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Ferrito N, Báez-Flores J, Rodríguez-Martín M, Sastre-Rodríguez J, Coppola A, Isidoro-García M, Prieto-Matos P, Lacal J. Biomarker Landscape in RASopathies. Int J Mol Sci 2024; 25:8563. [PMID: 39201250 PMCID: PMC11354534 DOI: 10.3390/ijms25168563] [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: 07/06/2024] [Revised: 07/28/2024] [Accepted: 08/02/2024] [Indexed: 09/02/2024] Open
Abstract
RASopathies are a group of related genetic disorders caused by mutations in genes within the RAS/MAPK signaling pathway. This pathway is crucial for cell division, growth, and differentiation, and its disruption can lead to a variety of developmental and health issues. RASopathies present diverse clinical features and pose significant diagnostic and therapeutic challenges. Studying the landscape of biomarkers in RASopathies has the potential to improve both clinical practices and the understanding of these disorders. This review provides an overview of recent discoveries in RASopathy molecular profiling, which extend beyond traditional gene mutation analysis. mRNAs, non-coding RNAs, protein expression patterns, and post-translational modifications characteristic of RASopathy patients within pivotal signaling pathways such as the RAS/MAPK, PI3K/AKT/mTOR, and Rho/ROCK/LIMK2/cofilin pathways are summarized. Additionally, the field of metabolomics holds potential for uncovering metabolic signatures associated with specific RASopathies, which are crucial for developing precision medicine. Beyond molecular markers, we also examine the role of histological characteristics and non-invasive physiological assessments in identifying potential biomarkers, as they provide evidence of the disease's effects on various systems. Here, we synthesize key findings and illuminate promising avenues for future research in RASopathy biomarker discovery, underscoring rigorous validation and clinical translation.
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Affiliation(s)
- Noemi Ferrito
- Laboratory of Functional Genetics of Rare Diseases, Department of Microbiology and Genetics, University of Salamanca (USAL), 37007 Salamanca, Spain; (N.F.); (J.B.-F.); (J.S.-R.); (A.C.)
- GIR of Biomedicine of Rare Diseases, University of Salamanca (USAL), 37007 Salamanca, Spain;
- Institute of Biomedical Research of Salamanca (IBSAL), 37007 Salamanca, Spain;
| | - Juan Báez-Flores
- Laboratory of Functional Genetics of Rare Diseases, Department of Microbiology and Genetics, University of Salamanca (USAL), 37007 Salamanca, Spain; (N.F.); (J.B.-F.); (J.S.-R.); (A.C.)
- GIR of Biomedicine of Rare Diseases, University of Salamanca (USAL), 37007 Salamanca, Spain;
- Institute of Biomedical Research of Salamanca (IBSAL), 37007 Salamanca, Spain;
| | - Mario Rodríguez-Martín
- Laboratory of Functional Genetics of Rare Diseases, Department of Microbiology and Genetics, University of Salamanca (USAL), 37007 Salamanca, Spain; (N.F.); (J.B.-F.); (J.S.-R.); (A.C.)
- GIR of Biomedicine of Rare Diseases, University of Salamanca (USAL), 37007 Salamanca, Spain;
- Institute of Biomedical Research of Salamanca (IBSAL), 37007 Salamanca, Spain;
| | - Julián Sastre-Rodríguez
- Laboratory of Functional Genetics of Rare Diseases, Department of Microbiology and Genetics, University of Salamanca (USAL), 37007 Salamanca, Spain; (N.F.); (J.B.-F.); (J.S.-R.); (A.C.)
| | - Alessio Coppola
- Laboratory of Functional Genetics of Rare Diseases, Department of Microbiology and Genetics, University of Salamanca (USAL), 37007 Salamanca, Spain; (N.F.); (J.B.-F.); (J.S.-R.); (A.C.)
- GIR of Biomedicine of Rare Diseases, University of Salamanca (USAL), 37007 Salamanca, Spain;
- Institute of Biomedical Research of Salamanca (IBSAL), 37007 Salamanca, Spain;
| | - María Isidoro-García
- Institute of Biomedical Research of Salamanca (IBSAL), 37007 Salamanca, Spain;
- Clinical Biochemistry Department, University Hospital of Salamanca, 37007 Salamanca, Spain
- Clinical Rare Diseases Reference Unit DiERCyL, 37007 Castilla y León, Spain
- Department of Medicine, University of Salamanca (USAL), 37007 Salamanca, Spain
| | - Pablo Prieto-Matos
- GIR of Biomedicine of Rare Diseases, University of Salamanca (USAL), 37007 Salamanca, Spain;
- Institute of Biomedical Research of Salamanca (IBSAL), 37007 Salamanca, Spain;
- Department of Pediatrics, University Hospital of Salamanca, 37007 Salamanca, Spain
- Department of Biomedical and Diagnostics Science, University of Salamanca (USAL), 37007 Salamanca, Spain
| | - Jesus Lacal
- Laboratory of Functional Genetics of Rare Diseases, Department of Microbiology and Genetics, University of Salamanca (USAL), 37007 Salamanca, Spain; (N.F.); (J.B.-F.); (J.S.-R.); (A.C.)
