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Duan ZB, Zheng JF, Huang SY, Hu LL. Long non-coding RNA MALAT1 triggers ferroptosis via interaction with FUS to enhance ACSF2 mRNA stabilization in septic acute kidney injury. Kaohsiung J Med Sci 2024. [PMID: 39390627 DOI: 10.1002/kjm2.12898] [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: 05/08/2024] [Revised: 09/04/2024] [Accepted: 09/08/2024] [Indexed: 10/12/2024] Open
Abstract
Septic acute kidney injury (AKI) is a fatal disease in the intensive care unit, with ferroptosis playing a crucial role in its pathogenesis. Long non-coding RNA (LncRNA) metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) has been implicated in septic-induced AKI inflammation and apoptosis. However, its regulatory role in ferroptosis and underlying mechanisms remain unclear. In vivo and in vitro models of septic AKI were established using cecal ligation and puncture (CLP) and lipopolysaccharide (LPS) challenge, respectively. Serum levels of creatinine (Cr), blood urea nitrogen (BUN), kidney injury molecule-1 (Kim-1), neutrophil gelatinase-associated lipocalin (NGAL), and inflammatory cytokine in kidney tissues were determined by ELISA kits. Histopathological alterations and apoptosis were evaluated by HE staining and TUNEL. Ferroptosis was accessed by measuring MDA, GSH, Fe2+, total and lipid ROS levels, and mitochondrial ultrastructure changes. Target molecular levels were determined using RT-qPCR, Western blotting, and immunofluorescence. Interactions among MALAT1, acyl-CoA synthetase family member 2 (ACSF2) and FUS RNA binding protein (FUS) were validated by RIP and RNA-pull down. MALAT1 level was significantly elevated in both in vivo and in vitro septic AKI models, of which knockdown impeded ferroptosis to alleviate septic AKI. Mechanistically, high MALAT1 expression increased ACSF2 mRNA stability via interaction with FUS. Rescue experiments showed that ACSF2 overexpression partially reversed the ferroptosis inhibition mediated by MALAT1 silencing. MALAT1 induces ferroptosis and exacerbates septic AKI by stabilizing ACSF2 mRNA with the assistance of FUS. These findings provide theoretical evidence for MALAT1 as a potential therapeutic target for septic AKI.
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Affiliation(s)
- Zhi-Bing Duan
- Department of Nephrology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi Province, China
| | - Ji-Fu Zheng
- Department of Hematology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi Province, China
| | - Si-Yue Huang
- Department of Nephrology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi Province, China
| | - Li-Li Hu
- Department of Nephrology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi Province, China
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2
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Jia QH, Cao YZ, Xing YX, Guan HB, Ma CL, Li X, Tian WH, Li ZJ, Tian YD, Li GX, Jiang RR, Kang XT, Liu XJ, Li H. LncRNA lncLLM Facilitates Lipid Deposition by Promoting the Ubiquitination of MYH9 in Chicken LMH Cells. Int J Mol Sci 2024; 25:10316. [PMID: 39408647 DOI: 10.3390/ijms251910316] [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: 08/22/2024] [Revised: 09/21/2024] [Accepted: 09/24/2024] [Indexed: 10/19/2024] Open
Abstract
The liver plays an important role in regulating lipid metabolism in animals. This study investigated the function and mechanism of lncLLM in liver lipid metabolism in hens at the peak of egg production. The effect of lncLLM on intracellular lipid content in LMH cells was evaluated by qPCR, Oil Red O staining, and detection of triglyceride (TG) and cholesterol (TC) content. The interaction between lncLLM and MYH9 was confirmed by RNA purification chromatin fractionation (CHIRP) and RNA immunoprecipitation (RIP) analysis. The results showed that lncLLM increased the intracellular content of TG and TC and promoted the expression of genes related to lipid synthesis. It was further found that lncLLM had a negative regulatory effect on the expression level of MYH9 protein in LMH cells. The intracellular TG and TC content of MYH9 knockdown cells increased, and the expression of genes related to lipid decomposition was significantly reduced. In addition, this study confirmed that the role of lncLLM is at least partly through mediating the ubiquitination of MYH9 protein to accelerate the degradation of MYH9 protein. This discovery provides a new molecular target for improving egg-laying performance in hens and treating fatty liver disease in humans.
