Biology subjects

Shen, M. M.

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

13 recordsLinked to original sources

bioRxiv2025

Dual pathway regulation of castration response and ferroptosis in the prostate epithelium

Understanding how sex hormones maintain tissue integrity--and how their disruption can promote cancer--is a central question in biology. In the prostate, androgen signaling is crucial for development, homeostasis, and cancer, yet the molecular mechanisms underlying tissue regression after androgen-deprivation have remained unknown. Here we show that castration induces epithelial regression via ferroptosis in the normal mouse and human prostate, as well as in prostate tumors. Using in vivo analyses in genetically-engineered mice, supported by validation in human organotypic cultures, we demonstrate that androgen receptor (AR) signaling controls castration response through two distinct pathways: an intrinsic luminal epithelial pathway regulated by the prostate-specific transcription factor NKX3.1, and an extrinsic stromal signal mediated by the secreted factor pleiotrophin (PTN). Together, these AR signaling pathways coordinately regulate biosynthesis of monounsaturated fatty acid (MUFA) phospholipids and GPX4 expression to suppress prostate epithelial ferroptosis. Our findings reveal a sex hormone-regulated ferroptotic program that governs tissue homeostasis and suggest that ferroptosis induction could represent a new therapeutic strategy for prostate cancer.

developmental biology↗

bioRxiv2024

Identification of Myeloid Protein Kinase C - Epsilon as a Novel Atheroprotective Gene

BACKGROUNDAtherosclerosis is a chronic inflammatory disease driven by macrophages (MO). Protein Kinase C - epsilon (PKC{varepsilon}) is a serine/threonine kinase involved in diverse cellular processes including migration, growth, differentiation, and survival. PKC{varepsilon} acts in a context dependent manner within the heart, however, its role in atherosclerosis is unknown. METHODSBone marrow derived MO from global PKC{varepsilon} knockout mice were tested for lipid retention and cytokine secretion. Public geneset analysis assessed raw counts of PRKCE in human atheromas to determine translational relevance. A LysM Cre PKC{varepsilon}fl/fl (m{varepsilon}KO) mouse was developed to study the impact of myeloid PKC{varepsilon} on atherosclerosis. After confirming myeloid selective PKC{varepsilon} deletion, human-like hypercholesterolemia was induced and multiple metrics of atherosclerosis were compared in WT and m{varepsilon}KO plaques. RNA sequencing was used to provide unbiased insight into possible mechanisms by which PKC{varepsilon} regulates atherosclerosis. RESULTSPublic geneset analysis of human atherosclerotic plaque tissue revealed that PKC{varepsilon} expression is inversely correlated with plaque vulnerability. Similarly, peritoneal MO from WT hypercholesterolemic mice have significantly lower PKC{varepsilon} expression, providing a translational rational for generation of the m{varepsilon}KO mouse. qPCR revealed no differences between genotypes in the expression of genes related to atherosclerosis, at either steady state or upon lipid loading, suggesting that loss of PKC{varepsilon} does not fundamentally change the basal state and that differences seen are a result of a more complex pathway. Comparing descending aorta and aortic root plaques from WT and m{varepsilon}KO hypercholesterolemic mice revealed that m{varepsilon}KO plaques are larger, have larger foam cells and regions of necrosis, and thinner collagen caps. Upon lipid loading in vitro and in vivo, m{varepsilon}KO MO retained significantly more cholesterol and lipid droplets than WT; Gene Ontology suggests higher expression of genes related to endocytosis in m{varepsilon}KO MO compared to WT. CONCLUSIONSPKC{varepsilon} expression is decreased in vulnerable human plaques and decreases in mouse MO upon lipid loading. m{varepsilon}KO plaques are larger and exhibit markers of vulnerability. With no differences in scavenger receptor (SR) expression, the impact of PKC{varepsilon} deletion is more subtle than simple SR dysregulation. RNA sequencing implicates higher expression of genes involved in endocytosis and m{varepsilon}KO MO have significantly more lipid-containing endosomes. The data define the atherophenotype of m{varepsilon}KO mice and demonstrate that PKC{varepsilon} restricts lipid uptake into MO by a mechanism independent of SR expression. Taken together, these studies identify PKC{varepsilon} as a novel atheroprotective gene, laying the foundation for mechanistic studies on the endocytic signaling networks responsible for the phenotype. GRAPHIC ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=170 HEIGHT=200 SRC="FIGDIR/small/627650v5_ufig1.gif" ALT="Figure 1"> View larger version (65K): org.highwire.dtl.DTLVardef@1873e8org.highwire.dtl.DTLVardef@161a63eorg.highwire.dtl.DTLVardef@1e95b36org.highwire.dtl.DTLVardef@1634ecd_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIA novel murine model in which PKC{varepsilon} is floxed (PKC{varepsilon}fl/fl) on both alleles haas been generated, backcrossed, and deposited into Jackson Laboratories (B6(Cg)-Prkcetm1.1Akv/LennMmjax). Then, PKC{varepsilon}fl/fl LysM Cre (m{varepsilon}KO) mice have been generated. C_LIO_LIDeletion of PKC{varepsilon} has no basal affects on other PKC isoforms, lipid handling markers, or inflammatory markers. C_LIO_LIUpon (in vitro) lipid loading of BMDM or isolating lipid loaded pMACs from hypercholesterolemic mice (in vivo), m{varepsilon}KO BMDMs retain more cholesterol. C_LIO_LILong term (16 wk) hypercholesterolemis generates larger lesions, more necrosis, and thinner plaque caps (i.e., a more vulnerable plaque phenotype) in m{varepsilon}KO mice. C_LIO_LIRNA sequencing suggests PKC{varepsilon} regulates endocytosis mechanisms post initial uptake of LDL and has been confirmed in a model of synchronized endocytosis. C_LIO_LIThese findings identify myeloid PKC{varepsilon} as a novel atheroprotective molecule whose expression impacts multiple metrics of atherosclerosis. This opens new avenues of investigation to uncover the PKC{varepsilon} signaling network responsible for the phenotype. Understanding how myeloid PKC{varepsilon} slows atherosclerosis development will aid in the development of novel preventative and therapeutic treatments. C_LI