- GIR of Biomedicine of Rare Diseases, University of Salamanca (USAL), 37007 Salamanca, Spain;
- Institute of Biomedical Research of Salamanca (IBSAL), 37007 Salamanca, Spain;
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Yeh J, Chen Y, Chou Y, Su S, Chang L, Chen Y, Lin C, Yang S. Interactive effects of CDKN2B-AS1 gene polymorphism and habitual risk factors on oral cancer. J Cell Mol Med 2023; 27:3395-3403. [PMID: 37724356 PMCID: PMC10623535 DOI: 10.1111/jcmm.17966] [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: 07/05/2023] [Revised: 08/02/2023] [Accepted: 09/08/2023] [Indexed: 09/20/2023] Open
Abstract
Oral squamous cell carcinoma (OSCC) is a common malignant disease associated with a high mortality rate and heterogeneous disease aetiology. Cyclin dependent kinase inhibitor 2B antisense RNA 1 (CDKN2B-AS1), is a long noncoding RNA that has been shown to act as a scaffold, sponge, or signal hub to promote carcinogenesis. Here, we attempted to assess the effect of CDKN2B-AS1 single-nucleotide polymorphisms (SNPs) on the susceptibility to OSCC. Five CDKN2B-AS1 SNPs, including rs564398, rs1333048, rs1537373, rs2151280 and rs8181047, were analysed in 1060 OSCC cases and 1183 cancer-free controls. No significant association of these five SNPs with the risk of developing OSCC was detected between the case and control group. However, while examining the clinical characteristics, patients bearing at least one minor allele of rs1333048 (CA and CC) were more inclined to develop late-stage (stage III/IV, adjusted OR, 1.480; 95% CI, 1.129-1.940; p = 0.005) and large-size (greater than 2 cm in the greatest dimension, adjusted OR, 1.347; 95% CI, 1.028-1.765; p = 0.031) tumours, as compared with those homologous for the major allele (AA). Further stratification analyses demonstrated that this genetic correlation with the advanced stage of disease was observed only in habitual betel quid chewers (adjusted OR, 1.480; 95% CI, 1.076-2.035; p = 0.016) or cigarette smokers (adjusted OR, 1.531; 95% CI, 1.136-2.063; p = 0.005) but not in patients who were not exposed to these major habitual risks. These data reveal an interactive effect of CDKN2B-AS1 rs1333048 with habitual exposure to behavioural risks on the progression of oral cancer.
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Affiliation(s)
- Jung‐Chun Yeh
- School of Dentistry, Chung Shan Medical UniversityTaichungTaiwan
- Department of DentistryChung Shan Medical University HospitalTaichungTaiwan
| | - Yi‐Tzu Chen
- School of Dentistry, Chung Shan Medical UniversityTaichungTaiwan
- Department of DentistryChung Shan Medical University HospitalTaichungTaiwan
| | - Ying‐Erh Chou
- School of Medicine, Chung Shan Medical UniversityTaichungTaiwan
- Department of Medical ResearchChung Shan Medical University HospitalTaichungTaiwan
| | - Shih‐Chi Su
- Whole‐Genome Research Core Laboratory of Human Diseases, Chang Gung Memorial HospitalKeelungTaiwan
- Department of Dermatology, Drug Hypersensitivity Clinical and Research CenterChang Gung Memorial HospitalLinkouTaiwan
| | - Lun‐Ching Chang
- Department of Mathematical SciencesFlorida Atlantic UniversityBoca RatonFloridaUSA
| | - Yen‐Lin Chen
- School of Dentistry, Chung Shan Medical UniversityTaichungTaiwan
- Department of DentistryChung Shan Medical University HospitalTaichungTaiwan
| | - Chiao‐Wen Lin
- Department of DentistryChung Shan Medical University HospitalTaichungTaiwan
- Institute of Oral Sciences, Chung Shan Medical UniversityTaichungTaiwan
| | - Shun‐Fa Yang
- Department of Medical ResearchChung Shan Medical University HospitalTaichungTaiwan
- Institute of Medicine, Chung Shan Medical UniversityTaichungTaiwan
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3
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Sanchez A, Lhuillier J, Grosjean G, Ayadi L, Maenner S. The Long Non-Coding RNA ANRIL in Cancers. Cancers (Basel) 2023; 15:4160. [PMID: 37627188 PMCID: PMC10453084 DOI: 10.3390/cancers15164160] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/14/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023] Open
Abstract
ANRIL (Antisense Noncoding RNA in the INK4 Locus), a long non-coding RNA encoded in the human chromosome 9p21 region, is a critical factor for regulating gene expression by interacting with multiple proteins and miRNAs. It has been found to play important roles in various cellular processes, including cell cycle control and proliferation. Dysregulation of ANRIL has been associated with several diseases like cancers and cardiovascular diseases, for instance. Understanding the oncogenic role of ANRIL and its potential as a diagnostic and prognostic biomarker in cancer is crucial. This review provides insights into the regulatory mechanisms and oncogenic significance of the 9p21 locus and ANRIL in cancer.