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Affiliation(s)
- Qi-Hui Jia
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Yu-Zhu Cao
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Yu-Xin Xing
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Hong-Bo Guan
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Cheng-Lin Ma
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Xin Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Wei-Hua Tian
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Zhuan-Jian Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
- Key Laboratory of Livestock and Poultry Resources (Poultry) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Henan Agricultural University, Zhengzhou 450046, China
- International Joint Research Laboratory for Poultry Breeding of Henan, Henan Agricultural University, Zhengzhou 450046, China
| | - Ya-Dong Tian
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
- Key Laboratory of Livestock and Poultry Resources (Poultry) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Henan Agricultural University, Zhengzhou 450046, China
- International Joint Research Laboratory for Poultry Breeding of Henan, Henan Agricultural University, Zhengzhou 450046, China
| | - Guo-Xi Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
- Key Laboratory of Livestock and Poultry Resources (Poultry) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Henan Agricultural University, Zhengzhou 450046, China
- International Joint Research Laboratory for Poultry Breeding of Henan, Henan Agricultural University, Zhengzhou 450046, China
| | - Rui-Rui Jiang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
- Key Laboratory of Livestock and Poultry Resources (Poultry) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Henan Agricultural University, Zhengzhou 450046, China
- International Joint Research Laboratory for Poultry Breeding of Henan, Henan Agricultural University, Zhengzhou 450046, China
| | - Xiang-Tao Kang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
- Key Laboratory of Livestock and Poultry Resources (Poultry) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Henan Agricultural University, Zhengzhou 450046, China
- International Joint Research Laboratory for Poultry Breeding of Henan, Henan Agricultural University, Zhengzhou 450046, China
| | - Xiao-Jun Liu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
- Key Laboratory of Livestock and Poultry Resources (Poultry) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Henan Agricultural University, Zhengzhou 450046, China
- International Joint Research Laboratory for Poultry Breeding of Henan, Henan Agricultural University, Zhengzhou 450046, China
| | - Hong Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
- Key Laboratory of Livestock and Poultry Resources (Poultry) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Henan Agricultural University, Zhengzhou 450046, China
- International Joint Research Laboratory for Poultry Breeding of Henan, Henan Agricultural University, Zhengzhou 450046, China
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Tang H, Zhu D, Li W, Zhang G, Zhang H, Peng Q. Exosomal AFAP1-AS1 Promotes the Growth, Metastasis, and Glycolysis of Pituitary Adenoma by Inhibiting HuR Degradation. Mol Neurobiol 2024:10.1007/s12035-024-04387-y. [PMID: 39090353 DOI: 10.1007/s12035-024-04387-y] [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: 03/15/2024] [Accepted: 07/19/2024] [Indexed: 08/04/2024]
Abstract
Exosomal long noncoding RNAs (lncRNAs), which are highly expressed in tumor-derived exosomes, regulate various cellular behaviors such as cell proliferation, metastasis, and glycolysis by facilitating intercellular communication. Here, we explored the role and regulatory mechanism of tumor-derived exosomal lncRNAs in pituitary adenomas (PA). We isolated exosomes from PA cells, and performed in vitro and in vivo assays to examine their effect on the proliferation, metastasis, and glycolysis of PA cells. In addition, we conducted RNA pull-down, RNA immunoprecipitation, co-immunoprecipitation, and ubiquitination assays to investigate the downstream mechanism of exosomal AFAP1-AS1. Exosomes from PA cells augmented the proliferation, mobility, and glycolysis of PA cells. Moreover, AFAP1-AS1 was significantly enriched in these exosomes and stimulated the growth, migration, invasion, and glycolysis of PA cells in vitro, as well as tumor metastasis in vivo. It also enhanced the binding affinity between Hu antigen R (HuR) and SMAD-specific E3 ubiquitin protein ligase 1 (SMURF1), resulting in HuR ubiquitination and degradation accompanied by enhanced expression of hexokinase 2 (HK2) and pyruvate kinase M2 (PKM2). Moreover, HuR overexpression alleviated the exosomal AFAP1-AS1-mediated promotion of growth, metastasis, and glycolysis effects. These findings indicate that tumor-derived exosomal AFAP1-AS1 modulated SMURF1-mediated HuR ubiquitination and degradation to upregulate HK2 and PKM2 expression, thereby enhancing PA cell growth, metastasis, and glucose metabolism. This suggests targeting exosomal AFAP1-AS1 may be a potential strategy for the treatment of PA.
