Epigenetic research in cancer epidemiology: trends, opportunities, and challenges

Epigenetic Features in Uterine Leiomyosarcoma and Endometrial Stromal Sarcomas: An Overview of the Literature

There is a consensus that epigenetic alterations play a key role in cancer initiation and its biology. Studies evaluating the modification in the DNA methylation and chromatin remodeling patterns, as well as gene regulation profile by non-coding RNAs (ncRNAs) have led to the development of novel therapeutic approaches to treat several tumor types. Indeed, despite clinical and translational challenges, combinatorial therapies employing agents targeting epigenetic modifications with conventional approaches have shown encouraging results. However, for rare neoplasia such as uterine leiomyosarcomas (LMS) and endometrial stromal sarcomas (ESS), treatment options are still limited. LMS has high chromosomal instability and molecular derangements, while ESS can present a specific gene fusion signature. Although they are the most frequent types of “pure” uterine sarcomas, these tumors are difficult to diagnose, have high rates of recurrence, and frequently develop resistance to current treatment options. The challenges involving the management of these tumors arise from the fact that the molecular mechanisms governing their progression have not been entirely elucidated. Hence, to fill this gap and highlight the importance of ongoing and future studies, we have cross-referenced the literature on uterine LMS and ESS and compiled the most relevant epigenetic studies, published between 2009 and 2022.

A critical review of datasets and computational suites for improving cancer theranostics and biomarker discovery

Cancer has been constantly evolving and so is the research pertaining to cancer diagnosis and therapeutic regimens. Early detection and specific therapeutics are the key features of modern cancer therapy. These requirements can only be fulfilled with the integration of diverse high-throughput technologies. Integration of advanced omics methodology involving genomics, epigenomics, proteomics, and transcriptomics provide a clear understanding of multi-faceted cancer. In the past few years, tremendous high-throughput data have been generated from cancer genomics and epigenomic analyses, which on further methodological analyses can yield better biological insights. The major epigenetic alterations reported in cancer are DNA methylation levels, histone post-translational modifications, and epi-miRNA regulating the oncogenes and tumor suppressor genes. While the genomic analyses like gene expression profiling, cancer gene prediction, and genome annotation divulge the genetic alterations in oncogenes or tumor suppressor genes. Also, systems biology approach using biological networks is being extensively used to identify novel cancer biomarkers. Therefore, integration of these multi-dimensional approaches will help to identify potential diagnostic and therapeutic biomarkers. Here, we reviewed the critical databases and tools dedicated to various epigenomic and genomic alterations in cancer. The review further focuses on the multi-omics resources available for further validating the identified cancer biomarkers. We also highlighted the tools for cancer biomarker discovery using a systems biology approach utilizing genomic and epigenomic data. Biomarkers predicted using such integrative approaches are shown to be more clinically relevant.

Associations of DNA methylation algorithms of aging and cancer risk: Results from a prospective cohort study

Background

Previous studies have shown that three DNA methylation (DNAm) based algorithms of aging, DNAm PhenoAge acceleration (AgeAccelPheno), DNAm GrimAge acceleration (AgeAccelGrim), and mortality risk score (MRscore), to be strong predictors of mortality and aging related outcomes. We aimed to investigate if and to what extent these algorithms predict cancer.

Methods

In four subsets (n = 727, 1003, 910, and 412) of a population-based cohort from Germany, DNA methylation in whole blood was measured using the Infinium Methylation EPIC BeadChip kit or the Infinium HumanMethylation450K BeadChip Assay (Illumina.Inc, San Diego, CA, USA). AgeAccelPheno, AgeAccelGrim, and a revised MRscore based on 8 CpGs only (MRscore-8CpGs), were calculated. Hazard ratios (HRs) were calculated to assess associations of the three DNAm algorithms with total cancer risk and risk of invasive breast, lung, prostate, and colorectal cancer incidence.

Findings

During 17 years of follow-up, a total of 697 malignant tumors (thereof breast cancer = 75, lung cancer = 146, prostate cancer = 114, colorectal cancer = 155) were observed. All three algorithms showed strong positive associations with lung cancer risk in a dose response manner, with adjusted HRs per SD increase in AgeAccelPheno, AgeAccelGrim, and MRscore-8CpGs, of 1·37 (1·03-1·82), 1·74 (1·11-2·73), and 2·06 (1·39-3·06), respectively. By contrast, strong inverse associations were seen with breast cancer risk [adjusted HRs 0·65 (0·49-0·86), 0·45 (0·25-0·80), and 0·42 (0·25-0·70), respectively]. Weak positive associations of MRscore-8CpGs were seen with total cancer risk.

Interpretation

The DNAm algorithms, particularly the MRscore-8CpGs, have potential to contribute to site-specific cancer risk prediction.

Funding

The ESTHER study was funded by grants from the Baden-Württemberg state Ministry of Science, Research and Arts (Stuttgart, Germany), the Federal Ministry of Education and Research (Berlin, Germany), the Federal Ministry of Family Affairs, Senior Citizens, Women and Youth (Berlin, Germany), and the Saarland State Ministry of Health, Social Affairs, Women and the Family (Saarbrücken, Germany). The work of Xiangwei Li was supported by a grant from Fondazione Cariplo (Bando Ricerca Malattie invecchiamento, #2017-0653).

