scholarly journals Comprehensive Analysis of a tRNA-Derived Small RNA in Colorectal Cancer

2021 ◽  
Vol 11 ◽  
Author(s):  
Yong Zhu ◽  
Shaoqiu Chen ◽  
Zhougui Ling ◽  
Andrew Winnicki ◽  
Lilly Xu ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Small Rna ◽  
Interaction Network ◽  
Diagnostic Methods ◽  
Cancer Prognosis ◽  
Diagnostic Model ◽  
Tissue Samples ◽  
Mrna Targets ◽  
Diagnostic Panel ◽  
New Biomarkers

Colorectal cancer often presents as a highly variable disease with myriad forms that are at times difficult to detect in early screenings with sufficient accuracy, for which novel diagnostic methods are an attractive and valuable area of improvement. To improve colorectal cancer diagnosis and prognosis, new biomarkers that can be assembled into a diagnostic panel must be identified, and tRNA-derived small RNAs (tsRNAs) are a particularly interesting and increasingly visible new class of molecules to examine. In this study, small RNA-seq data were profiled for the expression of 104 human tsRNAs in tumor tissue and adjacent normal tissue samples, and a diagnostic model was built based on four differentially expressed tsRNAs: tRF-22-WB86Q3P92, tRF-22-WE8SPOX52, tRF-22-WE8S68L52, tRF-18-8R1546D2. Furthermore, the diagnostic model was validated by two independent validation datasets (AUC was 0.97 and 0.99), and a LASSO model was applied to develop a seven-tsRNA-based risk score model for colorectal cancer prognosis. Finally, a tsRNA-mRNA interaction network was established according to potential mRNA targets predicted by bioinformatic methods. In conclusion, the results suggest that abnormal expression of tsRNA in colorectal cancer may have a functional effect on tumor action and moreover, that some of the tsRNAs identified in this study with diagnostic and prognostic potential could be of clinical significance.

scholarly journals Colorectal Cancer Study with Nanostructured Sensors: Tumor Marker Screening of Patient Biopsies

Nanomaterials ◽  
2020 ◽  
Vol 10 (4) ◽  
pp. 606 ◽  
Author(s):  
Michele Astolfi ◽  
Giorgio Rispoli ◽  
Gabriele Anania ◽  
Veronica Nevoso ◽  
Elena Artioli ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Principal Component ◽  
Human Colon ◽  
Diagnostic Methods ◽  
Human Colon Cancer ◽  
Discrimination Power ◽  
Tissue Samples ◽  
Chemoresistive Sensors ◽  
One Year ◽  
Nanostructured Sensors

Despite the great progress in screening techniques and medical treatments, colorectal cancer remains one of the most widespread cancers in both sexes, with a high death rate. In this work, the volatile compounds released from human colon cancer tissues were detected by a set of four different chemoresistive sensors, made with a nanostructured powder of metal-oxide materials, inserted into an innovative patented device. The sensor responses to the exhalation of a primary cancer sample and of a healthy sample (both of the same weight, collected during colorectal surgery from the intestine of the same patient) were statistically analyzed. The sensors gave reversible, reproducible, and fast responses for at least one year of continuous use, making them quite superior in respect to the existing diagnostic methods. Preliminary results obtained using principal component analysis of the sensor responses to samples removed from 13 patients indicate that the nanostructured sensors employed in this study were able to distinguish between healthy and tumor tissue samples with coherent responses (the discrimination power of the most sensitive sensor was about 17%), highlighting a strong potential for clinical practice.

scholarly journals Identification of Hub Genes Related to Liver Metastasis of Colorectal Cancer by Integrative Analysis

2021 ◽  
Vol 11 ◽  
Author(s):  
Sicheng Liu ◽  
Yaguang Zhang ◽  
Su Zhang ◽  
Lei Qiu ◽  
Bo Zhang ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Liver Metastasis ◽  
Expression Profiles ◽  
Interaction Network ◽  
Rank Aggregation ◽  
Marker Genes ◽  
Peroxisome Proliferator ◽  
Hub Genes ◽  
Peroxisome Proliferator Activated Receptor ◽  
New Biomarkers

