Epigenetic alterations in the gastrointestinal tract: Current and emerging use for biomarkers of cancer

An overview of potential of natural compounds to regulate epigenetic modifications in colorectal cancer: a recent update

Colorectal cancer (CRC) remains an alarming global health concern despite advancements in treatment modalities over recent decades. Among the various factors contributing to CRC, this review emphasizes the critical role of epigenetic mechanisms in its pathogenesis and progression. This review also describes the potential role of natural compounds in altering the epigenetic landscape, focused mainly on DNA methylation, histone modification, and non-coding RNAs. Publications from the previous five years were searched and retrieved using well-known search engines and databases like PubMed, Google Scholar, and ScienceDirect. Keywords like CRC/colorectal cancer, CAC/Colitis associated CRC, inflammasomes, epigenetic modulation, genistein, curcumin, quercetin, resveratrol, anthocyanins, sulforaphane, and epigallocatechin-3-gallate were used in various combinations during the search. These natural compounds predominantly affect pathways such as Wnt/β-catenin, NF-κB, and PI3K/AKT to suppress CRC cell proliferation and oxidative stress and enhance anti-inflammation and apoptosis. However, their clinical use is restricted due to their low bioavailability. However, multiple methods exist to overcome challenges like this, including but not limited to structural modifications, nanoparticle encapsulations, bio-enhancers, and novel advanced delivery systems. These methods improve their potential as supportive therapies that target CRC progression epigenetically with fewer side effects. Current research focuses on enhancing epigenetic targeting to control CRC progression while minimizing side effects, emphasizing improved specificity, bioavailability, and efficacy as standalone or synergistic therapies.

Role of SMYD2 in gastrointestinal cancer progression (Review)

Gastrointestinal cancer is one of the most prevalent malignancies in humans and is often associated with a poor prognosis. Understanding the molecular mechanisms underlying cancer progression and severity is essential for the development of effective cancer therapies. Abnormal protein methylation is associated with the occurrence and advancement of cancer, highlighting the importance of protein methyltransferase research. SET and MYND domain-containing protein 2 (SMYD2), a lysine methyltransferase, has emerged as a promising small molecule target for cancer treatment. Notably, SMYD2 is implicated in the pathogenesis of several diseases, including gastrointestinal cancer. SMYD2 is closely associated with the tumorigenesis, proliferation, migration and other biological processes of gastrointestinal cancer, indicating its potential as a novel therapeutic target. The present review offers an in-depth analysis of SMYD2, covering its structural characteristics, regulatory pathways and functional significance. By assessing the biological roles and therapeutic potential of SMYD2, the current review presents fresh insights and perspectives for advancing research in different types of gastrointestinal cancer.

Helicobacter pylori induces GBA1 demethylation to inhibit ferroptosis in gastric cancer

This research investigates potential therapeutic targets for gastric cancer, focusing on ferroptosis-related genes. Gastric cancer is known for its lower survival rates, necessitating new treatment strategies. This study employed Mendelian randomization to identify ferroptosis-related genes and methylation sites in gastric cancer, examining correlations between Helicobacter pylori infection, GBA1 gene expression, and promoter methylation with single-cell datasets and the TCGA-STAD database. We used Helicobacter pylori-infected gastric cancer cell models and used next-generation sequencing to monitor methylation changes pre- and post-infection. GBA1 expression levels were assessed via qRT-PCR and Western blot both before and after infection. The effect of Helicobacter pylori on GC cell proliferation was analyzed using CCK-8 and EdU assays after knocking down the GBA1 gene. The association between Helicobacter pylori infection and ferroptosis, including its reversibility after GBA1 knockdown, was evaluated using FerrOrange, GSH, MDA, and C11-BODIPY assays. Mass spectrometry measured the impact of Helicobacter pylori and GBA1 knockdown on lipid metabolism. An in vivo subcutaneous tumor-bearing model was also established to confirm these findings. Mendelian randomization analysis revealed that high GBA1 expression and reduced methylation levels of its promoter are risk factors for gastric cancer. Single-cell sequencing and TCGA-STAD datasets indicated a positive correlation between Helicobacter pylori infection and GBA1 expression, with a concurrent negative correlation between GBA1 promoter methylation and GBA1 expression. In gastric cancer cell lines, Helicobacter pylori infection was observed to enhance GBA1 expression and decrease methylation levels at its promoter. Additionally, Helicobacter pylori promoted GC cell proliferation, an effect mitigated by knocking down GBA1. Infection also reduced lipid peroxidation, increased glutathione levels, and impeded ferroptosis in GC cells; however, these effects were reversed following GBA1 knockdown. Changes in sphingolipid metabolism induced by I were detected in GC cell lines. In vivo experiments using a subcutaneous tumor-bearing model demonstrated that Helicobacter pylori infection fosters tumorigenesis in GC cells. Our study demonstrates that Helicobacter pylori infection triggers demethylation and upregulation of GBA1, subsequently inhibiting ferroptosis in gastric cancer cells. These findings suggest that targeting the GBA1 pathway may offer a novel therapeutic approach for managing gastric cancer.

