Search bioRxiv⌕ Search

Biology subjects

Madan, E.

Publications and source records attributed to Madan, E..

3 recordsLinked to original sources

SC2Spa: a deep learning based approach to map transcriptome to spatial origins at cellular resolution

BackgroundUnderstanding cellular heterogeneity within tissues hinges on knowledge of their spatial context. However, it is still challenging to accurately map cells to their spatial coordinates. ResultsWe present SC2Spa, a deep learning-based approach that learns intricate spatial relationships from spatial transcriptomics (ST) data. Benchmarking tests show that SC2Spa outperformed other predictors and accurately detected tissue architecture from transcriptome. SC2Spa successfully mapped single cell RNA sequencing (scRNA-seq) to Visium assay, providing an approach to enhance the resolution for low resolution ST data. Our test showed that SC2Spa performs well for various ST technologies and robust to spatial resolution. In addition, SC2Spa can suggest spatially variable genes that cannot be identified from previous approaches. ConclusionsSC2Spa is a robust and accurate approach to provide single cells with their spatial location and identify spatially meaningful genes.

bioinformatics↗

Sphingosine-1-phosphate regulates Plasmodium histone deacetylase activity and exhibits epigenetic control over cell death and differentiation

Histone deacetylases (HDACs) play a key role in cellular processes by the regulation of gene transcription. This study contributes a novel insight how Plasmodium falciparum HDAC (PfHDAC-1) is regulated by S1P produced by host erythrocyte SphK-1. The binding of S1P with endogenous nuclear extract PfHDAC-1 and recombinant PfHDAC-1 blocks their activity. A significant modulation in transcriptional regulation of P. falciparum HDAC regulated genes resulted upon inhibition of S1P production through blocking of hSphK-1 by clinical SphK-1 inhibitor PF-543. PF-543 led to profound decrease in S1P in the parasites nuclear fraction. The significant modulation of PfHDAC-1 regulated specific candidate genes related to gametocytogenesis, virulence and proliferation was observed in parasite treated with SphK-1 inhibitor, suggesting S1P targets PfHDAC-1 and participates in epigenetic regulation of these key cellular processes. The epigenetic modulation of parasite cell growth and differentiation by host provides a novel approach for the developmenthost-targeted therapeutics.

molecular biology↗

Leishmania parasite arginine deprivation response pathway influences the host macrophage lysosomal arginine sensing machinery

Extensive interaction between the host and pathogen metabolic networks decidedly shapes the outcome of infection. Infection with Leishmania donovani, an intracellular protozoan parasite, leads to a competition for arginine between the host and the parasite. L. donovani transports arginine via a high-affinity transporter LdAAP3, encoded by the two genes LdAAP3.1 and LdAAP3.2. Earlier reports show that upon arginine starvation, cultured Leishmania parasites promptly activate an Arginine Deprivation Response (ADR) pathway, resulting in the stoichiometric up-regulation of LdAAP3.2 mRNA, protein and activity. Lysosomes, on the other hand, are known to employ a specific sensor and an arginine-activated amino acid transporter, solute carrier family 38 member 9 (SLC38A9) that monitors intra-lysosome arginine sufficiency and subsequently up-regulates cellular mTORkinase activity. The present study investigates the interaction between Leishmania and macrophage-lysosome arginine sensing machinery. We show that infection with L. donovani activates SLC38A9 arginine sensing in the human monocyte like-macrophage cell line (THP-1) when grown under physiological concentrations of arginine (0.1 mM). However, supplementing the macrophage growth medium with excess arginine (1.5 mM) followed by infection led to the down-regulation of SLC38A9. Similarly, THP-1 cells infected with LdAAP3.2 null mutants grown in 0.1 mM arginine resulted in reduced expression of SLC38A9 and mTOR. These results indicate that inside the host macrophage, Leishmania overcome low arginine levels by up-regulating the transport of arginine via LdAAP3 and SLC38A9 signalling. Furthermore, while LdAAP3.2 null mutants were impaired in their ability to develop inside THP-1 macrophages, their infectivity and intracellular growth were restored in SLC38A9 silenced macrophages. This study provides the first identification of regulatory role of SLC38A9 in the expression and role of LdAAP3. Author SummaryLeishmania donovani, the causative agent of kala-azar, exhibits a digenetic life cycle. Following infection of the mammalian host, promastigotes differentiate into intracellular amastigotes within the phagolysosome of macrophages. Arginine is a central point of competition between the host and the pathogen. L. donovani senses lack of arginine in the surrounding micro-environment and activates a unique ADR pathway, thus upregulating the expression of the arginine transporter (LdAAP3). The arginine-activated amino acid transporter SLC38A9 localizes to the lysosome surface of mammalian cells and acts as a sensor that transmits information about arginine levels in the lysosome lumen to the mechanistic target of rapamycin (mTOR) kinase. In the present study, we identified the functional interaction of host SLC38A9 and parasite LdAAP3 in macrophages infected with L. donovani. We report that host SLC38A9 upregulation is critical for enhancing and maintaining high LdAAP3 levels in intracellular L. donovani. Our results decode crucial information regarding the molecular mechanism involved in the arginine sensing response in L. donovani-infected host cells. These findings increase our understanding of the interaction of signalling intermediates during Leishmania infection which may lead to the discovery of novel therapeutic interventions.

molecular biology↗