Biology subjects

Nath, S. K.

Publications and source records attributed to Nath, S. K..

4 recordsLinked to original sources

bioRxiv2023

A Non-Coding Variant in SLC15A4 Drives Lysosomal Deacidification and Lupus Susceptibility

Systemic lupus erythematosus (SLE) is a complex autoimmune disease with a strong genetic basis. Despite the identification of several single nucleotide polymorphisms (SNPs) near the SLC15A4 gene that are significantly associated with SLE across multiple populations, specific causal SNP(s) and molecular mechanisms responsible for disease susceptibility are unknown. To address this gap, we employed bioinformatics, expression quantitative trait loci (eQTLs), and 3D chromatin interaction analysis to nominate a likely functional variant, rs35907548, in an active intronic enhancer of SLC15A4. Through luciferase reporter assays followed by chromatin immunoprecipitation (ChIP)-qPCR, we observed significant allele-specific enhancer effects of rs35907548 in diverse cell lines. The rs35907548 risk allele T is associated with increased regulatory activity and target gene expression, as shown by eQTLs and chromosome conformation capture (3C)-qPCR. The latter revealed long-range chromatin interactions between the rs35907548 enhancer and the promoters of SLC15A4, GLTLD1, and an uncharacterized lncRNA. The enhancer-promoter interactions and expression effects were validated by CRISPR/Cas9 knock-out (KO) of the locus in HL60 promyeloblast cells. KO cells also displayed dramatically dysregulated endolysosomal pH regulation. Together, our data show that the rs35907548 risk allele affects multiple aspects of cellular physiology and may directly contribute to SLE.

genetics↗

bioRxiv2023

Increased atherosclerotic plaque and anti-oxidized low density lipoprotein in anti-Ro60 SLE autoantibody subset

ObjectivePremature atherosclerosis is associated with systemic lupus erythematosus (SLE). We previously showed an association of anti-Ro60/La/Ro52 to anti-oxidized LDL in SLE. Here, we hypothesized that atherosclerotic plaque will be associated with anti-oxidized LDL (anti-oxLDL)/anti-lipoprotein lipase (ALPL) in a specific SLE autoantibody sub-set (anti-Ro60 positive, anti-RNP positive or extractable nuclear antigen antibody negative). MethodsWe carried out a case-control study (one time-point testing) of plaque, ALPL, anti-oxLDL, anti-low density lipoprotein (ALDL) or anti-LDL in 114 SLE and 117 age/sex matched controls. Total cholesterol, LDL, HDL, triglycerides, and HDL-Trig were also measured. Students t test was used for statistical analysis ResultsInterestingly, plaque was highest in SLE subset with anti-Ro60 (23/114). Plaque and anti-oxLDL were statistically significantly elevated in the anti-Ro60 SLE subset (1.3 +/-1.66, p<0.01; 0.26 +/-0.16, p<0.002 respectively) compared to controls (0.54 +/-1.26; 0.165 +/-0.13 respectively), but not anti-LPL/anti-LDL. Plaque was significantly elevated (0.9 +/-1.71; p< 0.05) in the SLE subset without anti-ENA (63/114) compared to controls. Other antibodies in this subset were not statistically different compared to other SLE subsets or controls. Only anti-oxLDL was significantly elevated (0.29 +/-0.27; p<0.005) in SLE subset with anti-RNP (14/114) compared to controls, while none were elevated in anti-SmRNP subset (6/114). We did not find significant differences in lipids between various SLE subsets. ConclusionPlaque segregates in anti-Ro and ENA negative groups either with or without anti-oxLDL. It will be clinically important if cardiovascular events are augmented in SLE anti-Ro subset having elevated anti-oxidized LDL antibodies. Key pointsO_LIPlaque and anti-oxLDL significantly elevated in anti-Ro60 SLE subset C_LIO_LIOnly plaque significantly elevated in SLE subset without antibodies against extractable nuclear antigens C_LIO_LIIt will be clinically important to see if augmented cardiovascular events occur in SLE anti-Ro subset having elevated anti-oxidized LDL antibodies. C_LI

biochemistry↗

bioRxiv2022

Penetratin inhibits α-synuclein fibrillation and improves locomotor functions in mice model of Parkinsons disease

