scholarly journals Potential Applications of DNA, RNA and Protein Biomarkers in Diagnosis, Therapy and Prognosis for Colorectal Cancer: A Study from Databases to AI-Assisted Verification

2018 ◽  
Author(s):  
Xueli Zhang ◽  
Xiao-feng Sun ◽  
Stephen T. A. Rush ◽  
Bairong Shen ◽  
Hong Zhang
Keyword(s):  
Colorectal Cancer ◽  
Protein Biomarkers ◽  
Potential Applications ◽  
Diagnosis Therapy

scholarly journals Potential Applications of DNA, RNA and Protein Biomarkers in Diagnosis, Therapy and Prognosis for Colorectal Cancer: A Study from Databases to AI-Assisted Verification

Cancers ◽  
2019 ◽  
Vol 11 (2) ◽  
pp. 172 ◽  
Author(s):  
Xueli Zhang ◽  
Xiao-Feng Sun ◽  
Bairong Shen ◽  
Hong Zhang
Keyword(s):  
Colorectal Cancer ◽  
Cellular Proliferation ◽  
Pathway Enrichment Analysis ◽  
Protein Biomarkers ◽  
Go Annotation ◽  
Diagnosis And Prognosis ◽  
Ppi Networks ◽  
Potential Applications ◽  
Multiple Biomarkers ◽  
Diagnosis Therapy

In order to find out the most valuable biomarkers and pathways for diagnosis, therapy and prognosis in colorectal cancer (CRC) we have collected the published CRC biomarkers and established a CRC biomarker database (CBD: http://sysbio.suda.edu.cn/CBD/index.html). In this study, we analysed the single and multiple DNA, RNA and protein biomarkers as well as their positions in cancer related pathways and protein-protein interaction (PPI) networks to describe their potential applications in diagnosis, therapy and prognosis. CRC biomarkers were collected from the CBD. The RNA and protein biomarkers were matched to their corresponding DNAs by the miRDB database and the PubMed Gene database, respectively. The PPI networks were used to investigate the relationships between protein biomarkers and further detect the multiple biomarkers. The Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway enrichment analysis and Gene Ontology (GO) annotation were used to analyse biological functions of the biomarkers. AI classification techniques were utilized to further verify the significances of the multiple biomarkers in diagnosis and prognosis for CRC. We showed that a large number of the DNA, RNA and protein biomarkers were associated with the diagnosis, therapy and prognosis in various degrees in the CRC biomarker networks. The CRC biomarkers were closely related to the CRC initiation and progression. Moreover, the biomarkers played critical roles in cellular proliferation, apoptosis and angiogenesis and they were involved in Ras, p53 and PI3K pathways. There were overlaps among the DNA, RNA and protein biomarkers. AI classification verifications showed that the combined multiple protein biomarkers played important roles to accurate early diagnosis and predict outcome for CRC. There were several single and multiple CRC protein biomarkers which were associated with diagnosis, therapy and prognosis in CRC. Further, AI-assisted analysis revealed that multiple biomarkers had potential applications for diagnosis and prognosis in CRC.

scholarly journals The crucial roles of N6-methyladenosine (m6A) modification in the carcinogenesis and progression of colorectal cancer

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Zhihao Fang ◽  
Yiqiu Hu ◽  
Jinhui Hu ◽  
Yanqin Huang ◽  
Shu Zheng ◽  
...  
Keyword(s):  
Gene Expression ◽  
Colorectal Cancer ◽  
Nuclear Export ◽  
Messenger Rna ◽  
Regulatory Proteins ◽  
Biological Processes ◽  
The Past ◽  
Common Cancer ◽  
Potential Applications ◽  
Regulated Gene Expression

AbstractAs the predominant modification in RNA, N6-methyladenosine (m6A) has attracted increasing attention in the past few years since it plays vital roles in many biological processes. This chemical modification is dynamic, reversible and regulated by several methyltransferases, demethylases and proteins that recognize m6A modification. M6A modification exists in messenger RNA and affects their splicing, nuclear export, stability, decay, and translation, thereby modulating gene expression. Besides, the existence of m6A in noncoding RNAs (ncRNAs) could also directly or indirectly regulated gene expression. Colorectal cancer (CRC) is a common cancer around the world and of high mortality. Increasing evidence have shown that the changes of m6A level and the dysregulation of m6A regulatory proteins have been implicated in CRC carcinogenesis and progression. However, the underlying regulation laws of m6A modification to CRC remain elusive and better understanding of these mechanisms will benefit the diagnosis and therapy. In the present review, the latest studies about the dysregulation of m6A and its regulators in CRC have been summarized. We will focus on the crucial roles of m6A modification in the carcinogenesis and development of CRC. Moreover, we will also discuss the potential applications of m6A modification in CRC diagnosis and therapeutics.

