Biology subjects

Jaiswal, R.

Publications and source records attributed to Jaiswal, R..

5 recordsLinked to original sources

bioRxiv2025

A switch from histone methyltransferase-EZH2 to demethylase KDM6A activity marks reinitiation of proliferation of drug treated colorectal cancer cells

Colorectal cancer (CRC) is one of the deadliest cancers, ranking third in cancer incidence worldwide. These tumor cells often adopt unique strategies under drug stress to attain a reversible drug-tolerant state and evade cell death. However, the molecular adaptations associated with this transitory emergence of the drug-tolerant state remain elusive. Herein, epigenetic alterations often dictate such reversible dynamic changes, and this study aims to characterize the role of specific epigenetic modifiers governing CRC cell survival under drug pressure and their subsequent relapse. We observed that under drug stress there is a drastic increase in the histone-repressive mark-H3K27me3, linked to an enhanced expression of EZH2 driving transcriptional inhibition of cell proliferation-associated genes and a proliferative arrest. Interestingly, drug-induced oxidative stress increased the expression of the P65 protein, which was found to interact and regulate EZH2 expression. Quenching of ROS, drug vacation, or P65 inactivation compromised EZH2 activity concurrent with a re-initiation of cell proliferation. Interestingly, this reversal to proliferative state was associated with an elevated activity of the histone lysine demethylase-KDM6A. The promoter elements of the proliferative genes were now occupied by KDM6A instead of EZH2. Accordingly, a genetic knockdown or pharmacological inhibition of KDM6A in vitro not only resulted in increased cell death but also prevented emergence of the re-proliferative CRC cells. Furthermore, KDM6A inhibition in combination with chemotherapy drug, resulted in an increased tumor regression in vivo. Our study thus highlights the importance of KDM6A as a therapeutic target in preventing CRC growth and relapse which can have future therapeutic implications.

cancer biology↗

bioRxiv2024

Cryo-EM Structure of AAV2 Rep68 bound to integration site AAVS1: Insights into the mechanism of DNA melting

The Rep68 protein from Adeno-Associated Virus (AAV) is a multifunctional SF3 helicase that performs most of the DNA transactions required for the viral life cycle. During AAV DNA replication, Rep68 assembles at the origin and catalyzes the DNA melting and nicking reactions during the hairpin rolling replication process to complete the second-strand synthesis of the AAV genome. Here, we report the Cryo-EM structures of Rep68 bound to double-stranded DNA (dsDNA) containing the sequence of the AAVS1 integration site in different nucleotide-bound states. In the apo state, Rep68 forms a heptameric complex around DNA, with three Origin Binding Domains (OBDs) bound to the Rep Binding Site (RBS) sequence and three other OBDs forming transient dimers with them. The AAA+ domains form an open ring with no interactions between subunits and with DNA. We hypothesize the heptameric quaternary structure is necessary to load onto dsDNA. In the ATP{gamma}S-bound state, a subset of three subunits binds the nucleotide, undergoing a large conformational change, inducing the formation of intersubunit interactions interaction and interaction with three consecutive DNA phosphate groups. Moreover, the induced conformational change positions three phenylalanine residues to come in close contact with the DNA backbone, producing a distortion in the DNA. We propose that the phenylalanine residues can potentially act as a hydrophobic wedge in the DNA melting process.

biochemistry↗

bioRxiv2020

The Cryo-EM structure of AAV2 Rep68 in complex with ssDNA reveals a malleable AAA+ machine that can switch between oligomeric states.

The adeno-associated virus (AAV) Rep proteins use a unique AAA+ domain to catalyze DNA replication, transcription regulation, and genome packaging. Also, they mediate site-specific integration during a latent phase. To understand the mechanisms underlying AAV Rep function, we investigated the cryo-EM and X-ray structures of Rep68-ssDNA complexes. Surprisingly, Rep68 generates hybrid ring structures where the Origin-Binding-Domain (OBD) forms octameric rings while the helicase domain (HD) forms heptamers. Moreover, the binding to ATP{gamma}S promotes a large conformational change in the entire AAA+ domain that leads the HD to form both heptamer and hexamers. The HD oligomerization is driven by an interdomain linker region that acts as a latch to catch the neighboring HD subunit and is flexible enough to permit the formation of different stoichiometric ring structures. Overall, our studies show the structural basis of AAV Reps structural flexibility required to fulfill its multifunctional role during the AAV life cycle.

biochemistry↗

bioRxiv2017

Inferring propensity amongst lung and breast carcinomas via overlapped gene expression profiles

Reconstruction of biological networks for topological analyses helps in correlation identification between various types of biomarkers. These networks have been vital components of System Biology in present era. Genes are the basic physical and structural unit of heredity. Genes act as instructions to make molecules called proteins. Alterations in the normal sequence of these genes are the root cause of various diseases and cancer is the prominent example disease caused by gene alteration or mutation. These slight alterations can be detected by microarray analysis. The high throughput data obtained by microarray experiments aid scientists in reconstructing cancer specific gene regulatory networks. The purpose of experiment performed is to find out the overlapping of the gene expression profiles of breast and lung cancer data, so that the common hub genes can be sifted and utilized as drug targets which could be used for the treatment of diseased conditions. In this study, first the differentially expressed genes have been identified (lung cancer and breast cancer), followed by a filtration approach and most significant genes are chosen using paired t-test and gene regulatory network construction. The obtained result has been checked and validated with the available databases and literature.

systems biology↗

bioRxiv2017

WDR88, CCDC11, and ARPP21 genes indulge profoundly in the desmoplastic retort to prostate and breast cancer metastasis.

Abstract.Microarray technology has unlocked doors to a multitude of open analysis problems that if conceived with efficacy may uncover varied genotypic and phenotypic traits. Algorithms belonging to different cultures in computer science have been applied to gene expression data to derive correlation and stratification parameters. While most outcomes are subject to clinical validation, majority of which get declined, the search for the precisely targeted therapeutic agents is still on. This paper is an effort in the similar direction and strives to delineate genes with significant stromal signatures. We suggest a corroborative indulgence of a human laterality disorder gene, CCDC11 in the metastasis, in addition to the role of WDR88 and ARPP21 genes has been further materialized in the analysis. Another standout aspect of the study has been the associated implications of the genes in rare disorders of male breast and female prostate cancers. There is also a threshold proposal that stratifies \"safe\" expression space for genes. Complimentarily, the manuscript serves as an expedient protocol for anyone seeking microarray data analysis, particularly in R.

systems biology↗