Mutational analysis guides therapeutic decision making in patients with advanced‐stage gastrointestinal stromal tumors (GISTs). We evaluated three targeted next‐generation sequencing (NGS) assays, ...consecutively used over 4 years in our laboratory for mutational analysis of 162 primary GISTs: Agilent GIST MASTR, Illumina TruSight 26 and an in‐house developed 96 gene panels. In addition, we investigated the feasibility of a more comprehensive approach by adding targeted RNA sequencing (Archer FusionPlex, 11 genes) in an attempt to reduce the number of Wild Type GISTs. We found KIT or PDGFRA mutations in 149 out of 162 GISTs (92.0%). Challenging KIT exon 11 alterations were initially missed by different assays in seven GISTs and typically represented deletions at the KIT intron 10‐exon 11 boundary or large insertions/deletions (>24 base pairs). Comprehensive analysis led to the additional identification of driver alterations in 8/162 GISTs (4.9%): apart from BRAF and SDHA mutations (one case each), we found five GISTs harboring somatic neurofibromatosis type 1 (NF1) alterations (3.1%) and one case with an in‐frame TRIM4‐BRAF fusion not reported in GIST before. Eventually, no driver alteration was found in two out of 162 GISTs (1.2%) and three samples (1.9%) failed analysis. Our study shows that a comprehensive targeted NGS approach is feasible for routine mutational analysis of GIST, thereby substantially reducing the number of Wild Type GISTs, and highlights the need to optimize assays for challenging KIT exon 11 alterations.
Sclerosing epithelioid fibrosarcoma (SEF) is a highly aggressive soft tissue sarcoma closely related to low-grade fibromyxoid sarcoma (LGFMS). Some tumors display morphologic characteristics of both ...SEF and LGFMS, hence they are known as hybrid SEF/LGFMS. Despite the overlap of gene fusion variants between these two tumor types, SEF is much more aggressive. The current study aimed to further characterize SEF and hybrid SEF/LGFMS genetically to better understand the role of the characteristic fusion genes and possible additional genetic alterations in tumorigenesis.
We performed whole-exome sequencing, SNP array analysis, RNA sequencing (RNA-seq), global gene expression analyses, and/or IHC on a series of 13 SEFs and 6 hybrid SEF/LGFMS. We also expressed the
and
fusion genes conditionally in a fibroblast cell line; these cells were subsequently analyzed by RNA-seq, and expression of the CD24 protein was assessed by FACS analysis.
The SNP array analysis detected a large number of structural aberrations in SEF and SEF/LGFMS, many of which were recurrent, notably
microdeletions. RNA-seq identified
and
as alternative fusion genes in one SEF each.
was strongly upregulated, presumably a direct target of the fusion proteins. This was further confirmed by the gene expression analysis and FACS analysis on Tet-On 3G cells expressing
Although gene fusions are the primary tumorigenic events in both SEF and LGFMS, additional genomic changes explain the differences in aggressiveness and clinical outcome between the two types. CD24 and DMD constitute potential therapeutic targets.
.
Endometrial stromal sarcomas (ESSs) are a genetically heterogeneous group of rare uterine neoplasms that are commonly driven by recurrent gene rearrangements. In conventional low‐grade ESS, ...JAZF1‐SUZ12, PHF1‐JAZF1, EPC1‐PHF1 and MEAF6‐PHF1, and recently described ZC3H7‐BCOR chimeric fusions have been reported in > 50% of cases. Conversely, oncogenic t(10;17)(q22;p13) translocation yields YWHAE‐FAM22A/B chimeric proteins that are associated with histologically high‐grade and clinically more aggressive ESS. Integrating whole‐transcriptome paired‐end RNA sequencing with fluorescence in situ hybridization (FISH) and banding cytogenetics, we identified MBTD1 (malignant brain tumor domain‐containing 1) and CXorf67 (chromosome X open reading frame 67) as the genes involved in the novel reciprocal t(X;17)(p11.2;q21.33) translocation in two independent low‐grade ESS of classical histology. The presence of the MBTD1‐CXorf67 fusion transcript was validated in both cases using reverse‐transcription polymerase chain reaction followed by Sanger sequencing. A specific FISH assay was developed to detect the novel t(X;17) translocation in formalin‐fixed paraffin‐embedded material, and resulted in identification of an additional low‐grade ESS case positive for the MBTD1‐CXorf67 fusion among 25 uterine stromal tumors 14 ESS and 11 undifferentiated endometrial sarcomas (UESs) that were negative for JAZF1 and YWHAE rearrangements. Gene expression profiles of seven ESS (including three with YWHAE and two with JAZF1 rearrangements) and four UES without specific chromosomal aberrations indicated clustering of tumors with MBTD1‐CXorf67 fusion together with low‐grade JAZF1‐associated ESS. The chimeric MBTD1‐CXorf67 fusion identifies yet another cytogenetically distinct subgroup of low‐grade ESS and offers the opportunity to shed light on the functions of two poorly characterized genes.
