Biology subjects

Muralidharan, S.

Publications and source records attributed to Muralidharan, S..

15 recordsLinked to original sources

bioRxiv2026

A System for Live Sorting of Neuronal Spiking Activity from Large-scale Recordings

Online monitoring of neuronal activity has tremendous value for closed-loop control in both experimental and clinical settings, yet established methods rely primarily on thresholded neural activity, rather than sorted single-neuron spikes. The recent introduction of large-scale electrophysiological tools has greatly expanded single-neuron recording capacity in animals and humans highlighting the need to sort spikes during data collection. Here, we describe a system for live spike sorting (LSS) populations of hundreds of neurons with millisecond-scale latency. Using neurophysiological recordings from macaque visual cortex with Neuropixels probes, we show that LSS closely replicates the temporal responses and tuning of single neurons obtained using offline sorting. We further show that decoding neural signals with LSS achieves the same performance as that obtained from offline sorting. Lastly, we demonstrate the capacity of LSS to enable closed-loop interventions based on the activity of specific neuronal subclasses.

neuroscience↗

bioRxiv2025

Rapid apical actin filament turnover is required for non-centrosomal microtubule organization in epithelium

Epithelial cells rely on the precise coordination of actin and microtubule cytoskeletons to maintain their polarized structure and function. Within polarized epithelial cells, microtubules form longitudinal non-centrosomal arrays essential for organelle positioning and facilitate directional cargo trafficking whereas the apical actin cytoskeleton supports cell shape and tissue architecture. This study investigates the interplay between disrupted apical actin dynamics and microtubule organization in vivo within Drosophila epithelial tissue. Loss of actin turnover promoting Cyclase-Associated Protein (CAP) results in the excessive accumulation of stable actin structures at the apical cortex. We show that accumulated apical actin sterically excludes microtubules and membrane-bound vesicles. Consequently, non-centrosomal microtubule-dependent processes are impaired, leading to nuclear mispositioning, disrupted apical cargo transport, and defective microvilli formation in CAP mutant cells. Our findings highlight that dense apical actin, due to impaired actin turnover catalyzed by CAP, disrupts the apical organization of non-centrosomal microtubules. This suggests that spatially regulated actin filament turnover is important for microtubule organization and sustaining the polarized functions of epithelial tissues.

cell biology↗

bioRxiv2024

Life stage impact on the human skin ecosystem: lipids and the microbial community

While research into gut-microbe interactions is common and advanced, with multiple defined impacts on human health, studies exploring the significance of skin-microbe interactions remain underrepresented. Skin is the largest human organ, has a vast surface area, and is inhabited by a plethora of microorganisms which metabolise sebaceous lipids. Sebaceous free fatty acids are metabolized into bioactive lipid mediators with immune-modulatory properties by skin-resident microbes, including Malassezia. Intriguingly, many of the same lipid mediators are also found on human skin, implying these compounds may have microbial or mixed microbial/human origin. To support this hypothesis, we isolated lipids and microbial DNA from the skin of prepubescent, adult, pre- and post-menopausal volunteers and performed correlational analyses using skin lipidomics and metagenomics to compare lipid mediator profiles and microbiome compositions on skin with either low or high sebaceous gland activity. We found that specific microbial taxonomies were positively and negatively correlated with skin lipid mediator species with high statistical significance. 2D in vitro co-cultures with Malassezia and keratinocytes also directly linked the production of specific lipid mediators, detected on healthy human skin, to secretion of immuno-stimulatory cytokines. Together, these findings further support the hypothesis that microbial-derived skin lipid mediators influence healthy skin homeostasis and skin disease development and progression, thereby spotlighting the relevance of the skin microbiomes footprint on human health.

microbiology↗

bioRxiv2023

Characterizing heterogeneity along EMT and metabolic axes in colorectal cancer reveals underlying consensus molecular subtype-specific trends

