The microRNA signature of patients with sunitinib failure: regulation of UHRF1 pathways by microRNA-101 in renal cell carcinoma

Molecular targeted therapy is a standard treatment for patients with advanced renal cell carcinoma (RCC). Sunitinib is one of the most common molecular-targeted drugs for metastatic RCC. Molecular mechanisms of sunitinib resistance in RCC cells is still ambiguous. The microRNA (miRNA) expression signature of patients with sunitinib failure in RCC was constructed using a polymerase chain reaction (PCR)-based array. Several miRNAs that were aberrantly expressed in RCC tissues from patients treated with sunitinib were identified in this analysis. MicroRNA-101 (miR- 101) was markedly suppressed in sunitinib treated RCC tissues. Restoration of miR-101 significantly inhibited cell migration and invasion in Caki-1 and 786-O cells. Ubiquitin-like with PHD and ring finger domains 1 (UHRF1) was directly suppressed by miR-101 in RCC cells, and overexpression of UHRF1 was confirmed in sunitinib-treated RCC tissues. The pathways of nucleotide excision repair and mismatch repair were significantly suppressed by knockdown of UHRF1. Our findings showed that antitumor miR-101- mediated UHRF1 pathways may be suppressed by sunitinib treatment.


INTRODUCTION
Renal cell carcinoma (RCC) accounts for over 80% of kidney cancers, and 338,000 new cases were diagnosed worldwide in 2012 [1].The incidence of RCC is increasing due to recent improvements in screening technologies, such as ultrasound and computed tomography.Although molecular-targeted anti-angiogenic multi-tyrosine kinase inhibitors have been developed, they show limited effects, particularly in patients with advanced RCC; consequently, the prognosis of advancedstage RCC is still poor [2].
Sunitinib is one of the most common moleculartargeted drugs for metastatic RCC.A phase 3 clinical trial of sunitinib versus interferon alpha in patients with metastatic RCC ushered in the molecular-targeted era in the treatment of RCC [3].Although side effects, such as hand-foot syndrome, thrombocytopenia, general fatigue, and hypothyroidism, often occur with sunitinib treatment, sunitinib is still a standard treatment for metastatic RCC due to the relatively longer progression-free survival time and higher response rate [4][5][6].Additionally, sunitinib therapy is often associated with treatment failure in patients with metastatic RCC.
MicroRNAs (miRNAs) are small noncoding RNAs that function as a fine tuner of protein-coding or noncoding gene expression [7,8].A growing body of evidence suggests that aberrantly expressed miRNAs contribute to cancer pathogenesis and drug resistance [9,10].We have sequentially identified antitumor miRNA-mediated RCC pathways based on RCC miRNA signatures [11][12][13].The next challenge in our RCC study is to identify key molecules and novel pathways involved in the resistance of molecular-targeted therapies for RCC.

Expression levels of miR-101 in RCC clinical specimens and RCC cell lines
Using RT-qPCR, we evaluated the expression levels of miR-101 in normal kidney (n = 41), primary RCC (n = 42), and sunitinib-treated RCC (n = 11) tissues.Normal kidney tissues were adjacent to primary RCC tissues.The histological type of all primary RCC specimens was clear cell RCC, and 81.0% of patient tissues were classified as pT1 tumors according to the TNM classification (Table 3).
The expression levels of miR-101 were significantly downregulated (P = 0.022) in primary RCC tissues compared with that in normal kidney tissues (Figure 1A).Furthermore, the levels of miR-101 were significantly downregulated (P = 0.0013) in sunitinib-treated RCC tissues compared with those in normal kidney tissues (Figure 1A).miR-101 expression levels were low in the RCC cell lines 786-O and Caki-1.

Effects of restoring miR-101 expression on cell proliferation, migration, and invasion in RCC cells
To investigate the functional roles of miR-101 in RCC, we performed gain-of-function studies in 786-O and Caki-1 cells by transfecting the cells with miRNA mimics.

