Novel Diagnostic Biomarkers in Colorectal Cancer

A simple and enzyme-free method for sensitive p53 analysis based on DNAzyme-mediated signal amplification

There is an urgent demand for a simple yet extremely accurate biosensor to analyze tumorigenesis. Herein, we present a novel fluorescent and enzyme-free approach for detecting p53 gene cascading proximity ligation-mediated catalytic hairpin assembly and DNAzyme-assisted signal reaction. When the target p53 gene is present, the interaction between p53 and L1 and L2 chains initiates catalytic hairpin assembly and subsequently exposes DNAzyme in the P3 probe. The exposed DNAzyme binds with the loop region of the P4 probe and generates a nicking site, resulting in the release of a significant amount of ATMND that is conjugated in the stem section of P4. This leads to an amplified fluorescence response, which serves as a fluorescence signal for the detection of the p53 gene. This method allows for the accurate and sensitive identification of the p53 gene, exhibiting a linear reaction range of 1 fM to 1 nM, with a limit of detection as low as 0.23 fM. Furthermore, this fluorescent method has been utilized for the examination of clinical samples with a favorable recovery rate. Crucially, this versatile platform may be expanded to analyze different targets by changing the corresponding recognition unit, showing great potential for point-of-care testing in tumorigenesis analysis.

mirSNPs as Potential Colorectal Cancer Biomarkers: A Systematic Review

Colorectal cancer (CRC) is the third most common neoplasm in the world and the second with the highest mortality rate. Single nucleotide polymorphisms (SNPs) in microRNA (miRNA) genes known as mirSNPs may be related to dysregulated miRNA expression in several neoplasms. This systematic review aims to investigate studies that investigate SNPs located in regions of miRNA genes that influence their expression and are associated with CRC, as well as their potential as biomarkers for the disease, based on the available literature. For this, searches were performed in public databases, including MEDLINE/PubMed, Embase, Web of Science, and Scopus. The rigorous review of the PRISMA 2020 guidelines and the methodological quality of these studies was assessed using the Newcastle-Ottawa scale and the Mixed Methods Assessment Tool. Of the 175 studies identified, 26 were considered eligible: 18 of them highlighted mirSNPs as potential biomarkers of risk and prognosis for CRC; 4 studies suggested a protective role; 1 study linked mirSNPs to treatment; 3 studies found no relevant evidence. These results highlight the importance of conducting further research on the topic, given the potential of these biomarkers to contribute to risk assessment, prognosis, and the development of therapeutic strategies for patients with CRC.

Liquid biopsy in cancer current: status, challenges and future prospects

Cancer has a high mortality rate across the globe, and tissue biopsy remains the gold standard for tumor diagnosis due to its high level of laboratory standardization, good consistency of results, relatively stable samples, and high accuracy of results. However, there are still many limitations and drawbacks in the application of tissue biopsy in tumor. The emergence of liquid biopsy provides new ideas for early diagnosis and prognosis of tumor. Compared with tissue biopsy, liquid biopsy has many advantages in the diagnosis and treatment of various types of cancer, including non-invasive, quickly and so on. Currently, the application of liquid biopsy in tumor detection has received widely attention. It is now undergoing rapid progress, and it holds significant potential for future applications. Around now, liquid biopsies encompass several components such as circulating tumor cells, circulating tumor DNA, exosomes, microRNA, circulating RNA, tumor platelets, and tumor endothelial cells. In addition, advances in the identification of liquid biopsy indicators have significantly enhanced the possibility of utilizing liquid biopsies in clinical settings. In this review, we will discuss the application, advantages and challenges of liquid biopsy in some common tumors from the perspective of diverse systems of tumors, and look forward to its future development prospects in the field of cancer diagnosis and treatment.

Tetrahedral DNA nanostructures-assisted electrochemical assay for detecting circulating tumor DNA by combining a masking tactic with 3D-hybridization chain reactions

Circulating tumor DNA (ctDNA) is a remarkable noninvasive tumor marker that plays a crucial role in tumor diagnosis, prognosis and treatment. However, detecting low-abundance ctDNA from a substantial amount of nucleic acids originating from healthy cells is challenging. Herein, we proposed a tetrahedral DNA nanostructures (TDNs)-assisted electrochemical biosensor for ctDNA detection. This biosensor combines a masking tactic with 3D-hybridization chain reactions. Masking hairpins (MHs) were initially introduced to prevent interference from wild-type (WT) DNA. Then, the initiator sequence was transferred to the electrode surface modified with TDNs by the target ctDNA. The initiator sequence triggers the 3D self-assembly of hairpin strands, leading to the formation of DNA networks or even DNA hydrogels (long reaction time). This process generates numerous evenly distributed biotin molecules that can bind to streptavidin peroxidase to considerably amplify the signal. This method exhibits high sensitivity (the minimum concentration for detecting ctDNA is 1 aM, which corresponds to 60 ctDNA molecules in 100 μl sample) and excellent specificity (single mismatch). More importantly, this high-performance sensor can detect ctDNA with other mutation sites and their mixtures by modifying the corresponding capture probes on the TDNs. Furthermore, this ultrasensitive sensor effectively detects target ctDNA (0.001 %) at high levels of WT DNA and in complex matrices such as serum. These findings suggest that the sensor has promising potential as a noninvasive tool for early tumor diagnosis.

Neo-RAS Wild Type or RAS Conversion in Metastatic Colorectal Cancer: A Comprehensive Narrative Review

The management of metastatic colorectal cancer in patients harboring RAS mutations primarily involves chemotherapy, often combined with bevacizumab, as a standard first-line treatment. However, emerging evidence suggests that tumors in a subset of these patients may experience a conversion from RAS-mutant status to RAS wild type (wt) during or after chemotherapy, a process referred to as "RAS conversion" or "neo-RAS wt". Understanding the mechanisms driving the neo-RAS wt phenomenon is crucial for its application in personalized medicine. Hypotheses suggest that selective pressure from chemotherapy may lead to a decrease in the number of mutant RAS clones or an outgrowth of pre-existing RAS wt clones. Further research is needed to validate these mechanisms and understand the impact of the neo-RAS wt phenomenon on long-term outcomes, such as overall survival and progression-free survival. This review provides a comprehensive overview of the current understanding of the neo-RAS wt phenomenon, including its incidence, potential mechanisms, and clinical implications.

GC-MS and multivariate analysis reveal partial serum metabolome restoration by bevacizumab in a colon cancer rat model: An untargeted metabolomics investigation

Bevacizumab is an anti-angiogenic therapeutic agent that targets vascular endothelial growth factor (VEGF) and has been approved for the treatment of several types of cancer, including colon cancer. Herein, a GC-MS based metabolomics approach was employed to investigate the impact of bevacizumab on the serum metabolome of colon cancer rats. Multivariate chemometric analysis models such as PCA and PLS-DA showed a clear separation between the control, cancer and bevacizumab-treated groups, suggesting that bevacizumab administration induced significant metabolic alterations. Furthermore, pairwise comparisons between the studied groups using the OPLS-DA model in addition to univariate analysis identified several discriminatory metabolites belonged to various chemical classes including amino acids, organic acids and fatty acids that were perturbed between the studied groups. Interestingly, bevacizumab treatment was able to partially restore some of the cancer-induced metabolic disturbances, indicating its potential therapeutic efficacy via improving the tumor vasculature and nutrient delivery. Besides, pathway analysis of the differential metabolites identified key metabolic pathways affected by bevacizumab, which included valine, leucine and isoleucine metabolism, pyruvate metabolism and butanoate metabolism. However, little effects were observed on lipid metabolites such as palmitic acid and stearic acid and consequently their related metabolic pathways such as fatty acid biosynthesis metabolism suggesting that bevacizumab has more prominent effect on energy and amino acid metabolisms as compared to fatty acid metabolism in colon cancer rats. Overall, our study provided novel insights into the metabolic mechanisms underlying the therapeutic effects of bevacizumab in colon cancer rats via the use of a comprehensive GC-MS metabolomics approach.

Construction of Prognostic Prediction Models for Colorectal Cancer Based on Ferroptosis-Related Genes: A Multi-Dataset and Multi-Model Analysis

Background

Colorectal cancer (CRC) remains a significant health burden globally, necessitating a deeper understanding of its molecular landscape and prognostic markers. This study characterized ferroptosis-related genes (FRGs) to construct models for predicting overall survival (OS) across various CRC datasets.

Methods

In TCGA-COAD dataset, differentially expressed genes (DEGs) were identified between tumor and normal tissues using DESeq2 package. Prognostic genes were identified associated with OS, disease-specific survival, and progression-free interval using survival package. Additionally, FRGs were downloaded from FerrDb website, categorized into unclassified, marker, and driver genes. Finally, multiple models (Coxboost, Elastic Net, Gradient Boosting Machine, LASSO Regression, Partial Least Squares Regression for Cox Regression, Ridge Regression, Random Survival Forest [RSF], stepwise Cox Regression, Supervised Principal Components analysis, and Support Vector Machines) were employed to predict OS across multiple datasets (TCGA-COAD, GSE103479, GSE106584, GSE17536, GSE17537, GSE29621, GSE39084, GSE39582, and GSE72970) using intersection genes across DEGs, OS, disease-specific survival, and progression-free interval, and FRG categories.

