Analysis of DNA methylation in cancer: location revisited

Prognostic gene expression profile of colorectal cancer

Colorectal cancer is a major global health burden, with significant heterogeneity in clinical outcomes among patients. Identifying robust prognostic gene expression signatures can help stratify patients, guide treatment decisions, and improve clinical management. This review provides an overview of current prognostic gene expression profiles in colorectal cancer research. We have synthesized evidence from numerous published studies investigating the association between tumor gene expression patterns and patient survival outcomes. The reviewed literature reveals several promising gene signatures that have demonstrated the ability to predict disease-free survival and overall survival in CRC patients, independent of standard clinicopathological risk factors. These genes are crucial in fundamental biological processes, including cell cycle control, epithelial-mesenchymal transition, and immune regulation. The implementation of prognostic gene expression tests in clinical practice holds great potential for enabling more personalized management strategies for colorectal cancer.

The role of PAX1 and JAM3 methylation in predicting the pathological upgrading of cervical intraepithelial neoplasia before conization

To explore the effect of PAX1 and JAM3 gene methylation on pathological upgrading before conization. A total of 549 patients who underwent colposcopy at our hospital were enrolled for analysis from December 2020 to April 2022. PAX1 and JAM3 gene methylation results in preoperative cervical exfoliated cells were collected. Univariate analysis and multivariate logistic regression analysis were conducted to identify the independent risk factors influencing the pathological upgrading of conization, aiming to establish a prediction model. A total of 88 patients were finally included for statistical analysis according to the inclusion and exclusion criteria. Based on univariate analysis and multivariate logistic regression analysis, ∆Ct PAX1 (P = 0.016, OR: 0.784, 95%CI 0.644-0.956) and cervical canal lesions (P = 0.048, OR: 3.469, 95%CI 1.014-11.870) were identified as independent risk factors for pathological upgrading for conization. Using the above results, we established a prediction model for pathological upgrading and plotted the receiver operator characteristic curve (ROC). The area under the curve (AUC) was calculated when the Youden index was maximized with an AUC value of 0.818 (95%CI 0.720-0.916), specificity of 94.4%, sensitivity of 60%. The cut-off value for ∆Ct PAX1 was determined as 4.34 when maximizing the Youden index. PAX1 could be a promising triage marker in predicting the pathological upgrading of CIN before conization. We found that if the ∆Ct PAX1 cut-off value is lower than 4.34, it is highly suggestive of pathological upgrading.

Accurate Mapping of 5-Glyceryl-methylcytosine Using Nanopore Sequencing

5-Glyceryl-methylcytosine (5gmC) is an epigenetic modification recently discovered in the genome of Chlamydomonas reinhardtii. It is formed by attaching a glyceryl group of vitamin C to the methyl moiety of 5mC, a process catalyzed by the CMD1 protein. 5gmC has been shown to play a role in promoting active DNA demethylation and photoacclimation. However, the precise localization of 5gmC and its role in gene transcription remain largely unexplored. To efficiently and economically map the distribution of 5gmC across the genome, we investigated the feasibility of nanopore sequencing for identifying this DNA modification. By introducing 5gmC into a set of model strands, significant current decreases associated with 5gmC were consistently observed during nanopore sequencing. This characteristic current signal enables direct identification of multiple 5gmC sites as well as 5gmC across various sequence contexts with reliable accuracy and single-molecule sensitivity. Moreover, we were able to discriminate between 5gmC and 5mC, as 5mC unambiguously increases the ionic current. These results demonstrate the feasibility of nanopore sequencing for mapping 5gmC at the genomic level and provide new insights into the exploration of the roles of 5gmC as a stable epigenetic mark.

Comprehensive analysis of the LINC01122/TPD52 axis as a predictive biomarker in prostate adenocarcinoma

Prostate cancer (PCa) ranks among the most prevalent malignant tumors worldwide. The pivotal role of competitive endogenous RNA (ceRNA) regulatory networks in numerous cancer types has been underscored. However, the specific characteristics of the ceRNA network in PCa remained unknown. This study aims to elucidate the ceRNA regulatory network associated with phosphatase and tensin homolog (PTEN) and to identify potential prognostic markers for PCa. The Cancer Genome Atlas (TCGA) database was employed to extract the expression patterns of long non-coding RNAs (lncRNAs), microRNAs (miRNAs), and messenger RNAs (mRNAs). LINC01122-hsa-miR-34c-5p/hsa-miR-449a-TPD52 ceRNA network regarding the prognosis of PCa was explored via bioinformatics analysis. Through correlation analysis, we investigated the LINC01122/TPD52 axis within the ceRNA network, identifying it as a significant clinical prognostic marker for PCa. Subsequent analyses indicated that hypomethylation was responsible for the abnormal upregulation of the LINC01122/TPD52 axis. Furthermore, immune infiltration analysis revealed the impact of the LINC01122/TPD52 axis on the tumor immune microenvironment and the progression of PCa. Finally, a nomogram was constructed to forecast the 1-year, 3-year, and 5-year survival probabilities of PCa patients. In summary, our study demonstrates the significant role of the ceRNA-based LINC01122/TPD52 axis in the progression of PCa and its correlation with prognosis.

A Comprehensive Review on LncRNAs/miRNAs-DNMT1 Axis in Human Cancer: Mechanistic and Clinical Application

Cancer constitutes a significant public health concern, and addressing the challenge of cancer holds paramount importance and requires immediate attention. Epigenetic alterations, encompassing DNA methylation, have emerged as pivotal contributors to the development of diverse cancer types. These modifications exert their influence by modulating chromatin structure, gene expression patterns and other nuclear processes, thereby influencing cancer pathogenesis. Over the last two decades, an increasing body of evidence has established the involvement of DNA methyltransferase 1 (DNMT1) in various aspects of cancer development, including tumorigenesis, aggressiveness and treatment response. Furthermore, non-coding RNAs (ncRNAs), such as microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), are increasingly recognised as significant modulators in diverse biological processes, encompassing metastasis, apoptosis, cell proliferation and differentiation. Several recent studies have elucidated the intricate relationship between epigenetic machinery, specifically DNMT1, and the expression of ncRNAs in the context of cancer. In this review, we provide a comprehensive overview of the interaction between DNMT1 and ncRNAs in cancer pathogenesis. Furthermore, we discuss the important role of the ncRNAs-DNMT1 axis in cancer stem cells and cancer therapy resistance as critical issues in cancer therapy. Finally, we demonstrate that herbal medicine and synthetic RNA molecules regulate DNMT1 activity and hold great promise in cancer treatment.

STEAP Proteins: Roles in disease biology and potential for therapeutic intervention

Iron and copper are essential metal ions, and maintaining their metabolic balance is critical for organismal health. The Six-Transmembrane Epithelial Antigen of the Prostate (STEAP) protein family, comprising STEAP1, STEAP2, STEAP3, and STEAP4, plays a vital role in cellular metal homeostasis. These proteins are located on the cell membrane and are characterized by six transmembrane domains. With the exception of STEAP1, the STEAP proteins function as metal oxidoreductases due to their F420H2:NADP+ oxidoreductase (FNO)-like domain. However, STEAP1 contributes to metal metabolism through its heme group and interaction with other STEAP proteins. Beyond metal metabolism, STEAP proteins are involved in critical cellular processes, including the regulation of the cell cycle, proliferation, differentiation, and apoptosis. Notably, STEAP proteins are recognized as potential biomarkers and therapeutic targets in human cancers, particularly prostate cancer. This review outlines the structural features and functional roles of STEAP proteins in various diseases, including cancers, insulin resistance, non-alcoholic fatty liver disease (NAFLD), and benign prostatic hyperplasia, with a focus on their potential for therapeutic intervention.

Targeting redox-sensitive MBD2-NuRD condensate in cancer cells

Transcriptional silencing of hypermethylated tumour suppressor genes is a hallmark of tumorigenesis but the underlying mechanism remains enigmatic. Here we show that methyl-CpG-binding domain protein 2 (MBD2) forms nuclear condensate in diverse cancer cells, where it assembles and navigates the chromatin remodeller NuRD complex to these gene loci for transcriptional suppression, thus fuelling tumour growth. Disturbance of MBD2 condensate reduces the level of NuRD complex-specific proteins, destabilizes heterochromatin foci, facilitates chromatin relaxation and consequently impedes tumour progression. We demonstrate that MBD2 condensate is redox sensitive, mediated by C359. Pro-oxidative interventions disperse MBD2-NuRD condensate, thereby alleviating the transcriptional repression of tumour suppressor genes. Our findings illuminate a hitherto unappreciated function of MBD2 condensate in sustaining a repressive chromatin state essential for cancer cell proliferation and suggest an oxidative stress targeting approach for malignancies with excessive MBD2 condensate.

