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Abd El Fattah YK, Abulsoud AI, AbdelHamid SG, AbdelHalim S, Hamdy NM. CCDC144NL-AS1/hsa-miR-143-3p/HMGA2 interaction: In-silico and clinically implicated in CRC progression, correlated to tumor stage and size in case-controlled study; step toward ncRNA precision. Int J Biol Macromol 2023; 253:126739. [PMID: 37690651 DOI: 10.1016/j.ijbiomac.2023.126739] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 08/06/2023] [Accepted: 08/25/2023] [Indexed: 09/12/2023]
Abstract
Unravel the regulatory mechanism of lncRNA CCDC144NL-AS1 in CRC hsa-miR-143-3p, downstream protein HMGA2 interaction arm, association with clinicopathological characteristics. Using peripheral blood as liquid biopsy from 60 CRC patients and 30 controls. The expression levels of CCDC144NL-AS1 and hsa-miR-143-3p detected by qRT-PCR. CCDC144NL-AS1 expression was significantly upregulated in CRC patients' sera, associated with worse CRC clinicopathological features regarding the depth of tumor invasion and highly significant difference between tumor stages 3 and 4 and tumor stages 2 and 4. While, hsa-miR-143-3p expression was downregulated in CRC patients by 4.5-fold change when compared to the control subjects (p < 0.0001) and HMGA2 increased in CRC patients than controls 19.59 ng/μL and 5.377 ng/μL, respectively (p < 0.0001) with significant difference between tumor stages 3 and 4 as well as tumor stages 2 and 4. CRC patients with large tumor size showed upregulation in CCDC144NL-AS1 expression and HMGA2 levels compared to those with small tumor size (p-value = 0.0365 and 0.013, respectively). CCDC144NL-AS1 and HMGA2 were positively correlated, whereas lncRNA CCDC144NL-AS1 and hsa-miR-143-3p were negatively correlated. Conclusion: As an interaction arm CCDC144NL-AS1/hsa-miR-143-3p/HMGA2 were correlated to CRC stages 2-4. Therefore, this interaction arm expression clinically and in silico approved, would direct treatment precision in the near future.
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Affiliation(s)
- Yasmine K Abd El Fattah
- Biochemistry Department, Faculty of Pharmacy, Heliopolis University, El Salam City, 11785, Cairo, Egypt
| | - Ahmed I Abulsoud
- Biochemistry Department, Faculty of Pharmacy, Heliopolis University, El Salam City, 11785, Cairo, Egypt; Biochemistry Department, Faculty of Pharmacy (Boy's Branch), Al-Azhar University, Nasr City, 11884, Cairo, Egypt
| | - Sherihan G AbdelHamid
- Biochemistry Department, Faculty of Pharmacy, Ain Shams University, Abbassia, 11566, Cairo, Egypt
| | - Sherif AbdelHalim
- Department of General surgery, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Nadia M Hamdy
- Biochemistry Department, Faculty of Pharmacy, Ain Shams University, Abbassia, 11566, Cairo, Egypt.
