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Lin Y, Zhao W, Lv Z, Xie H, Li Y, Zhang Z. The functions and mechanisms of long non-coding RNA in colorectal cancer. Front Oncol 2024; 14:1419972. [PMID: 39026978 PMCID: PMC11254705 DOI: 10.3389/fonc.2024.1419972] [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: 04/19/2024] [Accepted: 06/18/2024] [Indexed: 07/20/2024] Open
Abstract
CRC poses a significant challenge in the global health domain, with a high number of deaths attributed to this disease annually. If CRC is detected only in its advanced stages, the difficulty of treatment increases significantly. Therefore, biomarkers for the early detection of CRC play a crucial role in improving patient outcomes and increasing survival rates. The development of a reliable biomarker for early detection of CRC is particularly important for timely diagnosis and treatment. However, current methods for CRC detection, such as endoscopic examination, blood, and stool tests, have certain limitations and often only detect cases in the late stages. To overcome these constraints, researchers have turned their attention to molecular biomarkers, which are considered a promising approach to improving CRC detection. Non-invasive methods using biomarkers such as mRNA, circulating cell-free DNA, microRNA, LncRNA, and proteins can provide more reliable diagnostic information. These biomarkers can be found in blood, tissue, stool, and volatile organic compounds. Identifying molecular biomarkers with high sensitivity and specificity for the early and safe, economic, and easily measurable detection of CRC remains a significant challenge for researchers.
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Affiliation(s)
- Yuning Lin
- Medical Laboratory, Xiamen Humanity Hospital, Fujian Medical University, Xiamen, China
| | - Wenzhen Zhao
- Medical Laboratory, Xiamen Humanity Hospital, Fujian Medical University, Xiamen, China
| | - Zhenyi Lv
- Medical Laboratory, Xiamen Humanity Hospital, Fujian Medical University, Xiamen, China
| | - Hongyan Xie
- Medical Laboratory, Xiamen Humanity Hospital, Fujian Medical University, Xiamen, China
| | - Ying Li
- Ultrasonography Department, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen, China
| | - Zhongying Zhang
- Medical Laboratory, Xiamen Humanity Hospital, Fujian Medical University, Xiamen, China
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Wang Z, Wang R, Niu L, Zhou X, Han J, Li K. EPB41L4A-AS1 is required to maintain basal autophagy to modulates Aβ clearance. NPJ AGING 2024; 10:24. [PMID: 38704365 PMCID: PMC11069514 DOI: 10.1038/s41514-024-00152-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 04/22/2024] [Indexed: 05/06/2024]
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disorder characterized by the deposition of β-amyloid (Aβ) plaques. Aβ is generated from the cleavage of the amyloid precursor protein by β and γ-secretases and cleared by neuroglial cells mediated autophagy. The imbalance of the intracellular Aβ generation and clearance is the causative factor for AD pathogenesis. However, the exact underlying molecular mechanisms remain unclear. Our previous study reported that EPB41L4A-AS1 is an aging-related long non-coding RNA (lncRNA) that is repressed in patients with AD. In this study, we found that downregulated EPB41L4A-AS1 in AD inhibited neuroglial cells mediated-Aβ clearance by decreasing the expression levels of multiple autophagy-related genes. We found that EPB41L4A-AS1 regulates the expression of general control of amino acid synthesis 5-like 2, an important histone acetyltransferase, thus affecting histone acetylation, crotonylation, and lactylation near the transcription start site of autophagy-related genes, ultimately influencing their transcription. Collectively, this study reveals EPB41L4A-AS1 as an AD-related lncRNA via mediating Aβ clearance and provides insights into the epigenetic regulatory mechanism of EPB41L4A-AS1 in gene expression and AD pathogenesis.
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Affiliation(s)
- Ziqiang Wang
- Department of Nuclear Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, 250014, China.
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250062, China.
| | - Ruomei Wang
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250062, China
| | - Lixin Niu
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250062, China
| | - Xiaoyan Zhou
- Department of Nuclear Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, 250014, China
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250062, China
| | - Jinxiang Han
- Department of Nuclear Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, 250014, China.
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250062, China.
| | - Kun Li
- Department of Nuclear Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, 250014, China.
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3
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Su T, Trang N, Zhu J, Kong L, Cheung D, Chou V, Ellis L, Huang C, Camden N, McHugh CA. GRAS1 non-coding RNA protects against DNA damage and cell death by binding and stabilizing NKAP. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.20.545783. [PMID: 38645172 PMCID: PMC11030241 DOI: 10.1101/2023.06.20.545783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Non-coding RNA (ncRNA) gene products are involved in diverse biological processes including splicing, epigenetic regulation, gene expression, proliferation, and metabolism. The biological mechanisms by which ncRNAs contribute to cell survival remain poorly understood. We found that the Growth Regulator Antisense 1 (GRAS1) long non-coding RNA (lncRNA) transcript promotes growth in multiple human cell types by protecting against DNA damage. Knockdown of GRAS1 induced DNA damage and cell death, along with significant expression changes in DNA damage response, intrinsic apoptotic signaling, and cellular response to environmental stimulus genes. Extensive DNA damage occurred after GRAS1 knockdown, with numerous double strand breaks occurring in each cell. The number of cells undergoing apoptosis and with fragmented nuclei increased significantly after GRAS1 knockdown. We used RNA antisense purification and mass spectrometry (RAP-MS) to identify the NF-κB activating protein (NKAP) as a direct protein interaction partner of GRAS1 lncRNA. NKAP protein was degraded after GRAS1 knockdown, in a proteasome-dependent manner. Overexpression of GRAS1 or NKAP mitigated the DNA damage effects of GRAS1 knockdown. In summary, GRAS1 and NKAP directly interact to protect against DNA damage and cell death in multiple human cell lines.
