Biology subjects

Mandal, A. K.

Publications and source records attributed to Mandal, A. K..

10 recordsLinked to original sources

bioRxiv2026

Plasma Metabolomic Profiling of COPD Patients Stratified by Smoking Status: A GC-MS- Based Approach

BackgroundChronic obstructive pulmonary disease, primarily caused by exposure to cigarette smoke, is a heterogeneous lung condition characterized by complex metabolic alterations. The metabolic changes associated with smoking status have not been thoroughly investigated. Our study aims to explore the metabolite profile of COPD patients categorised by their smoking habits, including smokers, ex-smokers, and non-smokers. MethodsIn this study, the plasma metabolome of smoking stratified COPD patients were assessed using gas chromatography coupled to mass spectrometry. We applied multivariate and univariate statistical analysis to identify the differentially abundant metabolites. ResultsWe identified 23 altered metabolites in the smokers and 36 in the ex-smokers COPD subgroups. Interestingly, in comparison to the control group, no significant alteration was observed in the plasma of non-smoker COPD patients. Additionally, pathway enrichment analysis revealed top dysregulated metabolic pathways, including biosynthesis of unsaturated fatty acids, galactose metabolism, phenylalanine, tyrosine, and tryptophan biosynthesis, and glycosylphosphatidylinositol (GPI)-anchor biosynthesis. The receiver operating characteristic curve screened five metabolites, such as tetradecanoic acid, 2,4-di-tert-butylphenol, chloroxylenol, tetradecanal, and 1-dodecene, with the highest diagnostic performance (AUC > 0.8). ConclusionThis study reveals distinct plasma metabolic signatures across COPD subgroups categorized by cigarette smoking history.

biochemistry↗

bioRxiv2026

Structural insights into the inhibition of sickle hemoglobin polymerization by asymmetric hemoglobin tetramer HbFS (α2γβS)

Sickle cell disease (SCD) is caused by a single amino acid substitution in the {beta}S globin chain at 6th position (6E[->]V). This results in polymerization of deoxy state of sickle hemoglobin (HbS), followed by its precipitation and subsequent sickling of erythrocytes. These deformed cells can block small capillaries (vaso-occlusion), causing cardiovascular complications, ultimately leading to ischemia-reperfusion injury, severe oxygen deficiency, and progressive systemic damage. Occasionally, patients with SCD have been observed to produce exorbitantly high levels of fetal hemoglobin (HbF), which has been linked with the inhibition of HbS polymerization. One of the effects of hydroxyurea, the most commonly used therapeutic for SCD, is to elevate HbF levels. However, the mechanism of inhibitory role of HbF on HbS polymerization is largely unknown. This study attempts to gain insights into the mechanisms involved in this process by means of native mass spectrometry, ion mobility mass spectrometry, and hydrogen deuterium exchange-based mass spectrometry (H/DX-MS). The conformational flexibility of asymmetric hemoglobin, HbFS (2{gamma}{beta}S), for the observed regions in the tetrameric molecule appears to be more in the deoxy state as compared to the oxy state, eventually leading to reduced polymerization of sickle hemoglobin in patients with SCD that express elevated HbF levels.

biochemistry↗

bioRxiv2026

Interplay of Cullin5-HECTD3 ubiquitin ligases regulates stability of CRAF mutant associated with hypertrophy

Proteostatic imbalance caused by CRAF (Raf1) kinase mutation alters MAPK signaling and contributes to RASopathies. CRAF proteostasis is maintained by chaperones, Hsp90 which aids in folding, maturation, and activation; whereas Hsp70 recruits ubiquitin ligase CHIP for proteasomal degradation. However, the proteostasis of disease-associated CRAF mutants remains undefined. Here, we identify HECTD3, a HECT-ubiquitin ligase in promoting degradation of hypertrophic CRAF mutants. Interestingly, increased Hsp90 binding to CRAF plays a determinant factor in degradation via HECTD3. Transient increase in Hsp90-CRAF association upon Hsp90 inhibition promote ubiquitination, whereas prolonged inhibition stabilizes mutant CRAF, indicating temporally distinct chaperone functions. Notably, HECTD3 undergoes proteosomal degradation under stress via Cullin-RING ubiquitin ligase Cul5 in a neddylation-dependent manner. Overexpression of Cul5 thus reduces HECTD3 level resulted in stabilization of CRAFD486N, while promoting degradation of wild-type CRAF. Therefore, modulation of the Cul5-HECTD3 axis alters hypertrophic signaling in cardiomyocyte cells. These results establish a hierarchical proteostasis mechanism in which Hsp90 binding primes substrate for HECTD3-mediated ubiquitination, and Cul5-controlled ligase turnover collectively determine mutant CRAF fate.

