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Tekin L, Edgünlü T, Genç D. Immunohistochemical and molecular evaluation of TUSC2 expression in breast cancer. Mol Biol Rep 2024; 51:394. [PMID: 38446366 DOI: 10.1007/s11033-024-09320-z] [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: 11/27/2023] [Accepted: 02/05/2024] [Indexed: 03/07/2024]
Abstract
OBJECTIVE Tumor suppressor candidate 2 has shown to be deleted in lung, colon, and bladder cancer types. In the present study, we aimed to investigate the expression of TUSC2 in breast cancer. MATERIALS AND METHODS A total of thirty patients with breast cancer were included in the study. Normal and tumor tissue samples from fresh mastectomy materials were stored at -80 C until the number of cases was completed for gene expression analysis. Histopathological examination was carried out with routine hematoxylin & eosin method. TUSC2 staining was performed for immunohistochemical analysis. RESULTS The tumors of thirteen patients were Luminal A, fourteen patients were Luminal B, one patient was cerbB2(+), and tumors of two patients were triple-negative. Ki67 proliferation index was less than 14% in fifteen cases and tumor size was less than 2 cm in seven cases. Lymphovascular invasion and lymph node metastasis were present in thirteen cases. Statistically, TUSC2 expression significantly decreased or was lost in breast tumor tissues compared to normal tissues (p < 0.0001). TUSC2 expression decreased as the Ki67 proliferation index increased (p = 0.0003), and TUSC2 expression decreased as tumor size increased (p = 0.0483). The loss or decrease in the TUSC2 expression was significant as the tumor grade increased (p = 0.3740). Gene expression analysis correlated with immunohistochemistry results. CONCLUSION The results of the present study demonstrated a decrease or loss of TUSC2 expression in breast cancer tissue compared to normal tissue. A correlation was found between TUSC2 expression and Ki67 proliferation index and tumor size.
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Affiliation(s)
- Leyla Tekin
- Faculty of Medicine, Pathology Department, Muğla Sıtkı Koçman University, Muğla, Turkey.
| | - Tuba Edgünlü
- Faculty of Medicine, Genetics Department, Muğla Sıtkı Koçman University, Muğla, Turkey
| | - Deniz Genç
- Faculty of Health Sciences, Muğla Sıtkı Koçman University, Muğla, Turkey
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2
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Karimi B, Mokhtari K, Rozbahani H, Peymani M, Nabavi N, Entezari M, Rashidi M, Taheriazam A, Ghaedi K, Hashemi M. Pathological roles of miRNAs and pseudogene-derived lncRNAs in human cancers, and their comparison as prognosis/diagnosis biomarkers. Pathol Res Pract 2024; 253:155014. [PMID: 38128189 DOI: 10.1016/j.prp.2023.155014] [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: 10/23/2023] [Revised: 12/02/2023] [Accepted: 12/02/2023] [Indexed: 12/23/2023]
Abstract
This review examines and compares the diagnostic and prognostic capabilities of miRNAs and lncRNAs derived from pseudogenes in cancer patients. Additionally, it delves into their roles in cancer pathogenesis. Both miRNAs and pseudogene-derived lncRNAs have undergone thorough investigation as remarkably sensitive and specific cancer biomarkers, offering significant potential for cancer detection and monitoring. . Extensive research is essential to gain a complete understanding of the precise roles these non-coding RNAs play in cancer, allowing the development of novel targeted therapies and biomarkers for improved cancer detection and treatment approaches.
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Affiliation(s)
- Bahareh Karimi
- Department of Cellular and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Khatere Mokhtari
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Hossein Rozbahani
- Department of Psychology, North Tehran Branch, Islamic Azad University, Tehran, Iran; Department of Psychology, West Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Maryam Peymani
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Noushin Nabavi
- Department of Urologic Sciences and Vancouver Prostate Centre, University of British Columbia, Vancouver, BC V6H3Z6, Canada
| | - Maliheh Entezari
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Mohsen Rashidi
- Department Pharmacology, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran; The Health of Plant and Livestock Products Research Center, Mazandaran University of Medical Sciences, Sari, Iran.
| | - Afshin Taheriazam
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Orthopedics, Faculty of medicine, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
| | - Kamran Ghaedi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran.
| | - Mehrdad Hashemi
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
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3
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Nakamura-García AK, Espinal-Enríquez J. Pseudogenes in Cancer: State of the Art. Cancers (Basel) 2023; 15:4024. [PMID: 37627052 PMCID: PMC10452131 DOI: 10.3390/cancers15164024] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 07/24/2023] [Accepted: 07/26/2023] [Indexed: 08/27/2023] Open
Abstract
Pseudogenes are duplicates of protein-coding genes that have accumulated multiple detrimental alterations, rendering them unable to produce the protein they encode. Initially disregarded as "junk DNA" due to their perceived lack of functionality, research on their biological roles has been hindered by this assumption. Nevertheless, recent focus has shifted towards these molecules due to their abnormal expression in cancer phenotypes. In this review, our objective is to provide a thorough overview of the current understanding of pseudogene formation, the mechanisms governing their expression, and the roles they may play in promoting tumorigenesis.