Identification of target genes suppressed by miR-101 in RCC
To identify target genes of miR-101, we performed in silico analysis with the TargetScan program and GEO database.Analysis by the TargetScan program demonstrated that miR-101 could target 3,013 genes according to the sequences of their 3ʹUTRs.Among these genes, 790 had broadly conserved miR-101 sites across vertebrates.To gain further insights into which genes were suppressed by tumour-suppressive miR-101 in RCC, we investigated their expression statuses in RCC clinical specimens and examined gene expression profiles in the GEO database (accession numbers: GSE36985 and GSE22541) to evaluate upregulated genes in RCC specimens.Consequently, among the 790 putative conserved target genes of miR-101, 43 genes were significantly upregulated in RCC specimens compared with those in normal kidney tissues (log 2 ratio > 1.0).We sorted these candidate genes in order of expression levels in RCC from the GEO database, because genes with high expression in RCC tissues are thought to function as oncogenes in RCC.Among genes which have conserved target sites for miR-101, UHRF1 was the most upregulated gene.Among genes with multiple conserved target sites for miR-101, EZH2 showed the greatest upregulation (Table 4).
Thus, we focused on UHRF1 and EZH2 for further studies.Our strategy for selection of miR-101-targeted genes is shown in Figure 2.

UHRF1 and EZH2 were downregulated by miR-101 transfection in RCC cells
Next, we performed real-time RT-qPCR in 786-O and Caki-1 cells to analyze whether restoration of miR-101 altered the expression levels of the UHRF1 and

miR-101 directly suppressed UHRF1 in RCC cells
We performed luciferase reporter assays in 786-O cells to determine whether UHRF1 was directly suppressed by miR-101.The TargetScan database predicted that the putative miR-101 target site in UHRF1 was position 1030-1036 in the 3ʹ UTR.We used two vectors: a vector encoding a partial wild-type sequence of the 3ʹ UTR of UHRF1 mRNA including the predicted miR-101 target   putative target sites for miR-101 in their 3′ UTRs.Among these genes, 790 had conserved target sites among vertebrates for miR-101.Then, we assessed the expression levels of these genes in RCC clinical specimens using GEO expression profiles (GSE36985 and GSE22541).
Finally, genes upregulated in RCC (log 2 ratio > 1.0) were selected as putative target genes.
site, and a vector lacking the miR-101 target site.We found that the luminescence intensity was significantly reduced by cotransfection with miR-101 and the vector carrying the wildtype 3ʹUTR of UHRF1.However, the luminescence intensity was not decreased when the seed sequence of the target site was deleted from the vectors (P < 0.0001; Figure 3C).

Knockdown of UHRF1 significantly inhibited cell proliferation, migration, and invasion in RCC cell lines
To investigate the functional role of UHRF1 in RCC, we carried out loss-of-function studies by siRNA transfection.First, we evaluated the knockdown efficiency of si-UHRF1 transfection in 786-O and Caki-1 cells.RT-qPCR and western blotting indicated that si-UHRF1 transfection effectively downregulated UHRF1 and UHRF1 in 786-O and Caki-1 cells (P < 0.0001; Figure 5A and 5B).
In functional assays, si-UHRF1 transfection significantly inhibited cell proliferation compared with that in mock-or si-control-transfected 786-O and Caki-1 cells.Furthermore, cell migration and invasion were significantly inhibited by si-UHRF1 transfection compared with mock-or si-control-transfection in 786-O and Caki-1 cells (P < 0.0001; Figure 5C-5E).

Identification of pathways suppressed by UHRF1 knockdown in RCC cells
To further investigate which genes and pathways are suppressed by miR-101/UHRF1 signaling, we performed genome wide gene expression analysis using knockdown of UHRF1 by siRNA in 786-O cells.We deposited these data in the GEO (accession number: GSE77790).Genes which were significantly downregulated by si-UHRF1 (Log2 [si-UHRF1/mock] < -1.0) were categorized by KEGG pathway analysis using the GeneCodis program.Table 5 shows pathways that were significantly downregulated by knockdown of UHRF1.Pathways related to posttranscriptional modification, including the nucleotide excision repair and mismatch repair pathways, were significantly suppressed by knockdown of UHRF1.

