Biology subjects

Samaiya, A.

Publications and source records attributed to Samaiya, A..

7 recordsLinked to original sources

bioRxiv2026

A CTCF-LDHB axis converts nuclear lactate availability into an H3K18 acylation switch that directs alternative splicing in hypoxic breast cancer

Lactate accumulating in hypoxic tumours lactylates histones, coupling metabolic state to chromatin. Why it differs between tumours of comparable glycolytic rate has remained unresolved. Here we show that nuclear, rather than total intracellular, lactate availability determines histone H3K18 lactylation in breast cancer, and that CCCTC-binding factor (CTCF) and lactate dehydrogenase B (LDHB) jointly set it. CTCF sustains glycolytic gene expression under hypoxia and drives LDHB in triple-negative breast cancer (TNBC), whereas a CTCF-ER complex represses LDHB in non-TNBC. LDHB consumes lactate favouring H3K18 acetylation; where LDHB is low, CTCF-dependent MCT1 delivers lactate into the nucleus and sustains lactylation. At a CTCF site downstream of TACC3 exon 3, an invariant polymerase II pause couples kinetic and adaptor control of splicing, with the mark deciding the outcome: H3K18la recruits SMARCA4 and hnRNPA1 to skip the exon, generating an isoform that drives EMT, whereas H3K18ac recruits TRIM33 and SRSF10 to include it, generating one that confers stemness. Inhibiting LDHB restores exon skipping and suppresses tumour growth in vivo. Nuclear lactate availability therefore acts as a metabolic switch that converts hypoxic stress into subtype-specific splicing decisions and identifies LDHB as a tractable target in TNBC.

cancer biology↗

bioRxiv2024

PRMT5-mediated histone methylation regulates alternative splicing via MECP2-PTBP1 to promote EMT in breast cancer hypoxia

Tumor hypoxia induced alterations in the epigenetic landscape and alternative splicing influence cellular adaptations. PRMT5 is a type II protein arginine methyltransferase that regulates several tumorigenic events in many cancer types. However, the regulation of PRMT5 and its direct implication on aberrant alternative splicing under hypoxia remains unexplored. In this study, we observed hypoxia induced upregulation of PRMT5 via the CCCTC binding factor, CTCF. Further, PRMT5-mediated symmetric arginine dimethylation H4R3me2s and H3R8me2s directly regulated the alternative splicing of Transcription Factor 3 (TCF3). Under hypoxia, PRMT5-mediated histone dimethylation at the intronic conserved region (ICR) present between TCF3 exon 18a and exon 18b recruits DNA methyltransferase 3A (DNMT3A), resulting in DNA methylation. DNA methylation at the TCF3-ICR is recognized and bound by Methyl CpG binding protein (MECP2) resulting in RNA-Pol II pausing, promoting the recruitment of the negative splicing factor PTBP1 to the splicing locus of TCF3 mRNA. PTBP1 promotes the exclusion of exon 18a which results in the production of the pro-invasive TCF3-18B (E47) isoform which promotes EMT and invasion of breast cancer cells under hypoxia. Collectively, our results indicate PRMT5-mediated symmetric arginine dimethylation of histones regulates alternative splicing of TCF3 gene thereby enhancing EMT and invasion in breast cancer hypoxia.

cancer biology↗

bioRxiv2024

Interplay of YEATS2 and GCDH mediates histone crotonylation and drives EMT in head and neck cancer

The regulation of gene expression is an integral cellular process orchestrated by epigenetic marks like histone modifications. Perturbations in the activity or abundance of epigenetic factors can lead to tumorigenesis. Remarkably, several metabolites influence the epigenetic landscape in cells. Here, we investigated the interplay between a highly expressed epigenetic factor, YEATS2, and a metabolic enzyme, GCDH, in regulating epithelial-to-mesenchymal transition in head and neck cancer. We report that the histone reader YEATS2 is responsible for increased invasive potential in head and neck cancer in an SP1-dependent manner. YEATS2 functions by maintaining histone crotonylation, and its abrogation leads to a global decrease in the H3K27cr mark. Mechanistically, we report that YEATS2 maintains high promoter H3K27cr levels by assisting in the recruitment of crotonyltransferase p300 at the promoter of the EMT-promoting gene SPARC. Further, we found that the addition of the H3K27cr mark is also dependent on the crotonyl-CoA-producing enzyme GCDH. Overall, we describe a novel mechanism of interplay between epigenetics and metabolism in head and neck tumorigenesis, which results in the enhanced expression of EMT-related genes in a histone crotonylation-dependent manner.

cancer biology↗

bioRxiv2023

Oncometabolite lactate enhances breast cancer progression by orchestrating histone lactylation-dependent c-Myc expression

Owing to the enhanced glycolytic rate, cancer cells generate lactate copiously, which in turn, promotes lactylation of histone. Even though histone lactylation has been explored to alter the expression of few genes, the role of this epigenetic modification in regulating the expression of oncogenes is largely unchartered. In this study, using breast cancer cell lines their mutants (which exhibit lactate-deficient metabolome), we have identified that intracellular lactate promotes histone lactylation-dependent c-Myc upregulation. Furthermore, we report that the c-Myc upregulates serine/arginine splicing factor 10 (SRSF10) to drive alternative splicing in breast cancer cells. Our findings provide novel mechanistic insights into the role assayed by aerobic glycolysis in orchestrating alternative splicing that collectively drive breast tumorigenesis. Moreover, we also envisage that chemotherapeutic interventions attenuating glycolytic rate can restrict breast cancer progression by impeding the c-Myc-SRSF10 axis.

