Biology subjects

Vaidya, S.

Publications and source records attributed to Vaidya, S..

9 recordsLinked to original sources

bioRxiv2024

TEAD-targeting small molecules induce a cofactor switch to regulate the Hippo pathway

TEAD proteins are the main transcriptional effectors of the Hippo signaling pathway and a pharmacological target in oncology. Most TEAD-targeting small molecules act by disrupting interaction with the oncogenic transcriptional activators YAP and TAZ. Here, we describe an alternative mechanism for TEAD lipid pocket binding molecules. We report that select sulfonamide-containing compounds promote TEAD interaction with the transcriptional repressor VGLL4 to induce a small molecule-mediated cofactor switch from YAP to VGLL4. Chemically induced VGLL4-TEAD complexes counteract YAP activity at chromatin to repress pro-growth gene networks, including genes involved in cellular proliferation and mechanosignaling. VGLL4 is required for an anti-proliferative response to these select compounds, and genetic deletion of VGLL4 causes resistance to these molecules in vitro and in vivo. Our data reveal a category of molecules that facilitate the repressive VGLL4-TEAD interaction and open up new understandings for curbing the oncogenic activity of Hippo pathway deregulation.

cancer biology↗

bioRxiv2024

Comparative Analysis of Commercial Single-Cell RNA Sequencing Technologies

This study evaluates ten commercially available single-cell RNA sequencing (scRNA-seq) approaches across four technology groups: Emulsion-based kits from 10x Genomics and Fluent Biosciences; Microwell-based kits from Becton Dickinson, Honeycomb Technologies and Singerlon Technologies; Combinatorial-indexing kits from Parse Biosciences and Scale Biosciences; and a Matrigel-based kit from Scipio Biosciences. Peripheral blood mononuclear cells (PBMCs) from a single donor were used to assess analytical performance. Key features such as sample compatibility, cost, and experimental duration were also compared. Notably, superior analytical performance was demonstrated by the Chromium Fixed RNA Profiling kit from 10x Genomics, which uniquely features probe hybridization for transcript detection. Additionally, the Rhapsody WTA kit from Becton Dickinson provided a cost-effective balance of performance and expense per cell. With a rich dataset of 218,154 cells, this work provides a basis for differentiating commercial scRNA-seq technologies, which is intended to facilitate the effective application and further methodological development of single cell transcriptomics.

molecular biology↗

bioRxiv2024

Comparative Analysis of DNA Structural Parameters and the Corresponding Computational Tools to Differentiate Regulatory DNA Motifs and Promoters

Analyzing and distinguishing functionally distinct DNA regions is crucial for various applications, including predicting DNA motifs and promoters, and exploring the mechanisms of gene expression regulation in disease conditions. Our understanding of mammalian promoters, particularly those associated with differentially expressed genes (DEGs), particularly remains limited. However, existing methods for such analysis require refinement. Despite the value of DNA Structural Parameters (DSPs), users often struggle to objectively select parameters and tools, especially given the limited options available. This study addresses this challenge by thoroughly investigating DSP-tool combinations - particularly the local structural parameters that can be analyzed via web-interfaces, with a goal to discern human DNA motifs and promoters. What sets this study apart are the following aspects: a) examination of disease-associated promoters; b) attention to regulatory specific DNA motifs; c) compilation and comparison of all publicly available online tools and parameters for analyzing DNA structures, and test all available DSP-tool combinations. Through the execution of over half a million queries, the study identified DSP-tool combinations that consistently outperformed others in differentiating DNA sequences across various types of analyses. Notably, the propeller twist emerged as a standout DSP, while DNAshape, complemented by DNAshapeR scripts, demonstrated exceptional performance among the tools across four distinct types of analyses: testing motifs, sequences post motif insertion, comparing promoters with control sequences, and analyzing promoters of genes either up- or down-regulated under disease conditions. Significant alterations were observed in the values of multiple DSPs for 100-nucleotide-long promoter and control sequences following the insertion of single motifs such as triplex target sites (TTS), quadruplex-forming structural motifs (QSFM), and transcription factor binding sites (TFBS). However, no single combination proved universally successful. For instance, when analyzing promoters associated with differential gene expression, different combinations proved effective across various human diseases. These findings provide valuable insights for making informed selections among available options for sequence-based queries.

bioinformatics↗

bioRxiv2022

Dkk1 inhibition normalizes limb phenotypes in a mouse model of Fzd2 associated omodysplasia Robinow syndromes

