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Guo YG, Zhang LL, Hu P, Li ZZ, Zhang RB, Lv X, Yi Q, Zhan LB, Feng XL. Correlation analysis of bone marrow microvessel density and miRNA expression on drug resistance in patients with chronic myelogenous leukemia after tyrosine kinase inhibitor treatment. Hematology 2024; 29:2304488. [PMID: 38299685 DOI: 10.1080/16078454.2024.2304488] [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: 08/11/2023] [Accepted: 01/06/2024] [Indexed: 02/02/2024] Open
Abstract
OBJECTIVE This study analyzed the relationship between bone marrow microvessel density (MVD) and the expression of four miRNAs with chronic myelogenous leukemia (CML) resistance after tyrosine kinase inhibitor (TKI) treatment. METHODS 234 CML patients were divided into resistance and non-resistance groups in terms of the results of the 5-year follow-up. Patients were divided into the Optimum response group and the Warning/Failure group based on TKI response. MVD was determined by immunohistochemistry, and the expression levels of four miRNAs (miR-106a, miR-155, miR-146a, and miR-340) in bone marrow biopsy specimens were examined by qPCR. We evaluated the association of MVD with four miRNAs and them predictive value for CML resistance after TKI treatment. RESULTS The MVD and the levels of miR-106a, miR-155, and miR-146a were significantly higher while the miR-340 level was lower in the resistance group than the non-resistance group. Besides, MVD had a significant correlation with the levels of miR-340 and miR-155. According to the results of survival analysis, MVD as well as miR-340 and miR-155 levels were observably correlated with 5-year survival of patients without TKI resistance. The results of the ROC curve indicated that the MVD, miR-106a, miR-340, and miR-155 had good predictive accuracy for CML resistance after TKI treatment. As for the results of multivariate analysis, disease stage, risk level (high risk), high MVD, low miR-340 expression, and high miR-155 expression were all independent risk factors for CML resistance. CONCLUSION MVD and the expression of miR-340 and miR-155 are closely associated with CML resistance after TKI treatment.
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MESH Headings
- Humans
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Bone Marrow/pathology
- Tyrosine Kinase Inhibitors
- Microvascular Density
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology
- Protein Kinase Inhibitors/pharmacology
- Protein Kinase Inhibitors/therapeutic use
- Drug Resistance, Neoplasm/genetics
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Affiliation(s)
- Yi-Gang Guo
- Department of Hematology, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, People's Republic of China
| | - Lu-Lu Zhang
- Department of Hematology, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, People's Republic of China
| | - Ping Hu
- Department of Hematology, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, People's Republic of China
| | - Zhang-Zhi Li
- Department of Hematology, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, People's Republic of China
| | - Rui-Bo Zhang
- Children's Medical Center, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, People's Republic of China
| | - Xi Lv
- Department of Hematology, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, People's Republic of China
| | - Qiong Yi
- Department of Hematology, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, People's Republic of China
| | - Ling-Bo Zhan
- Department of Hematology, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, People's Republic of China
| | - Xue-Lian Feng
- Children's Medical Center, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, People's Republic of China
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Leng X, Zhang M, Xu Y, Wang J, Ding N, Yu Y, Sun S, Dai W, Xue X, Li N, Yang Y, Shi Z. Non-coding RNAs as therapeutic targets in cancer and its clinical application. J Pharm Anal 2024; 14:100947. [PMID: 39149142 PMCID: PMC11325817 DOI: 10.1016/j.jpha.2024.02.001] [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: 10/27/2023] [Revised: 01/12/2024] [Accepted: 02/01/2024] [Indexed: 08/17/2024] Open
Abstract
Cancer genomics has led to the discovery of numerous oncogenes and tumor suppressor genes that play critical roles in cancer development and progression. Oncogenes promote cell growth and proliferation, whereas tumor suppressor genes inhibit cell growth and division. The dysregulation of these genes can lead to the development of cancer. Recent studies have focused on non-coding RNAs (ncRNAs), including circular RNA (circRNA), long non-coding RNA (lncRNA), and microRNA (miRNA), as therapeutic targets for cancer. In this article, we discuss the oncogenes and tumor suppressor genes of ncRNAs associated with different types of cancer and their potential as therapeutic targets. Here, we highlight the mechanisms of action of these genes and their clinical applications in cancer treatment. Understanding the molecular mechanisms underlying cancer development and identifying specific therapeutic targets are essential steps towards the development of effective cancer treatments.
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Affiliation(s)
- Xuejiao Leng
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Mengyuan Zhang
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Yujing Xu
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Jingjing Wang
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Ning Ding
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Yancheng Yu
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Shanliang Sun
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Weichen Dai
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Xin Xue
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Nianguang Li
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Ye Yang
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Zhihao Shi
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, Nanjing, 211198, China
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Shafaee Arani S, Nejati M, Rastgoufar S, Raisi A, Eshraghi R, Ostadian A, Matini AH, Rahimain N, Mirzaei H. Evaluation of expression level of BANCR, MALAT1 and FER1L4 and their target genes in coumarin-treated AGS cell line. Pathol Res Pract 2024; 257:155291. [PMID: 38643553 DOI: 10.1016/j.prp.2024.155291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/23/2024] [Accepted: 04/02/2024] [Indexed: 04/23/2024]
Abstract
Because long non-coding RNAs (lncRNAs) can affect several interconnected processes, its value as a predictive marker for gastric cancer has been demonstrated. Coumarin - a natural compound known to contain some beneficial antitumor qualities - was tested for its effects on AGS gastric cancer cells. In this study, we investigated the expression level of selected cellular lncRNAs (BANCR, MALAT1 and FER1L4) and their target genes (PTEN, p-PI3K and p-AKT) in coumarin-treated AGS cell line. The expressions of the three lncRNAs: BANCR, MALAT1 and FER1L4, as well as their specified targets, PTEN, PI3K and AKT, were measured by qRT-PCR. To gauge the impact of coumarin on the AGS cells, a MTT assay was utilized. A Western blot has been employed to assess variations in PTEN, p-PI3K, and p-AKT expression. The experiment's results showed that AGS viability diminished with increasing doses of coumarin. Compared to the control cells, the cells exposed to coumarin had showed reduced levels of mRNAs which are known targets of the lncRNA BANCR. At the same time, levels of lncRNAs MALAT1 and FER1L4 within coumarin group have been higher comparing to those within control group. Additionally, the Western blot analysis revealed that the coumarin-treated cells expressed lower levels of p-PI3K, PTEN as well as p-AKT compared to control group. This information points to coumarin being a possible option in a treatment regimen for gastric cancer due to its ability to affect lncRNAs and the molecules they target.
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Affiliation(s)
- Shirin Shafaee Arani
- Department of Pathology and Histology, School of Medicine, Shahid Beheshti Hospital, Kashan University of Medical Sciences, Kashan, Iran
| | - Majid Nejati
- Anatomical Sciences Research Center, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
| | - Sepide Rastgoufar
- Department of Pathology and Histology, School of Medicine, Shahid Beheshti Hospital, Kashan University of Medical Sciences, Kashan, Iran
| | - Arash Raisi
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran; Research Committee, Kashan University of Medical Sciences, Kashan, Iran; Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
| | - Reza Eshraghi
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran; Research Committee, Kashan University of Medical Sciences, Kashan, Iran; Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
| | - Amirreza Ostadian
- Department of Laboratory Medicine, School of Allied Medical Sciences, Kashan University of Medical Sciences, Kashan, Iran
| | - Amir Hassan Matini
- Department of Pathology and Histology, School of Medicine, Shahid Beheshti Hospital, Kashan University of Medical Sciences, Kashan, Iran.
| | - Neda Rahimain
- Endocrine Research Center, Institute of Endocrinology and Metabolism, Iran University of Medical Sciences (IUMS), Tehran, Iran; Department of Internal Medicine, School of Medicine, Firoozgar Hospital, Iran University of Medical Sciences, Tehran, Iran.
| | - Hamed Mirzaei
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran.
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Hu Y, Sun Y, Yuan H, Liu J, Chen L, Liu D, Xu Y, Zhou X, Ding L, Zhang Z, Xiong L, Xue L, Wang T. Vof16-miR-185-5p-GAP43 network improves the outcomes following spinal cord injury via enhancing self-repair and promoting axonal growth. CNS Neurosci Ther 2024; 30:e14535. [PMID: 38168094 PMCID: PMC11017428 DOI: 10.1111/cns.14535] [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: 08/29/2022] [Revised: 10/31/2023] [Accepted: 11/04/2023] [Indexed: 01/05/2024] Open
Abstract
INTRODUCTION Self-repair of spinal cord injury (SCI) has been found in humans and experimental animals with partial recovery of neurological functions. However, the regulatory mechanisms underlying the spontaneous locomotion recovery after SCI are elusive. AIMS This study was aimed at evaluating the pathological changes in injured spinal cord and exploring the possible mechanism related to the spontaneous recovery. RESULTS Immunofluorescence staining was performed to detect GAP43 expression in lesion site after spinal cord transection (SCT) in rats. Then RNA sequencing and gene ontology (GO) analysis were employed to predict lncRNA that correlates with GAP43. LncRNA smart-silencing was applied to verify the function of lncRNA vof16 in vitro, and knockout rats were used to evaluate its role in neurobehavioral functions after SCT. MicroRNA sequencing, target scan, and RNA22 prediction were performed to further explore the underlying regulatory mechanisms, and miR-185-5p stands out. A miR-185-5p site-regulated relationship with GAP43 and vof16 was determined by luciferase activity analysis. GAP43-silencing, miR-185-5p-mimic/inhibitor, and miR-185-5p knockout rats were also applied to elucidate their effects on spinal cord neurite growth and neurobehavioral function after SCT. We found that a time-dependent increase of GAP43 corresponded with the limited neurological recovery in rats with SCT. CRNA chip and GO analysis revealed lncRNA vof16 was the most functional in targeting GAP43 in SCT rats. Additionally, silencing vof16 suppressed neurite growth and attenuated the motor dysfunction in SCT rats. Luciferase reporter assay showed that miR-185-5p competitively bound the same regulatory region of vof16 and GAP43. CONCLUSIONS Our data indicated miR-185-5p could be a detrimental factor in SCT, and vof16 may function as a ceRNA by competitively binding miR-185-5p to modulate GAP43 in the process of self-recovery after SCT. Our study revealed a novel vof16-miR-185-5p-GAP43 regulatory network in neurological self-repair after SCT and may underlie the potential treatment target for SCI.
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Affiliation(s)
- Yue Hu
- Department of Anesthesiology, Institute of Neurological Disease, Translational Neuroscience Center, West China HospitalSichuan UniversityChengduChina
- Department of Anesthesia Operation, The First People's Hospital of Shuangliu DistrictWest China Airport Hospital of Sichuan UniversityChengduChina
| | - Yi‐Fei Sun
- Department of Anesthesiology, Institute of Neurological Disease, Translational Neuroscience Center, West China HospitalSichuan UniversityChengduChina
| | - Hao Yuan
- Laboratory Zoology Department, Institute of NeuroscienceKunming Medical UniversityKunmingChina
| | - Jia Liu
- Laboratory Zoology Department, Institute of NeuroscienceKunming Medical UniversityKunmingChina
| | - Li Chen
- Department of Anesthesiology, Institute of Neurological Disease, Translational Neuroscience Center, West China HospitalSichuan UniversityChengduChina
| | - Dong‐Hui Liu
- Clinical and Health SciencesUniversity of South AustraliaAdelaideSouth AustraliaAustralia
| | - Yang Xu
- Department of Anesthesiology, Institute of Neurological Disease, Translational Neuroscience Center, West China HospitalSichuan UniversityChengduChina
| | - Xin‐Fu Zhou
- Clinical and Health SciencesUniversity of South AustraliaAdelaideSouth AustraliaAustralia
| | - Li Ding
- Department of Anesthesiology, Institute of Neurological Disease, Translational Neuroscience Center, West China HospitalSichuan UniversityChengduChina
| | - Ze‐Tao Zhang
- Department of Anesthesiology, Institute of Neurological Disease, Translational Neuroscience Center, West China HospitalSichuan UniversityChengduChina
| | - Liu‐Lin Xiong
- Department of AnesthesiologyAffiliated Hospital of Zunyi Medical UniversityZunyiGuizhouChina
| | - Lu‐Lu Xue
- State Key Laboratory of BiotherapySichuan UniversityChengduSichuanChina
| | - Ting‐Hua Wang
- Department of Anesthesiology, Institute of Neurological Disease, Translational Neuroscience Center, West China HospitalSichuan UniversityChengduChina
- Laboratory Zoology Department, Institute of NeuroscienceKunming Medical UniversityKunmingChina
- State Key Laboratory of BiotherapySichuan UniversityChengduSichuanChina
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5
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Zhang X, Li Y, Cao Y, Wu Y, Cheng G. The Role of Noncoding RNA in the Transmission and Pathogenicity of Flaviviruses. Viruses 2024; 16:242. [PMID: 38400018 PMCID: PMC10892091 DOI: 10.3390/v16020242] [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: 12/11/2023] [Revised: 01/28/2024] [Accepted: 01/31/2024] [Indexed: 02/25/2024] Open
Abstract
Noncoding RNAs (ncRNAs) constitute a class of RNA molecules that lack protein-coding capacity. ncRNAs frequently modulate gene expression through specific interactions with target proteins or messenger RNAs, thereby playing integral roles in a wide array of cellular processes. The Flavivirus genus comprises several significant members, such as dengue virus (DENV), Zika virus (ZIKV), and yellow fever virus (YFV), which have caused global outbreaks, resulting in high morbidity and mortality in human populations. The life cycle of arthropod-borne flaviviruses encompasses their transmission between hematophagous insect vectors and mammalian hosts. During this process, a complex three-way interplay occurs among the pathogen, vector, and host, with ncRNAs exerting a critical regulatory influence. ncRNAs not only constitute a crucial regulatory mechanism that has emerged from the coevolution of viruses and their hosts but also hold potential as antiviral targets for controlling flavivirus epidemics. This review introduces the biogenesis of flavivirus-derived ncRNAs and summarizes the regulatory roles of ncRNAs in viral replication, vector-mediated viral transmission, antiviral innate immunity, and viral pathogenicity. A profound comprehension of the interplay between ncRNAs and flaviviruses will help formulate efficacious prophylactic and therapeutic strategies against flavivirus-related diseases.