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2
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Shi W, Ling L, Li C, Wu R, Zhang M, Shao F, Wang Y. LncRNA UCA1 promoted cisplatin resistance in lung adenocarcinoma with HO1 targets NRF2/HO1 pathway. J Cancer Res Clin Oncol 2023; 149:1295-1311. [PMID: 35792913 DOI: 10.1007/s00432-022-04152-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/13/2022] [Indexed: 01/05/2023]
Abstract
PURPOSE Our previous experiments have demonstrated that lncRNA UCA1 (UCA1) promoted cisplatin resistance in lung adenocarcinoma (LUAD). This study aimed to explore the potential downstream target genes regulated by UCA1 and how this downstream gene promotes cisplatin resistance in LUAD. METHODS Here, we measured the expression level of Heme oxygenase1 (HO1) in LUAD cell lines by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) based on UCA1 overexpression cell lines and UCA1 knockdown cell lines. HO1 was knocked down in the UCA1 overexpression cell line, and HO1 was overexpressed in the UCA1 knockdown cell line, and the half maximal inhibitory concentration (IC50) trends were observed by adding cisplatin containing a certain concentration gradient. Cell functional assays were performed to observe the changes in the biological behavior of HO1 after overexpression and knockdown, and the tumorigenic assay in nude mice was performed to verify the effect of UCA1 in regulating the growth and cisplatin resistance of HO1 on LUAD cells in vivo. RESULTS The results showed that HO1 and UCA1 expression were both upregulated in LUAD tissues and LUAD cisplatin-resistant cell lines, and there was a significant positive correlation between the expression of HO1 and UCA1. In vitro experiments showed that HO1 overexpression could reverse the reduced sensitivity to cisplatin caused by UCA1 knockdown in A549/DDP cells, and HO1 knockdown could reduce cisplatin resistance in A549 UCA1 overexpressing cells. Tumorigenic assays in nude mice further confirmed the role of HO1 in the regulation of UCA1 by activating the NRF2/HO1 pathway against LUAD cisplatin resistance. CONCLUSION Our findings suggested that UCA1 regulates HO1 targets the UCA1/NRF2-HO1 pathway to exert cisplatin resistance in LUAD.
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Affiliation(s)
- Wenjing Shi
- Department of Laboratory Medicine, Key Laboratory of Clinical Laboratory Diagnosis and Translation Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Nanbaixiang Street, Ouhai District, Wenzhou, 325000, Zhejiang Province, China
| | - Liqun Ling
- Department of Laboratory Medicine, Key Laboratory of Clinical Laboratory Diagnosis and Translation Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Nanbaixiang Street, Ouhai District, Wenzhou, 325000, Zhejiang Province, China
| | - Changhong Li
- Department of Laboratory Medicine, Key Laboratory of Clinical Laboratory Diagnosis and Translation Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Nanbaixiang Street, Ouhai District, Wenzhou, 325000, Zhejiang Province, China
| | - Ruihao Wu
- Department of Laboratory Medicine, Key Laboratory of Clinical Laboratory Diagnosis and Translation Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Nanbaixiang Street, Ouhai District, Wenzhou, 325000, Zhejiang Province, China
| | - Meijuan Zhang
- Department of Laboratory Medicine, Key Laboratory of Clinical Laboratory Diagnosis and Translation Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Nanbaixiang Street, Ouhai District, Wenzhou, 325000, Zhejiang Province, China
| | - Fanggui Shao
- Department of Laboratory Medicine, Key Laboratory of Clinical Laboratory Diagnosis and Translation Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Nanbaixiang Street, Ouhai District, Wenzhou, 325000, Zhejiang Province, China
| | - Yumin Wang
- Department of Laboratory Medicine, Key Laboratory of Clinical Laboratory Diagnosis and Translation Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Nanbaixiang Street, Ouhai District, Wenzhou, 325000, Zhejiang Province, China.
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Role of Long Intergenic Noncoding RNAs in Cancers with an Overview of MicroRNA Binding. Mol Diagn Ther 2023; 27:29-47. [PMID: 36287372 PMCID: PMC9813052 DOI: 10.1007/s40291-022-00619-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2022] [Indexed: 02/04/2023]
Abstract
Long intergenic noncoding RNAs are transcripts originating from the regions without annotated coding genes. They are located mainly in the nucleus and regulate gene expression. Long intergenic noncoding RNAs can be also found in the cytoplasm acting as molecular sponges of certain microRNAs. This is crucial in various biological and signaling pathways. Expression levels of many long intergenic noncoding RNAs are disease related. In this article, we focus on the long intergenic noncoding RNAs and their relation to different types of cancer. Studies showed that abnormal expression of long intergenic noncoding RNA deregulates signaling pathways due to the disrupted free microRNA pool. Hampered signaling pathways leads to abnormal cell proliferation and restricts cell death, thus resulting in oncogenesis. This review highlights promising therapeutic targets and enables the identification of potential biomarkers specific for a certain type of cancer. Moreover, we provide an outline of long intergenic noncoding RNAs/microRNA axes, which might be applied in further detailed experiments broadening our knowledge about the cellular role of those RNA species.
