Colon cancer (CC) remains a significant global health burden, and the search for novel prognostic biomarkers and therapeutic targets is crucial. This study comprehensively analyzed the role of SIX2 (Sine Oculis Homeobox Homolog 2) in CC. Utilizing data from TCGA, GTEx, and CCLE databases, differential expression of SIX2 was observed in multiple cancers, with significant upregulation in many tumors compared to normal tissues. In CC, SIX2's differential expression was notable. Cox regression analysis revealed its prognostic significance, with overexpression associated with poor survival outcomes. SIX2 was strongly associated with gene alterations and correlated with key signaling pathways like WNT and TGF-β. In the tumor microenvironment, SIX2 was related to immune cell infiltration and immune-related molecules. Notably, in CC, it was associated with immunosuppressive cells and checkpoint molecules. Additionally, ABT737 was found to sensitize tumor immunotherapy in the context of SIX2. Animal experiments demonstrated that ABT737 effectively restricted the growth of CC in mice, and its combination with antiPD-1 immunotherapy was more effective. It could reduce the infiltration of CD163+ tumor-associated macrophages but without significantly increasing the infiltration of CD8+ T cells. Our findings suggest that SIX2 is a potential key player in CC, offering insights into future research and the development of targeted therapies.

The growing interest in RNA-based therapeutics has positioned small interfering RNA (siRNA) as a promising tool for gene silencing with high specificity and efficacy. However, the successful clinical application of siRNA therapies requires efficient delivery systems to overcome extracellular and intracellular barriers. Chitosan, a naturally derived polysaccharide, has gained significant attention as a non-viral vector due to its biodegradability, biocompatibility, mucoadhesive properties, and capacity to enhance cellular uptake. These attributes make chitosan an attractive alternative to lipid-based nanoparticles, which currently dominate siRNA delivery platforms. Recent advancements in chitosan-based nanoformulations, including chemical modifications and functionalization strategies, have improved siRNA stability, targeting efficiency, and transfection potential, addressing key limitations such as low bioavailability and immunogenicity. Despite these advances, challenges remain in achieving optimal release kinetics, scalability, and consistent therapeutic efficacy. Future research efforts will focus on engineering chitosan derivatives with enhanced physicochemical properties, integrating multifunctional nanocarriers, and refining formulation strategies to bridge the gap between preclinical research and clinical translation. The continued development of chitosan-based siRNA therapeutics holds significant potential for advancing precision medicine and expanding treatment options for a variety of diseases, including cancer, metabolic disorders, and inflammatory conditions.

Colorectal cancer (CRC) remains a leading cause of cancer-related illness and death worldwide, arising from a complex interplay of genetic predisposition, environmental influences, and epigenetic dysregulation. Among these factors, epigenetic modifications-reversible and heritable changes in gene expression-serve as crucial regulators of CRC progression. Understanding these modifications is essential for identifying potential biomarkers for early diagnosis and developing targeted therapeutic strategies. Epigenetic drugs (epidrugs) such as DNA methyltransferase inhibitors (e.g., decitabine) and bromodomain inhibitors (e.g., JQ1) have shown promise in modulating aberrant epigenetic changes in CRC. However, challenges such as drug specificity, delivery, and safety concerns limit their clinical application. Advances in CRISPR-Cas9-based epigenetic editing offer a more precise approach to modifying specific epigenetic markers, presenting a potential breakthrough in CRC treatment. Despite its promise, CRISPR-based epigenome editing may result in unintended genetic modifications, necessitating stringent regulations and safety assessments. Beyond pharmacological interventions, lifestyle factors-including diet and gut microbiome composition-play a significant role in shaping the epigenetic landscape of CRC. Nutritional and microbiome-based interventions have shown potential in preventing CRC development by maintaining intestinal homeostasis and reducing tumor-promoting epigenetic changes. This review provides a comprehensive overview of epigenetic alterations in CRC, exploring their implications for diagnosis, prevention, and treatment. By integrating multi-omics approaches, single-cell technologies, and model organism studies, future research can enhance the specificity and efficacy of epigenetic-based therapies. Shortly, a combination of advanced gene-editing technologies, targeted epidrugs, and lifestyle interventions may pave the way for more effective and personalized CRC treatment strategies.

Triclosan (TCS) and triclocarban (TCC) are widely used as antimicrobial agents in personal care products. Their widespread use has become a potential environmental contaminant. This review reviews the mechanisms of intestinal toxicity of TCS and TCC and their potential nutritional intervention strategies. TCS and TCC can be metabolized to glucuronic acid conjugates in the host and subsequently uncoupled by microorganisms in the intestine to regenerate free forms of TCS and TCC. TCS and TCC are unique metabolic pathways that lead to accumulation in the gut, altering the structure of intestinal flora, increasing the relative abundance of pathogenic bacteria, while reducing the abundance of beneficial bacteria, thereby disrupting the balance of intestinal flora. In addition, they can interfere with the self-renewal and differentiation of ISCs, thereby weakening intestinal barrier function. TCS and TCC can also activate the TLR4-NFκB signaling pathway, inducing and exacerbating inflammatory responses. These mechanisms together lead to intestinal toxicity and have a significant negative impact on intestinal health. In order to cope with the intestinal toxicity caused by these mechanisms of action, this paper believes that prebiotics, probiotics, vitamins, minerals and herbal extracts can be used as potential nutritional interventions to reduce the intestinal toxicity of TCS and TCC by regulating intestinal microbiota, enhancing intestinal barrier function and inhibiting inflammatory response. Although preliminary studies have shown the potential benefits of these interventions, their specific efficacy and safety still need further study.

A high-fat diet (HFD) exerts complex effects on the risk of colitis-associated cancer (CAC). Nodakenin, a key phytochemical isolated from the dried roots of Angelicae gigas Nakai (Umbelliferae), possesses anti-inflammatory and anti-adipogenic properties and shows potential as a therapeutic agent for colorectal cancer (CRC). In this study, we investigated the protective effects and underlying molecular mechanisms of nodakenin in an animal model of CRC induced by HFD, azoxymethane (AOM), and dextran sodium sulfate (DSS). Oral administration of nodakenin significantly alleviated clinical symptoms, such as recovery of weight, spleen weight, and colon length, and suppressed tumor progression in the colonic tissues of HFD/AOM/DSS-induced CRC mice. Nodakenin inhibited the activation of STAT3-related inflammatory mediators and downregulated proteins involved in the Wnt/β-catenin signaling pathway. These effects contributed to the disruption of epithelial-mesenchymal transition (EMT) and the restoration of tight junction integrity within the colonic tissue. Furthermore, nodakenin treatment improved the composition of the gut microbiota, leading to observable species-level differences. Network analysis revealed significant correlations between clinical parameters, inflammatory markers, EMT and apoptotic factors, and the composition of the gut microbiota. Specifically, negative correlations were observed between spleen weight and Alistipes, as well as between MCP-1 and Clostridium_g21. Positive correlations with spleen weight were observed with species belonging to Anaerotruncus, Emergencia, and Parvibacter. Bacteroidaceae_uc and Bacteroides correlated positively with MCP-1, Streptococcus correlated positively with PUMA, and Harryflintia, Odoribacteraceae_uc, and Roseburia correlated positively with cleaved caspase-3. Overall, our findings suggested that nodakenin effectively alleviates HFD/AOM/DSS-induced CRC by targeting inflammatory pathways (STAT3 and Wnt/β-catenin), suppressing EMT, and restoring gut microbiota balance. These multiple mechanisms underscore its potential as a promising agent for the prevention and treatment of colitis-associated colorectal cancer.

