Biology subjects

Nanda, R. K.

Publications and source records attributed to Nanda, R. K..

8 recordsLinked to original sources

bioRxiv2026

Orthogonal perturbation of sulfur availability reveals antibiotic-induced synthetic lethality in Mycobacterium tuberculosis

Despite its essential role in growth, the impact of sulfur limitation on mycobacterial physiology and antibiotic responsiveness remains poorly understood. Here, we combined chemical-genetic perturbations and infection models to investigate the consequences of sulfur limitation in Mycobacterium tuberculosis (M. tuberculosis). We report that sulfur limitation restricted bacterial growth by rewiring metabolism, resembling nutrient starvation. CRISPR interference of the sulfate transporter (ST) revealed severe vulnerability and sensitised M. tuberculosis to anti-TB drugs. Inhibition of H2S production in macrophages further compromised the fitness of ST-deficient M. tuberculosis, indicating that the bacteria depend on host-derived sulfur during infection. Importantly, preventing sulfur acquisition attenuated both the drug-sensitive H37Rv and the drug-resistant clinical strain of M. tuberculosis, while enhancing the efficacy of Isoniazid (INH) in the murine model, resulting in sterilisation of infected lung tissues. Combined, our findings suggest that restricting sulfur uptake highlights a therapeutic vulnerability that enhances the efficacy of existing anti-TB drugs.

microbiology↗

bioRxiv2025

Methionine metabolism shapes immune response against Mycobacterium tuberculosis

The methionine metabolism is central to epigenetic reprogramming to produce pro-inflammatory cytokines. Disruptions in methionine metabolism contribute to complex disorders, providing an important target for nutrient interventions. Here, Mycobacterium tuberculosis (Mtb) H37Rv-infected C57BL/6 mice showed functional heterogeneity between alveolar and non-alveolar macrophage (AMs/Non-AMs) with major metabolic reprogramming in Non-AMs. Global metabolite and proteome analysis of Mtb-infected bone marrow-derived macrophages (BMDMs) showed a diversion of flux from methionine metabolism toward increased nucleotide salvage and glutathione (GSH) production. Carbon units of 13C5-methionine via isotopomer analysis contributed to polyamine synthesis, fuelling the nucleotide salvage node in Mtb-infected BMDMs. Methionine supplementation increased mycobacterial clearance in C57BL/6 mice and in BMDMs by promoting a pro-inflammatory response, as evident by increased IL-1{beta} and IFN-{gamma}. Increased IL-1{beta} production is mainly contributed to by increased H3K4 trimethylation in macrophages. These findings reveal an important strategy by which methionine supplementation in macrophages and mice remodels host metabolism to enhance acute pro-inflammatory responses and exploit dietary supplementation to improve nutritional immunity in TB. HighlightsO_LIMycobacterium tuberculosis (Mtb) infection decreases intracellular methionine levels and increases purine levels in primary macrophages. C_LIO_LIMethionine carbon units contribute to nucleotide salvage, and their restriction lowers IL-1 response and mycobacterial clearance. C_LIO_LIEx vivo methionine supplementation in Mtb-infected macrophages increases H3K4me3 at the Il-1b gene promoter and gene body, leading to an increased pro-inflammatory response and improved mycobacterial clearance. C_LIO_LIIn vivo methionine supplementation improved pro-inflammatory response in lungs, spleen and bone marrow, leading to accelerated mycobacterial clearance upon Mtb-H37Rv infection. C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=157 SRC="FIGDIR/small/680834v2_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@1bf5corg.highwire.dtl.DTLVardef@ba4dbdorg.highwire.dtl.DTLVardef@145f23dorg.highwire.dtl.DTLVardef@122b2a2_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

Macrophages of diabetes and tuberculosis co-morbid conditions show perturbed differentiation and metabolic signatures

Diabetes negatively impacts the host immune system, leading to allergies, recurring infections, and lameness. Its impact on the distribution and molecular phenotypes of the bone marrow-derived macrophages (BMDMs) needs attention and, more importantly, in co-morbid conditions like diabetes and tuberculosis (DM-TB). In this study, total bone marrow cells were harvested at 3 w.p.i., from the low aerosol dose (100-120 CFU) of Mycobacterium tuberculosis H37Rv infected control and NA-STZ induced diabetic C57BL/6 mice. The bone marrow cells were differentiated into BMDMs, and CD11c, CD11b and F4/80 marker expressions were monitored using flow cytometry. BMDMs stimulated with Mtb H37Rv lysate were subjected to global transcriptome profiling to identify the perturbed metabolic and molecular landscape. The BMDMs of the DM-TB comorbid mice showed low CD11c, CD11b and higher F4/80 expression. The macrophages of the DM group showed a skewed pro-inflammatory response, characterized by perturbed complement response, NF-kB pathway and fatty acid metabolism, whereas macrophages of the DM-TB group showed deregulated ceramide and amino acid metabolism. Macrophages from the DM and DM-TB group stimulated with Mtb H37Rv lysate, showed a deregulated transcript signature that impacts humoral response. The dampened immune response observed in the DM-TB group macrophages highlights the importance of identifying novel targets for developing tailored drugs for comorbid conditions.

