SMARCB1 protein and mRNA loss is not caused by promoter and histone hypermethylation in epithelioid sarcoma

Gerg Papp, Yi Che Changchien, Bálint Péterfia, Loránd Pecsenka, Thomas Krausz, Thomas P. Stricker, Andras Khoor, Ludvik Donner, Zoltán Sápi

Research output: Contribution to journalArticle

17 Citations (Scopus)

Abstract

About 10% of epithelioid sarcomas have biallelic mutation of the SMARCB1 (SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily b, member 1) gene resulting in a lack of this nuclear protein. It has been suggested that SMARCB1 may be silenced by epigenetic changes in the remaining 90% of tumors. Thus, we hypothesized that the promoter of SMARCB1 is hypermethylated. We also examined SMARCB1 mRNA level to determine if a post-translational change was possible. Thirty-six cases of epithelioid sarcomas were studied. Immunohistochemistry and mutation analysis of the SMARCB1 gene were performed to select appropriate cases. Methylation status was assessed by methylation-specific PCR. Laser capture microdissection of tumor cells followed by real-time PCR was applied to examine the expression of SMARCB1 mRNA. Of 36 epithelioid sarcomas, 31 (86%) displayed a lack of SMARCB1 nuclear protein. In all, 4 (13%) of 31 SMARCB1-negative cases harbored biallelic deletion while 9 (33%) cases showed single-allelic deletion. One (4%) frameshift deletion of exon 3 and one point mutation of exon 7 were also found. In 16 (59%) cases, both alleles were intact. Altogether, 25/31 (81%) SMARCB1-negative cases had at least one intact allele. None of these cases demonstrated promoter hypermethylation. Low levels of SMARCB1 mRNA were found in all cases with tumor tissue extracted RNA (because of the minimal normal cell contamination) but no mRNA could be detected in laser dissected cases (containing only tumor cells). Enhancer of zeste homolog 2 (EZH2) overexpression was not characteristic of epithelioid sarcoma. Thus, loss of SMARCB1 expression in epithelioid sarcoma is caused neither by DNA hypermethylation nor by post-translational modifications. Most likely it is the microRNA destruction of SMARCB1 mRNA but further investigations are needed to elucidate this issue.

Original languageEnglish (US)
Pages (from-to)393-403
Number of pages11
JournalModern Pathology
Volume26
Issue number3
DOIs
StatePublished - Mar 2013

Fingerprint

Sarcoma
Histones
Chromatin
Actins
Messenger RNA
Proteins
Nuclear Proteins
Methylation
Exons
Neoplasms
Alleles
Laser Capture Microdissection
Mutation
Post Translational Protein Processing
MicroRNAs
Point Mutation
Epigenomics
Genes
Real-Time Polymerase Chain Reaction
Lasers

Keywords

  • epithelioid sarcoma
  • histone methylation
  • laser capture microdissection
  • methylation-specific PCR
  • promoter hypermethylation
  • SMARCB1

ASJC Scopus subject areas

  • Pathology and Forensic Medicine

Cite this

Papp, G., Changchien, Y. C., Péterfia, B., Pecsenka, L., Krausz, T., Stricker, T. P., ... Sápi, Z. (2013). SMARCB1 protein and mRNA loss is not caused by promoter and histone hypermethylation in epithelioid sarcoma. Modern Pathology, 26(3), 393-403. https://doi.org/10.1038/modpathol.2012.190

SMARCB1 protein and mRNA loss is not caused by promoter and histone hypermethylation in epithelioid sarcoma. / Papp, Gerg; Changchien, Yi Che; Péterfia, Bálint; Pecsenka, Loránd; Krausz, Thomas; Stricker, Thomas P.; Khoor, Andras; Donner, Ludvik; Sápi, Zoltán.

In: Modern Pathology, Vol. 26, No. 3, 03.2013, p. 393-403.

