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Ohno-Oishi M, Meiai Z, Sato K, Kanno S, Kawano C, Ishikawa M, Nakazawa T. SH-SY5Y human neuronal cells with mutations of the CDKN2B-AS1 gene are vulnerable under cultured conditions. Biochem Biophys Rep 2024; 38:101723. [PMID: 38737728 PMCID: PMC11088231 DOI: 10.1016/j.bbrep.2024.101723] [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: 09/14/2023] [Revised: 03/19/2024] [Accepted: 04/26/2024] [Indexed: 05/14/2024] Open
Abstract
Glaucoma is a common cause of blindness worldwide. Genetic effects are believed to contribute to the onset and progress of glaucoma, but the underlying pathological mechanisms are not fully understood. Here, we set out to introduce mutations into the CDKN2B-AS1 gene, which is known as being the closely associated with glaucoma, in a human neuronal cell line in vitro. We introduced gene mutations with CRISPR/Cas9 into exons and introns into the CDKN2B-AS1 gene. Both mutations strongly promoted neuronal cell death in normal culture conditions. RNA sequencing and pathway analysis revealed that the transcriptional factor Fos is a target molecule regulating CDKN2B-AS1 overexpression. We demonstrated that gene mutation of CDKN2B-AS1 is directly associated with neuronal cell vulnerability in vitro. Additionally, Fos, which is a downstream signaling molecule of CDKN2B-AS1, may be a potential source of new therapeutic targets for neuronal degeneration in diseases such as glaucoma.
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Affiliation(s)
- Michiko Ohno-Oishi
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Zou Meiai
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Kota Sato
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Sendai, Japan
- Department of Advanced Ophthalmic Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Seiya Kanno
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Chihiro Kawano
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Makoto Ishikawa
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Sendai, Japan
- Department of Ophthalmic Imaging and Information Analytics, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Toru Nakazawa
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Sendai, Japan
- Department of Advanced Ophthalmic Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
- Department of Ophthalmic Imaging and Information Analytics, Tohoku University Graduate School of Medicine, Sendai, Japan
- Collaborative Program for Ophthalmic Drug Discovery, Tohoku University Graduate School of Medicine, Sendai, Japan
- Department of Retinal Disease Control, Tohoku University Graduate School of Medicine, Miyagi, Japan
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2
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Zhang X, Bolck HA, Rupp NJ, Moch H. Genomic alterations and diagnosis of renal cancer. Virchows Arch 2024; 484:323-337. [PMID: 37999735 PMCID: PMC10948545 DOI: 10.1007/s00428-023-03700-9] [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: 08/28/2023] [Revised: 10/24/2023] [Accepted: 11/04/2023] [Indexed: 11/25/2023]
Abstract
The application of molecular profiling has made substantial impact on the classification of urogenital tumors. Therefore, the 2022 World Health Organization incorporated the concept of molecularly defined renal tumor entities into its classification, including succinate dehydrogenase-deficient renal cell carcinoma (RCC), FH-deficient RCC, TFE3-rearranged RCC, TFEB-altered RCC, ALK-rearranged RCC, ELOC-mutated RCC, and renal medullary RCC, which are characterized by SMARCB1-deficiency. This review aims to provide an overview of the most important molecular alterations in renal cancer, with a specific focus on the diagnostic value of characteristic genomic aberrations, their chromosomal localization, and associations with renal tumor subtypes. It may not yet be the time to completely shift to a molecular RCC classification, but undoubtedly, the application of molecular profiling will enhance the accuracy of renal cancer diagnosis, and ultimately guide personalized treatment strategies for patients.
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Affiliation(s)
- Xingming Zhang
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Schmelzbergstr. 12, 8091, Zurich, Switzerland
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Hella A Bolck
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Schmelzbergstr. 12, 8091, Zurich, Switzerland
| | - Niels J Rupp
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Schmelzbergstr. 12, 8091, Zurich, Switzerland
- Faculty of Medicine, University of Zurich, Zurich, Switzerland
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Schmelzbergstr. 12, 8091, Zurich, Switzerland.
- Faculty of Medicine, University of Zurich, Zurich, Switzerland.
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Mahato RK, Bhattacharya S, Khullar N, Sidhu IS, Reddy PH, Bhatti GK, Bhatti JS. Targeting long non-coding RNAs in cancer therapy using CRISPR-Cas9 technology: A novel paradigm for precision oncology. J Biotechnol 2024; 379:98-119. [PMID: 38065367 DOI: 10.1016/j.jbiotec.2023.12.003] [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: 09/08/2023] [Revised: 11/30/2023] [Accepted: 12/03/2023] [Indexed: 12/25/2023]
Abstract
Cancer is the second leading cause of death worldwide, despite recent advances in its identification and management. To improve cancer patient diagnosis and care, it is necessary to identify new biomarkers and molecular targets. In recent years, long non-coding RNAs (lncRNAs) have surfaced as important contributors to various cellular activities, with growing proof indicating their substantial role in the genesis, development, and spread of cancer. Their unique expression profiles within specific tissues and their wide-ranging functionalities make lncRNAs excellent candidates for potential therapeutic intervention in cancer management. They are implicated in multiple hallmarks of cancer, such as uncontrolled proliferation, angiogenesis, and immune evasion. This review article explores the innovative application of CRISPR-Cas9 technology in targeting lncRNAs as a cancer therapeutic strategy. The CRISPR-Cas9 system has been widely applied in functional genomics, gene therapy, and cancer research, offering a versatile platform for lncRNA targeting. CRISPR-Cas9-mediated targeting of lncRNAs can be achieved through CRISPR interference, activation or the complete knockout of lncRNA loci. Combining CRISPR-Cas9 technology with high-throughput functional genomics makes it possible to identify lncRNAs critical for the survival of specific cancer subtypes, opening the door for tailored treatments and personalised cancer therapies. CRISPR-Cas9-mediated lncRNA targeting with other cutting-edge cancer therapies, such as immunotherapy and targeted molecular therapeutics can be used to overcome the drug resistance in cancer. The synergy of lncRNA research and CRISPR-Cas9 technology presents immense potential for individualized cancer treatment, offering renewed hope in the battle against this disease.
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Affiliation(s)
- Rahul Kumar Mahato
- Laboratory of Translational Medicine and Nanotherapeutics, Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India
| | - Srinjan Bhattacharya
- Laboratory of Translational Medicine and Nanotherapeutics, Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India
| | - Naina Khullar
- Department of Zoology, Mata Gujri College, Fatehgarh Sahib, Punjab, India
| | - Inderpal Singh Sidhu
- Department of Zoology, Sri Guru Gobind Singh College, Sector 26, Chandigarh, India
| | - P Hemachandra Reddy
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA; Department of Pharmacology & Neuroscience, Texas Tech University Health Sciences Center, Lubbock, TX, USA; Departments of Neurology, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA; Public Health Department of Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center, Lubbock, TX, USA; Department of Speech, Language and Hearing Sciences, School Health Professions, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Gurjit Kaur Bhatti
- Department of Medical Lab Technology, University Institute of Applied Health Sciences, Chandigarh University, Mohali, India.
| | - Jasvinder Singh Bhatti
- Laboratory of Translational Medicine and Nanotherapeutics, Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India.
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Beihaghi M, Sahebi R, Beihaghi MR, Nessiani RK, Yarasmi MR, Gholamalizadeh S, Shahabnavaie F, Shojaei M. Evaluation of rs10811661 polymorphism in CDKN2A / B in colon and gastric cancer. BMC Cancer 2023; 23:985. [PMID: 37845622 PMCID: PMC10577985 DOI: 10.1186/s12885-023-11461-6] [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: 02/10/2023] [Accepted: 09/28/2023] [Indexed: 10/18/2023] Open
Abstract
One of the causes of colon and gastric cancer is the dysregulation of carcinogenic genes, tumor inhibitors, and micro-RNA. The purpose of this study is to apply rs10811661 polymorphism in CDKN2A /B gene as an effective biomarker of colon cancer and early detection of gastric cancer. As a result,400 blood samples, inclusive of 200 samples from healthy individuals and 200 samples (100 samples from intestinal cancer,100 samples from stomach cancer) from the blood of someone with these cancers, to determine the genotype of genes in healthful and ill people through PCR-RFLP approach and Allelic and genotypic tests of SPSS software. To observe the connection between gastric cancer and bowel cancer risk and genotypes, the t-student test for quantitative variables and Pearson distribution for qualitative variables have been tested and the results have been evaluated using the Chi-square test. The effects confirmed that the highest frequency of TT genotypes is in affected individuals and CC genotype is in healthful individuals. In addition, it confirmed that women were more inclined than men to T3 tumor invasion and most grade II and III colon cancers, and in older sufferers with gastric cancer, the grade of tumor tended to be grade I. Among genetic variety and rs10811661, with invasiveness, there is a tumor size and degree in the affected person. In summary, our findings suggest that the rs10811661 polymorphism of the CDKN2A / B gene is strongly associated with the occurrence of intestinal cancer and stomach is linked to its potential role as a prognostic biomarker for the management of bowel cancer and stomach.
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Affiliation(s)
- Maria Beihaghi
- Department of Biology, Kavian Institute of Higher Education, Mashhad, Iran.
- School of Science and Technology, The University of Georgia, Tbilisi, Georgia.
| | - Reza Sahebi
- Department of Modern Sciences and Technologies, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Reza Beihaghi
- Department of Public Health, Sheffield Hallam University, Sheffield, South Yorkshire, England
| | | | | | | | | | - Mitra Shojaei
- Department of Modern Sciences and Technologies, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
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Asadi-Tarani M, Saravani M, Ghasemi M, Rezaei M, Salimi S. Maternal and placental ANRIL polymorphisms and preeclampsia susceptibility. Per Med 2023; 20:445-452. [PMID: 37850322 DOI: 10.2217/pme-2023-0073] [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] [Indexed: 10/19/2023]
Abstract
Aim: The possible effects of maternal and placental ANRIL polymorphisms on preeclampsia were examined. Methods: The maternal blood of 315 preeclamptic and 317 control women and the placentas of 103 preeclamptic and 133 control women were enrolled in the study. ANRIL polymorphisms were genotyped using a PCR-RFLP method. Results: The maternal ANRIL rs1333048C variant showed a relationship with a lower risk of preeclampsia in codominant and dominant models. The maternal ANRIL rs4977574G variant had a relationship with a lower risk of preeclampsia in codominant and recessive models. There was an association between the placental rs1333048C variant and a lower risk of preeclampsia in codominant and dominant models. Conclusion: Maternal ANRIL rs1333048C and rs4977574G variants and placental rs1333048 variant showed a relationship with a lower risk of preeclampsia.
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Affiliation(s)
- Mina Asadi-Tarani
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Mohsen Saravani
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
- Cellular & Molecular Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Marzieh Ghasemi
- Department of Obstetrics & Gynecology, Pregnancy Health Research Center, Zahedan University of Medical Sciences, Zahedan, Iran
- Pregnancy Health Research Center, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Mahnaz Rezaei
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
- Cellular & Molecular Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Saeedeh Salimi
- Cellular & Molecular Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran
- Department of Clinical Biochemistry, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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6
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Takasugi M, Yoshida Y, Hara E, Ohtani N. The role of cellular senescence and SASP in tumour microenvironment. FEBS J 2023; 290:1348-1361. [PMID: 35106956 DOI: 10.1111/febs.16381] [Citation(s) in RCA: 39] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 12/04/2021] [Accepted: 01/31/2022] [Indexed: 01/01/2023]
Abstract
Cellular senescence refers to a state of irreversible cell cycle arrest that can be induced by various cellular stresses and is known to play a pivotal role in tumour suppression. While senescence-associated growth arrest can inhibit the proliferation of cancer-prone cells, the altered secretory profile of senescent cells, termed the senescence-associated secretory phenotype, can contribute to the microenvironment that promotes tumour development. Although the senescence-associated secretory phenotype and its effects on tumorigenesis are both highly context dependent, mechanisms underlying such diversity are becoming better understood, thereby allowing the creation of new strategies to effectively target the senescence-associated secretory phenotype and senescent cells for cancer therapy. In this review, we discuss the current knowledge on cellular senescence and the senescence-associated secretory phenotype to develop a structural understanding of their roles in the tumour microenvironment and provide perspectives for future research, including the possibility of senotherapy for the treatment of cancer.
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Affiliation(s)
- Masaki Takasugi
- Department of Pathophysiology, Graduate School of Medicine, Osaka City University, Japan
| | - Yuya Yoshida
- Department of Pathophysiology, Graduate School of Medicine, Osaka City University, Japan
| | - Eiji Hara
- Research Institute for Microbial Diseases, Osaka University, Japan.,Immunology Frontier Research Center (IFReC), Osaka University, Japan.,Center for Infectious Disease Education and Research (CiDER), Osaka University, Japan
| | - Naoko Ohtani
- Department of Pathophysiology, Graduate School of Medicine, Osaka City University, Japan.,AMED-CREST, AMED, Japan Agency for Medical Research and Development, Tokyo, Japan
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7
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Li Z, Qiao J, Ma W, Zhou J, Gu L, Deng D, Zhang B. P14AS upregulates gene expression in the CDKN2A/2B locus through competitive binding to PcG protein CBX7. Front Cell Dev Biol 2022; 10:993525. [PMID: 36176277 PMCID: PMC9513069 DOI: 10.3389/fcell.2022.993525] [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: 07/13/2022] [Accepted: 08/24/2022] [Indexed: 12/27/2022] Open
Abstract
Background: It is well known that P16 INK4A , P14 ARF , P15 INK4B mRNAs, and ANRIL lncRNA are transcribed from the CDKN2A/2B locus. LncRNA P14AS is a lncRNA transcribed from antisense strand of P14 ARF promoter to intron-1. Our previous study showed that P14AS could upregulate the expression level of ANRIL and P16 INK4A and promote the proliferation of cancer cells. Because polycomb group protein CBX7 could repress P16 INK4A expression and bind ANRIL, we wonder whether the P14AS-upregulated ANRIL and P16 INK4A expression is mediated with CBX7. Results: In this study, we found that the upregulation of P16 INK4A , P14 ARF , P15 INK4B and ANRIL expression was induced by P14AS overexpression only in HEK293T and HCT116 cells with active endogenous CBX7 expression, but not in MGC803 and HepG2 cells with weak CBX7 expression. Further studies showed that the stable shRNA-knockdown of CBX7 expression abolished the P14AS-induced upregulation of these P14AS target genes in HEK293T and HCT116 cells whereas enforced CBX7 overexpression enabled P14AS to upregulate expression of these target genes in MGC803 and HepG2 cells. Moreover, a significant association between the expression levels of P14AS and its target genes were observed only in human colon cancer tissue samples with high level of CBX7 expression (n = 38, p < 0.05), but not in samples (n = 37) with low level of CBX7 expression, nor in paired surgical margin tissues. In addition, the results of RNA immunoprecipitation (RIP)- and chromatin immunoprecipitation (ChIP)-PCR analyses revealed that lncRNA P14AS could competitively bind to CBX7 protein which prevented the bindings of CBX7 to both lncRNA ANRIL and the promoters of P16 INK4A , P14 ARF and P15 INK4B genes. The amounts of repressive histone modification H3K9m3 was also significantly decreased at the promoters of these genes by P14AS in CBX7 actively expressing cells. Conclusions: CBX7 expression is essential for P14AS to upregulate the expression of P16 INK4A , P14 ARF , P15 INK4B and ANRIL genes in the CDKN2A/2Blocus. P14AS may upregulate these genes' expression through competitively blocking CBX7-binding to ANRIL lncRNA and target gene promoters.
