Novel MicroRNA Biomarkers for Colorectal Cancer Early Diagnosis and 5-Fluorouracil Chemotherapy Resistance but Not Prognosis: A Study from Databases to AI-Assisted Verifications

Novel biomarkers for neoplastic progression from ulcerative colitis to colorectal cancer: a systems biology approach

In recent studies, the void of evaluation and in-depth understanding of unknown clinically relevant potential molecular biomarkers involved in colorectal cancer (CRC) from the inflammatory stage of ulcerative colitis (UC) to CRC metastasis, which can be suitable therapeutic targets, is deeply felt. The regulation and interaction among different cancer-promoting molecules, including messenger RNAs (mRNAs) and micro RNAs (miRNAs) in CRC and its progression, were the aim we pursued in this study. Using microarray data, we investigated the differential expression for five datasets, including mRNA and microRNA samples related to UC, tumor/normal. Then, using robust data analysis, separate lists of differentially expressed genes (DEGs) and differentially expressed miRNAs (DEmiRNAs) were identified, which were used for robust rank aggregation (RRA) and co-expression network analysis. Then, comprehensive computational systems biology analyses, including gene ontology and Kyoto encyclopedia of genes and genomic pathway enrichment analyses, mRNA-miRNA regulatory network, and survival analysis, were employed to achieve the aim of this study. Finally, we used clinical samples to validate this potential and new target. According to this systems biology approach, a total of 98 DEGs and 8 DEmiRNAs with common differential expression were identified. By combining the distinct results of RRA and network, several potential therapeutic targets, and predictive and prognostic biomarkers for UC and CRC were identified. These targets include six common hub genes, CXCL1, CXCL8, MMP7, SLCA16A9, PLAU, and TIMP1, which are upregulated. Among these, the important and new biomarker SLC16A9 is negatively regulated by hsa-mir-194-5p, and hsa-miR-378a-5p take. The findings of the present study provide new insight into the pathogenesis of CRC in UC. Our study suggests future evaluation of the functional role of SLC16A9 and hsa-mir-194-5p and hsa-miR-378a-5p in CRC development.

Identification of potential microRNA diagnostic panels and uncovering regulatory mechanisms in breast cancer pathogenesis

Early diagnosis of breast cancer (BC), as the most common cancer among women, increases the survival rate and effectiveness of treatment. MicroRNAs (miRNAs) control various cell behaviors, and their dysregulation is widely involved in pathophysiological processes such as BC development and progress. In this study, we aimed to identify potential miRNA biomarkers for early diagnosis of BC. We also proposed a consensus-based strategy to analyze the miRNA expression data to gain a deeper insight into the regulatory roles of miRNAs in BC initiation. Two microarray datasets (GSE106817 and GSE113486) were analyzed to explore the differentially expressed miRNAs (DEMs) in serum of BC patients and healthy controls. Utilizing multiple bioinformatics tools, six serum-based miRNA biomarkers (miR-92a-3p, miR-23b-3p, miR-191-5p, miR-141-3p, miR-590-5p and miR-190a-5p) were identified for BC diagnosis. We applied our consensus and integration approach to construct a comprehensive BC-specific miRNA-TF co-regulatory network. Using different combination of these miRNA biomarkers, two novel diagnostic models, consisting of miR-92a-3p, miR-23b-3p, miR-191-5p (model 1) and miR-92a-3p, miR-23b-3p, miR-141-3p, and miR-590-5p (model 2), were obtained from bioinformatics analysis. Validation analysis was carried out for the considered models on two microarray datasets (GSE73002 and GSE41922). The model based on similar network topology features, comprising miR-92a-3p, miR-23b-3p and miR-191-5p was the most promising model in the diagnosis of BC patients from healthy controls with 0.89 sensitivity, 0.96 specificity and area under the curve (AUC) of 0.98. These findings elucidate the regulatory mechanisms underlying BC and represent novel biomarkers for early BC diagnosis.

Loss of CHGA Protein as a Potential Biomarker for Colon Cancer Diagnosis: A Study on Biomarker Discovery by Machine Learning and Confirmation by Immunohistochemistry in Colorectal Cancer Tissue Microarrays

Simple Summary

The identification of effective novel biomarkers is emergently needed in colon cancer patients. In the present study, firstly we predicted that CHGA could be a biomarker for colon cancer based on the protein–protein interaction network of all the reported biomarkers that were collected from our colorectal cancer biomarker database (CBD). Then we verified our results using a diagnostic test in gene expression data and an immunohistochemistry test. The results of this study suggest that a loss of CHGA expression from the normal colon and adjacent mucosa to colon cancer may be used as a valuable biomarker for early diagnosis of colon cancer patients.

