Microarray analysis identifies coding and non-coding RNA markers of liver injury in whole body irradiated mice

Abstract

Radiation injury from medical, accidental, or intentional sources can induce acute and long-term hepatic dysregulation, fibrosis, and cancer. This long-term hepatic dysregulation decreases quality of life and may lead to death. Our goal in this study is to determine acute changes in biological pathways and discover potential RNA biomarkers predictive of radiation injury. We performed whole transcriptome microarray analysis of mouse liver tissue (C57BL/6 J) 48 h after whole-body irradiation with 1, 2, 4, 8, and 12 Gray to identify significant expression changes in mRNAs, lncRNAs, and miRNAs, We also validated changes in specific RNAs through qRT-PCR. We used Ingenuity Pathway Analysis (IPA) to identify pathways associated with gene expression changes. We observed significant dysregulation of multiple mRNAs across all doses. In contrast, miRNA dysregulation was observed upwards of 2 Gray. The most significantly upregulated mRNAs function as tumor suppressors: Cdkn1a, Phlda3, and Eda2r. The most significantly downregulated mRNAs were involved in hemoglobin synthesis, inflammation, and mitochondrial function including multiple members of Hbb and Hba. The most significantly upregulated miRNA included: miR-34a-5p, miR-3102-5p, and miR-3960, while miR-342-3p, miR-142a-3p, and miR-223-3p were most significantly downregulated. IPA predicted activation of cell cycle checkpoint control pathways and inhibition of pathways relevant to inflammation and erythropoietin. Clarifying expression of mRNA, miRNA and lncRNA at a short time point (48 h) offers insight into potential biomarkers, including radiation markers shared across organs and animal models. This information, once validated in human models, can aid in development of bio-dosimetry biomarkers, and furthers our understanding of acute pathway dysregulation.

Biomarkers for Biodosimetry and Their Role in Predicting Radiation Injury

“…Research to discover biomarkers of radiation in normal tissue injury has highlighted multiple genes within the p53 pathway and DNA repair pathways. These results are observable in vitro and in vivo with notable genes including CDKN1A, PCNA, PHLDA3, BBC3, GDF15, and the hemoglobin family members (Hbb, Hba) [Ghandhi et al, 2019;Li et al, 2019;Aryankalayil et al, 2021Aryankalayil et al, , 2023.…”

Connection between Radiation-Regulating Functions of Natural Products and miRNAs Targeting Radiomodulation and Exosome Biogenesis

“…miR-518b was upregulated in endothelium-derived cells after irradiation [53], and its radiation target EGR1 was identified (Table 2). Radiation downregulated miR-223-3p in the mouse liver [95] and human peripheral mononuclear blood cells [52], and its radiation target MDM2 was identified (Table 2). Radiation upregulated serum miR-375-3p in mice [55], and its radiation target MAP3K20 was identified (Table 2).…”

“…Some natural-product-regulated miRNAs, such as miR-34a-5p and miR-107, have been included in both non-cancer and cancer radiation studies (Table 2) [7,95,103]. For ex-ample, miR-34a-5p was upregulated in mouse liver tissue after whole-body irradiation [95].…”

“…Some natural-product-regulated miRNAs, such as miR-34a-5p and miR-107, have been included in both non-cancer and cancer radiation studies (Table 2) [7,95,103]. For ex-ample, miR-34a-5p was upregulated in mouse liver tissue after whole-body irradiation [95]. EGCG improved the apoptosis and radiosensitivity of liver cancer cells by upregulating miR-34a-5p [7], and its radiation targets TMEM109 and GATA3 were identified (Table 2).…”

“…As mentioned above, most of the natural-product-regulated miRNAs shown in Table 2 are associated with radiation-modulating effects and miRDB results for radiation-modulating targets. However, other natural-product-regulated miRNAs [52,61,68,[95][96][97][98][99][100][101][102], such as miR-3960 [95], miR-217-3p [61], miR-22-3p [96,97], miR-126-3p [52], miR-33a-5p [98,99], miR-574-3p [100], miR-370-3p [101], miR-149-5p [102], and miR-451a [52], have only been reported in the context of radiation-modulating effects, without available miRDB results for radiationmodulating targets.…”