An evaluation of the National Institutes of Health grants portfolio: identifying opportunities and challenges for multi-omics research that leverage metabolomics data

BACKGROUND

Through the systematic large-scale profiling of metabolites, metabolomics provides a tool for biomarker discovery and improving disease monitoring, diagnosis, prognosis, and treatment response, as well as for delineating disease mechanisms and etiology. As a downstream product of the genome and epigenome, transcriptome, and proteome activity, the metabolome can be considered as being the most proximal correlate to the phenotype. Integration of metabolomics data with other -omics data in multi-omics analyses has the potential to advance understanding of human disease development and treatment.

AIM OF REVIEW

To understand the current funding and potential research opportunities for when metabolomics is used in human multi-omics studies, we cross-sectionally evaluated National Institutes of Health (NIH)-funded grants to examine the use of metabolomics data when collected with at least one other -omics data type. First, we aimed to determine what types of multi-omics studies included metabolomics data collection. Then, we looked at those multi-omics studies to examine how often grants employed an integrative analysis approach using metabolomics data.

KEY SCIENTIFIC CONCEPTS OF REVIEW

We observed that the majority of NIH-funded multi-omics studies that include metabolomics data performed integration, but to a limited extent, with integration primarily incorporating only one other -omics data type. Some opportunities to improve data integration may include increasing confidence in metabolite identification, as well as addressing variability between -omics approach requirements and -omics data incompatibility.

Chronic Stress Effects on Tumor: Pathway and Mechanism

Chronic stress is an emotional experience that occurs when people encounter something they cannot adapt to. Repeated chronic stress increases the risk of a variety of diseases, such as cardiovascular disease, depression, endocrine disease, inflammation and cancer. A growing body of research has shown that there is a link between chronic stress and tumor occurrence in both animal studies and clinical studies. Chronic stress activates the neuroendocrine system (hypothalamic-pituitary-adrenal axis) and sympathetic nervous system. Stress hormones promote the occurrence and development of tumors through various mechanisms. In addition, chronic stress also affects the immune function of the body, leading to the decline of immune monitoring ability and promote the occurrence of tumors. The mechanisms of chronic stress leading to tumor include inflammation, autophagy and epigenetics. These factors increase the proliferation and invasion capacity of tumor cells and alter the tumor microenvironment. Antagonists targeting adrenergic receptors have played a beneficial role in improving antitumor activity, as well as chemotherapy resistance and radiation resistance. Here, we review how these mechanisms contribute to tumor initiation and progression, and discuss whether these molecular mechanisms might be an ideal target to treat tumor.

Targeting long non coding RNA by natural products: Implications for cancer therapy

In spite of achieving substantial progress in its therapeutic strategies, cancer-associated prevalence and mortality are persistently rising globally. However, most malignant cancers either cannot be adequately diagnosed at the primary phase or resist against multiple treatments such as chemotherapy, surgery, radiotherapy as well as targeting therapy. In recent decades, overwhelming evidences have provided more convincing words on the undeniable roles of long non-coding RNAs (lncRNAs) in incidence and development of various cancer types. Recently, phytochemical and nutraceutical compounds have received a great deal of attention due to their inhibitory and stimulatory effects on oncogenic and tumor suppressor lncRNAs respectively that finally may lead to attenuate various processes of cancer cells such as growth, proliferation, metastasis and invasion. Therefore, application of phytochemicals with anticancer characteristics can be considered as an innovative approach for treating cancer and increasing the sensitivity of cancer cells to standard prevailing therapies. The purpose of this review was to investigate the effect of various phytochemicals on regulation of lncRNAs in different human cancer and evaluate their capabilities for cancer treatment and prevention.

Targeting microRNAs with thymoquinone: a new approach for cancer therapy

Cancer is a global disease involving transformation of normal cells into tumor types via numerous mechanisms, with mortality among all generations, in spite of the breakthroughs in chemotherapy, radiotherapy and/or surgery for cancer treatment. Since one in six deaths is due to cancer, it is one of the overriding priorities of world health. Recently, bioactive natural compounds have been widely recognized due to their therapeutic effects for treatment of various chronic disorders, notably cancer. Thymoquinone (TQ), the most valuable constituent of black cumin seeds, has shown anti-cancer characteristics in a wide range of animal models. The revolutionary findings have revealed TQ's ability to regulate microRNA (miRNA) expression, offering a promising approach for cancer therapy. MiRNAs are small noncoding RNAs that modulate gene expression by means of variation in features of mRNA. MiRNAs manage several biological processes including gene expression and cellular signaling pathways. Accordingly, miRNAs can be considered as hallmarks for cancer diagnosis, prognosis and therapy. The purpose of this study was to review the various molecular mechanisms by which TQ exerts its potential as an anti-cancer agent through modulating miRNAs.

