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Luo S, Hu Q, Jiang B, Zhang Z, Sun D. Bioinformatics analysis for constructing a cellular senescence-related age-related macular degeneration diagnostic model and identifying relevant disease subtypes to guide treatment. Aging (Albany NY) 2024; 16:8044-8069. [PMID: 38742956 PMCID: PMC11131993 DOI: 10.18632/aging.205804] [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: 11/07/2023] [Accepted: 04/10/2024] [Indexed: 05/16/2024]
Abstract
Age-related macular degeneration (AMD) is a condition causing progressive central vision loss. Growing evidence suggests a link between cellular senescence and AMD. However, the exact mechanism by which cellular senescence leads to AMD remains unclear. Employing machine learning, we established an AMD diagnostic model. Through unsupervised clustering, two distinct AMD subtypes were identified. GO, KEGG, and GSVA analyses explored the diverse biological functions associated with the two subtypes. By WGCNA, we constructed a coexpression network of differential genes between the subtypes, revealing the regulatory role of hub genes at the level of transcription factors and miRNAs. We identified 5 genes associated with inflammation for the construction of the AMD diagnostic model. Additionally, we observed that the level of cellular senescence and pathways related to programmed cell death (PCD), such as ferroptosis, necroptosis, and pyroptosis, exhibited higher expression levels in subtype B than A. Immune microenvironments also differed between the subtypes, indicating potentially distinct pathogenic mechanisms and therapeutic targets. In summary, by leveraging cellular senescence-associated gene expression, we developed an AMD diagnostic model. Furthermore, we identified two subtypes with varying expression patterns of senescence genes, revealing their differential roles in programmed cell death, disease progression, and immune microenvironments within AMD.
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Affiliation(s)
- Shan Luo
- Department of Ophthalmology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Qiang Hu
- Department of Ophthalmology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Bo Jiang
- Department of Ophthalmology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Zhongyu Zhang
- Department of Ophthalmology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Dawei Sun
- Department of Ophthalmology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
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Wang S, Liu H, Yang P, Wang Z, Ye P, Xia J, Chen S. A role of inflammaging in aortic aneurysm: new insights from bioinformatics analysis. Front Immunol 2023; 14:1260688. [PMID: 37744379 PMCID: PMC10511768 DOI: 10.3389/fimmu.2023.1260688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 08/23/2023] [Indexed: 09/26/2023] Open
Abstract
Introduction Aortic aneurysms (AA) are prevalent worldwide with a notable absence of drug therapies. Thus, identifying potential drug targets is of utmost importance. AA often presents in the elderly, coupled with consistently raised serum inflammatory markers. Given that ageing and inflammation are pivotal processes linked to the evolution of AA, we have identified key genes involved in the inflammaging process of AA development through various bioinformatics methods, thereby providing potential molecular targets for further investigation. Methods The transcriptome data of AA was procured from the datasets GSE140947, GSE7084, and GSE47472, sourced from the NCBI GEO database, whilst gene data of ageing and inflammation were obtained from the GeneCards Database. To identify key genes, differentially expressed analysis using the "Limma" package and WGCNA were implemented. Protein-protein intersection (PPI) analysis and machine learning (ML) algorithms were employed for the screening of potential biomarkers, followed by an assessment of the diagnostic value. Following the acquisition of the hub inflammaging and AA-related differentially expressed genes (IADEGs), the TFs-mRNAs-miRNAs regulatory network was established. The CIBERSORT algorithm was utilized to investigate immune cell infiltration in AA. The correlation of hub IADEGs with infiltrating immunocytes was also evaluated. Lastly, wet laboratory experiments were carried out to confirm the expression of hub IADEGs. Results 342 and 715 AA-related DEGs (ADEGs) recognized from GSE140947 and GSE7084 datasets were procured by intersecting the results of "Limma" and WGCNA analyses. After 83 IADEGs were obtained, PPI analysis and ML algorithms pinpointed 7 and 5 hub IADEGs candidates respectively, and 6 of them demonstrated a high diagnostic value. Immune cell infiltration outcomes unveiled immune dysregulation in AA. In the wet laboratory experiments, 3 hub IADEGs, including BLNK, HLA-DRA, and HLA-DQB1, finally exhibited an expression trend in line with the bioinformatics analysis result. Discussion Our research identified three genes - BLNK, HLA-DRA, and HLA-DQB1- that play a significant role in promoting the development of AA through inflammaging, providing novel insights into the future understanding and therapeutic intervention of AA.