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Affiliation(s)
| | | | | | | | | | - Dajun Deng
- *Correspondence: Dajun Deng, ; Baozhen Zhang,
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8
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Wang Y, Zhang H, Hua L, Wang Z, Geng S, Zhang H, Zeng Z, Zhao J, Wang X, Wang Y. Curcumin prevents Alzheimer's disease progression by upregulating JMJD3. Am J Transl Res 2022; 14:5280-5294. [PMID: 36105064 PMCID: PMC9452350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 03/09/2022] [Indexed: 06/15/2023]
Abstract
The main purpose of this research was to explore the molecular mechanisms of Jumonji Domain-Containing Protein 3 (JMJD3) in Alzheimer's disease (AD) and to analyze its role in the anti-AD mechanism of curcumin (CUR). In the in vitro study of AD, JMJD3 overexpression promoted the trimethylation of histone H3 lysine 27 (H3K27me3), downregulated brain-derived neurotrophic factor (BDNF ), improved the abnormality of mitochondrial stress response (MSR) markers, Aβ accumulation, increased cell proliferation and inhibited apoptosis. Upregulating BDNF also achieved above similar results. Knockout of JMJD3 could downregulate BDNF, upregulate the level of H3K27me3 methylation and inhibit MSR markers, while transfection of JMJD3 RNAi could counteract the upregulated effect of BDNF. Then, MSR activator could also improve AD. In addition, JMJD3 in AD in vitro models was obviously upregulated under CUR stimulation, and it triggered a series of reactions as mentioned above. In the in vivo study, the levels of JMJD3, the mRNA and protein levels of BDNF in the right brain tissues of AD mice were downregulated, the methylation of H3K27me3 increased, and the MSR markers (ClpP, HSP6, HSP-60, ATFS-1, etc.) were downregulated; the above indexes were improved in varying degrees with the intervention of CUR. Thus, we conclude that CUR can induce the upregulation of JMJD3 and improve BDNF expression by promoting the demethylation of H3K27me3, thereby maintaining the balance of MSR and thus, preventing AD development.
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Affiliation(s)
- Yutong Wang
- Qilu Medical CollegeZibo, Shandong 255300, PR China
| | - Hong Zhang
- Department of Neurology, 960th Hospital of PLAZibo 255300, Shandong, PR China
| | - Linlin Hua
- Department of Neurology, The Second Affiliated Hospital of Zhengzhou UniversityZhengzhou 450014, Henan, PR China
| | - Zhen Wang
- Department of Neurology, 960th Hospital of PLAZibo 255300, Shandong, PR China
| | - Shuang Geng
- Department of Neurology, 960th Hospital of PLAZibo 255300, Shandong, PR China
| | - Hui Zhang
- Department of Neurology, 960th Hospital of PLAZibo 255300, Shandong, PR China
| | - Zhilei Zeng
- Department of Neurology, The Second Affiliated Hospital of Zhengzhou UniversityZhengzhou 450014, Henan, PR China
| | - Jing Zhao
- Department of Neurology, 960th Hospital of PLAZibo 255300, Shandong, PR China
| | - Xiaoyan Wang
- Department of Neurology, 960th Hospital of PLAZibo 255300, Shandong, PR China
| | - Yunliang Wang
- Qilu Medical CollegeZibo, Shandong 255300, PR China
- Department of Neurology, The Second Affiliated Hospital of Zhengzhou UniversityZhengzhou 450014, Henan, PR China
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Sardarzadeh N, Khojasteh-Leylakoohi F, Damavandi S, Khalili-Tanha G, Dashtiahangar M, Khalili-Tanha N, Avan A, Amoueian S, Hassanian SM, Esmaily H, Khazaei M, Ferns G, Khooei A, Aliakbarian M. Association of a Genetic Variant in the Cyclin-Dependent Kinase Inhibitor 2B with Risk of Pancreatic Cancer. Rep Biochem Mol Biol 2022; 11:336-343. [PMID: 36164638 PMCID: PMC9455181 DOI: 10.52547/rbmb.11.2.336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 03/27/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Pancreatic cancer (PC) is among the most aggressive tumors with a poor prognosis, indicating the need for the identification of a novel prognostic biomarker for risk stratifications. Recent genome-wide association studies have demonstrated common genetic variants in a region on chromosome 9p21 associated with an increased risk of different malignancies. METHODS In the present study, we explore the possible relationship between genetic variant, rs10811661, and gene expression of CDKN2B in 75 pancreatic cancer patients, and 188 healthy individuals. DNAs were extracted and genotyping and gene expression were performed by TaqMan real-time PCR and RT-PCR, respectively. Logistic regression was used to assess the association between risk and genotypes, while the significant prognostic variables in the univariate analysis were included in multivariate analyses. RESULTS The patients with PDAC had a higher frequency of a TT genotype for rs10811661 than the control group. Also, PDAC patients with dominant genetic model, (TT + TC), was associated with increased risk of developing PDAC (OR= 14.71, 95% CI [1.96-110.35], p= 0.009). Moreover, patients with CC genotype had a higher expression of CDKN2B, in comparison with TT genotype. CONCLUSION Our findings demonstrated that CDKN2A/B was associated with the risk of developing PDAC, supporting further investigations in the larger and multicenter setting to validate the potential value of this gene as an emerging marker for PDAC.
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Affiliation(s)
- Newsha Sardarzadeh
- Surgical Oncology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Fatemeh Khojasteh-Leylakoohi
- Metabolic syndrome Research center, Mashhad University of Medical Sciences, Mashhad, Iran.
- Basic Medical Sciences Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Sedigheh Damavandi
- Metabolic syndrome Research center, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Ghazaleh Khalili-Tanha
- Basic Medical Sciences Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
- Medical Genetics Research center, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Mohammad Dashtiahangar
- Metabolic syndrome Research center, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Nima Khalili-Tanha
- Metabolic syndrome Research center, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Amir Avan
- Metabolic syndrome Research center, Mashhad University of Medical Sciences, Mashhad, Iran.
- Basic Medical Sciences Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
- Medical Genetics Research center, Mashhad University of Medical Sciences, Mashhad, Iran.
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Sakineh Amoueian
- Department of Pathology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Seyed Mahdi Hassanian
- Metabolic syndrome Research center, Mashhad University of Medical Sciences, Mashhad, Iran.
- Basic Medical Sciences Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Habibollah Esmaily
- Metabolic syndrome Research center, Mashhad University of Medical Sciences, Mashhad, Iran.
- Basic Medical Sciences Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Majid Khazaei
- Metabolic syndrome Research center, Mashhad University of Medical Sciences, Mashhad, Iran.
- Basic Medical Sciences Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Gordon Ferns
- Brighton & Sussex Medical School, Division of Medical Education, Falmer, Brighton, Sussex BN1 9PH, UK.
| | - Alireza Khooei
- Department of Pathology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Mohsen Aliakbarian
- Surgical Oncology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
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10
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Iakovou E, Kourti M. A Comprehensive Overview of the Complex Role of Oxidative Stress in Aging, The Contributing Environmental Stressors and Emerging Antioxidant Therapeutic Interventions. Front Aging Neurosci 2022; 14:827900. [PMID: 35769600 PMCID: PMC9234325 DOI: 10.3389/fnagi.2022.827900] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 05/10/2022] [Indexed: 12/15/2022] Open
Abstract
Introduction Aging is a normal, inevitable, irreversible, and progressive process which is driven by internal and external factors. Oxidative stress, that is the imbalance between prooxidant and antioxidant molecules favoring the first, plays a key role in the pathophysiology of aging and comprises one of the molecular mechanisms underlying age-related diseases. However, the oxidative stress theory of aging has not been successfully proven in all animal models studying lifespan, meaning that altering oxidative stress/antioxidant defense systems did not always lead to a prolonged lifespan, as expected. On the other hand, animal models of age-related pathological phenotypes showed a well-correlated relationship with the levels of prooxidant molecules. Therefore, it seems that oxidative stress plays a more complicated role than the one once believed and this role might be affected by the environment of each organism. Environmental factors such as UV radiation, air pollution, and an unbalanced diet, have also been implicated in the pathophysiology of aging and seem to initiate this process more rapidly and even at younger ages. Aim The purpose of this review is to elucidate the role of oxidative stress in the physiology of aging and the effect of certain environmental factors in initiating and sustaining this process. Understanding the pathophysiology of aging will contribute to the development of strategies to postpone this phenomenon. In addition, recent studies investigating ways to alter the antioxidant defense mechanisms in order to prevent aging will be presented. Conclusions Careful exposure to harmful environmental factors and the use of antioxidant supplements could potentially affect the biological processes driving aging and slow down the development of age-related diseases. Maybe a prolonged lifespan could not be achieved by this strategy alone, but a longer healthspan could also be a favorable target.
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Affiliation(s)
- Evripides Iakovou
- Department of Life Sciences, European University Cyprus, Nicosia, Cyprus
| | - Malamati Kourti
- Department of Life Sciences, European University Cyprus, Nicosia, Cyprus
- Angiogenesis and Cancer Drug Discovery Group, Basic and Translational Cancer Research Center, Department of Life Sciences, European University Cyprus, Nicosia, Cyprus
- *Correspondence: Malamati Kourti
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11
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Li J, Wang S, Zhang S, Cheng D, Yang X, Wang Y, Yin H, Liu Y, Liu Y, Bai H, Geng S, Wang Y. Curcumin slows the progression of Alzheimer's disease by modulating mitochondrial stress responses via JMJD3-H3K27me3-BDNF axis. Am J Transl Res 2021; 13:13380-13393. [PMID: 35035682 PMCID: PMC8748089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 08/09/2021] [Indexed: 06/14/2023]
Abstract
Disturbance of mitochondrial proteins by amyloid beta-protein (Aβ) that associates with mitochondrial stress responses (MSR) is one of the pathological mechanisms of Alzheimer's disease (AD). This study tried to explore whether the axis of Jumonji domain-containing protein 3 (JMJD3)-trimethylated lysine 27 on histone H3 (H3K27me3)-brain derived neurotrophic factor (BDNF) is involved in the regulation of MSR which in turn intervenes in the process of AD, and whether curcumin (CUR) has a protective role against AD by influencing this axis, aiming to provide insights into AD treatment. AD mouse models presented a significant aggregation of Aβ, with conspicuous pathological changes in brain tissues and an increase in neuronal apoptosis. Moreover, the mRNA and protein levels of JMJD3 and BDNF were down-regulated, H3K27me3 methylation levels were increased, and the MSR markers (ClpP, HSP6, HSP-60, and ATFS-1) showed abnormal alterations. In in-vitro cellular models of AD, up-regulation of either JMJD3 or BDNF up-regulated BDNF levels, down-regulated H3K27me3 methylation levels, mitigated abnormalities of MSR markers and Aβ aggregation, and increased cell proliferation and inhibited apoptosis. JMJD3 was confirmed to regulate Aβ and MSR via BDNF. In addition, CUR was confirmed to modulate JMJD3-H3K27me3-BDNF axis. Furthermore, moderate and high doses of CUR could improve the morphology and histopathology of the brain, inhibit Aβ aggregation and cell apoptosis, and maintain MSR balance at least partly by modulating the JMJD3-H3K27me3-BDNF axis. To sum up, moderate and high doses of CUR regulate the progression of AD via MSR JMJD3-H3K27me3-BDNF axis.
