Epigenetic Alteration in Colorectal Cancer: Potential Diagnostic and Prognostic Implications

Construction and Value Analysis of a Prognostic Assessment Model Based on Radiomics and Genetic Data for Colorectal Cancer

Aims/Background Colorectal cancer (CRC) is one of the major global health problems, with high morbidity and mortality, underscoring the need for new diagnostic and prognostic tools. Therefore, this study aims to evaluate the significance of integrating radiomics with genetic data in CRC prognostic assessment and improve the accuracy of prognosis prediction. Methods This study included computed tomography (CT) images from 225 CRC patients and RNA-seq information from 654 patients, obtained from the TICA database. Key radiomics features and genes were identified through radiomics feature extraction, least absolute shrinkage and selection operator (LASSO) regression analysis, and Kaplan-Meier survival analysis. Furthermore, a CRC prognostic model was constructed using these key genes and radiomics features. Results This study identified 170 key radiomics features. Out of them, five were significantly associated with CRC prognosis. Transcriptome data analysis identified 8 key genes, among which the high expressions of Inhibin Subunit Beta B (INHBB), Potassium Voltage-Gated Channel Subfamily Q Member 2 (KCNQ2), and Ubiquilin Like (UBQLNL) were significantly correlated with poor prognosis. Age, tumor stage, pathological T stage, and pathological N stage were determined as independent prognostic factors. Moreover, immune infiltration analysis demonstrated that the immune score of the low-risk group was higher than that of the high-risk group, with significant differences in some immune cells, and key genes were correlated with immune cells. Additionally, the constructed CRC prognostic model incorporating three genes, INHBB, KCNQ2, and UBQLNL, exhibited high prediction accuracy in the validation set, with area under the curve (AUC) values of 0.80, 0.87, and 0.84 at 1-year, 3-year, and 5-year, respectively, indicating good prediction performance and reliability of the model. Conclusion The multimodal data combining radiomics features and gene expression data can improve the accuracy of CRC prognostic assessment, providing a valuable prognostic prediction tool for clinical practice and helping to guide the selection and optimization of treatment regimens.

Insight into the role of DNA methylation in prognosis and treatment response prediction of gastrointestinal cancers

Gastrointestinal (GI) cancers impose a significant disease burden, underscoring the critical importance of accurate prognosis prediction and treatment response evaluation. DNA methylation, one of the most extensively studied epigenetic modifications, has gained prominence due to its reliable measurement across various sample types. Numerous studies have reported that DNA methylation was linked to the diagnosis, prognosis and treatment response in malignancies, including GI cancers. While its diagnostic role in GI cancers has been comprehensively reviewed. Recent research has increasingly highlighted its potential in prognosis prediction and treatment response evaluation. However, no existing reviews have exclusively focused on these two aspects. In this review, we retrieved relevant studies and included 230 of them in our discussion, thereby providing an overview of the clinical applicability of aberrant DNA methylation in these two fields among patients with esophageal, gastric, colorectal, pancreatic cancers, and hepatocellular carcinomas. Additionally, we discuss the limitations of the current literature and propose directions for future research. Specifically, we emphasize the need for standardized DNA methylation methodologies and advocate for the integration of gene panels, rather than single genes, to address tumor heterogeneity more effectively.

Mechanisms and Strategies to Overcome Drug Resistance in Colorectal Cancer

Colorectal cancer (CRC) is a major cause of cancer-related mortality worldwide, with a significant impact on public health. Current treatment options include surgery, chemotherapy, radiotherapy, molecular-targeted therapy, and immunotherapy. Despite advancements in these therapeutic modalities, resistance remains a significant challenge, often leading to treatment failure, poor progression-free survival, and cancer recurrence. Mechanisms of resistance in CRC are multifaceted, involving genetic mutations, epigenetic alterations, tumor heterogeneity, and the tumor microenvironment. Understanding these mechanisms at the molecular level is crucial for identifying novel therapeutic targets and developing strategies to overcome resistance. This review provides an overview of the diverse mechanisms driving drug resistance in sporadic CRC and discusses strategies currently under investigation to counteract this resistance. Several promising strategies are being explored, including targeting drug transport, key signaling pathways, DNA damage response, cell death pathways, epigenetic modifications, cancer stem cells, and the tumor microenvironment. The integration of emerging therapeutic approaches that target resistance mechanisms aims to enhance the efficacy of current CRC treatments and improve patient outcomes.

