DNA methylation profiles in cancer diagnosis and therapeutics

Polymeric immunoglobulin receptor (pIgR) in cancer progression: a critical role and potential therapeutic target

Polymeric immunoglobulin receptor (pIgR) is a crucial receptor that primarily mediates the transcytosis of immunoglobulins A and M across epithelial cells, emerging as an essential participant in modulating both mucosal immunity and innate immunity. Recently, pIgR dysregulation in cancer has garnered widespread attention. It exhibits distinct mechanisms and effects across various cancer types with significant clinical value as a biomarker for malignant tumor diagnosis and prognosis evaluation. Recent therapeutic advances have revealed promising strategies, including dimeric IgA-based approaches targeting intracellular oncogenic drivers through pIgR-mediated transcytosis, small molecule modulators such as bufalin, and targeting EV-pIgR with neutralizing antibodies. Integrating these approaches with conventional therapies presents opportunities for enhanced treatment efficacy. Specifically, blocking EV-pIgR with neutralizing antibodies, when integrated with conventional hepatocellular carcinoma therapies such as sorafenib or other therapeutic agents, or a dIgA-targeting approach combined with immune checkpoint inhibitors, may enhance treatment efficacy. This review also addresses current challenges and future directions in pIgR-targeted cancer therapy, emphasizing the need for a deeper understanding of pIgR's regulatory mechanisms. These insights reveal that pIgR is an emerging therapeutic target with significant potential for the development of novel cancer treatment strategies.

STEAP Proteins: Roles in disease biology and potential for therapeutic intervention

Iron and copper are essential metal ions, and maintaining their metabolic balance is critical for organismal health. The Six-Transmembrane Epithelial Antigen of the Prostate (STEAP) protein family, comprising STEAP1, STEAP2, STEAP3, and STEAP4, plays a vital role in cellular metal homeostasis. These proteins are located on the cell membrane and are characterized by six transmembrane domains. With the exception of STEAP1, the STEAP proteins function as metal oxidoreductases due to their F420H2:NADP+ oxidoreductase (FNO)-like domain. However, STEAP1 contributes to metal metabolism through its heme group and interaction with other STEAP proteins. Beyond metal metabolism, STEAP proteins are involved in critical cellular processes, including the regulation of the cell cycle, proliferation, differentiation, and apoptosis. Notably, STEAP proteins are recognized as potential biomarkers and therapeutic targets in human cancers, particularly prostate cancer. This review outlines the structural features and functional roles of STEAP proteins in various diseases, including cancers, insulin resistance, non-alcoholic fatty liver disease (NAFLD), and benign prostatic hyperplasia, with a focus on their potential for therapeutic intervention.

Translational Advances in Oncogene and Tumor-Suppressor Gene Research

Cancer, characterized by the uncontrolled proliferation of cells, is one of the leading causes of death globally, with approximately one in five people developing the disease in their lifetime. While many driver genes were identified decades ago, and most cancers can be classified based on morphology and progression, there is still a significant gap in knowledge about genetic aberrations and nuclear DNA damage. The study of two critical groups of genes-tumor suppressors, which inhibit proliferation and promote apoptosis, and oncogenes, which regulate proliferation and survival-can help to understand the genomic causes behind tumorigenesis, leading to more personalized approaches to diagnosis and treatment. Aberration of tumor suppressors, which undergo two-hit and loss-of-function mutations, and oncogenes, activated forms of proto-oncogenes that experience one-hit and gain-of-function mutations, are responsible for the dysregulation of key signaling pathways that regulate cell division, such as p53, Rb, Ras/Raf/ERK/MAPK, PI3K/AKT, and Wnt/β-catenin. Modern breakthroughs in genomics research, like next-generation sequencing, have provided efficient strategies for mapping unique genomic changes that contribute to tumor heterogeneity. Novel therapeutic approaches have enabled personalized medicine, helping address genetic variability in tumor suppressors and oncogenes. This comprehensive review examines the molecular mechanisms behind tumor-suppressor genes and oncogenes, the key signaling pathways they regulate, epigenetic modifications, tumor heterogeneity, and the drug resistance mechanisms that drive carcinogenesis. Moreover, the review explores the clinical application of sequencing techniques, multiomics, diagnostic procedures, pharmacogenomics, and personalized treatment and prevention options, discussing future directions for emerging technologies.

Nanotechnology-leveraged CRISPR/Cas systems: icebreaking in trace cancer-related nucleic acids biosensing

As promising noninvasive biomarkers, nucleic acids provide great potential to innovate cancer early detection methods and promote subsequent diagnosis to improve the survival rates of patient. Accurate, straightforward and sensitive detection of such nucleic acid-based cancer biomarkers in complex biological samples holds significant clinical importance. However, the low abundance creates huge challenges for their routine detection. As the next-generation diagnostic tool, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated protein (Cas) with their high programmability, sensitivity, fidelity, single-base resolution, and precise nucleic acid positioning capabilities are extremely attractive for trace nucleic acid-based cancer biomarkers (NABCBs), permitting rapid, ultra-sensitive and specific detection. More importantly, by combing with nanotechnology, it can solve the long-lasting problems of poor sensitivity, accuracy and simplicity, as well as to achieve integrated miniaturization and portable point-of-care testing (POCT) detection. However, existing literature lacks specific emphasis on this topic. Thus, we intend to propose a timely one for the readers. This review will bridge this gap by providing insights for CRISPR/Cas-based nano-biosensing development and highlighting the current state-of-art, challenges, and prospects. We expect that it can provide better understanding and valuable insights for trace NABCBs detection, thereby facilitating advancements in early cancer screening/detection/diagnostics and win practical applications in the foreseeable future.

Integrative analysis of DNA methylation and gene expression in skin cutaneous melanoma by bioinformatic approaches

Skin cutaneous melanoma represents a significant threat among skin cancers. Investigating key methylated genes with prognostic implications remains an area ripe for exploration in this field. This study aims to identify survival-associated methylated genes and their specific methylation sites in skin cutaneous melanoma through integrated bioinformatic analysis. Utilizing data from the Cancer Genome Atlas database, gene methylation and expression files were analyzed. The results indicate that patients with skin cutaneous melanoma exhibiting high expression of hypomethylated HHEX experience better outcomes compared to those with low expression of hypermethylated HHEX. Furthermore, fifteen methylation sites within HHEX were found to significantly correlate with its expression levels. Expression of HHEX demonstrated a downward trend across pathological stages I-IV. The identified driven gene, HHEX, likely plays a crucial role in the survival of skin cutaneous melanoma patients. These findings provide new epigenetic insights and potential targets for early prognosis prediction in skin cutaneous melanoma.

Molecular profiling of breast cancer methylation pattern in triple negative versus non- triple negative breast cancer

Epigenetic alterations, especially promotor methylation, have a significant impact on gene expression, molecular subtyping, prognosis, and outcome of breast cancer (BC). The methylation profile was assessed for 22 genes of the BC tissue using the EpiTect Methyl II PCR System in 40 triple-negative BC (TNBC) patients compared to 50 non-TNBC group. The data were corelated with the disease-free (DFS) and overall survival (OS) of the patients. Genes that were differentially hypermethylated in TNBC patients compared to those with non-TNBC included CCND2, CDKN2A, ESR1, CDH1, BRCA1, GSTP, RASSF1, SLIT2, MGMT, PTEN, TP73, and PRDM2. These panel achieved 95% sensitivity, 98% specificity, 97.44% positive predictive value (PPV), 94.23% negative predictive value (NPV), and AUC of 0.993. Hypermethylation of BRCA1, CDH1, CDKN2A, ESR1, GSTP, HIC1, MGMT, PRDM2, PTEN, PYCARDM, RASSF1M, THBS1, and TP73 associated significantly with worse OS and DFS in TNBC cohort. Meanwhile, CCNA1 and CDH1 hypermethylation demonstrated significant associations with poor DFS but did not show significant relationships with OS in TNBC patients. PTGS2 and TNFRSF10C methylation were associated with better DFS and OS rates in TNBC patients. On multivariate Cox regression, CCND2 and PTEN hypermethylation were independent predictors of DFS in the overall BC patients. The hypermethylation of BRCA1 and GSTP were independent predictors of DFS, while PTEN hypermethylation was an independent predictor of OS in the TNBC cohort. The identification of hypermethylated genes, such as BRCA1, CCND2, CDH1, ESR1, GSTP, RASSF1, SLIT2, MGMT, and PTEN may serve as potential biomarkers or therapeutic targets for TNBC.

