Dilys Lam

Neoadjuvant chemotherapy (NAC) is used to treat triple-negative breast cancer (TNBC) prior to resection. Biomarkers that accurately predict a patient’s response to NAC are needed to individualise therapy and avoid chemotoxicity from unnecessary chemotherapy. We performed whole-genome DNA methylation profiling on diagnostic TNBC biopsy samples from the Sequential Evaluation of Tumours Undergoing Preoperative (SETUP) NAC study. We found 9 significantly differentially methylated regions (DMRs) at diagnosis which were associated with response to NAC. We show that 4 of these DMRs are associated with TNBC overall survival (P < 0.05). Our results highlight the potential of DNA methylation biomarkers for predicting NAC response in TNBC.

There is a major clinical need for accurate biomarkers for prostate cancer prognosis, to better inform treatment strategies and disease monitoring. Current clinically recognised prognostic factors, including prostate-specific antigen (PSA) levels, lack sensitivity and specificity in distinguishing aggressive from indolent disease, particularly in patients with localised intermediate grade prostate cancer. There has therefore been a major focus on identifying molecular biomarkers that can add prognostic value to existing markers, including investigation of DNA methylation, which has a known role in tumorigenesis. In this review, we will provide a comprehensive overview of the current state of DNA methylation biomarker studies in prostate cancer prognosis, and highlight the advances that have been made in this field. We cover the numerous studies into well-established candidate genes, and explore the technological transition that has enabled hypothesis-free genome-wide studies and the subsequent discovery of novel prognostic genes.

Background: Multiplex bisulphite PCR sequencing is a convenient and scalable method to comprehensively profile DNA methylation at selected loci. The method is useful for validation of methylation biomarker panels on large clinical cohorts, as it can be applied to DNA isolated from fresh tissue, archival formalin fixed paraffin embedded tissue (FFPET) or circulating cell free DNA in plasma. However, successful clinical implementation of DNA methylation biomarkers for disease detection using multiplex bisulphite PCR sequencing, requires user-friendly sample analysis methods and a diversity of visualisation options, which are not met by current tools.Results: We have developed a computational pipeline with an interactive graphical interface, calledMethPanel, in order to rapidly analyse multiplex bisulphite PCR sequencing data.MethPanelcomprises a complete analysis workflow from genomic alignment to DNA methylation calling and supports an unlimited number of PCR amplicons and input samples. Moreover,MethPaneloffers important and unique features, such as calculation of a polymorphism score and bisulphite PCR bias correction capabilities.MethPanelis designed so that the methylation data from all samples can be run in parallel on either a personal computer or a high performance computer. The outputs are also automatically forwarded to a shinyApp for convenient display, visualisation and sharing data with collaborators and clinicians. Importantly the data is centralised in one location, which aids storage management.Availability and Implementation: MethPanelis freely available athttps://github.com/thinhong/MethPanelConclusion: MethPanelprovides a novel parallel pipeline and interactive analysis tool for multiplex bisulphite PCR sequencing to assess DNA methylation marker panels for disease detection.

Disrupted serotonergic signaling is often a feature of depression and the role of the serotonin transporter gene (SLC6A4), responsible for serotonin re-uptake, has received much attention in this regard. Most studies have focused on the polymorphic 5-HTTLPR upstream repeat, or DNA methylation at the promoter CpG island. Few studies have explored the influence of genetic variation across the gene on DNA methylation, and their combined association with depression risk. The aim of this study was to determine whether genetic variation in the SLC6A4 gene influences promoter DNA methylation, and whether these are associated with depression status. The ESPRIT study involves a community-based population of older individuals (> 65 years of age). Major depressive disorder (MDD) was diagnosed according to DSM-IV (American Psychiatric Association, 1994) criteria, and severe depressive symptoms assessed by the Centre for Epidemiological Studies Depression (CES-D) Scale. Sequenom MassARRAY was used to measure SLC6A4 methylation status (n = 302). Nominally significant associations were observed between SLC6A4 genetic variants (5-HTTLPR, rs140700, rs4251417, rs6354, rs25528, rs25531) and DNA methylation at several CpG sites. In multivariate regression, DNA methylation was associated with depression status, but only in the presence of specific genotypes. In individuals homozygous for the short 5-HTTLPR and 5-HTTLPR/r25531 alleles, lower methylation at two CpGs was associated with depression (β = − 0.44 to β = − 0.31; p = 0.001 to p = 0.038). We present evidence for genotype-dependent associations between SLC6A4 methylation and depression. Genetic variants may also play a role in influencing promoter methylation levels and its association with depression.