No effect of different bariatric surgery procedures on LINE-1 DNA methylation in diabetic and nondiabetic morbidly obese patients

Retrotransposons and Diabetes Mellitus

Retrotransposons are invasive genetic elements, which replicate by copying and pasting themselves throughout the genome in a process called retrotransposition. The most abundant retrotransposons by number in the human genome are Alu and LINE-1 elements, which comprise approximately 40% of the human genome. The ability of retrotransposons to expand and colonize eukaryotic genomes has rendered them evolutionarily successful and is responsible for creating genetic alterations leading to significant impacts on their hosts. Previous research suggested that hypomethylation of Alu and LINE-1 elements is associated with global hypomethylation and genomic instability in several types of cancer and diseases, such as neurodegenerative diseases, obesity, osteoporosis, and diabetes mellitus (DM). With the advancement of sequencing technologies and computational tools, the study of the retrotransposon's association with physiology and diseases is becoming a hot topic among researchers. Quantifying Alu and LINE-1 methylation is thought to serve as a surrogate measurement of global DNA methylation level. Although Alu and LINE-1 hypomethylation appears to serve as a cellular senescence biomarker promoting genomic instability, there is sparse information available regarding their potential functional and biological significance in DM. This review article summarizes the current knowledge on the involvement of the main epigenetic alterations in the methylation status of Alu and LINE-1 retrotransposons and their potential role as epigenetic markers of global DNA methylation in the pathogenesis of DM.

Different effects of bariatric surgery on epigenetic plasticity in skeletal muscle of individuals with and without type 2 diabetes

AIM

Bariatric surgery is highly effective for the treatment of obesity in individuals without (OB1) and in those with type 2 diabetes (T2D2). However, whether bariatric surgery triggers similar or distinct molecular changes in OB and T2D remains unknown. Given that individuals with type 2 diabetes often exhibit more severe metabolic deterioration, we hypothesized that bariatric surgery induces distinct molecular adaptations in skeletal muscle, the major site of glucose uptake, of OB and T2D after surgery-induced weight loss.

METHODS

All participants (OB, n = 13; T2D, n = 13) underwent detailed anthropometry before and one year after the surgery. Skeletal muscle biopsies were isolated at both time points and subjected to transcriptome and methylome analyses using a comprehensive bioinformatic pipeline.

RESULTS

Before surgery, T2D had higher fasting glucose and insulin levels but lower whole-body insulin sensitivity, only glycemia remained higher in T2D than in OB after surgery. Surgery-mediated weight loss affected different subsets of genes with 2,013 differentially expressed in OB and 959 in T2D. In OB differentially expressed genes were involved in insulin, PPAR signaling and oxidative phosphorylation pathways, whereas ribosome and splicesome in T2D. LASSO regression analysis revealed distinct candidate genes correlated with improvement of phenotypic traits in OB and T2D. Compared to OB, DNA methylation was less affected in T2D in response to bariatric surgery. This may be due to increased global hydroxymethylation accompanied by decreased expression of one of the type 2 diabetes risk gene, TET2, encoding a demethylation enzyme in T2D.

CONCLUSION

OB and T2D exhibit differential skeletal muscle transcriptome responses to bariatric surgery, presumably resulting from perturbed epigenetic flexibility.

Effects of obesity, and of weight loss following bariatric surgery, on methylation of DNA from the rectal mucosa and in cell-free DNA from blood

BACKGROUND

DNA methylation is an epigenetic mechanism through which environmental factors including nutrition and inflammation influence health. Obesity is a major modifiable risk factor for many common diseases including cardiovascular diseases and cancer. In particular, obesity-induced inflammation resulting from aberrantly-methylated inflammatory genes may drive risk of several non-communicable diseases including colorectal cancer (CRC). This study is the first to investigate the effects of weight loss induced by bariatric surgery (BS) on DNA methylation in the rectum and in cell-free DNA (cfDNA) from blood.

