Biology subjects

Sanyal, P.

Publications and source records attributed to Sanyal, P..

5 recordsLinked to original sources

bioRxiv2025

Sec and Tat mediated secretion safeguards Mycobacterium tuberculosis membrane homeostasis

Protein secretion drives Mycobacterium tuberculosis (Mtb) physiology and pathogenesis, yet a unified picture of the machinery and its role in cell membrane homeostasis is still lacking. By comprehensively curating published evidence, we assembled a systems-level map of Mtb secretion encompassing 92 components and 198 mechanistic reactions across Sec, Tat, and ESX pathways. The secretory components identified were integrated with high-throughput ChIP-Seq and transcriptome datasets to elucidate the regulation of the secretion system. Using CRISPRi, conditional depletion of SecA1 or TatA impaired growth in vitro and survival ex vivo. Quantitative secretome revealed decreased export of SecA1- and TatA-dependent substrates, with enrichment of cytosolic proteins in culture filtrates, indicating increased membrane permeability. Membrane proteomics showed depletion dependent increased metabolic/lipid-degrading proteins and decreased cell-wall/cell-process proteins, consistent with loss of membrane stability. Ultrastructural defects and increased ethidium bromide uptake confirmed impaired membrane integrity. Together, our multi-omics and functional genetics established SecA1 and TatA as essential guardians of Mtb membrane integrity which provided valuable datasets and a framework for secretion-dependent Mtb pathogenesis.

microbiology↗

bioRxiv2023

A hepatocyte-specific transcriptional program driven by Rela and Stat3 exacerbates experimental colitis in mice by modulating bile synthesis

Hepatic factors secreted by the liver promote homeostasis and are pivotal for maintaining the liver-gut axis. Bile acid metabolism is one such example wherein, bile acid synthesis occurs in the liver and its biotransformation happens in the intestine. Dysfunctional interactions between the liver and the intestine stimulate varied pathological outcomes through its bidirectional portal communication. Indeed, aberrant bile acid metabolism has been reported in inflammatory bowel disease (IBD). However, the molecular mechanisms underlying these crosstalks that perpetuate intestinal permeability and inflammation remain obscure. Here, we identify a novel hepatic gene program regulated by Rela and Stat3 that accentuates the inflammation in an acute experimental colitis model. Hepatocyte-specific ablation of Rela and Stat3 reduces the levels of primary bile acids in both the liver and the gut and shows a restricted colitogenic phenotype. On supplementation of chenodeoxycholic acid (CDCA), knock-out mice exhibit enhanced colitis-induced alterations. This study provides persuasive evidence for the development of multi-organ strategies for treating IBD and identifies a hepatocyte-specific rela-stat3 network as a promising therapeutic target.

immunology↗

bioRxiv2022

GWAS and functional studies implicate a role for altered DNA repair in the evolution of drug resistance in Mycobacterium tuberculosis

The emergence of drug resistance in Mycobacterium tuberculosis (Mtb) is alarming and demands in-depth knowledge for timely diagnosis. We performed genome-wide association analysis (GWAS) using 2237 clinical strains of Mtb to identify novel genetic factors that evoke drug resistance. In addition to the known direct targets, for the first time, we identified a strong association between the mutations in the DNA repair genes and the multidrug-resistant phenotype. To evaluate the impact of variants identified in the clinical samples in the evolution of drug resistance, we utilized knockouts and complemented strains in Mycobacterium smegmatis (Msm) and Mtb. Results show that variant mutations abrogated the function of MutY and UvrB. MutY variant showed enhanced survival compared with wild-type (Rv) when the Mtb strains were subjected to multiple rounds of ex vivo antibiotic stress. Notably, in an in vivo Guinea pig infection model, the MutY variant outcompeted the wild-type strain. Collectively, we show that novel variant mutations in the DNA repair genes abrogate their function and contribute to better survival under antibiotic/host stress conditions.

microbiology↗

bioRxiv2021

A machine learning model for screening of body fluid cytology smears

IntroductionBody fluid cytology is one of the commonest investigations performed in indoor patients, both for diagnosis of suspected carcinoma as well as staging of known carcinoma. Carcinoma is diagnosed in body fluids by the pathologist through microscopic examination and searching for malignant epithelial cell clusters. The process of screening body fluid smears is a time consuming and error prone process. AimWe have attempted to construct a machine learning model which can screen body fluid cytology smears for malignant cells. Materials and methodsMGG stained Ascitic / pleural fluid cytology smears were included from 21 cases (14 malignant, 07 benign) in this study. A total of 693 microphotographs were taken at 40x magnification at the same illumination and after correction of white balance. A Magnus Microphotography system was used for photography. The images were split into the training set (195 images), test set (120 images) and validation set (378 images). A machine learning model, a convolutional neural network, was developed in the Python programming language using the Keras deep learning library. The model was trained with the images of the training set. After completion of training, the model was evaluated on the test set of images. ResultsEvaluation of the model on the test set produced a sensitivity of 97.87%, specificity 85.26%, PPV 95.18%, NPV 93.10% In 06 images, the model has failed to detect singly scattered malignant cells/ clusters. 14 (3.7%) false positives was reported by the model. The machine learning model shows potential utility as a screening tool. However, it needs improvement in detecting singly scattered malignant cells and filtering inflammatory infiltrate.

pathology↗

bioRxiv2020

A study of conventional histological parameters in excision specimens of breast cancer over a 7 year period and association with immunohistochemical categories

Background Along with conventional histological examination, immunohistochemistry (IHC) is a useful adjunct to assessment of a breast cancer excision specimen. Previous studies have shown differences in behavior of neoplasms depending on their histopathological as well as immunohistochemical categories; in particular, triple negative breast cancers (on IHC) show the worst prognosis.Objectives To find association, if any, within conventional histopathological characteristics (size, grade, stage, mitotic count, desmoplasia, dense inflammatory infiltrate, lymphovascular invasion) and between the conventional parameters and immunohistochemical categories of breast cancer, in both primary and post neo adjuvant chemotherapy (NACT) specimens.Methods 177 breast cancer excision specimens examined over last 7 years were assessed retrospectively, their histopathological parameters were recorded. In cases where immunohistochemistry was performed (N=108) the specimen was placed in one of the immunohistochemical categories: Luminal A, Luminal B, Her2 and Triple negative cancers. The data was then analysed by standard statistical methods.Results No statistically significant association was found between the histopathological parameters and IHC category was. However, a strong correlation was seen between lymphovascular invasion within the primary tumor and increasing lymph node involvement. There was also a reduction in ER and PR expression in neoplasms post NACT, while HER2 expression remained largely unchanged.Conclusion There might be additional genetic subtypes underlying the immunohistochemical phenotypes which determine the morphological characteristics of the neoplasm.Competing Interest StatementThe authors have declared no competing interest.View Full Text

pathology↗