Distinct genomic, transcriptomic, and immune profiles for tumor and non-tumor mucosal regions in early gastric cancer

In early gastric cancer, local recurrence develops after endoscopic resection by field cancerization. Understanding the nature of cancer-prone environments is important to establish effective strategies to prevent recurrence. We hypothesized that the molecular/immune profiles in non-tumor (cancer-prone) tissue differ according to the relative distance from the gastric tumor. For this purpose, we performed whole-exome and transcriptome sequencing of 16 early gastric cancer samples with paired non-tumor mucosa 1 cm (N1) and 3 cm (N3) away from the tumor. The whole exome sequencing revealed mutations in both the tumor and non-tumor mucosa. TTN was the most frequently altered gene in tumors (31 %) and was the second most frequently altered gene in N1 (25 %) samples; however, the mutation rate was significantly lower in N3 (12 %) samples (P = 0.0046). Moreover, the expression levels of TTN mRNA were higher in tumors than in the N1 and N3 samples and were significantly associated with TTN mutations (P = 0.04). TP53 mutations were mainly observed in tumors (50 %) and in 6.3 % of N1, with no mutation detected in N3 samples. Transcriptome sequencing revealed that the expression of the epithelial-mesenchymal transition signature, mesenchymal signature, and proliferation signature was increased in tumors, whereas programmed death-ligand 1 expression was decreased in the non-tumor mucosa. In the tumor, although the numbers of M0/M1 macrophages, neutrophils, and eosinophils increased, plasma cell numbers were markedly decreased compared to non-tumor mucosa. In conclusion, non-tumor mucosa at 1 cm and 3 cm from the tumor harbored different genomic, transcriptomic, and immune cell profiles. The non-tumor mucosa closer to the tumor (1 cm) exhibited similar genomic and transcriptomic features. These findings can offer clinical guidance for acquiring a safe horizontal margin in endoscopic resection for early gastric cancer.

Deciphering the potential role of post-translational modifications of histones in gastrointestinal cancers: a proteomics-based review with therapeutic challenges and opportunities

Oncogenesis is a complex and multi-step process, controlled by several factors including epigenetic modifications. It is considered that histone modifications are critical components in the regulation of gene expression, protein functions, and molecular interactions. Dysregulated post-translationally modified histones and the related enzymatic systems are key players in the control of cell proliferation and differentiation, which are associated with the onset and progression of cancers. The most of traditional investigations on cancer have focused on mutations of oncogenes and tumor suppressor genes. However, increasing evidence indicates that epigenetics, especially histone post-translational modifications (PTMs) play important roles in various cancer types. Mass spectrometry-based proteomic approaches have demonstrated tremendous potential in PTMs profiling and quantitation in different biological systems. In this paper, we have made a proteomics-based review on the role of histone modifications involved in gastrointestinal cancers (GCs) tumorigenesis processes. These alterations function not only as diagnostic or prognostic biomarkers for GCs, but a deeper comprehension of the epigenetic regulation of GCs could facilitate the treatment of this prevalent malignancy through the creation of more effective targeted therapies.

Erythropoietin-induced hepatocyte receptor A2 regulates effect of pyroptosis on gastrointestinal colorectal cancer occurrence and metastasis resistance

Erythropoietin-induced hepatocyte receptor A2 (EphA2) is a receptor tyrosine kinase that plays a key role in the development and progression of a variety of tumors. This article reviews the expression of EphA2 in gastrointestinal (GI) colorectal cancer (CRC) and its regulation of pyroptosis. Pyroptosis is a form of programmed cell death that plays an important role in tumor suppression. Studies have shown that EphA2 regulates pyrodeath through various signaling pathways, affecting the occurrence, development and metastasis of GI CRC. The overexpression of EphA2 is closely related to the aggressiveness and metastasis of GI CRC, and the inhibition of EphA2 can induce pyrodeath and improve the sensitivity of cancer cells to treatment. In addition, EphA2 regulates intercellular communication and the microenvironment through interactions with other cytokines and receptors, further influencing cancer progression. The role of EphA2 in GI CRC and its underlying mechanisms provide us with new perspectives and potential therapeutic targets, which have important implications for future cancer treatment.

Alteration in DNA methylation patterns: Epigenetic signatures in gastrointestinal cancers

Abnormalities in epigenetic modifications can cause malignant transformations in cells, leading to cancers of the gastrointestinal (GI) tract, which accounts for 20% of all cancers worldwide. Among the epigenetic alterations, DNA hypomethylation is associated with genomic instability. In addition, CpG methylation and promoter hypermethylation have been recognized as biomarkers for different malignancies. In GI cancers, epigenetic alterations affect genes responsible for cell cycle control, DNA repair, apoptosis, and tumorigenic-specific signaling pathways. Understanding the pattern of alterations in DNA methylation in GI cancers could help scientists discover new molecular-based pharmaceutical treatments. This study highlights alterations in DNA methylation in GI cancers. Understanding epigenetic differences among GI cancers may improve targeted therapies and lead to the discovery of new diagnostic biomarkers.