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Affiliation(s)
- Jingna Li
- Department of Neurology, Second Affiliated Hospital of Zhengzhou UniversityZhengzhou 450014, Henan, China
| | - Shanshan Wang
- Department of Neurology, 960 Hospital of PLAZibo 255300, Shandong, China
| | - Simiao Zhang
- Department of Neurology, Second Affiliated Hospital of Zhengzhou UniversityZhengzhou 450014, Henan, China
| | - Dan Cheng
- Department of Neurology, Second Affiliated Hospital of Zhengzhou UniversityZhengzhou 450014, Henan, China
| | - Xiaopeng Yang
- Department of Neurology, Second Affiliated Hospital of Zhengzhou UniversityZhengzhou 450014, Henan, China
| | - Yutong Wang
- Qilu Medical CollegeZibo 255300, Shandong, China
| | - Honglei Yin
- Department of Neurology, 960 Hospital of PLAZibo 255300, Shandong, China
| | - Yajun Liu
- Department of Neurology, Second Affiliated Hospital of Zhengzhou UniversityZhengzhou 450014, Henan, China
| | - Yanqiu Liu
- Department of Neurology, Second Affiliated Hospital of Zhengzhou UniversityZhengzhou 450014, Henan, China
| | - Hongying Bai
- Department of Neurology, 960 Hospital of PLAZibo 255300, Shandong, China
| | - Shuang Geng
- Department of Neurology, Second Affiliated Hospital of Zhengzhou UniversityZhengzhou 450014, Henan, China
| | - Yunliang Wang
- Department of Neurology, Second Affiliated Hospital of Zhengzhou UniversityZhengzhou 450014, Henan, China
- Qilu Medical CollegeZibo 255300, Shandong, China
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12
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Wang S, C Ordonez-Rubiano S, Dhiman A, Jiao G, Strohmier BP, Krusemark CJ, Dykhuizen EC. Polycomb group proteins in cancer: multifaceted functions and strategies for modulation. NAR Cancer 2021; 3:zcab039. [PMID: 34617019 PMCID: PMC8489530 DOI: 10.1093/narcan/zcab039] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 08/24/2021] [Accepted: 09/10/2021] [Indexed: 12/12/2022] Open
Abstract
Polycomb repressive complexes (PRCs) are a heterogenous collection of dozens, if not hundreds, of protein complexes composed of various combinations of subunits. PRCs are transcriptional repressors important for cell-type specificity during development, and as such, are commonly mis-regulated in cancer. PRCs are broadly characterized as PRC1 with histone ubiquitin ligase activity, or PRC2 with histone methyltransferase activity; however, the mechanism by which individual PRCs, particularly the highly diverse set of PRC1s, alter gene expression has not always been clear. Here we review the current understanding of how PRCs act, both individually and together, to establish and maintain gene repression, the biochemical contribution of individual PRC subunits, the mis-regulation of PRC function in different cancers, and the current strategies for modulating PRC activity. Increased mechanistic understanding of PRC function, as well as cancer-specific roles for individual PRC subunits, will uncover better targets and strategies for cancer therapies.
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Affiliation(s)
- Sijie Wang
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University and Purdue University Center for Cancer Research, 201 S. University St., West Lafayette, IN 47907 USA
| | - Sandra C Ordonez-Rubiano
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University and Purdue University Center for Cancer Research, 201 S. University St., West Lafayette, IN 47907 USA
| | - Alisha Dhiman
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University and Purdue University Center for Cancer Research, 201 S. University St., West Lafayette, IN 47907 USA
| | - Guanming Jiao
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University and Purdue University Center for Cancer Research, 201 S. University St., West Lafayette, IN 47907 USA
| | - Brayden P Strohmier
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University and Purdue University Center for Cancer Research, 201 S. University St., West Lafayette, IN 47907 USA
| | - Casey J Krusemark
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University and Purdue University Center for Cancer Research, 201 S. University St., West Lafayette, IN 47907 USA
| | - Emily C Dykhuizen
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University and Purdue University Center for Cancer Research, 201 S. University St., West Lafayette, IN 47907 USA
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13
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Adamou A, Mavrovounis G, Beltsios ET, Liampas I, Tsouris Z, Aloizou AM, Siokas V, Dardiotis E. The rs13330s40 and rs10757278 9p21 locus polymorphisms in patients with intracranial aneurysm: a Meta-analysis. Int J Neurosci 2021:1-12. [PMID: 34511017 DOI: 10.1080/00207454.2021.1976171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Introduction: The formation of intracranial aneurysms (IAs) has been associated with genetic polymorphisms. A few genome-wide (GWAS) and candidate gene association studies (CGAS) have reported that single nucleotide polymorphisms (SNPs) in locus 9p21 have been associated with the formation of IAs.Materials & Methods: We performed a meta-analysis of case-control studies to investigate the association of two SNPs (rs1333040, rs10757278), located at the 9p21 locus, with the formation of IAs. MEDLINE, EMBASE, Google Scholar and CENTRAL databases were comprehensively searched.Results: For the rs1333040 (C > T) polymorphism, a significant association with IA was observed in the dominant [OR (95% CI): 1.39 (1.24, 1.56); Pz <0.00001], recessive [OR (95% CI): 1.38 (1.28, 1.49); Pz <0.00001] and over-dominant [OR (95% CI): 0.85 (0.79, 0.91); Pz <0.00001] models. For the rs10757278(A > G) SNP, we observed a statistically significant association with IAs in the dominant [OR (95% CI): 1.41 (1.28, 1.56); Pz <0.01] and recessive [OR (95% CI): 1.42 (1.29, 1.56); Pz <0.01] models, while statistical significance was not revealed in the over-dominant model [OR (95% CI): 1.01 (0.93, 1.10); Pz=0.83].Discussion: A possible association between the two SNPs and IAs was indicated. The associations reported by our meta-analysis need to be further studied and validated by larger CGAS and GWAS.
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Affiliation(s)
- Antonis Adamou
- Department of Neurology, Laboratory of Neurogenetics, Faculty of Medicine, University of Thessaly, University Hospital of Larissa, Biopolis, Larissa, Greece
| | - Georgios Mavrovounis
- Department of Neurology, Laboratory of Neurogenetics, Faculty of Medicine, University of Thessaly, University Hospital of Larissa, Biopolis, Larissa, Greece
| | - Eleftherios T Beltsios
- Department of Neurology, Laboratory of Neurogenetics, Faculty of Medicine, University of Thessaly, University Hospital of Larissa, Biopolis, Larissa, Greece
| | - Ioannis Liampas
- Department of Neurology, Laboratory of Neurogenetics, Faculty of Medicine, University of Thessaly, University Hospital of Larissa, Biopolis, Larissa, Greece
| | - Zisis Tsouris
- Department of Neurology, Laboratory of Neurogenetics, Faculty of Medicine, University of Thessaly, University Hospital of Larissa, Biopolis, Larissa, Greece
| | - Athina-Maria Aloizou
- Department of Neurology, Laboratory of Neurogenetics, Faculty of Medicine, University of Thessaly, University Hospital of Larissa, Biopolis, Larissa, Greece
| | - Vasileios Siokas
- Department of Neurology, Laboratory of Neurogenetics, Faculty of Medicine, University of Thessaly, University Hospital of Larissa, Biopolis, Larissa, Greece
| | - Efthimios Dardiotis
- Department of Neurology, Laboratory of Neurogenetics, Faculty of Medicine, University of Thessaly, University Hospital of Larissa, Biopolis, Larissa, Greece
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14
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Abstract
Diabetic retinopathy (DR), which is known as a severe complication of type 2 diabetes mellitus, can cause varying degrees of damage to visual acuity. The pathogenesis of DR is multifactorial and not fully understood. Many previous research studies have revealed that an aberrant level of some long non-coding RNAs (lncRNAs) may accelerate the development of DR. These lncRNAs are regulatory factors and research related to them is always underway. In this review, we will update several types of lncRNAs based on the previous studies which are related to the development of DR and discuss its potential mechanisms of action and connections. Generally, the review will help us know more about lncRNAs and provide directions for future research related to DR.
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Affiliation(s)
- Qinying Huang
- Shantou University Medical College, Shantou, Guangdong, China
- Department of Ophthalmology, Peking University Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Jinying Li
- Department of Ophthalmology, Peking University Shenzhen Hospital, Shenzhen, Guangdong, China
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15
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Jolissaint JS, Soares KC, Seier KP, Kundra R, Gönen M, Shin PJ, Boerner T, Sigel C, Madupuri R, Vakiani E, Cercek A, Harding JJ, Kemeny NE, Connell LC, Balachandran VP, D'Angelica MI, Drebin JA, Kingham TP, Wei AC, Jarnagin WR. Intrahepatic Cholangiocarcinoma with Lymph Node Metastasis: Treatment-Related Outcomes and the Role of Tumor Genomics in Patient Selection. Clin Cancer Res 2021; 27:4101-4108. [PMID: 33963001 DOI: 10.1158/1078-0432.ccr-21-0412] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/24/2021] [Accepted: 05/04/2021] [Indexed: 12/11/2022]
Abstract
PURPOSE Lymph node metastasis (LNM) drastically reduces survival after resection of intrahepatic cholangiocarcinoma (IHC). Optimal treatment is ill defined, and it is unclear whether tumor mutational profiling can support treatment decisions. EXPERIMENTAL DESIGN Patients with liver-limited IHC with or without LNM treated with resection (N = 237), hepatic arterial infusion chemotherapy (HAIC; N = 196), or systemic chemotherapy alone (SYS; N = 140) at our institution between 2000 and 2018 were included. Genomic sequencing was analyzed to determine whether genetic alterations could stratify outcomes for patients with LNM. RESULTS For node-negative patients, resection was associated with the longest median overall survival [OS, 59.9 months; 95% confidence interval (CI), 47.2-74.31], followed by HAIC (24.9 months; 95% CI, 20.3-29.6), and SYS (13.7 months; 95% CI, 8.9-15.9; P < 0.001). There was no difference in survival for node-positive patients treated with resection (median OS, 19.7 months; 95% CI, 12.1-27.2) or HAIC (18.1 months; 95% CI, 14.1-26.6; P = 0.560); however, survival in both groups was greater than SYS (11.2 months; 95% CI, 14.1-26.6; P = 0.024). Node-positive patients with at least one high-risk genetic alteration (TP53 mutation, KRAS mutation, CDKN2A/B deletion) had worse survival compared to wild-type patients (median OS, 12.1 months; 95% CI, 5.7-21.5; P = 0.002), regardless of treatment. Conversely, there was no difference in survival for node-positive patients with IDH1/2 mutations compared to wild-type patients. CONCLUSIONS There was no difference in OS for patients with node-positive IHC treated by resection versus HAIC, and both treatments had better survival than SYS alone. The presence of high-risk genetic alterations provides valuable prognostic information that may help guide treatment.
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Affiliation(s)
- Joshua S Jolissaint
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Surgery, Brigham and Women's Hospital, Boston, Massachusetts
| | - Kevin C Soares
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kenneth P Seier
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ritika Kundra
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mithat Gönen
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Paul J Shin
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Thomas Boerner
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Carlie Sigel
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ramyasree Madupuri
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Efsevia Vakiani
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Andrea Cercek
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - James J Harding
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nancy E Kemeny
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Louise C Connell
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Vinod P Balachandran
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael I D'Angelica
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jeffrey A Drebin
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - T Peter Kingham
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Alice C Wei
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - William R Jarnagin
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York.
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16
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Kattan SW, Hobani YH, Shaheen S, Mokhtar SH, Hussein MH, Toraih EA, Fawzy MS, Abdalla HA. Association of cyclin-dependent kinase inhibitor 2B antisense RNA 1 gene expression and rs2383207 variant with breast cancer risk and survival. Cell Mol Biol Lett 2021; 26:14. [PMID: 33849428 PMCID: PMC8045214 DOI: 10.1186/s11658-021-00258-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 04/03/2021] [Indexed: 02/08/2023] Open
Abstract
Background The expression signature of deregulated long non-coding RNAs (lncRNAs) and related genetic variants is implicated in every stage of tumorigenesis, progression, and recurrence. This study aimed to explore the association of lncRNA cyclin-dependent kinase inhibitor 2B antisense RNA 1 (CDKN2B-AS1) gene expression and the rs2383207A>G intronic variant with breast cancer (BC) risk and prognosis and to verify the molecular role and networks of this lncRNA in BC by bioinformatics gene analysis. Methods Serum CDKN2B-AS1 relative expression and rs2383207 genotypes were determined in 214 unrelated women (104 primary BC and 110 controls) using real-time PCR. Sixteen BC studies from The Cancer Genome Atlas (TCGA) including 8925 patients were also retrieved for validation of results. Results CDKN2B-AS1 serum levels were upregulated in the BC patients relative to controls. A/A genotype carriers were three times more likely to develop BC under homozygous (OR = 3.27, 95% CI 1.20–8.88, P = 0.044) and recessive (OR = 3.17, 95% CI 1.20–8.34, P = 0.013) models. G/G homozygous patients had a higher expression level [median and quartile values were 3.14 (1.52–4.25)] than A/G [1.42 (0.93–2.35)] and A/A [1.62 (1.33–2.51)] cohorts (P = 0.006). The Kaplan–Meier curve also revealed a higher mean survival duration of G/G cohorts (20.6 months) compared to their counterparts (A/A: 15.8 and A/G: 17.2 months) (P < 0.001). Consistently, BC data sets revealed better survival in cohorts with high expression levels (P = 0.003). Principal component analysis (PCA) showed a deviation of patients who had shorter survival towards A/A and A/G genotypes, multiple lesions, advanced stage, lymphovascular invasion, and HER2+ receptor staining. Ingenuity Pathway Analysis (IPA) showed key genes highly enriched in BC with CDKN2B-AS1. Conclusions The findings support the putative role of CDKN2B-AS1 as an epigenetic marker in BC and open a new avenue for its potential use as a therapeutic molecular target in this type of cancer. Supplementary Information The online version contains supplementary material available at 10.1186/s11658-021-00258-9.
