Biology subjects

Prabhu, J. S.

Publications and source records attributed to Prabhu, J. S..

9 recordsLinked to original sources

bioRxiv2026

Endocrine therapy-specific lineage and partial epithelial-mesenchymal reprogramming defines divergent resistant cell-states in ER+ breast cancer

Acquired resistance to endocrine therapy remains a primary obstacle in the clinical management of estrogen receptor-positive (ER+) breast cancer. While resistance is frequently accompanied by transcriptional rewiring and lineage plasticity, how specific pharmacological modalities dictate divergent resistance trajectories remains poorly understood. Here, we integrate multi-omic profiling, spanning bulk and single-cell transcriptome, chromatin architecture (Hi-C), and the cistrome, to systematically compare the mechanisms involved in adaptive resistance to selective estrogen receptor modulators (SERMs, e.g., tamoxifen) and degraders (SERDs, e.g., fulvestrant), and the mechanism driven by constitutive ESR1 mutation, to characterize how mode of ER perturbation influences lineage identity and epithelial-mesenchymal state. We found that tamoxifen resistant (TamR) cells occupy a distinct transcriptional state characterized by coordinated luminal erosion, partial basal lineage activation, and stabilization of a partial epithelial-mesenchymal (pEMT) program. In contrast, fulvestrant resistant (FulR) cells primarily suppress ER signaling without extensive lineage reprogramming. Finally, ESR1 mutant cells recapitulate ligand-driven ER hyperactivation with limited engagement of mesenchymal and basal gene expression programs. Chromatin profiling further revealed that SERM resistance is accompanied by higher-order genome reorganization, including A-to-B compartment switching at luminal regulators such as GATA3 and ESR1, redistribution of ER and FOXA1 binding, and consequent activation of a pEMT program. Furthermore, we show that SERM-induced reprogramming is accompanied by a distinct mode of immune evasion where the reprogrammed cells do not engage classical T-cell exhaustion programs but instead exhibit coordinated loss of major histocompatibility complex (MHC) class I antigen presentation and establishment of a pro-tumorigenic signaling that strongly predicts adverse survival outcomes in patient cohorts. Together, these findings indicate that endocrine resistance does not converge on a single molecular endpoint but instead reflects drug-specific adaptive states defined by ER signaling context, lineage identity, and chromatin architecture. Our study establishes the basal-pEMT axis as a coordinated, epigenetically encoded module of SERM-induced plasticity and reframes endocrine resistance as a multidimensional evolutionary process shaped by therapeutic mechanisms of action.

cancer biology↗

bioRxiv2025

TIF1γ drives oral cancer recurrence by the transcriptional regulation of self-renewal genes, such as HES1

TIF1{gamma} is an E3 ubiquitin ligase and key mediator of the noncanonical TGF-{beta} signaling pathway. Initially characterized for its developmental functions, TIF1{gamma} is essential for maintaining the pluripotency of adult stem cells, including long-term hematopoietic stem cells. Although TGF-{beta} signaling contributes to cancer progression and recurrence, TIF1{gamma} has traditionally been regarded as a tumor suppressor due to its inhibition of oncogenes involved in epithelial-mesenchymal transition. However, clinical reports have associated high TIF1{gamma} expression at advanced cancer stages with poor prognosis. To elucidate the mechanism underlying this paradox, we identify a previously unrecognized role of TIF1{gamma} in promoting the self-renewal capacity of oral cancer cells, thereby contributing to disease recurrence. Phosphoproteomic profiling of self-renewal-enriched cells revealed activation of a noncanonical TGF-{beta} pathway. Using extreme limiting dilution assays, an ALDH1A1-DsRed2 cancer stem cell reporter, multiple oral cancer cell lines, primary 3D cultures on alginate matrix, and orthotopic mouse models, we demonstrate that TIF1{gamma} depletion significantly reduces self-renewal and prolongs disease-free survival. Immunoprecipitation (IP)-LC/MS/MS analysis identified transcriptional regulators within the TIF1{gamma} interactome, including TRRAP and H2A.Z, which were validated by IP and FRET assays. ChIP and IP studies further revealed that during self-renewal enrichment, TRRAP acetylates H2A.Z, decreasing the chromatin occupancy of its unacetylated form. Acetylated H2A.Z is subsequently recognized by TIF1{gamma}, which monoubiquitinates H2B at promoters of self-renewal genes such as HES1, initiating transcription. In alignment with findings from mouse neocortical development, where a Notch-independent Hes1-expressing (NIHes1) population defines primitive quiescent stem cells, we show that TIF1{gamma} acts as an acetylation reader specifically at the NIHES1 promoter region of HES1. TIF1{gamma} depletion drives NIHES1 cells toward a Notch-dependent HES1 (NDHES1) identity. RNA-seq confirmed reversal of 100 NIHES1-specific genes following TIF1{gamma} loss, along with downregulation of pluripotency-associated genes found in embryonic stem cells, supporting a critical role for TIF1{gamma} in maintaining primitive cancer stem cell states. Consistent with our in vivo findings, primary oral cancer samples showed that increased frequencies of TIF1{gamma}+/TRRAP+/H2A.Z- cells strongly predict recurrence. Given that the histone acetylation-reader function of TIF1{gamma} drives poor prognosis, our findings suggest the TIF1{gamma} bromodomain as a potential therapeutic target requiring further investigation.

