DNA methylation analysis for minimal-invasive Breast cancer diagnostic testing

Veränderungen im Methylierungsmuster der DNA geschehen früh in der Entwicklung von Tumoren. Zumeist sind Promoter-Regionen von Tumorsupressor-Genen und Onko-Genen betroffen, die einen Wachstumsvorteil der Krebszellen zur Folge haben. In dieser Studie wurde die Möglichkeit der Detektion dieser epigenetischen Aberrationen in zellfreier DNA aus Serum von Brustkrebspatienten untersucht, da diese potenzielle Biomarker zur minimal-invasiven Diagnostik darstellen. Hierzu wurden unterschiedliche DNA–Isolationsverfahren und Amplifikationsmethoden zur Anreicherung methylierter DNA getestet. Mit den optimierten Methoden wurde Serum-DNA von Brustkrebspatienten mit A) malignen Neoplasmen (n=40), B) nicht invasiv wachsenden Tumoren (n=18) und C) gesunden Kontrollprobandinnen (n=24) isoliert. Der DNA Gehalt im Serum von Brustkrebspatienten mit metastasierenden Tumoren [45,64ng/ml ± 32,31ng] war gegenüber gesunden Probanden [10,58ng/ml ± 9,71ng] signifikant erhöht (p = 0,0013; Wilcoxon-Rangsummentest). Die methylierte DNA Fraktion der Proben wurde mit einem Restriktionsenzymen – basierten Verfahren und einer „Rolling Circle Amplifikation“ (RCA) genomweit angereichert. Nach erfolgreicher Prozessierung von 72 der 82 DNA Proben konnte ein Biomarker-Screening zur Unterscheidung der Patientengruppen durchgeführt werden. Dazu wurden 360 ausgewählte DNA Bereiche in Multiplex-PCR Reaktionen amplifiziert und die PCR-Produkte durch Hybridisierung auf einem „targeted-micro-array“ detektiert. Die Micro-Array Analyse erlaubte eine Unterscheidung zwischen den Brustkrebspatienten und den Normal Kontrollen, wobei jedoch nach kritischer Betrachtung ein experimenteller Bias welcher zu diesen Unterschieden beiträgt nicht ausgeschlossen werden kann. In dieser Arbeit konnte somit ein Protokoll erarbeitet werden, das ein genomweites Biomarker-Screening zur Auffindung von DNA-Methylierungsmarkern für die minimal invasive Diagnostik aus geringsten Mengen zellfreier Serum DNA ermöglicht.Changes in DNA-methylation patterns are an early event in cancer development. Many promoter regions of tumor suppressor genes or oncogenes change their methylation status due to growth advantages of the cancer cell. During this study we investigated detection of these epigenetic aberrations in cell free DNA derived from serum of breast cancer patients, for elucidation of potential biomarkers for minimal invasive diagnostics. Therefore several DNA isolation approaches and genome wide amplification methods for enrichment of methylated DNA were tested. Applying these optimized methods serum-DNA was isolated form sera of A) breast cancer patients with malign neoplasm (n=40), B) sera of patients with a non-invasive cancer phenotype (n= 18) and C) healthy normal controls (n=24). The DNA concentrations in serum of patients with a metastasizing tumor (45,64 ng/ml +/- 32,31ng) was significantly increased when compared to serum-concentrations of normal controls (10,58ng/ml +/- 9,71ng), (p = 0.0013, Wilcoxon-test). The methylated fraction of the sample DNA was genome wide enriched, using a restriction enzyme based approach combined with a subsequent “Rolling Circle Amplification” (RCA). After successful sample preparation of 72 out of 82 DNA samples, a biomarker screening to distinguish between the patient study groups was performed. Therefore 360 selected DNA sequences were amplified within a multiplex-PCR approach and amplicons detected upon hybridization onto a target micro-array. Micro-array analyses enabled identification of marker-candidates for classification of study groups. However upon critical examination of our experimental setup, we can not exclude that some experimental bias contributes to this discrimination. In this work a protocol was established which enables a genome wide biomarker screening for elucidation of DNA methylation markers for minimal invasive diagnostic testing using spurious amounts of cell free serum DNA

