Metabolic reprogramming and epigenetic modifications in cancer: from the impacts and mechanisms to the treatment potential

Microbiome, metabolome, and ionome profiling of cyst fluids reveals heterogeneity in pancreatic cystic neoplasms

Pancreatic cystic neoplasms (PCNs) carry variable malignant potential, requiring precise clinical management. However, the heterogeneity and progression of PCNs remain poorly understood. This study analyzed the microbiome, metabolome, and ionome profiles of cyst fluids from 188 patients, including 165 with PCNs and 23 with other cyst types, using PacBio full-length 16S/ITS sequencing, LC-MS/MS, and ICP-MS. Bioinformatic analyses were performed, and metabolic enzyme and endoplasmic reticulum (ER) stress-related gene expression were examined using the PAAD TCGA dataset. PCNs were classified into distinct histopathological subtypes, including mucinous cystic lesions (MCLs) and serous cystic lesions (SCLs). MCLs demonstrated lower microbial diversity compared to SCLs, indicating microbial instability. Streptococcus and Staphylococcus were identified as key taxa in intraductal papillary mucinous neoplasms (IPMNs) and mucinous cystic neoplasms (MCNs), respectively. MCLs exhibited metabolic shifts towards lipid metabolism, while IPMNs showed distinct metabolic profiles potentially reflecting inflammation-related metabolic reprogramming. Ionic diversity varied among subtypes, with MCLs showing reduced diversity and IPMNs presenting broader ionic profiles. Palmitic acid (PA), a metabolite linked to Streptococcus, may contribute to pro-inflammatory metabolic alterations in IPMN. Our preliminary experiments demonstrated that co-culturing Streptococcus orails (S. orails) with ASAN-PaCa cells promoted their proliferation, accompanied by an elevation of PA levels in the supernatant. This integrative microbiome-metabolome-ionome analysis highlights histopathological heterogeneity among PCNs. While mechanistic associations remain to be fully defined, mucinous lesions may be more susceptible to microbe-driven metabolic disruption, with Streptococcus-associated lipid alterations as a potential contributing factor.

Targeted inhibition of JMJD2C/MALAT1 axis compensates for the deficiency of metformin in reversing ovarian cancer platinum resistance

AIMS

We explored JMJD2C's role in platinum resistance in ovarian cancer and its modulation by metformin to propose strategies for overcoming treatment limitations.

MATERIALS AND METHODS

JMJD2C and MALAT1 expression was assessed via RT-qPCR, western blotting, and immunohistochemical assays using OC cell lines, tissue from OC patients, and xenograft treatment with or without metformin. CCK-8 assays, flow cytometry, inductively coupled plasma mass spectrometry, luciferase reporter assays, and ChIP assays were employed to evaluate the impact of JMJD2C/MALAT1 on PR and the effects of metformin on JMJD2C. The effects of metformin in combination with JMJD2C knockdown were assessed in vitro and in vivo.

KEY FINDINGS

JMJD2C and MALAT1 expression was higher in tissue samples from platinum-resistant phase compared to those from paired platinum-sensitive phase. JMJD2C upregulated MALAT1 in platinum-resistant ovarian cancer (PROC) cells by demethylating its promoter at sites H3K9m3 and H3K36m3. Overexpression of JMJD2C or MALAT1 promoted PR by activating NF-κB/P-gp and P38 MAPK/ERCC1 signaling pathways, with their knockdown produced the opposite effect. Metformin increased JMJD2C expression in tumor tissue, cell lines, and a xenograft model of OC; however, elevated JMJD2C expression attenuated the PR-reversal efficacy of low-concentration metformin. Low-dose metformin combined with JMJD2C-knockdown effectively reversed PR both in in vitro and in vivo, achieving better results than either treatment alone.

SIGNIFICANCE

JMJD2C drives PR in OC by demethylating the MALAT1 promoter. Metformin upregulated JMJD2C expression, thus necessitating a higher effective dosage of metformin. Targeted inhibition of JMJD2C synergistically enhanced the efficacy of low-dose metformin in overcoming PR, thus providing a promising approach for addressing PR.

A pyrimidine metabolism-related gene signature for prognosis prediction and immune microenvironment description of breast cancer

BACKGROUND

Metabolic reprogramming is a hallmark in cancer. Pyrimidine metabolism (PM), a part of nucleotide metabolism, has been shown to be associated with the progression of various cancers, and the prognostic predictive ability of pyrimidine metabolism-related genes (PMG) in breast cancer has not been elucidated. This paper was designed to identify pyrimidine metabolism-related prognostic marker of breast cancer and potential targeted therapeutic options.

METHODS

The cohort in the TCGA-BRCA dataset was used for patient information, and 108 pyrimidine metabolism-related genes were identified from the MSigDB KEGG pathways. We identified PM clusters in breast cancer and established a PM risk score model based on 10 pyrimidine metabolism-related genes. The status of immune infiltration was assessed in different groups. Further we identified the relevant hub gene and analyzed its significance for breast cancer metastasis and explored patterns of combination therapy.

RESULTS

We identified three types of PM clusters in breast cancer and clarified that PM cluster C with inferior prognosis possessed activation of tumor proliferation-associated pathways. The high-risk group in PM risk score model was found to be characterized by an immunosuppressive microenvironment. The hub gene POLR2C (RNA polymerase II subunit C) was further identified and verified as a potential prognostic marker. Furthermore, targeting POLR2C in combination with anti-PD-1 and anti-angiogenic therapies demonstrated a promising tumor suppression effect, suggesting a potential therapeutic direction.

CONCLUSIONS

These findings provide additional insights into the link between breast cancer and PMG, offering potential strategies for breast cancer management and treatment.

Nuclear-localized metabolic enzymes: emerging key players in tumor epigenetic regulation

Advancements in tumor research have highlighted the potential of epigenetic therapies as a targeted approach to cancer treatment. However, the application of these therapies has faced challenges due to the issue of substrate availability since the discovery of epigenetic modifications. Interestingly, metabolic changes are closely associated with epigenetic changes, and notably, certain metabolic enzymes exhibit nuclear localization within epigenetically active cellular contexts. This suggests that nuclear localization of metabolic enzymes may provide a mechanistic foundation for addressing substrate availability issues in epigenetic regulation. To date, there has been limited progress in synthesizing this information systematically. In this study, we provide an overview of the interplay between metabolic enzymes and epigenetic mechanisms, highlighting their critical roles. Subsequently, we summarize recent advances regarding the nuclear localization of metabolic enzymes, shedding light on their emerging roles in epigenetic regulation and oncogenesis.

The impact of radiotherapy on the prognosis of metastatic clear cell renal cell carcinoma after surgery

Clear cell renal cell carcinoma, one of the most common types of renal cell carcinoma, has been increasing in incidence year by year. This study aims to investigate the impact of radiotherapy on the prognosis of patients with metastatic clear cell renal cell carcinoma (mccRCC) undergoing cytoreductive surgery. Clinical data of patients with mccRCC who underwent cytoreductive surgery were collected from the SEER database (2000-2021). This study employed propensity score matching (PSM) and R software to evaluate the overall survival (OS) of radiotherapy. Univariate and multivariate COX regression analyses were conducted to explore the impact of different variables on prognosis. Finally, a nomogram was developed to predict patient survival rates. A total of 2076 patients with mccRCC who underwent cytoreductive surgery were included in this study, with 538 (25.92%) in the radiotherapy group and 1539 (74.08%) in the non-radiotherapy group. After propensity score matching (PSM), there were 300 cases in each group. Kaplan-Meier values and the Cox proportional hazards model were used to plot the overall survival (OS) curves, which showed that the median survival time in the radiotherapy group was significantly lower than that in the non-radiotherapy group. Additionally, multivariate Cox regression analysis revealed that tumor grade, N stage, radiotherapy, lung metastasis, and liver metastasis were independent factors affecting the prognosis of patients with mccRCC undergoing cytoreductive surgery. Lastly, a nomogram was developed to estimate the survival rates of patients with mccRCC after cytoreductive surgery. Radiotherapy after cytoreductive surgery may have an adverse impact on the prognosis of patients with mccRCC.