LINE-1 methylation status and survival outcomes in colorectal cancer patients: A systematic review and meta-analysis

Colorectal cancer (CRC) is a leading cause of cancer-related mortality worldwide. DNA hypomethylation, particularly of Long Interspersed Nuclear Element-1 (LINE-1) repetitive sequences, has been implicated in CRC development and progression. The purpose of this meta-analysis and systematic review was to evaluate the prognostic value of LINE-1 methylation level in patients with CRC. Relevant studies were identified through systematic database searches, and summary hazard ratios (HRs) with 95 % confidence intervals (CIs) were calculated for relations between LINE-1 hypomethylation and overall survival (OS), disease-free survival (DFS), and cancer-specific survival (CSS). The current systematic review protocol was registered on International Prospective Register of Systematic Reviews (PROSPERO, CRD42024496615). A total of 19 studies comprising 8169 CRC patients were included. The pooled analysis showed no significant association between LINE-1 hypomethylation and OS in the overall population (HR = 1.70, 95 % CI: 0.97-2.96). However, in stage II/III patients, LINE-1 hypomethylation was significantly associated with poorer OS (HR = 1.92, 95 % CI: 1.26-2.91) and DFS (HR = 2.81, 95 % CI: 1.33-5.93). No significant association was found between LINE-1 hypomethylation and CSS (HR = 1.39, 95 % CI: 0.68-2.83). Substantial heterogeneity was observed across studies. The study suggests that LINE-1 methylation level could be a valuable prognostic biomarker for advanced-stage CRC patients, potentially improving personalized care and highlighting areas for future research to establish standardized methodologies.

Diagnostic and Prognostic Significance of a Four-miRNA Signature in Colorectal Cancer

Colorectal cancer (CRC) is the fourth most commonly diagnosed cancer and one of the leading causes of cancer death worldwide. Despite diagnostic and therapeutic advances, CRC mortality remains high, especially in industrialized countries. Numerous studies have highlighted the pathogenetic role of altered microRNA (miRNA) expression among the various factors contributing to the development and progression of colorectal cancer (CRC). However, the data regarding specific miRNAs involved in CRC pathogenesis remain inconsistent, and no miRNAs have been recognized so far as reliable or effective biomarkers for the diagnosis of this tumor type. To identify novel miRNA biomarkers in CRC, this study validated the expression levels of a four-miRNA signature predicted to be involved in CRC by analyzing both tissue and liquid biopsy samples. Our experimental and bioinformatics results highlighted the diagnostic potential of hsa-miR-21-5p, hsa-miR-503-5p, and hsa-miR-375, as well as the potential prognostic value of hsa-miR-497-5p overexpression and hsa-miR-375-3p downregulation. Overall, the results obtained suggest the diagnostic and prognostic significance of this four-miRNA signature in CRC.

Advancements in immunotherapy for colorectal cancer treatment: a comprehensive review of strategies, challenges, and future prospective

PURPOSE

Colorectal cancer (CRC) remains one of the leading causes of cancer-related mortality worldwide. Metastatic colorectal cancer (mCRC) continues to present significant challenges, particularly in patients with proficient mismatch repair/microsatellite stable (pMMR/MSS) tumors. This narrative review aims to provide recent developments in immunotherapy for CRC treatment, focusing on its efficacy and challenges.

METHODS

This review discussed the various immunotherapeutic strategies for CRC treatment, including immune checkpoint inhibitors (ICIs) targeting PD-1 and PD-L1, combination therapies involving ICIs with other modalities, chimeric antigen receptor T-cell (CAR-T) cell therapy, and cancer vaccines. The role of the tumor microenvironment and immune evasion mechanisms was also explored to understand their impact on the effectiveness of these therapies.