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Arrigo A, Regua AT, Najjar MK, Lo HW. Tumor Suppressor Candidate 2 (TUSC2): Discovery, Functions, and Cancer Therapy. Cancers (Basel) 2023; 15:2455. [PMID: 37173921 PMCID: PMC10177220 DOI: 10.3390/cancers15092455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/20/2023] [Accepted: 04/23/2023] [Indexed: 05/15/2023] Open
Abstract
Tumor Suppressor Candidate 2 (TUSC2) was first discovered as a potential tumor suppressor gene residing in the frequently deleted 3p21.3 chromosomal region. Since its discovery, TUSC2 has been found to play vital roles in normal immune function, and TUSC2 loss is associated with the development of autoimmune diseases as well as impaired responses within the innate immune system. TUSC2 also plays a vital role in regulating normal cellular mitochondrial calcium movement and homeostasis. Moreover, TUSC2 serves as an important factor in premature aging. In addition to TUSC2's normal cellular functions, TUSC2 has been studied as a tumor suppressor gene that is frequently deleted or lost in a multitude of cancers, including glioma, sarcoma, and cancers of the lung, breast, ovaries, and thyroid. TUSC2 is frequently lost in cancer due to somatic deletion within the 3p21.3 region, transcriptional inactivation via TUSC2 promoter methylation, post-transcriptional regulation via microRNAs, and post-translational regulation via polyubiquitination and proteasomal degradation. Additionally, restoration of TUSC2 expression promotes tumor suppression, eventuating in decreased cell proliferation, stemness, and tumor growth, as well as increased apoptosis. Consequently, TUSC2 gene therapy has been tested in patients with non-small cell lung cancer. This review will focus on the current understanding of TUSC2 functions in both normal and cancerous tissues, mechanisms of TUSC2 loss, TUSC2 cancer therapeutics, open questions, and future directions.
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Affiliation(s)
- Austin Arrigo
- Department of Neurosurgery, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA (A.T.R.); (M.K.N.)
- Graduate School of Arts and Sciences, Wake Forest University, Winston-Salem, NC 27101, USA
| | - Angelina T. Regua
- Department of Neurosurgery, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA (A.T.R.); (M.K.N.)
| | - Mariana K. Najjar
- Department of Neurosurgery, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA (A.T.R.); (M.K.N.)
- Graduate School of Arts and Sciences, Wake Forest University, Winston-Salem, NC 27101, USA
| | - Hui-Wen Lo
- Department of Neurosurgery, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA (A.T.R.); (M.K.N.)
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Yang X, Shen Z, Tian M, Lin Y, Li L, Chai T, Zhang P, Kang M, Lin J. LncRNA C9orf139 can regulate the progression of esophageal squamous carcinoma by mediating the miR-661/HDAC11 axis. Transl Oncol 2022; 24:101487. [PMID: 35917643 PMCID: PMC9352544 DOI: 10.1016/j.tranon.2022.101487] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 07/04/2022] [Accepted: 07/09/2022] [Indexed: 12/03/2022] Open
Abstract
LncRNA C9orf139 was highly expressed in ESCC. LncRNA C9orf139 could negatively regulate miR-661 expression. HDAC11 expression was negatively regulated by miR-661. LncRNA C9orf139 regulates the progression of ESCC through the miR-661/HDAC11 axis.
Increasing evidence has indicated that long non-coding RNAs (LncRNAs) play multiple functions in the development of cancer and function as indicators of diagnosis and prognosis. This aim of this study was to investigate the roles LncRNA C9orF139 had in the progression of esophageal squamous carcinoma (ESCC). We found C9orf139 was highly expressed in ESCC and knock down the expression of C9orf139 significantly suppressed cell proliferation, promoted apoptosis, and inhibited migration and invasion. C9orf139 was able to negatively regulate miR-661 expression. At the same time, HDAC11 expression was negatively regulated by miR-661. The C9orf139/miR-661/HDAC11 axis was further involved in regulating the expression of the NF-κB signaling pathway. The association between the C9orf139 knockdown and the reduced tumor growth and size was observed during in vivo study. C9orf139 is highly expressed in ESCC, and is thus qualified to be used as a potential diagnostic and prognostic marker for ESCC. Its promotion of ESCC progression is achieved by mediating the miR-661/HDAC11 axis.
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Affiliation(s)
- Xiaojie Yang
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, No. 29 Xinquan Road, Fuzhou 350001, China; Key Laboratory of Cardio-Thoracic Surgery (Fujian Medical University), Fujian Province University, Fuzhou, Fujian, China
| | - Zhimin Shen
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, No. 29 Xinquan Road, Fuzhou 350001, China; Key Laboratory of Cardio-Thoracic Surgery (Fujian Medical University), Fujian Province University, Fuzhou, Fujian, China
| | - Mengyue Tian
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Yukang Lin
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, No. 29 Xinquan Road, Fuzhou 350001, China; Key Laboratory of Cardio-Thoracic Surgery (Fujian Medical University), Fujian Province University, Fuzhou, Fujian, China
| | - Liming Li
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, No. 29 Xinquan Road, Fuzhou 350001, China; Key Laboratory of Cardio-Thoracic Surgery (Fujian Medical University), Fujian Province University, Fuzhou, Fujian, China
| | - Tianci Chai
- Key Laboratory of Cardio-Thoracic Surgery (Fujian Medical University), Fujian Province University, Fuzhou, Fujian, China; Department of Cardiovascular Surgery, Fujian Medical University Union Hospital, Fuzhou, China
| | - Peipei Zhang
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, No. 29 Xinquan Road, Fuzhou 350001, China; Key Laboratory of Cardio-Thoracic Surgery (Fujian Medical University), Fujian Province University, Fuzhou, Fujian, China
| | - Mingqiang Kang
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, No. 29 Xinquan Road, Fuzhou 350001, China; Key Laboratory of Cardio-Thoracic Surgery (Fujian Medical University), Fujian Province University, Fuzhou, Fujian, China.