Integrative genome-wide aberrant DNA methylation and transcriptome analysis identifies diagnostic markers for colorectal cancer

Colorectal cancer remains a major cause of cancer mortality, with limited sensitivity in current diagnostics. Aberrant DNA methylation in expression-regulating sites shows biomarker potential, though few studies explore such methylation-based diagnostic tools for colorectal cancer. We conducted genome-wide DNA methylation and RNA sequencing on matched colorectal cancer and normal tissues to identify expression-related differentially methylated CpG sites (DMCs). Diagnostic models were constructed with training and validation sets of 689 samples. Machine learning techniques (random forest, elastic net, support vector machine) were employed to identify optimal diagnostic markers. Methylation-specific PCR confirmed marker-host gene regulatory relationships, and targeted bisulfite sequencing validated these markers in an independent cohort of 200 samples. Host genes roles in colorectal cancer pathogenesis were further investigated through in vivo and in vitro assays and tissue microarray analysis. We identified 64,824 DMCs in colorectal cancer, with 442 associated with gene expression. These sites impact transcription factor binding, and their host genes are linked to chemotherapy resistance. Diagnostic panels showed high efficacy, with methylation changes significantly impacting RNA and protein expression of host genes. Markers cg16851417, cg19498960, and cg16302790 were validated in blood for noninvasive screening. Clustering expression-related DMCs with similar methylation patterns may facilitate diagnostic tools development. Host genes SIM2, PDX1, and TNS4 influence colorectal cancer progression and may impact therapy response. Expression-related DMCs hold strong potential as colorectal cancer biomarkers, with implications for prognosis and therapy. The specific expression patterns of these DMCs in host genes support development of non-invasive blood-based diagnostic tools.

YEATS2: a novel cancer epigenetic reader and potential therapeutic target

YEATS2, an evolutionarily conserved reader of histone acylation marks (H3K27ac, H3K27cr, H3K27bz), functions as a central oncogenic driver in diverse cancers, including non-small cell lung cancer (NSCLC), pancreatic ductal adenocarcinoma (PDAC), and hepatocellular carcinoma (HCC). Its structurally plastic YEATS domain bridges acyl-CoA metabolism to chromatin remodeling, amplifying transcription of survival genes such as MYC, BCL2, and PD-L1. YEATS2 orchestrates malignancy-specific programs-sustaining ribosome biogenesis in NSCLC through ATAC complex recruitment, enhancing NF-κB-dependent immune evasion in PDAC, and activating PI3K/AKT-driven metabolic rewiring in HCC. Structural studies demonstrate a unique aromatic cage architecture that selectively engages diverse acylated histones. Although pyrazolopyridine-based inhibitors targeting the YEATS domain show preclinical efficacy, developing isoform-selective agents remains challenging. Clinically, YEATS2 overexpression correlates with therapy resistance and may synergize with immune checkpoint blockade. This review integrates mechanistic insights into the role of YEATS2 in epigenetic regulation, evaluates its therapeutic potential, and proposes future directions: elucidating full-length complex topologies, mapping synthetic lethal interactors, and optimizing selective inhibitors. Disrupting YEATS2-mediated epigenetic adaptation presents novel opportunities for precision cancer therapy.

Epigenetic-modification associated hnRNPA3 acts as a prognostic biomarker and promotes malignant progression of HCC

OBJECTIVE

hnRNPA3 is highly expressed in numerous malignancies, including hepatocellular carcinoma (HCC), but its function and mechanism has not been elucidated. In this study, we performed a comprehensive bioinformatics analysis of hnRNPA3 in the TCGA-LIHC dataset and several experiments in vitro to investigate the function and potential mechanisms of hnRNPA3 in HCC.

METHODS

Pan-cancer expression including hnRNPA3 levels as well as DNA methylation, associated ceRNA, immune infiltration, and immune checkpoint genes of hnRNPA3 in TCGA-LIHC dataset were assessed. Logistic regression, receiver operating characteristic curve (ROC), Kaplan-Meier analysis, and nomogram modeling were used to evaluate prognostic values of hnRNPA3 in HCC. hnRNPA3 level in cell subtypes in HCC tumor microenvironment was analysed through spatial transcriptomic. "pRRophetic" package was used to predict potential chemotherapeutic drugs sensitivity. hnRNPA3 level in HCC patients and cell lines were detected by qRT-PCR or WB. hnRNPA3's impact on proliferation, migration were studied in SNU449 and HuH7 cell lines. RNA-seq showed hnRNPA3 controled different important singaling passways in HCC.

RESULTS

hnRNPA3 was significantly elevated in HCC tumors compared to controls. hnRNPA3 levels correlated with Age, HCC stage, histologic grade, and tumor status, and may independently predict the overall and disease-specific survival. Significant associations were found between hnRNPA3 levels and DNA methylation. hsa-miR-22-3p may act as a regulatory factor for hnRNPA3 and form a ceRNA network with multiple lncRNAs.Analysis of immune infiltration and immune checkpoint genes revealed a correlation between hnRNPA3 expression and macrophages. The similar conclusion also occurred in the spatial transcriptomic detection. 5-Fluorouracil, Doxorubicin, Etoposide, et al., may be potential sensitive drugs in therapy of high-hnRNPA3 HCC patients. Silencing hnRNPA3 expression in SNU449 and HuH7 cells resulted in reducing proliferation and migration. RNA-seq showed hnRNPA3 played an important regulatory role in the malignant progression of HCC.

CONCLUSION

hnRNPA3 was found to represent a promising biomarker within HCC diagnosis and prognosis and maybe a potential drug-target in HCC therapy.

Overexpression of FOS enhances the malignant potential of eutopic endometrial stromal cells in patients with endometriosis‑associated ovarian cancer

Endometrial cysts of the ovary (EMC) may develop into endometriosis (EM)‑associated ovarian cancer over time (EAOC), but the pathogenesis of this disease has not been determined. In the present study, RNA sequencing was used to identify a feasible biomarker, and the molecular function of this biomarker in eutopic endometrial cells from EAOC and EMC patients was evaluated to explore the potential mechanism related to EAOC and orthotopic endometrial tissue. RNA sequencing was performed on 5 EAOC and 4 EMC tissue samples, and differential expression analysis was performed. To identify biomarkers, differentially expressed genes were subjected to protein‑protein interaction network design, Gene Ontology pathway enrichment, and Gene Set Enrichment Analysis pathway enrichment. The expression of FOS in the endometrium was detected via immunohistochemical staining. Lv‑FOS was utilized to upregulate FOS in human endometrial stromal cells (hEnSCs), and Cell Counting Kit‑8, colony formation and scratch assays were performed to assess cell viability, proliferation and migration, respectively. Western blotting was used to determine protein expression. In total, 249 genes, including FOS, were differentially expressed. Pathway enrichment analysis demonstrated that the MAPK, AP‑1, ERK and other signaling pathways were involved in the EMC‑to‑EAOC conversion. FOS upregulation in hEnSCs increased cell viability, proliferation and migration. Western blot results revealed that after FOS expression was inhibited, P21 expression was upregulated, and CDK4, Cyclin D1, p‑Stat3, MMP2 and MMP9 expression was downregulated. In conclusion, mitosis and the cell cycle were found to affect the progression of EMC to EAOC. The expression of FOS, a novel biomarker, was identified to enhance the malignant potential of eutopic endometrial stromal cells in patients with EM‑associated ovarian cancer.

Highly Sensitive and Specific Lateral Flow Detection for DNA Methylation Based on GIaI-Mediated Specific-Terminal-Mediated Polymerase Chain Reaction

Sensitive and specific detection of DNA methylation is crucial for the early diagnosis of various human diseases, particularly cancers. However, conventional methylation detection methods often face challenges in balancing both sensitivity and specificity. In this study, we present a novel approach that integrates the high specificity of methylation-dependent restriction endonuclease (GlaI) digestion with the amplification efficiency of specific terminal-mediated polymerase chain reaction (STEM-PCR). This combination enables selective amplification of methylated DNA, which is then detected through lateral flow detection (LFD), providing a simple, visual readout. As a proof of concept, a STEM-PCR-LFD assay was applied to detect methylated Septin 9, a biomarker for colorectal cancer. The assay demonstrated a sensitivity of approximately 0.1% (10 copies of methylated template per reaction), with no cross-reactivity observed when 10,000 copies of unmethylated DNA were included as background. Furthermore, the assay was validated with ten formalin-fixed paraffin-embedded (FFPE) tissue samples, achieving 100% consistency with standard real-time STEM-PCR. This method offers a highly sensitive, specific, and accessible platform for DNA methylation detection, with potential for early disease diagnosis.

Molecular subtyping of renal clear cell carcinoma based on prognostic RASSF family genes and validation of C1QL1 as a key prognostic marker

RASSF family proteins play crucial roles in mitosis, apoptosis, cell migration, adhesion, and immune functions, primarily acting as tumor suppressors. Their roles in renal clear cell carcinoma (ccRCC) are not fully understood. We analyzed the expression and prognostic significance of RASSF genes in 573 ccRCC samples from TCGA and GEO, identifying two molecular subtypes with distinct characteristics. We developed a RAS score to assess prognosis and molecular status and investigated the key gene C1QL1 through in vitro assays. Four RASSF genes were identified as associated with prognosis and progression in ccRCC. Based on their co-expression, we defined two patient subtypes, one with poorer prognosis. A higher RAS score correlated with advanced disease and worse outcomes but indicated a favorable response to specific inhibitors, supporting personalized treatment strategies. Additionally, VHL mutations may cause abnormal SFMBT1 expression, leading to high C1QL1 levels, which promote tumor progression via the YAP-EMT pathway. Our findings highlight the potential of RASSF-based molecular subtypes and scoring systems in personalizing ccRCC treatment. Understanding C1QL1's role may facilitate the development of novel therapeutic approaches.