Epigene functional diversity: isoform usage, disordered domain content, and variable binding partners

BACKGROUND

Epigenes are defined as proteins that perform post-translational modification of histones or DNA, reading of post-translational modifications, form complexes with epigenetic factors or changing the general structure of chromatin. This specialized group of proteins is responsible for controlling the organization of genomic DNA in a cell-type specific fashion, controlling normal development in a spatial and temporal fashion. Moreover, mutations in epigenes have been implicated as causal in germline pediatric disorders and as driver mutations in cancer. Despite their importance to human disease, to date, there has not been a systematic analysis of the sources of functional diversity for epigenes at large. Epigenes' unique functions that require the assembly of pools within the nucleus suggest that their structure and amino acid composition would have been enriched for features that enable efficient assembly of chromatin and DNA for transcription, splicing, and post-translational modifications.

RESULTS

In this study, we assess the functional diversity stemming from gene structure, isoforms, protein domains, and multiprotein complex formation that drive the functions of established epigenes. We found that there are specific structural features that enable epigenes to perform their variable roles depending on the cellular and environmental context. First, epigenes are significantly larger and have more exons compared with non-epigenes which contributes to increased isoform diversity. Second epigenes participate in more multimeric complexes than non-epigenes. Thirdly, given their proposed importance in membraneless organelles, we show epigenes are enriched for substantially larger intrinsically disordered regions (IDRs). Additionally, we assessed the specificity of their expression profiles and showed epigenes are more ubiquitously expressed consistent with their enrichment in pediatric syndromes with intellectual disability, multiorgan dysfunction, and developmental delay. Finally, in the L1000 dataset, we identify drugs that can potentially be used to modulate expression of these genes.

CONCLUSIONS

Here we identify significant differences in isoform usage, disordered domain content, and variable binding partners between human epigenes and non-epigenes using various functional genomics datasets from Ensembl, ENCODE, GTEx, HPO, LINCS L1000, and BrainSpan. Our results contribute new knowledge to the growing field focused on developing targeted therapies for diseases caused by epigene mutations, such as chromatinopathies and cancers.

Unveiling DNA methylation: early diagnosis, risk assessment, and therapy for endometrial cancer

Endometrial cancer (EC), one of the most common gynecologic malignancies worldwide, poses a significant burden particularly among young women, with poor treatment outcomes and prognosis for advanced and recurrent patients. Epigenetic changes, encompassing DNA methylation, are involved in the occurrence and progression of tumors and hold promise as effective tools for screening, early diagnosis, treatment strategy, efficacy evaluation, and prognosis analysis. This review provides a comprehensive summary of DNA methylation-based early diagnostic biomarkers in EC, with a focus on recent valuable research findings published in the past two years. The discussion is organized according to sample sources, including cervical scraping, vaginal fluid, urine, blood, and tissue. Additionally, we outline the role of DNA methylation in EC risk assessment, such as carcinogenesis risk, feasibility of fertility preservation approaches, and overall prognosis, aiming to provide personalized treatment decisions for patients. Finally, we review researches on DNA methylation in resistance to first-line treatment of EC and the development of new drugs, and envision the future applications of DNA methylation in EC.

Lysine acetylation and its role in the pathophysiology of acute pancreatitis

Acute pancreatitis (AP) represents a severe inflammatory condition of the exocrine pancreas, precipitating systemic organ dysfunction and potential failure. The global prevalence of acute pancreatitis is on an ascending trajectory. The condition carries a significant mortality rate during acute episodes. This underscores the imperative to elucidate the etiopathogenic pathways of acute pancreatitis, enhance comprehension of the disease's intricacies, and identify precise molecular targets coupled with efficacious therapeutic interventions. The pathobiology of acute pancreatitis encompasses not only the ectopic activation of trypsinogen but also extends to disturbances in calcium homeostasis, mitochondrial impairment, autophagic disruption, and endoplasmic reticulum stress responses. Notably, the realm of epigenetic regulation has garnered extensive attention and rigorous investigation in acute pancreatitis research over recent years. One of these modifications, lysine acetylation, is a reversible post-translational modification of proteins that affects enzyme activity, DNA binding, and protein stability by changing the charge on lysine residues and altering protein structure. Numerous studies have revealed the importance of acetylation modification in acute pancreatitis, and that it is a favorable target for the design of new drugs for this disease. This review centers on lysine acetylation, examining the strides made in acute pancreatitis research with a focus on the contributory role of acetylomic alterations in the pathophysiological landscape of acute pancreatitis, thereby aiming to delineate novel therapeutic targets and advance the development of more efficacious treatment modalities.

Multiomic characterization, immunological and prognostic potential of SMAD3 in pan-cancer and validation in LIHC

SMAD3, a protein-coding gene, assumes a pivotal role within the transforming growth factor-beta (TGF-β) signaling pathway. Notably, aberrant SMAD3 expression has been linked to various malignancies. Nevertheless, an extensive examination of the comprehensive pan-cancer impact on SMAD3's diagnostic, prognostic, and immunological predictive utility has yet to be undertaken. Bioinformatics methods were employed to systematically investigate the potential carcinogenic impact of SMAD3. We extensively harnessed data from authoritative sources, including The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression (GTEx), cBioPortal, Human Protein Atlas (HPA), UALCAN, and various other databases. Our study encompassed a comprehensive analysis of the following aspects: differential SMAD3 expression and its association with prognosis across diverse cancer types, gene mutations, immune cell infiltration, single-cell sequencing analysis, DNA methylation patterns, and drug sensitivity profiles. In vitro experiments were conducted with the primary objective of appraising both the expression profile and the precise functional attributes of SMAD3 within the milieu of Liver Hepatocellular Carcinoma (LIHC). Our findings revealed significant variations in SMAD3 expression between cancerous and adjacent normal tissues. High levels of SMAD3 expression were consistently associated with unfavorable prognoses across multiple cancer types,. Additionally, our analysis of SMAD3 methylation patterns in human cancers unveiled a favorable prognosis linked to elevated DNA methylation levels in pan-cancer. Furthermore, we identified positive associations between SMAD3 expression and RNAm6A methylation-related genes in the majority of cancers. Moreover, SMAD3 expression displayed substantial correlations with immune cell infiltration. Notably, immune checkpoint genes exhibited significant associations with SMAD3 expression across diverse cancers. Single-cell sequencing results elucidated the pan-cancer single-cell expression landscape of SMAD3. Within specific cancer subtypes, SMAD3 expression exhibited a noteworthy positive association with distinctive facets of malignancy. Finally, in our comprehensive analysis of drug sensitivity, we discerned a catalog of prospective therapeutic agents. In our comprehensive analysis across multiple cancer types, we observed a significant disparity in SMAD3 expression compared to normal tissues, and this findings suggest that SMAD3 holds promise as both a prognostic biomarker and a therapeutic target against various cancers. Difference displayed a noteworthy association with patient prognosis.

miR-143-3p/TET1 Axis Regulates GPC1 Through DNA Methylation and Impairs the Malignant Biological Behaviour of HCC via the Hippo Signalling Pathway

Hepatocellular carcinoma (HCC) is a malignant tumour that poses a serious threat to human health and places a heavy burden on individuals and society. However, the role of GPC1 in the malignant progression of HCC is unknown. In this study, we analysed the expression of GPC1 in HCC, and its association with poor patient prognosis. The effects of GPC1 on the proliferation, invasion and migration of HCC were analysed through cellular functional experiments in vitro and in vivo. Mechanistically, DNA methylation of GPC1 was analysed by DNA extraction, methylation-specific PCR and bisulfite Sanger sequencing (BSP), and the target genes TET1 and miRNA regulating DNA methylation of GPC1 were found through the bioinformatics database. The results revealed that GPC1 was highly expressed in HCC, and its high expression was significantly associated with poor prognosis of HCC patients. Inhibiting the expression of GPC1 can inhibit the proliferation, invasion and migration of HCC cells. GPC1 was hypomethylated in HCC, and its methylation level was regulated by TET1. miR-143-3p can significantly regulated the expression of TET1 and affect the methylation level and protein expression of GPC1. Furthermore, GPC1 also affects the malignant biological behaviour of HCC by regulating the expression of Hippo signalling pathway. In summary, miR-143-3p regulates the expression of TET1, affects the expression of GPC1 through DNA methylation and regulates the malignant progression of HCC via Hippo signalling pathway.

A two-phase epigenome-wide four-way gene-smoking interaction study of overall survival for early-stage non-small cell lung cancer

High-order interactions associated with non-small cell lung cancer (NSCLC) survival may elucidate underlying molecular mechanisms and identify potential therapeutic targets. Our previous work has identified a three-way interaction among pack-year of smoking (the number of packs of cigarettes smoked per day multiplied by the number of years the person has smoked) and two DNA methylation probes (cg05293407TRIM27 and cg00060500KIAA0226). However, whether a four-way interaction exists remains unclear. Therefore, we adopted a two-phase design to identify the four-way gene-smoking interactions by a hill-climbing strategy on the basis of the previously detected three-way interaction. One CpG probe, cg16658473SHISA9, was identified with FDR-q ≤ 0.05 in the discovery phase and P ≤ 0.05 in the validation phase. Meanwhile, the four-way interaction improved the discrimination ability for the prognostic prediction model, as indicated by the area under the receiver operating characteristic curve (AUC) for both 3- and 5-year survival. In summary, we identified a four-way interaction associated with NSCLC survival among pack-year of smoking, cg05293407TRIM27, cg00060500KIAA0226 and g16658473SHISA9, providing novel insights into the complex mechanisms underlying NSCLC progression.