Ethyl p-methoxycinnamate inhibits tumor growth by suppressing of fatty acid synthesis and depleting ATP

Cancer cells reprogram their energy metabolism pathways, but the mechanisms that enable them to meet their energy demands remain poorly understood. This study investigates the anticancer effects of ethyl p-methoxycinnamate (EMC) in Ehrlich ascites tumor cells (EATCs) and reveals that de novo fatty acid synthesis, rather than glycolysis, plays a pivotal role in sustaining energy homeostasis in cancer cells. EMC significantly reduced ATP levels despite enhancing glycolytic activity. It suppressed the expression of key enzymes involved in de novo fatty acid synthesis, including Acly, Acc1, and Fasn, resulting in decreased intracellular triglyceride (TG) levels. The addition of exogenous palmitic acid reversed EMC-induced ATP depletion and mitigated its anti-proliferative effects. Mechanistically, the ATP reduction caused by EMC was associated with inhibition of the c-Myc/SREBP1 pathway and arrest of the G1/S cell cycle transition. These findings demonstrate that EMC inhibits EATC proliferation by reducing ATP levels via suppression of de novo fatty acid synthesis. This study highlights the critical role of de novo fatty acid synthesis, rather than glycolysis, in maintaining energy homeostasis in cancer cells and provides novel insights into targeting cancer metabolism.

Emerging Multifunctional Biomaterials for Addressing Drug Resistance in Cancer

Drug resistance remains a major barrier to effective cancer treatment, contributing to poor patient outcomes. Multifunctional biomaterials integrating electrical and catalytic properties offer a transformative strategy to target diverse resistance mechanisms. This review explores their ability to modulate cellular processes, remodel the tumor microenvironment (TME), and enhance drug delivery. Electrically active biomaterials enhance drug uptake and apoptotic sensitivity by altering membrane potentials, ion channels, and intracellular signaling, synergizing with chemotherapy. Catalytic biomaterials generate reactive oxygen species (ROS), activate prodrugs, reprogram hypoxic and acidic TME, and degrade the extracellular matrix (ECM) to improve drug penetration. Hybrid nanomaterials (e.g., conductive hydrogels, electrocatalytic nanoparticles), synergize electrical and catalytic properties for localized, stimuli-responsive therapy and targeted drug release, minimizing systemic toxicity. Despite challenges in biocompatibility and scalability, future integration with immunotherapy, personalized medicine, and intelligent self-adaptive systems capable of real-time tumor response promises to accelerate clinical translation. The development of these adaptive biomaterials, alongside advancements in nanotechnology and AI-driven platforms, represents the next frontier in precision oncology. This review highlights the potential of multifunctional biomaterials to revolutionize cancer therapy by addressing multidrug resistance at cellular, genetic, and microenvironmental levels, offering a roadmap to improve therapeutic outcomes and reshape oncology practice.

CRISPR/Cas-mediated macromolecular DNA methylation editing: Precision targeting of DNA methyltransferases in cancer therapy

Epigenetic modifications, particularly DNA methylation, play a pivotal role in gene regulation, influencing tumor suppressor silencing and oncogene activation in cancer. DNA methyltransferases (DNMTs), Ten-eleven translocation (TET) enzymes, and associated chromatin regulators are key biological macromolecules that mediate these epigenetic processes. Targeting aberrant DNA methylation holds great promise for cancer therapy, but traditional approaches lack precision and specificity. CRISPR/Cas-based epigenetic editing has emerged as a transformative tool for macromolecular DNA methylation reprogramming, offering targeted modifications without altering the genetic sequence. This review explores the role of DNMTs, TET enzymes, and chromatin-associated proteins in cancer epigenetics and discusses how CRISPR/dCas9 fused with DNMT3A or TET1 enables locus-specific DNA methylation editing. We highlight recent advances, including dCas9-DNMT3A for precise hypermethylation and dCas9-TET1 for targeted demethylation, and discuss their applications in reactivating tumor suppressor genes or silencing oncogenic pathways. Novel epigenetic editing systems, such as SunTag-based amplification, KRAB-MeCP2 repression, further enhance targeting efficiency and therapeutic potential. CRISPR/Cas-mediated macromolecular epigenetic editing represents a paradigm shift in cancer therapy, providing unprecedented control over DNA methylation and chromatin regulation. Despite challenges such as tumor heterogeneity and off-target effects, integrating CRISPR-based methylation reprogramming with precision oncology holds immense promise for future clinical applications.

The Synergistic Mechanisms and Prospects of Transarterial Chemoembolization Combined with Immunotherapy for Hepatocellular Carcinoma

Hepatocellular carcinoma (HCC) represents a highly aggressive form of liver neoplasm that presents various therapeutic obstacles. Recently, the synergistic use of transarterial chemoembolization (TACE) in conjunction with immunotherapy has attracted considerable interest within the medical community. This review aims to explore the synergistic mechanisms between TACE and immunotherapy, analyze the current research evidence, and discuss their potential applications in the treatment of HCC. By examining how TACE can enhance the efficacy of immunotherapy, we seek to provide direction for future research and emphasize the importance of personalized treatment strategies in managing HCC.

Lysine methyltransferase SETD7 in cancer: functions, molecular mechanisms and therapeutic implications

Since its discovery as a histone methyltransferase, SETD7 has been implicated in many signaling pathways and carcinogenesis. SETD7 catalyzes the methylation of histone H3 and non-histone proteins, regulating their translation, stability and activity. SETD7 is frequently abnormally expressed and has a significant influence on cell proliferation, invasion, autophagy and immune response. As cancer is a complex disease, an outstanding concept in cancer biology is the "hallmarks of cancer". In this review, we focus on the involvement of SETD7 in the hallmarks of cancer, describing its functions and underlying mechanisms in detail. Additionally, we discuss non-coding RNAs and chemical inhibitors targeting SETD7, highlighting the potential and importance of SETD7 in cancer therapy.

The current findings on the gut-liver axis and the molecular basis of NAFLD/NASH associated with gut microbiome dysbiosis

Recent research has highlighted the complex relationship between gut microbiota, metabolic pathways, and nonalcoholic fatty liver disease (NAFLD) progression. Gut dysbiosis, commonly observed in NAFLD patients, impairs intestinal permeability, leading to the translocation of bacterial products like lipopolysaccharides, short-chain fatty acids, and ethanol to the liver. These microbiome-associated mechanisms contribute to intestinal and hepatic inflammation, potentially advancing NAFLD to NASH. Dietary habits, particularly those rich in saturated fats and fructose, can modify the microbiome composition, leading to dysbiosis and fatty liver development. Metabolomic approaches have identified unique profiles in NASH patients, with specific metabolites like ethanol linked to disease progression. While bariatric surgery has shown promise in preventing NAFLD progression, the role of gut microbiome and metabolites in this improvement remains to be proven. Understanding these microbiome-related pathways may provide new diagnostic and therapeutic targets for NAFLD and NASH. A comprehensive review of current literature was conducted using multiple medical research databases, including PubMed, Scopus, Web of Science, Embase, Cochrane Library, ClinicalTrials.gov, ScienceDirect, Medline, ProQuest, and Google Scholar. The review focused on studies that examine the relationship between gut microbiota composition, metabolic pathways, and NAFLD progression. Key areas of interest included microbial dysbiosis, endotoxin production, and the influence of diet on gut microbiota. The analysis revealed that gut dysbiosis contributes to NAFLD through several mechanisms, diet significantly influences gut microbiota composition, which in turn affects liver function through the gut-liver axis. High-fat diets can lead to dysbiosis, altering microbial metabolic activities and promoting liver inflammation. Specifically, gut microbiota-mediated generation of saturated fatty acids, such as palmitic acid, can activate liver macrophages and increase TNF-α expression, contributing to NASH development. Different dietary components, including cholesterol, fiber, fat, and carbohydrates, can modulate the gut microbiome and influence NAFLD progression. This gut-liver axis plays a crucial role in maintaining immune homeostasis, with the liver responding to gut-derived bacteria by activating innate and adaptive immune responses. Microbial metabolites, such as bile acids, tryptophan catabolites, and branched-chain amino acids, regulate adipose tissue and intestinal homeostasis, contributing to NASH pathogenesis. Additionally, the microbiome of NASH patients shows an elevated capacity for alcohol production, suggesting similarities between alcoholic steatohepatitis and NASH. These findings indicate that targeting the gut microbiota may be a promising approach for NASH treatment and prevention. Recent research highlights the potential of targeting gut microbiota for managing nonalcoholic fatty liver disease (NAFLD). The gut-liver axis plays a crucial role in NAFLD pathophysiology, with dysbiosis contributing to disease progression. Various therapeutic approaches aimed at modulating gut microbiota have shown promise, including probiotics, prebiotics, synbiotics, fecal microbiota transplantation, and dietary interventions. Probiotics have demonstrated efficacy in human randomized controlled trials, while other interventions require further investigation in clinical settings. These microbiota-targeted therapies may improve NAFLD outcomes through multiple mechanisms, such as reducing inflammation and enhancing metabolic function. Although lifestyle modifications remain the primary recommendation for NAFLD management, microbiota-focused interventions offer a promising alternative for patients struggling to achieve weight loss targets.

