Biology subjects

Ramnarayanan, S.

Publications and source records attributed to Ramnarayanan, S..

5 recordsLinked to original sources

bioRxiv2026

Pan-cancer discovery of driver mutations in long noncoding RNAs reveals widespread functional rewiring of RNA regulatory elements

Most somatic mutations in cancer occur outside protein-coding genes, yet the functional impact of these mutations remains largely unknown. Long noncoding RNAs (lncRNAs) represent a major class of cancer-promoting genes whose molecular mechanisms are poorly understood. While individual driver mutations in lncRNAs have been identified, detecting such driver lncRNAs at scale requires large tumour genome cohorts. We analyse 12,631 cancer genomes from the 100,000 Genomes Project (100kGP) and identify 121 lncRNAs under positive selection across 19 cancer types. These driver lncRNAs are independently supported by functional genomic screens, germline predisposing variants, mutual exclusivity with protein-coding drivers, and independent oncogenic lncRNA catalogues. Overall, approximately two-thirds of analysed tumours harbour at least one lncRNA driver mutation. Leveraging the depth of this dataset, we demonstrate that somatic mutations preferentially target and remodel RNA-binding protein (RBP) interaction sites to potentiate oncogenic lncRNAs, including MALAT1, SNHG14 and NEAT1. From these data, we derive a model in which somatic mutations liberate oncogenic lncRNAs from repressive RNA:protein interactions. This work expands the number and nature of cancer driver genes, identifies targets for RNA-directed therapies, and demonstrates that with large tumour mutation catalogues we can dissect the molecular mechanisms of noncoding genes.

Cancer Biology↗

bioRxiv2025

Robust CRISPR Screens Identify TPL1 as a Novel Long Noncoding RNA Driving Triple-Negative Breast Cancer Hallmarks

Despite the growing catalog of long noncoding RNAs (lncRNAs), the functional roles of their vast majority in cancer remain poorly defined. To systematically explore lncRNA dependencies in triple-negative breast cancer (TNBC), we compiled a comprehensive annotation by merging GENCODE, BIGTranscriptome, and MiTranscriptome databases and performed a CRISPR-Cas9 deletion screen targeting 1,029 TNBC-enriched lncRNAs. The screen revealed several essential lncRNAs and those modulating doxorubicin sensitivity, with TPL1 emerging among top hits. TPL1 silencing significantly impaired TNBC cell proliferation in both 2D and 3D cultures and reduced invasive capacity in an organ-on-chip model. Transcriptomic and proteomic profiling following TPL1 knockdown revealed downregulation of genes involved in ECM-receptor interaction, focal adhesion, cell migration, and PI3K-Akt signaling. Mechanistically, TPL1 directly interacted with key proteins including EIF4B, MDM2, TARBP2, TLE5, and GTPase RAN, suggesting TPL1 could regulate RNA processing, transcriptional repression, and translation, as well as modulate GTPase signaling pathways. Additionally, TPL1 functioned as a competing endogenous RNA (ceRNA), sequestering miR-10396b-5p, miR-486-3p, and miR-450a-2-3p, among others, thereby modulating expression of pro-tumorigenic targets. Clinically, TPL1 was significantly overexpressed in TNBC tissues, particularly in the BLIS subtype. Collectively, our findings highlight TPL1 as a key regulator of TNBC molecular networks and a promising therapeutic target.

cancer biology↗

bioRxiv2024

Enhancer lncRNA LOC730338 limits the innate immune response against lymphoma cells, inhibiting ADAR2-dependent alternative transcription.

