ArticleCellular immunology2016
Droplet digital PCR quantifies host inflammatory transcripts in feces reliably and reproducibly.
Article in Cellular immunology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers, 1 of them a synthesis that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
18 citing papers in PubMed, 1 synthesis or guideline pooled it, 24 citations in OpenAlex.
- Environmental enteric dysfunction pathways and child stunting: A systematic review.PLoS neglected tropical diseases · 2018Pooled it
- The Impact of Milk on Gut Permeability, Fecal 16S rRNA Gene Microbiota Profiling, and Fecal Metabolomics in Children with Moderate Malnutrition in Sierra Leone: A Double-Blind, Randomized Controlled Trial.The American journal of clinical nutrition · 2024Trial
- Selection of optimal extraction and RT-PCR protocols for stool RNA detection of colorectal cancer associated immune genes.Scientific reports · 2024Article
- Highly accurate and sensitive absolute quantification of bacterial strains in human fecal samples.Microbiome · 2024Article
- Stool biomarkers as measures of enteric pathogen infection in infants from Addis Ababa informal settlements.PLoS neglected tropical diseases · 2023Article
- Review
- Biomarkers of environmental enteric dysfunction are differently associated with recovery and growth among children with moderate acute malnutrition in Sierra Leone.The American journal of clinical nutrition · 2021Article
- Multitarget Stool mRNA Test for Detecting Colorectal Cancer Lesions Including Advanced Adenomas.Cancers · 2021Article
- Article
- Omics in gut microbiome analysis.Journal of microbiology (Seoul, Korea) · 2021Review
- Investigating the gut-brain axis in a neurodevelopmental rodent model of schizophrenia.Brain, behavior, & immunity - health · 2020Article
- Mapping gastrointestinal gene expression patterns in wild primates and humans via fecal RNA-seq.BMC genomics · 2019Article
- Localization of Secretory Mucins MUC5AC and MUC5B in Normal/Healthy Human Airways.American journal of respiratory and critical care medicine · 2019Article
- Detection and interpretation of fecal host mRNA in rural Malawian infants aged 6-12 months at risk for environmental enteric dysfunction.Experimental biology and medicine (Maywood, N.J.) · 2018Observational
- Fecal Host Transcriptomics for Non-Invasive Human Mucosal Immune Profiling: Proof of Concept inPathogens & immunity · 2018Article
- Droplet digital PCR for quantification ofWorld journal of gastroenterology · 2017Article
- Environmental Enteric Dysfunction and the Fecal Microbiota in Malawian Children.The American journal of tropical medicine and hygiene · 2017Article
- Environmental Enteric Dysfunction Is Associated With Poor Linear Growth and Can Be Identified by Host Fecal mRNAs.Journal of pediatric gastroenterology and nutrition · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The gut is the most extensive, interactive, and complex interface between the human host and the environment and therefore a critical site of immunological activity. Non-invasive methods to assess the host response in this organ are currently lacking. Feces are the available analyte which have been in proximity to the gut tissue. We applied a method of concentrating host transcripts from fecal specimens using a existing bead-based affinity separation method for nucleic acids and quantified transcripts using droplet digital PCR (ddPCR) to determine the copy numbers of a variety of key transcripts in the gut immune system. ddPCR compartmentalizes the reaction in a small aqueous droplet suspended in oil, and counts droplets as either fluorescent or non-fluorescent. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was used to normalize transcript concentration. This method was applied to 799 fecal samples from rural Malawian children, and over 20,000 transcript concentrations were quantified. Host mRNA was detected in >99% samples, a threshold for target detection was established at an average expression of 0.02 copies target/GAPDH, above which correlation coefficient between duplicate measurements is >0.95. Quantities of transcript detected using ddPCR were greater than standard qPCR. Fecal sample preservation at the time of collection did not require immediate freezing or the addition of buffers or enzymes. Measurements of transcripts encoding immunoactive proteins correlated with a measure of gut inflammation in the study children, thereby substantiating their relevance. This method allows investigators to interrogate gene expression in the gut.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.