Vulvar malignant pleomorphic adenoma in a patient with lichen sclerosus

Lichen sclerosus (LS) is a chronic inflammatory skin disease presenting mainly on the anogenital area. The relationship between female genital LS and squamous cell carcinoma (SCC) has been established, with a lifetime risk of 4% to 5% for SCC development on female patients.1 Vulvar malignant pleomorphic adenoma, also termed carcinoma ex pleomorphic adenoma, is a rare tumor, with only 2 cases reported previously.2,3 The benign counterpart, pleomorphic adenoma (PA), is a commonly diagnosed benign tumor in the salivary glands but may also occur at a variety of other sites. Only about 10 cases of vulvar PA have been reported in the literature.4 There are no previous reports of PA or malignant PA in a patient with LS. Here we report a third case of vulvar malignant PA, and the first, to our knowledge, in a patient with LS.</p

Molekyylipatologia osana syöpäpotilaan hoitoa : patologin uusi rooli

Teema : geeniohjatun syövän hoidon työryhm

Molecular subtype diagnosis of endometrial carcinoma: comparison of the next-generation sequencing panel and Proactive Molecular Risk Classifier for Endometrial Cancer classifier

The Cancer Genome Atlas -based molecular classification of endometrial carcinoma (EC) has the potential to better identify those patients whose disease is likely to behave differently than predicted when using traditional risk stratification; however, the optimal approach to molecular subtype assignment in routine practice remains undetermined. The aim of this study was to compare the results of two different widely available approaches to diagnosis the EC molecular subtype. EC specimens from 60 patients were molecularly subclassified using two different methods, by using the FoundationOne CDx next-generation sequencing (NGS) panel and using the Proactive Molecular Risk Classifier for Endometrial Cancer (ProMisE) classifier and performing immunostaining for mismatch repair proteins and p53. POLE mutation status was derived from FoundationOne results in both settings. Molecular classification based on ProMisE was successful for all 60 tumors. Microsatellite instability status could be determined based on the NGS panel results in 53 of 60 tumors, so ProMisE and NGS molecular subtype assignment could be directly compared for these 53 tumors. Molecular subtype diagnosis based on NGS and ProMisE was in agreement for 52 of 53 tumors. One tumor was microsatellite stable but showed loss of MLH1 and PMS2 expression. Molecular subtype diagnosis of EC based on the NGS panel of formalin-fixed paraffin-embedded ECs and based primarily on immunostaining (ProMisE) yields identical results in 98.1% (52/53, kappa Z 0.97) of cases. Although results obtained using these two approaches are comparable, each has advantages and disadvantages that will influence the choice of the method to be used in clinical practice

Expression of Transcription Factor CREM in Human Tissues

AbstractCyclic AMP element modulator (CREM) is a transcription factor best known for its intricate involvement in spermatogenesis. The CREM gene encodes for multiple protein isoforms, which can enhance or repress transcription of target genes. Recent studies have identified fusion genes, with CREM as a partner gene in many neoplastic diseases. EWSR1-CREM fusion genes have been found in several mesenchymal tumors and in salivary gland carcinoma. These genes encode fusion proteins that include the C-terminal DNA-binding domain of CREM. We used a transcriptomic approach and immunohistochemistry to study the expression of CREM isoforms that include DNA-binding domains across human tissues. We found that CREM protein is widely expressed in almost all normal human tissues. A transcriptomic analysis of normal tissues and cancer showed that transcription of CREM can be altered in tumors, suggesting that also wild-type CREM may be involved in cancer biology. The wide expression of CREM protein in normal human tissues and cancer may limit the utility of immunohistochemistry for identification of tumors with CREM fusions.</p

No Link Between Striatal Dopaminergic Axons and Dopamine Transporter Imagingin Parkinson’s Disease

Background:Brain dopamine transporter binding hasbeen considered a possible biomarker for nigrostriataldegeneration in PD.Objective:To investigate whether dopamine trans-porter binding is associated with the number of dopa-minergic neurites in the putamen.Methods:Tyrosine hydroxylase–positive nervefiberswere counted from postmortem putamen sections takenfrom 14 parkinsonism patients who had been scannedwith dopamine transporter single-photon emission com-puted tomography antemortem. Fiber counts were cor-related with putamen dopamine transporter binding andSN neuron counts.Results:The putamen dopamine transporter specificbinding ratio did not correlate with the putamen tyrosinehydroxylase–positive axon counts (r = 0.00;P= 1.0; PDpatients: r = 0.07;P= 0.86). The nigra neuron counts had a positive correlation with the putamen tyrosinehydroxylase–positive axon counts.Conclusions:Striatal dopamine transporter imagingdoes not associate with axonal nor somal loss of thenigrostriatal neurons in PD. It may reflect dopaminergicactivity rather than number of surviving neurons or theirstriatal projection axons.</p

Tool evaluation for the detection of variably sized indels from next generation whole genome and targeted sequencing data

