Epigenetic regulation in the tumor microenvironment: molecular mechanisms and therapeutic targets

Role of gut microbiome in suppression of cancers

The pathogenesis of cancer is closely related to the disruption of homeostasis in the human body. The gut microbiome plays crucial roles in maintaining the homeostasis of its host throughout lifespan. In recent years, a large number of studies have shown that dysbiosis of the gut microbiome is involved in the entire process of cancer initiation, development, and prognosis by influencing the host immune system and metabolism. Some specific intestinal bacteria promote the occurrence and development of cancers under certain conditions. Conversely, some other specific intestinal bacteria suppress the oncogenesis and progression of cancers, including inhibiting the occurrence of cancers, delaying the progression of cancers and boosting the therapeutic effect on cancers. The promoting effects of the gut microbiome on cancers have been comprehensively discussed in the previous review. This article will review the latest advances in the roles and mechanisms of gut microbiome in cancer suppression, providing a new perspective for developing strategies of cancer prevention and treatment.

Unravelling the epigenetic based mechanism in discovery of anticancer phytomedicine: Evidence based studies

Epigenetic mechanisms play a crucial role in the normal development and maintenance of tissue-specific gene expression patterns in mammals. Disruption of these processes can result in changes to gene function and the transformation of cells into a malignant state. Cancer is characterized by widespread alterations in the epigenetic landscape, revealing that it involves not only genetic mutations but also epigenetic abnormalities. Recent progress in the field of cancer epigenetics has demonstrated significant reprogramming of various components of the epigenetic machinery in cancer, such as DNA methylation, modifications to histones, positioning of nucleosomes, and the expression of non-coding RNAs, particularly microRNAs. The ability to reverse epigenetic abnormalities has given rise to the hopeful field of epigenetic therapy, which has shown advancement with the recent approval by the FDA of three drugs targeting epigenetic mechanisms for the treatment of cancer. In the present manuscript, a comprehensive review has been presented about the role of understanding the epigenetic link between cancer and mechanisms by which phytomedicine offers treatment avenues. Further, this review deciphers the significance of natural products in the identification of epigenetic therapeutics, the diversity of their molecular targets, the use of nanotechnology, and the creation of new strategies for overcoming the inherent clinical challenges associated with developing these drug leads.

N6-methyladenosine-modified RNF220 induces cisplatin resistance and immune escape via regulating PDE10A K48-linked ubiquitination in bladder cancer

Bladder cancer (BCa) remains one of the most prevalent malignancies worldwide, with cisplatin-based combination chemotherapy as the cornerstone of adjuvant treatment. However, cisplatin resistance frequently arises in advanced BCa, limiting therapeutic efficacy. Comparative proteomic analysis of cisplatin-sensitive and -resistant BCa cells identified phosphodiesterase 10A (PDE10A) as significantly downregulated at the protein level in resistant cells, despite unchanged mRNA levels, indicating post-transcriptional regulation. Functional assays demonstrated that PDE10A enhanced cisplatin sensitivity by promoting apoptosis. Mechanistically, the E3 ubiquitin ligase RNF220 directly interacted with PDE10A, facilitating its ubiquitination and degradation under cisplatin-resistant conditions. RNF220 overexpression markedly reinforced cisplatin resistance in vitro and in vivo. Furthermore, N6-methyladenosine (m6A) modification mediated by METTL3 stabilized RNF220 mRNA in an IGF2BP2-dependent manner. Additionally, RNF220 promoted PD-L1 expression by destabilizing PDE10A, thereby facilitating immune evasion in BCa. These findings establish RNF220 as a pivotal ubiquitinase that drives both cisplatin resistance and immune escape through PDE10A destabilization, highlighting its potential as a therapeutic target to enhance chemotherapy and immunotherapy efficacy in advanced BCa.

MicroRNA-induced reprogramming of tumor-associated macrophages for modulation of tumor immune microenvironment

Tumor-associated macrophages (TAMs) are abundant in the tumor microenvironment and typically exhibit pro-tumoral phenotypes. TAMs overexpress the signal regulatory protein alpha (SIRPα) receptor on their surface, which interacts with CD47 on tumor cells to inhibit their phagocytic activity. In this study, we developed lipid nanoparticles modified with an anti-SIRPα antibody (aSIRPα) for the targeted delivery of microRNA-155 (miR155@aSIRPα-LNP) to TAMs, aiming to enhance their anti-tumoral phenotypes within the tumor microenvironment. The aSIRPα modification not only facilitated nanoparticle uptake by TAMs rather than B16F10 cells, but also blocked the anti-phagocytosis signal by disrupting the interaction between SIRPα and CD47 on cancer cells. This dual functionality enhanced the expression of anti-tumoral phenotype markers in TAMs and activated macrophage-mediated phagocytosis of tumor cells. In a melanoma model, intratumoral administration of miR155@aSIRPα-LNP to B16F10 tumor-bearing mice reprogrammed TAMs toward anti-tumoral phenotypes. The anti-tumoral cytokines released by these TAMs remodeled the immunosuppressive tumor microenvironment, increasing cytotoxic T cell infiltration and reducing the regulatory T cell population, inhibiting tumor progression. This approach indicates the potential of miRNA-based therapies to overcome the limitations of current immunotherapies in treating cold solid tumors. Overall, the results suggest that delivering miR155 to TAMs by targeting SIRPα is a promising strategy for modulating the immunosuppressive tumor microenvironment in cancer immunotherapy.

Pharmacology of epitranscriptomic modifications: Decoding the therapeutic potential of RNA modifications in drug resistance

RNA modifications, collectively known as epitranscriptomic modifications, have emerged as critical regulators of gene expression, cellular adaptation, and therapeutic resistance. This review explores the pharmacological potential of targeting RNA modifications, including N6-methyladenosine (m6A) and 5-methylcytosine (m5C), as strategies to overcome drug resistance in cancer. We examine key regulatory enzymes, writers, erasers, and readers-and their roles in modulating RNA stability, translation, and splicing. Advances in combination therapies, integrating RNA modification modulators with conventional chemotherapies and immune checkpoint inhibitors, have shown promising outcomes in reversing multidrug resistance (MDR). Emerging RNA-targeting technologies, such as CRISPR/Cas13 systems and advanced RNA sequencing platforms, further enable precision manipulation of RNA molecules, opening new therapeutic frontiers. However, several challenges persist, including issues related to pharmacokinetics, acquired resistance, and the complexity of epitranscriptomic networks. This review underscores the need for innovative delivery systems, such as lipid nanoparticles and tissue-specific targeting strategies, and highlights the dynamic nature of RNA modifications in response to environmental and therapeutic stress. Ongoing research into non-coding RNA modifications and the interplay between epitranscriptomics and epigenetics offers exciting possibilities for developing novel RNA-targeting therapies. The continued evolution of RNA-based technologies will be crucial in advancing precision medicine, addressing drug resistance, and improving clinical outcomes across multiple diseases.

CHD1 dysregulation in cancer: bridging chromatin instability, therapy resistance, and immune evasion

Chromodomain-Helicase-DNA-binding protein 1 (CHD1) is a central regulator of chromatin dynamics, profoundly influencing gene expression, DNA repair, and genomic stability. This review critically explores CHD1's role in cancer biology, emphasizing its complex, context-dependent functions. In prostate cancer, CHD1 acts as both a tumour suppressor and a facilitator of neuroendocrine differentiation, with its loss linked to aggressive phenotypes, resistance to androgen receptor therapies, and synthetic lethality with PTEN loss. Beyond prostate cancer, CHD1 is implicated in breast, ovarian, and hematological cancers, where it modulates chromatin accessibility, transcription regulation, and therapy resistance. Despite its promise as a biomarker and therapeutic target, CHD1 presents challenges due to its dual roles and cancer-specific effects. The review also highlights critical gaps, including the need for high-resolution studies on CHD1's interactions with immune pathways, synthetic lethality mechanisms, and chromatin remodelling in treatment resistance. Leveraging CHD1's molecular complexities could show the way for innovative diagnostic and therapeutic strategies in cancer, but its role in non-prostate cancers remains underexplored, warranting further investigation.