Multi-omic analyses reveal aberrant DNA methylation patterns and the associated biomarkers of nasopharyngeal carcinoma and its cancer stem cells

Aberrant DNA methylation is a hallmark of nasopharyngeal carcinoma (NPC) pathogenesis. The aberrant DNA methylation patterns in NPC, particularly in its cancer stem cells (CSCs), and their underlying significance require further elucidation. We integratively performed DNA methylome and transcriptome combined with single-nucleus RNA sequencing to investigate DNA methylation and gene expression patterns of NPC and CSCs. Unlike Epstein-Barr virus (EBV)-negative cells, NPC and CSCs harboring EBV displayed global DNA hypermethylation and they were more oncogenic and immunosuppressive. By correlating DNA methylation and gene expression profiles, we disclosed potential relationships between aberrant DNA methylation, tumorigenesis, metastasis, immunotherapy response, and radiotherapy resistance of NPC. After validating with datasets from GEO and TCGA, we identified aberrant DNA methylation-associated biomarkers including 9 NPC-specific diagnostic markers that had significantly higher DNA methylation levels in NPC than in normal tissues and 8 types of cancers, and 12 potential prognostic markers that were highly correlated to cell cycle dysregulation. Notably, 2 of these potential biomarkers highly expressed in CSCs were validated at the single-cell level. Our study not only identified new potential diagnostic and prognostic biomarkers but also provided new insight into aberrant DNA methylation-associated pathogenesis of NPC, which is beneficial for the development of precision diagnosis and treatment schemes.

A urine DNA methylation assay for early detection of renal cancer

Renal cancer (RC) is the most lethal urological malignancy with 30% late diagnosis. Over 50% RCs are asymptomatic and discovered incidentally. Current RC detection relies on imaging while it lacks satisfactory sensitivity for detecting small-size tumors. A sensitive and robust diagnostic tool is needed to facilitate standardized RC early detection. Herein, we performed genome-wide methylation sequencing on both tissues and urine samples for RC DNA methylation makers discovery and developed a PCR-based RC early detector (RED) using a cohort of 93 RC and 35 non-RC urine samples. RED further achieved sensitivities of 82.2% and 80.7%, and specificities of 77.1% and 75% in a testing cohort (90 RC vs. 35 non-RC) and a validation cohort (119 RC vs. 48 non-RC), respectively. Importantly, RED exhibited 89.5% sensitivity for tumors in diameter <2 cm. It can detect 83.6% clear cell renal cell carcinoma, 75.0% of translocational renal cell carcinoma, 100% of primitive neuroectodermal tumors, renal malignant masenchymomas and mucinous tubular and spindle cell carcinoma. RED showed promising performance for RC detection with early stage and small size and have potential to be used in conjunction with imaging.

Design and Synthesis of Novel Deazapurine DNMT 1 Inhibitors with In Vivo Efficacy in DLBCL

The application of drugs to regulate abnormal epigenetic changes has become an important means of tumor treatment. In this study, we employed computer-aided design methods to develop a novel deazapurine compound targeting DNA methyltransferase 1 (DNMT1). Through screening for enzyme activity, selectivity, and cellular efficacy, we optimized three structural skeletons, ultimately yielding compound 55, exhibiting an IC50 of 2.42 μM for DNMT1. Compound 55 displayed excellent in vitro inhibitory effects on various hematological tumor and solid tumor cell lines, especially lymphoma cells, with IC50 values in the nanomolar range. In vitro studies confirmed compound 55 selectively inhibited DNMT1 and exhibited demethylation ability. In vivo mouse model validated the DNA methylation inhibition of compound 55. Compound 55 demonstrated good antitumor activity in vivo. Specifically, compound 55 combined with chidamide demonstrated a superior therapeutic effect over the first-line therapy RTX-CHOP in both the DEL and TP53 mutant DLBCL PDX tumor models.

Histone H3 lysine 9 tri-methylation is associated with pterygium

BACKGROUND

Pterygium, abnormal growths of conjunctival tissue onto the cornea, are common ocular surface conditions with a high risk of recurrence after surgery and potential ophthalmic complications. The exact cause of pterygium remains unclear, and the triggers are still unknown. This study aims to investigate the relationship between pterygium and epigenetics to uncover the cause of pterygium and identify biomarkers for its diagnosis.

METHODS

We performed a ChIP-seq assay to compare genome-wide histone modification levels between normal conjunctiva and stage 3 pterygium samples.

RESULTS

In this study, we investigate the epigenetic profiles of patients with pterygium, focusing on histone H3 lysine 4 (H3K4) and lysine 9 (H3K9) trimethylation (me3). While H3K4me3 levels showed no significant genome-wide change, they were significantly altered in genes related to development and ocular diseases. Conversely, H3K9me3 levels were markedly elevated genome-wide, particularly at the promoters of 82 genes involved in developmental pathways. Furthermore, we identify six genes, ANK2, AOAH, CBLN2, CDH8, CNTNAP4, and DPP6, with decreased gene expression correlated with substantially increased H3K9me3, suggesting their potential as biomarkers for pterygium.

CONCLUSION

This study represents the first report linking histone modification to pterygium progression, providing valuable insights into therapeutic strategies and potential drug targets.

Loss of AXIN1 regulates response to lenvatinib through a WNT/KDM5B/p15 signalling axis in hepatocellular carcinoma

BACKGROUND AND PURPOSE

As a highly heterogeneous cancer, hepatocellular carcinoma (HCC) shows different response rates to the multi-kinase inhibitor lenvatinib. Thus, it is important to explore genetic biomarkers for precision lenvatinib therapy in HCC.

EXPERIMENTAL APPROACH

The effect and mechanism of AXIN1 mutation on HCC were revealed by cell proliferation assay, long-term clone formation assay, sphere formation assay and small molecule inhibitor library screening. A new therapeutic strategy targeting HCC with AXIN1 mutation was evaluated in humanized models (patient-derived xenograft [PDX] and patient-derived organoid [PDO]).

KEY RESULTS

Based on The Cancer Genome Atlas (TCGA) data, we screened 6 most frequently lost tumour suppressor genes in HCC (TP53, ARID1A, AXIN1, CDKN2A, ARID2 and PTEN) and identified AXIN1 as the most crucial gene for lenvatinib sensitivity. Further study showed that AXIN1-knockout HCC cells had a more malignant phenotype and lower sensitivity to lenvatinib in vitro and in vivo. Mechanistically, the WNT pathway and its target gene c-Myc were activated when AXIN1 was missing, and the expression of tumour suppressor p15 was inhibited by transcription co-repressors c-Myc and Miz-1, resulting in the exacerbation of the resistant phenotype. Screening of a library of epigenetic-related enzyme inhibitors showed that a KDM5B inhibitor up-regulated p15 expression, leading to increased sensitivity to lenvatinib in vitro and in vivo.

CONCLUSION AND IMPLICATIONS

AXIN1-deficient patients have a lower response to lenvatinib, which may be associated with suppression of p15 mediated by WNT pathway activation. KDM5B inhibitors can restore p15 levels, resulting in efficient killing of resistant cells in HCC.

Identification of EXO1 as a potential biomarker associated with prognosis and tumor immune microenvironment for specific human cancers

Exonuclease 1 (EXO1) is an evolutionarily conserved exonuclease, which have function on maintaining genomic stability. Elevated expression of EXO1 has been reported in certain cancers. However, a comprehensive pan-cancer analysis of EXO1 is still lacking and its role in human cancer development remains poorly understood. This study aims to investigate the genetic alterations and expression perturbations of EXO1 and evaluate its potential clinical relevance in different cancer types. By employing powerful bioinformatics tools and utilizing data sourced from The Cancer Genome Atlas and the Genotype-Tissue Expression datasets, a comprehensive pan-cancer analysis of EXO1 was conducted, including an examination of gene expression, alterations in genetics, DNA methylation patterns, survival outcomes, clinical traits, immune features, and functional enrichment analysis. EXO1 was found to be highly expressed across 20 tumor types, including lung adenocarcinoma, lung squamous cell carcinoma, and breast invasive carcinoma. The expression levels of EXO1 are frequently associated with later clinical stages and unfavorable outcomes. Genetic alterations in EXO1 were predominantly found to be amplified in a pan-cancer context. A total of 131 missense mutations, 24 truncation mutations, 1 in-frame mutation, 6 splice site mutations, and 1 fusion mutation were identified. Interestingly, a significant co-occurrence of alterations in EXO1 with other ten gene alterations were identified. The expression of EXO1 in multiple tumors showed a significant correlation with tumor mutational burden, microsatellite instability, and genes related to immunological checkpoints. In most types of cancer, a strong correlation exists between the expression of EXO1 and the infiltration of CD4+ Th2 cells, memory CD4+ T cells, myeloid-derived suppressor cells, and common lymphoid progenitors. Analysis of 150 genes related to EXO1 demonstrate an enrichment in processes such as cell cycle regulation, DNA damage repair, and relevant signaling pathways, suggesting a possible mechanism through which EXO1 may facilitate tumor development. This study offers a deep insight into the role of EXO1 in different types of human cancers, indicating that EXO1 could act as an important prognostic biomarker and a therapeutic target for certain types of cancer.

