Biology subjects

Venkatraman, S.

Publications and source records attributed to Venkatraman, S..

5 recordsLinked to original sources

bioRxiv2025

Analysis of menstrual effluent uncovers endometriosis-specific cell populations and impaired cellular pathway processes

Endometriosis is a chronic gynecological disease affecting 1 in 10 reproductive-aged women and is characterized by the ectopic presence of endometrial tissue outside the uterus. The leading hypothesis for disease etiology is via the reflux of menstrual effluent (ME) into the peritoneal cavity. ME is a complex mixture of viable endometrial tissue, proteins, and immune cells which serve specialized functions during menstruation to support and repair the endometrium. We hypothesized shifts in the subpopulations of immune cells present during retrograde menstruation may alter the microenvironment of the peritoneal cavity leading to a favorable environment for uterine tissue attachment and survival of endometriotic lesions. Menstrual effluent collected on days 1 and 2 of menstruation identified from women with endometriosis distinct morphological features, increased subpopulations of aged neutrophils, increased anti-inflammatory macrophages, and overall impaired clearance pathways that hijack endometrial clearance likely contributing to the development and progression of endometriosis.

immunology↗

bioRxiv2025

Potassium channels mediate the inhibitory effect of exosomes on anti-tumor immunity in head and neck cancer

Head and neck squamous cell carcinomas (HNSCC) are aggressive cancers with a relatively low response rate to immunotherapy. Anti-tumor immune responses rely on cytotoxic T and NK cells infiltrating the tumor microenvironment to eliminate cancer cells. However, tumors activate multiple mechanisms to evade these responses. Tumor-derived small extracellular vesicles, also known as exosomes, reshape the tumor microenvironment by impairing cytotoxic T and NK cell function, promoting immune escape and metastasis. Transcriptomic analysis of healthy donor peripheral blood mononuclear cells (PBMCs) exposed to exosomes from HPV-negative HNSCC patient primary cancer cells revealed reduced cytotoxic cells and suppressed immune responses including cytotoxicity, chemokine production, and NK and T cell functions. Bead-based multiplex immunoassay showed that HNSCC-derived exosomes inhibited the release of effector cytokines (IL-2, TNF-, IFN-{gamma}) and cytotoxic molecules from activated CD8 T cells. While ion channels regulate Ca{superscript 2}-dependent cytotoxicity and cytokine production and release, their role in exosome-mediated immune suppression is unexplored. We found that tumor-derived exosomes selectively inhibit KCa3.1 channel activity in CD8 T cells by downregulating calmodulin, ultimately impairing Ca{superscript 2} signaling and IFN-{gamma} release. This study identifies a novel mechanism of exosome-mediated immunosuppression, positioning KCa3.1 as a promising therapeutic target to enhance immune surveillance and immunotherapy response in HNSCC.

immunology↗

bioRxiv2022

Time series transcriptome analysis uncovers regulatory networks and a role for the circadian clock in the Drosophila melanogaster female's response to Sex Peptide

Sex Peptide, a seminal fluid protein of D. melanogaster males, has been described as driving a virgin-to-mated switch in females, through eliciting an array of responses, including increased egg laying, activity and food intake and a decreased re-mating rate. While it is known that Sex Peptide achieves this, at least in part, by altering neuronal signaling in females, the identity of key molecular regulators that act downstream of Sex Peptide is not known. Here, we used a high-resolution time series RNA-sequencing dataset of female heads at 10 time points within the first 24 hours after mating to investigate the genetic architecture, at the gene- and exon-level, of the females response to Sex Peptide. We find that Sex Peptide is not essential to trigger a virgin-to-mated transcriptional switch, which involves changes in a metabolic gene regulatory network. However, Sex Peptide is needed to maintain and diversify metabolic changes and to trigger changes in a neuronal gene regulatory network. We further find that Sex Peptide might interact with the females circadian clock to orchestrate transcriptional changes across different regulatory networks. That a male seminal fluid protein can alter a females rhythmic gene expression has implications for our understanding of both reproductive and circadian behaviors.

genomics↗

bioRxiv2021

An Empirical Bayes Approach to Estimating Dynamic Models of Co-regulated Gene Expression

Time-course gene expression datasets provide insight into the dynamics of complex biological processes, such as immune response and organ development. It is of interest to identify genes with similar temporal expression patterns because such genes are often biologically related. However, this task is challenging due to the high dimensionality of these datasets and the nonlinearity of gene expression time dynamics. We propose an empirical Bayes approach to estimating ordinary differential equation (ODE) models of gene expression, from which we derive a similarity metric between genes called the Bayesian lead-lag R2 (LLR2). Importantly, the calculation of the LLR2 leverages biological databases that document known interactions amongst genes; this information is automatically used to define informative prior distributions on the ODE models parameters. As a result, the LLR2 is a biologically-informed metric that can be used to identify clusters or networks of functionally-related genes with co-moving or time-delayed expression patterns. We then derive data-driven shrinkage parameters from Steins unbiased risk estimate that optimally balance the ODE models fit to both data and external biological information. Using real gene expression data, we demonstrate that our methodology allows us to recover interpretable gene clusters and sparse networks. These results reveal new insights about the dynamics of biological systems.

genomics↗

bioRxiv2021

Next generation vaccine platform: polymersomes as stable nanocarriers for a highly immunogenic and durable SARS-CoV-2 spike protein subunit vaccine

Multiple successful vaccines against SARS-CoV-2 are urgently needed to address the ongoing Covid-19 pandemic. In the present work, we describe a subunit vaccine based on the SARS-CoV-2 spike protein co-administered with CpG adjuvant. To enhance the immunogenicity of our formulation, both antigen and adjuvant were encapsulated with our proprietary artificial cell membrane (ACM) polymersome technology. Structurally, ACM polymersomes are self-assembling nanoscale vesicles made up of an amphiphilic block copolymer comprising of polybutadiene-b-polyethylene glycol and a cationic lipid 1,2-dioleoyl-3-trimethylammonium-propane. Functionally, ACM polymersomes serve as delivery vehicles that are efficiently taken up by dendritic cells, which are key initiators of the adaptive immune response. Two doses of our formulation elicit robust neutralizing titers in C57BL/6 mice that persist at least 40 days. Furthermore, we confirm the presence of memory CD4+ and CD8+ T cells that produce Th1 cytokines. This study is an important step towards the development of an efficacious vaccine in humans.

immunology↗