Biology subjects

Mahata, J.

Publications and source records attributed to Mahata, J..

3 recordsLinked to original sources

bioRxiv2024

The Role of ISG15 in Cancer Biology: Systematic Evaluation of ISG15 Expression and Its Molecular Interactions in a Pan-Cancer Context

Background: Interferon-stimulated gene 15 (ISG15) is a ubiquitin-like modifier induced by inflammatory cues, yet its functional relevance in cancer remains unclear and context dependent. Although frequently used as an interferon marker, whether ISG15 reflects effective antitumor immunity or dysfunctional immune states across cancers has not been systematically resolved. Methods: We performed an integrative pan-cancer analysis using TCGA, CPTAC, GEO, and immunotherapy and single-cell RNA-seq cohorts. ISG15 was examined at transcriptomic, proteomic, epigenetic, genetic, immune-infiltration, and phosphoproteomic levels. Survival-modeling, mutation and copy-number analyses, pathway-enrichment, protein-protein interaction networks, and kinase enrichment were used to define functional associations, with focused comparisons between renal clear cell carcinoma (KIRC) and chromophobe carcinoma (KICH). Results: ISG15 was upregulated in all studied cancers but downregulated in KICH. Its prognostic associations were bidirectional, correlating with poor survival in KIRC, LIHC, COAD, and LGG, yet favorable outcomes in SKCM, MESO, and OV. In KIRC, high ISG15 was associated with early promoter hypomethylation, interferon signaling, immune infiltration, T-cell exhaustion signatures, and broad immune-associated phosphokinase activity. In contrast, KICH showed preserved methylation, weak interferon coupling, limited immune engagement, and phosphoproteomic enrichment of structural and trafficking pathways. Genetic alterations and deep deletions of ISG15 were associated with shorter progression-free survival. Conclusion: This study indicates that ISG15 is associated with dysfunctional immune states rather than a direct effector of tumor control. These findings highlight ISG15 as a context-specific biomarker whose functional impact likely depends on tumor type and microenvironment, warranting further mechanistic and experimental validation.

bioinformatics↗

bioRxiv2024

Pathways in the brain, heart, and lung influenced by SARS-CoV-2 NSP6 and SARS-CoV-2 regulated miRNAs: an in silico study hinting cancer incidence

The influence of SARS-CoV-2 non-structural protein in the hosts tissue-specific complexities remains a mystery and needs more in-depth attention because of COVID-19 recurrence and long COVID. Here we investigated the influence of SARS-CoV-2 transmembrane protein NSP6 (Non-structural protein 6) in three major organs - the brain, heart, and lung in silico. To elucidate the interplay between NSP6 and host proteins, we analyzed the protein-protein interaction network of proteins regulated after SARS-CoV-2 infection and that are interacting with NSP6 interacting proteins. Pathway enrichment analyses provided global insights into biological pathways governed by differentially regulated genes in the three tissues after COVID-19 infection. Many drugs targeting hub genes of tissue-specific protein interactome were found that could be candidates for COVID-19 management. MiRNA-gene network for the tissue-specific regulated proteins was also deduced and comparing gene list targeted by SARS-CoV-2 regulated miRNAs, we found three and two common genes in the brain and lung respectively. Among the five common proteins revealed as potential therapeutic targets across the three tissues, Galectin3 (LGALS3) that was upregulated in the heart and brain after COVID-19 infection is reported to be influencing all the ten hallmarks of cancer positively and is found in multiple cancers. COVID-19 infection also causes myocardial inflammation and heart failure (HF). HF is observed to be increasing cancer incidence. Our bioinformatics and systems study hints probable effect of COVID-19 infection in cancer incidence and warrants in-depth studies in this direction and cancer surveillance especially with the present scenario of long COVID-19 and recurrent COVID-19 infections. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/578752v2_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@f10223org.highwire.dtl.DTLVardef@c34b64org.highwire.dtl.DTLVardef@18aaf59org.highwire.dtl.DTLVardef@1fe0b35_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2023

COVID-19 ORF3a Viroporin Influenced Common and Unique Cellular Signalling Cascades in Lung, Heart and Brain Choroid Plexus Organoids with Additional Enriched MicroRNA Network Analyses for Lung and Brain Tissues

Tissue specific implications of SARS-CoV-2 encoded accessory proteins are not fully understood. SARS-CoV-2 infection can severely affect three major organs - the heart, lung, and brain. We analysed SARS-CoV-2 ORF3a interacting host proteins in these three major organs. Further we identified common and unique interacting host proteins, their targeting miRNAs (lung and brain), and delineated associated biological processes reanalysing RNA-seq data from the brain (COVID-19 infected/uninfected Choroid Plexus Organoids study), lung tissue from COVID-19 patients/healthy subjects, and cardiomyocyte cells based transcriptomics analyses. Our in silico studies showed ORF3a interacting proteins could vary depending upon tissues. Number of unique ORF3a interacting proteins in brain, lung and heart were 10, 7 and 1 respectively. Though common pathways influenced by SARS-CoV-2 infection were more, unique 21 brain and 7 heart pathways were found. One unique pathway for heart was negative regulation of calcium ion transport. Reported observations of COVID-19 patients with the history of hypertension taking calcium channel blockers (CCBs) or dihydorpyridine CCBs had elevated rate of intubation or increased rate of intubation/death respectively. Also likelihood of hospitalization of chronic CCB users with COVID-19 was more in comparison to long term Angiotensin Converting Enzyme inhibitors/Angiotensin Receptor Blockers users. Further studies are necessary to confirm this. miRNA analysis of ORF3a interacting proteins in brain and lung revealed, 2 of 37 brain miRNAs and 1 of 25 lung miRNAs with high degree and betweenness indicating their significance as hubs in the interaction network. Our study could help in identifying potential tissue specific COVID-19 drug/drug repurposing targets.

bioinformatics↗