Impact of Intermittent Fasting with a Ketogenic Diet on AMPK Levels in Breast Cancer Patients Receiving Chemotherapy

Adenosine monophosphate-activated protein kinase (AMPK), a metabolic sensor activated by nutrient starvation, plays a multifaceted role in cancer. Whether AMPK is beneficial or malevolent is controversial. This study aimed to investigate AMPK levels in breast cancer patients receiving chemotherapy and compare the effects of intermittent fasting combined with different diets on these levels. Forty-five breast cancer patients were divided into three groups: a control, a group practicing 23:1-h intermittent fasting (IF) with a routine diet (RD), and another with a ketogenic diet (KD) over 4 weeks. Body mass index (BMI), Carbohydrate Antigen 15-3 (CA 15-3) levels, and serum AMPK levels were measured pre and post-intervention. Results showed a significant increase in AMPK levels in both the fasting groups and no significant difference in the non-fasting group, with the keto diet group showing the most significant growth. CA 15-3 levels were reduced in all the groups but significantly reduced in the KD group as compared to the RD group. This study shows that intermittent fasting with the keto diet improves AMPK levels and may serve as a valuable non-pharmacological complementary strategy for reducing or eliminating the tumor and, simultaneously, preventing the healthy cells from the toxic side effects of chemotherapy.

From Data to Cure: A Comprehensive Exploration of Multi-omics Data Analysis for Targeted Therapies

In the dynamic landscape of targeted therapeutics, drug discovery has pivoted towards understanding underlying disease mechanisms, placing a strong emphasis on molecular perturbations and target identification. This paradigm shift, crucial for drug discovery, is underpinned by big data, a transformative force in the current era. Omics data, characterized by its heterogeneity and enormity, has ushered biological and biomedical research into the big data domain. Acknowledging the significance of integrating diverse omics data strata, known as multi-omics studies, researchers delve into the intricate interrelationships among various omics layers. This review navigates the expansive omics landscape, showcasing tailored assays for each molecular layer through genomes to metabolomes. The sheer volume of data generated necessitates sophisticated informatics techniques, with machine-learning (ML) algorithms emerging as robust tools. These datasets not only refine disease classification but also enhance diagnostics and foster the development of targeted therapeutic strategies. Through the integration of high-throughput data, the review focuses on targeting and modeling multiple disease-regulated networks, validating interactions with multiple targets, and enhancing therapeutic potential using network pharmacology approaches. Ultimately, this exploration aims to illuminate the transformative impact of multi-omics in the big data era, shaping the future of biological research.

Functions and mechanisms of non-histone post-translational modifications in cancer progression

Protein post-translational modifications (PTMs) refer to covalent and enzymatic alterations to folded or nascent proteins during or after protein biosynthesis to alter the properties and functions of proteins. PTMs are modified in a variety of types and affect almost all aspects of cell biology. PTMs have been reported to be involved in cancer progression by influencing multiple signaling pathways. The mechanism of action of histone PTMs in cancer has been extensively studied. Notably, evidence is mounting that PTMs of non-histone proteins also play a vital role in cancer progression. In this review, we provide a systematic description of main non-histone PTMs associated with cancer progression, including acetylation, lactylation, methylation, ubiquitination, phosphorylation, and SUMOylation, based on recent studies.

Cell Progression and Survival Functions of Enzymes Secreted in Extracellular Vesicles Associated with Breast and Prostate Cancers

Extracellular vesicles (EVs) are membrane-bound cargoes secreted by normal and pathological cells. Through their protein, nucleic acid, and lipid cargoes, EVs mediate several cellular processes, such as cell-cell communication, cell development, immune response, and tissue repair. Most importantly, through their enzyme cargo, EVs mediate pathophysiological processes, including the pathogenesis of cancer. In this review, we enumerate several enzymes secreted in EVs (EV enzyme cargo) from cells and patient clinical samples of breast and prostate cancers and detail their contributions to the progression and survival of both cancers. Findings in this review reveal that the EV enzyme cargo could exert cell progression functions via adhesion, proliferation, migration, invasion, and metastasis. The EV enzyme cargo might also influence cell survival functions of chemoresistance, radioresistance, angiogenesis, cell death inhibition, cell colony formation, and immune evasion. While the current literature provides evidence of the possible contributions of the EV enzyme cargo to the progression and survival mechanisms of breast and prostate cancers, future studies are required to validate that these effects are modified by EVs and provide insights into the clinical applications of the EV enzyme cargo in breast and prostate cancer.

Machine learning reveals glycolytic key gene in gastric cancer prognosis

Glycolysis is recognized as a central metabolic pathway in the neoplastic evolution of gastric cancer, exerting profound effects on the tumor microenvironment and the neoplastic growth trajectory. However, the identification of key glycolytic genes that significantly affect gastric cancer prognosis remains underexplored. In this work, five machine-learning algorithms were used to elucidate the intimate association between the glycolysis-associated gene phosphofructokinase fructose-bisphosphate 3 (PFKFB3) and the prognosis of gastric cancer patients. Validation across multiple independent datasets confirmed the prognostic significance of PFKFB3. Further, we delved into the functional implications of PFKFB3 in modulating immune responses and biological processes within gastric cancer patients, as well as its broader relevance across multiple cancer types. Results underscore the potential of PFKFB3 as a prognostic biomarker and therapeutic target in gastric cancer. Our project can be found at https://github.com/PiPiNam/ML-GCP .

SRSF9 mediates oncogenic RNA splicing of SLC37A4 via liquid-liquid phase separation to promote oral cancer progression

INTRODUCTION

Oral cancer represents a significant proportion of head and neck malignancies, accounting for approximately 3 % of all malignant tumors worldwide.

OBJECTIVES

Alternative splicing (AS), a post-transcriptional regulatory mechanism, is increasingly linked to cancer development. The precise impact of AS on oral cancer progression is not well understood.

METHODS

Bioinformatics, semi-quantitative RT-PCR, and minigene reporter system to detect the skipping of SLC37A4 exon 7 in oral cancer. FRAP, live cell immunofluorescence demonstrates that SRSF9 can undergo liquid-liquid phase separation (LLPS). In vivo and in vitro experiments with subcutaneous graft tumors, CCK8, EdU, transwell, and others were used to detect the effects of SRSF9 and its induced SLC37A4-S isoforms on the malignant phenotype of oral cancer cells.

RESULTS

Our investigation revealed a multitude of aberrant alternative splicing events within head and neck tumor tissues, most notably the pronounced skipping of exon 7 in the SLC37A4 gene. This splicing anomaly leads to the production of a truncated isoform, SLC37A4-S, which is associated with a poor prognosis and significantly augments the proliferation and metastatic potential of oral cancer cells relative to the wild-type isoform, SLC37A4-L. Mechanically, SRSF9 may play a regulatory role in the aberrant splicing of SLC37A4. Furthermore, SRSF9 is capable of undergoing LLPS, a process driven by its arginine-serine-rich (RS) domain. Disruption of SRSF9 LLPS through the use of inhibitors or mutants effectively prevents its regulatory influence on the splicing of SLC37A4. Significantly, our research demonstrates that both SRSF9 and its regulated splicing isoforms of SLC37A4-S contribute to cisplatin chemotherapy resistance in oral cancer cells.

CONCLUSION

This study elucidates the mechanism by which SRSF9 phase separation mediates splicing in oral cancer, thereby establishing a basis for considering SRSF9 and its associated SLC37A4-S isoforms as potential therapeutic targets for oral cancer treatment.

HOTAIR Participation in Glycolysis and Glutaminolysis Through Lactate and Glutamate Production in Colorectal Cancer

Metabolic reprogramming plays a crucial role in cancer biology and the mechanisms underlying its regulation represent a promising study area. In this regard, the discovery of non-coding RNAs opened a new regulatory landscape, which is in the early stages of investigation. Using a differential expression model of HOTAIR, we evaluated the expression level of metabolic enzymes, as well as the metabolites produced by glycolysis and glutaminolysis. Our results demonstrated the regulatory effect of HOTAIR on the expression of glycolysis and glutaminolysis enzymes in colorectal cancer cells. Specifically, through the overexpression and inhibition of HOTAIR, we determined its influence on the expression of the enzymes PFKFB4, PGK1, LDHA, SLC1A5, GLUD1, and GOT1, which had a direct impact on lactate and glutamate production. These findings indicate that HOTAIR plays a significant role in producing "oncometabolites" essential to maintaining the bioenergetics and biomass necessary for tumor cell survival by regulating glycolysis and glutaminolysis.