Molecular profiling of breast cancer methylation pattern in triple negative versus non- triple negative breast cancer

Epigenetic alterations, especially promotor methylation, have a significant impact on gene expression, molecular subtyping, prognosis, and outcome of breast cancer (BC). The methylation profile was assessed for 22 genes of the BC tissue using the EpiTect Methyl II PCR System in 40 triple-negative BC (TNBC) patients compared to 50 non-TNBC group. The data were corelated with the disease-free (DFS) and overall survival (OS) of the patients. Genes that were differentially hypermethylated in TNBC patients compared to those with non-TNBC included CCND2, CDKN2A, ESR1, CDH1, BRCA1, GSTP, RASSF1, SLIT2, MGMT, PTEN, TP73, and PRDM2. These panel achieved 95% sensitivity, 98% specificity, 97.44% positive predictive value (PPV), 94.23% negative predictive value (NPV), and AUC of 0.993. Hypermethylation of BRCA1, CDH1, CDKN2A, ESR1, GSTP, HIC1, MGMT, PRDM2, PTEN, PYCARDM, RASSF1M, THBS1, and TP73 associated significantly with worse OS and DFS in TNBC cohort. Meanwhile, CCNA1 and CDH1 hypermethylation demonstrated significant associations with poor DFS but did not show significant relationships with OS in TNBC patients. PTGS2 and TNFRSF10C methylation were associated with better DFS and OS rates in TNBC patients. On multivariate Cox regression, CCND2 and PTEN hypermethylation were independent predictors of DFS in the overall BC patients. The hypermethylation of BRCA1 and GSTP were independent predictors of DFS, while PTEN hypermethylation was an independent predictor of OS in the TNBC cohort. The identification of hypermethylated genes, such as BRCA1, CCND2, CDH1, ESR1, GSTP, RASSF1, SLIT2, MGMT, and PTEN may serve as potential biomarkers or therapeutic targets for TNBC.

Identification of a novel hypermethylation marker, ZSCAN18, and construction of a diagnostic model in cervical cancer

PURPOSE

Cervical cancer (CC), a common female malignancy, has been linked to alterations in DNA methylation. This study employed an integrated "dry-wet lab" strategy combining bioinformatics, machine learning, and experimental validation to identify novel methylation biomarkers for CC.

METHODS

Methylome and transcriptome data from the TCGA and GEO cohorts (n=349 discovery, n=414 validation) were analyzed to identify differentially methylated CpGs. The top candidates were validated by pyrosequencing, methylation-specific PCR, and quantitative assays. Diagnostic models were developed, and functional studies were performed for the target markers.

RESULTS

Eighteen differentially methylated CpGs were identified, with five top candidates (three in the ZSCAN18 promoter) showing diagnostic potential. ZSCAN18 promoter methylation levels and positivity rates were significantly greater in CC tissues than in normal tissues (p<0.05), reaching 77.8% (21/27) in ThinPrep cytology test (TCT) samples. The ridge regression diagnostic model achieved an AUC of 0.9421 in the validation cohort. Similarly, ZSCAN18 overexpression suppressed CC cell proliferation (p<0.05).

CONCLUSIONS

This study established a rapid, effective and systematic systemic research strategy to screen novel methylation markers for CC. ZSCAN18 promoter methylation correlates with cervical lesion severity, and the diagnostic model enhances the diagnostic ability. These findings highlight the dual role of ZSCAN18 as a diagnostic marker and potential therapeutic target.

An "Outer Piezoelectric and Inner Epigenetic" Logic-Gated PANoptosis for Osteosarcoma Sono-Immunotherapy and Bone Regeneration

The precise manipulation of PANoptosis, a newly defined cell death pathway encompassing pyroptosis, apoptosis, and necroptosis, is highly desired to achieve safer cancer immunotherapy with tumor-specific inflammatory responses and minimal side effects. Nonetheless, this objective remains a formidable challenge. Herein, an "AND" logic-gated strategy for accurately localized PANoptosis activation, utilizing composite 3D-printed bioactive glasses scaffolds integrated with epigenetic regulator-loaded porous piezoelectric SrTiO3 nanoparticles is proposed. The "logic-gated" strategy is co-programmed by an "outer" input signal of exogenous ultrasound irradiation to produce reactive oxygen species and an "inner" input signal of acid tumor microenvironment to ensure the epigenetic demethylation regulation, guaranteeing the tumor-specific PANoptosis. Specifically, immunogenic PANoptosis triggers dendritic cell maturation and cytotoxic T cell activation, amplifying antitumor immune responses and significantly suppressing osteosarcoma growth, with a suppression rate of ≈73.47 ± 5.2%. In addition, the well-known bioactivities of Sr-doped scaffolds expedite osteogenic differentiation and reinforce bone regeneration. Therefore, this work provides a paradigm of logic-gated sono-piezoelectric biomaterial platform with concurrently exogenous/endogenous activated PANoptosis for controlled sono-immunotherapy of osteosarcoma, and related bone defects repair.

Deregulated methylation and expression of PCDHGB7 in patients with non-small cell lung cancer: a novel prognostic and immunological biomarker

Backgrounds

Protocadherin gamma subfamily B, 7 (PCDHGB7), a member of the protocadherin family, plays critical roles in neuronal connections and has been implicated in female reproductive system cancers. Its function in lung cancer has not been elucidated.

Methods

We comprehensively investigated PCDHGB7 expression, prognosis, biological function, methylation patterns, and it's relationship with immune infiltration and immunotherapy response through public datasets (HPA, TCGA, GEO, OncoDB and MEXPRESS). Two lung cancer immunotherapy cohorts from our clinical center were enrolled to detect the relationship between methylation and protein levels of PCDHGB7 in plasma and immunotherapy outcomes.

Results

PCDHGB7 expression was downregulated in lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) and associated with tumor prognosis. PCDHGB7 demonstrated a positive correlation with inhibitory immune cells and a negative correlation with tumor mutational burden (TMB) and homologous recombination deficiency (HRD). The methylation level of PCDHGB7 was upregulated in tumor tissue and negatively correlated with PCDHGB7 mRNA level. In immunotherapy cohort studies, patients with higher PCDHGB7 tissue expression showed worse prognosis. Patients with PCDHGB7 hypermethylation in baseline plasma had shorter progression-free survival (PFS) and overall survival (OS), while those with early reduction of PCDHGB7 methylation had the best prognosis. Plasma PCDHGB7 protein levels could predict responses to immune checkpoint inhibitors and function as a prognostic marker for PFS.

Conclusion

PCDHGB7 expression and methylation are prognostic and immunological biomarkers in non-small cell lung cancer. Plasma PCDHGB7 methylation and protein levels can be used as novel biomarkers for predicting the efficacy of immunotherapy in lung cancer.

Human immune system: Exploring diversity across individuals and populations

The immune response is an intricate system that involves the complex connection of cellular and molecular components, each with distinct functional specialisations. It has a distinct capacity to adjust and mould the immune response in accordance with specific stimuli, influenced by both genetic and environmental factors. The presence of genetic diversity, particularly across different ethnic and racial groups, significantly contributes to the impact of incidence of diseases, disease susceptibility, autoimmune disorders, and cancer risks in specific regions and certain populations. Environmental factors, including geography and socioeconomic status, further modulate the variety of the immune system responses. These, in turn, affect the susceptibility to infectious diseases and development of autoimmune disorders. Despite the complexity of the relationship, there remains a gap in understanding the specificity of immune indices across races, immune reference ranges among populations, highlighting the need for deeper understanding of immune diversity for personalized approaches in diagnostics and therapeutics. This review systematically organizes these findings, with the goal of emphasizing the potential of targeted interventions to address health disparities and advance translational research, enabling a more comprehensive strategy. This approach promises significant advancements in identifying specific immunological conditions, focusing on personalized interventions, through both genetic and environmental factors.