cell biology↗

bioRxiv2026

Saliva Metabolomics Reveals Distinct Metabolic Signatures in Patients with Chronic Obstructive Pulmonary Disease: A GC-MS-based approach.

Chronic obstructive pulmonary disease (COPD), a chronic lung disease, involves complex metabolic disturbances that remain poorly characterized using non-invasive matrices. The metabolic alterations associated with cigarette smoke (CS), one of the major drivers of disease progression in COPD patients, have not been explored in detail. This study primarily aimed to investigate the metabolic signatures in COPD patients categorized into smoker (n=15), ex-smoker (n=11), and non-smoker (n=3) subgroups. Utilizing saliva as a noninvasive sample, we identified 26 metabolites with differential expression in smokers and 31 in ex-smokers. However, no such significant alteration was observed in the non-smokers subgroup. The multivariate analysis distinctly separated the COPD subgroups from healthy controls. Additionally, pathway enrichment analysis revealed perturbations in key metabolic pathways, including unsaturated fatty acid biosynthesis, arginine biosynthesis, the tricarboxylic acid (TCA) cycle, and pyruvate metabolism. Moreover, univariate Random forest analysis identified four metabolites (cyclopentanone, tetradecane 4-methyl, acetophenone, and scyllo-inositol) as potential biomarkers distinguishing COPD subgroups from healthy controls. This study offers novel molecular insights into the association of smoking with disease progression and provides a mechanistic understanding of COPD in different subgroups for better management of the disease. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=163 SRC="FIGDIR/small/717654v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@1c3be84org.highwire.dtl.DTLVardef@10ce0aorg.highwire.dtl.DTLVardef@1470712org.highwire.dtl.DTLVardef@2163b6_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2025

Spatial differentiation of proteome in cervical cancer tissues using Imaging Mass Spectrometry

Cervical cancer, which is the fourth most common gynaecological cancer across the globe, has a poorly understood molecular pathogenesis and etiology. Current methods of diagnosis are based on cytology, histology and presence of Human Papillomavirus (HPV). Shortcomings of these methods lie with poor quality of smears which is very common in Papanicolaou (pap) smears, limited sensitivity in terms of early detection, dependence on presence of HPV, etc. Due to its high sensitivity and non-targeted approach, Matrix Assisted Laser Desorption Ionization based Imaging Mass Spectrometry (MALDI-IMS) might be advantageous to understand the pathogenesis, molecular mechanism, precise identification of surgical margins and identification of novel biomarkers. Since it can also identify proteins in the extracellular matrix, it is especially beneficial for the tissue types with sparse cells and excessive extracellular matrix. Although tissue proteome profiling for cervical cancer were reported, the heterogeneous distribution of proteins across cervical cancer tissues havent been explored. In this study, we employed a non-targeted MALDI-IMS based approach to profile the spatial distribution of proteins within cervical cancer tissues. We observed overexpression of Keratin 5 and Prelamin A/C in the region of cervical cancer tissues which were categorically labelled with cancerous morphology using histopathological examination. Both these proteins have been earlier associated with progression and aggressiveness of other cancers like breast and prostate cancers. However, no such reports are available for cervical cancer. Further studies are required on a large dataset to validate and quantitate these proteins as biomarkers for early diagnosis and prognosis of cervical cancer.

