Molecular genomic research designs

An Overview of DNA Methylation Indicators for the Course of Oral Precancer

DNA methylation is a physiologically epigenetic alteration that happens when a methyl group is introduced to a CpG dinucleotide in the gene-regulating sequence of DNA. However, the majority of oral cancers have a well-defined precancerous stage; there are few clinical and morphological parameters for detecting and signalling the progression of precancerous to malignant tumours. DNA methylation forms are dynamic and reversible, allowing them to adjust to environmental or therapeutic changes. We did an extensive investigation to compile the data supporting aberrant DNA methylation forms as a possible biomarker for prediction. According to two longitudinal studies, p16 hypermethylation was considerably higher in precancerous lesions that progressed to cancer than in lesions that shrank. Most of the studies examined for this study were tiny cross-sectional research with scant validation and inadequately specified control groups. Existing evidence suggests that DNA methylation sequences can be relevant as a diagnostic biomarker for OPS development; however, sample size and research design restrictions make it difficult to draw definitive conclusions. Strong studies, including extensive epigenome-wide methylation scans of OPS with longitudinal monitoring, are necessary in this study in order to corroborate the recently discovered signals and discover new risk loci and disease progression molecular pathways.

A contemporary narrative review to guide molecular epidemiology of oral submucous fibrosis

Oral submucous Fibrosis (OSMF) is a chronic disease that mainly affects the upper part of the aerodigestive tract. Areca nut and betel quid chewing has been established as the most significant causative factor for this condition. While OSMF is a predominantly Asian disease, the migrant populations from the region have taken the disease across the globe. Additionally, areca nut is now easily accessible in flavors and aggressively marketed. Many research activities have been undertaken for decades to understand the etiopathogenesis and risk factors of OSMF. Although OSMF is a slowly progressing disease, it has the potential to transform to an oral malignancy. This article is an attempt to review the literature and provide an update on its prevalence, etiopthogenesis and its diagnosis. We also highlight certain clinical, histopathological and molecular features that aid in the diagnosis and prognostication of OSMF, highlighting the importance of identifying the possibly high risk OSMF that is prone to malignant transformation. Using this information, future directions can be developed to include treatmentof OSMF through a dynamic gene-specific approach.

The Influence of Physical Activity and Epigenomics On Cognitive Function and Brain Health in Breast Cancer

The risk of breast cancer increases with age, with the majority of women diagnosed with breast cancer being postmenopausal. It has been estimated that 25-75% of women with breast cancer experience changes in cognitive function (CF) related to disease and treatment, which compromises psychological well-being, decision making, ability to perform daily activities, and adherence to cancer therapy. Unfortunately, the mechanisms that underlie neurocognitive changes in women with breast cancer remain poorly understood, which in turn limits the development of effective treatments and prevention strategies. Exercise has great potential as a non-pharmaceutical intervention to mitigate the decline in CF in women with breast cancer. Evidence suggests that DNA methylation, an epigenetic mechanism for gene regulation, impacts CF and brain health (BH), that exercise influences DNA methylation, and that exercise impacts CF and BH. Although investigating DNA methylation has the potential to uncover the biologic foundations for understanding neurocognitive changes within the context of breast cancer and its treatment as well as the ability to understand how exercise mitigates these changes, there is a dearth of research on this topic. The purpose of this review article is to compile the research in these areas and to recommend potential areas of opportunity for investigation.

Interferon gamma and interleukin 8 gene polymorphisms in patients with hepatitis C virus related oral lichen planus

OBJECTIVES

This study aimed to determine the association of rs2430561 and rs4073 polymorphisms in the Interferon gamma (IFN-ɤ) and Interleukin 8 (IL-8) genes, respectively, with hepatitis C virus-related oral lichen planus and disease severity.

DESIGN

This is a case-control study. 60 subjects were equally divided into patients with and without oral lichen planus. They were further subdivided into hepatitis C virus seropositive and seronegative patients. All patients were genotyped for IFN-γ rs2430561 thymine to adenine (T > A) and IL-8 rs4073 adenine to thymine (A > T) polymorphisms. All patients with oral lichen planus had their lesions measured and documented using the Escudier scoring system.

RESULTS

Disease activity was significantly higher in the "oral lichen planus/hepatitis C virus-positive" patients than in the "oral lichen planus/hepatitis C virus-negative" patients (P = 0.003). IFN-γ rs2430561 T > A and IL-8 rs4073 A > T genotypes and allele frequencies were not associated with the oral lichen planus group or the normal group. Stratification of the two groups into HCV and non-HCV-infected patients or into erosive and non-erosive types revealed no significant associations. The "A-allele-containing" genotypes of IL-8 rs4073 A > T were significantly more prevalent in the patients with oral lichen planus than in those without.

CONCLUSION

Hepatitis C virus infection is associated with the development of erosive oral lichen planus. The A-allele of IL-8 rs4073 A > T may have a role in the development and progression of oral lichen planus.

Rationale and Design of a Genetic Study on Cardiometabolic Risk Factors: Protocol for the Tehran Cardiometabolic Genetic Study (TCGS)

BACKGROUND

Cardiometabolic risk factors comprise cardiovascular diseases and/or diabetes, and need to be evaluated in different fields.

OBJECTIVE

The primary aim of the Tehran Cardiometabolic Genetic Study (TCGS) is to create a comprehensive genome-wide database of at least 16,000 Tehranians, who are participants of the ongoing Tehran Lipid and Glucose Study (TLGS) cohort.