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Snyder M, Iraola-Guzmán S, Saus E, Gabaldón T. Discovery and Validation of Clinically Relevant Long Non-Coding RNAs in Colorectal Cancer. Cancers (Basel) 2022; 14:cancers14163866. [PMID: 36010859 PMCID: PMC9405614 DOI: 10.3390/cancers14163866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/04/2022] [Accepted: 08/04/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Recent efforts in biomedical research have focused on the identification of molecular biomarkers to improve the diagnosis, prognosis and eventually treatment of the most common human diseases worldwide, including cancer. In this context, a large number of studies point to a pivotal role of long non-coding RNAs (lncRNAs) in the pathophysiology of carcinogenesis, suggesting diagnostic or therapeutic potential. However, for most of them, supporting evidence is scarce and often based on a single large-scale analysis. Here, focusing on colorectal cancer (CRC), we present an overview of the main approaches for discovering and validating lncRNA candidate molecules, and provide a curated list of the most promising lncRNAs associated with this malignancy. Abstract Colorectal cancer (CRC) is the third most prevalent cancer worldwide, with nearly two million newly diagnosed cases each year. The survival of patients with CRC greatly depends on the cancer stage at the time of diagnosis, with worse prognosis for more advanced cases. Consequently, considerable effort has been directed towards improving population screening programs for early diagnosis and identifying prognostic markers that can better inform treatment strategies. In recent years, long non-coding RNAs (lncRNAs) have been recognized as promising molecules, with diagnostic and prognostic potential in many cancers, including CRC. Although large-scale genome and transcriptome sequencing surveys have identified many lncRNAs that are altered in CRC, most of their roles in disease onset and progression remain poorly understood. Here, we critically review the variety of detection methods and types of supporting evidence for the involvement of lncRNAs in CRC. In addition, we provide a reference catalog that features the most clinically relevant lncRNAs in CRC. These lncRNAs were selected based on recent studies sorted by stringent criteria for both supporting experimental evidence and reproducibility.
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Affiliation(s)
- Madison Snyder
- Barcelona Supercomputing Centre (BSC-CNS), Plaça Eusebi Güell, 1-3, 08034 Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Susana Iraola-Guzmán
- Barcelona Supercomputing Centre (BSC-CNS), Plaça Eusebi Güell, 1-3, 08034 Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Ester Saus
- Barcelona Supercomputing Centre (BSC-CNS), Plaça Eusebi Güell, 1-3, 08034 Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Toni Gabaldón
- Barcelona Supercomputing Centre (BSC-CNS), Plaça Eusebi Güell, 1-3, 08034 Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
- Centro de Investigación Biomédica En Red de Enfermedades Infecciosas (CIBERINFEC), 08028 Barcelona, Spain
- Correspondence:
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5
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Blood-derived lncRNAs as biomarkers for cancer diagnosis: the Good, the Bad and the Beauty. NPJ Precis Oncol 2022; 6:40. [PMID: 35729321 PMCID: PMC9213432 DOI: 10.1038/s41698-022-00283-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 05/13/2022] [Indexed: 11/24/2022] Open
Abstract
Cancer ranks as one of the deadliest diseases worldwide. The high mortality rate associated with cancer is partially due to the lack of reliable early detection methods and/or inaccurate diagnostic tools such as certain protein biomarkers. Cell-free nucleic acids (cfNA) such as circulating long noncoding RNAs (lncRNAs) have been proposed as a new class of potential biomarkers for cancer diagnosis. The reported correlation between the presence of tumors and abnormal levels of lncRNAs in the blood of cancer patients has notably triggered a worldwide interest among clinicians and oncologists who have been actively investigating their potentials as reliable cancer biomarkers. In this report, we review the progress achieved (“the Good”) and challenges encountered (“the Bad”) in the development of circulating lncRNAs as potential biomarkers for early cancer diagnosis. We report and discuss the diagnostic performance of more than 50 different circulating lncRNAs and emphasize their numerous potential clinical applications (“the Beauty”) including therapeutic targets and agents, on top of diagnostic and prognostic capabilities. This review also summarizes the best methods of investigation and provides useful guidelines for clinicians and scientists who desire conducting their own clinical studies on circulating lncRNAs in cancer patients via RT-qPCR or Next Generation Sequencing (NGS).
