Biology subjects

Volik, S.

Publications and source records attributed to Volik, S..

9 recordsLinked to original sources

bioRxiv2025

Longitudinal single-cell analysis reveals RUNX1T1 as an early driver in treatment-induced neuroendocrine transdifferentiation

Treatment-induced neuroendocrine prostate cancer (t-NEPC) is a lethal form of advanced prostate cancer that can emerge from adenocarcinoma under androgen receptor pathway inhibition, but the tumor-cell states and regulators underlying this transition remain incompletely defined. Here, we analyzed longitudinal single-cell RNA sequencing data from the LTL331/331R patient-derived xenograft model across seven disease stages, comprising 32,269 tumor-cell transcriptomes from treatment-naive adenocarcinoma, post-castration regression, and relapsed NEPC. We identified an AR-low/NE-low intermediate state that emerged after castration and before overt relapse, as well as two transcriptionally distinct terminal NEPC states marked by ASCL1high/FOXA2low and ASCL1low/FOXA2high programs. RUNX1T1 was induced in the intermediate state and remained elevated across both terminal states. RUNX1T1 enhanced NE-associated features and cell viability during enzalutamide treatment in adenocarcinoma cells, whereas its knockdown in NCI-H660 cells reduced NE-associated transcriptional programs, proliferation, and survival and shifted the transcriptome toward an intermediate-like state. Chromatin interactome analysis and co-immunoprecipitation linked RUNX1T1 to G9A/LASP1-containing chromatin repressor complexes. These findings define a temporal framework for treatment-induced NEPC progression and identify RUNX1T1 as an early-induced and sustained regulator of NE lineage transition and maintenance of established NEPC.

cancer biology↗

bioRxiv2025

Longitudinal single-cell RNA sequencing of a neuroendocrine transdifferentiation model reveals transcriptional reprogramming in treatment-induced neuroendocrine prostate cancer

Neuroendocrine transdifferentiation (NEtD) of prostate adenocarcinoma (PRAD) leads to aggressive neuroendocrine prostate cancer (NEPC). The LTL331 patient-derived xenograft (PDX) model consistently progresses to NEPC following castration, mimicking clinical responses to androgen-deprivation therapy. Here we tracked NEtD using longitudinal single-cell RNA sequencing (scRNA-seq) across eight time points in LTL331 from pre- to post-castration. Castration led to the loss of AR-high PRAD cells, expansion of AR-low populations, and emergence of an AR- and NE-negative (AR-/NE-) intermediate state that transitioned into NEPC. We delineate a model in which pre-EMT cells enriched in ciliogenesis and cell-adhesion pathways differentiate into EMT-like populations before branching into distinct ASCL1+ and ASCL1- NEPC states. The EMT-enriched intermediate, marked by progenitor and neural crest stem-cell genes, acts as a transition bridge, suggesting EMT-associated stemness underlies lineage plasticity. A terminal ASCL1-NEPC state also suggests that ASCL1 is not essential for NEPC maintenance. Gene regulatory analysis highlighted key regulators driving NEtD, including MSX1 and ASCL1 in early EMT-like and NEPC states, respectively. These transcriptional states were validated in both patient-derived bulk and scRNA-seq data. Our findings offer insights into intervention strategies to delay or prevent NEtD with the potential of identifying novel prognostic and therapeutic targets.

cancer biology↗

bioRxiv2025

AR-V7 condensates drive androgen-independent transcription in castration resistant prostate cancer