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Affiliation(s)
- Xianwen Zhang
- Shenzhen Bay Laboratory, Institute of Infectious Diseases, Shenzhen 518000, China
| | - Yuhan Li
- New Cornerstone Science Laboratory, Tsinghua University-Peking University Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China; (Y.L.); (Y.C.)
| | - Yingyi Cao
- New Cornerstone Science Laboratory, Tsinghua University-Peking University Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China; (Y.L.); (Y.C.)
| | - Ying Wu
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Medical School, Wuhan University, Wuhan 430072, China;
| | - Gong Cheng
- New Cornerstone Science Laboratory, Tsinghua University-Peking University Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China; (Y.L.); (Y.C.)
- Institute of Pathogenic Organisms, Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, China
- Southwest United Graduate School, Kunming 650092, China
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Zhao Y, Xiong W, Li C, Zhao R, Lu H, Song S, Zhou Y, Hu Y, Shi B, Ge J. Hypoxia-induced signaling in the cardiovascular system: pathogenesis and therapeutic targets. Signal Transduct Target Ther 2023; 8:431. [PMID: 37981648 PMCID: PMC10658171 DOI: 10.1038/s41392-023-01652-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/10/2023] [Accepted: 09/13/2023] [Indexed: 11/21/2023] Open
Abstract
Hypoxia, characterized by reduced oxygen concentration, is a significant stressor that affects the survival of aerobic species and plays a prominent role in cardiovascular diseases. From the research history and milestone events related to hypoxia in cardiovascular development and diseases, The "hypoxia-inducible factors (HIFs) switch" can be observed from both temporal and spatial perspectives, encompassing the occurrence and progression of hypoxia (gradual decline in oxygen concentration), the acute and chronic manifestations of hypoxia, and the geographical characteristics of hypoxia (natural selection at high altitudes). Furthermore, hypoxia signaling pathways are associated with natural rhythms, such as diurnal and hibernation processes. In addition to innate factors and natural selection, it has been found that epigenetics, as a postnatal factor, profoundly influences the hypoxic response and progression within the cardiovascular system. Within this intricate process, interactions between different tissues and organs within the cardiovascular system and other systems in the context of hypoxia signaling pathways have been established. Thus, it is the time to summarize and to construct a multi-level regulatory framework of hypoxia signaling and mechanisms in cardiovascular diseases for developing more therapeutic targets and make reasonable advancements in clinical research, including FDA-approved drugs and ongoing clinical trials, to guide future clinical practice in the field of hypoxia signaling in cardiovascular diseases.
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Affiliation(s)
- Yongchao Zhao
- Department of Cardiology, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, China
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, 200032, China
| | - Weidong Xiong
- Department of Cardiology, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, China
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, 200032, China
- Key Laboratory of Viral Heart Diseases, National Health Commission, Shanghai, 200032, China
- Key Laboratory of Viral Heart Diseases, Chinese Academy of Medical Sciences, Shanghai, 200032, China
| | - Chaofu Li
- Department of Cardiology, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, China
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, 200032, China
| | - Ranzun Zhao
- Department of Cardiology, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, China
| | - Hao Lu
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, 200032, China
- National Clinical Research Center for Interventional Medicine, Shanghai, 200032, China
- Shanghai Clinical Research Center for Interventional Medicine, Shanghai, 200032, China
| | - Shuai Song
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, 200032, China
- National Clinical Research Center for Interventional Medicine, Shanghai, 200032, China
- Shanghai Clinical Research Center for Interventional Medicine, Shanghai, 200032, China
| | - You Zhou
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, 200032, China
- National Clinical Research Center for Interventional Medicine, Shanghai, 200032, China
- Shanghai Clinical Research Center for Interventional Medicine, Shanghai, 200032, China
| | - Yiqing Hu
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, 200032, China.
| | - Bei Shi
- Department of Cardiology, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, China.
| | - Junbo Ge
- Department of Cardiology, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, China.
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, 200032, China.
- Key Laboratory of Viral Heart Diseases, National Health Commission, Shanghai, 200032, China.
- Key Laboratory of Viral Heart Diseases, Chinese Academy of Medical Sciences, Shanghai, 200032, China.
- National Clinical Research Center for Interventional Medicine, Shanghai, 200032, China.
- Shanghai Clinical Research Center for Interventional Medicine, Shanghai, 200032, China.
- Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China.
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Liu J, Pan Y, Liu Y, Wei W, Hu X, Xin W, Chen N. The regulation of PTEN: Novel insights into functions as cancer biomarkers and therapeutic targets. J Cell Physiol 2023; 238:1693-1715. [PMID: 37334436 DOI: 10.1002/jcp.31053] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 05/10/2023] [Accepted: 05/17/2023] [Indexed: 06/20/2023]
Abstract
This review summarizes the implications of the primary tumor suppressor protein phosphatase and tensin homolog (PTEN) in aggressive cancer development. PTEN interacts with other cellular proteins or factors suggesting the existence of an intricate molecular network that regulates their oncogenic function. Accumulating evidence has shown that PTEN exists and plays a role in the cytoplasmic organelles and in the nucleus. PTEN blocks phosphoinositide 3-kinases (PI3K)-protein kinase B-mammalian target of rapamycin signaling pathway by dephosphorylating phosphatidylinositol (PI)-3,4,5-triphosphate to PI-4,5-bisphosphate thus counteracting PI3K function. Studies have shown that PTEN expression is tightly regulated at transcriptional, posttranscriptional, and posttranslational levels (including protein-protein interactions and posttranslational modifications). Despite recent advances in PTEN research, the regulation and function of the PTEN gene remain largely unknown. How mutation or loss of specific exons in the PTEN gene occurs and involves in cancer development is not clear. This review illustrates the regulatory mechanisms of PTEN expression and discusses how PTEN participates in tumor development and/or suppression. Future prospects for the clinical applications are also highlighted.
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Affiliation(s)
- Jie Liu
- Department of Dermatology, Skin Research, Peking University Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Yongli Pan
- Department of Neurology, University Medical Center Göttingen, Göttingen, Germany
| | - Yuheng Liu
- Department of Neurology, University Medical Center Göttingen, Göttingen, Germany
| | - Wei Wei
- Department of Neurology, University Medical Center Göttingen, Göttingen, Germany
| | - Xiaoping Hu
- Department of Dermatology, Skin Research, Peking University Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Wenqiang Xin
- Department of Neurology, University Medical Center Göttingen, Göttingen, Germany
| | - Nan Chen
- Department of Gastroenterology, Liaocheng People's Hospital, Liaocheng, China
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8
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Yin X, Wang S, Ge R, Chen J, Gao Y, Xu S, Yang T. Long non-coding RNA DNMBP-AS1 promotes prostate cancer development by regulating LCLAT1. Syst Biol Reprod Med 2023; 69:142-152. [PMID: 36602957 DOI: 10.1080/19396368.2022.2129520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 09/22/2022] [Indexed: 01/06/2023]
Abstract
Prostate cancer (PCa) is as a serious threat to male's health around the world. Recent studies have indicated that long non-coding RNAs (lncRNAs) occupy an important position in various human cancers. However, the function and mechanism of lncRNA DNMBP antisense RNA 1 (DNMBP-AS1) in PCa is rarely investigated. RT-qPCR analysis was used to test gene expression. CCK-8, colony formation, EdU staining and transwell assays were conducted to assess the function of DNMBP-AS1 on PCa cell behaviors. RNA pull down, RIP and luciferase reporter assays were implemented to verify the mechanism of DNMBP-AS1. DNMBP-AS1 was obviously up-regulated in PCa cell lines. Functionally, DNMBP-AS1 knockdown weakened cell proliferation, migration and invasion of PCa. Mechanistically, DNMBP-AS1 sponged microRNA-6766-3p (miR-6766-3p) to regulate lysocardiolipin acyltransferase 1 (LCLAT1) expression. Furthermore, DNMBP-AS1 could stabilize LCLAT1 expression by recruiting ELAV like RNA binding protein 1 (ELAVL1). Consequently, rescue assays demonstrated that DNMBP-AS1 regulated PCa cell proliferation, migration and invasion through enhancing LCLAT1 expression. Collectively, we elucidated the function and regulatory mechanism of DNMBP-AS1 and provided the first evidence of DNMBP-AS1 as a driver for PCa.
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Affiliation(s)
- Xiangang Yin
- Department of Diagnosis, Ningbo Diagnostic Pathology Center, Ningbo, China
| | - Suying Wang
- Department of Diagnosis, Ningbo Diagnostic Pathology Center, Ningbo, China
| | - Rong Ge
- Department of Diagnosis, Ningbo Diagnostic Pathology Center, Ningbo, China
| | - Jinping Chen
- Department of Diagnosis, Ningbo Diagnostic Pathology Center, Ningbo, China
| | - Youliang Gao
- Department of Diagnosis, Ningbo Diagnostic Pathology Center, Ningbo, China
| | - Shanshan Xu
- Department of Diagnosis, Ningbo Diagnostic Pathology Center, Ningbo, China
| | - Ting Yang
- Beijing Jinglai Huake Biotechnology Co., Ltd, Beijing, China
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Yu N, Qin H, Zhang F, Liu T, Cao K, Yang Y, Chen Y, Cai J. The role and mechanism of long non-coding RNAs in homologous recombination repair of radiation-induced DNA damage. J Gene Med 2023; 25:e3470. [PMID: 36537017 DOI: 10.1002/jgm.3470] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/29/2022] [Accepted: 12/04/2022] [Indexed: 12/24/2022] Open
Abstract
DNA double-strand breaks can seriously damage the genetic information that organisms depend on for survival and reproduction. Therefore, cells require a robust DNA damage response mechanism to repair the damaged DNA. Homologous recombination (HR) allows error-free repair, which is key to maintaining genomic integrity. Long non-coding RNAs (lncRNAs) are RNA molecules that are longer than 200 nucleotides. In recent years, a number of studies have found that lncRNAs can act as regulators of gene expression and DNA damage response mechanisms, including HR repair. Moreover, they have significant effects on the occurrence, development, invasion and metastasis of tumor cells, as well as the sensitivity of tumors to radiotherapy and chemotherapy. These studies have therefore begun to expose the great potential of lncRNAs for clinical applications. In this review, we focus on the regulatory roles of lncRNAs in HR repair.
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Affiliation(s)
- Nanxi Yu
- School of Public Health and Management, Wenzhou Medical University, University Town, Wenzhou, China.,South Zhejiang Institute of Radiation Medicine and Nuclear Technology, Wenzhou, China
| | - Hongran Qin
- Department of Nuclear Radiation, Shanghai Pulmonary Hospital,School of Medicine, Tongji University, Shanghai, China
| | - Fangxiao Zhang
- School of Public Health and Management, Wenzhou Medical University, University Town, Wenzhou, China
| | - Tingting Liu
- Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, Shanghai, China
| | - Kun Cao
- Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, Shanghai, China
| | - Yanyong Yang
- Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, Shanghai, China
| | - Yuanyuan Chen
- South Zhejiang Institute of Radiation Medicine and Nuclear Technology, Wenzhou, China.,Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, Shanghai, China
| | - Jianming Cai
- School of Public Health and Management, Wenzhou Medical University, University Town, Wenzhou, China.,South Zhejiang Institute of Radiation Medicine and Nuclear Technology, Wenzhou, China
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10
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Epigenetic regulation in hematopoiesis and its implications in the targeted therapy of hematologic malignancies. Signal Transduct Target Ther 2023; 8:71. [PMID: 36797244 PMCID: PMC9935927 DOI: 10.1038/s41392-023-01342-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 01/03/2023] [Accepted: 01/19/2023] [Indexed: 02/18/2023] Open
Abstract
Hematologic malignancies are one of the most common cancers, and the incidence has been rising in recent decades. The clinical and molecular features of hematologic malignancies are highly heterogenous, and some hematologic malignancies are incurable, challenging the treatment, and prognosis of the patients. However, hematopoiesis and oncogenesis of hematologic malignancies are profoundly affected by epigenetic regulation. Studies have found that methylation-related mutations, abnormal methylation profiles of DNA, and abnormal histone deacetylase expression are recurrent in leukemia and lymphoma. Furthermore, the hypomethylating agents and histone deacetylase inhibitors are effective to treat acute myeloid leukemia and T-cell lymphomas, indicating that epigenetic regulation is indispensable to hematologic oncogenesis. Epigenetic regulation mainly includes DNA modifications, histone modifications, and noncoding RNA-mediated targeting, and regulates various DNA-based processes. This review presents the role of writers, readers, and erasers of DNA methylation and histone methylation, and acetylation in hematologic malignancies. In addition, this review provides the influence of microRNAs and long noncoding RNAs on hematologic malignancies. Furthermore, the implication of epigenetic regulation in targeted treatment is discussed. This review comprehensively presents the change and function of each epigenetic regulator in normal and oncogenic hematopoiesis and provides innovative epigenetic-targeted treatment in clinical practice.