Results

Six intersection genes (ASNS, TIMP1, H19, CDKN2A, HOTAIR, and ASMTL-AS1) were identified, upregulated in tumor tissues, and associated with poor survival outcomes. In the TCGA-COAD dataset, the RSF model demonstrated the highest concordance index. Kaplan-Meier analysis revealed significantly lower OS probabilities in high-risk groups identified by the RSF model. The RSF model exhibited high accuracy with AUC values of 0.978, 0.985, and 0.965 for 1-, 3-, and 5-year survival predictions, respectively. Calibration curves demonstrated excellent agreement between predicted and observed survival probabilities. Decision curve analysis confirmed the clinical utility of the RSF model. Additionally, the model's performances were validated in GSE29621 dataset.

Conclusions

The study underscores the prognostic relevance of 6 intersection genes in CRC, providing insights into potential therapeutic targets and biomarkers for patient stratification. The RSF model demonstrates robust predictive performance, suggesting its utility in clinical risk assessment and personalized treatment strategies.

WDR77 in Pan-Cancer: Revealing expression patterns, genetic insights, and functional roles across diverse tumor types, with a spotlight on colorectal cancer

OBJECTIVE

Despite its involvement in regulating various cellular functions, the expression and role of WD repeat-containing protein 77 (WDR77) in cancer remain elusive. This study aims to explore the expression and potential roles of WDR77 across multiple cancers, with a particular focus on its relevance in colorectal cancer (CRC).

METHODS

We obtained WDR77 RNA-seq data, mutations, CNVs, and DNA methylation data from the TCGA, GTEx, and GEO databases to investigate its expression patterns and prognostic value. Additionally, we examined the correlation between WDR77 expression and somatic mutations, copy number variations, DNA methylation, and mRNA modifications. We utilized GSVA, GSEA algorithms, and CRISPR KO data from the Dependency Map database to explore WDR77's potential biological functions. The association between WDR77 and the tumor immune microenvironment was investigated using ESTIMATE and IOBR algorithms. Finally, we assessed WDR77 expression in CRC and its impact on cell proliferation through qRT-PCR, Western blotting, immunohistochemistry, CCK8, colony formation, and EdU assays.

RESULTS

WDR77 was upregulated in various tumors and correlated with poor patient prognosis. Its high expression positively correlated with pathways related to cell proliferation and negatively correlated with immune-related pathways. In CRC, WDR77 expression was associated with specific clinical features, genomic alterations, and immune microenvironment characteristics. Experimental validation confirmed upregulated WDR77 expression in CRC tissues and cells, with WDR77 knockdown significantly inhibiting CRC cell proliferation.

CONCLUSION

WDR77 holds potential as an oncogene and biological marker in various cancers, particularly CRC.

Circulating exosomal PCAT1 as a complement of carcinoembryonic antigen for early colorectal cancer diagnosis

Backgrounds

Given the global prevalence of colorectal cancer (CRC), advancements in prompt and accurate diagnosis are crucial. Long non-coding RNAs (lncRNAs) in serum exosomes are emerging as potential diagnostic biomarkers. This study evaluated the feasibility of using serum exosomal lncRNAs for early-stage CRC diagnosis in clinical practice.

Methods

Candidate serum exosomal lncRNAs were identified through an integrated analysis of two GEO datasets (GSE100206 and GSE100063) containing non-coding RNA expression profiles in serum exosomes. Exosomes isolated from participants' serum were validated using transmission electron microscopy (TEM) and immunoblotting. The expression levels of serum exosomal PCAT1 were measured by quantitative real-time polymerase chain reaction (qRT-PCR). Diagnostic accuracy was assessed using receiver operating characteristic (ROC) analysis.

Results

Serum exosomal PCAT1 levels were evaluated in 150 CRC patients, 66 patients with benign colorectal lesions, and 128 healthy controls. ROC analysis demonstrated high diagnostic efficacy of serum exosomal PCAT1 for CRC. Notably, the predictive performance was sufficient to distinguish early-stage CRC patients. Additionally, the diagnostic value was significant for CRC patients with low serum carcinoembryonic antigen (CEA) levels. Measuring serum exosomal PCAT1 could complement CEA assessment, enhancing CRC diagnostic accuracy.

Conclusions

Serum exosomal PCAT1 can complement CEA assessment, aiding in early CRC diagnosis and helping to differentiate the disease, especially in patients with low CEA levels.

Serum extracellular vesicles 3'tRF-ThrCGTand 3'tRF-mtlleGAT combined with tumor markers can serve as minimally invasive diagnostic predictors for colorectal cancer

Background

Colorectal cancer (CRC) is a leading cause of morbidity and mortality, and timely diagnosis and intervention are crucial for cancer patients. Transfer RNA-derived fragments (tRFs) play a noncoding regulatory role in organisms. Serum EV(extracellular vesicles), as an integral mediator of intercellular transmission of genetic information vesicles in Transfer RNA-derived fragment (tRF RNA), are expected to be minimally invasive diagnostic and predictive biologic factors of CRC.

Methods

Collect serum samples from 205 CRC patients, and then isolate extracellular vesicles from the serum. Captured the physical morphology of EV through transmission electron microscopy. The particle size was detected by particle size assay, and protein expression on the surface of EV was verified by Western blot. Gene microarrays were screened for differentially expressed tRF-RNA. TRF RNAs were verified by qPCR for differential expression in 205 CRC patients and 201 healthy donors, assessing the CRC diagnostic efficiency by area under the curve (AUC).

Results

Compared with 201 healthy donors, CRC patients experienced significantly down-regulated serum EV 3'tRF-ThrCGT while significantly up-regulated 3'tRF-mtlleGAT. Serum EV 3'tRF-ThrCGT and 3'tRF-mtlleGAT predictive diagnostic efficiency: 0.669 and 0.656, and the combination of CEA and CA724 predictive diagnostic efficiency was 0.938.

Conclusion

The study data showed that 3'tRF-ThrCGT and 3'tRF-mtlelGAT can be minimally invasive diagnostic CRC indicators. The combination of tumor markers CEA and CA724 has important diagnostic significance.

Novel drug delivery systems in colorectal cancer: Advances and future prospects

Colorectal cancer (CRC) is an abnormal proliferation of cells within the colon and rectum, leading to the formation of polyps and disruption of mucosal functions. The disease development is influenced by a combination of factors, including inflammation, exposure to environmental mutagens, genetic alterations, and impairment in signaling pathways. Traditional treatments such as surgery, radiation, and chemotherapy are often used but have limitations, including poor solubility and permeability, treatment resistance, side effects, and post-surgery issues. Novel Drug Delivery Systems (NDDS) have emerged as a superior alternative, offering enhanced drug solubility, precision in targeting cancer cells, and regulated drug release. Thereby addressing the shortcomings of conventional therapies and showing promise for more effective CRC management. The present review sheds light on the pathogenesis, signaling pathways, biomarkers, conventional treatments, need for NDDS, and application of NDDS against CRC. Additionally, clinical trials, ongoing clinical trials, marketed formulations, and patents on CRC are also covered in the present review.

Emerging methods and techniques for cancer biomarker discovery

Modern cancer research depends heavily on the identification and validation of biomarkers because they provide important information about the diagnosis, prognosis, and response to treatment of the cancer. This review will provide a comprehensive overview of cancer biomarkers, including their development phases and recent breakthroughs in transcriptomics and computational techniques for detecting these biomarkers. Blood-based biomarkers have great potential for non-invasive tumor dynamics and treatment response monitoring. These include circulating tumor DNA, exosomes, and microRNAs. Comprehensive molecular profiles are provided by multi-omic technologies, which combine proteomics, metabolomics, and genomes to support the identification of biomarkers and the targeting of therapeutic interventions. Genetic changes are detected by next-generation sequencing, and patterns of protein expression are found by protein arrays and mass spectrometry. Tumor heterogeneity and clonal evolution can be understood using metabolic profiling and single-cell studies. It is projected that the use of several biomarkers-genetic, protein, mRNA, microRNA, and DNA profiles, among others-will rise, enabling multi-biomarker analysis and improving individualised treatment plans. Biomarker identification and patient outcome prediction are further improved by developments in AI algorithms and imaging techniques. Robust biomarker validation and reproducibility require cooperation between industry, academia, and doctors. Biomarkers can provide individualized care, meet unmet clinical needs, and enhance patient outcomes despite some obstacles. Precision medicine will continue to take shape as scientific research advances and the integration of biomarkers with cutting-edge technologies continues to offer a more promising future for personalized cancer care.

In vitro and in vivo antineoplastic activities of solamargine in colorectal cancer through the suppression of PI3K/AKT pathway

PURPOSE

Previous research has demonstrated the efficacy of SM in inhibiting tumor growth in various cancer types. The objective of this study was to examine the antineoplastic effects and molecular mechanisms of Solamargine (SM) in colorectal cancer.

METHODS

Colorectal cancer (CRC) cells were treated with different concentrations of SM to evaluate the anticancer concentration for further experimental measurements. Additionally, the antitumor efficacy of SM was assessed in a subcutaneously implanted tumor model of colorectal cancer. RNA-seq and bioinformatics analyses were employed to identify differentially expressed genes (DEGs) and elucidate the underlying molecular mechanisms in LoVo cells. Subsequently, the specific mechanism of SM-mediated anti-tumor activities was analyzed by protein expression methods.

RESULTS

The results of in vitro assays demonstrated that SM exhibits significant inhibitory effects on cell proliferation, clone formation, and invasion, while also promoting apoptosis in SW48 and LoVo cells. In a mouse xenograft tumor model, intragastric administration of SM at doses of 5 or 10 mg/kg effectively suppressed tumor volume and weight, and induced cell apoptosis in vivo. SM treatment also down-regulated PCNA and Cyclin E protein expression, contributing to the regulation of apoptosis. Further analysis using RNA-seq, bioinformatics, and experimental measurements revealed that SM treatment upregulates PTEN expression, while significantly reducing the phosphorylation levels of Akt and mTOR in LoVo cells.

