Biology subjects

Newhart, V.

Publications and source records attributed to Newhart, V..

3 recordsLinked to original sources

bioRxiv2026

Single-cell profiling reveals disruption of cell-cycle homeostasis following JDP2 depletion in colorectal epithelial cells

Intestinal epithelial cells (IECs) undergo rapid and continuous renewal to maintain gut epithelial homeostasis and barrier integrity at the interface with luminal microbiota, dietary antigens, and enteric pathogens. IEC proliferation is tightly regulated by a complex machinery of cell cycle regulators and effectors, and genetic or transcriptional dysregulation of cell-cycle regulatory pathways is a hallmark of colorectal cancer development and progression. Previously, JDP2 (Jun dimerization protein 2) has been shown to be involved in cell cycle control and is associated with an array of cancers. JDP2 functions as a transcription factor or epigenetic regulator depending on cellular context, disease, and cancer types. However, the role of JDP2 in CRC, cell cycle homeostasis of colon cancer cells, and their fate remains poorly defined. In this study, we found that patients with higher JDP2 expression have significantly worse survival than patients with lower JDP2 expression. Our functional assays showed that JDP2 depletion increased EdU incorporation during S phase and PHH3 abundance, which is consistent with increased proliferative and mitotic activity. Our single-cell RNA sequencing and transcriptomic profiling further revealed reprogramming of cell-cycle-associated transcriptional states following JDP2 depletion. Differential-expression and pathway analysis identified changes in mitotic and cell-cycle regulatory genes, including programs involving cyclins, cyclin-dependent kinases, chromosome segregation, and mitotic progression. We also found that lower residual JDP2 expression was associated with escalated G2/M representation and a change toward later states along a G1 - S - G2/M-associated transcriptional trajectory. Furthermore, low-JDP2 cells showed significantly greater late-state occupancy than High-JDP2 cells (33.6% versus 24.0%; paired P=0.048). Among the JDP2-siRNA-treated cells, analysis of residual JDP2-expressing cells also revealed heterogeneous associations of JDP2 with cell-cycle, survival, apoptotic, and stress-response programs, consistent with JDP2's context-dependent transcriptional functions. Together, these data identify JDP2 as an important component of intestinal epithelial cell-cycle homeostasis and transcriptional landscape and suggest that JDP2 depletion perturbs the balance of proliferative cell states.

molecular biology↗

bioRxiv2026

Campylobacter jejuni Infection Is Associated With Cell-Cycle, Redox, and Metabolic Remodeling of Human Intestinal Epithelial Cells at Single-Cell Resolution

Campylobacter jejuni is the leading cause of bacterial enteric infections worldwide, including in the US. It is also a zoonotic pathogen that is transmitted by food and water, causing diarrhea and intestinal inflammation, and is responsible for high morbidity and mortality in young children, the elderly, and immunocompromised patients. During infection, C. jejuni profoundly perturbs intestinal epithelial physiology, leading to widespread mucosal damage and inflammatory response. However, the heterogeneity and coordination of host transcriptional responses remain incompletely defined. We performed single-cell RNA sequencing of Caco-2 intestinal epithelial cells from uninfected Control and C. jejuni-infected biological samples using 10x Genomics GEM-X Flex chemistry. Our dataset comprised 159,088 cells and 18,142 measured features. A Seurat workflow resolved 19 transcriptional states and revealed a highly reproducible condition-associated redistribution of clusters across biological replicates. Our study demonstrated that C. jejuni infection was associated with increased representation of G2/M-classified cells and coordinated induction of checkpoint and mitotic-spindle genes, including CDKN1A, WEE1, MAD2L1, BUB1B, PLK1, CDC20, CDK1, and UBE2C. Furthermore, ranked enrichment independently identified a C. jejuni-enriched Reactome mitotic spindle checkpoint program (NES ~1.67, FDR ~0.013), while Hallmark analysis identified strong TNF/NF-kB, hypoxia, G2M checkpoint, TGF-beta, glycolysis, apoptosis, p53, and mTORC1-associated programs. Infection was also associated with significantly decreased JDP2 and higher NOX1 and DUOX2 gene expression. Furthermore, scMetabolism/AUCell identified 20 KEGG metabolic pathways at FDR <0.05 in a balanced 10,000-cell analysis, with 12 lower and 8 higher in infection. Together, these data support a model in which C. jejuni dramatically restructures epithelial transcriptional states and is accompanied by mitotic-checkpoint, inflammatory/stress, redox, and metabolic remodeling.

microbiology↗

bioRxiv2025

Pro-restitutive Bacteroides thetaiotaomicron reprograms the transcriptome of intestinal epithelial cells by modulating the expression of genes essential for proliferation and migration.

The mammalian intestine harbors a highly complex, very diverse, and numerically vast community of symbiotic microorganisms, which profoundly influence the development and maintenance of the intestinal barrier function. Alterations in microbial composition, known as dysbiosis, are observed in Inflammatory Bowel Disease (IBD), colorectal cancer (CRC), and gastrointestinal infections; however, the exact causal relationship between these changes and the resolution of intestinal inflammation and the repair of damaged mucosa remains unclear. Notably, IBD is not only marked by dysbiosis but also by changes in microbial metabolic pathways and metabolite landscape in the intestinal lumen. The small molecules and microbial metabolites present in the intestinal lumen have emerged as potential regulators of gut pathology, cancer, and mucosal repair. Investigating how altered microbiota and microbial metabolic activities influence intestinal epithelial cells (IEC) can provide insights into their role in the regeneration of mucosal epithelia and restoration of gut barrier functions. This knowledge can be harnessed to promote intestinal homeostasis, prevent relapse, and prolong remission of IBD. To dissect the complex interplay between the gut microbiome and IEC, we focused on the overrepresented bacterium Bacteroides thetaiotaomicron. Here, we show that B. thetaiotaomicron and Akkermansia muciniphila, the dominant members of gut microbiota, expand during the repair & resolution phase of the chemically induced acute murine colitis. Furthermore, our bioinformatics analysis demonstrated that the elevated relative abundance of B. thetaiotamicron was also accompanied by rewiring of bacterial metabolic programs towards the essential amino acid metabolism, polyamine synthesis and utilization, stress response mechanisms, cell envelope biogenesis, and nutrient scavenging. Our RNA sequencing and transcriptomic analysis of primary human colonic epithelial cells cocultured with B. thetaiotaomicron showed that B. thetaiotaomicron stimulates the expression of genes and pathways involved in different cellular functions, including proliferation, differentiation, adhesion, lipid metabolism, migration, chemotaxis, and receptor expression. Our study emphasizes the crucial functions of the gut microbiome and metabolic activities in regulating the functions of intestinal epithelial cells during the repair of injured gut mucosa. Thus, these microorganisms and their metabolism hold promise as potential therapeutic agents.

microbiology↗