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11
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Li F, Zhou C, Li S, Wang J, Li M, Mu H. Bioinformatic analysis of differentially expressed profiles of lncRNAs and miRNAs with their related ceRNA network in endometrial cancer. Medicine (Baltimore) 2023; 102:e32573. [PMID: 36701720 PMCID: PMC9857477 DOI: 10.1097/md.0000000000032573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Increasing evidence suggests that long non-coding riboneucleic acids (lncRNAs), as competing endogenous RNA (ceRNA), play a key role in the initiation, invasion, and metastasis of cancer. As a new hypothesis, the lncRNA-micro RNA (miRNA)-messenger RNA (mRNA), ceRNA regulatory network has been successfully constructed in a variety of cancers. However, lncRNA, which plays a ceRNA function in endometrial cancer (EC), is still poorly understood. In this study, we downloaded EC expression profiling from The Cancer Genome Atlas database and used the R software "edgeR" package to analyze the differentially expressed genes between EC and normal endometrium samples. Then, differentially expressed (DE) lncRNAs, miRNAs and mRNAs were selected to construct a lncRNA-miRNA-mRNA prognosis-related regulatory network based on interaction information. The Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis were performed on the genes in the network to predict the potential underlying mechanisms and functions of lncRNAs in EC. Kaplan-Meier method and the log-rank test were used for survival analysis. Based on the "ceRNA hypothesis," we constructed a co-expression network of mRNA and lncRNA genes mediated by miRNA in the process of tumor genesis. Furthermore, we successfully constructed a dysregulated lncRNA-associated ceRNA network containing 96 DElncRNAs, 27 DEmiRNAs, and 74 DEmRNAs. Through Kaplan-Meier curve analysis, we found that 9 lncRNAs, 3 miRNAs, and 12 mRNAs were significantly correlated with the overall survival rate of patients among all lncRNAs, miRNAs, and mRNAs involved in ceRNA (P < .05). Our research provides a new perspective for the interaction among lncRNAs, miRNAs, and mRNA and lays the foundation for further research on the mechanism of lncRNAs in the occurrence of EC.
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Affiliation(s)
- Fengfan Li
- The First Central Clinical College of Tianjin Medical University, Tianjin, China
| | - Chunlei Zhou
- Department of Clinical Laboratory, Tianjin First Central Hospital, School of Medicine, Nankai University, Tianjin, China
| | - Shuxuan Li
- Department of Clinical Laboratory, Tianjin First Central Hospital, School of Medicine, Nankai University, Tianjin, China
| | - Jingyu Wang
- Department of Clinical Laboratory, Tianjin First Central Hospital, School of Medicine, Nankai University, Tianjin, China
| | - Ming Li
- Department of Gynecology, Peking University Second Hospital, Beijing, China
| | - Hong Mu
- Department of Clinical Laboratory, Tianjin First Central Hospital, School of Medicine, Nankai University, Tianjin, China
- * Correspondence: Hong Mu, Tianjin First Central Hospital, No. 24 Fukang Road, Nankai District, Tianjin 300190, China (e-mail: )
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12
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Ghazimoradi MH, Karimpour-Fard N, Babashah S. The Promising Role of Non-Coding RNAs as Biomarkers and Therapeutic Targets for Leukemia. Genes (Basel) 2023; 14:131. [PMID: 36672872 PMCID: PMC9859176 DOI: 10.3390/genes14010131] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/02/2022] [Accepted: 12/05/2022] [Indexed: 01/05/2023] Open
Abstract
Early-stage leukemia identification is crucial for effective disease management and leads to an improvement in the survival of leukemia patients. Approaches based on cutting-edge biomarkers with excellent accuracy in body liquids provide patients with the possibility of early diagnosis with high sensitivity and specificity. Non-coding RNAs have recently received a great deal of interest as possible biomarkers in leukemia due to their participation in crucial oncogenic processes such as proliferation, differentiation, invasion, apoptosis, and their availability in body fluids. Recent studies have revealed a strong correlation between leukemia and the deregulated non-coding RNAs. On this basis, these RNAs are also great therapeutic targets. Based on these advantages, we tried to review the role of non-coding RNAs in leukemia. Here, the significance of several non-coding RNA types in leukemia is highlighted, and their potential roles as diagnostic, prognostic, and therapeutic targets are covered.
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Affiliation(s)
- Mohammad H. Ghazimoradi
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 1411713116, Iran
| | - Naeim Karimpour-Fard
- Department of Pharmacoeconomics and Pharmaceutical Administration, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran 1417614411, Iran
| | - Sadegh Babashah
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 1411713116, Iran
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13
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Jafari-Raddani F, Davoodi-Moghaddam Z, Yousefi AM, Ghaffari SH, Bashash D. An overview of long noncoding RNAs: Biology, functions, therapeutics, analysis methods, and bioinformatics tools. Cell Biochem Funct 2022; 40:800-825. [PMID: 36111699 DOI: 10.1002/cbf.3748] [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: 08/16/2022] [Revised: 09/05/2022] [Accepted: 09/06/2022] [Indexed: 12/15/2022]
Abstract
Long noncoding RNAs (lncRNAs) are a diverse class of RNAs whose functions are widespread in all branches of life and have been the focus of attention in the last decade. While a huge number of lncRNAs have been identified, there is still much work to be done and plenty to be learned. In the current review, we begin with the biogenesis and function of lncRNAs as they are involved in the different cellular processes from regulating the architecture of chromosomes to controlling translation and post-translation modifications. Questions on how overexpression, mutations, or deficiency of lncRNAs can affect the cellular status and result in the pathogenesis of various human diseases are responded to. Besides, we allocate an overview of several studies, concerning the application of lncRNAs either as diagnostic and prognostic biomarkers or novel therapeutics. We also introduce the currently available techniques to explore details of lncRNAs such as their function, cellular localization, and structure. In the last section, as exponentially growing data in this area need to be gathered and organized in comprehensive databases, we have a particular focus on presenting general and specialized databases. Taken together, with this review, we aim to provide the latest information on different aspects of lncRNAs to highlight their importance in physiopathologic states and take a step towards helping future studies.
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Affiliation(s)
- Farideh Jafari-Raddani
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zeinab Davoodi-Moghaddam
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Amir-Mohammad Yousefi
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Seyed H Ghaffari
- Hematology, Oncology and Stem Cell Transplantation Research Center, Shariati Hospital, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Davood Bashash
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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14
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Gasic V, Karan-Djurasevic T, Pavlovic D, Zukic B, Pavlovic S, Tosic N. Diagnostic and Therapeutic Implications of Long Non-Coding RNAs in Leukemia. Life (Basel) 2022; 12:1770. [PMID: 36362925 PMCID: PMC9695865 DOI: 10.3390/life12111770] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 10/27/2022] [Accepted: 10/29/2022] [Indexed: 08/26/2023] Open
Abstract
Leukemia is a heterogenous group of hematological malignancies categorized in four main types (acute myeloid leukemia (AML), acute lymphoblastic leukemia (ALL), chronic myeloid leukemia (CML) and chronic lymphocytic leukemia (CLL). Several cytogenetic and molecular markers have become a part of routine analysis for leukemia patients. These markers have been used in diagnosis, risk-stratification and targeted therapy application. Recent studies have indicated that numerous regulatory RNAs, such as long non-coding RNAs (lncRNAs), have a role in tumor initiation and progression. When it comes to leukemia, data for lncRNA involvement in its etiology, progression, diagnosis, treatment and prognosis is limited. The aim of this review is to summarize research data on lncRNAs in different types of leukemia, on their expression pattern, their role in leukemic transformation and disease progression. The usefulness of this information in the clinical setting, i.e., for diagnostic and prognostic purposes, will be emphasized. Finally, how particular lncRNAs could be used as potential targets for the application of targeted therapy will be considered.
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Affiliation(s)
- Vladimir Gasic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11042 Belgrade, Serbia
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15
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LRF Promotes Indirectly Advantageous Chromatin Conformation via BGLT3-lncRNA Expression and Switch from Fetal to Adult Hemoglobin. Int J Mol Sci 2022; 23:ijms23137025. [PMID: 35806029 PMCID: PMC9266405 DOI: 10.3390/ijms23137025] [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: 05/25/2022] [Revised: 06/21/2022] [Accepted: 06/22/2022] [Indexed: 02/01/2023] Open
Abstract
The hemoglobin switch from fetal (HbF) to adult (HbA) has been studied intensively as an essential model for gene expression regulation, but also as a beneficial therapeutic approach for β-hemoglobinopathies, towards the objective of reactivating HbF. The transcription factor LRF (Leukemia/lymphoma-related), encoded from the ZBTB7A gene has been implicated in fetal hemoglobin silencing, though has a wide range of functions that have not been fully clarified. We thus established the LRF/ZBTB7A-overexpressing and ZBTB7A-knockdown K562 (human erythroleukemia cell line) clones to assess fetal vs. adult hemoglobin production pre- and post-induction. Transgenic K562 clones were further developed and studied under the influence of epigenetic chromatin regulators, such as DNA methyl transferase 3 (DNMT3) and Histone Deacetylase 1 (HDAC1), to evaluate LRF’s potential disturbance upon the aberrant epigenetic background and provide valuable information of the preferable epigenetic frame, in which LRF unfolds its action on the β-type globin’s expression. The ChIP-seq analysis demonstrated that LRF binds to γ-globin genes (HBG2/1) and apparently associates BCL11A for their silencing, but also during erythropoiesis induction, LRF binds the BGLT3 gene, promoting BGLT3-lncRNA production through the γ-δ intergenic region of β-type globin’s locus, triggering the transcriptional events from γ- to β-globin switch. Our findings are supported by an up-to-date looping model, which highlights chromatin alterations during erythropoiesis at late stages of gestation, to establish an “open” chromatin conformation across the γ-δ intergenic region and accomplish β-globin expression and hemoglobin switch.
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16
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Lu SY, Hua J, Liu J, Wei MY, Liang C, Meng QC, Zhang B, Yu XJ, Wang W, Xu J. Construction of a paclitaxel-related competitive endogenous RNA network and identification of a potential regulatory axis in pancreatic cancer. Transl Oncol 2022; 20:101419. [PMID: 35413498 PMCID: PMC9018166 DOI: 10.1016/j.tranon.2022.101419] [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: 02/14/2022] [Revised: 03/17/2022] [Accepted: 03/30/2022] [Indexed: 11/28/2022] Open
Abstract
It is the first study to focus on paclitaxel sensitivity and construct ceRNA network in pancreatic cancer. We confirmed a potential PART1/hsa-mir-21/SCRN1 axis and verified it by qPCR. The exploration of the prognostic signature of paclitaxel is significant to its clinical chemotherapy and immune related therapy.
Background Increasing numbers of studies have elucidated the role of competitive endogenous RNA (ceRNA) networks in carcinogenesis. However, the potential role of the paclitaxel-related ceRNA network in the innate mechanism and prognosis of pancreatic cancer has not been identified. Methods Comprehensive bioinformatics analyses were performed to identify drug-related miRNAs (DRmiRNAs), drug-related mRNAs (DRmRNAs) and drug-related lncRNAs (DRlncRNAs) and construct a ceRNA network. The ssGSEA and CIBERSORT algorithms were utilized for immune cell infiltration analysis. Additionally, we validated our paclitaxel-related ceRNA regulatory axis at the gene expression level; functional experiments were conducted to explore the biological functions of the key genes. Results A total of 182 mRNAs, 13 miRNAs, and 53 lncRNAs were confirmed in the paclitaxel-related ceRNA network. In total, 6 mRNAs, 4 miRNAs, and 6 lncRNAs were identified to establish a risk signature and exhibited optimal prognostic effects. The mRNA signature can predict the abundance of immune cell infiltration and the sensitivity of different chemotherapeutic drugs and may also have a guiding effect in immune checkpoint therapy. A potential PART1/hsa-mir-21/SCRN1 axis was confirmed according to the ceRNA theory and was verified by qPCR. The results indicated that PART1 knockdown markedly increased hsa-mir-21 expression but inhibited SCRN1 expression, weakening the proliferation and migration abilities. Conclusions We hypothesized that the paclitaxel-related ceRNA network strongly influences the innate mechanism, prognosis, and immune infiltration of pancreatic cancer. Our risk signatures can accurately predict survival outcomes and provide a clinical basis.
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17
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Comprehensive Analysis of Potential Biomarkers of Acute Lymphoblastic Leukemia in Children by Using a Competing Endogenous RNA Network. JOURNAL OF ONCOLOGY 2022; 2022:4563523. [PMID: 35432537 PMCID: PMC9007646 DOI: 10.1155/2022/4563523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 02/27/2022] [Accepted: 03/10/2022] [Indexed: 11/30/2022]
Abstract
Acute lymphoblastic leukemia (ALL) is the most serious hematological carcinoma in adolescents. The significance of long noncoding RNAs (lncRNAs) and their regulative role in the proliferation and differentiation of myeloid cells in cancer has been recently reported. Nevertheless, key RNAs and the regulatory mechanism of competitive endogenous RNA (ceRNA) network affected by pediatric ALL are not fully illustrated. In this study, phase 2 and 3 pediatric ALL RNA profiles were extracted from the TARGET database and used to identify lncRNAs, microRNAs, and messenger RNAs in high-risk ALL and reconstruct the sponge ceRNA regulatory network. Results indicated that 44 lncRNAs, 25 miRNAs, and 115 mRNA were up/downregulated. Functional analysis with differentially expressed RNAs (DERNAs) showed enriched significant signaling pathways, including PI3K-Akt and p53 signaling cascades and other pathways associated with the tumor. Seventeen differential hub RNAs, including LINC00909, BZRAP1-AS1, C17orf76-AS1, HCG11, MIAT, SNHG5, SNHG15, and TP73-AS1, were identified. The Cox model of correlation indicated that 14 of these RNAs were associated with the progression of pediatric ALL. These findings would help clarify the regulatory role of several lncRNAs as well as provide insights into the leukemogenesis of pediatric ALL to further explore novel prognostic markers/therapeutic targets for ALL.
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18
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Chen X, Kong X, Niu G, Qin F, Duan Y, Ren F. Long non-coding RNA PAXIP-AS1 promotes viability, invasion, and migration of HTR-8/SVneo cells through miR-210-3p/BDNF axis. Hypertens Pregnancy 2022; 41:107-115. [PMID: 35317685 DOI: 10.1080/10641955.2022.2056194] [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] [Indexed: 11/04/2022]
Abstract
OBJECTIVE The aim of this research was to explore the role and potential mechanism of long non-coding RNA PAXIP-AS1 in preeclampsia. METHODS To investigate the effects of PAXIP-AS1 on cell viability, migration, and invasion. The miR-210-3p-targeted relationship with lncRNA PAXIP-AS1 or BDNF was verified. RESULTS PAXIP-AS1 was inversely correlated with miR-210-3p and BDNF was targeted by miR-210-3p. BDNF was positively correlated with PAXIP-AS1 in the serum of preeclampsia patients. The promotion effects of PAXIP-AS1 on cell viability, migration, and invasion were reversed by miR-210-3p up-regulation or BDNF knockdown in trophoblast cells. CONCLUSION PAXIP-AS1 promoted the viability, migration, and invasion of trophoblast cells by regulating the miR-210-3p/BDNF axis.