UHRF1 and EZH2 expression in sunitinibtreated clinical RCC specimens
Finally, we examined UHRF1 expression status in clinical RCC specimens.
In a study with a relatively large sample size in GSE65615, higher UHRF1 expression was observed in sunitinib-treated RCC specimens compared with that in sunitinib-naïve RCC specimens (P = 0.0049; Figure 6A).To examine whether UHRF1 expression predicted overall survival, we used the TCGA-KIRC database (https:// tcga-data.nci.nih.gov/tcga/).A total of 533 patients who underwent surgery for RCC and were pathologically diagnosed as having clear cell RCC were divided into two groups: z-score > 0 and z-score < 0 [16,17].Higher expression of UHRF1 was associated with shorter overall survival (P < 0.0001; Figure 6B).Multivariate Cox proportional hazards models were used to assess independent predictors of overall survival times, including disease stage, pT stage, age at diagnosis, gender, and UHRF1 expression.High UHRF1 expression was one of the significant prognostic factors in patients with RCC (hazard ratio = 2.027, 95% confidence interval = 1.490-2.759,P < 0.0001; Figure 6C).To analyze UHRF1 protein expression, immunohistochemistry was performed with sunitinib-treated specimens.Immunohistochemical staining of UHRF1 in these specimens demonstrated high expression of UHRF1 in sunitinib-treated RCC cells (Figure 6D).
Similarly, we analyzed EZH2 status in clinical specimens.In GSE65615, we did not find significant difference of EZH2 expression between sunitinib-treated RCC specimens and sunitinib-naïve RCC specimens (Figure 7A).Higher expression of EZH2 was associated with shorter overall survival (P < 0.0001; Figure 7B).High EZH2 expression was one of the significant prognostic factors in patients with RCC (hazard ratio = 1.828, 95% confidence interval = 1.348-2.493,P < 0.0001; Figure 7C).High expression of EZH2 was observed in several sunitinib-treated RCC specimens (Figure 7D).
Our research group has sequentially identified novel RCC oncogenic pathways based on antitumor miRNAs identified using RCC miRNA signatures [11,13,25,26].Our miRNA-mediated RNA network analysis may provide many insights into RCC pathogenesis.In this study, we constructed a miRNA expression signature using autopsy specimens from patients with RCC who showed sunitinib failure.We believe that this miRNA signature will contribute to analysis of the mechanisms mediating resistance to sunitinib treatment.We identified 40 microRNAs that were downregulated in sunitinib-treated RCC tissues compared with that in untreated RCC tissues.Among these downregulated miRNAs, we identified miR-29b, which has been reported to suppress the extracellular matrix (ECM).In RCC cells, miR-29b directly suppresses the lysyl oxidase-like 2 (LOXL2) gene, leading to inhibition of cancer cell invasion [25].Furthermore, miR-23b, miR-10b, miR-135a, miR-29c, miR-27b, miR-1, and miR-26b have been reported as tumour-suppressive miRNAs in RCC by different research groups [12,[26][27][28][29][30].In particular, let-7c sensitizes cells to 5-FU in RCC cells in vitro, and miR-27b sensitizes cells to doxorubicin, sorafenib, gefitinib in RCC cells [31,32].Chemoresistance and miRNAs listed in this signature have been reported previously in a variety of cancers: miR-29b in ovarian cancer, miR-128 in breast cancer, miR-23b in gastric cancer, and miR-10b in colorectal and breast cancer [33][34][35][36].Therefore, miRNAs listed in this signature would have importance in resistance to both chemotherapy and molecular targeted therapy.These facts ensure the reliability of the data in this signature.
In this study, we focused on the miR-101 because miR-101 was the most strongly downregulated miRNA in sunitinib-treated tissues.Our present data showed that miR-101 functioned as an antitumor miRNA in RCC cells.The antitumor roles of miR-101 have been reported in various types of cancers, including hepatocellular carcinoma, gastric cancer, breast cancer, and lung cancer [37][38][39][40].Furthermore, miR-101 restoration enhances chemosensitivity in lung cancer and salivary gland adenoid cystic carcinoma [41,42].Thus, our data are consistent with previous studies of miR-101 in cancer research.
One interesting capacity of miRNA analyses is identification of miRNA-regulated genes in the human genome and investigation of the functional roles of these miRNA-regulated genes in cancer cells.In this study, we found that UHRF1, the master regulator of epigenetic modifications, was directly suppressed by miR-101 in RCC cells and that its expression enhanced cancer cell migration and invasion.Moreover, overexpression of UHRF1 was confirmed in sunitinib-treated RCC tissues, and higher expression of UHRF1 was associated with shorter overall survival after surgery for RCC.Because sunitinib is the first-line treatment option for recurrent RCC after surgical treatment, this association is consistent with other results.Ablation of UHRF1 induces genomic hypomethylation, and overexpression of UHRF1 has been reported in several cancers [43,44].UHRF1 consists of   five recognizable domains: PHD, Tudor, SRA, RING, and UBL [45].UHRF1 is required for DNA methyltransferase 1 (DNMT1) function through direct binding to DNMT1 and activation of DNMT1 function for maintenance of DNA methylation [46].
We found that miR-101 directly suppressed UHRF1; however, previous reports have indicated that EZH2 is also directly suppressed by miR-101 [14,47].Consistent with this, we confirmed that EZH2 was suppressed by miR-101 in RCC cells (Figure 4).Interestingly, EZH2 has also been reported to be a master regulator of transcription by modulation of histone modification or methylation [48,49].miR-101 can target and suppress both UHRF1 and EZH2 in RCC cells.Previous report indicated that UHRF1 and EZH2 synergistically and independently silence tumor suppressors by methylation: UHRF1 induce methylation of tumor suppressor gene DNA CpGs and H3-K9me3, and EZH2 induce methylation of H3-K27 [50].Overexpression of both UHRF1 and EZH2 coordinately suppressed antitumor genes and contributed to prostate cancer pathogenesis and metastasis [50].More recently, patient-derived clear cell RCC xenografts with sunitinib resistant phenotype showed increased EZH2 expression, and inhibition of EZH2 resulted in enhancement of the antitumor effects of sunitinib [51].Consequently, we speculate that overexpression of UHRF1 and EZH2 coordinately suppressed antitumor genes and deeply contribute to sunitinib resistant processes in RCC cells.In sunitinib-treated RCC tissues, loss of antitumor miR-101 may lead to upregulation of UHRF1 and EZH2, and consequently, post-transcriptional modification of multiple genes would promote cancer-related phenotypes in cells.Moreover, we investigated the downstream pathways suppressed by knockdown of UHRF1 and found that pathways such as cell cycle, DNA replication, and RNA degradation were enriched in RCC cells.Thus, antitumor miR-101-mediated UHRF1 pathways may be suppressed by sunitinib treatment.Our present data will contribute to our understanding of drug-resistance mechanisms in RCC cells.