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Affiliation(s)
| | | | - Jonathan Zhu
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
| | - Lingbo Kong
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
| | - Darin Cheung
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
| | - Vita Chou
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
| | - Lauren Ellis
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
| | - Calvin Huang
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
| | - Nichelle Camden
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
| | - Colleen A. McHugh
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
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Khattab RH, Abo-Hammam RH, Salah M, Hanora AM, Shabayek S, Zakeer S. Multi-omics analysis of fecal samples in colorectal cancer Egyptians patients: a pilot study. BMC Microbiol 2023; 23:238. [PMID: 37644393 PMCID: PMC10464353 DOI: 10.1186/s12866-023-02991-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 08/21/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is a public health concern and the second most common disease worldwide. This is due to genetic coding and is influenced by environmental aspects, in which the gut microbiota plays a significant role. The purpose of this study was to compare the microbiota makeup of CRC patients with that of healthy control and to identify upregulated and downregulated proteins and metabolites in CRC patients. Using a next-generation sequencing approach, fecal samples of five females (4 CRC patients and one healthy control) were analyzed by BGI DNBSEQ-T7, Hong Kong, China. Furthermore, proteomics and metabolomics analysis were performed using LC-MS/MS technique. RESULTS Dysbiosis of gut microbiota has been observed in patients with CRC, with an increase in microbiota diversity at all taxonomic levels relative to healthy control. Where, at the functional level the bacterial species participate in many different pathways among them de novo nucleotide synthesis and amino acids pathways were aberrantly upregulated in CRC patients. Proteomics and metabolomics profiles of CRC patients showed different proteins and metabolites, a total of 360 and 158 proteins and metabolites, respectively were highly expressed compared to healthy control with fold change ≥ 1.2. Among the highly expressed proteins were transketolase, sushi domain-containing protein, sulfide quinone oxidoreductase protein, AAA family ATPase protein, carbonic anhydrase, IgG Fc-binding protein, nucleoside diphosphate kinase protein, arylsulfatase, alkaline phosphatase protein, phosphoglycerate kinase, protein kinase domain-containing protein, non-specific serine/threonine protein kinase, Acyl-CoA synthetase and EF-hand domain-containing protein. Some of the differential metabolites, Taurine, Taurocholic acid, 7-ketodeoxycholic acid, Glycochenodeoxycholic acid, Glycocholic acid, and Taurochenodeoxycholic acid that belong to bile acids metabolites. CONCLUSIONS Some bacterial species, proteins, and metabolites could be used as diagnostic biomarkers for CRC. Our study paves an insight into using multi-omics technology to address the relationship between gut microbiota and CRC.
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Affiliation(s)
- Randa H Khattab
- Department of Microbiology and Immunology, Al-Salam University, Tanta, Egypt
| | - Rana H Abo-Hammam
- Forensic toxicologist and narcotics expert, Ministry of Justice, Tanta, Egypt
| | - Mohammed Salah
- Department of Microbiology and Immunology, Faculty of pharmacy, Port-Said University, Port-Said, Egypt
| | - Amro M Hanora
- Department of Microbiology and Immunology, Faculty of pharmacy, Suez Canal University, Ismailia, Egypt.
| | - Sarah Shabayek
- Department of Microbiology and Immunology, Faculty of pharmacy, Suez Canal University, Ismailia, Egypt
| | - Samira Zakeer
- Department of Microbiology and Immunology, Faculty of pharmacy, Suez Canal University, Ismailia, Egypt
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Chen GR, Zhang YB, Zheng SF, Xu YW, Lin P, Shang-Guan HC, Lin YX, Kang DZ, Yao PS. Decreased SPTBN2 expression regulated by the ceRNA network is associated with poor prognosis and immune infiltration in low‑grade glioma. Exp Ther Med 2023; 25:253. [PMID: 37153896 PMCID: PMC10161196 DOI: 10.3892/etm.2023.11952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 02/24/2023] [Indexed: 05/10/2023] Open
Abstract
The majority of low-grade gliomas (LGGs) in adults invariably progress to glioblastoma over time. Spectrin β non-erythrocytic 2 (SPTBN2) is detected in numerous tumors and is involved in tumor occurrence and metastasis. However, the specific roles and detailed mechanisms of SPTBN2 in LGG are largely unknown. The present study performed pan-cancer analysis for the expression and prognosis of SPTBN2 in LGG using The Cancer Genome Atlas and The Genotype-Tissue Expression. Western blotting was used to detect the amount of SPTBN2 between glioma tissues and normal brain tissues. Subsequently, based on expression, prognosis, correlation and immune infiltration, non-coding RNAs (ncRNAs) were identified that regulated SPTBN2 expression. Finally, tumor immune infiltrates associated with SPTBN2 and prognosis were performed. Lower expression of SPTBN2 was correlated with an unfavorable outcome in LGG. A significant correlation between the low SPTBN2 mRNA expression and poor clinicopathological features was observed, including wild-type isocitrate dehydrogenase status (P<0.001), 1p/19q non-codeletion (P<0.001) and elders (P=0.019). The western blotting results revealed that, compared with normal brain tissues, the amount of SPTBN2 was significantly lower in LGG tissues (P=0.0266). Higher expression of five microRNAs (miRs/miRNAs), including hsa-miR-15a-5p, hsa-miR-15b-5p, hsa-miR-16-5p, hsa-miR-34c-5p and hsa-miR-424-5p, correlated with poor prognosis by targeting SPTBN2 in LGG. Subsequently, four long ncRNAs (lncRNAs) [ARMCX5-GPRASP2, BASP1-antisense RNA 1 (AS1), EPB41L4A-AS1 and LINC00641] were observed in the regulation of SPTBN2 via five miRNAs. Moreover, the expression of SPTBN2 was significantly correlated with tumor immune infiltration, immune checkpoint expression and biomarkers of immune cells. In conclusion, SPTBN2 was lowly expressed and correlated with an unfavorable prognosis in LGG. A total of six miRNAs and four lncRNAs were identified as being able to modulate SPTBN2 in a lncRNA-miRNA-mRNA network of LGG. Furthermore, the current findings also indicated that SPTBN2 possessed anti-tumor roles by regulating tumor immune infiltration and immune checkpoint expression.
