molecular biomarker testing
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Juxtaglomerular cell tumor (JxGCT) is a rare type of renal neoplasm demonstrating morphologic overlap with some mesenchymal tumors such as glomus tumor (GT) and solitary fibrous tumor (SFT). Its oncogenic drivers remain elusive, and only a few cases have been analyzed with modern molecular techniques. In prior studies, loss of chromosomes 9 and 11 appeared to be recurrent. Recently, whole-genome analysis identified alterations involving genes of MAPK-RAS pathway in a subset, but no major pathogenic alterations have been discovered in prior whole transcriptome analyses. Considering the limited understanding of the molecular features of JxGCTs, we sought to assess a collaborative series with a multiomic approach to further define the molecular characteristics of this entity. Fifteen tumors morphologically compatible with JxGCTs were evaluated using immunohistochemistry for renin, single-nucleotide polymorphism array (SNP), low-pass whole-genome sequencing, and RNA sequencing (fusion assay). In addition, methylation analysis comparing JxGCT, GT, and SFT was performed. All cases tested with renin (n=11) showed positive staining. Multiple chromosomal abnormalities were identified in all cases analyzed (n=8), with gains of chromosomes 1p, 10, 17, and 19 and losses of chromosomes 9, 11, and 21 being recurrent. A pathogenic HRAS mutation was identified in one case as part of the SNP array analysis. Thirteen tumors were analyzed by RNA sequencing, with 2 revealing in-frame gene fusions: TFG::GPR128 (interpreted as stochastic) and NAB2::STAT6 . The latter, originally diagnosed as JxGCT, was reclassified as SFT and excluded from the series. No fusions were detected in the remaining 11 cases; of note, no case harbored NOTCH fusions previously described in GT. Genomic methylation analysis showed that JxGCT, GT, and SFT form separate clusters, confirming that JxGCT represents a distinct entity (ie, different from GT). The results of our study show that JxGCTs are a distinct tumor type with a recurrent pattern of chromosomal imbalances that may play a role in oncogenesis, with MAPK-RAS pathway activation being likely a driver in a relatively small subset.
- MeSH
- dospělí MeSH
- epigeneze genetická MeSH
- epigenomika MeSH
- fúze genů * MeSH
- genetická predispozice k nemoci MeSH
- genomika MeSH
- imunohistochemie MeSH
- jednonukleotidový polymorfismus MeSH
- juxtaglomerulární aparát patologie MeSH
- lidé středního věku MeSH
- lidé MeSH
- metylace DNA MeSH
- nádorové biomarkery * genetika MeSH
- nádory ledvin * genetika patologie chemie MeSH
- sekvenování celého genomu MeSH
- senioři MeSH
- Check Tag
- dospělí MeSH
- lidé středního věku MeSH
- lidé MeSH
- mužské pohlaví MeSH
- senioři MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- multicentrická studie MeSH
BACKGROUNDS: SWI/SNF complexes represent a family of multi-subunit chromatin remodelers that are affected by alterations in >20% of human tumors. While mutations of SWI/SNF genes are relatively uncommon in prostate cancer (PCa), the literature suggests that deregulation of various subunits plays a role in prostate tumorigenesis. To assess SWI/SNF functions in a clinical context, we studied the mutually exclusive, paralogue accessory subunits SMARCD1, SMARCD2, and SMARCD3 that are included in every known complex and are sought to confer specificity. METHODS: Performing immunohistochemistry (IHC), the protein levels of the SMARCD family members were measured using a tissue microarray (TMA) comprising malignant samples and matching healthy tissue of non-metastatic PCa patients (n = 168). Moreover, IHC was performed in castration-resistant tumors (n = 9) and lymph node metastases (n = 22). To assess their potential role as molecular biomarkers, SMARCD1 and SMARCD3 protein levels were correlated with clinical parameters such as T stage, Gleason score, biochemical recurrence, and progression-free survival. RESULTS: SMARCD1 protein levels in non-metastatic primary tumors, lymph node metastases, and castration-resistant samples were significantly higher than in benign tissues. Likewise, SMARCD3 protein expression was elevated in tumor tissue and especially lymph node metastases compared to benign samples. While SMARCD1 levels in primary tumors did not exhibit significant associations with any of the tested clinical parameters, SMARCD3 exhibited an inverse correlation with pre-operative PSA levels. Moreover, low SMARCD3 expression was associated with progression to metastasis. CONCLUSIONS: In congruence with previous literature, our results implicate that both SMARCD1 and SMARCD3 may exhibit relevant functions in the context of prostate tumorigenesis. Moreover, our approach suggests a potential role of SMARCD3 as a novel prognostic marker in clinically non-metastatic PCa.