Human patient derived organoids: an emerging precision medicine model for gastrointestinal cancer research

Gastrointestinal cancers account for approximately one-third of the total global cancer incidence and mortality with a poor prognosis. It is one of the leading causes of cancer-related deaths worldwide. Most of these diseases lack effective treatment, occurring as a result of inappropriate models to develop safe and potent therapies. As a novel preclinical model, tumor patient-derived organoids (PDOs), can be established from patients' tumor tissue and cultured in the laboratory in 3D architectures. This 3D model can not only highly simulate and preserve key biological characteristics of the source tumor tissue in vitro but also reproduce the in vivo tumor microenvironment through co-culture. Our review provided an overview of the different in vitro models in current tumor research, the derivation of cells in PDO models, and the application of PDO model technology in gastrointestinal cancers, particularly the applications in combination with CRISPR/Cas9 gene editing technology, tumor microenvironment simulation, drug screening, drug development, and personalized medicine. It also elucidates the ethical status quo of organoid research and the current challenges encountered in clinical research, and offers a forward-looking assessment of the potential paths for clinical organoid research advancement.

A Green Synthesis of Au-Ag Alloy Nanoparticles using Polydopamine Chemistry: Evaluation of their Anticancer Potency Towards Both MCF-7 Cells and their Cancer Stem Cells Subgroup

BACKGROUND

Limited chemotherapy efficacy and cancer stem cells (CSCs)-induced therapeutic resistance are major difficulties for tumour treatment. Adopting more efficient therapies to eliminate bulk-sensitive cancer cells and resistant CSCs is urgently needed.

METHODS

Based on the potential and functional complementarity of gold and silver nanoparticles (AuNPs or AgNPs) on tumour treatment, bimetallic NPs (alloy) have been synthesized to obtain improved or even newly emerging bioactivity from a combination effect. This study reported a facile, green and economical preparation of Au-Ag alloy NPs using biocompatible polydopamine (PDA) as a reductant, capping, stabilizing and hydrophilic agent.

RESULTS

These alloy NPs were quasi-spherical with rough surfaces and recorded in diameters of 80 nm. In addition, these alloy NPs showed good water dispersity, stability and photothermal effect. Compared with monometallic counterparts, these alloy NPs demonstrated a dramatically enhanced cytotoxic/pro-apoptotic/necrotic effect towards bulk-sensitive MCF-7 and MDA-MB-231 cells. The underlying mechanism regarding the apoptotic action was associated with a mitochondria-mediated pathway, as evidenced by Au3+/Ag+ mediated Mitochondria damage, ROS generation, DNA fragmentation and upregulation of certain apoptotic-related genes (Bax, P53 and Caspase 3). Attractively, these Au-Ag alloy NPs showed a remarkably improved inhibitory effect on the mammosphere formation capacity of MCF-7 CSCs.

CONCLUSION

All the positive results were attributed to incorporated properties from Au, Ag and PDA, the combination effect of chemotherapy and photothermal therapy and the nano-scaled structure of Au-Ag alloy NPs. In addition, the high biocompatibility of Au-Ag alloy NPs supported them as a good candidate in cancer therapy.

NAT10 mediated mRNA acetylation modification patterns associated with colon cancer progression and microsatellite status

N4-acetylcytidine (ac4C) is one type of RNA modification found in eukaryotes. RNA acetylation modifications are gradually expanding in oncology. However, the role of RNA acetylation modifications in colorectal cancer and its association with colorectal cancer microsatellite status remain unclear. Using public databases and in vitro experiments, we verified the expression and biological function of NAT10, as the key RNA acetylation modification enzyme, in colorectal cancer. The results showed that NAT10 was highly expressed in colorectal cancer, and significantly promoted colorectal cancer cell proliferation. NAT10 was also involved in several aspects of cell homoeostasis such as ion transport, calcium-dependent phospholipid binding, and RNA stability. NAT10 expression positively correlated with immune infiltration in colorectal cancer. We further constructed a risk regression model for mRNA acetylation in colorectal cancer using acetylation-related differential genes. We found that tumour immune infiltration, microsatellite instability (MSI) proportion, tumour immune mutation burden, and patient response to immunotherapy were positively correlated with risk scores. For the first time, our study showed that the level of mRNA acetylation modification level is elevated in colorectal cancer and positively correlates with immune infiltration and microsatellite status of patients. Based on our findings, NAT10 may be a new target for colorectal cancer treatment.

