A comparative analysis of cell-type adjustment methods for epigenome-wide association studies based on simulated and real data sets

Technological advances and reduced costs of high-density methylation arrays have led to an increasing number of association studies on the possible relationship between human disease and epigenetic variability. DNA samples from peripheral blood or other tissue types are analyzed in epigenome-wide association studies (EWAS) to detect methylation differences related to a particular phenotype. Since information on the cell-type composition of the sample is generally not available and methylation profiles are cell-type specific, statistical methods have been developed for adjustment of cell-type heterogeneity in EWAS. In this study we systematically compared five popular adjustment methods: the factored spectrally transformed linear mixed model (FaST-LMM-EWASher), the sparse principal component analysis algorithm ReFACTor, surrogate variable analysis (SVA), independent SVA (ISVA) and an optimized version of SVA (SmartSVA). We used real data and applied a multilayered simulation framework to assess the type I error rate, the statistical power and the quality of estimated methylation differences according to major study characteristics. While all five adjustment methods improved false-positive rates compared with unadjusted analyses, FaST-LMM-EWASher resulted in the lowest type I error rate at the expense of low statistical power. SVA efficiently corrected for cell-type heterogeneity in EWAS up to 200 cases and 200 controls, but did not control type I error rates in larger studies. Results based on real data sets confirmed simulation findings with the strongest control of type I error rates by FaST-LMM-EWASher and SmartSVA. Overall, ReFACTor, ISVA and SmartSVA showed the best comparable statistical power, quality of estimated methylation differences and runtime

FirebrowseR: an R client to the Broad Institute's Firehose Pipeline

With its Firebrowse service (http://firebrowse.org/) the Broad Institute is making large-scale multi-platform omics data analysis results publicly available through a Representational State Transfer (REST) Application Programmable Interface (API). Querying this database through an API client from an arbitrary programming environment is an essential task, allowing other developers and researchers to focus on their analysis and avoid data wrangling. Hence, as a first result, we developed a workflow to automatically generate, test and deploy such clients for rapid response to API changes. Its underlying infrastructure, a combination of free and publicly available web services, facilitates the development of API clients. It decouples changes in server software from the client software by reacting to changes in the RESTful service and removing direct dependencies on a specific implementation of an API. As a second result, FirebrowseR, an R client to the Broad Institute's RESTful Firehose Pipeline, is provided as a working example, which is built by the means of the presented workflow. The package's features are demonstrated by an example analysis of cancer gene expression data

Performance of the CHARGE-AF risk model for incident atrial fibrillation in the EPIC Norfolk cohort

Background Identification of individuals at risk for developing atrial fibrillation (AF) will help to target screening and preventive interventions. We aimed to validate the CHARGE-AF model (including variables age, race, height, weight, blood pressure, smoking, antihypertensive medication, diabetes, myocardial infarction and heart failure) for prediction of five-year incident AF in a representative European population with a wide age range. Methods and results The CHARGE-AF model was calculated in 24,020 participants of the population-based EPIC Norfolk study with 236 cases of hospitalization with diagnosis of AF within five years. The model showed good discrimination (c-statistic 0.81, 95% confidence interval (CI) 0.75-0.85), but weak calibration (Chi(2)-statistic 142) with an almost two-fold overestimation of AF incidence. A recalibration to characteristics of the European Prospective Investigation into Cancer and Nutrition (EPIC) Norfolk cohort improved calibration considerably (Chi(2)-statistic 13.3), with acceptable discrimination in participants both >65 and 65 years of age (c-statistics 0.70, 95% CI 0.61-0.77 and 0.83, 95% CI 0.74-0.88). The recalibrated model also showed good discrimination in participants free of cardiovascular disease (c-statistics 0.80, 95% CI 0.75-0.84). Categories of predicted risk (5%) showed good concordance with observed five-year AF incidence of 0.62%, 3.49% and 8.74% (log rank test p<0.001), respectively. Conclusion A recalibration of the CHARGE-AF model is necessary for accurate predictions of five-year risk of AF in the EPIC Norfolk population. The recalibrated model showed good discrimination across a wide age range and in individuals free of cardiovascular disease, and hence is broadly applicable in primary care to identify people at risk for development of AF

Family matters: How MYC family oncogenes impact small cell lung cancer

Small cell lung cancer (SCLC) is one of the most deadly cancers and currently lacks effective targeted treatment options. Recent advances in the molecular characterization of SCLC has provided novel insight into the biology of this disease and raises hope for a paradigm shift in the treatment of SCLC. We and others have identified activation of MYC as a driver of susceptibility to Aurora kinase inhibition in SCLC cells and tumors that translates into a therapeutic option for the targeted treatment of MYC-driven SCLC. While MYC shares major features with its paralogs MYCN and MYCL, the sensitivity to Aurora kinase inhibitors is unique for MYC-driven SCLC. In this review, we will compare the distinct molecular features of the 3 MYC family members and address the potential implications for targeted therapy of SCLC