cancer biology↗

bioRxiv2025

HSF1 Activator Azadiradione Ameliorates Parkinson Disease and Extends Lifespan in Preclinical Models: Analysis of Underlying Molecular Mechanism

Parkinsons disease (PD) affects millions worldwide, with no efficient therapy currently available. A major cause of the initiation and progression of this degenerative disease is the dysfunctional cellular protein quality control system (PQC), leading to the accumulation of toxic protein aggregates in neurons. We previously reported azadiradione (AZD), a small molecule (MW 451 Da), as a potent inducer of heat shock factor 1 (HSF1) activity, which could alleviate cellular toxicity induced by misfolded proteins by upregulating the levels of inducible molecular chaperones and proteasome activity. Here, we show the multifaceted effect of AZD in enhancing the capacity of PQC machinery in cells, fruit flies, and a PD mouse model. AZD activated HSF1 by promoting its phosphorylation at S326 through MEK. In parallel, AZD boosted protein degradation through increased chymotrypsin-like proteasome activity, upregulation of the ubiquitin ligase CHIP. AZD induced autophagy, marked by elevated levels of Beclin 1, ATG7, and ULK1 phosphorylation at S555, along with mTORC1 inhibition via AMPK activation. Surprisingly, the calorie restriction pathway was also upregulated upon AZD treatment, as demonstrated by the enhanced phosphorylation of FOXO3 and FOXO1, along with increased activity of their target enzymes SOD and catalase. Notably, AKT activity was also suppressed in AZD-treated cells. In vivo, AZD improved motor function, dopaminergic neuron survival, and tyrosine hydroxylase activity in an MPTP-induced mouse model of PD, and extended lifespan in Drosophila without compromising fertility or mobility. These findings highlight AZD as a promising therapeutic candidate for restoring PQC and mitigating PD pathology.

molecular biology↗

bioRxiv2024

Effect of p-benzoquinone, a cigarette smoke-derived component, on the architecture and function of human RBC

p-benzoquinone (pBQ), a cigarette smoke-derived component, stands as one of the lethal oxidants of cigarette smoke. Health hazards caused by cigarette smoking are a profound global health concern. It has been reported to contribute significantly to several health disorders, such as lung cancer, chronic obstructive pulmonary disease (COPD), cardiovascular diseases, etc. These adverse health effects might be attributed to the complex mixture of approximately 4,000 chemicals present in cigarette smoke, such as nicotine, tar, nitric oxide, and p-benzosemiquinone (pBSQ). pBSQ, ranging from 100-200 {micro}g per cigarette, gets oxidized to pBQ in the lungs of smokers and subsequently enters into the bloodstream. In the present study, we investigated the detrimental effect of pBQ on the architecture of human RBCs. Previously, we showed that the covalent modification of human hemoglobin with pBQ results in an alteration in its structure and function. In addition, we explored the potential neutralizing role of N-acetyl cysteine (NAC) in the reactivity of pBQ. Our results demonstrated that pBQ exposure to human red blood cells (RBCs), ex vivo, significantly decreases the reduced glutathione (GSH) content of RBCs, leading to the elevation of reactive oxygen species (ROS) and consequently causing oxidative damage to cellular components. pBQ exposure resulted in increased RBC sedimentation, altered membrane fluidity, enhanced lipid peroxidation, and significant morphological changes, such as bulging and distortion on the surface of RBCs, which eventually compromise membrane integrity. In addition, the coexistence of NAC with pBQ was found to be effective in neutralizing pBQ, thereby restoring GSH levels and RBC membrane architecture. These findings highlight the potential of NAC in mitigating the harmful effects of cigarette smoke on RBCs. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=172 SRC="FIGDIR/small/619387v1_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@8c3d58org.highwire.dtl.DTLVardef@10f7655org.highwire.dtl.DTLVardef@21d140org.highwire.dtl.DTLVardef@30d65c_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2023

Hsp70/Hsp90 organizing protein (HOP) maintains CRAF kinase activity and regulates MAPK signaling by enhancing Hsp90-CRAF association