| | - Jiangbo Lin
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, No. 29 Xinquan Road, Fuzhou 350001, China; Key Laboratory of Cardio-Thoracic Surgery (Fujian Medical University), Fujian Province University, Fuzhou, Fujian, China.
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Lu J, Zhu D, Li L. Biological Functions and Molecular Mechanisms of MiR-608 in Cancer. Front Oncol 2022; 12:870983. [PMID: 35387124 PMCID: PMC8977622 DOI: 10.3389/fonc.2022.870983] [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: 02/07/2022] [Accepted: 02/28/2022] [Indexed: 11/13/2022] Open
Abstract
In recent years, microRNAs (miRNAs) have attracted much attention because of their prominent role in cancer. An increasing number of studies have shown that miRNAs play an important role in a variety of tumors. miR-608 has been reported to be decreased in cancers, especially in solid tumors. miR-608 is regarded as a tumor suppressor, which has been verified through a large number of experiments both in vivo and in vitro. miR-608 participates in many biological processes, including cell proliferation, invasion, migration, and apoptosis, by inhibiting transmembrane proteins and many signaling pathways. Here, we summarize the expression profile and biological functions and mechanism of miR-608, suggesting that miR-608 is an ideal diagnostic and prognostic biomarker and a treatment target for cancer.
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Affiliation(s)
- Juan Lu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Danhua Zhu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
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7
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The microRNA-520a-3p inhibits invasion and metastasis by targeting NF-kappaB signaling pathway in non-small cell lung cancer. Clin Transl Oncol 2022; 24:1569-1579. [PMID: 35247196 DOI: 10.1007/s12094-022-02797-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 01/25/2022] [Indexed: 10/18/2022]
Abstract
PURPOSE To identify the expression of miR-520a-3p and AKT1 in non-small cell lung cancer cells (NSCLC) and the mechanism in inhibiting cell invasion and metastasis by targeting NF-kappaB signaling pathway. METHODS Bioinformatics analysis and dual luciferase reporter gene assay were used to predict and verify the targeting relationship between miR-520a-3p and AKT1. EdU assay was used to detect the proliferation of NSCLC cells. Flow cytometry detected the apoptosis of NSCLC cells. Transwell assay tested the invasion ability of NSCLC cells. qRT-PCR measured the expression of miR-520a-3p and AKT1 mRNA in NSCLC cells; while western blotting was adopted to detect the protein expressions of AKT1, Ki67, CyclinD1, Bax, Bcl-2, MMP-2, MMP-9, NF-kB p65, IkBs kinase (IKK), NF-kB inducing kinase (NIK). RESULTS Bioinformatics analysis suggested that miR-520a-3p could target AKT1. miR-520a-3p could regulate the expression of AKT1 negatively. Compared to mimic-NC group, miR-520a-3p mimic group had increased expressions of miR-520a-3p and Bax, while decreased expressions of AKT1, Ki67, CyclinD1, Bcl-2, MMP-2, MMP-9, NF-kB p65, IKK and NIK, reduced cell proliferation, invasion, and increased cell apoptosis rate (all P < 0.05). Compared to inhibitor NC group, miR-520a-3p inhibitor group had decreased expressions of miR-520a-3p and Bax, but increased expressions of AKT1, Ki67, CyclinD1, Bcl-2, MMP-2, MMP-9, NF-kB p65, IKK and NIK, promoted cell proliferation, invasion, and suppressed cell apoptosis rate (all P < 0.05). CONCLUSION Overexpression of miR-520a-3p can target and downregulate the expression of AKT1 to inhibit the invasion and metastasis of NSCLC via suppressing the activation of NF-kappaB signaling pathway.
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8
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miR-520a-5p regulates Frizzled 9 expression and mediates effects of cigarette smoke and iloprost chemoprevention. Sci Rep 2022; 12:2388. [PMID: 35149732 PMCID: PMC8837775 DOI: 10.1038/s41598-022-06292-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 01/20/2022] [Indexed: 12/19/2022] Open
Abstract
Expression of Frizzled 9 (FZD9) is critical to the activity of the lung cancer chemoprevention agent and prostacyclin analogue, iloprost. FZD9 is required in lung epithelial cells for iloprost to activate peroxisome proliferator activated receptor gamma (PPARG) and related anti-tumor signaling. We aimed to investigate which miRNA regulate FZD9 in the context of cigarette smoke exposure and iloprost treatment. We found that miR-520a-5p binds the FZD9 3’UTR in lung cell lines and alters activity and expression of FZD9 downstream targets. Cigarette smoke condensate (CSC) increases expression of miR-520a-5p, while iloprost decreases expression. Cancer promoting effects of a miR-520a-5p mimic were rescued with iloprost treatment, and effects of cigarette smoke were partially rescued with a miR-520a-5p inhibitor. Here we confirm miR-520a-5p as a regulator of FZD9 activity and a mediator of CSC and iloprost effects in the lung. Targeting miR-520a-5p could be an approach to restoring FZD9 expression and improving response to iloprost lung cancer chemoprevention.
