Targeted Bisulfite Sequencing Reveals DNA Methylation Changes in Zinc Finger Family Genes Associated With KRAS Mutated Colorectal Cancer

HOXD1 inhibits lung adenocarcinoma progression and is regulated by DNA methylation

The homeobox (HOX) gene family encodes a number of highly conserved transcription factors and serves a crucial role in embryonic development and tumorigenesis. Homeobox D1 (HOXD1) is a member of the HOX family, whose biological functions in lung cancer are currently unclear. The University of Alabama at Birmingham Cancer data analysis Portal of HOXD1 expression patterns demonstrated that HOXD1 was downregulated in lung adenocarcinoma (LUAD) patient samples compared with adjacent normal tissue. Western blotting analysis demonstrated low HOXD1 protein expression levels in lung LUAD cell lines. The Kaplan‑Meier plotter database demonstrated that reduced HOXD1 expression levels in LUAD correlated with poorer overall survival. Meanwhile, an in vitro study showed that HOXD1 overexpression suppressed LUAD cell proliferation, migration and invasion. In a mouse tumor model, upregulated HOXD1 was demonstrated to inhibit tumor growth. In addition, targeted bisulfite sequencing and chromatin immunoprecipitation assays demonstrated that DNA hypermethylation occurred in the promoter region of the HOXD1 gene and was associated with the action of DNA methyltransferases. Moreover, upregulated HOXD1 served as a transcriptional factor and increased the transcriptional expression of bone morphogenic protein (BMP)2 and BMP6. Taken together, the dysregulation of HOXD1 mediated by DNA methylation inhibited the initiation and progression of LUAD by regulating the expression of BMP2/BMP6.

Signaling pathways involved in colorectal cancer: pathogenesis and targeted therapy

Colorectal cancer (CRC) remains one of the leading causes of cancer-related mortality worldwide. Its complexity is influenced by various signal transduction networks that govern cellular proliferation, survival, differentiation, and apoptosis. The pathogenesis of CRC is a testament to the dysregulation of these signaling cascades, which culminates in the malignant transformation of colonic epithelium. This review aims to dissect the foundational signaling mechanisms implicated in CRC, to elucidate the generalized principles underpinning neoplastic evolution and progression. We discuss the molecular hallmarks of CRC, including the genomic, epigenomic and microbial features of CRC to highlight the role of signal transduction in the orchestration of the tumorigenic process. Concurrently, we review the advent of targeted and immune therapies in CRC, assessing their impact on the current clinical landscape. The development of these therapies has been informed by a deepening understanding of oncogenic signaling, leading to the identification of key nodes within these networks that can be exploited pharmacologically. Furthermore, we explore the potential of integrating AI to enhance the precision of therapeutic targeting and patient stratification, emphasizing their role in personalized medicine. In summary, our review captures the dynamic interplay between aberrant signaling in CRC pathogenesis and the concerted efforts to counteract these changes through targeted therapeutic strategies, ultimately aiming to pave the way for improved prognosis and personalized treatment modalities in colorectal cancer.

Association of KRAS Mutation and Gene Pathways in Colorectal Carcinoma: A Transcriptome- and Methylome-Wide Study and Potential Implications for Therapy

Kirsten Rat Sarcoma (KRAS) is the most commonly mutated oncogene in colorectal carcinoma (CRC). We have previously reported the interactions between microsatellite instability (MSI), DNA promoter methylation, and gene expression. In this study, we looked for associations between KRAS mutation, gene expression, and methylation that may help with precision medicine. Genome-wide gene expression and DNA methylation were done in paired CRC tumor and surrounding healthy tissues. The results suggested that (a) the magnitude of dysregulation of many major gene pathways in CRC was significantly greater in patients with the KRAS mutation, (b) the up- and down-regulation of these dysregulated gene pathways could be correlated with the corresponding hypo- and hyper-methylation, and (c) the up-regulation of CDKN2A was more pronounced in tumors with the KRAS mutation. A recent cell line study showed that there were higher CDKN2A levels in 5-FU-resistant CRC cells and that these could be down-regulated by Villosol. Our findings suggest the possibility of a better response to anti-CDKN2A therapy with Villosol in KRAS-mutant CRC. Also, the more marked up-regulation of genes in the proteasome pathway in CRC tissue, especially with the KRAS mutation and MSI, may suggest a potential role of a proteasome inhibitor (bortezomib, carfilzomib, or ixazomib) in selected CRC patients if necessary.

Mechanism of Dahuang Mudan Decotion in the treatment of colorectal cancer based on network pharmacology and experimental validation

Objective

The objective of this study was to assess the pharmacological activity and therapeutic mechanism of Dahuang Mudan Decotion (DHMDD) for colorectal cancer using ultra-performance liquid chromatography tandem mass spectrometry (UPLC-MS), network pharmacology and in vitro experiments.

Methods

The chemical components of DHMDD were identified by UPLC-MS. Network pharmacological analysis was utilized to screen the active ingredients and targets associated with DHMDD for colorectal cancer. Based on the results of network pharmacology, the potential mechanism of DHMDD on colorectal cancer predicted was experimentally studied and verified in vitro.

