Expression profiles of microRNAs in familial or sporadic PMAH cases compared with normal control
MicroRNA microarray analysis was respectively performed on tissue samples from 3 cases of patients with familial PMAH (Group1), 2 sporadic cases (Group2) as well as 3 normal control tissues (Group3) to compare the difference on microRNA expression levels. The differences on microRNAs expression were analyzed between patients with familial PMAH and normal controls to identify potential microRNA which may play important roles in the pathogenesis of familial PMAH. 16 microRNAs passed the FDR cutoff value of 0.05. 7 miRNAs were upregulated (hsa-miR-4306,hsa-miR-130a,hsa-miR-20b,hsa-miR-20a,hsa-miR-15a,hsa-miR-106a,hsa-miR-17) and 3 miRNAs were downregulated (hsa-miR-197, hsa-miR-3656, hsa-miR-3196) (Table 1). However, the following microRNAs exhibit differentially expression levels with statistical significance but signal intensities were very low, such as: hsa-miR-17*, hsa-miR-18b, hsa-miR-1976, has-miR-454, has-miR-629*, has-miR-629. Although we could detect some difference on microRNAs expression levels between the group of patients with familial PMAH and normal controls, expression levels of these microRNAs were statistically insignificant with p-value more than 0.05. After filtering low-intensity miRNAs, raw signal intensities were normalized by median. The differentially expressed miRNAs passed volcano plot filtering(Fig. 3A).
Similar analysis was performed on the differences of microRNAs expression levels between 2 sporadic patients with PMAH and 3 normal controls. Through filtering according to FDR cutoff value of 0.05 and expression signal intensities, 8 microRNAs were differentially expressed between above 2 groups, 1 miRNAs were upregulated (hsa-miR-3196) and 2 miRNAs were downregulated (hsa-miR-342-3p, hsa-miR-532-3p) (Table 2). However there was 5 microRNAs meeting requirements of statistical significance but their signal intensities were not strong enough, including hsa-miR-1976, hsa-miR-485-3p, hsa-miR-3195, hsa-miR-3180 and hsa-miR-445. After filtering low-intensity miRNAs, raw signal intensities were normalized by median. The differentially expressed miRNAs passed volcano plot filtering (Fig. 3B). The other microRNAs were found no expression difference in sporadic patients with PMAH compared to that of normal controls.
In order to identify the microRNAs which were differentially expressed between patients with familial and sporadic PMAH , we compared the microRNAs expression profiles of these two independent groups of samples. The same criteria of FDR cutoff value and expression intensities were applied to filter the candidate microRNAs. Results showed that, 2 miRNAs were upregulated (hsa-miR-342-3p, hsa-miR-532-3p) and 9 miRNAs were downregulated (hsa-miR-4306, hsa-miR-20b, hsa-miR-20a, hsa-miR-106a, hsa-miR-17, hsa-miR-101, hsa-miR-16, hsa-miR-26a, hsa-miR-106b) (Table 3). After filtering low-intensity miRNAs, raw signal intensities were normalized by median. The differentially expressed miRNAs passed volcano plot filtering (Fig.3C).
Validation of microRNA arrays by qRT-PCR
With the purpose of validating the results from microRNA microarrays, qRT-PCR was performed on total RNA extracted from familial and sporadic PMAH surgical tissues compared with the normal controls respectively. We evaluated microRNA level of has-miR-20b that, based on our microarray data, was differentially expressed in tissues from familial patients with PMAH compared with normal controls. The expression level of has-miR-20b in familial patients with PMAH was 1.56 fold higher than normal controls with p-value of 0.01165 which was in accordance with the results from microRNA arrays (3.11 fold higher with p-value=0.003463). The expression levels of has-miR-342-3p (0.68 fold downregulated with p-value=0.005814) were determined by qRT-PCR respectively in sporadic patients with PMAH and normal control samples to validate the comparison of microRNA expression profile between these 2 groups, which was consistent with the result from microRNA array (hsa-miR-342-3p was 0.21 fold downregulated in sporadic patients with PMAH versus normal controls). Similarly, hsa-miR-342-3p and hsa-miR-101 were selected to validate the different microRNA expression levels between familial and sporadic patients with PMAH, qRT-PCR results showed that, hsa-miR-342-3p was 1.58 fold upregulated while hsa-miR-101 was 0.40 fold downregulated in familial patients with PMAH compared to sporadic patients. These qRT-PCR test results were consistent with those from microRNA arrays in which hsa-miR-342-3p was 3.6 fold upregulated and hsa-miR-101 was 0.24 fold downregulated in familial patients with PMAH versus sporadic patients.
