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Kozhevnikova OS, Fursova AZ, Derbeneva AS, Nikulich IF, Devyatkin VA, Kolosova NG. Pharmacogenetic Association between Allelic Variants of the Autophagy-Related Genes and Anti-Vascular Endothelial Growth Factor Treatment Response in Neovascular Age-Related Macular Degeneration. Biomedicines 2023; 11:3079. [PMID: 38002079 PMCID: PMC10669692 DOI: 10.3390/biomedicines11113079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 11/13/2023] [Accepted: 11/15/2023] [Indexed: 11/26/2023] Open
Abstract
BACKGROUND Age-related macular degeneration (AMD) is the leading cause of late-onset blindness in elderly. The occurrence and development of AMD is a multifactorial complex process where autophagy plays an important role. The first-line drugs for neovascular AMD (nAMD) are inhibitors of VEGF, with up to 30% of patients having an incomplete response to treatment. Genetic factors may influence the response to anti-VEGF therapy and explain treatment outcome variability. We aimed to estimate the role of polymorphic markers of the MTOR (rs1064261, rs1057079, rs11121704, rs2295080), SQSTM1 (rs10277), ULK1 (rs11246867, rs3088051), MAP1LC3A (rs73105013) and ATG5 (rs573775) genes in the development of nAMD and the efficacy of anti-VEGF therapy response. METHODS Genotyping by allele-specific PCR was performed in 317 controls and 315 nAMD patients in the Russian population. Of them, 196 treatment-naive nAMD patients underwent three monthly intravitreal injections (IVIs) of aflibercept. Genotypic frequencies were compared with OCT markers of therapy effectiveness and best-corrected visual acuity (BCVA) measures. The main outcomes were the BCVA gain and decrease in central retinal thickness (CRT). RESULTS MTOR-rs1057079-C, MTOR-rs11121704-C and MTOR-rs2295080-G alleles were associated with an increased risk of nAMD. The BCVA was increased in 117 (59.7%) patients by 10 [5-20] letters, did not changed in 59 (30.1%), and was decreased in 20 (10.2%) patients. ULK1-rs3088051 was associated with BCVA change. Among patients with the TT and CT genotypes for ULK1-rs3088051, an improvement in visual acuity was noted in 67.6% and 53.8% of cases, while in patients with the CC genotype, an increase in BCVA was recorded in 37.5% of cases (p = 0.01). The decrease in CRT was associated with SQSTM1-rs10277 (p = 0.001): it was significantly higher in TT (93 [58-122] mkm) and CT (66 [30-105] mkm) carriers compared to the CC genotype (47 [24-68] mkm). Other SNPs did not show significant associations with the outcome of anti-VEGF treatment. CONCLUSIONS MTOR gene polymorphisms are moderately associated with the risk of nAMD. SQSTM1-rs10277 and ULK1-rs3088051 may influence short-term response to intravitreal anti-VEGF treatment. The results suggest that autophagy could be a target for future drugs to overcome resistance to anti-VEGF therapy.
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Affiliation(s)
- Oyuna S. Kozhevnikova
- Federal Research Center Institute of Cytology and Genetics SB RAS, Pr. Lavrentiev, 10, 630090 Novosibirsk, Russia; (A.Z.F.); (A.S.D.); (I.F.N.); (V.A.D.); (N.G.K.)
| | - Anzhella Zh. Fursova
- Federal Research Center Institute of Cytology and Genetics SB RAS, Pr. Lavrentiev, 10, 630090 Novosibirsk, Russia; (A.Z.F.); (A.S.D.); (I.F.N.); (V.A.D.); (N.G.K.)
- State Novosibirsk Regional Clinical Hospital, St. Nemirovich-Danchenko, 130, 630087 Novosibirsk, Russia
- Department of Ophthalmology, Novosibirsk State Medical University, Pr. Krasny, 52, 630091 Novosibirsk, Russia
| | - Anna S. Derbeneva
- Federal Research Center Institute of Cytology and Genetics SB RAS, Pr. Lavrentiev, 10, 630090 Novosibirsk, Russia; (A.Z.F.); (A.S.D.); (I.F.N.); (V.A.D.); (N.G.K.)