Results

DHMDD primarily exerts its effects on colorectal cancer through 52 active ingredients. AKT1, ESR1, HSP90AA1, JUN, PIK3CA, PIK3CB, PIK3R1, SRC, STAT3, TP53 were the top 10 targets. The top 10 ingredient nodes were Quercetin, Physcione, Pontigenin, Crysophanol, Linolenic acid, Piceatannol, Adenosine, Emodin, Sambunigrin, and Prunasin. The main compounds and the target proteins exhibited strong binding ability in molecular docking studies. The results of cell experiments demonstrated that DHMDD can inhibit the proliferation, invasion and migration of CRC cells through the PI3K/Akt pathway.

Conclusion

Through network pharmacology analysis and cell experiments, this study suggests that DHMDD can exert its therapeutic effects on colorectal cancer through a combination of multiple components and targets.

DNA methylation modulates epigenetic regulation in colorectal cancer diagnosis, prognosis and precision medicine

Colorectal cancer (CRC) is a multifaceted disease influenced by the interplay of genetic and environmental factors. The clinical heterogeneity of CRC cannot be attributed exclusively to genetic diversity and environmental exposures, and epigenetic markers, especially DNA methylation, play a critical role as key molecular markers of cancer. This review compiles a comprehensive body of evidence underscoring the significant involvement of DNA methylation modifications in the pathogenesis of CRC. Moreover, this review explores the potential utility of DNA methylation in cancer diagnosis, prognostics, assessment of disease activity, and prediction of drug responses. Recognizing the impact of DNA methylation will enhance the ability to identify distinct CRC subtypes, paving the way for personalized treatment strategies and advancing precision medicine in the management of CRC.

The role of zinc finger proteins in malignant tumors

Zinc finger proteins (ZNFs) are the largest family of transcriptional factors in mammalian cells. Recently, their role in the development, progression, and metastasis of malignant tumors via regulating gene transcription and translation processes has become evident. Besides, their possible involvement in drug resistance has also been found, indicating that ZNFs have the potential to become new biological markers and therapeutic targets. In this review, we summarize the oncogenic and suppressive roles of various ZNFs in malignant tumors, including lung, breast, liver, gastric, colorectal, pancreatic, and other cancers, highlighting their role as prognostic markers, and hopefully provide new ideas for the treatment of malignant tumors in the future.

Circulating DNA methylation level of CXCR5 correlates with inflammation in patients with rheumatoid arthritis

OBJECTIVES

To assess the differences in circulating DNA methylation levels of CXCR5 between rheumatoid arthritis (RA) and osteoarthritis (OA) and healthy controls (HC), and the correlation of methylation changes with clinical characteristics of RA patients.

METHODS

Peripheral blood samples were collected from 239 RA patients, 30 patients with OA, and 29 HC. Target region methylation sequencing to the promoter region of CXCR5 was achieved using MethylTarget. The methylation level of cg04537602 and methylation haplotype were compared among the three groups, and the correlation between methylation levels and clinical characteristics of RA patients was performed by Spearman's rank correlation analysis.

RESULTS

The methylation level of cg04537602 was significantly higher in the peripheral blood of RA patients compared with OA patients (p = 1.3 × 10-3 ) and in the HC group (p = 5.5 × 10- 4 ). The sensitivity was enhanced when CXCR5 methylation level combined with rheumatoid factor and anti-cyclic citrullinated peptide with area under curve (AUC) of 0.982 (95% confidence interval 0.970-0.995). The methylation level of cg04537602 in RA was positively correlated with C-reactive protein (CRP) (r = .16, p = .01), and in RA patients aged 60 years and above, cg04537602 methylation levels were positively correlated with CRP (r = .31, p = 4.7 × 10- 4 ), tender joint count (r = .21, p = .02), visual analog scales score (r = .21, p = .02), Disease Activity Score in 28 joints (DAS28) using the CRP level DAS28-CRP (r = .27, p = 2.1 × 10- 3 ), and DAS28-ESR (r = .22, p = .01). We also observed significant differences of DNA methylation haplotypes in RA patients compared with OA patients and HC, which was consistent with single-loci-based CpG methylation measurement.

CONCLUSION

The methylation level of CXCR5 was significantly higher in RA patients than in OA and HC, and correlated with the level of inflammation in RA patients, our study establishes a link between CXCR5 DNA methylation and clinical features that may help in the diagnosis and disease management of RA patients.

Deciphering the Prognostic and Therapeutic Significance of Cell Cycle Regulator CENPF: A Potential Biomarker of Prognosis and Immune Microenvironment for Patients with Liposarcoma

Liposarcoma (LPS) is one of the most common subtypes of sarcoma with a high recurrence rate. CENPF is a regulator of cell cycle, differential expression of which has been shown to be related with various cancers. However, the prognostic value of CENPF in LPS has not been deciphered yet. Using data from TCGA and GEO datasets, the expression difference of CENPF and its effects on the prognosis or immune infiltration of LPS patients were analyzed. As results show, CENPF was significantly upregulated in LPS compared to normal tissues. Survival curves illustrated that high CENPF expression was significantly associated with adverse prognosis. Univariate and multivariate analysis suggested that CENPF expression could be an independent risk factor for LPS. CENPF was closely related to chromosome segregation, microtubule binding and cell cycle. Immune infiltration analysis elucidated a negative correlation between CENPF expression and immune score. In conclusion, CENPF not only could be considered as a potential prognostic biomarker but also a potential malignant indicator of immune infiltration-related survival for LPS. The elevated expression of CENPF reveals an unfavorable prognostic outcome and worse immune score. Thus, therapeutically targeting CENPF combined with immunotherapy might be an attractive strategy for the treatment of LPS.