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Affiliation(s)
- Guo-Rong Chen
- Department of Neurosurgery, Neurosurgical Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350005, P.R. China
- Department of Neurosurgery, National Regional Medical Center, Binhai Campus of The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350212, P.R. China
| | - Yi-Bin Zhang
- Department of Neurosurgery, Neurosurgical Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350005, P.R. China
- Department of Neurosurgery, National Regional Medical Center, Binhai Campus of The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350212, P.R. China
| | - Shu-Fa Zheng
- Department of Neurosurgery, Neurosurgical Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350005, P.R. China
- Department of Neurosurgery, National Regional Medical Center, Binhai Campus of The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350212, P.R. China
| | - Ya-Wen Xu
- Department of Neurosurgery, Neurosurgical Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350005, P.R. China
- Department of Neurosurgery, National Regional Medical Center, Binhai Campus of The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350212, P.R. China
| | - Peng Lin
- Department of Pain, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350005, P.R. China
| | - Huang-Cheng Shang-Guan
- Department of Neurosurgery, Neurosurgical Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350005, P.R. China
- Department of Neurosurgery, National Regional Medical Center, Binhai Campus of The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350212, P.R. China
| | - Yuan-Xiang Lin
- Department of Neurosurgery, Neurosurgical Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350005, P.R. China
- Fujian Key Laboratory of Precision Medicine for Cancer, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350005, P.R. China
| | - De-Zhi Kang
- Department of Neurosurgery, Neurosurgical Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350005, P.R. China
- Department of Neurosurgery, National Regional Medical Center, Binhai Campus of The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350212, P.R. China
- Fujian Key Laboratory of Precision Medicine for Cancer, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350005, P.R. China
- Key Laboratory of Radiation Biology of Fujian Higher Education Institutions, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350005, P.R. China
- Fujian Provincial Institutes of Brain Disorders and Brain Sciences, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350005, P.R. China
- Correspondence to: Professor De-Zhi Kang or Dr Pei-Sen Yao, Department of Neurosurgery, Neurosurgical Research Institute, The First Affiliated Hospital, Fujian Medical University, 20 Chazhong Road, Taijiang, Fuzhou, Fujian 350005, P.R. China
| | - Pei-Sen Yao
- Department of Neurosurgery, Neurosurgical Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350005, P.R. China
- Department of Neurosurgery, National Regional Medical Center, Binhai Campus of The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350212, P.R. China
- Correspondence to: Professor De-Zhi Kang or Dr Pei-Sen Yao, Department of Neurosurgery, Neurosurgical Research Institute, The First Affiliated Hospital, Fujian Medical University, 20 Chazhong Road, Taijiang, Fuzhou, Fujian 350005, P.R. China
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Mokhtari K, Peymani M, Rashidi M, Hushmandi K, Ghaedi K, Taheriazam A, Hashemi M. Colon cancer transcriptome. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2023; 180-181:49-82. [PMID: 37059270 DOI: 10.1016/j.pbiomolbio.2023.04.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/31/2023] [Accepted: 04/06/2023] [Indexed: 04/16/2023]
Abstract
Over the last four decades, methodological innovations have continuously changed transcriptome profiling. It is now feasible to sequence and quantify the transcriptional outputs of individual cells or thousands of samples using RNA sequencing (RNA-seq). These transcriptomes serve as a connection between cellular behaviors and their underlying molecular mechanisms, such as mutations. This relationship, in the context of cancer, provides a chance to unravel tumor complexity and heterogeneity and uncover novel biomarkers or treatment options. Since colon cancer is one of the most frequent malignancies, its prognosis and diagnosis seem to be critical. The transcriptome technology is developing for an earlier and more accurate diagnosis of cancer which can provide better protectivity and prognostic utility to medical teams and patients. A transcriptome is a whole set of expressed coding and non-coding RNAs in an individual or cell population. The cancer transcriptome includes RNA-based changes. The combined genome and transcriptome of a patient may provide a comprehensive picture of their cancer, and this information is beginning to affect treatment decision-making in real-time. A full assessment of the transcriptome of colon (colorectal) cancer has been assessed in this review paper based on risk factors such as age, obesity, gender, alcohol use, race, and also different stages of cancer, as well as non-coding RNAs like circRNAs, miRNAs, lncRNAs, and siRNAs. Similarly, they have been examined independently in the transcriptome study of colon cancer.
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Affiliation(s)
- Khatere Mokhtari
- Department of Modern Biology, ACECR Institute of Higher Education (Isfahan Branch), Isfahan, Iran
| | - Maryam Peymani
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran.
| | - Mohsen Rashidi
- Department Pharmacology, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, 4815733971, Iran; The Health of Plant and Livestock Products Research Center, Mazandaran University of Medical Sciences, Sari, 4815733971, Iran
| | - Kiavash Hushmandi
- Department of Food Hygiene and Quality Control, Division of Epidemiology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Kamran Ghaedi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran.
| | - Afshin Taheriazam
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Orthopedics, Faculty of Medicine, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
| | - Mehrdad Hashemi
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
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Yan Y, Liu X, Li Y, Yan J, Zhao P, Yang L. EPB41L4A-AS1 and UNC5B-AS1 have diagnostic and prognostic significance in osteosarcoma. J Orthop Surg Res 2023; 18:261. [PMID: 36998043 PMCID: PMC10064547 DOI: 10.1186/s13018-023-03754-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 03/24/2023] [Indexed: 04/01/2023] Open
Abstract
BACKGROUND Deregulation of lncRNAs has been observed in human osteosarcoma. This study explored the diagnostic and prognostic significance of EPB41L4A-AS1 and UNC5B-AS1 in osteosarcoma. METHODS Relative levels of EPB41L4A-AS1 and UNC5B-AS1 were detected in osteosarcoma tissue samples and cells. The ability to distinguish osteosarcoma from health was assessed by receiver operating characteristic (ROC) curve construction. Kaplan-Meier (K-M) and Cox proportional-hazards analyses were performed for prognosis factors. The bioinformatics approach was used to identify targeting miRNA for EPB41L4A-AS1 and UNC5B-AS1. Kaplan-Meier survival curves and Whitney Mann U tests were conducted for validating the statistical significance. In cell culture experiments, the influence of EPB41L4A-AS1 and UNC5B-AS1 on proliferation, migration, and invasion of the osteosarcoma cell line was examined by CCK-8 and Transwell assays. RESULTS Levels of EPB41L4A-AS1 and UNC5B-AS1 were upregulated in osteosarcoma patients and cells compared with the healthy participants and normal cell lines. EPB41L4A-AS1 and UNC5B-AS1 have a potent ability to distinguish the patients with osteosarcoma from the health. EPB41L4A-AS1 and UNC5B-AS1 levels correlated with SSS stage. Patients with high levels of EPB41L4A-AS1 and UNC5B-AS1 had significantly shorter survival times. EPB41L4A-AS1 and UNC5B-AS1 were independent prognostic indexes for overall survival. miR-1306-5p was a common target for EPB41L4A-AS1 and UNC5B-AS1. A propulsive impact on cell proliferation, migration, and invasion by EPB41L4A-AS1 and UNC5B-AS1 was observed, but can be rescued by miR-1306-5p. CONCLUSIONS It was concluded that upregulations of EPB41L4A-AS1 and UNC5B-AS1 expression were diagnostic and prognostic biomarkers for human osteosarcoma. EPB41L4A-AS1 and UNC5B-AS1 contribute to the biological behavior of osteosarcoma via miR-1306-5p.
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Affiliation(s)
- Ying Yan
- Shanghai Baoshan Center for Disease Control and Prevention, Shanghai, 201901, China
| | - Xiaochuan Liu
- Clinical Research Center, Shanghai Baoshan Luodian Hospital, No. 121 Luoxi Road, Baoshan District, Shanghai, 201908, China
| | - Yamei Li
- Clinical Research Center, Shanghai Baoshan Luodian Hospital, No. 121 Luoxi Road, Baoshan District, Shanghai, 201908, China
| | - Jingyi Yan
- Juquan New Town Community Health Service Center, Gucun Town, Baoshan District, Shanghai, 201907, China
| | - Ping Zhao
- Clinical Research Center, Shanghai Baoshan Luodian Hospital, No. 121 Luoxi Road, Baoshan District, Shanghai, 201908, China.
| | - Lu Yang
- Clinical Research Center, Shanghai Baoshan Luodian Hospital, No. 121 Luoxi Road, Baoshan District, Shanghai, 201908, China.