Risk stratification of gastric cancer screening in community population based on oral contrast-enhanced ultrasonography examination: A 3-year follow-up analysis report

Objective

This study aimed to retrospectively investigate the use of oral contrast-enhanced ultrasonography (O-CEUS) in assessing the thickness of the gastric wall for gastric cancer (GC) screening and to establish screening strategies for GC with different risk stratifications based on the gastric wall thickness.

Methods

From January 2015 to March 2020, people who underwent O-CEUS at the Physical Examination Center of our hospital with at least three years of follow-up were included in this study. The thickness of the gastric wall measured by O-CEUS was divided into three groups using 6 mm and 9 mm as cutoff values. The occurrence of GC in each group was observed. The imaging and clinical information of these populations were recorded and analyzed. Kaplan-Meier survival analysis and Cox's proportional hazards regression were performed to calculate the risk of GC occurrence.

Results

A total of 4,047 people were finally included in this study. During the follow-up period, GC occurred in 7 individuals (incidence rate 0.17%). Among them, according to the thickness of the gastric wall, one case occurred in Group A (< 6 mm), two cases occurred in Group B (6-9 mm), and four cases occurred in Group C (>9mm). Based on Kaplan-Meier survival analysis, the curves of the three groups were significantly different (P < 0.01). The risk of GC occurrence in Group C and Group B were higher than that in Group A (4.76E+2-fold and 1.50E+2-fold).

Conclusion

O-CEUS is a convenient, economical, safe, and noninvasive screening method for GC. Measuring the thickness of the gastric wall is helpful to predict the risk of GC occurrence according to our stratification screening system.

Unveiling the genetic and epigenetic landscape of colorectal cancer: new insights into pathogenic pathways

Colorectal cancer (CRC) is a complex disease characterized by genetic and epigenetic alterations, playing a crucial role in its development and progression. This review aims to provide insights into the emerging landscape of these alterations in CRC pathogenesis to develop effective diagnostic tools and targeted therapies. Genetic alterations in signaling pathways such as Wnt/β-catenin, and PI3K/Akt/mTOR are pivotal in CRC development. Genetic profiling has identified distinct molecular subtypes, enabling personalized treatment strategies. Epigenetic modifications, including DNA methylation and histone modifications, also contribute to CRC pathogenesis by influencing critical cellular processes through gene silencing or activation. Non-coding RNAs have emerged as essential players in epigenetic regulation and CRC progression. Recent research highlights the interplay between genetic and epigenetic alterations in CRC. Genetic mutations can affect epigenetic modifications, leading to dysregulated gene expression and signaling cascades. Conversely, epigenetic changes can modulate genetic expression, amplifying or dampening the effects of genetic alterations. Advancements in understanding pathogenic pathways have potential clinical applications. Identifying genetic and epigenetic markers as diagnostic and prognostic biomarkers promises more accurate risk assessment and early detection. Challenges remain, including validating biomarkers and developing robust therapeutic strategies through extensive research and clinical trials. The dynamic nature of genetic and epigenetic alterations necessitates a comprehensive understanding of their temporal and spatial patterns during CRC progression. In conclusion, the genetic and epigenetic landscape of CRC is increasingly being unraveled, providing valuable insights into its pathogenesis. Integrating genetic and epigenetic knowledge holds great potential for improving diagnostics, prognostics, and personalized therapies in CRC. Continued research efforts are vital to translate these findings into clinical practice, ultimately improving patient outcomes.

Bidirectional Mediation Effects between Intratumoral Microbiome and Host DNA Methylation Changes Contribute to Stomach Adenocarcinoma

The induction of aberrant DNA methylation is the major pathway by which Helicobacter pylori infection induces stomach adenocarcinoma (STAD). The involvement of the non-H. pylori gastric microbiota in this mechanism remains to be examined. RNA sequencing data, clinical information, and DNA methylation data were obtained from The Cancer Genome Atlas (TCGA) STAD project. The Kraken 2 pipeline was employed to explore the microbiome profiles. The microbiome was associated with occurrence, distal metastasis, and prognosis, and differential methylation changes related to distal metastasis and prognosis were analyzed. Bi-directional mediation effects of the intratumoral microbiome and host DNA methylation changes on the metastasis and prognosis of STAD were identified by mediation analysis. The expression of the ZNF215 gene was verified by real-time quantitative PCR (RT-qPCR). A cell counting kit 8 (CCK8) cell proliferation experiment and a cell clone formation experiment were used to evaluate the proliferation and invasion abilities of gastric cells. Our analysis revealed that H. pylori and other cancer-related microorganisms were related to the occurrence, progression, or prognosis of STAD. The related methylated genes were particularly enriched in related cancer pathways. Kytococcus sedentarius and Actinomyces oris, which interacted strongly with methylation changes in immune genes, were associated with prognosis. Cell experiments verified that Staphylococcus saccharolyticus could promote the proliferation and cloning of gastric cells by regulating the gene expression level of the ZNF215 gene. Our study suggested that the bi-directional mediation effect between intratumoral microorganisms and host epigenetics was key to the distal metastasis of cancer cells and survival deterioration in the tumor microenvironment of stomach tissues of patients with STAD. IMPORTANCE The burgeoning field of oncobiome research declared that members of the intratumoral microbiome besides Helicobacter pylori existed in tumor tissues and participated in the occurrence and development of gastric cancer, and the methylation of host DNA may be a potential target of microbes and their metabolites. Current research focuses mostly on species composition, but the functional genes of the members of the microbiota are also key to their interaction with the host. Therefore, we focused on characterizing the species composition and functional gene composition of microbes in gastric cancer, and we suggest that microbes may further participate in the occurrence and development of cancer by influencing abnormal epigenetic changes in the host. Some key bioinformatics analysis results were verified by in vitro experiments. Thus, we consider that the tumor microbiota-host epigenetic axis of gastric cancer microorganisms and the host explains the mechanism of the microbiota participating in cancer occurrence and development, and we make some verifiable experimental predictions.

