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Reva, B.

Publications and source records attributed to Reva, B..

6 recordsLinked to original sources

Pancreatic cancer fibrosis activates protumorigenic Schwann cells through a nuclear mechanosensing mechanism.

BackgroundFibrosis and tumor innervation are two features of the tumor microenvironment (TME) that contribute directly to the lethality of pancreatic ductal adenocarcinoma (PDAC), but their potential interactions have not been explored. Moreover, although it is known that activated Schwann cells (SCs) stimulate cancer cell invasion, it remains unclear how SCs are activated. ObjectiveWe determined how SCs are activated in the pancreatic fibrotic microenvironment. DesignThe correlation between physical features of the microenvironment and SC activation was assessed in human patient samples and in mice by SC c-Jun phosphorylation monitoring, atomic force microscopy and multiphoton live imaging. Several in vitro models in which forces were applied to SCs expressing a reporter for c-Jun phosphorylation and RNA-Seq analysis were used to decipher the cellular and molecular mechanisms of SC activation. ResultsNerves surrounded by stiff stroma present higher SC activation. Intravital imaging shows a matrix dependent SC activation. Mechanical forces on SCs induce c-Jun phosphorylation in SCs in a non-canonical manner that involves a nuclear sensing machinery with the proinflammatory enzyme Phospholipase A2. ConclusionFibrosis enhances the protumorigenic impact of innervation by activating SCs via a mechanism in which nuclear compression triggers non-canonical activation of the AP-1 transcription factor complex. Pancreatic fibrosis alone, without cancer cells, is sufficient to activate SCs, suggesting this mechanism may be common across non-malignant pancreatic diseases. Notably, SCs are more sensitive to mechanical activation than PDAC cells. These findings reveal TME interactions that may guide future microenvironment-targeted PDAC therapies. What is already known on this topicThe pancreatic cancer tumor microenvironment is highly innervated and fibrotic, two components of the tumor microenvironment that regulate tumorigenesis. How they impact each other is unknown. Schwann cells have emerged as a significant protumorigenic player, but the triggers of Schwann cell activation remain undefined. What this study addsWe establish that fibrosis induces Schwann cell activation and characterize the mechanism by which it occurs. We uncovered a mechanical mode of action that deforms nuclear membrane and activates c-Jun in Schwann cells, which contradicts the traditional view of c-Jun activation through a stimulus detected at the plasma membrane. How this study might affect research, practice or policyThis study provides a better understanding of the biology of pancreatic ductal adenocarcinoma and supports the development of novel precision therapies that target the fibrotic microenvironment to impact the protumorigenic effect of tumor innervation.

cancer biology↗

MutationAssessor in cBioPortal

MutationAssessor (MA) helps researchers evaluate the likely functional impact of somatic and germline mutations in cancer. It provides an evolution-based functional impact score (FIS) to classify mutations based on their likely effect on protein function. FIS scores are based on analysis of patterns of conservation in protein families (conserved residues) and subfamilies (specificity residues). In this new version (r4) we have (1) refined the combinatorial entropy analysis of conservation patterns, (2) recalculated full-length protein multiple sequence alignments covering a larger fraction of human proteins and making use of the explosive growth of protein sequence data, (3) compared predicted functional impact with the pathogenic-benign classification of sequence variants in curated knowledge bases, such as ClinVar, (4) observed the inverse relationship between predicted high functional impact and variant frequency in germline genome sequences and (5) explore the evaluation of switch-of-function mutational effects. Functional impact of [~]4 million somatic amino-acid changing mutations across more than 320K human tumor samples are now available in the widely used cBioPortal for Cancer Genomics.

cancer biology↗

Reprogrammed Schwann cells organize into dynamic tracks that promote pancreatic cancer invasion

Nerves are a component of the tumor microenvironment contributing to cancer progression, but the role of cells from nerves in facilitating cancer invasion remains poorly understood. Here we show that Schwann cells (SCs) activated by cancer cells collectively function as Tumor Activated Schwann cell Tracks (TASTs) that promote cancer cell migration and invasion. Non-myelinating SCs form TASTs and have cell gene expression signatures that correlate with diminished survival in patients with pancreatic ductal adenocarcinoma. In TASTs, dynamic SCs form tracks that serve as cancer pathways and apply forces on cancer cells to enhance cancer motility. These SCs are activated by c-Jun, analogous to their reprogramming during nerve repair. This study reveals a mechanism of cancer cell invasion that co-opts a wound repair process and exploits the ability of SCs to collectively organize into tracks. These findings establish a novel paradigm of how cancer cells spread and reveal therapeutic opportunities. SIGNIFICANCEHow the tumor microenvironment participates in pancreatic cancer progression is not fully understood. Here, we show that Schwann cells are activated by cancer cells and collectively organize into tracks that dynamically enable cancer invasion in a c-Jun dependent manner.

