An Integrated Multi-Omic Approach to Assess Radiation Injury on the Host-Microbiome Axis

Abstract

Medical responders to radiological and nuclear disasters currently lack sufficient high-throughput and minimally invasive biodosimetry tools to assess exposure and injury in the affected populations. For this reason, we have focused on developing robust radiation exposure biomarkers in easily accessible biofluids such as urine, serum and feces. While we have previously reported on urine and serum biomarkers, here we assessed perturbations in the fecal metabolome resulting from exposure to external X radiation in vivo. The gastrointestinal (GI) system is of particular importance in radiation biodosimetry due to its constant cell renewal and sensitivity to radiation-induced injury. While the clinical GI symptoms such as pain, bloating, nausea, vomiting and diarrhea are manifested after radiation exposure, no reliable bioindicator has been identified for radiation-induced gastrointestinal injuries. To this end, we focused on determining a fecal metabolomic signature in X-ray irradiated mice. There is overwhelming evidence that the gut microbiota play an essential role in gut homeostasis and overall health. Because the fecal metabolome is tightly correlated with the composition and diversity of the microorganism in the gut, we also performed fecal 16S rRNA sequencing analysis to determine the changes in the microbial composition postir-radiation. We used in-house bioinformatics tools to integrate the 16S rRNA sequencing and metabolomic data, and to elucidate the gut integrated ecosystem and its deviations from a stable host-microbiome state that result from irradiation. The 16S rRNA sequencing results indicated that radiation caused remarkable alterations of the microbiome in feces at the family level. Increased abundance of common members of Lactobacillaceae and Staphylococcaceae families, and decreased abundances of Lachnospiraceae, Ruminococcaceae and Clostridiaceae families were found after 5 and 12 Gy irradiation. The metabolomic data revealed statistically significant changes in the microbial-derived products such as pipecolic acid, glutaconic acid, urobilinogen and homogentisic acid. In addition, significant changes were detected in bile acids such as taurocholic acid and 12-ketodeoxycholic acid. These changes may be associated with the observed shifts in the abundance of intestinal microbes, such as R. gnavus, which can transform bile acids.

Nonhuman primates as models for the discovery and development of radiation countermeasures

“…There are several studies identifying proteins [129,130], metabolites as biomarkers for radiation exposure in blood [131–133], urine [131,134,135], and the gut using NHP models [135–139]. In addition, there are ample studies with lipidomics [132], microbiome [140], and mRNA [141]. Considering space limitations for this article, it is not possible to discuss this aspect in depth and readers may go through recent reviews [98,137].…”

Metabolomic applications in radiation biodosimetry: exploring radiation effects through small molecules

“…Fecal material can be easily obtained and analyzed in a similar manner as urine, serum, saliva, and sebum. This was demonstrated in mice irradiated with 5 or 12 Gy and evaluated at 3 days post-irradiation (Goudarzi et al, 2016). Marked decreases in several species were observed after 16S rRNA sequencing, most notably in the Lactobacillaceae , Staphylococcaceae , Lachnospiraceae , Ruminococcaceae , and Clostridiaceae families.…”

Differential mobility spectrometry (DMS) reveals the elevation of urinary acetylcarnitine in non‐human primates (NHPs) exposed to radiation

“…The need for examination of small molecule metabolites from non‐invasively obtained biological samples has become particularly important as a result of the identification of diagnostic biomarkers for radiation exposure . These studies have emphasized the importance of rapid methods for screening large populations of patients who might require medical treatment due to radiation injury from industrial accidents or terrorist attacks .…”

“…The need for examination of small molecule metabolites from non-invasively obtained biological samples has become particularly important as a result of the identification of diagnostic biomarkers for radiation exposure. 1,[10][11][12][13][14][15][16][17][18][19][20][21][22] These studies have emphasized the importance of rapid methods for screening large populations of patients who might require medical treatment due to radiation injury from industrial accidents or terrorist attacks. 23,24 In line with these considerations, we have explored a non-chromatographic approach: the use of differential mobility spectrometry (DMS) in combination with mass spectrometry (MS), as a high throughput method for the analysis of acetylcarnitine in urine.…”