Transcription factor MAZ activates the transcription of hypomethylated TYMP in ccRCC

Clear cell renal cell carcinoma (ccRCC) is a highly malignant tumor characterized by a significant propensity for recurrence and metastasis. DNA methylation has emerged as a critical epigenetic mechanism with substantial utility in cancer diagnosis. In this study, multi-omics data were utilized to investigate the target genes regulated by the transcription factor MYC-associated zinc finger protein (MAZ) in ccRCC, leading to the identification of thymidine phosphorylase (TYMP) as a gene with notably elevated expression in ccRCC. The interaction between MAZ and TYMP was confirmed through chromatin immunoprecipitation (ChIP) assays and bioinformatics analysis. It was found that the binding of MAZ to the TYMP promoter is associated with the methylation status of this promoter region. Furthermore, the methylation of the TYMP promoter appears to be correlated with both the clinicopathological stage and overall survival of ccRCC patients. Further exploration of genes within the "nucleotide metabolism" pathway, identified through Gene Ontology (GO) enrichment analysis, revealed that uridine phosphorylase 1 (UPP1) interacts with TYMP. Interestingly, UPP1 was also shown to be activated by MAZ, suggesting a coordinated regulatory mechanism. Based on these findings, we propose that the TYMP-UPP1 complex, co-regulated by MAZ, plays a pivotal role in nucleotide metabolism in ccRCC. These results suggest that TYMP may contribute to the pathophysiology of ccRCC and that promoter methylation offers potential as a prognostic indicator, providing novel insights into the molecular underpinnings of ccRCC and potential avenues for therapeutic intervention.

CYP24A1 DNA Methylation in Colorectal Cancer as Potential Prognostic and Predictive Markers

The DNA methylation of CYP24A1 can regulate its gene expression and may play a role in the occurrence and progression of colorectal cancer (CRC). However, the association between CYP24A1 DNA methylation and the prognosis of CRC patients has not yet been reported. In this study, differential methylation analysis was conducted in both blood and tissue cohorts, and differential expression analysis was performed in the tissue cohort with in vitro validation. GO and KEGG enrichment analyses were performed on CYP24A1-related genes. A correlation between CYP24A1 promoter methylation and its gene expression was explored. Kaplan-Meier survival and Cox regression analyses were performed to investigate the impact of CYP24A1 DNA methylation on the prognosis of CRC patients. Prognostic risk scores were constructed for survival prediction. Immune infiltration analysis was also conducted. Our results showed that the hypermethylation of cg02712555 in tumor tissues (hazard ratio, 0.48; 95% confidence interval, 0.24-0.94; p = 0.032) and CpG site 41 in peripheral leukocytes (HR, 0.35; 95%CI, 0.14-0.84; p = 0.019) were both associated with decreased overall mortality in CRC patients. Prognostic risk scores showed robust predictive capabilities of these two CpG loci for the prognosis of CRC patients. CYP24A1 hypermethylation was positively correlated with infiltration levels of activated CD4 + T cells, activated CD8 + T cells, activated B cells, activated dendritic cells, and macrophages. Taken together, our findings indicate that the methylation levels of specific CpG sites within the CYP24A1 promoter region in blood leukocytes and tumors are potential prognostic and predictive markers for overall survival in CRC patients.

LKB1 inactivation promotes epigenetic remodeling-induced lineage plasticity and antiandrogen resistance in prostate cancer

Epigenetic regulation profoundly influences the fate of cancer cells and their capacity to switch between lineages by modulating essential gene expression, thereby shaping tumor heterogeneity and therapy response. In castration-resistant prostate cancer (CRPC), the intricacies behind androgen receptor (AR)-independent lineage plasticity remain unclear, leading to a scarcity of effective clinical treatments. Utilizing single-cell RNA sequencing on both human and mouse prostate cancer samples, combined with whole-genome bisulfite sequencing and multiple genetically engineered mouse models, we investigated the molecular mechanism of AR-independent lineage plasticity and uncovered a potential therapeutic strategy. Single-cell transcriptomic profiling of human prostate cancers, both pre- and post-androgen deprivation therapy, revealed an association between liver kinase B1 (LKB1) pathway inactivation and AR independence. LKB1 inactivation led to AR-independent lineage plasticity and global DNA hypomethylation during prostate cancer progression. Importantly, the pharmacological inhibition of TET enzymes and supplementation with S-adenosyl methionine were found to effectively suppress AR-independent prostate cancer growth. These insights shed light on the mechanism driving AR-independent lineage plasticity and propose a potential therapeutic strategy by targeting DNA hypomethylation in AR-independent CRPC.

A combined model of circulating tumor DNA methylated SHOX2/SCT/HOXA7 and clinical features facilitates the discrimination of malignant from benign pulmonary nodules

BACKGROUND

Despite the advancements in early lung cancer detection attributed to the widespread use of low-dose computed tomography (LDCT), this technology has also led to an increasing number of pulmonary nodules (PNs) of indeterminate significance being identified. Therefore, this study was aimed to develop a model that leverages plasma methylation biomarkers and clinical characteristics to distinguish between malignant and benign PNs.

METHODS

In a training cohort of 210 patients with PNs, we evaluated plasma circulating tumor DNA (ctDNA) for the presence of three lung cancer-specific methylation markers: SHOX2, SCT, and HOXA7. Subsequently, we constructed a combined model utilizing methylated SHOX2/SCT/HOXA7 (mSHOX2/SCT/HOXA7) ctDNA levels, the largest nodule size measured by LDCT, and age, employing the binary logistic regression algorithm. Furthermore, we compared the diagnostic performances of the combined model with the Mayo Clinic model and the single mSHOX2/SCT/HOXA7 model by analyzing the area under the receiver operating characteristic curve (AUC) for each.

RESULTS

The combined model demonstrated an impressive AUC of 0.87 and an accuracy of 0.75 in the training cohort, using pathologic diagnoses as the gold standard. This performance was significantly superior to that of the single mSHOX2/SCT/HOXA7 panel (AUC = 0.81, P < 0.0001) and the Mayo model (AUC = 0.65, P = 0.0005). Further validation in a cohort of 82 patients with PNs confirmed the diagnostic value of the combined model. Additionally, we observed that as the size of the nodule increased, the diagnostic accuracy of the combined model also improved.

CONCLUSIONS

A combined model incorporating the ctDNA-based methylation status of SHOX2/SCT/HOXA7 genes, the largest nodule size measured by LDCT, and age can serve as a supplementary approach to LDCT for lung cancer. This model enhances the precision in identifying high-risk individuals and optimizes the clinical management strategies for PNs detected by CT.

Advances in the diagnosis of colorectal cancer: the application of molecular biomarkers and imaging techniques: a literature review

Background

Following neoplasms of the lung and breast, colorectal cancer (CRC) is the third most frequent malignancy globally. Screening for CRC at the age of 50 years is strongly encouraged for prompt earlier diagnosis owing to prognoses being greatly correlated with time of detection and cancer staging.

Aim

This review aimed to elucidate the most recent advancements in the detection of CRC, with an emphasis on the latest innovations in diagnostic molecular biomarkers in conjunction with radiological imaging alongside stool-based tests for CRC screening.

Methods

A comprehensive review of the literature was performed, focusing on specific terms in different electronic databases, including that of PubMed/MEDLINE. Keywords pertaining to "colorectal cancer," "diagnosis," "screening," "imaging," and "biomarkers," among others, were employed in the search strategy. Articles screened and evaluated were deemed relevant to the study aim and were presented in the medium of the English language.

Results

There have been several innovations in the diagnostics and identification of CRC. These generally comprise molecular biomarkers, currently being studied for suitability in disease detection. Examples of these include genetic, epigenetic, and protein biomarkers. Concurrently, recent developments in CRC diagnostics highlight the advancements made in radiological imaging that offer precise insights on tumor biology in addition to morphological information. Combining these with statistical methodologies will increase the sensitivity and specificity of CRC diagnostics. However, putting these strategies into reality is hampered by several issues.

Conclusion

Progress in diagnostic technology alongside the identification of a few prognostic predictive molecular biomarkers suggested great promise for prompt detection and management of CRC. This clearly necessitates further efforts to learn more in this specific sector.

Attenuated sex-related DNA methylation differences in cancer highlight the magnitude bias mediating existing disparities

BACKGROUND

DNA methylation (DNAm) influences both sex differences and cancer development, yet the mechanisms connecting these factors remain unclear.

METHODS

Utilizing data from The Cancer Genome Atlas, we conducted a comprehensive analysis of sex-related DNAm effects in nine non-reproductive cancers, compared to paired normal adjacent tissues (NATs), and validated the results using independent datasets. First, we assessed the extent of sex differential DNAm between cancers and NATs to explore how sex-related DNAm differences change in cancerous tissues. Next, we employed a multivariate adaptive shrinkage approach to model the covariance of cancer-related DNAm effects between sexes, aiming to elucidate how sex impacts aberrant DNAm patterns in cancers. Finally, we investigated correlations between the methylome and transcriptome to identify key signals driving sex-biased DNAm regulation in cancers.