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Affiliation(s)
- Shahad W Kattan
- Department of Medical Laboratory, College of Applied Medical Sciences, Taibah University, Yanbu, Saudi Arabia
| | - Yahya H Hobani
- Department of Medical Laboratory Technology, College of Applied Medical Sciences, Jazan University, Jazan, Kingdom of Saudi Arabia
| | - Sameerah Shaheen
- Anatomy Department and Stem Cell Unit, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Sara H Mokhtar
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohammad H Hussein
- Department of Surgery, Tulane University, School of Medicine, New Orleans, LA, USA
| | - Eman A Toraih
- Department of Surgery, Tulane University, School of Medicine, New Orleans, LA, USA.,Genetics Unit, Department of Histology and Cell Biology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
| | - Manal S Fawzy
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt. .,Department of Biochemistry, College of Medicine, Northern Border University, Arar, Saudi Arabia.
| | - Hussein Abdelaziz Abdalla
- Department of Medical Biochemistry, Faculty of Medicine, Taibah University, Medina, Saudi Arabia.,Department of Medical Biochemistry, Faculty of Medicine, Mansoura University, Mansoura, Egypt
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17
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Roupakia E, Markopoulos GS, Kolettas E. Genes and pathways involved in senescence bypass identified by functional genetic screens. Mech Ageing Dev 2021; 194:111432. [PMID: 33422562 DOI: 10.1016/j.mad.2021.111432] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 12/30/2020] [Accepted: 01/01/2021] [Indexed: 10/22/2022]
Abstract
Cellular senescence is a state of stable and irreversible cell cycle arrest with active metabolism, that normal cells undergo after a finite number of divisions (Hayflick limit). Senescence can be triggered by intrinsic and/or extrinsic stimuli including telomere shortening at the end of a cell's lifespan (telomere-initiated senescence) and in response to oxidative, genotoxic or oncogenic stresses (stress-induced premature senescence). Several effector mechanisms have been proposed to explain senescence programmes in diploid cells, including the induction of DNA damage responses, a senescence-associated secretory phenotype and epigenetic changes. Senescent cells display senescence-associated-β-galactosidase activity and undergo chromatin remodeling resulting in heterochromatinisation. Senescence is established by the pRb and p53 tumour suppressor networks. Senescence has been detected in in vitro cellular settings and in premalignant, but not malignant lesions in mice and humans expressing mutant oncogenes. Despite oncogene-induced senescence, which is believed to be a cancer initiating barrier and other tumour suppressive mechanisms, benign cancers may still develop into malignancies by bypassing senescence. Here, we summarise the functional genetic screens that have identified genes, uncovered pathways and characterised mechanisms involved in senescence evasion. These include cell cycle regulators and tumour suppressor pathways, DNA damage response pathways, epigenetic regulators, SASP components and noncoding RNAs.
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Affiliation(s)
- Eugenia Roupakia
- Laboratory of Biology, School of Medicine, Faculty of Health Sciences, University of Ioannina, Ioannina, 45100, Greece; Biomedical Research Division, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Ioannina, 45110, Greece
| | - Georgios S Markopoulos
- Laboratory of Biology, School of Medicine, Faculty of Health Sciences, University of Ioannina, Ioannina, 45100, Greece; Biomedical Research Division, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Ioannina, 45110, Greece
| | - Evangelos Kolettas
- Laboratory of Biology, School of Medicine, Faculty of Health Sciences, University of Ioannina, Ioannina, 45100, Greece; Biomedical Research Division, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Ioannina, 45110, Greece.
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18
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Manjula G, Pranavchand R, Kumuda I, Reddy BS, Reddy BM. The SNP rs7865618 of 9p21.3 locus emerges as the most promising marker of coronary artery disease in the southern Indian population. Sci Rep 2020; 10:21511. [PMID: 33298998 PMCID: PMC7726101 DOI: 10.1038/s41598-020-77080-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 11/05/2020] [Indexed: 11/09/2022] Open
Abstract
Development of coronary artery disease (CAD) is primarily due to the process of atherosclerosis, however the prognosis of CAD depends on pleiotropic effects of the genes located at 9p21.3 region. Genome wide association studies revealed association of variants in this region with CAD pathology. However, specific marker in predicting CAD development or progression is not yet identified. In the present study, 35 SNPs at 9p21.3 region, located in the cyclin dependent kinase inhibitor (CDKN2A/CDKN2B) genes, were genotyped among 350 CAD cases and 480 controls from the southern Indian population of Hyderabad using fluidigm nanofluidic SNP genotyping system and the data were analyzed using PLINK and R softwares. Of the 35 SNPs analysed, only one SNP, rs7865618, was found to be highly significantly associated with CAD, even after correction for multiple testing (p = 0.008). The AG and GG genotypes of this SNP conferred 3.08 and 1.93 folds increased risk for CAD respectively. In particular, this SNP was significantly associated with severe anatomic (triple vessel disease p = 0.023) and phenotypic (acute coronary syndrome p = 0.007) categories of CAD. Pair wise SNP interaction analysis between the SNPs of 9p21.3 and 11q23.3 regions revealed significantly increased risk of three SNPs of 11q23.3 region that were not associated individually, in conjunction with rs7865618 of 9p21.3.
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Affiliation(s)
- Gorre Manjula
- Department of Genetics, Osmania University, Hyderabad, India
| | | | - Irgam Kumuda
- Department of Genetics, Osmania University, Hyderabad, India
| | - B Sriteja Reddy
- Dr Pinnamaneni, Siddhartha Institute of Medical Sciences and Research Foundation, Vijayawada, India
| | - Battini Mohan Reddy
- Department of Genetics, Osmania University, Hyderabad, India. .,Molecular Anthropology Group, Indian Statistical Institute, Hyderabad, India. .,Emeritus Scientist (ICMR), Department of Genetics, Osmania University, Hyderabad, 500007, India.
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19
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Rahmani F, Avan A, Amerizadeh F, Ferns GA, Talebian S, Shahidsales S. The association of a genetic variant in CDKN2A/B gene and the risk of colorectal cancer. EXCLI JOURNAL 2020; 19:1316-1321. [PMID: 33122978 PMCID: PMC7588726 DOI: 10.17179/excli2020-2051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 09/14/2020] [Indexed: 11/10/2022]
Abstract
Colorectal cancer is among the most aggressive tumors, and its development involves an interplay between various genetic and environmental familial risk factors. Several genetic polymorphisms have been reported to be associated with colorectal cancer in recent studies. In this current study, we aimed to evaluate the possible relationship between a CDKN2A/B, single nucleotide polymorphisms (SNP) (rs10811661), with the risk of colorectal cancer. A total of 541 individuals with, or without cancer were recruited. DNA was extracted, and genotyped using a Taq-Man based real-time PCR method. The rs10811661 SNP was associated with an increased risk of colorectal cancer (additive model: OR=3.46, CI= 1.79-6.69, p<0.0001 and recessive model: 5.72, CI= 3.12-10.49, p<0.0001). The distribution of minor alleles in the total population for homozygote allele was 9.2 %, while this was 20.1 % for heterozygotes. In summary, our findings indicate that the rs10811661 polymorphism of the CDKN2A/B gene was strongly related to the occurrence of colorectal cancer suggesting its potential role as a prognostic biomarker for the management of colorectal cancer.
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Affiliation(s)
- Farzad Rahmani
- Iranshahr University of Medical Sciences, Iranshahr, Iran.,Cancer Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amir Avan
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Forouzan Amerizadeh
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Gordon A Ferns
- Brighton & Sussex Medical School, Division of Medical Education, Falmer, Brighton, Sussex BN1 9PH, UK
| | - Sahar Talebian
- Cancer Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
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20
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Lou N, Liu G, Pan Y. Long noncoding RNA ANRIL as a novel biomarker in human cancer. Future Oncol 2020; 16:2981-2995. [PMID: 32986472 DOI: 10.2217/fon-2020-0470] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The long noncoding RNA ANRIL, located in the human chromosome 9p21 region, has been reported to be involved in tumor progression. ANRIL regulates gene expression via recruiting PRC2 or titrating miRNA; it also participates in signaling pathways. Evidence has indicated that ANRIL is overexpressed in many cancer types and is capable of enhancing cell proliferation and cell cycle progression and inhibiting apoptosis and senescence. ANRIL has the potential to serve as a biomarker for diagnosis and prognosis in cancer. In this article we focus on recent advances in studies of the oncogenic role of ANRIL and its potential role in cancer medicine.
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Affiliation(s)
- Ning Lou
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei, 430071, PR China
| | - Guohong Liu
- Department of Radiology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei, 430071, PR China
| | - Yunbao Pan
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei, 430071, PR China
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21
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Bar C, Cohen I, Zhao D, Pothula V, Litskevitch A, Koseki H, Zheng D, Ezhkova E. Polycomb Repressive Complex 1 Controls Maintenance of Fungiform Papillae by Repressing Sonic Hedgehog Expression. Cell Rep 2020; 28:257-266.e5. [PMID: 31269445 PMCID: PMC6921245 DOI: 10.1016/j.celrep.2019.06.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 04/22/2019] [Accepted: 06/03/2019] [Indexed: 12/28/2022] Open
Abstract
How tissue patterns are formed and maintained are fundamental questions. The murine tongue epithelium, a paradigm for tissue patterning, consists of an array of specialized fungiform papillae structures that harbor taste cells. The formation of fungiform papillae is preceded by pronounced spatial changes in gene expression, in which taste cell genes such as Shh, initially diffused in lingual epithelial progenitors, become restricted to taste cells when their specification progresses. However, the requirement of spatial restriction of taste cell gene expression for patterning and formation of fungiform papillae is unknown. Here, we show that a chromatin regulator, Polycomb repressive complex (PRC) 1, is required for proper maintenance of fungiform papillae by repressing Shh and preventing ectopic SHH signaling in non-taste cells. Ablation of SHH signaling in PRC1-null non-taste cells rescues the maintenance of taste cells. Altogether, our studies exemplify how epigenetic regulation establishes spatial gene expression patterns necessary for specialized niche structures. Formation and maintenance of patterns are critical for tissue development. Bar et al. show that PRC1, an epigenetic regulator, is critical for lingual papillae development. Specifically, PRC1 regulates maintenance of the developing fungiform papillae, harboring taste cells, by repressing Shh expression in the non-gustatory epithelium surrounding taste cells.
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Affiliation(s)
- Carmit Bar
- Black Family Stem Cell Institute, The Tisch Cancer Institute, Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA
| | - Idan Cohen
- Black Family Stem Cell Institute, The Tisch Cancer Institute, Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA
| | - Dejian Zhao
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Venu Pothula
- Black Family Stem Cell Institute, The Tisch Cancer Institute, Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA
| | - Anna Litskevitch
- Department of Molecular & Cell Biology, University of California, Berkeley, 142 Life Sciences Addition, Berkeley, CA 94720, USA
| | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (RIKEN-IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan; AMED-CREST, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA; Department of Neurology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA; Department of Neuroscience, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Elena Ezhkova
- Black Family Stem Cell Institute, The Tisch Cancer Institute, Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA.
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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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23
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Shahryari A, Moya N, Siehler J, Wang X, Karolina Blöchinger A, Burtscher I, Bakhti M, Mowla SJ, Lickert H. Generation of a human iPSC line harboring a biallelic large deletion at the INK4 locus (HMGUi001-A-5). Stem Cell Res 2020; 47:101927. [PMID: 32739881 DOI: 10.1016/j.scr.2020.101927] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 07/17/2020] [Accepted: 07/20/2020] [Indexed: 12/14/2022] Open
Abstract
The INK4 locus is considered as a hot-spot region for the complex genetic disorders, including cancer, type 2 diabetes (T2D) and coronary artery disease (CAD). By CRISPR/Cas9 gene editing, we generated a human induced pluripotent stem cell (hiPSC) line (HMGUi001-A-5) deleting an 8 kb genomic DNA encompassing six T2D-associated SNPs at the INK4 locus. The resulting hiPSC line revealed a normal karyotype, preserved pluripotency and was able to differentiate towards germ layers, endoderm, mesoderm and ectoderm. Thus, the HMGUi001-A-5 line could provide a valuable cellular model to explore the molecular mechanisms linking these SNPs to T2D and other genetic disorders.
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Affiliation(s)
- Alireza Shahryari
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran; Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, D-85764 Neuherberg, Germany; Institute of Stem Cell Research, Helmholtz Zentrum München, D-85764 Neuherberg, Germany; Technical University of Munich, School of Medicine, Department of Human Genetics, Klinikum Rechts der Isar, 81675 München, Germany; Stem Cell Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Noel Moya
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, D-85764 Neuherberg, Germany; Institute of Stem Cell Research, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
| | - Johanna Siehler
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, D-85764 Neuherberg, Germany; Institute of Stem Cell Research, Helmholtz Zentrum München, D-85764 Neuherberg, Germany; Technical University of Munich, School of Medicine, Department of Human Genetics, Klinikum Rechts der Isar, 81675 München, Germany
| | - Xianming Wang
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, D-85764 Neuherberg, Germany; Institute of Stem Cell Research, Helmholtz Zentrum München, D-85764 Neuherberg, Germany; Technical University of Munich, School of Medicine, Department of Human Genetics, Klinikum Rechts der Isar, 81675 München, Germany
| | - Anna Karolina Blöchinger
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, D-85764 Neuherberg, Germany; Institute of Stem Cell Research, Helmholtz Zentrum München, D-85764 Neuherberg, Germany; Technical University of Munich, School of Medicine, Department of Human Genetics, Klinikum Rechts der Isar, 81675 München, Germany
| | - Ingo Burtscher
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, D-85764 Neuherberg, Germany; Institute of Stem Cell Research, Helmholtz Zentrum München, D-85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Mostafa Bakhti
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, D-85764 Neuherberg, Germany; Institute of Stem Cell Research, Helmholtz Zentrum München, D-85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Seyed Javad Mowla
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
| | - Heiko Lickert
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, D-85764 Neuherberg, Germany; Institute of Stem Cell Research, Helmholtz Zentrum München, D-85764 Neuherberg, Germany; Technical University of Munich, School of Medicine, Department of Human Genetics, Klinikum Rechts der Isar, 81675 München, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany.
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24
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Cohen I, Bar C, Ezhkova E. Activity of PRC1 and Histone H2AK119 Monoubiquitination: Revising Popular Misconceptions. Bioessays 2020; 42:e1900192. [PMID: 32196702 PMCID: PMC7585675 DOI: 10.1002/bies.201900192] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 02/12/2020] [Indexed: 12/21/2022]
Abstract
Polycomb group proteins are evolutionary conserved chromatin-modifying complexes, essential for the regulation of developmental and cell-identity genes. Polycomb-mediated transcriptional regulation is provided by two multi-protein complexes known as Polycomb repressive complex 1 (PRC1) and 2 (PRC2). Recent studies positioned PRC1 as a foremost executer of Polycomb-mediated transcriptional control. Mammalian PRC1 complexes can form multiple sub-complexes that vary in their core and accessory subunit composition, leading to fascinating and diverse transcriptional regulatory mechanisms employed by PRC1 complexes. These mechanisms include PRC1-catalytic activity toward monoubiquitination of histone H2AK119, a well-established hallmark of PRC1 complexes, whose importance has been long debated. In this review, the central roles that PRC1-catalytic activity plays in transcriptional repression are emphasized and the recent evidence supporting a role for PRC1 complexes in gene activation is discussed.