KMT2C is a potential biomarker of prognosis and chemotherapy sensitivity in breast cancer

PURPOSE

Epigenetic regulation plays critical roles in cancer progression, and high-frequency mutations or expression variations in epigenetic regulators have been frequently observed in tumorigenesis, serving as biomarkers and targets for cancer therapy. Here, we aimed to explore the function of epigenetic regulators in breast cancer.

METHODS

The mutational landscape of epigenetic regulators in breast cancer samples was investigated based on datasets from the Cancer Genome Atlas. The Kaplan-Meier method was used for survival analysis. RNA sequencing (RNA-seq) in MCF-7 cells transfected with control siRNA or KMT2C siRNA was performed. Quantitative reverse transcription-PCR and chromatin immunoprecipitation were used to validate the RNA-seq results.

RESULTS

Among the 450 epigenetic regulators, KMT2C was frequently mutated in breast cancer samples. The tumor mutational burden (TMB) was elevated in breast cancer samples with KMT2C mutations or low KMT2C mRNA levels compared to their counterparts with wild-type KMT2C or high KMT2C mRNA levels. Somatic mutation and low expression of KMT2C were independently correlated with the poor overall survival (OS) and disease-free survival (DFS) of the breast cancer samples, respectively. RNA-seq analysis combined with chromatin immunoprecipitation and qRT-PCR assays revealed that the depletion of KMT2C remarkably affected the expression of DNA damage repair-related genes. More importantly, the low expression of KMT2C was related to breast cancer cell sensitivity to chemotherapy and longer OS of breast cancer patients who underwent chemotherapy.

CONCLUSION

We conclude that KMT2C could serve as a potential biomarker of prognosis and chemotherapy sensitivity by affecting the DNA damage repair-related genes of breast cancer.

Recent developments in epigenetic cancer therapeutics: clinical advancement and emerging trends

Epigenetic drug discovery field has evidenced significant advancement in the recent times. A plethora of small molecule inhibitors have progressed to clinical stage investigations and are being explored exhaustively to ascertain conclusive benefits in diverse malignancies. Literature precedents indicates that substantial amount of efforts were directed towards the use of epigenetic tools in monotherapy as well as in combination regimens at the clinical level, however, the preclinical/preliminary explorations were inclined towards the identification of prudent approaches that can leverage the anticancer potential of small molecule epigenetic inhibitors as single agents only. This review article presents an update of FDA approved epigenetic drugs along with the epigenetic inhibitors undergoing clinical stage investigations in different cancer types. A detailed discussion of the pragmatic strategies that are expected to steer the progress of the epigenetic therapy through the implementation of emerging approaches such as PROTACS and CRISPR/Cas9 along with logical ways for scaffold fabrication to selectively approach the enzyme isoforms in pursuit of garnering amplified antitumor effects has been covered. In addition, the compilation also presents the rational strategies for the construction of multi-targeting scaffold assemblages employing previously identified pharmacophores as potential alternatives to the combination therapy.

MOF Regulates TNK2 Transcription Expression to Promote Cell Proliferation in Thyroid Cancer

MOF is a well-known histone acetyltransferase to catalyze acetylation of histone H4 lysine 16 (K16), and it is relevant to diverse biological processes, such as gene transcription, cell cycle, early embryonic development and tumorigenesis. Here, we identify MOF as an oncogene in most thyroid cancer. It is found that expression level of MOF was significantly upregulated in most thyroid cancer tissue samples and cell lines. MOF-deficient in both BHP-10-3 and TT2609 cell lines inhibited cell proliferation by blocking the cell cycle in G1 phase and enhanced cell apoptosis. Mechanistically, MOF bound the TNK2 promoter to activate TNK2 transcription. Furthermore, the expression level of TNK2 was decreased with the histone acetyltransferase inhibitor. Besides, MOF promoted proliferation of thyroid cancer cells through increased phosphorylation of AKT, thus activating the PI3K/AKT pathway. Ultimately, our findings indicated that MOF played an oncogene role in development and progression of thyroid cancer and may be a potential novel target for the treatment of thyroid cancer.

Peripheral Blood Leukocyte N6-methyladenosine is a Noninvasive Biomarker for Non-small-cell Lung Carcinoma

Background

N6-methyladenosine (m6A) triggers a new layer of epi-transcription. However, the potential noninvasive screening and diagnostic value of peripheral blood m6A for cancer are still unknown. Here, we intend to investigate whether leukocyte m6A can be a novel biomarker for non-small-cell lung cancer (NSCLC).

Materials and Methods

Peripheral blood was collected from 119 NSCLC patients and 74 age-matched healthy controls. Total RNA was isolated from leukocytes for m6A measurement, and clinical information of participants was reviewed. The sensitivity, specificity, and area under the curve (AUC) of m6A for cancer diagnosis were evaluated by the receiver-operating characteristic (ROC) curve analysis. Flow cytometry and the Human Protein Atlas (HPA) database were used to characterize m6A in leukocyte differentials. Pearson's correlation was applied to indicate the relationship between m6A level and hematology variables. qPCR and bioinformatic analysis were used to identity the expression of m6A regulators in leukocyte.

