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- Andersson-Evelönn, Emma, 1983-
(författare)
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DNA methylation as a prognostic marker in clear cell Renal Cell Carcinoma
- 2020
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Clear cell renal cell carcinoma (ccRCC) is the most common type of renal cell carcinoma worldwide. Metastatic ccRCC is correlated to poor prognosis whereas non-metastatic disease has a 5-year survival rate up to 90%. Due to increased accessibility to different types of diagnostic imaging the frequency of metastatic ccRCC at diagnosis has decreased since the beginning of the 21st century. This has led to an earlier detection of primary tumors before patients present symptoms. However, 20-30% of the non-metastatic patients at diagnosis will progress and metastasize within five years of primary nephrectomy. Identifying patients at high risk of tumor progression at an early stage after diagnosis is of importance to improve outcome and survival. Currently, in Sweden, the Mayo scoring system is used to divide tumors into low, intermediate or high risk for tumor progression.DNA methylation has been associated with tumor development and progression in different malignancies. In this thesis, Illumina Infinium HumanMeth27 BeadChip Arrays and Human Meth450K BeadChip Arrays have been used to evaluate the relationship between methylation and clinicopathological variables as well as ccRCC outcome in 45 and 115 patients.Our studies identified an association between higher level of promoter-associated DNA methylation and clinicopathological variables in ccRCC. There was a significant stepwise increase of average methylation from tumor-free tissue, via non-metastatic tumors to metastatic disease. Cluster analysis divided patients into two distinct groups that differed in average methylation levels, TNM stage, Fuhrman nuclear grade, tumor size, survival and tumor progression. We also presented two prognostic classifiers for non-metastatic tumors; the promoter methylation classifier (PMC) panel and the triple classifier. The PMC panel divided tumors depending on the methylation level, PMC low or PMC high, with significantly worse prognosis in the PMC high group. This data was verified in an independent, publically available cohort. The triple classifier was created using a combination of clinicopathological variables, previously identified CpGs biomarkers and a novel cluster analysis approach (Directed Cluster Analysis). The triple classifier had a higher specificity compared to the clinically used Mayo scoring system and predicted tumor progression with higher accuracy at a fixed sensitivity.The identification of two epigenetic classifiers that predicted outcome in non-metastatic ccRCC further establishes the role of DNA methylation as a prognostic marker. This knowledge can contribute to identification of patients with a high risk of tumor progression and can be of importance in the decision regarding adjuvant treatment post-nephrectomy.
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| 2. |
- Andersson Evelönn, Emma, 1983-, et al.
(författare)
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DNA methylation associates with survival in non-metastatic clear cell renal cell carcinoma
- 2019
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Ingår i: BMC Cancer. - : BioMed Central. - 1471-2407. ; 19
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Tidskriftsartikel (refereegranskat)abstract
- Background: Clear cell renal cell carcinoma (ccRCC) is the most common subtype among renal cancer and is associated with poor prognosis if metastasized. Up to one third of patients with local disease at diagnosis will develop metastasis after nephrectomy, and there is a need for new molecular markers to identify patients with high risk of tumor progression. In the present study, we performed genome-wide promoter DNA methylation analysis at diagnosis to identify DNA methylation profiles associated with risk for progress.Method: Diagnostic tissue samples from 115 ccRCC patients were analysed by Illumina HumanMethylation450K arrays and methylation status of 155,931 promoter associated CpGs were related to genetic aberrations, gene expression and clinicopathological parameters.Results: The ccRCC samples separated into two clusters (cluster A/B) based on genome-wide promoter methylation status. The samples in these clusters differed in tumor diameter (p < 0.001), TNM stage (p < 0.001), morphological grade (p < 0.001), and patients outcome (5 year cancer specific survival (pCSS5yr) p < 0.001 and cumulative incidence of progress (pCIP5yr) p < 0.001. An integrated genomic and epigenomic analysis in the ccRCCs, revealed significant correlations between the total number of genetic aberrations and total number of hypermethylated CpGs (R = 0.435, p < 0.001), and predicted mitotic age (R = 0.407, p < 0.001). We identified a promoter methylation classifier (PMC) panel consisting of 172 differently methylated CpGs accompanying progress of disease. Classifying non-metastatic patients using the PMC panel showed that PMC high tumors had a worse prognosis compared with the PMC low tumors (pCIP5yr 38% vs. 8%, p = 0.001), which was confirmed in non-metastatic ccRCCs in the publically available TCGA-KIRC dataset (pCIP5yr 39% vs. 16%, p < 0.001).Conclusion: DNA methylation analysis at diagnosis in ccRCC has the potential to improve outcome-prediction in non-metastatic patients at diagnosis.
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| 3. |
- Andersson Evelönn, Emma, 1983-, et al.
