Úvod: Incidence nádorů štítné žlázy celosvětově stoupá. Mezi nejčastější zhoubné nádory štítné žlázy patří dobře diferencované karcinomy (WDTC), zejména papilární karcinom štítné žlázy (PTC) a folikulární karcinom štítné žlázy (FTC), které patří mezi nejčastější zhoubné nádory endokrinního systému. Méně často je diagnostikován medulární karcinom štítné žlázy (MTC). Genetické změny určují agresivní chování nádorů a zvyšují metastatický potenciál nádorů štítné žlázy. Cílem práce je zjistit incidenci bodových mutací genů a fúzních genů u pacientů s cytologií Bethesda III–VI jako možného prediktoru indikace rozsahu chirurgických výkonů na štítné žláze. Metodika: Studie byla prospektivně-retrospektivní a zahrnovala pacienty operované na Klinice otorinolaryngologie a maxilofaciální chirurgie 3. LF UK a ÚVN Praha v období 1. 7. 2019 do 1. 7. 2022, tedy období 36 měsíců. Do studie bylo zařazeno celkem 273 osob. V detekci BRAF V600E genu byla použita alela specifického realtime PCR (LC480, Roche). Mutace TERT byla detekována přímou sekvenací (CEQ 8000, BeckmanCoulter), vzorky byly analyzovány PCR (MiSeq, Illumina) a dále byl použit Thyro-ID panel (4base) detekce dalších 12 genů. Dále bylo testováno 23 fúzních genů včetně ALK, BRAF, GLIS3, NTRK1, NTRK3, PPARG, RET genu využitím realtime PCR, MTC test mutací genu RET a RAS. Výsledky: Do souboru bylo zařazeno 273 operovaných s předoperační cytologií Bethesda III–VI. V souboru bylo 21 (7,7 %) mužů a 256 (93,77 %) žen. Histologicky bylo potvrzeno 103 (37,72 %) karcinomů a ve 170 případech (62,27 %) s nálezem nezhoubného nádoru. Bethesda III benigních histologií bylo 118 (63,78%), 67 pacientů (36,21 %) si vyslechlo diagnózu karcinomu. Bethesda IV benigních histologií bylo 50 (70,42 %) a 21 (29,58 %) maligních nádorů. Bodová mutace BRAF V600E byla detekována u 63,85 % PTC a jen jednou u benigního nádoru a jednoho NIFTP nálezu. V souboru bylo zastoupení PTC 83 (76,14 %), FTC a jeho varianty 14 (12,84 %) a MTC byl detekován u 6 (5,5 %) nádorů souboru. Závěry: Bodová mutace BRAF V600E byla detekována u 63,85 % PTC a jen jednou u benigního nádoru a jednoho NIFTP nálezu.
Introduction: The incidence of thyroid tumours is increasing worldwide. The most common malignant tumours of the thyroid gland include well-differentiated carcinomas (WDTC), especially papillary thyroid carcinoma (PTC) and follicular thyroid carcinoma (FTC). Medullary thyroid carcinoma (MTC) is less commonly diagnosed. Genetic changes determine the aggressive behavior of tumours and increase the metastatic potential of thyroid tumours. The aim of the study is to determine the incidence of point gene mutations and gene fusions in patients with Bethesda III–VI cytology as a possible predictor of indication of the extent of surgical procedures on the thyroid gland. Materials and methods: The study was prospective-retrospective and included patients operated on at the Department of Otorhinolaryngology and Maxillofacial Surgery of the 3rd Faculty of Medicine, Charles University and the Military University Hospital from July 1, 2019 to July 1, 2022, i.e. a period of 36 months. In the detection of the BRAF V600E gene, the allele of specific Real-Time PCR (LC480, Roche), the TERT gene mutation by direct sequencing (CEQ 8000, Beckman Coulter) was used, samples were analyzed by PCR (MiSeq, Illumina), and the Thyro-ID panel (4base) was used to detect another 12 genes. In addition, 23 fusion genes were tested, including ALK, BRAF, GLIS3, NTRK1, NTRK3, PPARG, and RET gene using Real-Time PCR, and MTC test for mutations in the RET gene and RAS. Results: The study included 273 patients with preoperative cytology Bethesda III–VI. The study was based on 21 (7.7%) men and 256 (93.77%) women. In the group, 103 (37.72%) cancers were histologically confirmed and 170 (62.27%) were found to have a benign tumour. Bethesda III were benign histologies with 118 (63.78%) that were verified, and 67 patients (36.21%) were diagnosed with any type of carcinoma. In Bethesda IV, there were 50 (70.42%) confirmed benign histologies and 21 patients (29.58%) had malignant tumours. BRAF V600E point mutation was detected in 63.85% of papillary thyroid carcinoma and only once in a benign tumour, and one NIFTP case was confirmed. Papillary carcinoma was presented in 83 (76.14%) patients, follicular carcinoma and its variants was in 14 (12.84%) patients, and medullary carcinoma was detected in 6 (5.5%) cases in the group. Conclusions: BRAF V600E point mutation was detected in 63.85% of well differentiated thyroid carcinomas and in other diagnoses, any mutation detected was rare.