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Affiliation(s)
- Shilin Wang
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hao Liu
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Peiwen Yang
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhiwen Wang
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ping Ye
- Department of Cardiology, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiahong Xia
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shu Chen
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Zhou X, Zhang J, Ding Y, Huang H, Li Y, Chen W. Predicting late-stage age-related macular degeneration by integrating marginally weak SNPs in GWA studies. Front Genet 2023; 14:1075824. [PMID: 37065470 PMCID: PMC10101437 DOI: 10.3389/fgene.2023.1075824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 03/17/2023] [Indexed: 04/18/2023] Open
Abstract
Introduction: Age-related macular degeneration (AMD) is a progressive neurodegenerative disease and the leading cause of blindness in developed countries. Current genome-wide association studies (GWAS) for late-stage age-related macular degeneration are mainly single-marker-based approaches, which investigate one Single-Nucleotide Polymorphism (SNP) at a time and postpone the integration of inter-marker Linkage-disequilibrium (LD) information in the downstream fine mappings. Recent studies showed that directly incorporating inter-marker connection/correlation into variants detection can help discover novel marginally weak single-nucleotide polymorphisms, which are often missed in conventional genome-wide association studies, and can also help improve disease prediction accuracy. Methods: Single-marker analysis is performed first to detect marginally strong single-nucleotide polymorphisms. Then the whole-genome linkage-disequilibrium spectrum is explored and used to search for high-linkage-disequilibrium connected single-nucleotide polymorphism clusters for each strong single-nucleotide polymorphism detected. Marginally weak single-nucleotide polymorphisms are selected via a joint linear discriminant model with the detected single-nucleotide polymorphism clusters. Prediction is made based on the selected strong and weak single-nucleotide polymorphisms. Results: Several previously identified late-stage age-related macular degeneration susceptibility genes, for example, BTBD16, C3, CFH, CFHR3, HTARA1, are confirmed. Novel genes DENND1B, PLK5, ARHGAP45, and BAG6 are discovered as marginally weak signals. Overall prediction accuracy of 76.8% and 73.2% was achieved with and without the inclusion of the identified marginally weak signals, respectively. Conclusion: Marginally weak single-nucleotide polymorphisms, detected from integrating inter-marker linkage-disequilibrium information, may have strong predictive effects on age-related macular degeneration. Detecting and integrating such marginally weak signals can help with a better understanding of the underlying disease-development mechanisms for age-related macular degeneration and more accurate prognostics.
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Affiliation(s)
- Xueping Zhou
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, United States
| | - Jipeng Zhang
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, United States
| | - Ying Ding
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, United States
| | - Heng Huang
- Department of Electrical and Computer Engineering, University of Pittsburgh, Pittsburgh, PA, United States
| | - Yanming Li
- Department of Biostatistics and Data Science, University of Kansas Medical Center, Kansas, KS, United States
| | - Wei Chen
- Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, United States
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Senabouth A, Daniszewski M, Lidgerwood GE, Liang HH, Hernández D, Mirzaei M, Keenan SN, Zhang R, Han X, Neavin D, Rooney L, Lopez Sanchez MIG, Gulluyan L, Paulo JA, Clarke L, Kearns LS, Gnanasambandapillai V, Chan CL, Nguyen U, Steinmann AM, McCloy RA, Farbehi N, Gupta VK, Mackey DA, Bylsma G, Verma N, MacGregor S, Watt MJ, Guymer RH, Powell JE, Hewitt AW, Pébay A. Transcriptomic and proteomic retinal pigment epithelium signatures of age-related macular degeneration. Nat Commun 2022; 13:4233. [PMID: 35882847 PMCID: PMC9325891 DOI: 10.1038/s41467-022-31707-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 06/29/2022] [Indexed: 11/08/2022] Open
Abstract
There are currently no treatments for geographic atrophy, the advanced form of age-related macular degeneration. Hence, innovative studies are needed to model this condition and prevent or delay its progression. Induced pluripotent stem cells generated from patients with geographic atrophy and healthy individuals were differentiated to retinal pigment epithelium. Integrating transcriptional profiles of 127,659 retinal pigment epithelium cells generated from 43 individuals with geographic atrophy and 36 controls with genotype data, we identify 445 expression quantitative trait loci in cis that are asssociated with disease status and specific to retinal pigment epithelium subpopulations. Transcriptomics and proteomics approaches identify molecular pathways significantly upregulated in geographic atrophy, including in mitochondrial functions, metabolic pathways and extracellular cellular matrix reorganization. Five significant protein quantitative trait loci that regulate protein expression in the retinal pigment epithelium and in geographic atrophy are identified - two of which share variants with cis- expression quantitative trait loci, including proteins involved in mitochondrial biology and neurodegeneration. Investigation of mitochondrial metabolism confirms mitochondrial dysfunction as a core constitutive difference of the retinal pigment epithelium from patients with geographic atrophy. This study uncovers important differences in retinal pigment epithelium homeostasis associated with geographic atrophy.