CircXPO6 promotes breast cancer progression through competitively inhibiting the ubiquitination degradation of c-Myc

The number of breast cancer (BC) patients is increasing year by year, which is severely endangering to human life and health. c-Myc is a transcription factor, studies have shown that it is a very significant factor in tumor progression, but how it is regulated in BC is still not well understood. Here, we used the RIP microarray sequencing to confirm circXPO6, which had a high affinity with c-Myc and highly expressed in triple-negative breast cancer (TNBC) tissues and cells. CircXPO6 overexpression promoted tumor growth in vivo and in vitro. Furthermore, circXPO6 largely promoted the expression of genes related to glucose metabolism, such as GLUT1, HK2, and MCT4 in TNBC cells. Finally, high levels of circXPO6 expression were found to be closely associated with malignant pathological factors, such as tumor size, lymph node metastasis, TNM staging, and histopathological grading of TNBC. Mechanistically, circXPO6 interacted with c-Myc to prevent speckle-type POZ-mediated c-Myc ubiquitination and degradation, thus promoting TNBC progression. Through the regulation of c-Myc-mediated signal transduction, circXPO6 plays a key role in TNBC progresses. This discovery can provide new ideas for TNBC molecular targeted therapy.

Protein lactylation in cancer: mechanisms and potential therapeutic implications

Increased glycolysis, which leads to high lactate production, is a common feature of cancer cells. Recent evidence suggests that lactate plays a role in the post-translational modification of histone and nonhistone proteins via lactylation. In contrast to genetic mutations, lactylation in cancer cells is reversible. Thus, reversing lactylation can be exploited as a pharmacological intervention for various cancers. Here we discuss recent advances in histone and nonhistone lactylation in cancer, including L-, D- and S-lactylation, as well as alanyl-tRNA synthetase as a novel lactyltransferase. We also discuss potential approaches for targeting lactylation as a therapeutic opportunity in cancer treatment.

YY2-CYP51A1 signaling suppresses hepatocellular carcinoma progression by restraining de novo cholesterol biosynthesis

Lipid accumulation is a frequently observed characteristic of cancer. Lipid accumulation is closely related to tumor progression, metastasis, and drug resistance; however, the mechanism underlying lipid metabolic reprogramming in tumor cells is not fully understood. Yin yang 2 (YY2) is a C2H2‑zinc finger transcription factor that exerts tumor-suppressive effects. However, its involvement in tumor cell lipid metabolic reprogramming remains unclear. In the present study, we identified YY2 as a novel regulator of cholesterol metabolism. We showed that YY2 suppressed cholesterol accumulation in hepatocellular carcinoma (HCC) cells by downregulating the transcriptional activity of cytochrome P450 family 51 subfamily A member 1 (CYP51A1), a key enzyme in de novo cholesterol biosynthesis. Subsequently, through in vitro and in vivo experiments, we demonstrated that this downregulation is crucial for the YY2 tumor suppressive effect. Together, our findings unraveled a previously unprecedented regulation of HCC cells cholesterol metabolism, and eventually, their tumorigenic potential, through YY2 negative regulation on CYP51A1 expression. This study revealed a novel regulatory mechanism of lipid metabolic reprogramming in tumor cells and provided insights into the molecular mechanism underlying the YY2 the suppressive effect. Furthermore, our findings suggest a potential antitumor therapeutic strategy targeting cholesterol metabolic reprogramming using YY2.

Bioinformatics Identification of Lactate-Associated Genes in Hepatocellular Carcinoma: G6PD's Role in Immune Modulation

BACKGROUND

Hepatocellular carcinoma (HCC) is a major global health issue, with poor prognosis often associated with dysregulated metabolic pathways, especially lactate metabolism. This study explored the prognostic significance of lactate-associated genes in HCC and their potential as therapeutic targets.

METHODS

We analyzed RNA-seq and clinical data from 374 patients with HCC from The Cancer Genome Atlas (TCGA) database. Using Cox regression, LASSO analysis, and Kaplan-Meier survival curves, we identified key lactate-associated genes associated with patient outcomes. Functional validations, including Western blot, flow cytometry, and molecular docking studies, were performed to confirm the biological impact of these genes.

RESULTS

G6PD, IK, and CALML5 were identified as significant prognostic markers for HCC. A prognostic model was developed that effectively stratified patients into risk groups, which correlated with survival. G6PD's role in immune modulation and its potential as a drug target were validated through biochemical assays and computational analyses. Functional assays in HepG2 cells confirmed that alterations in G6PD expression affect T cell activity, with knockdown enhancing IFN-γ production and overexpression inhibiting it, demonstrating G6PD's role in immune evasion.

CONCLUSIONS

This study establishes lactate metabolism genes, particularly G6PD, as key prognostic markers in HCC. The validation of G6PD's immunomodulatory effects further supports its potential as a therapeutic target for strategies aimed at enhancing immune surveillance and treatment outcomes in HCC.

Machine Learning-Based Glycolipid Metabolism Gene Signature Predicts Prognosis and Immune Landscape in Oesophageal Squamous Cell Carcinoma

Using machine learning approaches, we developed and validated a novel prognostic model for oesophageal squamous cell carcinoma (ESCC) based on glycolipid metabolism-related genes. Through integrated analysis of TCGA and GEO datasets, we established a robust 15-gene signature that effectively stratified patients into distinct risk groups. This signature demonstrated superior prognostic value and revealed significant associations with immune infiltration patterns. High-risk patients exhibited reduced immune cell infiltration, particularly in B cells and NK cells, alongside increased tumour purity. Single-cell RNA sequencing analysis uncovered unique cellular composition patterns and enhanced interaction intensities in the high-risk group, especially within epithelial and smooth muscle cells. Functional validation confirmed MECP2 as a promising therapeutic target, with its knockdown significantly inhibiting tumour progression both in vitro and in vivo. Drug sensitivity analysis identified specific therapeutic agents showing potential efficacy for high-risk patients. Our study provides both a practical prognostic tool and novel insights into the relationship between glycolipid metabolism and tumour immunity in ESCC, offering potential strategies for personalised treatment.

A comprehensive prognostic and immune analysis of LAPTM4B in pan-cancer and Philadelphia chromosome-positive acute lymphoblastic leukemia

Introduction

Lysosomal-associated protein transmembrane-4 beta (LAPTM4B) protein expression was increased in solid tumors, whereas few studies were performed in hematologic malignancies. We aimed to study the effect of the LAPTM4B gene in pan-cancer and Philadelphia chromosome-positive acute B cell lymphoblastic leukemia (Ph+ B-ALL).

Methods

The differential expression, diagnosis, prognosis, genetic and epigenetic alterations, tumor microenvironment, stemness, immune infiltration cells, function enrichment, single-cell analysis, and drug response across cancers were conducted based on multiple computational tools. Additionally, Ph+ B-ALL transgenic mouse model with Laptm4b knockout was used to analyze the function of LAPTM4B in vivo. BrdU incorporation method, flow cytometry, and Witte-lock Witte culture were used to evaluate the roles of LAPTM4B in vitro.

Results

We identified that LAPTM4B expression was increased in various cancers, with significant associations with clinical outcomes. LAPTM4B expression correlated with DNA and RNA methylation patterns and was associated with drug resistance. It also influenced the tumor immune microenvironment, with implications for immunotherapy response. In leukemia, LAPTM4B was expressed in stem cells and associated with specific subtypes. Knockout of LAPTM4B impeded B-ALL progression in mice and reduced cell proliferation and caused G0/G1 arrest in vitro.

Discussion

Our study elucidated the role LAPTM4B that promoted the development and progression in Ph+ B-ALL. Furthermore, LAPTM4B played a diagnostic, prognostic, and immunological factor.

The association of metabolic disorders and prognosis in cancer patients

OBJECTIVE

Metabolic disorders are common in cancer patients. This study aimed to classify the metabolic disorder status of cancer patients using hematological indicators and to examine the association between disorder types and prognosis.