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9
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Mao J, Zhang Z, Chen Y, Wu T, Fersht V, Jin Y, Meng J, Zhang M. Sea cucumber peptides inhibit the malignancy of NSCLC by regulating miR-378a-5p targeted TUSC2. Food Funct 2021; 12:12362-12371. [PMID: 34788772 DOI: 10.1039/d1fo02267a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Lung cancer is a common cancer with high mortality worldwide, and non-small cell lung cancer (NSCLC) accounts for the majority. The clinical treatment effect of NSCLC is not ideal. The aim of this study was to investigate the inhibitory effect of sea cucumber peptide (SCP) on NSCLC and its mechanism. The results showed that SCP could effectively inhibit the proliferation, migration and invasion of A549 cells. In addition, SCP can also inhibit the formation of pleural effusion and tumor growth in lung cancer mice, reduce liver and kidney injury, increase the levels of IL-2 and IL-12, decrease the levels of IL-6 and TNF-α, and prolong the survival time of mice. The microRNA sequencing and immunohistochemistry of mouse tumors showed that the tumor suppressor gene TUSC2 targeted by miR-378a-5p was involved in the inhibition of tumor growth by SCP. This study provides an experimental basis for the further development of SCP as an anti-tumor nutritional supplement, and provides a new idea for exploring the molecular mechanism of food derived active peptides in anti-tumor applications.
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Affiliation(s)
- Jing Mao
- State Key Laboratory of Food Nutrition and Safety, Food Biotechnology Engineering Research Center of Ministry of Education, College of food Science and Engineering, Tianjin University of Science & Technology, Tianjin 300457, China.
| | - Zhuchi Zhang
- State Key Laboratory of Food Nutrition and Safety, Food Biotechnology Engineering Research Center of Ministry of Education, College of food Science and Engineering, Tianjin University of Science & Technology, Tianjin 300457, China.
| | - Yongde Chen
- Bestlife Biological Technology Co., Ltd, Hebei Province, China
| | - Tao Wu
- State Key Laboratory of Food Nutrition and Safety, Food Biotechnology Engineering Research Center of Ministry of Education, College of food Science and Engineering, Tianjin University of Science & Technology, Tianjin 300457, China.
| | - Viktor Fersht
- Center for Applied Medicine and Food Safety "Biomed", Lomonosov Moscow State University, Moscow, Russia
| | - Yan Jin
- State Key Laboratory of Food Nutrition and Safety, Food Biotechnology Engineering Research Center of Ministry of Education, College of food Science and Engineering, Tianjin University of Science & Technology, Tianjin 300457, China.
| | - Jing Meng
- State Key Laboratory of Food Nutrition and Safety, Food Biotechnology Engineering Research Center of Ministry of Education, College of food Science and Engineering, Tianjin University of Science & Technology, Tianjin 300457, China.
- Tianjin International Joint Academy of Biomedicine, Tianjin, China
| | - Min Zhang
- State Key Laboratory of Food Nutrition and Safety, Food Biotechnology Engineering Research Center of Ministry of Education, College of food Science and Engineering, Tianjin University of Science & Technology, Tianjin 300457, China.
- China-Russia Agricultural Products Processing Joint Laboratory, Tianjin Agricultural University, Tianjin 300384, PR China
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Stasiak M, Kolenda T, Kozłowska-Masłoń J, Sobocińska J, Poter P, Guglas K, Paszkowska A, Bliźniak R, Teresiak A, Kazimierczak U, Lamperska K. The World of Pseudogenes: New Diagnostic and Therapeutic Targets in Cancers or Still Mystery Molecules? Life (Basel) 2021; 11:life11121354. [PMID: 34947885 PMCID: PMC8705536 DOI: 10.3390/life11121354] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/01/2021] [Accepted: 12/02/2021] [Indexed: 02/07/2023] Open
Abstract
Pseudogenes were once considered as “junk DNA”, due to loss of their functions as a result of the accumulation of mutations, such as frameshift and presence of premature stop-codons and relocation of genes to inactive heterochromatin regions of the genome. Pseudogenes are divided into two large groups, processed and unprocessed, according to their primary structure and origin. Only 10% of all pseudogenes are transcribed into RNAs and participate in the regulation of parental gene expression at both transcriptional and translational levels through senseRNA (sRNA) and antisense RNA (asRNA). In this review, about 150 pseudogenes in the different types of cancers were analyzed. Part of these pseudogenes seem to be useful in molecular diagnostics and can be detected in various types of biological material including tissue as well as biological fluids (liquid biopsy) using different detection methods. The number of pseudogenes, as well as their function in the human genome, is still unknown. However, thanks to the development of various technologies and bioinformatic tools, it was revealed so far that pseudogenes are involved in the development and progression of certain diseases, especially in cancer.