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Affiliation(s)
- Hengxin Tang
- Department of Neurosurgery, Guangzhou First People's Hospital, South China University of Technology, 105 Fengze East Road, Nansha District, Guangzhou, 511457, Guangdong, China.
| | - Delong Zhu
- Department of Neurosurgery, Guangzhou First People's Hospital, South China University of Technology, 105 Fengze East Road, Nansha District, Guangzhou, 511457, Guangdong, China
| | - Wenxiang Li
- Department of Neurosurgery, Guangzhou First People's Hospital, South China University of Technology, 105 Fengze East Road, Nansha District, Guangzhou, 511457, Guangdong, China
| | - Guozhi Zhang
- Department of Neurosurgery, Guangzhou First People's Hospital, South China University of Technology, 105 Fengze East Road, Nansha District, Guangzhou, 511457, Guangdong, China
| | - Heng Zhang
- Department of Neurosurgery, Guangzhou First People's Hospital, South China University of Technology, 105 Fengze East Road, Nansha District, Guangzhou, 511457, Guangdong, China
| | - Qiujiao Peng
- Department of Neurosurgery, Guangzhou First People's Hospital, South China University of Technology, 105 Fengze East Road, Nansha District, Guangzhou, 511457, Guangdong, China
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Hashemi M, Mousavian Roshanzamir S, Orouei S, Daneii P, Raesi R, Zokaee H, Bikarannejad P, Salmani K, Khorrami R, Deldar Abad Paskeh M, Salimimoghadam S, Rashidi M, Hushmandi K, Taheriazam A, Entezari M. Shedding light on function of long non-coding RNAs (lncRNAs) in glioblastoma. Noncoding RNA Res 2024; 9:508-522. [PMID: 38511060 PMCID: PMC10950594 DOI: 10.1016/j.ncrna.2024.02.002] [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: 12/07/2023] [Revised: 01/29/2024] [Accepted: 02/04/2024] [Indexed: 03/22/2024] Open
Abstract
The brain tumors and especially glioblastoma, are affecting life of many people worldwide and due to their high mortality and morbidity, their treatment is of importance and has gained attention in recent years. The abnormal expression of genes is commonly observed in GBM and long non-coding RNAs (lncRNAs) have demonstrated dysregulation in this tumor. LncRNAs have length more than 200 nucleotides and they have been located in cytoplasm and nucleus. The current review focuses on the role of lncRNAs in GBM. There two types of lncRNAs in GBM including tumor-promoting and tumor-suppressor lncRNAs and overexpression of oncogenic lncRNAs increases progression of GBM. LncRNAs can regulate proliferation, cell cycle arrest and metastasis of GBM cells. Wnt, STAT3 and EZH2 are among the molecular pathways affected by lncRNAs in GBM and for regulating metastasis of GBM cells, these RNA molecules mainly affect EMT mechanism. LncRNAs are involved in drug resistance and can induce resistance of GBM cells to temozolomide chemotherapy. Furthermore, lncRNAs stimulate radio-resistance in GBM cells. LncRNAs increase PD-1 expression to mediate immune evasion. LncRNAs can be considered as diagnostic and prognostic tools in GBM and researchers have developed signature from lncRNAs in GBM.