- Klíčová slova
- BRAF mutace,
- MeSH
- bodová mutace * genetika MeSH
- incidence MeSH
- lidé MeSH
- nádory štítné žlázy * diagnóza genetika klasifikace patologie MeSH
- onkogenní fúze genetika MeSH
- prospektivní studie MeSH
- retrospektivní studie MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- práce podpořená grantem MeSH
BACKGROUND/AIM: Gliomas are primary malignancies of the central nervous system (CNS). High-grade gliomas are associated with poor prognosis and modest survival rates despite intensive multimodal treatment strategies. Targeting gene fusions is an emerging therapeutic approach for gliomas that allows application of personalized medicine principles. The aim of this study was to identify detectable fusion oncogenes that could serve as predictors of currently available or newly developed targeted therapeutics in cross-sectional samples from glioma patients using next-generation sequencing (NGS). PATIENTS AND METHODS: A total of 637 patients with glial and glioneuronal tumours of the CNS who underwent tumour resection between 2017 and 2020 were enrolled. Detection of fusion transcripts in FFPE tumour tissue was performed by a TruSight Tumour 170 assay and two FusionPlex kits, Solid Tumour and Comprehensive Thyroid and Lung. RESULTS: Oncogene fusions were identified in 33 patients. The most common fusion was the KIAA1549-BRAF fusion, detected in 13 patients, followed by FGFR fusions (FGFR1-TACC1, FGFR2-CTNNA3, FGFR3-TACC3, FGFR3-CKAP5, FGFR3-AMBRA1), identified in 10 patients. Other oncogene fusions were also infrequently diagnosed, including MET fusions (SRPK2-MET and PTPRZ1-MET) in 2 patients, C11orf95-RELA fusions in 2 patients, EGFR-SEPT14 fusion in 2 patients, and individual cases of SRGAP3-BRAF, RAF1-TRIM2, EWSR1-PALGL1 and TERT-ALK fusions. CONCLUSION: The introduction of NGS techniques provides additional information about tumour molecular alterations that can aid the multimodal management of glioma patients. Patients with gliomas positive for particular targetable gene fusions may benefit from experimental therapeutics, enhancing their quality of life and prolonging survival rates.
- MeSH
- adaptorové proteiny signální transdukční genetika MeSH
- gliom * genetika patologie MeSH
- kvalita života MeSH
- lidé MeSH
- onkogenní fúze * MeSH
- onkogeny genetika MeSH
- protein-serin-threoninkinasy MeSH
- proteiny asociované s mikrotubuly genetika MeSH
- průřezové studie MeSH
- tyrosinfosfatasy receptorového typu, třída 5 genetika MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
Large-scale molecular profiling studies in recent years have shown that central nervous system (CNS) tumors display a much greater heterogeneity in terms of molecularly distinct entities, cellular origins and genetic drivers than anticipated from histological assessment. DNA methylation profiling has emerged as a useful tool for robust tumor classification, providing new insights into these heterogeneous molecular classes. This is particularly true for rare CNS tumors with a broad morphological spectrum, which are not possible to assign as separate entities based on histological similarity alone. Here, we describe a molecularly distinct subset of predominantly pediatric CNS neoplasms (n = 60) that harbor PATZ1 fusions. The original histological diagnoses of these tumors covered a wide spectrum of tumor types and malignancy grades. While the single most common diagnosis was glioblastoma (GBM), clinical data of the PATZ1-fused tumors showed a better prognosis than typical GBM, despite frequent relapses. RNA sequencing revealed recurrent MN1:PATZ1 or EWSR1:PATZ1 fusions related to (often extensive) copy number variations on chromosome 22, where PATZ1 and the two fusion partners are located. These fusions have individually been reported in a number of glial/glioneuronal tumors, as well as extracranial sarcomas. We show here that they are more common than previously acknowledged, and together define a biologically distinct CNS tumor type with high expression of neural development markers such as PAX2, GATA2 and IGF2. Drug screening performed on the MN1:PATZ1 fusion-bearing KS-1 brain tumor cell line revealed preliminary candidates for further study. In summary, PATZ1 fusions define a molecular class of histologically polyphenotypic neuroepithelial tumors, which show an intermediate prognosis under current treatment regimens.