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Affiliation(s)
- Xuejuan Chen
- Department of Gynecology and Obstetrics, Shengli Oilfield Central Hospital, Dongying City, Shandong Province, China
| | - Xiang Kong
- Department of Gynecology and Obstetrics, Shengli Oilfield Central Hospital, Dongying City, Shandong Province, China
| | - Gang Niu
- Department of Reproductive Medicine, Shengli Oilfield Central Hospital, Dongying City, Shandong Province, China
| | - Fengjin Qin
- Department of Reproductive Medicine, Shengli Oilfield Central Hospital, Dongying City, Shandong Province, China
| | - Yan Duan
- Department of Gynecology and Obstetrics, Shengli Oilfield Central Hospital, Dongying City, Shandong Province, China
| | - Fengjiao Ren
- Department of Gynecology and Obstetrics, Shengli Oilfield Central Hospital, Dongying City, Shandong Province, China
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Identification of Novel Prognostic Signatures for Clear Cell Renal Cell Carcinoma Based on ceRNA Network Construction and Immune Infiltration Analysis. DISEASE MARKERS 2022; 2022:4033583. [PMID: 35320950 PMCID: PMC8938059 DOI: 10.1155/2022/4033583] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 02/20/2022] [Accepted: 03/02/2022] [Indexed: 12/11/2022]
Abstract
Objective. Clear cell renal cell carcinoma (ccRCC) carries significant morbidity and mortality globally and is often resistant to conventional radiotherapy and chemotherapy. Immune checkpoint blockade (ICB) has received attention in ccRCC patients as a promising anticancer treatment. Furthermore, competitive endogenous RNA (ceRNA) networks are crucial for the occurrence and progression of various tumors. This study was aimed at identifying reliable prognostic signatures and exploring potential mechanisms between ceRNA regulation and immune cell infiltration in ccRCC patients. Methods and Results. Gene expression profiling and clinical information of ccRCC samples were obtained from The Cancer Genome Atlas (TCGA) database. Through comprehensive bioinformatic analyses, differentially expressed mRNAs (DEmRNAs;
), lncRNAs (DElncRNAs;
), and miRNAs (DEmiRNAs;
) were identified to establish ceRNA networks. The CIBERSORT algorithm was applied to calculate the proportion of 22 types of tumor-infiltrating immune cells (TIICs) in ccRCC tissues. Subsequently, univariate Cox, Lasso, and multivariate Cox regression analyses were employed to construct ceRNA-related and TIIC-related prognostic signatures. In addition, we explored the relationship between the crucial genes and TIICs via coexpression analysis, which revealed that the interactions between MALAT1, miR-1271-5p, KIAA1324, and follicular helper T cells might be closely correlated with the progression of ccRCC. Ultimately, we preliminarily validated that the potential MALAT1/miR-1271-5p/KIAA1324 axis was consistent with the ceRNA theory by qRT-PCR in the ccRCC cell lines. Conclusion. On the basis of the ceRNA networks and TIICs, we constructed two prognostic signatures with excellent predictive value and explored possible molecular regulatory mechanisms, which might contribute to the improvement of prognosis and individualized treatment for ccRCC patients.
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20
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Liu Y, Li H, Zhao Y, Li D, Zhang Q, Fu J, Fan S. Knockdown of ADORA2A antisense RNA 1 inhibits cell proliferation and enhances imatinib sensitivity in chronic myeloid leukemia. Bioengineered 2022; 13:2296-2307. [PMID: 35034552 PMCID: PMC8973732 DOI: 10.1080/21655979.2021.2024389] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Long non-coding RNAs (LncRNAs) exert important regulatory roles in chronic myeloid leukemia (CML). In this study, we aimed to investigate the potential role and molecular mechanism of lncRNA ADORA2A antisense RNA 1 (ADORA2A-AS1) in CML. We found that the expression of ADORA2A-AS1 was upregulated in CML. Further, knockdown of ADORA2A-AS1 inhibited the proliferation, induced apoptosis, arrested cell cycle, and enhanced imatinib sensitivity in CML cells. Besides, ADORA2A-AS1 promoted the expression of transforming growth factor-beta receptor 1 (TGFBR1) and ATP binding cassette subfamily C member 2 (ABCC2) via sponging miR-665, thereby exerting a tumor-promoting activity. Collectively, our results confirmed the oncogenic effect of ADORA2A-AS1 in CML, indicating that ADORA2A-AS1 is a promosing therapeutic target for CML.
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Affiliation(s)
- Yabo Liu
- Department of Hematology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Huibo Li
- Department of Hematology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Yanqiu Zhao
- Department of Hematology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Dandan Li
- Department of Hematology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Qian Zhang
- Department of Hematology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Jinyue Fu
- Department of Hematology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Shengjin Fan
- Department of Hematology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
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21
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Abstract
Most of the transcribed human genome codes for noncoding RNAs (ncRNAs), and long noncoding RNAs (lncRNAs) make for the lion's share of the human ncRNA space. Despite growing interest in lncRNAs, because there are so many of them, and because of their tissue specialization and, often, lower abundance, their catalog remains incomplete and there are multiple ongoing efforts to improve it. Consequently, the number of human lncRNA genes may be lower than 10,000 or higher than 200,000. A key open challenge for lncRNA research, now that so many lncRNA species have been identified, is the characterization of lncRNA function and the interpretation of the roles of genetic and epigenetic alterations at their loci. After all, the most important human genes to catalog and study are those that contribute to important cellular functions-that affect development or cell differentiation and whose dysregulation may play a role in the genesis and progression of human diseases. Multiple efforts have used screens based on RNA-mediated interference (RNAi), antisense oligonucleotide (ASO), and CRISPR screens to identify the consequences of lncRNA dysregulation and predict lncRNA function in select contexts, but these approaches have unresolved scalability and accuracy challenges. Instead-as was the case for better-studied ncRNAs in the past-researchers often focus on characterizing lncRNA interactions and investigating their effects on genes and pathways with known functions. Here, we focus most of our review on computational methods to identify lncRNA interactions and to predict the effects of their alterations and dysregulation on human disease pathways.
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22
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Ma Y, Guo G, Li T, Wen F, Yang J, Chen B, Wang X, Chen JL. A novel imatinib-upregulated long noncoding RNA plays a critical role in inhibition of tumor growth induced by Abl oncogenes. Mol Cancer 2022; 21:5. [PMID: 34980123 PMCID: PMC8722111 DOI: 10.1186/s12943-021-01478-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 12/06/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Dysregulation of long noncoding RNAs (lncRNAs) has been linked to various human cancers. Bcr-Abl oncogene that results from a reciprocal translocation between human chromosome 9 and 22, is associated with several hematological malignancies. However, the role of lncRNAs in Bcr-Abl-induced leukemia remains largely unexplored. METHODS LncRNA cDNA microarray was employed to identify key lncRNAs involved in Bcr-Abl-mediated cellular transformation. Abl-transformed cell survival and xenografted tumor growth in mice were evaluated to dissect the role of imatinib-upregulated lncRNA 1 (IUR1) in Abl-induced tumorigenesis. Primary bone marrow transformation and in vivo leukemia transplant using lncRNA-IUR1 knockout (KO) mice were further conducted to address the functional relevance of lncRNA-IUR1 in Abl-mediated leukemia. Transcriptome RNA-seq and Western blotting were performed to determine the mechanisms by which lncRNA-IUR1 regulates Bcr-Abl-induced tumorigenesis. RESULTS We identified lncRNA-IUR1 as a critical negative regulator of Bcr-Abl-induced tumorigenesis. LncRNA-IUR1 expressed in a very low level in Bcr-Abl-positive cells from chronic myeloid leukemia patients. Interestingly, it was significantly induced in Abl-positive leukemic cells treated by imatinib. Depletion of lncRNA-IUR1 promoted survival of Abl-transformed human leukemic cells in experiments in vitro and xenografted tumor growth in mice, whereas ectopic expression of lncRNA-IUR1 sensitized the cells to apoptosis and suppressed tumor growth. In concert, silencing murine lncRNA-IUR1 in Abl-transformed cells accelerated cell survival and the development of leukemia in mice. Furthermore, lncRNA-IUR1 deficient mice were generated, and we observed that knockout of murine lncRNA-IUR1 facilitated Bcr-Abl-mediated primary bone marrow transformation. Moreover, animal leukemia model revealed that lncRNA-IUR1 deficiency promoted Abl-transformed cell survival and development of leukemia in mice. Mechanistically, we demonstrated that lncRNA-IUR1 suppressed Bcr-Abl-induced tumorigenesis through negatively regulating STAT5-mediated GATA3 expression. CONCLUSIONS These findings unveil an inhibitory role of lncRNA-IUR1 in Abl-mediated cellular transformation, and provide new insights into molecular mechanisms underlying Abl-induced leukemogenesis.
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Affiliation(s)
- Yun Ma
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guijie Guo
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Tingting Li
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Faxin Wen
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jianling Yang
- Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, 100191, China
| | - Biao Chen
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuefei Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
| | - Ji-Long Chen
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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Naik A, Dalpatraj N, Thakur N. Global Gene Expression Regulation Mediated by TGFβ Through H3K9me3 Mark. Cancer Inform 2022; 21:11769351221115135. [PMID: 35923287 PMCID: PMC9340917 DOI: 10.1177/11769351221115135] [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: 03/10/2022] [Accepted: 07/02/2022] [Indexed: 11/30/2022] Open
Abstract
Background: Epigenetic alterations play an important part in carcinogenesis. Different biological responses, including cell proliferation, migration, apoptosis, invasion, and senescence, are affected by epigenetic alterations in cancer. In addition, growth factors, such as transforming growth factor beta (TGFβ) are important regulators of tumorigenesis. Our understanding of the interplay between the epigenetic bases of tumorigenesis and growth factor signaling in tumorigenesis is rudimentary. Some studies suggest a link between TGFβ signaling and the heterochromatinizing histone mark H3K9me3. There is evidence for signal-dependent interactions between R-Smads and histone methyltransferases. However, the effects of TGFβ signaling on genome wide H3K9me3 landscape remains unknown. Our research examines TGFβ -induced genome-wide H3K9me3 in prostate cancer. Method: Chromatin-Immunoprecipitation followed by sequencing was performed to analyze genome-wide association of H3K9me3 epigenetic mark. DAVID Functional annotation tool was utilized to understand the involvement of different Biological Processes and Molecular Function. MEME-ChIP tool was also used to analyze known and novel DNA-binding motifs. Results: H3K9me3 occupancy appears to increase at intronic regions after short-term (6 hours) TGFβ stimulation and at distal intergenic regions during long-term stimulation (24 hours). We also found evidence for a possible association of SLC transporters with H3K9me3 mark in presence of TGFβ during tumorigenesis. No direct correlation was found between the occupancy of H3K9me3 mark and the expression of various genes. The epigenetic mechanisms-mediated regulation of gene expression by TGFβ was concentrated at promoters rich in SRY and FOXJ3 binding sites. Conclusion: Our results point toward a positive association of oncogenic function of TGFβ and the H3K9me3 mark and provide a context to the role of H3K9me3 in TGFβ-induced cell migration and cell adhesion. Interestingly, these functions of TGFβ through H3K9me3 mark regulation seem to depend on transcriptional activation in contrast to the conventionally known repressive nature of H3K9me3.
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Affiliation(s)
- Ankit Naik
- Biological and Life Sciences, School of Arts and Sciences, Ahmedabad University, Ahmedabad, Gujarat, India
| | - Nidhi Dalpatraj
- Biological and Life Sciences, School of Arts and Sciences, Ahmedabad University, Ahmedabad, Gujarat, India
| | - Noopur Thakur
- Biological and Life Sciences, School of Arts and Sciences, Ahmedabad University, Ahmedabad, Gujarat, India
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24
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Wang L, Zhang Z, Wang H. Downregulation of lncRNA GAS5 prevents mitochondrial apoptosis and hypoxic-ischemic brain damage in neonatal rats through the microRNA-128-3p/Bax/Akt/GSK-3β axis. Neuroreport 2021; 32:1395-1402. [PMID: 34718247 DOI: 10.1097/wnr.0000000000001730] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
OBJECTIVE Hypoxic/ischemic brain damage (HIBD) results in increased neonatal mortality and serious neurologic morbidity. Long noncoding RNAs (lncRNAs) are shown as essential modulators of various neurological diseases. Here, we determined the mechanisms of lncRNA GAS5 in mitochondrial apoptosis in HIBD rats. METHODS The HIBD neonatal rat model was established and treated with shRNA-GAS5 or antagomir miR-128-3p. The morphological changes and apoptosis rate were observed by histological staining. Expressions of GAS5, miR-128-3p, and Bax mRNA in brain tissues of HIBD neonatal rats were determined. The binding relationships between GAS5 and miR-128-3p, and miR-128-3p and Bax were confirmed by dual-luciferase assay. Subsequently, the mitochondrial membrane potential and apoptosis-related factors in brain tissues of HIBD neonatal rats were detected. Western blot analysis was performed to detect the expression of Akt/GSK3β pathway-associated proteins. RESULTS The neurons in the brain tissue of HIBD neonatal rats decreased with disordered arrangement, and showed vacuolization and nuclear pyknosis, obvious brain damage, increased neuronal apoptosis, and enhanced mitochondrial apoptotic pathway. Downregulated miR-128-3p and upregulated GAS5 and Bax mRNA were found in HIBD neonatal rats. There were binding relationships between GAS5 and miR-128-3p, and miR-128-3p and Bax mRNA. Inhibition of lncRNA GAS5 in HIBD neonatal rats suppressed mitochondrial apoptosis. miR-128-3p knockdown annulled the inhibitory effect of inhibiting lncRNA GAS5 on mitochondrial apoptosis. Silencing GAS5 increased the phosphorylation levels of Akt and GSK3β. CONCLUSION Downregulation of lncRNA GAS5 prevents mitochondrial apoptosis in neonatal HIBD rats by regulating the miR-128-3p/Bax/Akt/GSK-3β axis.
