Biology subjects

Singh, K.

Publications and source records attributed to Singh, K..

8 recordsLinked to original sources

bioRxiv2026

Microbial valerate is associated with CAR T dysbiosis and its supplementation enhances CAR T function in B-cell lymphoma

Anaerobe-depleting antibiotic exposure is associated with inferior progression-free survival after CD19 CAR T-cell therapy in large B-cell lymphoma, yet the cellular mechanisms linking gut dysbiosis to the CAR T-cell product and whether this imprint is reversible have remained undefined. In two independent CAR-T candidate cohorts, low stool valerate at the time of CAR-T eligibility identified a multi-metabolite-deficient dysbiotic gut microbiome state marked by depletion of fiber-fermenting commensals and loss of carbohydrate-fermentation, SCFA-biosynthesis, and amino-acid metabolism pathways. Reanalysis of single-cell RNA sequencing from 42 lymphoma patients stratified by piperacillin-tazobactam/imipenem/meropenem (PIM) exposure revealed that PIM-exposed CAR T-cell products were CD4-skewed, with significantly elevated AP-1/immediate-early gene (IEG) and cellular activation signatures that together predicted inferior progression-free survival. Ex vivo conditioning of CAR T-cells with valerate produced a chromatin and transcription factor program distinct from butyrate or propionate, characterized by KLF/SP/EGR family engagement, KLF4 promoter opening, and broad induction of AP-1/IEG and MHC class II transcripts, whereas butyrate drove broader chromatin remodeling with TBX21/EOMES/NF-{kappa}B gains and KLF2 promoter closure, and propionate induced an NFY-centered program with preferential commitment to low-mitochondrial-content states. Untargeted metabolomics confirmed valerate uptake and mitochondrial {beta}-oxidation in CAR T-cells, while dietary sodium valerate supplementation in meropenem-treated mice bearing A20 lymphoma significantly reduced tumor burden and extended survival compared with CAR T-cells alone. These findings identify stool valerate as a bedside-deployable biomarker of dysbiosis-imprinted CAR T-cell dysfunction and support ex vivo or dietary valerate supplementation as a clinically tractable strategy to improve CAR-T anti-tumor function in patients with disrupted gut microbiomes.

cancer biology↗

bioRxiv2018

A strain of an emerging Indian pathotype of Xanthomonas oryzae pv. oryzae defeats the rice bacterial blight resistance gene xa13 without inducing a clade III SWEET gene and is nearly identical to a recent Thai isolate

The rice bacterial blight pathogen Xanthomonas oryzae pv. oryzae (Xoo) injects transcription activator-like effectors (TALEs) that bind and activate host susceptibility (S) genes important for disease. Clade III SWEET genes are major S genes for bacterial blight. The resistance genes xa5, which reduces TALE activity generally, and xa13, a SWEET11 allele not recognized by the cognate TALE, have been effectively deployed. However, strains that defeat both resistance genes individually were recently reported in India and Thailand. To gain insight into the mechanism(s), we completely sequenced the genome of one such strain from each country and examined the encoded TALEs. Strikingly, the two strains are clones, sharing nearly identical TALE repertoires, including a TALE known to activate SWEET11 strongly enough to be effective even when diminished by xa5. We next investigated SWEET gene induction by the Indian strain. The Indian strain induced no clade III SWEET in plants harbouring xa13, indicating a pathogen adaptation that relieves dependence on these genes for susceptibility. The findings open a door to mechanistic understanding of the role SWEET genes play in susceptibility and illustrate the importance of complete genome sequence-based monitoring of Xoo populations in developing varieties with effective disease resistance.

pathology↗

bioRxiv2018

Analysis of genetic control and QTL mapping of essential wheat grain quality traits in a recombinant inbred population