- MeSH
- dítě MeSH
- fúzní onkogenní proteiny genetika MeSH
- lidé MeSH
- nádorové biomarkery genetika MeSH
- nádory mozku genetika patologie MeSH
- neuroepitelové nádory genetika patologie MeSH
- onkogenní fúze MeSH
- předškolní dítě MeSH
- represorové proteiny genetika MeSH
- transkripční faktory Krüppel-like genetika MeSH
- Check Tag
- dítě MeSH
- lidé MeSH
- mužské pohlaví MeSH
- předškolní dítě MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Ependymomas encompass a heterogeneous group of central nervous system (CNS) neoplasms that occur along the entire neuroaxis. In recent years, extensive (epi-)genomic profiling efforts have identified several molecular groups of ependymoma that are characterized by distinct molecular alterations and/or patterns. Based on unsupervised visualization of a large cohort of genome-wide DNA methylation data, we identified a highly distinct group of pediatric-type tumors (n = 40) forming a cluster separate from all established CNS tumor types, of which a high proportion were histopathologically diagnosed as ependymoma. RNA sequencing revealed recurrent fusions involving the pleomorphic adenoma gene-like 1 (PLAGL1) gene in 19 of 20 of the samples analyzed, with the most common fusion being EWSR1:PLAGL1 (n = 13). Five tumors showed a PLAGL1:FOXO1 fusion and one a PLAGL1:EP300 fusion. High transcript levels of PLAGL1 were noted in these tumors, with concurrent overexpression of the imprinted genes H19 and IGF2, which are regulated by PLAGL1. Histopathological review of cases with sufficient material (n = 16) demonstrated a broad morphological spectrum of tumors with predominant ependymoma-like features. Immunohistochemically, tumors were GFAP positive and OLIG2- and SOX10 negative. In 3/16 of the cases, a dot-like positivity for EMA was detected. All tumors in our series were located in the supratentorial compartment. Median age of the patients at the time of diagnosis was 6.2 years. Median progression-free survival was 35 months (for 11 patients with data available). In summary, our findings suggest the existence of a novel group of supratentorial neuroepithelial tumors that are characterized by recurrent PLAGL1 fusions and enriched for pediatric patients.
- MeSH
- dítě MeSH
- ependymom genetika MeSH
- lidé MeSH
- nádorové supresorové proteiny genetika MeSH
- onkogenní fúze MeSH
- proteiny buněčného cyklu genetika MeSH
- supratentoriální nádory genetika MeSH
- transkripční faktory genetika MeSH
- Check Tag
- dítě MeSH
- lidé MeSH
- mužské pohlaví MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
A single primary cilium projects from most vertebrate cells to guide cell fate decisions. A growing list of signaling molecules is found to function through cilia and control ciliogenesis, including the fibroblast growth factor receptors (FGFR). Aberrant FGFR activity produces abnormal cilia with deregulated signaling, which contributes to pathogenesis of the FGFR-mediated genetic disorders. FGFR lesions are also found in cancer, raising a possibility of cilia involvement in the neoplastic transformation and tumor progression. Here, we focus on FGFR gene fusions, and discuss the possible mechanisms by which they function as oncogenic drivers. We show that a substantial portion of the FGFR fusion partners are proteins associated with the centrosome cycle, including organization of the mitotic spindle and ciliogenesis. The functions of centrosome proteins are often lost with the gene fusion, leading to haploinsufficiency that induces cilia loss and deregulated cell division. We speculate that this complements the ectopic FGFR activity and drives the FGFR fusion cancers.
