Machine learning based identification of hub genes in renal clear cell carcinoma using multi-omics data.

von Hippel-Lindau Exonic Methylation Analysis Using MALDI-TOF Mass Spectrometry

BackgroundIt is estimated that there are 338,000 new renal-cell carcinoma releases every year in the world. Renal cell carcinoma (RCC) is a heterogeneous tumor, of which more than 70% is clear cell renal cell carcinoma (ccRCC). It is estimated that about 30% of new renal-cell carcinoma patients have metastases at the time of diagnosis. However, the pathogenesis of renal clear cell carcinoma has not been elucidated. Therefore, it is necessary to further study the pathogenesis of ccRCC. MethodsTwo expression profiling datasets (GSE68417, GSE71963) were downloaded from the GEO database. Differentially expressed genes (DEGs) between ccRCC and normal tissue samples were identified by GEO2R. Functional enrichment analysis was made by the DAVID tool. Protein-protein interaction (PPI) network was constructed. The hub genes were excavated. The clustering analysis of expression level of hub genes was performed by UCSC (University of California Santa Cruz) Xena database. The hub gene on overall survival rate (OS) in patients with ccRCC was performed by Kaplan-Meier Plotter. Finally, we used the ccRCC renal tissue samples to verify the hub genes. Results1182 common DEGs between the two datasets were identified. The results of GO and KEGG analysis revealed that variations in were predominantly enriched in intracellular signaling cascade, oxidation reduction, intrinsic to membrane, integral to membrane, nucleoside binding, purine nucleoside binding, pathways in cancer, focal adhesion, cell adhesion molecules. 10 hub genes ITGAX, CD86, LY86, TLR2, TYROBP, FCGR2A, FCGR2B, PTPRC, ITGB2, ITGAM were identified. FCGR2B and TYROBP were negatively correlated with the overall survival rate in patients with ccRCC (P < 0.05). RT-qPCR analysis showed that the relative expression levels of CD86, FCGR2A, FCGR2B, TYROBP, LY86, and TLR2 were significantly higher in ccRCC samples, compared with the adjacent renal tissue groups. ConclusionsIn summary, bioinformatics technology could be a useful tool to predict the progression of ccRCC. In addition, there are DEGs between ccRCC tumor tissue and normal renal tissue, and these DEGs might be considered as biomarkers for ccRCC.

Clinical research priorities in renal cell carcinoma: renal cell carcinoma chemoprevention strategies including target populations, proposed agents, and clinical trial designs--Workgroup No. 6. Union Internationale Contre le Cancer (UICC) and the American Joint Committee on Cancer (AJCC).

Hypermethylation associated inactivation of RASSF1A tumor suppressor gene at chromosome 3p21.3 has been observed in several human malignancies. Relatively high (91%) or low (23%) frequencies were reported in the methylation status of promoter region of the RASSF1A gene in clear cell renal carcinoma (RCC) depending on the country the report was from. To clarify exact contribution of the hypermethylation of RASSF1A gene in the development of RCC in Japan, we analyzed the methylation status of the RASSF1A promoter region in 50 Japanese clear cell RCC and RCC cell lines. Although relatively high frequency of hypermethylation in RASSF1A promoter (39 of 50 tumors, 78%) was observed, most of matched proximal normal tissue DNA also showed weak methylation. By comparison with methylation level of adapted normal kidney tissue DNA, tumor preferential hypermethylation in RASSF1A promoter was recognized as 40% (20/50 matched sets) of primary clear cell RCCs. Hypermethylation in RASSF1A promoter was observed in 36% (15/42) and 64% (5/8) of stage I-II or III-IV tumors, and also observed in 42% (11/26) and 38% (9/24) of our tumor samples with pathological grade I or II, respectively. In addition, 16 of 19 RCC cell lines (84%) showed complete or partial methylation of RASSF1A promoter region. There was no association between the frequency of RASSF1A methylation and inactivation of VHL tumor suppressor gene in either primary RCCs or RCC cell lines. Our results showed tumor specific RASSF1A promoter hypermethylation in up to 40% of low grade or low stage clear cell RCCs. It is essential to compare the methylation status of RASSF1A promoter in tumor with normal tissue to understand tumor specific hypermethylation. Since considerable cases of normal kidney are hypermethylated, contribution of the RASSF1A for the development and progression of kidney cancer may be more complex than expected.