Prognosis and survival study in patients with gastric adenocarcinoma and its relationship with pRb expression alteration: A retrospective IHC-based study

Background and Objective

Among cancers, gastric cancer has the fifth highest incidence worldwide and is the third most common mortality factor, which may have been due to inadequate knowledge of its molecular pathogenesis. The retinoblastoma gene (RB1), a tumor suppressor gene, may have a role in gastric cancer. This research aims to assess Rb expression as a prognostic marker to obtain more insight regarding gastric cancer.

Methods

This retrospective analytical study was done on 61 patients (45 males and 16 females) with gastric adenocarcinoma admitted from 2010 to 2012 in Shahid Sadoughi and Mortaz hospitals, Yazd, Iran. Demographic data, including age, gender, clinical signs and symptoms, and pathology reports, were retrieved from patients' hospital folders. Then, the altered Retinoblastoma gene expression was evaluated by immunohistochemistry studies. Acquired data were analyzed by SPSS software v.16. p < 0.05 was statistically considered meaningful.

Results

In this study, the ratio of men to women was higher (2.81:1), and the mean age of patients was 62.44 years. About 90.2% of patients died during the study. There was no meaningful relationship between the presence of pRb, the intensity of staining, the percentage of staining with patients' age, gender, tumor grading, and survival rate (p > 0.05). There was only a meaningful relationship between the grade of tumors and survival rate (p = 0.039).

Conclusion

Altered pRB expression is not common in gastric cancer and does not impact the survival and grading of tumors. Poorly differentiated tumors had an ominous outcome with the lowest survival time.

Epigenetic orchestration of host immune defences by Mycobacterium tuberculosis

Being among the top 10 causes of adult deaths, tuberculosis (TB) disease is considered a major global public health concern to address. The human tuberculosis pathogen, Mycobacterium tuberculosis (Mtb), is an extremely competent and well-versed pathogen that promotes pathogenesis by evading the host immune systems through numerous tactics. Investigations revealed that Mtb could evade the host defense mechanisms by reconfiguring the host gene transcription and causing epigenetic changes. Although results indicate the link between epigenetics and disease manifestation in other bacterial infections, little is known regarding the kinetics of the epigenetic alterations in mycobacterial infection. This literature review discusses the studies in Mtb-induced epigenetic alterations inside the host and its contribution in the host immune evasion strategies. It also discusses how the Mtb-induced alterations could be used as 'epibiomarkers' to diagnose TB. Additionally, this review also discusses therapeutic interventions to be enhanced through remodification by 'epidrugs'.

DNMT3b affects colorectal cancer development by regulating FLI1 through DNA hypermethylation

Friend leukemia integration 1 (FLI1) is an ETS transcription factor family member. Here, we identified cg11017065 as the most hyper-methylated cytosine and guanine (CpG) in colorectal cancer (CRC), which belongs to the FLI1 gene. Moreover, integrated bioinformatics prediction and analysis of our cohort showed that FLI1 expression was downregulated and DNA methylation was elevated in CRC. Bioinformatics prediction also indicated that patients overexpressing FLI1 had higher survival rates than those with low FLI1 expression. CRC cells with ectopic expression of FLI1 had reduced invasion, migration, cloning ability and increased apoptosis. Furthermore, DNA-methyltransferase 3b (DNMT3b) was found to be significantly overexpressed in CRC, and low DNMT3b expression predicted a prolonged survival. DNMT3b bound to the FLI1 promoter. Inhibition of DNMT3b increased FLI1 expression and inhibited the malignant phenotype of CRC cells. Inhibition of FLI1 reversed the phenotypic modulation by DNMT3b depletion in vitro and in vivo. In conclusion, our data indicate that DNMT3b potentiates CRC cell proliferation, migration, and invasion through downregulating FLI1.