The Wnt signaling pathway is a critical regulatory mechanism that governs cell cycle progression, apoptosis, epithelial-mesenchymal transition (EMT), angiogenesis, stemness, and the tumor immune microenvironment, while also maintaining tissue homeostasis. Dysregulated activation of this pathway is implicated in various cancers, closely linked to tumor initiation, progression, and metastasis. The Wnt/β-catenin axis plays a central role in the pathogenesis of common cancers, including colorectal cancer (CRC), breast cancer (BC), liver cancer, and lung cancer. Unlike traditional chemotherapy, targeted therapy offers a more precise approach to cancer treatment. As a key regulator of oncogenesis, the Wnt pathway represents a promising target for clinical interventions. This review provides a comprehensive analysis of the Wnt signaling pathway, exploring its roles in tumor biology and its implications in human malignancies. It further examines the molecular mechanisms and modes of action across different cancers, detailing how the Wnt pathway contributes to tumor progression through mechanisms such as metastasis promotion, immune modulation, drug resistance, and enhanced cellular proliferation. Finally, therapeutic strategies targeting Wnt pathway components are discussed, including inhibitors targeting extracellular members, as well as those within the cell membrane, cytoplasm, and nucleus. The potential of these targets in the development of novel therapeutic agents underscores the critical importance of intervening in the Wnt signaling pathway for effective cancer treatment.

Ferroptosis, a regulated form of cell death dependent on iron and marked by lipid peroxidation, is increasingly recognized for its role in a wide array of diseases, including cancers, neurodegenerative disorders, and tissue damage. This review examines the dynamic interaction between ferroptosis and the Wnt/β-catenin signaling pathway, focusing on how Wnt surface receptors, ligands, antagonists, and associated components influence the regulation of ferroptosis. Key elements such as Frizzled receptors, Wnt ligands, and antagonists like DKK1 are shown to affect ferroptosis by altering oxidative stress, lipid dynamics, and iron metabolism. A central aspect of this interaction is the role of the destruction complex, particularly GSK-3β, which regulates ferroptosis through its upstream modulation by the AKT pathway and downstream control over NRF2, GPX4, and SLC7A11. Furthermore, the involvement of β-catenin/TCF transcription factors in the regulation of ferroptosis emphasizes the significance of this pathway in promoting cell survival and resisting ferroptosis, particularly in various cancers. Multiple cancers, including colorectal, breast, ovarian, and lung cancers, are affected by disruptions in the Wnt/ferroptosis axis, where enhanced Wnt signaling helps cancer cells evade ferroptosis and develop resistance to treatments. Beyond cancer, this axis also plays a crucial role in neurodegenerative diseases and conditions like myocardial infarction. Additionally, natural compounds have shown potential in modulating the Wnt/ferroptosis pathway, offering promising therapeutic approaches for a variety of diseases. This review highlights the molecular mechanisms of the Wnt/ferroptosis axis, paving the way for innovative treatment options in cancer and other diseases.

Kaiso, a potential target for the treatment of lung cancer. Our research focuses on Kaiso inhibitros. Through virtual screening and molecular dynamic simulations, we discovered a promising Kaiso inhibitor called compound 5 (ZINC20577650). By modifying the structure of compound 5, a series of novel Kaiso inhibitors that contain a diphenyl ether ring were synthesized. Among them, compound 20 exhibited the strongest inhibitory activity against A549 cells (IC50 = 0.34 μM). Notably, its inhibitory activity surpassed that of the positive control MIRA-1 (IC50 = 654.065 μM). Molecular docking and dynamic studies revealed that the binding of the compound's amino and ester moieties to the active site of kaiso protein, as well as the extension of the benzene ring towards the Asn561 position in the cavity, contributed significantly to its potency. These findings provide valuable insights for the development of new Kaiso inhibitors.

Breast cancer (BC) and gynecological malignancies, including cervical, ovarian, and uterine cancers, are significant global health challenges due to their high prevalence, complex nature, and elevated mortality rates. Dysregulation of the Wnt/β-catenin signaling pathway is a common feature in gynecological malignancies, contributing to cancer cell growth, progression, migration, and metastasis. Recent studies have highlighted the pivotal role of non-coding RNAs (ncRNAs), particularly circular RNAs (circRNAs), in modulating the Wnt/β-catenin signaling pathway. Acting as sponges for microRNAs (miRNAs), circRNAs regulate key oncogenic and tumor-suppressive processes by influencing Wnt-related components. This research explores the role of circRNAs in breast and gynecological malignancies, focusing on their regulatory effects on the Wnt/β-catenin pathway. The findings reveal that circRNAs modulate critical cellular processes such as proliferation, apoptosis, autophagy, and metastasis, with potential implications for therapeutic interventions. Targeting circRNA-mediated dysregulation of Wnt signaling could offer novel strategies for improving diagnostic precision, treatment efficacy, and survival outcomes in breast and gynecological cancers.

Currently, the incidence of digestive system tumors has been increasing annually, thus becoming a prevalent cause of cancer‑related mortalities. Although significant strides have been made in targeting the molecular mechanisms that underpin the development of these tumors, their treatment and prognosis still pose substantial challenges. This is primarily due to the ambiguity of early diagnostic indicators and the fact that most digestive system tumors are detected at an advanced stage. However, epigenetic modifications are capable of altering the expression of oncogenes and regulating biological processes in cancer. In recent years, the study of methylation in relation to tumor pathogenesis has become a focus of prominent research. Among the various types of methylation, 5‑methylcytosine (m5C) methylation plays a crucial role in the development of digestive system tumors and is anticipated to serve as a novel therapeutic target. However, to date, a comprehensive and systematic review concerning the role of m5C methylation in digestive system tumors is lacking. Consequently, the present study reviewed the role of m5C methylation in digestive system tumors such as esophageal cancer, gastric cancer and hepatocellular carcinoma, with the aim of providing a valuable reference for future research endeavors.