Colorectal cancer (CRC) is highly heterogenous with variable survival outcomes and therapeutic vulnerabilities. A commonly used classification system in CRC is the Consensus Molecular Subtypes (CMS) based on gene expression patterns. However, how these CMS categories connect to axes of phenotypic plasticity and heterogeneity remains unclear. Here, we analyze 101 bulk transcriptomic datasets, along with patient tumor samples from TCGA and single-cell RNA sequencing data, to evaluate the extent of variation among CMS subtypes across metabolic plasticity and EMT axes. Our results show that CMS2 and CMS3 samples were relatively more epithelial as compared to CMS1 and CMS4. Single-cell RNA-seq analysis of CMS1 revealed two subpopulations: one close to CMS4 (more mesenchymal) and the other closer to CMS2 or CMS3 (more epithelial), indicating a partial EMT-like behavior. Further, in our meta-analysis and in TCGA data, epithelial phenotype score was positively correlated with scores of glycolysis, OXPHOS and FAO pathways, while mesenchymal scores showed CMS subtype-specific associations with metabolic axes. PD-L1 activity scores, however, consistently correlated positively with mesenchymal signature ones and negatively with epithelial signature ones, across the four CMS categories. Together, our results quantify the patterns of two interconnected axes of phenotypic heterogeneity - EMT and metabolic reprogramming - at a CMS subtype level in CRC.

cancer biology↗

bioRxiv2023

PROTEOMICS OF HYPOTHERMIC ADAPTATION REVEALS THAT RBM3 ENHANCES MITOCHONDRIAL METABOLISM AND MUSCLE STEM-CELL DIFFERENTIATION

Adaptation to hypothermic stress is important for skeletal muscle cells, but a comprehensive knowledge of molecular mediators is lacking. We show that adaptation to mild hypothermia (320C) improves the ability of skeletal muscle myoblasts to differentiate into myotubes in vitro. We performed proteomic analysis of mouse myoblasts exposed to mild hypothermia for various time points and identified dynamic changes in mitochondrial metabolism and proteostasis. This revealed that RBM3, an RNA-binding protein, increases progressively with acute and chronic exposure to hypothermic stress, and is necessary for the enhanced differentiation upon hypothermic adaptation. We also demonstrate that overexpression of RBM3 at physiological temperatures is sufficient to (i) enhance mitochondrial metabolism as judged by a decrease in the AMPK energy-sensing pathway, (ii) increase levels of proteins associated with translation and increase levels of 4E-BP1 phosphorylation, (iii) increase stem cell markers (MyoD1, PAX7), and improve differentiation of myoblasts from both young and aged mice.

biochemistry↗

bioRxiv2022

PD-L1 activity is associated with partial EMT and metabolic reprogramming in carcinomas

Immune evasion and metabolic reprogramming are hallmarks of cancer progression often associated with a poor prognosis and frequently present significant challenge for cancer therapies. Recent studies have emphasized on the dynamic interaction between immunosuppression and the dysregulation of energy metabolism in modulating the tumor microenvironment to promote cancer aggressiveness. However, a pan-cancer association among these two hallmarks, and a potent common driver for them - Epithelial-Mesenchymal Transition (EMT) - remains to be done. Here, our meta-analysis across 184 publicly available transcriptomic datasets as well as The Cancer Genome Atlas (TCGA) data reveals that an enhanced PD-L1 activity signature along with other immune checkpoint markers correlate positively with a partial EMT and elevated glycolysis signature but a reduced OXPHOS signature in many carcinomas. These trends were also recapitulated in single-cell RNA-seq time-course EMT induction data across cell lines. Furthermore, across multiple cancer types, concurrent enrichment of glycolysis and PD-L1 results in worse outcomes in terms of overall survival as compared to enrichment for only PD-L1 activity or expression. Our results highlight potential functional synergy among these interconnected axes of cellular plasticity in enabling metastasis and/or multi-drug resistance in cancer.

cancer biology↗

bioRxiv2022

Investigating the mechanistic role of painful self-experience in emotional contagion: an effect of auto-conditioning?

Emotional contagion refers to the transmission of emotions from one conspecific to another. Previous research in rodents has demonstrated that the self-experience of footshocks enhances how much an observer is affected by the emotional state of a conspecific in pain or distress. We hypothesized auditory auto-conditioning to contribute to this enhancement: during the observers own experience of shocks, the animal associates its own audible nocifensive responses, i.e. its pain squeaks, with the negative affective state induced by the shock. When the animal later witnesses a cage mate receive shocks and hears it squeak, the previously strengthened connection between fear and squeaks could be a mechanism eliciting the enhanced fearful response in the observer. As hypothesized, in a first study, we found pre-exposure to shocks to increase freezing and 22 kHz vocalizations associated with distress upon the playback of pain squeaks. Freezing was also increased during the playbacks of phase-scrambled squeaks, but 22 kHz calls were more frequent during the playback of regular squeaks. Core to the notion of auto-conditioning is that the effect of pre-exposure is due to the pairing of a pain-state with hearing ones own pain squeaks. In a second study, we therefore compared the response to squeak playbacks after animals had been pre-exposed to pairings of a CO2 laser with a squeak playback against three control groups that were pre-exposed to the CO2 laser alone, to squeak playbacks alone or to neither of these conditions. We however could not find any differences in freezing or 22 kHz calls among all experimental groups. In summary, we demonstrate the sufficiency of pain squeaks to trigger fear in a way that critically depends on the nature of an animals prior experience and discuss why the pairing of a CO2 laser with pain squeaks cannot substitute footshock pre-exposure.