SUBJECTS AND METHODS

DNA methylation was quantified in rectal mucosal biopsies and cfDNA from serum of 28 participants with obesity before and 6 months after BS, as well as in 12 participants without obesity (control group) matched for age and sex from the Biomarkers Of Colorectal cancer After Bariatric Surgery (BOCABS) Study. DNA methylation of LEP, IL6, POMC, LINE1, MAPK7 and COX2 was quantified by pyrosequencing.

RESULTS

BMI decreased significantly from 41.8 kg/m2 pre-surgery to 32.3 kg/m2 at 6 months after BS. Compared with the control group, obesity was associated with lower LEP methylation in both the rectal mucosa and in cfDNA from serum. BS normalised LEP methylation in DNA from the rectal mucosa but not in cfDNA. BS decreased methylation of some CpG sites of LINE1 in the rectal mucosal DNA and in cfDNA to levels comparable with those in participants without obesity. Methylation of POMC in rectal mucosal DNA was normalised at 6 months after BS.

CONCLUSION

BS reversed LINE1, POMC and LEP methylation in the rectal mucosa of patients with obesity to levels similar to those in individuals without obesity. These findings support current evidence of effects of BS-induced weight loss on reversibility of DNA methylation in other tissues. The DNA methylation changes in the rectal mucosa shows promise as a biomarker for objective assessment of effects of weight loss interventions on risk of cancer and other diseases.

DNA Methylation Remodeling after Bariatric Surgery Correlates with Clinical Parameters

The altered functions of adipose tissue are one of the main issues in obesity. Bariatric surgery is associated with improvement of obesity associated comorbidities. Here DNA methylation remodeling in adipose tissue after bariatric surgery is examined. After six months postoperative, DNA methylation shows changes in 1155 CpG sites, 66 of these sites correlate with body mass index. Some sites also show correlation with LDL-C, HDL-C, total cholesterol, and triglycerides. CpG sites are located in genes that have not previously been linked to obesity or metabolic diseases. GNAS complex locus is one of those that presented CpG site with the greatest changes after surgery, and the most significant correlation with BMI and lipid profiles. These results show that epigenetic regulation may be involved in the alteration of adipose tissue functions in obesity.

Clinical epigenetics and restoring of metabolic health in severely obese patients undergoing batriatric and metabolic surgery

Epigenetic-sensitive mechanisms, mainly DNA methylation, mirror the relationship between environmental and genetic risk factors able to affect the sensitiveness to development of obesity and its comorbidities. Bariatric and metabolic surgery may reduce obesity-related cardiovascular risk through tissue-specific DNA methylation changes. Among the most robust results, differential promoter methylation of ACACA, CETP, CTGF, S100A8, and S100A9 genes correlated significantly with the levels of mRNA before and after gastric bypass surgery (RYGB) in obese women. Additionally, promoter hypermethylation of NFKB1 gene was significantly associated with reduced blood pressure in obese patients after RYGB suggesting useful non-invasive biomarkers. Of note, sperm-related DNA methylation signatures of genes regulating the central control of appetite, such as MC4R, BDNF, NPY, and CR1, and other genes including FTO, CHST8, and SH2B1 were different in obese patients as compared to non-obese subjects and patients who lost weight after RYGB surgery. Importantly, transgenerational studies provided relevant evidence of the potential effect of bariatric and metabolic surgery on DNA methylation. For example, peripheral blood biospecimens isolated from siblings born from obese mothers before bariatric surgery showed different methylation signatures in the insulin receptor and leptin signaling axis as compared to siblings born from post-obese mothers who underwent surgery. This evidence suggests that bariatric and metabolic surgery of mothers may affect the epigenetic profiles of the offspring with potential implication for primary prevention of severe obesity. We update on tissue-specific epigenetic signatures as potential mechanisms underlying the restoration of metabolic health after surgery suggesting useful predictive biomarkers.

SERPINE-1 Gene Methylation and Protein as Molecular Predictors of Laparoscopic Sleeve Gastrectomy Outcome

BACKGROUND

Body weight is subjected to genetic and epigenetic modifiers that might affect the success of weight loss interventions. Because of its possible complications and disparity in patients' response, identification of predictors to the outcome of bariatric surgery is indispensable.