CONCLUSION

Our study provides further evidence to support the notion that SM primarily induces apoptosis in colorectal cancer cells through the inhibition of the PI3K/Akt signaling pathway. Additionally, our investigation demonstrated the favorable safety profile of SM in a mouse model of colorectal cancer, thereby suggesting its potential as a promising therapeutic approach for the management of CRC.

Contribution of PKS+ Escherichia coli to colon carcinogenesis through the inhibition of exosomal miR-885-5p

Objectives

About 90 % of all colorectal cancer (CRC) fatalities are caused by the metastatic spread of primary tumors, which is closely correlated with patient survival and spreads by circulating tumor cells (CTCs). The epithelial-mesenchymal transition (EMT) that characterizes CTCs is associated with a poor prognosis. Organotropic metastasis is dictated by the transmission of miRNAs by cancer-derived exosomes. The purpose of this research is to examine PKS + E's function. Coli in CRC metastases and exosomal miR-885-5p suppression.

Methods

A cohort of 100 patients (50 CRC, 50 healthy) underwent colonoscopy screenings from February 2018 to August 2021. Exosomes were isolated using ultracentrifugation, and exosomal miRNA was analyzed using sequencing and qPCR.

Results

Among the patients, 40 tested positive for E. coli (12 CRC, 23 healthy). Serotyping revealed that 68.57 % harbored the PKS gene. Exosomal miR-885-5p levels were significantly altered in CRC patients with PKS + E. coli. Intriguingly, our findings indicate that exosomes derived from EMT-CRC cells did not affect miR-885-5p synthesis in HUVECs. Moreover, we observed that the levels of miR-885-5p in both exosomes and the total CRC-conditioned medium were comparable upon isolation of exosomes from CRC cells. What's more, an increased expression of miR-558-5p within the tumors, and the group that received exosome treatment, as well as the EMT-HCT116 group, exhibited a higher occurrence of distant metastasis.

Conclusion

PKS + E. By inhibiting exosomal miR-885-5p, coli is linked to CRC metastases, offering a possible target for therapeutic intervention.

Personalised medicine based on host genetics and microbiota applied to colorectal cancer

Colorectal cancer (CRC) ranks second in incidence and third in cancer mortality worldwide. This situation, together with the understanding of the heterogeneity of the disease, has highlighted the need to develop a more individualised approach to its prevention, diagnosis and treatment through personalised medicine. This approach aims to stratify patients according to risk, predict disease progression and determine the most appropriate treatment. It is essential to identify patients who may respond adequately to treatment and those who may be resistant to treatment to avoid unnecessary therapies and minimise adverse side effects. Current research is focused on identifying biomarkers such as specific mutated genes, the type of mutations and molecular profiles critical for the individualisation of CRC diagnosis, prognosis and treatment guidance. In addition, the study of the intestinal microbiota as biomarkers is being incorporated due to the growing scientific evidence supporting its influence on this disease. This article comprehensively addresses the use of current and emerging diagnostic, prognostic and predictive biomarkers in precision medicine against CRC. The effects of host genetics and gut microbiota composition on new approaches to treating this disease are discussed. How the gut microbiota could mitigate the side effects of treatment is reviewed. In addition, strategies to modulate the gut microbiota, such as dietary interventions, antibiotics, and transplantation of faecal microbiota and phages, are discussed to improve CRC prevention and treatment. These findings provide a solid foundation for future research and improving the care of CRC patients.

Overexpression of Osteopontin-a and Osteopontin-c Splice Variants Are Worse Prognostic Features in Colorectal Cancer

Background: Osteopontin (OPN) is a glycoprotein involved in various physiological and pathological processes, and its aberrant expression in cancer cells is closely linked to tumor progression. In colorectal cancer (CRC), OPN is overexpressed, but the roles of its splice variants (OPN-SVs), OPNa, OPNb, and OPNc, are not well understood. This study aimed to characterize the expression patterns of OPN-SVs and their potential diagnostic and prognostic implications in CRC using transcriptomic data deposited in TSVdb and TCGA. Methods: The expression patterns of each OPN-SV were analyzed using transcriptomic data deposited in TSVdb and TCGA, which were correlated to patient data available at cBioPortal. Results: Bioinformatic analysis revealed that OPNa, OPNb, and OPNc are overexpressed in CRC samples compared to non-tumor samples. Notably, OPNa and OPNc are overexpressed in CRC stages (II, III, and IV) compared to stage I. Higher levels of OPNa and OPNc transcripts are associated with worse overall survival (OS) and shorter progression-free survival (PFS) in CRC patients. Additionally, the expression of OPNa, OPNb, and OPNc is correlated with BRAFV600E mutations in CRC samples. Conclusions: These findings suggest that OPNa and OPNc, in particular, have potential as diagnostic and prognostic biomarkers, paving the way for their further evaluation in CRC diagnosis and prognosis.

Potential of sonobiopsy as a novel diagnosis tool for brain cancer

Brain tumors have a poor prognosis. Early, accurate diagnosis and treatment are crucial. Although brain surgical biopsy can provide an accurate diagnosis, it is highly invasive and risky and is not suitable for follow-up examination. Blood-based liquid biopsies have a low detection rate of tumor biomarkers and limited evaluation ability due to the existence of the blood-brain barrier (BBB). The BBB is composed of brain capillary endothelial cells through tight junctions, which prevents the release of brain tumor markers to the human peripheral circulation, making it more difficult to diagnose, predict prognosis, and evaluate therapeutic response through brain tumor markers than other tumors. Focused ultrasound (FUS)-enabled liquid biopsy (sonobiopsy) is an emerging technique using FUS to promote the release of tumor markers into the circulatory system and cerebrospinal fluid, thus facilitating tumor detection. The feasibility and safety data from both animal models and clinical trials support sonobiopsy as a great potential in the diagnosis of brain diseases.

TRIM24/ZFX affects the stemness and resistance to 5-FU of colorectal cancer cells

Colorectal cancer (CRC) is the second leading cause of cancer death, and about 10% of all malignancies are CRC. Cancer stem cells are considered main culprits in CRC treatment resistance and disease recurrence. This study explored the effects of tripartite motif containing 24 (TRIM24) and zinc finger protein, X-linked (ZFX) on CRC cell stemness and 5-FU resistance. A 5-FU-resistant cell line (HT29-5-FU) was constructed for functional analysis of CRC 5-FU-resistant cells. qRT-PCR and western blot (WB) were employed to analyze mRNA and protein levels of ZFX in 5-FU resistant cells and sensitive cells. WB was also utilized to analyze the surface markers of stem cells in each group. CCK-8 assay determined the IC50 values of different cell groups treated with 5-FU. The sphere-forming ability of cells in each group was determined using tumor sphere assay. Dual-luciferase reporter gene assay validated binding of ZFX to TRIM24. ZFX was highly expressed in HT29-5-FU cells. Silencing ZFX significantly reduced the 5-FU resistance and IC50 value of HT29-5-FU cells, and the surface markers and cell sphere-forming ability of stem cells were also significantly reduced. The function of HT29 cells was opposite when ZFX was overexpressed. In CRC cells, TRIM24 was an upstream transcription factor of ZFX, and they interacted with each other. TRIM24 activated the expression of ZFX to influence the stemness and 5-FU resistance of cells. The TRIM24/ZFX regulatory axis affected the stemness of CRC cells and their sensitivity to 5-FU, providing potential drug targets for novel therapeutic avenues for CRC.

Quantitative parameters of dual-layer spectral detector computed tomography for evaluating differentiation grade and lymphovascular and perineural invasion in colorectal adenocarcinoma

PURPOSE

To explore the predictive value of dual-layer spectral detector CT (SDCT) quantitative parameters for determining differentiation grade, lymphovascular invasion (LVI) and perineural invasion (PNI) in colorectal adenocarcinoma (CRAC) patients.

METHODS

A total of 106 eligible patients with CRAC were included in this study. Spectral parameters, including CT values at 40 and 100 keV, the effective atomic number (Zeff), the iodine concentration (IC), the slope of the spectral Hounsfield unit (HU) curve (λHU), and the normalized iodine concentration (NIC) in the arterial phase (AP) and venous phase (VP), were compared according to the differentiation grade and the status of LVI and PNI. The diagnostic accuracies of the quantitative parameters with statistical significance were determined via receiver operating characteristic (ROC) curves, and the area under the curve (AUC) was calculated.

RESULTS

There were 57 males and 49 females aged 43-86 (69 ± 10) years. The measured values of the spectral quantitative parameters of the CRAC were consistent within the observer (ICC range: 0.800-0.926). The 40 keV-AP, IC-AP, NIC-AP, 40 keV-VP, and IC-VP were significantly different among the different differentiation grades in the CRAC (P = 0.040, AUC = 0.673; P = 0.035, AUC = 0.684; P = 0.031, AUC = 0.639; P = 0.044, AUC = 0.663 and P = 0.035, AUC = 0.666, respectively). A statistically significant difference was observed in 40 keV-VP, 100 keV-VP, Zeff-VP, IC-VP, and λHU-VP between LVI-positive and LVI-negative patients (P = 0.003, AUC = 0.688; P = 0.015, AUC = 0.644; P = 0.001, AUC = 0.688; P = 0.001, AUC = 0.703 and P = 0.003, AUC = 0.677, respectively). There were no statistically significant differences in the values of the spectral parameters of the PNI state of patients with CRAC (P > 0.05).

