Project description:HuMiChip was used to analyze human oral and gut microbiomes, showing significantly different functional gene profiles between oral and gut microbiome. The results were used to demonstarte the usefulness of applying HuMiChip to human microbiome studies.
Project description:HuMiChip was used to analyze human oral and gut microbiomes, showing significantly different functional gene profiles between oral and gut microbiome.
Project description:Multiple sclerosis (MS) is a chronic demyelinating disease of the central nervous system, which currently lacks effective therapies that provide regeneration and stop disease progression. A suggested link is anticipated between the development of progressive MS (PMS) and aging, as suggested by recent work identifying hallmarks of cellular senescence in numerous cell types both in vitro with patient cell lines and in vivo in the post-mortem MS brain, including neural stem cells (NSCs). Using an inducible system, directly reprogramming human fibroblasts into induced NSCs (iNSCs), we generated control and PMS iNSC cell lines, which was found to maintain epigenetic age. Here we performed multi-omics, including bulk RNA, single-cell (sc) RNA, single-nucleus (sn) RNA and ATAC, and whole genome bisulfite sequencing. Here, we show that PMS iNSCs have overall increases in senescence and inflammatory associated genes using bulk sequencing. We next identified a unique subcluster of cells within the PMS iNSCs that have a pro-inflammatory and senescent phenotype, associated with interferon gene activation using sc-RNA seq. Within this specific subcluster there is higher expression of genes associated with inflammatory protein secretion, as well as the senescence associated secretory phenotype (SASP). A similar clustering pattern was observed in the ATAC-seq data, a large main cluster and a small inflammatory cluster primarily comprising of PMS iNSCs. Differentially accessible regions within the PMS cluster revealed promoter sites of inflammatory-associated genes to be more accessible correlating with gene expression. Our results highlight a novel cellular mechanism in PMS wherein NSCs are interferon-responsive and senescent-like which may impact other cells within the lesion leading to chronic inflammation.
Project description:The objectives of this study were to establish a microbiome profile for oral epithelial dysplasia using archival lesion swab samples to characterize the community variations and the functional potential of the microbiome using 16S rRNA gene sequencing
Project description:To investigate the immune function of SEPT2 in the regulation of viral infection, we obtained SEPT2-deficient PMs from SEPT2 conditional knockout mice. We then performed gene expression profiling analysis using data obtained from RNA-seq of wild-type and SEPT2-deficient PMs with VSV or HSV-1 infection.
Project description:Head and neck cancers are a complex malignancy comprising multiple anatomical sites, with cancer of the oral cavity ranking among the deadliest and most disfiguring cancers globally. Oral cancer (OC) constitutes a subset of head and neck cancer cases, presenting primarily as tobacco- and alcohol-associated oral squamous cell carcinoma (OSCC), with a 5-year survival rate of ~65%, partly due to the lack of early detection and effective treatments. OSCC arises from premalignant lesions (PMLs) in the oral cavity through a multi-step series of clinical and histopathological stages, including varying degrees of epithelial dysplasia. To gain insights into the molecular mechanisms associated with the progression of PMLs to OSCC, we profiled the whole transcriptome of 66 human PMLs comprising leukoplakia with dysplasia and hyperkeratosis non-reactive (HkNR) pathologies, alongside healthy controls and OSCC. Our data revealed that PMLs were enriched in gene signatures associated with cellular plasticity, such as partial EMT (p-EMT) phenotypes, and with immune response. Integrated analyses of the host transcriptome and microbiome further highlighted a significant association between differential microbial abundance and PML pathway activity, suggesting a contribution of the oral microbiome towards PML evolution to OSCC. Collectively, this study reveals molecular processes associated with PML progression that may help early diagnosis and disease interception at an early stage.
Project description:The widespread use of potassium peroxymonosulfate (PMS) in aquaculture raises concerns about its ecological risks. This study evaluated acute toxicity of PMS to Chlorella pyrenoidosa over 24-96 h to establish a 96 h EC₅₀. Chronic exposure groups (0, 1.70, 3.40, 8.49 mg/L, corresponding to 0, 0.1, 0.2, and 0.5 of the EC₅₀) were cultured for 12 days. Cell growth, oxidative stress, ultrastructure, chlorophyll fluorescence, and transcriptomic genes were measured on days 0, 3, 6, 9, and 12. PMS decomposition products were monitored and correlated with physiological and Biochemical responses. PMS rapid decomposition increased breakdown products, inhibiting algal growth during days 0-3 and causing surface wrinkling, plasmolysis, chloroplast damage, and thylakoid disarray. Oxidative stress rose and growth_x001e_related genes were down_x001e_regulated. After day 6, with the cessation of PMS decomposition and the subsequent reduction in its byproducts, growth recovered, cellular structures were restored, oxidative stress decreased, and ribosome‑related genes were up_x001e_regulated. These findings contribute to the assessment of the potential risks of PMS to C.pyrenoidosa and provide new insights for the application of PMS in aquaculture practices.