CTSG is a prognostic marker involved in immune infiltration and inhibits tumor progression though the MAPK signaling pathway in non-small cell lung cancer

PURPOSE

This study aims to investigate the biological roles and molecular mechanisms of Cathepsin G (CTSG) in the progression of non-small cell lung cancer (NSCLC).

METHODS

Western blotting and immunohistochemistry analyses of clinical samples were performed to determine the expression levels of CTSG in patients with NSCLC. Bioinformatic analysis of clinical datasets was conducted to evaluate the correlation between CTSG and lymph node metastasis, tumor stage, and immune cell infiltration. Gain-of-function assays and tumor implantation experiments were employed to determine the effects of CTSG on malignant behaviors of NSCLC cells. Transcriptome sequencing and subsequent bioinformatic analysis were performed to explore the signaling pathways regulated by CTSG. Western blotting and qPCR were utilized to assess the influence of CTSG on the MAPK and EMT signaling pathways.

RESULTS

CTSG is expressed at low levels and serves as a prognostic marker in NSCLC. The downregulation of CTSG expression was associated with lymph node metastasis, tumor stage, and immune cell infiltration. CTSG inhibits NSCLC cell proliferation, migration, and invasion as well as tumor growth in nude mice. There exists a significant correlation between CTSG expression and endoplasmic reticulum function, cell cycling, and the IL-17 signaling pathway. CTSG suppresses the MAPK and EMT signaling pathways in NSCLC cells. Moreover, DNA methylation and histone deacetylation have been identified as crucial mechanisms contributing to the decreased expression of CTSG.

CONCLUSION

CTSG inhibits NSCLC development by suppressing the MAPK signaling pathway and is also associated with tumor immunity.

Genetics and Molecular Pathogenesis of the Chondrosarcoma: A Review of the Literature

The chondrosarcoma, a cartilage-forming bone tumor, presents significant clinical challenges due to its resistance to chemotherapy and radiotherapy. Surgical excision remains the primary treatment, but high-grade chondrosarcomas are prone to recurrence and metastasis, necessitating the identification of reliable biomarkers for diagnosis and prognosis. This review explores the genetic alterations and molecular pathways involved in chondrosarcoma pathogenesis. These markers show promise in distinguishing between benign enchondromas and malignant chondrosarcomas, assessing tumor aggressiveness, and guiding treatment. While these advancements offer hope for more personalized and targeted therapeutic strategies, further clinical validation of these biomarkers is essential to improve prognostic accuracy and patient outcomes in chondrosarcoma management.

SQLE-a promising prognostic biomarker in cervical cancer: implications for tumor malignant behavior, cholesterol synthesis, epithelial-mesenchymal transition, and immune infiltration

BACKGROUND

Cervical cancer, encompassing squamous cell carcinoma and endocervical adenocarcinoma (CESC), presents a considerable risk to the well-being of women. Recent studies have reported that squalene epoxidase (SQLE) is overexpressed in several cancers, which contributes to cancer development.

METHODS

RNA sequencing data for SQLE were obtained from The Cancer Genome Atlas. In vitro experiments, including colorimetry, colony formation, Transwell, RT-qPCR, and Western blotting were performed. Furthermore, a transplanted CESC nude mouse model was constructed to validate the tumorigenic activity of SQLE in vivo. Associations among the SQLE expression profiles, differentially expressed genes (DEGs), immune infiltration, and chemosensitivity were examined. The prognostic value of genetic changes and DNA methylation in SQLE were also assessed.

RESULTS

SQLE mRNA expression was significantly increased in CESC. ROC analysis revealed the strong diagnostic ability of SQLE toward CESC. Patients with high SQLE expression experienced shorter overall survival. The promotional effects of SQLE on cancer cell proliferation, metastasis, cholesterol synthesis, and EMT were emphasized. DEGs functional enrichment analysis revealed the signaling pathways and biological processes. Notably, a connection existed between the SQLE expression and the presence of immune cells as well as the activation of immune checkpoints. Increased SQLE expressions exhibited increased chemotherapeutic responses. SQLE methylation status was significantly associated with CESC prognosis.

CONCLUSION

SQLE significantly affects CESC prognosis, malignant behavior, cholesterol synthesis, EMT, and immune infiltration; thereby offering diagnostic and indicator roles in CESC. Thus, SQLE can be a novel therapeutic target in CESC treatment.

Epigenetics: Mechanisms, potential roles, and therapeutic strategies in cancer progression

Mutations or abnormal expression of oncogenes and tumor suppressor genes are known to cause cancer. Recent studies have shown that epigenetic modifications are key drivers of cancer development and progression. Nevertheless, the mechanistic role of epigenetic dysregulation in the tumor microenvironment is not fully understood. Here, we reviewed the role of epigenetic modifications of cancer cells and non-cancer cells in the tumor microenvironment and recent research advances in cancer epigenetic drugs. In addition, we discussed the great potential of epigenetic combination therapies in the clinical treatment of cancer. However, there are still some challenges in the field of cancer epigenetics, such as epigenetic tumor heterogeneity, epigenetic drug heterogeneity, and crosstalk between epigenetics, proteomics, metabolomics, and other omics, which may be the focus and difficulty of cancer treatment in the future. In conclusion, epigenetic modifications in the tumor microenvironment are essential for future epigenetic drug development and the comprehensive treatment of cancer. Epigenetic combination therapy may be a novel strategy for the future clinical treatment of cancer.

The role of TET2 in solid tumors and its therapeutic potential: a comprehensive review

Indeed, tumors are a significant health concern worldwide, and understanding the underlying mechanisms of tumor development is crucial for effective prevention and treatment. Epigenetics, which refers to changes in gene expression that are not caused by alterations in the DNA sequence itself, plays a critical role in the entire process of tumor development. It goes without saying that the effect of methylation on tumors is a significant aspect of epigenetics. Among the methylation modifications, DNA methylation is an important part, which plays a regulatory role in tumor-related genes. Ten-eleven translocation 2 (TET2) is a highly influential protein involved in the modification of DNA methylation. Its primary role is associated with the suppression of tumor development, making it a significant player in cancer research. However, TET2 is frequently mentioned in hematological diseases, its role in solid tumors has received little attention. Studying the changes of TET2 in solid tumors and the regulatory mechanism will facilitate its investigation as a clinical target for targeted therapy and may also provide directions for clinical treatment of malignant tumors.

DNA methylation in cardiovascular disease and heart failure: novel prediction models?

BACKGROUND

Cardiovascular diseases (CVD) affect over half a billion people worldwide and are the leading cause of global deaths. In particular, due to population aging and worldwide spreading of risk factors, the prevalence of heart failure (HF) is also increasing. HF accounts for approximately 36% of all CVD-related deaths and stands as the foremost cause of hospitalization. Patients affected by CVD or HF experience a substantial decrease in health-related quality of life compared to healthy subjects or affected by other diffused chronic diseases.

MAIN BODY

For both CVD and HF, prediction models have been developed, which utilize patient data, routine laboratory and further diagnostic tests. While some of these scores are currently used in clinical practice, there still is a need for innovative approaches to optimize CVD and HF prediction and to reduce the impact of these conditions on the global population. Epigenetic biomarkers, particularly DNA methylation (DNAm) changes, offer valuable insight for predicting risk, disease diagnosis and prognosis, and for monitoring treatment. The present work reviews current information relating DNAm, CVD and HF and discusses the use of DNAm in improving clinical risk prediction of CVD and HF as well as that of DNAm age as a proxy for cardiac aging.

CONCLUSION

DNAm biomarkers offer a valuable contribution to improving the accuracy of CV risk models. Many CpG sites have been adopted to develop specific prediction scores for CVD and HF with similar or enhanced performance on the top of existing risk measures. In the near future, integrating data from DNA methylome and other sources and advancements in new machine learning algorithms will help develop more precise and personalized risk prediction methods for CVD and HF.

DNA methylation detection is a significant biomarker for screening endometrial cancer in premenopausal women with abnormal uterine bleeding

OBJECTIVE

The aim of our study was to explore the value of DNA (CDO1m/CELF4m) methylation detection in exfoliated cervical cells collected for screening endometrial cancer in premenopausal women with abnormal uterine bleeding.

