Biology subjects

Thakar, M.

Publications and source records attributed to Thakar, M..

3 recordsLinked to original sources

bioRxiv2026

Intrathecal antibodies cross-react with EBV BRRF2 and human antigens in multiple sclerosis

Intrathecal antibody synthesis is a hallmark of multiple sclerosis (MS). Although some intrathecally synthesized antibodies in MS are known to target viral antigens, the spectrum of their antigenic specificities remains incompletely defined. We combined proteome-wide antibody profiling by Phage ImmunoPrecipitation Sequencing (PhIP-Seq) with cross-compartment analytics (MICAR) to study intrathecal antibody synthesis at peptide resolution in paired CSF and serum samples from individuals with MS (n = 40) and non-MS controls (n = 83). While intrathecal antibody responses in MS were polyspecific and included reactivities to various viruses, we identified a subset of individuals with a convergent intrathecal antibody reactivity to a previously described motif within the Epstein-Barr virus (EBV) protein BRRF2 (BRRF2408-415). This motif-directed response showed co-reactivity with multiple CNS-expressed human antigens. In an independent cohort of n = 909 individuals with MS and n = 311 controls, including individuals with NMOSD and MOGAD, serum antibodies to BRRF2408-415 were detected in 8.36% of MS individuals and in 0.64% of non-MS controls, corresponding to an odds ratio for MS of 14.1 (95% CI: 4.4-86.04). Within MS individuals, BRRF2408-415 seropositivity was associated with increased intrathecal IgG synthesis. Cross-reactivity of antibodies to BRRF2408-415 with human targets, including TRIM71 and RTN2, was confirmed by competition ELISA and cell-based assays. Together, these data define an intrathecal EBV BRRF2-linked antibody signature with human target cross-reactivity in a subset of MS individuals. This signature identifies a highly specific serological marker in MS and may support future stratification of the heterogeneous MS spectrum.

immunology↗

bioRxiv2021

The evolution of regulatory elements in the emerging promoter variant strains of HIV-1

In a multicentric, observational, investigator-blinded, and longitudinal clinical study of 764 ART-naive subjects, we identified nine different promoter-variant strains of HIV-1 subtype C (HIV-1C) emerging in the Indian population, with some of these variants being reported for the first time. Unlike several previous studies, our work here focuses on the evolving viral regulatory elements, not coding sequences. The emerging viral strains contain additional copies of the existing transcription factor binding sites (TFBS), including TCF-1/LEF-1, RBEIII, AP-1, and NF-{kappa}B, created by sequence duplication. The additional TFBS are genetically diverse and may blur the distinction between the modulatory region of the promoter and the viral enhancer. In a follow-up analysis, we found trends, but not significant associations between any specific variant promoter and prognostic markers, probably because the emerging viral strains might not have established mono infections yet. Illumina sequencing of four clinical samples containing a co-infection indicated the domination of one strain over the other and establishing a stable ratio with the second strain at the follow-up time-points. Since a single promoter regulates viral gene expression and constitutes the master regulatory circuit with Tat, the acquisition of additional and variant copies of the TFBS may significantly impact viral latency and latent reservoir characteristics. Further studies are urgently warranted to understand how the diverse TFBS profiles of the viral promoter may modulate the characteristics of the latent reservoir, especially following the initiation of antiretroviral therapy. Significance StatementA unique conglomeration of TFBS enables the HIV-1 promoter to accomplish two diametrically opposite functions - transcriptional activation and transcriptional silencing. The various phases of viral latency -establishment, maintenance, and reversal -collectively determine the replication fitness of individual viral strains. A profound variation in the TFBS composition of the viral promoter may significantly alter the viral latency properties and the latent reservoir characteristics. Although the duplication of certain TFBS remains a quality unique to HIV-1C, the high-level genetic recombination of HIV-1 may promote the transfer of such molecular properties to the other HIV-1 subtypes. The emergence of several promoter-variant viral strains may make the task of a functional cure more challenging in HIV-1C.

microbiology↗

bioRxiv2017

Untangling The Gene-Epigenome Networks: Timing Of Epigenetic Regulation Of Gene Expression In Acquired Cetuximab Resistance

BACKGROUNDTargeted therapies specifically act by blocking the activity of proteins that are encoded by genes critical for tumorigenesis. However, most cancers acquire resistance and long-term disease remission is rarely observed. Understanding the time course of molecular changes responsible for the development of acquired resistance could enable optimization of patients treatment options. Clinically, acquired therapeutic resistance can only be studied at a single time point in resistant tumors. To determine the dynamics of these molecular changes, we obtained high throughput omics data weekly during the development of cetuximab resistance in a head and neck cancer in vitro model.\n\nRESULTSAn unsupervised algorithm, CoGAPS, was used to quantify the evolving transcriptional and epigenetic changes. Applying a PatternMarker statistic to the results from CoGAPS enabled novel heatmap-based visualization of the dynamics in these time course omics data. We demonstrate that transcriptional changes result from immediate therapeutic response or resistance, whereas epigenetic alterations only occur with resistance. Integrated analysis demonstrates delayed onset of changes in DNA methylation relative to transcription, suggesting that resistance is stabilized epigenetically.\n\nCONCLUSIONSGenes with epigenetic alterations associated with resistance that have concordant expression changes are hypothesized to stabilize resistance. These genes include FGFR1, which was associated with EGFR inhibitor resistance previously. Thus, integrated omics analysis distinguishes the timing of molecular drivers of resistance. Our findings provide a relevant towards better understanding of the time course progression of changes resulting in acquired resistance to targeted therapies. This is an important contribution to the development of alternative treatment strategies that would introduce new drugs before the resistant phenotype develops.

cancer biology↗