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Manyam, G. C.

Publications and source records attributed to Manyam, G. C..

2 recordsLinked to original sources

Tumor emboli-associated adaptive stress response signatures identify aggressive disease features in inflammatory breast cancer

Inflammatory breast cancer (IBC) is an aggressive breast cancer subtype characterized by tumor emboli, lymphovascular invasion (LVI), and early dissemination. Herein, we establish adaptive stress response (ASR) as a biologic feature linking stress adaptation to tumor emboli survival, lymphatic dissemination, therapeutic response, and disparities. Using a previously defined 226 ASR-related genes, complementary preclinical models of tumor emboli and lymphatic circulating cell clusters, and independent patient cohorts, we identified ASR genes enriched for XIAP-NF{kappa}B, oxidative stress response, inflammatory, and immune pathways. CXCL8 emerged as one of the most highly upregulated transcripts in tumor emboli and was shared across both models; however, CXCL8, IL6, and PTGS2 were downregulated in lymphatic circulating cell clusters and LVI-positive triple-negative IBC patients, suggesting dynamic remodeling of inflammatory signaling during dissemination. CYP4B1 was associated with ER status, LVI, and therapeutic response across multiple cohorts, implicating metabolic stress adaptation in dissemination. IL6 and PTGS2 were elevated in self-reported Black patients with triple-negative IBC compared to White patients. Pharmacologic inhibition of XIAP-NF{kappa}B and oxidative stress pathways suppressed tumor emboli formation. Collectively, these findings identify ASR signaling as a framework linking tumor emboli survival, dissemination, and therapeutic vulnerability in IBC.

cancer biology↗

OmicPioneer-sc: an integrated, interactive visualization environment for single-cell sequencing data

OmicPioneer-sc is an open-source data visualization/analysis package that integrates dimensionality-reduction plots (DRPs) such as t-SNE and UMAP with Next-Generation Clustered Heat Maps (NGCHMs) and Pathway Visualization Modules (PVMs) in a seamless, highly interactive exploratory environment. It includes fluent zooming and navigation, a statistical toolkit, dozens of link-outs to external public bioinformatic resources, high-resolution graphics that meet the requirements of all major journals, and the ability to store all metadata needed to reproduce the visualizations at a later time. A user-friendly, multi-panel graphical interface enables non-informaticians to interact with the system without programming, asking and answering questions that require navigation among the three types of modules or extension from them to the Gene Ontology or information on therapies. The visual integration can be useful for detective work to identify and annotate cell-types for color-coding of the DRPs, and multiple NGCHMs can be layered on top of each other (with toggling among them) as an aid to multi-omic analysis. The tools are available in containerized form with APIs to facilitate incorporation as a plug-in to other bioinformatic environments. The capabilities of OmicPioneer-sc are illustrated here through application to a single-cell RNA-seq airway dataset pertinent to the biology of both cancer and COVID-19. [Supplemental material is available for this article.]

bioinformatics↗