The characteristic comparison between PTDM and T2D mouse model
Mice remained in good condition throughout the experimental period (Fig. 1A). Compared with the T2D group, the PTDM group showed higher body weight and lower fasting glucose (Fig. 1B-C, both P < 0.05). Besides, the PTDM group showed higher plasma insulin levels (Fig. 1G, P < 0.05). The PTDM group had higher alanine aminotransferase (P < 0.05) and aspartate aminotransferase (P < 0.05), while GSP was not significant (Fig. 1D-F). Interestingly, the PTDM group showed lower glucose levels after insulin injection (Fig. 1H, P < 0.05), as well as smaller areas under the ITT curves (Fig. 1I, P < 0.05). In GTT, the PTDM group showed lower glucose levels (Fig. 1J, P < 0.05) and smaller areas under the GTT curves after injection of insulin (Fig. 1K, P < 0.05) compared with the T2D group.(Fig. 1)
Transcriptomics analysis among the liver, pancreas and adipose tissue
Difference analysis showed that 149 genes upregulated (FDR < 0.05, log2(FC) > 1) and 236 genes downregulated in liver (FDR < 0.05, log2(FC)< -1) (Fig. 2A). Difference analysis showed that 94 genes upregulated (FDR < 0.05, log2(FC) > 1) and 350 genes downregulated in the pancreas (FDR < 0.05, log2(FC)< -1) (Fig. 2B). Difference analysis showed that 130 genes upregulated (FDR < 0.05, log2(FC) > 1) and 490 genes downregulated in Adipose (FDR < 0.05, log2(FC)< -1) (Fig. 2C). The Venn diagram clearly illustrates a shared upregulation of five genes—serpinh1, slc38a3, prepl, mocs2, and plekha7—in all three tissues: liver, pancreas, and adipose tissue (Fig. 2D, Supplementary Table 1, all p < 0.05). Conversely, 31 genes, such as syt13, nfasc, ngp, and ighg1, exhibited a consistent downregulation across these same tissues. (Fig. 2E, Supplementary Table 2, all p < 0.05). Figure 2F showed that ighg1 and ngp genes expressed higher in the T2D than PTDM in the pancreas, while slc38a3 expressed higher in the PTDM than T2D in the liver, and serpinh1 expressed higher in the PTDM than T2D in the adipose tissue. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses unveiled substantial alterations in various pathways across different tissues. In the liver (Fig. 2G), noteworthy changes were observed in the MAPK pathway, EGFR pathway, and leukocyte migration. Within the pancreas (Fig. 2H), there were significant shifts in the differentiation of Th17, Th1, and Th2 cells, as well as T cell activation. Similarly, in adipose tissue (Fig. 2I), we identified notable modifications in the MAPK signaling pathway, leukocyte migration, and Rap1 pathways. These results underscore the substantial impact of the immune system, particularly in terms of leukocyte migration, on the development of PTDM.(Fig. 2)
Weighted gene co-expression network analysis (WGCNA) showed the module correlated with glucose levels
WGCNA was employed to identify the module most relevant to glucose metabolism, as depicted in Fig. 3A. Modules with interconnected characteristics were selected based on a combination of network analysis, correlation coefficients, and hierarchical clustering. Notably, the lightcyan module emerged as highly correlated with blood glucose levels (R = 0.47, P = 0.03, Fig. 3B). This module encompasses genes such as treh, acsm4, cyp2c65, cyp2c66, cyp2d11, and cyp4a12b, with detailed information available in Supplementary Table 3. Of particular significance, treh and acsm4 are genes associated with glycolysis.
Furthermore, we conducted a comparative analysis between the genes within the lightcyan module and those identified in the differential analysis of liver, pancreas, and adipose tissue. Intriguingly, approximately 7.5%, 0.5%, and 2% of these genes were found to be shared among the liver, pancreas, and adipose tissue, respectively. This observation suggests that the liver may play a predominant role in the development of PTDM.
The results of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses further accentuated the importance of the lightcyan module. These analyses indicated significant alterations in pathways related to steroid hormone biosynthesis, insulin secretion, and oxidoreductase activity (Fig. 3C-F). (Fig. 3)
Comparison of ceRNA networks between PTDM and T2D in liver and pancreas tissues
Furthermore, we constructed a network encompassing mRNAs, circRNAs, and lncRNAs, which serve as targets for key miRNAs and exhibit strong correlations within the ceRNA network. Specifically, within the lincRNA-associated ceRNA network, we identified 4 crucial miRNAs (mmu-miR-369-3p, mmu-miR-494-3p, mmu-miR-495-3p, mmu-miR-6240) and 4 lncRNAs (chr11:67687120–67688930, ENSMUST00000236340, XR_871293.4, XR_877383.3) in a subnetwork that play pivotal roles in shaping PTDM in the liver (Fig. 4A), the details were in Supplementary Table 4. In the circRNA-associated ceRNA network, we identified 6 significant miRNAs (mmu-miR-369-3p, mmu-miR-376b-3p, mmu-miR-409-3p, mmu-miR-411-5p, mmu-miR-494-3p, mmu-miR-495-3p) and 1 circRNA (15_3457930_3551685) within a subnetwork that influencing the development of PTDM in the liver (Fig. 4B), the details were in Supplementary Table 5.