Plasma vitamin C and risk of hospitalisation with diagnosis of atrial fibrillation in men and women in EPIC-Norfolk prospective study

Background: Fruit and vegetable intake has been associated with lower risk for cardiovascular risk factors and disease. Data on its association with atrial fibrillation are lacking. Methods and results: We examined the prospective association of plasma vitamin C concentration as a biomarker for fruit and vegetable intake with the risk of hospitalisation with diagnosis of atrial fibrillation in apparently healthy 8,760 men and 10,530 women aged 39-79 participating in the EPIC-study in Norfolk. The hazard ratios of atrial fibrillation comparing each quartile of plasma vitamin C concentration with the lowest were 0.76 (95% CI 0.57-1.00), 0.73 (95% CI 0.55-0.98) and 0.77 (95% CI 0.58-1.01) in women (p for trend 0.05) and 0.81 (95% CI 0.63-1.03), 0.96 (95% CI 0.76-1.22) and 1.01 (95% CI 0.79-1.28) in men (p for trend 0.66) after adjustment for age, smoking, alcohol consumption, physical activity, systolic blood pressure, diabetes, use of blood pressure medication and body-mass index, with a significant gender x vitamin C interaction (p = 0.03). Assuming a linear association, a 20 mu mol/l increase in plasma vitamin C concentration (1 standard deviation) was associated with a 13% (95% CI 3-22%) relative reduction in risk of atrial fibrillation in women. Conclusion: Plasma vitamin C was inversely associated with the risk of atrial fibrillation in women, but there was no such association in men. Our findings suggest that intake of food rich in vitamin C might be preventive for atrial fibrillation with a significant benefit particularly in women with low baseline intake. (C) 2014 Elsevier Ireland Ltd. All rights reserved

CDK19 as a diagnostic marker for high-grade prostatic intraepithelial neoplasia

High-grade prostatic intraepithelial neoplasia (HGPIN) is a facultative precursor lesion of prostate cancer (PCa). Multifocal HGPIN in needle biopsies in the absence of PCa indicates a higher risk of cancer detection in subsequent biopsies. Therefore, a reliable diagnosis of HGPIN is of high clinical relevance guiding the management of patients with cancer-negative biopsies. Detection of HGPIN is merely based on morphological features while biomarkers aiding in the diagnosis of HGPIN and its differentiation from benign glands and other glandular lesions are lacking yet. Here, we investigated the expression of cyclin-dependent kinase 19 (CDK19) by immunohistochemistry on prostate needle biopsies of 140 patients who were all diagnosed with PCa using whole-tissue sections and compared CDK19 levels between HGPIN, PCa, and adjacent benign glands. In addition, CDK19 was compared with AMACR expression in a subset of intraductal carcinomas (IDCs) on radical prostatectomy (RP) specimens. HGPIN was present in 65.7% of biopsies and in 88% associated to adjacent PCa. CDK19 overexpression defined as moderate to high CDK19 expression visible at low magnification was found in 82.6% of HGPIN. In contrast, 89.3% of benign glands were CDK19-negative or demonstrated only low CDK19 expression highlighting a high sensitivity and specificity to accurately detect HGPIN based on CDK19 expression levels. CDK19 was overexpressed in 59% of PCa but did not correlate significantly with the expression of intermingled HGPIN. On RP, CDK19 and AMACR showed no significant difference in the detection rate of IDC. In summary, assessment of CDK19 facilitates accurate and simplified diagnosis of HGPIN with high sensitivity and specificity and aides the differentiation to non-neoplastic glandular alterations. Considering the high clinical significance of diagnosis HGPIN that still has a limited reproducibility among pathologists, we suggest CDK19 as diagnostic biomarker for HGPIN. (C) 2021 Elsevier Inc. All rights reserved