- State Novosibirsk Regional Clinical Hospital, St. Nemirovich-Danchenko, 130, 630087 Novosibirsk, Russia
- Department of Ophthalmology, Novosibirsk State Medical University, Pr. Krasny, 52, 630091 Novosibirsk, Russia
| | - Ida F. Nikulich
- Federal Research Center Institute of Cytology and Genetics SB RAS, Pr. Lavrentiev, 10, 630090 Novosibirsk, Russia; (A.Z.F.); (A.S.D.); (I.F.N.); (V.A.D.); (N.G.K.)
- State Novosibirsk Regional Clinical Hospital, St. Nemirovich-Danchenko, 130, 630087 Novosibirsk, Russia
- Department of Ophthalmology, Novosibirsk State Medical University, Pr. Krasny, 52, 630091 Novosibirsk, Russia
| | - Vasiliy A. Devyatkin
- Federal Research Center Institute of Cytology and Genetics SB RAS, Pr. Lavrentiev, 10, 630090 Novosibirsk, Russia; (A.Z.F.); (A.S.D.); (I.F.N.); (V.A.D.); (N.G.K.)
| | - Nataliya G. Kolosova
- Federal Research Center Institute of Cytology and Genetics SB RAS, Pr. Lavrentiev, 10, 630090 Novosibirsk, Russia; (A.Z.F.); (A.S.D.); (I.F.N.); (V.A.D.); (N.G.K.)
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Grosjean I, Roméo B, Domdom MA, Belaid A, D’Andréa G, Guillot N, Gherardi RK, Gal J, Milano G, Marquette CH, Hung RJ, Landi MT, Han Y, Brest P, Von Bergen M, Klionsky DJ, Amos CI, Hofman P, Mograbi B. Autophagopathies: from autophagy gene polymorphisms to precision medicine for human diseases. Autophagy 2022; 18:2519-2536. [PMID: 35383530 PMCID: PMC9629091 DOI: 10.1080/15548627.2022.2039994] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 01/20/2022] [Accepted: 02/06/2022] [Indexed: 12/15/2022] Open
Abstract
At a time when complex diseases affect globally 280 million people and claim 14 million lives every year, there is an urgent need to rapidly increase our knowledge into their underlying etiologies. Though critical in identifying the people at risk, the causal environmental factors (microbiome and/or pollutants) and the affected pathophysiological mechanisms are not well understood. Herein, we consider the variations of autophagy-related (ATG) genes at the heart of mechanisms of increased susceptibility to environmental stress. A comprehensive autophagy genomic resource is presented with 263 single nucleotide polymorphisms (SNPs) for 69 autophagy-related genes associated with 117 autoimmune, inflammatory, infectious, cardiovascular, neurological, respiratory, and endocrine diseases. We thus propose the term 'autophagopathies' to group together a class of complex human diseases the etiology of which lies in a genetic defect of the autophagy machinery, whether directly related or not to an abnormal flux in autophagy, LC3-associated phagocytosis, or any associated trafficking. The future of precision medicine for common diseases will lie in our ability to exploit these ATG SNP x environment relationships to develop new polygenetic risk scores, new management guidelines, and optimal therapies for afflicted patients.Abbreviations: ATG, autophagy-related; ALS-FTD, amyotrophic lateral sclerosis-frontotemporal dementia; ccRCC, clear cell renal cell carcinoma; CD, Crohn disease; COPD, chronic obstructive pulmonary disease; eQTL, expression quantitative trait loci; HCC, hepatocellular carcinoma; HNSCC, head and neck squamous cell carcinoma; GTEx, genotype-tissue expression; GWAS, genome-wide association studies; LAP, LC3-associated phagocytosis; LC3-II, phosphatidylethanolamine conjugated form of LC3; LD, linkage disequilibrium; LUAD, lung adenocarcinoma; MAF, minor allele frequency; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; NSCLC, non-small cell lung cancer; OS, overall survival; PtdIns3K CIII, class III phosphatidylinositol 3 kinase; PtdIns3P, phosphatidylinositol-3-phosphate; SLE, systemic lupus erythematosus; SNPs, single-nucleotide polymorphisms; mQTL, methylation quantitative trait loci; ULK, unc-51 like autophagy activating kinase; UTRs, untranslated regions; WHO, World Health Organization.
