Biology subjects

Sampath, D.

Publications and source records attributed to Sampath, D..

5 recordsLinked to original sources

bioRxiv2025

Loss of white matter tracts and persistent microglial activation in the chronic phase of ischemic stroke in female rats and the effect of miR-20a-3p treatment

Our previous studies showed that intravenous injections of the small non-coding RNA mir-20a-3p is neuroprotective for stroke in the acute phase and attenuates long-term cognitive impairment in middle-aged female rats. In this study, we evaluated postmortem brain pathology at 100+d after stroke in a set of behaviorally characterized animals. This included Sham (no stroke) controls or stroke animals that received either mir20a-3p at 4h, 24h and 70d iv post stroke (MCAo+mir20a-3p) or a scrambled oligo (MCAo+Scr). Brain volumetric features were analyzed with T2 weighted and Diffusion Tensor magnetic resonance imaging (MRI) followed by histological analysis. Principal component analysis of Fractional Anisotropy (FA)-diffusion tensor MRI measures showed that MCAo+Scr and MCAo+mir20a-3p groups differed significantly in the volume of white matter but not gray matter. Weil myelin-stained sections confirmed decreased volume of the corpus callosum, internal capsule and the anterior commissure in the ischemic hemisphere of MCAo+Scr animals compared to the non-ischemic hemisphere, while sham and MCAo+Mir-20a-3p showed no hemispheric asymmetries. The MCAo+Scr group also exhibited asymmetry in hemisphere and lateral ventricle volumes, with ventricular enlargement in the ischemic hemisphere as compared to the non-ischemic hemisphere. The numbers of microglia were significantly elevated in white matter tracts in the MCAo+Scr group, with a trend towards increased myelin phagocytic microglia in these tracts. Regression analysis indicated that performance on an episodic memory test (novel object recognition test; NORT) was associated with decreased white matter volume and increased microglial numbers. These data support the hypothesis that stroke-induced cognitive impairment is accompanied by white matter attrition and persistent microglial activation and is consistent with reports that cognitive deterioration resulting from vascular diseases, such as stroke, is associated with secondary neurodegeneration in regions distal from the initial infarction.

neuroscience↗

bioRxiv2024

Long-read single-cell RNA sequencing enables the study of cancer subclone-specific genotype and phenotype in chronic lymphocytic leukemia

Brutons tyrosine kinase (BTK) inhibitors are effective for the treatment of chronic lymphocytic leukemia (CLL) due to BTKs role in B cell survival and proliferation. Treatment resistance is most commonly caused by the emergence of the hallmark BTKC481S mutation that inhibits drug binding. In this study, we aimed to investigate whether the presence of additional CLL driver mutations in cancer subclones harboring a BTKC481S mutation accelerates subclone expansion. In addition, we sought to determine whether BTK-mutated subclones exhibit distinct transcriptomic behavior when compared to other cancer subclones. To achieve these goals, we employ our recently published method (Qiao et al. 2024) that combines bulk DNA sequencing and single-cell RNA sequencing (scRNA-seq) data to genotype individual cells for the presence or absence of subclone-defining mutations. While the most common approach for scRNA-seq includes short-read sequencing, transcript coverage is limited due to the vast majority of the reads being concentrated at the priming end of the transcript. Here, we utilized MAS-seq, a long-read scRNAseq technology, to substantially increase transcript coverage across the entire length of the transcripts and expand the set of informative mutations to link cells to cancer subclones in six CLL patients who acquired BTKC481S mutations during BTK inhibitor treatment. We found that BTK-mutated subclones often acquire additional mutations in CLL driver genes, leading to faster subclone proliferation. When examining subclone-specific gene expression, we found that in one patient, BTK-mutated subclones are transcriptionally distinct from the rest of the malignant B cell population with an overexpression of CLL-relevant genes.

genomics↗

bioRxiv2021

RTK-dependent inducible degradation of mutant PI3K alpha drives GDC-0077 (Inavolisib) efficacy

PIK3CA is one of the most frequently mutated oncogenes; the p110 protein it encodes plays a central role in tumor cell proliferation and survival. Small molecule inhibitors targeting the PI3K p110 catalytic subunit have entered clinical trials, with early-phase GDC-0077 (Inavolisib) studies showing anti-tumor activity and a manageable safety profile in patients with PIK3CA-mutant, hormone receptor-positive breast cancer as a single agent or in combination therapy. Despite this, preclinical studies have shown that PI3K pathway inhibition releases negative feedback and activates receptor tyrosine kinase signaling, reengaging the pathway and attenuating drug activity. Here we discover that GDC-0077 and taselisib more potently inhibit mutant PI3K pathway signaling and cell viability through unique HER2-dependent degradation. Both are more effective than other PI3K inhibitors at maintaining prolonged pathway suppression, resulting in enhanced apoptosis and greater efficacy. This unique mechanism against mutant p110 reveals a new strategy for creating inhibitors that specifically target mutant tumors with selective degradation of the mutant oncoprotein and also provide a strong rationale for pursuing PI3K degraders in patients with HER2-positive breast cancer.

cancer biology↗

bioRxiv2020

HDAC1 regulates the chromatin landscape to establish transcriptional dependencies in chronic lymphocytic leukemia

HDAC1 is a key regulator of gene expression in cancer. We identified a critical role for HDAC1 in establishing the transcriptional dependencies essential for survival in chronic lymphocytic leukemia (CLL) by profiling HDAC1 with BRD4, H3K27Ac superenhancers, H4K9Ac, chromatin accessibility signatures, Pol2 measurements and expression signatures to generate a regulatory chromatin landscape. Superenhancers marked by high levels of acetylation and BRD4 paradoxically also recruited the highest levels of HDAC1. HDAC inhibition poisoned transcription at these loci to selectively disrupt B-cell transcription factors and B-cell receptor signaling. HDAC1 was also recruited genome-wide at promoters without superenhancers to repress expression; HDAC inhibition induces these genes which include key microRNA networks that reciprocally downregulate CLL specific survival and driver genes. Our work provides a compelling rationale for profiling HDAC1 across cancers to characterize its role in driving the transcriptional dysregulation that is a hallmark of most cancers and develop epigenetic therapeutic strategies. SignificanceOur work definitively establishes the composition of the regulatory chromatin that enables HDAC1 to function as an activator and repressor at distinct target genes within the same tumor to drive transcriptional dysregulation and allow the expression of B cell specific signaling and survival networks that are critical for survival.

cancer biology↗

bioRxiv2019

Identification and comparison of genes differentially regulated by transcription factors and miRNAs

Transcription factors and microRNAs (miRNA) both play a critical role in gene regulation and in the development of many diseases such as cancer. Understanding how transcription factors and miRNAs influence gene expression is thus important to understand, but complicated due to the large and interconnected nature of the human genome. To help better understand what genes are being regulated by transcription factors and/or miRNAs we looked at it over 8000 patient samples from 32 different cancer types collected from The Cancer Genome Atlas (TCGA). We started by clustering the transcription factors and miRNAs using Thresher to reduce the number of features. Using both the mRNA and miRNA sequencing data we constructed linear models to calculate the coefficient of determination (R2) for each mRNA based on the Thresher cluster expression. We generated three types of linear models: transcription factor, miRNA and transcription factor plus miRNA. We then determined genes that were highly explained or poorly explained by each of the three models based on the genes R2 value. We performed downstream gene enrichment analysis using ToppGene on the sets of well and poorly explained genes. This identified differences in gene regulation between transcription factors and miRNAs and showed what groups of gene are differentially regulated.

systems biology↗