Globally, colorectal cancer (CRC) is the third most common type of cancer, and its treatment frequently includes the utilization of drugs based on antibodies and small molecules. The development of CRC has been linked to various signaling pathways, with the Wnt/β-catenin pathway identified as a key target for intervention.

We have explored the impact of imidazopyridine-tethered chalcone-C (CHL-C) in CRC models.

To determine the influence of CHL-C on apoptosis and autophagy, Western blot analysis, annexin V assay, cell cycle analysis, acridine orange staining, and immunocytochemistry were performed. Next, the activation of the Wnt/β-catenin signaling pathway and the anti-cancer effects of CHL-C in vivo were examined in an orthotopic HCT-116 mouse model.

We describe the synthesis and biological assessment of the CHL series as inhibitors of the viability of HCT-116, SW480, HT-29, HCT-15, and SNU-C2A CRC cell lines. Further biological evaluations showed that CHL-C induced apoptosis and autophagy in down-regulated β-catenin, Wnt3a, FZD-1, Axin-1, and p-GSK-3β (Ser9), and up-regulated p-GSK3β (Tyr216) and β-TrCP. In-depth analysis using structure-based bioinformatics showed that CHL-C strongly binds to β-catenin, with a binding affinity comparable to that of ICG-001, a well-known β-catenin inhibitor. Additionally, our in vivo research showed that CHL-C markedly inhibited tumor growth and triggered the activation of both apoptosis and autophagy in tumor tissues.

CHL-C is capable of inducing apoptosis and autophagy by influencing the Wnt/β-catenin signaling pathway.

The glioma microenvironment is critical for tumor growth, where reprogramming M2-polarized tumor-associated macrophages/microglia (TAMs) to an antitumor M1 phenotype represents a promising therapeutic strategy. While the potassium channel regulatory subunit KCNE3 has been implicated in tumorigenesis across malignancies, its functional role in shaping the glioma microenvironment remains undefined. Here, we leveraged transcriptome data from the Gene Expression Omnibus (GEO) to identify KCNE3 as a TAM-enriched gene in gliomas. To interrogate its mechanistic contributions, we generated KCNE3-knockdown and overexpressing macrophages and evaluated their impact on glioma cells in coculture systems. Silencing KCNE3 in macrophages significantly attenuated glioma cell proliferation, migration, and invasion in vitro, accompanied by enhanced M1 polarization. Mechanistically, KCNE3 depletion suppressed Wnt/β-catenin signaling, driving increased secretion of pro-inflammatory cytokines TNF-α, IL-6, and IL-12. Conversely, KCNE3 overexpression reversed these effects, promoting M2-like characteristics and tumor-supportive behaviors. These findings establish KCNE3 as a key modulator of TAM phenotype and glioma progression, suggesting that targeted KCNE3 inhibition may disarm pro-tumorigenic immune responses to improve therapeutic outcomes. This study uncovers a novel actionable method in glioma immunotherapy.

As traditional medicinal fungi, Ganoderma lucidum and Sanghuangporus vaninii are widely used in the treatment of tumor related diseases and cancer adjuvant therapy with potent anticancer effects. However, the anticancer effect and mechanism of action of their compound extract remain unclear.

To investigate the anticancer effect of Ganoderma lucidum and Sanghuangporus vaninii compound extract and explore the underlying mechanism.

First, MTT assay was performed to investigate the effect of 8 different extracts on tumor cell viability. Moreover, the synergistic effect of Ganoderma lucidum spore and Sanghuangporus vaninii was evaluated by Chou-Talalay method. Subsequently, the fractional extractions were conducted to further isolate anti-tumor active components. Next, network pharmacology combined with transcriptomics was used to explore the potential mechanisms underlying the anticancer effect of compound extract. Finally, the mechanism of action was verified using in vitro and in vivo models.

Among all 8 extracts, Ganoderma lucidum spore and Sanghuangporus vaninii compound ethanol extract (GSEE) showed the most significant cell viability inhibitory effect on cancer cells, especially colorectal cancer (CRC) cells, which was even better than combination of Sanghuangporus vaninii ethanol extract (SVEE) and Ganoderma lucidum spore ethanol extract (GLEE). The ethyl acetate fraction of GSEE (GSEAE) was screened as the anti-tumor active fraction of GSEE and could suppress CRC proliferation in vitro and in vivo. The CYP24A1-mediated Vitamin D receptor (VDR) pathway and TERT-mediated Wnt signaling pathway were identified as the main mechanisms of GSEAE against CRC. Multiple CRC models confirmed that GSEAE suppressed CRC metastasis, arrested cell cycle and induced mitochondrial apoptosis of CRC cells via VDR pathway and Wnt signaling pathway.

Collectively, our data suggest that compound extract GSEAE exerts anti-CRC effects via CYP24A1-mediated VDR pathway and TERT-mediated Wnt signaling pathway.

Inhibiting permeability glycoprotein (P-gp) efflux is a strategy to enhance drug efficacy or overcome multidrug resistance in tumors. However, whether P-gp aptamer (APTP-gp, an 81 bp ssDNA) inhibits P-gp efflux is unknown. Increased Rho123 uptake was observed in the rat brain and intestine. Bidirectional transport of Rho123 indicated that 100 nM of APTP-gp inhibited P-gp activity with inhibition ratios of 75.0 % in Caco-2 and 60.5 % in hCMEC/D3 cells. The apparent permeability coefficients (Papp) from the apical (AP) to basolateral (BL) sides significantly increased by 129.4 % in Caco-2 and 8.0 % in hCMEC/D3 cells, respectively. The Papp from the BL→AP sides in the two cell lines decreased. P-gp mRNA and protein expression in the rat ileum, brain, and two cell lines markedly decreased following APTP-gp exposure. APTP-gp downregulated Wnt3, pho-Dvl2, β-catenin expression and decreased the ratio of pho-GSK-3β to GSK-3β in the rat ileum and brain. Molecular docking analysis suggested that APTP-gp interact with Wnt/β-catenin signaling pathway proteins at various amino acid sites. The present study reports a novel a novel nucleic acid-based P-gp inhibitor, which may benefit for enhancing drug efficacy or overcome multidrug resistance in clinical application.