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Zhang H, Liu Y, Wang W, Liu F, Wang W, Su C, Zhu H, Liao Z, Zhang B, Chen X. ALKBH5-mediated m 6A modification of lincRNA LINC02551 enhances the stability of DDX24 to promote hepatocellular carcinoma growth and metastasis. Cell Death Dis 2022; 13:926. [PMID: 36335087 PMCID: PMC9637195 DOI: 10.1038/s41419-022-05386-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/27/2022] [Accepted: 10/27/2022] [Indexed: 11/08/2022]
Abstract
As the most important RNA epigenetic regulation in eukaryotic cells, N6-metheyladenosine (m6A) modification has been demonstrated to play significant roles in cancer progression. However, this modification in long intergenic non-coding RNAs (lincRNAs) and the corresponding functions remain elusive. Here, we showed a lincRNA LINC02551 was downregulated by AlkB Homolog 5 (ALKBH5) overexpression in a m6A-dependent manner in hepatocellular carcinoma (HCC). Functionally, LINC02551 was required for the growth and metastasis of HCC. Mechanistically, LINC02551, a bona fide m6A target of ALKBH5, acted as a molecular adaptor that blocked the combination between DDX24 and a E3 ligase TRIM27 to decrease the ubiquitination and subsequent degradation of DDX24, ultimately facilitating HCC growth and metastasis. Thus, ALKBH5-mediated LINC02551 m6A methylation was required for HCC growth and metastasis.
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Affiliation(s)
- Hongwei Zhang
- grid.33199.310000 0004 0368 7223Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 China ,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, 430030 China
| | - Yachong Liu
- grid.33199.310000 0004 0368 7223Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 China ,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, 430030 China
| | - Wei Wang
- grid.33199.310000 0004 0368 7223Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 China ,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, 430030 China
| | - Furong Liu
- grid.33199.310000 0004 0368 7223Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 China ,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, 430030 China
| | - Weijian Wang
- grid.33199.310000 0004 0368 7223Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 China ,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, 430030 China
| | - Chen Su
- grid.33199.310000 0004 0368 7223Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 China ,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, 430030 China
| | - He Zhu
- grid.33199.310000 0004 0368 7223Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 China ,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, 430030 China
| | - Zhibin Liao
- grid.33199.310000 0004 0368 7223Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 China ,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, 430030 China
| | - Bixiang Zhang
- grid.33199.310000 0004 0368 7223Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 China ,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, 430030 China ,Key Laboratory of Organ Transplantation, Ministry of Education and Ministry of Health, Wuhan, 430030 China
| | - Xiaoping Chen
- grid.33199.310000 0004 0368 7223Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 China ,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, 430030 China ,Key Laboratory of Organ Transplantation, Ministry of Education and Ministry of Health, Wuhan, 430030 China
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Ghafouri-Fard S, Safarzadeh A, Akhavan-Bahabadi M, Hussen BM, Taheri M, Dilmaghani NA. Expression pattern of non-coding RNAs in non-functioning pituitary adenoma. Front Oncol 2022; 12:978016. [PMID: 36119500 PMCID: PMC9478794 DOI: 10.3389/fonc.2022.978016] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
Non-functioning pituitary adenoma (NFPA) is a benign tumor arising from the adenohypophyseal cells. They can be associated with symptoms arising from mass effect. Although these tumors are regarded to be benign tumors, they are associated with increased comorbidity and mortality. Several studies have indicated abnormal expression of genes in these tumors. In the current study, we have used existing methods to identify differentially expressed genes (DEGs) including DE long non-coding RNAs (DElncRNAs) and DE microRNAs (DEmiRNAs) in NFPAs compared with normal samples. Then, we have assessed the relation between these genes and important signaling pathways. Our analyses led to identification of 3131 DEGs, including 189 downregulated DEGs (such as RPS4Y1 and DDX3Y) and 2898 upregulated DEGs (such as ASB3 and DRD4), and 44 DElncRNAs, including 8 downregulated DElncRNAs (such as NUTM2B-AS1 and MALAT1) and 36 upregulated DElncRNAs (such as BCAR4 and SRD5A3-AS1). GnRH signaling pathway, Tight junction, Gap junction, Melanogenesis, DNA replication, Nucleotide excision repair, Mismatch repair and N-Glycan biosynthesis have been among dysregulated pathways in NFPAs. Taken together, our study has revealed differential expression of several genes and signaling pathways in this type of tumors.
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Affiliation(s)
- Soudeh Ghafouri-Fard
- Men’s Health and Reproductive Health Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Arash Safarzadeh
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Bashdar Mahmud Hussen
- Department of Pharmacognosy, College of Pharmacy, Hawler Medical University, Erbil, Iraq
- Center of Research and Strategic Studies, Lebanese French University, Erbil, Iraq
| | - Mohammad Taheri
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
- *Correspondence: Mohammad Taheri, ; Nader Akbari Dilmaghani,
| | - Nader Akbari Dilmaghani
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- *Correspondence: Mohammad Taheri, ; Nader Akbari Dilmaghani,
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10
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Chen M, Deng Y, Li A, Tan Y. Inferring Latent Disease-lncRNA Associations by Label-Propagation Algorithm and Random Projection on a Heterogeneous Network. Front Genet 2022; 13:798632. [PMID: 35186029 PMCID: PMC8854791 DOI: 10.3389/fgene.2022.798632] [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: 12/07/2021] [Accepted: 01/18/2022] [Indexed: 11/13/2022] Open
Abstract
Long noncoding RNA (lncRNA), a type of more than 200 nucleotides non-coding RNA, is related to various complex diseases. To precisely identify the potential lncRNA–disease association is important to understand the disease pathogenesis, to develop new drugs, and to design individualized diagnosis and treatment methods for different human diseases. Compared with the complexity and high cost of biological experiments, computational methods can quickly and effectively predict potential lncRNA–disease associations. Thus, it is a promising avenue to develop computational methods for lncRNA-disease prediction. However, owing to the low prediction accuracy ofstate of the art methods, it is vastly challenging to accurately and effectively identify lncRNA-disease at present. This article proposed an integrated method called LPARP, which is based on label-propagation algorithm and random projection to address the issue. Specifically, the label-propagation algorithm is initially used to obtain the estimated scores of lncRNA–disease associations, and then random projections are used to accurately predict disease-related lncRNAs.The empirical experiments showed that LAPRP achieved good prediction on three golddatasets, which is superior to existing state-of-the-art prediction methods. It can also be used to predict isolated diseases and new lncRNAs. Case studies of bladder cancer, esophageal squamous-cell carcinoma, and colorectal cancer further prove the reliability of the method. The proposed LPARP algorithm can predict the potential lncRNA–disease interactions stably and effectively with fewer data. LPARP can be used as an effective and reliable tool for biomedical research.