The Exploration of Indole-Based LSD1-Targeted Inhibitors for Enhanced Immune Response in Gastric Cancer via the PD-L1/PD-1 Axis

Gastric cancer is one of the major health threats to human beings and has a low response rate to emerging immunotherapy. We herein reported a novel indole-based LSD1-targeted antigastric agent 7ae, which was able to enhance the sensitivity of gastric cancer cells to a T-cell-mediated immune response. It exhibited potent LSD1 inhibitory activity (IC50 = 0.080 ± 0.002 μM) and reduced the expression of PD-L1, which in turn promoted the T-cell killing response in gastric cancer cells. As a result, 7ae acted as an active LSD1 inhibitor, exerting excellent anti-invasion and anti-migration effects in gastric cancer cells and leading to significant suppression of the growth of xenograft gastric tumors without obvious toxicity in vivo. Collectively, 7ae has been demonstrated to be a novel, potent LSD1 inhibitor with the potential to be used as an antigastric agent, as well as a useful tool compound for exploratory studies of T-cell-mediated immunity and/or immunotherapy in gastric cancer.

Tumors and their microenvironments: Learning from pediatric brain pathologies

Early clues to tumors and their microenvironments come from embryonic development. Here we review the literature and consider whether the embryonic brain and its pathologies can serve as a better model. Among embryonic organs, the brain is the most heterogenous and complex, with multiple lineages leading to wide spectrum of cell states and types. Its dysregulation promotes neurodevelopmental brain pathologies and pediatric tumors. Embryonic brain pathologies point to the crucial importance of spatial heterogeneity over time, akin to the tumor microenvironment. Tumors dedifferentiate through genetic mutations and epigenetic modulations; embryonic brains differentiate through epigenetic modulations. Our innovative review proposes learning developmental brain pathologies to target tumor evolution-and vice versa. We describe ways through which tumor pharmacology can learn from embryonic brains and their pathologies, and how learning tumor, and its microenvironment, can benefit targeting neurodevelopmental pathologies. Examples include pediatric low-grade versus high-grade brain tumors as in rhabdomyosarcomas and gliomas.

A phase 2 study of chidamide in combination with CAG and venetoclax-azacitidine in acute myeloid leukemia: Clinical safety, efficacy, and correlative analysis

Acute myeloid leukemia (AML) is a highly heterogeneous hematopoietic malignancy characterized by elevated mortality. Epigenetic therapy plays an essential role in the treatment of AML. However, the clinical outcomes of the combination of multiple epigenetic agents and conventional chemotherapy remain unclear. We conducted a phase 2 study to evaluate the clinical safety and efficacy of chidamide combined with CAG and venetoclax-azacitidine (referred to as CACAG-VEN) in AML patients (NCT05659992). Patients received induction treatment with aclarubicin (10 mg/m2/d on days 1, 3, and 5), azacitidine (75 mg/m2 on days 1-7), cytarabine (75 mg/m2 bid on days 1-5), chidamide (30 mg, twice/week for 2 weeks), and venetoclax (100 mg on day 1, 200 mg on day 2, 400 mg on days 3-14). Granulocyte colony-stimulating factor 5 μg/kg/day was administered. After one cycle of CACAG-VEN, the overall response rate was 96.7 %, with a composite complete response (CRc) rate of 93.3 %. The CRc rates (86.7 %) were remarkable among patients with adverse NCCN risk. Patients receiving two cycles of CACAG-VEN achieved a CRc rate of 100 %. The 12-month overall survival rate was 69.7 %. The median time to recovery was 19 days for platelets ≥50,000/μL and 17 days for an absolute neutrophil count ≥500 cells/μL after induction therapy. The single-cell RNA sequence showed most immune cells exhibited no significant change in proportion after removing tumor cells. In conclusion, this regimen resulted in a high CRc rate in newly diagnosed AML patients, particularly in adverse-risk patients. And this regimen had minimal impact on immune cells.

It's all downstream from here: RTK/Raf/MEK/ERK pathway resistance mechanisms in glioblastoma

BACKGROUND

The receptor tyrosine kinase (RTK)/Ras/Raf/MEK/ERK signaling pathway is one of the most tumorigenic pathways in cancer, with its hyperactivation strongly linked to the aggressive nature of glioblastoma (GBM). Although extensive research has focused on developing therapeutics targeting this pathway, clinical success remains elusive due to the emergence of resistance mechanisms.

OBJECTIVE

This review investigates how inhibition of the RTK/Ras/Raf/MEK/ERK pathway alters transcription factors, contributing to acquired resistance mechanisms in GBM. It also highlights the critical role of transcription factor dysregulation in therapeutic resistance.

METHODS & RESULTS

Findings from key studies on the RTK/Ras/Raf/MEK/ERK pathway in GBM were synthesized to explore the role of transcription factor dysregulation in resistance to targeted therapies, radiation, and chemotherapy. The review highlights that transcription factors undergo significant dysregulation following RTK/Ras/Raf/MEK/ERK pathway inhibition, contributing to therapeutic resistance.

CONCLUSION

Transcription factors are promising targets for overcoming treatment resistance in GBM, with cotreatment strategies combining RTK/Ras/Raf/MEK/ERK pathway inhibitors and transcription factor-targeted therapies presenting a novel approach. Despite the challenges of targeting complex structures and interactions, advancements in drug development and precision technologies hold great potential. Continued research is essential to refine these strategies and improve outcomes for GBM and other aggressive cancers.

RGFP966 inhibits palmitic acid induced VSMCs phenotypic transition by targeting ATGL

BACKGROUND

The phenotypic switch of vascular smooth muscle cells (VSMCs) underlies the pathology of many cardiovascular diseases. Histone deacetylase 3 (HDAC3) is reported to upregulate in several cardiovascular diseases. RGFP966 is a highly selective HDAC3 inhibitor. This study aimed to explore the effects of RGFP966 on the phenotypic switch of VSMCs.

METHOD

First, we conducted an analysis of HDAC3 expression utilizing pertinent Gene Expression Omnibus (GEO) datasets. Then CCK-8, Edu, and wound healing assays were used to explore the effects of RGFP966 on the proliferation and migration of VSMCs and potential mechanisms at the cellular level.

RESULTS

Our results showed that palmitic acid (PA) induced the accumulation of lipid droplets in VSMCs, downregulated Adipose triglyceride lipase (ATGL), and increased VSMC viability and migration, which were significantly reversed by RGFP966. Additionally, siRNA targeting ATGL dramatically enhanced the VSMCs injury induced by PA. The autophagy inhibitor 3-Methyladenine (3-MA) partially reversed the decreased ATGL expression caused by PA. Furthermore, the p-mTOR/mTOR ratio decreased under PA induction and rebounded after administration of RGFP966.

CONCLUSION

RGFP966 has a protective effect against VSMCs phenotype transitions, potentially related to the regulation of ATGL.

Histone acetylation modulators in breast cancer

Breast cancer is the most prevalent cancer in women worldwide. Aberrant epigenetic reprogramming such as dysregulation of histone acetylation has been associated with the development of breast cancer. Histone acetylation modulators have been targeted as potential treatments for breast cancer. This review comprehensively discusses the roles of these modulators and the effects of their inhibitors on breast cancer. In addition, epigenetic reprogramming not only affects breast cancer cells but also the immunosuppressive myeloid cells, which can facilitate breast cancer progression. Therefore, the review also highlights the roles of these immunosuppressive myeloid cells and summarizes how histone acetylation modulators affect their functions and phenotypes. This review provides insights into histone acetylation modulators as potential therapeutic targets for breast cancer.

