The interactions between DNA methylation machinery and long non-coding RNAs in tumor progression and drug resistance

Endocrine toxicity of atrazine and its underlying mechanisms

Atrazine (ATR) is one of the most widely utilized herbicides globally and is prevalent in the environment due to its extensive use and long half-life. It can infiltrate the human body through drinking water, ingestion, and dermal contact, and has been recognized as an environmental endocrine disruptor. This study aims to comprehensively outline the detrimental impacts of ATR on the endocrine system. Previous research indicates that ATR is harmful to various bodily systems, including the reproductive system, nervous system, adrenal glands, and thyroi d gland. The toxic effects of ATR on the endocrine system and its underlying molecular mechanisms are summarized as follows: influencing the expression of kisspeptin in the HPG axis, consequently affecting steroid synthesis; disrupting DNA synthesis and meiosis, as well as modifying DNA methylation levels, leading to reproductive and developmental toxicity; impacting dopamine by altering Nurr1, VMAT2, and DAT expression, consequently affecting dopamine synthesis and transporter expression, and influencing other neurotransmitters, resulting in neurotoxicity; and changing adipose tissue synthesis and metabolism by reducing basal metabolism, impairing cellular oxidative phosphorylation, and inducing insulin resistance. Additionally, a compilation of natural products used to mitigate the toxic effects of ATR has been provided, encompassing melatonin, curcumin, quercetin, lycopene, flavonoids, vitamin C, vitamin E, and other natural remedies. It is important to note that existing research predominantly relies on in vitro and ex vivo experiments, with limited population-based empirical evidence available.

Roles of post-translational modifications of UHRF1 in cancer

UHRF1 as a member of RING-finger type E3 ubiquitin ligases family, is an epigenetic regulator with five structural domains. It has been involved in the regulation of a series of biological functions, such as DNA replication, DNA methylation, and DNA damage repair. Additionally, aberrant overexpression of UHRF1 has been observed in over ten cancer types, indicating that UHRF1 is a typical oncogene. The overexpression of UHRF1 repressed the transcription of such tumor-suppressor genes as CDKN2A, BRCA1, and CDH1 through DNMT1-mediated DNA methylation. In addition to the upstream transcription factors regulating gene transcription, post-translational modifications (PTMs) also contribute to abnormal overexpression of UHRF1 in cancerous tissues. The types of PTM include phosphorylation, acetylation, methylationand ubiquitination, which regulate protein stability, histone methyltransferase activity, intracellular localization and the interaction with binding partners. Recently, several novel PTM types of UHRF1 have been reported, but the detailed mechanisms remain unclear. This comprehensive review summarized the types of UHRF1 PTMs, as well as their biological functions. A deep understanding of these crucial mechanisms of UHRF1 is pivotal for the development of novel UHRF1-targeted anti-cancer therapeutic strategies in the future.

Deciphering drug resistance in gastric cancer: Potential mechanisms and future perspectives

Gastric cancer (GC) is a malignant tumor that originates from the epithelium of the gastric mucosa. The latest global cancer statistics show that GC ranks fifth in incidence and fourth in mortality among all cancers, posing a serious threat to public health. While early-stage GC is primarily treated through surgery, chemotherapy is the frontline option for advanced cases. Currently, commonly used chemotherapy regimens include FOLFOX (oxaliplatin + leucovorin + 5-fluorouracil) and XELOX (oxaliplatin + capecitabine). However, with the widespread use of chemotherapy, an increasing number of cases of drug resistance have emerged. This article primarily explores the potential mechanisms of chemotherapy resistance in GC patients from five perspectives: cell death, tumor microenvironment, non-coding RNA, epigenetics, and epithelial-mesenchymal transition. Additionally, it proposes feasibility strategies to overcome drug resistance from four angles: cancer stem cells, tumor microenvironment, natural products, and combined therapy. The hope is that this article will provide guidance for researchers in the field and bring hope to more GC patients.

