MicroRNA Expression in Melanocytic Nevi: The Usefulness of Formalin-Fixed, Paraffin-Embedded Material for miRNA Microarray Profiling

Glud, Martin; Klausen, Mikkel; Gniadecki, Robert; Rossing, Maria; Hastrup, Nina; Nielsen, Finn C.; Drzewiecki, Krzysztof T.

doi:10.1038/jid.2008.347

Cited by 80 publications

(77 citation statements)

References 17 publications

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“…The correlation coefficients have been similar to previous reports studying formalin-fixed paraffin-embedded samples from other tissues. 15,25,26 These findings confirm the applicability of archived formalin-fixed paraffin-embedded blocks for miRNA expression analysis of human pheochromocytoma samples.…”

Section: Discussionsupporting

confidence: 70%

“…Storage up to 7 years did not cause significant deterioration of miRNA quality, but older samples may exhibit loss of small RNA quality due to oxidation and fixation in nonbuffered formalin. 24 Formalin-fixed paraffin-embedded samples have already been successfully used for miRNA expression profiling in various tissues, 15,25,26 but there have been no data on their applicability for miRNA expression analysis in pheochromocytomas. We have observed good correlation between miRNA microarray results retrieved from three matched frozen and formalin-fixed paraffin-embedded samples derived from the same pheochromocytoma tissues.…”

Section: Discussionmentioning

confidence: 99%

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MicroRNA expression profiling in benign (sporadic and hereditary) and recurring adrenal pheochromocytomas

et al. 2010

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MicroRNAs are involved in the pathogenesis of several tumors, however, there have been no data on microRNA expression in pheochromocytomas to date. The objective of our study was to perform microRNA expression profiling in sporadic and hereditary benign, and recurring adrenomedullary tumors. Furthermore, the applicability of formalin-fixed paraffin-embedded tissue samples for the analysis of microRNA expression in pheochromocytomas was examined. MicroRNA expression data of three matched frozen and formalin-fixed paraffin-embedded samples were correlated. A total of 21 formalin-fixed paraffin-embedded samples (sporadic benign, multiple endocrine neoplasia 2, von Hippel-Lindau disease, sporadic recurring) were subjected to microRNA expression profiling using microarrays. MicroRNAs with significant differences in expression were validated and sample sizes were extended including tumors from neurofibromatosis type 1 patients by real-time quantitative reverse-transcription PCR (n ¼ 33). MicroRNA target prediction was carried out by TargetScan and MicroCosm Targets. Pathway analysis of targets was performed by Ingenuity Pathway Analysis and DIANA mirPath. Furthermore, microRNA expression profiles of a malignant pheochromocytoma and a pair of primary and recurrent tumors were studied by TaqMan Human MicroRNA Cards. MicroRNA expression correlated well between frozen and formalin-fixed paraffinembedded samples (70-92%). Microarray analysis revealed 16 significantly differentially expressed microRNAs. Five of these were validated by real-time RT-PCR. miR-139-3p, miR-541 and miR-765 were significantly differentially expressed between sporadic benign and von Hippel-Lindau-related pheochromocytomas. Significantly higher expression of miR-885-5p and miR-1225-3p was found in multiple endocrine neoplasia type 2 and sporadic recurring pheochromocytomas, respectively. Pathway analysis revealed the possible involvement of Notch-and G-proteincoupled receptor signaling in tumor recurrence. MicroRNA expression profiles in the primary recurrent and recurring malignant comparisons have been similar. In conclusion, we have proved that formalin-fixed paraffinembedded samples can be used for the analysis of microRNA expression in pheochromocytomas. MicroRNA expression patterns differ between various sporadic, hereditary and recurring tumors and miR-1225-3p may be useful for identifying recurring pheochromocytomas.

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Section: Discussionsupporting

confidence: 70%

Section: Discussionmentioning

confidence: 99%

MicroRNA expression profiling in benign (sporadic and hereditary) and recurring adrenal pheochromocytomas

et al. 2010

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“…The validity of using formalin-fixed, paraffinembedded samples for Agilent microarray analysis (Agilent Technologies Inc., Santa Clara, CA) was confirmed by previous studies. 20,21 The Faculty of Health Sciences Ethics Board at Queen's University approved the study.…”

Section: Clinical Specimensmentioning

confidence: 99%

miR-193b Regulates Mcl-1 in Melanoma

Chen

Zhang

Lentz

et al. 2011

The American Journal of Pathology

101

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“…2 Many subsequent reports of miRNAs in cancer have been reviewed. 3 In melanoma, miRNAs can be readily analyzed from formalin-fixed paraffin-embedded tissue, 4 show high frequency genetic alterations, 5 and exhibit a melanoma-specific signature. 6 In addition, miRNAs have shown prognostic value in melanoma.…”

mentioning

confidence: 99%

microRNA-10b is a prognostic biomarker for melanoma

et al. 2016

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Malignant melanoma is an aggressive form of skin cancer. Recently, drug therapy of advanced disease has been revolutionized by new agents. More therapeutic options, coupled with the desire to extend treatment to the adjuvant setting mean that prognostic biomarkers that can be assayed from formalin-fixed paraffin-embedded clinical would be valuable. microRNAs have potential to fill this need. We analyzed 377 microRNAs in 79 primary melanomas and 32 metastases using a split sample discovery strategy. From a discovery analysis using 40 thick primary melanomas (20 cases with metastasis and 20 controls without metastasis at 5 years), microRNA expression was measured by quantitative RT-PCR (QRT-PCR). MiR-10b emerged as a candidate prognostic microRNA. This was confirmed in an independent validation set of thick primary melanomas (20 cases with metastasis and 19 controls without metastasis at 5 years). In the combined discovery and validation cohorts (n = 79), miR-10b expression showed a 3.7-fold increase in expression between cases and controls (P = 0.005) and showed a trend of increasing expression between primary melanomas and their matched metastases (Po 0.001). In situ hybridization showed expression was in melanoma cells and correlated with expression measured by QRT-PCR (P = 0.0005). We used the combined discovery and validation samples to verify the prognostic value of additional candidate microRNAs identified from other studies, and proceeded to analyze miR-200b. We demonstrated that miR-10b and miR-200b showed independent prognostic value (P = 0.002 and 0.047, respectively) in multivariable analysis alongside known clinico-pathological prognostic features (eg, Breslow thickness) using a Cox proportional hazards regression model. Furthermore, the addition of these microRNAs to the clinico-pathological features led to an improved regression model with better identification of aggressive thick melanomas. Taken together, these data suggest that miR-10b is a new prognostic microRNA for melanoma and that there could be a place for microRNA analysis in stratifying melanoma for therapy.

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MicroRNA Expression in Melanocytic Nevi: The Usefulness of Formalin-Fixed, Paraffin-Embedded Material for miRNA Microarray Profiling

Cited by 80 publications

References 17 publications

MicroRNA expression profiling in benign (sporadic and hereditary) and recurring adrenal pheochromocytomas

MicroRNA expression profiling in benign (sporadic and hereditary) and recurring adrenal pheochromocytomas

miR-193b Regulates Mcl-1 in Melanoma

microRNA-10b is a prognostic biomarker for melanoma

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