cancer biology↗

bioRxiv2025

Repurposing statins in combination therapy for effective ablation of metastatic breast cancer

Metastatic breast cancer (mBC) remains an incurable disease with limited treatment options, highlighting the need for novel therapeutic approaches. Combination therapy with chemotherapeutic agents along with targeted therapy are the most common methods of treatment used in the terminal stages of the disease. Eventual development of resistance to these approaches, leading to fatal outcomes suggests the presence or emergence of a heterogenous population of cells intrinsically resistant to commonly used regimens. Previous work identified a heterogeneous population of metastatic tumor cells with distinct molecular characteristics driven by Macc1 (Metastasis Associated in Colon Cancer 1) overexpression, which could be targeted by lovastatin (transcriptional inhibitor of Macc1). Building on this foundation, the efficacy of lovastatin in targeting metastatic cells with high Macc1 expression was evaluated in lung metastasis, and the regulatory pathways governing Macc1 expression and lovastatin treatment in mBC were investigated. The expression of Macc1, in breast cancer biopsies provides insights into the intra and inter tumor heterogeneity of the Macc1 gene and its correlation with disease outcomes. While some studies suggest synergistic effects between statins and chemotherapeutic agents, comprehensive evaluations of various combinations and their therapeutic outcomes are still needed. The therapeutic efficacy of lovastatin combined with chemotherapy to determine the most effective treatment regimen that maximizes tumor cell ablation demonstrated that lovastatin can effectively ablate the chemoresistant tumor cells in mBC. The translational implications of this research will identify patient subgroups that may benefit most from statin-chemotherapy combinations that could support the repurposing of statins as cost-effective adjuvant therapies for mBC.

cancer biology↗

bioRxiv2025

EPHA2-dependent Ephrin-B1 signaling supports self-renewal ability and recurrence of oral cancer

Eph-Ephrin pathway that drives a bidirectional signaling regulates a plethora of biological activities with its varied level of complexity. While the canonical trans-interaction of the ligand and receptor on neighboring cells initiates forward signaling that brings about biological activities, their cis-interaction on the same cell attenuates the forward signaling, modulating the biological effects. Yet, non-canonical cis-interactions with heterotypic surface proteins and kinases regulate certain biological effects. In cancer, the canonical signaling is believed to be tumor suppressive, while the ligand-independent non-canonical signaling drives tumor progression and poor prognosis. Self-renewal ability of cancer cells is a major underlying cause of recurrence and poor prognosis of cancer. Using SILAC-based proteomics, we identified Ephrin-B1 signaling as a crucial regulator of oral cancer self-renewal. Though Ephrin-B1 is known to regulate normal stem cells, its role in cancer remains underexplored. Our biochemical analyses show that Ephrin-B1 binds to a nonconventional receptor EPHA2, which is known to regulate cancer stem cells (CSCs), though the mechanism is less explored. Contrary to the belief that the cis-interaction of receptors and ligands is a means to block functional signaling, our immunoprecipitation, FRET facilitated photoswitching analysis, proximity ligation assay, and in vitro kinase assay provide evidence for the Ephrin-B1-EPHA2 cis-interaction leading to the phosphorylation of EphrinB1 at Y324/329 and Y317. Extreme limiting dilution assay in vitro and in vivo confirmed that this cis-interaction promotes CSC enrichment. Substantiating our in vitro results, mouse orthotopic models showed that Ephrin-B1/EPHA2 interaction regulates prognosis. The clinical relevance of the finding was validated using a TCGA data set and immunohistochemical analysis of tissue microarray using samples from oral cancer patients with recurrence in comparison to patients, who showed disease-free survival. Given that Ephrin-B interacts with EphB for normal stem cell homeostasis, this unconventional EPHA2/Ephrin-B1 cis-interaction, specifically manifested in CSC niches, might serve as an attractive target for therapy, warranting further validation.