Colorectal cancer (CRC) is the third most common cause of death worldwide and has high mortality and a poor prognosis. Long non-coding RNAs (lncRNAs) are non-coding RNAs longer than 200 nucleotides that play roles in cancer through multiple mechanisms. TMEM51-AS1 is a newly discovered 40,650 bp lncRNA. Our results showed that TMEM51-AS1 expression was significantly downregulated in CRC tissues (fold change = 0.74, P < 0.0001). This finding was confirmed in 20 pairs of CRC carcinoma and paracancerous tissues (fold change = 0.5, P < 0.001). Additionally, TMEM51-AS1 expression was found to be significantly reduced in CRC cell lines compared to normal human intestinal epithelial cells (P < 0.001). Bioinformatic analysis revealed that TMEM51-AS1 expression was associated with immune escape, RNA methylation, and DNA damage and repair. TMEM51-AS1 may also activate energy metabolism pathways to participate in cancer development. Drug sensitivity analysis confirmed that several drugs are more effective in CRC patients with high expression of TMEM51-AS1. In conclusion, our study demonstrates that TMEM51-AS1 can suppress the progression of CRC.

This comprehensive review delves into the pivotal role of intestinal epithelial cells in the context of various diseases. It provides an in-depth analysis of the diverse types and functions of these cells, explores the influence of multiple signaling pathways on their differentiation, and elucidates their critical roles in a spectrum of diseases. The significance of the gastrointestinal tract in maintaining overall health is extremely important and cannot be exaggerated. This complex and elongated organ acts as a crucial link between the internal and external environments, making it vulnerable to various harmful influences. Preserving the normal structure and function of the gut is essential for well-being. Intestinal epithelial cells serve as the primary defense mechanism within the gastrointestinal tract and play a crucial role in preventing harmful substances from infiltrating the body. As the main components of the digestive system, they not only participate in the absorption and secretion of nutrients and the maintenance of barrier function but also play a pivotal role in immune defense. Therefore, the health of intestinal epithelial cells is of vital importance for overall health.

This review aims to elucidate the neural mechanisms driving colorectal cancer (CRC) growth, metastasis, and therapeutic resistance, summarizing the roles of neurotransmitters, neurotrophic factors, and neural signaling in carcinogenesis. It further explores therapeutic strategies targeting neural dependencies in CRC.

A comprehensive PubMed search was conducted using the keywords colorectal cancer and tumor innervation, focusing on studies published between 2000 and 2024. The review synthesizes evidence across four domains: neurotransmitter-receptor interactions, gut-brain-microbiota axis dynamics, neuroimmune modulation, and neural regulation of cancer stem cells, discussing their collective impact on CRC pathophysiology.

Neural innervation significantly influences CRC progression. For instance, the neurotransmitter serotonin promotes tumor growth and metastasis via paracrine and autocrine stimulation, while neurotrophic mediators like nerve growth factor (NGF) and brain-derived neurotrophic factor (BDNF) activate oncogenic signaling through receptor tyrosine kinases (RTKs). Downstream pathways, such as Wnt/β-catenin signaling, are modulated by neural inputs, underscoring CRC's neurodevelopmental dependency and highlighting their potential as therapeutic targets.

Neural mechanisms are pivotal in CRC progression, revealing novel therapeutic avenues. Strategies targeting neurotransmitter synthesis, neurotrophic signaling, or neuroimmune crosstalk may disrupt tumorigenic loops while preserving systemic nervous system integrity. Future research must prioritize translating these insights into clinical interventions to improve patient outcomes. Elucidating the intricate interplay between neural mediators and cancer pathogenesis, coupled with developing therapies specifically targeting the neurogenic basis of CRC aggressiveness, represents a critical frontier in oncology.

Colon adenocarcinoma (COAD) is increasingly prevalent among patients under 50 years old, and the 5-year survival rate for patients with metastasis is less than 20%. Identifying significant biomarkers and therapeutic targets is crucial. We investigated the expression of LRP2 in COAD and its prognostic value utilizing single-cell sequencing and transcriptomics datasets, which was conducted preliminary validation at the patient samples and cellular levels as well.

Based on differential gene expression of tumor samples and normal tissues in The Cancer Genome Atlas (TCGA), we performed consensus clustering, univariate and multivariate Cox regression analysis applying 1,234 mitochondrial metabolism-related genes (MMRGs) to identify some essential genes associated with poor prognosis in COAD patients. We validated survival outcome and biological function of the target gene leveraging single-cell sequencing and transcriptomics datasets from Gene Expression Omnibus (GEO), and evaluated the value of the target gene in the clinical pathology stage of COAD patients. Simultaneously, the expression levels of critical gene were detected in the diverse tissues of COAD by immunohistochemistry (IHC) staining. Transcriptomics data was continuously implemented to compare the discrepancy between the expression levels of the target gene and somatic mutation burden, inspecting the key pathways of the target gene by gene set enrichment analysis (GSEA) and examining its drug sensitivity synthetically in the CellMiner databases. The proliferative capacity augmented in LRP2-overexpressed colon cancer cells was determined employing cell counting kit-8 (CCK-8) and flow cytometry assays.

LRP2 served as a key mitochondrial metabolism-related gene was assessed clinical prognosis in COAD patients according to the TCGA database. High expression of LRP2 was prominently associated with poor prognosis in COAD patients (P < 0.05), which was validated by GEO databases, and the expression levels of LRP2 were positively related to clinical pathological stage simultaneously (P < 0.05). Some specific cell types were clustered and proliferation pathways were immensely enriched, which were correlated with LRP2 in two single-cell sequencing datasets. The mutation profiles displayed remarkable differences in two levels of LRP2, we also observed high expressions of LRP2 were immensely correlated with high tumor mutation burden (TMB) and unfavorable prognosis in these patients (P < 0.05). LRP2 was significantly enriched in multiple cancer proliferation-related pathways, and the noteworthy correlation between LRP2 and the sensitivity to various drugs was identified (P < 0.05). The expression levels of LRP2 were multifarious in different COAD patients based on IHC staining. LRP2-overpression could stimulate the proliferation capability of HCT116 and SW480 cell lines markedly (P < 0.05).

The expression levels of LRP2 were intimately correlated with gene mutations, prognosis, pathological stage and the sensitivity to anticancer drugs in COAD. Augmented levels of LRP2 would manifest poor prognosis, which furnished novel insights for clinical diagnosis and treatment in COAD. LRP2 could extensively facilitate the proliferation ability of colon cell lines.