cancer biology↗

CPTAC Pancancer Phosphoproteomics Kinase Enrichment Analysis with ProKAP Provides Insights into Immunogenic Signaling Pathways

The National Cancer Institute (NCI) Clinical Proteomic Tumor Analysis Consortium (CPTAC) initiative has generated extensive phosphoproteomics and proteomics data for tumor and tumor-adjacent normal tissue across multiple cancer types. This dataset provides an unprecedented opportunity to systematically characterize pan-cancer kinase activities, which is essential for coupling tumor subtypes with kinase inhibitors as potential treatment. In this work, we performed Kinase Enrichment Analysis (KEA) using a CPTAC phosphoproteomics dataset to identify putative differences in kinase state between tumor and normal tissues within and across five types of cancer. We then implemented an interactive web-portal, the ProTrack Kinase Activity Portal (ProKAP), for querying, visualizing, and downloading the derived pan-cancer kinase activity scores together with the corresponding sample metadata, and protein and phosphoprotein expression profiles. To illustrate the usage of this digital resource, we analyzed the association between kinase activity scores and immune subtypes of clear cell renal cell carcinoma (ccRCC) derived from the CPTAC ccRCC study. We found multiple kinases, whose inhibition has been suggested to have therapeutic effect in other tumor types, are highly active in CD8+-enriched ccRCC tumors. The ProTrack Kinase Activity Portal (ProKAP) is available at: https://pancan-kea3.cptac-data-view.org.

bioinformatics↗

Prioritization prostate cancer to immune checkpoint therapy by ranking tumors along IFN-γ axis and identification of immune resistance mechanisms

We propose priotirization of prostate cancer patients to PD-L1 checkpoint therapy by assessing activity of IFN-{gamma}/PD-L1 signaling in tumor from transcriptional profile. To this end, we introduced a new approach for inferring pathway activity and suppression (IPAS) by assessing significance of positioning pathways genes expression levels at top (activation) or bottom (suppression) in gene expression profile of a given tumor. By ordering tumors along IFN-{gamma}/PD-L1 axis, we determined distinct "IFN-{gamma}-depleted" and "IFN-{gamma}-enriched" immune subtypes, genes involved in immune evasion and potential targets for combination therapy. Using IPAS scoring method, we proposed biomarker panels for accurate ranking tumors along IFN-{gamma}/PD-L1 axis.

bioinformatics↗

ProTrack: An Interactive Multi-Omics Data Browser for Proteogenomic Studies

The Clinical Proteomic Tumor Analysis Consortium (CPTAC) initiative has generated extensive multi-omics data resources of deep proteogenomic profiles for multiple cancer types. To enable the broader community of biological and medical researchers to intuitively query, explore, and download data and analysis results from various CPTAC projects, we built a prototype user-friendly web application called "ProTrack" with the CPTAC clear cell renal cell carcinoma (ccRCC) data set (http://ccrcc.cptac-data-view.org). Here we describe the salient features of this application which provides a dynamic, comprehensive, and granular visualization of the rich proteogenomic data. Statement of SignificanceThe CPTAC initiative (https://proteomics.cancer.gov/) has generated multi-omics data for multiple cancer types to understand the proteogenomic aberrations of these malignancies. Collectively this effort has so far produced a large data resource for the research community, including high-throughput profiles for proteome, phosphoproteome, whole exome, whole genome, transcriptome, and DNA methylome. To make this valuable data-resource useful to the larger research community, there is a pressing need for development of user-friendly, readily accessible, and easily shared analytic and visualization tools for aligning multi-omics data and exploring alterations in key cancer genes, to drive and support new biological hypotheses. To bridge this gap, we have developed CPTAC ProTrack, an interactive web application which uses a multilayered, client-server architecture in order to deliver an interactive web experience to any user of a modern web-browser. This tool is intentionally designed accessible for researchers, biologists, and clinicians who are interested in multi-omic data without any need to code.

bioinformatics↗