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Alharbi KS. The ncRNA-TGF-β axis: Unveiling new frontiers in colorectal cancer research. Pathol Res Pract 2024; 254:155138. [PMID: 38266458 DOI: 10.1016/j.prp.2024.155138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 01/07/2024] [Accepted: 01/11/2024] [Indexed: 01/26/2024]
Abstract
Colorectal cancer (CRC) poses a substantial global challenge, necessitating a deeper understanding of the molecular underpinnings governing its onset and progression. The transforming growth factor beta (TGF-β) network has been a well-recognized cornerstone in advancing CRC. Nevertheless, a recent study has highlighted the growing importance of non-coding RNAs (ncRNAs) in this context. This comprehensive review aims to present an extensive examination of the interaction between ncRNAs and TGF-signaling. Noncoding RNAs (ncRNAs), encompassing circular RNAs (circRNAs), long-ncRNAs (lncRNAs), and microRNAs (miRNAs), have surfaced as pivotal modulators governing various aspects of TGF-β signaling. MiRNAs have been discovered to target elements within the TGF-β signaling, either enhancing or inhibiting signaling, depending on the context. LncRNAs have been associated with CRC progression, functioning as miRNA sponges or directly influencing TGF-β pathway elements. Even circRNAs, a relatively recent addition to the ncRNA family, have impacted CRC, affecting TGF-β signaling through diverse mechanisms. This review encompasses recent progress in comprehending specific ncRNAs involved in TGF-β signaling, their functional roles, and their clinical relevance in CRC. We investigate the possibility of ncRNAs as targets for detection, prognosis, and therapy. Additionally, we explore the interaction of TGF-β and other pathways in CRC and the role of ncRNAs within this intricate network. As we unveil the intricate regulatory function of ncRNAs in the TGF-β signaling in CRC, we gain valuable insights into the disease's pathogenesis. Incorporating these discoveries into clinical settings holds promise for more precise diagnosis, prognosis, and targeted therapeutic approaches, ultimately enhancing the care of CRC patients. This comprehensive review underscores the ever-evolving landscape of ncRNA research in CRC and the potential for novel interventions in the battle against this formidable disease.
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Affiliation(s)
- Khalid Saad Alharbi
- Department of Pharmacology and Toxicology, Unaizah College of Pharmacy, Qassim University, Qassim 51452, Saudi Arabia.
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Zhao Q, Li H, Li W, Guo Z, Jia W, Xu S, Chen S, Shen X, Wang C. Identification and verification of a prognostic signature based on a miRNA-mRNA interaction pattern in colon adenocarcinoma. Front Cell Dev Biol 2023; 11:1161667. [PMID: 37745305 PMCID: PMC10511881 DOI: 10.3389/fcell.2023.1161667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 08/04/2023] [Indexed: 09/26/2023] Open
Abstract
The expression characteristics of non-coding RNA (ncRNA) in colon adenocarcinoma (COAD) are involved in regulating various biological processes. To achieve these functions, ncRNA and a member of the Argonaute protein family form an RNA-induced silencing complex (RISC). The RISC is directed by ncRNA, especially microRNA (miRNA), to bind the target complementary mRNAs and regulate their expression by interfering with mRNA cleavage, degradation, or translation. However, how to identify potential miRNA biomarkers and therapeutic targets remains unclear. Here, we performed differential gene screening based on The Cancer Genome Atlas dataset and annotated meaningful differential genes to enrich related biological processes and regulatory cancer pathways. According to the overlap between the screened differential mRNAs and differential miRNAs, a prognosis model based on a least absolute shrinkage and selection operator-based Cox proportional hazards regression analysis can be established to obtain better prognosis characteristics. To further explore the therapeutic potential of miRNA as a target of mRNA intervention, we conducted an immunohistochemical analysis and evaluated the expression level in the tissue microarray of 100 colorectal cancer patients. The results demonstrated that the expression level of POU4F1, DNASE1L2, and WDR72 in the signature was significantly upregulated in COAD and correlated with poor prognosis. Establishing a prognostic signature based on miRNA target genes will help elucidate the molecular pathogenesis of COAD and provide novel potential targets for RNA therapy.