- MeSH
- centrozom metabolismus MeSH
- cilie * metabolismus patologie MeSH
- lidé MeSH
- nádorová transformace buněk patologie MeSH
- nádory * metabolismus patologie MeSH
- onkogenní fúze MeSH
- receptory fibroblastových růstových faktorů metabolismus MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- přehledy MeSH
Thyroid-like follicular renal cell carcinoma is an uncommon kidney tumor with no distinct molecular alteration described to date. This cohort of eight women with mean and median ages of 45 and 46 years, respectively (range 19-65 years), had unencapsulated, well-circumscribed tumors composed of tightly packed anastomosing follicle-like cysts filled with eosinophilic colloid-like material and lined by cuboidal cells with high nuclear to cytoplasmic ratios, oval to elongated nuclei with perpendicular arrangement toward the lumens, and prominent nuclear overlapping. The stroma between these was minimal with the exception of two tumors. Calcifications and necrosis were absent. Immunohistochemically, the tumors were positive for KRT19 (7/7), PAX8 (5/5), cyclin D1 (6/6), KRT7 (5/7), and AMACR (1/5; focal, weak), and were negative for WT1, TTF1 (transcription termination factor-1), and thyroglobulin. In three of three tumors tested molecularly, EWSR1-PATZ1 fusion was identified by RNA sequencing and confirmed by RT-PCR and Sanger sequencing. Over a follow-up period of 1-7 years, no evidence of recurrence or metastasis has been detected. The EWSR1-PATZ1 fusion has been recognized as a recurrent alteration in a subset of round to spindle cell sarcomas with EWSR1-non-ETS fusions (EWSR1-PATZ1 sarcoma) and in several central nervous system tumors. The finding of an EWSR1-PATZ1 fusion in all three of the thyroid-like follicular renal cell carcinomas for which sufficient tissue was available for genomic profiling provides the first distinct molecular abnormality in thyroid-like follicular renal cell carcinomas, supporting its designation as a distinct diagnostic entity.
- MeSH
- dospělí MeSH
- karcinom z renálních buněk genetika patologie MeSH
- lidé středního věku MeSH
- lidé MeSH
- mladý dospělý MeSH
- nádory ledvin genetika patologie MeSH
- onkogenní fúze * MeSH
- protein EWS vázající RNA genetika MeSH
- represorové proteiny genetika MeSH
- senioři MeSH
- transkripční faktory Krüppel-like genetika MeSH
- Check Tag
- dospělí MeSH
- lidé středního věku MeSH
- lidé MeSH
- mladý dospělý MeSH
- mužské pohlaví MeSH
- senioři MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
Myoepithelial carcinoma of salivary glands is an underrecognized and challenging entity with a broad morphologic spectrum, including an EWSR1-rearranged clear cell variant. Myoepithelial carcinoma is generally aggressive with largely unknown genetic features. A retrospective review of Salivary Gland Tumor Registry in Pilsen searching for the key words "clear cell myoepithelial carcinoma," "hyalinizing clear cell," and "clear cell malignant myoepithelioma" yielded 94 clear cell myoepithelial carcinomas (CCMCs) for molecular analysis of EWSR1 rearrangement using fluorescence in situ hybridization (FISH). Tumors positive for EWSR1 gene rearrangement were tested by next-generation sequencing (NGS) using fusion-detecting panels. NGS results were confirmed by reverse-transcription polymerase chain reaction or by FISH. Twenty-six tumors originally diagnosed as CCMC (26/94, 27.6%) revealed split signals for EWSR1 by FISH. Six of these tumors (6/26, 23%) displayed amplification of the EWSR1 locus. Fifteen cases were analyzable by NGS, whereas 9 were not, and tissue was not available in 2 cases. None of the CCMCs with EWSR1 rearrangements detected by FISH had an EWSR1 fusion transcript. Fusion transcripts were detected in 6 cases (6/15, 40%), including LIFR-PLAG1 and CTNNB1-PLAG1, in 2 cases each, and CHCHD7-PLAG1 and EWSR1-ATF1 fusions were identified in 1 case each. Seven cases, including those with PLAG1 fusion, were positive for PLAG1 rearrangement by FISH, with notable exception of CHCHD7-PLAG1, which is an inversion not detectable by FISH. One single case with EWSR1-ATF1 fusion in NGS showed ATF1 gene rearrangement by FISH and was reclassified as clear cell carcinoma (CCC). In addition, another 4 cases revealed ATF1 rearrangement by FISH and were reclassified as CCC as well. Moreover, 12/68 (17%) CCMCs with intact EWSR1 gene were selected randomly and analyzed by NGS. PLAG1 fusions were found in 5 cases (5/12, 41.6%) with LIFR (2 cases), FGFR1 (2 cases), and CTNNB1 (1 case) as partner genes. Overall, PLAG1 gene rearrangements were detected in 10/38 (26%) tested cases. None of the tumors had SMARCB1 loss by immunohistochemistry as a possible explanation for the EWSR1 abnormalities in FISH. Novel findings in our NGS study suggest that EWSR1-FISH positive CCMC is a gene fusion-driven disease with frequent oncogenic PLAG1 fusions, including LIFR-PLAG1 and CTNNB1-PLAG1 in most cases. Productive EWSR1 fusions are found only in a minority of EWSR1-ATF1-rearranged cases, which were in part reclassifiable as CCCs. Detectable EWSR1-FISH abnormality in CCMCs without gene fusion perhaps represents a passenger mutation with minor or no oncologic effect.