Moving to the pancreas, in the lincRNA-associated ceRNA network, we pinpointed 2 miRNAs (mmu-miR-196b-5p, mmu-miR-410-3p) and 6 lncRNAs (chr2:174710024–174710821, chr8:15030633–15033329, ENSMUST00000185694, ENSMUST00000226736, XR_001780381.3, XR_003951655.1) in a subnetwork that shaping the development of PTDM (Fig. 4C), the details were in Supplementary Table 6. Similarly, in the circRNA-associated ceRNA network of the pancreas, we identified 2 miRNAs (mmu-miR-196b-5p, mmu-miR-410-3p) and 2 circRNAs (17_51803431_51809287, 19_6341903_6343176) within a subnetwork that serve as crucial regulators influencing the development of PTDM (Fig. 4D), the details were in Supplementary Table 7.
This comprehensive approach provides a deeper understanding and introduces a novel perspective on which ceRNA networks are different between PTDM and T2D, particularly in the liver and pancreas, respectively. (Fig. 4)
Difference Analysis of Metabolomics both in the liver and pancreas
To assess the alterations in metabolomics within solid organs, we conducted a comparative analysis between the liver and pancreas. Figures 5A-B visually depict the discrimination between the PTDM and T2D groups based on metabolite profiles, as determined by orthogonal partial least squares discriminant analysis (OPLA-DA).
In the negative ionization mode, several metabolites exhibited significant differences between the PTDM and T2D groups in both the liver and pancreas. In the liver (Fig. 5C, 5E, 5G), metabolites such as 2,2-dimethylsuccinic acid, D-2,3-Dihydroxypropanoic acid, Succinic acid semialdehyde, D-Ribose, Methylsuccinic acid, (R)-lipoic acid, Resveratrol, Pyrrole-2-carboxylic acid, Aldehydo-D-xylose, and Nicotinic acid were notably changed in the PTDM group compared to the T2D group.
Similarly, in the pancreas (Fig. 5D, 5F, 5H), metabolites including 2,2-dimethylsuccinic acid, L-Serine, L-Leucine, N-Acetylserine, and Ketoleucine displayed a significant change in the PTDM group compared to the T2D group.
In the positive ionization mode, distinct metabolites were found to be significantly decreased in the PTDM group as compared to the T2D group. In the liver, metabolites such as Pinostrobin chalcone and PC(18:1(11Z)/P-16:0) exhibited notable increases. Similarly, in the pancreas, metabolites including Pinostrobin chalcone, Caffeine, D-Galactose, and PC(22:4(7Z,10Z,13Z,16Z)/15:0) were significantly decreased in the PTDM group compared to the T2D group (Supplementary Table 8).
These findings underscore the significant metabolic differences between the PTDM and T2D groups within the liver and pancreas, shedding light on the unique metabolic signatures associated with PTDM.(Fig. 5)
Combination analysis of transcriptomics and metabolomics
Through a comprehensive analysis combining transcriptomics and metabolomics following differential analysis with permutation test, we observed intriguing correlations involving 2510002D24RIK. In the liver (Fig. 6A), this gene was found to be correlated with changes in Resveratrol, Aldehydo-D-xylose, 3-Hydroxybutyric acid, 5-Aminoimidazole-4-carboxamide, Leucinic acid and (R)-lipoic acid. Figure 6B showed that 2510002D24RIK was significantly increased in the PTDM group compared to T2D group (P = 0.049). Figure 6C-H provide a detailed visualization of the correlations between above metabolites and 2510002D24RIK in the liver, while we did not see a correlation of 2510002D24RIK and metabolites in the pancreas.
To further validate our findings that PTDM group had a lower glucose than T2D group, we assessed the glucose and triglyceride content in liver tissues and adipose tissues using PAS staining and Oil red O staining respectively (Fig. 6I-P). Consistently, our results indicated lower liver glycogen content and reduced fat content in the PTDM group, aligning with the outcomes of our biochemical experiments. These findings collectively contribute to our understanding of the intricate interplay between gene expression and metabolite profiles, especially that liver played an important role in the PTDM development.(Fig. 6)