Liver metastasis of colorectal cancer (LMCRC) severely damages patient health, causing poor prognosis and tumor relapse. Marker genes associated with LMCRC identified by previous study did not meet therapeutic demand. Therefore, it is necessary to identify new biomarkers regulating the metastasis network and screen potential drugs for future treatment. Here, we identified that cell adhesion molecules and peroxisome proliferator-activated receptor (PPAR) signaling pathway were significantly enriched by analyzing the integrated-multiple expression profiles. Moreover, analysis with robust rank aggregation approach revealed a total of 138 differentially expressed genes (DEGs), including 108 upexpressed and 30 downexpressed genes. With establishing protein–protein interaction network, we also identified the subnetwork significantly enriching the metastasis-associated hub genes including ALB, APOE, CDH2, and ORM1. ESR2, FOXO3, and SRY were determined as key transcription factors regulating hub genes. In addition, ADH-1, epigallocatechin, CHEMBL1945287, and cochinchinenin C were predicted as potential therapeutic drugs. Moreover, the antimigration capacity of ADH-1 and epigallocatechin were confirmed in CRC cell lines. In conclusion, our findings not only offer opportunities to understand metastasis mechanism but also identify potential therapeutic targets for CRC.

scholarly journals DNA methylation markers for diagnosis and prognosis of common cancers

2017 ◽  
Vol 114 (28) ◽  
pp. 7414-7419 ◽  
Author(s):  
Xiaoke Hao ◽  
Huiyan Luo ◽  
Michal Krawczyk ◽  
Wei Wei ◽  
Wenqiu Wang ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Dna Methylation ◽  
Cancer Biology ◽  
Normal Tissue ◽  
Diagnostic Methods ◽  
Adjacent Normal Tissue ◽  
Tissue Samples ◽  
Diagnosis And Prognosis ◽  
Cancer Metastases ◽  
Colorectal Cancer Metastases

The ability to identify a specific cancer using minimally invasive biopsy holds great promise for improving the diagnosis, treatment selection, and prediction of prognosis in cancer. Using whole-genome methylation data from The Cancer Genome Atlas (TCGA) and machine learning methods, we evaluated the utility of DNA methylation for differentiating tumor tissue and normal tissue for four common cancers (breast, colon, liver, and lung). We identified cancer markers in a training cohort of 1,619 tumor samples and 173 matched adjacent normal tissue samples. We replicated our findings in a separate TCGA cohort of 791 tumor samples and 93 matched adjacent normal tissue samples, as well as an independent Chinese cohort of 394 tumor samples and 324 matched adjacent normal tissue samples. The DNA methylation analysis could predict cancer versus normal tissue with more than 95% accuracy in these three cohorts, demonstrating accuracy comparable to typical diagnostic methods. This analysis also correctly identified 29 of 30 colorectal cancer metastases to the liver and 32 of 34 colorectal cancer metastases to the lung. We also found that methylation patterns can predict prognosis and survival. We correlated differential methylation of CpG sites predictive of cancer with expression of associated genes known to be important in cancer biology, showing decreased expression with increased methylation, as expected. We verified gene expression profiles in a mouse model of hepatocellular carcinoma. Taken together, these findings demonstrate the utility of methylation biomarkers for the molecular characterization of cancer, with implications for diagnosis and prognosis.

scholarly journals Alterations, Interactions, and Diagnostic Potential of Gut Bacteria and Viruses in Colorectal Cancer

2021 ◽  
Vol 11 ◽  
Author(s):  
Renyuan Gao ◽  
Yefei Zhu ◽  
Cheng Kong ◽  
Kai Xia ◽  
Hao Li ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Relative Abundance ◽  
Gut Microbiome ◽  
Fusobacterium Nucleatum ◽  
Gut Bacteria ◽  
Microbial Interactions ◽  
Diagnostic Model ◽  
Metagenomic Sequencing ◽  
Diagnostic Potential ◽  
Diagnostic Panel