Renal cell carcinoma: ESMO Clinical Practice Guidelines for diagnosis, treatment and follow-up†.

Clear cell renal cell carcinoma (CCRCC) is the most common pathological type of renal cell carcinoma and the main cause of renal carcinoma mortality. NDRG2, a new member of the N-Myc downstream-regulated gene (NDRG) family, is a focus for study at present. Up to now, its expression and function in carcinoma remain unclear. The aim of this study was to investigate its expression in CCRCC tissues and several renal carcinoma cell lines. The expression of NDRG2 was evaluated in renal cell carcinoma cell lines, tumor and adjacent non-tumor tissues from same clear cell renal cell carcinoma patients, by using immunohistochemistry, immunofluorescence, RT-PCR and Western blot. By immunohistochemistry and immunofluorescence we found that NDRG2 was predominantly located in the cytoplasm and membrane of renal carcinoma cancer cells, and the positive rate of NDRG2 in renal carcinoma specimens was 30.3% (40/132), which is significantly lower than 91.67% (121/132) in normal renal tissues (p<0.01). The average staining score in normal renal tissues was significantly higher than renal carcinoma (6.12+/-1.84 versus 2.65+/-1.23, p<0.01). Moreover, NDRG2 mRNA and protein were down-regulated in 6 fresh CCRCC tissues compared with their adjacent noncancerous tissues and normal tissues. Its expression was also lower in the human CCRCC-derived cell lines A-498 and 786-O than in the human proximal tubular cell lines HK-2 and HKC. These results indicated that NDRG2 might play an important role in the carcinogenesis and development of CCRCC and may function as a tumor suppressor in CCRCC.

Kidney renal clear cell carcinoma (KIRC) is the most common renal cell carcinoma (RCC). However, patients with KIRC usually have poor prognosis due to limited biomarkers for early detection and prognosis prediction. In this study, we analysed key genes and pathways involved in KIRC from an array dataset including 26 tumour and 26 adjacent normal tissue samples. Weighted gene co-expression network analysis (WGCNA) was performed with the WGCNA package, and 20 modules were characterized as having the highest correlation with KIRC. The upregulated genes in the tumour samples are involved in the innate immune response, whereas the downregulated genes contribute to the cellular catabolism of glucose, amino acids and fatty acids. Furthermore, the key genes were evaluated through a protein-protein interaction (PPI) network combined with a co-expression network. The comparatively lower expression of AGXT, PTGER3 and SLC12A3 in tumours correlates with worse prognosis in KIRC patients, while higher expression of ALOX5 predicts reduced survival. Our integrated analysis illustrated the hub genes involved in KIRC tumorigenesis, shedding light on the development of prognostic markers. Further understanding of the function of the identified KIRC hub genes could provide deep insights into the molecular mechanisms of KIRC.

To analyze characteristic imagery of renal cell carcinoma with distinct histological subtypes and to increase the level of the diagnose and treatment in renal cell carcinoma. 32 cases of parenchymatous renal cell cancer consisting of 26 conventional clear cell renal cell carcinoma, 5 cases of indolent papillary and 1 case of chromophobe carcinomas were compared with the different imagery features. All parenchymatous renal cell cancer patients underwent ultrasound, renal lesions showed parenchymatous echo of cortex renis. Most of the clear-cell carcinoma (20/26) demonstrated a low echo-level, papillary carcinoma (4/5) showed an ambly-high-level echo, chromophobe carcinoma showed a high-level echo. There was a significant differences the echo level between the conventional clear cell renal cell carcinoma and nonconventional clear cell RCC (P=0.005). 29 of 32 case, including 23 cases of conventional clear cell tumors and 6 cases of nonconventional clear cell RCC, underwent CT scanning: all renal lesions showed soft tissue density, but there was a significant difference between conventional and nonconventional clear cell renal cell carcinoma in contrast enhancement in either inhomogeneous enhancement (22/23 vs 3/6, P=0.004). 17 cases (11 with conventional clear cell renal cell carcinoma, 1 with chromophobe carcinoma and 5 with papillary carcinoma) underwent MRI. 10 of the conventional clear cell renal cell carcinoma showed hyperintense on T2WI (10/11) cases papillary tumor showed hypointensity on T2WI (5/5) them (P<0.01). The different imagery features in conventional and nonconventional clear cell renal cell carcinoma according to preoperative imaging examination (ultrasound and computed tomography and magnetic resonance imaging) are helpful in the diagnosis and treatment of renal cell carcinoma.