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Affiliation(s)
| | | | | | - Lilia Ayadi
- CNRS, Université de Lorraine, IMoPA, F-54000 Nancy, France
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4
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Bettinaglio P, Mangano E, Tritto V, Bordoni R, Paterra R, Borghi A, Volontè M, Battaglia C, Saletti V, Cesaretti C, Natacci F, Melone MAB, Eoli M, Riva P. New insights into the molecular basis of spinal neurofibromatosis type 1. Eur J Hum Genet 2023; 31:931-938. [PMID: 37217626 PMCID: PMC10400572 DOI: 10.1038/s41431-023-01377-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 04/19/2023] [Accepted: 04/27/2023] [Indexed: 05/24/2023] Open
Abstract
Spinal neurofibromatosis (SNF) is a form of neurofibromatosis type 1 (NF1) characterized by bilateral neurofibromas involving all spinal roots. The pathogenic mechanisms determining the SNF form are currently unknown. To verify the presence of genetic variants possibly related to SNF or classic NF1, we studied 106 sporadic NF1 and 75 SNF patients using an NGS panel of 286 genes encoding RAS pathway effectors and neurofibromin interactors and evaluated the expression of syndecans (SDC1, SDC2, SDC3, SDC4), the NF1 3' tertile interactors, by quantitative real-time PCR. We previously identified 75 and 106 NF1 variants in SNF and NF1 cohorts, respectively. The analysis of the distribution of pathogenic NF1 variants in the three NF1 tertiles showed a significantly higher prevalence of NF1 3' tertile mutations in SNF than in the NF1 cohort. We hypothesized a potential pathogenic significance of the 3' tertile NF1 variants in SNF. The analysis of syndecan expression on PBMCs RNAs from 16 SNF, 16 classic NF1 patients and 16 healthy controls showed that the expression levels of SDC2 and SDC3 were higher in SNF and NF1 patients than in controls; moreover, SDC2, SDC3 and SDC4 were significantly over expressed in patients mutated in the 3' tertile compared to controls. Two different mutational NF1 spectra seem to characterize SNF and classic NF1, suggesting a pathogenic role of NF1 3' tertile and its interactors, syndecans, in SNF. Our study, providing new insights on a possible role of neurofibromin C-terminal in SNF, could address effective personalized patient management and treatments.
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Affiliation(s)
- Paola Bettinaglio
- Department of Medical Biotechnology and Translational Medicine (BIOMETRA), University of Milan, 20054, Segrate, Milan, Italy
| | - Eleonora Mangano
- Institute of Biomedical Technologies (ITB) National Research Center (CNR), ITB-CNR, 20054, Segrate, Milan, Italy
| | - Viviana Tritto
- Department of Medical Biotechnology and Translational Medicine (BIOMETRA), University of Milan, 20054, Segrate, Milan, Italy
| | - Roberta Bordoni
- Institute of Biomedical Technologies (ITB) National Research Center (CNR), ITB-CNR, 20054, Segrate, Milan, Italy
| | - Rosina Paterra
- Molecular Neuro-Oncology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133, Milan, Italy
| | - Arianna Borghi
- Molecular Neuro-Oncology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133, Milan, Italy
| | - Marinella Volontè
- Department of Medical Biotechnology and Translational Medicine (BIOMETRA), University of Milan, 20054, Segrate, Milan, Italy
| | - Cristina Battaglia
- Department of Medical Biotechnology and Translational Medicine (BIOMETRA), University of Milan, 20054, Segrate, Milan, Italy
- Institute of Biomedical Technologies (ITB) National Research Center (CNR), ITB-CNR, 20054, Segrate, Milan, Italy
| | - Veronica Saletti
- Developmental Neurology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Mariani Foundation Center for Complex Disabilities, 20054, Milan, Italy
| | - Claudia Cesaretti
- Medical Genetics Unit, Woman-Child-Newborn Department, Fondazione IRCCS Ca' Granda-Ospedale Maggiore Policlinico, 20122, Milan, Italy
| | - Federica Natacci
- Medical Genetics Unit, Woman-Child-Newborn Department, Fondazione IRCCS Ca' Granda-Ospedale Maggiore Policlinico, 20122, Milan, Italy
| | - Mariarosa A B Melone
- Department of Advanced Medical and Surgical Sciences, 2nd Division of Neurology, Center for Rare Diseases and InterUniversity Center for Research in Neurosciences, University of Campania Luigi Vanvitelli, 80131, Naples, Italy
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, Temple University, Philadelphia, PA, 19122-6078, USA
| | - Marica Eoli
- Molecular Neuro-Oncology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133, Milan, Italy.
| | - Paola Riva
- Department of Medical Biotechnology and Translational Medicine (BIOMETRA), University of Milan, 20054, Segrate, Milan, Italy.