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Affiliation(s)
- Qiwu Zhao
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Haosheng Li
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wenchang Li
- Department of Interventional Radiography, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zichao Guo
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wenqing Jia
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shuiyu Xu
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Sixia Chen
- Tongji Hospital, Tongji University School of Medicine, Tongji University, Shanghai, China
| | - Xiaonan Shen
- Department of Gastroenterology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Changgang Wang
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Wu F, Zhang X, Zhang S, Zhang Y, Feng Y, Jiang Z, Shi Y, Zhang S, Tu W. Construction of an immune-related lncRNA-miRNA-mRNA regulatory network in radiation-induced esophageal injury in rats. Int Immunopharmacol 2023; 122:110606. [PMID: 37423154 DOI: 10.1016/j.intimp.2023.110606] [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: 04/19/2023] [Revised: 06/20/2023] [Accepted: 07/03/2023] [Indexed: 07/11/2023]
Abstract
Radiation-induced esophageal injury (RIEI) is an adverse reaction of radiation therapy in patients with esophageal cancer, lung cancer and other malignant tumors. Competitive endogenous RNA (ceRNA) network is known to play a significant role in the onset and progression of many diseases, but the exact mechanism of ceRNA in RIEI has not been fully elucidated. In this study, rat esophaguses were obtained after conducting irradiation under different doses (0 Gy, 25 Gy, 35 Gy). Total RNA was extracted and mRNA, lncRNA, circRNA, and miRNA sequencing was performed. Multiple dose-dependent differentially expressed RNAs (dd-DERs), including 870 lncRNAs, 82 miRNAs, 2478 mRNAs, were obtained through the integration of differential expression analysis and dose-dependent screening (35 Gy ≥ 25 Gy > 0 Gy, or 35 Gy ≤ 25 Gy < 0 Gy). Co-expression analysis and prediction of the binding site in dd-DER were conducted and 27 lncRNAs, 20 miRNAs, and 168 mRNAs were selected to construct a ceRNA network. As the immune microenvironment is crucial for RIEI progression, we constructed an immune-related ceRNA network consisting of 11 lncRNAs, 9 miRNAs, and 9 mRNAs. The expression levels of these immune-related RNAs were verified by RT-qPCR. Immune infiltration analysis showed that the RNAs in the immune-related ceRNA network were mainly associated with the proportion of monocytes, M2 macrophages, activated NK cells, and activated CD4+ memory T cells. Drug sensitivity analysis was conducted based on the expression levels of mRNAs in the immune-related ceRNA network, and small molecule drugs with preventive and therapeutic effects on RIEI were identified. In summary, an immune-related ceRNA network associated with RIEI progression was constructed in this study. The findings provide useful information on new potential targets for the prevention and treatment of RIEI.
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Affiliation(s)
- Fengping Wu
- Department of Nuclear Medicine, The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu 610051, China
| | - Xiaolin Zhang
- Department of Nuclear Medicine, The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu 610051, China
| | - Shuaijun Zhang
- Laboratory of Radiation Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China; Laboratory of Radiation Medicine, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Yuehua Zhang
- Laboratory of Radiation Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China; Laboratory of Radiation Medicine, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Yahui Feng
- Department of Nuclear Medicine, The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu 610051, China; NHC Key Laboratory of Nuclear Technology Medical Transformation (Mianyang Central Hospital), Mianyang, China
| | - Zhiqiang Jiang
- Department of Nuclear Medicine, The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu 610051, China
| | - Yuhong Shi
- Department of Nuclear Medicine, The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu 610051, China
| | - Shuyu Zhang
- Department of Nuclear Medicine, The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu 610051, China; Laboratory of Radiation Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China; Laboratory of Radiation Medicine, West China Second University Hospital, Sichuan University, Chengdu, China; NHC Key Laboratory of Nuclear Technology Medical Transformation (Mianyang Central Hospital), Mianyang, China.
| | - Wenling Tu
- Department of Nuclear Medicine, The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu 610051, China; School of Bioscience and Technology, Chengdu Medical College, Chengdu, 610500, China; NHC Key Laboratory of Nuclear Technology Medical Transformation (Mianyang Central Hospital), Mianyang, China.
