pilot study, we evaluated the feasibility of real-time deep analysis of serial tumor samples from triple negative breast cancer patients to identify mechanisms of resistance and treatment opportunities as...
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Article
Chemokine signaling in cancer-stroma communications
Cancer is a multi-faceted disease in which spontaneous mutation(s) in a cell leads to the growth and development of a malignant new organ that if left undisturbed will grow in size and lead to eventual death o...
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Article
Open AccessSensitivity to targeted therapy differs between HER2-amplified breast cancer cells harboring kinase and helical domain mutations in PIK3CA
HER2-amplified breast cancer is a clinically defined subtype of breast cancer for which there are multiple viable targeted therapies. Resistance to these targeted therapies is a common problem, but the mechanisms...
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Article
Open AccessRelevance of circulating hybrid cells as a non-invasive biomarker for myriad solid tumors
Metastatic progression defines the final stages of tumor evolution and underlies the majority of cancer-related deaths. The heterogeneity in disseminated tumor cell populations capable of seeding and growing i...
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Article
Open AccessCharacterizing advanced breast cancer heterogeneity and treatment resistance through serial biopsies and comprehensive analytics
Molecular heterogeneity in metastatic breast cancer presents multiple clinical challenges in accurately characterizing and treating the disease. Current diagnostic approaches offer limited ability to assess he...
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Article
Open AccessVISTA: VIsual Semantic Tissue Analysis for pancreatic disease quantification in murine cohorts
Mechanistic disease progression studies using animal models require objective and quantifiable assessment of tissue pathology. Currently quantification relies heavily on staining methods which can be expensive...
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Article
Open AccessSHIFT: speedy histological-to-immunofluorescent translation of a tumor signature enabled by deep learning
Spatially-resolved molecular profiling by immunostaining tissue sections is a key feature in cancer diagnosis, subty**, and treatment, where it complements routine histopathological evaluation by clarifying ...
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Article
Open AccessDevelopment and implementation of the SUM breast cancer cell line functional genomics knowledge base
Several years ago, the SUM panel of human breast cancer cell lines was developed, and these cell lines have been distributed to hundreds of labs worldwide. Our lab and others have developed extensive omics dat...
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Article
Open AccessRESTORE: Robust intEnSiTy nORmalization mEthod for multiplexed imaging
Recent advances in multiplexed imaging technologies promise to improve the understanding of the functional states of individual cells and the interactions between the cells in tissues. This often requires comp...
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Chapter and Conference Paper
Activation vs. Organization: Prognostic Implications of T and B Cell Features of the PDAC Microenvironment
Pancreatic ductal adenocarcinoma (PDAC) patients, who often present with stage III or IV disease, face a dismal prognosis as the 5-year survival rate remains below 10%. Recent studies have revealed that CD4 ...
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Protocol
Cyclic Multiplexed-Immunofluorescence (cmIF), a Highly Multiplexed Method for Single-Cell Analysis
Immunotherapy harnesses the power of the adaptive immune system and has revolutionized the field of oncotherapy, as novel therapeutic strategies have been introduced into clinical use. The development of immun...
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Chapter and Conference Paper
cmIF: A Python Library for Scalable Multiplex Imaging Pipelines
Histological staining and analysis of tissue sections is integral to diagnosis and treatment of many diseases, including cancer. Multiplex imaging technologies (e.g., cyclic immunostaining) have dramatically ...
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Article
Open AccessImplementing a comprehensive translational oncology platform: from molecular testing to actionability
In order to establish the workflows required to implement a real-time process involving multi-omic analysis of patient samples to support precision-guided therapeutic intervention, a tissue acquisition and ana...
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Article
Open AccessDifferentiation-state plasticity is a targetable resistance mechanism in basal-like breast cancer
Intratumoral heterogeneity in cancers arises from genomic instability and epigenomic plasticity and is associated with resistance to cytotoxic and targeted therapies. We show here that cell-state heterogeneity...