FRIZZLED-2 (FZD2) is a transmembrane Wnt ligand receptor. We previously identified a pathogenic human FZD2 variant, encoding for a protein with a premature stop and loss of 17 amino acids. This includes a portion of the consensus DISHEVELLED binding sequence required for Wnt signal transduction. Patients with this variant exhibited FZD2-associated autosomal dominant Robinow Syndrome. To model this variant, we utilized zygote microinjection and i-GONAD-based CRISPR/Cas9-mediated genome editing to generate an allelic series in the mouse. Embryos mosaic for humanized Fzd2W553* knock-in exhibited cleft palate and shortened limbs, consistent with FZD2W548* patient phenotypes. We also generated two germline mouse alleles with small deletions, Fzd2D3 and Fzd2D4. Homozygotes for each allele survive embryonic development at normal ratios but exhibit a highly penetrant cleft palate phenotype, shortened limbs compared to wild-type and perinatal lethality. Fzd2D4 craniofacial tissues indicated decreased canonical WNT signaling. In utero treatment with IIIC3a (DKK inhibitor) normalized the limb lengths in Fzd2D4 homozygotes. The in vivo replication represents an approach to further investigate the mechanism of FZD2 phenotypes and validates the utility of CRISPR knock-in mice as a tool for demonstrating pathogenicity of human genetic variants. We also present evidence for a potential therapeutic intervention.

developmental biology↗

bioRxiv2021

Multispecies phase diagram reveals biophysical principles of bacterial biofilm architectures

Bacterial biofilms are among the most abundant multicellular structures on Earth and play essential roles in a wide range of ecological, medical, and industrial processes. However, general principles that govern the emergence of biofilm architecture across different species remain unknown. Here, we combine experiments, simulations and statistical analysis to identify shared biophysical mechanisms that determine biofilm architecture development at the single-cell level, for the species Vibrio cholerae, Escherichia coli, Salmonella enterica, and Pseudomonas aeruginosa. Our data-driven analysis reveals that despite the many molecular differences between these species, the biofilm architecture differences can be described by only two control parameters: cellular aspect ratio and cell density. Further experiments using single-species mutants for which the cell aspect ratio and the cell density are systematically varied, and mechanistic simulations, show that tuning these two control parameters reproduces biofilm architectures of different species. Altogether, our results show that early-stage biofilm architecture is determined by mechanical cell-cell interactions which are conserved across different species and, therefore, provide a unifying understanding of biofilm architecture development.

microbiology↗

bioRxiv2020

Drug screening linked to molecular profiling identifies novel dependencies in patient-derived primary cultures of paediatric high grade glioma and DIPG

Paediatric high grade glioma and diffuse midline glioma (including DIPG) are comprised of multiple biological and clinical subgroups, the majority of which urgently require novel therapies. Patient-derived in vitro primary cell cultures represent potentially useful tools for mechanistic and preclinical investigation based upon their retention of key features of tumour subgroups under experimental conditions amenable to high-throughput approaches. We present 17 novel primary cultures derived from patients in London, Dublin and Belfast, and together with cultures established or shared from Barcelona, Brisbane, Rome and Stanford, assembled a panel of 52 models under 2D (laminin matrix) and/or 3D (neurospheres) conditions, fully credentialed by phenotypic and molecular comparison to the original tumour sample (methylation BeadArray, panel/exome sequencing, RNAseq). In screening a subset of these against a panel of ~400 approved chemotherapeutics and small molecules, we identified specific dependencies associated with tumour subgroups and/or specific molecular markers. These included MYCN-amplified cells and ATM/DNA-PK inhibitors, and DIPGs with PPM1D activating truncating mutations and inhibitors of MDM2 or PARP1. Specific mutations in PDGFRA were found to confer sensitivity to a range of RTK inhibitors, though not all such mutations conferred sensitivity to targeted agents. Notably, dual PDGFRA/FGFR and downstream pathway MEK inhibitors showed profound effects against both PDGFRA-sensitising mutant and FGFR1-dependent non-brainstem pHGG and DIPG. In total, 85% cells were found to have at least one drug screening hit in short term assays linked to the underlying biology of the patients tumour, providing a rational approach for individualised clinical translation.

cancer biology↗

bioRxiv2019

BiofilmQ, a software tool for quantitative image analysis of microbial biofilm communities

Biofilms are now considered to be the most abundant form of microbial life on Earth, playing critical roles in biogeochemical cycles, agriculture, and health care. Phenotypic and genotypic variations in biofilms generally occur in three-dimensional space and time, and biofilms are therefore often investigated using microscopy. However, the quantitative analysis of microscopy images presents a key obstacle in phenotyping biofilm communities and single-cell heterogeneity inside biofilms. Here, we present BiofilmQ, a comprehensive image cytometry software tool for the automated high-throughput quantification and visualization of 3D and 2D community properties in space and time. Using BiofilmQ does not require prior knowledge of programming or image processing and provides a user-friendly graphical user interface, resulting in editable publication-quality figures. BiofilmQ is designed for handling fluorescence images of any spatially structured microbial community and growth geometry, including microscopic, mesoscopic, macroscopic colonies and aggregates, as well as bacterial biofilms in the context of eukaryotic hosts.