RESULTS

Our analysis revealed a significant attenuation of sex differences in DNAm within cancerous tissues compared to baseline differences in normal tissues. We identified 3,452 CpGs (Pbonf < 0.05) associated with this reduction, with 72% of the linked genes involved in X chromosome inactivation. Through covariance analysis, we demonstrated that sex differences in cancer are predominantly driven by variations in the magnitude of shared DNAm signals, referred to as "amplification." Based on these patterns, we classified cancers into female- and male-biased groups and identified key CpGs exhibiting sex-specific amplification. These CpGs were enriched in binding sites of critical transcription factors, including P53, SOX2, and CTCF. Integrative multi-omics analyses uncovered 48 CpG-gene-cancer trios for females and 380 for males, showing similar magnitude differences in DNAm and gene expression, pointing to a sex-specific regulatory role of DNAm in cancer risk. Notably, several genes regulated by these trios were previously identified as drug targets for cancers, highlighting their potential as sex-specific therapeutic targets.

CONCLUSIONS

These findings advance our understanding of how sex, DNAm, and gene expression interact in cancer, offering insights into the development of sex-specific biomarkers and precision medicine.

Interpretable deep cross networks unveiled common signatures of dysregulated epitranscriptomes across 12 cancer types

Cancer is a complex and multifaceted group of diseases characterized by uncontrolled cell growth that leads to the formation of malignant tumors. Recent studies suggest that N6-methyladenosine (m6A) RNA methylation plays pivotal roles in cancer pathology by influencing various cellular processes. However, the degree to which these mechanisms are shared across different cancer types remains unclear. In this study, we analyze an expansive array of 167 m6A epitranscriptome profiles covering 12 distinct cancer types and their originating normal tissues. We trained 12 distinct, cancer type-specific interpretable deep cross network models, which successfully distinguish between specific pairs of normal and cancer m6A contexts using integrated information from both the sequences and curated genomic knowledge. Interestingly, cross-cancer type testing indicated the existence of shared genomic patterns across various cancers at the epitranscriptome level. A pan-cancer model was subsequently developed to identify these shared patterns that could not be observed in a single cancer type. Our analysis uncovered, for the first time, a common epitranscriptome signature shared across multiple cancer types, particularly associated with RNA hybridization process and aberrant splicing. This highlights the importance of a comprehensive understanding of the pan-cancer epitranscriptome and holding potential implications in the development of RNA methylation-based therapeutics for various cancers.

Current status and new directions for hepatocellular carcinoma diagnosis

Liver cancer ranks as the sixth most common cancer globally, with hepatocellular carcinoma (HCC) accounting for approximately 75%-85% of cases. Most patients present with moderately advanced disease, while those with advanced HCC face limited and ineffective treatment options. Despite diagnostic efforts, no ideal tumor marker exists to date, highlighting the urgent clinical need for improved early detection of HCC. A key research objective is the development of assays that target specific pathways involved in HCC progression. This review explores the pathological origin and development of HCC, providing insights into the mechanistic rationale, clinical statistics, and the advantages and limitations of commonly used diagnostic tumor markers. Additionally, it discusses the potential of emerging biomarkers for early diagnosis and offers a brief overview of relevant assay methodologies. This review aims to summarize existing markers and investigate new ones, providing a basis for subsequent research.

Comprehensive pan-cancer analysis unveils the significant prognostic value and potential role in immune microenvironment modulation of TRIB3

TRIB3, a pseudokinase, was previously studied within only some specific cancer types, leaving its comprehensive functions in pan-cancer contexts largely unexplored. Here, we performed an integrated analysis of TRIB3 expression, prognosis, genetic alterations, functional enrichment and tumor immune-related characteristics in 33 cancer types. Our results showed that TRIB3 exhibits high expression levels across 24 different cancer types and correlates closely with unfavorable prognoses. Meanwhile, TRIB3 shows mutations in a wide spectrum of 22 distinct cancer types, with the predominant mutation types being missense mutations and gene amplifications, and significant changes in DNA methylation levels in 14 types of cancer. We further discovered that TRIB3 expression is significantly associated with cancer immune-related genome mutations, such as tumor mutational burden (TMB), microsatellite instability (MSI) and DNA mismatch repair (MMR), and infiltration of immunosuppressive cells, such as CD4+ Th2 cells and myeloid-derived suppressor cells (MDSCs), into the tumor microenvironment. These results indicated that the expression of TRIB3 might reshape the tumor immune microenvironment (TIME) and lead to immunosuppressive "cold" tumors. In addition, our results confirmed that the loss of function of TRIB3 inhibits cell proliferation, promotes apoptosis, and leads to significant enrichment of "hot" tumor-related immune pathways, at least in breast cancer cells, which further supports the important role of TRIB3 in cancer prognosis and TIME regulation. Together, this pan-cancer investigation provided a comprehensive understanding of the critical role of TRIB3 in human cancers, and suggested that TRIB3 might be a promising prognostic biomarker and a potential target for cancer immunotherapy.

Mechanisms and cross-talk of regulated cell death and their epigenetic modifications in tumor progression

Cell death is a fundamental part of life for metazoans. To maintain the balance between cell proliferation and metabolism of human bodies, a certain number of cells need to be removed regularly. Hence, the mechanisms of cell death have been preserved during the evolution of multicellular organisms. Tumorigenesis is closely related with exceptional inhibition of cell death. Mutations or defects in cell death-related genes block the elimination of abnormal cells and enhance the resistance of malignant cells to chemotherapy. Therefore, the investigation of cell death mechanisms enables the development of drugs that directly induce tumor cell death. In the guidelines updated by the Cell Death Nomenclature Committee (NCCD) in 2018, cell death was classified into 12 types according to morphological, biochemical and functional classification, including intrinsic apoptosis, extrinsic apoptosis, mitochondrial permeability transition (MPT)-driven necrosis, necroptosis, ferroptosis, pyroptosis, PARP-1 parthanatos, entotic cell death, NETotic cell death, lysosome-dependent cell death, autophagy-dependent cell death, immunogenic cell death, cellular senescence and mitotic catastrophe. The mechanistic relationships between epigenetic controls and cell death in cancer progression were previously unclear. In this review, we will summarize the mechanisms of cell death pathways and corresponding epigenetic regulations. Also, we will explore the extensive interactions between these pathways and discuss the mechanisms of cell death in epigenetics which bring benefits to tumor therapy.

Multi-omics analysis of the biological function of the VEGF family in colon adenocarcinoma

The vascular endothelial growth factor (VEGF) family plays a crucial role in cancer progression, but the prognostic significance and biological functions of VEGF family members in colon adenocarcinoma (COAD) remain unclear. Using data from The Cancer Genome Atlas, Gene Expression Omnibus, Gene Set Cancer Analysis, cBioPortal, GeneMANIA, String, MethSurv and starBase database, we identified vascular endothelial growth factor B (VEGFB) as a key gene associated with COAD prognosis, with its abnormal expression linked to methylation dysregulation. In vitro experiments confirmed VEGFB expression was significantly higher in colon cancer tissues compared to normal tissues, as shown by Real-time quantitative PCR and immunohistochemistry. Cell Counting Kit-8 and colony formation assay showed that decreased VEGFB expression in SW480 cells resulted in decreased cell viability and proliferation ability. Scratch assay showed that VEGFB downregulation impaired SW480 cell migration. In addition, our research suggests that VEGFB not only promotes angiogenesis but is also involved in the tumor microenvironment and immune regulation. The SHNG17-miR-375-VEGFB regulatory axis provides a potential therapeutic target for COAD, highlighting VEGFB's role in immune activation during anti-angiogenic therapy and potential reversal of drug resistance.

Methylation modification is a poor prognostic factor in non-small cell lung Cancer and regulates the tumor microenvironment: mRNA molecular structure and function

Non-small cell lung cancer (NSCLC) is the most common and deadly type of lung cancer, and its poor prognosis is closely related to the complex interactions of the tumor microenvironment. Through methylation analysis of tumor tissue samples from NSCLC patients, combined with high-throughput sequencing technology, the methylation status and structural characteristics of mRNA molecules were studied. Bioinformatics tools were used to analyze the regulatory effects of methylation modification on mRNA expression and genes associated with the tumor microenvironment. The results showed that the methylation level of specific mRNA was significantly correlated with the expression changes of tumor microenvironment-related factors. In addition, methylation modification affected mRNA stability and translation efficiency, further altering the metabolic activity and immune escape capacity of tumor cells. The results showed that mRNA with high methylation level was significantly associated with poor prognosis. Methylation modification profoundly affects the tumor microenvironment and prognosis of non-small cell lung cancer by altering the structure and function of mRNA molecules.