Cytosine 5-Hydroxymethylation of the LZTS1 Gene Is Reduced in Breast Cancer

Change of DNA cytosine methylation (5mC) is an early event in the development of cancer, and the recent discovery of a 5-hydroxymethylated form (5hmC) of cytosine suggests a regulatory epigenetic role that might be different from 5-methylcytosine. Here, we aimed at elucidating the role of 5hmC in breast cancer. To interrogate the 5hmC levels of the leucine zipper, putative tumor suppressor 1 (LZTS1) gene in detail, we analyzed 75 primary breast cancer tissue samples from initial diagnosis and 12 normal breast tissue samples derived from healthy persons. Samples were subjected to 5hmC glucosyltransferase treatment followed by restriction digestion and segment-specific amplification of 11 polymerase chain reaction products. Nine of the 11 5′LZTS1 fragments showed significantly lower (fold change of 1.61–6.01, P < .05) 5hmC content in primary breast cancer tissue compared to normal breast tissue samples. No significant differences were observed for 5mC DNA methylation. Furthermore, both LZTS1 and TET1 mRNA expressions were significantly reduced in tumor samples (n = 75, P < .001, Student's t test), which correlated significantly with 5hmC levels in samples. 5hmC levels in breast cancer tissues were associated with unfavorable histopathologic parameters such as lymph node involvement (P < .05, Student's t test). A decrease of 5hmC levels of LZTS1, a classic tumor suppressor gene known to influence metastasis in breast cancer progression, is correlated to down-regulation of LZTS1 mRNA expression in breast cancer and might epigenetically enhance carcinogenesis. The study provides support for the novel hypothesis that suggests a strong influence of 5hmC on mRNA expression. Finally, one may also consider 5hmC as a new biomarker

Cytosine 5-Hydroxymethylation of the LZTS1 Gene Is Reduced in Breast Cancer

Change of DNA cytosine methylation (5mC) is an early event in the development of cancer, and the recent discovery of a 5-hydroxymethylated form (5hmC) of cytosine suggests a regulatory epigenetic role that might be different from 5-methylcytosine. Here, we aimed at elucidating the role of 5hmC in breast cancer. To interrogate the 5hmC levels of the leucine zipper, putative tumor suppressor 1 (LZTS1) gene in detail, we analyzed 75 primary breast cancer tissue samples from initial diagnosis and 12 normal breast tissue samples derived from healthy persons. Samples were subjected to 5hmC glucosyltransferase treatment followed by restriction digestion and segment-specific amplification of 11 polymerase chain reaction products. Nine of the 11 5′LZTS1 fragments showed significantly lower (fold change of 1.61–6.01, P < .05) 5hmC content in primary breast cancer tissue compared to normal breast tissue samples. No significant differences were observed for 5mC DNA methylation. Furthermore, both LZTS1 and TET1 mRNA expressions were significantly reduced in tumor samples (n = 75, P < .001, Student's t test), which correlated significantly with 5hmC levels in samples. 5hmC levels in breast cancer tissues were associated with unfavorable histopathologic parameters such as lymph node involvement (P < .05, Student's t test). A decrease of 5hmC levels of LZTS1, a classic tumor suppressor gene known to influence metastasis in breast cancer progression, is correlated to down-regulation of LZTS1 mRNA expression in breast cancer and might epigenetically enhance carcinogenesis. The study provides support for the novel hypothesis that suggests a strong influence of 5hmC on mRNA expression. Finally, one may also consider 5hmC as a new biomarker

Systematic review of lung function and COPD with peripheral blood DNA methylation in population based studies

Background Epigenetic variations in peripheral blood have potential as biomarkers for disease. This systematic review assesses the association of lung function and chronic obstructive pulmonary disease (COPD) with DNA methylation profiles in peripheral blood from population-based studies. Methods Online databases Medline, Embase, and Web of Science were searched. Google Scholar was searched to identify grey literature. After removing duplicate articles, 1155 articles were independently screened by two investigators. Peer reviewed reports on population-based studies that examined peripheral blood DNA methylation in participants with measured lung function (FEV1, FEV1/FVC ratio) or known COPD status were selected for full-text review. Six articles were suitable for inclusion. Information regarding study characteristics, designs, methodologies and conclusions was extracted. A narrative synthesis was performed based on published results. Results Three of the six articles assessed the association of COPD with DNA methylation, and two of these also included associations with lung function. Overall, five reports examined the association of lung function with DNA methylation profiles. Five of the six articles reported ‘significant’ results. However, no consistent CpG sites were identified across studies for COPD status or lung function values. Conclusions DNA methylation patterns in peripheral blood from individuals with reduced lung function or COPD may be different to those in people with normal lung function. However, this systematic review did not find any consistent associations of lung function or COPD with differentially methylated CpG sites. Large studies with a longitudinal design to address reverse causality may prove a more fruitful area of research

Non-IgE-reactive allergen peptides deteriorate the skin barrier in house dust mite-sensitized atopic dermatitis patients

Atopic dermatitis (AD) is a chronic inflammatory skin disease characterized by type 2 cytokine-driven skin inflammation and epithelial barrier dysfunction. The latter is believed to allow the increased penetration of chemicals, toxins, and allergens into the skin. House dust mite allergens, particularly Der p 2, are important triggers in sensitized individuals with AD; the precise actions of these allergens in epithelial biology remain, however, incompletely understood. In this study, we compared the effects of the protein allergen Der p 2 and a mix of non-IgE-reactive Der p 2 peptides on skin cells using patch tests in AD patients and healthy participants. We then analyzed mRNA expression profiles of keratinocytes by single-cell RNA-sequencing. We report that existing barrier deficiencies in the non-lesional skin of AD patients allow deep penetration of Der p 2 and its peptides, leading to local microinflammation. Der p 2 protein specifically upregulated genes involved in the innate immune system, stress, and danger signals in suprabasal KC. Der p 2 peptides further downregulated skin barrier genes, in particular the expression of genes involved in cell–matrix and cell–cell adhesion. Peptides also induced genes involved in hyperproliferation and caused disturbances in keratinocyte differentiation. Furthermore, inflammasome-relevant genes and IL18 were overexpressed, while KRT1 was downregulated. Our data suggest that Der p 2 peptides contribute to AD initiation and exacerbation by augmenting hallmark features of AD, such as skin inflammation, barrier disruption, and hyperplasia of keratinocytes

