DNA hypomethylation mediates immune response in pan-cancer

Research progress of DNA methylation in the diagnosis and treatment of thyroid carcinoma

Thyroid cancer is the most prevalent endocrine malignancy, and its timely and accurate diagnostic and prognostic assessments are crucial for enhancing patient survival rates. As an important epigenetic modification, DNA methylation plays a key role in the regulation of gene expression and tumorigenesis. Recent studies increasingly indicate that abnormal DNA methylation patterns are closely associated with the onset and progression of thyroid cancer. This review discusses the role of DNA methylation in diagnosing thyroid adenocarcinoma, its impact on prognosis, and its potential utility in cancer immunotherapy. Additionally, it explores the prospect of using DNA methylation as a biomarker and highlights its significant potential in the personalized treatment of thyroid cancer. This article aims to serve as a resource for future research and clinical applications to advance the diagnosis and treatment of thyroid cancer.

Pan-cancer characterization of C-C motif chemokine ligand 5 (CCL5) identifies its role as biomarker and therapeutic target

OBJECTIVES

C-C Motif Chemokine Ligand 5 (CCL5) is known for its role in immune regulation and has been implicated in cancer progression. However, its expression and prognostic significance in pan-cancer require comprehensive evaluation. This study was initiated to decipher the pan-cancer role of CCL5 genes.

METHODS

In silico analyses involving various online databases and molecular experiments involving CCL5 knockdown experiments in KIRC cell lines evaluated its role in cell proliferation, colony formation, and migration.

RESULTS

CCL5 expression was significantly up-regulated in several cancers. High CCL5 expression correlated with poorer overall survival in kidney renal cell carcinoma (KIRC) and esophageal cancer (ESCA) patients. Promoter hypomethylation correlated with elevated CCL5 expression and poorer prognosis. CCL5 mutations were rare; indicating its role in cancer is driven by overexpression rather than genetic alterations. Positive correlations with immune inhibitory and MHC genes suggested CCL5's role in fostering an immunosuppressive tumor microenvironment. High CCL5 expression correlated with increased immune cell infiltration, particularly CD8 T cells and macrophages. CCL5 expression did not significantly influence drug sensitivity. CCL5 knockdown in resulted in reduced proliferation, colony formation, and migration, underscoring its critical role in cancer cell dynamics.

CONCLUSION

Our study highlights the significance of CCL5 in cancer progression and prognosis, particularly in KIRC and ESCA. CCL5's role in modulating the tumor immune microenvironment and its potential as a therapeutic target warrant further investigation.

DNA methylation status classifies pleural mesothelioma cells according to their immune profile: implication for precision epigenetic therapy

BACKGROUND

Co-targeting of immune checkpoint inhibitors (ICI) CTLA-4 and PD-1 has recently become the new first-line standard of care therapy of pleural mesothelioma (PM) patients, with a significant improvement of overall survival (OS) over conventional chemotherapy. The analysis by tumor histotype demonstrated greater efficacy of ICI therapy compared to standard chemotherapy in non-epithelioid (non-E) vs. epithelioid (E) PM, although some E PM patients also benefit from ICI treatment. This evidence suggests that molecular tumor features, beyond histotype, could be relevant to improve the efficacy of ICI therapy in PM. Among these, tumor DNA methylation emerges as a promising factor to explore, due to its potential role in driving the immune phenotype of cancer cells. Therefore, we utilized a panel of cultured PM cells of different histotype to provide preclinical evidence supporting the role of the tumor methylation landscape, along with its pharmacologic modulation, to prospectively improve the efficacy of ICI therapy of PM patients.

METHODS

The methylome profile (EPIC array) of distinct E (n = 5) and non-E (n = 9) PM cell lines was analyzed, followed by integrated analysis with their associated transcriptomic profile (Clariom S array), before and after in vitro treatment with the DNA hypomethylating agent (DHA) guadecitabine. The most variable methylated probes were selected to calculate the methylation score (CIMP index) for each cell line at baseline. Genes that were differentially expressed (DE) and differentially methylated (DM) were then selected for gene ontology analysis.