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García-Padilla C, Dueñas Á, García-López V, Aránega A, Franco D, Garcia-Martínez V, López-Sánchez C. Molecular Mechanisms of lncRNAs in the Dependent Regulation of Cancer and Their Potential Therapeutic Use. Int J Mol Sci 2022; 23:764. [PMID: 35054945 PMCID: PMC8776057 DOI: 10.3390/ijms23020764] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 12/31/2021] [Accepted: 01/08/2022] [Indexed: 12/16/2022] Open
Abstract
Deep whole genome and transcriptome sequencing have highlighted the importance of an emerging class of non-coding RNA longer than 200 nucleotides (i.e., long non-coding RNAs (lncRNAs)) that are involved in multiple cellular processes such as cell differentiation, embryonic development, and tissue homeostasis. Cancer is a prime example derived from a loss of homeostasis, primarily caused by genetic alterations both in the genomic and epigenetic landscape, which results in deregulation of the gene networks. Deregulation of the expression of many lncRNAs in samples, tissues or patients has been pointed out as a molecular regulator in carcinogenesis, with them acting as oncogenes or tumor suppressor genes. Herein, we summarize the distinct molecular regulatory mechanisms described in literature in which lncRNAs modulate carcinogenesis, emphasizing epigenetic and genetic alterations in particular. Furthermore, we also reviewed the current strategies used to block lncRNA oncogenic functions and their usefulness as potential therapeutic targets in several carcinomas.
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Affiliation(s)
- Carlos García-Padilla
- Department of Experimental Biology, University of Jaen, 23071 Jaen, Spain; (Á.D.); (A.A.); (D.F.)
- Department of Human Anatomy and Embryology, University of Extremadura, 06006 Badajoz, Spain; (V.G.-L.); (V.G.-M.)
- Institute of Molecular Pathology Biomarkers, University of Extremadura, 06006 Badajoz, Spain
| | - Ángel Dueñas
- Department of Experimental Biology, University of Jaen, 23071 Jaen, Spain; (Á.D.); (A.A.); (D.F.)
- Department of Human Anatomy and Embryology, University of Extremadura, 06006 Badajoz, Spain; (V.G.-L.); (V.G.-M.)
- Institute of Molecular Pathology Biomarkers, University of Extremadura, 06006 Badajoz, Spain
| | - Virginio García-López
- Department of Human Anatomy and Embryology, University of Extremadura, 06006 Badajoz, Spain; (V.G.-L.); (V.G.-M.)
- Institute of Molecular Pathology Biomarkers, University of Extremadura, 06006 Badajoz, Spain
| | - Amelia Aránega
- Department of Experimental Biology, University of Jaen, 23071 Jaen, Spain; (Á.D.); (A.A.); (D.F.)
- Fundación Medina, 18016 Granada, Spain
| | - Diego Franco
- Department of Experimental Biology, University of Jaen, 23071 Jaen, Spain; (Á.D.); (A.A.); (D.F.)
- Fundación Medina, 18016 Granada, Spain
| | - Virginio Garcia-Martínez
- Department of Human Anatomy and Embryology, University of Extremadura, 06006 Badajoz, Spain; (V.G.-L.); (V.G.-M.)
- Institute of Molecular Pathology Biomarkers, University of Extremadura, 06006 Badajoz, Spain
| | - Carmen López-Sánchez
- Department of Human Anatomy and Embryology, University of Extremadura, 06006 Badajoz, Spain; (V.G.-L.); (V.G.-M.)
- Institute of Molecular Pathology Biomarkers, University of Extremadura, 06006 Badajoz, Spain
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