animal behavior and cognition↗

bioRxiv2022

Mapping phenotypic heterogeneity in melanoma onto the epithelial-hybrid-mesenchymal axis

Epithelial to mesenchymal transition (EMT) is a well-studied hallmark of epithelial-like cancers that is characterized by loss of epithelial markers and gain of mesenchymal markers. Interestingly, melanoma, which is derived from melanocytes of the skin, also undergo phenotypic plasticity toward mesenchymal-like phenotypes under the influence of various micro-environmental cues. Our study connects EMT to the phenomenon of de-differentiation (i.e., transition from proliferative to more invasive phenotypes) observed in melanoma cells during drug treatment. By analyzing 78 publicly available transcriptomic melanoma datasets, we found that de-differentiation in melanoma is accompanied by upregulation of mesenchymal genes, but not necessarily a concomitant loss of an epithelial program, suggesting a more "one-dimensional" EMT that leads to a hybrid epithelial/ mesenchymal phenotype. Samples lying in the hybrid epithelial/mesenchymal phenotype also correspond to the intermediate phenotypes in melanoma along the proliferative-invasive axis - neural crest and transitory ones. Interestingly, as melanoma cells progress along the invasive axis, the mesenchymal signature does not increase monotonically. Instead, we observe a peak in mesenchymal scores followed by a decline, as cells further de-differentiate. This biphasic response recapitulates the dynamics of melanocyte development, suggesting close interactions among genes controlling differentiation and mesenchymal programs in melanocytes. Similar trends were noted for metabolic changes often associated with EMT in carcinomas in which progression along mesenchymal axis correlates with the downregulation of oxidative phosphorylation, while largely maintaining glycolytic capacity. Overall, these results provide an explanation for how EMT and dedifferentiation axes overlap with respect to their transcriptional and metabolic programs in melanoma.

cancer biology↗

bioRxiv2022

Glypican-3 (GPC3) is associated with MCPyV-negative status and impaired outcome in Merkel Cell Carcinoma

BackgroundMerkel cell carcinoma (MCC) is an aggressive skin cancer, related to the Merkel Cell Polyomavirus (MCPyV) in 80% of cases. Immune checkpoint inhibitors provide sustained benefit in about half of MCC patients with advanced disease. Glypican-3 (GPC3) is an oncofetal tumor antigen that is an attractive target for chimeric antigen receptor T cell therapy due to its highly restricted expression on normal tissue and high prevalence in several solid tumors. GPC3 was previously found to be expressed in MCC but its association with tumor characteristics or prognosis has not been reported. ObjectivesTo investigate the expression of GPC3 in MCC by immunohistochemistry (IHC) and its association with tumor characteristics, MCPyV status, and patient outcome. MethodsThe GC33 antibody clone was validated for GPC3 IHC staining of tumor specimens in comparison to an established GPC3 IHC antibody. A tissue microarray of tumors collected from an ongoing cohort of MCC patients was stained for GPC3 by IHC using GC33 antibody. Association of GPC3 positivity with baseline characteristics, MCPyV status (quantitative PCR) and outcome (death from MCC, recurrence) were assessed by Fishers exact tests and Cox regression analysis. ResultsAmong 62 tumors from 59 patients, 42 samples (67.7%) were GPC3-positive. GPC3 expression was more frequently observed in females (p=0.048) and MCPyV-negative tumors (p=0.021). In the multivariate analysis, GPC3 expression was associated with increased death from disease (CSS) (hazard ratio [HR] 4.05, 95% CI 1.06-15.43), together with advanced age (HR 4.85, 95% CI 1.39-16.9) and male gender (HR 4.64, 95% CI 1.31-16.41). ConclusionsGPC3 expression is frequently expressed in MCC tumors, especially MCPyV-negative cases, and is associated with increased risk of death. The high prevalence of surface GPC3 makes it a putative drug target.