RESULTS

This review provides a comprehensive update of recent advancements in immunotherapy for CRC, highlighting the potential of various immunotherapeutic approaches, including immune checkpoint inhibitors, combination therapies, CAR-T therapy, and vaccination strategies. The results of checkpoint inhibitors, particularly in patients with MSI-H/dMMR tumors, which have significant improvements in survival rates have been observed. Furthermore, this review also addresses the challenges faced in treating pMMR/MSS CRC, which remains resistant to immunotherapy.

CONCLUSION

Immunotherapy plays a significant role in the treatment of CRC, particularly in patients with MSI-H/dMMR tumors. However, many challenges remain, especially in treating pMMR/MSS CRC. This review discussed the need for further research into combination therapies, biomarker development, CAR-T cell therapy, and a deeper understanding of immune evasion mechanisms for CRC treatment.

Closing Editorial: Colorectal Cancer-A Molecular Genetics Perspective

Colorectal cancer (CRC) remains a significant global health challenge, ranking third in incidence and second in mortality among all cancers [...].

Targeting non-histone methylation in gastrointestinal cancers: From biology to clinic

Gastrointestinal (GI) cancers, encompassing a range of malignancies within the digestive tract, present significant challenges in both diagnosis and treatment, reflecting a dire need for innovative therapeutic strategies. This article delves into the profound influence of non-histone methylation on the pathogenesis and evolution of gastrointestinal (GI) cancers. Non-histone proteins, undergoing methylation by enzymes such as Protein Arginine Methyltransferases (PRMTs) and Lysine Methyltransferases (KMTs), play pivotal roles in cellular signaling, metabolism, chromatin remodeling, and other processes crucial for cancer development. This review illuminates the complex mechanisms by which non-histone methylation affects key aspects of tumor biology, including oncogenesis, growth, proliferation, invasion, migration, metabolic reprogramming, and immune escape in GI malignancies. Highlighting recent discoveries, this work underscores the importance of non-histone methylation in cancer biology and its potential as a target for innovative therapeutic strategies aimed at improving outcomes for patients with GI cancers.

The implication of TET1, miR-200, and miR-494 expression with tumor formation in colorectal cancer: through targeting Wnt signaling

OBJECTIVE

Colorectal cancer (CRC) is a diverse and multifaceted disease characterized by genetic and epigenetic changes that contribute to tumor initiation and progression. CRC pathophysiology has been linked to the deregulation of the Wnt signaling pathway and the ten-eleven translocation (TET) DNA demethylases. This study aimed to evaluate the expression level of selective miRNAs (miR-200 and miR-494), TET1, and Wnt1 in colorectal polyps, actual colorectal tumors, and normal adjacent tissues. We also evaluated the effect of 5-aza cytidine on the expression level of TET1 and wnt1 in the HT29 cell line.

MATERIALS AND METHODS

In this study, we assessed TET1 and Wnt1 expression in 5-azacytidine-treated HT29 cells, a demethylating agent commonly used in cancer therapy. Additionally, we enrolled 114 individuals who underwent radical surgical colon resection, including 47 with cancerous tissues and 67 with polyps. We utilized qRT-PCR to measure miR-200, miR-494, TET1, and Wnt1 mRNA levels in colorectal polyps, actual colorectal tumors, and normal adjacent tissues.

RESULTS

Our study revealed that TET1 expression was notably lower in both polyps and CRC tissue compared to adjacent normal tissue, with higher TET1 expression in tumors than polyps. We also observed significant differences in miR-200 and miR-494 expression in tumor samples compared to adjacent normal tissue. Our in vitro experiments revealed that 5-azacytidine administration increased TET1 and decreased Wnt1 expression in CRC cell lines. This suggests that DNA-demethylating drugs may have a therapeutic role in modifying TET1 and Wnt signaling in the development of CRC.

CONCLUSIONS

Overall, our findings shed light on the intricate interactions between TET1, Wnt1, and specific miRNAs in colorectal cancer (CRC) and their potential implications for diagnosis and treatment.

Serum Pyridoxal 5'-Phosphate and Pyridoxic Acid Ratio Index with Prognosis of Colorectal Cancer: A Prospective Cohort Study

BACKGROUND

Studies on the association between serum vitamin B6 status and colorectal cancer prognosis are limited and have yielded inconsistent results. This study investigated the association of pyridoxal 5'-phosphate (PLP) and pyridoxic acid ratio (PAr) index with colorectal cancer survival.