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Affiliation(s)
- Iris Grosjean
- University Côte d’Azur, CNRS, INSERM, IRCAN, FHU-OncoAge, Centre Antoine Lacassagne, France
| | - Barnabé Roméo
- University Côte d’Azur, CNRS, INSERM, IRCAN, FHU-OncoAge, Centre Antoine Lacassagne, France
| | - Marie-Angela Domdom
- University Côte d’Azur, CNRS, INSERM, IRCAN, FHU-OncoAge, Centre Antoine Lacassagne, France
| | - Amine Belaid
- Université Côte d’Azur (UCA), INSERM U1065, C3M, Team 5, F-06204, France
| | - Grégoire D’Andréa
- University Côte d’Azur, CNRS, INSERM, IRCAN, FHU-OncoAge, Centre Antoine Lacassagne, France
- ENT and Head and Neck surgery department, Institut Universitaire de la Face et du Cou, CHU de Nice, University Hospital, Côte d’Azur University, Nice, France
| | - Nicolas Guillot
- University Côte d’Azur, CNRS, INSERM, IRCAN, FHU-OncoAge, Centre Antoine Lacassagne, France
| | - Romain K Gherardi
- INSERM U955 Team Relais, Faculty of Health, Paris Est University, France
| | - Jocelyn Gal
- University Côte d’Azur, Centre Antoine Lacassagne, Epidemiology and Biostatistics Department, Nice, France
| | - Gérard Milano
- Université Côte d’Azur, Centre Antoine Lacassagne, UPR7497, Nice, France
| | - Charles Hugo Marquette
- University Côte d’Azur, CNRS, INSERM, IRCAN, FHU-OncoAge, Centre Antoine Lacassagne, France
- University Côte d’Azur, FHU-OncoAge, Department of Pulmonary Medicine and Oncology, CHU de Nice, Nice, France
| | - Rayjean J. Hung
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada; Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Younghun Han
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Patrick Brest
- University Côte d’Azur, CNRS, INSERM, IRCAN, FHU-OncoAge, Centre Antoine Lacassagne, France
| | - Martin Von Bergen
- Helmholtz Centre for Environmental Research GmbH - UFZ, Dep. of Molecular Systems Biology; University of Leipzig, Faculty of Life Sciences, Institute of Biochemistry, Leipzig, Germany
| | - Daniel J. Klionsky
- University of Michigan, Life Sciences Institute, Ann Arbor, MI, 48109, USA
| | - Christopher I. Amos
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Paul Hofman
- University Côte d’Azur, CNRS, INSERM, IRCAN, FHU-OncoAge, Centre Antoine Lacassagne, France
- University Côte d’Azur, FHU-OncoAge, CHU de Nice, Laboratory of Clinical and Experimental Pathology (LPCE) Biobank(BB-0033-00025), Nice, France
| | - Baharia Mograbi
- University Côte d’Azur, CNRS, INSERM, IRCAN, FHU-OncoAge, Centre Antoine Lacassagne, France
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Zhu Y, Rao J, Wei J, Liu L, Huang S, Lan J, Xue C, Li W. Gene polymorphisms in ULK1 and PIK3CA are associated with the risk of microscopic polyangiitis in the Guangxi Zhuang Autonomous Region in China. PeerJ 2021; 9:e12377. [PMID: 34820172 PMCID: PMC8588863 DOI: 10.7717/peerj.12377] [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: 06/23/2021] [Accepted: 10/03/2021] [Indexed: 11/20/2022] Open
Abstract
Background Microscopic polyangiitis (MPA) is a systemic autoimmune disease characterized by inflammation of small- and medium-sized blood vessels. Autophagy-related protein polymorphisms are involved in autoimmune disease. The aim of this study was to evaluate the effects of single-nucleotide polymorphisms (SNPs) in the ULK1 and PIK3CA genes on the risk of MPA. Method A total of 208 patients with MPA and 211 controls in the Guangxi Zhuang Autonomous Region were recruited and analyzed. The SNPs selected were detected by polymerase chain reaction and high-throughput sequencing. The differences in allele and genotype frequency, various genetic models, and stratification analyses were evaluated, haplotype evaluation was performed after linkage disequilibrium analysis, and the interaction between gene alleles was analyzed. Results A statistically significant difference was detected in the genotypic distribution of two SNPs between the two groups: ULK1rs4964879 (p = 0.019) and PIK3CArs1607237 (p = 0.002). The results of the genetic models revealed that ULK1rs4964879 and rs9481 were statistically significantly associated with an increased risk of MPA, whereas PIK3CArs1607237 was associated with a reduced risk. The association between SNPs and MPA risk was affected by age, sex, and ethnicity. The ULK1 haplotype (G-T-A-C-G-A) and PIK3CA haplotype (T-G) were associated with a reduced risk of MPA, while the PIK3CA haplotype (C-G) was associated with an increased risk. Conclusion In this study, polymorphisms in the autophagy-related genes ULK1 and PIK3CA and their association with MPA were examined. The results showed that the polymorphisms in ULK1 (rs4964879 and rs9481) and PIK3CA (rs1607237) were significantly associated with MPA risk in the Guangxi population. However, the molecular mechanisms are still unclear; basic science research and studies with larger samples are needed to confirm our conclusions and explore the underlying mechanisms.
