Project description:The main purpose of this study is to investigate the differences between the gene expression profiles of common warts and healthy skin in HPV-positive individuals by RNA sequencing on the Illumina HiSeq 2500. After obtaining shave biopsies of common warts and healthy skin from twelve Arab males, we were able to analyze the transcriptomes of 24 paired cases and controls.
Project description:mRNA array analysis was carried out using total RNA of skin biopsies from lesional and non-lesional skin of three atopic dermatitits patients and four healthy individuals.
Project description:Human saliva microbiota is phylogenetically divergent among host individuals yet their roles in health and disease are poorly appreciated. We employed a microbial functional gene microarray, HuMiChip 1.0, to reconstruct the global functional profiles of human saliva microbiota from ten healthy and ten caries-active adults. Saliva microbiota in the pilot population featured a vast diversity of functional genes. No significant distinction in gene number or diversity indices was observed between healthy and caries-active microbiota. However, co-presence network analysis of functional genes revealed that caries-active microbiota was more divergent in non-core genes than healthy microbiota, despite both groups exhibited a similar degree of conservation at their respective core genes. Furthermore, functional gene structure of saliva microbiota could potentially distinguish caries-active patients from healthy hosts. Microbial functions such as Diaminopimelate epimerase, Prephenate dehydrogenase, Pyruvate-formate lyase and N-acetylmuramoyl-L-alanine amidase were significantly linked to caries. Therefore, saliva microbiota carried disease-associated functional signatures, which could be potentially exploited for caries diagnosis. The DMFT INDEX (Decayed, Missing, Filled [DMF] teeth index used in dental epidemiology) values are provided for each sample We employed a microbial functional gene microarray, HuMiChip 1.0, to reconstruct the global functional profiles of human saliva microbiota from ten healthy and ten caries-active adults.
Project description:Objective: The dietary xanthophylls, lutein and zeaxanthin, accumulate in primate brain and may be beneficial for cognition. Brain xanthophyll content varies greatly among individuals and genetic factors are likely to be significant contributors. Subspecies of rhesus macaques originating from different geographic locations differ genetically, but the effect of origin on gene expression and carotenoid status has not been determined. The study objective was to determine whether xanthophyll status and expression of carotenoid-related genes, as well as genes with known variants between subspecies, differ between the brains of adult rhesus monkeys of Indian and Chinese origin. Methods: Next generation RNA sequencing was used to determine differentially expressed carotenoid-related genes and genes with known variants among rhesus monkey subspecies in the prefrontal cortex, cerebellum, and striatum of Indian-origin monkeys (n=3) versus Chinese-origin monkeys (n=3). Serum and brain xanthophylls were determined using HPLC. FastQC was performed on raw sequenced reads to determine the quality of each read. Reads were mapped to the Rhesus Macaque reference genome and differences in gene expression (FPKM) were determined using TopHat and Cuffdiff, respectively. Findings from RNAseq were validated using RT-PCR. Results: Indian-origin monkeys had higher xanthophyll levels in brain tissue compared to Chinese-origin monkeys despite consuming similar amounts of dietary carotenoids. In a region-specific manner, 4 genes related to carotenoid and fatty acid metabolism (BCO2, RPE65, ELOVL4, FADS2) and 4 genes involved in the immune response (CD4, CD74, CXCL12 LTBR) were differentially expressed between Indian- and Chinese-origin monkeys. Expression of all four genes involved in carotenoid and fatty acid metabolism were correlated with brain xanthophyll concentration in a region-specific manner. Conclusions: These results indicate that origin is related to differences in both gene expression and xanthophyll content in the brain. Findings from this study may have important implications regarding genetic diversity, lutein status, and cognition in primates.
Project description:In this study, we used RNA-sequencing to profile the long non-coding RNA (lncRNA) transcriptome in lesional skin from psoriasis patients before (PP) and after treatment (PT) with adalimumab and in normal skin from healthy individuals (NN). For this we sequenced total RNA from 18 psoriasis patients (before and after treatment) and 16 healthy controls. We created our own reference set of long non-coding RNAs by merging three long non-coding RNA reference data sets. The combined reference had 67,157 lncRNA transcripts with no overlaps. We identified differential expression of 971 lncRNAs between PP and NN, 157 between PP and PT, and 377 between PT and NN. Based on differentially expressed (DE) lncRNAs between PP and NN, we identified a molecular lncRNA signature that distinguishes psoriatic skin from healthy skin .
Project description:Type 2 inflammation contributes to the pathology of pruritic skin diseases such as atopic dermatitis (AD). Chronic pruritus of unknown origin (CPUO) is a skin condition of unknown etiology that typically has minimal inflammation. Yet, some patients with CPUO display signs of mildly increased type 2 inflammation. This study aims to compare skin transcriptional profiles in CPUO to healthy skin and to skin from AD, a classical type 2 inflammatory condition.
Project description:In this study, a comprehensive assessment of human miRNA was performed on leprosy skin lesions using DNA chip microarrays, which included the entire spectrum of the disease along with its reactional states. Sixty-eight samples from leprotic lesions (10TT, 10BT, 10BB, 10BL, 4LL, 14R1, and 10R2) and nine skin biopsies from healthy individuals were used as controls (CC) (ages ranged from 06 to 83 years, 48 were male and 29 female). The evaluation identified differentially expressed miRNAs [Fold Change (FC)≥2.0, p<0.05] in disease lesions versus healthy controls or between them. Some of these miRNAs were validated by RT-PCR.
Project description:Human skin provides both physical integrity and immunological protection from the external environment, using functionally distinct layers, cell types and extracellular matrix. Despite its central role in human health and disease, the constituent proteins of skin have not been systematically characterized. Here, we combined advanced tissue dissection methods, flow cytometry and state-of-the-art proteomics to describe a spatially-resolved quantitative proteomic atlas of human skin. We quantified 10,701 proteins as a function of their spatial location and cellular origin. The resulting protein atlas and our initial data analyses demonstrate the value of proteomics for understanding cell-type diversity within the skin. We describe here the quantitative distribution of structural proteins, known and novel proteins specific to cellular subsets and those with specialized immunological funtions such as cytokines and chemokines. We anticipate this proteomic atlas of human skin will become an essential community resource for basic and translational research (www.skin.science).