Results

Leukocyte m6A was significantly elevated in 119 NSCLC patients compared with 74 healthy controls (P<0.001). We did not find significant association between m6A and age or gender. Elevated m6A level in NSCLC was associated with tumor stage (P<0.05) and tumor differentiation (P<0.05), and was significantly reduced after surgery (P<0.01). ROC curve analysis revealed that leukocyte m6A could significantly discriminate patients with lung adenocarcinoma (LUAD) (AUC=0.736, P<0.001) and lung squamous cell carcinoma (LUSC) (AUC=0.963, P<0.001) from healthy individuals. m6A displayed superior sensitivity (100%) and specificity (85.7%) for LUSC than squamous cell carcinoma (SCC) antigen and cytokeratin fragment 211 (Cyfra211). Flow cytometry analysis showed m6A modification was mainly localized on T cells and monocytes among leukocyte differentials. Leukocyte m6A was positively correlated with the number of lymphocytes and negatively correlated with monocytes in NSCLC but not in healthy controls. qPCR and bioinformatic analysis showed that elevated leukocyte m6A in NSCLC was caused by upregulated methyltransferase complex and downregulated FTO and ALKBH5.

Conclusion

Leukocyte m6A represents a potential noninvasive biomarker for NSCLC screening, monitoring and diagnosis.

Assessment of tumor suppressor promoter methylation in healthy individuals

Background

The number of tumor suppressor genes for which germline mutations have been linked to cancer risk is steadily increasing. However, while recent reports have linked constitutional normal tissue promoter methylation of BRCA1 and MLH1 to ovarian and colon cancer risk, the role of epigenetic alterations as cancer risk factors remains largely unknown, presenting an important area for future research. Currently, we lack fast and sensitive methods for assessment of promoter methylation status across known tumor suppressor genes.

Results

In this paper, we present a novel NGS-based approach assessing promoter methylation status across a large panel of defined tumor suppressor genes to base-pair resolution. The method omits the limitations related to commonly used array-approaches. Our panel includes 565 target regions covering the promoters of 283 defined tumor suppressors, selected by pre-specified criteria, and was applied for rapid targeted methylation-specific NGS. The feasibility of the method was assessed by analyzing normal tissue DNA (white blood cells, WBC) samples from 34 healthy postmenopausal women and by performing preliminary assessment of the methylation landscape of tumor suppressors in these individuals. The mean target coverage was 189.6x providing a sensitivity of 0.53%, sufficient for promoter methylation assessment of low-level methylated genes like BRCA1. Within this limited test-set, we detected 206 regions located in the promoters of 149 genes to be differentially methylated (hyper- or hypo-) at > 99% confidence level. Seven target regions in gene promoters (CIITA, RASSF1, CHN1, PDCD1LG2, GSTP1, XPA, and ZNF668) were found to be hyper-methylated in a minority of individuals, with a > 20 percent point difference in mean methylation across the region between individuals. In an exploratory hierarchical clustering analysis, we found that the individuals analyzed may be grouped into two main groups based on their WBC methylation profile across the 283 tumor suppressor gene promoters.

Conclusions

Methylation-specific NGS of our tumor suppressor panel, with detailed assessment of differential methylation in healthy individuals, presents a feasible method for identification of novel epigenetic risk factors for cancer.

Epigenetic regulation in the pathophysiology of Lewy body dementia

Lewy body dementia encompasses both dementia with Lewy bodies and Parkinson's disease dementia. Although both are common causes of dementia, they remain relatively understudied. The review summarises the clinico-pathologic characteristics of Lewy Body dementia and discusses the genetic and environmental evidence contributing to the risk of developing the condition. Considering that the pathophysiology of Lewy body dementia is not yet fully understood, here we focus on the role of epigenetic mechanisms as potential key mediators of gene-environment interactions in the development of the disease. We examine available important data on genomics, epigenomics, gene expression and proteomic studies in Lewy body dementia on human post-mortem brain and peripheral tissues. Genetic variation and epigenetic modifications in key genes involved in the disorder, such as apolipoprotein E (APOE), α-synuclein (SNCA) and glucocerobrosidase (GBA), suggest a central involvement of epigenetics in DLB but conclusive evidence is scarce. This is due to limitations of existing literature, such as small sample sizes, lack of replication and lack of studies interrogating cell-type specific epigenetic modifications in the brain. Future research in the field can improve the understanding of this common but complex and rapidly progressing type of dementia and potentially open early diagnostic and effective therapeutic targets.

Patterns of Reliability: Assessing the Reproducibility and Integrity of DNA Methylation Measurement

DNA methylation plays an important role in both normal human development and risk of disease. The most utilized method of assessing DNA methylation uses BeadChips, generating an epigenome-wide “snapshot” of >450,000 observations (probe measurements) per assay. However, the reliability of each of these measurements is not equal, and little consideration is paid to consequences for research. We correlated repeat measurements of the same DNA samples using the Illumina HumanMethylation450K and the Infinium MethylationEPIC BeadChips in 350 blood DNA samples. Probes that were reliably measured were more heritable and showed consistent associations with environmental exposures, gene expression, and greater cross-tissue concordance. Unreliable probes were less replicable and generated an unknown volume of false negatives. This serves as a lesson for working with DNA methylation data, but the lessons are equally applicable to working with other data: as we advance toward generating increasingly greater volumes of data, failure to document reliability risks harming reproducibility.