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Affiliation(s)
- Idan Cohen
- The Shraga Segal Department of Microbiology, Immunology and Genetics; Faculty of Health Science; Ben-Gurion University of the Negev; Beer Sheva 84105; Israel
- These authors contributed equally to this work
| | - Carmit Bar
- Black Family Stem Cell Institute, Department of Cell, Developmental, and Regenerative Biology; Icahn School of Medicine at Mount Sinai; 1 Gustave L. Levy Place, New York, NY 10029; USA
- These authors contributed equally to this work
| | - Elena Ezhkova
- The Shraga Segal Department of Microbiology, Immunology and Genetics; Faculty of Health Science; Ben-Gurion University of the Negev; Beer Sheva 84105; Israel
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25
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Yaghoubi Hariri F, Salahshourifar I, Zare Karizi S. Association between Coronary Artery Disease and rs10757278 and rs1333049 Polymorphisms in 9p21 Locus in Iran. Rep Biochem Mol Biol 2020; 9:58-63. [PMID: 32821752 DOI: 10.29252/rbmb.9.1.58] [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] [Indexed: 12/17/2022]
Abstract
Background Coronary arteries disease (CAD) has been recognized as one of the most common causes of death worldwide, with an estimated seven million deaths annually. Methods Two hundred blood samples from Iranian CAD patients and normal healthy controls were collected. CAD and the 9p21 locus variants rs1333049 and rs10757278 were analyzed for potential associations. Results No significant differences in rs10757278 and rs1333049 polymorphisms were found between patients and controls, but a significant relationship was found between rs10757278 and rs1333049 in CAD patients at the genotype level (p= 0.0323). At the haplotype level and on the basis of diplotype analysis, a significant relationship was found between patients and controls (OR= 5.16, p= 0.047, 95% CI: 1.02-26.0). In CAD patients, rs10757278 and rs1333049 were associated at locus 9p21. Conclusion The inconsistency between the results of this and other studies on different CAD populations may be due to high population, different ethnicities, low prevalence of some alleles in populations, and interactions of different genes.
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Affiliation(s)
- Farbod Yaghoubi Hariri
- Department of biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Iman Salahshourifar
- Department of biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Shohreh Zare Karizi
- Department of Genetics and Biotechnology, School of Biological Science, Varamin-Pishva Branch, Islamic Azad University, Varamin, Iran
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26
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Kaur N, Singh J, Reddy S. ANRIL rs1333049 C/G polymorphism and coronary artery disease in a North Indian population - Gender and age specific associations. Genet Mol Biol 2020; 43:e20190024. [PMID: 32191788 PMCID: PMC7197980 DOI: 10.1590/1678-4685-gmb-2019-0024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 12/15/2019] [Indexed: 11/30/2022] Open
Abstract
Many studies conducted worldwide substantiate a role of genetic polymorphisms in
non-coding regions linked with coronary artery disease (CAD). One such single
nucleotide polymorphism (SNP) of a non-coding RNA in the INK4 locus (ANRIL)
i.e. rs1333049 C/G in the vicinity of cell cycle regulating
genes is documented to have a role in CAD risk. In this study we aimed to
determine the association of ANRIL rs1333049 C/G with CAD in a North Indian
population. Five hundred disease free controls and 500 CAD patients were
genotyped using allele specific ARMS-PCR method. High risk association of
rs1333049 was seen in both heterozygous and mutant genotypes (OR=2.883, 95%
CI=1.475-5.638 and p=0.002 and OR=6.717, 95% CI=3.444-13.102 and p < 0.001
respectively). Gender stratified analysis revealed risk association in both
heterozygous and mutant genotypes in males. However, risk association in the
mutant genotype and females was documented. Similarly, risk association was seen
in subjects above 40 years of age in heterozygous and mutant genotypes.
Similarly, risk association was reported in obese, sedentary lifestyle, positive
family history and smoking in the heterozygous and mutant genotype and with
diabetes in the mutant GG genotype. The study revealed high risk association of
ANRIL rs1333049 with CAD and other risk factors.
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Affiliation(s)
- Naindeep Kaur
- Department of Biotechnology, Panjab University, Chandigarh, India
| | - Jagtar Singh
- Department of Biotechnology, Panjab University, Chandigarh, India
| | - Sreenivas Reddy
- Department of Cardiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
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27
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Roshdy F, Farag MMS, El-Ahwany E, Mahmode O, Mousa AA, El Talkawy M, Essawy F. Long non-coding RNA HOTAIR and HOTTIP as potential biomarkers for hepatitis C virus genotype 4-induced hepatocellular carcinoma. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2020. [DOI: 10.1186/s43042-020-0048-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Abstract
Background
Long non-coding RNAs (lncRNAs) homeobox (Hox) transcript antisense intergenic RNA (HOTAIR) and HOXA transcript at the distal tip (HOTTIP) have been suggested to be implicated in liver cancer tumorigenesis and progression; however, little is known about the role of the plasma HOTAIR and HOTTIP in liver cancer diagnosis and prognosis. The current study aimed at measuring the plasma levels of long non-coding RNAs (HOTAIR and HOTTIP) expression in chronic liver disease (CLD) due to HCV genotype 4 infection with/without cirrhosis and HCC patients in an attempt to evaluate the potential benefits of these new circulating as non-invasive diagnostic biomarkers and a novel therapeutic strategy for liver cirrhosis and carcinogenesis of Egyptian patients. Hundred subjects were included in this study, divided into two groups; group I (50 patients) were classified into subgroup Ia (CLD without cirrhosis, n = 25) and subgroup Ib (CLD with cirrhosis, n = 25), group II (CLD patients with HCC, n = 25), and control (healthy volunteer, n = 25). The expression of lncRNAs (HOTAIR and HOTTIP) genes was analyzed by real-time PCR.
Results
LncRNAs (HOTAIR and HOTTIP) showed upregulation in all diseased groups, which was in consistent with the progression of the disease toward the HCC stage. In addition, HOTAIR and HOTTIP showed a diagnostic ability to discriminate between cases of cirrhosis and HCC compared with healthy control (p < 0.001), while HOTAIR and HOTTIP did not show a discrimination significant differences between cirrhotic cases and non-cirrhotic cases. By using receiver operating characteristic curve (ROC) analysis, it was found that LncRNAs (HOTAIR and HOTTIP) could diagnose liver cancer with 64.0% sensitivity and 86.0% specificity and 48.0% sensitivity and 88.0% specificity. Furthermore, both genes can be considered as the predictor and prognostic parameters for cirrhosis (OR = 1.111, p = 0.05) and (OR = 1.07, p = 0.05) respectively, and HCC (OR = 1.047, p = 0.01) and (OR = 1.05, p = 0.003). The increased HOTAIR and HOTTIP expression were associated with advanced tumor stages and higher grades.
Conclusion
These results strongly prompt us that HOTAIR and HOTTIP genes can be used as non-invasive prognostic biomarkers and new therapeutic targets for HCV genotype 4-induced HCC.
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28
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Li Y, Li X, Yang Y, Li M, Qian F, Tang Z, Zhao J, Zhang J, Bai X, Jiang Y, Zhou J, Zhang Y, Zhou L, Xie J, Li E, Wang Q, Li C. TRlnc: a comprehensive database for human transcriptional regulatory information of lncRNAs. Brief Bioinform 2020; 22:1929-1939. [PMID: 32047897 DOI: 10.1093/bib/bbaa011] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 01/09/2020] [Indexed: 12/20/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) have been proven to play important roles in transcriptional processes and biological functions. With the increasing study of human diseases and biological processes, information in human H3K27ac ChIP-seq, ATAC-seq and DNase-seq datasets is accumulating rapidly, resulting in an urgent need to collect and process data to identify transcriptional regulatory regions of lncRNAs. We therefore developed a comprehensive database for human regulatory information of lncRNAs (TRlnc, http://bio.licpathway.net/TRlnc), which aimed to collect available resources of transcriptional regulatory regions of lncRNAs and to annotate and illustrate their potential roles in the regulation of lncRNAs in a cell type-specific manner. The current version of TRlnc contains 8 683 028 typical enhancers/super-enhancers and 32 348 244 chromatin accessibility regions associated with 91 906 human lncRNAs. These regions are identified from over 900 human H3K27ac ChIP-seq, ATAC-seq and DNase-seq samples. Furthermore, TRlnc provides the detailed genetic and epigenetic annotation information within transcriptional regulatory regions (promoter, enhancer/super-enhancer and chromatin accessibility regions) of lncRNAs, including common SNPs, risk SNPs, eQTLs, linkage disequilibrium SNPs, transcription factors, methylation sites, histone modifications and 3D chromatin interactions. It is anticipated that the use of TRlnc will help users to gain in-depth and useful insights into the transcriptional regulatory mechanisms of lncRNAs.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Chunquan Li
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
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Ros G, Pegoraro S, De Angelis P, Sgarra R, Zucchelli S, Gustincich S, Manfioletti G. HMGA2 Antisense Long Non-coding RNAs as New Players in the Regulation of HMGA2 Expression and Pancreatic Cancer Promotion. Front Oncol 2020; 9:1526. [PMID: 32010621 PMCID: PMC6978849 DOI: 10.3389/fonc.2019.01526] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 12/18/2019] [Indexed: 02/06/2023] Open
Abstract
Background: Natural antisense long non-coding RNAs (lncRNAs) are regulatory RNAs transcribed from the opposite strand of either protein coding or non-coding genes, able to modulate their own sense gene expression. Hence, their dysregulation can lead to pathologic processes. Cancer is a complex class of diseases determined by the aberrant expression of a variety of factors, among them, the oncofetal chromatin architectural proteins High Mobility Group A (HMGA) modulate several cancer hallmarks. Thus, we decided to investigate the presence of natural antisense lncRNAs in HMGA1 and HMGA2 loci, and their possible involvement in gene expression regulation. Methods: We used FANTOM5 data resources, FANTOM-CAT genome browser and Zenbu visualization tool, which employ 1,829 human CAGE and RNA-sequencing libraries, to determine expression, ontology enrichment, and dynamic regulation of natural antisense lncRNAs in HMGA1 and HMGA2 loci. We then performed qRT-PCR in different cancer cell lines to validate the existence of HMGA2-AS1 transcripts. We depleted HMGA2-AS1 transcripts with siRNAs and investigated HMGA2 expression by qRT-PCR and western blot analyses. Moreover, we evaluated cell viability and migration by MTS and transwell assays, and EMT markers by qRT-PCR and immunofluorescence. Furthermore, we used bioinformatics approaches to evaluate HMGA2 and HMGA2-AS1 correlation and overall survival in tumor patients. Results: We found the presence of a promoter-associated lncRNA (CATG00000088127.1) in the HMGA1 gene and three antisense genes (RPSAP52, HMGA2-AS1, and RP11-366L20.3) in the HMGA2 gene. We studied the uncharacterized HMGA2-AS1 transcripts, validating their existence in cancer cell lines and observing a positive correlation between HMGA2 and HMGA2-AS1 expression in a cancer-derived patient dataset. We showed that HMGA2-AS1 transcripts positively modulate HMGA2 expression and migration properties of PANC1 cells through HMGA2. In addition, Kaplan-Meier analysis showed that high level of HMGA2-AS1 is a negative prognostic factor in pancreatic cancer patients. Conclusions: Our results describe novel antisense lncRNAs associated with HMGA1 and HMGA2 genes. In particular, we demonstrate that HMGA2-AS1 is involved in the regulation of its own sense gene expression, mediating tumorigenesis. Thus, we highlight a new layer of complexity in the regulation of HMGA2 expression, providing new potential targets for cancer therapy.
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Affiliation(s)
- Gloria Ros
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Silvia Pegoraro
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Paolo De Angelis
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Riccardo Sgarra
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Silvia Zucchelli
- Department of Health Sciences, Center for Autoimmune and Allergic Diseases, Interdisciplinary Research Center of Autoimmune Diseases, University of Piemonte Orientale, Novara, Italy
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Pérez-Cremades D, Cheng HS, Feinberg MW. Noncoding RNAs in Critical Limb Ischemia. Arterioscler Thromb Vasc Biol 2020; 40:523-533. [PMID: 31893949 DOI: 10.1161/atvbaha.119.312860] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Peripheral artery disease, caused by chronic arterial occlusion of the lower extremities, affects over 200 million people worldwide. Peripheral artery disease can progress into critical limb ischemia (CLI), its more severe manifestation, which is associated with higher risk of limb amputation and cardiovascular death. Aiming to improve tissue perfusion, therapeutic angiogenesis held promise to improve ischemic limbs using delivery of growth factors but has not successfully translated into benefits for patients. Moreover, accumulating studies suggest that impaired downstream signaling of these growth factors (or angiogenic resistance) may significantly contribute to CLI, particularly under harsh environments, such as diabetes mellitus. Noncoding RNAs are essential regulators of gene expression that control a range of pathophysiologies relevant to CLI, including angiogenesis/arteriogenesis, hypoxia, inflammation, stem/progenitor cells, and diabetes mellitus. In this review, we summarize the role of noncoding RNAs, including microRNAs and long noncoding RNAs, as functional mediators or biomarkers in the pathophysiology of CLI. A better understanding of these ncRNAs in CLI may provide opportunities for new targets in the prevention, diagnosis, and therapeutic management of this disabling disease state.
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Affiliation(s)
- Daniel Pérez-Cremades
- From the Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (D.P.-C., H.S.C., M.W.F.).,Department of Physiology, University of Valencia and INCLIVA Biomedical Research Institute, Spain (D.P.-C.)
| | - Henry S Cheng
- From the Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (D.P.-C., H.S.C., M.W.F.)
| | - Mark W Feinberg
- From the Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (D.P.-C., H.S.C., M.W.F.)