OBJECTIVES

This prospective study aims to investigate serpin peptidase inhibitor type 1 (SERPINE-1) protein and gene methylation as molecular predictors to the outcome of bariatric surgery.

PATIENTS AND METHODS

One hundred participants were enrolled and divided to control group (n = 50) and obese patients who underwent laparoscopic sleeve gastrectomy (LSG) (n = 50). Anthropometric measurements were assessed and blood samples were collected preoperatively and 6 months postoperatively for assessment of SERPINE-1 protein and gene methylation, C-reactive protein (CRP), and homeostatic model assessment of insulin resistance (HOMA-IR). Moreover, subjects were followed for 2 years for weight loss parameters.

RESULTS

Patients with obesity showed high baseline SERPINE-1 protein and gene hypermethylation where LSG was followed by a drop in SERPINE-1 protein level but not gene hypermethylation. Baseline SERPINE-1 gene methylation was negatively related to postoperative weight loss and was the independent predictor to weight loss after LSG. Likewise, postoperative SERPINE-1 protein was negatively related to weight loss with independent expression from its gene methylation state. Furthermore, postoperative SERPINE-1 gene methylation correlated to CRP and HOMA-IR.

CONCLUSION

Baseline SERPINE-1 gene methylation might be a predictor of weight loss after LSG. Meanwhile, postoperative SERPINE-1 protein could be a predictor to weight loss maintenance after LSG. Lastly, postoperative SERPINE-1 gene methylation might serve as an index to postoperative changes in obesity-related comorbidities.

Effects of bariatric surgery on DNA methylation in adults: a systematic review and meta-analysis

BACKGROUND

DNA methylation is an epigenetic mechanism through which environmental factors, including obesity, influence health. Obesity is a major modifiable risk factor for many common diseases, including cardiovascular diseases and cancer. Obesity-induced metabolic stress and inflammation are key mechanisms that affect disease risk and that may result from changes in methylation of metabolic and inflammatory genes.

OBJECTIVES

This review aims to report the effects of weight loss induced by bariatric surgery (BS) on DNA methylation in adults with obesity focusing on changes in metabolic and inflammatory genes.

METHODS

A systematic review was performed using MEDLINE, EMBASE, and Scopus, to identify studies in adult humans that reported DNA methylation after BS.

RESULTS

Of 15,996 screened titles, 15 intervention studies were identified, all of which reported significantly lower body mass index postsurgery. DNA methylation was assessed in 5 different tissues (blood = 7 studies, adipose tissues = 4, skeletal muscle = 2, liver, and spermatozoa). Twelve studies reported significant changes in DNA methylation after BS. Meta-analysis showed that BS increased methylation of PDK4 loci in skeletal muscle and blood in 2 studies, while the effects of BS on IL6 methylation levels in blood were inconsistent. BS had no overall effect on LINE1 or PPARGC1 methylation.

CONCLUSION

The current evidence supports the reversibility of DNA methylation at specific loci in response to BS-induced weight loss. These changes are consistent with improved metabolic and inflammatory profiles of patients after BS. However, the evidence regarding the effects of BS on DNA methylation in humans is limited and inconsistent, which makes it difficult to combine and compare data across studies.

Meta-Analysis of Differential miRNA Expression after Bariatric Surgery

Bariatric surgery is an efficient treatment for weight loss in obese patients and for resolving obesity comorbidities. However, the mechanisms behind these outcomes are unclear. Recent studies have indicated significant alterations in the transcriptome after surgery, specifically in the differential expression of microRNAs. In order to summarize the recent findings, we conducted a systematic summary of studies comparing microRNA expression levels before and after surgery. We identified 17 animal model and human studies from four databases (Ovid, Scopus, Web of Science, and PubMed) to be enrolled in this meta-analysis. From these studies, we identified 14 miRNAs which had the same direction of modulation of their expression after surgery in at least two studies (downregulated: hsa-miR-93-5p, hsa-miR-106b-5p, hsa-let-7b-5p, hsa-let-7i-5p, hsa-miR-16-5p, hsa-miR-19b-3p, hsa-miR-92a-3p, hsa-miR-222-3p, hsa-miR-142-3p, hsa-miR-140-5p, hsa-miR-155-5p, rno-miR-320-3p; upregulated: hsa-miR-7-5p, hsa-miR-320c). Pathway analysis for these miRNAs was done using database resources (DIANA-TarBase and KEGG pathway database) and their predicted target genes were discussed in relation with obesity and its comorbidities. Discrepancies in study design, such as miRNA source, bariatric surgery type, time of observation after surgery, and miRNA profiling methods, were also discussed.