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11
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Ranasinghe R, Mathai M, Zulli A. A synopsis of modern - day colorectal cancer: Where we stand. Biochim Biophys Acta Rev Cancer 2022; 1877:188699. [DOI: 10.1016/j.bbcan.2022.188699] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 01/30/2022] [Accepted: 02/14/2022] [Indexed: 02/07/2023]
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12
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Utility of RGNEF in the Prediction of Clinical Prognosis in Patients with Rectal Cancer Receiving Preoperative Concurrent Chemoradiotherapy. Life (Basel) 2021; 12:life12010018. [PMID: 35054411 PMCID: PMC8778573 DOI: 10.3390/life12010018] [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: 11/14/2021] [Revised: 12/08/2021] [Accepted: 12/16/2021] [Indexed: 11/17/2022] Open
Abstract
Rectal cancer is a heterogeneous malignancy with different clinical responses to preoperative concurrent chemoradiotherapy (CCRT). To discover the significant genes associated with CCRT response, we performed data mining of a transcriptomic dataset (GSE35452), including 46 rectal cancer patients who received preoperative CCRT and underwent standardized curative resection. We identified ARHGEF28 as the most significantly upregulated gene correlated with resistance to CCRT among the genes related to Rho guanyl-nucleotide exchange factor activity (GO:0005085). We enrolled 172 patients with rectal cancer receiving CCRT with radical surgery. The expression of ARHGEF28 encoded protein, Rho guanine nucleotide exchange factor (RGNEF), was assessed using immunohistochemistry. The results showed that upregulated RGNEF immunoexpression was considerably correlated with poor response to CCRT (p = 0.018), pre-CCRT positive nodal status (p = 0.004), and vascular invasion (p < 0.001). Furthermore, high RGNEF expression was significantly associated with worse local recurrence-free survival (p < 0.0001), metastasis-free survival (MeFS) (p = 0.0029), and disease-specific survival (DSS) (p < 0.0001). The multivariate analysis demonstrated that RGNEF immunoexpression status was an independent predictor of DSS (p < 0.001) and MeFS (p < 0.001). Using Gene Ontology enrichment analysis, we discovered that ARHGEF28 overexpression might be linked to Wnt/β-catenin signaling in rectal cancer progression. In conclusion, high RGNEF expression was related to unfavorable pathological characteristics and independently predicted worse clinical prognosis in patients with rectal cancer undergoing CCRT, suggesting its role in risk stratification and clinical decision making.
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13
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Naz F, Tariq I, Ali S, Somaida A, Preis E, Bakowsky U. The Role of Long Non-Coding RNAs (lncRNAs) in Female Oriented Cancers. Cancers (Basel) 2021; 13:6102. [PMID: 34885213 PMCID: PMC8656502 DOI: 10.3390/cancers13236102] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/14/2021] [Accepted: 11/30/2021] [Indexed: 12/15/2022] Open
Abstract
Recent advances in molecular biology have discovered the mysterious role of long non-coding RNAs (lncRNAs) as potential biomarkers for cancer diagnosis and targets for advanced cancer therapy. Studies have shown that lncRNAs take part in the incidence and development of cancers in humans. However, previously they were considered as mere RNA noise or transcription byproducts lacking any biological function. In this article, we present a summary of the progress on ascertaining the biological functions of five lncRNAs (HOTAIR, NEAT1, H19, MALAT1, and MEG3) in female-oriented cancers, including breast and gynecological cancers, with the perspective of carcinogenesis, cancer proliferation, and metastasis. We provide the current state of knowledge from the past five years of the literature to discuss the clinical importance of such lncRNAs as therapeutic targets or early diagnostic biomarkers. We reviewed the consequences, either oncogenic or tumor-suppressing features, of their aberrant expression in female-oriented cancers. We tried to explain the established mechanism by which they regulate cancer proliferation and metastasis by competing with miRNAs and other mechanisms involved via regulating genes and signaling pathways. In addition, we revealed the association between stated lncRNAs and chemo-resistance or radio-resistance and their potential clinical applications and future perspectives.
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Affiliation(s)
- Faiza Naz
- Punjab University College of Pharmacy, Allama Iqbal Campus, University of the Punjab, Lahore 54000, Pakistan;
| | - Imran Tariq
- Punjab University College of Pharmacy, Allama Iqbal Campus, University of the Punjab, Lahore 54000, Pakistan;
- Department of Pharmaceutics and Biopharmaceutics, University of Marburg, Robert-Koch-Str. 4, 35037 Marburg, Germany or (S.A.); (A.S.); (E.P.)
| | - Sajid Ali
- Department of Pharmaceutics and Biopharmaceutics, University of Marburg, Robert-Koch-Str. 4, 35037 Marburg, Germany or (S.A.); (A.S.); (E.P.)
- Angström Laboratory, Department of Chemistry, Uppsala University, 75123 Uppsala, Sweden
| | - Ahmed Somaida
- Department of Pharmaceutics and Biopharmaceutics, University of Marburg, Robert-Koch-Str. 4, 35037 Marburg, Germany or (S.A.); (A.S.); (E.P.)
| | - Eduard Preis
- Department of Pharmaceutics and Biopharmaceutics, University of Marburg, Robert-Koch-Str. 4, 35037 Marburg, Germany or (S.A.); (A.S.); (E.P.)
| | - Udo Bakowsky
- Department of Pharmaceutics and Biopharmaceutics, University of Marburg, Robert-Koch-Str. 4, 35037 Marburg, Germany or (S.A.); (A.S.); (E.P.)
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14
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Olovo CV, Huang X, Zheng X, Xu M. Faecal microbial biomarkers in early diagnosis of colorectal cancer. J Cell Mol Med 2021; 25:10783-10797. [PMID: 34750964 PMCID: PMC8642680 DOI: 10.1111/jcmm.17010] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 10/04/2021] [Accepted: 10/07/2021] [Indexed: 12/26/2022] Open
Abstract
Colorectal cancer (CRC) is ranked as the second most common cause of cancer deaths and the third most common cancer globally. It has been described as a 'silent disease' which is often easily treatable if detected early-before progression to carcinoma. Colonoscopy, which is the gold standard for diagnosis is not only expensive but is also an invasive diagnostic procedure, thus, effective and non-invasive diagnostic methods are urgently needed. Unfortunately, the current methods are not sensitive and specific enough in detecting adenomas and early colorectal neoplasia, hampering treatment and consequently, survival rates. Studies have shown that imbalances in such a relationship which renders the gut microbiota in a dysbiotic state are implicated in the development of adenomas ultimately resulting in CRC. The differences found in the makeup and diversity of the gut microbiota of healthy individuals relative to CRC patients have in recent times gained attention as potential biomarkers in early non-invasive diagnosis of CRC, with promising sensitivity, specificity and even cost-effectiveness. This review summarizes recent studies in the application of these microbiota biomarkers in early CRC diagnosis, limitations encountered in the area of the faecal microbiota studies as biomarkers for CRC, and future research exploits that address these limitations.