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Affiliation(s)
- Mehrdad Hashemi
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Sophie Mousavian Roshanzamir
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Sima Orouei
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Pouria Daneii
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Rasoul Raesi
- Department of Nursing, Torbat Jam Faculty of Medical Sciences, Torbat Jam, Iran
- Department of Health Services Management, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Haleh Zokaee
- Department of Oral and Maxillofacial Medicine, Dental Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Pooria Bikarannejad
- Young Researchers and Elite Club, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Kiana Salmani
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Ramin Khorrami
- Department of Food Hygiene and Quality Control, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Mahshid Deldar Abad Paskeh
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Shokooh Salimimoghadam
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Mohsen Rashidi
- Department Pharmacology, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
- The Health of Plant and Livestock Products Research Center, Mazandaran University of Medical Sciences, Sari, Iran
| | - Kiavash Hushmandi
- Department of Food Hygiene and Quality Control, Division of Epidemiology & Zoonoses, Faculty of Veterinary Medicine, University of Tehran, Tehran, 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
| | - Maliheh Entezari
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
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5
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Zhang L, Yang L, Du K. Exosomal HSPB1, interacting with FUS protein, suppresses hypoxia-induced ferroptosis in pancreatic cancer by stabilizing Nrf2 mRNA and repressing P450. J Cell Mol Med 2024; 28:e18209. [PMID: 38682349 PMCID: PMC11056849 DOI: 10.1111/jcmm.18209] [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: 08/10/2023] [Revised: 01/20/2024] [Accepted: 02/14/2024] [Indexed: 05/01/2024] Open
Abstract
Ferroptosis is a new type of programmed cell death, which has been involved in the progression of tumours. However, the regulatory network of ferroptosis in pancreatic cancer is still largely unknown. Here, using datasets from GEO and TCGA, we screened HSPB1, related to the P450 monooxygenase signalling, a fuel of ferroptosis, to be a candidate gene for regulating pancreatic cancer cell ferroptosis. We found that HSPB1 was enriched in the exosomes derived from human pancreatic cancer cell lines SW1990 and Panc-1. Then, hypoxic SW1990 cells were incubated with exosomes alone or together with HSPB1 siRNA (si-HSPB1), and we observed that exosomes promoted cell proliferation and invasion and suppressed ferroptosis, which was reversed by si-HSPB1. Moreover, we found a potential binding affinity between HSPB1 and FUS, verified their protein interaction by using dual-colour fluorescence colocalization and co-IP assays, and demonstrated the promoting effect of FUS on oxidative stress and ferroptosis in hypoxic SW1990 cells. Subsequently, FUS was demonstrated to bind with and stabilize the mRNA of Nrf2, a famous anti-ferroptosis gene that negatively regulates the level of P450. Furthermore, overexpressing FUS and activating the Nrf2/HO-1 pathway (using NK-252) both reversed the inhibitory effect of si-HSPB1 on exosome functions. Finally, our in vivo studies showed that exosome administration promote tumour growth in nude mice of xenotransplantation, which was able to be eliminated by knockdown of HSPB1. In conclusion, exosomal HSPB1 interacts with the RNA binding protein FUS and decreases FUS-mediated stability of Nrf2 mRNA, thus suppressing hypoxia-induced ferroptosis in pancreatic cancer.
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Affiliation(s)
- Lun Zhang
- Department of Hepatobiliary SurgeryThe First Affiliated Hospital of Xi'an Jiaotong UniversityXi'anShaanxiP.R. China
| | - Liuxu Yang
- Health Science CenterXi'an Jiaotong UniversityXi'anShaanxiP.R. China
| | - Keyuan Du
- Health Science CenterXi'an Jiaotong UniversityXi'anShaanxiP.R. China
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6
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Swaminathan G, Rogel-Ayala DG, Armich A, Barreto G. Implications in Cancer of Nuclear Micro RNAs, Long Non-Coding RNAs, and Circular RNAs Bound by PRC2 and FUS. Cancers (Basel) 2024; 16:868. [PMID: 38473229 DOI: 10.3390/cancers16050868] [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: 01/04/2024] [Revised: 02/13/2024] [Accepted: 02/16/2024] [Indexed: 03/14/2024] Open
Abstract
The eukaryotic genome is mainly transcribed into non-coding RNAs (ncRNAs), including different RNA biotypes, such as micro RNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), among others. Although miRNAs are assumed to act primarily in the cytosol, mature miRNAs have been reported and functionally characterized in the nuclei of different cells. Further, lncRNAs are important regulators of different biological processes in the cell nucleus as part of different ribonucleoprotein complexes. CircRNAs constitute a relatively less-characterized RNA biotype that has a circular structure as result of a back-splicing process. However, circRNAs have recently attracted attention in different scientific fields due to their involvement in various biological processes and pathologies. In this review, we will summarize recent studies that link to cancer miRNAs that have been functionally characterized in the cell nucleus, as well as lncRNAs and circRNAs that are bound by core components of the polycomb repressive complex 2 (PRC2) or the protein fused in sarcoma (FUS), highlighting mechanistic aspects and their diagnostic and therapeutic potential.