METHODS

A cohort of 6307 patients from INSCOC was classified into three clusters via K-means clustering based on hematological indicators. Logistic regression and Cox models assessed each cluster's impact on adverse outcomes.

RESULTS

A total of 6,307 participants were included in the study, K-means clustering divided the population into three groups, Cluster 1 (Normal Group, NG), Cluster 2 (Mild Disorder Group, MDG) and Cluster 3 (Severe Disorder Group, SDG). Compared to NG, MDG (OR = 2.268; 95% CI: 1.967-2.616) and SDG (OR = 4.317; 95% CI: 2.441-7.634) had significantly higher risks of sarcopenia. MDG (OR = 1.943; 95% CI: 1.717-2.198) was associated with a higher risk of moderate malnutrition, and both MDG (OR = 3.786; 95% CI: 3.282-4.368) and SDG (OR = 14.501; 95% CI: 6.847-30.709) were identified as risk factors for severe malnutrition (p < 0.05). Cox regression analysis indicated that MDG and SDG were independent risk factors for all-cause mortality (MDG: HR = 1.460, 95% CI: 1.341-1.590; SDG: HR = 2.257, 95% CI: 1.622-3.140) and cancer-specific mortality (MDG: HR = 1.192, 95% CI: 1.039-1.367; SDG: HR = 2.068, 95% CI: 1.825-2.343) (p < 0.05).

CONCLUSION

K-means clustering effectively categorized metabolic disorder subgroups, supporting targeted interventions and demonstrating a significant link between disorder severity and adverse outcomes.

Analysis of microarray and single-cell RNA-seq identifies gene co-expression, cell-cell communication, and tumor environment associated with metabolite interconversion enzyme in prostate cancer

BACKGROUND

Prostate cancer (PCa) is the second most common malignant neoplasm in males and is the fifth leading cause of cancer-related mortality. Due to the use of prostate-specific antigen (PSA) screening and improved biopsy techniques, persons identified with early-stage prostate cancer often have a positive prognosis after comprehensive treatment. Nonetheless, prostate cancer is a latent illness that may present as an asymptomatic tumor in individuals aged 20-30. The overall survival (OS) of men with advanced PCa is significantly diminished. Consequently, there is an immediate want for innovative, accurate biomarkers to detect early prostate cancer.

METHODS

This research analyzed the interaction network of differentially expressed genes (DEGs) related to metabolite interconversion enzymes in PCa by gene expression microarray data, single-cell RNA sequencing, oncogenes, and tumor suppressor genes (TSGs) utilizing bioinformatics techniques. This kind of analysis has not been documented in prior studies.

RESULTS

We then used a dataset acquired by the Cancer Genome Atlas (TCGA) to confirm our findings. Genes including CYP3A5, PDE8B, AOX1, BNIPL, FADS2, RRM2, ALDH3B2, and GSTM2 may be significant in the diagnosis and treatment of PCa.

CONCLUSION

Our objective was to provide new perspectives on the molecular properties and pathways of DEGs in PCa and to uncover potential biomarkers that play a crucial role in the genesis and progression of PCa.

Tumor dormancy and relapse: understanding the molecular mechanisms of cancer recurrence

Cancer recurrence, driven by the phenomenon of tumor dormancy, presents a formidable challenge in oncology. Dormant cancer cells have the ability to evade detection and treatment, leading to relapse. This review emphasizes the urgent need to comprehend tumor dormancy and its implications for cancer recurrence. Despite notable advancements, significant gaps remain in our understanding of the mechanisms underlying dormancy and the lack of reliable biomarkers for predicting relapse. This review provides a comprehensive analysis of the cellular, angiogenic, and immunological aspects of dormancy. It highlights the current therapeutic strategies targeting dormant cells, particularly combination therapies and immunotherapies, which hold promise in preventing relapse. By elucidating these mechanisms and proposing innovative research methodologies, this review aims to deepen our understanding of tumor dormancy, ultimately facilitating the development of more effective strategies for preventing cancer recurrence and improving patient outcomes.

Metabolic crossroads: unravelling immune cell dynamics in gastrointestinal cancer drug resistance

Metabolic reprogramming within the tumor microenvironment (TME) plays a critical role in driving drug resistance in gastrointestinal cancers (GI), particularly through the pathways of fatty acid oxidation and glycolysis. Cancer cells often rewire their metabolism to sustain growth and reshape the TME, creating conditions such as nutrient depletion, hypoxia, and acidity that impair antitumor immune responses. Immune cells within the TME also undergo metabolic alterations, frequently adopting immunosuppressive phenotypes that promote tumor progression and reduce the efficacy of therapies. The competition for essential nutrients, particularly glucose, between cancer and immune cells compromises the antitumor functions of effector immune cells, such as T cells. Additionally, metabolic by-products like lactate and kynurenine further suppress immune activity and promote immunosuppressive populations, including regulatory T cells and M2 macrophages. Targeting metabolic pathways such as fatty acid oxidation and glycolysis presents new opportunities to overcome drug resistance and improve therapeutic outcomes in GI cancers. Modulating these key pathways has the potential to reinvigorate exhausted immune cells, shift immunosuppressive cells toward antitumor phenotypes, and enhance the effectiveness of immunotherapies and other treatments. Future strategies will require continued research into TME metabolism, the development of novel metabolic inhibitors, and clinical trials evaluating combination therapies. Identifying and validating metabolic biomarkers will also be crucial for patient stratification and treatment monitoring. Insights into metabolic reprogramming in GI cancers may have broader implications across multiple cancer types, offering new avenues for improving cancer treatment.

The role of lactylation in tumor growth and cancer progression

Background

Lactate's perception of lactate has changed over the last 30 years from a straightforward metabolic byproduct to a complex chemical with important biological activities, such as signal transduction, gluconeogenesis, and mitochondrial respiration. In addition to its metabolic contributions, lactate has far-reaching repercussions. This review highlights the role of lactate in the course of cancer by highlighting lactylation as a unique epigenetic alteration. The purpose of this review is to clarify the functions of lactate in the biology of tumors, with a particular focus on the translational potential of lactylation pathways in cancer diagnosis and treatment approaches.

Methods

This review summarizes research on the relationship between lactate and cancer, with an emphasis on histone lactylation, its effect on gene expression, and its influence on the tumor microenvironment. By establishing a connection between metabolic byproducts and epigenetic gene regulation, we investigated how lactylation affects immune regulation, inflammation, and cellular repair.

Findings

Histone lactylation, or the addition of lactate to lysine residues on histone proteins, increases transcriptional activity and facilitates the expression of genes involved in homeostasis and repair. These findings have important implications for cancer treatment. Lactylation, for example, activates genes such as Arg1, which is a hallmark of the M2 macrophage phenotype implicated in immunosuppression and tumor growth. The ability of lactate to dynamically alter gene expression is further supported by its function as a histone deacetylase(HDAC)inhibitor and its impact on histone acetylation. Its wide-ranging involvement in cellular metabolism and epigenetic control has been demonstrated by the discovery of particular lactylation sites on histones in various cell types, including cancer cells.

JQ1 Treatment and miR-21 Silencing Activate Apoptosis of CD44+ Oral Cancer Cells

Oral cancer ranks in the top 10 most prevalent malignancies worldwide. It is an aggressive tumor with frequent relapses and metastases and relatively modest survival rates that do not improve in spite of constantly evolving treatment modalities. Cancer stem cells are a subpopulation of tumor cells considered to be responsible not only for tumor initiation but also its aggressive behavior. Many efforts are directed at targeting those cells specifically. A class of small molecules, inhibitors of BET proteins (iBET), is emerging as a novel anticancer tool. Modulating the expression of microRNAs could also be a valid approach in cancer therapy. We aimed to study the effect of the iBET JQ1 combined with miR-21 silencing on oral cancer stem cells (CD44+ cells). CD44+ cells were sorted by flow cytometry and treated with JQ1 alone or in combination with miRNA-21 silencing. Following treatment, MTT, spheroid formation, invasion, and annexin V assays were performed, along with cell cycle and gene expression analyses. JQ1 in conjunction with miR-21 silencing showed considerable cytotoxicity led to a significant downregulation of cyclin D1, consistent with G1 cell cycle arrest, a significant caspase 3 upregulation in accordance with activation of apoptosis. The combined treatment approach also reduced CD44+ cell invasion capacity. Modulating chromatin structure with iBETs and silencing miRNA could be suitable epigenetic adjuncts to oral cancer treatment.