Methylation-Mediated Silencing of miR-124-3 Regulates LRRC1 Expression and Promotes Oral Cancer Progression

Background: Epigenetic alterations, including DNA methylation, play a crucial role in the development of oral squamous cell carcinoma (OSCC) by regulating the expression of tumor suppressor genes and oncogenes. This study investigated the methylation status of miR-124-3 and its role in OSCC progression. Methods: This study applied the Illumina Infinium MethylationEPIC BeadChip assay to profile >850,000 CpG sites in paired OSCC and normal tissues. The methylation data were validated by further analyzing the methylation level of miR-124-3 by using a bisulfite pyrosequencing assay. We investigated whether miR-124-3 acts as a tumor suppressor by establishing miR-124-3-overexpressing OSCC cells and subjecting them to cell proliferation, colony formation, and migration assays. Dual-luciferase reporter assay was used to validate the target genes of miR-124-3 in OSCC cells. Results: The Infinium MethylationEPIC BeadChip and bisulfite pyrosequencing assays consistently identified hypermethylation of miR-124-3 in OSCC tissues relative to normal oral tissues. It was especially notable that miR-124-3 methylation levels were markedly higher in late-stage tumors than in early-stage, and differed significantly between early-stage tumor and normal tissues, indicating that miR-124-3 methylation is an early event in OSCC development. Methylation of miR-124-3 contributes markedly to the downregulation of the gene, leading to the increased expression of its target gene, leucine-rich repeat-containing 1 (LRRC1), which is considered to be positively associated with cancer progression. Moreover, overexpression of miR-124-3 suppressed the proliferation and migration of OSCC cells, while silencing the expression of LRRC1 produced similar tumor-suppressive effects. Luciferase reporter assays confirmed that miR-124-3 directly targets the 3' untranslated region of LRRC1 to downregulate LRRC1 expression. Conclusions: Hypermethylation-mediated downregulation of miR-124-3 results in increased LRRC1 expression, which drives OSCC progression. These findings highlight DNA methylation of miR-124-3 as a potential biomarker for the early detection of OSCC and a therapeutic target for OSCC treatments.

NCOR2 represses MHC class I molecule expression to drive metastatic progression of breast cancer

Metastatic progression depends upon the ability of disseminated tumor cells to evade immune surveillance. MHC molecule expression facilitates T cell recognition and activation to permit the eradication of metastatic tumor cells. We identified nuclear corepressor 2 (NCOR2) as a key epigenetic regulator of MHC class I molecule expression on breast tumor cells. Patients with triple negative breast cancers (TNBC) that expressed high levels of NCOR2 also exhibited reduced metastasis free survival and decreased MHC class I expression, and the metastatic lesions in patients with TNBC had high nuclear NCOR2 and reduced CD8 T cell levels and activity. Genetically and experimentally reducing NCOR2 expression in tumor cells permitted interferon gamma upregulation of MHC class I, and potentiated CD8 T cell activity and induction of apoptosis to repress metastatic progression of disseminated breast cancer cells. These studies provide evidence to support NCOR2 as a targetable epigenetic regulator of metastasis towards which therapies could be developed to reduce patient mortality.

Bridging epigenomics and tumor immunometabolism: molecular mechanisms and therapeutic implications

Epigenomic modifications-such as DNA methylation, histone acetylation, and histone methylation-and their implications in tumorigenesis, progression, and treatment have emerged as a pivotal field in cancer research. Tumors undergo metabolic reprogramming to sustain proliferation and metastasis in nutrient-deficient conditions, while suppressing anti-tumor immunity in the tumor microenvironment (TME). Concurrently, immune cells within the immunosuppressive TME undergo metabolic adaptations, leading to alterations in their immune function. The complicated interplay between metabolites and epigenomic modulation has spotlighted the significance of epigenomic regulation in tumor immunometabolism. In this review, characteristics of the epigenomic modification associated with tumors are systematically summarized alongside with their regulatory roles in tumor metabolic reprogramming and immunometabolism. Classical and emerging approaches are delineated to broaden the boundaries of research on the crosstalk research on the crosstalk between tumor immunometabolism and epigenomics. Furthermore, we discuss potential therapeutic strategies that target tumor immunometabolism to modulate epigenomic modifications, highlighting the burgeoning synergy between metabolic therapies and immunotherapy as a promising avenue for cancer treatment.

Blocking WNT7A Enhances MHC-I Antigen Presentation and Enhances the Effectiveness of Immune Checkpoint Blockade Therapy

The limited infiltration of CD8+ T cells in tumors hampers the effectiveness of T cell-based immunotherapy, yet the mechanisms that limit tumor infiltration by CD8+ T cells remain unclear. Through bulk RNA sequencing of human tumors, we identified a strong correlation between WNT7A expression and reduced CD8+ T-cell infiltration. Further investigation demonstrated that inhibiting WNT7A substantially enhanced MHC-I expression on tumor cells. Mechanistically, WNT7A inhibition inactivated the Wnt/β-catenin signaling pathway and thus resulted in reduced physical interaction between β-catenin and p65 in the cytoplasm, which increased the nuclear translocation of p65 and activated the NF-κB pathway, ultimately promoting the transcription of genes encoding MHC-I molecules. We found that our lead compound, 1365-0109, disrupted the protein-protein interaction between WNT7A and its receptor FZD5, resulting in the upregulation of MHC-I expression. In murine tumor models, both genetic and pharmaceutical suppression of WNT7A led to increased MHC-I levels on tumor cells, and consequently enhanced the infiltration and functionality of CD8+ T cells, which bolstered antitumor immunity and improved the effectiveness of immune checkpoint blockade therapy. These findings have elucidated the intrinsic mechanisms of WNT7A-induced immune suppression, suggesting that therapeutic interventions targeting WNT7A hold promise for enhancing the efficacy of immunotherapy.

Epigenetic modifications in early stage lung cancer: pathogenesis, biomarkers, and early diagnosis

The integration of liquid biopsy with epigenetic markers offers significant potential for early lung cancer detection and personalized treatment. Epigenetic alterations, including DNA methylation, histone modifications, and noncoding RNA changes, often precede genetic mutations and are critical in cancer progression. In this study, we explore how liquid biopsy, combined with epigenetic markers, can provide early detection of lung cancer, potentially predicting onset up to 4 years before clinical diagnosis. We discuss the challenges of targeting epigenetic regulators, which could disrupt cellular balance if overexploited, and the need for maintaining key gene expressions in therapeutic applications. This review highlights the promise and challenges of using liquid biopsy and epigenetic markers for early-stage lung cancer diagnosis, with a focus on optimizing treatment strategies for personalized and precision medicine.

Harnessing phytochemicals: Innovative strategies to enhance cancer immunotherapy

Cancer immunotherapy has revolutionized cancer treatment, but therapeutic ineffectiveness-driven by the tumor microenvironment and immune evasion mechanisms-continues to limit its clinical efficacy. This challenge underscores the need to explore innovative approaches, such as multimodal immunotherapy. Phytochemicals, bioactive compounds derived from plants, have emerged as promising candidates for overcoming these barriers due to their immunomodulatory and antitumor properties. This review explores the synergistic potential of phytochemicals in enhancing immunotherapy by modulating immune responses, reprogramming the tumor microenvironment, and reducing immunosuppressive factors. Integrating phytochemicals with conventional immunotherapy strategies represents a novel approach to mitigating resistance and enhancing therapeutic outcomes. For instance, nab-paclitaxel has shown the potential in overcoming resistance to immune checkpoint inhibitors, while QS-21 synergistically enhances the efficacy of tumor vaccines. Furthermore, we highlight recent advancements in leveraging nanotechnology to engineer phytochemicals for improved bioavailability and targeted delivery. These innovations hold great promise for optimizing the clinical application of phytochemicals. However, further large-scale clinical studies are crucial to fully integrate these compounds into immunotherapeutic regimens effectively.

Tumor suppressor genes in the tumor microenvironment

Tumor suppressor genes (TSGs) are thought to suppress tumor development primarily via cancer cell-autonomous mechanisms. However, the tumor microenvironment (TME) also significantly influences tumorigenesis. In this context, a role for TSGs in the various cell types of the TME in regulating tumor growth is emerging. Indeed, expression analyses of TSGs in clinical samples, along with data from mouse models in which TSGs were deleted selectively in the TME, indicate a functional role for them in tumor development. In this Perspective, using TP53 and PTEN as examples, we posit that TSGs play a significant role in cells of the TME in regulating tumor development, and postulate both a 'pro-active' and 'reactive' model for their contribution to tumor growth, dependent on the temporal sequence of initiating events. Finally, we discuss the need to consider a 2-in-1 cancer-treatment strategy to improve the efficacy of clearance of cancer cells and the cancer-promoting TME.