RESULTS

The CIMP index stratified PM cell lines into two distinct classes, CIMP (hyper-methylated; n = 7) and LOW (hypo-methylated; n = 7), regardless of their E or non-E histotype. Integrated methylome and transcriptome analyses revealed that CIMP PM cells exhibited a substantial number of hyper-methylated, silenced genes, which negatively impacted their immune phenotype compared to LOW PM cells. Treatment with DHA reverted the methylation-driven immune-compromised profile of CIMP PM cells and enhanced the constitutive immune-favorable profile of LOW PM cells.

CONCLUSION

The study highlighted the relevance of DNA methylation in shaping the constitutive immune classification of PM cells, independent of their histological subtypes. The identified role of DHA in shifting the phenotype of PM cells towards an immune-favorable state highlights its potential for evaluation in phase I/II clinical trials investigating the efficacy of epigenetic-based ICI combinations to reverse cancer immune resistance mechanisms.

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.

Defining high confidence targets of differential CpG methylation in response to in utero arsenic exposure and implications for cancer risk

Arsenic is a relatively abundant metalloid that impacts DNA methylation and has been implicated in various adverse health outcomes including several cancers and diabetes. However, uncertainty remains about the identity of genomic CpGs that are sensitive to arsenic exposure, in utero or otherwise. Here we identified a high confidence set of CpG sites whose methylation is sensitive to in utero arsenic exposure. To do so, we analyzed methylation of infant CpGs as a function of maternal urinary arsenic in cord blood and placenta from geographically and ancestrally distinct human populations. Independent analyses of these distinct populations were followed by combination of results across sexes and populations/tissue types. Following these analyses, we concluded that both sex and tissue type are important drivers of heterogeneity in methylation response at several CpGs. We also identified 17 high confidence CpGs that were hypermethylated across sex, tissue type and population; 11 of these were located within protein coding genes. This pattern is consistent with hypotheses that arsenic increases cancer risk by inducing the hypermethylation of genic regions. This study represents an opportunity to understand consistent, reproducible patterns of epigenomic responses after in utero arsenic exposure and may aid towards novel biomarkers or signatures of arsenic exposure. Identifying arsenic-responsive sites can also contribute to our understanding of the biological mechanisms by which arsenic exposure can affect biological function and increase risk of cancer and other age-related diseases.

Betulinic acid regulates tumor-associated macrophage M2 polarization and plays a role in inhibiting the liver cancer progression

OBJECTIVE

To investigate the regulatory role and mechanism of betulinic acid (BET) in tumor-associated M2 macrophage polarization.

METHODS

For in vitro experiments, RAW246.7 and J774A.1 cells were used, and differentiation of M2 macrophages was induced using recombinant interleukin-4/13. The levels of M2 cell marker cytokines were measured, and the proportion of F4/80+CD206+ cells was evaluated using flow cytometry. Furthermore, STAT6 signaling was detected, and H22 and RAW246.7 cells were cocultured to assess the effect of BET on M2 macrophage polarization. Changes in the malignant behavior of H22 cells after coculturing were observed and a tumor-bearing mouse model was constructed to determine CD206 cell infiltration after BET intervention.

RESULTS

In vitro experiments showed that BET inhibited M2 macrophage polarization and phospho-STAT6 signal modification. Moreover, the ability to promote the malignant behavior of H22 cells was reduced in BET-treated M2 macrophages. Furthermore, in vivo experiments indicated that BET decreased M2 macrophage polarization and infiltration in the microenvironment of liver cancer. BET was noted to predominantly bind to the STAT6 site to inhibit STAT6 phosphorylation.

CONCLUSION

BET bound chiefly to STAT6 to inhibit STAT6 phosphorylation and decrease M2 polarization in the microenvironment of liver cancer. These findings suggest that BET exerts an antitumor effect by modulating M2 macrophage function.