Analysis of CpG methylation sites and CGI among human papillomavirus DNA genomes

<p>Abstract</p> <p>Background</p> <p>The Human Papillomavirus (HPV) genome is divided into early and late coding sequences, including 8 open reading frames (ORFs) and a regulatory region (LCR). Viral gene expression may be regulated through epigenetic mechanisms, including cytosine methylation at CpG dinucleotides. We have analyzed the distribution of CpG sites and CpG islands/clusters (CGI) among 92 different HPV genomes grouped in function of their preferential tropism: cutaneous or mucosal. We calculated the proportion of CpG sites (PCS) for each ORF and calculated the expected CpG values for each viral type.</p> <p>Results</p> <p>CpGs are underrepresented in viral genomes. We found a positive correlation between CpG observed and expected values, with mucosal high-risk (HR) virus types showing the smallest O/E ratios. The ranges of the PCS were similar for most genomic regions except <it>E4</it>, where the majority of CpGs are found within islands/clusters. At least one CGI belongs to each <it>E2/E4 </it>region. We found positive correlations between PCS for each viral ORF when compared with the others, except for the LCR against four ORFs and <it>E6 </it>against three other ORFs. The distribution of CpG islands/clusters among HPV groups is heterogeneous and mucosal HR-HPV types exhibit both lower number and shorter island sizes compared to cutaneous and mucosal Low-risk (LR) HPVs (all of them significantly different).</p> <p>Conclusions</p> <p>There is a difference between viral and cellular CpG underrepresentation. There are significant correlations between complete genome PCS and a lack of correlations between several genomic region pairs, especially those involving LCR and <it>E6</it>. <it>L2 </it>and <it>L1 </it>ORF behavior is opposite to that of oncogenes <it>E6 </it>and <it>E7</it>. The first pair possesses relatively low numbers of CpG sites clustered in CGIs while the oncogenes possess a relatively high number of CpG sites not associated to CGIs. In all HPVs, <it>E2/E4 </it>is the only region with at least one CGI and shows a higher content of CpG sites in every HPV type with an identified <it>E4</it>. The mucosal HR-HPVs show either the shortest CGI size, followed by the mucosal LR-HPVs and lastly by the cutaneous viral subgroup, and a trend to the lowest CGI number, followed by the cutaneous viral subgroup and lastly by the mucosal LR-HPVs.</p

Differential Methylation of the HPV 16 Upstream Regulatory Region during Epithelial Differentiation and Neoplastic Transformation

High risk human papillomaviruses are squamous epitheliotropic viruses that may cause cervical and other cancers. HPV replication depends on squamous epithelial differentiation. Transformation of HPV-infected cells goes along with substantial alteration of the viral gene expression profile and preferentially occurs at transformation zones usually at the uterine cervix. Methylation of the viral genome may affect regulatory features that control transcription and replication of the viral genome. Therefore, we analyzed the methylation pattern of the HPV16 upstream regulatory region (URR) during squamous epithelial differentiation and neoplastic transformation and analyzed how shifts in the HPV URR methylome may affect viral gene expression and replication. HPV 16 positive biopsy sections encompassing all stages of an HPV infection (latent, permissive and transforming) were micro-dissected and DNA was isolated from cell fractions representing the basal, intermediate, and superficial cell layers, each, as well as from transformed p16INK4a-positive cells. We observed fundamental changes in the methylation profile of transcription factor binding sites in the HPV16 upstream regulatory region linked to the squamous epithelial differentiation stage. Squamous epithelial transformation indicated by p16INK4a overexpression was associated with methylation of the distal E2 binding site 1 leading to hyper-activation of the HPV 16 URR. Adjacent normal but HPV 16-infected epithelial areas retained hyper-methylated HPV DNA suggesting that these viral genomes were inactivated. These data suggest that distinct shifts of the HPV 16 methylome are linked to differentiation dependent transcription and replication control and may trigger neoplastic transformation

Design of a cluster-randomized trial of the effectiveness and cost-effectiveness of metformin on prevention of type 2 diabetes among prediabetic Mexican adults (the PRuDENTE initiative of Mexico City)

IntroductionType 2 diabetes (T2D) is a global epidemic, and nations are struggling to implement effective healthcare strategies to reduce the burden. While efficacy studies demonstrate that metformin can reduce incident T2D by half among younger, obese adults with prediabetes, its real-world effectiveness are understudied, and its use for T2D prevention in primary care is low. We describe the design of a pragmatic trial to evaluate the incremental effectiveness of metformin, as an adjunct to a simple lifestyle counseling.MethodsThe "Prevención de la Diabetes con Ejercicio, Nutrición y Tratamiento" [Diabetes Prevention with Exercise, Nutrition and Treatment; PRuDENTE, (Spanish acronym)] is a cluster-randomized trial in Mexico City's public primary healthcare system. The study randomly assigns 51 clinics to deliver one of two interventions for 36 months: 1) lifestyle only; 2) lifestyle plus metformin, to 3060 patients ages 30-65 with impaired fasting glucose and obesity. The primary endpoint is incident T2D (fasting glucose ≥126 mg/dL, or HbA1c ≥6.5%). We will also measure a range of implementation-related process outcomes at the clinic-, clinician- and patient-levels to inform interpretations of effectiveness and enable efforts to refine, adapt, adopt and disseminate the model. We will also estimate the cost-effectiveness of metformin as an adjunct to lifestyle counseling in Mexico.DiscussionFindings from this pragmatic trial will generate new translational knowledge in Mexico and beyond, both with respect to metformin's real-world effectiveness among an 'at-risk' population, and uncovering facilitators and barriers to the reach, adoption and implementation of metformin preventive therapy in public primary care settings.Trial registrationThis trial is registered at Clinicaltrials.gov (NCT03194009)