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Affiliation(s)
- Maciej Stasiak
- Greater Poland Cancer Centre, Laboratory of Cancer Genetics, Garbary 15, 61-866 Poznan, Poland; (M.S.); (J.K.-M.); (J.S.); (K.G.); (A.P.); (R.B.); (A.T.)
- Greater Poland Cancer Centre, Research and Implementation Unit, Garbary 15, 61-866 Poznan, Poland;
| | - Tomasz Kolenda
- Greater Poland Cancer Centre, Laboratory of Cancer Genetics, Garbary 15, 61-866 Poznan, Poland; (M.S.); (J.K.-M.); (J.S.); (K.G.); (A.P.); (R.B.); (A.T.)
- Greater Poland Cancer Centre, Research and Implementation Unit, Garbary 15, 61-866 Poznan, Poland;
- Correspondence: or (T.K.); or (K.L.)
| | - Joanna Kozłowska-Masłoń
- Greater Poland Cancer Centre, Laboratory of Cancer Genetics, Garbary 15, 61-866 Poznan, Poland; (M.S.); (J.K.-M.); (J.S.); (K.G.); (A.P.); (R.B.); (A.T.)
- Greater Poland Cancer Centre, Research and Implementation Unit, Garbary 15, 61-866 Poznan, Poland;
- Faculty of Biology, Institute of Human Biology and Evolution, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
| | - Joanna Sobocińska
- Greater Poland Cancer Centre, Laboratory of Cancer Genetics, Garbary 15, 61-866 Poznan, Poland; (M.S.); (J.K.-M.); (J.S.); (K.G.); (A.P.); (R.B.); (A.T.)
- Greater Poland Cancer Centre, Research and Implementation Unit, Garbary 15, 61-866 Poznan, Poland;
| | - Paulina Poter
- Greater Poland Cancer Centre, Research and Implementation Unit, Garbary 15, 61-866 Poznan, Poland;
- Greater Poland Cancer Center, Department of Oncologic Pathology and Prophylaxis, Poznan University of Medical Sciences, Garbary 15, 61-866 Poznan, Poland
- Department of Pathology, Pomeranian Medical University, Rybacka 1, 70-204 Szczecin, Poland
| | - Kacper Guglas
- Greater Poland Cancer Centre, Laboratory of Cancer Genetics, Garbary 15, 61-866 Poznan, Poland; (M.S.); (J.K.-M.); (J.S.); (K.G.); (A.P.); (R.B.); (A.T.)
- Greater Poland Cancer Centre, Research and Implementation Unit, Garbary 15, 61-866 Poznan, Poland;
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, 61 Zwirki and Wigury, 02-091 Warsaw, Poland
| | - Anna Paszkowska
- Greater Poland Cancer Centre, Laboratory of Cancer Genetics, Garbary 15, 61-866 Poznan, Poland; (M.S.); (J.K.-M.); (J.S.); (K.G.); (A.P.); (R.B.); (A.T.)
- Greater Poland Cancer Centre, Research and Implementation Unit, Garbary 15, 61-866 Poznan, Poland;
- Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Renata Bliźniak
- Greater Poland Cancer Centre, Laboratory of Cancer Genetics, Garbary 15, 61-866 Poznan, Poland; (M.S.); (J.K.-M.); (J.S.); (K.G.); (A.P.); (R.B.); (A.T.)
- Greater Poland Cancer Centre, Research and Implementation Unit, Garbary 15, 61-866 Poznan, Poland;
| | - Anna Teresiak
- Greater Poland Cancer Centre, Laboratory of Cancer Genetics, Garbary 15, 61-866 Poznan, Poland; (M.S.); (J.K.-M.); (J.S.); (K.G.); (A.P.); (R.B.); (A.T.)
- Greater Poland Cancer Centre, Research and Implementation Unit, Garbary 15, 61-866 Poznan, Poland;
| | - Urszula Kazimierczak
- Department of Cancer Immunology, Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland;
| | - Katarzyna Lamperska
- Greater Poland Cancer Centre, Laboratory of Cancer Genetics, Garbary 15, 61-866 Poznan, Poland; (M.S.); (J.K.-M.); (J.S.); (K.G.); (A.P.); (R.B.); (A.T.)
- Greater Poland Cancer Centre, Research and Implementation Unit, Garbary 15, 61-866 Poznan, Poland;
- Correspondence: or (T.K.); or (K.L.)
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Ciomborowska-Basheer J, Staszak K, Kubiak MR, Makałowska I. Not So Dead Genes-Retrocopies as Regulators of Their Disease-Related Progenitors and Hosts. Cells 2021; 10:cells10040912. [PMID: 33921034 PMCID: PMC8071448 DOI: 10.3390/cells10040912] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 03/30/2021] [Accepted: 04/13/2021] [Indexed: 12/12/2022] Open
Abstract
Retroposition is RNA-based gene duplication leading to the creation of single exon nonfunctional copies. Nevertheless, over time, many of these duplicates acquire transcriptional capabilities. In human in most cases, these so-called retrogenes do not code for proteins but function as regulatory long noncoding RNAs (lncRNAs). The mechanisms by which they can regulate other genes include microRNA sponging, modulation of alternative splicing, epigenetic regulation and competition for stabilizing factors, among others. Here, we summarize recent findings related to lncRNAs originating from retrocopies that are involved in human diseases such as cancer and neurodegenerative, mental or cardiovascular disorders. Special attention is given to retrocopies that regulate their progenitors or host genes. Presented evidence from the literature and our bioinformatics analyses demonstrates that these retrocopies, often described as unimportant pseudogenes, are significant players in the cell’s molecular machinery.