Wheat cultivars are genetically crossed for improving end use quality for apt traits as per need of baking industry and broad consumers preferences. The processing and baking qualities of bread wheat underlie into genetic make-up of a variety and influence by environmental factors and their interactions. WL711 and C306 derived recombinant inbred lines (RILs) population of 206 was used for phenotyping of quality related traits in three different environmental conditions. The genetic analysis of quality traits showed considerable variation for measurable quality traits with normal distribution and transgressive segregation across the years. From the 206 RIL, few RILs found to be superior to those of the parental cultivars for key quality traitsindicating their potential usefor improvement of end use quality and also suggestingprobability of finding new alleles and allelic combinations from the RIL population. A genetic linkage map including 346 markers was constructed withtotal map distance of 4526.8cM andinterval distance between adjacent markersof 12.9cM. Mapping analysis identified 38 putative QTLs for 13 quality related traits with QTLs explaining 7.9% - 16.8% phenotypic variation spanning over 14 chromosomes i.e. 1A, 1B, 1D, 2A, 2D, 3B, 3D, 4A, 4B, 4D, 5D, 6A, 7A and 7B. Major novel QTLs regions for quality traits have been identified on several chromosome in studied RIL population posing their potential role in marker assisted selection for better bread making quality after validation.

genetics↗

bioRxiv2018

A Patient-Derived Cellular Model for Huntington Disease Reveals Phenotypes at Clinically Relevant CAG Lengths

The huntingtin protein participates in several cellular processes that are disrupted when the polyglutamine tract is expanded beyond a threshold of 37 CAG DNA repeats in Huntingtons disease (HD). Cellular biology approaches to understand these functional disruptions in HD have primarily focused on cell lines with synthetically long CAG length alleles that clinically represent outliers in this disease and a more severe form of HD that lacks age-onset. Patient-derived fibroblasts are limited to a finite number of passages before succumbing to cellular senescence. We used human telomerase reverse transcriptase (hTERT) to immortalize fibroblasts taken from individuals of varying age, sex, disease onset and CAG repeat length, which we have termed TruHD cells. TruHD cells display classic HD phenotypes of altered morphology, size and growth rate, increased sensitivity to oxidative stress, aberrant ADP/ATP ratios and hypophosphorylated huntingtin protein. We additionally observed dysregulated ROS-dependent huntingtin localization to nuclear speckles in HD cells. We report the generation and characterization of a human, clinically relevant cellular model for investigating disease mechanisms in HD at the single cell level, which, unlike transformed cell lines, maintains TP53 function critical for huntingtin transcriptional regulation and genomic integrity.

cell biology↗

bioRxiv2017

Bcl11b is a Newly Identified Regulator of Vascular Smooth Muscle Phenotype and Arterial Stiffness

B-cell leukemia 11b (Bcl11b) is a zinc-finger transcription factor known as master regulator of T lymphocytes and neuronal development during embryogenesis. Bcl11b-interacting protein COUP-TFII is required for atrial development and vasculogenesis, however a role of Bcl11b in the adult cardiovascular system is unknown. A genome-wide association study (GWAS) recently showed that a gene desert region downstream of BCL11B and known to function as BCL11B enhancer harbors single nucleotide polymorphisms (SNPs) associated with increased arterial stiffness. Based on these human findings, we sought to examine relations between Bcl11b and arterial function using mice with Bcl11b deletion. We report for the first time that Bcl11b is expressed in vascular smooth muscle (VSM) and transcriptionally regulates the expression of VSM contractile proteins smooth muscle myosin and smooth muscle -actin. Lack of Bcl11b in VSM-specific Bcl11b null mice (BSMKO) resulted in increased expression of Ca++-calmodulin-dependent serine/threonine phosphatase calcineurin in BSMKO VSM cells, cultured in serum-free condition, and in BSMKO aortas, which showed an inverse correlation with levels of phosphorylated VASPS239, a regulator of cytoskeletal actin rearrangements. Moreover, decreased pVASPS239 in BSMKO aortas was associated with increased actin polymerization (F/G actin ratio). Functionally, aortic force, stress and wall tension, measured ex vivo in organ baths, were increased in BSMKO aortas and BSMKO mice had increased pulse wave velocity, the in vivo index of arterial stiffness, compared to WT littermates. Despite having no effect on baseline blood pressure or angiotensin II-induced hypertension, Bcl11b deletion in VSM increased the incidence of aortic aneurysms in BSMKO mice. Aneurysmal aortas from angII-treated BSMKO mice had increased number of apoptotic VSM cells. In conclusion, we identified VSM Bcl11b as a novel and crucial regulator of VSM cell phenotype and vascular structural and functional integrity.