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Affiliation(s)
- Anne Senabouth
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
| | - Maciej Daniszewski
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC, 3010, Australia
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, 3002, Australia
| | - Grace E Lidgerwood
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC, 3010, Australia
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, 3002, Australia
| | - Helena H Liang
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, 3002, Australia
| | - Damián Hernández
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC, 3010, Australia
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, 3002, Australia
| | - Mehdi Mirzaei
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Stacey N Keenan
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Ran Zhang
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
| | - Xikun Han
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Drew Neavin
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
| | - Louise Rooney
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | | | - Lerna Gulluyan
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Linda Clarke
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, 3002, Australia
| | - Lisa S Kearns
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, 3002, Australia
| | | | - Chia-Ling Chan
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
| | - Uyen Nguyen
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
| | - Angela M Steinmann
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
| | - Rachael A McCloy
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
| | - Nona Farbehi
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
| | - Vivek K Gupta
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - David A Mackey
- Lions Eye Institute, Centre for Vision Sciences, University of Western Australia, Perth, WA, 6009, Australia
- School of Medicine, University of Tasmania, Hobart, TAS, 7005, Australia
| | - Guy Bylsma
- Lions Eye Institute, Centre for Vision Sciences, University of Western Australia, Perth, WA, 6009, Australia
| | - Nitin Verma
- School of Medicine, University of Tasmania, Hobart, TAS, 7005, Australia
| | - Stuart MacGregor
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Matthew J Watt
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Robyn H Guymer
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, 3002, Australia
- Department of Surgery, Ophthalmology, Royal Victorian Eye and Ear Hospital, The University of Melbourne, East Melbourne, VIC, 3002, Australia
| | - Joseph E Powell
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia.
- UNSW Cellular Genomics Futures Institute, University of New South Wales, Sydney, NSW, 2052, Australia.
| | - Alex W Hewitt
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, 3002, Australia.
- School of Medicine, University of Tasmania, Hobart, TAS, 7005, Australia.
- Department of Surgery, Ophthalmology, Royal Victorian Eye and Ear Hospital, The University of Melbourne, East Melbourne, VIC, 3002, Australia.
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, 7000, Australia.
| | - Alice Pébay
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC, 3010, Australia.
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, 3002, Australia.
- Department of Surgery, Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC, 3010, Australia.