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Huang LA, Lin C, Yang L. Plumbing mysterious RNAs in "dark genome" for the conquest of human diseases. Mol Ther 2023; 31:1577-1595. [PMID: 37165619 PMCID: PMC10278048 DOI: 10.1016/j.ymthe.2023.05.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 04/11/2023] [Accepted: 05/05/2023] [Indexed: 05/12/2023] Open
Abstract
Next-generation sequencing has revealed that less than 2% of transcribed genes are translated into proteins, with a large portion transcribed into noncoding RNAs (ncRNAs). Among these, long noncoding RNAs (lncRNAs) represent the largest group and are pervasively transcribed throughout the genome. Dysfunctions in lncRNAs have been found in various diseases, highlighting their potential as therapeutic, diagnostic, and prognostic targets. However, challenges, such as unknown molecular mechanisms and nonspecific immune responses, and issues of drug specificity and delivery present obstacles in translating lncRNAs into clinical applications. In this review, we summarize recent publications that have explored lncRNA functions in human diseases. We also discuss challenges and future directions for developing lncRNA treatments, aiming to bridge the gap between functional studies and clinical potential and inspire further exploration in the field.
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Affiliation(s)
- Lisa A Huang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; The Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Chunru Lin
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; The Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Liuqing Yang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; The Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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Khosravi T, Oladnabi M. The role of miRNAs and lncRNAs in neurofibromatosis type 1. J Cell Biochem 2023; 124:17-30. [PMID: 36345594 DOI: 10.1002/jcb.30349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 10/24/2022] [Accepted: 11/04/2022] [Indexed: 11/09/2022]
Abstract
Neurofibromatosis Type 1 (NF1) is a frequent cancer predisposition syndrome. The common hallmark of patients with this multisystemic genetic disorder is the formation of peripheral nerve sheath tumors, which can be seen as either dermal, plexiform, and malignant forms. MicroRNA (miRNA) is an essential gene regulation factor and consists of 22-25 nucleotides. MiRNAs are identified to act as both tumor suppressors and oncogenes (oncomirs) in a wide variety of human cancers. They play multiple roles in molecular pathways responsible for tumor homing, progression, and invasion. Long noncoding RNA (lncRNA) also has a key role in cancer transcriptomics. Altered lncRNA expression levels have been found in various malignancies. This review aims to summarize the role of two noncoding RNA groups, miRNAs and lncRNAs, in NF1 establishment, development, and progression. We also highlight their potential for future clinical interventions and devising new diagnostic tools.
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Affiliation(s)
- Teymoor Khosravi
- Student Research Committee, Golestan University of Medical Sciences, Gorgan, Iran
| | - Morteza Oladnabi
- Gorgan Congenital Malformations Research Center, Golestan University of Medical Sciences, Gorgan, Iran.,Ischemic Disorders Research Center, Golestan University of Medical Sciences, Gorgan, Iran
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Huang D, He L, Xiong M, Sun Q. Study on the value of multi-dimensional conformal radiotherapy and functional imaging in tumor bioimaging. Transl Cancer Res 2022; 11:3780-3789. [PMID: 36388020 PMCID: PMC9641124 DOI: 10.21037/tcr-22-2005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 09/14/2022] [Indexed: 01/25/2023]
Abstract
BACKGROUND To explore the diagnostic and therapeutic effects of multi-dimensional conformal radiotherapy (MD-CRT) combined with functional imaging in tumor bioimaging. METHODS A total of 150 cases of patients with brain metastases in First Affiliated Hospital of Xi'an Jiaotong University between December 2020 and December 2021 were retrospectively selected as the research cohort. Participants underwent whole brain imaging guided by MD-CRT combined with volume assessment to assess the patient's recent treatment effect, statistically acceptable dose irradiation treatment, and the incidence of adverse reactions. All patients were followed up to evaluate the long-term efficacy. RESULTS Among the 150 patients, 24 cases were in complete remission, 72 cases were in partial remission, 36 cases were in a stable condition, 18 cases were in deterioration, and the treatment of 96 cases (64.00%) was deemed effective. All participants were followed up, the mean survival was (62.37±1.24) months, 96 cases (64.00%) survived, and 54 cases (36.00%) had died. The average dose was (62.09±3.94) Gy. In terms of adverse reactions: brain edema occurred in 57 patients, accounting for 38.00%. CONCLUSIONS The MD-CRT and functional imaging techniques for patients with metastatic tumor have high therapeutic accuracy, are associated with improved local control rate, prolonged survival, and cause little damage to normal tissues, with significant therapeutic effect, and can be widely used in clinical practice.
