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Mollanoori H, Ghelmani Y, Hassani B, Dehghani M. Integrated whole transcriptome profiling revealed a convoluted circular RNA-based competing endogenous RNAs regulatory network in colorectal cancer. Sci Rep 2024; 14:91. [PMID: 38167453 PMCID: PMC10761719 DOI: 10.1038/s41598-023-50230-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 12/17/2023] [Indexed: 01/05/2024] Open
Abstract
Recently, it has been identified that circRNAs can act as miRNA sponge to regulate gene expression in various types of cancers, associating them with cancer initiation and progression. The present study aims to identify colorectal cancer-related circRNAs and the underpinning mechanisms of circRNA/miRNA/mRNA networks in the development and progress of Colorectal Cancer. Differentially expressed circRNAs, miRNAs, and mRNAs were identified in GEO microarray datasets using the Limma package of R. The analysis of differentially expressed circRNAs resulted in 23 upregulated and 31 downregulated circRNAs. CeRNAs networks were constructed by intersecting the results of predicted and experimentally validated databases, circbank and miRWalk, and by performing DEMs and DEGs analysis using Cytoscape. Next, functional enrichment analysis was performed for DEGs included in ceRNA networks. Followed by survival analysis, expression profile assessment using TCGA and GEO data, and ROC curve analysis we identified a ceRNA sub-networks that revealed the potential regulatory effect of hsa_circ_0001955 and hsa_circ_0071681 on survival-related genes, namely KLF4, MYC, CCNA2, RACGAP1, and CD44. Overall, we constructed a convoluted regulatory network and outlined its likely mechanisms of action in CRC, which may contribute to the development of more effective approaches for early diagnosis, prognosis, and treatment of CRC.
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Affiliation(s)
- Hasan Mollanoori
- Medical Genetics Research Center, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Yaser Ghelmani
- Clinical Research Development Center, Shahid Sadoughi Hospital, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Bita Hassani
- Sarem Gynecology, Obstertrics and Infertility Research Center, Sarem Women's Hospital, Iran University of Medical Sciences (IUMS), Tehran, Iran
| | - Mohammadreza Dehghani
- Medical Genetics Research Center, Shahid Sadoughi University of Medical Sciences, Yazd, Iran.
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Zhang Y, Luo J, Yang W, Ye WC. CircRNAs in colorectal cancer: potential biomarkers and therapeutic targets. Cell Death Dis 2023; 14:353. [PMID: 37296107 PMCID: PMC10250185 DOI: 10.1038/s41419-023-05881-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 05/09/2023] [Accepted: 05/31/2023] [Indexed: 06/12/2023]
Abstract
Globally, colorectal cancer (CRC) is the third most prevalent cancer and the second leading cause of cancer-related deaths. Circular RNAs (circRNAs) are single-stranded RNA with covalently closed-loop structures and are highly stable, conserved, and abundantly expressed in various organs and tissues. Recent research found abnormal circRNA expression in CRC patients' blood/serum, cells, CRC tissues, and exosomes. Furthermore, mounting data demonstrated that circRNAs are crucial to the development of CRC. CircRNAs have been shown to exert biological functions by acting as microRNA sponges, RNA-binding protein sponges, regulators of gene splicing and transcription, and protein/peptide translators. These characteristics make circRNAs potential markers for CRC diagnosis and prognosis, potential therapeutic targets, and circRNA-based therapies. However, further studies are still necessary to improve the understanding of the roles and biological mechanisms of circRNAs in the development of CRC. In this review, up-to-date research on the role of circRNAs in CRC was examined, focusing on their potential application in CRC diagnosis and targeted therapy, which would advance the knowledge of the functions of circRNAs in the development and progression of CRC.
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Affiliation(s)
- Yuying Zhang
- Central Laboratory, Shenzhen Longhua Maternity and Child Healthcare Hospital, Shenzhen, 518109, China
| | - Jingyan Luo
- Forevergen Biosciences Centre, Guangzhou International Biotech Island, Guangzhou, 510300, China
| | - Weikang Yang
- Department of Prevention and Healthcare, Shenzhen Longhua Maternity and Child Healthcare Hospital, Shenzhen, 518109, China
| | - Wen-Chu Ye
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China.