- MeSH
- chromozomální proteiny, nehistonové * genetika metabolismus MeSH
- imunohistochemie MeSH
- lidé středního věku MeSH
- lidé MeSH
- lokální recidiva nádoru patologie metabolismus genetika MeSH
- lymfatické metastázy MeSH
- nádorové biomarkery * genetika metabolismus MeSH
- nádory prostaty rezistentní na kastraci patologie genetika metabolismus MeSH
- nádory prostaty * patologie metabolismus genetika MeSH
- prognóza MeSH
- senioři MeSH
- stupeň nádoru MeSH
- transkripční faktory genetika metabolismus MeSH
- Check Tag
- lidé středního věku MeSH
- lidé MeSH
- mužské pohlaví MeSH
- senioři MeSH
- Publikační typ
- časopisecké články MeSH
AIMS: CIC-rearranged sarcomas (CRS) are clinically aggressive undifferentiated round cell sarcomas (URCS), commonly driven by CIC::DUX4. Due to the repetitive nature of DUX4 and the variability of the fusion breakpoints, CIC::DUX4 fusion may be missed by molecular testing. Immunohistochemical (IHC) stains have been studied as surrogates for the CIC::DUX4 fusion. We aim to assess the performance of DUX4 IHC in the work-up of CRS and its expression in non-CRS round cell or epithelioid neoplasms. METHODS AND RESULTS: Cases of molecularly confirmed CRS (n = 48) and non-CRS (n = 105) were included. CRS cases consisted of 35 females and 13 males, with ages ranging from less than 1 year to 67 years (median = 41 years). Among the molecularly confirmed non-CRS cases, C-terminal DUX4 expression was investigated in Ewing sarcomas (38 cases), alveolar rhabdomyosarcomas (18 cases), desmoplastic small round cell tumours (12 cases) and synovial sarcomas (n = five), as well as in non-mesenchymal neoplasms such as SMARCA4/SMARCB1-deficient tumours (n = five), carcinomas of unknown primary (n = three) and haematolymphoid neoplasms (four cases). DUX4 IHC was considered positive when strong nuclear expression was detected in more than 50% of neoplastic cells. When used as a surrogate for the diagnosis of CRS, the sensitivity and specificity of DUX4 IHC was 98 and 100%, respectively. Only one CRS case was negative for DUX4 IHC and harboured a CIC::FOXO4 fusion. CONCLUSIONS: DUX4 IHC is a highly sensitive and specific surrogate marker for the presence of CIC::DUX4 fusion, demonstrating its utility in establishing a diagnosis of CRS.