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Merle H, Béral L, Rocher M, Pierre M, Jean-Charles A, Béra O, Rosamont LA, Robert PY, Lézin A. Class II Human Leukocyte Antigen (HLA) and Susceptibility to Polypoidal Choroidal Vasculopathy in Afro-Caribbean Descent. Clin Ophthalmol 2022; 16:1047-1053. [PMID: 35418742 PMCID: PMC8995864 DOI: 10.2147/opth.s337084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 12/13/2021] [Indexed: 11/25/2022] Open
Abstract
Purpose To evaluate how the HLA genotype is associated to the polypoidal choroidal vasculopathy (PCV) in a population of patients of Afro-Caribbean descent. Methods Forty-seven patients were diagnosed with PCV. The number of control patients was 457. All affected patients and control patients were of Afro-Caribbean descent and natives to Martinique. HLA typing was based on blood sample, using the polymerase chain reaction technique. Comparison of HLA alleles between the 2 groups was done using chi-2 test, odds ratio (OR) and confidence interval using Woolf’s method. The Bonferroni correction was considered significant when p-value ≤0.05. Alleles frequency was analyzed for DRB1 and DQB1 locus. Results HLA-DRB1*13 allele was significantly associated to PCV (OR = 2.02, CI = [1.3; 3.13], p = 0.003). In group DRB1, the Bonferroni correction significance threshold was <0.004. HLA-DQB1*04 allele was significantly associated to PCV (OR = 3.5, CI = [1.48; 8.3], p = 0.006). In group DQB1, the Bonferroni correction significance threshold was <0.006. Conclusion Two HLA alleles are positively associated to PCV. The possible association between PCV and certain alleles suggest HLA implication in PCV pathogeny, most likely by modeling the immune system response.
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Affiliation(s)
- Harold Merle
- Department of Ophthalmology, University Hospital of Martinique, Fort de France, French West Indies, France
- Correspondence: Harold Merle, Department of Ophthalmology, University Hospital of Martinique, Hôpital Pierre Zobda Quitman, BP 632, Martinique, Fort de France, 97261 Cedex, French West Indies, France, Tel +596 596 552 251, Fax +596 596 758 447, Email
| | - Laurence Béral
- Department of Ophthalmology, University Hospital of Guadeloupe, Pointe à Pitre, French West Indies, France
| | - Maxime Rocher
- Department of Ophthalmology, University Hospital of Limoges, France
| | - Mitta Pierre
- Department of Ophthalmology, University Hospital of Martinique, Fort de France, French West Indies, France
| | - Albert Jean-Charles
- Department of Ophthalmology, University Hospital of Martinique, Fort de France, French West Indies, France
| | - Odile Béra
- Department of Genetics, University Hospital of Martinique, Fort de France, French West Indies, France
| | - Laurie-Anne Rosamont
- Department of Genetics, University Hospital of Martinique, Fort de France, French West Indies, France
| | | | - Agnes Lézin
- Department of Genetics, University Hospital of Martinique, Fort de France, French West Indies, France
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Pugazhendhi A, Hubbell M, Jairam P, Ambati B. Neovascular Macular Degeneration: A Review of Etiology, Risk Factors, and Recent Advances in Research and Therapy. Int J Mol Sci 2021; 22:1170. [PMID: 33504013 PMCID: PMC7866170 DOI: 10.3390/ijms22031170] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/11/2021] [Accepted: 01/19/2021] [Indexed: 12/14/2022] Open
Abstract
Neovascular age-related macular degeneration (exudative or wet AMD) is a prevalent, progressive retinal degenerative macular disease that is characterized by neovascularization of the choroid, mainly affecting the elderly population causing gradual vision impairment. Risk factors such as age, race, genetics, iris color, smoking, drinking, BMI, and diet all play a part in nvAMD's progression, with anti-vascular endothelial growth factor (anti-VEGF) therapy being the mainstay of treatment. Current therapeutic advancements slow the progression of the disease but do not cure or reverse its course. Newer therapies such as gene therapies, Rho-kinase inhibitors, and levodopa offer potential new targets for treatment.
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Affiliation(s)
- Arunbalaji Pugazhendhi
- Knights Campus for Accelerating Scientific Impact, University of Oregon, Eugene, OR 97403, USA; (A.P.); (M.H.)
| | - Margaret Hubbell
- Knights Campus for Accelerating Scientific Impact, University of Oregon, Eugene, OR 97403, USA; (A.P.); (M.H.)
| | - Pooja Jairam
- Vagelos College of Physicians & Surgeons, Columbia Irving Medical Center, Columbia University, New York, NY 10032, USA;
| | - Balamurali Ambati
- Knights Campus for Accelerating Scientific Impact, University of Oregon, Eugene, OR 97403, USA; (A.P.); (M.H.)