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Foruzandeh Z, Alivand MR, Ghiami-Rad M, Zaefizadeh M, Ghorbian S. Identification and validation of miR-583 and mir-877-5p as biomarkers in patients with breast cancer: an integrated experimental and bioinformatics research. BMC Res Notes 2023; 16:72. [PMID: 37158948 PMCID: PMC10169388 DOI: 10.1186/s13104-023-06343-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 04/28/2023] [Indexed: 05/10/2023] Open
Abstract
OBJECTIVES Breast cancer (BC) is one of the most common cancers with a high mortality rate in women worldwide. The advantages of early cancer diagnosis are apparent, and it is a critical factor in increasing the patient's life and survival. According to mounting evidence, microRNAs (miRNAs) may be crucial regulators of critical biological processes. miRNA dysregulation has been linked to the beginning and progression of various human malignancies, including BC, and can operate as tumor suppressors or oncomiRs. This study aimed to identify novel miRNA biomarkers in BC tissues and non-tumor adjacent tissues of patients with BC. Microarray datasets GSE15852 and GSE42568 for differentially expressed genes (DEGs) and GSE45666, GSE57897, and GSE40525 for differentially expressed miRNAs (DEMs) retrieved from the Gene Expression Omnibus (GEO) database were analyzed using "R" software. A protein-protein interaction (PPI) network was created to identify the hub genes. MirNet, miRTarBase, and MirPathDB databases were used to predict DEMs targeted genes. Functional enrichment analysis was used to demonstrate the topmost classifications of molecular pathways. The prognostic capability of selected DEMs was evaluated through a Kaplan-Meier plot. Moreover, the specificity and sensitivity of detected miRNAs to discriminate BC from adjacent controls were assessed by area under the curve (AUC) using the ROC curve analysis. In the last phase of this study, gene expression on 100 BC tissues and 100 healthy adjacent tissues were analyzed and calculated by using the Real-Time PCR method. RESULTS This study declared that miR-583 and miR-877-5p were downregulated in tumor samples in comparison to adjacent non-tumor samples (|logFC|< 0 and P ≤ 0.05). Accordingly, ROC curve analysis demonstrated the biomarker potential of miR-877-5p (AUC = 0.63) and miR-583 (AUC = 0.69). Our results showed that has-miR-583 and has-miR-877-5p could be potential biomarkers in BC.
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Affiliation(s)
- Zahra Foruzandeh
- Department of Molecular Genetics, Ahar Branch, Islamic Azad University, Ahar, Iran
| | - Mohammad Reza Alivand
- Eye Research Center, The Five Senses Health Institute, Rassoul Akram Hospital, Iran University of Medical Sciences, Tehran, Iran.
- Stem Cell and Regenerative Medicine Research Center, Iran University of Medical Sciences, Tehran, Iran.
| | - Mehdi Ghiami-Rad
- Department of Microbiology, Faculty of Basic Sciences, Ahar Branch, Islamic Azad University, Ahar, Iran
| | | | - Saeid Ghorbian
- Department of Molecular Genetics, Ahar Branch, Islamic Azad University, Ahar, Iran
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Fang G, Xu D, Zhang T, Wang G, Qiu L, Gao X, Miao Y. Biological functions, mechanisms, and clinical significance of circular RNA in colorectal cancer. Front Oncol 2023; 13:1138481. [PMID: 36950552 PMCID: PMC10025547 DOI: 10.3389/fonc.2023.1138481] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 02/20/2023] [Indexed: 03/08/2023] Open
Abstract
Colorectal cancer (CRC) is a leading cause of cancer-related death worldwide due to the lack of effective diagnosis and prognosis biomarkers and therapeutic targets, resulting in poor patient survival rates. Circular RNA (circRNA) is a type of endogenous non-coding RNA (ncRNA) with a closed-loop structure that plays a crucial role in physiological processes and pathological diseases. Recent studies indicate that circRNAs are involved in the diagnosis, prognosis, drug resistance, and development of tumors, particularly in CRC. Therefore, circRNA could be a potential new target for improving CRC diagnosis, prognosis, and treatment. This review focuses on the origin and biological functions of circRNA, summarizes recent research on circRNA's role in CRC, and discusses the potential use of circRNAs as clinical biomarkers for cancer diagnosis and prognosis, as well as therapeutic targets for CRC treatment.