A review on the role of KCNQ1OT1 lncRNA in human disorders

KCNQ1OT1 is an lncRNA located within KCNQ1 gene on chromosome 11p15.5. This lncRNAs participates in the pathogenesis of a diversity of cancers as well as non-cancerous conditions. In most types of cancers, KCNQ1OT1 is regarded as an oncogene. In a wide array of cancers, high level of KCNQ1OT1 is associated with lower overall survival time. This lncRNA has been found to adsorb a variety of miRNAs, namely miR-15a, miR-211-5p, hsa-miR-107, miR-145, miR-34a, miR-204-5p, miR-129-5p, miR-372-3p, miR-491-5p, miR-153, miR-185-5p, miR-124-3p, miR-211-5p, miR-149, miR-148a-3p, miR-140-5p, miR-125b-5p, miR-9, miR-329-3p, miR-760, miR-296-5p, miR-3666 and miR-129-5p, thus regulating the downstream targets of these miRNAs. In this manuscript, our attention is on this lncRNA and its biomolecular roles in human cancers and other disorders. KCNQ1OT1 plays significant roles in the tumorigenesis and may function as a prospective target for cancer therapy.

Plasma Cell-Free Tumor Methylome as a Biomarker in Solid Tumors: Biology and Applications

DNA methylation is a fundamental mechanism of epigenetic control in cells and its dysregulation is strongly implicated in cancer development. Cancers possess an extensively hypomethylated genome with focal regions of hypermethylation at CPG islands. Due to the highly conserved nature of cancer-specific methylation, its detection in cell-free DNA in plasma using liquid biopsies constitutes an area of interest in biomarker research. The advent of next-generation sequencing and newer computational technologies have allowed for the development of diagnostic and prognostic biomarkers that utilize methylation profiling to diagnose disease and stratify risk. Methylome-based predictive biomarkers can determine the response to anti-cancer therapy. An additional emerging application of these biomarkers is in minimal residual disease monitoring. Several key challenges need to be addressed before cfDNA-based methylation biomarkers become fully integrated into practice. The first relates to the biology and stability of cfDNA. The second concerns the clinical validity and generalizability of methylation-based assays, many of which are cancer type-specific. The third involves their practicability, which is a stumbling block for translating technologies from bench to clinic. Future work on developing pan-cancer assays with their respective validities confirmed using well-designed, prospective clinical trials is crucial in pushing for the greater use of these tools in oncology.

Prognostic evaluation of the novel blueprint of DNA methylation sites by integrating bulk RNA-sequencing and methylation modification data in endometrial cancer

INTRODUCTION

Endometrial cancer (EC) is a prevalent malignancy affecting the female population, with an increasing incidence among younger age groups. DNA methylation, a common epigenetic modification, is well-established to play a key role in cancer progression. We suspected whether DNA methylation could be used as biomarkers for EC prognosis.

METHODS

In the present study, we analyzed bulk RNA-sequencing data from 544 EC patients and DNA methylation data from 430 EC patients in the TCGA-UCEC cohort. We applied weighted correlation network analysis to select a key gene set associated with panoptosis. We conducted correlation analysis between transcriptomic data of the selected key genes and DNA methylation data to identify valuable DNA methylation sites. These sites were further screened by Cox regression and least absolute shrinkage and selection operator analysis. Immune microenvironment differences between high-risk and low-risk groups were assessed using single-sample gene set enrichment analysi, xCell and MCPcounter algorithms.

RESULTS

Our results identified five DNA methylation sites (cg03906681, cg04549977, cg06029846, cg10043253 and cg15658376) with significant prognostic value in EC. We constructed a prognostic model using these sites, demonstrating satisfactory predictive performance. The low-risk group showed higher immune cell infiltration. Notably, methylation of site cg03906681 was negatively related to CD8 T cell infiltration, whereas cg04549977 exhibited positive correlations with immune infiltration, particularly in macrophages, activated B cells, dendritic cells and myeloid-derived suppressor cells. PD0325901_1060 was strongly correlated with risk scores, indicating a potential therapeutic response for high-risk EC patients.

CONCLUSION

We have developed a robust DNA methylation-based prognostic model for EC, which holds promise for improving prognosis prediction and personalized treatment approaches. These findings may contribute to better management of EC patients, particularly in identifying those at higher risk who may benefit from tailored interventions.