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Affiliation(s)
- Yan Zhu
- The Second Affiliated Hospital of Guangxi Medical University, Department of Nephrology, Nanning, Guangxi, China.,The First Affiliated Hospital, Department of Nephrology, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Jinlan Rao
- The Second Affiliated Hospital of Guangxi Medical University, Department of Nephrology, Nanning, Guangxi, China
| | - Jingsi Wei
- The Second Affiliated Hospital of Guangxi Medical University, Department of Nephrology, Nanning, Guangxi, China
| | - Liu Liu
- The Second Affiliated Hospital of Guangxi Medical University, Department of Nephrology, Nanning, Guangxi, China
| | - Shanshan Huang
- The Second Affiliated Hospital of Guangxi Medical University, Department of Nephrology, Nanning, Guangxi, China
| | - Jingjing Lan
- The Second Affiliated Hospital of Guangxi Medical University, Department of Nephrology, Nanning, Guangxi, China
| | - Chao Xue
- The Second Affiliated Hospital of Guangxi Medical University, Department of Nephrology, Nanning, Guangxi, China
| | - Wei Li
- The Second Affiliated Hospital of Guangxi Medical University, Department of Nephrology, Nanning, Guangxi, China
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Tamargo-Gómez I, Fernández ÁF, Mariño G. Pathogenic Single Nucleotide Polymorphisms on Autophagy-Related Genes. Int J Mol Sci 2020; 21:ijms21218196. [PMID: 33147747 PMCID: PMC7672651 DOI: 10.3390/ijms21218196] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 10/28/2020] [Accepted: 10/30/2020] [Indexed: 02/06/2023] Open
Abstract
In recent years, the study of single nucleotide polymorphisms (SNPs) has gained increasing importance in biomedical research, as they can either be at the molecular origin of a determined disorder or directly affect the efficiency of a given treatment. In this regard, sequence variations in genes involved in pro-survival cellular pathways are commonly associated with pathologies, as the alteration of these routes compromises cellular homeostasis. This is the case of autophagy, an evolutionarily conserved pathway that counteracts extracellular and intracellular stressors by mediating the turnover of cytosolic components through lysosomal degradation. Accordingly, autophagy dysregulation has been extensively described in a wide range of human pathologies, including cancer, neurodegeneration, or inflammatory alterations. Thus, it is not surprising that pathogenic gene variants in genes encoding crucial effectors of the autophagosome/lysosome axis are increasingly being identified. In this review, we present a comprehensive list of clinically relevant SNPs in autophagy-related genes, highlighting the scope and relevance of autophagy alterations in human disease.
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Affiliation(s)
- Isaac Tamargo-Gómez
- Instituto de Investigación Sanitaria del Principado de Asturias, 33011 Oviedo, Spain;
- Departamento de Biología Funcional, Universidad de Oviedo, 33011 Oviedo, Spain
| | - Álvaro F. Fernández
- Instituto de Investigación Sanitaria del Principado de Asturias, 33011 Oviedo, Spain;
- Departamento de Biología Funcional, Universidad de Oviedo, 33011 Oviedo, Spain
- Correspondence: (Á.F.F.); (G.M.); Tel.: +34-985652416 (G.M.)
| | - Guillermo Mariño
- Instituto de Investigación Sanitaria del Principado de Asturias, 33011 Oviedo, Spain;
- Departamento de Biología Funcional, Universidad de Oviedo, 33011 Oviedo, Spain
- Correspondence: (Á.F.F.); (G.M.); Tel.: +34-985652416 (G.M.)
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