Patients and clinical RCC specimens
Clinical kidney specimens were obtained from patients admitted to Kagoshima University Hospital and Teikyo University Chiba Medical Centre Hospital from 2004 to 2014.A total of 42 pairs of clear cell renal carcinoma and adjacent noncancerous tissue were obtained by nephrectomy.Three patients who died of RCC after sunitinib treatment failure underwent autopsies.RCC tissues (n = 42), adjacent noncancerous kidney tissues (n = 41), and sunitinib-treated RCC tissues (n = 11) were used.The patients' backgrounds and characteristics are summarized in Tables 1 and 3. Samples were staged according to the UICC TNM classification.Written consent for tissue donation for research purposes was obtained from each patient before sample collection.The protocol was approved by the Institutional Review Board of Chiba University, Kagoshima University and Teikyo University.

Construction of the miRNA expression signature of sunitinib-treated RCC
miRNA expression patterns were evaluated using a TaqMan LDA Human microRNA Panel v2.0 (Applied Biosystems, Foster City, CA, USA).A cut-off P-value of less than 0.05 was used to narrow down the candidates after global normalization of the raw data.After global normalization, additional normalization was carried out with the U6 gene.The procedure was performed as described previously [11,52].

Cell culture
Human RCC cell lines (786-O and Caki-1 cells) were obtained from the American Type Culture Collection (Manassas, VA, USA).Cells were maintained in RPMI-1640 medium supplemented with 10% fetal bovine serum in a humidified atmosphere containing 5% CO 2 and 95% air at 37°C.

Figure 1 :
Figure 1: Analysis of miR-101 expression in RCC clinical specimens and functional analysis of miR-101 transfection in 786-O and Caki-1 cells.(A) Expression levels of miR-101 in RCC clinical specimens.RNU48 was used for normalization.(B) Cell proliferation was assessed 72 h after transfection with miR-101 using XTT assays.(C) Cell migration was assessed 48 h after transfection with miR-101 using uncoated Transwell polycarbonate membrane filters.(D) Cell invasion was assessed 48 h after transfection with miR-101 using Matrigel invasion assays.*P < 0.0001.The bars indicate SDs.