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Measurements of DNA methylation made using BeadChip probes are differentially reliable

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Unreliable probes were less heritable, less replicable, and less functionally relevant

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This has serious implications for reporting and evaluating DNA methylation findings

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Reliability joins replicability and reproducibility to make three fundamental Rs of STEM

Although DNA methylation data are used widely by researchers in many fields, the reliability of these data are surprisingly variable. Our findings remind us that, in an age of increasingly big data, research is only as robust as its foundations. We hope that our findings will improve the integrity of DNA methylation studies. We also hope that our findings serve as a cautionary reminder for those generating and implementing big data of any type: reliability is a fundamental aspect of replicability. Conducting analysis with reliable data will improve chances of replicable findings, which might lead to more actionable targets for further research. To the extent that reliable data improve replicability, the knock-on effect will be more public confidence in research and less effort spent trying to replicate findings that are bound to fail.

Enriching Personalized Endometrial Cancer Research with the Harmonization of Biobanking Standards

Endometrial cancer is the commonest gynecological cancer, with an incidence predicted to escalate by a further 50–100% before 2025, due to the rapid rise in risk factors such as obesity and increased life expectancy. Endometrial cancer associated mortality is also rising, depicting the need for translatable research to improve our understanding of the disease. Rapid translation of scientific discoveries will facilitate the development of new diagnostic, prognostic and therapeutic strategies. Biobanks play a vital role in providing biospecimens with accompanying clinical data for personalized translational research. Wide variation in collection, and pre-analytic variations in processing and storage of bio-specimens result in divergent and irreproducible data from multiple studies that are unsuitable for collation to formulate robust conclusions. Harmonization of biobanking standards is thus vital, in facilitating international multi-center collaborative studies with valuable outcomes to improve personalized treatments. This review will detail the pitfalls in the biobanking of biosamples from women with cancer in general, and describe the recent international harmonization project that developed standardized research tools to overcome these challenges and to enhance endometrial cancer research, which will facilitate future development of personalized novel diagnostic strategies and treatments.

Epigenetic role of thymoquinone: impact on cellular mechanism and cancer therapeutics

Thymoquinone is a natural product known for its anticancer activity. Preclinical studies indicated numerous mechanisms of action by which thymoquinone exerts its effects on cancer cells. Recent evidence has indicated that thymoquinone can modulate epigenetic machinery, like modifying histone acetylation and deacetylation, DNA methylation and demethylation, which are among the major epigenetic changes that can contribute to carcinogenesis. Moreover, thymoquinone can alter the genetic expression of various noncoding RNAs, such as miRNA and lncRNA, which are the key parts of cellular epigenetics. This review focuses on cellular epigenetic systems, epigenetic changes responsible for cancer and the counteraction of thymoquinone to target epigenetic challenges, which might be among the mechanisms of the thymoquinone effect in cancer cells.

Epigenetically regulated imprinted gene expression associated with IVF and infertility: possible influence of prenatal stress and depression

PURPOSE

Despite the growing body of research implying an impact of in vitro fertilization (IVF) on imprinted genes and epigenetics, few studies have examined the effects of underlying subfertility or prenatal stress on epigenetics, particularly in terms of their role in determining infant birthweights. Both subfertility and prenatal stressors have been found to impact epigenetics and may be confounding the effect of IVF on epigenetics and imprinted genes. Like IVF, both of these exposures-infertility and prenatal stressors-have been associated with lower infant birthweights. The placenta, and specifically epigenetically regulated placental imprinted genes, provides an ideal but understudied mechanism for evaluating the relationship between underlying genetics, environmental exposures, and birthweight.

METHODS AND RESULTS

In this review, we discuss the impacts of IVF and infertility on birthweight, epigenetic mechanisms and genomic imprinting, and the role of these mechanisms in the IVF population and discuss the role and importance of the placenta in infant development. We then highlight recent work on the relationships between infertility, IVF, and prenatal stressors in terms of placental imprinting.

CONCLUSIONS

In combination, the studies discussed, as well as two recent projects of our own on placental imprinted gene expression, suggest that lower birthweights in IVF infants are secondary to a combination of exposures including the infertility and prenatal stress that couples undergoing IVF are experiencing. The work highlighted herein emphasizes the need for appropriate control populations that take infertility into account and also for consideration of prenatal psychosocial stressors as confounders and causes of variation in IVF infant outcomes.