Parkinsons disease (PD) is the second most common neurodegenerative disease. The presence of lewy bodies, primarily consisting of -synuclein (-syn) aggregates is one of the common features seen in the substantia nigra region of the brain in PD patients. The disease remains incurable and only symptomatic relief is available. We screened various cell-penetrating peptides and reveal that penetratin is a potent inhibitor of -syn aggregation in-vitro, and significantly improved locomotor coordination in mice models of PD in-vivo. The peptide inhibits -syn aggregation in vitro as well as in yeast, and C.elegans models. We further made a cyclic derivative of penetratin by disulfide coupling of N- and C-terminal cysteine residues. Both penetratin and its cyclized derivative interact with -syn. NMR studies show that both linear as well as cyclic derivative interact at the acidic C-terminal tail of the protein. Similar to penetratin, its cyclic derivative inhibited -syn aggregation in the C.elegans model of Parkinsons disease, and also improved worm motility. Molecular Dynamics studies show that penetratin interacts with -synuclein and prevents its conformational transition from disordered into {beta}-sheet rich structure. The therapeutic efficacy of penetratin was further confirmed in a transgenic mice model of the disease, wherein penetratin treatment over a period of 90 days improved locomotor coordination, and halted disease progression. Overall, the present work provides a potent therapeutic agent that could be further explored in the management of PD.

neuroscience↗

bioRxiv2019

Mechanistic characterization of RASGRP1 variants identifies an hnRNP K-regulated transcriptional enhancer contributing to SLE susceptibility

Systemic lupus erythematosus (SLE) is an autoimmune disease with a strong genetic component. We recently identified a novel SLE susceptibility locus near RASGRP1, which governs the ERK/MAPK kinase cascade and B-/T-cell differentiation and development. However, precise causal RASGRP1 functional variant(s) and their mechanisms of action in SLE pathogenesis remain undefined. Our goal was to fine-map this locus, prioritize genetic variants according to likely functionality, experimentally validate the contribution of three SNPs to SLE risk, and experimentally determine their biochemical mechanisms of action. We performed a meta-analysis across six Asian and European cohorts (9,529 cases; 22,462 controls), followed by in silico bioinformatic and epigenetic analyses to prioritize potentially functional SNPs. We experimentally validated the functional significance and mechanism of action of three SNPs in cultured T-cells. Meta-analysis identified 18 genome-wide significant (p<5x10-8) SNPs, mostly concentrated in two haplotype blocks, one intronic and the other intergenic. Epigenetic fine-mapping, allelic, eQTL and imbalance analyses predicted three transcriptional regulatory regions with four SNPs (rs7170151, rs11631591-rs7173565, and rs9920715) prioritized for functional validation. Luciferase reporter assays indicated significant allele-specific enhancer activity for intronic rs7170151 and rs11631591-rs7173565 in T-lymphoid (Jurkat) cells, but not in HEK293 cells. Following up with EMSA, mass spectrometry and ChIP-qPCR, we detected allele-dependent interactions between heterogeneous nuclear ribonucleoprotein K (hnRNP-K) and rs11631591. Furthermore, inhibition of hnRNP-K in Jurkat and primary T-cells downregulated RASGRP1 and ERK/MAPK signaling. Comprehensive association, bioinformatics, and epigenetic analyses yielded putative functional variants of RASGRP1, which were experimentally validated. Notably, intronic variant (rs11631591) is located in a cell type-specific enhancer sequence, where its risk allele binds to the hnRNP-K protein and modulates RASGRP1 expression in Jurkat and primary T-cells. As risk allele dosage of rs11631591 correlates with increased RASGRP1 expression and ERK activity, we suggest that this SNP may underlie SLE risk at this locus.

genetics↗