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Affiliation(s)
- Chinasa Valerie Olovo
- Department of Biochemistry and Molecular BiologySchool of MedicineJiangsu UniversityZhenjiangChina
- Department of MicrobiologyFaculty of Biological SciencesUniversity of NigeriaNsukkaNigeria
| | - Xinxiang Huang
- Department of Biochemistry and Molecular BiologySchool of MedicineJiangsu UniversityZhenjiangChina
| | - Xueming Zheng
- Department of Biochemistry and Molecular BiologySchool of MedicineJiangsu UniversityZhenjiangChina
| | - Min Xu
- Department of GastroenterologyAffiliated Hospital of Jiangsu UniversityZhenjiangChina
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15
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Zhang Y, Chen M, Huang L, Xie X, Li X, Jin H, Wang X, Wei H. Fusion of KATZ measure and space projection to fast probe potential lncRNA-disease associations in bipartite graphs. PLoS One 2021; 16:e0260329. [PMID: 34807960 PMCID: PMC8608294 DOI: 10.1371/journal.pone.0260329] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 11/06/2021] [Indexed: 11/19/2022] Open
Abstract
It is well known that numerous long noncoding RNAs (lncRNAs) closely relate to the physiological and pathological processes of human diseases and can serves as potential biomarkers. Therefore, lncRNA-disease associations that are identified by computational methods as the targeted candidates reduce the cost of biological experiments focusing on deep study furtherly. However, inaccurate construction of similarity networks and inadequate numbers of observed known lncRNA–disease associations, such inherent problems make many mature computational methods that have been developed for many years still exit some limitations. It motivates us to explore a new computational method that was fused with KATZ measure and space projection to fast probing potential lncRNA-disease associations (namely KATZSP). KATZSP is comprised of following key steps: combining all the global information with which to change Boolean network of known lncRNA–disease associations into the weighted networks; changing the similarities calculation into counting the number of walks that connect lncRNA nodes and disease nodes in bipartite graphs; obtaining the space projection scores to refine the primary prediction scores. The process to fuse KATZ measure and space projection was simplified and uncomplicated with needing only one attenuation factor. The leave-one-out cross validation (LOOCV) experimental results showed that, compared with other state-of-the-art methods (NCPLDA, LDAI-ISPS and IIRWR), KATZSP had a higher predictive accuracy shown with area-under-the-curve (AUC) value on the three datasets built, while KATZSP well worked on inferring potential associations related to new lncRNAs (or isolated diseases). The results from real cases study (such as pancreas cancer, lung cancer and colorectal cancer) further confirmed that KATZSP is capable of superior predictive ability to be applied as a guide for traditional biological experiments.
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Affiliation(s)
- Yi Zhang
- School of Information Science and Engineering, Guilin University of Technology, Guilin, China
- Guangxi Key Laboratory of Embedded Technology and Intelligent System, Guilin University of Technology, Guilin, China
| | - Min Chen
- School of Computer Science and Technology, Hunan Institute of Technology, Hengyang, China
| | - Li Huang
- Academy of Arts and Design, Tsinghua University, Beijing, China
- The Future Laboratory, Tsinghua University, Beijing, China
| | - Xiaolan Xie
- School of Information Science and Engineering, Guilin University of Technology, Guilin, China
| | - Xin Li
- School of Information Science and Engineering, Guilin University of Technology, Guilin, China
| | - Hong Jin
- School of Information Science and Engineering, Guilin University of Technology, Guilin, China
| | - Xiaohua Wang
- Pharmacy School, Guilin Medical University, Guilin, China
| | - Hanyan Wei
- Pharmacy School, Guilin Medical University, Guilin, China
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16
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Hegre SA, Samdal H, Klima A, Stovner EB, Nørsett KG, Liabakk NB, Olsen LC, Chawla K, Aas PA, Sætrom P. Joint changes in RNA, RNA polymerase II, and promoter activity through the cell cycle identify non-coding RNAs involved in proliferation. Sci Rep 2021; 11:18952. [PMID: 34556693 PMCID: PMC8460802 DOI: 10.1038/s41598-021-97909-w] [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: 04/07/2021] [Accepted: 07/26/2021] [Indexed: 11/09/2022] Open
Abstract
Proper regulation of the cell cycle is necessary for normal growth and development of all organisms. Conversely, altered cell cycle regulation often underlies proliferative diseases such as cancer. Long non-coding RNAs (lncRNAs) are recognized as important regulators of gene expression and are often found dysregulated in diseases, including cancers. However, identifying lncRNAs with cell cycle functions is challenging due to their often low and cell-type specific expression. We present a highly effective method that analyses changes in promoter activity, transcription, and RNA levels for identifying genes enriched for cell cycle functions. Specifically, by combining RNA sequencing with ChIP sequencing through the cell cycle of synchronized human keratinocytes, we identified 1009 genes with cell cycle-dependent expression and correlated changes in RNA polymerase II occupancy or promoter activity as measured by histone 3 lysine 4 trimethylation (H3K4me3). These genes were highly enriched for genes with known cell cycle functions and included 57 lncRNAs. We selected four of these lncRNAs-SNHG26, EMSLR, ZFAS1, and EPB41L4A-AS1-for further experimental validation and found that knockdown of each of the four lncRNAs affected cell cycle phase distributions and reduced proliferation in multiple cell lines. These results show that many genes with cell cycle functions have concomitant cell-cycle dependent changes in promoter activity, transcription, and RNA levels and support that our multi-omics method is well suited for identifying lncRNAs involved in the cell cycle.
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Affiliation(s)
- Siv Anita Hegre
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway
| | - Helle Samdal
- Department of Computer Science, Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway
| | - Antonin Klima
- Department of Computer Science, Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway
| | - Endre B Stovner
- Department of Computer Science, Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway.,K.G. Jebsen Center for Genetic Epidemiology, Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway
| | - Kristin G Nørsett
- Department of Computer Science, Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway.,Department of Biomedical Laboratory Science, Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway
| | - Nina Beate Liabakk
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway
| | - Lene Christin Olsen
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway.,Bioinformatics Core Facility-BioCore, Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway.,The Central Norway Regional Health Authority, St. Olavs Hospital HF, Trondheim, Norway
| | - Konika Chawla
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway.,Bioinformatics Core Facility-BioCore, Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway
| | - Per Arne Aas
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway
| | - Pål Sætrom
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway. .,Department of Computer Science, Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway. .,K.G. Jebsen Center for Genetic Epidemiology, Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway. .,Bioinformatics Core Facility-BioCore, Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway.