Insertions and deletions (indels) in human genomes are associated with a wide range of phenotypes, including various clinical disorders. High-throughput, next generation sequencing (NGS) technologies enable the detection of short genetic variants, such as single nucleotide variants (SNVs) and indels. However, the variant calling accuracy for indels remains considerably lower than for SNVs. Here we present a comparative study of the performance of variant calling tools for indel calling, evaluated with a wide repertoire of NGS datasets. While there is no single optimal tool to suit all circumstances, our results demonstrate that the choice of variant calling tool greatly impacts the precision and recall of indel calling. Furthermore, to reliably detect indels, it is essential to choose NGS technologies that offer a long read length and high coverage coupled with specific variant calling tools.Author summaryThe development of next generation sequencing (NGS) technologies and computational algorithms enabled the large scale, simultaneous detection of a wide range of genetic variants, such as single nucleotide variants as well as insertions and deletions (indels), which may confer potential clinical significance. Recently, many studies have been conducted to evaluate variant calling tools for indel calling. However, the optimal indel size range for different variant calling tools remains unclear. A good benchmarking dataset for indel calling evaluation should contain biologically representative high-confident indels with a wide size range and preferably come from various sequencing settings. In this article, we created a semi-simulated whole genome sequencing dataset where the sequencing data were computationally generated. The indels in the semi-simulated genome were incorporated from a real human sample to represent biologically realistic indels and to avoid the inclusion of variants due to potential technical sequencing errors. Furthermore, we used three real-world NGS datasets generated by whole genome or targeted sequencing to further evaluate our candidate tools. Our results demonstrated that variant calling tools vary greatly in calling different sizes of indels. Deletion calling and insertion calling also showed differences among the tools. The sequencing settings in coverage and read length also had a great impact on indel calling. Our results suggest that the accuracy of indel calling was dependent on the combination of a variant calling tool, indel size range, and sequencing settings.</p

Comprehensive genomic profiling of Finnish lung adenocarcinoma cohort reveals high clinical actionability and SMARCA4 altered tumors with variable histology and poor prognosis

Introduction: Lung adenocarcinoma is the most common type of lung cancer and typically carries a high number of mutations. However, the genetic background of the tumors varies according to patients' ethnic background and smoking status. Little data is available on the mutational landscape and the frequency of actionable genomic alterations in lung adenocarcinoma in the Finnish population. Materials and methods: We evaluated the gene alteration frequencies of 135 stage I-IV lung adenocarcinomas operated at Turku University Hospital between 2004 and 2017 with a large commercial comprehensive genomic profiling panel. Additionally, we correlated the alterations in selected genes with disease outcomes in 115 stage I-III patients with comprehensive follow-up data. The genomic alterations in a sub-cohort of 30 never-smokers were assessed separately. Results: Seventy percent of patients in the overall cohort and 77% in the never-smoker sub-cohort harbored an alteration or a genomic signature targetable by FDA and/or EMA approved drug for non-small cell carcinoma, respectively. In multivariable analysis for disease-specific survival, any alteration in SMARCA4 (DSS; HR 3.911, 95%CI 1.561-9.795, P = 0.004) exhibited independent prognostic significance along with stage, tumor mutation burden, and predominant histological subtypes. Conclusions: Over two thirds of our overall cohort, and especially never-smokers had an actionable genomic alteration or signature. SMARCA4 alterations, detected in 7.4% of the tumors, independently predicted a shortened overall and disease-specific survival regardless of the alteration type. Most SMARCA4 alterations in our cohort were missense mutations associated with differentiated predominant histological subtypes and immunohistochemical SMARCA4/BRG1 and TTF-1 positive status.</p

High tumor mutation burden predicts favorable outcome among patients with aggressive histological subtypes of lung adenocarcinoma : A population-based single-institution study

Objectives: Tumor mutation burden (TMB) is an emerging predictive cancer biomarker. Few studies have addressed the prognostic role of TMB in non-small cell lung carcinoma, with conflicting results. Moreover, the association of TMB with different histological subtypes of lung adenocarcinoma has hitherto not been systematically evaluated. Here we studied the prognostic value of TMB and its distribution in different histological subtypes of lung adenocarcinomas in a retrospective cohort using the most recent updated classification guidelines. Materials and methods: 176 surgically resected stage I-IV lung adenocarcinomas were histologically reclassified according to WHO 2015 guidelines. A modified classification subdividing the acinar subtype into classic acinar, complex glandular and cribriform subtypes was further applied and potentially prognostic histopathological characteristics such as tumor-infiltrating lymphocytes were evaluated. 148 patients with stage I-III tumors and complete follow-up data were included in the survival analyses. TMB was determined by a commercial next generation sequencing panel from 131 tumors, out of which 105 had survival data available. Results: Predominant micropapillary, solid and complex glandular as well as nonpredominant cribriform histological subtypes were associated with significantly shorter survival. High TMB concentrated in micropapillary, solid and acinar predominant subtypes. Interestingly, TMB >= 14 mutations/MB conferred a stage- and histology-independent survival benefit compared to TMB <14 in multivariable analysis for overall (HR 0.284, 95% CI 0.14-0.59, P=0.001) and disease-specific survival (HR 0.213, 95% CI 0.08-0.56, P=0.002). Conclusion: TMB was an independent biomarker of favorable prognosis in our cohort of lung adenocarcinoma despite being associated with predominant histological subtypes considered aggressive.Peer reviewe