Exploring the fascinating interplay of epigenetically modified DNA bases with two dimensional bare and P-doped Si2BN and BN sheets for biosensing applications: A compelling DFT perspective

Detecting epigenetically modified (EM) bases is crucial for disease detection, biosensing, and DNA sequencing. Two-dimensional P-doped Si2BN and BN sheets are used as sensing substrates in density functional theory (DFT) studies. Both the sheets are doped with a phosphorous atom at various atomic sites to examine the sheet's potential in detecting 5-hydroxymethylcytosine (5hmc), 5-methylcytosine (5mc), 7-methylguanine (7mg) and 8-oxoguanine (8oxg) bases. Doping of the P atom in the Si2BN sheet improves the adsorption energy (Ead) of Ab+5hmc (-107.16 kcal/mol) and Ab+5mc (-78.36 kcal/mol), As+7mg (-84.31 kcal/mol) in the gas and aqueous phase Ab+5hmc (-93.28 kcal/mol), An+7mg (-78.92 kcal/mol) and As+5mc (-77.52 kcal/mol) respectively. Standard deviation (θ) indicates that As complexes have high θ values ranging from 4.55 to 37.77, suggesting a high likelihood of distinguishing the bases. The P-doped BN complexes exhibit noticeable work functional shifting (Δϕ%) recommended that they can be used as ϕ-based sensors. Time-dependent DFT results suggest that when EM bases interact with P-doped Si2BN complexes, significant blue shifts (hypsochromic) and red shifts (bathochromic) are observed in the visible and near-infrared spectrum. Hence, the above finding suggests that P-doped Si2BN sheets are highly effective for sensing EM bases and are recommended for DNA/RNA sequencing applications.

Potential Role of AKR1B1 Gene Methylation in Diagnosis of Patients With Breast Cancer

Background

In addition to the great challenge of early diagnosis and prognosis in breast cancer (BC), the role of gene promoters in BC remains largely unexplored. This study aimed to evaluate aldo-keto reductase family 1 member B1 (AKR1B1) methylation as noninvasive biomarker for early BC diagnosis.

Methods

A total of 200 (120 with BC, 40 with benign breast diseases, 40 healthy) Egyptian women were enrolled. AKR1B1 methylation level was determined using EpiTect Methyl II QPCR assay quantitative polymerase chain reaction.

Results

Findings revealed that hypermethylation AKR1B1 was reported to be associated (P < .0001) with BC cases (93.2 [75.4-98.6]) compared with benign (23.9 [22.6-48.3]) or healthy (15.5 [10.6-16]) controls. It had a great diagnostic power (area under the curve [AUC] = 0.909) that was superior to cancer antigen (CA) 15-3 (AUC = 0.681) and carcinoembryonic antigen (CEA) (AUC = 0.539). Interestingly, AKR1B1 hypermethylation was reported to be significant in identifying BC early stages (AUC = 0.899) and grades (AUC = 0.903). Independent to hormonal status and HER2neu expression, AKR1B1 hypermethylation was related to some tumor severity features, including advanced stages, high histological grades, and lymph node invasion. Also, AKR1B1 high degrees of methylation were significantly correlated with the increase in CEA (r = .195; P = .027), CA-15.3 (r = .351; P = .0001) and tumor stages (r = .274; P = .014), grades (r = .253; P = .024), and lymph node invasion (r = .275; P = .014).

Conclusions

This study revealed that aberrant AKR1B1 methylation could facilitate early BC detection from benign br0east disorders. Hypermethylated AKR1B1 was related to BC aggressiveness suggesting its potential role as diagnostic and prognostic BC biomarker.

Pan-cancer analysis of the prognostic and immunological roles of SHP-1/ptpn6

SHP-1, a nonreceptor protein tyrosine phosphatase encoded by ptpn6, has been regarded as a regulatory protein of hematopoietic cell biology for years. However, there is now increasing evidence to support its role in tumors. Thus, the role of ptpn6 for prognosis and immune regulation across 33 tumors was investigated, aiming to explore its functional heterogeneity and clinical significance in pan-cancer. Differential expression of ptpn6 was found between cancer and adjacent normal tissues, and its expression was significantly correlated with the prognosis of tumor patients. In most cancers, ptpn6 expression was significantly associated with immune infiltration. This was further confirmed by ptpn6-related genes/proteins enrichment analysis. Additionally, genetic alterations in ptpn6 was observed in most cancers. As for epigenetic changes, it's phosphorylation levels significantly altered in 6 tumors, while methylation levels significantly altered in 12 tumors. Notably, the methylation levels of ptpn6 were significantly decreased in 11 tumors, accompanied by its increased expression in 8 of them, suggesting that the hypomethylation may be related to its increased expression. Our results show that ptpn6 plays a specific role in tumor immunity and exerts a pleiotropic effect in a variety of tumors. It can serve as a prognostic factor for some cancers. Especially in LGG, KIRC, UCS and TGCT, the increased expression of ptpn6 is associated with poor prognosis and high immune infiltration. This aids in understanding the role of ptpn6 in tumor biology, and can provide insight into presenting a potential biomarker for poor prognosis and immune infiltration in cancers.

DNA methylation-regulated HK1 overexpression contributes to irradiation-resistance by promoting glycolysis in non-small cell lung cancer

Irradiation-resistance presents a substantial challenge in the successful application of radiotherapy for non-small-cell lung cancer (NSCLC). However, the specific molecular mechanisms responsible for irradiation-resistance have yet to be completely understood. In this research, the DNA methylation and gene expression patterns resulting from irradiation treatment were produced using the DNA methylation BeadChip and RNA-Seq. An integrated analysis was carried out to identify the genes that are differentially expressed and regulated by DNA methylation. As results, the upregulation of gene expression and downregulation of DNA methylation of hexokinase 1 (HK1), a protein associated with glycolysis, were observed in irradiation-resistant NSCLC cells. Additionally, treatment with the DNA demethylating agent 5-aza-2'-deoxycytidine (5-Aza-dC) resulted in increased expression of HK1. Furthermore, it was found that overexpression of HK1 could enhance irradiation-resistance by impacting glycolysis. Collectively, our study indicate that irradiation-induced alterations in DNA methylation lead to the upregulation of HK1, which in turn promotes glycolysis and contributes to radiotherapy resistance in NSCLC. Therefore, targeting HK1 presents a potential novel strategy for addressing the issue of radiotherapy failure in NSCLC.

STUB1-mediated K63-linked ubiquitination of UHRF1 promotes the progression of cholangiocarcinoma by maintaining DNA hypermethylation of PLA2G2A

BACKGROUND

Cholangiocarcinoma (CCA) is a highly malignant tumor characterized by a lack of effective targeted therapeutic strategies. The protein UHRF1 plays a pivotal role in the preservation of DNA methylation and works synergistically with DNMT1. Posttranscriptional modifications (PTMs), such as ubiquitination, play indispensable roles in facilitating this process. Nevertheless, the specific PTMs that regulate UHRF1 in CCA remain unidentified.

METHODS

We confirmed the interaction between STUB1 and UHRF1 through mass spectrometry analysis. Furthermore, we investigated the underlying mechanisms of the STUB1-UHRF1/DNMT1 axis via co-IP experiments, denaturing IP ubiquitination experiments, nuclear‒cytoplasmic separation and immunofluorescence experiments. The downstream PLA2G2A gene, regulated by the STUB1-UHRF1/DNMT1 axis, was identified via RNA-seq.  The negative regulatory mechanism of PLA2G2A was explored via bisulfite sequencing PCR (BSP) experiments to assess changes in promoter methylation. The roles of PLA2G2A and STUB1 in the proliferation, invasion, and migration of CCA cells were assessed using the CCK-8 assay, colony formation assay, Transwell assay, wound healing assay and xenograft mouse model. We evaluated the effects of STUB1/UHRF1 on cholangiocarcinoma by utilizing a primary CCA mouse model.

RESULTS

This study revealed that STUB1 interacts with UHRF1, resulting in an increase in the K63-linked ubiquitination of UHRF1. Consequently, this facilitates the nuclear translocation of UHRF1 and enhances its binding affinity with DNMT1. The STUB1-UHRF1/DNMT1 axis led to increased DNA methylation of the PLA2G2A promoter, subsequently repressing its expression. Increased STUB1 expression in CCA was inversely correlated with tumor progression and overall survival. Conversely, PLA2G2A functions as a tumor suppressor in CCA by inhibiting cell proliferation, invasion and migration.

CONCLUSIONS

These findings suggest that the STUB1-mediated ubiquitination of UHRF1 plays a pivotal role in tumor progression by epigenetically silencing PLA2G2A, underscoring the potential of STUB1 as both a prognostic biomarker and therapeutic target for CCA.

Unraveling the key role of chromatin structure in cancer development through epigenetic landscape characterization of oral cancer

Epigenetic alterations, such as those in chromatin structure and DNA methylation, have been extensively studied in a number of tumor types. But oral cancer, particularly oral adenocarcinoma, has received far less attention. Here, we combined laser-capture microdissection and muti-omics mini-bulk sequencing to systematically characterize the epigenetic landscape of oral cancer, including chromatin architecture, DNA methylation, H3K27me3 modification, and gene expression. In carcinogenesis, tumor cells exhibit reorganized chromatin spatial structures, including compromised compartment structures and altered gene-gene interaction networks. Notably, some structural alterations are observed in phenotypically non-malignant paracancerous but not in normal cells. We developed transformer models to identify the cancer propensity of individual genome loci, thereby determining the carcinogenic status of each sample. Insights into cancer epigenetic landscapes provide evidence that chromatin reorganization is an important hallmark of oral cancer progression, which is also linked with genomic alterations and DNA methylation reprogramming. In particular, regions of frequent copy number alternations in cancer cells are associated with strong spatial insulation in both cancer and normal samples. Aberrant methylation reprogramming in oral squamous cell carcinomas is closely related to chromatin structure and H3K27me3 signals, which are further influenced by intrinsic sequence properties. Our findings indicate that structural changes are both significant and conserved in two distinct types of oral cancer, closely linked to transcriptomic alterations and cancer development. Notably, the structural changes remain markedly evident in oral adenocarcinoma despite the considerably lower incidence of genomic copy number alterations and lesser extent of methylation alterations compared to squamous cell carcinoma. We expect that the comprehensive analysis of epigenetic reprogramming of different types and subtypes of primary oral tumors can provide additional guidance to the design of novel detection and therapy for oral cancer.