CONCLUSION

The quantitative parameters of SDCT had good diagnostic efficacy in differentiating between different grades and statuses of LVI in patients with CRAC; however, SDCT did not have value for identifying the state of PNI.

Gut microbiota in colorectal cancer: From pathogenesis to clinic

Colorectal cancer is the third most common type of cancer, with a significant burden on healthcare and social systems. Its incidence is constantly rising, due to the spread of unhealthy lifestyle, i.e. Western diet. Increasing evidence suggests that westernization-driven microbiome alterations may play a critical role in colorectal tumorigenesis. The current screening strategies for this neoplasm, mainly fecal immunochemical tests, are burdened by unsatisfactory accuracy. Novel, non-invasive biomarkers are rising as the new frontier of colorectal cancer screening, and the microbiome-based ones are showing positive and optimistic results. This Review describes our current knowledge on the role of gut microbiota in colorectal cancer, from its pathogenetic action to its clinical potential as diagnostic biomarker.

Urolithin C suppresses colorectal cancer progression via the AKT/mTOR pathway

Urolithin families are gut-microbial metabolites of ellagic acid (EA). Although urolithin A (UA) and urolithin B (UB) were reported to have antiproliferative activities in cancer cells, the role and related mechanisms of urolithin C (UC) in colorectal cancer (CRC) have not yet been clarified. In this study, we assess the antitumor activities of UC in vitro and in vivo and further explore the underlying mechanisms in CRC cell lines. We found that UC inhibited the proliferation and migration of CRC cells, induced apoptosis, and arrested the cell cycle at the G2/M phase in vitro, and UC inhibited tumor growth in a subcutaneous transplantation tumor model in vivo. Mechanically, UC blocked the activation of the AKT/mTOR signaling pathway by decreasing the expression of Y-box binding protein 1(YBX1). The AKT agonist SC79 could reverse the suppression of cell proliferation in UC-treated CRC cells. In conclusion, our research revealed that UC could prevent the progression of CRC by blocking AKT/mTOR signaling, suggesting that it may have potential therapeutic values.

Identification of hub genes and potential molecular mechanisms in MSS/MSI classifier primary colorectal cancer based on multiple datasets

OBJECTIVE

MSI has a better prognosis than MSS in colorectal cancer patients, and the main objective of this study was to screen for differentially expressed molecules between MSI and MSS primary colorectal cancers using bioinformatics.

MATERIAL AND METHODS

Two gene expression datasets (GSE13294 and GSE13067) were downloaded from GEO, and differential expressed genes (DEGs) were analyzed using GEO2R. Gene Ontology, Kyoto Encyclopedia of Genomes, and Gene Set Enrichment Analysis were conducted using the DEGs. Furthermore, a Protein-Protein Interaction Networks (PPI) was constructed to screen for significant modules and identify hub genes. The hub genes were analyzed in colorectal cancer using GEPIA. The expression of hub genes in clinical samples was visualized using the online Human Protein Atlas (HPA).

RESULTS

A total of 265 common DEGs were identified in MSS primary colorectal cancer compared to MSI primary colorectal cancer. Among these, 178 DEGs were upregulated, and 87 DEGs were downregulated. Enrichment analysis showed that these DEGs were associated with the response to mechanical stimulus, regulation of cellular response to stress, G protein-coupled receptor binding, and other processes. A total of 5 hub genes was identified by cytoHubba: HNRNPL, RBM39, HNRNPH1, TRA2A, SRSF6. GEPIA software online analysis, 5 hub gene expression in colorectal cancer survival curve did not have significant differences. The expression of RBM39 was significantly different in different stages of colorectal cancer. The HPA online database results showed that the expression of the five hub proteins varied widely in CRC patients.

CONCLUSION

The hub genes, such as HNRNPH1and RBM39, and the spliceosome resulting from DEGs, which may provide novel insights and evidence for the future diagnosis and targeted therapy of MSS/MSI PCRC.

Serum Uric Acid Level May Be a Predictive Factor for BRAF V600E Mutation in Older Patients with Metastatic Colorectal Cancer: An Exploratory Analysis

INTRODUCTION

This study aimed to show the relationship between the serum uric acid level measured at diagnosis and the BRAF mutation status in the primary tumor tissue in patients with metastatic colorectal cancer.

METHODS

In this retrospective cross-sectional study, 264 patients (64% male) whose serum uric acid level was measured at the time of diagnosis and whose BRAF mutation status in the primary tumor was determined were included.

RESULTS

The BRAF mutation rate was 14% (n = 37). The median serum uric acid levels of all patients were 6.9 mg/dL (25%, 75% percentile range 3.7, 8.2). The serum uric acid level cut-off value was 6.6 mg/dL. Sensitivity and specificity for BRAF mutated patients were 84% and 27%, respectively. These rates were calculated as 85% and 70% in BRAF-mutated patients aged 65 and over. There was a significant correlation between BRAF mutation and high serum uric acid level, female gender, tumor located in the ascending colon, and multiple metastatic sites. The independent factors affecting BRAF mutation were age 65 and over, tumor in the ascending colon, and high serum uric acid level.

CONCLUSION

As a result, we concluded that high serum uric acid level measured during diagnosis in metastatic colorectal cancer is an accessible and economical biomarker that can predict BRAF mutation in patients aged 65 and over.

Association of body composition indicators with colorectal cancer: a hospital-based case-control study

PURPOSE

Colorectal cancer (CRC) is a common malignancy that affects adults worldwide, causing a high disease burden. Few studies have examined the relationship between body composition (BC) measures and the prevalence of CRC. Our purpose was to investigate the relationship between pertinent BC indicators and CRC.

METHODS

Bioelectrical impedance analysis, laboratory test results, face-to-face questionnaire investigation, and nutritional risk assessment (Nutritional Risk Screening 2002 and Patient-Generated Subjective Global Assessment) were used in this case-control study. Bioelectrical impedance analysis in the case group was performed prior to antitumor therapy/surgery.

RESULTS

From June 2018 to January 2019, a total of 303 cases and 286 controls were included. The results showed that low body fat percentage (BFP) and high visceral adiposity index (VAI) groups had a higher risk of developing CRC in comparison to the normal BFP and normal VAI groups. The risk of CRC decreased with the increase of BFP. The group with a normal BC had a lower risk of developing CRC compared to those with a greater VAI and a lower BFP, as indicated by the results of the pairwise and total combinations of VAI, fat-free mass index (FFMI), and BFP. Additionally, FFMI and VAI had positive correlations with prealbumin, serum albumin, and nutritional risk scores.

CONCLUSION

Low BFP and high VAI are associated with higher CRC risk. FFMI and VAI are positively correlated with prealbumin, serum albumin, and nutritional risk scores in CRC patients.

Serum biomarkers REG1A and REG3A combined with the traditional CEA represent a novel nomogram for the screening and risk stratification of colorectal cancer

BACKGROUND

To develop and validate a serum protein nomogram for colorectal cancer (CRC) screening.

METHODS

The serum protein characteristics were extracted from an independent sample containing 30 colorectal cancer and 12 polyp tissues along with their paired samples, and different serum protein expression profiles were validated using RNA microarrays. The prediction model was developed in a training cohort that included 1345 patients clinicopathologically confirmed CRC and 518 normal participants, and data were gathered from November 2011 to January 2017. The lasso logistic regression model was employed for features selection and serum nomogram building. An internal validation cohort containing 576 CRC patients and 222 normal participants was assessed.

RESULTS

Serum signatures containing 27 secreted proteins were significantly differentially expressed in polyps and CRC compared to paired normal tissue, and REG family proteins were selected as potential predictors. The C-index of the nomogram1 (based on Lasso logistic regression model) which contains REG1A, REG3A, CEA and age was 0.913 (95% CI, 0.899 to 0.928) and was well calibrated. Addition of CA199 to the nomogram failed to show incremental prognostic value, as shown in nomogram2 (based on logistic regression model). Application of the nomogram1 in the independent validation cohort had similar discrimination (C-index, 0.912 [95% CI, 0.890 to 0.934]) and good calibration. The decision curve (DCA) and clinical impact curve (ICI) analysis demonstrated that nomogram1 was clinically useful.

CONCLUSIONS

This study presents a serum nomogram that included REG1A, REG3A, CEA and age, which can be convenient for screening of colorectal cancer.

Mechanisms and clinical landscape of N6-methyladenosine (m6A) RNA modification in gastrointestinal tract cancers

Epigenetics encompasses reversible and heritable chemical modifications of non-nuclear DNA sequences, including DNA and RNA methylation, histone modifications, non-coding RNA modifications, and chromatin rearrangements. In addition to well-studied DNA and histone methylation, RNA methylation has emerged as a hot topic in biological sciences over the past decade. N6-methyladenosine (m6A) is the most common and abundant modification in eukaryotic mRNA, affecting all RNA stages, including transcription, translation, and degradation. Advances in high-throughput sequencing technologies made it feasible to identify the chemical basis and biological functions of m6A RNA. Dysregulation of m6A levels and associated modifying proteins can both inhibit and promote cancer, highlighting the importance of the tumor microenvironment in diverse biological processes. Gastrointestinal tract cancers, including gastric, colorectal, and pancreatic cancers, are among the most common and deadly malignancies in humans. Growing evidence suggests a close association between m6A levels and the progression of gastrointestinal tumors. Global m6A modification levels are substantially modified in gastrointestinal tumor tissues and cell lines compared to healthy tissues and cells, possibly influencing various biological behaviors such as tumor cell proliferation, invasion, metastasis, and drug resistance. Exploring the diagnostic and therapeutic potential of m6A-related proteins is critical from a clinical standpoint. Developing more specific and effective m6A modulators offers new options for treating these tumors and deeper insights into gastrointestinal tract cancers.