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Affiliation(s)
| | - Diana G Rogel-Ayala
- Université de Lorraine, CNRS, Laboratoire IMoPA, UMR 7365, F-54000 Nancy, France
- Lung Cancer Epigenetics, Max-Planck-Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Amine Armich
- Université de Lorraine, CNRS, Laboratoire IMoPA, UMR 7365, F-54000 Nancy, France
| | - Guillermo Barreto
- Université de Lorraine, CNRS, Laboratoire IMoPA, UMR 7365, F-54000 Nancy, France
- Lung Cancer Epigenetics, Max-Planck-Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
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7
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Zhou W, Hu Y, Wang B, Yuan L, Ma J, Meng X. Aberrant expression of PELI1 caused by Jagged1 accelerates the malignant phenotype of pancreatic cancer. Cell Signal 2023; 111:110877. [PMID: 37657587 DOI: 10.1016/j.cellsig.2023.110877] [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: 05/09/2023] [Revised: 08/13/2023] [Accepted: 08/29/2023] [Indexed: 09/03/2023]
Abstract
Pancreatic cancer is one of the most aggressive cancers. PELI1 has been reported to promote cell survival and proliferation in multiple cancers. As of now, the role of PELI1 in pancreatic cancer is largely unknown. Here, we found that the PELI1 mRNA was higher expressed in pancreatic tumor tissues than in adjacent normal tissues, and the high PELI1 level in pancreatic cancer patients had a short survival time compared with the low level. Moreover, the results showed that PELI1 promoted cell proliferation, migration, and invasion, and inhibited apoptosis in vitro. Xenograft tumor experiments were used to determine the biological function of PELI1, and the results showed that PELI1 promoted tumor growth in vivo. Additionally, we found that Jagged1 activated PELI1 transcription in pancreatic cancer cells. To sum up, our results show that PELI1 affects the malignant phenotype of pancreatic cancer.
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Affiliation(s)
- Wenyang Zhou
- Department of Pathology, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, China
| | - Yuying Hu
- Department of Pathology, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, China
| | - Baosheng Wang
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning Province, China
| | - Lina Yuan
- Department of Pathology, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, China
| | - Jia Ma
- Department of Gastroenterology, The Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning Province, China.
| | - Xiangpeng Meng
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning Province, China.
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Shukla N, Kour B, Sharma D, Vijayvargiya M, Sadasukhi TC, Medicherla KM, Malik B, Bissa B, Vuree S, Lohiya NK, Suravajhala P. Towards Understanding the Key Signature Pathways Associated from Differentially Expressed Gene Analysis in an Indian Prostate Cancer Cohort. Diseases 2023; 11:diseases11020072. [PMID: 37218885 DOI: 10.3390/diseases11020072] [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: 02/20/2023] [Revised: 04/13/2023] [Accepted: 04/18/2023] [Indexed: 05/24/2023] Open
Abstract
Prostate cancer (PCa) is one of the most prevalent cancers among men in India. Although studies on PCa have dealt with genetics, genomics, and the environmental influence in the causality of PCa, not many studies employing the Next Generation Sequencing (NGS) approaches of PCa have been carried out. In our previous study, we identified some causal genes and mutations specific to Indian PCa using Whole Exome Sequencing (WES). In the recent past, with the help of different cancer consortiums such as The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC), along with differentially expressed genes (DEGs), many cancer-associated novel non-coding RNAs have been identified as biomarkers. In this work, we attempt to identify differentially expressed genes (DEGs) including long non-coding RNAs (lncRNAs) associated with signature pathways from an Indian PCa cohort using the RNA-sequencing (RNA-seq) approach. From a cohort of 60, we screened six patients who underwent prostatectomy; we performed whole transcriptome shotgun sequencing (WTSS)/RNA-sequencing to decipher the DEGs. We further normalized the read counts using fragments per kilobase of transcript per million mapped reads (FPKM) and analyzed the DEGs using a cohort of downstream regulatory tools, viz., GeneMANIA, Stringdb, Cytoscape-Cytohubba, and cbioportal, to map the inherent signatures associated with PCa. By comparing the RNA-seq data obtained from the pairs of