immunology↗

bioRxiv2024

A forward genetic screen identifies Sirtuin1 as a driver of neuroendocrine prostate cancer

Although localized prostate cancer is relatively indolent, advanced prostate cancer manifests with aggressive and often lethal variants, including neuroendocrine prostate cancer (NEPC). To identify drivers of aggressive prostate cancer, we leveraged Sleeping Beauty (SB) transposon mutagenesis in a mouse model based on prostate-specific loss-of-function of Pten and Tp53. Compared with control mice, SB mice developed more aggressive prostate tumors, with increased incidence of metastasis. Notably, a significant percentage of the SB prostate tumors display NEPC phenotypes, and the transcriptomic features of these SB mouse tumors recapitulated those of human NEPC. We identified common SB transposon insertion sites (CIS) and prioritized associated CIS-genes differentially expressed in NEPC versus non-NEPC SB tumors. Integrated analysis of CIS-genes encoding for proteins representing upstream, post-translational modulators of master regulators controlling the transcriptional state of SB-mouse and human NEPC tumors identified sirtuin 1 (Sirt1) as a candidate mechanistic determinant of NEPC. Gain-of-function studies in human prostate cancer cell lines confirmed that SIRT1 promotes NEPC, while its loss-of-function or pharmacological inhibition abrogates NEPC. This integrative analysis is generalizable and can be used to identify novel cancer drivers for other malignancies. SummaryUsing an unbiased forward mutagenesis screen in an autochthonous mouse model, we have investigated mechanistic determinants of aggressive prostate cancer. SIRT1 emerged as a key regulator of neuroendocrine prostate cancer differentiation and a potential target for therapeutic intervention.

cancer biology↗

bioRxiv2024

The regulatory architecture of the primed pluripotent cell state

Although numerous studies have focused on defining transcriptional cell states in normal and disease contexts, the gene regulatory architecture that governs and defines specific mammalian cell states remains poorly understood. Here we present an integrative computational and experimental systems biology approach to elucidate the regulatory architecture of a conserved cell state of critical importance in development and stem cell biology, namely primed state pluripotency. We have used an unbiased approach to analyze protein activity profiles from mouse epiblast stem cells (EpiSCs), leading to identification and experimental confirmation of 132 transcription factors that are master regulators (MRs) of primed state pluripotency. These MRs include known as well as novel factors, many of which were further validated for their role in lineage-specific differentiation using CRISPR-mediated functional assays. To assemble a comprehensive regulatory network, we silenced each of the 132 MRs to assess their effects on the other MRs and their transcriptional targets, yielding a network of 1,273 MR[->]MR interactions. Network architecture analyses revealed four functionally distinct MR modules (communities), largely independent of lineage-specific differentiation, and identified key Speaker and Mediator MRs based on their hierarchical rank and centrality in mediating information flow in the pluripotent cell. Taken together, our findings elucidate the de-centralized logic of a "communal interaction" model in which the balanced activities of four MR communities maintain pluripotency, and define the primed pluripotent cell state in terms of its transcriptional regulatory network.

