| 51 |
IPD6047 |
Nuclear-injuries by aberrant dynein-forces defeat proteostatic purposes of Lewy Body-like InclusionsNuclear-injuries by aberrant dynein-forces defeat proteostatic purposes of Lewy Body-like Inclusions |
Dr Swasti Raychaudhuri |
Biogenesis of inclusion bodies (IBs) facilitates protein quality control (PQC). Canonical aggresomes execute degradation of misfolded proteins while non-degradable amyloids quarantine into Insoluble Protein Deposits. Lewy Bodies (LBs) are well-known neurodegenerative IBs of α-Synuclein but PQC-benefits and drawbacks associated with LBs remain underexplored. Here, we report that a crosstalk between...
Biogenesis of inclusion bodies (IBs) facilitates protein quality control (PQC). Canonical aggresomes execute degradation of misfolded proteins while non-degradable amyloids quarantine into Insoluble Protein Deposits. Lewy Bodies (LBs) are well-known neurodegenerative IBs of α-Synuclein but PQC-benefits and drawbacks associated with LBs remain underexplored. Here, we report that a crosstalk between LBs and aggresome-like IBs of α-Synuclein (Syn-aggresomes) buffer amyloidogenic α-Synuclein load. LBs possess unorthodox PQC-capacities of self-quarantining Syn-amyloids and being degradable upon receding fresh amyloidogenesis. Syn-aggresomes equilibrate biogenesis of LBs by facilitating spontaneous degradation of soluble α-Synuclein and opportunistic turnover of Syn-amyloids. LBs overgrow at the perinucleus once amyloidogenesis sets in and are misidentified by cytosolic BICD2 as cargos for motor-protein dynein. Simultaneously, microtubules surrounding the perinuclear LBs are distorted misbalancing the dynein motor-force on nucleoskeleton leading to widespread lamina injuries. Like typical Laminopathies, nucleocytoplasmic mixing, DNA-damage, and deregulated transcription of stress chaperones defeat the proteostatic purposes of LBs.
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Centre for Cellular & Molecular Biology (CCMB |
Gel-based experiment |
2024-11-16 |
38477372
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| 52 |
IPD4200 |
A comprehensive comparison of Rapid and Deep Plasma Proteomics workflows to identify and quantify biomarkers of Sickle Cell Anaemia |
Dr. Swasti Raychaudhuri |
Plasma serves as a rich source of protein biomarkers but in-depth proteomic analysis is challenging due to the vast dynamic range of protein abundance. Pre-fractionation of plasma proteins is commonly practiced to improve the proteome coverage but the protocols are time-expensive, suffer from flowchart complexity, and often less reproducible. Here,...
Plasma serves as a rich source of protein biomarkers but in-depth proteomic analysis is challenging due to the vast dynamic range of protein abundance. Pre-fractionation of plasma proteins is commonly practiced to improve the proteome coverage but the protocols are time-expensive, suffer from flowchart complexity, and often less reproducible. Here, we explore multiple strategies of shotgun proteomics to optimize biomarker discovery workflows for Sickle Cell Anaemia (SCA) patients from remote India. A deep proteomics workflow via off-line reverse phase Ultra High-Pressure Liquid Chromatography based fractionation of tryptic digested plasma peptides followed by optimized pooling of peptides based on charge and hydrophobicity yielded the best depth of plasma proteome with a trade-off of significantly long experimental time. Alternatively, a rapid analysis of tryptic digested plasma peptides via a shorter gradient mass spectrometry run saves time but quantifies only ~ 50% of the proteins than the deep workflow. Intriguingly, despite the difference in proteome coverage, more than 80% of known FDA and SCA biomarkers quantified in the deep workflow are also quantified in the rapid workflow. Given the practical difficulties of sample collection and plasma preservation in rural India, we propose the deep proteomics workflow for biomarker discovery in smaller cohorts and the rapid workflow for biomarker validations in larger cohorts. Additional targeted proteomics based strategies may be designed for the validation of missing biomarkers in the rapid workflow.