Association between multiple gene promoter hypermethylation and the risk of gastric cancer: A systematic review and meta-analysis

BACKGROUND

Several studies have demonstrated an association between multiple gene hypermethylation and gastric cancer. However, the intrinsic mechanisms remain elusive and highly debatable. To this end, our study aims to investigate the correlation between the methylation status of multiple gene promoters and gastric cancer.

METHODS

PubMed, EMBASE, CNKI, WanFang, Cqvip, and Cochrane Library were queried from inception to May 2021, and the relationship between the methylation status of the CpG islands and gastric cancer risk was systematically assessed under the inclusion and exclusion criteria. The incidence of DNA methylation between tumor and non-tumor tissues was compared, and the clinicopathological significance of DNA methylation in gastric carcinoma was further evaluated. The odds ratio (OR) was estimated with a 95% confidence interval (CI), and forest plots were generated using the fixed-effects or random-effects model.

RESULTS

In total, 201 studies were enrolled, and a higher frequency of CpG islands methylation was identified in gastric cancer tissues than in non-neoplastic tissues. This suggests that aberrant polygene methylation might be associated with the initial onset and progression of gastric cancer.

CONCLUSION

This study sheds light on the significance of polygene methylation status in gastric cancer. The DNA methylation of these genes may serve as underlying epigenetic biomarkers, providing a promising molecular diagnostic approach for human gastric cancer clinical diagnosis. More large randomized trials are needed to confirm the findings.

A Comprehensive Study on the Anti-cancer Effects of Quercetin and Its Epigenetic Modifications in Arresting Progression of Colon Cancer Cell Proliferation

Colon cancer etiology involves a wide spectrum of genetic and epigenetic alterations, finding it challenging to find effective therapeutic strategies. Quercetin exhibits potent anti-proliferative/apoptotic properties. In the present study, we aimed to elucidate the anti-cancer and anti-aging effect of quercetin in colon cancer cell lines. The anti-proliferative effect of quercetin was assessed in vitro by CCK-8 in normal and colon cancer cell lines. To check the anti-aging potential of quercetin, collagenase, elastase, and hyaluronidase inhibitory activity assays were performed. The epigenetic and DNA damage assays were performed using the human NAD-dependent deacetylase Sirtuin-6, proteasome 20S, Klotho, Cytochrome-C, and telomerase ELISA kits. Furthermore, the aging-associated miRNA expression profiling was performed on colon cancer cells. The treatment with quercetin inhibited cell proliferation of colon cancer cells in a dose-dependent manner. Quercetin arrested colon cancer cell growth by modulating expression of aging proteins including Sirtuin-6 and Klotho and also by inhibiting telomerase activity to restrict the telomere length which is evident from qPCR analysis. Quercetin also exhibited DNA damage protection by reducing proteasome 20S levels. The miRNA expression profiling results displayed differential expression of miRNA in colon cancer cell, and in addition, the highly upregulated miRNA was involved in the regulation of cell cycle, proliferation, and transcription. Our data suggest that quercetin treatment inhibited cell proliferation in colon cancer cells through regulating the anti-aging protein expression and provides better understanding for quercetin's potential use in colon cancer treatment.

Altered genome‑wide hydroxymethylation analysis for neoadjuvant chemoradiotherapy followed by surgery in esophageal cancer

Esophageal cancer has high incidence rate in China. Neoadjuvant chemoradiotherapy (nCRT) has become the standard treatment for esophageal squamous cell carcinoma (ESCC). However, there are few reliable epigenetic parameters for patients with ESCC undergoing neoadjuvant therapy. Genomic extract from tumor tissue was amplified and sequenced using the Illumina HiSeq4000 to quantify genes associated methylation or hydromethylation in 12 patients with ESCC undergoing nCRT. The genome-wide hydroxymethylation were analyzed by methylated and hydroxymethylated DNA immunoprecipitation sequencing by MACS2 software and UCSC RefSeq database. Abnormal DNA methylation was statistically different between nCRT-well (showed a pathological complete response to nCRT) and nCRT-poor (showed incomplete pathological response to nCRT) patients. Levels of ten-eleven translocation 1, 2 and 3 mRNA and protein were higher in tumor tissue in nCRT-well group patients than in nCRT-poor group patients. Illumina HiSeq 4000 sequencing identified 2925 hypo-differentially hydroxymethylated region (DhMRs) and 292 hyper-DhMRs in promoter between nCRT-well and nCRT-poor patients. Biological processes associated with hyper-DhMRs included 'snRNA processing', 'hormone-mediated signaling pathway' and 'cellular response'. Metabolic processes were associated with hypo-DhMRs. These data may explain the functional response to nCRT in patients with abnormal promoter of methylation gene-associated mRNA expression. The present results implied that hyper-DhMRs and hypo-DhMRs affect molecular pathways, such as hippo and Notch signaling pathways, highlighting epigenetic modifications associated with clinical response to nCRT in patients with esophageal cancer.