Role of DNA methylation in the association of lung function with body mass index: a two-step epigenetic Mendelian randomisation study

Low lung function has been associated with increased body mass index (BMI). The aim of this study was to investigate whether the effect of BMI on lung function is mediated by DNA methylation.; We used individual data from 285,495 participants in four population-based cohorts: the European Community Respiratory Health Survey, the Northern Finland Birth Cohort 1966, the Swiss Study on Air Pollution and Lung Disease in Adults, and the UK Biobank. We carried out Mendelian randomisation (MR) analyses in two steps using a two-sample approach with SNPs as instrumental variables (IVs) in each step. In step 1 MR, we estimated the causal effect of BMI on peripheral blood DNA methylation (measured at genome-wide level) using 95 BMI-associated SNPs as IVs. In step 2 MR, we estimated the causal effect of DNA methylation on FEV; 1; , FVC, and FEV; 1; /FVC using two SNPs acting as methQTLs occurring close (in cis) to CpGs identified in the first step. These analyses were conducted after exclusion of weak IVs (F statistic < 10) and MR estimates were derived using the Wald ratio, with standard error from the delta method. Individuals whose data were used in step 1 were not included in step 2.; In step 1, we found that BMI might have a small causal effect on DNA methylation levels (less than 1% change in methylation per 1 kg/m2 increase in BMI) at two CpGs (cg09046979 and cg12580248). In step 2, we found no evidence of a causal effect of DNA methylation at cg09046979 on lung function. We could not estimate the causal effect of DNA methylation at cg12580248 on lung function as we could not find publicly available data on the association of this CpG with SNPs.; To our knowledge, this is the first paper to report the use of a two-step MR approach to assess the role of DNA methylation in mediating the effect of a non-genetic factor on lung function. Our findings do not support a mediating effect of DNA methylation in the association of lung function with BMI

DNA methylation links prenatal smoking exposure to later life health outcomes in offspring

Abstract Background Maternal smoking during pregnancy is associated with adverse offspring health outcomes across their life course. We hypothesize that DNA methylation is a potential mediator of this relationship. Methods We examined the association of prenatal maternal smoking with offspring blood DNA methylation in 2821 individuals (age 16 to 48 years) from five prospective birth cohort studies and perform Mendelian randomization and mediation analyses to assess whether methylation markers have causal effects on disease outcomes in the offspring. Results We identify 69 differentially methylated CpGs in 36 genomic regions (P value < 1 × 10−7) associated with exposure to maternal smoking in adolescents and adults. Mendelian randomization analyses provided evidence for a causal role of four maternal smoking-related CpG sites on an increased risk of inflammatory bowel diseases or schizophrenia. Further mediation analyses showed some evidence of cg25189904 in GNG12 gene mediating the effect of exposure to maternal smoking on schizophrenia-related outcomes. Conclusions DNA methylation may represent a biological mechanism through which maternal smoking is associated with increased risk of psychiatric morbidity in the exposed offspring

Genetic analysis in European ancestry individuals identifies 517 loci associated with liver enzymes

Plasma levels of liver enzymes provide insights into hepatic function and related diseases. Here, the authors perform a genome-wide association study on three liver enzymes, identifying genetic variants associated with their plasma concentration as well as links to metabolic and cardiovascular diseases. Serum concentration of hepatic enzymes are linked to liver dysfunction, metabolic and cardiovascular diseases. We perform genetic analysis on serum levels of alanine transaminase (ALT), alkaline phosphatase (ALP) and gamma-glutamyl transferase (GGT) using data on 437,438 UK Biobank participants. Replication in 315,572 individuals from European descent from the Million Veteran Program, Rotterdam Study and Lifeline study confirms 517 liver enzyme SNPs. Genetic risk score analysis using the identified SNPs is strongly associated with serum activity of liver enzymes in two independent European descent studies (The Airwave Health Monitoring study and the Northern Finland Birth Cohort 1966). Gene-set enrichment analysis using the identified SNPs highlights involvement in liver development and function, lipid metabolism, insulin resistance, and vascular formation. Mendelian randomization analysis shows association of liver enzyme variants with coronary heart disease and ischemic stroke. Genetic risk score for elevated serum activity of liver enzymes is associated with higher fat percentage of body, trunk, and liver and body mass index. Our study highlights the role of molecular pathways regulated by the liver in metabolic disorders and cardiovascular disease