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Huang S, Liao Q, Li W, Deng G, Jia M, Fang Q, Ji H, Meng M. The lncRNA PTTG3P promotes the progression of CRPC via upregulating PTTG1. Bull Cancer 2021; 108:359-368. [PMID: 33743960 DOI: 10.1016/j.bulcan.2020.11.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 11/25/2020] [Accepted: 11/26/2020] [Indexed: 11/18/2022]
Abstract
BACKGROUND Overexpression of certain long non-coding RNAs (lncRNAs) promotes the progression of castration-resistant prostate cancer (CRPC). The significance and potential role of the lncRNA designated pituitary tumour-transforming 3, pseudogene (PTTG3P) in CRPC is unknown. METHODS We detected PTTG3P expression by qPCR. Upregulated PTTG3P expression was performed to explore the role of PTTG3P in PCa cells resistant to ADT (androgen deprivation therapy). The relationship among PTTG3P, mir-146a-3p and PTTG1 were validated by qPCR, western blot and luciferase assay. RESULTS PTTG3P levels were significantly increased in the androgen-independent PC cell lines, as well as in CRPC tissues compared with those of the androgen-dependent prostate cancer cell line LNCaP and tumour tissues of patients with hormone-naive prostate cancers. Enforced expression of PTTG3P in androgen-deprived LNCaP cells significantly enhanced survival, clonogenicity, and tumorigenicity. Further, PTTG3P acted as a competing endogenous RNA (ceRNA, natural miRNA sponge) to upregulate PTTG1 expression by competing for mir-146a-3p in the progression to CRPC. CONCLUSION Our findings suggest that PTTG3P promotes the resistance of prostate cancer cells to androgen-deprivation therapy via upregulating PTTG1. PTTG3P may therefore represent a potential target for therapy of CRPC.
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MESH Headings
- Adenocarcinoma/genetics
- Adenocarcinoma/pathology
- Androgen Antagonists/therapeutic use
- Anilides/therapeutic use
- Animals
- Antineoplastic Agents, Hormonal/therapeutic use
- Binding, Competitive
- Cell Line, Tumor
- Drug Resistance, Neoplasm
- Heterografts
- Humans
- Male
- Mice, Nude
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Neoplasm Transplantation
- Nitriles/therapeutic use
- Prostatic Neoplasms, Castration-Resistant/genetics
- Prostatic Neoplasms, Castration-Resistant/pathology
- Pseudogenes
- RNA, Long Noncoding/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Neoplasm/genetics
- RNA, Neoplasm/metabolism
- Securin/biosynthesis
- Securin/genetics
- Tosyl Compounds/therapeutic use
- Tumor Stem Cell Assay
- Up-Regulation
- Mice
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Affiliation(s)
- Shengquan Huang
- Chongqing medical university, The third affiliated hospital (General Hospital), Department of urology, 401120 Chongqing, China
| | - Qianjin Liao
- Chongqing north KuanRen hospital, 400000 Chongqing, China
| | - Weibing Li
- Chongqing medical university, The third affiliated hospital (General Hospital), Department of urology, 401120 Chongqing, China
| | - Guoxian Deng
- Chongqing medical university, The third affiliated hospital (General Hospital), Department of urology, 401120 Chongqing, China
| | - Ming Jia
- Chongqing medical university, The third affiliated hospital (General Hospital), Department of urology, 401120 Chongqing, China
| | - Qiang Fang
- Chongqing medical university, The third affiliated hospital (General Hospital), Department of urology, 401120 Chongqing, China
| | - Huixiang Ji
- Chongqing medical university, The third affiliated hospital (General Hospital), Department of urology, 401120 Chongqing, China.
| | - Mingsen Meng
- Chongqing medical university, The third affiliated hospital (General Hospital), Department of urology, 401120 Chongqing, China.
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Xue W, Zheng Y, Shen Z, Li L, Fan Z, Wang W, Zhu Z, Zhai Y, Zhao J, Kan Q. Involvement of long non-coding RNAs in the progression of esophageal cancer. Cancer Commun (Lond) 2021; 41:371-388. [PMID: 33605567 PMCID: PMC8118593 DOI: 10.1002/cac2.12146] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 12/12/2020] [Accepted: 02/02/2021] [Indexed: 02/06/2023] Open
Abstract
Esophageal cancer (EC) is one of the most common malignant tumors of the digestive system with high incidence and mortality rate worldwide. Therefore, exploring the pathogenesis of EC and searching for new targeted therapies are the current research hotspot for EC treatment. Long non‐coding RNAs (lncRNAs) are endogenous RNAs with more than 200 nucleotides, but without protein‐coding function. In recent years, lncRNAs have gradually become the focuses in the field of non‐coding RNA. Some lncRNAs have been proved to be closely related to the pathogenesis of EC. Many lncRNAs are abnormally expressed in EC and participate in many biological processes including cell proliferation, apoptosis, and metastasis by inhibiting or promoting target gene expression. LncRNAs can also regulate the progression of EC through epithelial‐mesenchymal transformation (EMT), which is closely related to the occurrence, development, and prognosis of EC. In this article, we review and discuss the involvement of lncRNAs in the progression of EC.
