Infantile fibrosarcoma with an EGFR kinase domain duplication: underlining a close relationship with congenital mesoblastic nephroma and highlighting a similar morphological spectrum

Infantile fibrosarcoma (IFS) and congenital mesoblastic nephroma (CMN) are locally aggressive tumors primarily occurring in infants. Both IFS and the cellular subtype of CMN show overlapping morphological features and an ETV6-NTRK3 fusion, suggesting a close relationship. An activating alteration of EGFR, based on an EGFR kinase domain duplication (KDD), occurs in a subset of CMNs lacking an NTRK3 rearrangement, especially in the classic and mixed type. So far no EGFR-KDDs have been detected in IFS.We describe four pediatric tumors at the extremities (leg, n = 2; foot and arm n = 1) with histological features of IFS/CMN. Two cases showed classic IFS morphology while two were similar to classic/mixed type CMN. In all cases, an EGFR-KDD was identified without detection of a fusion gene. There were no abnormalities of the kidneys in any of the patients.This is the first description of IFS with an EGFR-KDD as driver mutation, supporting that IFS and CMN are similar lesions with the same morphological and genetic spectrum. Pathologists should be aware of the more fibrous variant of IFS, similar to classic/mixed type CMN. Molecular analyses are crucial to treat these lesions adequately, especially with regard to the administration of tyrosine kinase inhibitors.Orthopaedics, Trauma Surgery and Rehabilitatio

The biogenesis and function of small RNAs in C. elegans

RNAi is the process by which double-stranded RNA (dsRNA) induces sequence-specific mRNA degradation. DsRNA is diced into small interfering RNAs (siRNAs) of ~21-23 nt by a complex containing the RNaseIII enzyme DICER. The mature siRNAs are subsequently bound by Argonaute proteins and incorporated into an RNA-induced silencing complex (RISC), which cleaves homologous mRNAs. This process is involved in viral resistance and transposon silencing. Here we describe the identification of two proteins involved in the siRNA pathway; RRF-2 and RDE-2. The first is an RNA-directed RNA polymerase, the latter is a Caenorhabditae-specific protein, binding to MUT-7. Both RRF-2 and RDE-2 are required for an efficient RNAi response in C. elegans. A process closely related to the RNAi pathway is the microRNA (miRNA) pathway. MiRNAs are transcribed from the genome as long transcripts that can snap-back on themselves (primary miRNA or pri-miRNA) and are processed into ~70 nt stem-loop structures (precursor miRNA or pre-miRNA) by Drosha in the nucleus (Lee et al. 2003). The pre-miRNA serves as a template for Dicer which processes the pre-miRNA into the double-stranded miRNA of ~21 nt. These miRNAs are, like siRNAs, bound by Argonaute proteins and can bind to mRNAs (usually to the 3' UTR), but unlike siRNA that degrade mRNAs, miRNAs primarily inhibit translation. MiRNAs play a role in developmental timing, stress responses and fine-tuning gene-regulation. Here we describe the identification of Pasha (partner of Drosha) in Drosophila and C. elegans. Pasha is an essential protein, that associates with Drosha in the nucleus and is required for processing of pri-miRNAs into pre-miRNAs. We also discuss the role of the two Argonaute proteins, ALG-1 and ALG-2, that function in the miRNA pathway in C. elegans and present data supporting specialized roles for these Argonautes in this pathway. We show that a cluster of miRNAs, mir-35-41, regulates sex-determination in C. elegans. These miRNAs re-enforce decisions at several levels in the sex-determination pathway, that result in hermaphrodite-specific development. One of the targets of mir-35-41 is the fem-2 gene. Finally we discuss the pros and cons of the methods currently used to predict/verify miRNA targets, illustrated by a C. elegans example

Desmoid-type fibromatosis of the head and neck region in the paediatric population: a clinicopathological and genetic study of seven cases