cancer biology↗

bioRxiv2022

E.PAGE: A curated database and enrichment tool to predict modules associated with gene-environment interactions

BackgroundThe purpose of this study was to manually and semi-automatically curate a database and develop an R package that will provide a comprehensive resource to uncover associations between biological processes and environmental factors in health and disease. We followed a two-step process to achieve the objectives of this study. First, we conducted a systematic review of existing gene expression datasets to identify those with integrated genomic and environmental factors. This enabled us to curate a comprehensive genomic-environmental database for four key environmental factors (smoking, diet, infections and toxic chemicals) associated with various autoimmune and chronic conditions. Second, we developed a statistical analysis package that allows users to interrogate the relationships between differentially expressed genes and environmental factors under different disease conditions. ResultsThe initial database search run on the Gene Expression Omnibus (GEO) and the Molecular Signature Database (MSigDB) retrieved a total of 90,018 articles. After title and abstract screening against pre-set criteria, a total of 186 studies were selected. From those, 243 individual sets of genes, or "gene modules", were obtained. We then curated a database containing four environmental factors, namely cigarette smoking, diet, infections and toxic chemicals, along with a total of 25789 genes that had an association with one or more of these gene modules. In six case studies, the database and statistical analysis package were then tested with lists of differentially expressed genes obtained from the published literature related to type 1 diabetes, rheumatoid arthritis, small cell lung cancer, COVID-19, cobalt exposure and smoking. On testing, we uncovered statistically enriched biological processes, which revealed pathways associated with environmental factors and the genes. ConclusionsA novel curated database and software tool is provided as an R Package. Users can enter a list of genes to discover associated environmental factors under various disease conditions.

genomics↗

bioRxiv2021

Quantifying the patterns of metabolic plasticity and heterogeneity along the epithelial-hybrid-mesenchymal spectrum in cancer

Cancer metastasis is the leading cause of cancer-related mortality and the process of Epithelial to Mesenchymal Transition (EMT) is crucial for cancer metastasis. Either a partial or complete EMT have been reported to influence the metabolic plasticity of cancer cells in terms of switching among oxidative phosphorylation, fatty acid oxidation and glycolysis pathways. However, a comprehensive analysis of these major metabolic pathways their associations with EMT across different cancers is lacking. Here, we analyse more than 180 cancer cell datasets and show diverse associations of these metabolic pathways with the EMT status of cancer cells. Our bulk data analysis shows that EMT generally positively correlates with glycolysis but negatively with oxidative phosphorylation and fatty acid metabolism. These correlations are also consistent at the level of their molecular master regulators, namely AMPK and HIF1. Yet, these associations are shown to not be universal. Analysis of singlecell data of EMT induction shows dynamic changes along the different axes of metabolic pathways, consistent with general trends seen in bulk samples. Together, our results reveal underlying patterns of metabolic plasticity and heterogeneity as cancer cells traverse through the epithelial-hybrid-mesenchymal spectrum of states.

cancer biology↗

bioRxiv2021

BOXR1030, an anti-GPC3 CAR with exogenous GOT2 expression, shows enhanced T cell metabolism and improved antitumor activity

PurposeThe solid tumor microenvironment (TME) drives T cell dysfunction and inhibits the effectiveness of immunotherapies such as chimeric antigen receptor-based T cell (CAR T) cells. Early data has shown that modulation of T cell metabolism can improve intratumoral T cell function in preclinical models. Experimental DesignWe evaluated GPC3 expression in human normal and tumor tissue specimens. We developed and evaluated BOXR1030, a novel CAR T therapeutic co-expressing glypican-3 (GPC3)-targeted CAR and exogenous glutamic-oxaloacetic transaminase 2 (GOT2) in terms of CAR T cell function both in vitro and in vivo. ResultsExpression of tumor antigen GPC3 was observed by immunohistochemical staining in tumor biopsies from hepatocellular carcinoma, liposarcoma, squamous lung cancer, and Merkel cell carcinoma patients. Compared to control GPC3 CAR alone, BOXR1030 (GPC3-targeted CAR T cell that co-expressed GOT2) demonstrated superior in vivo efficacy in aggressive solid tumor xenograft models, and showed favorable attributes in vitro including an enhanced cytokine production profile, a less-differentiated T cell phenotype with lower expression of stress and exhaustion markers, an enhanced metabolic profile and increased proliferation in TME-like conditions. ConclusionsTogether, these results demonstrated that co-expression of GOT2 can substantially improve the overall antitumor activity of CAR T cells by inducing broad changes in cellular function and phenotype. These data show that BOXR1030 is an attractive approach to targeting select solid tumors. To this end, BOXR1030 will be explored in the clinic to assess safety, dose- finding, and preliminary efficacy (NCT05120271).