From silent partners to potential therapeutic targets: macrophages in colorectal cancer

Cancer cells grow and survive in the tumor microenvironment, which is a complicated process. As a key part of how colorectal cancer (CRC) progresses, tumor-associated macrophages (TAMs) exhibit a double role. Through angiogenesis, this TAM can promote the growth of cancers. Although being able to modify and adjust immune cells is a great advantage, these cells can also exhibit anti-cancer properties including direct killing of cancer cells, presenting antigens, and aiding T cell-mediated responses. The delicate regulatory mechanisms between the immune system and tumors are composed of a complex network of pathways regulated by several factors including hypoxia, metabolic reprogramming, cytokine/chemokine signaling, and cell interactions. Decoding and figuring out these complex systems become significant in building targeted treatment programs. Targeting TAMs in CRC involves disrupting chemokine signaling or adhesion molecules, reprogramming them to an anti-tumor phenotype using TLR agonists, CD40 agonists, or metabolic modulation, and selectively removing TAM subsets that promote tumor growth. Multi-drug resistance, the absence of an accurate biomarker, and drug non-specificity are also major problems. Combining macrophage-targeted therapies with chemotherapy and immunotherapy may revolutionize treatment. Macrophage studies will advance with new technology and multi-omics methodologies to help us understand CRC and build specific and efficient treatments.

Epigenetic marvels: exploring the landscape of colorectal cancer treatment through cutting-edge epigenetic-based drug strategies

Epigenetics is currently considered the investigation of inheritable changes in gene expression that do not rely on DNA sequence alteration. Significant epigenetic procedures are involved, such as DNA methylations, histone modifications, and non-coding RNA actions. It is confirmed through several investigations that epigenetic changes are associated with the formation, development, and metastasis of various cancers, such as colorectal cancer (CRC). The difference between epigenetic changes and genetic mutations is that the former could be reversed or prevented; therefore, cancer treatment and prevention could be achieved by restoring abnormal epigenetic events within the neoplastic cells. These treatments, consequently, cause the anti-tumour effects augmentation, drug resistance reduction, and host immune response stimulation. In this article, we begin our survey by exploring basic epigenetic mechanisms to understand epigenetic tools and strategies for treating colorectal cancer in monotherapy and combination with chemotherapy or immunotherapy.

Molecular Mechanisms of Immune Regulation: A Review

BACKGROUND

The immune system must carefully balance fighting pathogens with minimization of inflammation and avoidance of autoimmune responses. Over the past ten years, researchers have extensively studied the mechanisms regulating this delicate balance. Comprehending these mechanisms is essential for developing treatments for inflammatory conditions.

AIM

This review aims to synthesize knowledge of immunoregulatory processes published from 2014-2024 and to highlight discoveries that provide fresh perspectives on this complex balance.

METHODS

The keywords "molecular mechanisms", "immune regulation", "immune signaling pathways", and "immune homeostasis" were used to search PubMed for articles published between 2014 and 2024, with a preference for articles published in the past three years.

RESULTS

Recent research has pinpointed the impact of factors such as cytokine signaling, T-cell regulation, epigenetic regulation, and immunometabolism on immune function.

DISCUSSION

New research highlights the intricate interactions between the immune system and other molecular elements. A key area of interest is the impact of non-coding RNAs and metabolic pathways on the regulation of immune responses.

CONCLUSIONS

Exploring the mechanisms by which the immune system is regulated will provide new avenues for developing treatments to address autoimmune and inflammatory conditions.

Enzyme-Activated Orthogonal Proteolysis Chimeras for Tumor Microenvironment-Responsive Immunomodulation

Precise modulation of dynamic and complex tumor microenvironment (TME) to disrupt tumorigenesis and reshape intratumoral immune infiltration has emerged as promising approaches for enhanced cancer therapy. Among recent innovations, proteolysis-targeting chimeras (PROTACs) represent a burgeoning chemical knockdown technology capable of degrading oncogenic protein homeostasis and inducing dynamic alternations within carcinoma settings, offering potential for antitumor manipulation. However, achieving selectivity in PROTACs that respond to disease environmental stimulation and precisely perturb on-target proteins remains challenging. The multi-step synthesis and limited permeability, attributed to high-molecular-weight and heterobifunctional structures, further hinder their in vivo efficacy. Herein, we present a unique TME-responsive enzyme-activated clickable PROTACs, which features a short peptide-tagged pomalidomide derivative to undergo tumor-specific cleavage by cathepsin protease to induce orthogonal crosslinking of the exposed cysteine with 2-cyanobenzothiazole-labeled epigenetic protein-ligand JQ1, facilitating in situ degrader formation within tumor regions only. Systematic protein profiling and proteomic analysis revealed that such TME-specific clickable-PROTACs not only selectively eliminate epigenetic proteins without tedious pre-synthesis to bridge disparate small-molecule bi-warhead fragments, but also demonstrated superior tumor penetration compared to conventional high-molecular-weight PROTACs. Importantly, these clickable-PROTACs efficiently downregulated immune checkpoint programmed death-ligand 1 (PD-L1) both in vitro and in vivo, remodeling TME for enhanced therapeutics, especially in anti-tumoral immunomodulation.

Novel Epigenetics Control (EpC) Nanocarrier for Cancer Therapy Through Dual-Targeting Approach to DNA Methyltransferase and Ten-Eleven Translocation Enzymes

BACKGROUND/OBJECTIVES

Aberrant hypermethylation in the promoter regions of tumor suppressor genes facilitates the pathogenesis and progression of cancer. Therefore, inhibitors targeting DNA methyltransferase (DNMT) have been tested in clinical studies. However, the current monotherapy of DNMT inhibitors shows limited efficacy. Furthermore, the mechanism of action of DNMT inhibitors is DNA replication-dependent. To address these limitations, we developed a novel core-shell-type "epigenetics control (EpC) nanocarrier" that encapsulated decitabine (5-aza-dC) in the PLGA core nanoparticle and hybridized TET1 gene-encoding pDNA on the lipid shell surface. This study aimed to evaluate whether the dual delivery of DNMT inhibitors and pDNA of TET1 could synergistically enhance tumor suppressor gene expression and induce cell cycle arrest and/or apoptosis in cancer cells. Herein, we demonstrate the potential of the EpC carrier in HCT116 human colon cancer cells to upregulate tumor suppressor gene expression and rapidly achieve cell cycle arrest.

METHODS

PLGA core nanoparticles were prepared by the W/O/W double emulsion method. The formation of core-shell nanoparticles and complexation with pDNA were investigated and optimized by dynamic light scattering, zeta potential measurement, and agarose gel electrophoresis. The cellular uptake and transfection efficiency were measured by confocal laser scanning microscopy and a luciferase assay, respectively. The expression of p53 protein was detected by Western blotting. The anti-tumor effects of the EpC nanocarrier were evaluated by cell cycle analysis and an apoptosis assay.

RESULTS

The EpC nanocarrier delivered the DNMT inhibitor and TET gene-encoding pDNA into HCT116 cells. It promoted the expression of the tumor suppressor protein p53 and induced rapid cell cycle arrest in the G2/M phase in HCT116 cells.

CONCLUSIONS

Our findings suggest that the dual-targeting of DNMT and TET enzymes effectively repairs aberrant DNA methylation and induces growth arrest in cancer cells, and the dual-targeting strategy may contribute to the advancement of epigenetic cancer therapy.