Item does not contain fulltextAIMS: Desmoid-type fibromatosis (desmoid) is a locally aggressive (myo)fibroblastic lesion. It represents one of the more common fibrous tumours in children and adolescents. The head and neck region is more often involved than in adults. METHODS AND Results : We investigated the clinicopathological and genetic characteristics of seven paediatric desmoids at this anatomical site, including two cases of desmoplastic fibroma located in the mandible. There were two females and five males with an age range of 1.5-8 years. The sites of the soft tissue lesions were sinonasal (n = 4) and paramandibular (n = 1). All cases showed typical morphology and nuclear beta-catenin expression. CTNNB1 gene sequencing, performed successfully in five cases, revealed mutations in three cases with one p.T41A (bone lesion), one p.S37A and one novel mutation, p.D32V (sinonasal soft tissue lesions). Six patients were treated by excision with positive margins in five cases. Follow-up, available for six patients (median 4 years), showed no evidence of disease in four cases, slow progression in one case, and recurrence with stable disease in the last case. CONCLUSIONS: Our study provides evidence of genetic similarities in desmoid and desmoplastic fibroma. Additionally, we expanded the spectrum of mutations in CTNNB1 with one novel desmoid mutation

The homogeneous mutation status of a 22 gene panel justifies the use of serial sections of colorectal cancer tissue for external quality assessment

Contains fulltext : 154191.pdf (publisher's version ) (Open Access)Testing for treatment related biomarkers in clinical care, like Ras mutation status in colorectal cancer (CRC), has increased drastically over recent years. Reliable testing of these markers is pivotal for optimal treatment of patients. Participation in external quality assessment (EQA) programs is an important element in quality management and often obligatory to comply with regulations or for accreditation. Formalin-fixed paraffin-embedded (FFPE) clinical specimens would ideally form the basis for these assessments, as they represent the most common starting material for molecular testing. However, molecular heterogeneity of a lesion in a FFPE tissue block could potentially affect test results of participating laboratories, which might compromise reliability of the quality assessment results. To assess the actual impact of this potential problem, we determined the mutation status of 22 genes commonly mutated in colon cancer in four levels covering 360 mum of 30 FFPE tissue blocks, by Next Generation Sequencing. In each block, the genotype of these genes was identical at all four levels, with only little variation in mutation load. This result shows that the mutation status of the selected 22 genes in CRC specimens is homogeneous within a 360 mum segment of the tumor. These data justify the use of serial sections, within a defined segment of a CRC tissue block, for external quality assessment of mutation analysis

Next generation diagnostic molecular pathology: Critical appraisal of quality assurance in Europe

Contains fulltext : 136387.pdf (publisher's version ) (Open Access)Tumor evaluation in pathology is more and more based on a combination of traditional histopathology and molecular analysis. Due to the rapid development of new cancer treatments that specifically target aberrant proteins present in tumor cells, treatment decisions are increasingly based on the molecular features of the tumor. Not only the number of patients eligible for targeted precision medicine, but also the number of molecular targets per patient and tumor type is rising. Diagnostic molecular pathology, the discipline that determines the molecular aberrations present in tumors for diagnostic, prognostic or predictive purposes, is faced with true challenges. The laboratories have to meet the need of comprehensive molecular testing using only limited amount of tumor tissue, mostly fixed in formalin and embedded in paraffin (FFPE), in short turnaround time. Choices must be made for analytical methods that provide accurate, reliable and cost-effective results. Validation of the test procedures and results is essential. In addition, participation and good performance in internal (IQA) and external quality assurance (EQA) schemes is mandatory. In this review, we critically evaluate the validation procedure for comprehensive molecular tests as well as the organization of quality assurance and assessment of competence of diagnostic molecular pathology laboratories within Europe

EWSR1-ATF1 chimeric transcript in a myoepithelial tumor of soft tissue: a case report.

Item does not contain fulltextSoft tissue myoepithelial tumors, a recently defined entity, include benign and malignant lesions showing a considerable morphological and immunohistochemical heterogeneity. EWSR1 rearrangements are well recognized in this tumor type, and some of the partner genes have been identified. Herein we describe a soft tissue myoepithelioma arising in the pelvis with an EWSR1-ATF1 fusion, therefore extending the spectrum of partner genes of EWSR1. In addition, this case indicates that there are overlapping genetic features of myoepithelial tumors, clear cell sarcoma, angiomatoid fibrous histiocytoma, and hyalinizing clear-cell carcinoma of the salivary gland.1 mei 201

Comprehensive molecular and clinicopathological analysis of vascular malformations: A study of 319 cases