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Rutledge GA, Pratt SG, Richer SP, Huntjens B, Perry CB, Pratt G, Podella C. Foveal macular pigment dip in offspring of age-related macular degeneration patients is inversely associated with omega-3 index. BMC Ophthalmol 2020; 20:473. [PMID: 33267825 PMCID: PMC7709463 DOI: 10.1186/s12886-020-01742-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 11/23/2020] [Indexed: 12/23/2022] Open
Abstract
Background Offspring of parent(s) with age-related macular degeneration (AMD) have a 45% lifetime risk of developing the disease. High foveal macular pigment optical density (MPOD) is protective, whereas individuals with a “foveal macular pigment dip” (FMPD) are at increased risk. Shortage of the dietary carotenoids lutein, zeaxanthin as well as fish consumption are reported AMD risk factors. This Early Biomarkers of AMD (EBAMD) study evaluates serum factors that protect foveal MPOD architecture in Caucasian offspring of parent(s) with AMD. Methods N = 130 subjects [mean (SD) age 62.8 (8.6) years; 36/94 male/female] were recruited from Scripps Health/ Scripps Memorial Hospital/ Scripps Mericos Eye Institute between 2012 and 2017. Macula pigment 3D topography was evaluated using specular reflectance. Buccal genetic cheek swab, circulating serum dietary carotenoids and long-term RBC omega-3 fatty acid status, as well as common secondary clinical structural and vision function parameters were obtained. Results 41 % of offspring of AMD parent(s) presented with FMPD. These offspring were about 4 years younger than those without FMPD (controls; P = 0.012) and had thinner foveas (P = 0.010). There were no differences in gender, BMI, % body fat, visual acuity or contrast sensitivity between those with and without FMPD. % RBC membrane docosahexaenoic acid (DHA) was reduced in FMPD offspring vs. control offspring (P = 0.04). The Omega-3 Index was significantly decreased in the FMPD group (P = 0.03). Conclusions The percentage of FMPD in AMD offspring is nearly twice that reported for the general population in the scientific literature. Offspring presenting FMPD had similar AMD genetic risk, but significantly reduced % RBC membrane omega-3 fatty acids and thinner foveas compared with those without FMPD. Our data supports the importance of ‘essential fatty’ acids as an independent AMD risk factor.
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Affiliation(s)
- Grant A Rutledge
- Scripps Health/Scripps Memorial Hospital/Scripps Mericos Eye Institute - Scripps Clinical Research Service, La Jolla, CA, USA. .,Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA. .,USDA Human Nutrition Research Center on Aging, Boston, MA, USA.
| | - Steven G Pratt
- Scripps Health/Scripps Memorial Hospital/Scripps Mericos Eye Institute - Scripps Clinical Research Service, La Jolla, CA, USA
| | - Stuart P Richer
- Eye Clinics, Captain James A. Lovell Federal Health Care Center, North Chicago, IL, USA
| | - Byki Huntjens
- Centre for Applied Vision Research, Division of Optometry and Vision Sciences, City, University of London, London, UK
| | - C Blake Perry
- Scripps Health/Scripps Memorial Hospital/Scripps Mericos Eye Institute - Scripps Clinical Research Service, La Jolla, CA, USA
| | - Gunilla Pratt
- Scripps Health/Scripps Memorial Hospital/Scripps Mericos Eye Institute - Scripps Clinical Research Service, La Jolla, CA, USA
| | - Carla Podella
- Eye Clinics, Captain James A. Lovell Federal Health Care Center, North Chicago, IL, USA
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9
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Svendsen SG, Nilsson LL, Djurisic S, Funck T, Wu CL, Faber C, Falk MK, Singh A, Sørensen TL, Carosella ED, LeMaoult J, Hviid TVF, Nissen MH. Extended HLA-G haplotypes in patients with age-related macular degeneration. HLA 2018; 92:83-89. [PMID: 30009537 DOI: 10.1111/tan.13340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 06/14/2018] [Accepted: 07/12/2018] [Indexed: 11/29/2022]
Abstract
