Biology subjects

Shen, M. M.

Publications and source records attributed to Shen, M. M..

4 recordsLinked to original sources

bioRxiv2022

The OncoLoop network-based precision oncology framework

At present, prioritizing cancer treatments at the individual patient level remains challenging, and performing co-clinical studies using patient-derived models in real-time is often not feasible. To circumvent these challenges, we introduce OncoLoop, a precision medicine framework to predict and validate drug sensitivity in human tumors and their pre-existing high-fidelity (cognate) model(s) by leveraging perturbational profiles of clinically-relevant oncology drugs. As proof-of-concept, we applied OncoLoop to prostate cancer (PCa) using a series of genetically-engineered mouse models (GEMMs) that recapitulate a broad spectrum of disease states, including castration-resistant, metastatic, and neuroendocrine prostate cancer. Interrogation of published cohorts using Master Regulator (MR) conservation analysis revealed that most patients were represented by at least one cognate GEMM-derived tumor (GEMM-DT). Drugs predicted to invert MR activity in patients and their cognate GEMM-DTs were successfully validated, including in two cognate allografts and one cognate patient-derived xenograft (PDX). OncoLoop is a highly generalizable framework that can be extended to other cancers and potentially other diseases. Significance StatementOncoLoop is a transcriptomic-based experimental and computational framework that can support rapid-turnaround co-clinical studies to identify and validate drugs for individual patients, which can then be readily adapted to clinical practice. This framework should be applicable in many cancer contexts for which appropriate models and drug perturbation data are available.

cancer biology↗

bioRxiv2021

Platr4 is an ESC-specific lncRNA that exhibits its function downstream on meso/endoderm lineage commitment

The mammalian genome encodes thousands of long non-coding RNAs (lncRNAs) that are developmentally regulated and differentially expressed across tissues, suggesting possible roles in cellular differentiation. Despite this expression pattern, little is known about how lncRNAs influence lineage commitment at the molecular level. Here, we reveal that perturbation of an embryonic stem cell (ESC)-specific lncRNA, Pluripotency associated transcript 4 (Platr4), in ESCs directly influences the downstream meso/endoderm differentiation program without affecting pluripotency. We further show that Platr4 interacts with the TEA domain transcription factor 4 (Tead4) to regulate the expression of a downstream target gene crucial in the cardiac lineage program known as connective tissue growth factor (Ctgf). Importantly, Platr4 knockout mice exhibit myocardial atrophy, valve mucinous degenration associated with reduced cardiac output and sudden heart failure. Together, our findings provide evidence that Platr4 expression in undifferentiated ESCs is critical for downstream lineage differentiation, highlighting its importance in disease modeling and regenerative medicine.

developmental biology↗

bioRxiv2021

Intra-epithelial non-canonical Activin A signalling safeguards prostate progenitor quiescence

The healthy prostate is a relatively quiescent tissue. Yet, prostate epithelium overgrowth is a common condition during ageing, associated with urinary dysfunction and tumorigenesis. For over thirty years, TGF-{beta} ligands have been known to induce cytostasis in a large variety of epithelia, but the intracellular pathway mediating this signal in the prostate, as well as its relevance for quiescence, have remained elusive. Here, using mouse prostate organoids to model epithelial progenitors, we found that intra-epithelial non-canonical Activin A signalling inhibited cell proliferation in a Smad-independent manner. Mechanistically, Activin A triggered Tak1 and p38 MAPK activity, leading to p16 and p21 nuclear import. Spontaneous evasion from this quiescent state occurred upon prolonged culture, due to reduced Activin A secretion, a condition associated with DNA replication stress and aneuploidy. Organoids capable to escape quiescence in vitro were also able to implant with increased frequency into immunocompetent mice. Our study demonstrates that non-canonical Activin A signalling safeguards epithelial quiescence in the healthy prostate, with potential implications for the understanding of cancer initiation, and the development of therapies targeting quiescent tumour progenitors.

cancer biology↗

bioRxiv2020

A single-cell atlas of the mouse and human prostate reveals heterogeneity and conservation of epithelial progenitors

Understanding the cellular constituents of the prostate is essential for identifying the cell of origin for benign prostatic hyperplasia and prostate adenocarcinoma. Here we describe a comprehensive single-cell atlas of the adult mouse prostate epithelium, which demonstrates extensive heterogeneity. We observe distinct lobe-specific luminal epithelial populations (LumA, LumD, LumL, and LumV) in the distal region of the four prostate lobes, a proximally-enriched luminal population (LumP) that is not lobe-specific, as well as a periurethral population (PrU) that shares both basal and luminal features. Functional analyses suggest that LumP and PrU cells have multipotent progenitor activity in organoid formation and tissue reconstitution assays. Furthermore, we show that mouse distal and proximal luminal cells are most similar to human acinar and ductal populations, that a PrU-like population is conserved between species, and that the mouse lateral prostate is most similar to the human peripheral zone. Our findings elucidate new prostate epithelial progenitors, and help resolve long-standing questions about the anatomical relationships between the mouse and human prostate.

developmental biology↗