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17
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Jing H, Wang C, Zhao L, Cheng J, Qin P, Lin H. Propofol protects cardiomyocytes from hypoxia/reoxygenation injury via regulating MALAT1/miR-206/ATG3 axis. J Biochem Mol Toxicol 2021; 35:e22880. [PMID: 34383354 DOI: 10.1002/jbt.22880] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 06/06/2021] [Accepted: 07/29/2021] [Indexed: 01/24/2023]
Abstract
Previous studies have shown that propofol (PPF) plays a protective role in ischemia-reperfusion (I/R) in multiple organs and tissues. This study was aimed to explore the mechanism of PPF in ameliorating myocardial ischemia-reperfusion injury (MIRI). MIRI model was established with Sprague-Dawley rats, and PPF pretreatment was performed before reperfusion. Creatine kinase isoform (CK-MB), lactate dehydrogenase (LDH), and hematoxylin and eosin stain were used to evaluate the severity of MIRI. H9c2 cells were treated with hypoxia/reoxygenation (H/R) to simulate I/R injury in vitro. Real-time quantitative polymerase chain reaction (qPCR) was employed to assess MALAT1 and microRNA (miR)-206 expressions. Autophagy-related 3 (ATG3), LC3BⅡ/LC3BⅠ, and Beclin-1 expression were examined by western blot. Apoptosis was monitored using flow cytometry. Interaction between MALAT1 and miR-206 was determined by bioinformatics analysis, dual-luciferase reporter gene assay, RIP assay, and RNA pull-down assay. PPF pretreatment remarkably reduced CK-MB level, LDH level, myocardial infarct size, and LC3BⅡ/LC3BⅠ ratio and Beclin-1 expression in the rats with MIRI, and repressed the apoptosis of H9c2 cells exposed to H/R. PPF pretreatment markedly suppressed MALAT1 expression and enhanced miR-206 expression in both in vivo and in vitro models. MiR-206 was identified as a target of MALAT1 in cardiomyocytes, and MALAT1 could increase the expression of ATG3. Additionally, the upregulation of MALAT1 partially reversed the protective effect of PPF on cardiomyocytes in vitro. PPF modulated MALAT1/miR-206/ATG3 axis to protect cardiomyocytes against I/R injury.
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Affiliation(s)
- Haijuan Jing
- Department of Anesthesiology, Henan Provincial People's Hospital (Central China Fuwai Hospital of Zhengzhou University), Zhengzhou, Henan, China.,Department of Anesthesiology, Central China Fuwai Hospital (Central China Fuwai Hospital of Zhengzhou University), Zhengzhou, Henan, China
| | - Chuan Wang
- Department of Anesthesiology, Hebei North University, Zhangjiakou, Hebei, China
| | - Liang Zhao
- Department of Anesthesiology, Henan Provincial People's Hospital (Central China Fuwai Hospital of Zhengzhou University), Zhengzhou, Henan, China
| | - Jing Cheng
- Department of Anesthesiology, Henan Provincial People's Hospital (Central China Fuwai Hospital of Zhengzhou University), Zhengzhou, Henan, China
| | - Pengyu Qin
- Department of Anesthesiology, Henan Provincial People's Hospital (Central China Fuwai Hospital of Zhengzhou University), Zhengzhou, Henan, China
| | - Hongqi Lin
- Department of Anesthesiology, Henan Provincial People's Hospital (Central China Fuwai Hospital of Zhengzhou University), Zhengzhou, Henan, China.,Department of Anesthesiology, Central China Fuwai Hospital (Central China Fuwai Hospital of Zhengzhou University), Zhengzhou, Henan, China
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18
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Islam Khan MZ, Law HKW. Cancer Susceptibility Candidate 9 (CASC9) Promotes Colorectal Cancer Carcinogenesis via mTOR-Dependent Autophagy and Epithelial-Mesenchymal Transition Pathways. Front Mol Biosci 2021; 8:627022. [PMID: 34017854 PMCID: PMC8129023 DOI: 10.3389/fmolb.2021.627022] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 03/09/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is the third most common cancer worldwide. Many recent studies have demonstrated that different long non-coding RNAs (lncRNAs) are involved in the initiation, advancement, and metastasis of many cancers including CRC. Cancer susceptibility candidate 9 (CASC9) is an lncRNA that has been reported in many cancers, but its role in CRC is poorly understood. In this study, we aimed to examine the expression of CASC9 in CRC cell lines and to determine the mechanism of action of CASC9 in CRC carcinogenesis. METHODS The expression of CASC9 in CRC tissues was compared with normal samples from publicly available datasets in The Cancer Genome Atlas (TCGA) and The Encyclopedia of RNA Interactomes (ENCORI). CASC9 expression was further verified in four CRC cell lines (DLD1, HT-29, SW480, and HCT-116) and normal colorectal cell line (CCD-112CoN) by real-time quantitative polymerase chain reaction (RT-qPCR). After gene silencing in HCT-116 and SW480, Cell Counting Kit-8 assay, clonogenic assay, and wound healing assay were performed to evaluate cell proliferation, viability, and migration index of cells. Western blotting was used to explore the key pathways involved. RESULTS CASC9 was significantly upregulated as analyzed from both public datasets TCGA and ENCORI where its overexpression was associated with poor survival of CRC patients. Similarly, CASC9 was significantly overexpressed in the CRC cell lines compared with normal cells studied. The silencing of CASC9 in HCT-116 and SW480 attenuated cell proliferation and migration significantly. Furthermore, pathways investigations showed that silencing of CASC9 significantly induced autophagy, promoted AMP-activated protein kinase (AMPK) phosphorylation, inhibited mTOR and AKT signaling pathways, and altered epithelial-mesenchymal transition (EMT) marker protein expression. CONCLUSION We demonstrated that silencing of CASC9 contributes to the reduced CRC cell proliferation and migration by regulating autophagy and AKT/mTOR/EMT signaling. Therefore, CASC9 plays an important role in carcinogenesis, and its expression may act as a prognostic biomarker and a potential therapeutic target of CRC management.
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Affiliation(s)
| | - Helen Ka Wai Law
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Kowloon, Hong Kong
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19
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Yang Y, Yan X, Li X, Ma Y, Goel A. Long non-coding RNAs in colorectal cancer: Novel oncogenic mechanisms and promising clinical applications. Cancer Lett 2021; 504:67-80. [PMID: 33577977 PMCID: PMC9715275 DOI: 10.1016/j.canlet.2021.01.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 12/29/2020] [Accepted: 01/08/2021] [Indexed: 02/05/2023]
Abstract
Colorectal cancer (CRC) is the third most common malignancy and ranks as the second leading cause of cancer-related deaths worldwide. Despite the improvements in CRC diagnosis and treatment approaches, a considerable proportion of CRC patients still suffers from poor prognosis due to late disease detections and lack of personalized disease managements. Recent evidences have not only provided important molecular insights into their mechanistic behaviors but also indicated that identification of cancer-specific long non-coding RNAs (LncRNAs) could benefit earlier disease detections and improve treatment outcomes in patients suffering from CRC. LncRNAs have raised extensive attentions as they participate in various hallmarks of CRC. The mechanistic evidence gleaned in the recent decade clearly reveals that lncRNAs exert their oncogenic roles by regulating autophagy, epigenetic modifications, enhancing stem phenotype and modifying tumor microenvironment. In view of their pleiotropic functional roles in malignant progression, and their frequently dysregulated expression in CRC patients, they have great potential to be reliable diagnostic and prognostic biomarkers, as well as therapeutic targets for CRC. In the present review, we will focus on the oncogenic roles of lncRNAs and related mechanisms in CRC as well as discuss their clinical potential in the early diagnosis, prognostic prediction and therapeutic translation in patients with this malignancy.