Research output: Contribution to journalArticle

Papp, G, Changchien, YC, Péterfia, B, Pecsenka, L, Krausz, T, Stricker, TP, Khoor, A, Donner, L & Sápi, Z 2013, 'SMARCB1 protein and mRNA loss is not caused by promoter and histone hypermethylation in epithelioid sarcoma', Modern Pathology, vol. 26, no. 3, pp. 393-403. https://doi.org/10.1038/modpathol.2012.190
Papp, Gerg ; Changchien, Yi Che ; Péterfia, Bálint ; Pecsenka, Loránd ; Krausz, Thomas ; Stricker, Thomas P. ; Khoor, Andras ; Donner, Ludvik ; Sápi, Zoltán. / SMARCB1 protein and mRNA loss is not caused by promoter and histone hypermethylation in epithelioid sarcoma. In: Modern Pathology. 2013 ; Vol. 26, No. 3. pp. 393-403.
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abstract = "About 10{\%} of epithelioid sarcomas have biallelic mutation of the SMARCB1 (SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily b, member 1) gene resulting in a lack of this nuclear protein. It has been suggested that SMARCB1 may be silenced by epigenetic changes in the remaining 90{\%} of tumors. Thus, we hypothesized that the promoter of SMARCB1 is hypermethylated. We also examined SMARCB1 mRNA level to determine if a post-translational change was possible. Thirty-six cases of epithelioid sarcomas were studied. Immunohistochemistry and mutation analysis of the SMARCB1 gene were performed to select appropriate cases. Methylation status was assessed by methylation-specific PCR. Laser capture microdissection of tumor cells followed by real-time PCR was applied to examine the expression of SMARCB1 mRNA. Of 36 epithelioid sarcomas, 31 (86{\%}) displayed a lack of SMARCB1 nuclear protein. In all, 4 (13{\%}) of 31 SMARCB1-negative cases harbored biallelic deletion while 9 (33{\%}) cases showed single-allelic deletion. One (4{\%}) frameshift deletion of exon 3 and one point mutation of exon 7 were also found. In 16 (59{\%}) cases, both alleles were intact. Altogether, 25/31 (81{\%}) SMARCB1-negative cases had at least one intact allele. None of these cases demonstrated promoter hypermethylation. Low levels of SMARCB1 mRNA were found in all cases with tumor tissue extracted RNA (because of the minimal normal cell contamination) but no mRNA could be detected in laser dissected cases (containing only tumor cells). Enhancer of zeste homolog 2 (EZH2) overexpression was not characteristic of epithelioid sarcoma. Thus, loss of SMARCB1 expression in epithelioid sarcoma is caused neither by DNA hypermethylation nor by post-translational modifications. Most likely it is the microRNA destruction of SMARCB1 mRNA but further investigations are needed to elucidate this issue.",
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AU - Pecsenka, Loránd

AU - Krausz, Thomas

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N2 - About 10% of epithelioid sarcomas have biallelic mutation of the SMARCB1 (SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily b, member 1) gene resulting in a lack of this nuclear protein. It has been suggested that SMARCB1 may be silenced by epigenetic changes in the remaining 90% of tumors. Thus, we hypothesized that the promoter of SMARCB1 is hypermethylated. We also examined SMARCB1 mRNA level to determine if a post-translational change was possible. Thirty-six cases of epithelioid sarcomas were studied. Immunohistochemistry and mutation analysis of the SMARCB1 gene were performed to select appropriate cases. Methylation status was assessed by methylation-specific PCR. Laser capture microdissection of tumor cells followed by real-time PCR was applied to examine the expression of SMARCB1 mRNA. Of 36 epithelioid sarcomas, 31 (86%) displayed a lack of SMARCB1 nuclear protein. In all, 4 (13%) of 31 SMARCB1-negative cases harbored biallelic deletion while 9 (33%) cases showed single-allelic deletion. One (4%) frameshift deletion of exon 3 and one point mutation of exon 7 were also found. In 16 (59%) cases, both alleles were intact. Altogether, 25/31 (81%) SMARCB1-negative cases had at least one intact allele. None of these cases demonstrated promoter hypermethylation. Low levels of SMARCB1 mRNA were found in all cases with tumor tissue extracted RNA (because of the minimal normal cell contamination) but no mRNA could be detected in laser dissected cases (containing only tumor cells). Enhancer of zeste homolog 2 (EZH2) overexpression was not characteristic of epithelioid sarcoma. Thus, loss of SMARCB1 expression in epithelioid sarcoma is caused neither by DNA hypermethylation nor by post-translational modifications. Most likely it is the microRNA destruction of SMARCB1 mRNA but further investigations are needed to elucidate this issue.

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