Biomolecular condensates organize cellular environments and regulate key processes such as transcription. We previously showed that full-length androgen receptor (AR-FL), a major oncogenic driver in prostate cancer (PCa), forms nuclear condensates upon androgen stimulation in androgen-sensitive PCa cells. Disrupting these condensates impairs AR-FL transcriptional activity, highlighting their functional importance. However, resistance to androgen deprivation therapy often leads to castration-resistant prostate cancer (CRPC), driven by constitutively active splice variants like AR variant 7 (AR-V7). The mechanisms underlying AR-V7s role in CRPC remain unclear. In this study, we characterized the condensate-forming ability of AR-V7 and compared its phase behavior with AR-FL across a spectrum of PCa models and in vitro conditions. Our findings indicate that cellular context can influence AR-V7s condensate-forming capacity. Unlike AR-FL, AR-V7 spontaneously forms condensates in the absence of androgen stimulation and functions independently of AR-FL in CRPC models. However, AR-V7 requires a higher concentration to form condensates, both in cellular contexts and in vitro. We further reveal that AR-V7 drives transcription via both condensate-dependent and condensate-independent mechanisms. Using an AR-V7 mutant incapable of forming condensates, while retaining nuclear localization and DNA-binding ability, we reveal that the condensate-dependent regime activates part of the oncogenic KRAS pathway in CRPC models. Genes under this condensate-dependent regime were found to harbor significantly higher numbers of AR-binding sites and exhibited boosted expression in response to AR-V7. These findings uncover a previously unrecognized role of AR-V7 condensate formation in driving oncogenic transcriptional programs and shed light on its unique contribution to CRPC progression. HighlightsO_LIAR-V7 condensates form independently of both androgens and AR-FL in CRPC models. C_LIO_LIAR-V7 mediates condensate-dependent and independent transcription C_LIO_LICondensate-dependent transcription enables boosted expression of oncogenic KRAS genes C_LIO_LICondensate-dependent genes exhibit an exponential increase in expression, with a higher number of AR binding sites potentially playing a key role in their reliance on condensate formation. C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=99 SRC="FIGDIR/small/631986v1_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@16b50d1org.highwire.dtl.DTLVardef@86e3b6org.highwire.dtl.DTLVardef@1cfe7f3org.highwire.dtl.DTLVardef@8532a2_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2024

5'-S-(3-aminophenyl)-5'-thioadenosine, a novel chemoprotective agent for reducing toxic side effects of fluorouracil in treatment of MTAP-deficient cancers

BackgroundNucleobase analogue (NBA) drugs are effective chemotherapeutics, but their clinical use is limited by severe side effects. Compelling evidence suggests the use of S-methyl-5-thioadenosine (MTA) can selectively reduce NBA toxicity on normal tissues while maintaining the efficacy of NBAs on methylthioadenosine phosphorylase (MTAP)-deficient cancers. However, we found that MTA induced hypothermia at its effective dose, limiting its translational potential. We intended to find an MTA analogue that can exert MTA function while minimize the undesired side effects of MTA. Thus, such an analogue can be used in combination with NBAs in selectively targeting MTAP-deficient cancers. MethodsWe screened a library of MTA analogues for the following criteria: 1) being substrates of MTAP; 2) selectively protection on MTAP-expressing cells from NBA toxicity using MTAP-isogenic cell lines; 3) ability to protect the host from NBA toxicity without hypothermic effect; and 4) lack of interference on the tumor-suppressive effect of NBA in mice bearing MTAP-deficient tumors. ResultsWe identified 5-S-(3-aminophenyl)-5-thioadenosine (m-APTA) that did not induce hypothermia at the effective doses. We demonstrated that m-APTA could be converted to adenine by MTAP. Consequently, m-APTA selectively protected mouse hosts from 5-FU-induced toxicity (i.e. anemia); yet it did not interfere with the drug efficacy on MTAP-deficient bladder cancers. In silico docking studies revealed that, unlike MTA, m-APTA interact inefficiently with adenosine A1 receptor, providing a plausible explanation of the superior safety profile of m-APTA. Conclusionm-APTA can significantly improve the translational potential of the NBA toxicity reduction strategy in selectively targeting MTAP-deficient cancers.

cancer biology↗

bioRxiv2023

Clinical Phenotype Prediction From Single-cell RNA-seq Data using Attention-Based Neural Networks