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Affiliation(s)
- Wenhua Xue
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, P. R. China.,Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, Henan, 450052, P. R. China
| | - Yuanyuan Zheng
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, P. R. China.,Internet Medical and System Applications of National Engineering Laboratory, Zhengzhou, Henan, 450052, P. R. China
| | - Zhibo Shen
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, P. R. China.,Department of Oncology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, P. R. China.,Internet Medical and System Applications of National Engineering Laboratory, Zhengzhou, Henan, 450052, P. R. China
| | - Lifeng Li
- Department of Oncology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, P. R. China.,Internet Medical and System Applications of National Engineering Laboratory, Zhengzhou, Henan, 450052, P. R. China
| | - Zhirui Fan
- Department of Oncology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, P. R. China
| | - Wenbin Wang
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, P. R. China
| | - Zijia Zhu
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, P. R. China
| | - Yunkai Zhai
- Internet Medical and System Applications of National Engineering Laboratory, Zhengzhou, Henan, 450052, P. R. China
| | - Jie Zhao
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, P. R. China.,Internet Medical and System Applications of National Engineering Laboratory, Zhengzhou, Henan, 450052, P. R. China
| | - Quancheng Kan
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, P. R. China.,Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, Henan, 450052, P. R. China
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Abstract
Pseudogenes are commonly labeled as "junk DNA" given their perceived nonfunctional status. However, the advent of large-scale genomics projects prompted a revisit of pseudogene biology, highlighting their key functional and regulatory roles in numerous diseases, including cancers. Integrative analyses of cancer data have shown that pseudogenes can be transcribed and even translated, and that pseudogenic DNA, RNA, and proteins can interfere with the activity and function of key protein coding genes, acting as regulators of oncogenes and tumor suppressors. Capitalizing on the available clinical research, we are able to get an insight into the spread and variety of pseudogene biomarker and therapeutic potential. In this chapter, we describe pseudogenes that fulfill their role as diagnostic or prognostic biomarkers, both as unique elements and in collaboration with other genes or pseudogenes. We also report that the majority of prognostic pseudogenes are overexpressed and exert an oncogenic role in colorectal, liver, lung, and gastric cancers. Finally, we highlight a number of pseudogenes that can establish future therapeutic avenues.
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Hou X, Tang W. Pseudogene PA2G4P4 promotes oncogene PA2G4 expression and nuclear translocation to affect glioblastoma cell viability and apoptosis. Life Sci 2020; 265:118793. [PMID: 33220287 DOI: 10.1016/j.lfs.2020.118793] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 10/02/2020] [Accepted: 11/15/2020] [Indexed: 12/21/2022]
Abstract
Dysregulation of pseudogenes is involved in the progression of various types of cancer, including glioblastoma (GBM). Proliferation associated-2G4 (PA2G4) pseudogene 4 (PA2G4P4) has been shown to play an oncogenic role in bladder cancer development. Our study aimed to explore the role and mechanism of PA2G4P4 in GBM progression. PA2G4P4 and PA2G4 expression in GBM tissues was analyzed using the GEPIA database. Cell viability, apoptosis, and activities of caspase-3 and caspase-9 in GBM cells were explored by CCK-8, flow cytometry analysis, and colorimetric activity assay kits, respectively. GEPIA database showed that PA2G4P4 and PA2G4 were both upregulated in GBM tissues. PA2G4P4 expression was also boosted in GBM cells. Knockdown of PA2G4P4 or PA2G4 inhibited cell viability, induced apoptosis, and increased caspase-3 and caspase-9 activities in GBM cells. Data from UALCAN database showed that among top 15 genes correlated with PA2G4P4, PA2G4 had the highest correlation coefficient. Additionally, knockdown of PA2G4P4 inhibited PA2G4 expression and nuclear translocation in GBM cells. Overexpression of PA2G4 abolished the functions of PA2G4P4 knockdown on viability and apoptosis in GBM cells. Summarily, pseudogene PA2G4P4 promotes oncogene PA2G4 expression and nuclear translocation to affect cell viability and apoptosis in GBM cells.
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Affiliation(s)
- Xiaofeng Hou
- Department of Neurosurgery, The First Affiliated Hospital of Baotou Medical College, Inner Mongolia University of Science and Technology, Baotou 014010, China
| | - Wenhai Tang
- Department of Neurosurgery, Shanxian Central Hospital, Heze 274300, China.
