Targeted massively parallel sequencing of candidate regions on chromosome 22q predisposing to multiple schwannomas: An analysis of 51 individuals in a single‐center experience

Abstract

Constitutional LZTR1 or SMARCB1 pathogenic variants (PVs) have been found in ∼86% of familial and ∼40% of sporadic schwannomatosis cases. Hence, we performed massively parallel sequencing of the entire LZTR1, SMARCB1, and NF2 genomic loci in 35 individuals with schwannomas negative for constitutional first‐hit PVs in the LZTR1/SMARCB1/NF2 coding sequences; however, with 22q deletion and/or a different NF2 PV in each tumor, including six cases with only one tumor available. Furthermore, we verified whether any other LZTR1/SMARCB1/NF2 (likely) PVs could be found in 16 cases carrying a SMARCB1 constitutional variant in the 3′‐untranslated region (3′‐UTR) c.*17C>T, c.*70C>T, or c.*82C>T. As no additional variants were found, functional studies were performed to clarify the effect of these 3′‐UTR variants on the transcript. The 3′‐UTR variants c.*17C>T and c.*82C>T showed pathogenicity by negatively affecting the SMARCB1 transcript level. Two novel deep intronic SMARCB1 variants, c.500+883T>G and c.500+887G>A, resulting in out‐of‐frame missplicing of intron 4, were identified in two unrelated individuals. Further resequencing of the entire repeat‐masked genomics sequences of chromosome 22q in individuals negative for PVs in the SMARCB1/LZTR1/NF2 coding‐ and noncoding regions revealed five potential schwannomatosis‐predisposing candidate genes, that is, MYO18B, NEFH, SGSM1, SGSM3, and SBF1, pending further verification.

Updated diagnostic criteria and nomenclature for neurofibromatosis type 2 and schwannomatosis: An international consensus recommendation

“…Some SMARCB1/LZTR1 PVs, missed by current diagnostic methods, may reside in untranslated regions or nearby regions that may affect expression (position effect). 21,38 However, additional genes are likely to be discovered. For instance, a 3-generation family and an unrelated sporadic case with multiple schwannomas and multinodular goiter have now been described with the same DGCR8 PV (c.1552G>A; p.E518K) on chromosome 22q that showed the same 3 event/4 hit mechanism as SMARCB1/LZTR1 in 9 schwannomas, with 4 additional schwannomas showing somatic loss of the entire chromosome 22.…”

Screening of potential novel candidate genes in schwannomatosis patients

“…Indeed a deep intronic PV, NM_003073.5:c.795+1498C>T, leading to the inclusion of a cryptic exon and a truncated product, has previously been reported in intron 6 of SMARCB1 (Smith et al, 2020). In addition, a recent deep massive parallel sequencing study of 35 schwannomatosis cases (Piotrowski et al, 2021) reported two novel deep intronic variants in intron 4 of SMARCB1 (NM_003073.5:c.500+883T>G and NM_003073.5:c.500+887G>A). Both of these variants were further characterized by means of RNA analysis and demonstrated to result in retention of part of intron 4 and a truncated transcript.…”

“…The presence of copy number variants is also routinely assessed Primers were designed to target flanking sites at each side of exons for regions of COQ6 (NM_182476.2), DGCR8 (NM_022720.6), CDKN2A (NM_000077.4), and CDKN2B (NM_004936.3) and are listed in Supporting Information: Table S3. In addition, two intronic regions of SMARCB1 known to harbor PVs for schwannomatosis (Piotrowski et al, 2021;Smith et al, 2020) were also screened.…”

“…Primers were designed to target flanking sites at each side of exons for regions of COQ6 (NM_182476.2), DGCR8 (NM_022720.6), CDKN2A (NM_000077.4), and CDKN2B (NM_004936.3) and are listed in Supporting Information: Table . In addition, two intronic regions of SMARCB1 known to harbor PVs for schwannomatosis (Piotrowski et al, 2021; Smith et al, 2020) were also screened. Sanger sequencing of amplicons was then carried out using BigDye™ Terminator v3.1 Cycle Sequencing Kit (Thermo Fisher Scientific) and an ABI 3100 automated sequencer (Applied Biosystems).…”

Prognostic biomarker SGSM1 and its correlation with immune infiltration in gliomas

“…A recent study has found that SGSM1 degradation led to the invasion and metastasis of nasopharyngeal carcinoma [ 14 ]. Another parallel sequencing research has shown that SGSM1 was a potential candidate gene for schwannomatosis [ 15 ]. However, the role of SGSM1 has hardly been studied and its prognostic value in LGGs remained unclear.…”