physiology↗

bioRxiv2017

Necrosis triggered by Mycobacterium tuberculosis alters macrophage triglyceride metabolism and inflammatory response in a DGAT1-dependent manner

Tuberculosis granulomas represent a site of controlling bacterial dissemination at the cost of host tissue damage. Within the heterogenous array of TB granulomas, some contain triglyceride (TG) rich foamy macrophages, the etiology and function of which remains largely unexplained. Here we show that necrosis of tuberculosis lesions and M. tuberculosis (Mtb) infected macrophages elicits a bystander response of triglyceride storage. We elucidate a role for the RD1 region of mycobacterial genome to be a key player in this phenomenon. TG storage in necrosis associated foamy macrophages promoted the pro-inflammatory state of macrophages while silencing expression of diacylglycerol O-acyltransferase (DGAT1) suppressed expression of pro-inflammatory genes. Surprisingly, acute infection with Mtb led to lipolysis of host TG, rather than synthesis, suggesting mobilization of triglyceride stored within macrophage lipid droplets to be involved in the inflammatory response to infection. Our data is likely to open new avenues for management of the inflammatory response during infection.

immunology↗

bioRxiv2017

An indicator cell assay for blood-based diagnostics

We have established proof of principle for the Indicator Cell Assay Platform (iCAP), a broadly applicable tool for blood-based diagnostics that uses specifically-selected, standardized cells as biosensors, relying on their innate ability to integrate and respond to diverse signals present in patients blood. To develop an assay, indicator cells are exposed in vitro to serum from case or control subjects and their global differential response patterns are used to train reliable, cost-effective disease classifiers based on a small number of features. In a feasibility study, the iCAP detected pre-symptomatic disease in a murine model of amyotrophic lateral sclerosis (ALS) with 94% accuracy (p-Value=3.81E-6) and correctly identified samples from a murine Huntingtons disease model as non-carriers of ALS. In a preliminary human disease assay, the iCAP detected early stage Alzheimers disease with 72% cross-validated accuracy (p-Value=3.10E-3). For both assays, iCAP features were enriched for disease-related genes, supporting the assays relevance for disease research.

systems biology↗

bioRxiv2016

LOCALIZER: subcellular localization prediction of plant and effector proteins in the plant cell

Pathogens are able to deliver effector proteins into plant cells to enable infection. Some effectors have been found to enter subcellular compartments by mimicking host targeting sequences. Although many computational methods exist to predict plant protein subcellular localization, they perform poorly for effectors. We introduce LOCALIZER for predicting plant and effector protein localization to chloroplasts, mitochondria, and nuclei. LOCALIZER shows greater prediction accuracy for chloroplast and mitochondrial targeting compared to other methods for 652 plant proteins. For 108 eukaryotic effectors, LOCALIZER outperforms other methods and predicts a previously unrecognized chloroplast transit peptide for the ToxA effector, which we show translocates into tobacco chloroplasts. Secretome-wide predictions and confocal microscopy reveal that rust fungi might have evolved multiple effectors that target chloroplasts or nuclei. LOCALIZER is the first method for predicting effector localisation in plants and is a valuable tool for prioritizing effector candidates for functional investigations. LOCALIZER is available at http://localizer.csiro.au/.

bioinformatics↗