Histone Demethylase KDM5C Drives Prostate Cancer Progression by Promoting EMT

Simple Summary Prostate cancer is the most common cancer in men and is one of the leading causes of cancer-related deaths. During prostate cancer progression and metastasis, the epithelial cells can undergo epithelial-mesenchymal transition (EMT). Here, we show that the histone demethylase KDM5C is highly expressed in metastatic prostate cancer. We establish that stable clones silence KDM5C in prostate cancer cells. Knockdown of KDM5C leads to a reduced migratory and invasion capacity. This is associated with changes by multiple molecular mechanisms. This signaling subsequently modifies the expression of various transcription factors like Snail, Twist, and Zeb1/2, which are also known as master regulators of EMT. Taken together, our results indicate the potential to therapeutically target KDM5C either alone or in combination with Akt/mTOR-inhibitor in prostate cancer patients by targeting the EMT signaling pathways. Prostate cancer (PCa) poses a major public health problem in men. Metastatic PCa is incurable, and ultimately threatens the life of many patients. Mutations in tumor suppressor genes and oncogenes are important for PCa progression, whereas the role of epigenetic factors in prostate carcinogenesis is insufficiently examined. The histone demethylase KDM5C exerts important roles in tumorigenesis. KDM5C has been reported to be highly expressed in various cancer cell types, particularly in primary PCa. Here, we could show that KDM5C is highly upregulated in metastatic PCa. Functionally, in KDM5C knockdown cells migratory and invasion capacity was reduced. Interestingly, modulation of KDM5C expression influences several EMT signaling pathways (e.g., Akt/mTOR), expression of EMT transcription factors, epigenetic modifiers, and miR-205, resulting in increased expression of E-cadherin and reduced expression of N-cadherin. Mouse xenografts of KDM5C knockdown cells showed reduced tumor growth. In addition, the Akt/mTOR pathway is one of the classic signaling pathways to mediate tumor metabolic homeostasis, which is beneficial for tumor growth and metastasis. Taken together, our findings indicate that a combination of a selective KDM5C- and Akt/mTOR-inhibitor might be a new promising therapeutic strategy to reduce metastatic burden in PCa

CDK19 as a Potential HPV-Independent Biomarker for Recurrent Disease in HNSCC

The Mediator complex is a central integrator of transcription and a hub for the regulation of gene expression. Cyclin dependent kinase (CDK) 19 and its paralog CDK8 are part of its kinase domain and contribute to cancer progression in different cancer entities. STAT1 is an important immune modulator and a downstream substrate of CDK8/CDK19 mediated phosphorylation. So far, little is known about CDK19's role in head and neck squamous cell carcinoma (HNSCC) progression, its link to STAT1 activity, and related immune modulation. Immunohistochemistry for CDK19, activated pSTAT1, and PD-L1, known to be affected by STAT1, was conducted on samples of 130 primary tumors, 71 local recurrences, 32 lymph node metastases, and 25 distant metastases of HNSCC. Compared to primary tumors, CDK19 is overexpressed in local recurrences and distant metastases as well as in primary tumors that developed local recurrence after initial therapy. Patients with high-CDK19-expressing primary tumors have a significantly shorter disease-free survival. CDK19 expression correlates with pSTAT1 expression in primary tumors associated with recurrent disease, local recurrent tumors, lymph node metastases, and distant metastases. pSTAT1 expression correlates with PD-L1 expression in recurrent tumors. Our findings identify CDK19 as a potential biomarker in HNSCC to predict recurrent disease and support recent developments to target CDK19 and its paralog CDK8 in advanced cancer

Inhibition of Cyclin-Dependent Kinase 8/Cyclin-Dependent Kinase 19 Suppresses Its Pro-Oncogenic Effects in Prostate Cancer

Progression of prostate cancer (PCa) is characterized by metastasis and castration resistance after response to androgen deprivation. Therapeutic options are limited, causing high morbidity and lethality. Recent work reported pro-oncogenic implications of the Mediator subunits cyclin-dependent kinase (CDK) 8 and 19 for the progression of PCa. The current study explored the underlying molecular mechanisms of CDK8/CDK19 and tested effects of novel CDK8/CDK19 inhibitors. PC3, DU145, LNCaP, and androgen-independent LNCaP Abl were used for in vitro experiments. Two inhibitors and CDK19 over expression were used to modify CDK8/CDK19 activity. MTT assay, propidium iodide staining, wound healing assay, Boyden chamber assay, and adhesion assay were used to investigate cell viability, cell cycle, migration, and adhesion, respectively. Peptide-kinase screen using the PamGene platform was conducted to identify phosphorylated targets. Combining CDK8/CDK19 inhibitors with anti-androgens led to synergistic antiproliferative effects and sensitized androgen-independent cells to bicalutamide. CDK8/CDK19 inhibition resulted in reduced migration and increased collagen I-dependent adhesion. Phosphorylation of multiple peptides linked to cancer progression was identified to be dependent on CDK8/CDK19. In summary, this study substantially supports recent findings on CDK8/ CDK19 in PCa progression. These findings contribute to a better understanding of underlying prooncogenic effects, which is needed to develop CDK8/CDK19 as a therapeutic target in PCa.& nbsp