Exploring the methyl-verse: Dynamic interplay of epigenome and m6A epitranscriptome

The orchestration of dynamic epigenetic and epitranscriptomic modifications is pivotal for the fine-tuning of gene expression. However, these modifications are traditionally examined independently. Recent compelling studies have disclosed an interesting communication and interplay between m6A RNA methylation (m6A epitranscriptome) and epigenetic modifications, enabling the formation of feedback circuits and cooperative networks. Intriguingly, the interaction between m6A and DNA methylation machinery, coupled with the crosstalk between m6A RNA and histone modifications shape the transcriptional profile and translational efficiency. Moreover, m6A modifications interact also with non-coding RNAs, modulating their stability, abundance, and regulatory functions. In the light of these findings, m6A imprinting acts as a versatile checkpoint, linking epigenetic and epitranscriptomic layers toward a multilayer and time-dependent control of gene expression and cellular homeostasis. The scope of the present review is to decipher the m6A-coordinated circuits with DNA imprinting, chromatin architecture, and non-coding RNAs networks in normal physiology and carcinogenesis. Ultimately, we summarize the development of innovative CRISPR-dCas engineering platforms fused with m6A catalytic components (m6A writers or erasers) to achieve transcript-specific editing of m6A epitranscriptomes that can create new insights in modern RNA therapeutics.

The role of lncRNAs in the interplay of signaling pathways and epigenetic mechanisms in glioma

Gliomas, highly aggressive tumors of the central nervous system, present overwhelming challenges due to their heterogeneity and therapeutic resistance. Glioblastoma multiforme (GBM), the most malignant form, underscores this clinical urgency due to dismal prognosis despite aggressive treatment regimens. Recent advances in cancer research revealed signaling pathways and epigenetic mechanisms that intricately govern glioma progression, offering multifaceted targets for therapeutic intervention. This review explores the dynamic interplay between signaling events and epigenetic regulation in the context of glioma, with a particular focus on the crucial roles played by non-coding RNAs (ncRNAs). Through direct and indirect epigenetic targeting, ncRNAs emerge as key regulators shaping the molecular landscape of glioblastoma across its various stages. By dissecting these intricate regulatory networks, novel and patient-tailored therapeutic strategies could be devised to improve patient outcomes with this devastating disease.

Unveiling intricating roles and mechanisms of ferroptosis in melanoma

Melanoma is a highly invasive malignant tumor originating from melanocytes, with increasing incidence in recent years. Ferroptosis is an iron-dependent and non-apoptotic form of programmed cell death characterized by the accumulation of lipid peroxides and reactive oxygen species. Morphologically, ferroptosis exhibits the alteration in cells, such as reduced mitochondrial volume, increased density of bilayer membrane, and a decrease or disappearance of mitochondrial cristae. Ferroptosis has shown tremendous potential and applicability in regulating the development of melanoma. As melanoma progresses, certain biomarkers associated with ferroptosis display characteristic patterns of expression. These changes not only reveal the sensitivity of tumor cells to ferroptosis but also provide potential targets for diagnosis and treatment. Besides, inducing ferroptosis has been well-documented to inhibit the growth of melanoma and enhance the efficacy of tumor immunotherapy. Hence, this review emphasizes the roles and regulatory mechanisms of ferroptosis in melanoma development, the involved immune regulation, as well as the potential for diagnosis and treatment of melanoma. The continuous explorations will endow novel strategies for developing ferroptosis-based therapies for melanoma.

Turning cold into hot: emerging strategies to fire up the tumor microenvironment

The tumor microenvironment (TME) is a complex, highly structured, and dynamic ecosystem that plays a pivotal role in the progression of both primary and metastatic tumors. Precise assessment of the dynamic spatiotemporal features of the TME is crucial for understanding cancer evolution and designing effective therapeutic strategies. Cancer is increasingly recognized as a systemic disease, influenced not only by the TME, but also by a multitude of systemic factors, including whole-body metabolism, gut microbiome, endocrine signaling, and circadian rhythm. In this review, we summarize the intrinsic, extrinsic, and systemic factors contributing to the formation of 'cold' tumors within the framework of the cancer-immunity cycle. Correspondingly, we discuss potential strategies for converting 'cold' tumors into 'hot' ones to enhance therapeutic efficacy.

Getting the right combination to break the epigenetic code

Rapid advances in the field of epigenetics have facilitated the development of novel therapeutics targeting epigenetic mechanisms that are hijacked by cancer cells to support tumour growth and progression. Several epigenetic agents have been approved by the FDA for the treatment of cancer; however, the efficacy of these drugs is dependent on the underlying biology and drivers of the disease, with inherent differences between solid tumours and haematological malignancies. The efficacy of epigenetic drugs as single agents remains limited across most cancer types, which has spurred the clinical development of combination therapies, with the hope of attaining synergistic activity and/or overcoming treatment resistance. In this Review we discuss clinical advances that have been achieved with the use of epigenetic agents in combination with chemotherapies, immunotherapies or other targeted agents, including epigenetic-epigenetic combinations, as well as limitations and challenges associated with these combinatorial strategies. So far, the success of combination therapies targeting epigenetic mechanisms has generally been confined to haematological malignancies, with limited efficacy observed in patients with solid tumours. Nevertheless, this Review captures the field of epigenetic combination therapies across the spectra of haematology and oncology, highlighting opportunities for precision therapy to effectively harness the potential of epigenetic agents and produce meaningful improvements in clinical outcomes.

Unveiling the potential of gene editing techniques in revolutionizing Cancer treatment: A comprehensive overview

Gene editing techniques have emerged as powerful tools in biomedical research, offering precise manipulation of genetic material with the potential to revolutionize cancer treatment strategies. This review provides a comprehensive overview of the current landscape of gene editing technologies, including CRISPR-Cas systems, base editing, prime editing, and synthetic gene circuits, highlighting their applications and potential in cancer therapy. It discusses the mechanisms, advantages, and limitations of each gene editing approach, emphasizing their transformative impact on targeting oncogenes, tumor suppressor genes, and drug resistance mechanisms in various cancer types. The review delves into population-level interventions and precision prevention strategies enabled by gene editing technologies, including gene drives, synthetic gene circuits, and precision prevention tools, for controlling cancer-causing genes, targeting pre-cancerous lesions, and implementing personalized preventive measures. Ethical considerations, regulatory challenges, and future directions in gene editing research for cancer treatment are also addressed. This review highlights how gene editing could revolutionize precision medicine by enhancing patient care and advancing cancer treatments with targeted, personalized methods. For these benefits to be fully realized, collaboration among researchers, doctors, regulators, and patient advocates is crucial in fighting cancer and meeting clinical needs.

The molecular code of kidney cancer: A path of discovery for gene mutation and precision therapy

Renal cell carcinoma (RCC) is a malignant tumor with highly heterogeneous and complex molecular mechanisms. Through systematic analysis of TCGA, COSMIC and other databases, 24 mutated genes closely related to RCC were screened, including VHL, PBRM1, BAP1 and SETD2, which play key roles in signaling pathway transduction, chromatin remodeling and DNA repair. The PI3K/AKT/mTOR signaling pathway is particularly important in the pathogenesis of RCC. Mutations in genes such as PIK3CA, MTOR and PTEN are closely associated with metabolic abnormalities and tumor cell proliferation. Clinically, mTOR inhibitors and VEGF-targeted drugs have shown significant efficacy in personalized therapy. Abnormal regulation of metabolic reprogramming, especially glycolysis and glutamine metabolic pathways, provides tumor cells with continuous energy supply and survival advantages, and GLS1 inhibitors have shown promising results in preclinical studies. This paper also explores the potential of immune checkpoint inhibitors in combination with other targeted drugs, as well as the promising application of nanotechnology in drug delivery and targeted therapy. In addition, unique molecular mechanisms are revealed and individualized therapeutic strategies are explored for specific subtypes such as TFE3, TFEB rearrangement type and SDHB mutant type. The review summarizes the common gene mutations in RCC and their molecular mechanisms, emphasizes their important roles in tumor diagnosis, treatment and prognosis, and looks forward to the application prospects of multi-pathway targeted therapy, metabolic targeted therapy, immunotherapy and nanotechnology in RCC treatment, providing theoretical support and clinical guidance for individualized treatment and new drug development.