Early Diagnosis of Colorectal Cancer Based on Bisulfite-free Site-specific Methylation Identification PCR Strategy: High-Sensitivity, Accuracy, and Primary Medical Accessibility

Due to its decade-long progression, colorectal cancer (CRC) is most suitable for population screening to achieve a significant reduction in its incidence and mortality. DNA methylation has emerged as a potential marker for the early detection of CRC. However, the current mainstream methylation detection method represented by bisulfite conversion has issues such as tedious operation, DNA damage, and unsatisfactory sensitivity. Herein, a new high-performance CRC screening tool based on the promising specific terminal-mediated polymerase chain reaction (STEM-PCR) strategy is developed. CRC-related methylation-specific candidate CpG sites are first prescreened through The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases using self-developed bioinformatics. Next, 9 homebrew colorectal cancer DNA methylated STEM‒PCR assays (ColoC-mSTEM) with high sensitivity (0.1%) and high specificity are established to identify candidate sites. The clinical diagnostic performance of these selected methylation sites is confirmed and validated by a case-control study. The optimized diagnostic model has an overall sensitivity of 94.8% and a specificity of 95.0% for detecting early-stage CRC. Taken together, ColoC-mSTEM, based on a single methylation-specific site, is a promising diagnostic approach for the early detection of CRC which is perfectly suitable for the screening needs of CRC in primary healthcare institutions.

Targeting transposable elements in cancer: developments and opportunities

Transposable elements (TEs), comprising nearly 50% of the human genome, have transitioned from being perceived as "genomic junk" to key players in cancer progression. Contemporary research links TE regulatory disruptions with cancer development, underscoring their therapeutic potential. Advances in long-read sequencing, computational analytics, single-cell sequencing, proteomics, and CRISPR-Cas9 technologies have enriched our understanding of TEs' clinical implications, notably their impact on genome architecture, gene regulation, and evolutionary processes. In cancer, TEs, including long interspersed element-1 (LINE-1), Alus, and long terminal repeat (LTR) elements, demonstrate altered patterns, influencing both tumorigenic and tumor-suppressive mechanisms. TE-derived nucleic acids and tumor antigens play critical roles in tumor immunity, bridging innate and adaptive responses. Given their central role in oncology, TE-targeted therapies, particularly through reverse transcriptase inhibitors and epigenetic modulators, represent a novel avenue in cancer treatment. Combining these TE-focused strategies with existing chemotherapy or immunotherapy regimens could enhance efficacy and offer a new dimension in cancer treatment. This review delves into recent TE detection advancements, explores their multifaceted roles in tumorigenesis and immune regulation, discusses emerging diagnostic and therapeutic approaches centered on TEs, and anticipates future directions in cancer research.

The whole blood DNA methylation of RAB8A and RAP1A in autoimmune thyroiditis: evidence and validation of iodine exposure in a population from different water iodine areas

Our study aimed to identify and verify G protein-related methylated genes in AIT patients, while also investigate those genes in AIT patients exposed to iodine in different water iodine areas. Different areas were classified by median water iodine (MWI) concentrations: Iodine-Fortified Areas (IFA, MWI<10µg/L), Iodine-Adequate Areas (IAA, 40≤MWI≤100 µg/L), and Iodine-Excessive Areas (IEA, MWI>100 µg/L). We studied 176 AIT cases and 176 controls, with 89, 40, and 47 pairs in IFA, IAA, and IEA, respectively. Using the Illumina Human Methylation 850k BeadChip, we identified candidate methylated genes. MethylTargetTM and QRT-PCR validated DNA methylation and mRNA expression. Results showed hypomethylation and high expression of RAB8A and RAP1A in all 176 AIT cases. RAB8A's CpG sites were mainly hypomethylated in IFA and IEA, while RAP1A's sites were primarily hypomethylated in IEA. This study underscores how water iodine exposure may influence RAB8A and RAP1A methylation in AIT.

TNC upregulation promotes glioma tumourigenesis through TDG-mediated active DNA demethylation

Gliomas represent the most predominant primary malignant tumor in central nervous system. Thymine DNA glycosylase (TDG) is a central component in active DNA demethylation. However, the specific mechanisms of TDG-mediated active DNA demethylation in gliomas remain unclear. This research indicates TDG expression is overexpressed in gliomas and correlated with poor prognosis. TDG knockdown suppressed the malignant phenotype of gliomas both in vitro and vivo. Notably, RNA-seq analysis revealed a strong association between TDG and tenascin-C (TNC). ChIP-qPCR and MeDIP-qPCR assays were undertaken to confirm that TDG participates in TNC active DNA demethylation process, revealing decreased DNA methylation levels and elevated TNC expression as a result. Silencing TNC expression also suppressed the tumor malignant phenotype in both in vitro and in vivo experiments. Additionally, simultaneous silencing of TNC reduced or even reversed the glioma promotion caused by TDG overexpression. Based on our findings, we conclude that TDG exerts an indispensable role in TNC active DNA demethylation in gliomas. The DNA demethylation process leads to alternations in TNC methylation levels and promotes its expression, thereby contributing to the development of gliomas. These results suggest a novel epigenetic therapeutic strategy targeting active DNA demethylation in gliomas.

T cell proliferation-related subtypes, prognosis model and characterization of tumor microenvironment in head and neck squamous cell carcinoma

Background

Thirty-three synthetic driver genes of T-cell proliferation have recently been identified through genome-scale screening. However, the tumor microenvironment (TME) cell infiltration, prognosis, and response to immunotherapy mediated by multiple T cell proliferation-related genes (TRGs) in patients with head and neck squamous cell carcinoma (HNSC) remain unclear.

Methods

This study examined the genetic and transcriptional changes in 771 patients with HNSC by analyzing the TRGs from two independent datasets. Two different subtypes were analyzed to investigate their relationship with immune infiltrating cells in the TME and patient prognosis. The study also developed and validated a risk score to predict overall survival (OS). Furthermore, to enhance the clinical utility of the risk score, an accurate nomogram was constructed by combining the characteristics of this study.

Results

The low-risk score observed in this study was associated with high levels of immune checkpoint expression and TME immune activation, indicating a favorable OS outcome. Additionally, various factors related to risk scores were depicted.

Conclusion

Through comprehensive analysis of TRGs in HNSC, our study has revealed the characteristics of the TME and prognosis, providing a basis for further investigation into TRGs and the development of more effective immunotherapy and targeted therapy strategies.

Hypermethylated TAGMe as a universal-cancer-only methylation marker and its application in diagnosis and recurrence monitoring of urothelial carcinoma

BACKGROUND

Urothelial carcinoma (UC) is the second most common urological malignancy. Despite numerous molecular markers have been evaluated during the past decades, no urothelial markers for diagnosis and recurrence monitoring have shown consistent clinical utility.

METHODS

The methylation level of tissue samples from public database and clinical collected were analyzed. Patients with UC and benign diseases of the urinary system (BUD) were enrolled to establish TAGMe (TAG of Methylation) assessment in a training cohort (n = 567) using restriction enzyme-based bisulfite-free qPCR. The performance of TAGMe assessment was further verified in the validation cohort (n = 198). Urine samples from 57 UC patients undergoing postoperative surveillance were collected monthly for six months after surgery to assess the TAGMe methylation.

RESULTS

We identified TAGMe as a potentially novel Universal-Cancer-Only Methylation (UCOM) marker was hypermethylated in multi-type cancers and investigated its application in UC. Restriction enzyme-based bisulfite-free qPCR was used for detection, and the results of which were consistent with gold standard pyrosequencing. Importantly, hypermethylated TAGMe showed excellent sensitivity of 88.9% (95% CI: 81.4-94.1%) and specificity of 90.0% (95% CI: 81.9-95.3%) in efficiently distinguishing UC from BUD patients in urine and also performed well in different clinical scenarios of UC. Moreover, the abnormality of TAGMe as an indicator of recurrence might precede clinical recurrence by three months to one year, which provided an invaluable time window for timely and effective intervention to prevent UC upstaging.

CONCLUSION

TAGMe assessment based on a novel single target in urine is effective and easy to perform in UC diagnosis and recurrence monitoring, which may reduce the burden of cystoscopy. Trial registration ChiCTR2100052507. Registered on 30 October 2021.