cancer biology↗

bioRxiv2023

Multi-modal transcriptomic analysis unravels enrichment of hybrid epithelial/mesenchymal state and enhanced phenotypic heterogeneity in basal breast cancer

Intra-tumoral phenotypic heterogeneity promotes tumor relapse and therapeutic resistance and remains an unsolved clinical challenge. It manifests along multiple phenotypic axes and decoding the interconnections among these different axes is crucial to understand its molecular origins and to develop novel therapeutic strategies to control it. Here, we use multi-modal transcriptomic data analysis - bulk, single-cell and spatial transcriptomics - from breast cancer cell lines and primary tumor samples, to identify associations between epithelial-mesenchymal transition (EMT) and luminal-basal plasticity - two key processes that enable heterogeneity. We show that luminal breast cancer strongly associates with an epithelial cell state, but basal breast cancer is associated with hybrid epithelial/mesenchymal phenotype(s) and higher phenotypic heterogeneity. These patterns were inherent in methylation profiles, suggesting an epigenetic crosstalk between EMT and lineage plasticity in breast cancer. Mathematical modelling of core underlying gene regulatory networks representative of the crosstalk between the luminal-basal and epithelial-mesenchymal axes recapitulate and thus elucidate mechanistic underpinnings of the observed associations from transcriptomic data. Our systems-based approach integrating multi-modal data analysis with mechanism-based modeling offers a predictive framework to characterize intra-tumor heterogeneity and to identify possible interventions to restrict it.

systems biology↗

bioRxiv2023

Androgen Receptor driven gene score identifies tumors with Epithelial to Mesenchymal Transition features in triple negative breast cancer

BackgroundAndrogen receptor (AR) is considered marker associated with better prognosis within hormone receptor positive tumors. Its role in triple negative tumors however is controversial showing both better and worse prognosis and different methods are used for identification of AR driven tumors. Conflicting results could be due to intrinsic molecular differences or scoring method for AR positivity. We attempted to develop an AR driven gene score and examined its utility in subtypes of breast cancer (BC). MethodsA bioinformatic pipeline was constructed and applied on publicly available microarray data sets obtained from AR positive BC cell lines treated with dihydrotestosterone (DHT). Expression levels of genes identified through the pipeline along with set of epithelial mesenchymal transition (EMT) markers, proliferation associated genes and enzymes involved in intracrinal androgen metabolism was evaluated in a cohort of Indian Breast cancer patients. Tumors were divided into AR high and low based on the gene score and association with clinical parameters, circulating androgens, disease free survival, proliferation and EMT markers were examined, all results were further validated in external public datasets. ResultsAR driven gene score was calculated as average expression of the 6 genes selected through bioinformatic analysis. 53% (133/249) tumors were classified as AR high by the gene score and had significantly better clinical parameters such as higher age, smaller tumor size, lower grade and lower proliferation. Tumors with high AR driven gene score had significantly better disease-free survival (mean survival time of 86.13 vs 72.69 months, log rank p=0.032) when compared to the AR low tumors. A subset analysis within TNBC (N=66) showed 36% (24/66) were AR high and had significantly higher expression of EMT markers (p=0.024). Though circulating levels of total testosterone was not different between the groups, intratumoral levels of 5 alfa reductase (SRD5A1) was significantly high in tumors with high AR driven score. ConclusionRole of AR in breast cancer is debatable and difficult to decipher with protein detection alone. Our results support the context dependent function of AR in driving better prognosis, while identifying its role in driving EMT within TNBC tumors.

cancer biology↗

bioRxiv2023

BRCA1 expression, its correlation with clinicopathological features and response to neoadjuvant chemotherapy in high grade serous ovarian cancer from an Indian centre