Cell-free epigenomes enhanced fragmentomics-based model for early detection of lung cancer

BACKGROUND

Lung cancer is a leading cause of cancer mortality, highlighting the need for innovative non-invasive early detection methods. Although cell-free DNA (cfDNA) analysis shows promise, its sensitivity in early-stage lung cancer patients remains a challenge. This study aimed to integrate insights from epigenetic modifications and fragmentomic features of cfDNA using machine learning to develop a more accurate lung cancer detection model.

METHODS

To address this issue, a multi-centre prospective cohort study was conducted, with participants harbouring suspicious malignant lung nodules and healthy volunteers recruited from two clinical centres. Plasma cfDNA was analysed for its epigenetic and fragmentomic profiles using chromatin immunoprecipitation sequencing, reduced representation bisulphite sequencing and low-pass whole-genome sequencing. Machine learning algorithms were then employed to integrate the multi-omics data, aiding in the development of a precise lung cancer detection model.

RESULTS

Cancer-related changes in cfDNA fragmentomics were significantly enriched in specific genes marked by cell-free epigenomes. A total of 609 genes were identified, and the corresponding cfDNA fragmentomic features were utilised to construct the ensemble model. This model achieved a sensitivity of 90.4% and a specificity of 83.1%, with an AUC of 0.94 in the independent validation set. Notably, the model demonstrated exceptional sensitivity for stage I lung cancer cases, achieving 95.1%. It also showed remarkable performance in detecting minimally invasive adenocarcinoma, with a sensitivity of 96.2%, highlighting its potential for early detection in clinical settings.

CONCLUSIONS

With feature selection guided by multiple epigenetic sequencing approaches, the cfDNA fragmentomics-based machine learning model demonstrated outstanding performance in the independent validation cohort. These findings highlight its potential as an effective non-invasive strategy for the early detection of lung cancer.

KEYPOINTS

Our study elucidated the regulatory relationships between epigenetic modifications and their effects on fragmentomic features. Identifying epigenetically regulated genes provided a critical foundation for developing the cfDNA fragmentomics-based machine learning model. The model demonstrated exceptional clinical performance, highlighting its substantial potential for translational application in clinical practice.

Targeting the PD-1/PD-L1 Signaling Pathway for Cancer Therapy: Focus on Biomarkers

The PD1/PD-L1 axis plays an important immunosuppressive role during the T-cell-mediated immune response, which is essential for the physiological homeostasis of the immune system. The biology of the immunological microenvironment is extremely complex and crucial for the development of treatment strategies for immunotherapy. Characterization of the immunological, genomic or transcriptomic landscape of cancer patients could allow discrimination between responders and non-responders to anti-PD-1/PD-L1 therapy. Immune checkpoint inhibitor (ICI) therapy has shown remarkable efficacy in a variety of malignancies in landmark trials and has fundamentally changed cancer therapy. Current research focuses on strategies to maximize patient selection for therapy, clarify mechanisms of resistance, improve existing biomarkers, including PD-L1 expression and tumor mutational burden (TMB), and discover new biomarkers. In this review, we focus on the function of the PD-1/PD-L1 signaling pathway and discuss the immunological, genomic, epigenetic and transcriptomic landscape in cancer patients receiving anti-PD-1/PD-L1 therapy. Finally, we provide an overview of the clinical trials testing the efficacy of antibodies against PD-1/PD-L1.

Molecular insight into histone methylation as a novel target for oral squamous cell carcinoma: future hope in personalised medicine

Oral squamous cell carcinoma (OSCC) is the most prevalent type of malignant epithelial neoplasm that affects the oral cavity. It has been a significant health concern in many countries for a long time since it was usually treated with surgery, radiation, and/or chemotherapy. Drug resistance is the primary issue in patient populations and scientific research, which promotes OSCC tumour cell invasion and migration. Thus, identifying highly specific therapeutic targets could be the potential approach for more successful treatment of OSCC. It is still challenging to understand the genetic causes of oral carcinogenesis due to its highly varied clinic-pathological parameters. It is important to remember that signaling channels and complexes that affect chromatin accessibility control gene expression, which in turn affects cell development and differentiation. Histones undergo post-translational alteration to give this platform. Understanding the processes of gene regulation through histone methylation and its modifications could enhance the early detection, prognostic prediction, and therapy of OSCC. To be properly used as a therapeutic target, histone methylation in OSCC requires more investigation. This review details the dysregulated histone methylation and the modifying enzymes linked to the development and aetiology of OSCC. Furthermore, the part that lysine methylation plays in cell migration, chemo-resistance, and OSCC invasion is also investigated.

Development and pan-cancer validation of an epigenetics-based random survival forest model for prognosis prediction and drug response in OS

Background

Osteosarcoma (OS) exhibits significant epigenetic heterogeneity, yet its systematic characterization and clinical implications remain largely unexplored.

Methods

We analyzed single-cell transcriptomes of five primary OS samples, identifying cell type-specific epigenetic features and their evolutionary trajectories. An epigenetics-based Random Survival Forest (RSF) model was constructed using 801 curated epigenetic factors and validated in multiple independent cohorts.

Results

Our analysis revealed distinct epigenetic states in the OS microenvironment, with particular activity in OS cells and osteoclasts. The RSF model identified key predictive genes including OLFML2B, ACTB, and C1QB, and demonstrated broad applicability across multiple cancer types. Risk stratification analysis revealed distinct therapeutic response patterns, with low-risk groups showing enhanced sensitivity to traditional chemotherapy drugs while high-risk groups responded better to targeted therapies.

Conclusion

Our epigenetics-based model demonstrates excellent prognostic accuracy (AUC>0.997 in internal validation, 0.832-0.929 in external cohorts) and provides a practical tool for treatment stratification. These findings establish a clinically applicable framework for personalized therapy selection in OS patients.

Predicting immunotherapy efficacy in endometrial cancer: focus on the tumor microenvironment

Immunotherapy represents a groundbreaking therapeutic approach, based on the immune system's intrinsic capacity to interfere with tumor progression, that opens the horizons in the treatment of endometrial cancer. However, the clinical efficacy of immunotherapy is hampered by the development of resistance in patients. The resistance to immunotherapy is multifactorial mechanism, encompassed genetic and epigenetic alterations in tumor cells modulating immune checkpoint molecules, resulted in escaping immune surveillance. The tumor microenvironment can orchestrate an immunosuppressive milieu, attenuating the immune response and facilitating tumor progression. To overcome immunotherapeutic resistance in endometrial cancer we must bring to light the mechanisms of intricate interplay between neoplastic cells, the host immune system, and the tumor microenvironment. The identification of predictive biomarkers for immunotherapeutic response and the innovative agents capable of reversing resistance pathways must be developed. Our review summarizes accumulated data on the role of cells of the tumor microenvironment and their regulatory molecules in the mechanisms underlying therapeutic effects of immune checkpoint inhibitors, including resistance to therapy. Major question we raise here - which group of patients is the most favorable to achieve durable immunotherapy response in endometrial cancer?

Advancing precision cancer immunotherapy drug development, administration, and response prediction with AI-enabled Raman spectroscopy

Molecular characterization of tumors is essential to identify predictive biomarkers that inform treatment decisions and improve precision immunotherapy development and administration. However, challenges such as the heterogeneity of tumors and patient responses, limited efficacy of current biomarkers, and the predominant reliance on single-omics data, have hindered advances in accurately predicting treatment outcomes. Standard therapy generally applies a "one size fits all" approach, which not only provides ineffective or limited responses, but also an increased risk of off-target toxicities and acceleration of resistance mechanisms or adverse effects. As the development of emerging multi- and spatial-omics platforms continues to evolve, an effective tumor assessment platform providing utility in a clinical setting should i) enable high-throughput and robust screening in a variety of biological matrices, ii) provide in-depth information resolved with single to subcellular precision, and iii) improve accessibility in economical point-of-care settings. In this perspective, we explore the application of label-free Raman spectroscopy as a tumor profiling tool for precision immunotherapy. We examine how Raman spectroscopy's non-invasive, label-free approach can deepen our understanding of intricate inter- and intra-cellular interactions within the tumor-immune microenvironment. Furthermore, we discuss the analytical advances in Raman spectroscopy, highlighting its evolution to be utilized as a single "Raman-omics" approach. Lastly, we highlight the translational potential of Raman for its integration in clinical practice for safe and precise patient-centric immunotherapy.