immunology↗

bioRxiv2025

Diabetes mellitus and tuberculosis comorbidity induce unique microbial gut dysbiosis and associated metabolome.

BackgroundPatients with diabetes and tuberculosis (DMTB) often exhibit atypical disease progression and poor treatment outcomes. Alterations in gut microbiota may contribute to the impaired immune response in diabetes. Understanding the microbiota composition and associated metabolite profiles in DMTB could provide insights for developing targeted adjunctive therapies to improve patient prognosis. MethodNicotinamide (NA) and streptozotocin (STZ) induced diabetic C57BL/6 mice were aerosol infected with 100-120 CFU of Mycobacterium tuberculosis H37Rv. At different time points (2 days pre-infection and 3- and 8 weeks post-infection; wpi), faecal samples were collected for microbiome and metabolome profiling using 16S rRNA sequencing and gas chromatography-time of flight-mass spectrometry (GC-TOF-MS), respectively. ResultsDiabetic mice showed gut dysbiosis, with 16 bacterial genera significantly altered between DMTB and TB groups at 3 wpi, which reduced to 11 at 8 wpi. Among the 93 identified faecal metabolites, 11 and 10 metabolites were significantly deregulated (log2FC>{+/-}1.0, p<0.05) in the DMTB group compared to TB group at 3 and 8 wpi, respectively. A negative correlation between faecal valeric acid levels in DMTB with the abundances of Coriobacteriaceae, Granulicatella, Veillonella, Achromobacter, Erysipelatrichaceae, Atopobiaceae, Citrobacter, and Lactiplantibacillus were observed. Stronger correlations between microbiota and metabolite were observed in DMTB comorbidity compared to TB. Additionally, correlation analysis also revealed a phylogenetic distance-dependent synchrony in amino acid metabolism across five clades, each containing three or more bacterial genera. ConclusionThis study reveals significant differences in the gut microbiome and metabolome between DMTB and TB groups. The identified microbes and metabolic products may serve as potential prebiotic or probiotic candidates for improving recovery in DMTB comorbid conditions.

microbiology↗

bioRxiv2023

Chemical inhibition of histidine biosynthesis curtails M. tuberculosis infection

To overcome the drug resistance crisis and shorten the current duration of human tuberculosis (TB) therapy, new anti-TB molecules is required. In an earlier study, we have shown that Mycobacterium tuberculosis (Mtb), the causative agent of TB, with a fractured de novo histidine biosynthesis fails to mount TB infection in mouse model, emboldening that disrupting the function of this pathway may constitute a novel strategy to curtailing TB infection. In this study, through a target based approach we have designed a number of triazole scaffold molecules specific to imidazole glycerol phosphate dehydratase (IGPD; HisB) of this pathway and have delineated atomic level interactions between the enzyme and inhibitors which pinpointed the specificity and the inhibitory mechanism. Importantly, these molecules exhibited significant potency against free as well as macrophage-internalized wild-type and drug-resistant clinical isolates in culture medium. Notably, a couple of these compounds showed efficacy in reducing the bacterial burden in Mtb-infected mouse model. The chemical inhibition of IGPD induces histidine auxotrophy in Mtb and brings in new prospects to the area of anti-TB drug discovery.

biochemistry↗

bioRxiv2023

Seasonal plasticity and energy efficiency in migratory buntings is an assemblage of alterations in metabolic and gut microbe adaptations.