METHODS

A total of 296 premenopausal women with abnormal uterine bleeding admitted to the Department of Obstetrics and Gynecology at the Third Xiangya Hospital of Central South University from November 2021 to October 2022 were selected. Clinical characteristics, endometrial thickness measured by transvaginal ultrasound and serum CA125 were collected. Exfoliated cervical cells from the thinPrep cytogic test were collected for DNA (CDO1m/CELF4m) methylation testing. Endometrial tissue was collected under hysteroscopy for pathological diagnosis as the gold standard. A univariate logistic regression model was used to analyze risk factors for endometrial cancer. The receiver operating characteristic (ROC) curve and area under the curve (AUC) were used to measure the diagnostic efficacy of DNA methylation detection in endometrial cancer screening of women with abnormal uterine bleeding.

RESULTS

Univariate logistic regression analysis showed that age, body mass index (BMI) ≥25 kg/m2, endometrial thickness ≥11 mm, CDO1 methylation (CDO1mΔCt≤8.4), CELF4 methylation (CELF4mΔCt≤8.8), and dual gene methylation (CDO1mΔCt≤8.4 or CELF4mΔCt≤8.8) were independent risk factors for endometrial cancer in women with abnormal uterine bleeding. The odds ratio (OR) values (95% confidence interval (CI) were 0.87 (0.80-0.95), 4.76 (1.89-11.96), 8.41 (3.13-22.59), 64.49 (20.46-203.33), 12.79 (4.91-33.30), and 42.53 (11.90-152.04), respectively. Among these indicators, dual gene methylation had the higher sensitivity and specificity for endometrial cancer screening (85.7% and 87.6%). Moreover, dual gene methylation combined with BMI or endometrial thickness could further improve the screening efficiency of endometrial cancer in women with abnormal uterine bleeding.

CONCLUSIONS

In premenopausal women with abnormal uterine bleeding, the clinical efficacy of DNA (CDO1m/CELF4m) methylation detection in exfoliated cervical cells for endometrial cancer screening was better than that of other noninvasive clinical indicators. In addition, dual gene methylation combined with BMI or endometrial thickness was a good predictor of endometrial cancer screening.

Pan-cancer analyses reveal the molecular and clinical characteristics of TET family members and suggests that TET3 maybe a potential therapeutic target

The Ten-Eleven Translocation (TET) family genes are implicated in a wide array of biological functions across various human cancers. Nonetheless, there is a scarcity of studies that comprehensively analyze the correlation between TET family members and the molecular phenotypes and clinical characteristics of different cancers. Leveraging updated public databases and employing several bioinformatics analysis methods, we assessed the expression levels, somatic variations, methylation levels, and prognostic values of TET family genes. Additionally, we explored the association between the expression of TET family genes and pathway activity, tumor microenvironment (TME), stemness score, immune subtype, clinical staging, and drug sensitivity in pan-cancer. Molecular biology and cytology experiments were conducted to validate the potential role of TET3 in tumor progression. Each TET family gene displayed distinct expression patterns across at least ten detected tumors. The frequency of Single Nucleotide Variant (SNV) in TET genes was found to be 91.24%, primarily comprising missense mutation types, with the main types of copy number variant (CNV) being heterozygous amplifications and deletions. TET1 gene exhibited high methylation levels, whereas TET2 and TET3 genes displayed hypomethylation in most cancers, which correlated closely with patient prognosis. Pathway activity analysis revealed the involvement of TET family genes in multiple signaling pathways, including cell cycle, apoptosis, DNA damage response, hormone AR, PI3K/AKT, and RTK. Furthermore, the expression levels of TET family genes were shown to impact the clinical staging of tumor patients, modulate the sensitivity of chemotherapy drugs, and thereby influence patient prognosis by participating in the regulation of the tumor microenvironment, cellular stemness potential, and immune subtype. Notably, TET3 was identified to promote cancer progression across various tumors, and its silencing was found to inhibit tumor malignancy and enhance chemotherapy sensitivity. These findings shed light on the role of TET family genes in cancer progression and offer insights for further research on TET3 as a potential therapeutic target for pan-cancer.

PIWI-interacting RNAs (PiRNAs) as emerging biomarkers and therapeutic targets in biliary tract cancers: A comprehensive review

Cancers affecting the biliary tract, such as gallbladder cancer and cholangiocarcinoma, make up a small percentage of adult gastrointestinal malignancies, but their incidence is on the rise. Due to the lack of dependable molecular biomarkers for diagnosis and prognosis, these cancers are often not detected until later stages and have limited treatment options. Piwi-interacting RNAs (piRNAs) are a type of small noncoding RNA that interacts with Piwi proteins and has been linked to various diseases, especially cancer. Manipulation of piRNA expression has the potential to serve as an important biomarker and target for therapy. This review uncovers the relationship between PIWI-interacting RNA (piRNA) and a variety of gastrointestinal cancers, including biliary tract cancer (BTC). It is evident that piRNAs have the ability to impact gene expression and regulate key genes and pathways related to the advancement of digestive cancers. Abnormal expression of piRNAs plays a significant role in the development and progression of digestive-related malignancies. The potential of piRNAs as potential biomarkers for diagnosis and prognosis, as well as therapeutic targets in BTC, is noteworthy. Nevertheless, there are obstacles and limitations that require further exploration to fully comprehend piRNAs' role in BTC and to devise effective diagnostic and therapeutic approaches using piRNAs. In summary, this review underscores the value of piRNAs as valuable biomarkers and promising targets for treating BTC, as we delve into the association between piRNAs and various gastrointestinal cancers, including BTC, and how piRNAs can impact gene expression and control essential pathways for digestive cancer advancement. The present research consists of a thorough evaluation presented in a storytelling style. The databases utilized to locate original sources were PubMed, MEDLINE, and Google Scholar, and the search was conducted using the designated keywords.

The Role of Exhaled Breath Condensate in Chronic Inflammatory and Neoplastic Diseases of the Respiratory Tract

Asthma and chronic obstructive pulmonary disease (COPD) are among the most common chronic respiratory diseases. Chronic inflammation of the airways leads to an increased production of inflammatory markers by the effector cells of the respiratory tract and lung tissue. These biomarkers allow the assessment of physiological and pathological processes and responses to therapeutic interventions. Lung cancer, which is characterized by high mortality, is one of the most frequently diagnosed cancers worldwide. Current screening methods and tissue biopsies have limitations that highlight the need for rapid diagnosis, patient differentiation, and effective management and monitoring. One promising non-invasive diagnostic method for respiratory diseases is the assessment of exhaled breath condensate (EBC). EBC contains a mixture of volatile and non-volatile biomarkers such as cytokines, leukotrienes, oxidative stress markers, and molecular biomarkers, providing significant information about inflammatory and neoplastic states in the lungs. This article summarizes the research on the application and development of EBC assessment in diagnosing and monitoring respiratory diseases, focusing on asthma, COPD, and lung cancer. The process of collecting condensate, potential issues, and selected groups of markers for detailed disease assessment in the future are discussed. Further research may contribute to the development of more precise and personalized diagnostic and treatment methods.

Prediction of the binding mechanism of a selective DNA methyltransferase 3A inhibitor by molecular simulation

DNA methylation is an epigenetic mechanism that introduces a methyl group at the C5 position of cytosine. This reaction is catalyzed by DNA methyltransferases (DNMTs) and is essential for the regulation of gene transcription. The DNMT1 and DNMT3A or -3B family proteins are known targets for the inhibition of DNA hypermethylation in cancer cells. A selective non-nucleoside DNMT3A inhibitor was developed that mimics S-adenosyl-l-methionine and deoxycytidine; however, the mechanism of selectivity is unclear because the inhibitor-protein complex structure determination is absent. Therefore, we performed docking and molecular dynamics simulations to predict the structure of the complex formed by the association between DNMT3A and the selective inhibitor. Our simulations, binding free energy decomposition analysis, structural isoform comparison, and residue scanning showed that Arg688 of DNMT3A is involved in the interaction with this inhibitor, as evidenced by its significant contribution to the binding free energy. The presence of Asn1192 at the corresponding residues in DNMT1 results in a loss of affinity for the inhibitor, suggesting that the interactions mediated by Arg688 in DNMT3A are essential for selectivity. Our findings can be applied in the design of DNMT-selective inhibitors and methylation-specific drug optimization procedures.

