Small RNA profiling of low biomass samples: identification and removal of contaminants

Heintz‐Buschart, Anna; Yusuf, Dilmurat; Kaysen, Anne; Etheridge, Alton; Fritz, Joëlle V.; May, Patrick; Beaufort, Carine de; Upadhyaya, Bimal Babu; Ghosal, Anubrata; Galas, David J.; Wilmes, Paul

doi:10.1186/s12915-018-0522-7

Cited by 45 publications

(34 citation statements)

References 77 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The data the authors refer to were serum and plasma samples, exosome, cerebrospinal fluid, blood cells, liver, and brain. Two additional studies caution the interpretation of sequencing data to small RNA for potential contaminations in RNA extraction kits or artifacts . In this work, we applied primarily TaqMan‐based assay which provides greatest specificity for miRNAs.…”

Section: Discussionmentioning

confidence: 99%

Food‐Derived Xeno‐microRNAs: Influence of Diet and Detectability in Gastrointestinal Tract—Proof‐of‐Principle Study

Link

Thon

Schanze

et al. 2018

Molecular Nutrition Food Res

View full text Add to dashboard Cite

Scope Diet is amongst the most crucial factors contributing to the multistep process of carcinogenesis. The role of exogenous microRNAs (miRNAs) is still debatable. In this proof‐of‐principle work, the presence of miRNAs in a variety of foods, its stability to processing, and detectability in GI mucosa and feces are studied and the effect of short‐term diet on human‐ or plant‐derived miRNAs in feces and blood is examined. Methods and results Animal and plant miRNAs are detected in all foods irrespective of processing. Animal‐derived foods showed the highest miRNA level and the lowest is found in cheese and milk. The impact of the short‐term vegetarian or meat‐rich diet on blood and feces miRNA is evaluated in healthy subjects using qPCR and Affymetrix profiling. Diet is not associated with changes in ultraconserved miRNAs. However, a vegetarian diet is associated with an increase of miR‐168 in feces but not in blood. Overall, plant miR‐168 is detectable in normal GI mucosa and in colorectal cancer. Conclusions Food provides a great source of miRNAs and diet may be associated with changes in xenomiRs. Plant‐derived miR‐168 is ubiquitously present in feces, normal mucosa, and cancer. Further studies are needed to evaluate the functional interaction between diet‐derived miRNAs and GI tract.

show abstract

Section: Discussionmentioning

confidence: 99%

Food‐Derived Xeno‐microRNAs: Influence of Diet and Detectability in Gastrointestinal Tract—Proof‐of‐Principle Study

Link

Thon

Schanze

et al. 2018

Molecular Nutrition Food Res

View full text Add to dashboard Cite

show abstract

“…Bacterial reads in aqueous humor and CSF, two fluids with very low endogenous RNA content that were collected in a sterile setting (and thus presumed to be sterile), most likely reflect background contamination during the workflow 29 . To illustrate the biological relevance of the bacterial signal, we looked into reads mapping to Campylobacter concisus, a gram-negative bacterium that is known to primarily colonize the human oral cavity, with some strains translocated to the intestinal tract 30 .…”

Section: Fig 4 Circrnas Are Enriched In Biofluids Compared To Tissuesmentioning

confidence: 99%

“…As both CSF and aqueous humor display a very low relative RNA content, the exogenous sequences may represent bacterial contaminants introduced during the sample processing workflow. Contaminants can derive from contaminated spin columns used during RNA purification29 , enzymes produced in microorganisms42 , or various environmental sources43 . Such contaminant signals are likely underrepresented in samples with high concentration of endogenous exRNAs.…”

mentioning

confidence: 99%

Charting extracellular transcriptomes in The Human Biofluid RNA Atlas

Hulstaert

Morlion

Cobos

et al. 2019

Preprint

View full text Add to dashboard Cite

Extracellular RNAs present in biofluids have emerged as potential biomarkers for disease.Where most studies focus on plasma or serum, other biofluids may contain more informative RNA molecules, depending on the type of disease. Here, we present an unprecedented atlas of messenger, circular and small RNA transcriptomes of a comprehensive collection of 20 different human biofluids. By means of synthetic spike-in controls, we compared RNA content across biofluids, revealing a more than 10 000-fold difference in RNA concentration. The circular RNA fraction is increased in nearly all biofluids compared to tissues. Each biofluid transcriptome is enriched for RNA molecules derived from specific tissues and cell types. In addition, a subset of biofluids, including stool, sweat, saliva and sputum, contains high levels of bacterial RNAs. Our atlas enables a more informed selection of the most relevant biofluid to monitor particular diseases. To verify the biomarker potential in these biofluids, four validation cohorts representing a broad spectrum of diseases were profiled, revealing numerous differential RNAs between case and control subjects. Taken together, our results reveal novel insights in the RNA content of human biofluids and may serve as a valuable resource for future biomarker studies.

show abstract

“…It was argued that the occurrences of low quantity of plant miRNAs in publicly available animal small RNA sequencing datasets might be due to contamination in sequencing methodologies [49,50] It has been recently reviewed that plant miRNAs present in human sera are due to contamination (technical artifacts) rather than dietary intake (regulating the endogenous genes) [48]. This review was based on various experiments from different groups concluding that the exogenous miRNAs are found in humans are due to contamination [49,51,52]. These findings were based on non-detection of plant miRNAs after proper handling to exclude cross-sample contamination in human sperm cells [49].…”

Section: Cross-kingdom Gene Regulation or Contamination Of Plant Mirnmentioning

confidence: 99%

Dietary plant miRNAs as an augmented therapy: cross-kingdom gene regulation

et al. 2018

View full text Add to dashboard Cite

Cross-kingdom gene regulation by microRNAs (miRNAs) initiated a hot debate on the effective role of orally acquired plant miRNAs on human gene expression. It resulted in the expansion of gene regulation theories and role of plant miRNAs in cross-kingdom regulation of gene expression. This opened up the discussion that 'Whether we really get what we eat?' and 'Whether the orally acquired miRNAs really have a biologically important consequences after entering our digestive and circulatory system?' The reports of orally acquired plant miRNAs inside human alimentary canal have been a topic of discussion in the scientific community. The cross-kingdom gene regulations have raised our hopes to explore the exciting world of plant miRNAs as therapeutic potential and dietary supplements. However, there are reports which have raised concerns over any such cross-kingdom regulation and argued that technical flaws in the experiments might have led to such hypothesis. This review will give the complete understanding of exogenous application and cross-kingdom regulation of plant miRNAs on human health. Here, we provide update and discuss the consequences of plant miRNA mediated cross-kingdom gene regulation and possibilities for this exciting regulatory mechanism as an augmented therapy against various diseases. ARTICLE HISTORY

show abstract

Small RNA profiling of low biomass samples: identification and removal of contaminants

Cited by 45 publications

References 77 publications

Food‐Derived Xeno‐microRNAs: Influence of Diet and Detectability in Gastrointestinal Tract—Proof‐of‐Principle Study

Food‐Derived Xeno‐microRNAs: Influence of Diet and Detectability in Gastrointestinal Tract—Proof‐of‐Principle Study

Charting extracellular transcriptomes in The Human Biofluid RNA Atlas

Dietary plant miRNAs as an augmented therapy: cross-kingdom gene regulation

Contact Info

Product

Resources

About