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Affiliation(s)
- Dabei Huang
- Department of Medical Imaging, Zhongshan City People’s Hospital, Zhongshan, China
| | - Lan He
- Department of Medical Imagine, Ezhou Central Hospital, Ezhou, China
| | - Minchao Xiong
- Department of Medical Imagine, Ezhou Central Hospital, Ezhou, China
| | - Qing Sun
- Department of Medical Imaging, First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
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Che D, Fang Z, Mai H, Xu Y, Fu L, Zhou H, Zhang L, Pi L, Gu X. The lncRNA ANRIL Gene rs2151280 GG Genotype is Associated with Increased Susceptibility to Recurrent Miscarriage in a Southern Chinese Population. J Inflamm Res 2021; 14:2865-2872. [PMID: 34234511 PMCID: PMC8256094 DOI: 10.2147/jir.s304801] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 03/31/2021] [Indexed: 12/19/2022] Open
Abstract
Background Genetic factors may play an important role in susceptibility to recurrent miscarriage. Some cardiovascular disease-related candidate genes have been shown to be associated with recurrent miscarriage. Long noncoding RNA ANRIL has been confirmed to be associated with susceptibility to various diseases, such as cardiovascular disease. However, it remains unclear whether the ANRIL gene polymorphism is related to recurrent miscarriage susceptibility. Methods Three ANRIL gene polymorphisms (rs2151280, rs1063192 and rs564398) were genotyped in 819 controls and 610 recurrent miscarriage patients through TaqMan real-time polymerase chain reaction. The odds ratios and 95% confidence intervals (CIs) were used to assess the strength of each association. Results Our results showed that the ANRIL rs2151280 GG genotype was associated with increased susceptibility to recurrent miscarriage (GG vs AA: adjusted OR=1.527, 95% CI=1.051–2.218, p=0.0262; GG vs AG/AA adjusted OR=1.460, 95% CI=1.021–2.089, p=0.0381). By combining the analysis of the risk genotypes in the three SNPs, we found that individuals with 2–3 risk genotypes had a significantly increased risk of recurrent miscarriage compared with those with a 0–1 risk genotype (adjusted OR=1.728, 95% CI=1.112–2.683, p=0.0149). This risk was more significant in subgroups of women less than 35–40 years of age and women with 2–3 miscarriages. Conclusion These results suggested that a specific SNP in the ANRIL gene may be associated with increased susceptibility to recurrent miscarriage in a southern Chinese population.
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Affiliation(s)
- Di Che
- Department of Clinical Biological Resource Bank, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Zhenzhen Fang
- Program of Molecular Medicine, Guangzhou Women and Children's Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Hanran Mai
- Department of Clinical Biological Resource Bank, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Yufen Xu
- Department of Clinical Biological Resource Bank, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, People's Republic of China
| | - LanYan Fu
- Department of Clinical Biological Resource Bank, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Huazhong Zhou
- Department of Clinical Biological Resource Bank, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Linyuan Zhang
- Department of Clinical Biological Resource Bank, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Lei Pi
- Department of Clinical Biological Resource Bank, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Xiaoqiong Gu
- Department of Clinical Biological Resource Bank, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, People's Republic of China
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9
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Scala M, Schiavetti I, Madia F, Chelleri C, Piccolo G, Accogli A, Riva A, Salpietro V, Bocciardi R, Morcaldi G, Di Duca M, Caroli F, Verrico A, Milanaccio C, Viglizzo G, Traverso M, Baldassari S, Scudieri P, Iacomino M, Piatelli G, Minetti C, Striano P, Garrè ML, De Marco P, Diana MC, Capra V, Pavanello M, Zara F. Genotype-Phenotype Correlations in Neurofibromatosis Type 1: A Single-Center Cohort Study. Cancers (Basel) 2021; 13:cancers13081879. [PMID: 33919865 PMCID: PMC8070780 DOI: 10.3390/cancers13081879] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/10/2021] [Accepted: 04/12/2021] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Neurofibromatosis type 1 (NF1) is a complex disorder characterized by a multisystem involvement and cancer predisposition. It is caused by genetic variants in NF1, a large tumor suppressor gene encoding a cytoplasmatic protein (neurofibromin) with a regulatory role in essential cellular processes. Genotype–phenotype correlations in NF1 patients are so far elusive. We retrospectively reviewed clinical, radiological, and genetic data of 583 individuals with at least 1 National Institutes of Health (NIH) criterion for NF1 diagnosis, including 365 subjects fulfilling criteria for the diagnosis. Novel genotype–phenotype correlations were identified through uni- and multivariate statistical analysis. Missense variants negatively correlated with neurofibromas. Skeletal abnormalities were associated with frameshift variants and whole gene deletions. The c.3721C>T; p.