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Association between polymorphism in CDKN2B-AS1 gene and its interaction with smoking on the risk of lung cancer in a Chinese population. Hum Genomics 2019; 13:58. [PMID: 31775885 PMCID: PMC6880550 DOI: 10.1186/s40246-019-0240-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 10/01/2019] [Indexed: 01/06/2023] Open
Abstract
Background Long non-coding RNAs became the hot spots in the carcinogenesis of various tumors. This case-control study evaluated the association between the rs2151280 in lncRNA CDKN2B-AS1 and lung cancer risk. Methods This study included 507 lung cancer patients and 542 healthy individuals. Odds ratios and their 95% confidence intervals were calculated by unconditional logistic regression analysis to evaluate the association between the rs2151280 and lung cancer risk. Results Compared with individuals carrying TT genotype, individuals carrying CC genotype of rs2151280 had a decreased risk of lung cancer (OR = 0.640, 95%CI = 0.421–0.972, P = 0.036). In the recessive model, rs2151280 CC genotype was observed to reduce the risk of lung cancer (OR = 0.684). C allele was associated with non-small cell lung cancer risk (OR = 0.674). The rs2151280 was significantly associated with lung adenocarcinoma risk (CCvsTT: OR = 0.567, 95%CI = 0.333–0.965, P = 0.037; CCvsTC+TT: OR = 0.543, 95%CI 0.330–0.893, P = 0.016, respectively). However, there was no significant association between rs2151280 and lung squamous cell carcinoma risk in five models. The quantitative analysis suggested that there were no significant interactions of rs2151280 with smoking exposure to lung cancer susceptibility. Conclusions This hospital-based case-control study suggested that CDKN2B-AS1 rs2151280 T>C was associated with the risk of lung cancer.
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32
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Zhang X, Liu L, Yuan X, Wei Y, Wei X. JMJD3 in the regulation of human diseases. Protein Cell 2019; 10:864-882. [PMID: 31701394 PMCID: PMC6881266 DOI: 10.1007/s13238-019-0653-9] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 06/11/2019] [Indexed: 02/06/2023] Open
Abstract
In recent years, many studies have shown that histone methylation plays an important role in maintaining the active and silent state of gene expression in human diseases. The Jumonji domain-containing protein D3 (JMJD3), specifically demethylate di- and trimethyl-lysine 27 on histone H3 (H3K27me2/3), has been widely studied in immune diseases, infectious diseases, cancer, developmental diseases, and aging related diseases. We will focus on the recent advances of JMJD3 function in human diseases, and looks ahead to the future of JMJD3 gene research in this review.
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Affiliation(s)
- Xiangxian Zhang
- Laboratory of Aging Research and Nanotoxicology, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Li Liu
- Laboratory of Aging Research and Nanotoxicology, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xia Yuan
- Laboratory of Aging Research and Nanotoxicology, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yuquan Wei
- Laboratory of Aging Research and Nanotoxicology, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xiawei Wei
- Laboratory of Aging Research and Nanotoxicology, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China.
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Kokkinopoulou I, Maratou E, Mitrou P, Boutati E, Sideris DC, Fragoulis EG, Christodoulou MI. Decreased expression of microRNAs targeting type-2 diabetes susceptibility genes in peripheral blood of patients and predisposed individuals. Endocrine 2019; 66:226-239. [PMID: 31559537 DOI: 10.1007/s12020-019-02062-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 08/20/2019] [Indexed: 12/12/2022]
Abstract
AIM Certain microRNA molecules (miRNAs) that target genes involved in beta-cell growth and insulin resistance are found deregulated in patients with type-2 diabetes mellitus (T2D) and correlate with its complications. However, the expression profile of miRNAs that regulate genes bearing T2D-related single-nucleotide polymorphisms has been hardly studied. We recently reported that the mRNA patterns of specific T2D-susceptibility genes are impaired in patients, and associate with disease parameters and risk factors. The aim of this study was to explore the levels of miRNAs that target those genes, in peripheral blood of patients versus controls. METHODS A panel of 14 miRNAs validated to target the CDKN2A, CDK5, IGF2BP2, KCNQ1, and TSPAN8 genes, was developed upon combined search throughout the DIANNA TarBase v7.0, miRTarBase, miRSearch v3.0-Exiqon, miRGator v3.0, and miRTarget Link Human algorithms. Specifically developed poly(A)polyadenylation(PAP)-reverse transcription(RT)-qPCR protocols were applied in peripheral blood RNA samples from patients and controls. Possible correlations with the disease, clinicopathological parameters and/or risk factors were evaluated. RESULTS T2D patients expressed decreased levels of let-7b-5p, miR-1-3p, miR-24-3p, miR-34a-5p, miR-98-5p, and miR-133a-3p, compared with controls. Moreover, these levels correlated with certain disease features including insulin and % HbA1c levels in patients, as well as BMI, triglycerides' levels and family history in controls. CONCLUSIONS A T2D-specific expression profile of miRNAs that target disease-susceptibility genes is for the first time described. Future studies are needed to elucidate the associated transcription-regulatory mechanisms, perchance involved in T2D pathogenesis, and to evaluate the potential of these molecules as possible biomarkers for this disorder.
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Affiliation(s)
- Ioanna Kokkinopoulou
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece.
| | - Eirini Maratou
- Second Department of Internal Medicine and Research Institute, School of Medicine, National and Kapodistrian University of Athens, "Attikon" University Hospital, Athens, Greece
| | | | - Eleni Boutati
- Second Department of Internal Medicine and Research Institute, School of Medicine, National and Kapodistrian University of Athens, "Attikon" University Hospital, Athens, Greece
| | - Diamantis C Sideris
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Emmanuel G Fragoulis
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Maria-Ioanna Christodoulou
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece.
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK.
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Drak Alsibai K, Vacher S, Meseure D, Nicolas A, Lae M, Schnitzler A, Chemlali W, Cros J, Longchampt E, Cacheux W, Pignot G, Callens C, Pasmant E, Allory Y, Bieche I. High Positive Correlations between ANRIL and p16- CDKN2A/ p15- CDKN2B/ p14- ARF Gene Cluster Overexpression in Multi-Tumor Types Suggest Deregulated Activation of an ANRIL-ARF Bidirectional Promoter. Noncoding RNA 2019; 5:E44. [PMID: 31438464 PMCID: PMC6789474 DOI: 10.3390/ncrna5030044] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 08/08/2019] [Accepted: 08/15/2019] [Indexed: 01/10/2023] Open
Abstract
The CDKN2B-AS1 gene, also called ANRIL, is located at the human CDKN2A/B locus at 9p21.3 and transcribed by RNA polymerase II into a long non-coding RNA of 3834 bp. The CDKN2B-AS1 gene overlaps a critical region of 125 kb covering the CDKN2B gene. The CDKN2A/B locus encompasses three major tumor suppressors juxtaposed and joined into a p16-CDKN2A/p15-CDKN2B/p14-ARF gene cluster. CDKN2A encodes splice variants p16-CDKN2A and p14-ARF, and CDKN2B encodes p15-CDKN2B. ANRIL shares a bidirectional promoter with the p14-ARF gene and is transcribed from the opposite strand to the cluster. We performed an analysis of the expression level of ANRIL and tumor suppressor p16-CDKN2A, p15-CDKN2B, and p14-ARF genes using quantitative RT-PCR in a multitumor panel. We observed the overexpression of the four genes ANRIL, p16-CDKN2A, p15-CDKN2B, and p14-ARF in the great majority of the 17 different cancer types. ANRIL was upregulated in 13/17 tumors compared to normal tissues, ranging from 5% (prostate cancer) to 91% (cervix cancer), with variable expression of p16-CDKN2A, p15-CDKN2B, and p14-ARF genes. A high positive correlation was identified between levels of expression of ANRIL and the three tumor suppressors. The strongest positive association was observed with p14-ARF (p < 0.001) in all but one (lung squamous cell carcinoma) of the examined tumor types. This correlation suggests coordinated deregulated mechanisms in all cancer types through aberrant activation of a bidirectional p14-ARF/ANRIL promoter. Furthermore, significant positive correlation was unexpectedly established in prostatic carcinomas, in contradiction with previous data.
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Affiliation(s)
| | - Sophie Vacher
- Unit of Pharmacogenomics, Department of Genetics, Institut Curie, 75248 Paris, France
| | - Didier Meseure
- Platform of Experimental Pathology, Institut Curie, 75248 Paris, France.
- Unit of Pharmacogenomics, Department of Genetics, Institut Curie, 75248 Paris, France.
- Department of Diagnostic and Theranostic Medicine, Institut Curie, 75248 Paris, France.
| | - Andre Nicolas
- Platform of Experimental Pathology, Institut Curie, 75248 Paris, France
- Department of Diagnostic and Theranostic Medicine, Institut Curie, 75248 Paris, France
| | - Marick Lae
- Department of Diagnostic and Theranostic Medicine, Institut Curie, 75248 Paris, France
| | - Anne Schnitzler
- Unit of Pharmacogenomics, Department of Genetics, Institut Curie, 75248 Paris, France
| | - Walid Chemlali
- Unit of Pharmacogenomics, Department of Genetics, Institut Curie, 75248 Paris, France
| | - Jerome Cros
- Department of Pathology, Beaujon Hospital, APHP Nord, 92110 Clichy, France
| | | | - Wulfran Cacheux
- Unit of Pharmacogenomics, Department of Genetics, Institut Curie, 75248 Paris, France
| | - Geraldine Pignot
- Unit of Pharmacogenomics, Department of Genetics, Institut Curie, 75248 Paris, France
| | - Celine Callens
- Unit of Pharmacogenomics, Department of Genetics, Institut Curie, 75248 Paris, France
| | - Eric Pasmant
- Department of Genetics, Cochin Hospital, APHP, 75014 Paris, France
- Cochin Institute, Inserm U1016, Paris Descartes University, 75014 Paris, France
| | - Yves Allory
- Department of Diagnostic and Theranostic Medicine, Institut Curie, 75248 Paris, France
| | - Ivan Bieche
- Platform of Experimental Pathology, Institut Curie, 75248 Paris, France
- Department of Diagnostic and Theranostic Medicine, Institut Curie, 75248 Paris, France
- Department of Genetics, Cochin Hospital, APHP, 75014 Paris, France
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Leeper NJ, Maegdefessel L. Non-coding RNAs: key regulators of smooth muscle cell fate in vascular disease. Cardiovasc Res 2019; 114:611-621. [PMID: 29300828 DOI: 10.1093/cvr/cvx249] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 12/28/2017] [Indexed: 01/02/2023] Open
Abstract
The vascular smooth muscle cell (SMC) is one of the most plastic cells in the body. Understanding how non-coding RNAs (ncRNAs) regulate SMC cell-fate decision making in the vasculature has significantly enhanced our understanding of disease development, and opened up exciting new avenues for potential therapeutic applications. Recent studies on SMC physiology have in addition challenged our traditional view on their role and contribution to vascular disease, mainly in the setting of atherosclerosis as well as aneurysm disease, and restenosis after angioplasties. The impact of SMC behaviour on vascular disease is now recognized to be context dependent; SMC proliferation and migration can be harmful or beneficial, whereas their apoptosis, senescence, and switching into a more macrophage-like phenotype can promote inflammation and disease progression. This is in particular true for atherosclerosis-related diseases, where proliferation of SMCs was believed to promote lesion formation, but may also prevent plaque rupture by stabilizing the fibrous cap. Based on newer findings of genetic lineage tracing studies, it was revealed that SMC phenotypic switching can result in less-differentiated forms that lack classical SMC markers while exhibiting functions more related to macrophage-like cells. This switching can directly promote atherogenesis. The aim of this current review is to summarize and discuss how ncRNAs (mainly microRNAs and long ncRNAs) are involved in SMC plasticity, and how they directly affect vascular disease development and progression. Finally, we want to critically assess where potential future therapies could be useful to influence the burden of vascular diseases.
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Affiliation(s)
- Nicholas J Leeper
- Division of Vascular Surgery, Stanford University, Stanford, CA, USA
| | - Lars Maegdefessel
- Department of Vascular and Endovascular Surgery, Klinikum Rechts der Isar, Technical University Munich, and German Center for Cardiovascular Research Center (DZHK) Partner Site Munich, 81675 Munich, Germany.,Karolinska Institute, Center for Molecular Medicine, Stockholm, Sweden
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LncRNAs Regulatory Networks in Cellular Senescence. Int J Mol Sci 2019; 20:ijms20112615. [PMID: 31141943 PMCID: PMC6600251 DOI: 10.3390/ijms20112615] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 04/19/2019] [Accepted: 05/06/2019] [Indexed: 02/07/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are a class of transcripts longer than 200 nucleotides with no open reading frame. They play a key role in the regulation of cellular processes such as genome integrity, chromatin organization, gene expression, translation regulation, and signal transduction. Recent studies indicated that lncRNAs are not only dysregulated in different types of diseases but also function as direct effectors or mediators for many pathological symptoms. This review focuses on the current findings of the lncRNAs and their dysregulated signaling pathways in senescence. Different functional mechanisms of lncRNAs and their downstream signaling pathways are integrated to provide a bird’s-eye view of lncRNA networks in senescence. This review not only highlights the role of lncRNAs in cell fate decision but also discusses how several feedback loops are interconnected to execute persistent senescence response. Finally, the significance of lncRNAs in senescence-associated diseases and their therapeutic and diagnostic potentials are highlighted.