Gut microbiome alteration was closely associated with colorectal cancer (CRC). Previous studies had demonstrated the bacteria composition changes but lacked virome profiles, trans-kindom interactions, and reliable diagnostic model explorations in CRC. Hence, we performed metagenomic sequencing to investigate the gut microbiome and microbial interactions in adenoma and CRC patients. We found the decreased microbial diversity in CRC and revealed the taxonomic alterations of bacteria and viruses were highly associated with CRC at the species level. The relative abundance of oral-derived species, such as Fusobacterium nucleatum, Fusobacterium hwasookii, Porphyromonas gingivalis, and Bacteroides fragilis, increased. At the same time, butyrate-producing and anti-inflammatory microbes decreased in adenoma and CRC by non-parametric Kruskal-Wallis test. Despite that, the relative abundance of Escherichia viruses and Salmonella viruses increased, whereas some phages, including Enterobacteria phages and Uncultured crAssphage, decreased along with CRC development. Gut bacteria was negatively associated with viruses in CRC and healthy control by correlation analysis (P=0.017 and 0.002, respectively). Viruses were much more dynamic than the bacteria as the disease progressed, and the altered microbial interactions were distinctively stage-dependent. The degree centrality of microbial interactions decreased while closeness centrality increased along with the adenoma to cancer development. Uncultured crAssphage was the key bacteriophage that enriched in healthy controls and positively associated with butyrate-producing bacteria. Diagnostic tests based on bacteria by random forest confirmed in independent cohorts showed better performance than viruses for CRC. In conclusion, our study revealed the novel CRC-associated bacteria and viruses that exhibited specific differences and intensive microbial correlations, which provided a reliable diagnostic panel for CRC.

scholarly journals Elevated AA/EPA Ratio Represents an Inflammatory Biomarker in Tumor Tissue of Metastatic Colorectal Cancer Patients

2019 ◽  
Vol 20 (8) ◽  
pp. 2050 ◽  
Author(s):  
Valeria Tutino ◽  
Valentina De Nunzio ◽  
Maria Gabriella Caruso ◽  
Nicola Veronese ◽  
Dionigi Lorusso ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Tumor Tissue ◽  
Profile Analysis ◽  
Lipid Homeostasis ◽  
Tissue Samples ◽  
Inflammatory Microenvironment ◽  
Inflammatory Biomarker ◽  
Metastatic Process ◽  
New Biomarkers ◽  
Colorectal Cancer Patients

Chronic inflammation increases the risk of developing certain types of cancer, such as colorectal cancer (CRC). The oxidative metabolism of polyunsaturated fatty acids (PUFAs) has a strong effect on colonic tumorigenesis and the levels of arachidonic acid (AA) and eicosapentaenoic acid (EPA) can contribute to the development of an inflammatory microenvironment. Aim of this study was to evaluate the possible differences in the AA/EPA ratio tissue levels between CRC patients with and without synchronous metastases. Moreover, the expression of the most important inflammatory enzymes and mediators, linked with the AA/EPA ratio, have been also assessed. Sixty-eight patients with CRC were enrolled in the study, of which 33 patients with synchronous metastasis. Fatty acid profile analysis in tissue samples was done to examine the levels of AA and EPA. High levels of the AA/EPA ratio were detected in tumor tissue of patients with metastatic CRC. Moreover, an increase of expression of the main enzymes and mediators involved in inflammation was also detected in the same samples. The lipidomic approach of inflammation allows to evaluate lipid homeostasis changes that occur in cancer and in its metastatic process, in order to identify new biomarkers to be introduced into clinical practice.

scholarly journals Detection of Microsatellite Instability: State of the Art and Future Applications in Circulating Tumour DNA (ctDNA)