MotivationA patients disease phenotype can be driven and determined by specific groups of cells whose marker genes are either unknown, or can only be detected at late-stage using conventional bulk assays such as RNA-Seq technology. Recent advances in single-cell RNA sequencing (scRNA-seq) enable gene expression profiling in cell-level resolution, and therefore have the potential to identify those cells driving the disease phenotype even while the number of these cells is small. However, most existing methods rely heavily on accurate cell type detection, and the number of available annotated samples is usually too small for training deep learning predictive models. ResultsHere we propose the method ScRAT for clinical phenotype prediction using scRNA-seq data. To train ScRAT with a limited number of samples of different phenotypes, such as COVID and non-COVID, ScRAT first applies a mixup module to increase the number of training samples. A multi-head attention mechanism is employed to learn the most informative cells for each phenotype without relying on a given cell type annotation. Using three public COVID datasets, we show that ScRAT outperforms other phenotype prediction methods. The performance edge of ScRAT over its competitors increases as the number of training samples decreases, indicating the efficacy of our sample mixup. Critical cell types detected based on high-attention cells also support novel findings in the original papers and the recent literature. This suggests that ScRAT overcomes the challenge of missing marker genes and limited sample number with great potential revealing novel molecular mechanisms and/or therapies.

bioinformatics↗

bioRxiv2023

Patient and cell-type specific hiPSC-modeling of a truncating titin variant associated with atrial fibrillation

BackgroundProtein truncating mutations in the titin gene are associated with increased risk of atrial fibrillation (AF). However, little is known regarding the underlying pathophysiology. MethodsWe identified a heterozygous titin truncating variant in a patient with unexplained early-onset AF using whole exome sequencing. We used atrial and ventricular patient induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs), CRISPR/Cas9 genetic correction, and engineered heart tissue (EHT) constructs to evaluate the impact of the titin truncating variant on electrophysiology, sarcomere structure, contractility, and gene expression. ResultsWe generated atrial and ventricular iPSC-CMs from the AF patient with the titin truncating variant and a CRISPR/Cas9 genome corrected isogenic control. We demonstrate that the titin truncating variant increases susceptibility to pacing-induced arrhythmia (prevalence of arrhythmogenic phenotypes, 85.7% versus 14.2%; P = 0.03), promotes sarcomere disorganization (mean {+/-} SEM, 66.3 {+/-} 6.8% versus 88.0 {+/-} 2.9%; P = 0.04) in atrial iPSC-CMs, and reduces contractile force (0.013 {+/-} 0.003 mN versus 0.027 {+/-} 0.004 mN; P < 0.01) in atrial EHTs compared to isogenic controls. In ventricular iPSC-CMs, this variant led to altered electrophysiology (90.0% versus 33.3%; P = 0.02) and sarcomere organization (62.0 {+/-} 3.9% versus 82.9 {+/-} 2.9%; P < 0.01) with no change in EHT contractility compared to isogenic controls. RNA-sequencing revealed an upregulation of cell adhesion and extracellular matrix genes in the presence of the titin truncating variant for both atrial and ventricular EHTs. ConclusionsIn a patient with early-onset unexplained AF and normal ventricular function, iPSC-CMs with a titin truncating variant showed structural and electrophysiological abnormalities in both atrial and ventricular preparations, while only atrial EHTs demonstrated reduced contractility. Whole transcriptome sequencing showed upregulation of genes involved in cell-cell and cell-matrix interactions in both atrial and ventricular EHTs. Together, these findings suggest titin truncating variants promote the development of AF through remodeling of atrial cardiac tissue and provide insight into the chamber-specific effects of titin truncating variants.

cell biology↗

bioRxiv2020

Multiomics Characterization of Potential Therapeutic Vulnerabilities in Low-grade Serous Ovarian Carcinoma