Hierarchical clustering of microRNAs with different expression levels
In order to identify the special microRNAs expression signatures among different groups of patients, hierarchical clustering analysis was performed on all microRNAs expression levels in the form of signal intensities included in microarrays. This hierarchical clustering analysis clustered microRNAs together according to their expression levels and samples from different groups based on similarity of the investigated microRNA expression profiles[24]. Supervised hierarchical pairwise comparison among these 3 groups of samples, we could always identify a special group of microRNAs which could discriminate one group from the other. The 16 differential expressed microRNAs signature from the results in microarray could clearly discriminate between familial patients with PMAH and normal controls including 10 downregulated microRNAs and 6 upregulated microRNAs (Fig.4A). Similarly, the microRNAs signature containing 8 differentially expressed microRNAs could discriminate between the sporadic patients with PMAH and normal controls with statistical significance p-value of 0.05 (Fig.4B). The identified 11 differentially expressed microRNAs could well discriminate between familial and sporadic patients with PMAH (table 3).
Comprehensive target-network prediction of differential expressed microRNAs and Pathway analysis
Functional analysis of the altered microRNAs between the PMAH patients and normal controls revealed that some enriched pathways such as signal transduction, signaling molecules and interaction metabolic, were potentially associated with the pathogenesis of PMAH. When comparison analysis was performed between familial patients with PMAH and normal controls, all of the 16 altered microRNAs were imported into KEGG Pathway analysis software to reveal that Circadian Rhythm pathway was the most affected pathway by these microRNAs with 6 genes predicted as the potential targets, including NPAS2, CRY2, BHLHE40, BHLHE41, CRY1 and CLOCK. At the same time, however, renal cell carcinoma pathway, mTOR signaling pathway, glioma pathway, pancreatic cancer pathway and endocytosis pathway were ranked top most signaling pathways affected by these altered microRNAs (Fig.5A). When KEGG Pathway analysis was similarly performed on the differentially expressed 8 microRNAs between the sporadic patients with PMAH and normal controls, renal cell carcinoma pathway, dilated cardiomyopathy pathway, axon guidance pathway, Ubiquitin mediated proteolysis, endocytosis and MAPK signaling pathway were ranked top most affected pathways on the basis of predicted targets, while renal cell carcinoma pathway contained 5 genes which was predicted as the potential downstream targets for the altered microRNAs, including CDC42, CUL2, EP300, GRB2 and SLC2A1 (Fig.5B).
Interestingly, the renal cell carcinoma pathway was ranked at top 2 most affected pathways among all associated pathways containing potential targets of the altered microRNAs which were differentially expressed in familial or sporadic patients with PMAH compared to normal controls. In comparison of altered microRNAs between familial patients with PMAH and normal controls , renal cell carcinoma pathway contained 25 genes which were targeted by these microRNAs( including EGLN3, EGLN2, EGLN1, PAK6, PAK7, CUL2, CDC42, RAC1, SOS2, GAB1, SLC2A1, TGFA, PAK1, PIK3R1, AKT3, PIK3R2, MAP2K1, MET, RAF1, MAPK1, HIF1A, CRKL, VEGFA, RAP1A and CRK), while 5 genes (including CDC42, CUL2, EP300, GRB2 and SLC2A1) were targeted by microRNAs which were differentially expressed between sporadic patients with PMAH and normal controls. These results indicated that renal cell carcinoma pathway might play an important role in the pathogenesis of PMAH although PMAH was a benign hereditary endocrine abnormality without malignant characters (Fig.6).