(författare)
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DNA methylation status defines clinicopathological parameters including survival for patients with clear cell renal cell carcinoma (ccRCC)
- 2016
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Ingår i: Tumor Biology. - : Springer Science and Business Media LLC. - 1010-4283 .- 1423-0380. ; 37:8, s. 10219-10228
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Tidskriftsartikel (refereegranskat)abstract
- Epigenetic alterations in the methylome have been associated with tumor development and progression in renal cell carcinoma (RCC). In this study, 45 tumor samples, 12 tumor-free kidney cortex tissues, and 24 peripheral blood samples from patients with clear cell RCC (ccRCC) were analyzed by genome-wide promoter-directed methylation arrays and related to clinicopathological parameters. Unsupervised hierarchical clustering separated the tumors into two distinct methylation groups (clusters A and B), where cluster B had higher average methylation and increased number of hypermethylated CpG sites (CpGs). Furthermore, tumors in cluster B had, compared with cluster A, a larger tumor diameter (p = 0.033), a higher morphologic grade (p < 0.001), a higher tumor-node-metastasis (TNM) stage (p < 0.001), and a worse prognosis (p = 0.005). Higher TNM stage was correlated to an increase in average methylation level (p = 0.003) and number of hypermethylated CpGs (p = 0.003), whereas a number of hypomethylated CpGs were mainly unchanged. However, the predicted age of the tumors based on methylation profile did not correlate with TNM stage, morphological grade, or methylation cluster. Differently methylated (DM) genes (n = 840) in ccRCC samples compared with tumor-free kidney cortex samples were predominantly hypermethylated and a high proportion were identified as polycomb target genes. The DM genes were overrepresented by transcription factors, ligands, and receptors, indicating functional alterations of significance for ccRCC progression. To conclude, increased number of hypermethylated genes was associated with increased TNM stage of the tumors. DNA methylation classification of ccRCC tumor samples at diagnosis can serve as a clinically applicable prognostic marker in ccRCC.
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| 4. |
- Hedberg, Ylva, 1975-
(författare)
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Cell Cycle Regulation in Human Renal Cell Carcinoma
- 2003
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- ABSTRACTCell cycle regulation in human renal cell carcinomaYlva Hedberg, Departments of Medical Biosciences, Pathology, and Surgical andPerioperative Sciences, Urology Andrology, Umeå University, SwedenDeregulated growth control is a hallmark of neoplasia potentially caused by aberrant expression of cell cycle regulatory proteins. The importance of such aberrations in human renal cell carcinoma (RCC) has not been fully clarified. Therefore, the protein expressions of several G1/S regulatory proteins in human RCC were evaluated and their relation to clinico-pathological data was examined.Western blotting and immunohistochemistry were used to detect the proteinexpression of cyclin D1, D3, and E in 80 RCCs. Most tumors expressed higher levels of cyclin D1 (75%) and cyclin E (65%) compared to corresponding normal kidney cortex. In contrast, only 16 % of the tumors had high levels of cyclin D3. In conventional RCCs, low levels of cyclin D1 were associated with large tumor size, aneuploidy and a poor outcome for the patients. High expression of cyclin D3 and Ewere associated with aneuploidy, high proliferation, high TNM-stage, and high nuclear grade. Cyclin E was positively correlated to cyclin D3 but inversely associated with cyclin D1. Cyclin D3 and E were not associated with survival. The majority of RCCs had normal p27 levels, determined by immunohistochemistry, whereas the few tumors with low p27 levels were associated with large tumor size and poor survival.In order to confirm and extend our initial studies, a tissue microarray consisting of 218 RCCs was constructed and cyclin D1, D3, E, p27 were detected by immunohistochemistry. The tissue microarray results were validated by comparing the array data with western analyzes. Due to the large number of tumors analyzed we could evaluate potential differences in expression patterns of cell cycle regulators between conventional, papillary, and chromophobe RCCs. Interestingly, the protein expression differed between RCC types, showing that the conventional tumors generally had high cyclin D1 expression. In contrast, papillary and chromophobe RCCs had high cyclin E expression. Downregulation of p27 was found mostly in chromophobe RCCs. The retinoblastoma protein (pRb) was detected in all RCCs. Phosphorylation of pRb, detected by western blotting or immunohistochemistry and phospho-specific antibodies, was observed in approximately 50% of the tumors. The cdk-inhibitor p16 was not overexpressed suggesting that pRb was functional in the majority of RCCs.In summary, abnormal expression of G1-cyclins and the CDK-inhibitor p27 was common in RCC whereas the main G1/S-substrate, pRb, seemed to be functional. The aberrations further differed between the separate RCC subtypes and were linked to clinical behavior.
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