METHODS

A total of 1286 colorectal cancer patients diagnosed since 2010 were selected from the Guangdong Colorectal Cancer Cohort study. Serum levels of PLP, pyridoxal, and 4-pyridoxic acid were measured using ultra-high-performance liquid chromatography-tandem mass spectrometry. The study followed overall mortality and colorectal cancer-specific mortality until December 2023. Multivariable Cox proportional hazards regression models were applied to calculate hazard ratios (HRs) and 95% confidence intervals (95% CIs). Restricted cubic spline and stratified analysis were performed.

RESULTS

During a median follow-up of 77.36 months, 331 deaths were recorded, with 293 specifically attributed to colorectal cancer. Higher PLP levels were associated with a longer overall survival (HRQ4 vs. Q1, 0.63; 95% CI: 0.46, 0.87; p for trend = 0.008) and colorectal cancer-specific survival (HRQ4 vs. Q1, 0.62; 95% CI: 0.44, 0.87; p for trend = 0.006). Non-linear associations were observed between serum PLP and overall and colorectal cancer-specific survival (p for non-linear < 0.05). However, PAr was not significantly associated with either overall survival (HRQ4 vs. Q1, 1.03; 95% CI: 0.75, 1.41) or colorectal cancer-specific survival (HRQ4 vs. Q1, 1.01; 95% CI: 0.72, 1.42). The association between serum PLP and both overall survival and colorectal cancer-specific survival (p for interaction < 0.05) varied by alcohol drinking status.

CONCLUSIONS

Higher serum PLP levels, but not PAr, may be associated with improved overall and colorectal cancer-specific survival.

Integrating Machine Learning with Multi-Omics Technologies in Geroscience: Towards Personalized Medicine

Aging is a fundamental biological process characterized by a progressive decline in physiological functions and an increased susceptibility to diseases. Understanding aging at the molecular level is crucial for developing interventions that could delay or reverse its effects. This review explores the integration of machine learning (ML) with multi-omics technologies-including genomics, transcriptomics, epigenomics, proteomics, and metabolomics-in studying the molecular hallmarks of aging to develop personalized medicine interventions. These hallmarks include genomic instability, telomere attrition, epigenetic alterations, loss of proteostasis, disabled macroautophagy, deregulated nutrient sensing, mitochondrial dysfunction, cellular senescence, stem cell exhaustion, altered intercellular communication, chronic inflammation, and dysbiosis. Using ML to analyze big and complex datasets helps uncover detailed molecular interactions and pathways that play a role in aging. The advances of ML can facilitate the discovery of biomarkers and therapeutic targets, offering insights into personalized anti-aging strategies. With these developments, the future points toward a better understanding of the aging process, aiming ultimately to promote healthy aging and extend life expectancy.

Targeting LRP6: A new strategy for cancer therapy

Targeting specific molecular drivers of tumor growth is a key approach in cancer therapy. Among these targets, the low-density lipoprotein receptor-related protein 6 (LRP6), a vital component of the Wnt signaling pathway, has emerged as an intriguing candidate. As a cell-surface receptor and vital co-receptor, LRP6 is frequently overexpressed in various cancer types, implicating its pivotal role in driving tumor progression. The pursuit of LRP6 as a target for cancer treatment has gained substantial traction, offering a promising avenue for therapeutic intervention. Here, this comprehensive review explores recent breakthroughs in our understanding of LRP6's functions and underlying molecular mechanisms, providing a profound discussion of its involvement in cancer pathogenesis and drug resistance. Importantly, we go beyond discussing LRP6's role in cancer by discussing diverse potential therapeutic approaches targeting this enigmatic protein. These approaches encompass a wide spectrum, including pharmacological agents, natural compounds, non-coding RNAs, epigenetic factors, proteins, and peptides that modulate LRP6 expression or disrupt its interactions. In addition, also discussed the challenges associated with developing LRP6 inhibitors and their advantages over Wnt inhibitors, as well as the drugs that have entered phase II clinical trials. By shedding light on these innovative strategies, we aim to underscore LRP6's significance as a valuable and multifaceted target for cancer treatment, igniting enthusiasm for further research and facilitating translation into clinical applications.