Cerebral ischemia-reperfusion injury (CIRI) represents a multifaceted pathological phenomenon characterized by an array of molecular and cellular mechanisms, which significantly contribute to neurological dysfunction. Evidence suggests that calcium ions play an indispensable role in this context, as abnormal elevations in calcium concentrations exacerbate neuronal injury and intensify functional deficits. These ions are integral not only for intracellular signaling pathways but also for various pathological processes, such as programmed cell death, inflammatory responses, and oxidative stress. This review article elucidates the physiological framework of calcium homeostasis and the precise mechanisms through which calcium ions influence CIRI. Moreover, it addresses potential intervention strategies, including calcium channel blockers, calmodulin (CaM) inhibitors, antioxidants, and anti-inflammatory agents. Despite the proposal of certain intervention strategies, their effectiveness and safety in clinical settings warrant further scrutiny. In conclusion, the article highlights the limitations of current research and anticipates future investigative trajectories, aiming to provide a theoretical foundation and reference for the development of more efficacious treatment modalities.

We identified a subset of patients with colorectal cancer (CRC) enriched with "collagen-TAMs," designated the CM class, using large integrated colon cancer transcriptome and single-cell transcriptome datasets. This classification system could be used as an extension of the traditional CMS classification system for CRC to guide more accurate classification and treatment.We also screened CAF-derived THBS2 as a potential biomarker for CM and found that it plays an important role in CRC disease models in vitro and in vivo, promoting tumor development and metastasis as well as TAM recruitment. Targeting THBS2 combined with PD-1 therapy effectively improved the therapeutic effect of immunotherapy in vivo. The CM classification provides a new perspective for CRC treatment, and THBS2, which is highly expressed in CM cases, can be used as a new potential combined target for immunotherapy.

Colorectal cancer (CRC), a complex and multifactorial disease, has been associated with elevated expression of microRNA miR-182-5p, although its precise regulatory role in CRC progression remains unclear. This study aims to identify potential therapeutic targets to improve clinical outcomes and to decipher the intricate role of miR-182-5p in the pathobiology of CRC.

We conducted comprehensive bioinformatics analyses using GEO databases to investigate differences in miRNA expression between CRC and normal tissues, with a particular focus on miR-182-5p. Its expression levels in CRC cells and tumor tissues were quantified by quantitative real-time PCR (qRT-PCR). The expression of neurocalcin delta (NCALD) and proteins related to Wnt/β-catenin signalling was evaluated by qRT-PCR and Western blotting. Pathological changes in tumor-bearing mice as well as the proliferation, invasion, and migration of CRC cells, were assessed. Tumor cell proliferation and apoptosis were examined using Ki-67 immunohistochemistry and TUNEL staining, respectively. A dual luciferase reporter assay explored the regulatory interaction between miR-182-5p and NCALD.

Our findings reveal significantly elevated miR-182-5p levels in CRC tissues and cell lines, positively correlated with tumor invasion depth, differentiation degree, clinical stage, and lymph node metastasis. miR-182-5p appears to accelerate CRC progression in both cell lines and mouse models by downregulating NCALD, thereby enhancing Wnt/β-catenin signalling. This study identifies miR-182-5p as a pivotal enhancer of CRC progression, modulating Wnt/β-catenin signalling via NCALD regulation.

The findings position the miR-182-5p/NCALD axis as promising targets for CRC therapy, offering new avenues for treatment strategies.

Retrospectively registered.

NAG-1/GDF15, a tumor suppressor, is synthesized as a pro-form in colorectal cancer (CRC) cells and undergoes cleavage to generate its mature form. While the biological function of pro-NAG-1/GDF15 remains unclear, our study reveals its crucial role in suppressing oncogenic signaling. We demonstrate that pro-NAG-1/GDF15 is predominantly retained within cells, whereas its mature form is secreted into the media. The expression of NAG-1/GDF15, or uncleavable R193A mutant, inhibits β-catenin and NF-κB signaling, key pathways in CRC progression. Mechanistically, the pro-NAG-1/GDF15 interacts with EpCAM, preventing its cleavage and nuclear translocation, thereby reducing β-catenin and NF-κB activity. This inhibition correlates with decreased expression of oncogenic targets such as cyclin D1 and c-myc. In vivo, NAG-1/GDF15 expression significantly reduces tumor growth in cancer xenograft models, accompanied by decreased proliferation and increased apoptosis. Furthermore, analysis of public datasets suggests that high NAG-1/GDF15 expression is associated with improved CRC patient survival. These findings highlight NAG-1/GDF15 via the formation of pro-NAG-1/GDF15 as a promising therapeutic target for cancer, with potential applications in modulating tumorigenic signaling pathways.

The focus on breast cancer treatment has shifted from the cytotoxic effects of single drugs on tumor cells to multidimensional multi‑pathway synergistic intervention strategies targeting the tumor microenvironment (TME). The activation of the Wnt signaling pathway in the TME of breast cancer cells serves a key regulatory role in tissue homeostasis and is a key driver of the carcinogenic process. Modulating the crosstalk between the Wnt pathway and TME of breast cancer is key for understanding the biological behavior of breast cancer and advancing the development of novel antitumor drugs. The present review aimed to summarize the complex mechanisms of the Wnt signaling pathway in the breast cancer TME, interactions between the Wnt signaling pathway and components of the breast cancer TME and breast cancer‑associated genes, as well as the interactions between the Wnt signaling pathway and other signaling cascades at the molecular level. Furthermore, the present review aimed to highlight the unique advantages of the Wnt signaling pathway in the macro‑regulation of the TME and the current therapeutic strategies targeting the Wnt signaling pathway, their potential clinical value and future research directions in breast cancer treatment.

PEST-containing nuclear protein (PCNP), a short-lived small nuclear protein with 178 amino acids, is a nuclear protein containing two PEST sequences. PCNP is highly expressed in several malignant tumors such as cervical cancer, rectal cancer, and lung cancer. It is also associated with cell cycle regulation and the phosphoinositide 3-kinase/protein kinase B/mammalian target of rapamycin (PI3K/AKT/mTOR) and Wnt signaling pathways during tumor growth. The present article discuss how PCNP regulates the PI3K/AKT/mTOR and Wnt signaling pathways and related proteins, and the ubiquitination of PCNP regulates tumor cell cycle as well as the progress of the application of PCNP in the pathophysiology and treatment of colon cancer, human ovarian cancer, thyroid cancer, lung adenocarcinoma and oral squamous cell carcinoma. The main relevant articles were retrieved from PubMed, with keywords such as PEST-containing nuclear protein (PCNP), cancer (tumor), and signaling pathways as inclusion/exclusion criteria. Relevant references has been included and cited in the manuscript.