- MeSH
- dítě MeSH
- dospělí MeSH
- fúzní onkogenní proteiny * genetika MeSH
- genová přestavba MeSH
- homeodoménové proteiny * metabolismus genetika MeSH
- imunohistochemie * MeSH
- kojenec MeSH
- lidé středního věku MeSH
- lidé MeSH
- mladiství MeSH
- mladý dospělý MeSH
- nádorové biomarkery * metabolismus analýza genetika MeSH
- nádory měkkých tkání diagnóza patologie genetika metabolismus MeSH
- předškolní dítě MeSH
- sarkom * diagnóza patologie genetika metabolismus MeSH
- senioři MeSH
- senzitivita a specificita MeSH
- Check Tag
- dítě MeSH
- dospělí MeSH
- kojenec MeSH
- lidé středního věku MeSH
- lidé MeSH
- mladiství MeSH
- mladý dospělý MeSH
- mužské pohlaví MeSH
- předškolní dítě MeSH
- senioři MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
Current European/US guidelines recommend that molecular testing in advanced non-small cell lung cancer (aNSCLC) be performed using next-generation sequencing (NGS). However, the global uptake of NGS is limited, largely owing to reimbursement constraints. We compared real-world costs of NGS and single-gene testing (SGT) in nonsquamous aNSCLC. This observational study was conducted across 10 pathology centers in 10 different countries worldwide. Biomarker data collected via structured questionnaires (1 January-31 December 2021) were used to feed micro-costing analyses for three scenarios ['Starting Point' (SP; 2021-2022), 'Current Practice' (CP; 2023-2024), and 'Future Horizons' (FH; 2025-2028)] in both a real-world model, comprising all biomarkers tested by each center, and a standardized model, comprising the same sets of biomarkers across centers. Testing costs (including retesting) encompassed personnel costs, consumables, equipment, and overheads. Overall, 4,491 patients with aNSCLC were evaluated. Mean per-patient costs decreased for NGS relative to SGT over time, with real-world model costs 18% lower for NGS than for SGT in the SP scenario, and 26% lower for NGS than for SGT in the CP scenario. Mean per-biomarker costs also decreased over time for NGS relative to SGT. In the standardized model, the tipping point for the minimum number of biomarkers required for NGS to result in cost savings (per patient) was 10 and 12 in the SP and CP scenarios, respectively. Retesting had a negligible impact on cost analyses, and results were robust to variation in cost parameters. This study provides robust real-world global evidence for cost savings with NGS-based panels over SGT to evaluate predictive biomarkers in nonsquamous aNSCLC when the number of biomarkers to be tested exceeds 10. Widespread adoption of NGS may enable more efficient use of limited healthcare resources.
- MeSH
- analýza nákladů a výnosů MeSH
- genetické testování ekonomika metody MeSH
- lidé středního věku MeSH
- lidé MeSH
- nádorové biomarkery * genetika MeSH
- nádory plic * genetika patologie diagnóza MeSH
- náklady na zdravotní péči MeSH
- nemalobuněčný karcinom plic * genetika diagnóza patologie MeSH
- senioři MeSH
- vysoce účinné nukleotidové sekvenování * ekonomika MeSH
- Check Tag
- lidé středního věku MeSH
- lidé MeSH
- mužské pohlaví MeSH
- senioři MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- multicentrická studie MeSH
- pozorovací studie MeSH
- srovnávací studie MeSH
In addition to "classic" and eosinophilic subtype, chromophobe renal cell carcinoma (RCC) is well-known to demonstrate various morphological patterns including adenomatoid, microcystic, pigmented, multicystic, papillary, neuroendocrine-like, and small cell-like, all of which are important to appreciate for accurate diagnosis. Herein, we expand on a unique chromophobe RCC morphology not previously described consisting of tumor cells with extensive stromal retraction, mimicking upper urothelial tract micropapillary carcinoma (MPC). Twelve MPC-like chromophobe RCC nephrectomies were reviewed with clinicopathological features recorded; molecular testing was performed on 7 of 12 tumors. Patients were mostly men (n=10) with a mean age of 65 years. Mean tumor size was 6.4 cm with pathological stage distribution as follows: 4 (33%) T1a, 2 (17%) T1b, 1 (8%) T2b, and 3 (25%) T3a. The extent of MPC-like chromophobe RCC foci ranged from 10% to 40% (mean=26%; there was no correlation between the extent of MPC-like chromophobe RCC foci and tumor stage). Other chromophobe RCC morphological patterns were not identified. When performed, all (100%) tumors depicted prototypic chromophobe RCC staining pattern of KIT positivity/KRT7 positivity. Molecular showed 6 of 7 (86%) with multiple chromosomal losses. Clinically significant mutations were identified in NF1, TP53, FLCN (likely somatic), CHEK2, and ZFHX3 genes. Follow up available in 9 patients showed no evidence of disease (mean=23 months). Although the etiology behind the extensive stromal retraction in our tumors is unknown, this may likely be artifactual in nature. Nonetheless, it is important to include MPC-like chromophobe RCC in the spectrum of "variant" morphologies to avoid diagnostic pitfalls from micropapillary carcinoma.
