Figure 1
(A) Dot-plots depicting the differential distribution of mRNA levels (RQ units) of CDK5, CDKN2A and TSPAN8 in controls (CT) and T2D patients (T2D) (upper row of panels), as well as among controls without T2D risk factors (CTRF−), controls with T2D risk factors (CTRF+) and T2D patients (lower row of panels), as attested by appropriate non-parametric tests. Mann-Whitney analysis revealed that T2D patients are characterized by higher mRNA levels of CDK5, CDKN2A and TSPAN8, compared to controls (upper row). Jonckheere-Terpstra test showed a stepwise increase in the total mRNA levels of the abovementioned genes among the CTRF−, CTRF+ and T2D groups (lower row). P-values are designated by asterisks (*p < 0.05, **p < 0.01, ***p < 0.001), whereas horizontal bars represent the median value of the group (B). Area-proportional Euler diagrams showing the differentially expressed genes and transcripts variants between the samples of controls (CT) and T2D patients (T2D), as analysed by RNA-seq. a. Diagrams representing the differentially expressed genes between T2D patients and controls, within the total 24 genes-of-interest (T2D-susceptibility genes; grey circle). Based on our data, T2D patients expressed exclusively higher levels of total mRNA of 3 genes (namely CAPN10, KCNQ1, TCF7L2) and lower levels of total mRNA of 2 genes (namely CDKAL1 and IGF2BP2), compared to controls, while mRNA expression of one gene (THADA) was found to be either up- or- downregulated in T2D versus CT groups. Further analysis of the individual gene-transcript variants revealed that the levels of 6 out of the 77 transcript variants of interest [NM_023085 (CAPN10), NM_000218 (KCNQ1), NM_001198530, NM_001146284, NM_001198527 (all of TCF7L2), NR_073394 (THADA)] were increased, while 8 [NM_017774 (CDKAL1), NM_001291873, NM_001291872, NM_001291875 (all of IGF2BP2), NM_001271643, NM_001271644, NM_001083953, NM_022065 (all of THADA)] decreased in patients versus controls. Differential expression was considered as fold-change of the relative expression levels (mean of reads per kilobase million, RPKM) between the two groups (CT:T2D ratio) <0.5 or >2. (C) Dot-plots depicting the differential distribution of mRNA levels (RQ units) of CAPN10 tv3, CDK5 tv1, CDKN2A tv3, CDKN2A tv4, IGF2BP2 tv7, KCNQ1 tv1 and TSPAN8 in controls (CT) and T2D patients (T2D) (upper row of panels), as well as among controls without T2D risk factors (CTRF−), controls with T2D risk factors (CTRF+) and T2D patients (lower row of panels), as attested by appropriate non-parametric tests. Mann-Whitney analysis revealed that T2D patients are characterized by higher mRNA levels of CDK5 tv1, CDKN2A tv3, CDKN2A tv4, IGF2BP2 tv7, and TSPAN8, while lower levels of CAPN10 tv3 and KCNQ1 tv1, compared to controls (upper row). Jonckheere-Terpstra test showed that the mRNA levels’ distribution of the abovementioned transcripts followed a linear trend among the CTRF−, CTRF+ and T2D groups: increase in the cases of CDK5 tv1, CDKN2A tv3, CDKN2A tv4, IGF2BP2 tv7, and TSPAN8 and decrease in the cases of CAPN10 tv3 and KCNQ1 tv1 (lower row). P-values are designated by asterisks (*p < 0.05, **p < 0.01, ***p < 0.001), whereas horizontal bars represent the median value of the group; D. Dot-plots depicting the differential distribution of mRNA levels (RQ units) of CDK5 tv2 and THADA tv5 in controls (CT) and T2D patients (T2D) (upper row of panels), as well as among controls without T2D risk factors (CTRF−), controls with T2D risk factors (CTRF+) and T2D patients (lower row of panels), as attested by appropriate non-parametric tests. Mann-Whitney analysis revealed that T2D patients are characterized by higher mRNA levels of CDK5 tv2 and THADA tv5 (upper row). More specifically, there is a significant difference of these tv levels between T2D individuals and the group of controls with T2D risk factors (CTRF+), while not with the controls without such factors (lower row). P-values are designated by asterisks (*p < 0.05), whereas horizontal bars represent the median value of the group.
