3.3. Transcriptome Analysis of Kidney Injury Induced by T-2 Toxin
We collected mice kidney tissues at 1 d, 3 d, and 7 d after T-2 toxin exposure and performed RNA-seq. Each sample produced an average of 1.18 G of data. The raw data from sequencing contained low-quality, junction-contaminated, and high unknown base N reads, which needed to be removed prior to data analysis to ensure the reliability of the results. Then we utilized the reference genome (GCF_000001635.26_GRCm38.p6) of mice (species: Mus_musculus) in the NCBI database for functional annotation. A total of 97,608 mRNA, 103,339 IncRNA, and 1,976 miRNA were found in this study. The average comparison rate of the samples against the gene set was 96.62% and the average comparison rate against the gene set was 62.73% (
Table S2). A total of 19,513 genes were detected. Volcano plots for comparison of gene expression patten between TG_1d, TG_3d, and TG_7d were shown in
Figure 5A–C. The fragments per kilobase per million (FPKM) > 10 with fold change > 2 and adjusted p < 0.01 were filtered to screen the candidate DEGs. We identified a total of 1122, 58, and 391 genes that were predominantly expressed in kidney tissues at 1d, 3d, and 7d after T-2 toxin exposure, respectively (
Figure 5D). A total of seven genes (Hba-a2, Alas2, Kif20a, Mup3, Ugt2b35, Mmp12, and Myh4) were distributed in all the three TG groups. We then compared the expression of the DEGs between three different groups and most DEGs were up-regulated at TG_1d and TG_7d (
Figure 5E).
Next, we performed transcriptome profiling of mice kidney at 1d after T-2 toxin exposure. GO function enrichment analysis indicated that the DEGs were mainly enriched in cellular process, metabolic process, biological regulation, regulation of biological process, response to stimulus, etc (
Figure 6A). We conducted functional annotation of the gene lists using ConsensusPathDB [
29]. Intriguingly, the top-ranked pathway related to the cell cycle, p53 signaling pathway, and cellular senescence were over-presented in the TG_1d gene list. The top pathway including ribosome, proteasome, protein processing in endoplasmic reticulum, antigen processing and presentation, steroid biosynthesis, fatty acid elongation, alanine, aspartate and glutamate metabolism, terpenoid backbone biosynthesis, fatty acid degradation, measles, and circadian rhythm were overexpressed at 1 d after T-2 toxin exposure (
Figure 6B). Kegg pathway enrichment results showed that the DEGs induced by T-2 toxin were enriched in AMPK signaling pathway, FoxO signaling pathway, NOD-like receptor signaling pathway, and metabolic pathways (
Figure 6B). We found that the key seven genes including Bnip3, Tnfsf10, Ccnd1, Pten, Pck1, Sgk2, Prkag3 were involved in FoxO signaling pathway. A total of 44 ribosome related genes (e.g. Rps7, Rps21, Rpl4, Rps3a1, Rps2, etc) were over-presented after T-2 toxin exposure. Protein processing in endoplasmic reticulum including Eif2ak2, Hsp90b1, Hspa5, Lman1, Dnaja1, Svip, Hsp90ab1, and Hspbp1 was also disturbed in this exposure period. Some genes important for the AMPK signaling pathway (Fbp2, Eef2, Ppargc1a, Ccnd1, Eif4ebp1, Pck1, Ppp2r5a, Prkag3, and Pfkp genes) were also up-regulated in this acute T-2 toxin exposure.
GO analysis demonstrated that regulation of APC/C activators between G1/S and early anaphase, response to stilbenoid, regulation of cell cycle process, porphyrin metabolism, regulation of transferase activity, and MAPK cascade (
Figure S1A). Consistently, the top-ranked pathway for the T-2_3d group was cell cycle, p53 signaling pathway, and cellular senescence for the upregulated DEGs (
Figure S1A). Porphyrin metabolism, pentose and glucuronate interconversions, ascorbate and aldarate metabolism, chemical carcinogenesis - DNA adducts, drug metabolism, and retinol metabolism were significant pathway for the downregulated DEGs (
Figure S1B). Two genes Ccna2 and Slc2a4 were important for the AMPK signaling pathway and FoxO signaling pathway. Four genes (Ccna2, Cdc20, Ccnb1, and Cdk1) were involved in the cell cycle pathway to modulate the repair of the T-2 toxin induced nephrotoxicity (
Figure S2). For Wnt signaling pathway, we found that Frzb and Sfrp1 were involved in this exposure period. Importantly, p53 signaling pathway was affected by disturbing the expression of Ccnb1, Rrm2, and Cdk1genes. Porphyrin metabolism was over-expressed and Ugt2b35, Alas2, and Ugt2a2 genes were affected in this process. We also found that Reln gene was involved in the PI3K-Akt signaling pathway.
We further characterize the transcriptomic profile of T-2 toxin exposure at 7 d and the number of the DEGs was increased approximately 6.74-fold change compared with that at 3 d (
Figure 5D). Notably, most genes were upregulated in this exposure period (
Figure 5E). We speculated the mice might have a process of self-repairing protection, and this protection may be only temporary after acute exposure to T-2 toxin. GO analysis found that monocarboxylic acid metabolic process, metabolism of lipids, biological oxidations, steroid metabolic process, protein localization, metabolism of xenobiotics by cytochrome P450, PPAR signaling pathway, and mitochondrial long chain fatty acid beta oxidation were enriched using Metascape software (
Figure S3A). Kegg pathway analysis showed that peroxisome, porphyrin metabolism, PPAR signaling pathway, fatty acid degradation, butanoate metabolism, steroid hormone biosynthesis, ferroptosis and fatty acid metabolism were over-presented in T-2 toxin exposure (
Figure S3B). Slc3a2, Slc39a8, Map1lc3a, Hmox1, Gpx4, and Fth1were associated with ferroptosis pathway. MAPK signaling pathway was disturbed by regulating the expression of Cd36, Hmgcr, Ccnd1, Pck1, Pfkfb2, and Scd2 (
Figure S4).
3.4. Temporal Pattern and Network Analysis of Transcriptional Regulators
We identified the transcriptional regulators likely to be involved in the mice kidney after T-2 toxin exposure at three different time points. Activated regulators, such as Irf1, Cebpb, Nr3c1, Trp53, Nfkb1, Spic, Egr1, Foxo4, Ep300, Clock, and Stat1 may play important roles for T-2 toxin exposure at 1 d (
Figure S5A). On the other hand, at 3 d after exposure, Trp53 was important regulating genes involved in autophagy (
Figure S5B). There are two important regulatory gene Ppara and Bcl3 that are predicted to be activated in 7 d after T-2 toxin exposure (
Figure S5C). Molecular network analysis revealed that the DEGs (Rpl8, Rps15a, Rpl19, Rpl11, Rps18, Rps5, Rpl5, Rpl0, Rack1, and Rps3) were mainly involved in Ribosome-related pathway at 1 d after T-2 toxin exposure (
Figure 7A). At 3d after exposure, the key regulators including Cdc20, Top2a, Cona2, Ube2c, Kif20a, Prc1, Aspm, Mki67, Rrm2, and Cdk1 were referred to Cell cycle, cellular senescence, ubiquitin mediated proteolysis, and p53 signaling pathway (
Figure 7B). Notably, Cyp2e1, Cyp4a14, Ugt2b34, Ugt2b37, Ugt2b35, Ugt2b38, and Cyp2a4 were the important regulators and mainly involved in cellular metabolism at the exposure recovery period (
Figure 7C).