- MeSH
- DNA vazebné proteiny genetika MeSH
- dospělí MeSH
- genová přestavba MeSH
- lidé středního věku MeSH
- lidé MeSH
- myoepiteliální nádor genetika MeSH
- nádory slinných žláz genetika MeSH
- onkogenní fúze MeSH
- protein EWS vázající RNA genetika MeSH
- senioři MeSH
- stanovení celkové genové exprese MeSH
- Check Tag
- dospělí MeSH
- lidé středního věku MeSH
- lidé MeSH
- mužské pohlaví MeSH
- senioři MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Solitary fibrous tumors (SFTs) harbor activating NAB2-STAT6 gene fusions. Different variants of the NAB2-STAT6 gene fusion have been associated with distinct clinicopathologic features. Lipomatous SFTs are a morphologic variant of SFTs, characterized by a fat-forming tumor component. Our aim was to evaluate NAB2-STAT6 fusion variants and to further study the molecular genetic features in a cohort of lipomatous SFTs. A hybrid-capture-based next-generation sequencing panel was employed to detect NAB2-STAT6 gene fusions at the RNA level. In addition, the RNA expression levels of 507 genes were evaluated using this panel, and were compared with a control cohort of nonlipomatous SFTs. Notably, 5 of 11 (45%) of lipomatous SFTs in the current series harbored the uncommon NAB2 exon 4-STAT6 exon 4 gene fusion variant, which is observed in only 0.9% to 1.4% of nonlipomatous SFTs. Furthermore, lipomatous SFTs displayed significant differences in gene expression compared with their nonlipomatous counterparts, including up-regulation of the gene peroxisome proliferator activated receptor-γ (PPARG). Peroxisome proliferator activated receptor-γ is a nuclear receptor regulating adipocyte differentiation, providing a possible explanation for the fat-forming component in lipomatous SFTs. In summary, the current study provides a possible molecular genetic basis for the distinct morphologic features of lipomatous SFTs.
- MeSH
- buněčná diferenciace genetika MeSH
- dospělí MeSH
- lidé středního věku MeSH
- lidé MeSH
- onkogenní fúze MeSH
- PPAR gama genetika MeSH
- represorové proteiny genetika MeSH
- senioři MeSH
- solitární fibrózní tumory genetika patologie MeSH
- transkripční faktor STAT6 genetika MeSH
- tukové buňky patologie MeSH
- upregulace MeSH
- Check Tag
- dospělí MeSH
- lidé středního věku MeSH
- lidé MeSH
- mužské pohlaví MeSH
- senioři MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Infantile fibrosarcoma (IFS)/cellular congenital mesoblastic nephroma (cCMN) commonly harbors the classic ETV6-NTRK3 translocation. However, there are recent reports of mesenchymal tumors with IFS-like morphology harboring fusions of other receptor tyrosine kinases or downstream effectors, including NTRK1/2/3, MET, RET, and RAF1 fusions as well as one prior series with BRAF fusions. Discovery of these additional molecular drivers contributes to a more integrated diagnostic approach and presents important targets for therapy. Here we report the clinicopathologic and molecular features of 14 BRAF-altered tumors, of which 5 had BRAF point mutations and 10 harbored one or more BRAF fusions. Of the BRAF fusion-positive tumors, one harbored two BRAF fusions (FOXN3-BRAF, TRIP11-BRAF) and another harbored three unique alternative splice variants of EPB41L2-BRAF. Tumors occurred in ten males and four females, aged from birth to 32 years (median 6 months). Twelve were soft tissue based; two were visceral including one located in the kidney (cCMN). All neoplasms demonstrated ovoid to short spindle cells most frequently arranged haphazardly or in intersecting fascicles, often with collagenized stroma and a chronic inflammatory infiltrate. No specific immunophenotype was observed; expression of CD34, S100, and SMA was variable. To date, this is the largest cohort of BRAF-altered spindle cell neoplasms with IFS-like morphology, including not only seven novel BRAF fusion partners but also the first description of oncogenic BRAF point mutations in these tumors.
- MeSH
- bodová mutace MeSH
- dospělí MeSH
- kojenec MeSH
- lidé MeSH
- mladiství MeSH
- novorozenec MeSH
- onkogenní fúze MeSH
- plod MeSH
- protoonkogenní proteiny B-raf genetika MeSH
- sarkom genetika patologie MeSH
- Check Tag
- dospělí MeSH
- kojenec MeSH
- lidé MeSH
- mladiství MeSH
- mužské pohlaví MeSH
- novorozenec MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- kazuistiky MeSH