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Affiliation(s)
- Li Wang
- Department of Emergency Medicine, The Second Affiliated Hospital, Zhejiang University School of Medicine
| | - Zhe Zhang
- Department of Emergency Medicine, Yuhang Branch of the Second Affiliated Hospital of Zhejiang University School of Medicine, The First People's Hospital of Yuhang District
| | - Haibin Wang
- Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Translational Medicine Research Center, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China
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25
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Abdulmawjood B, Costa B, Roma-Rodrigues C, Baptista PV, Fernandes AR. Genetic Biomarkers in Chronic Myeloid Leukemia: What Have We Learned So Far? Int J Mol Sci 2021; 22:12516. [PMID: 34830398 PMCID: PMC8626020 DOI: 10.3390/ijms222212516] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/11/2021] [Accepted: 11/18/2021] [Indexed: 12/20/2022] Open
Abstract
Chronic Myeloid Leukemia (CML) is a rare malignant proliferative disease of the hematopoietic system, whose molecular hallmark is the Philadelphia chromosome (Ph). The Ph chromosome originates an aberrant fusion gene with abnormal kinase activity, leading to the buildup of reactive oxygen species and genetic instability of relevance in disease progression. Several genetic abnormalities have been correlated with CML in the blast phase, including chromosomal aberrations and common altered genes. Some of these genes are involved in the regulation of cell apoptosis and proliferation, such as the epidermal growth factor receptor (EGFR), tumor protein p53 (TP53), or Schmidt-Ruppin A-2 proto-oncogene (SRC); cell adhesion, e.g., catenin beta 1 (CTNNB1); or genes associated to TGF-β, such as SKI like proto-oncogene (SKIL), transforming growth factor beta 1 (TGFB1) or transforming growth factor beta 2 (TGFB2); and TNF-α pathways, such as Tumor necrosis factor (TNFA) or Nuclear factor kappa B subunit 1 (NFKB1). The involvement of miRNAs in CML is also gaining momentum, where dysregulation of some critical miRNAs, such as miRNA-451 and miRNA-21, which have been associated to the molecular modulation of pathogenesis, progression of disease states, and response to therapeutics. In this review, the most relevant genomic alterations found in CML will be addressed.
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Affiliation(s)
- Bilal Abdulmawjood
- i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal; (B.A.); (B.C.); (C.R.-R.)
- UCIBIO—Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
| | - Beatriz Costa
- i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal; (B.A.); (B.C.); (C.R.-R.)
- UCIBIO—Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
| | - Catarina Roma-Rodrigues
- i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal; (B.A.); (B.C.); (C.R.-R.)
- UCIBIO—Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
| | - Pedro V. Baptista
- i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal; (B.A.); (B.C.); (C.R.-R.)
- UCIBIO—Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
| | - Alexandra R. Fernandes
- i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal; (B.A.); (B.C.); (C.R.-R.)
- UCIBIO—Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
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26
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Zhou J, Wu H, Guo C, Li B, Zhou LL, Liang AB, Fu JF. A comprehensive genome-wide analysis of long non-coding RNA and mRNA expression profiles of JAK2V617F-positive classical myeloproliferative neoplasms. Bioengineered 2021; 12:10564-10586. [PMID: 34738870 PMCID: PMC8810098 DOI: 10.1080/21655979.2021.2000226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Aberrant expression of long non-coding RNAs (lncRNAs) is involved in the progression of myeloid neoplasms, but the role of lncRNAs in the JAK2V617F-positive subtype of classical myeloproliferative neoplasms (cMPNs) remains unclear. This study was conducted to clarify the expression and regulation patterns of lncRNAs in JAK2V617F-positive cMPNs, and to explore new potential carcinogenic factors of cMPNs. Bioinformatics analysis of microarray detection and wet testing verification were performed to study the expression and regulation signature of differentially expressed lncRNAs (DELs) and related genes (DEGs) in cMPNs. The expression of lncRNAs and mRNAs were observed to significantly dysregulated in JAK2V617F-positive cMPN patients compared with the normal controls. Co-expression analysis indicated that there were significant differences of the co-expression pattern of lncRNAs and mRNAs in JAK2V617F-positive cMPN patients compared to normal controls. GO and KEGG pathway analysis of DEGs and DELs showed the involvement of several pathways previously reported to regulate the pathogenesis of leukemia and cMPNs. Cis- and trans-regulation analysis of lncRNAs showed that ZNF141, DHX29, NOC2L, MAS1L, AFAP1L1, and CPN2 were significantly cis-regulated by lncRNA ENST00000356347, ENST00000456816, hsa-mir-449c, NR_026874, TCONS_00012136, uc003lqp.2, and ENST00000456816, respectively, and DELs were mostly correlated with transcription factors including CTBP2, SUZ12, REST, STAT2, and GATA4 to jointly regulate multiple target genes. In summary, expression profiles of lncRNAs and mRNAs were significantly altered in JAK2V617F-positive cMPNs, the relative signaling pathway, co-expression, cis- and trans-regulation were regulated by dysregulation of lncRNAs and several important genes, such as ITGB3, which may act as a promising carcinogenic factor, warrant further investigation.
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Affiliation(s)
- Jie Zhou
- Tongji University School of Medicine, Shanghai, 200092, China.,Department of Gastroenterology, Tongji Hospital of Tongji University, Shanghai, 200065, China
| | - Hao Wu
- Tongji University School of Medicine, Shanghai, 200092, China.,Department of Hematology, Tongji Hospital of Tongji University, Shanghai, 200065, China
| | - Cheng Guo
- Tongji University School of Medicine, Shanghai, 200092, China.,Department of Gastroenterology, Tongji Hospital of Tongji University, Shanghai, 200065, China
| | - Bing Li
- Tongji University School of Medicine, Shanghai, 200092, China.,Department of Hematology, Tongji Hospital of Tongji University, Shanghai, 200065, China
| | - Li-Li Zhou
- Tongji University School of Medicine, Shanghai, 200092, China.,Department of Hematology, Tongji Hospital of Tongji University, Shanghai, 200065, China
| | - Ai-Bin Liang
- Tongji University School of Medicine, Shanghai, 200092, China.,Department of Hematology, Tongji Hospital of Tongji University, Shanghai, 200065, China
| | - Jian-Fei Fu
- Tongji University School of Medicine, Shanghai, 200092, China.,Department of Hematology, Tongji Hospital of Tongji University, Shanghai, 200065, China
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27
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Russi M, Marson D, Fermeglia A, Aulic S, Fermeglia M, Laurini E, Pricl S. The fellowship of the RING: BRCA1, its partner BARD1 and their liaison in DNA repair and cancer. Pharmacol Ther 2021; 232:108009. [PMID: 34619284 DOI: 10.1016/j.pharmthera.2021.108009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 08/22/2021] [Accepted: 09/20/2021] [Indexed: 12/12/2022]
Abstract
The breast cancer type 1 susceptibility protein (BRCA1) and its partner - the BRCA1-associated RING domain protein 1 (BARD1) - are key players in a plethora of fundamental biological functions including, among others, DNA repair, replication fork protection, cell cycle progression, telomere maintenance, chromatin remodeling, apoptosis and tumor suppression. However, mutations in their encoding genes transform them into dangerous threats, and substantially increase the risk of developing cancer and other malignancies during the lifetime of the affected individuals. Understanding how BRCA1 and BARD1 perform their biological activities therefore not only provides a powerful mean to prevent such fatal occurrences but can also pave the way to the development of new targeted therapeutics. Thus, through this review work we aim at presenting the major efforts focused on the functional characterization and structural insights of BRCA1 and BARD1, per se and in combination with all their principal mediators and regulators, and on the multifaceted roles these proteins play in the maintenance of human genome integrity.
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Affiliation(s)
- Maria Russi
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Domenico Marson
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Alice Fermeglia
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Suzana Aulic
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Maurizio Fermeglia
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Erik Laurini
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Sabrina Pricl
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy; Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland.
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28
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Zhao M, Yang F, Sang C, Yan C, Wang Z. BGL3 inhibits papillary thyroid carcinoma progression via regulating PTEN stability. J Endocrinol Invest 2021; 44:2165-2174. [PMID: 33543443 DOI: 10.1007/s40618-021-01519-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 01/23/2021] [Indexed: 02/06/2023]
Abstract
PURPOSE BGL3, a novel long non-coding RNA (lncRNA) that plays a crucial role in several human malignancies. However, the clinical significance and biological function of BGL3 in papillary thyroid carcinoma (PTC) have not been explored. Herein, we aimed to investigate the role of BGL3 in human PTC. METHODS A total of 85 pairs of PTC and normal tissues were collected for clinicopathological analysis. Expression of BGL3 was determined by quantitative real-time polymerase chain reaction (qRT-PCR). The effects of BGL3 on PTC cells ware determined by CCK-8, colony formation, EdU and wound healing assays. The molecular mechanism underlying BGL3 was tested by ChIP, Co-IP, RNA pull-down and luciferase reporter assays. In vivo experiments were conducted using xenografts in nude mice. RESULTS BGL3 was significantly decreased in PTC tissues compared to adjacent normal thyroid tissues, and it was transcriptionally repressed by oncogene Myc. Low BGL3 is positively related to larger tumor size, lymph node metastasis, later TNM stage and poor prognosis. Overexpression of BGL3 inhibited PTC cell proliferation and migration in vitro, and reduced tumor size and lung metastasis nodules in vivo. BGL3 was mainly located in the cytoplasm, in which interacted with PTEN and recruited OTUD3, enhancing the de-ubiquitination effect of OTUD3 on PTEN, resulting in increasing PTEN protein stability and inactivating carcinogenic PI3K/AKT signaling. CONCLUSIONS Our data underscore the critical tumor-inhibiting role of BGL3 in PTC via post-translational regulation of PTEN protein stability, which may serve as a novel therapeutic target and prognostic biomarker in human PTC.
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Affiliation(s)
- M Zhao
- Department of General Surgery, Yanqing District Hospital, Beijing and Yanqing Hospital, Peking University Third Hospital, Beijing, People's Republic of China
| | - F Yang
- Department of Orthopedics, Yanqing District Hospital, Beijing and Yanqing Hospital, Peking University Third Hospital, Beijing, People's Republic of China
| | - C Sang
- Department of General Surgery, Yanqing District Hospital, Beijing and Yanqing Hospital, Peking University Third Hospital, Beijing, People's Republic of China
| | - C Yan
- Department of General Surgery, Yanqing District Hospital, Beijing and Yanqing Hospital, Peking University Third Hospital, Beijing, People's Republic of China
| | - Z Wang
- Department of General Surgery, Beijing Chaoyang Hospital, Capital Medical University, Beijing, People's Republic of China.
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Li L, Li L, Hu L, Li T, Xie D, Liu X. Long non‑coding RNA HAND2‑AS1/miR‑106a/PTEN axis re‑sensitizes cisplatin‑resistant ovarian cells to cisplatin treatment. Mol Med Rep 2021; 24:762. [PMID: 34476500 PMCID: PMC8436234 DOI: 10.3892/mmr.2021.12402] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 05/05/2021] [Indexed: 01/20/2023] Open
Abstract
Cisplatin (DDP) resistance in patients suffering from ovarian cancer is a considerable hurdle to successful treatment. The present study aimed to identify a possible long non‑coding RNA (lncRNA)‑microRNA (miRNA)‑mRNA axis participating in ovarian cancer DDP‑resistance based on the critical roles of non‑coding RNAs, including lncRNAs and miRNAs, in carcinogenesis. According to online data and experimental results, lncRNA HAND2‑AS1 expression was significantly downregulated within ovarian carcinoma, especially within recurrent and DDP‑resistant ovarian carcinoma. The expression of HAND2‑AS1 was also shown to be markedly inhibited in SKOV3/DDP (DDP) cells with resistance to DDP. In SKOV3/DDP cells, HAND2‑AS1 overexpression inhibited cell viability and promoted cell apoptosis upon DDP treatment through the Bcl‑2/caspase‑3 apoptotic signaling. It was hypothesized that PTEN mRNA expression was also markedly inhibited in SKOV3/DDP ovarian cancer cells, while HAND2‑AS1 overexpression rescued PTEN proteins and blocked PI3K/AKT signaling activation. Moreover, miR‑106a was found to bind directly to PTEN 3' UTR and HAND2‑AS1. Upon DDP treatment, miR‑106a overexpression in SKOV3/DDP cells promoted cell viability. It inhibited cell apoptosis through the Bcl‑2/caspase‑3 apoptotic signaling pathway and downregulated the protein levels of PTEN and upregulated PI3K/AKT signaling activity. Furthermore, miR‑106a overexpression partially reversed the effect of HAND2‑AS1 overexpression upon PTEN proteins and SKOV3/DDP cell proliferation upon DDP treatment. In conclusion, a lncRNA HAND2‑AS1/miR‑106a/PTEN axis that re‑sensitizes DDP‑resistant SKOV3/DDP cells to DDP treatment has been established.
