Project description:This is for Rigor and Reproducibility study to demonstrate the reproducibility of AFS SOP for EV separation, RNA isolation, and RNA analysis by using saliva samples from healthy individuals. Blinded saliva samples have been processed by two independent AFS operators for EV separation and subjected to miRNA-seq analysis. EV-associated miRNA seqeunces were used as a monitoring tool for Rigor and Reproducibility of AFS process between operators.
Project description:Exosomes were isolared from saliva od healthy individuals and head and neck cancer (HNSCC) patients.miRNA profiling of saliva-derived exosomes was perfomred using nCounter SPRINT system. Samples were grouped according to Healthy and Tumor based on their saliva-derived exosomal miRNA profile.
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
Project description:Saliva is a convenient non-invasive source of liquid biopsy to monitor human health and diagnose diseases. In particular, extracellular vesicles (EVs) in saliva can potentially reveal clinically relevant information for systemic health. Recent studies have shown that RNA in saliva EVs could be exploited as biomarkers for disease diagnosis. However, there is no standardized protocol for profiling RNA in saliva EV nor clear guideline on selecting saliva fractions for biomarker analysis. To address these issues, we established a robust protocol for small RNA profiling from fractionated saliva. With this method, we performed comprehensive small RNA sequencing of four saliva fractions, including cell-free saliva (CFS), EV-depleted saliva (EV-D), exosome (EXO), and microvesicle (MV) from ten healthy volunteers. Methods: To address these issues, we established a robust protocol for small RNA profiling from fractionated saliva. With this method, we performed comprehensive small RNA sequencing of four saliva fractions, including cell-free saliva (CFS), EV-depleted saliva (EV-D), exosome (EXO), and microvesicle (MV) from ten healthy volunteers.
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:Exosomes were isolated from plasma and saliva of healthy individuals and head and neck cancer (HNSCC) patients. miRNA profiling of plasma- and saliva-derived exosomes was performed using nCounter SPRINT system. Diagnostic panels were selected from the exosomal miRNA profile.
Project description:The investigation includes findings from our clinical trial, monitoring individualized response to pneumococcal vaccination, where we have carried out integrative profiling assessment of saliva pre and post vaccination in a single individual. This is to our knowledge the most extensive saliva-centered omics dataset on an individual, covering 100 timepoints over the course of one year. The time span covers a healthy period as well as comprehensive monitoring of innate and adaptive immune responses following pneumococcal vaccination. Protein and RNA from saliva were produced at each timepoint (100 timepoints), and mass spectrometry proteomics and RNA-sequencing were carried out for all samples in non-targeted comprehensive profiling. Specifically, a single individual (male, 38) was profiled over multiple timepoints during healthy periods, as well as post treatment with pneumococcal vaccine (PPSV23). Initially pre-immunization samples, including a 24 hour period with hourly sampling (samples P1052515H07-P1052615H08), were collected to provide a comparative baseline. A subsequent 24-hour time course was performed, with again hourly samples taken pre and post vaccination (P1060715H07-P1060815H06). The PPSV23 pneumococcal vaccine was admistered inbetween timepoints at approximately 10.30am, prior to datapoint P1060715H11. Following the vaccination, and after the 24 hour monitoring, daily samples were taken for about a month (up to sample P1070715H08), to capture innate and adaptive responses in saliva. Two more weekly samples followed, with then monthly sample till the end of the investigation. Omics sample analysis includes: RNA-sequencing of total RNA, small RNA sequencing in saliva extracellular vesicles and saliva mass spectrometry proteomics. Note on sample naming: The sample identifier/name P1MMDDYYHhh corresponds to: patient index:P1, date MMDDYY and hour hh preceded by H using 24 hour enumeration.
Project description:mRNA samples from bone marrow CD34+ cells (HSC) from healthy donors after co-culture assays (Control condition, with hMSCs and CD34+ cells from healthy donors; and AML condition, with hMSCs-AML and CD34+ cells from donors) were amplified, labeled and hybridized to the ClariomTM S Array human (Thermo Scientific, USA). Normalization and analysis of microarray data was performed using the Transcriptome Analysis Console (TAC) software (Affymetrix, USA).
Project description:miRNA differential expression in Rheumatoid arthritis(RA) blood: Microarray analysis of miRNAs in blood from RA and healthy donors.
Project description:We took saliva samples from 89 people with oesophageal cancer (plus 9 with high grade dysplasia, also labelled here as cancer) and 167 controls. We took replicate samples on 6 cancer samples and 4 controls to assess reproducibility. The cancer groups comprise people with invasive adenocarcinoma (61 and also 6 replicates), 28 people with intramucosal adenocarcinoma, 9 people with high-grade dysplasia arising in Barrett's esophagus, 52 patients with non-dysplastic Barrett's esophagus, 42 people with no positive diagnosis after endoscopy (ie no Barrett's, + 1 replicate), and 73 self-reported healthy volunteers (with 3 duplicates)