normal and PCa tissue samples using our benchmarked in-house cuffdiff pipeline, we observed some important genes specific to PCa, such as STEAP2, APP, PMEPA1, PABPC1, NFE2L2, and HN1L, and some other important genes known to be involved in different cancer pathways, such as COL6A1, DOK5, STX6, BCAS1, BACE1, BACE2, LMOD1, SNX9, CTNND1, etc. We also identified a few novel lncRNAs such as LINC01440, SOX2OT, ENSG00000232855, ENSG00000287903, and ENST00000647843.1 that need to be characterized further. In comparison with publicly available datasets, we have identified characteristic DEGs and novel lncRNAs implicated in signature PCa pathways in an Indian PCa cohort which perhaps have not been reported. This has set a precedent for us to validate candidates further experimentally, and we firmly believe this will pave a way toward the discovery of biomarkers and the development of novel therapies.
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Affiliation(s)
- Nidhi Shukla
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research (BISR), Statue Circle, Jaipur 302001, India
- Department of Chemistry, School of Basic Sciences, Manipal University Jaipur, Jaipur 303007, India
| | - Bhumandeep Kour
- Department of Biotechnology, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara 144001, India
| | - Devendra Sharma
- Department of Urology, Rukmani Birla Hospital, Jaipur 302018, India
| | - Maneesh Vijayvargiya
- Department of Pathology, Mahatma Gandhi University of Medical Sciences and Technology, Jaipur 302022, India
| | - T C Sadasukhi
- Department of Urology, Mahatma Gandhi University of Medical Sciences and Technology, Jaipur 302022, India
| | - Krishna Mohan Medicherla
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research (BISR), Statue Circle, Jaipur 302001, India
- Department of Bioengineering, Birla Institute of Technology, Mesra Jaipur Campus, 27-Malaviya Industrial Area, Jaipur 302017, India
| | - Babita Malik
- Department of Chemistry, School of Basic Sciences, Manipal University Jaipur, Jaipur 303007, India
| | - Bhawana Bissa
- Department of Biochemistry, Central University of Rajasthan, Ajmer 305817, India
| | - Sugunakar Vuree
- Bioclues.org, Hyderabad 500072, India
- MNR Foundation for Research & Innovation, MNR University, Sangareddy 502294, India
| | - Nirmal Kumar Lohiya
- Department of Zoology, Center for Advanced Studies, University of Rajasthan, Jaipur 302004, India
| | - Prashanth Suravajhala
- Bioclues.org, Hyderabad 500072, India
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 690525, India
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Xue C, Yang Z, Yang B, Xiong H, Ye W. LINC00460 Promotes Cutaneous Squamous Cell Carcinoma Progression Through Stabilizing ELAVL1 Protein. Mol Biotechnol 2022:10.1007/s12033-022-00631-9. [PMID: 36513874 DOI: 10.1007/s12033-022-00631-9] [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: 10/24/2022] [Accepted: 11/28/2022] [Indexed: 12/15/2022]
Abstract
Long intergenic noncoding ribonucleic acid (lncRNA) 460 is reportedly associated with carcinogenesis and progression in various types of cancer. However, the mechanisms underlying its action in cutaneous squamous cell carcinoma (CSCC) remain unclear. LINC00460 mRNA expression was analysed using data from the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. Cell growth, migration, and invasion were evaluated using Cell Counting Kit-8 (CCK-8), 5-ethynyl-2'-deoxyuridine (EdU), transwell migration and invasion assays after inducing LINC00460 knockdown. A xenograft tumour model was used to determine the effects of LINC00460 on tumour growth and metastasis in vivo. To examine the interaction between LINC00460 and ELAVL1, RNA pulldown and RNA immunoprecipitation assays were performed. LINC00460 was found to be significantly upregulated in CSCC tissues and cell lines. Functionally, LINC00460 knockdown inhibited cell proliferation, migration, and invasion in vitro. Consistent with this, when LINC00460 expression decreased, CSCC tumorigenesis and metastasis in vivo were inhibited. Mechanistically, LINC00460 binds to embryonic lethal abnormal vision like RNA binding protein 1 (ELAVL1) and enhances its stability by inhibiting the β-transducin repeats-containing protein (β-TrCP)-mediated ubiquitination of ELAVL1. Moreover, the effect of LINC00460 silencing on the proliferation, migration, and invasion of CSCC cells could be reversed by overexpressing ELAVL1. Our findings demonstrated that LINC00460 plays a critical role in regulating ELAVL1 function. This highlights the potential targets for the clinical diagnosis and treatment of CSCC.