scholarly journals Circulating Noncoding RNAs Have a Promising Future Acting as Novel Biomarkers for Colorectal Cancer

2019 ◽  
Vol 2019 ◽  
pp. 1-13 ◽  
Author(s):  
Jia-jun Wang ◽  
Xin Wang ◽  
Yong-xi Song ◽  
Jun-hua Zhao ◽  
Jing-xu Sun ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
General Population ◽  
Malignant Tumors ◽  
Noncoding Rnas ◽  
Screening Methods ◽  
Potential Applications ◽  
Novel Biomarkers ◽  
Noninvasive Biomarkers ◽  
Regulatory Functions ◽  
Resistance To Chemotherapy

Colorectal cancer (CRC) is one of the most common malignant tumors worldwide, causing a large number of cancer-related deaths each year. Patients are usually diagnosed at advanced and incurable stages due to the lack of suitable screening methods for early detection. Noncoding RNAs (ncRNAs), including small and long noncoding RNAs (lncRNA), are known to have significant regulatory functions, and accumulating evidence suggests that circulating ncRNAs have potential applications as noninvasive biomarkers for diagnosing CRC, evaluating its prognosis, or predicting chemosensitivity in the general population. In this review, we summarize the origins of circulating ncRNAs and provide details of single and multiple circulating ncRNAs that might have roles as diagnostic and prognostic biomarkers in CRC. We end by discussing circulating ncRNAs that may distinguish patients with resistance to chemotherapy.

scholarly journals Gel-Based Proteomics of Clinical Samples Identifies Potential Serological Biomarkers for Early Detection of Colorectal Cancer

2019 ◽  
Vol 20 (23) ◽  
pp. 6082 ◽  
Author(s):  
Stine Thorsen ◽  
Irina Gromova ◽  
Ib Christensen ◽  
Simon Fredriksson ◽  
Claus Andersen ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Early Detection ◽  
Biomarker Discovery ◽  
Real Life ◽  
Clinical Samples ◽  
Plasma Samples ◽  
Healthy Individuals ◽  
Protein Biomarkers ◽  
2D Gel ◽  
Cancer Diseases

The burden of colorectal cancer (CRC) is considerable—approximately 1.8 million people are diagnosed each year with CRC and of these about half will succumb to the disease. In the case of CRC, there is strong evidence that an early diagnosis leads to a better prognosis, with metastatic CRC having a 5-year survival that is only slightly greater than 10% compared with up to 90% for stage I CRC. Clearly, biomarkers for the early detection of CRC would have a major clinical impact. We implemented a coherent gel-based proteomics biomarker discovery platform for the identification of clinically useful biomarkers for the early detection of CRC. Potential protein biomarkers were identified by a 2D gel-based analysis of a cohort composed of 128 CRC and site-matched normal tissue biopsies. Potential biomarkers were prioritized and assays to quantitatively measure plasma expression of the candidate biomarkers were developed. Those biomarkers that fulfilled the preset criteria for technical validity were validated in a case-control set of plasma samples, including 70 patients with CRC, adenomas, or non-cancer diseases and healthy individuals in each group. We identified 63 consistently upregulated polypeptides (factor of four-fold or more) in our proteomics analysis. We selected 10 out of these 63 upregulated polypeptides, and established assays to measure the concentration of each one of the ten biomarkers in plasma samples. Biomarker levels were analyzed in plasma samples from healthy individuals, individuals with adenomas, CRC patients, and patients with non-cancer diseases and we identified one protein, tropomyosin 3 (Tpm3) that could discriminate CRC at a significant level (p = 0.0146). Our results suggest that at least one of the identified proteins, Tpm3, could be used as a biomarker in the early detection of CRC, and further studies should provide unequivocal evidence for the real-life clinical validity and usefulness of Tpm3.

scholarly journals Personalized Medicine in Screening for Malignant Disease: A Review of Methods and Applications