High methylation of the same promoter of lncRNA ZNF582-AS1/ZNF582 promotes malignant progression of esophageal cancer

Aim: This study aimed to investigate the functions of ZNF582-AS1 and ZNF582 in esophageal cancer (EC). Materials & methods: Bioinformatics analysis, qRT-PCR and western blot were used to analyze the expression levels. Biological functions were evaluated using cell-counting kit 8, colony formation, Transwell assays and flow cytometry. FISH was used to detect subcellular localization, and methylation-specific PCR determined gene methylation levels. Animal experiments validated the impact on tumor progression. Results: ZNF582-AS1 and ZNF582 were highly methylated and downregulated in EC. Overexpression of ZNF582-AS1 up-regulated the expression of ZNF582, thereby inhibiting EC cell viability and metastasis, promoting apoptosis and inhibiting tumor growth. Conclusion: Low expression of ZNF582-AS1/ZNF582 mediated by DNA hypermethylation facilitates the malignant progression of EC.

Effects of DNA methylation and its application in inflammatory bowel disease (Review)

Inflammatory bowel disease (IBD) is marked by persistent inflammation, and its development and progression are linked to environmental, genetic, immune system and gut microbial factors. DNA methylation (DNAm), as one of the protein modifications, is a crucial epigenetic process used by cells to control gene transcription. DNAm is one of the most common areas that has drawn increasing attention recently, with studies revealing that the interleukin (IL)‑23/IL‑12, wingless‑related integration site, IL‑6‑associated signal transducer and activator of transcription 3, suppressor of cytokine signaling 3 and apoptosis signaling pathways are involved in DNAm and in the pathogenesis of IBD. It has emerged that DNAm‑associated genes are involved in perpetuating the persistent inflammation that characterizes a number of diseases, including IBD, providing a novel therapeutic strategy for exploring their treatment. The present review discusses DNAm‑associated genes in the pathogenesis of IBD and summarizes their application as possible diagnostic, prognostic and therapeutic biomarkers in IBD. This may provide a reference for the particular form of IBD and its related methylation genes, aiding in clinical decision‑making and encouraging therapeutic alternatives.

Research progress of human key DNA and RNA methylation-related enzymes assay

Gene methylation-related enzymes (GMREs) are disfunction and aberrantly expressed in a variety of cancers, such as lung, gastric, and pancreatic cancers and have important implications for human health. Therefore，it is critical for early diagnosis and therapy of tumor to develop strategies that allow rapid and sensitive quantitative and qualitative detection of GMREs. With the development of modern analytical techniques and the application of various biosensors, there are numerous methods have been developed for analysis of GMREs. Therefore, this paper provides a systematic review of the strategies for level and activity assay of various GMREs including methyltransferases and demethylase. The detection methods mainly involve immunohistochemistry, colorimetry, fluorescence, chemiluminescence, electrochemistry, etc. Then, this review also addresses the coordinated role of various detection probes, novel nanomaterials, and signal amplification methods. The aim is to highlight potential challenges in the present field, to expand the analytical application of GMREs detection strategies, and to meet the urgent need for future disease diagnosis and intervention.

CRTAC1 identified as a promising diagnosis and prognostic biomarker in lung adenocarcinoma

CRTAC1, one of the pyroptosis-related genes, has been identified as a protective factor in certain kinds of cancer, such as gastric adenocarcinoma and bladder cancer. The study aimed to investigate the role of CRTAC1 in lung adenocarcinoma (LUAD). LUAD datasets were obtained from Gene Expression Omnibus (GEO) database and The Cancer Genome Atlas (TCGA), pyroptosis-related genes from GeneCard. Limma package used to find differentially expressed genes (DEGs), least absolute shrinkage and selection operator (LASSO) regression and weighted genes co-expression network analysis (WGCNA) to identify CRTAC1 as hub gene. CRTAC1 expression was confirmed in a real-world cohort using quantitative polymerase chain reaction (qPCR) and Western Blot (WB) analyses. Cellular experiments were conducted to investigate CRTAC1's potential oncogenic mechanisms. CRTAC1 mRNA expression was significantly lower in LUAD tissues (p < 0.05) and showed high accuracy in diagnosing LUAD. Reduced CRTAC1 expression was associated with a poor prognosis. Higher CRTAC1 expression correlated with increased immune cell infiltration. Individuals with high CRTAC1 expression showed increased drug sensitivity. Additionally, qPCR and WB analyses showed that CRTAC1 expression was lower in tumor tissue compared to adjacent normal tissue at both the RNA and protein levels. Upregulation of CRTAC1 significantly inhibited LUAD cell proliferation, invasion, and migration in cellular experiments. CRTAC1 has the potential to serve as a diagnostic and prognostic biomarker in LUAD.

DNMT3A-mediated DNA methylation and transcription inhibition of FZD5 suppresses lung carcinogenesis

Background

Based on the bioinformatics prediction, this study investigates the correlation between aberrant transcription factor Frizzled 5 (FZD5) expression and the establishment of non-small cell lung cancer (NSCLC).

Methods

A mouse model with regard to primary NSCLC was encouraged by intraperitoneal injection of urethane. Lentivirus-based FZD5 silencing was then administrated to examine its role in tumorigenesis in the mouse lung. Silencing of FZD5 was induced in two NSCLC cell lines to examine its function in the malignant behavior pertaining to cells in vitro. Quantitative methylation-specific PCR was employed to assess the DNA methylation level within the NSCLC cells. DNA methyltransferases (DNMTs) that administer FZD5 were assessed by chromatin immunoprecipitation assay. Consequently, overexpression of DNMT3A was introduced in mice and NSCLC cells to verify its regulation on FZD and its biological roles in NSCLC development.

Results

In NSCLC, FZD5 expression is elevated, and its knockdown reduced tumor incidence rate in the urethane-challenged mice. The FZD5 silencing also inhibited proliferation, migration, as well as invasion with regard to Calu-3 and NCI-H1299 cells in vitro. The aberrant upregulation with regard to FZD5 in NSCLC was due to at least partly by reduced promoter methylation level. DNMT3A, which bound to FZD5 promoter to suppress its transcription, was poorly expressed in NSCLC. Artificial upregulation of DNMT3A suppressed urethane-induced lung carcinogenesis in mice and suppressed the malignant phenotype pertaining to NSCLC cells in vitro.

Conclusion

This research demonstrates that the lack of DNA methylation level-induced activation of FZD5 is correlated with NSCLC's onset and progression.

Elevated serum homocysteine levels associated with poor recurrence-free and overall survival in patients with colorectal cancer

This study aimed to evaluate the significance of homocysteine (HCY) levels in predicting recurrence-free survival (RFS) and overall survival (OS) in colorectal cancer (CRC) patients. This retrospective study involved 1272 CRC patients. The risk of mortality increased with increasing HCY levels in CRC patients. The optimal HCY cutoff value in CRC patients was 15.2 μmol/L. The RFS (45.8% vs. 60.5%, p < 0.001) and OS (48.2% vs. 63.2%, p < 0.001) of patients with high HCY levels were significantly lower than those of patients with low HCY levels. Patients with high HCY levels were older, male, had large tumours, high carcinoembryonic antigen (CEA) levels, and long hospital stays, and incurred high hospitalisation costs. Multivariate analysis showed that when HCY levels exceeded 15.2 μmol/L, the risk of adverse RFS and OS increased by 55.7% and 61.4%, respectively. Subgroup analysis showed that HCY levels could supplement CEA levels and pathological staging. We constructed HCY-based prognostic nomograms, which demonstrated feasible discrimination and calibration values better than the traditional tumour, node, metastasis staging system for predicting RFS and OS. Elevated serum HCY levels were strongly associated with poor RFS and OS in CRC patients. HCY-based prognostic models are effective tools for a comprehensive evaluation of prognosis.

Early detection and prognosis evaluation for hepatocellular carcinoma by circulating tumour DNA methylation: A multicentre cohort study

BACKGROUND

Early diagnosis of hepatocellular carcinoma (HCC) can significantly improve patient survival. We aimed to develop a blood-based assay to aid in the diagnosis, detection and prognostic evaluation of HCC.

METHODS

A three-phase multicentre study was conducted to screen, optimise and validate HCC-specific differentially methylated regions (DMRs) using next-generation sequencing and quantitative methylation-specific PCR (qMSP).

RESULTS

Genome-wide methylation profiling was conducted to identify DMRs distinguishing HCC tumours from peritumoural tissues and healthy plasmas. The twenty most effective DMRs were verified and incorporated into a multilocus qMSP assay (HepaAiQ). The HepaAiQ model was trained to separate 293 HCC patients (Barcelona Clinic Liver Cancer (BCLC) stage 0/A, 224) from 266 controls including chronic hepatitis B (CHB) or liver cirrhosis (LC) (CHB/LC, 96), benign hepatic lesions (BHL, 23), and healthy controls (HC, 147). The model achieved an area under the curve (AUC) of 0.944 with a sensitivity of 86.0% in HCC and a specificity of 92.1% in controls. Blind validation of the HepaAiQ model in a cohort of 523 participants resulted in an AUC of 0.940 with a sensitivity of 84.4% in 205 HCC cases (BCLC stage 0/A, 167) and a specificity of 90.3% in 318 controls (CHB/LC, 100; BHL, 102; HC, 116). When evaluated in an independent test set, the HepaAiQ model exhibited a sensitivity of 70.8% in 65 HCC patients at BCLC stage 0/A and a specificity of 89.5% in 124 patients with CHB/LC. Moreover, HepaAiQ model was assessed in paired pre- and postoperative plasma samples from 103 HCC patients and correlated with 2-year patient outcomes. Patients with high postoperative HepaAiQ score showed a higher recurrence risk (Hazard ratio, 3.33, p < .001).