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Affiliation(s)
- Chunli Xue
- Department of Burn Surgery, Huizhou Municipal Central Hospital, Huizhou, 516001, China
| | - Zuxian Yang
- Department of Burn Surgery, Huizhou Municipal Central Hospital, Huizhou, 516001, China
| | - Ben Yang
- Department of Burn Surgery, Huizhou Municipal Central Hospital, Huizhou, 516001, China
| | - Hailin Xiong
- Department of Oncology, Huizhou Municipal Central Hospital, No.41, Erling North Road, Huizhou, 516001, China.
| | - Wei Ye
- Department of Burn Surgery, The First Clinical Medical College of Guangdong Medical University, Huizhou, 516001, China
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Shaath H, Vishnubalaji R, Elango R, Kardousha A, Islam Z, Qureshi R, Alam T, Kolatkar PR, Alajez NM. Long non-coding RNA and RNA-binding protein interactions in cancer: Experimental and machine learning approaches. Semin Cancer Biol 2022; 86:325-345. [PMID: 35643221 DOI: 10.1016/j.semcancer.2022.05.013] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 05/16/2022] [Accepted: 05/20/2022] [Indexed: 01/27/2023]
Abstract
Understanding the complex and specific roles played by non-coding RNAs (ncRNAs), which comprise the bulk of the genome, is important for understanding virtually every hallmark of cancer. This large group of molecules plays pivotal roles in key regulatory mechanisms in various cellular processes. Regulatory mechanisms, mediated by long non-coding RNA (lncRNA) and RNA-binding protein (RBP) interactions, are well documented in several types of cancer. Their effects are enabled through networks affecting lncRNA and RBP stability, RNA metabolism including N6-methyladenosine (m6A) and alternative splicing, subcellular localization, and numerous other mechanisms involved in cancer. In this review, we discuss the reciprocal interplay between lncRNAs and RBPs and their involvement in epigenetic regulation via histone modifications, as well as their key role in resistance to cancer therapy. Other aspects of RBPs including their structural domains, provide a deeper knowledge on how lncRNAs and RBPs interact and exert their biological functions. In addition, current state-of-the-art knowledge, facilitated by machine and deep learning approaches, unravels such interactions in better details to further enhance our understanding of the field, and the potential to harness RNA-based therapeutics as an alternative treatment modality for cancer are discussed.
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Affiliation(s)
- Hibah Shaath
- Translational Cancer and Immunity Center (TCIC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), PO Box 34110, Doha, Qatar
| | - Radhakrishnan Vishnubalaji
- Translational Cancer and Immunity Center (TCIC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), PO Box 34110, Doha, Qatar
| | - Ramesh Elango
- Translational Cancer and Immunity Center (TCIC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), PO Box 34110, Doha, Qatar
| | - Ahmed Kardousha
- College of Health & Life Sciences, Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), PO Box 34110, Doha, Qatar
| | - Zeyaul Islam
- Diabetes Research Center (DRC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, PO Box 34110, Doha, Qatar
| | - Rizwan Qureshi
- College of Science and Engineering, Hamad Bin Khalifa University (HBKU), Qatar Foundation, PO Box 34110, Doha, Qatar
| | - Tanvir Alam
- College of Science and Engineering, Hamad Bin Khalifa University (HBKU), Qatar Foundation, PO Box 34110, Doha, Qatar
| | - Prasanna R Kolatkar
- College of Health & Life Sciences, Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), PO Box 34110, Doha, Qatar; Diabetes Research Center (DRC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, PO Box 34110, Doha, Qatar
| | - Nehad M Alajez
- Translational Cancer and Immunity Center (TCIC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), PO Box 34110, Doha, Qatar; College of Health & Life Sciences, Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), PO Box 34110, Doha, Qatar.