microbiology↗

bioRxiv2019

Ontogeny and expression profiles of steroid hormone receptors in a mouse model of endometriosis

Endometriosis is a chronic incurable disorder of unknown etiology affecting a large proportion of women in reproductive age. In order to understand the pathogenesis and preclinical testing of drugs,animal models that recapitulate the key features of the disorder are highly desirous. Herein, we describe the ontogeny of the ectopic endometrial lesion in a mouse model where uterine tissue was ligated to the intestinal mesentery and the animals were followed up from day 5 to day 60 post-surgery. Out of 60 animals that underwent surgery, 58 developed endometriosis using this strategy. Most lesions were pale, fluid filled while red lesions were seen in ~10% of animals. Histologically, in most animals there was one large cystic gland with well differentiated epithelium, in 13% of animals there was mixed phenotype (well and poorly differentiated). There was extensive stromal compaction and increased number of macrophages in ectopic lesions. During the course of endometriosis, there was an increase in number of PCNA positive epithelial and stromal cells. The epithelial cells at all the time point were cytokeratin positive and the stroma was vimentin positive. However, at day 30 and 60, the stromal cells were also cytokeratin positive. The mRNA levels of estrogen receptors Esr1 and Gper1 were reduced while those of Esr2 were elevated as compared to normal endometrium, the levels of progesterone receptor (Pgr) were found to be downregulated in ectopic lesions as compared to control. However, these differences were not statistically significant due to high biological variability. Low abundance of Cyp19a1 transcripts (aromatase gene) were only detected in the ectopic endometrium. Immunohistochemically, the expression of ER and ER{beta} was significantly reduced only in stromal cells; the epithelial cell staining was maintained. GPER1 and PR immunoreactivity was significantly low in both epithelial and stromal cells. The immunostaining of all the steroid receptors was highly heterogeneous in the ectopic tissues with some areas of sections had stained intensely while others had negligible staining. We propose that temporal and spatial difference in the expression of steroid hormone receptors during the course of endometriosis development coupled with micro-heterogeneity may alter the effectiveness of steroid hormone analogues resulting in variable outcomes and often failure of therapy.

pathology↗

bioRxiv2017

Novel Locus Influencing Retinal Venular Tortuosity Is Also Associated With Risk Of Coronary Artery Disease

Structural variation in retinal blood vessels is associated with global vascular health in humans and may provide a readily accessible indicator of several diseases of vascular origin. Increasing evidence suggests variation in retinal vasculature is highly heritable. This study aimed to identify genetic determinants of retinal vascular traits. We reported a meta-analysis of genome-wide association studies (GWAS) for quantitative retinal vascular traits derived using semi-automatic image analysis of digital retinal photographs from the Genetics of Diabetes Audit and Research in Tayside (GoDARTS) (n=1736) and the Orkney Complex Disease Study (ORCADES) (n=1358) cohorts. We identified a novel genome-wide significant locus at 19q13 (ACTN4/CAPN12) for retinal venular tortuosity (TortV), and one at 13q34 (COL4A2) for retinal arteriolar tortuosity (TortA); these two loci were subsequently confirmed in three independent cohorts (n=1413). In the combined analysis in ACTN4/CAPN12 the lead single nucleotide polymorphism (SNP) was rs1808382 (n=4507; Beta=-0.109; standard error (SE) =0.015; P=2.39x10-13) and in COL4A2 it was rs7991229 (n=4507; Beta=0.103; SE=0.015; P=4.66x10-12). Notably, the ACTN4/CAPN12 locus associated with retinal TortV is also associated with coronary artery disease and heart rate. Our findings demonstrate the contribution of genetics in retinal tortuosity traits, and provide new insights into cardiovascular diseases.\n\nAuthor SummaryRetinal vascular features are associated with wide range of diseases related to vascular health and provide an opportunity to understand early structural changes in vasculature which may help to predict disease risk. Emerging evidence indicates that retinal tortuosity traits are both associated with vascular health and highly heritable. However, the genetic architecture of retinal vascular tortuosity has not been investigated. We therefore performed a genome-wide association study on retinal arteriolar tortuosity (TortA) and retinal venular tortuosity trait (TortV) using data from two independent discovery cohorts of 3094 individuals of European-heritage. We found a novel associations at 19q13 (ACTN4/CAPN12) for TortV, and one at 13q34 (COL4A2) for TortA at discovery stage and validated in three independent cohorts. A significant association was subsequently found between lead SNPs at 19q13 and coronary artery disease, cardiovascular vascular risk factors and heart rate. We also performed genome-wide association studies for retinal vascular calibres and optic disc radius (ODradius) and replicated previously reported locus at 10q21.3 for ODradius. Our findings highlight genetic impacts on retinal venular tortuosity and it is association with cardiovascular disease. This may provide a molecular pathophysiological foundation for use of retinal vascular traits as biomarkers for cardiovascular diseases.

genomics↗