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Chikenji TS, Saito Y, Konari N, Nakano M, Mizue Y, Otani M, Fujimiya M. p16 INK4A-expressing mesenchymal stromal cells restore the senescence-clearance-regeneration sequence that is impaired in chronic muscle inflammation. EBioMedicine 2019; 44:86-97. [PMID: 31129096 PMCID: PMC6604166 DOI: 10.1016/j.ebiom.2019.05.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 04/28/2019] [Accepted: 05/06/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND The therapeutic benefits of mesenchymal stromal cells (MSCs) include treatment of chronic inflammation. However, given the short-lived engraftment of these cells in vivo, their therapeutic efficacy remains mysterious. Transient induction of cellular senescence contributes to activation of immune cells, which promotes clearance of damaged cells during tissue remodelling. This may occur in tissue-resident mesenchymal progenitor cells during regeneration. Elucidation of the role of senescence in tissue-resident mesenchymal progenitor cells during regeneration would provide insight into the profile of therapeutic MSCs for treatment of chronic inflammatory disease. METHODS We evaluated multipotent mesenchymal progenitor cells, termed fibro/adipogenic progenitors (FAPs), and immune cells in acute muscle injury (AMI) model mice and mice with myosin-induced experimental autoimmune myositis, a model of chronic inflammatory myopathy (CIM). Human bone marrow MSCs were optimised for the treatment of CIM using placental extract. FINDING FAPs in AMI transiently expressed p16INK4A on days 1 and 2 after injury and recruited phagocytic immune cells, whereas in CIM, p16INK4A expression in FAPs was low. Cellular senescence occurs during the natural maturation of the placenta. Therefore, we used human placental extract to induce p16INK4A expression in therapeutic human bone marrow MSCs in culture. Treatment of CIM with p16INK4A-expressing MSCs promoted tissue remodelling by transiently increasing the abundance of engrafted MSCs, inducing cellular senescence in innate FAPs, and recruiting phagocytic immune cells. INTERPRETATION MSCs may exert their effect by remodelling the chronic inflammatory environment via senescence-related regenerative processes.
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Affiliation(s)
- Takako S Chikenji
- Department of Anatomy, Sapporo Medical University School of Medicine, Sapporo, Hokkaido 060-8556, Japan.
| | - Yuki Saito
- Department of Anatomy, Sapporo Medical University School of Medicine, Sapporo, Hokkaido 060-8556, Japan
| | - Naoto Konari
- Department of Anatomy, Sapporo Medical University School of Medicine, Sapporo, Hokkaido 060-8556, Japan
| | - Masako Nakano
- Department of Anatomy, Sapporo Medical University School of Medicine, Sapporo, Hokkaido 060-8556, Japan
| | - Yuka Mizue
- Department of Anatomy, Sapporo Medical University School of Medicine, Sapporo, Hokkaido 060-8556, Japan
| | - Miho Otani
- Department of Anatomy, Sapporo Medical University School of Medicine, Sapporo, Hokkaido 060-8556, Japan
| | - Mineko Fujimiya
- Department of Anatomy, Sapporo Medical University School of Medicine, Sapporo, Hokkaido 060-8556, Japan
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Kalpana B, Murthy DK, Balakrishna N, Aiyengar MT. Genetic variants of chromosome 9p21.3 region associated with coronary artery disease and premature coronary artery disease in an Asian Indian population. Indian Heart J 2019; 71:263-271. [PMID: 31543200 PMCID: PMC6796635 DOI: 10.1016/j.ihj.2019.04.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 04/01/2019] [Accepted: 04/26/2019] [Indexed: 01/29/2023] Open
Abstract
INTRODUCTION Asian Indians have a propensity for premature, severe, and diffuse coronary artery disease (CAD). Several single-nucleotide polymorphisms (SNPs) in the 'core CAD' region of the chromosomal region 9p21.3 are known to be strongly associated with CAD. OBJECTIVES We aimed to study SNPs in the 9p21.3 region associated with CAD and premature CAD and identify their association with demographic and clinical characteristics in an Asian Indian population. METHODS SNP genotyping was performed for 30 SNPs of the 9p21.3 region using MassARRAY® technology. Along with demographic and SNP data analysis, we also performed multivariate logistic regression analysis and multifactor dimensionality reduction analysis to study SNP-SNP and SNP-demographic/clinical variable interactions. RESULTS Our results suggest that females are at a higher risk of premature CAD. We found that SNPs rs1333045 (CC), rs16905599 (AA), rs2383206 (GG), rs2383208 (AG), and rs4977574 (GG) were significantly associated with premature CAD. When adjusted for covariates/confounders, we found that rs2383206 showed the strongest risk association with CAD followed by rs16905599 and rs2383208. Further, SNPs rs1333049 (CC) and rs4977574 (GG) were found to be exclusively associated with premature CAD cases, suggesting their potential as genetic markers for premature CAD in the local population. Upon gender-based stratification, it was found that rs10757272 (TT and TC) is significantly associated with eightfold to ninefold CAD risk specifically among females. SNP rs7865618 (GG) is significantly associated with more than 2.5-fold CAD risk specifically among males. CONCLUSION Our study suggests that SNPs at the 9p21 risk locus may be used to generate a reliable genetic risk score along with markers at other loci.
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Affiliation(s)
- Bellary Kalpana
- Department of Genetics & Biotechnology, Bhavan's Vivekananda College, Sainikpuri, Secunderabad 500094, Telangana State, India.
| | - Dwarkanath K Murthy
- Department of Genetics & Biotechnology, Osmania University, Hyderabad 500007, Telangana State, India.
| | - Nagalla Balakrishna
- Division of Biostatistics, National Institute of Nutrition, Hyderabad 500007, Telangana State, India.
| | - Mohini T Aiyengar
- Department of Genetics & Biotechnology, Bhavan's Vivekananda College, Sainikpuri, Secunderabad 500094, Telangana State, India.
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Bunch H, Choe H, Kim J, Jo DS, Jeon S, Lee S, Cho DH, Kang K. P-TEFb Regulates Transcriptional Activation in Non-coding RNA Genes. Front Genet 2019; 10:342. [PMID: 31068966 PMCID: PMC6491683 DOI: 10.3389/fgene.2019.00342] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 03/29/2019] [Indexed: 01/16/2023] Open
Abstract
Many non-coding RNAs (ncRNAs) serve as regulatory molecules in various physiological pathways, including gene expression in mammalian cells. Distinct from protein-coding RNA expression, ncRNA expression is regulated solely by transcription and RNA processing/stability. It is thus important to understand transcriptional regulation in ncRNA genes but is yet to be known completely. Previously, we identified that a subset of mammalian ncRNA genes is transcriptionally regulated by RNA polymerase II (Pol II) promoter-proximal pausing and in a tissue-specific manner. In this study, human ncRNA genes that are expressed in the early G1 phase, termed immediate early ncRNA genes, were monitored to assess the function of positive transcription elongation factor b (P-TEFb), a master Pol II pausing regulator for protein-coding genes, in ncRNA transcription. Our findings indicate that the expression of many ncRNA genes is induced in the G0–G1 transition and regulated by P-TEFb. Interestingly, a biphasic characteristic of P-TEFb-dependent transcription of serum responsive ncRNA genes was observed: Pol II carboxyl-terminal domain phosphorylated at serine 2 (S2) was largely increased in the transcription start site (TSS, -300 to +300) whereas overall, it was decreased in the gene body (GB, > +350) upon chemical inhibition of P-TEFb. In addition, the three representative, immediate early ncRNAs, whose expression is dependent on P-TEFb, metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), nuclear enriched abundant transcript 1 (NEAT1), and X-inactive specific transcript (XIST), were further analyzed for determining P-TEFb association. Taken together, our data suggest that transcriptional activation of many human ncRNAs utilizes the pausing and releasing of Pol II, and that the regulatory mechanism of transcriptional elongation in these genes requires the function of P-TEFb. Furthermore, we propose that ncRNA and mRNA transcription are regulated by similar mechanisms while P-TEFb inhibition unexpectedly increases S2 Pol II phosphorylation in the TSSs in many ncRNA genes. One Sentence Summary: P-TEFb regulates Pol II phosphorylation for transcriptional activation in many stimulus-inducible ncRNA genes.
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Affiliation(s)
- Heeyoun Bunch
- Department of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, South Korea
| | - Hyeseung Choe
- Department of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, South Korea
| | - Jongbum Kim
- Department of Transcriptome & Epigenome, Macrogen Incorporated, Seoul, South Korea
| | - Doo Sin Jo
- Institute of Life Science and Biotechnology, College of Natural Science, Kyungpook National University, Daegu, South Korea
| | - Soyeon Jeon
- Department of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, South Korea
| | - Sanghwa Lee
- Department of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, South Korea
| | - Dong-Hyung Cho
- Department of Life Science, College of Natural Science, Kyungpook National University, Daegu, South Korea
| | - Keunsoo Kang
- Department of Microbiology, College of Natural Sciences, Dankook University, Cheonan, South Korea
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Kangarlouei R, Irani S, Noormohammadi Z, Memari F, Mirfakhraie R. ANRIL and ANRASSF1 long noncoding RNAs are upregulated in gastric cancer. J Cell Biochem 2019; 120:12544-12548. [PMID: 30834580 DOI: 10.1002/jcb.28520] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 12/27/2018] [Accepted: 01/09/2019] [Indexed: 01/13/2023]
Abstract
Gastric cancer (GC) is the fifth most frequent cancer and the third-leading cause of cancer-related death worldwide. It is a highly heterogeneous disease regarding the morphological and molecular viewpoints. Since it is curable in primary stages, early detection could improve the survival rate. Long noncoding RNAs contribute to a variety of cellular mechanisms, and their dysregulation is reported in various diseases such as cancer. Thus, they have a great potential to be used as diagnostic and prognostic biomarkers and therapeutic targets as well. In the current study, ANRIL and ANRASSF1 expression levels were compared between GC tumors and the adjacent normal tissues collected from 39 Iranian patients using the quantitative real-time polymerase chain reaction method. Correlation between ANRIL and ANRASSF1 expression levels and other clinical parameters was also evaluated. ANRIL and ANRASSF1 were significantly overexpressed in GC tumors compared with adjacent tissues ( P < 0.0001 and P = 0.001, respectively). No significant correlation between ANRIL and ANRASSF1 expression levels and demographic information was found. This study suggests that ANRIL and ANRASSF1 may play a critical role in GC progression and can be considered as a potential diagnostic or therapeutics biomarkers.
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Affiliation(s)
- Roghayeh Kangarlouei
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Shiva Irani
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Zahra Noormohammadi
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Fereidoon Memari
- Cancer Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Reza Mirfakhraie
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Genomic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Sui A, Xu Y, Pan B, Guo T, Wu J, Shen Y, Yang J, Guo X. Histone demethylase KDM6B regulates 1,25‐dihydroxyvitamin D3‐induced senescence in glioma cells. J Cell Physiol 2019; 234:17990-17998. [PMID: 30825201 DOI: 10.1002/jcp.28431] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 02/04/2019] [Accepted: 02/14/2019] [Indexed: 12/30/2022]
Affiliation(s)
- Aixia Sui
- Department of Oncology Hebei General Hospital Shijiazhuang China
| | - Yongbing Xu
- Department of Oncology Hebei General Hospital Shijiazhuang China
- Graduate School, Hebei Medical University Shijiazhuang China
| | - Baogen Pan
- Department of Neurosurgery Hebei General Hospital Shijiazhuang China
| | - Tao Guo
- Department of Oncology Hebei General Hospital Shijiazhuang China
| | - Jiang Wu
- Department of Neurosurgery Hebei General Hospital Shijiazhuang China
| | - Yongqing Shen
- Department of Nursing Hebei University of Chinese Medicine Shijiazhuang China
| | - Junjie Yang
- Department of Oncology Hebei General Hospital Shijiazhuang China
| | - Xiaoqiang Guo
- The Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics Peking University Shenzhen Hospital Shenzhen China
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Blood-based analysis of type-2 diabetes mellitus susceptibility genes identifies specific transcript variants with deregulated expression and association with disease risk. Sci Rep 2019; 9:1512. [PMID: 30728419 PMCID: PMC6365563 DOI: 10.1038/s41598-018-37856-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 12/13/2018] [Indexed: 01/26/2023] Open
Abstract
Despite significant progress by genome-wide association studies, the ability of genetic variants to conduce to the prediction or prognosis of type-2 diabetes (T2D) is weak. Expression analysis of the corresponding genes may suggest possible links between single-nucleotide polymorphisms and T2D phenotype and/or risk. Herein, we investigated the expression patterns of 24 T2D-susceptibility genes, and their individual transcript variants (tv), in peripheral blood of T2D patients and controls (CTs), applying RNA-seq and real-time qPCR methodologies, and explore possible associations with disease features. Our data revealed the deregulation of certain transcripts in T2D patients. Among them, the down-regulation of CAPN10 tv3 was confirmed as an independent predictor for T2D. In patients, increased expression of CDK5 tv2, CDKN2A tv3 or THADA tv5 correlated positively with serum insulin levels, of CDK5 tv1 positively with % HbA1c levels, while in controls, elevated levels of TSPAN8 were associated positively with the presence of T2D family history. Herein, a T2D-specific expression profile of specific transcripts of disease-susceptibility genes is for the first time described in human peripheral blood. Large-scale studies are needed to evaluate the potential of these molecules to serve as disease biomarkers.
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The silencing of long non-coding RNA ANRIL suppresses invasion, and promotes apoptosis of retinoblastoma cells through the ATM-E2F1 signaling pathway. Biosci Rep 2018; 38:BSR20180558. [PMID: 30355646 PMCID: PMC6294646 DOI: 10.1042/bsr20180558] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 09/25/2018] [Accepted: 10/04/2018] [Indexed: 01/07/2023] Open
Abstract
As one of the most common primary intraocular carcinomas, retinoblastoma generally stems from the inactivation of the retinoblastoma RB1 gene in retinal cells. Antisense non-coding RNA in the INK4 locus (ANRIL), a long non-coding RNA (lncRNA), has been reported to affect tumorigenesis and progression of various cancers, including gastric cancer and non-small cell lung cancer. However, limited investigations emphasized the role of ANRIL in human retinoblastoma. Hence, the current study was intended to investigate the effects of ANRIL on the proliferation, apoptosis, and invasion of retinoblastoma HXO-RB44 and Y79 cells. The lentivirus-based packaging system was designed to aid the up-regulation of ANRIL and ATM expressions or employed for the down-regulation of ANRIL in human retinoblastoma cells. Afterward, ANRIL expression, mRNA and protein expression of ATM and E2F1, and protein expression of INK4b, INK4a, alternate reading frame (ARF), p53 and retinoblastoma protein (pRB) were determined in order to elucidate the regulation effect associated with ANRIL on the ATM-E2F1 signaling pathway. In addition, cell viability, apoptosis, and invasion were detected accordingly. The results indicated that the down-regulation of ANRIL or up-regulation of ATM led to an increase in the expressions of ATM, E2F1, INK4b, INK4a, ARF, p53, and pRB. The silencing of ANRIL or up-regulation of ATM exerted an inhibitory effect on the proliferation and invasion while improving the apoptosis of HXO-RB44 and Y79 cells. In conclusion, the key observations of our study demonstrated that ANRIL depletion could act to suppress retinoblastoma progression by activating the ATM-E2F1 signaling pathway. These results provide a potentially promising basis for the targetted intervention treatment of human retinoblastoma.