systems biology↗

bioRxiv2024

Rarγ-Foxa1 signaling promotes luminal identity in prostate progenitors and is disrupted in prostate cancer

Retinoic acid (RA) signaling is a master regulator of vertebrate development with crucial roles in directing body axis orientation and tissue differentiation, including in the reproductive system. However, a mechanistic understanding of how RA signaling promotes cell lineage identity in different tissues is often missing. Here, leveraging prostate organoid technology, we demonstrated that RA signaling orchestrates the commitment of adult mouse prostate progenitors to glandular identity, epithelial barrier integrity, and ultimately, proper specification of the prostatic lumen. Mechanistically, RA-dependent RAR{gamma} activation promotes the expression of the pioneer factor Foxa1, which synergizes with the androgen pathway for proper luminal expansion, cytoarchitecture and function. FOXA1 nucleotide variants are common in human prostate and breast cancers and considered driver mutations, though their pathogenic mechanism is incompletely understood. Combining functional genetics experiments with structural modeling of FOXA1 folding and chromatin binding analyses, we discovered that FOXA1F254E255 is a loss-of-function mutation leading to compromised transcriptional function and lack of luminal fate commitment of prostate progenitors. Overall, we define RA as a crucial instructive signal for glandular identity in adult prostate progenitors. We propose deregulation of vitamin A metabolism as a risk factor for benign and malignant prostate disease, and identified cancer associated FOXA1 indels affecting residue F254 as loss-of-function mutations promoting dedifferentiation of adult prostate progenitors. Summary: Retinoic acid signaling orchestrates luminal differentiation of adult prostate progenitors

cancer biology↗

bioRxiv2024

Meta-analyses of mouse and human prostate single-cell transcriptomes reveal widespread epithelial plasticity in tissue regression, regeneration, and cancer

Recent advances in single-cell RNA-sequencing (scRNA-seq) technology have facilitated studies of cell states and plasticity in tissue maintenance and cancer, including in the prostate. Here we present meta-analyses of multiple new and published scRNA-seq datasets to establish reference cell type classifications for the normal mouse and human prostate. Our analyses demonstrate transcriptomic similarities between epithelial cell states in the normal prostate, in the regressed prostate after androgen-deprivation, and in primary prostate tumors. During regression in the mouse prostate, all epithelial cells shift their expression profiles towards a proximal periurethral (PrU) state, demonstrating an androgen-dependent plasticity that is restored to normal during androgen restoration and regeneration. In the human prostate, we find progressive rewiring of transcriptional programs across epithelial cell types in benign prostate hyperplasia and treatment-naive prostate cancer. Notably, we detect copy number variants predominantly within Luminal Acinar cells in prostate tumors, suggesting a bias in their cell type of origin, as well as a larger field of transcriptomic alterations in non-tumor cells. Finally, we observe that Luminal Acinar tumor cells in treatment-naive prostate cancer display heterogeneous androgen receptor (AR) signaling activity, including a split between high-AR and low-AR profiles with similarity to PrU-like states. Taken together, our analyses of cellular heterogeneity and plasticity provide important translational insights into the origin and treatment response of prostate cancer.

cancer biology↗

bioRxiv2023

NSD2 maintains lineage plasticity and castration-resistance in neuroendocrine prostate cancer

The clinical use of potent androgen receptor (AR) inhibitors has promoted the emergence of novel subtypes of metastatic castration-resistant prostate cancer (mCRPC), including neuroendocrine prostate cancer (CRPC-NE), which is highly aggressive and lethal1. These mCRPC subtypes display increased lineage plasticity and often lack AR expression2-5. Here we show that neuroendocrine differentiation and castration-resistance in CRPC-NE are maintained by the activity of Nuclear Receptor Binding SET Domain Protein 2 (NSD2)6, which catalyzes histone H3 lysine 36 dimethylation (H3K36me2). We find that organoid lines established from genetically-engineered mice7 recapitulate key features of human CRPC-NE, and can display transdifferentiation to neuroendocrine states in culture. CRPC-NE organoids express elevated levels of NSD2 and H3K36me2 marks, but relatively low levels of H3K27me3, consistent with antagonism of EZH2 activity by H3K36me2. Human CRPC-NE but not primary NEPC tumors expresses high levels of NSD2, consistent with a key role for NSD2 in lineage plasticity, and high NSD2 expression in mCRPC correlates with poor survival outcomes. Notably, CRISPR/Cas9 targeting of NSD2 or expression of a dominant-negative oncohistone H3.3K36M mutant results in loss of neuroendocrine phenotypes and restores responsiveness to the AR inhibitor enzalutamide in mouse and human CRPC-NE organoids and grafts. Our findings indicate that NSD2 inhibition can reverse lineage plasticity and castration-resistance, and provide a potential new therapeutic target for CRPC-NE.

cancer biology↗

bioRxiv2023

Inactive PARP1 causes embryonic lethality and genome instability in a dominant-negative manner.