The study aims to determine if genetic polymorphisms in the human leukocyte antigen (HLA)-G gene are associated with age-related macular degeneration (AMD). HLA-G is important for immunological tolerance, and it is also known to have angiogenic effects. Polymorphisms in the 5'-upstream regulatory region (URR) and 3'-untranslated region (UTR) of HLA-G have been associated with a number of diseases, especially with respect to a 14 bp insertion/deletion (ins/del) polymorphism in the 3'UTR. Full gene sequencing was performed on a cohort of 146 AMD patients and 63 healthy controls aged 60 years or older and HLA-G haplotypes were determined. Analyses were performed on a publicly available gene expression dataset from the NCBI GEO database (accession number GSE29801) from which expression data for HLA-G, -C and -A were extracted. Analysis of the GEO dataset showed that both HLA-G and -C was expressed in the back of the eye and that expression was upregulated in the macular area of AMD. No differences were observed between patients and controls when analysing the distribution of haplotypes in the HLA-G promoter, coding region, 3'UTR or the 14 bp ins/del polymorphism of the 3'UTR. The increased expression of HLA-G in the macula of AMD patients indicates a role of HLA-G in the micro environment as part of the AMD pathogenesis. This is supported by the expression of HLA-C, which has previously been shown to play a role in AMD. The HLA-G haplotype distribution did not display any differences between AMD patients and controls. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Signe Goul Svendsen
- Department of Immunology and Microbiology, University of Copenhagen, Denmark
| | - Line Lynge Nilsson
- Centre for Immune Regulation and Reproductive Immunology (CIRRI), Department of Clinical Biochemistry, Zealand University Hospital, Denmark
- Department of Clinical Medicine, Faculty of Health Sciences, University of Copenhagen
| | - Snezana Djurisic
- Centre for Immune Regulation and Reproductive Immunology (CIRRI), Department of Clinical Biochemistry, Zealand University Hospital, Denmark
- Department of Clinical Medicine, Faculty of Health Sciences, University of Copenhagen
| | - Tina Funck
- Centre for Immune Regulation and Reproductive Immunology (CIRRI), Department of Clinical Biochemistry, Zealand University Hospital, Denmark
- Department of Clinical Medicine, Faculty of Health Sciences, University of Copenhagen
| | - Ching-Lien Wu
- Hemato-Immunology Research Department, CEA, Hospital Saint Louis, Paris
| | - Carsten Faber
- Department of Immunology and Microbiology, University of Copenhagen, Denmark
- Department of Ophthalmology, Rigshospitalet, Glostrup, Denmark
| | - Mads Krüger Falk
- Department of Ophthalmology, Rigshospitalet, Glostrup, Denmark
- Clinical Eye Research Unit, Department of Ophthalmology, Zealand University Hospital, Roskilde, Denmark
| | - Amardeep Singh
- Clinical Eye Research Unit, Department of Ophthalmology, Zealand University Hospital, Roskilde, Denmark
- Dept. of Ophthalmology, Skåne University Hospital & Lund University, Sweden
| | - Torben Lykke Sørensen
- Clinical Eye Research Unit, Department of Ophthalmology, Zealand University Hospital, Roskilde, Denmark
- Department of Clinical Medicine, Faculty of Health Sciences, University of Copenhagen
| | | | - Joël LeMaoult
- Hemato-Immunology Research Department, CEA, Hospital Saint Louis, Paris
| | - Thomas Vauvert F Hviid
- Centre for Immune Regulation and Reproductive Immunology (CIRRI), Department of Clinical Biochemistry, Zealand University Hospital, Denmark
- Department of Clinical Medicine, Faculty of Health Sciences, University of Copenhagen
| | - Mogens Holst Nissen
- Department of Immunology and Microbiology, University of Copenhagen, Denmark
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Wang W, Ollila HM, Whittemore AS, Demehri S, Ioannidis NM, Jorgenson E, Mignot E, Asgari MM. Genetic variants in the HLA class II region associated with risk of cutaneous squamous cell carcinoma. Cancer Immunol Immunother 2018; 67:1123-1133. [PMID: 29754218 DOI: 10.1007/s00262-018-2168-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 04/30/2018] [Indexed: 11/29/2022]
Abstract