Although the characteristics at the invasive tumour front in colorectal cancer (CRC) are simple to assess, they are not included in routine pathology reports because they lack reproducibility and standardisation. In this study, we aimed to validate alternative scoring methods at the invasive tumour front in a large cohort of stage I-III CRC. The retrospective analysis was performed on haematoxylin and eosin-stained sections from 538 patients. At the invasive tumour front, tumour characteristics were scored using three alternative methods: the Karamitopoulou method, which evaluates the percentage of infiltrative tumour; the Taskin method, a five-point grading scale; and the tumour growth pattern (TGP) method, which classifies patterns as pushing, intermediate, or infiltrative. For interobserver assessment, the Karamitopoulou and TGP methods showed good agreement while the Taskin method presented fair agreement. High scores with the Karamitopoulou and Taskin methods correlated significantly with adverse prognostic factors, particularly advanced T stage (p < 0.001), N stage (p < 0.001), and the presence of peritoneal involvement (p < 0.001). The survival rate of the TGP method demonstrated that patients with an infiltrative growth pattern had significantly worse CRC survival compared to those with pushing and intermediate growth patterns (p < 0.001) and the TGP method retained its independence as a prognostic factor in multivariable Cox regression analysis only for colon cancer-specific survival (p < 0.001). The TGP scoring method is an independent prognostic factor only for colon cancer with simple and inexpensive assessment, underlining its practicality in routine reporting. Additionally, this method could be included as an additional histopathological risk indicator with the potential to guide therapeutic decision making.

Colorectal cancer (CRC) is still one of the leading causes of cancer deaths worldwide. Even though there has been progress in cancer immunotherapy, the results of applying immune checkpoint inhibitors (ICIs) have been unsatisfactory, especially in microsatellite stable (MSS) CRC. Single-agent ICIs that target programmed cell death-1 (PD-1)/ PD-L1, cytotoxic T-lymphocyte-associated protein 4 (CTLA-4), T cell Ig- and mucin-domain-containing molecule-3 (TIM-3), and lymphocyte activation gene (LAG)-3 have emerged as having specific benefits. However, many primary and secondary resistance mechanisms are available in the tumor microenvironment (TME) that prevent it from happening. Combination strategies, such as the use of anti-PD-1 and anti-CTLA-4, can be effective in overcoming these resistance pathways, but toxicities remain a significant concern. Moreover, ICIs have been integrated with various treatment modalities, including chemotherapy, radiotherapy, antibiotics, virotherapy, polyadenosine diphosphate-ribose polymerase (PARP) inhibitors, and heat shock protein 90 (HSP90) inhibitors. The outcomes observed in both preclinical and clinical settings have been encouraging. Interestingly, manipulating gut microbiota via fecal microbiota transplantation (FMT) has been identified as a new strategy to increase the efficacy of immunotherapy in CRC patients. Therefore, integrating ICIs with other treatment approaches holds promise in enhancing the prognosis of CRC patients. This review focuses on the unmet need for new biomarkers to select patients for combination therapies and the ongoing work to overcome resistance and immune checkpoint blockade.

Hepatocellular carcinoma (HCC), originating from hepatocytes, is the most common type of primary liver cancer. HCC imposes a significant global health burden with high morbidity and mortality, making it a critical public concern. Surgical interventions, including hepatectomy and liver transplantation, are pivotal in achieving long-term survival for patients with HCC. Additionally, ablation therapy, endovascular interventional therapy, radiotherapy, and systemic anti-tumor therapies are commonly employed. However, these treatment modalities are often associated with considerable challenges, including high postoperative recurrence rates and adverse effects. Traditional Chinese medicine (TCM) and natural products have been utilized for centuries as a complementary approach in managing HCC and its complications, demonstrating favorable clinical outcomes. Various bioactive compounds derived from TCM and natural products have been identified and purified, and their mechanisms of action have been extensively investigated. This review aims to provide a comprehensive and up-to-date evaluation of the clinical efficacy of TCM, natural products and their active constituents in the treatment and management of HCC. Particular emphasis is placed on elucidating the potential molecular mechanisms and therapeutic targets of these agents, including their roles in inhibiting HCC cell proliferation, inducing apoptosis and pyroptosis, suppressing tumor invasion and metastasis, and restraining angiogenesis within HCC tissues.

With the significant challenges in using human embryonic stem cells (ESCs) for research and clinical applications, there is a growing impetus to seek alternative pluripotent cell sources. Embryonic stem-like (ES-like) cells emerge as a promising avenue in this pursuit. Our research demonstrates the potential for deriving ES-like cells from spermatogonial stem cells (SSCs) in a time-dependent manner under defined culture conditions. To better understand this process, we investigated the gene expression dynamics and underlying pathways associated with ES-like cell generation from SSCs. A deeper understanding of the signaling pathways underlying this biological process can lead us to refine protocols for ES-like cell generation, which could catalyze the development of more efficient and expedited methodologies inspired by the derivation pathway for future research in regenerative medicine. To identify differentially expressed genes (DEGs), we analyzed publicly available microarray data from murine cells obtained from the Gene Expression Omnibus (GEO). This analysis enabled the prediction of protein-protein interactions (PPIs), which were subsequently used for pathway enrichment analysis to identify biologically relevant pathways. Complementing these computational findings, we conducted in vitro experiments, including Fluidigm qPCR and immunostaining. These experiments serve as validation for our microarray data and the DEGs identified, providing reassurance about the reliability of our research. Among the identified enriched pathways in our investigation are the Toll-like receptor (TLR), GDNF/RET, interleukins (ILs), FGF/FGFR, and SMAD signaling pathway, along with the activation of NIMA kinases. Additionally, miR-410-3p, miRNA let-7e, Miat, and Xist are among some of the predicted non-coding RNAs.

The incidence of early-onset colorectal cancer (EOCRC) (< 50 years) has been steadily rising, with a parallel increase in metastatic and invasive cases. To elucidate the molecular mechanisms underlying this aggressive phenotype, we performed comprehensive multi-omics profiling to delineate the distinct features of EOCRC, with a focus on key drivers of metastatic and invasive potential.

We initially characterized the genome, epigenome, and transcriptome of tumors from 515 (69 EOCRC and 446 late-onset CRC [LOCRC]) cases in The Cancer Genome Atlas. Key candidate molecules were further validated using RNA-seq and scRNA-seq data. Multi-omics profiling revealed PIWIL1/piRNA as a hallmark of EOCRC, with further validation through in vitro functional assays, transcriptomic profiling, and Kaplan-Meier survival analysis.