cancer biology↗

bioRxiv2023

Hypoxia-induced CTCF mediates alternative splicing via coupling chromatin looping and RNA Pol II pause to promote EMT in breast cancer

Cancer cells experiencing hypoxic stress employ Epithelial-Mesenchymal Transition (EMT) to undergo metastasis through rewiring chromatin landscape, epigenetics, and importantly alternative splicing. Here, we investigated the role of CTCF, chromatin, epigenetic and alternative splicing modulator under hypoxia to promote EMT. Our result shows that hypoxia-induced epigenetic changes upregulate CTCF expression in breast cancer. We delineate that CTCF is a direct target of HIF1 and the hypoxia-induced HIF1-CTCF axis functionally contributes to promoting EMT in breast cancer cells. Finally, our work uncovers COL5A1, an EMT gene, as a direct target of CTCF. We demonstrated that hypoxia-mediated CTCF enrichment on COL5A1 promoter regulates expression as well as alternative splicing events to promote EMT. Here, we put forward an intricate mechanism of alternative splicing where CTCF-mediated promoter-exon upstream looping regulates DNA de-methylation and CTCF-mediated RNA Pol II pausing at COL5A1 exon 64A. Our global analysis of CTCF-ChIP-seq data reveals that the hypoxia-induced differential CTCF occupancy possibly regulates gene expression and alternative splicing events of many genes that are enriched in the EMT pathway, cancer cell motility and invasion, angiogenesis, and stemness under hypoxia, similarly to the proposed model. Finally, we employed the epigenetic modulator dCas9-DNMT3A system to specifically disrupt HIF1 or CTCF binding under hypoxia and hence the HIF1-CTCF-COL5A1exon64A axis that alleviates the EMT potential of breast cancer cells that may represent a novel therapeutic target in breast cancer. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=180 SRC="FIGDIR/small/539689v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@e15c15org.highwire.dtl.DTLVardef@1649a71org.highwire.dtl.DTLVardef@1d77481org.highwire.dtl.DTLVardef@21f148_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO C_FIG

molecular biology↗

bioRxiv2022

PKM2-mediated epigenetic reprogramming regulates hypoxic expression of PFKFB3 to promote breast cancer progression

The hypoxic milieu is a critical modulator of aerobic glycolysis, yet the regulatory mechanisms existing between the key glycolytic enzymes in hypoxic cancer cells are largely unexplored. In particular, M2 isoform of pyruvate kinase (PKM2) - the ratelimiting enzyme of glycolysis, is well-known to confer adaptive advantages under hypoxia. Herein, we report a non-canonical role of PKM2 in functioning as a co-activator of HIF-1 to govern the transcription of 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 (PFKFB3). Nuclear PKM2 enhances HIF-1 and p300 occupancy at PFKFB3 hypoxia responsive elements (HREs) resulting in its upregulation. Consequently, absence of nuclear PKM2 fails to recruit HIF-1 which activates an opportunistic occupancy of HIF-2 at PFKFB3 HREs. Enhanced binding of HDAC3 also occurs in the absence of PKM2 which prevents HIF-2 from efficiently inducing PFKFB3 to hamper proliferation of hypoxic breast cancer cells. In addition, clinical relevance of the study has been investigated by demonstrating that Shikonin blocks nuclear translocation of PKM2 to suppress PFKFB3 expression. Furthermore, MCF7 cells-derived xenograft tumors in mice exhibited substantial tumor growth inhibition when treated with shikonin, highlighting the vitality of targeting PKM2. Taken in concert, this work provides novel insights into contributions of PKM2 in modulating hypoxic transcriptome and a previously unreported molecular axis exhibited by the hypoxic breast cancer cells for ensuring the maintenance of PFKFB3 expression essential for achieving high glycolytic flux. Statement of significanceNuclear PKM2 orchestrates the binding of histone modifiers to epigenetically alter PFKFB3 promoter and affects the binding of HIF-2. Notably, targeting this axis attenuates proliferation of hypoxic breast cancer cells.

cancer biology↗

bioRxiv2020

Overexpressed Nup88 stabilized through interaction with Nup62 promotes NFκB dependent pathways in cancer

Nuclear pores control nucleo-cytoplasmic trafficking and directly or indirectly regulate vital cellular processes. Nup88, important for Crm1 mediated nuclear export process, is overexpressed in many cancers. A positive correlation exists between progressive stages of cancer and Nup88 expression. However, links between Nup88 overexpression and head and neck cancer are insignificant, and mechanistic details are non-existent. Here, we report that Nup88 exhibits positive correlation in head and neck cancer in addition to elevated Nup62 levels. We demonstrate that Nup88 interacts with Nup62 in a cell-cycle and glycosylation independent manner. The overexpression of Nup88 or Nup62 imparts proliferation and migration advantages to cells. We further report that the interaction with Nup62 stabilizes Nup88 by inhibiting proteasome-mediated degradation of overexpressed Nup88. Overexpressed Nup88 is stabile and partly inside the nucleus and can interact with NF{kappa}B (p65). Nup88 overexpression induces proliferative and inflammatory responses downstream of p65. Altogether, we suggest that simultaneous overexpression of Nup62 and Nup88 in head and neck cancer stabilizes overexpressed Nup88. Stable Nup88 interacts with p65 and induces inflammatory, proliferative, and migratory advantages to cells, which perhaps is the underlying mechanism driving tumorigenic transformations.

cancer biology↗