(R1241*) variant positively correlated with structural brain alterations, whereas the c.6855C>A; p.(Y2285*) variant was associated with a higher prevalence of Lisch nodules and endocrinological disorders. These novel NF1 genotype–phenotype correlations may have a relevant role in the implementation of patients’ care. Abstract Neurofibromatosis type 1 (NF1) is a proteiform genetic condition caused by pathogenic variants in NF1 and characterized by a heterogeneous phenotypic presentation. Relevant genotype–phenotype correlations have recently emerged, but only few pertinent studies are available. We retrospectively reviewed clinical, instrumental, and genetic data from a cohort of 583 individuals meeting at least 1 diagnostic National Institutes of Health (NIH) criterion for NF1. Of these, 365 subjects fulfilled ≥2 NIH criteria, including 235 pediatric patients. Genetic testing was performed through cDNA-based sequencing, Next Generation Sequencing (NGS), and Multiplex Ligation-dependent Probe Amplification (MLPA). Uni- and multivariate statistical analysis was used to investigate genotype–phenotype correlations. Among patients fulfilling ≥ 2 NIH criteria, causative single nucleotide variants (SNVs) and copy number variations (CNVs) were detected in 267/365 (73.2%) and 20/365 (5.5%) cases. Missense variants negatively correlated with neurofibromas (p = 0.005). Skeletal abnormalities were associated with whole gene deletions (p = 0.05) and frameshift variants (p = 0.006). The c.3721C>T; p.(R1241*) variant positively correlated with structural brain alterations (p = 0.031), whereas Lisch nodules (p = 0.05) and endocrinological disorders (p = 0.043) were associated with the c.6855C>A; p.(Y2285*) variant. We identified novel NF1 genotype–phenotype correlations and provided an overview of known associations, supporting their potential relevance in the implementation of patient management.
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Affiliation(s)
- Marcello Scala
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, 16132 Genoa, Italy; (M.S.); (C.C.); (A.A.); (A.R.); (V.S.); (R.B.); (P.S.); (C.M.); (P.S.); (F.Z.)
- Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, University of Genoa, 16147 Genoa, Italy; (G.P.); (G.M.); (M.T.); (M.C.D.)
| | - Irene Schiavetti
- Department of Health Sciences, Section of Biostatistics, University of Genova, 16132 Genoa, Italy;
| | - Francesca Madia
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, University of Genoa, 16147 Genoa, Italy; (F.M.); (M.D.D.); (F.C.); (S.B.); (M.I.); (P.D.M.); (V.C.)
| | - Cristina Chelleri
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, 16132 Genoa, Italy; (M.S.); (C.C.); (A.A.); (A.R.); (V.S.); (R.B.); (P.S.); (C.M.); (P.S.); (F.Z.)
- Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, University of Genoa, 16147 Genoa, Italy; (G.P.); (G.M.); (M.T.); (M.C.D.)
| | - Gianluca Piccolo
- Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, University of Genoa, 16147 Genoa, Italy; (G.P.); (G.M.); (M.T.); (M.C.D.)
| | - Andrea Accogli
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, 16132 Genoa, Italy; (M.S.); (C.C.); (A.A.); (A.R.); (V.S.); (R.B.); (P.S.); (C.M.); (P.S.); (F.Z.)
| | - Antonella Riva
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, 16132 Genoa, Italy; (M.S.); (C.C.); (A.A.); (A.R.); (V.S.); (R.B.); (P.S.); (C.M.); (P.S.); (F.Z.)
- Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, University of Genoa, 16147 Genoa, Italy; (G.P.); (G.M.); (M.T.); (M.C.D.)
| | - Vincenzo Salpietro
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, 16132 Genoa, Italy; (M.S.); (C.C.); (A.A.); (A.R.); (V.S.); (R.B.); (P.S.); (C.M.); (P.S.); (F.Z.)
- Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, University of Genoa, 16147 Genoa, Italy; (G.P.); (G.M.); (M.T.); (M.C.D.)
| | - Renata Bocciardi
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, 16132 Genoa, Italy; (M.S.); (C.C.); (A.A.); (A.R.); (V.S.); (R.B.); (P.S.); (C.M.); (P.S.); (F.Z.)
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, University of Genoa, 16147 Genoa, Italy; (F.M.); (M.D.D.); (F.C.); (S.B.); (M.I.); (P.D.M.); (V.C.)
| | - Guido Morcaldi
- Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, University of Genoa, 16147 Genoa, Italy; (G.P.); (G.M.); (M.T.); (M.C.D.)
| | - Marco Di Duca
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, University of Genoa, 16147 Genoa, Italy; (F.M.); (M.D.D.); (F.C.); (S.B.); (M.I.); (P.D.M.); (V.C.)
| | - Francesco Caroli
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, University of Genoa, 16147 Genoa, Italy; (F.M.); (M.D.D.); (F.C.); (S.B.); (M.I.); (P.D.M.); (V.C.)