Abstract

Background. The incidence of colorectal cancers has been constantly increasing. Although the mortality has slightly decreased, it is far from satisfaction. Precise early diagnosis for colorectal cancer has been a great challenge in order to improve patient survival. Patients and Methods. We started with searching for protein biomarkers based on our colorectal cancer biomarker database (CBD), finding differential expressed genes (GEGs) and non-DEGs from RNA sequencing (RNA-seq) data, and further predicted new biomarkers of protein–protein interaction (PPI) networks by machine learning (ML) methods. The best-selected biomarker was further verified by a receiver operating characteristic (ROC) test from microarray and RNA-seq data, biological network, and functional analysis, and immunohistochemistry in the tissue arrays from 198 specimens. Results. There were twelve proteins (MYO5A, CHGA, MAPK13, VDAC1, CCNA2, YWHAZ, CDK5, GNB3, CAMK2G, MAPK10, SDC2, and ADCY5) which were predicted by ML as colon cancer candidate diagnosis biomarkers. These predicted biomarkers showed close relationships with reported biomarkers of the PPI network and shared some pathways. An ROC test showed the CHGA protein with the best diagnostic accuracy (AUC = 0.9 in microarray data and 0.995 in RNA-seq data) among these candidate protein biomarkers. Furthermore, immunohistochemistry examination on our colon cancer tissue microarray samples further confirmed our bioinformatical prediction, indicating that CHGA may be used as a potential biomarker for early diagnosis of colon cancer patients. Conclusions. CHGA could be a potential candidate biomarker for diagnosing earlier colon cancer in the patients.

mRNA expression level of CDH2, LEP, POSTN, TIMP1 and VEGFC modulates 5-fluorouracil resistance in colon cancer cells

Drug resistance severely affects the clinical efficacy of therapeutic agents in patients with colon cancer. The aim of the present study was to identify genes involved in drug resistance in colon cancer using bioinformatics analysis and to identify the underlying mechanisms in vitro. Genes associated with cancer recurrence and chemotherapy resistance were identified using data mining. Immunohistochemistry was performed to analyze the protein expression level of genes of interest in human colon cancer tissues. Reverse transcription-quantitative PCR analysis was performed to analyze the gene expression level in patient samples and in colon cancer cell lines (HCT116 and LoVo). Cell viability was evaluated using the Cell Counting Kit-8 assay in the colon cancer cell lines. Apoptosis was measured using PI staining. The results from the present study revealed 602 genes using both ‘cancer recurrence’ and ‘chemoresistance’ terms on the GenCLiP3 website. Gene functional annotation was performed using the Database for Annotation, Visualization and Integrated Discovery then, the protein-protein interaction networks of the 602 genes were analyzed using STRING analysis. Further, in the GEPIA database, 14 genes (ATM, CDH2, CDKN2A, EPO, LEP, TGFB1, TIMP1, PGR, VEGFC, POSTN, BCL6, CYP19A1, NOTCH3 and XPA) were found to be upregulated in colon cancer tissue and were associated with poor prognosis in patients with colon cancer. Further analysis of 33 paired human colon cancer tissues revealed that 8 genes (ATM, CDH2, CDKN2A, LEP, PGR, TIMP1, POSTN and VEGFC) were significantly upregulated, which was consistent with the results obtained from the earlier analysis and 5 genes (CDH2, LEP, POSTN, TIMP1 and VEGFC) were associated with patient prognosis. Silencing of these 5 genes using small interfering RNAs significantly enhanced the sensitivity of colon cancer cells to the chemotherapeutic agent, 5-fluorouracil (5-FU). Taken together, the results suggested that CDH2, LEP, POSTN, TIMP1 and VEGFC might play a role in chemotherapeutic resistance in colon cancer and represent potential targets for overcoming 5-FU resistance in colon cancer.

Advances in Early Detection of Colorectal Cancer: A Focus on Non-invasive Biomarkers

BACKGROUND

Colorectal cancer (CRC) is the third most commonly diagnosed cancer worldwide. Currently, colonoscopy remains the gold standard diagnostic test for CRC detection. Nonetheless, this technique is invasive and expensive. Remarkable ongoing strategies are focusing on the development of affordable methods to diagnose CRC at earlier stages. The introduction of suitable noninvasive, sensitive and specified diagnostic tests for early CRC detection by employing biomarker analysis seems to be a fundamental need to reduce the numbers of unnecessary colonoscopies. In this review, we provide an overview of single- and multi-panel biomarkers (Genomic markers, transcriptome markers, proteomic markers, inflammatory markers, and microbiome markers) encompassing noninvasive tests in blood and stool for early CRC detection.

METHODS

A bibliographic search using PubMed/Medline, Web of Science, and EBSCOhost databases was performed to find relevant published studies over the last 6 years. Forty-three pertinent studies were included in this review.