DNA methylation screening after roux-en Y gastric bypass reveals the epigenetic signature stems from genes related to the surgery per se

Background/objectives

Obesity has been associated with gene methylation regulation. Recent studies have shown that epigenetic signature plays a role in metabolic homeostasis after Roux-en Y gastric bypass (RYGB). To conduct a genome-wide epigenetic analysis in peripheral blood to investigate whether epigenetic changes following RYGB stem from weight loss or the surgical procedure per se.

Subjects/methods

By means of the Infinium Human Methylation 450 BeadChip array, global methylation was analyzed in blood of 24 severely obese women before and 6 months after RYGB and in 24 normal-weight women (controls).

Results

In blood cells, nine DMCpG sites showed low methylation levels before surgery, methylation levels increased after RYGB and neared the levels measured in the controls. Additionally, 44 CpG sites associated with the Wnt and p53 signaling pathways were always differently methylated in the severely obese patients as compared to the controls and were not influenced by RYGB. Finally, 1638 CpG sites related to inflammation, angiogenesis, and apoptosis presented distinct methylation in the post-surgery patients as compared to the controls.

Conclusion

Bariatric surgery per se acts on CpGs related to inflammation, angiogenesis, and endothelin-signaling. However, the gene cluster associated with obesity remains unchanged, suggesting that weight loss 6 months after RYGB surgery cannot promote this effect.

Graphical abstract

Electronic supplementary material

The online version of this article (10.1186/s12920-019-0522-7) contains supplementary material, which is available to authorized users.

LINE-1 in Obesity and Cardiometabolic Diseases: A Systematic Review

Epigenetic mechanisms may play an important role in the etiology of obesity and cardiometabolic diseases, by activating or silencing the related-genes. Scientific evidence has suggested that LINE-1 methylation is associated with body composition and obesity-related diseases, including insulin resistance, type 2 diabetes mellitus, and cardiovascular disease (CVD). It also has been evaluated as predictor of weight loss. The studies' results are still conflicting, and positive and negative associations have been found to LINE-1 methylation regarding adiposity and cardiometabolic markers. Overall, this review presents observational (cross-sectional and longitudinal) studies and interventions (diet, exercises, and bariatric surgery) that evaluated the relationship of the LINE-1 methylation with obesity, weight loss, dyslipidemias, hypertension, insulin resistance, CVD, and metabolic syndrome. TEACHING POINTS Epigenetic mechanisms may play an important role in the etiology of obesity and cardiometabolic diseases. Many studies have related methylation of LINE-1 with cardiometabolic diseases; however, the results are still controversial. The relationship between the etiology of chronic diseases and the methylation of LINE-1 is not fully elucidated. With advances in epigenetic studies, related mechanisms may be early biomarkers in weight change and cardiometabolic risk.