To assess the usefulness of apparent diffusion coefficients (ADCs) for characterizing renal cell carcinoma (RCC) subtypes at 3.0 T. The Institutional Review Board approved this retrospective study, and informed consent was waived. Eighty-three patients underwent diffusion-weighted (DW) magnetic resonance (MR) imaging of 85 renal masses. In each patient, precontrast single-shot spin-echo echo-planar DW imaging was performed with b values of 0 and 500 and 0 and 800 sec/mm(2) by using a 3.0-T MR imaging system. Differences in ADCs between the RCC lesions and uninvolved renal parenchyma were tested by using a paired-samples t test. One-way analysis of variance was used to compare ADCs of the various RCC subtypes. Receiver operating characteristic (ROC) curve analysis was used to test the ability of ADCs in differentiating clear cell from non-clear cell RCCs. Pathologic diagnoses of the 85 tumors (median diameter, 4.4 cm) in the 83 patients (54 men, 29 women; age range, 23-75 years; mean age, 49.4 years) were clear cell RCC for 49 tumors, papillary RCC for 22 tumors, and chromophobic RCC for 14 tumors. With b values of 0 and 500 sec/mm(2), clear cell RCCs showed a significantly higher mean ADC (1.849 × 10(-3) mm(2)/sec) than papillary (1.087 × 10(-3) mm(2)/sec) and chromophobic (1.307 × 10(-3) mm(2)/sec) RCCs (P < .001); however, the difference between papillary and chromophobic RCCs was not significant (P = .068). With b values of 0 and 800 sec/mm(2), clear cell RCC showed the largest mean ADC (1.698 × 10(-3) mm(2)/sec) of the three subtypes, and the difference between each pair of subtypes was significant (P < .001). ADCs obtained with b values of 0 and 800 sec/mm(2) were more effective for distinguishing clear cell from non-clear cell RCC (area under the ROC curve, 0.973): A threshold value of 1.281 × 10(-3) mm(2)/sec permitted distinction with high sensitivity (95.9%) and specificity (94.4%). DW imaging with b values of 0 and 800 sec/mm(2) allows sensitive and specific differentiation of clear cell, papillary, and chromophobic RCCs, suggesting that DW imaging may be useful in the preoperative characterization of RCC.

miRNA Profiling for Clear Cell Renal Cell Carcinoma: Biomarker Discovery and Identification of Potential Controls and Consequences of miRNA Dysregulation

The prevalence of renal masses has escalated as a result of the augmented utilization of cross-sectional imaging techniques. The approach to managing renal masses may exhibit variability contingent upon the subtype of renal cell carcinoma (RCC). This research aimed to distinguish between clear cell and papillary RCCs, utilizing dynamic contrast magnetic resonance imaging (MRI) and diffusion-weighted imaging (DWI). The study assessed the MR images of 112 patients with RCC. Two radiologists independently analyzed tumor size, vascular involvement, signal characteristics in T1- and T2-weighted sequences, the presence of hemosiderin, both microscopic and macroscopic fat content, enhancement patterns, and apparent diffusion coefficient (ADC) values derived from b-values of 1000 s/mm². Seventy patients had clear cell RCC, and 42 had papillary. In the clear cell RCC, microscopic fat content was significantly higher than the papillary RCC (P < 0.001). However, in papillary RCC, hemosiderin content was substantially greater (P = 0.001). On T2-weighted MR images, clear cell RCCs were usually hyperintense, while papillary RCCs were hypointense (P < 0.001). Even though the rapid enhancement pattern was observed in clear cell RCCs, the progressive enhancement pattern was more prevalent in papillary RCCs (P < 0.001). Hyperintensity on T2-weighted images, microscopic fat content, and rapid enhancement pattern may be indicative of clear cell RCC, whereas hypointensity on T2-weighted images, hemosiderin content, and a progressive contrast pattern may be diagnostic for papillary RCC.

