Identification of Key Gene Targets for Sensitizing Colorectal Cancer to Chemoradiation: an Integrative Network Analysis on Multiple Transcriptomics Data

Manoochehri, Hamed; Jalali, Akram; Tanzadehpanah, Hamid; Taherkhani, Amir; Saidijam, Massoud

doi:10.1007/s12029-021-00690-2

Cited by 18 publications

(13 citation statements)

References 65 publications

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“…According to the prediction of the development of human diseases, the global population of CRC cases will reach more than 3 million in the next 20 years. 120,121 Therefore, the key to the treatment of CRC is early detection, early diagnosis, and early treatment. As special noncoding RNA molecules in eukaryotes, circRNAs are formed by irregular reverse splicing sequences in pre-mRNA through specific upstream and downstream splicing sites.…”

Section: Conclusion and Perspectivementioning

confidence: 99%

Circular RNA: A promising new star for the diagnosis and treatment of colorectal cancer

Zhang

Sun

et al. 2021

Cancer Medicine

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Colorectal cancer (CRC) is one of the most common malignant tumors of the digestive tract, and morbidity and mortality rank third and second in malignant tumors. [1][2][3] Currently, early screening for CRC can effectively improve the survival rate of patients with CRC, but approximately 25% of CRC patients develop metastatic disease from an early stage. [4][5][6] Therefore, a promising field of antimetastatic therapy lies in the targeted inhibition of cancer cells with high metastatic potential from the primary site. 7,8 Recently, there has been a qualitative leap in tumor medical technology, such as the application of laparoscopic surgery, nano-assembly technology, PET/ CT imaging technology, and dynamic network biomarker (DNB), etc. 9-11 However, the cure rate and survival rate of CRC are still very low, mainly lacking new drug treatment targets and biomarkers for the treatment of CRC. 12 According to the research of circular RNAs in the CRC field, circular RNAs are expected to be therapeutic targets

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Section: Conclusion and Perspectivementioning

confidence: 99%

Circular RNA: A promising new star for the diagnosis and treatment of colorectal cancer

Zhang

Sun

et al. 2021

Cancer Medicine

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“…1 The poor prognosis is due to the high recurrence rate and early metastasis of colon cancer, 2 which is closely related to the limitations of surgery, the lack of specificity of chemotherapy and radiotherapy, and the drug resistance of antitumor drugs. 3 However, attributable to the enormous differences in prognosis at the same stage, the most commonly used approach, the tumor-node-metastasis (TNM) classification system for predicting survival, can only provide limited information. 4 Therefore, there is an urgent need to develop reliable markers with sound recognition and survival prediction function for colon cancer.…”

Section: Introductionmentioning

confidence: 99%

“…5 Today, thanks to the development of highthroughput microarray technology, we can detect differentially expressed miRNAs between cancer tissues and normal tissues on a large scale. 3,6 The network-based screening method can help us identify treatment targets more accurately and efficiently and make up for the differences brought by different individuals. However, when we identify too many target genes, a very complex protein-protein interaction (PPI) network will bring difficulties to our further research, not to mention many false-positive targets.…”

Section: Introductionmentioning

confidence: 99%

A Novel Defined Necroptosis-Related miRNAs Signature for Predicting the Prognosis of Colon Cancer