EOCRC demonstrated a mutational landscape similar to that of LOCRC, with comparable oncogenic driver mutations and somatic copy-number alterations. However, EOCRC exhibited a higher frequency of deletion in chromosomes 6, 15, and 19 regions, along with metabolic reprogramming favoring aerobic glycolysis and lipid metabolism. Integrative transcriptomic and DNA methylation analyses identified six EOCRC-specific molecules, including PIWIL1. Notably, PIWIL1 was mainly expressed in epithelial cells, with lower expression in EOCRC versus LOCRC. Its downstream piRNAs (FR019019, FR019089, and FR132045) were also downregulated in EOCRC. Functional experiments demonstrated that FR019089/FR019019 overexpression suppressed migration and invasion. Clinically, low FR019089 levels correlated with significantly shorter progression-free and overall survival in EOCRC patients. Additionally, downstream pathways of FR019089 and FR019019 overexpression were enriched in anti-cancer-related signaling pathways.

Our multi-omics approach yields novel insights into the molecular underpinnings of EOCRC and we characterize the role of PIWIL1-associated piRNAs in modulating EOCRC metastasis and invasion. FR019089 shows promise as a prognostic biomarker with potential clinical utility in the risk stratification and management of EOCRC patients.

Colorectal cancer (CRC) progression occurs through three stages: adenoma (pre-cancerous lesion), carcinoma in situ (CIS) and adenocarcinoma, with tumor stage playing a pivotal role in the prognosis and treatment outcomes. Despite therapeutic advancements, the lack of stage-specific biomarkers hinders the development of accurate diagnostic tools and effective therapeutic strategies. This study aims to identify stage-specific gene expression profiles and key molecular mechanisms in CRC providing insights into molecular alterations across disease progression. Our methodological approach integrates the use of absolute gene set enrichment analysis (absGSEA) on formalin-fixed paraffin-embedded (FFPE)-derived transcriptomic data, combined with large-scale clinical validation and experimental confirmation. A comparative whole transcriptomic analysis (RNA-seq) was performed on FFPE samples including adenoma (n = 10), carcinoma in situ (CIS) (n = 8) and adenocarcinoma (n = 11) samples. Using absGSEA, we identified significant cellular pathways and putative molecular biomarkers associated with each stage of CRC progression. Key findings were then validated in a large independent CRC patient cohort (n = 1926), with survival analysis conducted from 1336 patients to assess the prognostic relevance of the candidate biomarkers. The key differentially expressed genes were experimentally validated using real-time PCR (RT-qPCR). Pathway analysis revealed that in CIS, apoptotic processes and Wnt signaling pathways were more prominent than in adenoma samples, while in adenocarcinoma, transcriptional co-regulatory mechanisms and protein kinase activity, which are critical for tumor growth and metastasis, were significantly enriched compared to adenoma. Additionally, extracellular matrix organization pathways were significantly enriched in adenocarcinoma compared to CIS. Distinct gene signatures were identified across CRC stages that differentiate between adenoma, CIS and adenocarcinoma. In adenoma, ARRB1, CTBP1 and CTBP2 were overexpressed, suggesting their involvement in early tumorigenesis, whereas in CIS, RPS3A and COL4A5 were overexpressed, suggesting their involvement in the transition from benign to malignant stage. In adenocarcinoma, COL1A2, CEBPZ, MED10 and PAWR were overexpressed, suggesting their involvement in advanced disease progression. Functional analysis confirmed that ARRB1 and CTBP1/2 were associated with early tumor development, while COL1A2 and CEBPZ were involved in extracellular matrix remodeling and transcriptional regulation, respectively. Experimental validation with RT-qPCR confirmed the differential expression of the candidate biomarkers (ARRB1, RPS3A, COL4A5, COL1A2 and MED10) across the three CRC stages reinforcing their potential as stage-specific biomarkers in CRC progression. These findings provide a foundation to distinguish between the CRC stages and for the development of accurate stage-specific diagnostic and prognostic biomarkers, which helps in the development of more effective therapeutic strategies for CRC.

Hepatocellular carcinoma (HCC) is one of the deadliest malignant tumors in the world, and its incidence and mortality have increased year by year. HCC research has increasingly focused on understanding its pathogenesis and developing treatments.The Wnt signaling pathway, a complex and evolutionarily conserved signal transduction system, has been extensively studied in the genesis and treatment of several malignant tumors. Recent investigations suggest that the pathogenesis of HCC may be significantly influenced by dysregulated Wnt/β-catenin signaling. This article aimed to examine the pathway that controls Wnt signaling in HCC and its mechanisms. In addition, we highlighted the role of this pathway in HCC etiology and targeted treatment.

Lung cancer remains the most prevalent carcinoma with a high mortality rate, yet the underlying mechanisms driving pulmonary neoplasia and disease progression are not fully understood. In our study, we conducted a comprehensive analysis of the transcriptome profiles and clinicopathological characteristics of 515 patients diagnosed with non-small cell lung cancer (NSCLC) from the TCGA database. We identified a significant upregulation of centromere protein M (CENPM) in NSCLC tissues, which was positively correlated with poor prognosis. Furthermore, overexpression of CENPM markedly promoted cell proliferation and increased the tumorigenic potential of NSCLC cell lines (A549/NCI-H1299), leading to accelerated tumor progression and reduced survival time in tumor-bearing mice. Mechanistically, CENPM activated the Wnt/β-catenin signaling pathway via the cell division cycle 20 (CDC20)/MYB proto-oncogene-like 2 (MYBL2) axis. Inhibition of either Wnt signaling or the CDC20/MYBL2 axis attenuated the tumorigenic potential and proliferative effects induced by CENPM. Our findings underscore the critical role of CENPM in driving NSCLC development and suggest that CENPM could serve as a novel biomarker for predicting NSCLC progression in clinical settings.

Chemoresistance and immunosuppression are common obstacles to the efficacy of chemo-immunotherapy in colorectal cancer (CRC) and are regulated by mitochondrial chaperone proteins. Here we show that the disruption of the tumour necrosis factor receptor-associated protein 1 (TRAP1) gene, which encodes a mitochondrial chaperone in tumour cells, causes the translocation of cyclophilin D in tumour cells. This process results in the continuous opening of the mitochondrial permeability transition pore, which enhances chemotherapy-induced cell necrosis and promotes immune responses. On the basis of this discovery we developed an oral CRISPR-Cas9 delivery system based on zwitterionic and polysaccharide polymer-coated nanocomplexes that disrupts the TRAP1 gene in CRC. This system penetrates the intestinal mucus layer and undergoes epithelial transcytosis, accumulating in CRC tissues. It enhances chemotherapeutic efficacy by overcoming chemoresistance and activating the tumour immune microenvironment in orthotopic, chemoresistant and spontaneous CRC models, with remarkable synergistic antitumour effects. This oral CRISPR-Cas9 delivery system represents a promising therapeutic strategy for the clinical management of CRC.