Effects of the Combination of Noise Reduction Earplugs with White Noise and Rational Emotional Therapy on Emotional States of Inpatients with Colorectal Cancer

OBJECTIVE

The aim of the study was to explore the effects of the combination of noise reduction earplugs with white noise and rational emotional therapy on the emotional states of inpatients with colorectal cancer (CRC).

METHODS

The study selected 152 CRC patients who received inpatient treatment in our hospital from January 2020 to January 2022 as the research objects. According to different nursing intervention modes, these patients were divided into the observation group (OG, n = 73, conventional nursing + noise reduction earplugs with white noise + rational emotional therapy) and the control group (CG, n = 79, conventional nursing) to compare the emotional status, sleep quality, and other indicators between the two groups.

RESULTS

After 2 and 6 weeks of intervention, the severity of illness and global impression in the OG were notably lower than those in the CG. The OG had remarkably higher efficacy indexes than the CG (p < 0.05). The OG had overtly lower Montgomery-Asberg Depression Scale (MADRS) scores and Pittsburgh sleep quality index (PSQI) scores than the CG (p < 0.05).

CONCLUSION

The combination of noise reduction earplugs with white noise and rational emotional therapy can improve the emotion and sleep states of patients, with certain positive effects, which can be used as a potential nursing plan for CRC patients.

Rechallenge with Anti-EGFR Treatment in RAS/BRAF wt Metastatic Colorectal Cancer (mCRC) in Real Clinical Practice: Experience of the GITuD Group

BACKGROUND

There are few third- and fourth-line therapeutic options for metastatic colorectal cancer (mCRC). In RAS/BRAF wild-type (wt) mCRC previously treated with anti-epidermal growth factor receptor (anti-EGFR) (first-line) and relapsed after a good response, retreatment with anti-EGFR (rechallenge) emerges as a therapeutic alternative.

OBJECTIVE

The aim was to show the activity and safety of anti-EGFR rechallenge in RAS/BRAF wt mCRC in real-world practice.

PATIENTS AND METHODS

A multicenter, retrospective, observational study (six hospitals of the Galician Group of Research in Digestive Tumors) was conducted. Adult patients with RAS/BRAF wt mCRC, evaluated by liquid biopsy, were included. They received anti-EGFR rechallenge (cetuximab, panitumumab) as monotherapy, or combined with chemotherapy, in third- or subsequent lines. Efficacy (overall response rate [ORR], disease control rate [DCR], overall survival [OS], and progression-free survival [PFS]) and safety (incidence of adverse events [AEs]) were assessed.

RESULTS

Thirty-one patients were analyzed. Rechallenge (median 6 cycles [range 1-27], mainly cetuximab [80.7%]), started at a median anti-EGFR-free time of 18.4 months (1.7-37.5 months) after two (38.7%) or more (61.3%) lines of treatment; 64.5% of patients received a full dose. Median OS and PFS were 9.8 months (95% confidence interval [CI] 8.2-11.4) and 2.6 months (95% CI 1.7-3.4), respectively. ORR was 10%, and DCR was 30%. The most common AEs were diarrhea (35.5%), anemia (29%), emesis (6.4%), and neutropenia (6.4%); < 5% grade ≥ 3; 48.4% of patients reported anti-EGFR-related skin toxicity (grade > 1). Hypomagnesemia required supplements in 29% of patients. Dose delays (≥ 3 days) and reduction (≥ 20%) were reported in 11 (35.5%) and seven patients (22.6%), respectively.

CONCLUSIONS

In RAS/BRAF wt mCRC patients, an anti-EGFR rechallenge provides a feasible therapeutic option with clinical benefit (survival) and a manageable safety profile.

Trends in management and outcomes of colon cancer in the United States over 15 years: Analysis of the National Cancer Database

Management of colon cancer has changed over the last few decades. We assessed the trends in management and outcomes using the US National Cancer Database (NCDB). A retrospective analysis of all patients with colonic adenocarcinoma between 2005 and 2019 was conducted. The cohort was divided into three equal time periods: Period 1 (2005-2009), Period 2 (2010-2014), and Period 3 (2015-2019) to examine treatment and outcomes trends. The primary outcome was 5-year overall survival (OS). The study included 923,275 patients. A significant increase in patients with stage IV disease was noted in Period 3 compared to Period 1 (47.9% vs. 27.9%, respectively), whereas a reciprocal reduction was seen in patients with locally advanced disease (stage II: 20.8%-12%; stage III: 14.5%-7.7%). Use of immunotherapy significantly increased from 0.3% to 7.6%. Mean 5-year OS increased (43.6 vs. 42.1 months) despite the increase in metastatic disease and longer time from diagnosis to definitive surgery (7 vs. 14 days). A reduction in 30-day readmission (5.1%-4.2%), 30- (3.9%-2.8%), and 90-day mortality (7.1%-5%) was seen. Laparoscopic and robotic surgery increased from 45.8% to 53.1% and 2.9% to 12.7%, respectively. Median postoperative length of hospital stay decreased by 2 days. Rate of positive resection margins (7.2%-6%) and median number of examined lymph nodes (14-16) also improved. Minimally invasive surgery and immunotherapy for colon cancer significantly increased in recent years. Patient outcomes including OS improved over time.

Atractylenolide II combined with Interferon-γ synergistically ameliorates colorectal cancer progression in vivo and in vitro by blocking the NF-kB p65/PD-L1 pathway

Purpose: Atractylodes macrocephala Koidz is a widely used classical traditional Chinese herbal medicine, that has shown remarkable efficacy in cancers. Colorectal cancer (CRC) is the most common malignant tumor globally. Interferon (IFN)-γ, a prominent cytokine involved in anti-tumor immunity that has cytostatic, pro-apoptotic, and immune-stimulatory properties for the detection and removal of transformed cells. Atractylenolides-II (AT-II) belongs to the lactone compound that is derived from Atractylodes macrocephala Koidz with anti-cancer activity. However, whether AT-II combined with IFN-γ modulates CRC progression and the underlying mechanisms remain unclear. The present study aimed to elucidate the efficacy and pharmaceutical mechanism of action of AT-II combined with IFN-γ synergistically against CRC by regulating the NF-kB p65/PD-L1 signaling pathway. Methods: HT29 and HCT15 cells were treated with AT-II and IFN-γ alone or in combination and cell viability, migration, and invasion were then analyzed using Cell Counting Kit-8 (CCK-8) and Transwell assays, respectively. Furthermore, the underlying mechanism was investigated through western blot assay. The role of AT-II combined with IFN-γ on tumor growth and lung metastases was estimated in vivo. Finally, the population of lymphocytes in tumor tissues of lung metastatic C57BL/6 mice and the plasma cytokine levels were confirmed by flow cytometry and enzyme-linked immunosorbent assay (ELISA). Results: AT-II or the combination IFN-γ significantly inhibited the growth and migration abilities of CRC cells in vitro and in vivo. The biological mechanisms behind the beneficial effects of AT-II combined with IFN-γ were also measured and inhibition of p38 MAPK, FAK, Wnt/β-catenin, Smad, and NF-kB p65/PD-L1 pathways was observed. Moreover, AT-II combined with IFN-γ significantly inhibited HCT15 xenograft tumor growth and lung metastases in C57BL/6 mice, which was accompanied by lymphocyte infiltration into the tumor tissues and inflammatory response inactivation. Conclusions: The results showed that the AT-II in combination with IFN-γ could be used as a potential strategy for tumor immunotherapy in CRC. More importantly, the mechanism by which AT-II suppressed CRC progressions was by inhibiting the NF-kB p65/PD-L1 signal pathway.

Role of artificial intelligence in colorectal cancer

The sphere of artificial intelligence (AI) is ever expanding. Applications for clinical practice have been emerging over recent years. Although its uptake has been most prominent in endoscopy, this represents only one aspect of holistic patient care. There are a multitude of other potential avenues in which gastrointestinal care may be involved. We aim to review the role of AI in colorectal cancer as a whole. We performed broad scoping and focused searches of the applications of AI in the field of colorectal cancer. All trials including qualitative research were included from the year 2000 onwards. Studies were grouped into pre-operative, intra-operative and post-operative aspects. Pre-operatively, the major use is with endoscopic recognition. Colonoscopy has embraced the use for human derived classifications such as Narrow-band Imaging International Colorectal Endoscopic, Japan Narrow-band Imaging Expert Team, Paris and Kudo. However, novel detection and diagnostic methods have arisen from advances in AI classification. Intra-operatively, adjuncts such as image enhanced identification of structures and assessment of perfusion have led to improvements in clinical outcomes. Post-operatively, monitoring and surveillance have taken strides with potential socioeconomic and environmental savings. The uses of AI within the umbrella of colorectal surgery are multiple. We have identified existing technologies which are already augmenting cancer care. The future applications are exciting and could at least match, if not surpass human standards.