FBXW7 metabolic reprogramming inhibits the development of colon cancer by down-regulating the activity of arginine/mToR pathways

FBXW7 is a tumor suppressor gene that regulates metabolism and is associated with the onset and progression of colorectal cancer (CRC)), however, the precise mechanism whereby FBXW7 participates in the metabolic reprogramming of CRC remains unclear. Here, the research aims to reveal the association between the expression of FBXW7 and clinical variables and to investigate the molecular mechanism by which FBXW7 plays a critical role in the development of CRC. The clinical importance of FBXW7 in CRC was determined by immunohistochemistry. Non-targeted metabolomics was utilized to explore the role of FBXW7 in the metabolic regulation of CRC. Low expression of FBXW7 was associated with poor prognosis in individuals with CRC, both at the mRNA and protein levels. FBXW7 over-expression inhibited CRC cell growth, colony formation, migration, and invasion. Non-targeted metabolomics unveiled that FBXW7 over-expression directly caused the deprivation of arginine which led to downmodulation of mTOR signaling pathway; meanwhile, FBXW7-related metabolites were primarily concentrated in the mTOR signaling pathway. In summary, the research identified a novel mechanism of action of FBXW7 in CRC. The research findings provide a theoretical foundation for the prognostic prediction and therapeutic planning of CRC based on metabolic reprogramming.

Spatially-resolved characterization of the metabolic and N-glycan alterations in colorectal cancer using matrix-assisted laser desorption/ionization mass spectrometry imaging

Colorectal cancer is the second leading cause of cancer-related deaths worldwide, and its development typically involves complex metabolic reprogramming. By mapping the spatial distributions of metabolites and N-glycans in heterogeneous colorectal cancer tissues, we can elucidate cancer-associated metabolic and N-glycan changes. Herein, we combine mass spectrometry imaging-based metabolomics and N-glycomics to characterize the spatially resolved reprogramming of metabolites and N-glycans in colorectal cancer tissues. The metabolic characteristics of different regions of colorectal cancer were evaluated through the utilization of orthogonal partial least squares discriminant analysis. In combination with metabolic pathway enrichment analysis, significant alterations were identified in the fatty acid metabolism, arginine and proline metabolism of colorectal cancer. Cancer cell regions exhibited a marked upregulation of saturated fatty acids, monounsaturated fatty acids, polyamines, and histidine. Additionally, we discovered that the high-mannose N-glycans were predominantly distributed in tumor tissue regions, whereas complex N-glycans were more commonly found in the normal tissue regions adjacent to the tumor. Such findings provide new insights into the spatial signatures of metabolites and N-glycans in colorectal cancer, thereby offering a crucial basis for the diagnosis of colorectal cancer and potential vulnerabilities that might be targeted for cancer therapy.

The roles of KRAS in cancer metabolism, tumor microenvironment and clinical therapy

KRAS is one of the most mutated genes, driving alternations in metabolic pathways that include enhanced nutrient uptaking, increased glycolysis, elevated glutaminolysis, and heightened synthesis of fatty acids and nucleotides. However, the beyond mechanisms of KRAS-modulated cancer metabolisms remain incompletely understood. In this review, we aim to summarize current knowledge on KRAS-related metabolic alterations in cancer cells and explore the prevalence and significance of KRAS mutation in shaping the tumor microenvironment and influencing epigenetic modification via various molecular activities. Given that cancer cells rely on these metabolic changes to sustain cell growth and survival, targeting these processes may represent a promising therapeutic strategy for KRAS-driven cancers.

Epigenetic Regulatory Processes Involved in the Establishment and Maintenance of Skin Homeostasis-The Role of Microbiota

Epigenetic mechanisms are central to the regulation of all biological processes. This manuscript reviews the current understanding of diverse epigenetic modifications and their role in the establishment and maintenance of normal skin functions. In healthy skin, these mechanisms allow for the precise control of gene expression, facilitating the dynamic balance between cell proliferation and differentiation necessary for effective barrier function. Furthermore, as the skin ages, alterations in epigenetic marks can lead to impaired regenerative capacity and increased susceptibility to environmental stressors. The interaction between skin microbiota and epigenetic regulation will also be explored, highlighting how microbial communities can influence skin health by modulating the host gene expression. Future research should focus on the development of targeted interventions to promote skin development, resilience, and longevity, even in an ever-changing environment. This underscores the need for integrative approaches to study these complex regulatory networks.

Mechanisms and technologies in cancer epigenetics

Cancer's epigenetic landscape, a labyrinthine tapestry of molecular modifications, has long captivated researchers with its profound influence on gene expression and cellular fate. This review discusses the intricate mechanisms underlying cancer epigenetics, unraveling the complex interplay between DNA methylation, histone modifications, chromatin remodeling, and non-coding RNAs. We navigate through the tumultuous seas of epigenetic dysregulation, exploring how these processes conspire to silence tumor suppressors and unleash oncogenic potential. The narrative pivots to cutting-edge technologies, revolutionizing our ability to decode the epigenome. From the granular insights of single-cell epigenomics to the holistic view offered by multi-omics approaches, we examine how these tools are reshaping our understanding of tumor heterogeneity and evolution. The review also highlights emerging techniques, such as spatial epigenomics and long-read sequencing, which promise to unveil the hidden dimensions of epigenetic regulation. Finally, we probed the transformative potential of CRISPR-based epigenome editing and computational analysis to transmute raw data into biological insights. This study seeks to synthesize a comprehensive yet nuanced understanding of the contemporary landscape and future directions of cancer epigenetic research.

APOM Modulates the Glycolysis Process in Liver Cancer Cells by Controlling the Expression and Activity of HK2 via the Notch Pathway

The metabolic pathway of aerobic glycolysis in tumor cells has garnered significant attention in tumor research because of its high activation in cancer cells. Previous research conducted by our team has demonstrated that Apolipoprotein M (APOM) exhibits potential as a factor against liver cancer. However, further investigations are needed to elucidate the precise approach and mechanism that are involved in this process. The findings of this study demonstrated that the inhibition of APOM gene expression led to a notable increase in glucose uptake within liver cancer cells, along with increased levels of lactate dehydrogenase A (LDHA) mRNA and protein expression, as well as increased lactate and adenosine triphosphate (ATP) levels (P < 0.05). These alterations in the cellular microenvironment may be associated with a significant increase in the expression level and enzyme activity of the pivotal enzyme hexokinase 2 (HK2) (P < 0.05). Subsequent investigations revealed notable enrichment of the Notch pathway in liver cancer samples exhibiting low expression of the APOM gene. Western blot experiments demonstrated that the inhibition of APOM gene expression triggers the activation of the Notch pathway in liver cancer cells. Furthermore, the administration of a γ-secretase inhibitor (DAPT) successfully mitigated the increase in HK2 levels, glucose uptake, lactate production, and proliferation of liver cancer cells induced by the downregulation of the APOM gene (P < 0.05). In conclusion, diminished APOM expression may facilitate the progression of liver cancer by stimulating the aerobic glycolysis pathway, which is mediated by the Notch signaling pathway.

Crosstalk between ROS-inflammatory gene expression axis in the progression of lung disorders

A significant number of deaths and disabilities worldwide are brought on by inflammatory lung diseases. Many inflammatory lung disorders, including chronic respiratory emphysema, resistant asthma, resistance to steroids, and coronavirus-infected lung infections, have severe variants for which there are no viable treatments; as a result, new treatment alternatives are needed. Here, we emphasize how oxidative imbalance contributes to the emergence of provocative lung problems that are challenging to treat. Endogenic antioxidant systems are not enough to avert free radical-mediated damage due to the induced overproduction of ROS. Pro-inflammatory mediators are then produced due to intracellular signaling events, which can harm the tissue and worsen the inflammatory response. Overproduction of ROS causes oxidative stress, which causes lung damage and various disease conditions. Invasive microorganisms or hazardous substances that are inhaled repeatedly can cause an excessive amount of ROS to be produced. By starting signal transduction pathways, increased ROS generation during inflammation may cause recurrent DNA damage and apoptosis and activate proto-oncogenes. This review provides information about new targets for conducting research in related domains or target factors to prevent, control, or treat such inflammatory oxidative stress-induced inflammatory lung disorders.