Tissue-Specific Trans Regulation of the Mouse Epigenome

The epigenetic landscape varies greatly among cell types. Although a variety of writers, readers, and erasers of epigenetic features are known, we have little information about the underlying regulatory systems controlling the establishment and maintenance of these features. Here, we have explored how natural genetic variation affects the epigenome in mice. Studying levels of H3K4me3, a histone modification at sites such as promoters, enhancers, and recombination hotspots, we found tissue-specific trans-regulation of H3K4me3 levels in four highly diverse cell types: male germ cells, embryonic stem cells, hepatocytes, and cardiomyocytes. To identify the genetic loci involved, we measured H3K4me3 levels in male germ cells in a mapping population of 59 BXD recombinant inbred lines. We found extensive trans-regulation of H3K4me3 peaks, including six major histone quantitative trait loci (QTL). These chromatin regulatory loci act dominantly to suppress H3K4me3, which at hotspots reduces the likelihood of subsequent DNA double-strand breaks. QTL locations do not correspond with genes encoding enzymes known to metabolize chromatin features. Instead their locations match clusters of zinc finger genes, making these possible candidates that explain the dominant suppression of H3K4me3. Collectively, these data describe an extensive, set of chromatin regulatory loci that control the epigenetic landscape.

Ethical, Legal, and Regulatory Issues for the Implementation of Omics-Based Risk Prediction of Women's Cancer: Points to Consider

BACKGROUND AND OBJECTIVE

Advances in omics open new opportunities for cancer risk prediction and risk-based screening interventions. However, implementation of risk prediction in clinical practice may impact the ethical, legal, and regulatory aspects of current cancer screening programs. In order to support decision-making, we analyzed the ethical, legal, and regulatory issues and developed a set of Points to Consider to support management of these issues.

METHODS

We analyzed the legal and policy frameworks applicable to breast and cervical cancer screening programs in 7 European countries. We identified the most relevant issues to be considered, and we developed considerations for their management, based on the literature, the legal and policy frameworks, and our experience with similar issues.

RESULTS

The considerations focus on five topics: (A) health services planning, (B) information and invitation, (C) consent and data/sample collection, (D) risk calculation and communication of results, and (E) storage of data and residual samples.

CONCLUSION

Current frameworks might not be adequate to implement a risk prediction approach using omics factors due to the different characteristics of such approaches.

Temporal variability of global DNA methylation and hydroxymethylation in buccal cells of healthy adults: Association with air pollution

BACKGROUND

Epigenetic changes, such as DNA methylation, are observed in response to environmental exposure and in the development of several chronic diseases. Consequently, DNA methylation alterations might serve as indicators of early effects. In this context, the aim of this study was to assess the temporal variability of global DNA methylation and hydroxymethylation levels in buccal cells from healthy adult volunteers.

METHODS

Global DNA methylation (%5mdC) and hydroxymethylation (%5hmdC) levels in human buccal cells, collected from 26 healthy adults at different time points, were quantified by UPLC-MS/MS. Associations between %5mdC and %5hmdC, respectively, and short-term exposure (1-7days) to air pollutants PM_2.5 and PM₁₀ were tested with mixed-effects models including various covariates.

RESULTS/DISCUSSION

Dynamic short-term changes in DNA methylation and hydroxymethylation levels in buccal cells were observed, which were inversely associated with exposure to PM_2.5 and PM₁₀. An IQR increase in PM_2.5 over a 7-day moving average period was significantly associated with a decrease of -1.47% (-1.74%, -1.20%) and -0.043% (-0.054%, -0.032%) in %5mdC and %5hmdC, respectively. Likewise, for PM₁₀, a decrease of -1.42% (-1.70, -1.13) and -0.040% (-0.051%, -0.028%) was observed.

CONCLUSION

Global DNA methylation and hydroxymethylatation varied over a time period of three weeks. The observed temporal variability was associated with exposure to ambient PM_2.5 and PM₁₀ levels. This should be taken into account when interpreting epigenetic alterations in buccal cells.

Evaluation of MiR-21 and MiR-10b Expression of Human Breast Cancer in West Sumatera

BACKGROUND

Abnormal expression of several microRNAs (miRNAs) has been demonstrated in many types of cancer tumor tissue. The miR-10b and miR-21 are an oncogenic miRNAs which play role in proliferation and invasion of Breast Cancer (BC) tumorigenesis. The aim of this study was to evaluate the miR-21 and miR-10b expression in BC in West Sumatran women, Indonesia.

MATERIALS AND METHODS

A total of 40 samples, consisting of 30 samples of breast cancer tissues (BC) and 10 samples of fibroadenoma tissues (FATs) as control and non-cancerous were analyzed. The miR-21 and miR-10b expression of each sample were investigated by using realtime PCR, followed by universal Reverse Transcription (RT) then real-time PCR amplification with specific primers. Hsa-miR-16-5p LNA PCR primer was used as an endogenous control.

RESULTS

The results showed that the expression level of miR-21 was more than 4 times higher in BC than in FATs. The expression level of miR-10b was lower in BC than FATs, by a factor of 3.34 fold. Both these differences were statistically different (p = 0.001).

CONCLUSION

In this study it was concluded that for this sample of West Sumatran Women miR-21 expression in BC was higher than in FATs, whereas miR-10b was lower in BC than in FATs.

Genome-wide association studies and epigenome-wide association studies go together in cancer control

Completion of the human genome a decade ago laid the foundation for: using genetic information in assessing risk to identify individuals and populations that are likely to develop cancer, and designing treatments based on a person's genetic profiling (precision medicine). Genome-wide association studies (GWAS) completed during the past few years have identified risk-associated single nucleotide polymorphisms that can be used as screening tools in epidemiologic studies of a variety of tumor types. This led to the conduct of epigenome-wide association studies (EWAS). This article discusses the current status, challenges and research opportunities in GWAS and EWAS. Information gained from GWAS and EWAS has potential applications in cancer control and treatment.