| | - Antonio Verrico
- Neuro-Oncology Unit, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy; (A.V.); (C.M.); (M.L.G.)
| | - Claudia Milanaccio
- Neuro-Oncology Unit, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy; (A.V.); (C.M.); (M.L.G.)
| | | | - Monica Traverso
- Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, University of Genoa, 16147 Genoa, Italy; (G.P.); (G.M.); (M.T.); (M.C.D.)
| | - Simona Baldassari
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, University of Genoa, 16147 Genoa, Italy; (F.M.); (M.D.D.); (F.C.); (S.B.); (M.I.); (P.D.M.); (V.C.)
| | - Paolo Scudieri
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, 16132 Genoa, Italy; (M.S.); (C.C.); (A.A.); (A.R.); (V.S.); (R.B.); (P.S.); (C.M.); (P.S.); (F.Z.)
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, University of Genoa, 16147 Genoa, Italy; (F.M.); (M.D.D.); (F.C.); (S.B.); (M.I.); (P.D.M.); (V.C.)
| | - Michele Iacomino
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, University of Genoa, 16147 Genoa, Italy; (F.M.); (M.D.D.); (F.C.); (S.B.); (M.I.); (P.D.M.); (V.C.)
| | - Gianluca Piatelli
- Neurosurgery Department, IRCCS Istituto Giannina Gaslini, University of Genoa, 16147 Genoa, Italy;
| | - Carlo Minetti
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, 16132 Genoa, Italy; (M.S.); (C.C.); (A.A.); (A.R.); (V.S.); (R.B.); (P.S.); (C.M.); (P.S.); (F.Z.)
- Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, University of Genoa, 16147 Genoa, Italy; (G.P.); (G.M.); (M.T.); (M.C.D.)
| | - Pasquale Striano
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, 16132 Genoa, Italy; (M.S.); (C.C.); (A.A.); (A.R.); (V.S.); (R.B.); (P.S.); (C.M.); (P.S.); (F.Z.)
- Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, University of Genoa, 16147 Genoa, Italy; (G.P.); (G.M.); (M.T.); (M.C.D.)
| | - Maria Luisa Garrè
- Neuro-Oncology Unit, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy; (A.V.); (C.M.); (M.L.G.)
| | - Patrizia De Marco
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, University of Genoa, 16147 Genoa, Italy; (F.M.); (M.D.D.); (F.C.); (S.B.); (M.I.); (P.D.M.); (V.C.)
| | - Maria Cristina Diana
- Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, University of Genoa, 16147 Genoa, Italy; (G.P.); (G.M.); (M.T.); (M.C.D.)
| | - Valeria Capra
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, University of Genoa, 16147 Genoa, Italy; (F.M.); (M.D.D.); (F.C.); (S.B.); (M.I.); (P.D.M.); (V.C.)
| | - Marco Pavanello
- Neurosurgery Department, IRCCS Istituto Giannina Gaslini, University of Genoa, 16147 Genoa, Italy;
- Correspondence:
| | - Federico Zara
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, 16132 Genoa, Italy; (M.S.); (C.C.); (A.A.); (A.R.); (V.S.); (R.B.); (P.S.); (C.M.); (P.S.); (F.Z.)
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, University of Genoa, 16147 Genoa, Italy; (F.M.); (M.D.D.); (F.C.); (S.B.); (M.I.); (P.D.M.); (V.C.)
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Woycinck Kowalski T, Brussa Reis L, Finger Andreis T, Ashton-Prolla P, Rosset C. Systems Biology Approaches Reveal Potential Phenotype-Modifier Genes in Neurofibromatosis Type 1. Cancers (Basel) 2020; 12:cancers12092416. [PMID: 32858845 PMCID: PMC7565824 DOI: 10.3390/cancers12092416] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/18/2020] [Accepted: 07/20/2020] [Indexed: 12/18/2022] Open
Abstract
Neurofibromatosis type (NF1) is a syndrome characterized by varied symptoms, ranging from mild to more aggressive phenotypes. The variation is not explained only by genetic and epigenetic changes in the NF1 gene and the concept of phenotype-modifier genes in extensively discussed in an attempt to explain this variability. Many datasets and tools are already available to explore the relationship between genetic variation and disease, including systems biology and expression data. To suggest potential NF1 modifier genes, we selected proteins related to NF1 phenotype and NF1 gene ontologies. Protein–protein interaction (PPI) networks were assembled, and network statistics were obtained by using forward and reverse genetics strategies. We also evaluated the heterogeneous networks comprising the phenotype ontologies selected, gene expression data, and the PPI network. Finally, the hypothesized phenotype-modifier genes were verified by a random-walk mathematical model. The network statistics analyses combined with the forward and reverse genetics strategies, and the assembly of heterogeneous networks, resulted in ten potential phenotype-modifier genes: AKT1, BRAF, EGFR, LIMK1, PAK1, PTEN, RAF1, SDC2, SMARCA4, and VCP. Mathematical models using the random-walk approach suggested SDC2 and VCP as the main candidate genes for phenotype-modifiers.