- MeSH
- artefakty * MeSH
- diferenciální diagnóza MeSH
- karcinom z přechodných buněk diagnóza patologie chirurgie MeSH
- karcinom z renálních buněk * diagnóza patologie chirurgie genetika MeSH
- lidé středního věku MeSH
- lidé MeSH
- nádorové biomarkery analýza genetika MeSH
- nádory ledvin * patologie diagnóza chirurgie genetika MeSH
- papilární karcinom patologie diagnóza chirurgie MeSH
- senioři nad 80 let MeSH
- senioři MeSH
- Check Tag
- lidé středního věku MeSH
- lidé MeSH
- mužské pohlaví MeSH
- senioři nad 80 let MeSH
- senioři MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
The immunohistochemical (IHC) or fluorescence/chromogenic in situ hybridization (FISH/CISH) assays for assessing HER2 are now recommended by the American Society of Clinical Oncologists and the College of American Pathologists, but there are an increasing number of published studies describing alternative diagnoses at the molecular level. Inspired by these studies, we established a laboratory-developed test (LDT) to analyze HER2 status not only at the gene expression level but also at the gene copy number. A precise copy number calculation was fulfilled including the Control Genomic DNA of known concentration, which allowed subsequent assay validation at the DNA level. The results were reported according to the concordant results of the DNA and RNA approaches. By comparing with IHC determination, completely identical results were found in ten blank samples, which underlines the legitimacy of molecular biological approaches in this diagnostic field. An equivocal sample that was positive by IHC and qPCR was found to be negative by the FISH and so it may change the choice of personalized medicine. The topic of this short communication will hopefully contribute to allowing IVD-certified diagnostics based on the HER2 gene expression profile or copy number to be tested in the Czech Republic as well.
- MeSH
- DNA genetika metabolismus MeSH
- genová dávka * MeSH
- hybridizace in situ fluorescenční * metody MeSH
- imunohistochemie * metody MeSH
- lidé MeSH
- nádorové biomarkery genetika metabolismus MeSH
- nádory prsu genetika metabolismus diagnóza MeSH
- receptor erbB-2 * genetika metabolismus MeSH
- RNA metabolismus genetika analýza MeSH
- Check Tag
- lidé MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
High-grade B-cell lymphomas (HGBCLs) are aggressive blood cancers with a severe disease course, especially when the central nervous system (CNS) is involved. Standard histological examination depends on tissue availability and is currently supplemented with molecular tests, as the status of MYC, BCL2, or BCL6 gene rearrangements is required for proper lymphoma classification. This case report demonstrates the relevance of cerebrospinal fluid (CSF) cell-free DNA testing by integrative next-generation sequencing (NGS) panel. The benefit of this approach resided in tumor genotyping alongside the proof of CNS progression despite MRI negativity, revealing a clonal relationship with the primary tumor lesion. In addition, our strategy allowed us to classify the tumor as DLBCL/HGBL-MYC/BCL2 entity. In clinical practice, such a minimally invasive approach provides a more sensitive tool than standard imaging and cell analyzing techniques, enabling more accurate disease monitoring and relapse prediction in particular cases.