Mechanistic and Technical Challenges in Studying the Human Microbiome and Cancer Epidemiology

This article reviews the significance of the microbiome in cancer epidemiology, mechanistic and technical challenges in the field, and characterization of the microbiome in different tumor types to identify biomarkers of risk, progression, and prognosis. Publications on the microbiome and cancer epidemiology were reviewed to analyze sample collection and processing, microbiome taxa characterization by 16S ribosomal RNA sequencing, and microbiome metabolite characterization (metabotyping) by nuclear magnetic resonance and mass spectrometry. The analysis identified methodology types, research design, sample types, and issues in integrating data from different platforms. Aerodigestive cancer epidemiology studies conducted by different groups demonstrated the significance of microbiome information in developing approaches to improve health. Challenges exist in sample preparation and processing (eg, standardization of methods for collection and analysis). These challenges relate to technology, data integration from "omics" studies, inherent bias in primer selection during 16S ribosomal RNA sequencing, the need for large consortia with well-characterized biospecimens, cause and effect issues, resilience of microbiota to exposure events (requires longitudinal studies), and expanding studies for fungal and viral diversity (most studies used bacterial 16S ribosomal RNA sequencing for microbiota characterization). Despite these challenges, microbiome and cancer epidemiology studies are significant and may facilitate cancer risk assessment, diagnosis, and prognosis. In the future, clinical trials likely will use microbiota modifications to improve the efficacy of existing treatments.

A 2015 survey of established or potential epigenetic biomarkers for the accurate detection of human cancers

Context The silencing or activation of cancer-associated genes by epigenetic mechanisms can ultimately lead to the clonal expansion of cancer cells. Objective The aim of this review is to summarize all relevant epigenetic biomarkers that have been proposed to date for the diagnosis of some prevalent human cancers. Methods A Medline search for the terms epigenetic biomarkers, human cancers, DNA methylation, histone modifications and microRNAs was performed. Results One hundred fifty-seven relevant publications were found and reviewed. Conclusion To date, a significant number of potential epigenetic cancer biomarkers of human cancer have been investigated, and some have advanced to clinical implementation.

Influence of environmental exposure on human epigenetic regulation

Environmental toxicants can alter epigenetic regulatory features such as DNA methylation and microRNA expression. As the sensitivity of epigenomic regulatory features may be greatest during the in utero period, when critical windows are narrow, and when epigenomic profiles are being set, this review will highlight research focused on that period. I will focus on work in human populations, where the impact of environmental toxicants in utero, including cigarette smoke and toxic trace metals such as arsenic, mercury and manganese, on genome-wide, gene-specific DNA methylation has been assessed. In particular, arsenic is highlighted, as this metalloid has been the focus of a number of studies and its detoxification mechanisms are well understood. Importantly, the tissues and cells being examined must be considered in context in order to interpret the findings of these studies. For example, by studying the placenta, it is possible to identify potential epigenetic adaptations of key genes and pathways that may alter the developmental course in line with the developmental origins of health and disease paradigm. Alternatively, studies of newborn cord blood can be used to examine how environmental exposure in utero can impact the composition of cells within the peripheral blood, leading to immunological effects of exposure. The results suggest that in humans, like other vertebrates, there is a susceptibility for epigenomic alteration by the environment during intrauterine development, and this may represent a mechanism of plasticity of the organism in response to its environment as well as a mechanism through which long-term health consequences can be shaped.

Epigenetic regulation in biopsychosocial pathways

Theory and empirical evidence suggest that psychological stress and other adverse psychosocial experiences can contribute to cancer progression. Research has begun to explore the potential role of epigenetic changes in these pathways. In basic, animal and human models, exposure to stressors or to the products of the physiological stress response (e.g., cortisol) has been associated with epigenetic changes, such as DNA methylation and microRNA (miR) expression, which may influence tumor growth, progression, metastasis, or chemoresistance. However, the specific biological pathways linking stress, epigenetic changes, and cancer outcomes remain unclear. Numerous opportunities exist to extend the preliminary evidence for the role of epigenetic mechanisms in the biopsychosocial pathways contributing to cancer progression. Such work will improve our understanding of how the psychosocial environment influences cancer risk and survival, potentially leading to improved prevention and treatment strategies.

Toxicoepigenomics and cancer: implications for screening

Scientists have long considered genetics to be the key mechanism that alters gene expression because of exposure to the environment and toxic substances (toxicants). Recently, epigenetic mechanisms have emerged as an alternative explanation for alterations in gene expression resulting from such exposure. The fact that certain toxic substances that contribute to tumor development do not induce mutations probably results from underlying epigenetic mechanisms. The field of toxicoepigenomics emerged from the combination of epigenetics and classical toxicology. High-throughput technologies now enable evaluation of altered epigenomic profiling in response to toxins and environmental pollutants. Furthermore, differences in the epigenomic backgrounds of individuals may explain why, although whole populations are exposed to toxicants, only a few people in a population develop cancer. Metals in the environment and toxic substances not only alter DNA methylation patterns and histone modifications but also affect enzymes involved in posttranslational modifications of proteins and epigenetic regulation, and thereby contribute to carcinogenesis. This article describes different toxic substances and environmental pollutants that alter epigenetic profiling and discusses how this information can be used in screening populations at high risk of developing cancer. Research opportunities and challengers in the field also are discussed.