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Affiliation(s)
- Lijun Li
- Obstetrics and Gynecology Department, The Fourth Hospital of Changsha, Changsha Hospital of Hunan Normal University, Changsha, Hunan 410006, P.R. China
| | - Li Li
- Obstetrics and Gynecology Department, The Fourth Hospital of Changsha, Changsha Hospital of Hunan Normal University, Changsha, Hunan 410006, P.R. China
| | - Lian Hu
- Obstetrics and Gynecology Department, The Fourth Hospital of Changsha, Changsha Hospital of Hunan Normal University, Changsha, Hunan 410006, P.R. China
| | - Ting Li
- Obstetrics and Gynecology Department, The Fourth Hospital of Changsha, Changsha Hospital of Hunan Normal University, Changsha, Hunan 410006, P.R. China
| | - Dan Xie
- Obstetrics and Gynecology Department, The Fourth Hospital of Changsha, Changsha Hospital of Hunan Normal University, Changsha, Hunan 410006, P.R. China
| | - Xiaoliu Liu
- Obstetrics and Gynecology Department, The Fourth Hospital of Changsha, Changsha Hospital of Hunan Normal University, Changsha, Hunan 410006, P.R. China
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30
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Wong NK, Luo S, Chow EYD, Meng F, Adesanya A, Sun J, Ma HMH, Jin W, Li WC, Yip SP, Huang CL. The Tyrosine Kinase-Driven Networks of Novel Long Non-coding RNAs and Their Molecular Targets in Myeloproliferative Neoplasms. Front Cell Dev Biol 2021; 9:643043. [PMID: 34414175 PMCID: PMC8369571 DOI: 10.3389/fcell.2021.643043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 07/09/2021] [Indexed: 01/16/2023] Open
Abstract
Recent research has focused on the mechanisms by which long non-coding RNAs (lncRNAs) modulate diverse cellular processes such as tumorigenesis. However, the functional characteristics of these non-coding elements in the genome are poorly understood at present. In this study, we have explored several mechanisms that involve the novel lncRNA and microRNA (miRNA) axis participating in modulation of drug response and the tumor microenvironment of myeloproliferative neoplasms (MPNs). We identified novel lncRNAs via mRNA sequencing that was applied to leukemic cell lines derived from BCR-ABL1-positive and JAK2-mutant MPNs under treatment with therapeutic tyrosine kinase inhibitors (TKI). The expression and sequence of novel LNC000093 were further validated in both leukemic cells and normal primary and pluripotent cells isolated from human blood, including samples from patients with chronic myelogenous leukemia (CML). Downregulation of LNC000093 was validated in TKI-resistant CML while a converse expression pattern was observed in blood cells isolated from TKI-sensitive CML cases. In addition to BCR-ABL1-positive CML cells, the driver mutation JAK2-V617F-regulated lncRNA BANCR axis was further identified in BCR-ABL1-negative MPNs. Further genome-wide validation using MPN patient specimens identified 23 unique copy number variants including the 7 differentially expressed lncRNAs from our database. The newly identified LNC000093 served as a competitive endogenous RNA for miR-675-5p and reversed the imatinib resistance in CML cells through regulating RUNX1 expression. The extrinsic function of LNC000093 in exosomal H19/miR-675-induced modulation for the microenvironment was also determined with significant effect on VEGF expression.
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Affiliation(s)
- Nonthaphat Kent Wong
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong
| | - Shumeng Luo
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong
| | - Eudora Y D Chow
- Department of Pathology, United Christian Hospital, Kwun Tong, Hong Kong
| | - Fei Meng
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong
| | - Adenike Adesanya
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong
| | - Jiahong Sun
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong.,Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Herman M H Ma
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong.,Department of Pathology, United Christian Hospital, Kwun Tong, Hong Kong
| | - Wenfei Jin
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Wan-Chun Li
- Institute of Oral Biology, College of Dentistry, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Shea Ping Yip
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong
| | - Chien-Ling Huang
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong
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Jiang L, Ge W, Cui Y, Wang X. The regulation of long non-coding RNA 00958 (LINC00958) for oral squamous cell carcinoma (OSCC) cells death through absent in melanoma 2 (AIM2) depending on microRNA-4306 and Sirtuin1 (SIRT1) in vitro. Bioengineered 2021; 12:5085-5098. [PMID: 34384029 PMCID: PMC8806533 DOI: 10.1080/21655979.2021.1955561] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) have been proposed as potential targets in OSCC gene therapy. Thus, the study aims to analyze how they exert functions in OSCC. LINC00958, AIM2, Gasdermin D (GSDMD) and tumor protein p53 (TP53) expression levels are analyzed by Quantitative Real-time PCR (qPCR) or Western blotting (WB) in OSCC cells lines. The roles of LINC00958 in cell proliferation, cell death, and GSDMD expression respectively were analyzed by Cell Counting Kit-8 (CCK8) assay, flow cytometry and Immunofluorescence (IF) assay. In addition, expressions of pyroptosis- and autophagy-related proteins are evaluated by WB detection. The targeted binding of LINC00958 and miR-4306 or AIM2 mRNA is predicted by bioinformatics analysis and detected by biodual luciferase system. RIP and qPCR assays analyze whether LINC00958 interacts with SIRT1. We found that LINC00958 showed upregulation in OSCC cells compared to normal oral epithelial cells. LINC00958 silencing significantly suppressed OSCC cell proliferation, induced cell death and reduced autophagy. LINC00958 regulated the levels of miR-4306 which binds to the 3'UTR of AIM2, and interacts with and modulates SIRT1 protein expression. LINC00958 regulated GSDMD and AIM2 levels, as well as p53 and SIRT1 levels. SIRT1 overexpression markedly reversed aforementioned effects of LINC00958. LINC00958 not only downregulated miR-4306 levels to activate the pyroptosis pathway mediated by AIM2 and promoted cancer cell survival but also induced a decrease in SIRT protein expression to further reduce p53 levels.
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Affiliation(s)
- Lei Jiang
- Department of Pathology, The Second Affiliated Hospital of Harbin Medical University, Heilongjiang. China
| | - Wenyu Ge
- Department of Stomatology, The Second Affiliated Hospital of Harbin Medical University. Harbin Institute of Technology, Heilongjiang Provincial Hospital, Heilongjiang, China
| | - Yifei Cui
- Department of Pathology, Harbin Medical University Cancer Hospital, Heilongjiang, China
| | - Xiaofeng Wang
- Department of Stomatology, The Second Affiliated Hospital of Harbin Medical University, Heilongjiang, China
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Varier KM, Dhandapani H, Liu W, Song J, Wang C, Hu A, Ben-David Y, Shen X, Li Y, Gajendran B. An immunotherapeutic approach to decipher the role of long non-coding RNAs in cancer progression, resistance and epigenetic regulation of immune cells. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2021; 40:242. [PMID: 34303380 PMCID: PMC8305593 DOI: 10.1186/s13046-021-01997-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 05/27/2021] [Indexed: 01/01/2023]
Abstract
Immunotherapeutic treatments are gaining attention due to their effective anti-tumor response. Particularly, the revolution of immune checkpoint inhibitors (ICIs) produces promising outcomes for various cancer types. However, the usage of immunotherapy is limited due to its low response rate, suggesting that tumor cells escape the immune surveillance. Rapid advances in transcriptomic profiling have led to recognize immune-related long non-coding RNAs (LncRNAs), as regulators of immune cell-specific gene expression that mediates immune stimulatory as well as suppression of immune response, indicating LncRNAs as targets to improve the efficacy of immunotherapy against tumours. Moreover, the immune-related LncRNAs acting as epigenetic modifiers are also under deep investigation. Thus, herein, is a summarised knowledge of LncRNAs and their regulation in the adaptive and innate immune system, considering their importance in autophagy and predicting putative immunotherapeutic responses.
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Affiliation(s)
- Krishnapriya M Varier
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, Guizhou Province, People's Republic of China.,The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academic of Sciences, Guiyang, 550014, Guizhou Province, People's Republic of China.,School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang, 550025, Guizhou Province, People's Republic of China
| | - Hemavathi Dhandapani
- Department of Molecular Oncology, Cancer Institute (WIA), Chennai, 600020, India.,Department of Biosciences & Bioengineering, Indian Institute of Technology Bombay, Mumbai, 400076, India
| | - Wuling Liu
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, Guizhou Province, People's Republic of China.,The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academic of Sciences, Guiyang, 550014, Guizhou Province, People's Republic of China
| | - Jialei Song
- Guizhou University of Traditional Chinese Medicine, Guiyang, 550025, Guizhou Province, People's Republic of China
| | - Chunlin Wang
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, Guizhou Province, People's Republic of China.,The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academic of Sciences, Guiyang, 550014, Guizhou Province, People's Republic of China
| | - Anling Hu
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, Guizhou Province, People's Republic of China.,The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academic of Sciences, Guiyang, 550014, Guizhou Province, People's Republic of China
| | - Yaacov Ben-David
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, Guizhou Province, People's Republic of China. .,The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academic of Sciences, Guiyang, 550014, Guizhou Province, People's Republic of China.
| | - Xiangchun Shen
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, Guizhou Province, People's Republic of China. .,The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academic of Sciences, Guiyang, 550014, Guizhou Province, People's Republic of China. .,School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang, 550025, Guizhou Province, People's Republic of China.
| | - Yanmei Li
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, Guizhou Province, People's Republic of China. .,The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academic of Sciences, Guiyang, 550014, Guizhou Province, People's Republic of China.
| | - Babu Gajendran
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, Guizhou Province, People's Republic of China. .,The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academic of Sciences, Guiyang, 550014, Guizhou Province, People's Republic of China. .,School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang, 550025, Guizhou Province, People's Republic of China.
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Abstract
Long noncoding RNAs (lncRNAs) are involved in numerous cellular processes. Increasing evidence suggests that some lncRNAs function in immunity through various complex mechanisms. However, implication of a large fraction of lncRNAs in antiviral innate immunity remains uncharacterized. Here, we identified a lncRNA called lncRNA IFITM4P that was transcribed from interferon induced transmembrane protein 4 pseudogene (IFITM4P), a pseudogene belonging to interferon induced transmembrane protein (IFITM) family. We found that expression of lncRNA IFITM4P was significantly induced by infection with several viruses including influenza A virus (IAV). Importantly, lncRNA IFITM4P acted as a positive regulator of innate antiviral immunity. Ectopic expression of lncRNA IFITM4P significantly suppressed IAV replication in vitro, whereas IFITM4P deficiency promoted the viral production. We further observed that expression of lncRNA IFITM4P was up-regulated by interferon (IFN) signaling during viral infection, and altering the expression of this lncRNA had significant effects on the mRNA levels of several IFITM family members including IFITM1, IFITM2 and IFITM3. Moreover, it was identified that lncRNA IFITM4P was a target of miR-24-3p that represses mRNA of IFITM1, IFITM2 and IFITM3. The experiments demonstrated that lncRNA IFITM4P was able to cross-regulate the expression of IFITM family members as a competing endogenous RNA (ceRNA), leading to increased stability of these IFITM mRNAs. Together, our results reveal that lncRNA IFITM4P, as a ceRNA, is involved in innate immunity against viral infection through the lncRNA IFITM4P-miR-24-3p- IFITM1/2/3 regulatory network. IMPORTANCE LncRNAs play important roles in various biological processes, but their involvement in host antiviral responses remains largely unknown. In this study, we revealed that the pseudogene IFITM4P belonging to IFITM family can transcribe a functional long noncoding RNA termed lncRNA IFITM4P. Importantly, results showed that lncRNA IFITM4P was involved in innate antiviral immunity, which resembles some interferon-stimulated genes (ISGs). Furthermore, lncRNA IFITM4P was identified as a target of miR-24-3p and acts as a ceRNA to inhibit the replication of IAV through regulating the mRNA levels of IFITM1, IFITM2 and IFITM3. These data provide a new insight into the role of a previously uncharacterized lncRNA encoded by a pseudogene in the host antiviral response, and a better understanding of the IFITM antiviral network.
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Identification of Potential Key lncRNAs in the Context of Mouse Myeloid Differentiation by Systematic Transcriptomics Analysis. Genes (Basel) 2021; 12:genes12050630. [PMID: 33922442 PMCID: PMC8146222 DOI: 10.3390/genes12050630] [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: 02/20/2021] [Revised: 04/09/2021] [Accepted: 04/21/2021] [Indexed: 11/17/2022] Open
Abstract
Hematopoietic differentiation is a well-orchestrated process by many regulators such as transcription factor and long non-coding RNAs (lncRNAs). However, due to the large number of lncRNAs and the difficulty in determining their roles, the study of lncRNAs is a considerable challenge in hematopoietic differentiation. Here, through gene co-expression network analysis over RNA-seq data generated from representative types of mouse myeloid cells, we obtained a catalog of potential key lncRNAs in the context of mouse myeloid differentiation. Then, employing a widely used in vitro cell model, we screened a novel lncRNA, named Gdal1 (Granulocytic differentiation associated lncRNA 1), from this list and demonstrated that Gdal1 was required for granulocytic differentiation. Furthermore, knockdown of Cebpe, a principal transcription factor of granulocytic differentiation regulation, led to down-regulation of Gdal1, but not vice versa. In addition, expression of genes involved in myeloid differentiation and its regulation, such as Cebpa, were influenced in Gdal1 knockdown cells with differentiation blockage. We thus systematically identified myeloid differentiation associated lncRNAs and substantiated the identification by investigation of one of these lncRNAs on cellular phenotype and gene regulation levels. This study promotes our understanding of the regulation of myeloid differentiation and the characterization of roles of lncRNAs in hematopoietic system.
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Long non-coding RNA SNHG16 regulates cell behaviors through miR-542-3p/HNF4α axis via RAS/RAF/MEK/ERK signaling pathway in pediatric neuroblastoma cells. Biosci Rep 2021; 40:224159. [PMID: 32412051 PMCID: PMC7251324 DOI: 10.1042/bsr20200723] [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: 04/09/2020] [Revised: 05/14/2020] [Accepted: 05/14/2020] [Indexed: 01/27/2023] Open
Abstract
Neuroblastoma (NB) is an extracranial solid tumor in children with complex mechanism. Increasing reports indicated that long non-coding RNA (lncRNA) small nucleolar RNA host gene 16 (SNHG16) account for the pathogenesis of NB. Nevertheless, the precise functions of SNHG16 needed to be further exposed in NB progression. Our data revealed that SNHG16 and hepatocyte nuclear factor 4 α (HNF4α) were up-regulated, but miR-542-3p was down-regulated in NB. Knockdown of SNHG16 or HNF4α could impede cell proliferation, migration, invasion, and epithelial-mesenchymal transition (EMT) in vitro. Interestingly, the role of SNHG16 detetion in cell behaviors was rescued by HNF4α overexpression in NB cells. Mechanically, SNHG16 modulated the progression of tumor growth via miR-542-3p/HNF4α axis in NB. Also, SNHG16 knockdown inactivated rat sarcoma/effector of RAS/mitogen-activated extracellular signal-regulated kinase/extracellular regulated protein kinases (RAS/RAF/MEK/ERK) signaling pathway through HNF4α. Therefore, SNHG16/miR-542-3p/HNF4α axis modified NB progression via RAS/RAF/MEK/ERK signaling pathway, might highlight a novel therapeutic approach for NB.