Figure 2 :
Figure 2: Selection strategy for target genes of miR-101.Analysis using the TargetScan program showed that 3,013 genes had

Figure 3 :
Figure 3: miR-101 directly downregulated UHRF1 expression in RCC cells.(A) UHRF1 mRNA expression 72 h after transfection with miR-101.GUSB was used as an internal control.(B) UHRF1 protein expression 72 h after transfection with miR-101.GAPDH was used as a loading control.(C) miR-101 binding sites in UHRF1 mRNA.Luciferase reporter assays were carried out using a vector encoding the putative miR-101 target site in the UHRF1 3ʹ-UTR (position 1030-1036) for wild-type and deletion constructs.*P < 0.002, **P < 0.0001.The bars indicate SDs.

Figure 4 :
Figure 4: Effects of miR-101 transfection on EZH2 mRNA and protein expression in RCC cells.(A) EZH2 mRNA expression was determined at 72 h after transfection with miR-101.GUSB was used as an internal control.(B) EZH2 protein expression was evaluated by western blotting at 72 h after transfection with miR-101.GAPDH was used as a loading control.*P < 0.005.The bars indicate SDs.

Figure 5 :
Figure 5: Effects of UHRF1 knockdown in RCC cells and impact of UHRF1 expression on clinical RCC specimens.(A) UHRF1 mRNA expression was determined at 72 h after transfection with si-UHRF1.GUSB was used as an internal control.(B) UHRF1 protein expression was evaluated by western blotting at 72 h after transfection with si-UHRF1.GAPDH was used as a loading control.*P < 0.0001.The bars indicate SDs.(C) Cell proliferation was assessed 72 h after transfection with si-UHRF1 using XTT assays.(D) Cell migration was assessed 48 h after transfection with si-UHRF1 using uncoated Transwell polycarbonate membrane filters.(E) Cell invasion was assessed 48 h after transfection with si-UHRF1 using Matrigel invasion assays.*P < 0.0001.The bars indicate SDs.

Figure 6 :
Figure 6: Clinical significance of UHRF1 expression in RCC.(A) UHRF1 was highly expressed in sunitinib-treated RCC compared with that in sunitinib-naïve RCC (P = 0.0049).(B) The overall survival rate of patients with high UHRF1 expression was significantly lower than that of patients with low UHRF1 expression (P < 0.0001).(C) Multivariate Cox proportional hazards model for prediction of overall survival showed high UHRF1 expression, advanced disease stage, and age at diagnosis were significant prognostic factors (P < 0.0001, P < 0.0001, P = 0.0005, respectively).(D) High expression of UHRF1 was observed in sunitinib-treated RCC specimens.

Figure 7 :
Figure 7: Clinical significance of EZH2 expression in RCC.(A) There was no significant difference of EZH2 expression between sunitinib-treated RCC specimens and sunitinib-naïve RCC specimens.(B) The overall survival rate of patients with high EZH2 expression was significantly lower than that of patients with low EZH2 expression (P < 0.0001).(C) Multivariate Cox proportional hazards model for prediction of overall survival showed high EZH2 expression, advanced disease stage, and age at diagnosis were significant prognostic factors (P < 0.0001, P < 0.0001, P = 0.0013, respectively).(D) High expression of EZH2 was observed in several sunitinib-treated RCC specimens.

Table 2 : Downregulated miRNAs in sunitinib-treated RCC (versus primary RCC) miRNA Log2 ratio (sunitinib failure/primary) Primary RCC Sunitinib failure RCC P-value
[14,15]actjournals.com/oncotargetEZH2genes.Additionally, western blotting was carried out to investigate the effects of miR-101 transfection on UHRF1 and EZH2 protein.The mRNA and protein expression levels of UHRF1 and EZH2 were significantly downregulated by miR-101 transfection as compared with those in mock-or miR-control-transfected cells (P < 0.002 and P < 0.005; Figure3A and 3B, Figure4A and 4B).Because direct regulation of EZH2 by miR-101 in RCC has been reported by several groups[14,15], we focused on the UHRF1 gene in this study.