- MeSH
- B-buněčný lymfom genetika patologie diagnóza diagnostické zobrazování MeSH
- cirkulující nádorová DNA genetika MeSH
- difúzní velkobuněčný B-lymfom genetika patologie MeSH
- lidé středního věku MeSH
- lidé MeSH
- lokální recidiva nádoru patologie genetika MeSH
- magnetická rezonanční tomografie * MeSH
- nádorové biomarkery genetika MeSH
- nádory centrálního nervového systému genetika patologie diagnostické zobrazování MeSH
- vysoce účinné nukleotidové sekvenování * MeSH
- Check Tag
- lidé středního věku MeSH
- lidé MeSH
- mužské pohlaví MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- kazuistiky MeSH
Adenoid cystic carcinomas (AdCC) of salivary gland origin have long been categorized as fusion-defined carcinomas owing to the almost universal presence of the gene fusion MYB::NFIB , or less commonly MYBL1::NFIB. Sinonasal AdCC is an aggressive salivary gland malignancy with no effective systemic therapy. Therefore, it is urgent to search for potentially targetable genetic alterations associated with AdCC. We have searched the authors' registries and selected all AdCCs arising in the sinonasal tract. The tumors were examined histologically, immunohistochemically, by next generation sequencing (NGS) and/or fluorescence in situ hybridization (FISH) looking for MYB/MYBL1 and/or NFIB gene fusions or any novel gene fusions and/or mutations. In addition, all tumors were tested for HPV by genotyping using (q)PCR. Our cohort comprised 88 cases of sinonasal AdCC, predominantly characterized by canonical MYB::NFIB (49 cases) and MYBL1::NFIB (9 cases) fusions. In addition, noncanonical fusions EWSR1::MYB ; ACTB::MYB; ESRRG::DNM3 , and ACTN4::MYB were identified by NGS, each of them in 1 case. Among nine fusion-negative AdCCs, FISH detected rearrangements in MYB (7 cases) , NFIB (1 case), and EWSR1 (1 case). Six AdCCs lacked fusions or gene rearrangements, while 11 cases were unanalyzable. Mutational analysis was performed by NGS in 31/88 (35%) AdCCs. Mutations in genes with established roles in oncogenesis were identified in 21/31 tumors (68%), including BCOR (4/21; 19%), NOTCH1 (3/21; 14%), EP300 (3/21; 14%), SMARCA4 (2/21; 9%), RUNX1 (2/21; 9%), KDM6A (2/21; 9%), SPEN (2/21; 9%), and RIT1, MGA, RB1, PHF6, PTEN, CREBBP, DDX41, CHD2, ROS1, TAF1, CCD1, NF1, PALB2, AVCR1B, ARID1A, PPM1D, LZTR1, GEN1 , PDGFRA , each in 1 case (1/21; 5%). Additional 24 cases exhibited a spectrum of gene mutations of uncertain pathogenetic significance. No morphologic differences were observed between AdCCs with MYBL1::NFIB and MYB::NFIB fusions. Interestingly, mutations in the NOTCH genes were seen in connection with both canonical and noncanonical fusions, and often associated with high-grade histology or metatypical phenotype, as well as with poorer clinical outcome. Noncanonical fusions were predominantly observed in metatypical AdCCs. These findings emphasize the value of comprehensive molecular profiling in correlating morphologic characteristics, genetic landscape, and clinical behavior in AdCC.
- MeSH
- adenoidně cystický karcinom * genetika patologie MeSH
- dospělí MeSH
- fenotyp MeSH
- fúze genů MeSH
- fúzní onkogenní proteiny genetika MeSH
- genetická predispozice k nemoci MeSH
- hybridizace in situ fluorescenční * MeSH
- imunohistochemie MeSH
- lidé středního věku MeSH
- lidé MeSH
- mladiství MeSH
- mladý dospělý MeSH
- mutace * MeSH
- mutační analýza DNA MeSH
- nádorové biomarkery * genetika MeSH
- nádory vedlejších dutin nosních * genetika patologie MeSH
- senioři nad 80 let MeSH
- senioři MeSH
- transkripční faktory NFI genetika MeSH
- vysoce účinné nukleotidové sekvenování * MeSH
- Check Tag
- dospělí MeSH
- lidé středního věku MeSH
- lidé MeSH
- mladiství MeSH
- mladý dospělý MeSH
- mužské pohlaví MeSH
- senioři nad 80 let MeSH
- senioři MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
Karcinom prostaty je jedním z nejčastějších onkologických onemocnění mužů ve světě. Diagnostika a stratifikace pacientů jsou klíčové pro zajištění včasné a adekvátní terapie. Současné standardy se opírají převážně o PSA, jehož nádorová specificita je limitována. Tento přehled se zaměřuje na neinvazivní potenciální onkomarkery získané z moči včetně oxidačního stresu, metabolomiky a analýzy nukleových kyselin. V rámci některých studií se ukazuje, že zvýšené hladiny markerů jako F2-isoprostanáza, sarcosin a PCA3 mohou indikovat přítomnost a agresivitu karcinomu prostaty. Nové kombinované testy Prostarix, Mi-Prostate Score, SelectMDX nebo ExoDX nabízejí potenciál pro zlepšení stratifikace pacientů a snížení počtu negativních biopsií. Klinické využití těchto nových markerů je zatím omezené. Vzhledem k heterogenitě tohoto onemocnění je nezbytné pokračovat ve výzkumu, který usnadní personalizovaný přístup v léčbě.