What's new?
Endometrial stromal tumors can be classified into three groups; among all the groups, the tumors frequently contain one of several possible chromosomal translocations. This study identified a new gene fusion that tends to occur in low‐grade endometrial tumors. Clinicians may find it useful to identify this gene fusion as a way to help classify tumors that don't clearly fall into one category or the other.
Clinical management of uterine sarcomas Amant, Frédéric, Prof; Coosemans, An, MD; Debiec-Rychter, Maria, Prof ...
The lancet oncology,
12/2009, Volume:
10, Issue:
12
Journal Article
Peer reviewed
Summary Malignant pure mesenchymal uterine tumours encompass endometrial stromal sarcoma (ESS), uterine leiomyosarcoma, and undifferentiated sarcomas. This Review discusses pathology, preoperative ...diagnosis, and standard treatment of uterine leiomyosarcoma and low-grade ESS (distinct from undifferentiated uterine sarcomas), with an emphasis on targeted treatment. We show that several features on ultrasonography and MRI can raise suspicion of a uterine sarcoma; however, there are no pathognomonic features on any imaging technique. For both ESS and uterine leiomyosarcoma, hysterectomy with bilateral salpingo-oophorectomy, but without lymphadenectomy, is the standard surgical treatment for early stage disease. The clinical benefit of chemotherapy is limited, which underscores the importance of targeted therapy. ESS and uterine leiomyosarcoma are driven by different pathways, resulting in a different clinical behaviour. ESS typically is a hormone-sensitive tumour with indolent growth. Uterine leiomyosarcoma is notorious for its aggressive growth and poor outcome. Individualisation of treatment is mandatory, because randomised trials are almost non-existent. The progesterone and oestrogen receptors are clinically important targets for most primarily advanced or recurrent ESS and a subset of recurrent uterine leiomyosarcomas. Potential future targets and targeted treatments that are under investigation are presented for both entities.
The clinical utility of circulating tumor DNA (ctDNA) monitoring has been shown in tumors that harbor highly recurrent mutations. Leiomyosarcoma represents a type of tumor with a wide spectrum of ...heterogeneous genomic abnormalities; thus, targeting hotspot mutations or a narrow genomic region for ctDNA detection may not be practical. Here, we demonstrate a combinatorial approach that integrates different sequencing protocols for the orthogonal detection of single-nucleotide variants (SNV), small indels, and copy-number alterations (CNA) in ctDNA.
We employed Cancer Personalized Profiling by deep Sequencing (CAPP-Seq) for the analysis of SNVs and indels, together with a genome-wide interrogation of CNAs by Genome Representation Profiling (GRP). We profiled 28 longitudinal plasma samples and 25 tumor specimens from 7 patients with leiomyosarcoma.
We detected ctDNA in 6 of 7 of these patients with >98% specificity for mutant allele fractions down to a level of 0.01%. We show that results from CAPP-Seq and GRP are highly concordant, and the combination of these methods allows for more comprehensive monitoring of ctDNA by profiling a wide spectrum of tumor-specific markers. By analyzing multiple tumor specimens in individual patients obtained from different sites and at different times during treatment, we observed clonal evolution of these tumors that was reflected by ctDNA profiles.
Our strategy allows for the comprehensive monitoring of a broad spectrum of tumor-specific markers in plasma. Our approach may be clinically useful not only in leiomyosarcoma but also in other tumor types that lack recurrent genomic alterations.
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Sclerosing epithelioid fibrosarcoma (SEF) is a rare, malignant fibroblastic neoplasm, morphologically composed of cords, nests or sheets of monotonous epithelioid cells within a collagenous matrix. ...It has been recently characterized by recurrent pathogenic EWS‐CREB3L1/2 or FUS‐CREB3L2 fusions and common MUC4 protein expression by immunohistochemistry. Typically SEF occur in middle‐aged adults and rarely have been reported within the abdominal cavity. Here we report an 18‐year‐old man with intraabdominal tumor and multiple disseminated liver metastases, presenting pure SEF histologic and immunophenotypic features. Fluorescence in situ hybridization analysis showed unbalanced rearrangement of Ewing sarcoma breakpoint region 1 (EWSR1) gene. Genomic profiling by array CGH, followed by RT‐PCR and sequencing analysis, revealed a previously not reported EWSR1 translocation partner, cAMP‐responsive element‐binding protein 3‐like 3 (CREB3L3). The novel EWSR1‐CREB3L3 fusion further extends the range of fusion types involving EWSR1 that are characteristic for SEF.
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