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Centre for Cellular & Molecular Biology (CCMB |
Shotgun proteomics |
2024-11-16 |
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| 53 |
IPD8972 |
Distinct Stress Response to Mitochondrial Inter-membrane Space and Matrix Proteotoxic Stress are Preferentially Modulated by TOM complex and Vms1, respectively |
Dr Swasti Raychaudhuri |
Double-membrane-bound architecture of mitochondria is essential for its ATP synthesis function; simultaneously such structure sub-divides the organelle into inter-membrane space (IMS) and matrix. IMS and matrix are inherently different in protein folding milieu due to their contrasting oxido-reductive environments and distinctly different protein quality control (PQC) machineries. By inducing proteotoxic...
Double-membrane-bound architecture of mitochondria is essential for its ATP synthesis function; simultaneously such structure sub-divides the organelle into inter-membrane space (IMS) and matrix. IMS and matrix are inherently different in protein folding milieu due to their contrasting oxido-reductive environments and distinctly different protein quality control (PQC) machineries. By inducing proteotoxic stress limited to IMS or matrix using varied stressor proteins, we decipher distinct cellular response to IMS and matrix stress. IMS stress leads to specific upregulation of IMS-resident chaperones and TOM complex components. In contrast, matrix stress leads to specific upregulation of matrix- chaperones and cytosolic PQC components. We report that cells respond to mitochondrial stress by an adaptive mechanism by adjourning mitochondrial respiration while upregulating glycolysis as a compensatory pathway. By systematic genetic interaction, we show that TOM complex components act as specific modulators of IMS-stress response while Vms1 preferentially modulates the matrix stress response
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Centre for Cellular & Molecular Biology (CCMB |
Top-down |
2024-11-16 |
35500842
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| 54 |
IPD8258 |
Cell membrane proteome analysis in HEK293T cells challenged with α-Synuclein amyloids |
Dr Swasti Raychaudhuri |
Amyloids interact with plasma membranes. Extracellular amyloids cross the plasma membrane barrier. Internalized extracellular amyloids are reported to trigger amyloidogenesis of endogenous proteins in recipient cells. To what extent these extracellular and intracellular amyloids perturb the plasma membrane proteome is not investigated. Using α-Synuclein as a model amyloid protein, we...
Amyloids interact with plasma membranes. Extracellular amyloids cross the plasma membrane barrier. Internalized extracellular amyloids are reported to trigger amyloidogenesis of endogenous proteins in recipient cells. To what extent these extracellular and intracellular amyloids perturb the plasma membrane proteome is not investigated. Using α-Synuclein as a model amyloid protein, we performed membrane shaving followed by mass spectrometry experiment to identify the conformational changes in the cell surface proteins after extracellular amyloid challenge. We also performed membrane proteomics after the biogenesis of intracellular α-Synuclein amyloids. Our results suggest that promiscuous interaction with extracellular amyloids stochastically alter the conformation of plasma membrane proteins. This affects the biological process through the plasma membrane and result in loss in cell viability. Cells that survive the extracellular amyloid shock can grow normally and gradually develop intracellular amyloids which do not directly impact the plasma membrane proteome and associated biological processes. Thus, α-Synuclein amyloids can damage the plasma membrane and related processes only during cell to cell transfer and not during their intracellular biogenesis.
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Centre for Cellular & Molecular Biology (CCMB |
Shotgun proteomics, Gel-based experiment |
2024-11-16 |
38973669
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| 55 |
IPD1873 |
Biogeographic venom variation in medically important Indian snakes and the inadequacy of antivenom therapy in snakebite hotspots |
Dr. Kartik Sunagar |
The project aims at investigating the snake venom variability of Daboia russelii populations from five different biogeographic zones across India.
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Evolutionary Venomics Lab, Center for Ecological Sciences, Indian Institute of Science, Bangalore, India |
Shotgun proteomics |
2024-11-24 |
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| 56 |
IPD8910 |
A wolf in another wolf’s clothing: Post-genomic regulation dictates venom profiles of medically-important cryptic kraits in India |
Dr. Kartik Sunagar |
This study investigates the widespread cryptic Bungarus caeruleus (Comman krait) in India and clinical repercussions of their bits by implementing multidisciplinary approach involving proteomics, transcripomics, and assessment of toxicity and efficacy of currently marketed anivenoms. The study also aims at understanding the evolutionary relationships between these phenotypically simillar kraits.