BACKGROUND The immune system has been implicated in the pathophysiology of cutaneous squamous cell carcinoma (cSCC) as evidenced by the substantially increased risk of cSCC in immunosuppressed individuals. Associations between cSCC risk and single nucleotide polymorphisms (SNPs) in the HLA region have been identified by genome-wide association studies (GWAS). The translation of the associated HLA SNPs to structural amino acids changes in HLA molecules has not been previously elucidated. METHODS Using data from a GWAS that included 7238 cSCC cases and 56,961 controls of non-Hispanic white ancestry, we imputed classical alleles and corresponding amino acid changes in HLA genes. Logistic regression models were used to examine associations between cSCC risk and genotyped or imputed SNPs, classical HLA alleles, and amino acid changes. RESULTS Among the genotyped SNPs, cSCC risk was associated with rs28535317 (OR = 1.20, p = 9.88 × 10- 11) corresponding to an amino-acid change from phenylalanine to leucine at codon 26 of HLA-DRB1 (OR = 1.17, p = 2.48 × 10- 10). An additional independent association was observed for a threonine to isoleucine change at codon 107 of HLA-DQA1 (OR = 1.14, p = 2.34 × 10- 9). Among the classical HLA alleles, cSCC was associated with DRB1*01 (OR = 1.18, p = 5.86 × 10- 10). Conditional analyses revealed additional independent cSCC associations with DQA1*05:01 and DQA1*05:05. Extended haplotype analysis was used to complement the imputed haplotypes, which identified three extended haplotypes in the HLA-DR and HLA-DQ regions. CONCLUSIONS Associations with specific HLA-DR and -DQ alleles are likely to explain previously observed GWAS signals in the HLA region associated with cSCC risk.
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Affiliation(s)
- Wei Wang
- Department of Health Research and Policy, Stanford University School of Medicine, Stanford, CA, USA
| | - Hanna M Ollila
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | - Alice S Whittemore
- Department of Health Research and Policy, Stanford University School of Medicine, Stanford, CA, USA
| | - Shadmehr Demehri
- Department of Dermatology, Massachusetts General Hospital, 50 Staniford Street, Suite 270, 02114, Boston, MA, USA
| | - Nilah M Ioannidis
- Department of Health Research and Policy, Stanford University School of Medicine, Stanford, CA, USA
| | - Eric Jorgenson
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Emmanuel Mignot
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | - Maryam M Asgari
- Department of Dermatology, Massachusetts General Hospital, 50 Staniford Street, Suite 270, 02114, Boston, MA, USA. .,Department of Population Medicine, Harvard Medical School, Boston, MA, USA.
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11
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SanGiovanni JP, SanGiovanni PM, Sapieha P, De Guire V. miRNAs, single nucleotide polymorphisms (SNPs) and age-related macular degeneration (AMD). Clin Chem Lab Med 2017; 55:763-775. [PMID: 28343170 DOI: 10.1515/cclm-2016-0898] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 02/27/2017] [Indexed: 12/15/2022]
Abstract
Advanced age-related macular degeneration (AAMD) is a complex sight-threating disease of public health significance. Micro RNAs (miRNAs) have been proposed as biomarkers for AAMD. The presence of certain single nucleotide polymorphisms (SNPs) may influence the explanatory value of these biomarkers. Here we present findings from an integrated approach used to determine whether AAMD-associated SNPs have the capacity to influence miRNA-mRNA pairing and, if so, to what extent such pairing may be manifested in a discrete AAMD transcriptome. Using a panel of 8854 SNPs associated with AAMD at p-values ≤5.0E-7 from a cohort of >30,000 elderly people, we identified SNPs in miRNA target-encoding constituents of: (1) regulator of complement activation (RCA) genes (rs390679, CFHR1, p≤2.14E-214 | rs12140421, CFHR3, p≤4.63E-29); (2) genes of major histocompatibility complex (MHC) loci (rs4151672, CFB, p≤8.91E-41 | rs115404146, HLA-C, p≤6.32E-12 | rs1055821, HLA-B, p≤1.93E-9 | rs1063355, HLA-DQB1, p≤6.82E-14); and (3) genes of the 10q26 AAMD locus (rs1045216, PLEKHA1, p≤4.17E-142 | rs2672603, ARMS2, p≤7.14E-46). We used these findings with existing data on AAMD-related retinal miRNA and transcript profiles for the purpose of making inferences on SNP-mRNA-miRNA-AAMD