Biology subjects

Basak, T.

Publications and source records attributed to Basak, T..

5 recordsLinked to original sources

bioRxiv2025

Deciphering the intra-tissue specific Collagen PTMs site-specific heterogeneity in Human Adrenal extracellular-matrix

The human adrenal is one of the pivotal glands of the endocrine system. Recently, the extracellular matrix (ECM) of the adrenal capsule and cortex was explored by dividing them into two fractions: outer (OF) and inner (IF). A significant variation in the levels of ECM proteins, including collagens, was documented. During the biosynthesis of collagen, it undergoes a plethora of PTMs exhibiting crucial roles such as cell-matrix interaction, adhesion, crosslinking, stability, etc. However, the site-specific identification and characterization of collagen PTMs remained challenging and is unknown for the human adrenal gland. We applied our in-house developed proteomics pipeline to identify several PTMS in 25 collagen chains from human adrenal-ECM. In the entire collagenome, we identified a total of 963 4-hydroxyproline (4-HyP), 201 3-hydroxyproline (3-HyP), 105 hydroxylysine (HyK), 17 galactosyl-hydroxylysine (G-HyK), and 35 glucosyl galactosyl-hydroxylysine (GG-HyK) sites. Although the site-specificity of collagen PTMs (3-HyP, HyK, G/GG-HyK) across fractions is conserved, the occupancies were different in a site-specific manner. Classically, a fully 3-hydroxylated site (P1164) of COL1A1 associated with osteogenesis imperfecta was found to be approximately fully hydroxylated ([~]99%) across fractions. Similarly, we also looked at the microheterogeneity of lysine modifications on one lysine residue (K862) of COL1A1. We observed that the hydroxylation level was higher in OF, while glycosylation levels were higher in IF. This may suggest a change in the crosslinking of collagen I across both fractions. Further, our analysis revealed much higher site-specific O-glycosylation in basement membrane collagen-IV, potentially facilitating the secretion of steroids from the adrenal gland. For the first time, we have annotated the collagen PTMs, developed a COL1A1 PTM map, and quantitated site-specific PTMs in the human adrenal gland. Taken together, this work revealed that intra-tissue-specific site-specific PTM collagen heterogeneity and lay the foundation for understanding their role in region-specific functions.

biochemistry↗

bioRxiv2025

Live access to the emotional dynamics of REM sleep dreams in lucid dreamers with narcolepsy

Sleep helps regulate emotions, but it is still unclear whether -and how- the emotions we experience in dreams contribute to this regulation. To uncover the potential function of dream emotions, we must first understand what they are and how they unfold in dreams. The emotional content of dreams has mostly been studied using post-sleep dream reports, which provide a biased and static snapshot of a complex and dynamic experience. In this study, we took a more direct approach, accessing dream emotions in real-time. We asked twenty-four lucid dreamers with narcolepsy to report the emotional valence of their dreams, - positive, negative or neutral-, while still asleep, using predefined facial codes during daytime naps monitored with polysomnography. Of the 126 naps recorded, 62 contained at least one emotional code during REM sleep, yielding 191 codes in total. The ratios of positive and negative codes were evenly balanced per nap. The 33 naps with at least two codes allowed us to track the dream emotional dynamics. Over half of these naps showed opposite emotional valences (positive and negative). By measuring the time elapsed between codes, we estimated the average duration of a given dreams emotional valence in REM sleep to be about one minute. Positive emotions emerged on average earlier than negative ones during lucid REM sleep. These findings confirm the highly emotional nature of dreams and, more importantly, highlight that emotions in REM sleep dreams are fluid and fast-changing. Such emotional dynamics during REM sleep dreams may help us to better understand the mechanisms of the emotional regulatory function of dreams.

neuroscience↗

bioRxiv2025

Integrative plasma lipidomics and proteomics profiling to decipher potential biomarkers of dilated cardiomyopathy

BackgroundDilated cardiomyopathy (DCM), primarily characterised by left ventricular dilatation and systolic dysfunction, is one of the leading causes of heart failure and requires a critical clinical investigative strategy. However, conventional imaging techniques such as echocardiography and MRI, along with some classical CVD markers (NTproBNP, cTnT), fall short in diagnosing DCM-specific phenotypes. Thus, the need for biochemical markers with enhanced accuracy to DCM is of enormous importance. Lipids and proteins play essential roles in maintaining myocardial function. The homeostatic disruption of such biomolecules might contribute to DCM pathogenesis, thus offering to serve as potential biomarkers for DCM. Moreover, the lack of global lipidomics studies and specific protein markers in DCM patients prompted us to explore the disease pathophysiology through an integrative omics-based analysis coupled with an ML-derived approach. ObjectiveTo identify accurate, precise and specific circulatory lipidomic and proteomic biomarkers of DCM using high-resolution mass spectrometry and machine learning (ML)-based approaches. MethodsHigh-resolution-mass-spectrometry-based lipidomics and proteomics were applied to identify lipid and protein biomarkers in a cohort (n=360) of healthy and DCM patients. Top protein classifiers were further evaluated using single-cell transcriptomics on publicly available datasets from DCM myocardium and validated using ELISA. A biomarker panel was built by the integration of lipidomics and validated proteomics data using machine-learning-based approaches. ResultsA total of 125 lipids and 10 proteins have been primarily discovered with significant alterations in DCM (0.8 [≥] FC [≥] 1.2; padj < 0.05). Using a Boruta-based ML approach, we identified 39 lipids and 10 proteins as primary discriminators between DCM and controls. ELISA validation confirmed the potential of B2M (6.85 {+/-} 2.86 g/ml vs. 4.26 {+/-} 1.25 g/ml; p < 0.0001) and Tetranectin (CLEC3B) (1.99 {+/-} 0.88 g/ml vs. 2.49 {+/-} 0.90 g/ml; p = 0.0006) to emerge as protein biomarkers of DCM. In line with that, the single-cell transcriptomic analysis showed a similar trend of alteration of tetranectin (CLEC3B) in cardiomyocytes and {beta}2microglobulin (B2M) in varied cell types of the myocardium. Further, Integrated ROC analysis combining the top 8 lipid discriminators with B2M and CLEC3B achieved an AUC of 0.995, demonstrating enhanced diagnostic precision compared to the classical CVD marker NTproBNP (0.965). ConclusionThis study offers a system-omics-based perspective on first-global lipidomic and proteomic changes associated with DCM pathophysiology, with a high potential for diagnostic application.