Background: Laminin subunit gamma 1 (LAMC1) protein is associated with tumor cell invasion and metastasis. However, its role in kidney cancer remains unclear. In this work, we sought to probe the expression as well as its carcinogenic mechanisms of LAMC1 in kidney renal papillary cell carcinoma (KIRP) and kidney renal clear cell carcinoma (KIRC). Methods: Public databases including TIMER, Oncomine, UALCAN, TISIDB, TCGA, Kaplan–Meier plotter, UCSC Xena, cBioPortal, SurvivalMeth, KEGG, GeneMANIA, Metascape, GSCALite and GDSC were adopted, and the expression, clinical pathological correlation, prognostic signatures, dominant factors influencing LAMC1 expression, DNA methylation levels, gene mutations, copy number variations, functional networks, and drug sensitivity were analyzed. Expression of LAMC1 protein in clinical KIRP and KIRC was validated using tissue array. Results: LAMC1 expression in KIRP and KIRC were significantly higher than those in normal tissues. High LAMC1 expression indicated poor overall survival in KIRP patients and better overall survival in KIRC patients. Through the univariate and multivariate Cox analysis, we found that high LAMC1 expression was a potential independent marker for poor prognosis in KIRP, however it implied a better prognosis in KIRC by univariate Cox analysis. In addition, the LAMC1 expression in KIRP and KIRC was negatively correlated with methylation levels of LAMC1 DNA. Interestingly, LAMC1 expression was positively correlated with the infiltration of CD8+ T cells, dendritic cells and neutrophils in KIRP; however, it was positively correlated with the infiltration of CD4+ T cells, macrophages and neutrophils but negatively correlated with B cells in KIRC. Moreover, high level of CD8+ T cells is beneficial for KIRC prognosis but opposite for KIRP. LAMC1 may participate in signaling pathways involved in formation of adherens junction and basement membrane in KIRP and KIRC, and the high expression of LAMC1 is resistant to most drugs or small molecules of the Genomics of Drug Sensitivity in Cancer database. Conclusion: Enhanced LAMC1 expression suggests a poor prognosis in KIRP while a better prognosis in KIRC, and these opposite prognostic signatures of LAMC1 may be related to different immune microenvironments.

Role of Inflammatory Related Gene Expression in Clear Cell Renal Cell Carcinoma Development and Clinical Outcomes

Objective To analyze the value of multi-slice spiral CT (SCT) scan in staging and subtyping of renal cell carcinoma (RCC). Methods The preoperative kidney SCT data and postoperative pathology results of 64 patients with RCC were retrospectively analyzed. The patients′ ages ranged from 33-78 years (average 54 years). There were 44 males and 20 females in the study group. According to the CUA Guidelines, the staging and subtyping of RCC were performed through the combined information of preoperative SCT attenuation in unenhanced, corticomedullary phase and enhancement pattern. The results were compared with the postoperative histopathological results. Results The SCT results showed 38 cases were clear cell RCC, 14 cases were papillary RCC and 12 cases were chromophobic cell RCC. Histopathological results showed that 40 cases were clear cell RCC, 16 cases were papillary RCC and 8 cases were chromophobic cell RCC. According to the standard of 40 HU of CT attenuation value, the sensitivity, specificity and accuracy were 75%, 79% and 78% for diagnosis of papillary RCC in the unenhanced phase. The sensitivity, specificity and accuracy by the standard of 90 HU of CT attenuation value was 90%, 88% and 89% for diagnosis of clear cell RCC in the corticomedullary phase. In chromophobic RCC, homogeneous enhancement was more common than in papillary RCC and clear cell RCC. There was no significant difference of staging and subtyping of RCC between SCT and pathological results (P>0.05). The accuracy of SCT in staging and subtyping of RCC was 88% in staging, and 89% in subtyping. Conclusions SCT is a useful preoperative tool to stage and subtype RCC Key words: Kidney neoplasms; Carcinoma; Tomography, X-ray computed; Neoplasm staging

Sequential Sorafenib and Sunitinib for Renal Cell Carcinoma