2013 ◽  
Vol 8 ◽  
pp. BMI.S11153 ◽  
Author(s):  
F. Schmalfuss ◽  
P.L. Kolominsky-Rabas
Keyword(s):  
Breast Cancer ◽  
Prostate Cancer ◽  
Colorectal Cancer ◽  
Personalized Medicine ◽  
Literature Search ◽  
Malignant Disease ◽  
Decisive Role ◽  
Routine Clinical Practice ◽  
Cancer Breast ◽  
Potential Applications

Personalized medicine (PM) is currently a hot topic in the professional world. It is often called the medicine of the future and has already achieved resounding success in the area of targeted therapy. Nevertheless, integration of the concepts of PM into routine clinical practice is slow. This review is intended to give an overview of current and potential applications of PM in oncology. PM could soon play a decisive role, especially in screening. The relevance of PM in screening was examined in the case of four common cancers (colorectal cancer, lung cancer, breast cancer, and prostate cancer). A literature search was performed. This showed that biomarkers in particular play a crucial role in screening. In summary, it can be emphasized that there are already numerous known promising biomarkers in malignant disease. This results in several possibilities for individualizing and revolutionizing screening.

scholarly journals The Long Noncoding RNA HOTAIR Promotes Colorectal Cancer Progression by Sponging miR-197

2018 ◽  
Vol 26 (3) ◽  
pp. 473-481 ◽  
Author(s):  
Xinyang Lu ◽  
Zhiqiang Liu ◽  
Xiaofei Ning ◽  
Lunhua Huang ◽  
Biao Jiang
Keyword(s):  
Colorectal Cancer ◽  
Cancer Progression ◽  
Long Noncoding Rna ◽  
Noncoding Rna ◽  
Migration And Invasion ◽  
Downstream Target ◽  
Potential Applications ◽  
Colorectal Cancer Progression

The long noncoding RNA HOX transcript antisense RNA (HOTAIR) has been found to be overexpressed in many human malignancies and involved in tumor progression and metastasis. Although the downstream target through which HOTAIR modulates tumor metastasis is not well known, evidence suggests that microRNA-197 (miR-197) might be involved in this event. In the present study, the significance of HOTAIR and miR-197 in the progression of colorectal cancer was detected in vitro and in vivo. We found that HOTAIR expression was significantly increased in colorectal cancer cells and tissues. In contrast, the expression of miR-197 was obviously decreased. We further demonstrated that HOTAIR knockdown promoted apoptosis and inhibited cell proliferation, migration, and invasion in vitro and in vivo. Moreover, HOTAIR modulated the progression of colorectal cancer by competitively binding miR-197. Taken together, our study has identified a novel pathway through which HOTAIR exerts its oncogenic role and provided a molecular basis for potential applications of HOTAIR in the prognosis and treatment of colorectal cancer.

scholarly journals Noninvasive urinary protein signatures associated with colorectal cancer diagnosis and metastasis

2020 ◽  
Author(s):  
Yulin Sun ◽  
Zhengguang Guo ◽  
Zongpan Jing ◽  
Jun Li ◽  
Lijun Yang ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Urinary Protein ◽  
Functional Study ◽  
Protein Biomarkers ◽  
Tissue Samples ◽  
Serum Carcinoembryonic Antigen ◽  
Diagnostic Signature ◽  
Increased Sensitivity ◽  
Noninvasive Biomarkers ◽  
Metastatic Risk

Abstract Currently, imaging and serum carcinoembryonic antigen (CEA) tests are not sufficient for early detection and evaluation of metastasis and recurrence in colorectal cancer (CRC). To comprehensively discover and validate more accurate noninvasive biomarkers in urine, we adopted a staged discovery-verification-validation pipeline in 657 urine and 665 tissue samples from healthy controls and CRC patients with a distinct metastatic risk. The diagnostic signature generated combined with serum CEA levels revealed a significantly increased sensitivity (+34.8%) compared to CEA alone. Moreover, over 50% of CEA-negative metastatic patients were correctly predicted by the metastatic signature generated for metastatic risk. The tissue validation and functional study showed that CORO1C was associated with distant metastasis and enhanced the invasion and metastasis of CRC cells via a novel integrin/FAK/SRC and relevant pathways. Our findings provide novel urinary protein biomarkers and potential interventional targets to reliably detect CRC, especially in patients with metastatic CRC.

Sign in / Sign up

Export Citation Format

Share Document