Circulatory system is the source of useful metabolites to enable organismal energy demands of muscle during different life states of birds including migration. In this study, we profiled the serum metabolites and fecal microbiome of redheaded buntings (Emberiza bruniceps) exhibiting diurnal non-migratory (nonM) pre-migratory (preM), migratory (M) and post-migratory (posM) states, when exposed to long days (14L:10D). Using gas chromatography, out of the identified 124 serum analytes, 38 showed significant variations (Fold change, VIP) between states. Out of these, 11 metabolites (short chain fatty acids, SCFAs-butanoate and hexanoate, lactate, pyruvate, ethylene and acetate oxime, pyridoxal phosphate (PLP), niacin, L-valine and carboximidic acids viz. phosphatidyl ethanolamine (PE) and diethyl carbamate) involved in energy pathways and enhanced immunity showed higher abundance in M state. While, upsurge of L-valine suggested energy contribution of glucogenic branched chain amino acids (BCAAs) in M state, that of leucine metabolite, was related to higher temperature in posM birds. Gut microbiota was analysed using faeces of buntings (n=6 each) during nonM and M states and alteration in bacterial compositions was observed; faeces of nonM birds were enriched in proteobacteria, while those of M were rich in firmicutes. This study reports the migratory state specific changes in the serum metabolome and faecal microbiome of the buntings and highlights the role of short chain fatty acids, SCFAs and branched chain amino acids, BCAAs during hypermetabolic state of migration.

animal behavior and cognition↗

bioRxiv2020

Kinetic isotope tracing of glycerol and de novo proteogenic amino acids in Human Lung Carcinoma cells using glucose

13C based Isotopic tracers of the media components can be used to kinetically track their contribution in the cell systems. A tracer ([U-13C6] glucose) was used to monitor its contribution into the central carbon metabolic pathways of human lung carcinoma (A549) cells by Gas chromatography-mass spectrometry (GC-MS) based mass isotopomer analysis. Calculated average 13C of methanolic extracts (glycerol: 5.46{+/-}3.53 % and lactate: 74.4{+/-}2.65 %), protein acid hydrolysates (serine: 4.51{+/-}0.21 %, glycine: 2.44{+/-}0.31 %, alanine: 24.56{+/-}0.59 %, glutamate: 8.81{+/-}0.85 %, proline: 6.96{+/-}0.53 % and aspartate: 10.72{+/-}0.95 %) and the culture filtrate (glycerol: 43.14{+/-}1.45 % and lactate: 81.67{+/-}0.91 %), showed significant contribution of 13C glucose. We observed the Warburg effect with higher levels of 13C lactate in the culture filtrate. 13C glycerol levels in culture supernatant showed significant increase with time and amino acids of glucogenic origin also contributed cellular protein biomass. The workflow adopted in this study for 13C analysis could be useful for the metabolic phenotyping of other mammalian cell systems under normal and perturbed (cancer and infection) conditions.

biochemistry↗

bioRxiv2020

CMTM6 drives cisplatin resistance in OSCC by regulating AKT mediated Wnt signaling

Chemoresistance is one of the important factors for treatment failure in OSCC, which can culminate in progressive tumor growth and metastatic spread. Rewiring tumor cells to undergo drug-induced apoptosis is a promising way to overcome chemoresistance, which can be achieved by identifying the causative factors for acquired chemoresistance. In this study, to explore the key cisplatin resistance triggering factors, we performed global proteomic profiling of OSCC lines representing with sensitive, early and late cisplatin-resistant patterns. The top ranked up-regulated protein appeared to be CMTM6. We found CMTM6 to be elevated in both early and late cisplatin-resistant cells with respect to the sensitive counterpart. Analyses of OSCC patient samples indicate that CMTM6 expression is upregulated in chemotherapy-non-responder tumors as compared to chemotherapy-naive tumors. Stable knockdown of CMTM6 restores cisplatin-mediated cell death in chemoresistant OSCC lines. Similarly, upon CMTM6 overexpression in CMTM6KD lines, the cisplatin resistant phenotype was efficiently rescued. Mechanistically, it was found that CMTM6 interacts with membrane bound Enolase-1 and stabilized its expression, which in turn activates the AKT-GSK3{beta} mediated Wnt signaling. CMTM6 triggers the translocation of {beta}-catenin into the nucleus, which elevates the Wnt target pro-survival genes like Cyclin D, c-Myc and CD44. Moreover, incubation with lithium chloride, a Wnt signaling activator, efficiently rescued the chemoresistant phenotype in CMTM6KD OSCC lines. In a patient-derived cell xenograft model of chemoresistant OSCC, knock-down of CMTM6 restores cisplatin induced cell death and results in significant reduction of tumor burden. CMTM6 has recently been identified as a stabilizer of PD-L1 and henceforth it facilitates immune evasion by tumor cells. Herewith for the first time, we uncovered another novel role of CMTM6 as one of the major driver of cisplatin resistance.

cancer biology↗