Biology subjects

Adivarahan, S.

Publications and source records attributed to Adivarahan, S..

4 recordsLinked to original sources

bioRxiv2026

SubCellSpace: Automated characterization of subcellular mRNA localization patterns in spatial transcriptomics

The localized translation of transcripts is a universal phenomenon across biological domains. Many examples of subcellular RNA localization and their functional importance have been described. However, these examples remain anecdotal, and a more systematic genome and cell-type-wide analysis is needed. Current spatial transcriptomic techniques can characterize hundreds to thousands of transcript species at subcellular resolutions, enabling the large-scale investigation of subcellular mRNA localization. Here we describe SubCellSpace, a computational framework to learn general representations of mRNA localization patterns. By embedding observed single-cell subcellular localization patterns (SLPs) to an interpretable latent space, SubCellSpace can detect and statistically infer the presence of SLPs, uncover colocalizing gene-pairs and characterize cellular heterogeneity for pattern-presentation. We benchmark SubCellSpace in both synthetic and real data, showing it can correctly detect previously described apical/basal polarized genes in the enterocytes of mouse small-intestine, as well as encode the enterocytes orientation. Additionally, we provide a tailored spatial transcriptomics validation dataset for benchmarking SLP identification based on transcripts previously described to be enriched near subcellular structures in HEK293T cells. We propose a practical and computationally-efficient classification workflow that automatically detects localized transcript species and quantifies their degree of patterning, while controlling false positive rates. Finally, we showcase SubCellSpace in both supervised and unsupervised settings, to either classify pre-determined SLPs or to explore spatial patterning without specifying pattern types a priori. Automated AI models such as SubCellSpace and their integration in spatial transcriptomics analysis workflows will help characterize previously undiscovered subcellular RNA localization phenomena, providing novel insights into post-transcriptional regulation mechanisms.

bioinformatics↗

bioRxiv2023

In vivo screening of tumor-hepatocyte interactions identifies Plexin B2 as a gatekeeper of liver metastasis

It is estimated that only 0.02% of disseminated tumor cells are able to seed overt metastases1. While this indicates the presence of environmental constraints to metastatic seeding, the landscape of host factors controlling this process remains largely unknown. Combining transposon technology2 and fluorescent niche labeling3, we developed an in vivo CRISPR activation screen to systematically investigate the influence of hepatocytes on metastatic seeding in the liver. Our approach enabled the identification of Plexin B2 as a critical host-derived regulator of metastasis. Plexin B2 upregulation in hepatocytes dramatically enhances grafting in colorectal and pancreatic cancer syngeneic models, and promotes seeding and survival of patient-derived organoids. Notably, ablation of Plexin B2 in hepatocytes prevents mesenchymal-to-epithelial transition of extravasated tumor cells and thereby almost entirely suppresses liver metastasis. We dissect a mechanism by which Plexin B2 interacts with class 4 semaphorins on tumor cells, activating Rac1 signaling and actin cytoskeleton remodeling, thereby promoting the acquisition of epithelial traits. Our findings highlight the essential role of signals from the liver parenchyma for the survival of disseminated tumor cells, prior to the establishment of a growth promoting niche. They further suggest that acquisition of epithelial traits is required for the adaptation of extravasated cells to their new tissue environment. Targeting of Plexin B2 on hepatocytes shields the liver from colonizing cells and thus presents an innovative therapeutic strategy for preventing metastasis. Finally, our screening technology, which evaluates host-derived extrinsic signals rather than tumor-intrinsic factors for their ability to promote metastatic seeding, is broadly applicable and lays a framework for the screening of environmental constraints on metastasis in other organs and cancer types.

cancer biology↗

bioRxiv2021

Single-molecule imaging suggests compact and spliceosome dependent organization of long introns

Intron removal from pre-mRNAs is a critical step in the processing of RNA polymerase II transcripts, required to create translation competent mRNAs. In humans, introns account for large portions of the pre-mRNA, with intronic sequences representing about 95% of most pre-mRNA. Intron length varies considerably; introns can be as short as a few to hundreds of thousands of nucleotides in length. How nascent long intronic RNA is organized during transcription to facilitate the communication between 5 and 3 splice-sites required for spliceosome assembly however is still poorly understood. Here, we use single-molecule fluorescent RNA in situ hybridization (smFISH) to investigate the spatial organization of co- and post-transcriptional long introns in cells. Using two long introns within the POLA1 pre-mRNA as a model, we show that introns are packaged into compact assemblies, and when fully transcribed, are organized in a looped conformation with their ends in proximity. This organization is observed for nascent and nucleoplasmic pre-mRNAs and requires spliceosome assembly, as disruption of U2 snRNP binding results in introns with separated 5 and 3 ends. Moreover, interrogating the spatial organization of partially transcribed co-transcriptional POLA1 intron 35 indicates that the 5 splice site is maintained proximal to the 3 splice site during transcription, supporting a model that 5 splice site tethering to the elongating polymerase might contribute to spliceosome assembly at long introns. Together, our study reveals details of intron and pre-mRNA organization in cells and provides a tool to investigate mechanisms of splicing for long introns.

cell biology↗

bioRxiv2017

Spatial organization of single mRNPs at different stages of the gene expression pathway

mRNAs form ribonucleoprotein complexes (mRNPs) by association with proteins that are crucial for mRNA metabolism. While the mRNP proteome has been well characterized, little is known about mRNP organization. Using a single molecule approach, we show that mRNA conformation changes depending on its cellular localization and translational state. Compared to nuclear mRNPs and lncRNPs, association with ribosomes decompacts individual mRNAs, while their sequestration into stress-granules leads to increased compaction. Moreover, translating mRNAs rarely show co-localizing 5 and 3 ends, indicating that mRNAs are either not translated in a closed-loop configuration, or that mRNA circularization is transient, suggesting that a stable closed-loop conformation is not a universal state for all translating mRNAs.\n\nOne Sentence SummarySingle mRNA studies in cells show RNA compaction changes depending on translational state, but mRNAs are not translated in closed-loop conformation.

molecular biology↗