Identification of cancer cell-intrinsic biomarkers associated with tumor progression and characterization of SFTA3 as a tumor suppressor in lung adenocarcinomas

BACKGROUND

Recent advancements in contemporary therapeutic approaches have increased the survival rates of lung cancer patients; however, the long-term benefits remain constrained, underscoring the pressing need for novel biomarkers. Surfactant-associated 3 (SFTA3), a long non-coding RNA predominantly expressed in normal lung epithelial cells, plays a crucial role in lung development. Nevertheless, its function in lung adenocarcinoma (LUAD) remains inadequately understood.

METHODS

Single-cell RNA sequencing data were utilized to identify novel cancer cell-intrinsic gene signatures associated with the progression of LUAD, and their roles in LUAD were comprehensively analyzed. Serum samples were collected to quantify the expression levels of SFTA3 in LUAD patients. Furthermore, a series of biological experiments, including cell viability assays, scratch wound healing assays, and colony formation assays, were conducted to demonstrate the tumor-suppressive effects of SFTA3. RNA sequencing was performed to elucidate the molecular mechanisms underlying the role of SFTA3 in lung cancer cells.

RESULTS

We constructed a prognostic model comprising eight genes: ALDOA, ATP5MD, SERPINH1, SFTA3, SLK, U2SURP, SCGB1A1, and SCGB1A3. The model effectively stratified patients into high- and low-risk categories, revealing that low-risk patients experienced superior clinical outcomes, exhibited an immunologically hot tumor microenvironment (TME), and had a greater probability of responding to immunotherapy. In contrast, the high-risk group exhibited a cold TME and may benefit more from chemotherapy. Furthermore, our study revealed that a progressive decrease in SFTA3 expression in cancer cells was correlated with tumor advancement. Notably, the serum levels of SFTA3 significantly decreased in patients with LUAD, suggesting its potential utility in liquid biopsy for LUAD diagnosis. Additionally, the knockdown of SFTA3 enhances the proliferation and migration of lung cancer cells, whereas its overexpression inhibits these phenotypes. The epithelial-mesenchymal transition pathway was significantly enriched following SFTA3 silencing, suggesting that SFTA3 may impact tumor progression by modulating this process. We also identified key transcription factors and epigenetic mechanisms implicated in the downregulation of SFTA3 in LUAD.

CONCLUSION

We developed a robust prognostic model and identified SFTA3 as a novel biomarker with potential applications in the diagnosis, prognosis, and personalized treatment of LUAD. Additionally, our findings offer new insights into the mechanisms underlying LUAD tumorigenesis and immune evasion.

Epigenetic Regulation of Stromal and Immune Cells and Therapeutic Targets in the Tumor Microenvironment

The tumor microenvironment (TME) plays a pivotal role in neoplastic initiation and progression. Epigenetic machinery, governing the expression of core oncogenes and tumor suppressor genes in transformed cells, significantly contributes to tumor development at both primary and distant sites. Recent studies have illuminated how epigenetic mechanisms integrate external cues and downstream signals, altering the phenotype of stromal cells and immune cells. This remolds the area surrounding tumor cells, ultimately fostering an immunosuppressive microenvironment. Therefore, correcting the TME by targeting the epigenetic modifications holds substantial promise for cancer treatment. This review synthesizes recent research that elucidates the impact of specific epigenetic regulations-ranging from DNA methylation to histone modifications and chromatin remodeling-on stromal and immune cells within the TME. Notably, we highlight their functional roles in either promoting or restricting tumor progression. We also discuss the potential applications of epigenetic agents for cancer treatment, envisaging their ability to normalize the ecosystem. This review aims to assist researchers in understanding the dynamic interplay between epigenetics and the TME, paving the way for better epigenetic therapy.

Histone-acetyl epigenome regulates TGF-β pathway-associated chemoresistance in colorectal cancer

TGF-β signaling pathway has been demonstrated to be closely related to chemoresistance, which is the major cause of recurrence and poor outcome in colorectal cancer (CRC), however, the comprehensive epigenetic landscape that functionally implicates in the regulation of TGF-β pathway-associated chemoresistance has not yet well established in CRC. In our study, chromatin immunoprecipitation sequencing (ChIP-seq) and Western blot were employed to investigate epigenetic modifications for histones in response to TGF-β1 intervene. We found that the activation of the TGF-β pathway was characterized by genome-wide high levels of H3K9ac and H3K18ac. Mechanistically, the activation of the TGF-β signaling pathway leads to the downregulation of the deacetylase HDAC4, resulting in the upregulation of H3K9ac and H3K18ac. Consequently, this cascade induces oxaliplatin chemoresistance in CRC by triggering the anti-apoptotic PI3K/AKT signaling pathway. Our in vivo experiment results confirmed that overexpression of HDAC4 significantly enhances the sensitivity of CRC to oxaliplatin chemotherapy. Moreover, the expression level of HDAC4 was positively correlated with patients' prognosis in CRC. Our data suggest that histone-acetyl modification demonstrates a crucial role in modulating TGF-β pathway-associated chemoresistance in CRC, and HDAC4 would be a biomarker for prognostic prediction and potential therapeutic target for treatment in CRC.

CBX3 Downregulates HLTF to Activate PI3K/AKT Signaling Promoting Cholangiocarcinoma

Cholangiocarcinoma (CCA) is an aggressive cancer with poor response to chemotherapy or radiation, necessitating novel therapeutic approaches. Epigenetic regulation, which is reversible, plays a significant role in cancer progression. CBX3 (HP1γ), a key heterochromatin protein, regulates gene expression by interacting with histone H3 lysine 9 trimethyl (H3K9me3) markers. While CBX3 is linked to tumor progression in various cancers, its role in CCA remains unclear. This study reveals that CBX3 and H3K9me3 enrich the HLTF promoter, a gene involved in chromatin remodeling and DNA repair. HLTF is often inactivated by hypermethylation in other cancers, suggesting tumor-suppressive properties. Depleting CBX3 in CCA cells elevates HLTF expression, reducing proliferation, while HLTF silencing reverses this effect. Furthermore, HLTF overexpression inhibits PI3K-AKT signaling activated by CBX3. These findings suggest CBX3 promotes CCA progression by suppressing HLTF expression.

Immune biomarkers and predictive signatures in gastric cancer: Optimizing immunotherapy responses

Gastric cancer is a malignant disease with a poor prognosis and few therapeutic options once it has advanced. Immunotherapy using ICIs has emerged as a viable therapeutic method; nevertheless, reliable immunological biomarkers are required to identify who may benefit from these therapies. It focuses on key immune biomarkers and predictive signatures in gastric cancer, such as PD-L1 expression, microsatellite instability (MSI), tumor mutational burden (TMB), and Epstein-Barr virus (EBV) status, to optimize gastric cancer patients' immunotherapy responses. PD-L1 expression is a popular biomarker for ICI effectiveness. Tumors with high MSI-H and TMB are the most susceptible to ICIs because they are highly immunogenic. EBV-positive stomach tumors are highly immunogenic, and immunotherapy has a high response rate. Combining composite biomarker panels with multi-omics-based techniques improved patient selection accuracy. In recent years, machine learning models have been integrated into next-generation sequencing. Dynamic, real-time-monitorable biomarkers for real-time immune response monitoring are also being considered. Thus, enhancing biomarker-driven immunotherapy is critical for improving clinical outcomes with gastric cancer. There is still more work to be done in this field, and verifying developing biomarkers will be an important component in the future of customized cancer therapy.

AH-6809 mediated regulation of lung adenocarcinoma metastasis through NLRP7 and prognostic analysis of key metastasis-related genes

Introduction

Lung adenocarcinoma (LUAD) has become one of the leading causes of cancer-related deaths globally, with metastasis representing the most lethal stage of the disease. Despite significant advances in diagnostic and therapeutic strategies for LUAD, the mechanisms enabling cancer cells to breach the blood-brain barrier remain poorly understood. While genomic profiling has shed light on the nature of primary tumors, the genetic drivers and clinical relevance of LUAD metastasis are still largely unexplored.