Changes in the Fecal Metabolome Accompany an Increase in Aberrant Crypt Foci in the Colon of C57BL/6 Mice Fed with a High-Fat Diet

High-fat diet (HFD)-induced obesity is a risk factor for colon cancer. Our previous data show that compared to an AIN-93 diet (AIN), a HFD promotes azoxymethane (AOM)-induced colonic aberrant crypt foci (ACF) formation and microbial dysbiosis in C57BL/6 mice. To explore the underlying metabolic basis, we hypothesize that AOM treatment triggers a different fecal metabolomic profile in C57BL/6 mice fed the HFD or the AIN. We found that 65 of 196 identified metabolites were significantly different among the four groups of mice (AIN, AIN + AOM, HFD, and HFD + AOM). A sparse partial least squares discriminant analysis (sPLSDA) showed that concentrations of nine fecal lipid metabolites were increased in the HFD + AOM compared to the HFD, which played a key role in overall metabolome group separation. These nine fecal lipid metabolite concentrations were positively associated with the number of colonic ACF, the cell proliferation of Ki67 proteins, and the abundance of dysbiotic bacteria. These data suggest that the process of AOM-induced ACF formation may increase selective fecal lipid concentrations in mice fed with a HFD but not an AIN. Collectively, the accumulation of these critical fecal lipid species may alter the overall metabolome during tumorigenesis in the colon.

CIMP-positive glioma is associated with better prognosis: A systematic analysis

BACKGROUND

CpG island methylator phenotype (CIMP) was closely related to the degree of pathological differentiation of tumors, and it's an important determinant of glioma pathogenicity. However, the molecular and pathological features of CIMP-positive glioma have not been fully elucidated. In addition, CIMP have been reported to be a useful prognostic marker in several human cancers, yet its prognostic value in gliomas is still controversial. Therefore, we aimed to evaluate gene mutations and pathological features of CIMP-positive glioma and explore the prognostic value of CIMP in gliomas.

METHODS

We comprehensively searched PubMed, Embase, and MEDLINE for studies describing gene mutations, pathological features and overall survival of gliomas stratified by CIMP status. Odds ratios (OR), hazard ratios (HR), and their 95% confidence intervals (CI) were used to estimate the correlation between CIMP and the outcome parameters.

RESULTS

Twelve studies with 2386 gliomas (1051 CIMP-positive and 1335 CIMP-negative) were included. Our results showed that CIMP was more frequent in isocitrate dehydrogenase 1 (IDH1)-mutated gliomas (OR 229.07; 95% CI 138.72-378.26) and 1p19q loss of heterozygosis (LOH) gliomas (OR 5.65; 95% CI 2.66-12.01). Pathological analysis showed that CIMP was common in low-malignant oligodendroglioma (OR 5.51; 95% CI 3.95-7.70) with molecular features including IDH1 mutations and 1p19q LOH, but rare in glioblastoma (OR 0.14; 95% CI 0.10-0.19). However, CIMP showed no obvious correlation with anaplastic oligoastrocytomas (OR 1.57; 95% CI 1.24-2.00) or oligoastrocytomas (OR 0.79; 95% CI 0.35-1.76). Concerning the prognosis, we found that CIMP-positive gliomas had longer overall survival (HR 0.57; 95% CI 0.97-0.16) than CIMP-negative gliomas.

CONCLUSIONS

CIMP could be used as a potential independent prognostic indicator for glioma.

Green Synthesis of Gold Nanoparticles and Study of Their Inhibitory Effect on Bulk Cancer Cells and Cancer Stem Cells in Breast Carcinoma

Chemo-resistance from cancer stem cells (CSCs) subpopulation is a current issue in cancer treatment. It is important to select alternative therapies to efficiently eradicate both bulk cancer cells and CSCs. Here, gold nanoparticles (AuNPs) have been selected regarding their biocompatibility, facile and controllable synthesis, potent anti-cancer activity and photothermal conversion performance. We reported a green synthesis of functionalized AuNPs using hyaluronic acid (HA) as a reductant, capping, stabilizing and hydrophilic substance. The resultant AuNPs were spherical-shaped with an average diameter of around 30 nm. These AuNPs displayed improved physico-chemical (yield, stability, photothermal effect) and biological properties (cellular uptake, cytotoxicity and apoptotic effect) against bulk MDA-MB-231 cells, in comparison with other organic anti-cancer drugs. The intensified bioactivity was dependent on a mitochondria-mediated cascade, reflected by the damage in mitochondria, oxidative stress, intensified Caspase 3 activity and increased/decreased expression of certain pro-apoptotic (Bax, P53, Caspase 3)/anti-apoptotic (Bcl-2) genes. Moreover, these AuNPs posed a dramatically improved inhibitory effect in cell viability and self-renewable capacity on CSC subpopulation. All the results were attributed from the nano-scaled structure of AuNPs and combined effect from NIR-induced hyperthermia. In addition, the biocompatible nature of these AuNPs supported them to be a potential candidate in the development of novel chemotherapeutic drugs.