CONCLUSIONS

HepaAiQ, a noninvasive qMSP assay, was developed to accurately measure HCC-specific DMRs and shows great potential for the diagnosis, detection and prognosis of HCC, benefiting at-risk populations.

Epigenetic regulation of FOXI2 promotes clear cell renal cell carcinoma progression

In recent decades, substantial advancements in epigenetics have unveiled a profound understanding of its mechanisms in tumorigenesis and have offered promising strategies for epigenetic therapy in cancer patients. In our study, through bioinformatics analysis, we discovered a significant downregulation and hypermethylation of FOXI2 in clear cell renal cell carcinoma (ccRCC), while the expression in chromophobe cell carcinoma (chRCC) exhibited the opposite trend. Moreover, we established a strong correlation between FOXI2 expression levels and the prognosis of ccRCC. Gene enrichment analysis and cell function experiments unequivocally demonstrate that FOXI2 possesses the capability to induce cell cycle arrest and inhibit cell proliferation. Our research findings demonstrate that the expression of FOXI2 in ccRCC is under the regulation of promoter hypermethylation. Furthermore, in vitro experiments have conclusively shown that the overexpression of FOXI2 induces cell cycle arrest and inhibits cell proliferation.

DNA methylation regulator-based molecular subtyping and tumor microenvironment characterization in hepatocellular carcinoma

Backgroud

Although recent studies have reported the regulation of the immune response in hepatocellular carcinoma (HCC) through DNA methylation, the comprehensive impact methylation modifications on tumor microenvironment characteristics and immunotherapy efficacy has not been fully elucidated.

Methods

In this research, we conducted a comprehensive assessment of the patterns of DNA methylation regulators and the profiles of the tumor microenvironment (TME) in HCC, focusing on 21 specific DNA methylation regulators. We subsequently developed a unique scoring system, a DNA methylation score (DMscore), to assess the individual DNA methylation modifications among the three distinct methylation patterns for differentially expressed genes (DEGs).

Results

Three distinct methylation modification patterns were identified with distinct TME infiltration characteristics. We demonstrated that the DMscore could predict patient subtype, TME infiltration, and patient prognosis. A low DMscore, characterized by an elevated tumor mutation burden (TMB), hepatitis B virus (HBV)/hepatitis C virus (HCV) infection, and immune activation, indicates an inflamed tumor microenvironment phenotype with a 5-year survival rate of 7.8%. Moreover, a low DMscore appeared to increase the efficacy of immunotherapy in the anti-CTLA-4/PD-1/PD-L1 cohort.

Conclusions

In brief, this research has enhanced our understanding of the correlation between modifications in DNA methylation patterns and the profile of the tumor microenvironment in individuals diagnosed with HCC. The DMscore may serve as an alternative biomarker for survival and efficacy of immunotherapy in patients with HCC.

Lau AT, Xu YM. The regulation of microRNAs on chemoresistance in triple-negative breast cancer: a recent update

Triple-negative breast cancer (TNBC) has negative expressions of ER, PR and HER2. Due to the insensitivity to both endocrine therapy and HER2-targeted therapy, the main treatment method for TNBC is cytotoxic chemotherapy. However, the curative effect of chemotherapy is limited because of the existence of acquired or intrinsic multidrug resistance. MicroRNAs (miRNAs) are frequently dysregulated in malignant tumors and involved in tumor occurrence and progression. Interestingly, growing studies show that miRNAs are involved in chemoresistance in TNBC. Thus, targeting dysregulated miRNAs could be a plausible way for better treatment of TNBC. Here, we present the updated knowledge of miRNAs associated with chemoresistance in TNBC, which may be helpful for the early diagnosis, prognosis and treatment of this life-threatening disease.

Novel milestones for early esophageal carcinoma: From bench to bed

Esophageal cancer (EC) is the seventh most common cancer worldwide, and esophageal squamous cell carcinoma (ESCC) accounts for the majority of cases of EC. To effectively diagnose and treat ESCC and improve patient prognosis, timely diagnosis in the initial phase of the illness is necessary. This article offers a detailed summary of the latest advancements and emerging technologies in the timely identification of ECs. Molecular biology and epigenetics approaches involve the use of molecular mechanisms combined with fluorescence quantitative polymerase chain reaction (qPCR), high-throughput sequencing technology (next-generation sequencing), and digital PCR technology to study endogenous or exogenous biomolecular changes in the human body and provide a decision-making basis for the diagnosis, treatment, and prognosis of diseases. The investigation of the microbiome is a swiftly progressing area in human cancer research, and microorganisms with complex functions are potential components of the tumor microenvironment. The intratumoral microbiota was also found to be connected to tumor progression. The application of endoscopy as a crucial technique for the early identification of ESCC has been essential, and with ongoing advancements in technology, endoscopy has continuously improved. With the advancement of artificial intelligence (AI) technology, the utilization of AI in the detection of gastrointestinal tumors has become increasingly prevalent. The implementation of AI can effectively resolve the discrepancies among observers, improve the detection rate, assist in predicting the depth of invasion and differentiation status, guide the pericancerous margins, and aid in a more accurate diagnosis of ESCC.

Multi-omics landscape analysis reveals the pan-cancer association of arginine biosynthesis genes with tumor immune evasion and therapy resistance

Background

The metabolism of arginine, a conditionally essential amino acid, plays a crucial role in cancer progression and prognosis. However, a more detailed understanding of the influence of arginine biosynthesis genes in cancer is currently unavailable.

Methods

We performed an integrative multi-omics analysis using The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases to determine the characteristics of these genes across multiple cancer types. To measure the overall activity of arginine biosynthesis genes in cancer, we calculated arginine biosynthesis scores based on gene expression.

Results

Our results indicated that the arginine biosynthesis score was negatively correlated with immune-related pathways, immune infiltration, immune checkpoint expression, and patient prognosis, and single-cell data further clarified that patients with high arginine biosynthesis scores showed a reduced proportion of T and B cells in an immune desert tumor microenvironment and were insensitive to immunotherapy. We also identified several potential drugs through the Cancer Therapeutic Response Portal (CTRP) and Genomics of Drug Sensitivity in Cancer (GDSC) databases that could target arginine biosynthesis genes and potentially improve the response rate to immunotherapy in patients with a high arginine biosynthesis fraction.

Conclusion

Overall, our analyses emphasize that arginine biosynthesis genes are associated with immune evasion in several cancers. Targeting these genes may facilitate more effective immunotherapy.

DNA methylation characteristics associated with chemotherapy resistance in epithelial ovarian cancer

Objective

The high mortality rate of epithelial ovarian cancer (EOC) is often attributed to the frequent development of chemoresistance. DNA methylation is a predictive biomarker for chemoresistance.

Methods

This study utilized DNA methylation profiles and relevant information from GEO and TCGA to identify different methylated CpG sites (DMCs) between chemoresistant and chemosensitive patients. Subsequently, we constructed chemoresistance risk models with DMCs. The genes corresponding to candidate DMCs in chemoresistance risk models were further analyzed to identify different methylated gene symbols (DMGs) associated with chemoresistance. The DMGs that showed a strong correlation with the corresponding DMCs were analyzed through immunohistochemistry.

Results

Compared to chemosensitive EOC patients, chemoresistant patients showed 423 hypermethylated CpGs and 1445 hypomethylated CpGs. The chemoresistance risk models based on DMCs have shown the improved predictive ability for chemoresistance in EOC (AUC = 65.0-76.2%). The methylations of cg25510164, cg13154880, cg15362155 and cg08665359 were strongly associated with decreased risk of chemoresistance. Conversely, the methylation of cg08872590 and cg14739437 significantly increased the risk. We identified 13 DMGs, from 47 DMCs corresponding genes, between chemosensitive and chemoresistant samples. Among the DMGs, the expression levels of DDR2 and OPCML exhibited strong correlations with the corresponding DMCs. DDR2 and OPCML both showed enhanced expression in chemoresistant ovarian microarray tissue.

Conclusions

Hypomethylated CpGs may play a significant role in DNA methylation associated with chemoresistance in EOC. The epigenetic modification of DDR2 could have important implications for the development of chemoresistance. Our study provides valuable insights for future research on DNA methylation in the chemoresistance of EOC.