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Antisense Non-Coding RNA in the INK4 Locus (ANRIL) in Human Cancers. INTERNATIONAL JOURNAL OF CANCER MANAGEMENT 2018. [DOI: 10.5812/ijcm.67864] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Ghobadi N, Mehramiz M, ShahidSales S, Rezaei Brojerdi A, Anvari K, Khazaei M, Rezayi M, Sadegh Khorrami M, Joudi‐Mashhad M, Ramshini H, Ahmadi‐Simab S, Moradi A, Hassanian SM, Ghayour‐Mobarhan M, Boroushaki MT, Ferns GA, Avan A. A genetic variant in
CDKN2A/2B
locus was associated with poor prognosis in patients with esophageal squamous cell carcinoma. J Cell Physiol 2018; 234:5070-5076. [PMID: 30238987 DOI: 10.1002/jcp.27310] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 08/02/2018] [Indexed: 12/13/2022]
Abstract
Esophageal squamous cell carcinoma (ESCC) is among the leading causes of cancer related death. Despite of extensive efforts in identifying valid cancer prognostic biomarkers, only a very small number of markers have been identified. Several genetic variants in the 9p21 region have been identified that are associated with the risk of multiple cancers. Here, we explored the association of two genetic variants in the 9p21 region, CDKN2A/B, rs10811661, and rs1333049 for the first time in 273 subjects with, or without ESCC. We observed that the patients with ESCC had a higher frequency of a TT genotype for rs10811661 than individuals in the control group, and this polymorphism was also associated with tumor size. Moreover, a CC genotype for the rs1333049 polymorphism was associated with a reduced overall survival (OS) of patients with ESCC. In particular, patients with a CC (rs1333049) genotype had a significantly shorter OS (CC genotype: 34.5 ± 8.9 months vs. CG+GG: 47.7 ± 5.9 months; p value = 0.03). We have also shown the association of a novel genetic variant in CDKN2B gene with clinical outcome of patients with ESCC. Further investigations are warranted in a larger population to explore the value of emerging markers as a risk stratification marker in ESCC.
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Affiliation(s)
- Niloofar Ghobadi
- Department of Biochemistry Faculty of Sciences, Payam‐e Noor University of Mashhad Mashhad Iran
- Department of Biology Payam e Noor University, Branch of Sabzevar Sabzevar Iran
| | - Mehrane Mehramiz
- Metabolic syndrome Research center, Mashhad University of Medical Sciences Mashhad Iran
| | | | | | - Kazem Anvari
- Cancer Research Center, Mashhad University of Medical Sciences Mashhad Iran
| | - Majid Khazaei
- Metabolic syndrome Research center, Mashhad University of Medical Sciences Mashhad Iran
| | - Majid Rezayi
- Metabolic syndrome Research center, Mashhad University of Medical Sciences Mashhad Iran
| | - Mohammad Sadegh Khorrami
- Department of Modern Sciences and Technologies School of Medicine, Mashhad University of Medical Sciences Mashhad Iran
| | - Mona Joudi‐Mashhad
- Cancer Research Center, Mashhad University of Medical Sciences Mashhad Iran
| | - Hassan Ramshini
- Department of Biology Payam e Noor University, Branch of Sabzevar Sabzevar Iran
| | | | - Ali Moradi
- Cancer Research Center, Mashhad University of Medical Sciences Mashhad Iran
| | - Seyed Mahdi Hassanian
- Metabolic syndrome Research center, Mashhad University of Medical Sciences Mashhad Iran
- Department of Medical Biochemistry School of Medicine, Mashhad University of Medical Sciences Mashhad Iran
| | | | - Mohammad Taher Boroushaki
- Department of Pharmacology and Pharmacological Research Center of Medicinal Plants Faculty of Medicine, Mashhad University of Medical Sciences Mashhad Iran
| | - Gordon A. Ferns
- Division of Medical Education Brighton & Sussex Medical School Brighton Sussex UK
| | - Amir Avan
- Metabolic syndrome Research center, Mashhad University of Medical Sciences Mashhad Iran
- Cancer Research Center, Mashhad University of Medical Sciences Mashhad Iran
- Department of Modern Sciences and Technologies School of Medicine, Mashhad University of Medical Sciences Mashhad Iran
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Gong Y, Mao J, Wu D, Wang X, Li L, Zhu L, Song R. Circ-ZEB1.33 promotes the proliferation of human HCC by sponging miR-200a-3p and upregulating CDK6. Cancer Cell Int 2018; 18:116. [PMID: 30123094 PMCID: PMC6090603 DOI: 10.1186/s12935-018-0602-3] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 07/23/2018] [Indexed: 12/23/2022] Open
Abstract
Background Accumulating data indicated that circRNA plays important roles in regulating many biological processes of the tumor, the present study is designated for exploring roles of the circ-ZEB1.33-miR-200a-3p-CDK6 regulating axis in human hepatocellular carcinoma (HCC). Methods The regulation axis as predicted by using online tool circNet, the expression and correlation of circ-ZEB1.33-miR-200a-3p-CDK6 was verified in human HCC. The diagnostic value of both tumor and serum circ-ZEB1.33 was estimated by using clinical samples. The roles of circ-ZEB1.33-miR-200a-3p-CDK6 in regulating cell cycle were explored by using in vitro studies. Results Overexpression of circ-ZEB1.33 and CDK6, downregulation of miR-200a-3p were detected in human HCC tissues, negative correlation between circ-ZEB1.33 and miR-200a-3p, positive correlation between circ-ZEB1.33 and CDK6 were confirmed in human HCC tissues. Tissue and serum circ-ZEB1.33 were related to different TMN stages and prognosis in HCC patients. RNA pull-down assay implied that circ-ZEB1.33 could decrease miR-200a-3p by sponging miR-200a-3p, and the luciferase reporter assay indicated that miR-200a-3p could downregulate CDK6 transcription by targeting its 3′UTR. The in vitro assays indicated that circ-ZEB1.33 could promote the proliferation of HCC cells by increasing the percentage of S phase regulated by CDK6/Rb. Conclusion Proliferation promotion roles of the circ-ZEB1.33-miR-200a-3p-CDK6 regulating axis are existed and verified in human HCC, both tumor and serum circ-ZEB1.33 can serve as an indicator for the prognosis of HCC patients. Electronic supplementary material The online version of this article (10.1186/s12935-018-0602-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yuhua Gong
- Department of Clinical Laboratory, The Third People's Hospital of Zhenjiang, 300 Daijiamen, Zhenjiang, 212005 Jiangsu China
| | - Jinzhong Mao
- Department of Radiology, The Third People's Hospital of Zhenjiang, 300 Daijiamen, Zhenjiang, 212005 Jiangsu China
| | - Di Wu
- Department of Hepatosis Inpatient, The Third People's Hospital of Zhenjiang, 300 Daijiamen, Zhenjiang, 212005 Jiangsu China
| | - Xuemei Wang
- Department of Clinical Laboratory, The Third People's Hospital of Zhenjiang, 300 Daijiamen, Zhenjiang, 212005 Jiangsu China
| | - Long Li
- Department of Clinical Laboratory, The Third People's Hospital of Zhenjiang, 300 Daijiamen, Zhenjiang, 212005 Jiangsu China
| | - Liang Zhu
- Department of Clinical Laboratory, The Third People's Hospital of Zhenjiang, 300 Daijiamen, Zhenjiang, 212005 Jiangsu China
| | - Rong Song
- Department of Clinical Laboratory, The Third People's Hospital of Zhenjiang, 300 Daijiamen, Zhenjiang, 212005 Jiangsu China
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Yang J, Gu L, Guo X, Huang J, Chen Z, Huang G, Kang Y, Zhang X, Long J, Su L. LncRNA ANRIL Expression and ANRIL Gene Polymorphisms Contribute to the Risk of Ischemic Stroke in the Chinese Han Population. Cell Mol Neurobiol 2018; 38:1253-1269. [DOI: 10.1007/s10571-018-0593-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 05/23/2018] [Indexed: 12/13/2022]
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Jalali S, Gandhi S, Scaria V. Distinct and Modular Organization of Protein Interacting Sites in Long Non-coding RNAs. Front Mol Biosci 2018; 5:27. [PMID: 29670884 PMCID: PMC5893854 DOI: 10.3389/fmolb.2018.00027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 03/14/2018] [Indexed: 12/11/2022] Open
Abstract
Background: Long non-coding RNAs (lncRNAs), are being reported to be extensively involved in diverse regulatory roles and have exhibited numerous disease associations. LncRNAs modulate their function through interaction with other biomolecules in the cell including DNA, RNA, and proteins. The availability of genome-scale experimental datasets of RNA binding proteins (RBP) motivated us to understand the role of lncRNAs in terms of its interactions with these proteins. In the current report, we demonstrate a comprehensive study of interactions between RBP and lncRNAs at a transcriptome scale through extensive analysis of the crosslinking and immunoprecipitation (CLIP) experimental datasets available for 70 RNA binding proteins. Results: Our analysis suggests that density of interaction sites for these proteins was significantly higher for specific sub-classes of lncRNAs when compared to protein-coding transcripts. We also observe a positional preference of these RBPs across lncRNA and protein coding transcripts in addition to a significant co-occurrence of RBPs having similar functions, suggesting a modular organization of these elements across lncRNAs. Conclusion: The significant enrichment of RBP sites across some lncRNA classes is suggestive that these interactions might be important in understanding the functional role of lncRNA. We observed a significant enrichment of RBPs which are involved in functional roles such as silencing, splicing, mRNA processing, and transport, indicating the potential participation of lncRNAs in such processes.
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Affiliation(s)
- Saakshi Jalali
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology, New Delhi, India.,CSIR Institute of Genomics and Integrative Biology, Academy of Scientific and Innovative Research, New Delhi, India
| | - Shrey Gandhi
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology, New Delhi, India
| | - Vinod Scaria
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology, New Delhi, India.,CSIR Institute of Genomics and Integrative Biology, Academy of Scientific and Innovative Research, New Delhi, India
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Elsayed ET, Salem PE, Darwish AM, Fayed HM. Plasma long non-coding RNA HOTAIR as a potential biomarker for gastric cancer. Int J Biol Markers 2018; 33:1724600818760244. [PMID: 29683069 DOI: 10.1177/1724600818760244] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) Hox transcript antisense intergenic RNA ( HOTAIR) has been suggested to be implicated in gastric cancer tumorigenesis and progression; however, little is known about the role of the plasma HOTAIR in gastric cancer diagnosis and prognosis. OBJECTIVE The current study was aimed at investigating the clinical relevance of plasma long non-coding HOTAIR as a non-invasive diagnostic biomarker in gastric cancer. METHODS Plasma HOTAIR expression was measured in 50 patients with newly diagnosed gastric cancer and 50 age- and sex-matched healthy controls using quantitative reverse transcription polymerase chain reaction. RESULTS Plasma level of HOTAIR was significantly higher in gastric cancer patients compared with healthy controls ( P < 0.001). By using receiver operating characteristic curve analysis, it was found that plasma HOTAIR could diagnose gastric cancer with 88% sensitivity and 84% specificity. Furthermore, increased HOTAIR expression was associated with advanced tumor stages, higher grades, and metastasis. CONCLUSION Plasma HOTAIR might serve as a potential non-invasive biomarker for diagnosis of gastric cancer.
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Affiliation(s)
- Eman T Elsayed
- 1 Clinical Pathology Department, Alexandria University, Egypt
| | - Perihan E Salem
- 2 Internal Medicine Department, Alexandria University, Egypt
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Inoue K, Fry EA. Aberrant Expression of p14 ARF in Human Cancers: A New Biomarker? TUMOR & MICROENVIRONMENT 2018; 1:37-44. [PMID: 30740529 PMCID: PMC6364748 DOI: 10.4103/tme.tme_24_17] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The ARF and INK4a genes are located on the CDKN2a locus, both showing tumor suppressive activity. ARF has been shown to monitor potentially harmful oncogenic signalings, making early stage cancer cells undergo senescence or programmed cell death to prevent cancer. Conversely, INK4a detects both aging and incipient cancer cell signals, and thus these two gene functions are different. The efficiency of detection of oncogenic signals is more efficient for the for the former than the latter in the mouse system. Both ARF and INK4a genes are inactivated by gene deletion, promoter methylation, frame shift, aberrant splicing although point mutations for the coding region affect only the latter. Recent studies show the splicing alterations that affect only ARF or both ARF and INK4a genes suggesting that ARF is inactivated in human tumors more frequently than what was previously thought. The ARF gene is activated by E2Fs and Dmp1 transcription factors while it is repressed by Bmi1, Tbx2/3, Twist1, and Pokemon nuclear proteins. It is also regulated at protein levels by Arf ubiquitin ligase named ULF, MKRN1, and Siva1. The prognostic value of ARF overexpression is controversial since it is induced in early stage cancer cells to eliminate pre-malignant cells (better prognosis); however, it may also indicate that the tumor cells have mutant p53 associated with worse prognosis. The ARF tumor suppressive protein can be used as a biomarker to detect early stage cancer cells as well as advanced stage tumors with p53 inactivation.
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Affiliation(s)
- Kazushi Inoue
- The Department of Pathology, Wake Forest University Health Sciences, Winston-Salem, NC 27157
| | - Elizabeth A. Fry
- The Department of Pathology, Wake Forest University Health Sciences, Winston-Salem, NC 27157
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