Metabolism of cancer cells and immune cells in the initiation, progression, and metastasis of cancer

The metabolism of cancer and immune cells plays a crucial role in the initiation, progression, and metastasis of cancer. Cancer cells often undergo metabolic reprogramming to sustain their rapid growth and proliferation, along with meeting their energy demands and biosynthetic needs. Nevertheless, immune cells execute their immune response functions through the specific metabolic pathways, either to recognize, attack, and eliminate cancer cells or to promote the growth or metastasis of cancer cells. The alteration of cancer niches will impact the metabolism of both cancer and immune cells, modulating the survival and proliferation of cancer cells, and the activation and efficacy of immune cells. This review systematically describes the key characteristics of cancer cell metabolism and elucidates how such metabolic traits influence the metabolic behavior of immune cells. Moreover, this article also highlights the crucial role of immune cell metabolism in anti-tumor immune responses, particularly in priming T cell activation and function. By comprehensively exploring the metabolic crosstalk between cancer and immune cells in cancer niche, the aim is to discover novel strategies of cancer immunotherapy and provide effective guidance for clinical research in cancer treatment. In addition, the review also discusses current challenges such as the inadequacy of relevant diagnostic technologies and the issue of multidrug resistance, and proposes potential solutions including bolstering foundational cancer research, fostering technological innovation, and implementing precision medicine approaches. In-depth research into the metabolic effects of cancer niches can improve cancer treatment outcomes, prolong patients' survival period and enhance their quality of life.

High-Fat Diet, Epigenetics, and Atherosclerosis: A Narrative Review

BACKGROUND/OBJECTIVES

Atherosclerosis is a chronic inflammatory disease developing and progressing in the presence of risk factors including hyperlipidemia, hypercholesterolemia, and chronic inflammation, among others. Atherosclerosis commonly precipitates as ischemic events, transient ischemic attacks, and myocardial infarction. Saturated fatty acids are risk factors; however, their association with epigenetics in the pathophysiology of atherosclerosis is not clearly understood. The preclinical and clinical trials associating atherosclerosis with epigenetics are scarcely documented, and most of the studies reported the use of drugs inhibiting methylation and histone modification to improve atherosclerosis. This narrative review aims to discuss various aspects and the association between a high-fat diet, epigenetic reprogramming, and atherosclerosis.

METHODS

A literature search with the keywords high-fat diet, epigenetics, and atherosclerosis, alone or in combination, was conducted to search for articles in the English language. Duplicate articles were removed, and articles related to the subject of this review article were included in this review.

RESULTS

A review of the literature suggests that a high-fat diet with saturated fatty acids is a risk factor for atherosclerosis, but this association is multifactorial, and epigenetics play a critical role. However, the connecting link and the underlying molecular and cellular mechanisms are not clearly understood yet and warrant more research.

CONCLUSIONS

A high-fat diet rich in saturated fatty acids is a risk factor for atherosclerosis involving epigenetic reprogramming and altered gene expression. The existing preclinical and clinical trials support the role of epigenetics and reversing it using drugs to attenuate atherosclerosis, but definitive evidence warrants larger clinical trials. Further, a high-fat diet in pregnant mothers can manifest as cardiovascular disease in offspring; caution must be taken in pregnant mothers for their diet and nutrients.

ACSL4-mediated H3K9 and H3K27 hyperacetylation upregulates SNAIL to drive TNBC metastasis

Triple-negative breast cancer (TNBC) has profound unmet medical need globally for its devastating clinical outcome associated with rapid metastasis and lack of targeted therapies. Recently, lipid metabolic reprogramming especially fatty acid oxidation (FAO) has emerged as a major driver of breast cancer metastasis. Analyzing the expression of major FAO regulatory genes in breast cancer, we found selective overexpression of acyl-CoA synthetase 4 (ACSL4) in TNBC, which is primarily attributed to the absence of progesterone receptor. Loss of ACSL4 function, by genetic ablation or pharmacological inhibition significantly reduces metastatic potential of TNBC. Global transcriptome analysis reveals that ACSL4 activity positively influences the gene expression related to TNBC migration and invasion. Mechanistically, ACSL4 modulates FAO and intracellular acetyl-CoA levels, leading to hyperacetylation of particularly H3K9ac and H3K27ac marks resulting in overexpression of SNAIL during the course of TNBC metastatic spread to lymph node and lung. Further, human TNBC metastasis exhibits positive correlation among ACSL4, H3K9ac, H3K27ac, and SNAIL expression. Altogether, our findings provide molecular insights regarding the intricate interplay between metabolic alterations and epigenetic modifications, intertwined to orchestrate TNBC metastasis, and posit a rational understanding for the development of ACSL4 inhibitors as a targeted therapy against TNBC.

PPDPF promotes esophageal squamous cell carcinoma progression by blocking PCCA binding to PCCB and inhibiting methionine catabolism

While metabolic reprogramming and remodeling of tumor microenvironment play important roles in the development of esophageal squamous cell carcinoma (ESCC), the mechanisms remain unclear. In this study, we found that pancreatic progenitor cell differentiation and proliferation factor (PPDPF) is upregulated in ESCC and its expression level is associated with lymph node metastasis. PPDPF was found to promote tumorigenesis, lymph node metastasis and distal metastasis of ESCC cells. Furthermore, the results of mass spectrometry analysis revealed that PPDPF interacts with PCCA, the subunit of the PCC, a key enzyme involved in the catabolism of methionine by the C-Vomit pathway. In addition, PPDPF increases methionine and SAM levels. Additionally, knockdown of PPDPF decreases the levels of methionine and SAM in vivo, and promotes the infiltration of CD8+ T cells in ESCC. Taken together, the results of this study suggest that PPDPF inhibits the interaction between PCCA and PCCB to downregulate methionine catabolism via the C-Vomit pathway, providing a new target for the treatment of ESCC.

Inflammation in myelodysplastic syndrome pathogenesis

Inflammation is a key driver of the progression of preleukemic myeloid conditions, such as clonal hematopoiesis of indeterminate potential (CHIP) and clonal cytopenia of undetermined significance (CCUS), to myelodysplastic syndromes (MDS). Inflammation is a critical mediator in the complex interplay of the genetic, epigenetic, and microenvironmental factors contributing to clonal evolution. Under inflammatory conditions, somatic mutations in TET2, DNMT3A, and ASXL1, the most frequently mutated genes in CHIP and CCUS, induce a competitive advantage to hematopoietic stem and progenitor cells, which leads to their clonal expansion in the bone marrow. Chronic inflammation also drives metabolic reprogramming and immune system deregulation, further promoting the expansion of malignant clones. This review underscores the urgent need to fully elucidate the role of inflammation in MDS initiation and highlights the potential of the therapeutical targeting of inflammatory pathways as an early intervention in MDS.

Tumor energy metabolism: implications for therapeutic targets

Tumor energy metabolism plays a crucial role in the occurrence, progression, and drug resistance of tumors. The study of tumor energy metabolism has gradually become an emerging field of tumor treatment. Recent studies have shown that epigenetic regulation is closely linked to tumor energy metabolism, influencing the metabolic remodeling and biological traits of tumor cells. This review focuses on the primary pathways of tumor energy metabolism and explores therapeutic strategies to target these pathways. It covers key areas such as glycolysis, the Warburg effect, mitochondrial function, oxidative phosphorylation, and the metabolic adaptability of tumors. Additionally, this article examines the role of the epigenetic regulator SWI/SNF complex in tumor metabolism, specifically its interactions with glucose, lipids, and amino acids. Summarizing therapeutic strategies aimed at these metabolic pathways, including inhibitors of glycolysis, mitochondrial-targeted drugs, exploitation of metabolic vulnerabilities, and recent developments related to SWI/SNF complexes as potential targets. The clinical significance, challenges, and future directions of tumor metabolism research are discussed, including strategies to overcome drug resistance, the potential of combination therapy, and the application of new technologies.

Multi-fusion strategy network-guided cancer subtypes discovering based on multi-omics data

Introduction

The combination of next-generation sequencing technology and Cancer Genome Atlas (TCGA) data provides unprecedented opportunities for the discovery of cancer subtypes. Through comprehensive analysis and in-depth analysis of the genomic data of a large number of cancer patients, researchers can more accurately identify different cancer subtypes and reveal their molecular heterogeneity.

Methods

In this paper, we propose the SMMSN (Self-supervised Multi-fusion Strategy Network) model for the discovery of cancer subtypes. SMMSN can not only fuse multi-level data representations of single omics data by Graph Convolutional Network (GCN) and Stacked Autoencoder Network (SAE), but also achieve the organic fusion of multi- -omics data through multiple fusion strategies. In response to the problem of lack label information in multi-omics data, SMMSN propose to use dual self-supervise method to cluster cancer subtypes from the integrated data.