PARP1 is recruited and activated by DNA strand breaks, catalyzing the generation of poly-ADP-ribose (PAR) chains from NAD+. PAR relaxes chromatin and recruits other DNA repair factors, including XRCC1 and DNA Ligase 3, to maintain genomic stability. Here we show that, in contrast to the normal development of Parp1-null mice, heterozygous expression of catalytically inactive Parp1 (E988A, Parp1+/A) acts in a dominant-negative manner to disrupt murine embryogenesis. As such, all the surviving F1 Parp1+/A mice are chimeras with mixed Parp1+/AN (neoR retention) cells that act similarly to Parp1+/-. Pure F2 Parp1+/A embryos were found at Mendelian ratios at the E3.5 blastocyst stage but died before E9.5. Compared to Parp1-/- cells, genotype and expression-validated pure Parp1+/A cells retain significant ADP-ribosylation and PARylation activities but accumulate markedly higher levels of sister chromatin exchange and mitotic bridges. Despite proficiency for homologous recombination and non-homologous end-joining measured by reporter assays and supported by normal lymphocyte and germ cell development, Parp1+/A cells are hypersensitive to base damages, radiation, and Topoisomerase I and II inhibition. The sensitivity of Parp1+/A cells to base damages and Topo inhibitors in particular exceed Parp1-/- controls. The findings show that the enzymatically inactive PARP1 protein has a dominant negative role and establishes a clear physiological difference between PARP1 inactivation vs. deletion. As a result, the enzymatically inactive PARP1 has a much more deteriorating impact on normal tissues than previously estimated, providing a mechanism for the on-target side effect of PARP inhibitors used for cancer therapy. Significance StatementPARP1 is the primary target of PARP enzymatic inhibitors. The use of PARP inhibitors for cancer therapy is based not only on the extreme sensitivity of BRCA1/2-deficient cancer cells to PARP1 inhibition but also on the nonessential role of PARP1 in normal tissues. Here we show that in contrast to the normal development of Parp1-null mice, the mouse model expressing the catalytically inactive Parp1 on only one allele (E988A, Parp1+/A) dies embryonically with high levels of genomic instability. The results reveal the severe dominant-negative impact of catalytically inactive PARP1, indicating the presence of enzymatically inactive PARP1 is much more damaging to normal tissues than previously anticipated. These findings provide a mechanism for clinical PARP inhibitors unexpected normal tissue toxicity.

genetics↗

bioRxiv2023

Integrated single-cell analysis defines the epigenetic basis of castration-resistant prostate luminal cells

Understanding prostate response to castration and androgen receptor signaling inhibitors (ARSI) is critical to improving long-term prostate cancer (PCa) patient survival. Here we use a multi-omics approach on 229,794 single cells to create a mouse single-cell reference atlas better suited to interpreting mouse prostate biology and castration response. Our reference atlas refines single-cell annotations and provides chromatin context, which, when coupled with mouse lineage tracing demonstrates that the castration-resistant luminal cells are distinct from the pre-existent urethra- proximal stem/progenitor cells. Molecular pathway analysis and therapeutic studies further implicate JUN/FOS, WNT/{beta}-Catenin, FOXQ1, NF{kappa}B, and JAK/STAT pathways as the major drivers of castration- resistant luminal populations with high relevance to human PCa. Importantly, we demonstrate the utility of our datasets, which can be explored through an interactive portal (https://visportal.roswellpark.org/data/tang/), to aid in developing novel combination treatments with ARSI for advanced PCa patients. O_FIG O_LINKSMALLFIG WIDTH=164 HEIGHT=200 SRC="FIGDIR/small/530998v1_ufig1.gif" ALT="Figure 1"> View larger version (62K): org.highwire.dtl.DTLVardef@8bd384org.highwire.dtl.DTLVardef@1ebc004org.highwire.dtl.DTLVardef@8b4dbforg.highwire.dtl.DTLVardef@19d7052_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

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↗