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Affiliation(s)
- Guida Fang
- Department of Gastrointestinal Surgery, Clinical College of Lianyungang Second People’s Hospital, Bengbu Medical College, Lianyungang, China
| | - Dalai Xu
- Department of Gastrointestinal Surgery, The Second People’s Hospital of Lianyungang City, Kangda College of Nanjing Medical University, Lianyungang, China
| | - Tao Zhang
- Department of Gastrointestinal Surgery, Clinical College of Lianyungang Second People’s Hospital, Bengbu Medical College, Lianyungang, China
| | - Gang Wang
- Department of Gastrointestinal Surgery, The Second People’s Hospital of Lianyungang City, Kangda College of Nanjing Medical University, Lianyungang, China
| | - Lei Qiu
- Department of Gastrointestinal Surgery, The Second People’s Hospital of Lianyungang City, Kangda College of Nanjing Medical University, Lianyungang, China
| | - Xuzhu Gao
- Department of Gastrointestinal Surgery, Clinical College of Lianyungang Second People’s Hospital, Bengbu Medical College, Lianyungang, China
- Department of Gastrointestinal Surgery, The Second People’s Hospital of Lianyungang City, Kangda College of Nanjing Medical University, Lianyungang, China
- Institute of Clinical Oncology, The Second People’s Hospital of Lianyungang City (Cancer Hospital of Lianyungang), Lianyungang, China
- *Correspondence: Yongchang Miao, ; Xuzhu Gao,
| | - Yongchang Miao
- Department of Gastrointestinal Surgery, Clinical College of Lianyungang Second People’s Hospital, Bengbu Medical College, Lianyungang, China
- Department of Gastrointestinal Surgery, The Second People’s Hospital of Lianyungang City, Kangda College of Nanjing Medical University, Lianyungang, China
- *Correspondence: Yongchang Miao, ; Xuzhu Gao,
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Yang Q, Luo Y, Lan B, Dong X, Wang Z, Ge P, Zhang G, Chen H. Fighting Fire with Fire: Exosomes and Acute Pancreatitis-Associated Acute Lung Injury. Bioengineering (Basel) 2022; 9:615. [PMID: 36354526 PMCID: PMC9687423 DOI: 10.3390/bioengineering9110615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/18/2022] [Accepted: 10/24/2022] [Indexed: 08/30/2023] Open
Abstract
Acute pancreatitis (AP) is a prevalent clinical condition of the digestive system, with a growing frequency each year. Approximately 20% of patients suffer from severe acute pancreatitis (SAP) with local consequences and multi-organ failure, putting a significant strain on patients' health insurance. According to reports, the lungs are particularly susceptible to SAP. Acute respiratory distress syndrome, a severe type of acute lung injury (ALI), is the primary cause of mortality among AP patients. Controlling the mortality associated with SAP requires an understanding of the etiology of AP-associated ALI, the discovery of biomarkers for the early detection of ALI, and the identification of potentially effective drug treatments. Exosomes are a class of extracellular vesicles with a diameter of 30-150 nm that are actively released into tissue fluids to mediate biological functions. Exosomes are laden with bioactive cargo, such as lipids, proteins, DNA, and RNA. During the initial stages of AP, acinar cell-derived exosomes suppress forkhead box protein O1 expression, resulting in M1 macrophage polarization. Similarly, macrophage-derived exosomes activate inflammatory pathways within endothelium or epithelial cells, promoting an inflammatory cascade response. On the other hand, a part of exosome cargo performs tissue repair and anti-inflammatory actions and inhibits the cytokine storm during AP. Other reviews have detailed the function of exosomes in the development of AP, chronic pancreatitis, and autoimmune pancreatitis. The discoveries involving exosomes at the intersection of AP and acute lung injury (ALI) are reviewed here. Furthermore, we discuss the therapeutic potential of exosomes in AP and associated ALI. With the continuous improvement of technological tools, the research on exosomes has gradually shifted from basic to clinical applications. Several exosome-specific non-coding RNAs and proteins can be used as novel molecular markers to assist in the diagnosis and prognosis of AP and associated ALI.
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Affiliation(s)
- Qi Yang
- Department of General Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, China
- Institute (College) of Integrative Medicine, Dalian Medical University, Dalian 116044, China
- Department of Traditional Chinese Medicine, The Second Affiliated Hospital of Dalian Medical University, Dalian 116023, China
| | - Yalan Luo
- Department of General Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, China
- Institute (College) of Integrative Medicine, Dalian Medical University, Dalian 116044, China
- Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, China
| | - Bowen Lan
- Department of General Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, China
- Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, China
| | - Xuanchi Dong
- Department of General Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, China
- Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, China
| | - Zhengjian Wang
- Department of General Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, China
- Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, China
| | - Peng Ge
- Department of General Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, China
- Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, China
| | - Guixin Zhang
- Department of General Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, China
- Institute (College) of Integrative Medicine, Dalian Medical University, Dalian 116044, China
- Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, China
| | - Hailong Chen
- Department of General Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, China
- Institute (College) of Integrative Medicine, Dalian Medical University, Dalian 116044, China
- Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, China
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