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Shakhpazyan NK, Mikhaleva LM, Bedzhanyan AL, Sadykhov NK, Midiber KY, Konyukova AK, Kontorschikov AS, Maslenkina KS, Orekhov AN. Long Non-Coding RNAs in Colorectal Cancer: Navigating the Intersections of Immunity, Intercellular Communication, and Therapeutic Potential. Biomedicines 2023; 11:2411. [PMID: 37760852 PMCID: PMC10525929 DOI: 10.3390/biomedicines11092411] [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: 07/12/2023] [Revised: 08/18/2023] [Accepted: 08/23/2023] [Indexed: 09/29/2023] Open
Abstract
This comprehensive review elucidates the intricate roles of long non-coding RNAs (lncRNAs) within the colorectal cancer (CRC) microenvironment, intersecting the domains of immunity, intercellular communication, and therapeutic potential. lncRNAs, which are significantly involved in the pathogenesis of CRC, immune evasion, and the treatment response to CRC, have crucial implications in inflammation and serve as promising candidates for novel therapeutic strategies and biomarkers. This review scrutinizes the interaction of lncRNAs with the Consensus Molecular Subtypes (CMSs) of CRC, their complex interplay with the tumor stroma affecting immunity and inflammation, and their conveyance via extracellular vesicles, particularly exosomes. Furthermore, we delve into the intricate relationship between lncRNAs and other non-coding RNAs, including microRNAs and circular RNAs, in mediating cell-to-cell communication within the CRC microenvironment. Lastly, we propose potential strategies to manipulate lncRNAs to enhance anti-tumor immunity, thereby underlining the significance of lncRNAs in devising innovative therapeutic interventions in CRC.
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Affiliation(s)
- Nikolay K. Shakhpazyan
- Avtsyn Research Institute of Human Morphology, Petrovsky National Research Center of Surgery, 119435 Moscow, Russia; (L.M.M.); (N.K.S.); (K.Y.M.); (A.K.K.); (A.S.K.); (K.S.M.); (A.N.O.)
| | - Liudmila M. Mikhaleva
- Avtsyn Research Institute of Human Morphology, Petrovsky National Research Center of Surgery, 119435 Moscow, Russia; (L.M.M.); (N.K.S.); (K.Y.M.); (A.K.K.); (A.S.K.); (K.S.M.); (A.N.O.)
| | - Arcady L. Bedzhanyan
- Department of Abdominal Surgery and Oncology II (Coloproctology and Uro-Gynecology), Petrovsky National Research Center of Surgery, 119435 Moscow, Russia;
| | - Nikolay K. Sadykhov
- Avtsyn Research Institute of Human Morphology, Petrovsky National Research Center of Surgery, 119435 Moscow, Russia; (L.M.M.); (N.K.S.); (K.Y.M.); (A.K.K.); (A.S.K.); (K.S.M.); (A.N.O.)
| | - Konstantin Y. Midiber
- Avtsyn Research Institute of Human Morphology, Petrovsky National Research Center of Surgery, 119435 Moscow, Russia; (L.M.M.); (N.K.S.); (K.Y.M.); (A.K.K.); (A.S.K.); (K.S.M.); (A.N.O.)
| | - Alexandra K. Konyukova
- Avtsyn Research Institute of Human Morphology, Petrovsky National Research Center of Surgery, 119435 Moscow, Russia; (L.M.M.); (N.K.S.); (K.Y.M.); (A.K.K.); (A.S.K.); (K.S.M.); (A.N.O.)
| | - Andrey S. Kontorschikov
- Avtsyn Research Institute of Human Morphology, Petrovsky National Research Center of Surgery, 119435 Moscow, Russia; (L.M.M.); (N.K.S.); (K.Y.M.); (A.K.K.); (A.S.K.); (K.S.M.); (A.N.O.)
| | - Ksenia S. Maslenkina
- Avtsyn Research Institute of Human Morphology, Petrovsky National Research Center of Surgery, 119435 Moscow, Russia; (L.M.M.); (N.K.S.); (K.Y.M.); (A.K.K.); (A.S.K.); (K.S.M.); (A.N.O.)
| | - Alexander N. Orekhov
- Avtsyn Research Institute of Human Morphology, Petrovsky National Research Center of Surgery, 119435 Moscow, Russia; (L.M.M.); (N.K.S.); (K.Y.M.); (A.K.K.); (A.S.K.); (K.S.M.); (A.N.O.)