In high grade serous ovarian cancers (HG-SOC), BRCA1/2 mutations have been reported as the most predominant mutations by various studies. However, the non-mutational mechanisms of BRCA pathway inactivation in HG-SOC are unclear. We aimed to evaluate BRCA1 inactivation by estimating its expression along with its repressor in primary and neoadjuvant chemotherapy (NACT) treated HG-SOC tumors with known therapeutic response. The expression pattern of BRCA1 protein was evaluated by immunohistochemistry (IHC) in 119 cases of HG-SOC from a hospital cohort consisting of primary (N= 69) and NACT treated (N=50) tumors. Histological patterns (SET), stromal infiltration by lymphocytes (sTILs) and chemotherapy response score (CRS) were estimated by microscopic examination. Gene expression levels of BRCA1, and its repressor ID4 was estimated by qPCR. Association of BRCA1 protein and mRNA with clinicopathological features was studied. Relevance of the BRCA1/ID4 ratio was evaluated in tumors with different CRS. BRCA1 protein expression was observed in 12% of primary and 19% of NACT treated HG-SOC tumors. Moderate concordance was observed between BRCA1 protein and mRNA expression (AUC-0.677). High BRCA1 mRNA expression was significantly associated with more frequent SET pattern (p=0.024), higher sTILs density (p=0.042), increased mitosis (p=0.028). BRCA1 negative tumors showed higher expression of ID4 though not statistically significant. Higher BRCA1/ID4 ratio was associated with high sTILs density in primary (p=0.042) and NACT treated tumors (p=0.040). Our findings show the utility of BRCA1/ID4 ratio to predict neoadjuvant therapy response, which needs further evaluation in larger cohort with long term outcomes.

cancer biology↗

bioRxiv2022

Acquisition of hybrid E/M phenotype associated with increased migration, drug resistance and stemness is mediated by reduced miR-18a levels in ER-negative breast cancer

The complexity of the ER-negative subtype of breast cancer arises due to the heterogeneous nature of the disease rendering them more aggressive and this poses a challenge to effective treatment and eventually the prognosis of the patients. We have explored the miRNA regulation of altered molecular signatures and the effect on tumour progression in ER-negative breast cancer. Using breast tumour specimens, gene expression data from public datasets and in-vitro and in-vivo model systems we have shown that low-levels of miR-18a in ER-negative tumours drives enrichment of hybrid Epithelial/Mesenchymal (E/M) cells with luminal attributes. On inhibition of miR-18a in ER-negative breast cancer cell lines, the cells showed traits of increased migration, stemness and drug-resistance. miR-18a/low tumours were also associated with increased expression of genes associated with EMT, stemness, drug resistance and immune-suppression. Further analysis of the miR-18a targets pointed out at a possible HIF-1 mediated signalling in these tumours. HIF-1 inhibition reduced the enrichment of the hybrid E/M cells and decreased the migratory ability of miR-18a/low cells. Our study reports for the first time a dual role of miR-18a in breast cancer that is subtype specific based on hormone receptor expression and a novel association of low miR-18a levels and enrichment of hybrid E/M cells. The results highlight the possibility of stratifying the ER-negative disease into clinically relevant groups by analysing epigenetic signatures.

cancer biology↗

bioRxiv2022

mTORC2 Drives ZFX-mediated Ganglioside Biosynthesis to Promote Breast Cancer Progression.

Sphingolipid and ganglioside metabolic pathways are crucial components of cell signalling, having established roles in tumor cell proliferation, invasion, and migration. However, regulatory mechanisms controlling sphingolipid and ganglioside biosynthesis in mammalian cells is less known. Here, we show that RICTOR, the regulatory subunit of mTORC2, regulates the synthesis of sphingolipids and gangliosides in luminal breast cancer-specific MCF-7 and BT-474 cells through transcriptional and epigenetic mechanisms. RICTOR regulates glucosylceramide levels by modulating the expression of UDP-Glucose Ceramide Glucosyl transferase (UGCG). We identify Zinc Finger protein X-linked (ZFX) as a RICTOR-responsive transcription factor whose recruitment to the UGCG promoter is regulated by DNA methyltransferases and histone demethylase (KDM5A) that are known AKT substrates. We further demonstrate that RICTOR regulates the synthesis of GD3 gangliosides through ZFX and UGCG, and triggers the activation of EGFR signalling pathway, thereby promoting tumor growth. In line with our findings in cell culture and mice models, we observe an elevated expression of RICTOR, ZFX, and UGCG in Indian luminal breast cancer tissues, and in TCGA and METABRIC datasets. Together, we establish a key regulatory circuit, RICTOR-AKT-ZFX-UGCG-Ganglioside-EGFR-AKT, and elucidate its contribution to breast cancer progression.

cancer biology↗