Contains fulltext : 204299.pdf (publisher's version ) (Open Access)Vascular malformations are part of overgrowth syndromes characterized by somatic mosaic mutations or rarely by germline mutations. Due to their similarities and diversity, clinicopathological classification can be challenging. A comprehensive targeted Next Generation Sequencing screen using Unique Molecular Identifiers with a technical sensitivity of 1% mutant alleles was performed for frequently mutated positions in >/=21 genes on 319 formalin-fixed paraffin-embedded samples. In 132 out of 319 cases pathogenic mosaic mutations were detected affecting genes previously linked to vascular malformations e.g. PIK3CA (n=80), TEK (TIE2) (n=11), AKT1 (n=1), GNAQ (n=7), GNA11 (n=4), IDH1 (n=3), KRAS (n=9), and NRAS (n=1). Six cases harbored a combination of mutations in PIK3CA and in GNA11 (n=2), GNAQ (n=2), or IDH1 (n=2). Aberrations in PTEN and RASA1 with a variant allele frequency approaching 50% suggestive of germline origin were identified in six out of 102 cases tested; four contained a potential second hit at a lower allele frequency. Ninety-one of the total 142 pathogenic mutations were present at a variant allele frequency <10% illustrating the importance of sensitive molecular analysis. Clinicopathological characteristics showed a broad spectrum and overlap when correlated with molecular data. Sensitive screening of recurrently mutated genes in vascular malformations may help to confirm the diagnosis and reveals potential therapeutic options with a significant contribution of PIK3CA/mTOR and RAS-MAPK pathway mutations. The co-existence of two activating pathogenic mutations in parallel pathways illustrates potential treatment challenges and underlines the importance of multigene testing. Detected germline mutations have major clinical impact

Genetic variants found in paediatric oncology patients with severe chemotherapy-induced toxicity: A case series

Paediatric oncology patients who develop severe chemotherapy-induced toxicity that requires dose reduction, delay or termination of treatment are at risk of decreased treatment efficacy. Previous research has provided evidence that genetic variants in TPMT, NUDT15, UGT1A1 and DPYD are associated with toxicity of anticancer drugs. This led to pharmacogenetic guidelines that are integrated into clinical practice in paediatric oncology. Recently, novel genetic variants have been associated with a higher risk of developing chemotherapy-induced toxicity. In this case series, we selected 21 novel variants and genotyped these in nine patients with excessive chemotherapy-induced toxicity using whole exome sequencing or micro-array data. We observed that six out of nine patients carried at least one variant that, according to recent studies, potentially increased the risk of developing methotrexate- or vincristine-induced toxicity. As patient-derived genetic data are becoming widely accessible in paediatric oncology, these variants could potentially enter clinical practice to mitigate chemotherapy-induced toxicity.Personalised Therapeutic

Using a semi-conductor sequencing-based panel for genotyping of HPV-positive and HPV-negative oropharyngeal cancer: a retrospective pilot study

Contains fulltext : 174696.pdf (publisher's version ) (Closed access)OBJECTIVES: The aim of this study was to assess the feasibility of testing actionable mutations in small amounts of formalin-fixed paraffin-embedded material in multiple genes of the receptor tyrosine kinase pathway and to determine the frequency of these mutations in human papillomavirus (HPV)-positive and HPV-negative oropharyngeal cancer (OPC). DESIGN: A retrospective pilot study was performed. SETTING: In OPC, no predictive markers for response to epidermal growth factor receptor inhibition are known. Therefore, identifying predictive biomarkers is of utmost importance, but is often hampered by the small amount of tumour material available. PARTICIPANTS: We included the archival material of 45 OPC, all treated with concomitant chemoradiotherapy between 2003 and 2010. MAIN OUTCOME MEASURES: Besides the HPV status, we assessed mutations using a gene panel that targets 16 genes in the receptor tyrosine kinase pathway and six other genes. The polymerase chain reaction required only 10 ng DNA. RESULTS: In total, 42 of the 45 biopsies have been successfully analysed. In total 20 of 42 samples were HPV-positive and 22 of 42 were HPV-negative. In the receptor tyrosine kinase pathway, mutations in PIK3CA were most frequently identified. A TP53 mutation was identified in one HPV-positive sample and in 13 HPV-negative samples. Additionally, three mutations in three different genes were found. CONCLUSIONS: We evaluated an assay to identify mutations in the receptor tyrosine kinase pathway. As only small amounts of formalin-fixed paraffin-embedded material are sufficient for reliable analysis, this test opens up new possibilities for personalised medicine