Biology subjects

Ramamurthy, A.

Publications and source records attributed to Ramamurthy, A..

4 recordsLinked to original sources

bioRxiv2026

Coupled Cell-Intrinsic and Microenvironmental Heterogeneity Drives Divergent Trajectories in Castration-Resistant Prostate Cancer

Castration-resistant prostate cancer emerges from coupling between cell-intrinsic heterogeneity and microenvironmental constraints. Mechanistically dissecting this coupling, rather than either factor in isolation, is the central aim of this study. To systematically study the effect of intrinsic and extrinsic spatial axes on disease trajectories, we developed an integrated multiscale framework: a cellular signaling model (MHS) parameterized with TCGA genomic data from control, biochemical recurrence (BR), and treatment-resistant (TR) cohorts, coupled to a spatial agent-based model (ABM). Machine learning surrogates trained on the MHS model identified PTEN, MDM4, and AR as dominant intrinsic drivers, using SHAP-based feature ranking. Clinical validation via Kaplan-Meier and Cox regression across cBioPortal cohorts confirmed these rankings: AR alterations (median OS 20 vs. 86 months), PTEN loss (54 vs. 77 months), and MDM4 amplification (33 vs. 75 months) predicted poor overall survival outcomes independently. At the tissue scale, ABM simulations were run to study the effect of microenvironmental (cell-extrinsic) factors such as physical confinement, androgen uptake kinetics, and adhesion-motility strength, on disease progression. This spatiotemporal analysis revealed that identical genetic alterations produce varied selection outcomes depending on microenvironmental context. Extending this coupling logic to the individual patient level, we parameterized the MHS model using gene expression profiles from 14 patients in the EUREKA1 prospective registry. Patient-specific androgen sensitivity ratios, the ratio of net cell growth under high versus low testosterone, stratified patients by model-predicted androgen dependence without requiring longitudinal PSA observations and showed that PTEN deletion shifts the proliferative response toward androgen independence in a patient-specific magnitude set by the broader expression background. This provides a model-based route from genomic data at diagnosis to personalized prediction of ADT resistance risk. Together, these findings establish that CRPC emergence is an emergent property of the intrinsic-extrinsic coupling, that neither molecular nor spatial analyses in isolation can predict clinical trajectories, and that mechanistic integration of both is required for accurate patient stratification.

systems biology↗

bioRxiv2025

Analysis of 14q12 microdeletions reveals novel regulatory loci for the neurodevelopmental disorder-related gene, FOXG1

Up to 17% of neurodevelopmental disorders (NDDs) can be explained by pathogenic structural variants (SVs) that disrupt coding regions and elicit gene dosage defects. However, noncoding SVs which can perturb cis-regulatory elements (CREs) and downstream gene expression are understudied. In this study, we describe multiple 14q12 deletions downstream of NDD-related gene FOXG1 in individuals with overlapping phenotypes of FOXG1 haploinsufficiency. We show that deletion of a minimum region of overlap (MRO) reduced FOXG1 expression, disrupted CREs and altered FOXG1s native genomic interactions. Deleting the MRO did not fully eliminate FOXG1 expression, indicating that multiple CREs likely cooperate to regulate FOXG1 and would need to be deleted to completely prevent expression. The transcriptomic profiles of MRO loss overlap in part with FOXG1 loss, including direct FOXG1 targets, indicating converging molecular pathways. These findings expand the scope of FOXG1s complex regulatory region, and more broadly, of regulatory SVs in NDD susceptibility.

genetics↗

bioRxiv2023

Long-read sequencing and profiling of RNA-binding proteins reveals the pathogenic mechanism of aberrant splicing of an SCN1A poison exon in epilepsy

Pathogenic loss-of-function SCN1A variants cause a spectrum of seizure disorders. We previously identified variants in individuals with SCN1A-related epilepsy that fall in or near a poison exon (PE) in SCN1A intron 20 (20N). We hypothesized these variants lead to increased PE inclusion, which introduces a premature stop codon, and, therefore, reduced abundance of the full-length SCN1A transcript and Nav1.1 protein. We used a splicing reporter assay to interrogate PE inclusion in HEK293T cells. In addition, we used patient-specific induced pluripotent stem cells (iPSCs) differentiated into neurons to quantify 20N inclusion by long and short-read sequencing and Nav1.1 abundance by western blot. We performed RNA-antisense purification with mass spectrometry to identify RNA-binding proteins (RBPs) that could account for the aberrant PE splicing. We demonstrate that variants in/near 20N lead to increased 20N inclusion by long-read sequencing or splicing reporter assay and decreased Nav1.1 abundance. We also identified 28 RBPs that differentially interact with variant constructs compared to wild-type, including SRSF1 and HNRNPL. We propose a model whereby 20N variants disrupt RBP binding to splicing enhancers (SRSF1) and suppressors (HNRNPL), to favor PE inclusion. Overall, we demonstrate that SCN1A 20N variants cause haploinsufficiency and SCN1A-related epilepsies. This work provides insights into the complex control of RBP-mediated PE alternative splicing, with broader implications for PE discovery and identification of pathogenic PE variants in other genetic conditions.

genetics↗

bioRxiv2020

Paired motor cortex and spinal cord epidural stimulation strengthens sensorimotor connections and improves forelimb function after cervical spinal cord injury in rats.

Associative plasticity occurs when two stimuli converge on a common neural target. Previous efforts to promote associative plasticity have targeted cortex, with variable and moderate effects. In addition, the targeted circuits are inferred, rather than tested directly. In contrast, we sought to target the strong convergence between motor and sensory systems in the spinal cord. We developed spinal cord associative plasticity (SCAP), precisely timed pairing of motor cortex and dorsal spinal cord stimulations, to target this interaction. We tested the hypothesis that properly timed paired stimulation would strengthen the sensorimotor connections in the spinal cord and improve recovery after spinal cord injury (SCI). We tested physiological effects of paired stimulation, the pathways that mediate it, and its function in a preclinical trial. Subthreshold spinal cord stimulation strongly augmented motor cortex evoked muscle potentials at the time they were paired, but only when they arrived synchronously in the spinal cord. This paired stimulation effect depended on both cortical descending motor and spinal cord proprioceptive afferents; selective inactivation of either of these pathways fully abrogated the paired stimulation effect. SCAP, repetitive pairing of these pathways for 5 or 30 minutes in awake rats, increased spinal excitability for hours after pairing ended. To apply SCAP as therapy, we optimized the parameters to promote strong and long-lasting effects. This effect was just as strong in rats with cervical SCI as in uninjured rats, demonstrating that spared connections after moderate SCI were sufficient to support plasticity. In a blinded trial, rats received a moderate C4 contusive SCI. Ten days after injury, they were randomized to 30 minutes of SCAP each day for 10 days or sham stimulation. Rats with SCAP had significantly improved function on the primary outcome measure, a test of dexterity during manipulation of food, at 50 days after SCI. In addition, rats with SCAP had persistently stronger responses to cortical and spinal stimulation than sham stimulation rats, indicating a spinal locus of plasticity. SCAP rats had lasting improvements in H-reflex modulation. The groups had no difference in the rat grimace scale, a measure of pain. We conclude that SCAP strengthens sensorimotor connections within the spinal cord, resulting in improved reflex modulation and forelimb function after moderate SCI. Since both motor cortex and spinal cord stimulation are performed routinely in humans, this approach can be trialed in people with SCI or other disorders that damage sensorimotor connections and impair dexterity.

neuroscience↗