RESULTS

The primary outcome highlights the sensitivity and specificity of single diagnostic biomarkers studied in blood or stool. The secondary outcome reveals the sensitivity and specificity of the biomarkers panel (combinations) in blood or stool. While some markers show better performance, others are not suitable for screening purposes.

CONCLUSION

There is a need to adjust experimental and analytical tests that can interfere with a robust result to replace or supplement those markers that are currently in use. Nevertheless, robust verification and validation with large clinical cohorts are needed for successful noninvasive tests that can fulfill the role of colonoscopy.

DECT in Detection of Vertebral Fracture-associated Bone Marrow Edema: A Systematic Review and Meta-Analysis with Emphasis on Technical and Imaging Interpretation Parameters

Background Dual-energy CT (DECT) shows promising performance in detecting bone marrow edema (BME) associated with vertebral body fractures. However, the optimal technical and image interpretation parameters are not well described. Purpose To conduct a systematic review and meta-analysis to determine the diagnostic performance of DECT in detecting BME associated with vertebral fractures (VFs), using different technical and image interpretation parameters, compared with MRI as the reference standard. Materials and Methods A systematic literature search was performed on July 9, 2020, to identify studies evaluating DECT performance for in vivo detection of vertebral BME. A random-effects model was used to derive estimates of the diagnostic accuracy parameters of DECT. The impact of relevant covariates in technical, image interpretation, and study design parameters on the diagnostic performance of DECT was investigated using subgroup analyses. Results Seventeen studies (with 742 of 2468 vertebrae with BME at MRI) met inclusion criteria. Pooled estimates of sensitivity, specificity, and area under the curve of DECT for vertebral body BME were 89% (95% CI: 84%, 92%), 96% (95% CI: 92%, 98%), and 96% (95% CI: 94%, 97%), respectively. Single-source consecutive scanning showed poor specificity (78%) compared with the dual-source technique (98%, P < .001). Specificity was higher using bone and soft-tissue kernels (98%) compared with using only soft-tissue kernels (90%, P = .001). Qualitative assessment had a better specificity (97%) versus quantitative assessment (90%) of DECT images (P = .01). Experienced readers showed considerably higher specificity (96%) compared with trainees (79%, P = .01). DECT sensitivity improved using a higher difference between low- and high-energy spectra (90% vs 83%, P = .04). Conclusion Given its high specificity, the detection of vertebral bone marrow edema with dual-energy CT (DECT) associated with vertebral fracture may obviate confirmatory MRI in an emergency setting. Technical parameters, such as the dual-source technique, both bone and soft-tissue kernels, and qualitative assessment by experienced readers, can ensure the high specificity of DECT. © RSNA, 2021 Online supplemental material is available for this article.

Down-Regulation of Circ_0032833 Sensitizes Colorectal Cancer to 5-Fluorouracil and Oxaliplatin Partly Depending on the Regulation of miR-125-5p and MSI1

Background

5-fluorouracil, leucovorin, and oxaliplatin (FOLFOX) is an effective chemotherapy for colorectal cancer (CRC) in clinic. It remains unclear regarding the effect of circular RNA (circRNA) circ_0032833 on regulating chemosensitivity in CRC.

Methods

Drug resistance analysis was performed by Cell Counting Kit-8 (CCK-8) assay. All RNA and protein levels were, respectively, measured via quantitative real-time polymerase chain reaction (qRT-PCR) and Western blot. Cellular colony capacity, apoptosis and metastasis were evaluated using colony formation assay, Annexin-FITC/PI flow cytometry and transwell migration/invasion assays. The molecular combination was notarized using dual-luciferase reporter and RNA immunoprecipitation (RIP) assays. The in vivo experiment was conducted via xenograft tumors in mice.

Results

Circ_0032833 was significantly up-regulated in FOLFOX-resistant CRC and associated with drug resistance. Knockdown of circ_0032833 could sensitize FOLFOX-resistant CRC cells to 5-fluorouracil and oxaliplatin. Circ_0032833 was a miR-125-5p sponge, and miR-125-5p overexpression was responsible for the effect of circ_0032833 knockdown on 5-fluorouracil and oxaliplatin sensitivities. Besides, miR-125-5p targeted Musashi1 (MSI1) to increase the susceptibility of 5-fluorouracil and oxaliplatin in FOLFOX-resistant CRC cells. We found that circ_0032833 generated the regulation on MSI1 by sponging miR-125-5p. Circ_0032833 down-regulation also promoted the 5-fluorouracil and oxaliplatin sensitivities partly through the miR-125-5p/MSI1 axis in vivo.

Conclusion

This study illuminated an unambiguous mechanism circ_0032833/miR-125-5p/MSI1 on regulating 5-fluorouracil and oxaliplatin sensitivities in FOLFOX therapy, maybe providing a deep insight of resistance formation and developing a novel strategy to enhance chemosensitivity in CRC.