Methylation Analysis of Urinary Sample in Non-Muscle-Invasive Bladder Carcinoma: Frequency and Management of Invalid Result

BACKGROUND

Numerous studies showed that methylation analysis represents a newly developed urinary marker based on DNA methylation changes in a panel of genomic biomarkers and it could represent a valid tool in terms of the diagnosis and prediction of high-grade urothelial carcinoma recurrences. One of the limits of the use of this new molecular method during a follow-up is represented by the number of invalid tests in routine practice.

METHOD

A total of 782 patients with a diagnosis of non-muscle-invasive high-grade carcinoma (NMIBC) was studied. The Bladder EpiCheck test (BE) was performed together with cytology in all cases within 1 year after the end of treatment. In 402 patients, the urinary samples were voided urine (UV), while, in 380 cases, the samples were collected after bladder washing (IU). For all the patients with invalid BE results, a second BE test was performed following the instructions for use that indicated the test should be repeated with a new urinary sample in the case of an invalid result.

RESULTS

Analyzing the two different groups (UV and IU), we found the invalid BE results seemed to be not related to urinary samples (p = 0.13 Fisher's exact test), suggesting that the collection method was not relevant in order to reduce the number of invalid tests.

CONCLUSIONS

In the follow-up for NMIBC, for patients for whom a BE test is planned, a combined approach of cytology and a methylation test is recommended in order to repeat the BE test with an invalid result only in those cases with a cytological diagnosis of atypical urothelial cells (AUC) suspicious for high-grade urothelial carcinoma (SHGUC) and high-grade urothelial carcinoma (HGUC).

Role of the NLRP3 inflammasome in gynecological disease

The NLR family pyrin domain containing 3 (NLRP3) inflammasome is involved in the innate immune system and is a three-part macromolecular complex comprising the NLRP3 protein, apoptosis-associated speck-like protein containing a CARD (ASC) and the cysteine protease pro-caspase-1. When the NLRP3 inflammasome is activated, it can produce interleukin (IL)- 1β and IL-18 and eventually lead to inflammatory cell pyroptosis. Related studies have demonstrated that the NLRP3 inflammasome can induce an immune response and is related to the occurrence and development of gynecological diseases, such as endometriosis, polycystic ovary syndrome and breast cancer. NLRP3 inflammasome inhibitors are beneficial for maintaining cellular homeostasis and tissue health and have been found effective in targeting some gynecological diseases. However, excessive inhibitor concentrations have been found to cause adverse effects. Therefore, proper control of NLRP3 inflammasome activity is critical. This paper summarizes the structure and function of the NLRP3 inflammasome and highlights the therapeutic potential of targeting it in gynecological diseases, such as endometriosis, polycystic ovary syndrome and breast cancer The application of NLRP3 inflammasome inhibitors is also discussed.

Prognostic significance of MALAT1 in clear cell renal cell carcinoma based on TCGA and GEO

Long noncoding RNAs metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) can regulate tumorigenesis and progression of various cancers. However, there is little known about the tumor biology and regulatory mechanism of MALAT1 in clear cell renal cell carcinoma (ccRCC). The objective of this study was to evaluate the prognostic value and potential functions of MALAT1 in ccRCC based on the cancer genome atlas. Through bioinformatics research, we analyzed the expression of MALAT1 in ccRCC, and the relationship with clinicopathological features, overall survival and infiltration of immune cells, and established the prognostic models. The results showed that MALAT1 was highly expressed in ccRCC tissues and predicted poor ccRCC patient outcome. The expression level of MALAT1 was significantly correlated with histologic grade, pathologic grade, T stage, M stage. ROC curve showed that MALAT1 had a good diagnostic accuracy, area under the curve of 0.752. The univariate and multivariate cox regression analysis showed that high MALAT1 expression was an independent prognostic factor for overall survival in the cancer genome atlas (hazard ratio = 2.271, 95% confidence interval: 1.435-3.593, P < .001). Gene set enrichment analysis revealed that MALAT1 expression was associated with the DNA methylation, epigenetic regulation of gene expression signaling pathway. In addition, the prognostic models were established to predict 1-, 3- and 5-year survival. This study showed that high expression of MALAT1 might be a potential diagnostic and prognostic biomarker.