WTAP-induced N6-methyladenosine of PD-L1 blocked T-cell-mediated antitumor activity under hypoxia in colorectal cancer

N6-Methyladenosine (m6A) is a important process regulating gene expression post-transcriptionally. Programmed death ligand 1 (PD-L1) is a major immune inhibitive checkpoint that facilitates immune evasion and is expressed in tumor cells. In this research we discovered that Wilms' tumor 1-associated protein (WTAP) degradation caused by ubiquitin-mediated cleavage in cancer cells (colorectal cancer, CRC) under hypoxia was inhibited by Pumilio homolog 1 (PUM1) directly bound to WTAP. WTAP enhanced PD-L1 expression in a way that was m6A-dependent. m6A "reader," Insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2) identified methylated PD-L1 transcripts and subsequently fixed its mRNA. Additionally, we found that T-cell proliferation and its cancer cell-killing effects were prevented by overexpression of WTAP in vitro and in vivo. Overexpression prevented T cells from proliferating and killing CRC by maintaining the expression of PD-L1. Further evidence supporting the WTAP-PD-L1 regulatory axis was found in human CRC and organoid tissues. Tumors with high WTAP levels appeared more responsive to anti-PD1 immunotherapy, when analyzing samples from patients undergoing treatment. Overall, our findings demonstrated a novel PD-L1 regulatory mechanism by WTAP-induced mRNA epigenetic regulation and the possible application of targeting WTAP as immunotherapy for tumor hypoxia.

RUNX1-induced upregulation of PTGS2 enhances cell growth, migration and invasion in colorectal cancer cells

Colorectal cancer (CRC) arises via the progressive accumulation of dysregulation in key genes including oncogenes and tumor-suppressor genes. Prostaglandin-endoperoxide synthase 2 (PTGS2, also called COX2) acts as an oncogenic driver in CRC. Here, we explored the upstream transcription factors (TFs) responsible for elevating PTGS2 expression in CRC cells. The results showed that PTGS2 silencing repressed cell growth, migration and invasion in HCT116 and SW480 CRC cells. The two fragments (499-981 bp) and (1053-1434 bp) were confirmed as the core TF binding profiles of the PTGS2 promoter. PTGS2 expression positively correlated with RUNX1 level in colon adenocarcinoma (COAD) samples using the TCGA-COAD dataset. Furthermore, RUNX1 acted as a positive regulator of PTGS2 expression by promoting transcriptional activation of the PTGS2 promoter via the 1086-1096 bp binding motif. In conclusion, our study demonstrates that PTGS2 upregulation induced by the TF RUNX1 promotes CRC cell growth, migration and invasion, providing an increased rationale for the use of PTGS2 inhibitors in CRC prevention and treatment.

Demographic characteristics and short-term outcomes of laparoscopic colon cancer surgeries at a newly developed cancer center in Peshawar, Pakistan

Objective

In Pakistan, colon cancer ranks fourth in incidence, exhibiting survival rates of 90% to 14%, contingent on TNM staging and early detection. This research focuses on the demographic involvement and short-term outcomes of elective colon cancer resections at a newly established tertiary care cancer center utilizing laparoscopic procedures.

Method

A retrospective analysis of elective laparoscopic colorectal resections at Shaukat Khanum Memorial Cancer Institute and Research Centre, Peshawar, from April 2021 to February 2022 was conducted. Out of 157 cases, 79 had colon cancer. Criteria included patients >18 years old with positive biopsies; consent non-providers were excluded. Statistical analysis employed descriptive statistics and cross-tabulations using SPSS-22.

Results

The study encompassed biopsy-confirmed colon cancers in patients >18 years. 157 colorectal cases were performed, including 79 colon cancers. The sample comprised 61 males (77.2%) and 18 females (22.7%), mean age 42 years. Most patients (33%) were in the 36-45 age group. Majority were from KPK (69.6%), followed by Afghanistan (24%). Tumors were predominantly in the ascending colon (30.3%). Most were moderately differentiated (70.8%). Mean lymph node yield was 19.0, with 1.2% requiring open laparotomy. Post-discharge, one readmission occurred within 30 days. Mortality within 90 days was 2%, attributed to aspiration pneumonia and chemotherapy-related effects.

Conclusions

Elective laparoscopic colonic surgery exhibits safety and efficacy in treating colon cancer. The study provides evidence of minimal morbidity and mortality, low readmission rates, and absence of anastomotic leaks. Hence, elective laparoscopic colonic surgery should be favored due to fewer post-operative complications and superior short-term outcomes. Larger studies on colon cancer are imperative for enhanced healthcare delivery.

Chemoprophylaxis of precancerous lesions in patients who are at a high risk of developing colorectal cancer (Review)

The diagnostics of colorectal cancer (CRC) and precancerous lesions in the colon is one of the most urgent matters to be considered for the modern protocols of complex examination, recommended for use from the age of 45 years, and including both instrumental and laboratory methods of research: Colonoscopy, CT colonography, flexible sigmoidoscopy, fecal occult blood test, fecal immunohistochemistry test and stool DNA test Nevertheless, the removal of those precancerous lesions does not solve the issue, and, apart from the regular endoscopic monitoring of patients who are at a high risk of developing CRC, the pharmacological treatment of certain key pathogenic mechanisms leading to the development of CRC is required. The present review to discusses the function of β-catenin in the transformation of precancerous colorectal lesions into CRC, when collaborating with PI3K/AKT/mTOR signaling pathway and other mechanisms. The existing methods for the early diagnostics and prevention of discovered anomalies are described and categorized. The analysis of the approaches to chemoprophylaxis of CRC, depending on the results of endoscopic, morphological and molecular-genetic tests, is presented.

CHL1 inhibits cell proliferation, migration and invasion by regulating the NF‑κB signaling pathway in colorectal cancer

Cell adhesion molecule close homolog of L1 (CHL1) is implicated in tumorigenesis of various malignancies. However, its role and underlying molecular mechanisms in colorectal cancer (CRC) remain unclear. The present study aimed to evaluate the specific biological functions and mechanisms of CHL1, in order to provide a theoretical basis for the use of CHL1 as a biological target in CRC. CHL1 expression was originally determined in CRC cell lines. Subsequently, CHL1 overexpression was induced by plasmid transfection in HT29 and SW480 cells, and cell proliferation, migration and invasion were evaluated using the Cell Counting Kit-8, clone formation, organoids formation and Transwell assays. Immunofluorescence and western blotting were performed to assess the protein expression of E-cadherin or N-cadherin. Differentially expressed genes (DEGs) were further evaluated using RNA-sequencing (RNA-seq) in HT29 and SW480 cells following CHL1 overexpression and functional enrichment analysis. Western blotting was performed to validate the expression of proteins related to the nuclear factor κB (NF-κB) signaling pathway. The TNMplot online database revealed the significant downregulation of CHL1 in CRC tissues. The results indicated that exogenous CHL1 overexpression significantly inhibited the proliferative, organoid-forming, migratory and invasive abilities of HT29 and SW480 cells, and increased E-cadherin protein expression. Additionally, CHL1 overexpression reduced xenograft tumor growth in vivo. RNA-seq and functional analysis revealed that DEGs in CHL1 overexpressing cells were mainly enriched in the NF-κB signaling pathway. The expression of p-p65 and p-p65/p65 ratio were significantly reduced in HT29 and SW480 cells, following CHL1 overexpression. Additionally, the inhibitory effects of CHL1 overexpression on CRC cell proliferation, organoid formation, migration and invasion were partially counteracted following the overexpression of p65 expression. Overall, the present study demonstrates that CHL1 inhibits CRC cell growth, migration and invasion through the inactivation of the NF-κB signaling pathway.

Holistic exploration of CHGA and hsa-miR-137 in colorectal cancer via multi-omic data Integration

Colorectal cancer (CRC) ranks among the most widespread malignancies globally, with early detection significantly influencing prognosis. Employing a systems biology approach, we aimed to unravel the intricate mRNA-miRNA network linked to CRC pathogenesis, potentially yielding diagnostic biomarkers. Through an integrative analysis of microarray, Bulk RNA-seq, and single-cell RNA-seq data, we explored CRC-related transcriptomes comprehensively. Differential gene expression analysis uncovered crucial genes, while Weighted Gene Co-expression Network Analysis (WGCNA) identified key modules closely linked to CRC. Remarkably, CRC manifested its strongest correlation with the turquoise module, signifying its pivotal role. From the cohort of genes showing high Gene Significance (GS) and Module Membership (MM), and Differential Expression Genes (DEGs), we highlighted the downregulated Chromogranin A (CHGA) as a notable hub gene in CRC. This finding was corroborated by the Human Protein Atlas database, which illustrated decreased CHGA expression in CRC tissues. Additionally, CHGA displayed elevated expression in primary versus metastatic cell lines, as evidenced by the CCLE database. Subsequent RT-qPCR validation substantiated the marked downregulation of CHGA in CRC tissues, reinforcing the significance of our differential expression analysis. Analyzing the Space-Time Gut Cell Atlas dataset underscored specific CHGA expression in epithelial cell subclusters, a trend persisting across developmental stages. Furthermore, our scrutiny of colon and small intestine Enteroendocrine cells uncovered distinct CHGA expression patterns, accentuating its role in CRC pathogenesis. Utilizing the WGCNA algorithm and TargetScan database, we validated the downregulation of hsa-miR-137 in CRC, and integrated assessment highlighted its interplay with CHGA. Our findings advocate hsa-miR-137 and CHGA as promising CRC biomarkers, offering valuable insights into diagnosis and prognosis. Despite proteomic analysis yielding no direct correlation, our multifaceted approach contributes comprehensive understanding of CRC's intricate regulatory mechanisms. In conclusion, this study advances hsa-miR-137 and CHGA as promising CRC biomarkers through an integrated analysis of diverse datasets and network interactions.