Obesity-Related Epigenetic Changes After Bariatric Surgery

Objective: In recent years, an increasing number of studies have begun focusing on epigenetics as a link between environmental factors and a greater predisposition to the development of obesity and its comorbidities. An important challenge in this field is the evaluation of the possibility of the reversal of obesity-related epigenetic marks by means of therapy to induce weight loss and if the beneficial effects of therapy in reducing obesity are mediated by epigenetic mechanisms. We aimed to offer an outline of the current results regarding to the impact of bariatric surgery on epigenetic regulation, as well as to show if the beneficial effect of this intervention could be mediated by epigenetic mechanisms. Methods: A review of the scientific publications in PubMed was performed by using key words related to obesity, epigenetics and bariatric surgery to provide an update of recent findings in this area of research. The most relevant and recently published articles and abstracts were selected to frame this review. Results: Previous studies have demonstrated the presence of differential DNA methylation after bariatric surgery and the differential expression of non-coding RNAs. Therefore, epigenetic regulation could mediate the benefit of bariatric surgery on body weight and the metabolic disturbances associated with excess body weight, such as insulin resistance, hypertension, and cardiovascular disease. This evidence is relatively new as epigenetic regulation was first evaluated in the obesity field only a few years ago. However, there is an urgent need to perform longitudinal studies to evaluate the capacity of epigenetic marks in the prediction of bariatric surgery response. Conclusions: Bariatric surgery appears to be capable of partially reversing the obesity-related epigenome. The identification of potential epigenetic biomarkers predictive for the success of bariatric surgery may open new doors to personalized therapy for severe obesity.

Decreased blood pressure is related to changes in NF-kB promoter methylation levels after bariatric surgery

BACKGROUND

Obesity is characterized by a chronic, low-grade inflammation, and bariatric surgery is proposed as an effective treatment for reducing the obesity-related co-morbidities. Epigenetic modifications could be involved in the metabolic improvement after surgery.

OBJECTIVE

The main aim of this study was to evaluate whether DNA methylation pattern from genes related to inflammation and insulin response is associated with the metabolic improvement after bariatric surgery in morbidly obese patients and if these changes depend on the surgical procedure.

SETTING

University hospital, Spain.

METHODS

We studied 60 severely obese patients; 31 underwent Roux-en-Y gastric bypass and 29 underwent laparoscopic sleeve gastrectomy. All patients were examined before and at 6 months after bariatric surgery. DNA methylation profile of genes related to the inflammatory response and insulin sensitivity was measured by pyrosequencing.

RESULTS

The promoter methylation levels of the NFKB1 gene were increased significantly after surgery (2.16 ± .9 versus 2.8 ± 1.03). The decrease in blood pressure, both systolic and diastolic, after surgery was significantly associated with the changes in the promoter methylation levels of the NFKB1 gene (β = -.513, P = .003 and β = -.543, P = .004, respectively). A decrease in inflammation status, measured by high sensitivity C-reactive protein values, was associated with changes in SLC19A1 methylation levels.

CONCLUSION

Our study shows for the first time an association between NFKB1 methylation levels and blood pressure after bariatric surgery, highlighting the possible function of this gene in the regulation of arterial pressure. Regarding SLC19A1, this gene could position as a potential target linking inflammation and insulin resistance.

Bariatric Surgery and Precision Nutrition

This review provides a literature overview of new findings relating nutritional genomics and bariatric surgery. It also describes the importance of nutritional genomics concepts in personalized bariatric management. It includes a discussion of the potential role bariatric surgery plays in altering the three pillars of nutritional genomics: nutrigenetics, nutrigenomics, and epigenetics. We present studies that show the effect of each patient's genetic and epigenetic variables on the response to surgical weight loss treatment. We include investigations that demonstrate the association of single nucleotide polymorphisms with obesity phenotypes and their influence on weight loss after bariatric surgery. We also present reports on how significant weight loss induced by bariatric surgery impacts telomere length, and we discuss studies on the existence of an epigenetic signature associated with surgery outcomes and specific gene methylation profile, which may help to predict weight loss after a surgical procedure. Finally, we show articles which evidence that bariatric surgery may affect expression of numerous genes involved in different metabolic pathways and consequently induce functional and taxonomic changes in gut microbial communities. The role nutritional genomics plays in responses to weight loss after bariatric surgery is evident. Better understanding of the molecular pathways involved in this process is necessary for successful weight management and maintenance.