Although cancer chemopreventive agents have been confirmed to effectively protect high-risk populations from cancer invasion or recurrence, only over ten drugs have been approved by the U.S. Food and Drug Administration. Therefore, screening potent cancer chemopreventive agents is crucial to reduce the constantly increasing incidence and mortality rate of cancer. Considering the lengthy prevention process, an ideal chemopreventive agent should be nontoxic, inexpensive, and oral. Natural compounds have become a natural treasure reservoir for cancer chemoprevention because of their superior ease of availability, cost-effectiveness, and safety. The benefits of natural compounds as chemopreventive agents in cancer prevention have been confirmed in various studies. In light of this, the present review is intended to fully delineate the entire scope of cancer chemoprevention, and primarily focuses on various aspects of cancer chemoprevention based on natural compounds, specifically focusing on the mechanism of action of natural compounds in cancer prevention, and discussing in detail how they exert cancer prevention effects by affecting classical signaling pathways, immune checkpoints, and gut microbiome. We also introduce novel cancer chemoprevention strategies and summarize the role of natural compounds in improving chemotherapy regimens. Furthermore, we describe strategies for discovering anticancer compounds with low abundance and high activity, revealing the broad prospects of natural compounds in drug discovery for cancer chemoprevention. Moreover, we associate cancer chemoprevention with precision medicine, and discuss the challenges encountered in cancer chemoprevention. Finally, we emphasize the transformative potential of natural compounds in advancing the field of cancer chemoprevention and their ability to introduce more effective and less toxic preventive options for oncology.

As an oncogenic driver, lysine-specific demethylase 5A (KDM5A) participates in regulating numerous tumor progression-related processes. Moreover, KDM5A functions as a histone demethylase, modulating the expression levels of its target genes by adjusting methylation levels. However, the underlying molecular mechanism of KDM5A in osteosarcoma remains elusive. To elucidate this mechanism, specifically how the KDM5A /Homeobox A5 (HOXA5) axis regulates osteosarcoma progression, we measured the expression levels of KDM5A and HOXA5 genes using reverse transcription-quantitative real-time PCR. The correlation between HOXA5 and KDM5A was analyzed via Pearson correlation analysis and further validated through chromatin immunoprecipitation-quantitative real-time PCR. Immunohistochemistry was conducted to determine the number of KDM5A-or HOXA5-positive cells present in osteosarcoma tissues. Additionally, Western blot analysis was utilized to quantify the protein levels of KDM5A, HOXA5, di- and tri-methylation of lysine 4 on histone H3, and β-catenin. Colony formation assays, wound healing assays and flow cytometry were used to detect cell proliferation, migration and apoptosis. The factors associated with the five-year survival rate of patients were analyzed. Our results illustrated that KDM5A was up-regulated in osteosarcoma and associated with a poor prognosis; KDM5A knockdown inhibited osteosarcoma cell proliferation and migration and promotes apoptosis. Subsequently, KDM5A knockdown induced HOXA5 expression by promoting di- and tri-methylation of lysine 4 on histone H3 demethylation, and HOXA5 overexpression inhibited osteosarcoma cell proliferation and migration, and promoted apoptosis by inhibiting the Wnt/β-catenin pathway. We finally proved that HOXA5 silence weakened the inhibitory effect of sh- KDM5A on osteosarcoma proliferation and migration and promoted apoptosis via activating Wnt/β-catenin pathway in vivo and in vitro. Our study demonstrated that the KDM5A /HOXA5 axis regulates osteosarcoma progression by activating the Wnt/β-catenin pathway.

Gene set analysis methods have played a major role in generating biological interpretations of omics data such as gene expression datasets. However, most methods focus on detecting homogenous pattern changes in mean expression while methods detecting pattern changes in variance remain poorly explored. While a few studies attempted to use gene-level variance analysis, such approach remains under-utilized. When comparing two phenotypes, gene sets with distinct changes in subgroups under one phenotype are overlooked by available methods although they reflect meaningful biological differences between two phenotypes. Multivariate sample-level variance analysis methods are needed to detect such pattern changes.

We used ranking schemes based on minimum spanning tree to generalize the Cramer-Von Mises and Anderson-Darling univariate statistics into multivariate gene set analysis methods to detect differential sample variance or mean. We characterized the detection power and Type I error rate of these methods in addition to two methods developed earlier using simulation results with different parameters. We applied the developed methods to microarray gene expression dataset of prednisolone-resistant and prednisolone-sensitive children diagnosed with B-lineage acute lymphoblastic leukemia and bulk RNA-sequencing gene expression dataset of benign hyperplastic polyps and potentially malignant sessile serrated adenoma/polyps. One or both of the two compared phenotypes in each of these datasets have distinct molecular subtypes that contribute to within phenotype variability and to heterogeneous differences between two compared phenotypes. Our results show that methods designed to detect differential sample variance provide meaningful biological interpretations by detecting specific hallmark gene sets associated with the two compared phenotypes as documented in available literature.

The results of this study demonstrate the usefulness of methods designed to detect differential sample variance in providing biological interpretations when biologically relevant but heterogeneous changes between two phenotypes are prevalent in specific signaling pathways. Software implementation of the methods is available with detailed documentation from Bioconductor package GSAR. The available methods are applicable to gene expression datasets in a normalized matrix form and could be used with other omics datasets in a normalized matrix form with available collection of feature sets.

Natural polysaccharides (PSs) have shown inhibitory effects on differentiated cancer cells (DCCs), but their activity against cancer stem cells (CSCs) remains poorly understood. Here, we report that PSs from wheat cell cultures (WCCPSs) inhibit the proliferation of both DCCs and CSCs derived from HCT-116 colorectal cancer cells. Among them, NA and DC fractions showed the strongest anti-CSC activity. NA, rich in xylose, was effective at lower concentrations, while DC, enriched in xylose and galacturonic acid (GalUA), exhibited higher potency, with a lower IC50 and preferential activity against CSCs at higher doses. WCCPSs reduced β-catenin levels, and some fractions also downregulated Ep-CAM, CD44, and c-Myc. Notably, DC increased caspase-3 without inducing cytochrome C and caspase-8 overexpression, suggesting a mechanism promoting CSC differentiation rather than apoptosis. Correlation analysis linked xylose content to reduced c-Myc expression, and GalUA levels to increased caspase-3. These results suggest that WCCPS bioactivity may be related to their monosaccharide composition. Overall, our findings support the potential of wheat-derived PSs as CSC-targeting agents that suppress self-renewal and promote differentiation, offering a promising approach to reduce tumor aggressiveness and recurrence.