Biomarker discovery and validation for gastrointestinal tumors: A comprehensive review of colorectal, gastric, and liver cancers

Gastrointestinal (GI) malignancies, encompassing gastric, hepatic, colonic, and rectal cancers, are prevalent forms of cancer globally and contribute substantially to cancer-related mortality. Although there have been improvements in methods for diagnosing and treating GI cancers, the chances of survival for these types of cancers are still extremely low. According to the World Cancer Research International Fund's most recent figures, stomach cancer was responsible for roughly one million deaths worldwide in 2020. This emphasizes the importance of developing more effective tools for detecting, diagnosing, and predicting the outcome of these cancers at an early stage. Biomarkers, quantitative indications of biological processes or disease states, have emerged as promising techniques for enhancing the diagnosis and prognosis of GI malignancies. Recently, there has been a considerable endeavor to discover and authenticate biomarkers for various GI cancers by the utilization of diverse methodologies, including genomics, proteomics, and metabolomics. This review provides a thorough examination of the current state of biomarker research in the field of gastrointestinal malignancies, with a specific emphasis on colorectal, stomach, and liver cancers. A thorough literature search was performed on prominent databases such as PubMed, Scopus, and Web of Science to find pertinent papers published until November, 2023 for the purpose of compiling this review. The diverse categories of biomarkers, encompassing genetic, epigenetic, and protein-based biomarkers, and their potential utility in the fields of diagnosis, prognosis, and treatment selection, are explored. Recent progress in identifying and confirming biomarkers, as well as the obstacles that persist in employing biomarkers in clinical settings are emphasized. The utilization of biomarkers in GI cancers has significant potential in enhancing patient outcomes. Ongoing research is expected to uncover more efficient biomarkers for the diagnosis and prognosis of these cancers.

The effect of genetic variants of SLC22A18 on proliferation, migration, and invasion of colon cancer cells

Solute carrier family (SLC) transporters are expressed in the digestive system and play important roles in maintaining physiological functions in the body. In addition, SLC transporters act as oncoproteins or tumor-suppressor proteins during the development, progression, and metastasis of various digestive system cancers. SLC22A18, a member of the SLC22 gene family, is an orphan transporter with an unknown endogenous substrate. Previous study revealed that SLC22A18 is downregulated in colorectal cancer tissues and that it acts as a suppressor in colorectal cancer, although the effects of SLC22A18 variants on colon cancer cell proliferation, migration, and invasion are unknown. Therefore, in this study, we identified SLC22A18 variants found in multiple populations by searching public databases and determined the in vitro effects of these missense variations on transporter expression and cancer progression. Our results indicated that three missense SLC22A18 variants-p.Ala6Thr, p.Arg12Gln, and p.Arg86His-had significantly lower cell expression than the wild type, possibly owing to intracellular degradation. Furthermore, these three variants caused significantly higher proliferation, migration, and invasion of colon cancer cells than the wild type. Our findings suggest that missense variants of SLC22A18 can potentially serve as biomarkers or prognostic tools that enable clinicians to predict colorectal cancer progression.

The Potential of Clostridium butyricum to Preserve Gut Health, and to Mitigate Non-AIDS Comorbidities in People Living with HIV

A dramatic reduction in mortality among people living with HIV (PLWH) has been achieved during the modern antiretroviral therapy (ART) era. However, ART does not restore gut barrier function even after long-term viral suppression, allowing microbial products to enter the systemic blood circulation and induce chronic immune activation. In PLWH, a chronic state of systemic inflammation exists and persists, which increases the risk of development of inflammation-associated non-AIDS comorbidities such as metabolic disorders, cardiovascular diseases, and cancer. Clostridium butyricum is a human butyrate-producing symbiont present in the gut microbiome. Convergent evidence has demonstrated favorable effects of C. butyricum for gastrointestinal health, including maintenance of the structural and functional integrity of the gut barrier, inhibition of pathogenic bacteria within the intestine, and reduction of microbial translocation. Moreover, C. butyricum supplementation has been observed to have a positive effect on various inflammation-related diseases such as diabetes, ulcerative colitis, and cancer, which are also recognized as non-AIDS comorbidities associated with epithelial gut damage. There is currently scant published research in the literature, focusing on the influence of C. butyricum in the gut of PLWH. In this hypothesis review, we speculate the use of C. butyricum as a probiotic oral supplementation may well emerge as a potential future synergistic adjunctive strategy in PLWH, in tandem with ART, to restore and consolidate intestinal barrier integrity, repair the leaky gut, prevent microbial translocation from the gut, and reduce both gut and systemic inflammation, with the ultimate objective of decreasing the risk for development of non-AIDS comorbidities in PLWH.

Sensitive and Specific Analyses of Colorectal Cancer Recurrence through Multiplex superRCA Mutation Detection in Blood Plasma

Mutation analysis of circulating tumor DNA (ctDNA) has applications in monitoring of colorectal cancer (CRC) patients for recurrence. Considering the low tumor fraction of ctDNA in cell-free DNA (cfDNA) isolated from blood plasma, the sensitivity of the detection method is important. Here, plasma DNA collected at diagnosis and follow-up from 25 CRC patients was analyzed using a multiplex superRCA mutation detection assay. The assay was also performed on genomic DNA (gDNA) from tumor and normal tissue from 20 of these patients. The lower limit of detection for most sequence variants was in the range of 10-5, while when analyzing cfDNA from plasma with a typical input of 33 ng, the practical detection limit was ~10-4 or 0.01% mutant allele frequency (MAF). In 17 of 19 patients with identified hotspot mutations in tumor gDNA, at least one hotspot mutation could be detected in plasma DNA at the time of diagnosis. The MAF increased at subsequent time points in four of the patients who experienced a clinical relapse. Multiplex superRCA analysis of the remaining six patients did not reveal any hotspot mutations. In conclusion, multiplex superRCA assays proved suitable for monitoring CRC patients by analyzing hotspot mutations in cfDNA, and dynamic changes in MAF were observed in patients with clinical relapse.

Predicting colorectal cancer prognosis based on long noncoding RNAs of disulfidptosis genes

BACKGROUND

A recently hypothesized cause of cell death called disulfidptosis has been linked to the expansion, emigration, and vascular rebuilding of cancer cells. Cancer can be treated by targeting the pathways that trigger cell death.

AIM

To discover the long non-coding RNA of the disulfidaptosis-related lncRNAs (DRLs), prognosis clinical survival, and treat patients with colorectal cancer with medications.

METHODS

Initially, we queried the Cancer Genome Atlas database to collect transcriptome, clinical, and genetic mutation data for colorectal cancer (CRC). Training and testing sets for CRC patient transcriptome data were generated randomly. Key long non-coding RNAs (lncRNAs) related to DRLs were then identified and evaluated using a least absolute shrinkage and selection operator procedure, as well as univariate and multivariate Cox regression models. A prognostic model was then created after risk scoring. Also, Immune infiltration analysis, immune checkpoint analysis, and medication susceptibility analysis were used to investigate the causes of the different prognoses between high and low risk groups. Finally, we validated the differential expression and biomarker potential of risk-predictive lncRNAs through induction using both NCM460 and HT-29 cell lines, as well as a disulfidptosis model.

RESULTS

In this work, eight significant lncRNAs linked to disulfidptosis were found. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses of differentially expressed genes between high- and low-risk groups from the prognostic model showed a close relationship with the immune response as well as significant enrichment in neutrophil extracellular trap formation and the IL-17 signaling pathway. Furthermore, significant immune cell variations between the high-risk and low-risk groups were seen, as well as a higher incidence of immunological escape risk in the high-risk group. Finally, Epirubicin, bortezomib, teniposide, and BMS-754807 were shown to have the lowest sensitivity among the four immunotherapy drugs.

CONCLUSION

Our findings emphasizes the role of disulfidptosis in regulating tumor development, therapeutic response, and patient survival in CRC patients. For the clinical treatment of CRC, these important LncRNAs could serve as viable therapeutic targets.

Experimental prognostic model integrating N6-methyladenosine-related programmed cell death genes in colorectal cancer

Colorectal cancer (CRC) intricacies, involving dysregulated cellular processes and programmed cell death (PCD), are explored in the context of N6-methyladenosine (m6A) RNA modification. Utilizing the TCGA-COADREAD/CRC cohort, 854 m6A-related PCD genes are identified, forming the basis for a robust 10-gene risk model (CDRS) established through LASSO Cox regression. qPCR experiments using CRC cell lines and fresh tissues was performed for validation. The CDRS served as an independent risk factor for CRC and showed significant associations with clinical features, molecular subtypes, and overall survival in multiple datasets. Moreover, CDRS surpasses other predictors, unveiling distinct genomic profiles, pathway activations, and associations with the tumor microenvironment. Notably, CDRS exhibits predictive potential for drug sensitivity, presenting a novel paradigm for CRC risk stratification and personalized treatment avenues.

Glutaredoxin 2 Protein (Grx2) as an Independent Prognostic Factor Associated with the Survival of Colon Adenocarcinoma Patients

Glutaredoxin 2 (Grx2; Glrx2) is a glutathione-dependent oxidoreductase located in mitochondria, which is central to the regulation of glutathione homeostasis and mitochondrial redox, and plays a crucial role in highly metabolic tissues. In response to mitochondrial redox signals and oxidative stress, Grx2 can catalyze the oxidation and S-glutathionylation of membrane-bound thiol proteins in mitochondria. Therefore, it can have a significant impact on cancer development. To investigate this further, we performed an immunohistochemical analysis of Grx2 protein expression in colon adenocarcinoma samples collected from patients with primary colon adenocarcinoma (stage I and II) and patients with metastasis to regional lymph nodes (stage III). The results of our study revealed a significant relationship between the immunohistochemical expression of Grx2 and tumor histological grade, depth of invasion, regional lymph node involvement, angioinvasion, staging, and PCNA immunohistochemical expression. It was found that 87% of patients with stage I had high levels of Grx2 expression. In contrast, only 33% of patients with stage II and 1% of patients with stage III had high levels of Grx2 expression. Moreover, the multivariate analysis revealed that the immunohistochemical expression of Grx2 protein apart from the grade of tumor differentiation was an independent prognostic factors for the survival of patients with colon adenocarcinoma. Studies analyzing Grx2 levels in patients' blood confirmed that the highest levels of serum Grx2 protein was also found in stage I patients, which was reflected in the survival curves. A higher level of Grx2 in the serum has been associated with a more favorable outcome. These results were supported by in vitro analysis conducted on colorectal cancer cell lines that corresponded to stages I, II, and III of colorectal cancer, using qRT-PCR and Western Blot.

