Epigenetic regulation and therapeutic targets in the tumor microenvironment

Cuproptosis-related DNA methylation signature predict prognosis and immune microenvironment in cutaneous melanoma

The prognosis for Cutaneous Melanoma (CM), a skin malignant tumor that is extremely aggressive, is not good. A recently identified type of controlled cell death that is intimately related to immunotherapy and the development of cancer is called cuproptosis. Using The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) database, we developed and validated a DNA-methylation located in cuproptosis death-related gene prognostic signature (CRG-located DNA-methylation prognostic signature) to predict CM's prognosis. Kaplan-Meier analysis of our TCGA and GEO cohorts showed that high-risk patients had a shorter overall survival. The area under the curve (AUC) for the TCGA cohort was 0.742, while for the GEO cohort it was 0.733, according to the receiver operating characteristic (ROC) analysis. Furthermore, this signature was discovered as an independent prognostic indicator over CM patients based on Cox-regression analysis. Immunogenomic profiling indicated that majority immune-checkpoints got an opposite relationship with the signature, and patients in the group at low risk got higher immunophenoscore. Several immune pathways were enriched, according to functional enrichment analysis. In conclusion, a prognostic methylation signature for CM patients was established and confirmed. Because of its close relationship to the immune landscape, this signature may help clinicians make more accurate and individualized choices regarding therapy.

Therapeutic Strategies for Angiogenesis Based on Endothelial Cell Epigenetics

With the in-depth investigation of various diseases, angiogenesis has gained increasing attention. Among the contributing factors to angiogenesis research, endothelial epigenetics has emerged as an influential player. Endothelial epigenetic therapy exerts its regulatory effects on endothelial cells by controlling gene expression, RNA, and histone modification within these cells, which subsequently promotes or inhibits angiogenesis. As a result, this therapeutic approach offers potential strategies for disease treatment. The purpose of this review is to outline the pertinent mechanisms of endothelial cell epigenetics, encompassing glycolysis, lactation, amino acid metabolism, non-coding RNA, DNA methylation, histone modification, and their connections to specific diseases and clinical applications. We firmly believe that endothelial cell epigenetics has the potential to become an integral component of precision medicine therapy, unveiling novel therapeutic targets and providing new directions and opportunities for disease treatment.

Identification and validation of immune-related methylated genes as diagnostic and prognostic biomarkers of nasopharyngeal carcinoma

BACKGROUND

Nasopharyngeal carcinoma (NPC) is a common malignancy occurring in the head and neck. Identification of immune-related methylated biomarkers might be helpful for NPC detection and prognostic evaluation.

METHODS

A co-methylation network based on WGCNA was constructed to identify modules associated with NPC and immune cells. In combination with differentially expressed genes (DEGs) and immune-related genes from ImmPort database, the candidate immune-related methylated genes (IRMGs) were obtained.

RESULTS

Our combined analysis identified 12 IRMGs. Among them, both the methylation and mRNA expression of CCL28, CSK, and PRKCB were correlated with the infiltration of B cells. CD1D, CR2, and GDF10 were favorable markers. Demethylation experiments validated that downregulation of GDF10, PRKCB, SLC40A1, and TGFBR3 in NPC resulted from promoter hypermethylation. Additionally, a diagnostic model was developed and exhibited high discriminative accuracy.

CONCLUSIONS

These results provided a group of immune-related methylated biomarkers that may help with the diagnosis and prognosis of NPC.

The molecular mechanism of actions and clinical utilities of tumor infiltrating lymphocytes in gastrointestinal cancers: a comprehensive review and future prospects toward personalized medicine

Gastrointestinal (GI) cancers remain a significant global health burden, accounting for a substantial number of cases and deaths. Regrettably, the inadequacy of dependable biomarkers hinders the precise forecasting of patient prognosis and the selection of appropriate therapeutic sequencing for individuals with GI cancers, leading to suboptimal outcomes for numerous patients. The intricate interplay between tumor-infiltrating lymphocytes (TILs) and the tumor immune microenvironment (TIME) has been shown to be a pivotal determinant of response to anti-cancer therapy and consequential clinical outcomes across a multitude of cancer types. Therefore, the assessment of TILs has garnered global interest as a promising prognostic biomarker in oncology, with the potential to improve clinical decision-making substantially. Moreover, recent discoveries in immunotherapy have progressively changed the landscape of cancer treatment and significantly prolonged the survival of patients with advanced cancers. Nonetheless, the response rate remains constrained within solid tumor sufferers, even when TIL landscapes appear comparable, which calls for the development of our understanding of cellular and molecular cross-talk between TIME and tumor. Hence, this comprehensive review encapsulates the extant literature elucidating the TILs' underlying molecular pathogenesis, prognostic significance, and their relevance in the realm of immunotherapy for patients afflicted by GI tract cancers. Within this review, we demonstrate that the type, density, and spatial distribution of distinct TIL subpopulations carries pivotal implications for the prediction of anti-cancer treatment responses and patient survival. Furthermore, this review underscores the indispensable role of TILs in modulating therapeutic responses within distinct molecular subtypes, such as those characterized by microsatellite stability or programmed cell death ligand-1 expression in GI tract cancers. The review concludes by outlining future directions in TIL-based personalized medicine, including integrating TIL-based approaches into existing treatment regimens and developing novel therapeutic strategies that exploit the unique properties of TILs and their potential as a promising avenue for personalized cancer treatment.

Single-cell mapping reveals several immune subsets associated with liver metastasis of pancreatic ductal adenocarcinoma

BACKGROUND

Identifying a metastasis-correlated immune cell composition within the tumor microenvironment (TME) of pancreatic ductal adenocarcinoma (PDAC) will help to develop promising and innovative therapeutic strategies. However, the dynamics of immune cell lineages in the TME of advanced PDAC remains elusive.

METHODS

Twenty-six samples from 11 patients (including 11 primary tumor tissues, 10 blood, and 5 lymph nodes) with different stages were used to develop a multiscale immune profile. High-dimensional single-cell analysis with mass cytometry was performed to search for metastasis-correlated immune changes in the microenvironment. The findings were further validated by published single-cell RNA sequencing (scRNA-seq) data and multiplex fluorescent immunohistochemistry.

FINDINGS

High-dimensional single-cell profiling revealed that the three immune-relevant sites formed a distinct immune atlas. Interestingly, the PDAC microenvironment with the potential for metastatic spread to the liver was characterized by a decreased proportion of CD103+PD-1+CD39+ T cells with cytotoxic and exhausted functional status and an increased proportion of CD73+ macrophages. Analysis of scRNA-seq data of PDAC further confirmed the identified subsets and revealed strong potential interactions via various ligand-receptor pairs between the identified T subsets and the macrophages. Moreover, stratified patients with different immune compositions correlated with clinical outcomes of PDAC.

CONCLUSIONS

Our study uncovered metastasis-correlated immune changes, suggesting that ecosystem-based patient classification in PDAC will facilitate the identification of candidates likely to benefit from immunotherapy.

FUNDING

This work was supported by the National Key Research and Development Program of China, the Shanghai International Science and Technology Collaboration Program, the Shanghai Sailing Program, and the Key Laboratory of diagnosis and treatment of severe hepato-pancreatic diseases of Zhejiang Province.