Survey of 800+ data sets from human tissue and body fluid reveals xenomiRs are likely artifacts

Abstract

miRNAs are small 22-nucleotide RNAs that can post-transcriptionally regulate gene expression. It has been proposed that dietary plant miRNAs can enter the human bloodstream and regulate host transcripts; however, these findings have been widely disputed. We here conduct the first comprehensive meta-study in the field, surveying the presence and abundances of cross-species miRNAs (xenomiRs) in 824 sequencing data sets from various human tissues and body fluids. We find that xenomiRs are commonly present in tissues (17%) and body fluids (69%); however, the abundances are low, comprising 0.001% of host human miRNA counts. Further, we do not detect a significant enrichment of xenomiRs in sequencing data originating from tissues and body fluids that are exposed to dietary intake (such as liver). Likewise, there is no significant depletion of xenomiRs in tissues and body fluids that are relatively separated from the main bloodstream (such as brain and cerebro-spinal fluids). Interestingly, the majority (81%) of body fluid xenomiRs stem from rodents, which are a rare human dietary contribution but common laboratory animals. Body fluid samples from the same studies tend to group together when clustered by xenomiR compositions, suggesting technical batch effects. Last, we performed carefully designed and controlled animal feeding studies, in which we detected no transfer of plant miRNAs into rat blood, or bovine milk sequences into piglet blood. In summary, our comprehensive computational and experimental results indicate that xenomiRs originate from technical artifacts rather than dietary intake.

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

“…Recently, Kang et al. reanalyzed >800 data sets from human tissues and body fluids sequenced using Illumina platform and concluded that majority of xenomiRs are likely artifacts . The data the authors refer to were serum and plasma samples, exosome, cerebrospinal fluid, blood cells, liver, and brain.…”

Milk MicroRNAs in Health and Disease

“…These observations, along with the conservation of microRNAs and their targets in species that can be part of the human food supply (Friedman et al., ; Lee et al., ; van Herwijnen et al., ) sparked the interest for dietary microRNAs’ (sometimes termed as xenomiRs) transfer and function in human consumers (Auerbach et al., ; Fabris & Calin, ; Kang et al., ; Witwer, ; Witwer & Halushka, ; Witwer & Hirschi, ; Witwer, McAlexander, Queen, & Adams, ).…”

“…First suggested for plant small RNA (Timmons & Fire, ; Whangbo & Hunter, ; Witwer & Zhang, ; Zhou et al., ) and more specifically rice microRNAs in a highly controversial study (Zhang et al., ), dietary microRNAs bioavailability found more solid ground when milk was considered as their carriers for transfer between individuals or species, yet not without sparking an intense debate (Auerbach et al., ; Fabris & Calin, ; Kang et al., ; Melnik et al., , ; Melnik & Schmitz, ; Witwer, , ; Witwer & Halushka, ; Witwer & Hirschi, ; Witwer et al., ; Zempleni, ; Zempleni et al., ; Zempleni et al., ; Zhou et al., ).…”

“…Milk microRNA bioavailability, meaning the possibility of their uptake by a whole organism, has been explored by several studies, sometimes with conflicting results, encouraging further the ongoing controversies (Auerbach et al., ; Bagci & Allmer, ; Baier et al., , ; Kang et al., ; Manca et al., ; Title, Denzler, & Stoffel, ; Wang et al., ; Witwer, ; Zempleni et al., , ).…”

“…Data from in silico analysis of small RNA‐sequencing databases in humans are still conflicting (Cui et al., ; Kang et al., ; Zempleni, ; Zhang, Vieira Resende, & Cui, ), mostly because microRNAs are conserved between the species. It is also because microRNAs isomeric sequences (isomiRs) are often not taken into account, which offers a supplementary challenge for milk microRNA investigations in various species (Guo & Chen, ; Rubio et al., ; Yu et al., ).…”