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Affiliation(s)
- Yufei Yang
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xuebing Yan
- Department of Oncology, Affiliated Hospital of Yangzhou University, Yangzhou, China
| | - Xinxiang Li
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Yanlei Ma
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Ajay Goel
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope Comprehensive Cancer Center, Duarte, CA, USA.
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20
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Liao Z, Nie H, Wang Y, Luo J, Zhou J, Ou C. The Emerging Landscape of Long Non-Coding RNAs in Colorectal Cancer Metastasis. Front Oncol 2021; 11:641343. [PMID: 33718238 PMCID: PMC7947863 DOI: 10.3389/fonc.2021.641343] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 01/29/2021] [Indexed: 12/11/2022] Open
Abstract
Colorectal cancer (CRC) is one of the most common gastrointestinal cancers, with extremely high rates of morbidity and mortality. The main cause of death in CRC is distant metastasis; it affects patient prognosis and survival and is one of the key challenges in the treatment of CRC. Long non-coding RNAs (lncRNAs) are a group of non-coding RNA molecules with more than 200 nucleotides. Abnormal lncRNA expression is closely related to the occurrence and progression of several diseases, including cancer. Recent studies have shown that numerous lncRNAs play pivotal roles in the CRC metastasis, and reversing the expression of these lncRNAs through artificial means can reduce the malignant phenotype of metastatic CRC to some extent. This review summarizes the major mechanisms of lncRNAs in CRC metastasis and proposes lncRNAs as potential therapeutic targets for CRC and molecular markers for early diagnosis.
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Affiliation(s)
- Zhiming Liao
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
| | - Hui Nie
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
| | - Yutong Wang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
| | - Jingjing Luo
- Teaching and Research Room of Biochemistry and Molecular Biology, Medical School of Hunan University of Traditional Chinese Medicine, Changsha, China
| | - Jianhua Zhou
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Chunlin Ou
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
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21
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Liu G, Liu D, Huang J, Li J, Wang C, Liu G, Ge S, Gong H. Comprehensive analysis of ceRNA network related to lincRNA in glioblastoma and prediction of clinical prognosis. BMC Cancer 2021; 21:98. [PMID: 33499813 PMCID: PMC7836476 DOI: 10.1186/s12885-021-07817-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 01/18/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Long intergenic non-coding RNAs (lincRNAs) are capable of regulating several tumours, while competitive endogenous RNA (ceRNA) networks are of great significance in revealing the biological mechanism of tumours. Here, we aimed to study the ceRNA network of lincRNA in glioblastoma (GBM). METHODS We obtained GBM and normal brain tissue samples from TCGA, GTEx, and GEO databases, and performed weighted gene co-expression network analysis and differential expression analysis on all lincRNA and mRNA data. Subsequently, we predicted the interaction between lincRNAs, miRNAs, and target mRNAs. Univariate and multivariate Cox regression analyses were performed on the mRNAs using CGGA data, and a Cox proportional hazards regression model was constructed. The ceRNA network was further screened by the DEmiRNA and mRNA of Cox model. RESULTS A prognostic prediction model was constructed for patients with GBM. We assembled a ceRNA network consisting of 18 lincRNAs, 6 miRNAs, and 8 mRNAs. Gene Set Enrichment Analysis was carried out on four lincRNAs with obvious differential expressions and relatively few studies in GBM. CONCLUSION We identified four lincRNAs that have research value for GBM and obtained the ceRNA network. Our research is expected to facilitate in-depth understanding and study of the molecular mechanism of GBM, and provide new insights into targeted therapy and prognosis of the tumour.
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Affiliation(s)
- Guangdong Liu
- Department of Neurosurgery, Hongqi Hospital Affiliated to Mudanjiang Medical University, No. 5, Tongxiang Road, Aimin, MuDanJiang, HeiLongJiang, China
| | - Danian Liu
- Department of Neurology, Hongqi Hospital Affiliated to Mudanjiang Medical University, MuDanJiang, China
| | - Jingjing Huang
- Department of Infectious Diseases, Hongqi Hospital Affiliated to Mudanjiang Medical University, MuDanJiang, China
| | - Jianxin Li
- Department of Neurosurgery, Jiaozuo People's Hospital, JiaoZuo, China
| | - Chuang Wang
- Department of Neurosurgery, Hongqi Hospital Affiliated to Mudanjiang Medical University, No. 5, Tongxiang Road, Aimin, MuDanJiang, HeiLongJiang, China
| | - Guangyao Liu
- Department of Neurosurgery, Hongqi Hospital Affiliated to Mudanjiang Medical University, No. 5, Tongxiang Road, Aimin, MuDanJiang, HeiLongJiang, China
| | - Shiqiang Ge
- Department of Neurosurgery, Hongqi Hospital Affiliated to Mudanjiang Medical University, No. 5, Tongxiang Road, Aimin, MuDanJiang, HeiLongJiang, China
| | - Haidong Gong
- Department of Neurosurgery, Hongqi Hospital Affiliated to Mudanjiang Medical University, No. 5, Tongxiang Road, Aimin, MuDanJiang, HeiLongJiang, China.
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22
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Zhou Z, Sun B, Nie A, Yu D, Bian M. Roles of Aminoacyl-tRNA Synthetases in Cancer. Front Cell Dev Biol 2020; 8:599765. [PMID: 33330488 PMCID: PMC7729087 DOI: 10.3389/fcell.2020.599765] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 11/09/2020] [Indexed: 12/18/2022] Open
Abstract
Aminoacyl-tRNA synthetases (ARSs) catalyze the ligation of amino acids to their cognate transfer RNAs (tRNAs), thus playing an important role in protein synthesis. In eukaryotic cells, these enzymes exist in free form or in the form of multi-tRNA synthetase complex (MSC). The latter contains nine cytoplasmic ARSs and three ARS-interacting multifunctional proteins (AIMPs). Normally, ARSs and AIMPs are regarded as housekeeping molecules without additional functions. However, a growing number of studies indicate that ARSs are involved in a variety of physiological and pathological processes, especially tumorigenesis. Here, we introduce the roles of ARSs and AIMPs in certain cancers, such as colon cancer, lung cancer, breast cancer, gastric cancer and pancreatic cancer. Furthermore, we particularly focus on their potential clinical applications in cancer, aiming at providing new insights into the pathogenesis and treatment of cancer.
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Affiliation(s)
- Zheng Zhou
- Department of Chinese Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Bao Sun
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, China.,Institution of Clinical Pharmacy, Central South University, Changsha, China
| | - Anzheng Nie
- Department of Chinese Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Dongsheng Yu
- Department of Chinese Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Meng Bian
- Department of Chinese Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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