Association Between Multiple Single Nucleotide Polymorphisms in Folate Metabolism Pathway and Breast Cancer Risk in Georgian Women: A Case-Control Study

Background

The folate metabolism pathway plays an integral part in DNA synthesis, methylation, and repair. Methylenetetrahydrofolate reductase (MTHFR) and methylenetetrahydrofolate dehydrogenase (MTHFD1) are both enzymes that are involved in this pathway, and the single nucleotide polymorphisms (SNPs) in genes coding for them have modulatory effects on DNA expression. This study aimed to investigate the relationship between MTHFR C677T (rs1801133) and MTHFD1 G1958A (rs2236225) polymorphisms and the risk of developing breast cancer in Georgian women.

Methods

A case-control study was performed examining the MTHFR C677T and MTHFD1 G1958A SNP in breast cancer-confirmed cases and healthy matched controls. Real time-polymerase chain reaction (PCR) was used to genotype SNPs. The case individuals' pathology reports were obtained following surgeries for cancer characteristic data. Statistical analysis was performed to investigate the significance of the acquired data.

Results

Statistical analysis of MTHFR C677T SNP revealed that the CT genotype increased the risk of breast cancer by 2.17 folds in the over-dominant model. Statistical analysis of MTHFD1 G1958A SNP showed that the GA genotype increased the risk of breast cancer by 4.12 folds in the codominant model and 2.41 folds in the over-dominant model. No statistically significant link was found between genotypes and lymph node status, however, patients with the CT genotype had higher percentages of proliferative activity.

Conclusions

Breast cancer seems to have a statistically significant association with the CT genotype in MTHFR C677T and the GA genotype in MTHFD1 G1958A in Georgian women.

TCHH as a Novel Prognostic Biomarker for Patients with Gastric Cancer by Bioinformatics Analysis

Background

This study aims to investigate the clinicopathological significance and prognostic value of Trichohyalin (TCHH) in gastric cancer patients through bioinformatics analysis.

Materials and Methods

Data on TCHH expression and clinicopathological information were sourced from The Cancer Genome Atlas (TCGA). The Wilcoxon signed-rank test was used for evaluating the correlation between TCHH mRNA expression levels and clinicopathological features. The predictive significance of TCHH mRNA expression for overall survival (OS), disease-specific survival (DSS), and progression-free interval (PFI) in patients with gastric cancer was assessed using Cox regression models. Furthermore, measures of immune cell infiltration in gastric cancer were made, and studies of gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment were also carried out to investigate the possible roles of TCHH in patients with gastric cancer.

Results

Compared to normal tissues, gastric cancer had a considerably higher expression of TCHH mRNA (P < 0.05). Wilcoxon analysis revealed a significant association between TCHH mRNA expression and the pathologic M stage (P = 0.017). High TPMT mRNA levels were also correlated with worse OS, DFS, and PFI in gastric cancer patients (both P < 0.05). TCHH showed significant negative correlations with the levels of NK CD56dim infiltration (r = -0.157, p = 0.002), Th17 cells infiltration (r = -0.235, P < 0.001), and Th2 infiltration (r = -0.195, P < 0.001). Furthermore, enrichment analysis indicated potential involvement in intermediate filament cytoskeleton organization, DNA methylation in gamete generation, cell-cell recognition, and G protein-coupled peptide receptor (GPCRs) activity.

Conclusion

The level of TCHH mRNA may serve as a novel prognostic biomarker for gastric cancer patients.

Twin study: genotype-dependent epigenetic factors affecting free thyroxine levels in the normal range

Aim: To explore the clinical application of DNA methylation affecting thyroid function, we evaluated the association of DNA methylation with free thyroxine (FT4) and TSH measurements in monozygotic twins. Materials & methods: Discordant pairs for FT4 or TSH levels were examined for the relationship between the within-pair difference of each measurement and the DNA methylation levels using epigenome-wide association studies. The contribution of polymorphisms to the methylation sensitivity was also examined. Results: We found two CpG sites significantly associated with FT4 levels, and also some CpG sites showing significant differences in their methylation levels within FT4-discordant pairs depending on the polymorphism in EPHB2. Conclusion: The FT4 level may be associated with a combination of methylation and polymorphisms in the EPHB2 gene.

Integrated multi-omics analyses reveal the TM4SF family genes with prognostic and therapeutic relevance in hepatocellular carcinoma

TM4SF family members (TM4SFs) have been shown to be aberrantly expressed in multiple types of cancer. However, a comprehensive investigation of the TM4SFs has yet to be performed in LIHC. The study comprehensively investigated the expression and prognostic value of TM4SFs. Then, a TM4SFs-based risk model and nomogram were constructed for prognostic prediction. Finally, functional loss of TM4SFs was performed to verify the potential role of TM4SFs in LIHC. We found that TM4SFs were significantly up-regulated in LIHC. High expression and hypomethylation of TM4SFs were associated with poor prognosis of LIHC patients. Then, a TM4SFs-based risk model was constructed that could effectively classify LIHC patients into high and low-risk groups. In addition, we constructed a prognostic nomogram that could predict the long-term survival of LIHC patients. Based on immune infiltration analysis, high-risk patients had a relatively higher immune status than low-risk patients. Moreover, the prediction module could predict patient responses to immunotherapy and chemotherapy. Finally, loss-of-function studies showed that TM4SF4 knockdown could substantially suppress the growth, migratory, and invasive abilities of LIHC cells. Targeting TM4SFs will contribute to effective immunotherapy strategies and improve the prognosis of liver cancer patients.

DNA Methyltransferase 3A: A Significant Target for the Discovery of Inhibitors as Potent Anticancer Drugs

DNA methyltransferase (DNMT) is a conserved family of Cytosine methylases, which plays a crucial role in the regulation of Epigenetics. They have been considered promising therapeutic targets for cancer. Among the DNMT family, mutations in the DNMT3A subtype are particularly important in hematologic malignancies. The development of specific DNMT3A subtype inhibitors to validate the therapeutic potential of DNMT3A in certain diseases is a significant task. In this review, we summarized the small molecule inhibitors of DNMT3A discovered in recent years and their inhibitory activities, and classified them based on their inhibitory mechanisms.

The Functions and Mechanisms of Long Non-coding RNA SNHGs in Gastric Cancer

Gastric cancer (GC) is one of the most common malignancies worldwide. Despite significant advancements in surgical and adjuvant treatments, patient prognosis remains unsatisfactory. Long non-coding RNAs (lncRNAs) are a class of RNA molecules that lack protein-coding capacity but can engage in the malignant biological behaviors of tumors through various mechanisms. Among them, small nucleolar host genes (SNHGs) represent a subgroup of lncRNAs. Studies have revealed their involvement not only in gastric cancer cell proliferation, invasion, migration, epithelial- mesenchymal transition (EMT), and apoptosis but also in chemotherapy resistance and tumor stemness. This review comprehensively summarizes the biological functions, molecular mechanisms, and clinical significance of SNHGs in gastric cancer. It provides novel insights into potential biomarkers and therapeutic targets for the exploration of gastric cancer.

A comprehensive review on anticancer evaluation techniques

The development of effective anticancer strategies and the improvement of our understanding of cancer need analytical tools. Utilizing a variety of analytical approaches while investigating anti-cancer medicines gives us a thorough understanding of the traits and mechanisms concerned to cancer cells, which enables us to develop potent treatments to combat them. The importance of anticancer research may be attributed to various analytical techniques that contributes to the identification of therapeutic targets and the assessment of medication efficacy, which are crucial things in expanding our understanding of cancer biology. The study looks at methods that are often used in cancer research, including cell viability assays, clonogenic assay, flow cytometry, 2D electrophoresis, microarray, immunofluorescence, western blot caspase activation assay, bioinformatics, etc. The fundamentals, applications, and how each technique analytical advances our understanding of cancer are briefly reviewed.

Conformation-dependent lesion bypass of bulky arylamine-dG adducts generated from 2-nitrofluorene in epigenetic sequence contexts

Sequence context influences structural characteristics and repair of DNA adducts, but there is limited information on how epigenetic modulation affects conformational heterogeneity and bypass of DNA lesions. Lesions derived from the environmental pollutant 2-nitrofluorene have been extensively studied as chemical carcinogenesis models; they adopt a sequence-dependent mix of two significant conformers: major groove binding (B) and base-displaced stacked (S). We report a conformation-dependent bypass of the N-(2'-deoxyguanosin-8-yl)-7-fluoro-2-aminofluorene (dG-FAF) lesion in epigenetic sequence contexts (d[5'-CTTCTC#G*NCCTCATTC-3'], where C# is C or 5-methylcytosine (5mC), G* is G or G-FAF, and N is A, T, C or G). FAF-modified sequences with a 3' flanking pyrimidine were better bypassed when the 5' base was 5mC, whereas sequences with a 3' purine exhibited the opposite effect. The conformational basis behind these variations differed; for -CG*C- and -CG*T-, bypass appeared to be inversely correlated with population of the duplex-destabilizing S conformer. On the other hand, the connection between conformation and a decrease in bypass for flanking purines in the 5mC sequences relative to C was more complex. It could be related to the emergence of a disruptive non-S/B conformation. The present work provides novel conformational insight into how 5mC influences the bypass efficiency of bulky DNA damage.

