Mining of public sequencing databases supports a non-dietary origin for putative foreign miRNAs in human tissues

Previous posts have tackled the question Will a GMO wheat silence human genes?.
The story started with claims of plant RNA appearing in human tissues.
It's likely contamination.
This report below offers new analysis that comes to the same conclusion as previous reports about contamination artefacts as the explanation for unexpected traces of plant microRNA in human tissues:

Mining of public sequencing databases supports a non-dietary origin for putative foreign miRNAs: underestimated effects of contamination in NGS [next gen sequencing].

The report that exogenous plant miRNAs are able to cross the mammalian gastrointestinal tract and exert gene-regulation mechanism in mammalian tissues has yielded a lot of controversy, both in the public press and the scientific literature. Despite the initial enthusiasm, reproducibility of these results was recently questioned by several authors. To analyze the causes of this unease, we searched for diet-derived miRNAs in deep-sequencing libraries performed by ourselves and others. We found variable amounts of plant miRNAs in publicly available small RNA-seq data sets of human tissues.

In human spermatozoa,exogenous RNAs reached extreme, biologically meaningless levels. On the contrary,plant miRNAs were not detected in our sequencing of human sperm cells, whichwas performed in the absence of any known sources of plant contamination. We designed an experiment to show that cross-contamination during library preparation is a source of exogenous RNAs. These contamination-derived exogenous sequences even resisted oxidation with sodium periodate. To test the assumption that diet-derived miRNAs were actually contamination-derived, we sought in the literature for previous sequencing reports performed by the same group which reported the initial finding. We analyzed the spectra of plant miRNAs in a small RNA sequencing study performed in amphioxus by this group in 2009 and we found a very strong correlation with the plant miRNAs which they later reported in human sera. Even though contamination with exogenous sequences may be easy to detect,cross-contamination between samples from the same organism can go completely unnoticed, possibly affecting conclusions derived from NGS transcriptomics.

RNA. 2014 Jun;20(6):754-7. doi: 10.1261/rna.044263.114. Epub 2014 Apr 11. Tosar JP, Rovira C, Naya H, Cayota A.

See previous posts with the RNAi miRNA dsRNA tag for further context

Key comment:

Next-generation sequencing technologies have become a widespread and indispensable tool in many research fields, and clinical use of a deep-sequencing platform has recently been approved by FDA (Collins and Hamburg 2013). These technologies have ... enough sensitivity to produce whole-transcriptome data from single cells (Tang et al. 2010). However...even low amounts of contaminant nucleic acids can be detected in biological samples. ...our main concern is what seems to be a widespread underestimation of the effects of contamination on deep-sequencing data. The case discussed here is simply a paradigmatic example but plant-derived miRNAs have been identified even in transcriptome analysis of cultured cells (Zhang et al. 2012b). Furthermore, we have analyzed sequencing data generated from all over the world, and detection of contaminant sequences was found to be ubiquitous (Fig. 1A) and in some cases reached extreme, biologically meaningless levels (Fig. 1B).