Gastrointestinal Tract Polyp Anomaly Segmentation on Colonoscopy Images Using Graft-U-Net

Computer-aided polyp segmentation is a crucial task that supports gastroenterologists in examining and resecting anomalous tissue in the gastrointestinal tract. The disease polyps grow mainly in the colorectal area of the gastrointestinal tract and in the mucous membrane, which has protrusions of micro-abnormal tissue that increase the risk of incurable diseases such as cancer. So, the early examination of polyps can decrease the chance of the polyps growing into cancer, such as adenomas, which can change into cancer. Deep learning-based diagnostic systems play a vital role in diagnosing diseases in the early stages. A deep learning method, Graft-U-Net, is proposed to segment polyps using colonoscopy frames. Graft-U-Net is a modified version of UNet, which comprises three stages, including the preprocessing, encoder, and decoder stages. The preprocessing technique is used to improve the contrast of the colonoscopy frames. Graft-U-Net comprises encoder and decoder blocks where the encoder analyzes features, while the decoder performs the features’ synthesizing processes. The Graft-U-Net model offers better segmentation results than existing deep learning models. The experiments were conducted using two open-access datasets, Kvasir-SEG and CVC-ClinicDB. The datasets were prepared from the large bowel of the gastrointestinal tract by performing a colonoscopy procedure. The anticipated model outperforms in terms of its mean Dice of 96.61% and mean Intersection over Union (mIoU) of 82.45% with the Kvasir-SEG dataset. Similarly, with the CVC-ClinicDB dataset, the method achieved a mean Dice of 89.95% and an mIoU of 81.38%.

Epigenetic regulation of autophagy in gastrointestinal cancers

The development of novel therapeutic approaches is necessary to manage gastrointestinal cancers (GICs). Considering the effective molecular mechanisms involved in tumor growth, the therapeutic response is pivotal in this process. Autophagy is a highly conserved catabolic process that acts as a double-edged sword in tumorigenesis and tumor inhibition in a context-dependent manner. Depending on the stage of malignancy and cellular origin of the tumor, autophagy might result in cancer cell survival or death during the GICs' progression. Moreover, autophagy can prevent the progression of GIC in the early stages but leads to chemoresistance in advanced stages. Therefore, targeting specific arms of autophagy could be a promising strategy in the prevention of chemoresistance and treatment of GIC. It has been revealed that autophagy is a cytoplasmic event that is subject to transcriptional and epigenetic regulation inside the nucleus. The effect of epigenetic regulation (including DNA methylation, histone modification, and expression of non-coding RNAs (ncRNAs) in cellular fate is still not completely understood. Recent findings have indicated that epigenetic alterations can modify several genes and modulators, eventually leading to inhibition or promotion of autophagy in different cancer stages, and mediating chemoresistance or chemosensitivity. The current review focuses on the links between autophagy and epigenetics in GICs and discusses: 1) How autophagy and epigenetics are linked in GICs, by considering different epigenetic mechanisms; 2) how epigenetics may be involved in the alteration of cancer-related phenotypes, including cell proliferation, invasion, and migration; and 3) how epidrugs modulate autophagy in GICs to overcome chemoresistance.

Gene Characteristics and Prognostic Values of m6A RNA Methylation Regulators in Nonsmall Cell Lung Cancer

Background

N⁶-methyladenosine (m⁶A) is the most common internal modification present in mRNAs and long noncoding RNAs (lncRNAs), associated with tumorigenesis and cancer progression. However, little is known about the roles of m⁶A and its regulatory genes in nonsmall cell lung cancer (NSCLC). Here, we systematically explored the roles and prognostic significance of m⁶A-associated regulatory genes in NSCLC.

Methods

The copy number variation (CNV), mutation, mRNA expression data, and corresponding clinical pathology information of 1057 NSCLC patients were downloaded from the cancer genome atlas (TCGA) database. The gain and loss levels of CNVs were determined by utilizing segmentation analysis and GISTIC algorithm. The GSEA was conducted to explore the functions related to different levels of m⁶A regulatory genes. Logrank test was utilized to assess the prognostic significance of m⁶A-related gene's CNV.

Results

The genetic alterations of ten m⁶A-associated regulators were identified in 102 independent NSCLC samples and significantly related to advanced tumor stage. Deletions or shallow deletions corresponded to lower mRNA expression while copy number gains or amplifications were related to increased mRNA expression of m⁶A regulatory genes. Survival analysis showed the patients with copy number loss of FTO with worse disease-free survival (DFS) or overall survival (OS). Besides, copy number loss of YTHDC2 was also with poor OS for NSCLC patients. Moreover, high FTO expression was significantly associated with oxidative phosphorylation, translation, and metabolism of mRNA.

Conclusion

Our findings provide novel insight for better understanding of the roles of m⁶A regulators and RNA epigenetic modification in the pathogenesis of NSCLC.