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Li J, Jiang L, Liu Z, Li Y, Xu Y, Liu H. Oncogenic pseudogene DUXAP10 knockdown suppresses proliferation and invasion and induces apoptosis of papillary thyroid carcinoma cells by inhibition of Akt/mTOR pathway. Clin Exp Pharmacol Physiol 2020; 47:1473-1483. [PMID: 32215944 DOI: 10.1111/1440-1681.13310] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 03/15/2020] [Accepted: 03/19/2020] [Indexed: 12/13/2022]
Abstract
Pseudogenes, another novel group of non-coding segments without protein-coding capacity, are closely associated with tumourigenesis and cancer progression. Double homeoboxA pseudogene 10 (DUXAP10) is reported to be robustly expressed in thyroid carcinoma. However, the functional role and underlying mechanism of DUXAP10 in papillary thyroid carcinoma (PTC) progression remain undefined. DUXAP10 expression in PTC cells was detected by qRT-PCR. Cell proliferation and invasion were determined using 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2-H-tetrazolium bromide (MTT) and Transwell invasion assay, respectively. Apoptosis was evaluated using flow cytometry. Protein expression of matrix metalloproteinase (MMP)-2, MMP-9, protein kinase B (Akt), phosphorylated Akt, mammalian target of rapamycin (mTOR), and phosphorylated mTOR was examined by western blot. Results showed that DUXAP10 was significantly overexpressed in PTC cells compared with normal thyroid follicular epithelium cells. DUXAP10 silencing suppressed cell proliferation and invasive ability, reduced the expression of MMP-2 and MMP-9, and increased apoptotic rate and caspase-3 activity in PTC cells. Additionally, the Akt/mTOR pathway was inhibited following DUXAP10 knockdown in PTC cells. Activation of the Akt/mTOR pathway by 740Y-P and MHY1485 attenuated DUXAP10 knockdown-induced proliferation reduction, invasion suppression and apoptosis in PTC cells. In conclusion, DUXAP10 knockdown suppressed proliferation and invasion and induced apoptosis in PTC cells at least partially by inhibition of the Akt/mTOR pathway.
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Affiliation(s)
- Jian Li
- Department of Head and Neck Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang, China
| | - Li Jiang
- Department of Head and Neck Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang, China
| | - Zhu Liu
- Department of Head and Neck Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang, China
| | - Yanguo Li
- Department of Head and Neck Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang, China
| | - Yang Xu
- Department of Head and Neck Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang, China
| | - Hongwei Liu
- Department of Head and Neck Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang, China
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Lou W, Ding B, Fu P. Pseudogene-Derived lncRNAs and Their miRNA Sponging Mechanism in Human Cancer. Front Cell Dev Biol 2020; 8:85. [PMID: 32185172 PMCID: PMC7058547 DOI: 10.3389/fcell.2020.00085] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 01/30/2020] [Indexed: 12/28/2022] Open
Abstract
Pseudogenes, abundant in the human genome, are traditionally considered as non-functional “junk genes.” However, recent studies have revealed that pseudogenes act as key regulators at DNA, RNA or protein level in diverse human disorders (including cancer), among which pseudogene-derived long non-coding RNA (lncRNA) transcripts are extensively investigated and has been reported to be frequently dysregulated in various types of human cancer. Growing evidence demonstrates that pseudogene-derived lncRNAs play important roles in cancer initiation and progression by serving as competing endogenous RNAs (ceRNAs) through competitively binding to shared microRNAs (miRNAs), thus affecting both their cognate genes and unrelated genes. Herein, we retrospect those current findings about expression, functions and potential ceRNA mechanisms of pseudogene-derived lncRNAs in human cancer, which may provide us with some crucial clues in developing potential targets for cancer therapy in the future.
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Affiliation(s)
- Weiyang Lou
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Program of Innovative Cancer Therapeutics, Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, Key Laboratory of Organ Transplantation, Zhejiang University, Hangzhou, China
| | - Bisha Ding
- Program of Innovative Cancer Therapeutics, Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, Key Laboratory of Organ Transplantation, Zhejiang University, Hangzhou, China
| | - Peifen Fu
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
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Chen X, Wan L, Wang W, Xi WJ, Yang AG, Wang T. Re-recognition of pseudogenes: From molecular to clinical applications. Theranostics 2020; 10:1479-1499. [PMID: 32042317 PMCID: PMC6993246 DOI: 10.7150/thno.40659] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 11/12/2019] [Indexed: 12/14/2022] Open
Abstract
Pseudogenes were initially regarded as "nonfunctional" genomic elements that did not have protein-coding abilities due to several endogenous inactivating mutations. Although pseudogenes are widely expressed in prokaryotes and eukaryotes, for decades, they have been largely ignored and classified as gene "junk" or "relics". With the widespread availability of high-throughput sequencing analysis, especially omics technologies, knowledge concerning pseudogenes has substantially increased. Pseudogenes are evolutionarily conserved and derive primarily from a mutation or retrotransposon, conferring the pseudogene with a "gene repository" role to store and expand genetic information. In contrast to previous notions, pseudogenes have a variety of functions at the DNA, RNA and protein levels for broadly participating in gene regulation to influence the development and progression of certain diseases, especially cancer. Indeed, some pseudogenes have been proven to encode proteins, strongly contradicting their "trash" identification, and have been confirmed to have tissue-specific and disease subtype-specific expression, indicating their own value in disease diagnosis. Moreover, pseudogenes have been correlated with the life expectancy of patients and exhibit great potential for future use in disease treatment, suggesting that they are promising biomarkers and therapeutic targets for clinical applications. In this review, we summarize the natural properties, functions, disease involvement and clinical value of pseudogenes. Although our knowledge of pseudogenes remains nascent, this field deserves more attention and deeper exploration.
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