Biology subjects

Khurana, J.

Publications and source records attributed to Khurana, J..

3 recordsLinked to original sources

bioRxiv2025

Discovery of the metalloenzyme IsmB revises a pathway for coprostanol formation by the human gut microbiome

High levels of circulating cholesterol are associated with human cardiovascular diseases and an altered gut microbiome. Still, major gaps exist in our understanding of the interactions of cholesterol with gut microbes. The reductive transformation of cholesterol to the poorly absorbed sterol coprostanol by human gut bacteria has long been known, but the genetic and biochemical basis for this activity is only partially elucidated. Here, we discover and characterize a gut bacterial enzyme that catalyzes the reduction of cholestenone to coprostanone, the second step in the intestinal sterol metabolism (ism) pathway for coprostanol production. We identify a gene encoding a previously unknown 5{beta}-reductase, IsmB, a new member of the Fe-S cluster flavoenzyme superfamily, in the coprostanol producing organism Eubacterium coprostanoligenes. Biochemical characterization of IsmB confirms it is an anaerobic Fe-S cluster flavoenzyme and reveals specificity for reduction of an unanticipated intermediate, 5-cholesten-3-one, to coprostanone, revising the ism pathway. We also identify and characterize homologs of IsmB encoded in uncultured human gut bacteria that also encode the previously identified ism pathway enzyme IsmA, further supporting the role of IsmB in coprostanol formation. Finally, analysis of human stool metagenomics and metabolomics datasets further confirms the relevance of IsmB in the human gut microbiome, and analyses of human serum metabolomics from Framingham Heart Study participants reveal negative correlation between serum cholesterol levels and the presence of IsmA/IsmB encoders in the gut. Together, these results show the utility of combining biochemistry and stool metagenomic analysis for gut microbial enzyme discovery, and suggests IsmA/IsmB-encoding gut bacteria carry potential benefits for cholesterol homeostasis and cardiovascular health.

biochemistry↗

bioRxiv2025

Complete Genome Sequencing and Molecular Characterization of Indigenous Enterovirus A71 Genogroups D and G of India

Enterovirus A71 (EV-A71), a neurotropic member of the Picornaviridae family, comprises seven recognized genogroups (A-G). Despite prior identification of D and G genogroups in India, comprehensive full-genome characterization of these indigenous lineages remains unreported. We performed next-generation sequencing (NGS) and molecular phylogenetic analyses on two Indian isolates: R13223-IND-02 (genogroup D) and V11-2209-01 (genogroup G). Phylogenetic reconstruction revealed robust clustering of these strains within distinct clades, divergent from globally prevalent genogroups B and C, considering bootstrap support [≥]99%. Both D and G genogroups appear geographically restricted to India, while genogroup D persists as an endemic lineage. Comparative genomic analyses demonstrated extensive nucleotide divergence, including numerous non-synonymous substitutions across both structural (VP1-VP4) and non-structural (2A-3D) coding regions. These findings highlight the evolutionary independence and sustained circulation of D and G genogroups in India, suggesting a unique regional evolutionary trajectory. The findings hold significant global relevance, offering valuable insights for molecular surveillance, advancing pathogenesis research, and supporting the development of genogroup-specific vaccine strategies tailored to diverse epidemiological landscapes.

genomics↗

bioRxiv2021

Somatic Mutations in Collagens are Associated with a Distinct Tumor Environment and Overall Survival in Gastric Cancer

BackgroundGastric cancer is a heterogeneous disease with poorly understood genetic and microenvironmental factors. Mutations in collagen genes are associated with genetic diseases that compromise tissue integrity, but their role in tumor progression has not been extensively reported. Aberrant collagen expression has been long associated with malignant tumor growth, invasion, chemoresistance, and patient outcomes. We hypothesized that somatic mutations in collagens could functionally alter the tumor extracellular matrix. MethodsWe used publicly available datasets including The Tumor Cancer Genome Atlas (TCGA) to interrogate somatic mutations in collagens in stomach adenocarcinomas. To demonstrate that collagens were significantly mutated above background mutation rates, we used a moderated Kolmogorov-Smirnov test along with combination analysis with a bootstrap approach to define the background accounting for mutation rates. Association between mutations and clinicopathological features was evaluated by Fisher or chi-squared tests. Association with overall survival was assessed by Kaplan-Meier and the Cox-Proportional Hazards Model. Gene Set Enrichment Analysis was used to interrogate pathways. Immunohistochemistry and in situ hybridization tested expression of COL7A1 in stomach tumors. ResultsIn stomach adenocarcinomas, we identified individual collagen genes and sets of collagen genes harboring somatic mutations at a high frequency compared to background in both microsatellite stable, and microsatellite instable tumors in TCGA. Many of the missense mutations resemble the same types of loss of function mutations in collagenopathies that disrupt tissue formation and destabilize cells providing guidance to interpret the somatic mutations. We identified combinations of somatic mutations in collagens associated with overall survival, with a distinctive tumor microenvironment marked by lower matrisome expression and immune cell signatures. Truncation mutations were strongly associated with improved outcomes suggesting that loss of expression of secreted collagens impact tumor progression and treatment response. Germline collagenopathy variants guided interpretation of impactful somatic mutations on tumors. ConclusionsThese observations highlight that many collagens, expressed in non-physiologically relevant conditions in tumors, harbor impactful somatic mutations in tumors, suggesting new approaches for classification and therapy development in stomach cancer. In sum, these findings demonstrate how classification of tumors by collagen mutations identified strong links between specific genotypes and the tumor environment. Research HighlightsCollagen mutations are prevalent in stomach cancer Collagen somatic missense mutations resemble collagenopathy mutations Collagen mutations associate with overall survival in stomach cancer Tumors with collagen mutations have distinct molecular pathways and tumor microenvironments

cancer biology↗