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Wu L, Zhang X, Luo L, Li X, Liu Y, Qin X. Altered expression of serum miR-106a, miR-19b, miR-17, and PTEN in patients with idiopathic membranous nephropathy. J Clin Lab Anal 2021; 35:e23737. [PMID: 33745222 PMCID: PMC8059741 DOI: 10.1002/jcla.23737] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 01/28/2021] [Accepted: 02/02/2021] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND To find new diagnostic markers for idiopathic membranous nephropathy (IMN) and also conduct preliminary explorations into the possible pathogenesis of IMN by comparing the expression of microRNA-451a (miR-451a), miR-106a, miR-19b, miR-17, and phosphatase and tensin homolog (PTEN) protein in the serum of patients with IMN and healthy controls. METHODS The expression levels of miR-451a, miR-106a, miR-19b, and miR-17 in the serum of patients in the IMN group (n = 55, age: 50.2 ± 12.1 years) and the control group (n = 58, age 47.4 ± 13.1 years) were measured by quantitative real-time polymerase chain reaction (qRT-PCR), and the concentration of serum PTEN protein was determined by enzyme-linked immunosorbent assay (ELISA). RESULTS Compared with the control group, the expression of miR-106a, miR-19b, and miR-17 was decreased significantly in the IMN group, whereas PTEN protein concentration was increased significantly in the IMN group. The areas under the receiver operating characteristic curve (AUC) of serum miR-106a, miR-19b, miR-17, and PTEN were 0.66 (95% confidence interval [CI], 0.56-0.76), 0.81 (95% CI, 0.73-0.89), 0.69 (95% CI, 0.59-0.79), and 0.86 (95% CI, 0.79-0.93), respectively. The level of serum PTEN protein was negatively correlated with the expression of miR-106a and miR-19b. PTEN concentration was positively correlated with serum urea (Urea), creatinine (Crea), cystatin C (Cysc), 24 h urine total protein (24 h-UP) and negatively correlated with albumin (Alb) and estimated glomerular filtration rate (eGFR). CONCLUSIONS MiR-106a, miR-19b, miR-17, and PTEN are involved in the pathogenesis of IMN and may become new biomarkers for the diagnosis of IMN.
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Affiliation(s)
- Lina Wu
- Department of Laboratory Medicine, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xinpeng Zhang
- Department of Laboratory Medicine, Shengjing Hospital of China Medical University, Shenyang, China.,Department of Laboratory Medicine, The People's Hospital of Liupanshui City, Liupanshui, China
| | - Lin Luo
- Department of Laboratory Medicine, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xiaoying Li
- Department of Laboratory Medicine, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yong Liu
- Department of Laboratory Medicine, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xiaosong Qin
- Department of Laboratory Medicine, Shengjing Hospital of China Medical University, Shenyang, China
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Johnson SJ, Cooper TA. Overlapping mechanisms of lncRNA and expanded microsatellite RNA. WILEY INTERDISCIPLINARY REVIEWS. RNA 2021; 12:e1634. [PMID: 33191580 PMCID: PMC7880542 DOI: 10.1002/wrna.1634] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 10/14/2020] [Accepted: 10/20/2020] [Indexed: 12/15/2022]
Abstract
RNA has major regulatory roles in a wide range of biological processes and a surge of RNA research has led to the classification of numerous functional RNA species. One example is long noncoding RNAs (lncRNAs) that are structurally complex transcripts >200 nucleotides (nt) in length and lacking a canonical open reading frame (ORF). Despite a general lack of sequence conservation and low expression levels, many lncRNAs have been shown to have functionality in diverse biological processes as well as in mechanisms of disease. In parallel with the growing understanding of lncRNA functions, there is a growing subset of microsatellite expansion disorders in which the primary mechanism of pathogenesis is an RNA gain of function arising from RNA transcripts from the mutant allele. Microsatellite expansion disorders are caused by an expansion of short (3-10 nt) repeats located within coding genes. Expanded repeat-containing RNA mediates toxicity through multiple mechanisms, the details of which remain only partially understood. The purpose of this review is to highlight the links between functional mechanisms of lncRNAs and the potential pathogenic mechanisms of expanded microsatellite RNA. These shared mechanisms include protein sequestration, peptide translation, micro-RNA (miRNA) processing, and miRNA sequestration. Recognizing the parallels between the normal functions of lncRNAs and the negative impact of expanded microsatellite RNA on biological processes can provide reciprocal understanding to the roles of both RNA species. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Sara J Johnson
- Department of Molecular & Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Thomas A Cooper
- Department of Molecular & Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, USA
- Department of Physiology and Biophysics, Baylor College of Medicine, Houston, Texas, USA
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Abstract
Long noncoding RNAs (lncRNAs) have recently been discovered and are increasingly recognized as vital components of modern molecular biology. Accumulating evidence shows that lncRNAs have emerged as important mediators in diverse biological processes such as cell differentiation, pluripotency, and tumorigenesis, while the function of lncRNAs in the field of normal and malignant hematopoiesis remains to be further elucidated. Here, we widely reviewed recent advances and summarize the characteristics and basic mechanisms of lncRNAs and keep abreast of developments of lncRNAs within the field of normal and malignant hematopoiesis. Based on gene regulatory networks at different levels of lncRNAs participation, lncRNAs have been shown to regulate gene expression from epigenetics, transcription and post transcription. The expression of lncRNAs is highly cell-specific and critical for the development and activation of hematopoiesis. Moreover, we also summarized the role of lncRNAs involved in hematological malignancies in recent years. LncRNAs have been found to play an emerging role in normal and malignant hematopoiesis, which may provide novel ideas for the diagnosis and therapeutic targets of hematological diseases in the foreseeable future.
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Zhang Y, Zhou H, Zhang M, Xing L, Yang C, Xia B, Lou G. Integrated analysis of a competing endogenous RNA network reveals an 11-lncRNA prognostic signature in ovarian cancer. Aging (Albany NY) 2020; 12:25153-25171. [PMID: 33223503 PMCID: PMC7803494 DOI: 10.18632/aging.104116] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 09/09/2020] [Indexed: 01/22/2023]
Abstract
Long noncoding RNA (lncRNA) can function as a competing endogenous RNA (ceRNA) involved in tumor initiation and progression. However, the prognostic roles of lncRNAs in the integrated analysis of the ceRNA network in ovarian cancer (OVC) are still lacking. This study aimed to identify lncRNAs associated with the prognosis of OVC. Differential expression analysis and WGCNA were used to screen OVC-specific RNAs. A lncRNA-miRNA-mRNA regulatory network consisting of 201 lncRNAs, 85 miRNA and 146 mRNAs was constructed, and functional enrichment and protein-protein network analyses were performed. Then, the OVC-specific RNAs were submitted to Cox regression analysis. Twelve differentially expressed lncRNAs and mRNAs were identified as significantly associated with OS of OVC patients. Meanwhile, 11 lncRNAs (including C4A-AS1, LINC02408, LINC00488) were established as prognostic risk formulas. The low-risk group had better OS and DFS than the high-risk group (P <0.01). Univariate and multivariate Cox regression analyses revealed the 11-lncRNA risk score as an independent prognostic factor. A prognostic nomogram was developed based on independent prognostic factors. Our data provide evidence that the 11-lncRNA signature could serve as an independent prognostic indicator. This study also suggests that these 11 lncRNAs potentially participate in the progression of OVC.
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Affiliation(s)
- Yongjian Zhang
- Department of Gynecology Oncology, Harbin Medical University Cancer Hospital, Harbin 150081, Heilongjiang Province, China
| | - Hu Zhou
- Department of Gynecology Oncology, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, Hefei 230001, Anhui Province, China
| | - Meiyin Zhang
- Department of Gynecology Oncology, Harbin Medical University Cancer Hospital, Harbin 150081, Heilongjiang Province, China
| | - Linan Xing
- Department of Gynecology Oncology, Harbin Medical University Cancer Hospital, Harbin 150081, Heilongjiang Province, China
| | - Chang Yang
- Department of Gynecology Oncology, Harbin Medical University Cancer Hospital, Harbin 150081, Heilongjiang Province, China
| | - Bairong Xia
- Department of Gynecology Oncology, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, Hefei 230001, Anhui Province, China
| | - Ge Lou
- Department of Gynecology Oncology, Harbin Medical University Cancer Hospital, Harbin 150081, Heilongjiang Province, China
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Wang H, Radomska HS, Phelps MA. Replication Study: Coding-independent regulation of the tumor suppressor PTEN by competing endogenous mRNAs. eLife 2020; 9:56651. [PMID: 33073769 DOI: 10.7554/elife.56651] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 09/18/2020] [Indexed: 12/19/2022] Open
Abstract
As part of the Reproducibility Project: Cancer Biology, we published a Registered Report (Phelps et al., 2016) that described how we intended to replicate selected experiments from the paper 'Coding-independent regulation of the tumor suppressor PTEN by competing endogenous mRNAs' (Tay et al., 2011). Here, we report the results. We found depletion of putative PTEN competing endogenous mRNAs (ceRNAs) in DU145 cells did not impact PTEN 3'UTR regulation using a reporter, while the original study reported decreased activity when SERINC1, VAPA, and CNOT6L were depleted (Figure 3C; Tay et al., 2011). Using the same reporter, we found decreased activity when ceRNA 3'UTRs were overexpressed, while the original study reported increased activity (Figure 3D; Tay et al., 2011). In HCT116 cells, ceRNA depletion resulted in decreased PTEN protein levels, a result similar to the findings reported in the original study (Figure 3G,H; Tay et al., 2011); however, while the original study reported an attenuated ceRNA effect in microRNA deficient (DicerEx5) HCT116 cells, we observed increased PTEN protein levels. Further, we found depletion of the ceRNAs VAPA or CNOT6L did not statistically impact DU145, wild-type HCT116, or DicerEx5 HCT116 cell proliferation. The original study reported increased DU145 and wild-type HCT116 cell proliferation when these ceRNAs were depleted, which was attenuated in the DicerEx5 HCT116 cells (Figure 5B; Tay et al., 2011). Differences between the original study and this replication attempt, such as variance between biological repeats, are factors that might have influenced the results. Finally, we report meta-analyses for each result.
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Affiliation(s)
- Hongyan Wang
- Pharmacoanalytic Shared Resource (PhASR), Comprehensive Cancer Center, The Ohio State University, Columbus, United States
| | - Hanna S Radomska
- Pharmacoanalytic Shared Resource (PhASR), Comprehensive Cancer Center, The Ohio State University, Columbus, United States
| | - Mitch A Phelps
- Pharmacoanalytic Shared Resource (PhASR), Comprehensive Cancer Center, The Ohio State University, Columbus, United States
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- Science Exchange, Palo Alto, United States.,Center for Open Science, Charlottesville, United States
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Lu YB, Shi C, Yang B, Lu ZF, Wu YL, Zhang RY, He X, Li LM, Hu B, Hu YW, Zheng L, Wang Q. Long noncoding RNA ZNF800 suppresses proliferation and migration of vascular smooth muscle cells by upregulating PTEN and inhibiting AKT/mTOR/HIF-1α signaling. Atherosclerosis 2020; 312:43-53. [PMID: 32971395 DOI: 10.1016/j.atherosclerosis.2020.09.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 06/19/2020] [Accepted: 09/08/2020] [Indexed: 01/31/2023]
Abstract
BACKGROUND AND AIMS Long noncoding RNAs (lncRNAs) have recently been implicated in many biological and disease processes, but the exact mechanism of their involvement in atherosclerosis is unclear. The aberrant proliferation and migration of vascular smooth muscle cells (VSMCs) is a major contributor to the development of atherosclerotic lesions. This study aimed to investigate the potential effects of lncRNA ZNF800, a previously uncharacterized lncRNA, on VSMC proliferation and migration. METHODS The expression of lncRNA ZNF800 in atherosclerotic plaque tissues was detected using reverse transcription-quantitative PCR (RT-qPCR), while the role and mechanism of lncRNA ZNF800 in proliferation and migration of VSMCs were investigated by CCK8 assay, transwell assay, scratch wound assay, RT-qPCR and Western blot. RESULTS We found that lncRNA ZNF800 was significantly more abundant in atherosclerotic plaque tissues, and substantially suppressed the proliferation and migration of VSMCs. LncRNA ZNF800 had no effect on phosphatase and tensin homolog deleted on chromosome 10 (PTEN) mRNA expression but dramatically increased the levels of PTEN protein. Enhanced lncRNA ZNF800 expression inhibited the activity of the AKT/mTOR/HIF-1α signaling pathway, downregulated the expression of vascular endothelial growth factor α (VEGF-α) and matrix metalloproteinase 1 (MMP1), and suppressed VSMC proliferation and migration. These inhibitory effects of lncRNA ZNF800 were abolished by knockdown of PTEN. The inhibitory effects of lncRNA ZNF800 on cell proliferation and migration and the expression of VEGF-α and MMP1 were exacerbated by HIF-1α knockdown in VSMCs. CONCLUSIONS These findings demonstrated that lncRNA ZNF800 suppressed VSMC proliferation and migration by interacting with PTEN through a mechanism involving AKT/mTOR/HIF-1α signaling. Therefore, it may play a key atheroprotective role and represent a potential therapeutic target for atherosclerosis-related diseases.
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Affiliation(s)
- Yuan-Bin Lu
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Chao Shi
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Biao Yang
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Zhi-Feng Lu
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Yi-Lin Wu
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Ru-Yi Zhang
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Xin He
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Li-Min Li
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Bing Hu
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Yan-Wei Hu
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China; Department of Clinical Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, China.
| | - Lei Zheng
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.
| | - Qian Wang
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.