systems biology↗

bioRxiv2023

DIGEST: An online tool for designing of multiple reaction monitoring assays

Targeted proteomics using multiple reaction monitoring (MRM) assays enables fast and sensitive detection of a preselected set of target peptides. This technique utilizes the specificity of precursors to product transitions for quantitative analysis of multiple proteins in a single sample. The success of an MRM experiment depends on the selection of transitions however, given the existing resources, accurately predicting signal intensity of peptides and their fragmentation patterns ab initio is challenging task. We present an alternative for rapid design of MRM transitions for proteomics research: DIGEST. Our method predicts the b and y ions with +1 and +2 charge produced in a collision cell of a mass spectrometer from peptides of multiple proteotypically digested proteins. Additionally, by using the existing knowledge of the fundamental rules for designing transitions, the tool provides optimal MRM transitions, negating the need to undertake prior "discovery" MS studies. We demonstrate that our algorithm is directed toward the selection of MRM precursor and product-ions pairs, and can avoid the pitfalls of interference due to cross-contamination of samples by selecting ion combinations that uniquely map to target peptides. Comparison with SRMAtlas showed that DIGEST successfully predicted the peptide and production pairs in the majority of cases. We believe that DIGEST will facilitate rapid design of MRM assays with increased specificity, reducing the overall time required to design an MRM assay for routine mass-spectrometry. DIGEST is available as a web-based tool at https://digest.raylab.iiitd.edu.in/

bioinformatics↗

bioRxiv2023

Decoding the comprehensive substrate-specificity and evidence of altered site-specific collagen prolyl-3-hydroxylation, lysyl-hydroxylation, and lysyl O-glycosylation in P4ha1 and P4ha2 deleted mutant mice

Collagens, the most abundant proteins in mammals, play pivotal roles in the maintenance of tissue structure, functions, cell-to-cell communication, cellular migration, behavior, and growth. Collagens are highly complex in structure due to the dynamic post-translational modifications (PTMs) such as hydroxylations (on prolines and lysine residues) and O-glycosylation (on hydroxylysines) enzymatically catalyzed during biosynthesis. The most prevalent modification in fibrillar collagens is prolyl 4-hydroxylation catalyzed by collagen prolyl 4-hydroxylases (C-P4hs). Prolyl 4-hydroxylation on collagens plays a critical role in collagen biosynthesis, thermostability, and cell-collagen interactions. However, the site-specificity of prolyl 4-hydroxylase 1 (P4ha1) and P4ha2 is not comprehensively studied yet. Further, the effect of P4ha1 and P4ha2 on the plethora of other site-specific collagen PTMs is not known to date. In-depth mass-spectrometry data (PXD008802) analysis of mice skin collagen I extracted from wild-type and different deletion mutants of C-P4hs revealed that partial or full deletion of prolyl 4-hydroxylases (P4ha1 and P4ha2) significantly decreases collagen deposition in ECM hinting towards perturbed biosynthesis. A total of 421 site-specific PTMs on fibrillar collagen chains (Col1a1, Col1a2, and Col3a1) were identified. Further, novel 23 P4ha1 specific, 8 P4ha2 specific, and 18 C-P4hs promiscuous sites on fibrillar collagen chains were identified. Partial deletion of P4ha1 and full deletion of P4ha2 also resulted in altered levels of the site-specific prolyl-3-hydroxylation occupancy in collagen I. Surprisingly, an increased level of site-specific lysyl hydroxylation (Col1a1-K731, Col1a2-K183,315) was documented upon partial deletion of P4ha1 and full deletion of P4ha2. Our findings showcased that the activity of prolyl 4-hydroxylases is not limited to 4-hydroxylation of specific proline sites, but simultaneously can perturb the entire biosynthetic network by modulating prolyl 3-hydroxylation and lysyl hydroxylation occupancy levels in the fibrillar collagen chains in a site-specific manner.

biochemistry↗