BackgroundLow-grade serous ovarian carcinoma (LGSOC) is a rare tumor subtype with high case fatality rates. As such, there is a pressing need to develop more effective treatments using newly available preclinical models for therapeutic discovery and drug evaluation. Here, we use a multiomics approach to interrogate a collection of LGSOC patient-derived cell lines to elucidate novel biomarkers and therapeutic vulnerabilities. MethodsFourteen LGSOC cell lines were interrogated using whole exome sequencing, RNA sequencing, and mass spectrometry-based proteomics. Somatic mutation, copy-number aberrations, gene and protein expression were analyzed and integrated using different computational approaches. LGSOC cell line data was compared to publicly available LGSOC tumor data (AACR GENIE cohort), and also used for predictive biomarker identification of MEK inhibitor (MEKi) efficacy. Protein interaction databases were evaluated to identify novel therapeutic targets. ResultsKRAS mutations were exclusively found in MEKi-sensitive and NRAS mutations mostly in MEKi-resistant cell lines. Analysis of COSMIC mutational signatures revealed distinct patterns of nucleotide substitution mutations in MEKi-sensitive and MEKi-resistant cell lines. Deletions of CDKN2A/B and MTAP genes (chromosome 9p21) were much more frequent in cell lines than tumor samples and possibly represent key driver events in the absence of KRAS/NRAS/BRAF mutations. For in-vitro MEKi efficacy prediction, proteomic data provided better discrimination than gene expression data. Condensin, MCM, and RFC protein complexes were identified as potential treatment targets in MEKi-resistant cell lines. ConclusionsOur LGSOC cell lines are representative models of the most common molecular aberrations found in LGSOC tumors. This study highlights the importance of using proteomic data in multiomics assessment of drug prediction and identification of potential therapeutic targets. CDKN2A/B and MTAP deficiency offer an opportunity to find synthetically lethal candidates for novel treatments. Multiomics approaches are crucial to improving our understanding of the molecular aberrations in LGSOC, establishing effective drug prediction programs and identifying novel therapeutic targets in LGSOC.

cancer biology↗

bioRxiv2019

Well-Differentiated Papillary Mesothelioma of the Peritoneum is Genetically Distinct from Malignant Mesothelioma

Well-differentiated papillary mesothelioma (WDPM) is an uncommon mesothelial proliferation that is most commonly encountered as an incidental finding in the peritoneal cavity. There is controversy in the literature about whether WDPM is a neoplasm or a reactive process, and if neoplastic, whether it is a variant or precursor of epithelial malignant mesothelioma or is a different entity. Using whole exome sequencing of five WDPM of the peritoneum, we have identified distinct mutations in EHD1, ATM, FBXO10, SH2D2A, CDH5, MAGED1, and TP73 shared by WDPM cases but not reported in malignant mesotheliomas. Furthermore, we show that WDPM is strongly enriched with C>A transversion substitution mutations, a pattern that is also not found in malignant mesotheliomas. The WDPMs lacked alterations involving BAP1, SETD2, NF2, CDKN2A/B, LASTS1/2, PBRM1, and SMARCC1 that are frequently altered in malignant mesotheliomas. We conclude that WDPMs are neoplasms that are genetically distinct from malignant mesotheliomas, and based on observed mutations do not appear to be precursors of malignant mesotheliomas.

cancer biology↗

bioRxiv2018

BAP1 Loss Predicts Therapeutic Vulnerability in Malignant Peritoneal Mesothelioma

BackgroundMalignant Peritoneal Mesothelioma (PeM) is a rare but frequently fatal cancer that originates from the peritoneal lining of the abdomen. Standard treatment of PeM is limited to cytoreductive surgery and/or chemotherapy, and no effective targeted therapies for PeM yet exist. In the search for novel therapeutic target candidates in PeM, we performed a comprehensive integrative multi-omics analysis of 19 treatment-naive PeM tumors.\n\nResultsThe analysis identified PeM tumors with BAP1 loss to form a distinct molecular subtype characterized by distinct expression patterns of genes involved in chromatin remodeling, DNA repair pathway, and immune checkpoint receptor activation. This PeM subtype could potentially benefit from immune checkpoint, PARP, or HDAC inhibition therapies.\n\nConclusionsOur findings uncover BAP1 as a trackable prognostic and predictive biomarker, and refine PeM disease classification. This integrated molecular characterization provides a comprehensive foundation for developing PeM precision medicine.

cancer biology↗