Objectives

This study aims to investigate the genomic differences between brain-metastatic and non-brain-metastatic LUAD, identify potential prognostic biomarkers, and evaluate the efficacy of AH-6809 in modulating key molecular pathways involved in LUAD metastasis, with a focus on post-translational modifications (PTMs).

Methods

Genomic analyses were performed using data from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO). Differentially expressed genes (DEGs) between brain-metastatic and non-metastatic LUAD samples were identified. Key gene modules were determined using Weighted Gene Co-expression Network Analysis (WGCNA), and their prognostic significance was assessed through Kaplan-Meier analysis. Cellular experiments, including CCK8 and qRT-PCR assays, were conducted to evaluate the anti-cancer effects of AH-6809 in LUAD cells. Apoptosis and inflammatory marker expression were assessed using immunofluorescence.

Results

Genomic analysis differentiated brain-metastatic from non-brain-metastatic LUAD and identified NLRP7, FIBCD1, and ELF5 as prognostic markers. AH-6809 significantly suppressed LUAD cell proliferation, promoted apoptosis, and modulated epithelial-mesenchymal transition (EMT) markers. These effects were reversed upon NLRP7 knockdown, highlighting its role in metastasis. Literature analysis further supported AH-6809's tumor-suppressive activity, particularly in NLRP7 knockdown cells, where it inhibited cell growth and facilitated apoptosis. AH-6809 was also found to affect SUMO1-mediated PTMs and downregulate EMT markers, including VIM and CDH2. NLRP7 knockdown partially reversed these effects. Immunofluorescence revealed enhanced apoptosis and inflammation in lung cancer cells, especially in NLRP7 knockdown cells treated with AH-6809. The regulatory mechanisms involve SUMO1-mediated post-translational modifications and NQO1. Further studies are required to elucidate the molecular mechanisms and assess the clinical potential of these findings.

Conclusion

These findings demonstrate the critical role of NLRP7 and associated genes in LUAD metastasis and suggest that AH-6809 holds promise as a potential therapeutic agent for brain-metastatic LUAD.

Tumor Methylation Burden (TMeB) in Non-Small Cell Lung Cancer: A New Way of Thinking About Epigenetics

Lung cancer represents a substantial proportion of cancer-associated mortality worldwide, with non-small cell lung cancer (NSCLC) accounting for most of these cases [...].

VIM-AS1, which is regulated by CpG methylation, cooperates with IGF2BP1 to inhibit tumor aggressiveness via EPHA3 degradation in hepatocellular carcinoma

Early tumor recurrence in hepatocellular carcinoma (HCC) remains a challenging area, as the mechanisms involved are not fully understood. While microvascular invasion is linked to early recurrence, established biomarkers for diagnosis and prognostication are lacking. In this study, our objective was to identify DNA methylation sites that can predict the outcomes of liver cancer patients and elucidate the molecular mechanisms driving HCC aggressiveness. Using DNA methylome data from HCC patient samples from the CGRC and TCGA databases, we pinpointed hypermethylated CpG sites in HCC. Our analysis revealed that cg02746869 acts as a crucial regulatory site for VIM-AS1 (vimentin antisense RNA1), a 1.8 kb long noncoding RNA. RNA sequencing of HCC cells with manipulated VIM-AS1 expression revealed EPHA3 as a pathogenic target of VIM-AS1, which performs an oncogenic function in HCC. Hypermethylation-induced suppression of VIM-AS1 significantly impacted HCC cell dynamics, particularly impairing motility and invasiveness. Mechanistically, reduced VIM-AS1 expression stabilized EPHA3 mRNA by enhancing the binding of IGF2BP1 to EPHA3 mRNA, leading to increased expression of EPHA3 mRNA and the promotion of HCC progression. In vivo experiments further confirmed that the VIM-AS1‒EPHA3 axis controlled tumor growth and the tumor microenvironment in HCC. These findings suggest that the downregulation of VIM-AS1 due to hypermethylation at cg02746869 increased EPHA3 mRNA expression via a m6A-dependent mechanism to increase HCC aggressiveness.

Epigenetic modulation of immune cells: Mechanisms and implications

Epigenetic modulation of the immune response entails modifiable and inheritable modifications that do not modify the DNA sequence. While there have been many studies on epigenetic changes in tumor cells, there is now a growing focus on epigenetically mediated changes in immune cells of both the innate and adaptive systems. These changes have significant implications for both the body's response to tumors and the development of potential therapeutic vaccines. This study primarily discusses the key epigenetic alterations, with a specific emphasis on pseudouridination, as well as non-coding RNAs and their transportation, which can lead to the development of cancer and the acquisition of new phenotypic traits by immune cells. Furthermore, the advancement of therapeutic vaccinations targeting the tumor will be outlined.

Connecting the dots: Involvement of methyltransferase-like 3, N6-methyladenosine modification, and ferroptosis in the pathogenesis of intracerebral hemorrhage pathogenesis

Intracerebral hemorrhage is a profoundly detrimental acute cerebrovascular condition with a low overall survival rate and a high post-onset disability rate. Secondary brain injury that ensues post-ICH is the primary contributor to fatality and disability. Hence, the mitigation of brain injury during intracerebral hemorrhage progression has emerged as a crucial aspect of clinical management. N6-methyladenosine is the most pervasive, abundant, and conserved internal co-transcriptional modification of eukaryotic ribonucleic acid and is predominantly expressed in the nervous system. Methyltransferase-like 3 is a key regulatory protein that is strongly associated with the development of the nervous system and numerous neurological diseases. Ferroptosis, a form of iron-associated cell death, is a typical manifestation of neuronal apoptosis in neurological diseases and plays an important role in secondary brain damage following intracerebral hemorrhage. Therefore, this review aimed to elucidate the connection between m6A modification (particularly methyltransferase-like 3) and ferroptosis in the context of intracerebral hemorrhage to provide new insights for future intracerebral hemorrhage management approaches.

A nomogram for cancer-specific survival of lung adenocarcinoma patients: A SEER based analysis

Background

Non-small cell lung cancer (NSCLC) accounts for 85 % of lung cancer cases. Among NSCLC subtypes, lung adenocarcinoma (LUAD) stands as the most prevalent. Regrettably, LUAD continues to exhibit a notably unfavorable overall prognosis. This study's primary aim was to develop and validate prognostic tools capable of predicting the likelihood of cancer-specific survival (CSS) in patients with LUAD.

Methods

We retrospectively collected 21,099 patients diagnosed with LUAD between 2010 and 2015, and 8290 patients diagnosed between 2004 and 2009 from SEER database. The cohort of 21,099 patients served as the prognostic group for the exploration of LUAD-related prognostic risk factors. The cohort of 8290 patients was designated for external validation. We created a training set and an internal validation set in the prognostic group for the development and internal validation of CSS nomograms. CSS predictors were identified through the least absolute shrinkage and selection operator (Lasso) regression analysis. Prognostic model was constructed via Cox hazard regression analysis, presented in the form of both static and dynamic network-based nomograms.

Results

Several independent prognostic factors were incorporated into the construction of nomogram. The nomogram accurately predicted CSS at 1, 3, and 5 years, with respective AUC values of 0.769, 0.761, and 0.748 for the training group, and 0.741, 0.752, and 0.740 for the testing group. The study demonstrated a strong agreement between anticipated and actual CSS values, supported by decision curve analysis (DCA) and time-dependent calibrated curves. High-risk patients based on the nomogram exhibiting significantly lower survival rates compared to their low-risk counterparts according to Kaplan-Meier (K-M) curves. The nomogram demonstrates excellent predictive power in the external validation cohort.

Conclusions

A dependable and user-friendly nomogram has been developed, available in both static and online dynamic calculator formats, to facilitate healthcare professionals in accurately estimating the likelihood of CSS for patients diagnosed LUAD.