Whole Exome- and mRNA-Sequencing of an AT/RT Case Reveals Few Somatic Mutations and Several Deregulated Signalling Pathways in the Context of SMARCB1 Deficiency

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Sandgren, JKarolinska Institutet (författare)

Whole Exome- and mRNA-Sequencing of an AT/RT Case Reveals Few Somatic Mutations and Several Deregulated Signalling Pathways in the Context of SMARCB1 Deficiency

Artikel/kapitelEngelska2015

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Hindawi Limited,2015

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LIBRIS-ID:oai:prod.swepub.kib.ki.se:131872665
http://kipublications.ki.se/Default.aspx?queryparsed=id:131872665URI
https://doi.org/10.1155/2015/862039DOI

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Sammanfattning på:engelska

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Background. AT/RTs are rare aggressive brain tumours, mainly affecting young children. Most cases present with genetic inactivation ofSMARCB1, a core member of the SWI/SNF chromatin-remodeling complex. We have performed whole exome- and mRNA-sequencing on an early onset AT/RT case for detection of genetic events potentially contributing to the disease.Results. Ade novogermline variant inSMARCB1, c.601C>T p.Arg201∗, in combination with somatic deletion of the healthy allele is likely the major tumour causing event. Only seven somatic small scale mutations were discovered (hittingSEPT03, H2BFM, ZIC4, HIST2H2AB, ZIK1, KRTAP6-3, andIFNA8). All were found with subclonal allele frequencies (range 5.7–17%) and none were expressed. However, besidesSMARCB1, candidate genes affected by predicted damaging germline variants that were expressed were detected (KDM5C, NUMA1, andPCM1). Analysis of differently expressed genes revealed many dysregulated pathways in the tumour, such as cell cycle, CXCR4 pathway, GPCR-signalling, and neuronal system.FGFR1, CXCR4, andMDKwere upregulated and may represent possible drug targets.Conclusion. The loss ofSMARCB1function leads to AT/RT development and deregulated genes and pathways. Additional predisposing events may however contribute. Studies utilizing NGS technologies in larger cohorts will probably identify recurrent genetic and epigenetic alterations and molecular subgroups with implications for clinical practice and development of targeted therapies.

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Holm, S (författare)
Marino, AM (författare)
Asmundsson, JKarolinska Institutet (författare)
Grillner, PKarolinska Institutet (författare)
Nister, MKarolinska Institutet (författare)
de Stahl, TDKarolinska Institutet (författare)
Karolinska Institutet (creator_code:org_t)

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Ingår i:BioMed research international: Hindawi Limited2015, s. 862039-2314-61412314-6133

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Av författaren/redakt...: Sandgren, J; Holm, S; Marino, AM; Asmundsson, J; Grillner, P; Nister, M; visa fler...; de Stahl, TD; visa färre...

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