METHODS

TCGS was designed in collaboration with the Research Institute for Endocrine Sciences and the genetic company deCODE. Participants had already been followed for over a 20-year period for major cardiometabolic-related health events including myocardial infarction, stroke, diabetes mellitus, hypertension, obesity, hyperlipidemia, and familial hypercholesterolemia.

RESULTS

The TCGS cohort described here comprises 17,186 (86.3%) of the 19,905 TLGS participants who provided a baseline blood sample that was adequate for plasma and deoxyribonucleic acid analysis. This study is comprised of 849 individuals and 3109 families with at least one member having genotype information. Finally, 5977 males and 7422 females with the total genotyping rate of 0.9854 were genotyped with HumanOmniExpress-24-v1-0 bead chips (containing 649,932 single-nucleotide polymorphism loci with an average mean distance of 4 kilobases).

CONCLUSIONS

Investigations conducted within the TCGS will seek to identify relevant patterns of genetic polymorphisms that could be related to cardiometabolic risk factors in participants from Tehran. By linking genome-wide data to the existing databank of TLGS participants, which includes comprehensive behavioral, biochemical, and clinical data on each participant since cohort inception in 1999, the TCGS will also allow exploration of gene-gene and gene-environment interactions as they relate to disease status.

DNA methylation markers for oral pre-cancer progression: A critical review

Although oral cancers are generally preceded by a well-established pre-cancerous stage, there is a lack of well-defined clinical and morphological criteria to detect and signal progression from pre-cancer to malignant tumours. We conducted a critical review to summarize the evidence regarding aberrant DNA methylation patterns as a potential diagnostic biomarker predicting progression. We identified all relevant human studies published in English prior to 30th April 2015 that examined DNA methylation (%) in oral pre-cancer by searching PubMed, Web-of-Science and Embase databases using combined key-searches. Twenty-one studies (18-cross-sectional; 3-longitudinal) were eligible for inclusion in the review, with sample sizes ranging from 4 to 156 affected cases. Eligible studies examined promoter region hyper-methylation of tumour suppressor genes in pathways including cell-cycle-control (n=15), DNA-repair (n=7), cell-cycle-signalling (n=4) and apoptosis (n=3). Hyper-methylated loci reported in three or more studies included p16, p14, MGMT and DAPK. Two longitudinal studies reported greater p16 hyper-methylation in pre-cancerous lesions transformed to malignancy compared to lesions that regressed (57-63.6% versus 8-32.1%; p<0.01). The one study that explored epigenome-wide methylation patterns reported three novel hyper-methylated loci (TRHDE; ZNF454; KCNAB3). The majority of reviewed studies were small, cross-sectional studies with poorly defined control groups and lacking validation. Whilst limitations in sample size and study design preclude definitive conclusions, current evidence suggests a potential utility of DNA methylation patterns as a diagnostic biomarker for oral pre-cancer progression. Robust studies such as large epigenome-wide methylation explorations of oral pre-cancer with longitudinal tracking are needed to validate the currently reported signals and identify new risk-loci and the biological pathways of disease progression.

Educating future nursing scientists: Recommendations for integrating omics content in PhD programs

Preparing the next generation of nursing scientists to conduct high-impact, competitive, sustainable, innovative, and interdisciplinary programs of research requires that the curricula for PhD programs keep pace with emerging areas of knowledge and health care/biomedical science. A field of inquiry that holds great potential to influence our understanding of the underlying biology and mechanisms of health and disease is omics. For the purpose of this article, omics refers to genomics, transcriptomics, proteomics, epigenomics, exposomics, microbiomics, and metabolomics. Traditionally, most PhD programs in schools of nursing do not incorporate this content into their core curricula. As part of the Council for the Advancement of Nursing Science's Idea Festival for Nursing Science Education, a work group charged with addressing omics preparation for the next generation of nursing scientists was convened. The purpose of this article is to describe key findings and recommendations from the work group that unanimously and enthusiastically support the incorporation of omics content into the curricula of PhD programs in nursing. The work group also calls to action faculty in schools of nursing to develop strategies to enable students needing immersion in omics science and methods to execute their research goals.

An overview of epigenetics in nursing

Epigenetic changes to the genome are biochemical alterations to the DNA that do not change an individual's genome but do change and influence gene expression. The nursing profession is qualified to conduct and integrate epigenetic-focused nursing research into practice. This article discusses current epigenetic nursing research, provides an overview of how epigenetic research relates to nursing practice, makes recommendations, and provides epigenetic online resources for nursing research. An overview of major epigenetic studies in nursing (specific to childbirth studies, preeclampsia, metabolic syndrome, immunotherapy cancer, and pain) is provided, with recommendations on next steps.

Current and emerging technology approaches in genomics

PURPOSE

To introduce current and emerging approaches that are being utilized in the field of genomics so the reader can conceptually evaluate the literature and appreciate how these approaches are advancing our understanding of health-related issues.

ORGANIZING CONSTRUCT

Each approach is described and includes information related to how it is advancing research, its potential clinical utility, exemplars of current uses, challenges related to technologies used for these approaches, and when appropriate information related to understanding the evidence base for clinical utilization of each approach is provided. Web-based resources are included for the reader who would like more in-depth information and to provide opportunity to stay up to date with these approaches and their utility.

CONCLUSIONS

The chosen approaches-genome sequencing, genome-wide association studies, epigenomics, and gene expression-are extremely valuable approaches for collecting research data to help us better understand the pathophysiology of a variety of health-related conditions, but they are also gaining in utility for clinical assessment and testing purposes.

CLINICAL RELEVANCE

Our increased understanding of the molecular underpinnings of disease will assist with better development of screening tests, diagnostic tests, tests that allow us to prognosticate, tests that allow for individualized treatments, and tests to facilitate post-treatment surveillance.