Cancers ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1491
Author(s):  
Pauline Gilson ◽  
Jean-Louis Merlin ◽  
Alexandre Harlé
Keyword(s):  
Microsatellite Instability ◽  
Liquid Biopsy ◽  
Treatment Decision ◽  
Molecular Techniques ◽  
Diagnostic Methods ◽  
Cancer Prognosis ◽  
Tumour Tissue ◽  
Repair System ◽  
Tissue Samples ◽  
Treatment Decision Making

Microsatellite instability (MSI) is a molecular scar resulting from a defective mismatch repair system (dMMR) and associated with various malignancies. MSI tumours are characterized by the accumulation of mutations throughout the genome and particularly clustered in highly repetitive microsatellite (MS) regions. MSI/dMMR status is routinely assessed in solid tumours for the initial screening of Lynch syndrome, the evaluation of cancer prognosis, and treatment decision-making. Currently, pentaplex PCR-based methods and MMR immunohistochemistry on tumour tissue samples are the standard diagnostic methods for MSI/dMMR. Other tissue methods such as next-generation sequencing or real-time PCR-based systems have emerged and represent viable alternatives to standard MSI testing in specific settings. The evolution of the standard molecular techniques has offered the opportunity to extend MSI determination to liquid biopsy based on the analysis of cell-free DNA (cfDNA) in plasma. This review aims at synthetizing the standard and emerging techniques used on tumour tissue samples for MSI/dMMR determination. We also provide insights into the MSI molecular techniques compatible with liquid biopsy and the potential clinical consequences for patients with solid cancers.

COMPARATIVE EVALUATION OF MULTIPARAMETRIC ENDORECTAL ULTRASOUND AND ENHANCED IMAGING COLONOSCOPY IN THE DIAGNOSIS OF EARLY COLORECTAL CANCER

2020 ◽  
Vol 19 (3) ◽  
pp. 49-64
Author(s):  
E. M. Bogdanova ◽  
Yu. L. Trubacheva ◽  
O. M. Yugai ◽  
S. V. Chernyshov ◽  
E. G. Rybakov ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Statistical Significance ◽  
Muscle Layer ◽  
Endorectal Ultrasound ◽  
Diagnostic Methods ◽  
Early Colorectal Cancer ◽  
Morphological Examination ◽  
Optical Magnification ◽  
The Difference ◽  
Enhanced Imaging

AIM: to compare multiparametric endorectal ultrasound (ERUS) and enhanced imaging colonoscopy in the diagnosis of early colorectal cancer.PATIENTS AND METHODS: the study included 78 patients with epithelial rectal tumor. All the patients underwent multiparametric ERUS and colonoscopy with examination by narrow beam imaging (NBI) at optical magnification. All the patients were operated.RESULTS: a morphological examination removed specimens revealed adenomas in 48 cases, in 19 specimens – adenocarcinomas in situ and T1, and in 11 specimens – adenocarcinomas with invasion of the muscle layer or deeper. When calculating the accuracy indicators of diagnostic methods for groups of patients with adenoma, Tis-T1 adenocarcinoma, and T2-T3 adenocarcinoma, the difference in the sensitivity and specificity of the methods in none of the presented groups did not reach the level of statistical significance (p>0.05).ROC analysis showed that ultrasound has a prognostic value comparable to colonoscopy. The area difference was 0.013 (p=0.85).CONCLUSION: endoscopy and ultrasound have similar value in the diagnosis of malignant transformation of rectal adenomas.

DIAGNOSING QUALITY OF FRICTION SYSTEMS OF MECHANISMS OF DEVICES

2019 ◽  
Vol 1 (7) ◽  
pp. 10-13
Author(s):  
D. Yu. Ershov ◽  
I. N. Lukyanenko ◽  
E. E. Aman
Keyword(s):  
Surface Defects ◽  
Diagnostic Methods ◽  
Design Parameters ◽  
Diagnostic Model ◽  
Mechanical Assemblies ◽  
Local Defects ◽  
Relationship Of ◽  
The Relationship ◽  
Production And Operation