- Laboratory of Angiopathology, Institute of General Pathology and Pathophysiology, 125315 Moscow, Russia
- Institute for Atherosclerosis Research, 121096 Moscow, Russia
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Ogbonnaya CN, Alsaedi BSO, Alhussaini AJ, Hislop R, Pratt N, Nabi G. Radiogenomics Reveals Correlation between Quantitative Texture Radiomic Features of Biparametric MRI and Hypoxia-Related Gene Expression in Men with Localised Prostate Cancer. J Clin Med 2023; 12:jcm12072605. [PMID: 37048688 PMCID: PMC10095552 DOI: 10.3390/jcm12072605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 03/23/2023] [Accepted: 03/28/2023] [Indexed: 04/14/2023] Open
Abstract
OBJECTIVES To perform multiscale correlation analysis between quantitative texture feature phenotypes of pre-biopsy biparametric MRI (bpMRI) and targeted sequence-based RNA expression for hypoxia-related genes. MATERIALS AND METHODS Images from pre-biopsy 3T bpMRI scans in clinically localised PCa patients of various risk categories (n = 15) were used to extract textural features. The genomic landscape of hypoxia-related gene expression was obtained using post-radical prostatectomy tissue for targeted RNA expression profiling using the TempO-sequence method. The nonparametric Games Howell test was used to correlate the differential expression of the important hypoxia-related genes with 28 radiomic texture features. Then, cBioportal was accessed, and a gene-specific query was executed to extract the Oncoprint genomic output graph of the selected hypoxia-related genes from The Cancer Genome Atlas (TCGA). Based on each selected gene profile, correlation analysis using Pearson's coefficients and survival analysis using Kaplan-Meier estimators were performed. RESULTS The quantitative bpMR imaging textural features, including the histogram and grey level co-occurrence matrix (GLCM), correlated with three hypoxia-related genes (ANGPTL4, VEGFA, and P4HA1) based on RNA sequencing using the TempO-Seq method. Further radiogenomic analysis, including data accessed from the cBioportal genomic database, confirmed that overexpressed hypoxia-related genes significantly correlated with a poor survival outcomes, with a median survival ratio of 81.11:133.00 months in those with and without alterations in genes, respectively. CONCLUSION This study found that there is a correlation between the radiomic texture features extracted from bpMRI in localised prostate cancer and the hypoxia-related genes that are differentially expressed. The analysis of expression data based on cBioportal revealed that these hypoxia-related genes, which were the focus of the study, are linked to an unfavourable survival outcomes in prostate cancer patients.
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Affiliation(s)
- Chidozie N Ogbonnaya
- Division of Imaging Science and Technology, University of Dundee, Dundee DD1 4HN, UK
- College of Basic Medical Sciences, Abia State University, Uturu 441103, Nigeria
| | - Basim S O Alsaedi
- Statistics Department, University of Tabuk, Tabuk 47512, Saudi Arabia
| | - Abeer J Alhussaini
- Division of Imaging Science and Technology, University of Dundee, Dundee DD1 4HN, UK
- Department of Medical Imaging, Al-Amiri Hospital, Ministry of Health, Sulaibikhat 1300, Kuwait
| | - Robert Hislop
- Cytogenetic, Human Genetics Unit, Ninewells Hospital and Medical School, Dundee DD1 9SY, UK
| | - Norman Pratt
- Cytogenetic, Human Genetics Unit, Ninewells Hospital and Medical School, Dundee DD1 9SY, UK
| | - Ghulam Nabi
- Division of Imaging Science and Technology, University of Dundee, Dundee DD1 4HN, UK
- School of Medicine, Ninewells Hospital, Dundee DD1 9SY, UK
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