Yang¹,

Lü²,

Wang³

et al. 2022

IJGM

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This study aims at exploring the relationship between necroptosis-related miRNAs and colon cancer prognosis. Methods: We downloaded the miRNA sequencing data from the TCGA, and eight differentially expressed necroptosis-related miRNAs were screened. Then, we used Cox regression analysis to establish a prediction model of necroptosis-related miRNA. Finally, the prognosis related miRNAs were used to predict the target genes, and functional analysis was used to explore the potential mechanism of these target genes. Results:The miRNA-seq data of 444 COAD cases were downloaded from TCGA. We identified 8 differentially expressed miRNAs (has-miR-16-5p, has-miR-141-3p, has-miR -148a-3p, has-miR-425-5p, has-miR-7-5p, has-miR-223-3p, has-miR-200a-5p, and has-miR -500a-3p), then Cox analysis was performed for determining eight-miRNA signature prognostic biomarkers with obviously different OS. The area under the curve (AUC) of receiver operating characteristic (ROC) curve for predicting 1-, 3-, and 5-year survival were 0.663, 0.653 and 0.639, respectively. The multivariate analysis also implied that the risk score was an independent prognostic factor considering other confounding factors (HR = 1.847, 95% CI = 1.197-2.848, P = 0.006). According to the Kaplan-Meier analysis, the expression of hsa-miR-500a-3p (P = 0.003), hsa-miR-16-5p (P = 0.004) and hsa-miR-148a-3p (P = 0.035) significantly affected OS outcomes. We predicted the target genes of these three miRNAs and then screened 10 hub genes (CCND1, SMAD3, SMAD2, CDK1, TGFB2, CDC25A, CHEK1, VEGFA, CCNE1, WEE1). In addition, CHEK1 was associated with the survival prognosis. Conclusion: Our study demonstrated that necroptosis is closely associated with colon cancer, and the model of eight necroptosis-related miRNAs are potentially useful prognostic biomarkers and therapeutic targets for colon cancer.

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“…Previously, other researchers have also identified multiple key tumor molecules through high-throughput technology. 28 , 29 For example, Manoochehri et al found that CDC25A is a key gene for the prognosis of colorectal cancer. 30 Khoei et al found that miR-299-5p is an important prognostic factor for a variety of tumors.…”

Section: Discussionmentioning

confidence: 99%

Identification of Significant Modules and Targets of Xian-Lian-Jie-Du Decoction Based on the Analysis of Transcriptomics, Proteomics and Single-Cell Transcriptomics in Colorectal Tumor

Yu¹,

Chen²,

Lu³

et al. 2022

JIR

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Purpose Colorectal cancer (CRC) remains the third most common tumor worldwide. Ulcerative colitis (UC) could cause chronic inflammation and ulcers in the colon and rectum. UC is a risk factor for a high incidence of CRC, and the incidence of UC-associated CRC (UC-CRC) is still increasing. Chinese medicine prescription, Xian-Lian-Jie-Du decoction (XLJDD), has been proven its efficacy in some UC-CRC patients. However, the mechanism of XLJDD in treating UC-CRC remains unknown. This study aimed to investigate the mechanism of XLJDD in treating UC-CRC. Methods We constructed an AOM/DSS mouse model that could simulate the various stages of UC-CRC in humans. XLJDD and its 5 main components are used to treat the AOM/DSS model, respectively. With the power of high-throughput sequencing technology, we described the mechanism of XLJDD from transcriptomics, proteomics, and single-cell transcriptomics. Results Our results showed that XLJDD could effectively suppress the occurrence and development of colorectal tumors. Using the weighted correlation network analysis (WGCNA), several mRNA and protein modules that respond to XLJDD have been identified. Moreover, two essential genes, Mfsd2a and Ccdc85c, were caught our attention. They were prognostic markers in CRC patients, and their expression could be significantly modulated by XLJDD, showing their potential as effective targets of XLJDD. In addition, we also discovered that XLJDD could affect the cell composition of the colorectal tumor environment, especially in the infiltration of B cells. Conclusion We demonstrated that XLJDD could prevent the initiation and development of colorectal tumors by modulating the expression of Mfsd2a and Ccdc85c and reducing the infiltration of B cells in the tumor microenvironment of colorectal tumor.

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Identification of Key Gene Targets for Sensitizing Colorectal Cancer to Chemoradiation: an Integrative Network Analysis on Multiple Transcriptomics Data

Cited by 18 publications

References 65 publications

Circular RNA: A promising new star for the diagnosis and treatment of colorectal cancer

Circular RNA: A promising new star for the diagnosis and treatment of colorectal cancer

A Novel Defined Necroptosis-Related miRNAs Signature for Predicting the Prognosis of Colon Cancer

Identification of Significant Modules and Targets of Xian-Lian-Jie-Du Decoction Based on the Analysis of Transcriptomics, Proteomics and Single-Cell Transcriptomics in Colorectal Tumor

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