Pan‑cancer analysis identified ARHGAP23 as a potential biomarker for pancreatic adenocarcinoma

Rho GTPASE-activating protein 23 (ARHGAP23) is known to activate RHO-GTPase and has an important role in the infiltration and metastasis of tumors. Although previous studies suggested its involvement in certain human cancers, its role in pan-cancer remains unclear. In the present study, the expression, prognosis and potential functions of ARHGAP23 in pan-cancer were evaluated through various public databases such as Human Protein Atlas, Tumor IMmune Estimation Resource, Gene Set Co-Expression Analysis, Gene Expression Profiling Interactive Analysis, cBio Cancer Genomics Portal, Tumor-Immune System Interactions Database (TISIDB) and others. Through these data combined with a variety of biological information analysis methods, the potential role of ARHGAP23 as a carcinogenic gene was explored in the present study. The present analysis revealed that ARHGAP23 expressed abnormalities in >10 tumors, which was associated with differences in prognosis. Furthermore, the findings of the present study indicated that ARHGAP23 is associated with DNA methylation and multiple immune cell infiltrations in these tumors. ARHGAP23 expression was related to clinical prognosis, DNA methylation and immune infiltration. These findings support the potential of ARHGAP23 as a prognostic biomarker and a molecular target for cancer treatment.

NXNL2 Promotes Colon Cancer Proliferation and Metastasis by Regulating AKT Pathway

This study aimed to explore the role of nucleoredoxin-like 2 (NXNL2) in colon cancer (CC). The GEPIA and UALCAN databases were analyzed to explore genes involved in the prognosis of CC patients. DLD1 cells were treated with the DNA methylation inhibitor 5-azacitidine to validate the above findings. The methyltransferase DNMT (DNA methylation) was further knocked down by shRNA, then the expression of NXNL2 was assessed by qPCR. The role of NXNL2 on cell proliferation and metastasis was examined using corresponding assays. NXNL2 was found to exhibit the greatest impact on the prognosis of CC patients. High NXNL2 correlated with poor survival outcomes of CC. The expression of NXNL2 was regulated by DNA methylation. NXNL2 promoted CC cell proliferation and metastasis. Also, NXNL2 promoted the AKT pathway activity. In conclusion, NXNL2 could affect the cancer cell proliferation and metastasis, and has a poor survival prognosis in CC.

Hypermethylated CDO1 and CELF4 in cytological specimens as triage strategy biomarkers in endometrial malignant lesions

Objective

Developing a non-invasive and reliable triage test for endometrial malignant lesions is an important goal, as it could help to reduce the number of invasive diagnostic procedures required and improve patient survival. We aimed to estimate the diagnostic value of DNA methylation levels in cervical cytological samples of endometrial cancer (EC) and endometrial atypical hyperplasia (AH).

Methods

A total of 607 women who had indications for endometrial biopsy in the Department of Obstetrics and Gynecology of Cangzhou Central Hospital from October 2022 to April 2023 were enrolled in this study. The cervical exfoliated cells were collected for gene methylation before endometrial biopsy. Clinical information, tumor biomarkers, and endometrial thickness (ET) of transvaginal ultrasonography (TVS) were also collected. With endometrial histopathology as the gold standard, multivariate unconditional logistic regression was applied to analyze the risk factors of endometrial malignant lesions. The role of cysteine dioxygenase type 1 (CDO1) and CUGBP Elav-like family member 4 (CELF4) gene methylation as a triage strategy biomarker in endometrial malignant lesions was specifically explored.

Results

Multivariate logistic regression analysis showed that premenopausal ET ≥ 11 mm or postmenopausal ET ≥ 5 mm, CDO1 ΔCt ≤ 8.4, or CELF4 ΔCt ≤ 8.8 were the risk factors for AH and EC, with odds ratios (ORs) (95%CI) of 5.03 (1.83-13.82) and 6.92 (1.10-43.44), respectively (p-values < 0.05). The sensitivity and specificity of CDO1/CELF4 dual-gene methylation assay for AH and EC reached 84.9% (95%CI: 75.3%-94.5%) and 86.6% (95%CI: 83.8%-89.5%), respectively. ET combined with DNA methylation detection further improved the specificity to (94.9%, 95%CI: 93.1%-96.8%).

Conclusion

The accuracy of cervical cytology DNA methylation is superior to that of other clinical indicators in the non-invasive examination of endometrial malignant lesions. DNA methylation combined with TVS can further improve the specificity and is a promising biomarker triage strategy in women with suspected endometrial lesions.

Brain Tumor Classification by Methylation Profile

The goal of the methylation classifier in brain tumor classification is to accurately classify tumors based on their methylation profiles. Accurate brain tumor diagnosis is the first step for healthcare professionals to predict tumor prognosis and establish personalized treatment plans for patients. The methylation classifier can be used to perform classification on tumor samples with diagnostic difficulties due to ambiguous histology or mismatch between histopathology and molecular signatures, i.e., not otherwise specified (NOS) cases or not elsewhere classified (NEC) cases, aiding in pathological decision-making. Here, the authors elucidate upon the application of a methylation classifier as a tool to mitigate the inherent complexities associated with the pathological evaluation of brain tumors, even when pathologists are experts in histopathological diagnosis and have access to enough molecular genetic information. Also, it should be emphasized that methylome cannot classify all types of brain tumors, and it often produces erroneous matches even with high matching scores, so, excessive trust is prohibited. The primary issue is the considerable difficulty in obtaining reference data regarding the methylation profile of each type of brain tumor. This challenge is further amplified when dealing with recently identified novel types or subtypes of brain tumors, as such data are not readily accessible through open databases or authors of publications. An additional obstacle arises from the fact that methylation classifiers are primarily research-based, leading to the unavailability of charging patients. It is important to note that the application of methylation classifiers may require specialized laboratory techniques and expertise in DNA methylation analysis.

An Update on Potential Molecular Biomarkers of Dietary Phytochemicals Targeting Lung Cancer Interception and Prevention

Since ancient times, dietary phytochemicals are known for their medicinal properties. They are broadly classified into polyphenols, terpenoids, alkaloids, phytosterols, and organosulfur compounds. Currently, there is considerable interest in their potential health effects against various diseases, including lung cancer. Lung cancer is the leading cause of cancer deaths with an average of five-year survival rate of lung cancer patients limited to just 14%. Identifying potential early molecular biomarkers of pre-malignant lung cancer cells may provide a strong basis to develop early cancer detection and interception methods. In this review, we will discuss molecular changes, including genetic alterations, inflammation, signal transduction pathways, redox imbalance, epigenetic and proteomic signatures associated with initiation and progression of lung carcinoma. We will also highlight molecular targets of phytochemicals during lung cancer development. These targets mainly consist of cellular signaling pathways, epigenetic regulators and metabolic reprogramming. With growing interest in natural products research, translation of these compounds into new cancer prevention approaches to medical care will be urgently needed. In this context, we will also discuss the overall pharmacokinetic challenges of phytochemicals in translating to humans. Lastly, we will discuss clinical trials of phytochemicals in lung cancer patients.

The role of dietary polyphenols in alternating DNA methylation in cancer

Natural products such as curcumin, quercetin, and resveratrol have been shown to have antitumor effectsand several studies have examined their role in treating cancer, either alone or in combination with other chemotherapeutic drugs. These compounds are capable of affecting different cancer-related mechanisms, such as proliferation, inflammation, invasion, and metastasis. Along with all of the benefits of these agents, affecting epigenetic processes is one of the most important aspects of their impact. Epigenetic modifications can be categorized into three main processes that include DNA methylation, histone modification, and regulation of small non-coding RNAs. Therefore, targeting DNA methylation can be used as a cancer treatment strategy by identifying or developing methylation modulators. Herein, we take a look into the studies investigating the role of natural products (e.g. curcumin, resveratrol, epigallocatechin gallate (EGCG), and quercetin) in alternating the DNA methylation status of various cancer cells. We discuss how these compounds reduce the expression of enzymes mediating the methylation of tumor suppressor genes and thereby, increasing the expression of tumor suppressors while reactivating antitumor signaling pathways.