Small nucleolar RNA and its potential role in the oncogenesis and development of colorectal cancer

Small nucleolar RNAs (snoRNAs) represent a class of non-coding RNAs that play pivotal roles in post-transcriptional RNA processing and modification, thereby contributing significantly to the maintenance of cellular functions related to protein synthesis. SnoRNAs have been discovered to possess the ability to influence cell fate and alter disease progression, holding immense potential in controlling human diseases. It is suggested that the dysregulation of snoRNAs in cancer exhibits differential expression across various cancer types, stages, metastasis, treatment response and/or prognosis in patients. On the other hand, colorectal cancer (CRC), a prevalent malignancy of the digestive system, is characterized by high incidence and mortality rates, ranking as the third most common cancer type. Recent research indicates that snoRNA dysregulation is associated with CRC, as snoRNA expression significantly differs between normal and cancerous conditions. Consequently, assessing snoRNA expression level and function holds promise for the prognosis and diagnosis of CRC. Nevertheless, current comprehension of the potential roles of snoRNAs in CRC remains limited. This review offers a comprehensive survey of the aberrant regulation of snoRNAs in CRC, providing valuable insights into the discovery of novel biomarkers, therapeutic targets, and potential tools for the diagnosis and treatment of CRC and furnishing critical cues for advancing research into CRC and the judicious selection of therapeutic targets.

The Inhibitory Effects of Propofol on Colorectal Cancer Progression through the NF-κB/HIF-1α Signaling Pathway

BACKGROUND AND OBJECTIVE

Colorectal cancer (CRC) is a neoplastic disease that gradually develops due to genetic variations and epigenetic changes. Surgical excision is the first-line treatment for CRC. Accumulating evidence has shown that total intravenous anesthesia has beneficial effects for CRC patients as it decreases the probability of tumor recurrence and metastasis. Propofol is one of the most frequently used intravenous anesthetics in clinical practice. However, it remains unknown whether it can reduce recurrence and metastasis after surgery in cancer patients.

METHODS

CRC cell lines (HCT116 and SW480) were cultured in vitro, and different concentrations of propofol were added to the cell culture medium. The proliferation effect of propofol on CRC cell lines was evaluated by CCK-8 assay. The effect of propofol on the migration and invasion of CRC cells was evaluated by scratch healing and Transwell experiments. The inhibitory effects of propofol on NF-κB and HIF-1α expressions in CRC cell lines were determined by Western blotting and immunofluorescence assays to further clarify the regulatory effects of propofol on NF-κB and HIF-1α.

RESULTS

Compared to the control, propofol significantly inhibited the proliferation, migration, and invasion abilities of CRC cells (HCT116 and SW480) (p < 0.0001). The expression levels of NF-κB and HIF-1α gradually decreased with increasing propofol concentration in both cell lines. After activation and inhibition of NF-κB, the expression of HIF-1α changed. Further studies showed that propofol inhibited LPS-activated NF-κB-induced expression of HIF-1α, similar to the NF-κB inhibitor Bay17083 (p < 0.0001).

CONCLUSION

In vitro, propofol inhibited the proliferation, migration, and invasion of CRC cells (HCT116 and SW480) in a dose-dependent manner, possibly by participating in the regulation of the NF-κB/HIF-1α signaling pathway.

Downregulation of Serum miR-133b and miR-206 Associate with Clinical Outcomes of Progression as Monitoring Biomarkers for Metastasis Colorectal Cancer Patients

BACKGROUND

Colorectal cancer (CRC) is the third most common cancer in the world. Noncoding RNAs or microRNAs (miRNAs; miRs) biomarkers can play a role in cancer carcinogenesis and progression. Specific KRAS and EGFR mutation are associated with CRC development playing a role in controlling the cellular process as epigenetic events. Circulating serum miRs can serve for early diagnosis, monitoring, and prognosis of CRC as biomarkers but it is still unclear, clinically.

OBJECTIVE

To determine potential biomarkers of circulating serum miR-133b and miR-206 in CRC patients Methods: Bioinformatic prediction of microRNA was screened followed by TargetScanHuman7.2, miRTar2GO, miRDB, MiRanda, and DIANA-microT-CDS. Forty-four CRC serum (19 locally advanced, 23 distant advanced CRC) and 12 normal serum samples were subsequently extracted for RNA isolation, cDNA synthesis, and miR validation. The candidate circulating serum miR-133b and miR-206 were validated resulting in a relative expression via quantitative RT-PCR. Relative expression was normalized to the spike-internal control and compared to normal samples as 1 using the -2ΔΔCt method in principle.

RESULTS

Our results represented 9 miRs of miR-206, miR-155-5p, miR-143-3p, miR-193a-3p, miR-30a- 5p, miR-30d-5p, miR-30e-5p, miR-543, miR-877-5p relate to KRAS-specific miRs, whereas, 9 miRs of miR-133b, miR-302a-3p, miR-302b-3p, miR-302d-3p, miR-302e, miR-520a-3p, miR-520b, miR-520c- 3p and miR-7-5p relevance to EGFR-specific miRs by using the bioinformatic prediction tools. Our results showed a decreased expression level of circulating serum miR-133b as well as miR-206 associating with CRC patients (local and advanced metastasis) when compared to normal (P < 0.05), significantly.

CONCLUSION

The circulating serum miR-133b and miR-206 can serve as significant biomarkers for monitoring the clinical outcome of progression with metastatic CRC patients. Increased drug-responsive CRC patients associated with crucial molecular intervention should be further explored, clinically.

Diet-Wide Association, Genetic Susceptibility and Colorectal Cancer Risk: A Prospective Cohort Study

BACKGROUND

Both genetic and dietary factors play significant roles in the etiology of colorectal cancer (CRC). To evaluate the relationship between certain food exposures and the risk of CRC, we carried out a large-scale association analysis in the UK Biobank.

METHODS

The associations of 139 foods and nutrients' intake with CRC risk were assessed among 118,210 participants. A polygenic risk score (PRS) of CRC was created to explore any interaction between dietary factors and genetic susceptibility in CRC risk. The hazard ratio (HR) and 95% confidence interval (CI) of CRC risk linked to dietary variables and PRS were estimated using Cox regression models. Multiple comparisons were corrected using the error discovery rate (FDR).

RESULTS

During a mean follow-up of 12.8 years, 1466 incidents of CRC were identified. In the UK Biobank, alcohol and white bread were associated with increased CRC risk, and their HRs were 1.08 (95% CI: 1.03-1.14; FDRP = 0.028) and 1.10 (95% CI: 1.05-1.16; FDRP = 0.003), whereas dietary fiber, calcium, magnesium, phosphorus, and manganese intakes were inversely associated. We found no evidence of any PRS-nutrient interaction relationship in relation to CRC risk.

CONCLUSIONS

Our results show that higher intakes of alcohol and white bread are associated with increased CRC risk, whilst dietary fiber, calcium, magnesium, phosphorus, and manganese are inversely associated.

Biological function and clinical application prospect of tsRNAs in digestive system biology and pathology

tsRNAs are small non-coding RNAs originating from tRNA that play important roles in a variety of physiological activities such as RNA silencing, ribosome biogenesis, retrotransposition, and epigenetic inheritance, as well as involvement in cellular differentiation, proliferation, and apoptosis. tsRNA-related abnormalities have a significant influence on the onset, development, and progression of numerous human diseases, including malignant tumors through affecting the cell cycle and specific signaling molecules. This review introduced origins together with tsRNAs classification, providing a summary for regulatory mechanism and physiological function while dysfunctional effect of tsRNAs in digestive system diseases, focusing on the clinical prospects of tsRNAs for diagnostic and prognostic biomarkers. Video Abstract.

Comparative analysis between 2D and 3D colorectal cancer culture models for insights into cellular morphological and transcriptomic variations

Drug development is a time-consuming and expensive process, given the low success rate of clinical trials. Now, anticancer drug developments have shifted to three-dimensional (3D) models which are more likely to mimic tumor behavior compared to traditional two-dimensional (2D) cultures. A comparative study among different aspects was conducted between 2D and 3D cultures using colorectal cancer (CRC) cell lines, in addition, Formalin-Fixed Paraffin-Embedded (FFPE) block samples of patients with CRC were used for evaluation. Compared to the 2D culture, cells grown in 3D displayed significant (p < 0.01) differences in the pattern of cell proliferation over time, cell death phase profile, expression of tumorgenicity-related genes, and responsiveness to 5-fluorouracil, cisplatin, and doxorubicin. Epigenetically, 3D cultures and FFPE shared the same methylation pattern and microRNA expression, while 2D cells showed elevation in methylation rate and altered microRNA expression. Lastly, transcriptomic study depending on RNA sequencing and thorough bioinformatic analyses showed significant (p-adj < 0.05) dissimilarity in gene expression profile between 2D and 3D cultures involving thousands of genes (up/down-regulated) of multiple pathways for each cell line. Taken together, the study provides insights into variations in cellular morphologies between cells cultured in 2D and 3D models.