The Spectrum of Circulating RNA: A Window into Systems Toxicology

Abstract

Adverse effects caused by therapeutic drugs are a serious and costly health concern. Despite the body's systemic responses to therapeutics, the liver is often the focus of damage and is usually the focus of studies of toxic effects due to its active roles in the metabolism of xenobiotics. It is extremely difficult, however, to assess systemic responses with currently available methods. Comprehensive cataloging of cell-free circulating RNAs using next-generation sequencing technology may open a window to assess drug-associated adverse effects at the systems level. To explore this potential, we conducted an RNA profiling study using the well-characterized acetaminophen overdose mouse model on liver and plasma with microarray and next-generation sequencing platforms, respectively. After drug treatment, the levels of a number of transcripts, both endogenous and exogenous RNAs, showed significant changes in plasma, reflecting not only the classical liver injury induced by acetaminophen overdose but also damage in tissues other than the liver. The changes in exogenous RNAs also reflect alteration on dieting behavior after acetaminophen overdose. Besides reporting an extensive list of circulating RNA-based biomarker candidates, this study illustrates the possibility of using circulating RNAs to assess global effects of therapeutics. This could also lead to a new approach for a more comprehensive assessment of the efficacy and safety of therapeutics.

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

“…Some in vivo studies support the initial finding that xenomiRs are present in body fluids of humans and other animals, however at a very low expression level (Wang et al 2012(Wang et al , 2013. The most highly abundant Brassica oleracea MIR172 was found in stomach, intestine, serum, and feces of mice that were fed plant RNA extracts.…”

“…These data sets included 215 serum and plasma samples and 37 exosome samples, since these are body fluids that have previously been described to contain xenomiRs (Wang et al 2012(Wang et al , 2013Zhang et al 2012;Liang et al 2015). We also selected 180 samples of cerebrospinal fluid (CSF), which is separated from the bloodstream by the brain-blood barrier (BBB), which unprotected small RNAs are unlikely to cross (Pardridge 2005;Boudreau et al 2011).…”

“…This is easily obtained with tissue samples, but it can be difficult to extract these amounts of RNA from body fluids (Burgos et al 2013). Therefore, sequencing of small RNAs from body fluids often use lower amounts of input material, in some cases down to 10 ng or 100 µL of input fluids for the RNA extraction (Wang et al 2012(Wang et al , 2013, and this can be compensated through additional cycles of PCR amplification (Wang et al 2012). This potentially means that very small amounts of contaminants can be amplified to yield detectable sequence read output.…”

Oxidative Balance in Brain After Exposure to Arsenic in Ex Vivo and in Vivo Models.

“…Moreover, arsenicals can release Fe by the activation of the enzyme heme-oxygenase (HO-1) (Albores et al, 1989). Negishi et al (2013) reported that the adverse effects of exposure to diphenyl arsenic acid (DPAA) in the drinking water during development could be due to an increase in HO-1 in the cerebellar astrocytes. Previously, Ahmad et al (2000) suggested the direct reduction of Ft Fe by dimethyl arsenic acid (DMAIII) as the predominant pathway, and that DMAIII and AH --mediated Fe-release from Ft (not via O 2ˉ) also may be a significant route in vivo.…”

Transcriptional profiling of reactive metabolites for elucidating toxicological mechanisms: a case study of quinoneimine-forming agents

“…Subsequent studies in mice have greatly expanded our understanding of the transcriptomic changes that occur in response to APAP exposure (Coen et al, 2004;Liu et al, 2003;Reilly et al, 2001a, Ruepp et al, 2002Wang et al, 2013;Welch et al, 2006;Williams et al, 2004;Tachibana et al, 2011). The consensus from these studies is that toxic doses of APAP lead to the increased expression of stressresponsive genes involved in heat shock protein expression, cell cycle-response, inflammatory-response, cell signaling, and cell metabolism.…”