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Fabris L, Juracek J, Calin G. Non-Coding RNAs as Cancer Hallmarks in Chronic Lymphocytic Leukemia. Int J Mol Sci 2020; 21:E6720. [PMID: 32937758 PMCID: PMC7554994 DOI: 10.3390/ijms21186720] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/23/2020] [Accepted: 09/10/2020] [Indexed: 01/02/2023] Open
Abstract
The discovery of non-coding RNAs (ncRNAs) and their role in tumor onset and progression has revolutionized the way scientists and clinicians study cancers. This discovery opened new layers of complexity in understanding the fine-tuned regulation of cellular processes leading to cancer. NcRNAs represent a heterogeneous group of transcripts, ranging from a few base pairs to several kilobases, that are able to regulate gene networks and intracellular pathways by interacting with DNA, transcripts or proteins. Deregulation of ncRNAs impinge on several cellular responses and can play a major role in each single hallmark of cancer. This review will focus on the most important short and long non-coding RNAs in chronic lymphocytic leukemia (CLL), highlighting their implications as potential biomarkers and therapeutic targets as they relate to the well-established hallmarks of cancer. The key molecular events in the onset of CLL will be contextualized, taking into account the role of the "dark matter" of the genome.
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Affiliation(s)
- Linda Fabris
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Jaroslav Juracek
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - George Calin
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
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Zhang XY, Mao L. Circular RNA Circ_0000442 acts as a sponge of MiR-148b-3p to suppress breast cancer via PTEN/PI3K/Akt signaling pathway. Gene 2020; 766:145113. [PMID: 32891771 DOI: 10.1016/j.gene.2020.145113] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 08/23/2020] [Accepted: 08/28/2020] [Indexed: 02/06/2023]
Abstract
Breast cancer remains the most common malignancy in women worldwide. Circular RNAs (circRNAs) are a newly validated type of endogenous non-coding RNAs and accumulating evidence suggests that aberrant circRNAs are involved in disease pathogenesis. However, the function of circRNAs in breast cancer remains largely unknown. This study is aimed to characterize the potential role and mechanism of hsa_circ_0000442 (circ_0000442) in breast cancer. The human breast epithelial cell line (MCF-10A), breast cancer cell lines (MCF-7, T47D, BT474, SK-BR-3, MDA-MB-231, SUM-1315) and the Balb/C Nude mice were used for exploration, and the qRT-PCR, western blot, dual-luciferase reporter assay, glo assay, colony formation assay, and tumor xenograft were carried out for investigation. In this study, the results showed a lower expression of circ_0000442 in breast cancer tumor tissues compared with the adjacent normal tissues. Subsequently, circ_0000442 was found to acted as the sponge of miR-148b-3p in breast cancer cells, thus exerting the tumor-suppressive effects. In the subsequent mechanism study, results showed that miR-148b-3p directly targeted PTEN, a well-known tumor suppressor which negatively regulats PI3K/Akt pathway, thus promoting tumor growth in breast cancer. Overall, this study for the first time identified the tumor-suppressive role of circ_0000442 in breast cancer and found PTEN as a novel direct target of miR-148b-3p. The regulatory role of circ_0000442/miR-148b-3p/PTEN/PI3K/Akt axis was preliminarily confirmed in breast cancer cells and mouse models. These findings suggest an important progress in our standing of breast cancer and lay the foundation for the further function, diagnosis, therapy and prognosis research of circular RNAs in breast cancer.
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Affiliation(s)
| | - Ling Mao
- Department of Thyroid and Breast Surgery, the Affiliated Huai'an Hospital of Xuzhou Medical University, the Second People's Hospital of Huai'an, No. 62, Huaihai Road (S.), Huai'an 223002, China.
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Liu Y, Sun P, Zhao Y, Liu B. The role of long non-coding RNAs and downstream signaling pathways in leukemia progression. Hematol Oncol 2020; 39:27-40. [PMID: 32621547 DOI: 10.1002/hon.2776] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/22/2020] [Accepted: 06/25/2020] [Indexed: 01/17/2023]
Abstract
The study of long non-coding RNAs (lncRNA) is a newly established field and our knowledge about them is rapidly growing. These kinds of RNAs are unchanged parts of the genome throughout evolution, that modulate cell growth, differentiation, and apoptosis during diverse physiological and pathological processes including leukemia development. They have the capability to be useful biomarkers for the diagnosis, clinical typing, prognosis, as well as potential therapeutic targets. In this study, we summarized the role of lncRNAs in the expression and function of white blood cells and oncogenic transformation into four main types of leukemia.
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Affiliation(s)
- Yadong Liu
- Department of Spine Surgery, The First Hospital of Jilin University, Changchun, China
| | - Penghao Sun
- Department of Andrology, The First Hospital of Jilin University, Changchun, China
| | - Yuhao Zhao
- Department of Neurosurgery, The First Hospital of Jilin University, Changchun, China
| | - Bin Liu
- Department of Hand Surgery, The First Hospital of Jilin University, Changchun, China
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Han C, Sun LY, Wang WT, Sun YM, Chen YQ. Non-coding RNAs in cancers with chromosomal rearrangements: the signatures, causes, functions and implications. J Mol Cell Biol 2020; 11:886-898. [PMID: 31361891 PMCID: PMC6884712 DOI: 10.1093/jmcb/mjz080] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 05/24/2019] [Accepted: 05/26/2019] [Indexed: 12/25/2022] Open
Abstract
Chromosomal translocation leads to the juxtaposition of two otherwise separate DNA loci, which could result in gene fusion. These rearrangements at the DNA level are catastrophic events and often have causal roles in tumorigenesis. The oncogenic DNA messages are transferred to RNA molecules, which are in most cases translated into cancerous fusion proteins. Gene expression programs and signaling pathways are altered in these cytogenetically abnormal contexts. Notably, non-coding RNAs have attracted increasing attention and are believed to be tightly associated with chromosome-rearranged cancers. These RNAs not only function as modulators in downstream pathways but also directly affect chromosomal translocation or the associated products. This review summarizes recent research advances on the relationship between non-coding RNAs and chromosomal translocations and on diverse functions of non-coding RNAs in cancers with chromosomal rearrangements.
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Affiliation(s)
- Cai Han
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Lin-Yu Sun
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Wen-Tao Wang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Yu-Meng Sun
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Yue-Qin Chen
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
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Benetatos L, Benetatou A, Vartholomatos G. Long non-coding RNAs and MYC association in hematological malignancies. Ann Hematol 2020; 99:2231-2242. [PMID: 32621182 DOI: 10.1007/s00277-020-04166-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 06/29/2020] [Indexed: 12/19/2022]
Abstract
Long non-coding RNAs (lncRNAs) have an established role in cell biology. Among their functions is the regulation of hematopoiesis. They characterize the different stages of hematopoiesis in a more lineage-restricted expression pattern than coding mRNAs. They affect hematopoietic stem cell renewal, proliferation, and differentiation of committed progenitors by interacting with master regulators transcription factors. Among these transcription factors, MYC has a prominent role. Similar to MYC's transcriptional activation/amplification of protein coding genes, MYC also regulates lncRNAs' expression profile, while it is also regulated by lncRNAs. Both myeloid and lymphoid malignancies are prone to the association of MYC with lncRNAs. Such interaction inhibits apoptosis, enhances cell proliferation, deregulates metabolism, and promotes genomic instability and resistance to treatment. In this review, we discuss the recent findings that encompass the crosstalk between lncRNAs and describe the pathways that very probably have a pathogenetic role in both acute and chronic hematologic malignancies.
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Affiliation(s)
| | - Agapi Benetatou
- Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece
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Su W, Wang L, Niu F, Zou L, Guo C, Wang Z, Yang X, Wu J, Lu Y, Zhang J, Beer DG, Yang Z, Chen G. LINC00857 knockdown inhibits cell proliferation and induces apoptosis via involving STAT3 and MET oncogenic proteins in esophageal adenocarcinoma. Aging (Albany NY) 2020; 11:2812-2821. [PMID: 31085800 PMCID: PMC6535059 DOI: 10.18632/aging.101953] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Accepted: 05/02/2019] [Indexed: 01/17/2023]
Abstract
Esophageal adenocarcinoma (EAC) is one of the leading causes of cancer-related death worldwide, and the molecular biology of this cancer remains poorly understood. Recent evidence indicates that long non-coding RNAs are dysregulated in a variety of cancers including EAC. In this study, siRNA mediated gene knockdown, Western blot, RT-PCR, as well as oncogenic function assay were performed. We found that the cell proliferation, colony formation, invasion and migration were decreased after LINC00857 knockdown in EAC cell lines. We also found that knockdown LINC00857 could induce apoptosis. Mechanistically, we found that the MET, STAT3, c-Myc and p-CREB proteins were decreased after LINC00857 knockdown. Our study suggests that LINC00857 may play an important oncogenic role in EAC via STAT3 and MET signaling.
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Affiliation(s)
- Wenmei Su
- Department of Pulmonary Oncology, Affiliated Hospital of Guangdong Medical University, Zhanjiang 524023, China
| | - Lihui Wang
- Key Laboratory of Longevity and Aging-related Diseases of Chinese Ministry of Education, Center for Translational Medicine & School of Preclinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, China
| | - Feiyu Niu
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou 510000, China
| | - Lei Zou
- Department of Organ Transplant, First Affiliated Hospital of Kunming Medical University, Kunming 650032, China
| | - Chunfang Guo
- Section of Thoracic Surgery, Department of Surgery, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Zhuwen Wang
- Section of Thoracic Surgery, Department of Surgery, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Xiao Yang
- Department of Pulmonary Oncology, Affiliated Hospital of Guangdong Medical University, Zhanjiang 524023, China
| | - Jiancong Wu
- Department of Pulmonary Oncology, Affiliated Hospital of Guangdong Medical University, Zhanjiang 524023, China
| | - Yi Lu
- School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China
| | - Jian Zhang
- School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China
| | - David G Beer
- Section of Thoracic Surgery, Department of Surgery, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Zhixiong Yang
- Department of Pulmonary Oncology, Affiliated Hospital of Guangdong Medical University, Zhanjiang 524023, China
| | - Guoan Chen
- School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China
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Long non-coding RNA RP11-59H7.3 promotes cell proliferation and invasion metastasis in colorectal cancer by miR-139-5p/NOTCH1 axis. Aging (Albany NY) 2020; 12:11653-11666. [PMID: 32507766 PMCID: PMC7343512 DOI: 10.18632/aging.103331] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 05/17/2020] [Indexed: 11/30/2022]
Abstract
Increasing evidence suggests long non-coding RNAs (lncRNAs) are distinctively expressed in several cancers. However, the functions of these lncRNAs in cancer development remain unknown. In the current study, we report high expression of a novel lncRNA, RP11-59H7.3, and its association with prognosis in colorectal cancer (CRC) patients. Functional analyses of this lncRNA revealed its role in promoting proliferation and progression of the cell cycle, as well as enhancement of cell migration and invasion. Furthermore, our results revealed that knockdown of RP11-59H7.3 promoted cell apoptosis, with luciferase reporter assays showing that it directly binds to miR-139-5p. Knockdown of this lncRNA significantly reduced expression of NOTCH1, a direct target of miR-139-5p. Additionally, we show that suppression NOTCH1 by miR-139-5p could be partially rescued by overexpressing RP11-59H7.3. Analysis of the relationship between RP11-59H7.3 and miR-139-5p, in CRC tissues, showed a negative correlation while a positive association was observed between the RP11-59H7.3 expression and levels of NOTCH1. Taken together, these results demonstrated that the RP11-59H7.3/miR-139-5p/NOTCH1 axis functions as a key regulator in CRC metastasis. RP11-59H7.3 represents a potential biomarker for CRC diagnosis and could be an important target for development of novel therapies to manage the disease.
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LncRNA SNHG16 induces proliferation and fibrogenesis via modulating miR-141-3p and CCND1 in diabetic nephropathy. Gene Ther 2020; 27:557-566. [PMID: 32504027 DOI: 10.1038/s41434-020-0160-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 05/11/2020] [Accepted: 05/26/2020] [Indexed: 12/15/2022]
Abstract
LncRNAs are reported to participate in the progression of various diseases including diabetic nephropathy. Currently, we reported that SNHG16 was obviously upregulated in db/db mice and high glucose-treated mice mesangial cells. Then, functional experiments showed that SNHG16 silencing significantly inhibited proliferation of mice mesangial cells, which induced the apoptosis and triggered cell cycle arrest. Meanwhile, proliferation-related biomarkers PCNA and Cyclin D1 (CCND1) were greatly repressed. Furthermore, western blot analysis was conducted to test fibrogenesis-associated genes Fibronectin and α-SMA. Meanwhile, the increased protein expression levels of Fibronectin and α-SMA under high glucose conditions were reversed by loss of SNHG16. miR-141-3p has been reported to be involved in various diseases. Then, RNA immunoprecipitation assay revealed the relation between SNHG16 and miR-141-3p. Downregulation of SNHG16 was able to induce expression of miR-141-3p, which was obviously reduced in db/db diabetic nephropathy mice. In addition, CCND1 is a crucial cell cycle master in human diseases. CCND1 was speculated as the target of miR-141-3p and miR-141-3p inhibited CCND1 expression significantly. Meanwhile, we observed that loss of CCND1 greatly repressed mice mesangial cell proliferation and induced cell apoptosis. Taken these together, we revealed for the first time that SNHG16 induced proliferation and fibrogenesis via modulating miR-141-3p and CCND1 in diabetic nephropathy. SNHG16/miR-141-3p/CCND1 axis can suggest a pathological mechanism of progression of diabetic nephropathy.
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Expression of non-coding RNAs in hematological malignancies. Eur J Pharmacol 2020; 875:172976. [DOI: 10.1016/j.ejphar.2020.172976] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 01/18/2020] [Accepted: 01/29/2020] [Indexed: 12/22/2022]
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