The stability and activity of CRAF kinase are stringently regulated by heat shock protein 90 (Hsp90). Hsp90-mediated client folding and maturation is governed by its co-chaperones, but their functionality in chaperoning CRAF/Raf1 kinase to accomplish signaling under physiological conditions remains poorly understood. Here, we show that Hsp70/Hsp90 organizing protein (HOP) associates with CRAF kinase for maintaining its kinase activity and facilitates the activation of the MAPK pathway. Such activation is mediated by TPR2A-2B-DP2 domain of HOP and requires efficient binding to Hsp90. Being a recruiter of Hsp90, Cdc37 is unable to supplement the function of HOP/Sti1. Downregulation of HOP/Sti1 in yeast and in vitro cell culture significantly reduces the CRAF signaling. Our data suggest that Hsp90 is recruited to CRAF in two steps, separately initiated by co-chaperones HOP and Cdc37 respectively during CRAF folding/maturation, and again upon CRAF activation mediated by HOP during MAPK signaling. Therefore, HOP is a regulator of CRAF kinase during activation of MAPK pathway and serves as a sensor of growth signaling beyond its client folding and maturation function.

cell biology↗

bioRxiv2020

Praja1 ubiquitin ligase facilitates degradation of polyglutamine proteins and suppresses polyglutamine-mediated toxicity

A network of chaperones and ubiquitin ligases sustain intracellular proteostasis, and is integral in preventing aggregation of misfolded proteins associated with various neurodegenerative diseases. Using cell-based studies of polyglutamine (polyQ) diseases: Spinocerebellar ataxia Type 3 (SCA3) and Huntingtons disease (HD), we aimed to identify crucial ubiquitin ligases that protect against polyQ aggregation. We report here that Praja1 (PJA1), a Ring-H2 ubiquitin ligase abundantly expressed in the brain is diminished when polyQ repeat proteins (Ataxin-3/Huntingtin) are expressed in cells. PJA1 interacts with polyQ proteins and enhances their degradation resulting in reduced aggregate formation. Down-regulation of PJA1 in neuronal cells increases polyQ protein levels vis-a-vis their aggregates rendering the cells vulnerable to cytotoxic stress. Finally, PJA1 suppresses polyQ toxicity in yeast and rescues eye degeneration in transgenic Drosophila model of SCA3. Thus, our findings establish PJA1 as a robust ubiquitin ligase of polyQ proteins and induction of which might serve as an alternative therapeutic strategy in handling cytotoxic polyglutamine aggregates.

cell biology↗

bioRxiv2019

Fluorescent Sp3 Defect-Tailored Carbon Nanotubes Enable NIR-II Single Particle Imaging in Live Brain Slices at Ultra-Low Excitation Doses

Cellular and tissue imaging in the second near-infrared window (NIR-II, [~]1000 - 1350 nm) is advantageous for in vivo studies because of low light extinction by biological constituents at these wavelengths. However, deep tissue imaging at the single molecule sensitivity has not been achieved in the NIR-II window due to lack of suitable bio-probes. Single-walled carbon nanotubes have emerged as promising near-infrared luminescent molecular bio-probes; yet, their inefficient photoluminescence (quantum yield [~]1%) drives requirements for sizeable excitation doses ([~]1-10 kW/cm2) that are significantly blue-shifted from the NIR-II region (<850 nm) and may thus ultimately compromise live tissue. Here, we show that single nanotube imaging can be achieved in live brain tissue using ultralow excitation doses ([~]100 W/cm2), an order of magnitude lower than those currently used. To accomplish this, we synthesized fluorescent sp3-defect tailored (6,5) carbon nanotubes which, when excited at their first order excitonic transition fluoresce brightly at [~]1160 nm. The biocompatibility of these functionalized nanotubes, which are wrapped by state-of-the-art encapsulation agents (phospholipid-polyethylene glycol), is demonstrated using standard cytotoxicity assays. Single molecule photophysical studies of these biocompatible nanotubes allowed us to identify the optimal luminescence properties in the context of biological imaging.

biophysics↗