cancer biology↗

bioRxiv2021

A mechanistic model captures the emergence and implications of non-genetic heterogeneity and reversible drug resistance in ER+ breast cancer cells

Resistance to anti-estrogen therapy is an unsolved clinical challenge in successfully treating ER+ breast cancer patients. Acquisition of mutations can confer heritable resistance to cancer cells, enabling their clonal selection to establish a drug-resistant population. Recent studies have demonstrated that cells can tolerate drug treatment without any genetic alterations too; however, the mechanisms and dynamics of such non-genetic adaptation remain elusive. Here, we investigate coupled dynamics of epithelial-mesenchymal transition (EMT) in breast cancer cells and emergence of reversible drug resistance. Our mechanism-based model for the underlying regulatory network reveals that these two axes can drive one another, thus conferring bidirectional plasticity. This network can also enable non-genetic heterogeneity in a population of cells by allowing for six co-existing phenotypes: epithelial-sensitive, mesenchymal-resistant, hybrid E/M-sensitive, hybrid E/M-resistant, mesenchymal-sensitive and epithelial-resistant, with the first two ones being most dominant. Next, in a population dynamics framework, we exemplify the implications of phenotypic plasticity (both drug-induced and intrinsic stochastic switching) and/or non-genetic heterogeneity in promoting population survival in a mixture of sensitive and resistant cells, even in the absence of any cell-cell cooperation. Finally, we propose the potential therapeutic use of MET (mesenchymal-epithelial transition) inducers besides canonical anti-estrogen therapy to limit the emergence of reversible drug resistance. Our results offer mechanistic insights into empirical observations on EMT and drug resistance and illustrate how such dynamical insights can be exploited for better therapeutic designs.

cancer biology↗

bioRxiv2021

Destabilization of β-cell FIT2 by saturated fatty acids contribute to ER stress and diabetes

Western type diets are linked to obesity and diabetes partly because of their high saturated fatty acid (SFA) content. We found that SFAs, but not unsaturated fatty acids (USFAs), reduced the number of lipid droplets (LDs) within pancreatic {beta}-cells. Mechanistically, SFAs but not USFAs disabled LD biogenesis by inducing palmitoylation and subsequent ERAD-C mediated degradation of LD formation protein, Fat storage-Inducing Transmembrane protein 2 (FIT2). Targeted ablation of FIT2 reduced {beta}-cell LD numbers, lowered {beta}-cell ATP levels, reduced Ca2+ signaling, downregulated {beta}-cell transcription factors (RNA sequencing analysis), and exacerbated diet-induced diabetes in mice. Subsequent mass spectrometry studies revealed increased C16:0 ceramide accumulation in islets of mice lacking {beta}-cell FIT2 under lipotoxic conditions. Inhibition of ceramide synthases ameliorated the enhanced ER stress. Overexpression of FIT2 increased number of intracellular LDs and rescued SFA-induced ER-stress and apoptosis thereby highlighting the protective role of FIT2 and LDs against {beta}-cell lipotoxicity and diet-induced diabetes.

biochemistry↗

bioRxiv2019

Long acyl chain ceramides govern cholesterol and cytoskeleton dependence of membrane outer leaflet dynamics

The cellular plasma membrane composition and organization is crucial for the regulation of biological processes. Based on our earlier work showing that the same lipid probe, DiI, exhibits different dynamics in CHO-K1 and RBL-2H3 cells, we investigate the molecular factors that govern these differences. First, we determined that the cytoskeleton-interacting Immunoglobulin E receptor (Fc{varepsilon}RI), which is abundant in RBL-2H3 but not in CHO-K1 cells, is not responsible for the DiI confinement found in RBL-2H3 cells. Second, lipid mass spectrometry of the plasma membrane of the two cells indicated differences in ceramide content, especially with long and very long acyl chains (C16 to C24). We, therefore, measure membrane dynamics by imaging total internal reflection fluorescence correlation spectroscopy in dependence on these ceramides. Our results show that C24 and C16 saturated ceramides uniquely alter the membrane dynamics by promoting the formation of cholesterol-independent domains and by elevating inter-leaflet coupling.

biophysics↗