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Affiliation(s)
- Thayne Woycinck Kowalski
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-007, Rio Grande do Sul, Brazil; (T.W.K.); (L.B.R.); (T.F.A.); (P.A.-P.)
- Programa de Pós-Graduação em Genética e Biologia Molecular, PPGBM, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Rio Grande do Sul, Brazil
- CESUCA - Faculdade Inedi, Cachoeirinha 94935-630, Rio Grande do Sul, Brazil
| | - Larissa Brussa Reis
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-007, Rio Grande do Sul, Brazil; (T.W.K.); (L.B.R.); (T.F.A.); (P.A.-P.)
- Programa de Pós-Graduação em Genética e Biologia Molecular, PPGBM, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Rio Grande do Sul, Brazil
| | - Tiago Finger Andreis
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-007, Rio Grande do Sul, Brazil; (T.W.K.); (L.B.R.); (T.F.A.); (P.A.-P.)
- Programa de Pós-Graduação em Genética e Biologia Molecular, PPGBM, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Rio Grande do Sul, Brazil
| | - Patricia Ashton-Prolla
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-007, Rio Grande do Sul, Brazil; (T.W.K.); (L.B.R.); (T.F.A.); (P.A.-P.)
- Programa de Pós-Graduação em Genética e Biologia Molecular, PPGBM, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Rio Grande do Sul, Brazil
- Serviço de Genética Médica, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-007, Rio Grande do Sul, Brazil
| | - Clévia Rosset
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-007, Rio Grande do Sul, Brazil; (T.W.K.); (L.B.R.); (T.F.A.); (P.A.-P.)
- Unidade de Pesquisa Laboratorial, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-007, Rio Grande do Sul, Brazil
- Correspondence: ; Tel.: +55-51-3359-7661
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Zhu B, Liu W, Liu H, Xu Q, Xu W. LINC01094 Down-Regulates miR-330-3p and Enhances the Expression of MSI1 to Promote the Progression of Glioma. Cancer Manag Res 2020; 12:6511-6521. [PMID: 32801889 PMCID: PMC7395698 DOI: 10.2147/cmar.s254630] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 06/23/2020] [Indexed: 01/15/2023] Open
Abstract
Background This study aims at probing into the expression, function, and mechanism of LINC01094 and miR-330-3p in glioma. Materials and Methods qRT-PCR was employed to examine LINC01094 and miR-330-3p expressions in gliomas. After gain-of-function and loss-of-function models were constructed, CCK-8 and Transwell assays were used to detect the proliferation, migration and invasion of LN229 and U251 cells, respectively. Additionally, dual luciferase reporter gene assay was utilized to verify the binding site between m4iR-330-3p and LINC01094, miR-330-3p, and the 3ʹUTR of musashi RNA binding protein 1 (MSI1). Then, RNA pull-down, RIP, qRT-PCR and Western blot were employed to detect the regulatory relationships among LINC01094, miR-330-3p, and MSI1. Results The expression of LINC01094 was elevated in glioma tissues and cell lines, and the high expression of LINC01094 was associated with high grade of glioma. In contrast, miR-330-3p was lowly expressed in glioma tissue. Overexpression of LINC01094 or down-regulation of miR-330-3p promoted the proliferation, migration, and invasion of glioma cells, while LINC01094 knockdown or miR-330-3p up-regulation impeded these processes. miR-330-3p was identified as a target miRNA of LINC01094, and it could be negatively regulated by LINC01094. In addition, miR-330-3p antagonized the function of LINC01094 by negatively regulating MSI1. Conclusion LINC01094 promotes the proliferation, migration, and invasion of glioma cells by adsorbing miR-330-3p and up-regulating the expression of MSI1.
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Affiliation(s)
- Bin Zhu
- Department of Neurosurgery, Huashan North Hospital, Baoshan Branch, Fudan University, Shanghai 200431, People's Republic of China
| | - Wei Liu
- Department of Neurosurgery, Huashan North Hospital, Baoshan Branch, Fudan University, Shanghai 200431, People's Republic of China
| | - Hongliang Liu
- Department of Neurosurgery, Huashan North Hospital, Baoshan Branch, Fudan University, Shanghai 200431, People's Republic of China
| | - Qiang Xu
- Department of Neurosurgery, Huashan North Hospital, Baoshan Branch, Fudan University, Shanghai 200431, People's Republic of China
| | - Wei Xu
- Department of Neurosurgery, Huashan North Hospital, Baoshan Branch, Fudan University, Shanghai 200431, People's Republic of China
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Analysis of ANRIL gene polymorphism rs4977574 association with kidney cancer development in Ukrainian population. MEDICNI PERSPEKTIVI (MEDICAL PERSPECTIVES) 2020. [DOI: 10.26641/2307-0404.2020.2.206360] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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