Epigenome-wide association studies (EWAS): past, present, and future

Just as genome-wide association studies (GWAS) grew from the field of genetic epidemiology, so too do epigenome-wide association studies (EWAS) derive from the burgeoning field of epigenetic epidemiology, with both aiming to understand the molecular basis for disease risk. While genetic risk of disease is currently unmodifiable, there is hope that epigenetic risk may be reversible and or modifiable. This review will take a look back at the origins of this field and revisit the past early efforts to conduct EWAS using the 27k Illumina methylation beadarrays, to the present where most investigators are using the 450k Illumina beadarrays and finally to the future where next generation sequencing based methods beckon. There have been numerous diseases, exposures and lifestyle factors investigated with EWAS, with several significant associations now identified. However, much like the GWAS studies, EWAS are likely to require large international consortium-based approaches to reach the numbers of subjects, and statistical and scientific rigor, required for robust findings.

Molecular profiling and companion diagnostics: where is personalized medicine in cancer heading?

The goal of personalized medicine is to use the right drug at the right dose - with minimal or no toxicity - for the right patient at the right time. Recent advances in understanding cell biology and pathways, and in using molecular 'omics' technologies to diagnose cancer, offer a strategic bridge to personalized medicine in cancer. Modern personalized medicine takes into account an individual's genetic makeup and disease history before developing a treatment regimen. The future of clinical oncology will be based on the use of predictive and prognostic biomarkers in patient management. Once implemented widely, personalized medicine will benefit patients and the healthcare system greatly.

Effects of selenium compounds on proliferation and epigenetic marks of breast cancer cells

Breast cancer is a global public health problem and the most frequent cause of cancer death among women. Mammary carcinogenesis is driven not only by genetic alterations but also by epigenetic disturbances. Because epigenetic marks are potentially reversible they represent promising molecular targets for breast cancer prevention interventions. Selenium is a promising anti-breast cancer trace element that has shown the modulation of DNA methylation and histone post-translational modifications in other malignancies. This study aimed to evaluate the effects of selenium compounds [methylseleninic acid (MSA) and selenite] on cell proliferation and death, expression of the tumor suppressor gene RASSF1A and epigenetic marks in MCF-7 human breast adenocarcinoma cells. Treatment with MSA or selenite markedly inhibited (P<0.05) in a dose-dependent manner the proliferation of MCF-7 cells. MSA induced (P<0.05) G2/M cell arrest while selenite presented the opposite effect. Regarding cell death induction, MSA acted mainly by inducing apoptosis (P<0.05), while selenite only induced necrosis (P<0.05). Furthermore selenite, but not MSA, markedly induced (P<0.05) cytotoxicity and increased (P<0.05) RASSF1A expression. Both selenium compounds inhibited (P<0.05) DNMT1 expression. MSA decreased (P<0.05) H3K9me3 and increased (P<0.05) H4K16ac, while selenite decreased (P<0.05) this latter histone mark. To the best of our knowledge this is the first report showing that selenite and MSA modulate epigenetic marks specifically in breast cancer cells. Our data reinforce the anti-breast cancer potential of selenium that is dependent on its chemical form. Furthermore the data show that epigenetic mechanisms represent relevant molecular targets involved in selenium inhibitory effects in breast cancer cells.

DNA methylation study of fetus genome through a genome-wide analysis

Background

DNA methylation is a crucial epigenetic modification of the genome which is involved in embryonic development, transcription, chromatin structure, X chromosome inactivation, genomic imprinting and chromosome stability. Consistent with these important roles, DNA methylation has been demonstrated to be required for vertebrate early embryogenesis and essential for regulating temporal and spatial expression of genes controlling cell fate and differentiation. Further studies have shown that abnormal DNA methylation is associated with human diseases including the embryonic development diseases. We attempt to study the DNA methylation status of CpG islands in fetus related to fetus growth and development.

Methods

GeneChip® Human Tiling 2.0R Array set is used for analysis of methylated DNA in a whole-genome wide in 8 pairs amniotic fluid and maternal blood DNA samples.

Results

We found 1 fetus hypermethylation DNA markers and 4 fetus hypomethylation DNA markers though a Genome-wide analysis. These DNA markers all found to be associated with the critical genes for fetus growth and development (SH2D3C gene, EML3 gene, TRIM71 gene, HOXA3 gene and HOXA5 gene).

Conclusions

These genes can be used as a biomarker for association studying of embryonic development, pathological pregnancy and so on. The present study has provided new and fundamental insights into the roles that DNA methylation has in embryonic development and in the pathological pregnancy.