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Wang J, He Z, Liu X, Xu J, Jiang X, Quan G, Jiang J. LINC00941 promotes pancreatic cancer malignancy by interacting with ANXA2 and suppressing NEDD4L-mediated degradation of ANXA2. Cell Death Dis 2022; 13:718. [PMID: 35977942 PMCID: PMC9385862 DOI: 10.1038/s41419-022-05172-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 08/04/2022] [Accepted: 08/08/2022] [Indexed: 01/21/2023]
Abstract
Recently, long non-coding RNAs (lncRNA) have been proven to regulate pancreatic cancer (PC) progression. We aimed to explore the pathogenesis of LINC00941 in PC regarding protein binding. By using PCR analysis, we found that LINC00941 was overexpressed in PC tissues and was higher in patients with liver metastasis than in patients without liver metastasis. In addition, high LINC00941 expression was associated with a poor prognosis. Functional experiments and mice models were respectively used to evaluate PC cell proliferation and migration in vitro and in vivo. The results suggested that LINC00941 overexpression promoted PC proliferation and metastasis. Subsequently, RNA pull-down, mass spectrometry (MS), and RNA-binding protein immunoprecipitation (RIP) were performed to identify LINC00941-interacting proteins. The results suggested that ANXA2 was the potential LINC00941-interacting protein. Nucleotides 500-1390 of LINC00941 could bind to the Annexin 1 domain of ANXA2. LINC00941-mediated malignant phenotype of PC was reversed by ANXA2 depletion. Co-immunoprecipitation (Co-IP) followed by MS was conducted to determine the potential interacting protein of LINC00941. The results illustrated that NEDD4L, an E3 ligase involved in ubiquitin-mediated protein degradation, bound to the Annexin 1 domain of ANXA2 and promoted its degradation. Mechanically, LINC00941 functioned as a decoy to bind to ANXA2 and suppressed its degradation by enclosing the domain that binds to NEDD4L. Eventually, LINC00941 upregulated ANXA2 and activated FAK/AKT signaling, increasing PC cell proliferation and metastasis. This study indicates that LINC00941 promotes PC proliferation and metastasis by binding ANXA2 and potentiating its stability, leading to the activation of FAK/AKT signaling. Our data demonstrate that LINC00941 may serve as a novel target for prognosis and therapy.
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Affiliation(s)
- Jie Wang
- grid.412632.00000 0004 1758 2270Department of Hepatobiliary Surgery, Renmin Hospital of Wuhan University, Wuhan, Hubei China
| | - Zhiwei He
- grid.412632.00000 0004 1758 2270Department of Hepatobiliary Surgery, Renmin Hospital of Wuhan University, Wuhan, Hubei China
| | - Xinyuan Liu
- grid.412632.00000 0004 1758 2270Department of Hepatobiliary Surgery, Renmin Hospital of Wuhan University, Wuhan, Hubei China
| | - Jian Xu
- grid.412632.00000 0004 1758 2270Department of Hepatobiliary Surgery, Renmin Hospital of Wuhan University, Wuhan, Hubei China
| | - Xueyi Jiang
- grid.412632.00000 0004 1758 2270Department of Hepatobiliary Surgery, Renmin Hospital of Wuhan University, Wuhan, Hubei China
| | - Gang Quan
- grid.412632.00000 0004 1758 2270Department of Hepatobiliary Surgery, Renmin Hospital of Wuhan University, Wuhan, Hubei China
| | - Jianxin Jiang
- grid.412632.00000 0004 1758 2270Department of Hepatobiliary Surgery, Renmin Hospital of Wuhan University, Wuhan, Hubei China
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