The Effect of Metabolic and Bariatric Surgery on DNA Methylation Patterns

PURPOSE OF REVIEW

Metabolic and bariatric surgery (MBS) is considered to be the most effective treatment for obesity. Not only due to the significant weight reduction but also because of the many health benefits associated with it. In the last 5 years, several studies have suggested that epigenetic modifications could be involved in the mechanisms underlying the response to bariatric surgery. In this review, we will compile the different studies (2012-2017) concerning the effect of this surgical procedure on DNA methylation patterns (the most studied epigenetic marker) and its association with metabolic improvement. This is an emerging area, and currently, there are not many studies in the literature. The aim is to show what has been done so far and what the future direction in this emerging area might be.

RECENT FINDINGS

Recent findings have shown how metabolic and bariatric surgery modifies the DNA methylation profile of the specific genes associated with the pathophysiology of the disease. The studies were performed in morbidly obese subjects, mainly in women, with the aim of reducing weight and improving the obesity-associated comorbidities. DNA methylation has been measured both in specific tissue and in peripheral blood samples. In general, studies about site-specific DNA methylation have shown a change in the methylation profile after surgery, whereas the studies analyzing global DNA methylation are not so conclusive. Summing up, metabolic and bariatric surgery can modify the DNA methylation profile of different genes and contributes to the metabolic health benefits that are often seen after metabolic and bariatric surgery. Although there are still many issues to be resolved, the capacity to revert the DNA methylation profile of specific sites opens a window for searching for target markers to treat obesity-related comorbidities.

Clinical significance of expression of proliferating cell nuclear antigen and E-cadherin in gastric carcinoma

AIM

to investigate the expression of proliferating cell nuclear antigen (PCNA) and E-cadherin in gastric carcinoma and to analyze their clinical significance.

METHODS

A total of 146 patients were selected for this study, including 38 patients with intestinal metaplasia, 42 with dysplasia, and 66 with primary gastric cancer. In addition, 40 patients with normal gastric tissues were selected as controls. The expression of PCNA and E-cadherin was detected by immunohistochemistry. Differences in PCNA and the E-cadherin labeling indexes among normal gastric mucosa, intestinal metaplasia, dysplasia, and gastric carcinoma were compared. Subjects with normal gastric tissues were assigned to a normal group, while gastric cancer patients were assigned to a gastric cancer group. The difference in PCNA and E-cadherin expression between these two groups was compared. The relationship between expression of PCNA and E-cadherin and clinicopathological features was also explored in gastric cancer patients. Furthermore, prognosis-related factors, as well as the expression of PCNA and E-cadherin, were analyzed in patients with gastric cancer to determine the 3-year survival of these patients.

RESULTS

The difference in PCNA and the E-cadherin labeling indexes among normal gastric mucosa, intestinal metaplasia, dysplasia, and gastric carcinoma was statistically significant (P < 0.05). During the transition of normal gastric mucosa to gastric cancer, the PCNA labeling index gradually increased, while the E-cadherin labeling index gradually decreased (P < 0.05). The PCNA labeling index was significantly higher and the E-cadherin labeling index was significantly lower in gastric cancer than in dysplasia (P < 0.05). The expression of PCNA was significantly higher in the gastric cancer group than in the normal group, but E-cadherin was weaker (P < 0.05). There was a negative correlation between the expression of PCNA and E-cadherin in gastric carcinoma (r = -0.741, P = 0.000). PCNA expression differed significantly between gastric cancer patients with and without lymph node metastasis and between patients at different T stages. E-cadherin expression also differed significantly between gastric cancer patients with and without lymph node metastasis (P < 0.05). High T stage and positive PCNA expression were risk factors for the prognosis of patients with gastric cancer (RR > 1), while the positive expression of E-cadherin was a protective factor (RR < 1). The sensitivity, specificity, and accuracy of PCNA positivity in predicting the 3-year survival of patients with gastric cancer were 93.33%, 38.89%, and 0.64, respectively; while these values for E-cadherin negativity were 80.0%, 41.67%, and 0.59, respectively. When PCNA positivity and E-cadherin negativity were combined, the sensitivity, specificity, and accuracy were 66.67%, 66.67%, and 0.67, respectively.

CONCLUSION

Combined detection of PCNA and E-cadherin can improve the accuracy of assessing the prognosis of patients with gastric cancer.