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Evolutionary Venomics Lab, Center for Ecological Sciences, Indian Institute of Science, Bangalore, India |
Shotgun proteomics |
2024-11-24 |
33477742
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| 57 |
IPD3987 |
The preclinical evaluation of a second-generation antivenom for treating snake envenoming in India |
Dr. Kartik Sunagar |
In this study, by employing chromatographic purification of the bulk, we have significantly enhanced the preclinical performance of the conventional Indian antivenom product. The effectiveness of the test batches of this ‘second-generation’ antivenom was evaluated using a variety of in vitro and in vivo preclinical assays, including venom recognition and...
In this study, by employing chromatographic purification of the bulk, we have significantly enhanced the preclinical performance of the conventional Indian antivenom product. The effectiveness of the test batches of this ‘second-generation’ antivenom was evaluated using a variety of in vitro and in vivo preclinical assays, including venom recognition and toxicity and pathology neutralisation. The outcomes of these experiments demonstrated the significantly superior performance of the purified product over all other major commercial Indian antivenoms.
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Evolutionary Venomics Lab, Center for Ecological Sciences, Indian Institute of Science, Bangalore, India |
Shotgun proteomics |
2024-11-24 |
35324665
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| 58 |
IPD6128 |
Stings on wings: venom proteomics and tissue transcriptomics of the lesser banded hornet, Vespa affinis |
Dr Kartik Sunagar |
The project aims at unraveling the venom repertoire of the lesser banded hornet (Vespa affinis) and investigate the regimes of natural selection underpinning their venom evolution. The study also sheds light on the clinical repercussions of the V. affinis venom.
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Evolutionary Venomics Lab, Center for Ecological Sciences, Indian Institute of Science, Bangalore, India |
Shotgun proteomics |
2024-11-24 |
36601583
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| 59 |
IPD3822 |
Fangs in the ghats: preclinical insights into the medical importance of endemic pit vipers from the Western Ghats |
Dr. Kartik Sunagar |
The socioeconomic burden of snakebite in India is largely attributed to the ‘big four’ snakes, completely neglecting the considerable impact of envenoming by many other snake species. Bites from the so-called ‘neglected many’ are often treated with a polyvalent antivenom that is manufactured against the ‘big four’ snakes - a...
The socioeconomic burden of snakebite in India is largely attributed to the ‘big four’ snakes, completely neglecting the considerable impact of envenoming by many other snake species. Bites from the so-called ‘neglected many’ are often treated with a polyvalent antivenom that is manufactured against the ‘big four’ snakes - a strategy that has been widely documented to fail. Yet, specific antivenoms are not commercially manufactured against these snakes. While the medical importance of various species of cobras, saw-scaled vipers, and kraits is very well-known, the clinical impact of pit vipers from the rainforests of the Western Ghats, northeastern India, and Andaman and Nicobar islands has remained elusive. Amongst the 90+ species of snakes found in the Western Ghats, the hump-nosed (Hypnale hypnale), Malabar (Craspedocephalus malabaricus) and bamboo (Craspedocephalus gramineus) pit vipers can potentially inflict clinically severe envenoming in humans. To evaluate the severity of toxicity inflicted by these snakes, we characterised their venom composition, biochemical and pharmacological activities, and toxicity- and morbidity-inducing potentials. Our findings highlight the therapeutic inadequacies of the generic Indian and Hypnale-specific Sri Lankan polyvalent antivenoms in neutralising morbidity and mortality resulting from pit viper envenomings and underscore the need for a regional antivenom therapy in India.
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Evolutionary Venomics Lab, Center for Ecological Sciences, Indian Institute of Science, Bangalore, India |
Shotgun proteomics |
2024-11-24 |
37298463
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| 60 |
IPD7258 |
The Arabian cousin: Comparative venomics of Daboia palaestinae and Daboia russelii |
Dr. Kartik Sunagar |
In this study, to unravel the influence of phylogenetic divergence and biogeography in shaping the composition and activity of Daboia venoms, we comparatively investigated the venoms of D. russelii from western India and D. palaestinae from Israel.
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Evolutionary Venomics Lab, Center for Ecological Sciences, Indian Institute of Science, Bangalore, India |
Shotgun proteomics |
2024-11-24 |
36355975
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