Prostate cancer is one of the most common oncological diseases among men worldwide. Accurate diagnosis and patient stratification are crucial for ensuring timely and appropriate therapy. Current standards primarily rely on PSA, whose tumor specificity is limited. This review focuses on non-invasive potential oncological markers derived from urine, including oxidative stress, metabolomics and nucleic acid analysis. Some studies indicate that elevated levels of markers such as F2-isoprostane, sarcosine or PCA3 may signify the presence and aggressiveness of prostate cancer. New combined tests Prostarix, Mi-Prostate Score, SelectMDX and ExoDX offer potential for improved diagnosis and patient stratification, as well as a reduction in negative biopsies. However, the clinical application of these new markers remains limited. Considering the heterogeneity of this disease, ongoing research is essential to support a personalized approach to treatment.
- MeSH
- aminokyseliny moč MeSH
- biopsie metody MeSH
- časná detekce nádoru metody MeSH
- diagnostické techniky molekulární MeSH
- exozómy fyziologie MeSH
- lidé MeSH
- metabolomika metody MeSH
- mikro RNA moč MeSH
- nádorové biomarkery * moč MeSH
- nádory prostaty * diagnóza MeSH
- oxidační stres fyziologie MeSH
- prostatický specifický antigen krev MeSH
- Check Tag
- lidé MeSH
U nádorů gastrointestinálního traktu dnes vedle stanovení histologické diagnózy, grade a stage hraje zásadní roli rovněž tzv. prediktivní testování. To slouží zejména k identifikaci molekulárních cílů pro moderní onkologickou terapii. U karcinomů jícnu a žaludku je dnes standardem vyšetření exprese a amplifikace HER2, exprese proteinů mismatch repair (MMR) systému a vyšetření exprese PD-L1. U karcinomu žaludku se v blízké budoucnosti testování rozšíří o další markery, zejména exprese claudinu 18.2 či receptoru FGFR2a. U kolorektálního karcinomu je standardem prediktivního vyšetření stanovení mutací RAS (KRAS a NRAS), BRAF a dále zhodnocení mikrosatelitní instability, jen vzácně lze nalézt rovněž terapeuticky cílitelné genové fúze. U karcinomu pankreatu se lze setkat s případy deficience MMR, mutacemi BRCA1/2, zcela raritně lze identifikovat další cílitelné aberace. U nádorů žlučníku a žlučových cest hledáme zejména mutace IDH1 a IDH2, fúze a mutace genu FGFR2, amplifikace či mutace HER2, mutace BRAF či mutace BRCA1/2. Všechny výsledky by měly být projednány v rámci molekulárního tumor boardu.
In addition to the histological diagnosis, grade and stage, predictive testing plays a crucial role in gastrointestinal tumours today. This is mainly used to identify molecular targets for modern cancer therapy. In esophageal and gastric cancers, HER2 expression and amplification, mismatch repair (MMR) system protein deficiency and PD-L1 expression are tested routinely. In colorectal cancer, it is namely detection of RAS (KRAS and NRAS) and BRAF mutations, as well as the assessment of microsatellite instability; targetable gene fusions are found rarely only. In pancreatic cancer, cases of MMR deficiency, BRCA1/2 mutations and other targetable aberrations can be identified quite rarely. In gallbladder and biliary tract cancers, we are mainly looking for IDH1 and IDH2 mutations, FGFR2 gene fusions and mutations, HER2 amplifications or mutations, as well as mutations of BRAF or BRCA1/2. All results should be discussed within the molecular tumor board.
- MeSH
- diagnostické techniky molekulární MeSH
- gastrointestinální nádory * diagnóza genetika klasifikace MeSH
- genetické testování MeSH
- lidé MeSH
- mutace genetika MeSH
- nádorové biomarkery * genetika MeSH
- prediktivní hodnota testů MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- práce podpořená grantem MeSH
- přehledy MeSH