relationships. Four of 12 miRNAs significantly elevated in AAMD retina (hsa-miR-155-5p, hsa-let-7a-5p, hsa-let-7b-5p hsa-let-7d-5p) also showed strong pairing capacity (TarBase 7.1 context++ score <-0.2, miRanda 3.3 pairing score >150) with miRNA target transcripts encoded by AAMD-associated SNPs resident in HLA-DQB1 (rs1063355, hsa-miR-155-5p) and TGFBR1 (rs868, hsa-let-7). Three of the 12 miRNAs overexpressed in AAMD retina are inducible by NFkB and have high affinity targets in the complement factor H (CFH) mRNA 3' UTR. We used ENSEMBL to identify polymorphic regions in the CFH mRNA 3' UTR with the capacity to disrupt miRNA-mRNA pairing. Two variants (rs766666504 and rs459598) existed in DNA sequence encoding the seed region of hsa-miR-146a-5p in the CFH mRNA 3' UTR - as this miRNA is also elevated in both vitreous and serum of people with AAMD, it shows great value as a biomarker. Our findings suggest that knowledge on the nature of DNA sequence variation may increase the explanatory power of miRNA biomarkers in genetically diverse populations, while yielding information with which to develop: (1) mechanistic tests on processes implicated in AMD pathogenesis; and, (2) site-specific small molecules (synthetic mimetics or anti-miRNAs) with preventive or therapeutic efficacy for AAMD.
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Affiliation(s)
- John Paul SanGiovanni
- Laboratory of Membrane Biochemistry and Biophysics, Section on Nutritional Neuroscience, NIAAA/NIH, Bethesda, MD
| | | | - Przemysław Sapieha
- Departments of Biochemistry and Ophthalmology, Maisonneuve-Rosemont Hospital Research Centre, University of Montreal, Montreal, Quebec
| | - Vincent De Guire
- Division of Clinical Biochemistry, Maisonneuve-Rosemont Hospital, University of Montreal, Department of Biochemistry and Molecular Medicine, Montreal, Quebec
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12
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Neville MJ, Lee W, Humburg P, Wong D, Barnardo M, Karpe F, Knight JC. High resolution HLA haplotyping by imputation for a British population bioresource. Hum Immunol 2017; 78:242-251. [PMID: 28111166 PMCID: PMC5367449 DOI: 10.1016/j.humimm.2017.01.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 12/03/2016] [Accepted: 01/17/2017] [Indexed: 12/02/2022]
Abstract
This study aimed to establish the occurrence and frequency of HLA alleles and haplotypes for a healthy British Caucasian population bioresource from Oxfordshire. We present the results of imputation from HLA SNP genotyping data using SNP2HLA for 5553 individuals from Oxford Biobank, defining one- and two-field alleles together with amino acid polymorphisms. We show that this achieves a high level of accuracy with validation using sequence-specific primer amplification PCR. We define six- and eight-locus HLA haplotypes for this population by Bayesian methods implemented using PHASE. We determine patterns of linkage disequilibrium and recombination for these individuals involving classical HLA loci and show how analysis within a haplotype block structure may be more tractable for imputed data. Our findings contribute to knowledge of HLA diversity in healthy populations and further validate future large-scale use of HLA imputation as an informative approach in population bioresources.
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Affiliation(s)
- Matt J Neville
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Old Road, Oxford OX3 7LJ, UK; Oxford NIHR Biomedical Research Centre, Churchill Hospital, Oxford, UK
| | - Wanseon Lee
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Peter Humburg
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Daniel Wong
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Martin Barnardo
- Transplant Immunology and Immunogenetics Laboratory, Oxford Transplant Centre, Churchill Hospital, Oxford OX3 7LJ, UK
| | - Fredrik Karpe
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Old Road, Oxford OX3 7LJ, UK; Oxford NIHR Biomedical Research Centre, Churchill Hospital, Oxford, UK
| | - Julian C Knight
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.
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