The article shows the need to develop diagnostic methods for monitoring the quality of lubrication systems, which makes it possible to study the dynamic processes of contacting elements of the friction systems of instrument mechanisms, taking into account roughness parameters, the presence of local surface defects of elements and the bearing capacity of a lubricant. In the present article, a modern diagnostic model has been developed to control the quality of the processes of production and operation of friction systems of instrument assemblies. With the help of the developed model, it becomes possible to establish the relationship of diagnostic and design parameters of the mechanical system, as well as the appearance of possible local defects and lubricant state, which characterize the quality of friction systems used in many mechanical assemblies of the mechanisms of devices. The research results are shown in the form of nomograms to assess the defects of the elements of friction mechanisms of the mechanisms of the devices.

scholarly journals The Role of the CpG Island Methylator Phenotype in Colorectal Cancer Prognosis Depends on Microsatellite Instability Screening Status

2010 ◽  
Vol 16 (6) ◽  
pp. 1845-1855 ◽  
Author(s):  
Anna M. Dahlin ◽  
Richard Palmqvist ◽  
Maria L. Henriksson ◽  
Maria Jacobsson ◽  
Vincy Eklöf ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Microsatellite Instability ◽  
Cpg Island ◽  
Cancer Prognosis ◽  
Cpg Island Methylator Phenotype ◽  
Methylator Phenotype

scholarly journals Association between colorectal cancer and Fusobacterium nucleatum and Bacteroides fragilis bacteria in Iranian patients: a preliminary study

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Aref Shariati ◽  
Shabnam Razavi ◽  
Ehsanollah Ghaznavi-Rad ◽  
Behnaz Jahanbin ◽  
Abolfazl Akbari ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Relative Abundance ◽  
Normal Tissue ◽  
Bacteroides Fragilis ◽  
Fusobacterium Nucleatum ◽  
Normal Mucosa ◽  
Clinicopathologic Characteristics ◽  
Tissue Samples ◽  
Adjacent Normal Mucosa ◽  
Iranian Patients

Abstract Background and aim Recent studies have proposed that commensal bacteria might be involved in the development and progression of gastrointestinal disorders such as colorectal cancer (CRC). Therefore, in this study, the relative abundance of Fusobacterium nucleatum, Bacteroides fragilis, Streptococcus bovis/gallolyticus, and Enteropathogenic Escherichia coli (EPEC) in CRC tissues, and their association with clinicopathologic characteristics of CRC was investigated in Iranian patients. Moreover, the role of these bacteria in the CRC-associated mutations including PIK3CA, KRAS, and BRAF was studied. Method To these ends, the noted bacteria were quantified in paired tumors and normal tissue specimens of 30 CRC patients, by TaqMan quantitative Real-Time Polymerase Chain Reaction (qPCR). Next, possible correlations between clinicopathologic factors and mutations in PIK3CA, KRAS, and BRAF genes were analyzed. Results In studied samples, B. fragilis was the most abundant bacteria that was detected in 66 and 60% of paired tumor and normal samples, respectively. Furthermore, 15% of the B. fragilis-positive patients were infected with Enterotoxigenic B. fragilis (ETBF) in both adenocarcinoma and matched adjacent normal samples. F. nucleatum was also identified in 23% of tumors and 13% of adjacent normal tissue samples. Moreover, the relative abundance of these bacteria determined by 2-ΔCT was significantly higher in CRC samples than in adjacent normal mucosa (p < 0.05). On the other hand, our findings indicated that S. gallolyticus and EPEC, compared to adjacent normal mucosa, were not prevalent in CRC tissues. Finally, our results revealed a correlation between F. nucleatum-positive patients and the KRAS mutation (p = 0.02), while analyses did not show any association between bacteria and mutation in PIK3CA and BRAF genes. Conclusion The present study is the first report on the analysis of different bacteria in CRC tissue samples of Iranian patients. Our findings revealed that F. nucleatum and B. fragilis might be linked to CRC. However, any link between gut microbiome dysbiosis and CRC remains unknown.

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