Results

We conducted experiments on three labeled and five unlabeled multi-omics datasets to distinguish potential cancer subtypes. Kaplan Meier survival curves and other results showed that SMMSN can obtain cancer subtypes with significant differences.

Discussion

In the case analysis of Glioblastoma Multiforme (GBM) and Breast Invasive Carcinoma (BIC), we conducted survival time and age distribution analysis, drug response analysis, differential expression analysis, functional enrichment analysis on the predicted cancer subtypes. The research results showed that SMMSN can discover clinically meaningful cancer subtypes.

Metabolically inducing defects in DNA repair sensitizes BRCA-wild-type cancer cells to replication stress

Metabolic reprogramming from oxidative respiration to glycolysis is generally considered to be advantageous for tumor initiation and progression. However, we found that breast cancer cells forced to perform glycolysis acquired a vulnerability to PARP inhibitors. Small-molecule inhibition of mitochondrial respiration-using glyceollin I, metformin, or phenformin-induced overproduction of the oncometabolite lactate, which acidified the extracellular milieu and repressed the expression of homologous recombination (HR)-associated DNA repair genes. These serial events created so-called "BRCAness," in which cells exhibit an HR deficiency phenotype despite lacking germline mutations in HR genes such as BRCA1 and BRCA2, and, thus, sensitized the cancer cells to clinically available poly(ADP-ribose) polymerase inhibitors. The increase in lactate repressed HR-associated gene expression by decreasing histone acetylation. These effects were selective to breast cancer cells; normal epithelial cells retained HR proficiency and cell viability. These mechanistic insights into the BRCAness-prone properties of breast cancer cells support the therapeutic utility and cancer cell-specific potential of mitochondria-targeting drugs.

Supercomputer-Based Virtual Screening for Deoxyribonucleic Acid Methyltransferase 1 Inhibitors as Novel Anticancer Agents

Targeting epigenetics is a new strategy to treat cancer and develop novel epigenetic drugs with anti-tumor activity. DNA methyltransferases transfer the methyl group from S-adenosyl-L-methionine (SAM) to the cytosine residue in a CpG island, leading to the transcription silencing of the gene. Hypermethylation can frequently be observed in several tumor types. Hence, the inhibition of DNMT1 has become a novel approach to cure cancer. In this study, virtual screening and molecular docking were performed for more than 11,000 ligands from the ZINC15 database to discover new hypomethylation agents. Four candidate compounds were further tested for their effects on DNMT1 in silico and in vitro. Compounds 2 and 4 showed the best DNMT1 inhibitory activity, but only compound 4 was able to inhibit the growth of several cancer cell lines. The hypomethylation of the luciferase gene by compound 4 was verified by a CMV- luciferase assay using KG-1 cells. Additionally, compound 4 suppressed cell migration in a dose- and time-dependent manner in the wound healing assay. Moreover, cell cycle analyses demonstrated that compound 4 arrested CCRF-CEM cells and MDA-MB-468 cells in the G0/G1 phase. Also, compound 4 significantly induced early and late apoptosis in a dose-dependent manner. In conclusion, we introduce compound 4 as a novel DNMT1 inhibitor with anticancer activity.

Altered glycosylation in cancer: molecular functions and therapeutic potential

Glycosylation, a key mode of protein modification in living organisms, is critical in regulating various biological functions by influencing protein folding, transportation, and localization. Changes in glycosylation patterns are a significant feature of cancer, are associated with a range of pathological activities in cancer-related processes, and serve as critical biomarkers providing new targets for cancer diagnosis and treatment. Glycoproteins like human epidermal growth factor receptor 2 (HER2) for breast cancer, alpha-fetoprotein (AFP) for liver cancer, carcinoembryonic antigen (CEA) for colon cancer, and prostate-specific antigen (PSA) for prostate cancer are all tumor biomarkers approved for clinical use. Here, we introduce the diversity of glycosylation structures and newly discovered glycosylation substrate-glycosylated RNA (glycoRNA). This article focuses primarily on tumor metastasis, immune evasion, metabolic reprogramming, aberrant ferroptosis responses, and cellular senescence to illustrate the role of glycosylation in cancer. Additionally, we summarize the clinical applications of protein glycosylation in cancer diagnostics, treatment, and multidrug resistance. We envision a promising future for the clinical applications of protein glycosylation.

Acid affairs in anti-tumour immunity

Metabolic rewiring of cancer cells is one of the hallmarks of cancer. As a consequence, the metabolic landscape of the tumour microenvironment (TME) differs compared to correspondent healthy tissues. Indeed, due to the accumulation of acid metabolites, such as lactate, the pH of the TME is generally acidic with a pH drop that can be as low as 5.6. Disruptions in the acid-base balance and elevated lactate levels can drive malignant progression not only through cell-intrinsic mechanisms but also by impacting the immune response. Generally, acidity and lactate dampen the anti-tumour response of both innate and adaptive immune cells favouring tumour progression and reducing the response to immunotherapy. In this review, we summarize the current knowledge on the functional, metabolic and epigenetic effects of acidity and lactate on the cells of the immune system. In particular, we focus on the role of monocarboxylate transporters (MCTs) and other solute carrier transporters (SLCs) that, by mediating the exchange of lactate (among other metabolites) and bicarbonate, participate in pH regulation and lactate transport in the cancer context. Finally, we discuss advanced approaches to target pH or lactate in the TME to enhance the anti-tumour immune response.

Pathogenic nsSNPs of protein kinase C-eta with hepatocellular carcinoma susceptibility

BACKGROUND

Hepatocellular carcinoma (HCC) is a global health concern. Due to late diagnosis and limited therapeutic strategies, HCC based mortality rate is exponentially increasing globally. Genetic predisposition is a non-avoidable intrinsic factor that could alter the genome sequence, ultimately leading to HCC. Protein kinase C eta (PKCη) is involved in key physiological roles, hence alteration in PKCη could aid in cancer progression. Research indicates association between non-synonymous (ns) SNPs and HCC onset. However, effect of nsSNP variants of PKCη on HCC development has not been explored yet. Hence, this study aimed to investigate the association between pathogenic nsSNPs of PKCη with HCC.

METHODS

Non-synonymous (missense) variants of PKCη were obtained from Ensembl genome browser. These variants were filtered out to obtain pathogenic nsSNPs of PKCη. Genotyping of nsSNPs was done through Tetra ARMS PCR. For that, blood samples of 348 HCC patients and 337 controls were collected. The clinical factors that influence HCC were studied. Relative risk (RR) and Odds Ratio (OR) with 95% confidence interval was calculated by Chi-square test and P-value < 0.05 was deemed significant.

RESULTS

Five nsSNP variants of PKCη including rs1162102190 (T/C), rs868127012 (G/T), rs750830348 (G/T), rs768619375 (T/C), and rs752329416 (T/C) were identified. The retrieved nsSNPs were frequently identified in HCC patients. However, rs752329416 T/C was significantly prevalent in patients having HCC family history. Moreover, all the variants were found in HCC patients manifesting the stage II than the advance stages of HCC.

CONCLUSION

This study can be utilized to identify potential genetic markers for early screening of HCC. Moreover, consideration of further clinical factors, and mechanistic approach would enhance the understanding that how alteration in nsSNPs could impact the HCC onset.

Insights into Metabolic Reprogramming in Tumor Evolution and Therapy

Background: Cancer remains a global health challenge, characterized not just by uncontrolled cell proliferation but also by the complex metabolic reprogramming that underlies its development and progression. Objectives: This review delves into the intricate relationship between cancer and its metabolic alterations, drawing an innovative comparison with the cosmological concepts of dark matter and dark energy to highlight the pivotal yet often overlooked role of metabolic reprogramming in tumor evolution. Methods: It scrutinizes the Warburg effect and other metabolic adaptations, such as shifts in lipid synthesis, amino acid turnover, and mitochondrial function, driven by mutations in key regulatory genes. Results: This review emphasizes the significance of targeting these metabolic pathways for therapeutic intervention, outlining the potential to disrupt cancer's energy supply and signaling mechanisms. It calls for an interdisciplinary research approach to fully understand and exploit the intricacies of cancer metabolism, pointing toward metabolic reprogramming as a promising frontier for developing more effective cancer treatments. Conclusion: By equating cancer's metabolic complexity with the enigmatic nature of dark matter and energy, this review underscores the critical need for innovative strategies in oncology, highlighting the importance of unveiling and targeting the "dark energy" within cancer cells to revolutionize future therapy and research.