Chronic antigenic stimulation is a central factor in the development of marginal zone lymphoma (MZL). While the pharmacological inhibition of the B-cell receptor (BCR) signaling by Brutons tyrosine kinase (BTK) inhibitors is initially effective, the development of resistance remains a challenge in treating MZL and other B-cell malignancies. Enhancer activation remodeling is a key epigenetic mechanism that enables tumor adaptation during therapy. The most active regulatory regions cluster in super-enhancers and produce enhancer RNAs (eRNAs), a class of unstable noncoding transcripts that primarily serve as scaffolds for chromatin looping. However, when stabilized, these eRNAs can evolve into long noncoding RNA (lncRNAs) with distinct functions. To investigate enhancer-associated long non-coding RNAs (elncRNAs) involved in shaping BCR pathway dependence, we conducted a CRISPR interference (CRISPRi) screen in MZL cells. We identified LOC730338, an elncRNA linked to A-to-I RNA editing, which we renamed ADARreg. ADARreg renders tumor cells refractory to BCR pathway inhibition by modulating ADAR2 nuclear translocation and altering RNA modification patterns in key regulatory isoforms through coordinated control of RNA stability and localization, as revealed through subcellular direct RNA sequencing (DRS). In addition, ADARreg induces an immune-suppressive transcriptional program, increasing the production of inhibitory cytokines and receptors that diminish NK cell-mediated cytotoxicity. Together, these findings uncover a novel role for elncRNAs in orchestrating immune evasion and provide a potential therapeutic strategy to overcome resistance in lymphoma and other immune-related diseases. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=116 SRC="FIGDIR/small/627805v2_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@1c3fa92org.highwire.dtl.DTLVardef@177b234org.highwire.dtl.DTLVardef@154a8fdorg.highwire.dtl.DTLVardef@122acfd_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIThe enhancer-associated long non-coding RNA ADARreg modulates RNA editing and alters the stability and localization of key immune-related transcripts, thereby enabling tumor immune evasion. C_LIO_LIADARreg has prognostic and therapeutic relevance, linking resistance mechanisms and immune modulation, which supports the development of RNA-based therapeutic strategies in cancer. C_LI

cancer biology↗

bioRxiv2021

Tumour mutations in long noncoding RNAs that enhance cell fitness

Long noncoding RNAs (lncRNAs) can act as tumour suppressors or oncogenes to repress/promote tumour cell proliferation via RNA-dependent mechanisms. Recently, genome sequencing has identified elevated densities of tumour somatic single nucleotide variants (SNVs) in lncRNA genes. However, this has been attributed to phenotypically-neutral "passenger" processes, and the existence of positively-selected fitness-altering "driver" SNVs acting via lncRNAs has not been addressed. We developed and used ExInAtor2, an improved driver-discovery pipeline, to map pancancer and cancer-specific mutated lncRNAs across an extensive cohort of 2583 primary and 3527 metastatic tumours. The 54 resulting lncRNAs are mostly linked to cancer for the first time. Their significance is supported by a range of clinical and genomic evidence, and display oncogenic potential when experimentally expressed in matched tumour models. Our results revealed a striking SNV hotspot in the iconic NEAT1 oncogene, which was ascribed by previous studies to passenger processes. To directly evaluate the functional significance of NEAT1 SNVs, we used in cellulo mutagenesis to introduce tumour-like mutations in the gene and observed a consequent increase in cell proliferation in both transformed and normal backgrounds. Mechanistic analyses revealed that SNVs alter NEAT1 ribonucleoprotein assembly and boost subnuclear paraspeckles. This is the first experimental evidence that mutated lncRNAs can contribute to the pathological fitness of tumour cells.

genomics↗

bioRxiv2019

Cytosolic Ca2+ modulates Golgi structure through PKC-mediated GRASP55 phosphorylation

It has been well documented that the endoplasmic reticulum (ER) responds to cellular stresses through the unfolded protein response (UPR), but it is unknown how the Golgi responds to similar stresses. In this study, we treated HeLa cells with ER stress inducers, thapsigargin (TG), tunicamycin (Tu) and Dithiothreitol (DTT), and found that only TG treatment caused Golgi fragmentation. TG induced Golgi fragmentation at a low dose and short time when UPR was undetectable, demonstrating that Golgi fragmentation occurs independently of ER stress. Further experiments demonstrated that TG induces Golgi fragmentation through elevated intracellular Ca2+ and protein kinase C (PKC) activity, which phosphorylates the Golgi stacking protein GRASP55. Significantly, activation of PKC with other activating or inflammatory agents, including Phorbol 12-myristate 13-acetate (PMA) and histamine, modulates the Golgi structure in a similar fashion. Hence, our study revealed a novel mechanism through which increased cytosolic Ca2+ modulates Golgi structure and function.

cell biology↗