Systems genomics in age-related macular degeneration

• Published in: Experimental eye research Vol. 225; p. 109248
• Main Authors: den Hollander, Anneke I., Mullins, Robert F., Orozco, Luz D., Voigt, Andrew P., Chen, Hsu-Hsin, Strunz, Tobias, Grassmann, Felix, Haines, Jonathan L., Kuiper, Jonas J.W., Tumminia, Santa J., Allikmets, Rando, Hageman, Gregory S., Stambolian, Dwight, Klaver, Caroline C.W., Boeke, Jef D., Chen, Hao, Honigberg, Lee, Katti, Suresh, Frazer, Kelly A., Weber, Bernhard H.F., Gorin, Michael B.
• Format: Journal Article
• Language: English
• Published: England Elsevier Ltd 01.12.2022
• Subjects: Age-related macular degeneration; Choroid - metabolism; Clinical trial; Complement Factor H - genetics; Complement Factor H - metabolism; Complement system; Complement System Proteins - metabolism; Expression quantitative trait locus; Genomics; High-Temperature Requirement A Serine Peptidase 1 - genetics; Humans; Induced pluripotent stem cells; iPSc-RPE; Macular Degeneration - genetics; Macular Degeneration - metabolism; Omics; Polygenic risk scores; Polymorphism, Single Nucleotide; Proteins - genetics; Retinal Pigment Epithelium - metabolism; Single cell sequencing; Systems genomics; Polygenic risk scores; Systems genomics; Single cell sequencing; Age-related macular degeneration; Induced pluripotent stem cells; Omics; iPSc-RPE; Clinical trial; Expression quantitative trait locus; Complement system
• ISSN: 0014-4835; 1096-0007
• DOI: 10.1016/j.exer.2022.109248

Genomic studies in age-related macular degeneration (AMD) have identified genetic variants that account for the majority of AMD risk. An important next step is to understand the functional consequences and downstream effects of the identified AMD-associated genetic variants. Instrumental for this next step are ‘omics’ technologies, which enable high-throughput characterization and quantification of biological molecules, and subsequent integration of genomics with these omics datasets, a field referred to as systems genomics. Single cell sequencing studies of the retina and choroid demonstrated that the majority of candidate AMD genes identified through genomic studies are expressed in non-neuronal cells, such as the retinal pigment epithelium (RPE), glia, myeloid and choroidal cells, highlighting that many different retinal and choroidal cell types contribute to the pathogenesis of AMD. Expression quantitative trait locus (eQTL) studies in retinal tissue have identified putative causal genes by demonstrating a genetic overlap between gene regulation and AMD risk. Linking genetic data to complement measurements in the systemic circulation has aided in understanding the effect of AMD-associated genetic variants in the complement system, and supports that protein QTL (pQTL) studies in plasma or serum samples may aid in understanding the effect of genetic variants and pinpointing causal genes in AMD. A recent epigenomic study fine-mapped AMD causal variants by determing regulatory regions in RPE cells differentiated from induced pluripotent stem cells (iPSC-RPE). Another approach that is being employed to pinpoint causal AMD genes is to produce synthetic DNA assemblons representing risk and protective haplotypes, which are then delivered to cellular or animal model systems. Pinpointing causal genes and understanding disease mechanisms is crucial for the next step towards clinical translation. Clinical trials targeting proteins encoded by the AMD-associated genomic loci C3, CFB, CFI, CFH, and ARMS2/HTRA1 are currently ongoing, and a phase III clinical trial for C3 inhibition recently showed a modest reduction of lesion growth in geographic atrophy. The EYERISK consortium recently developed a genetic test for AMD that allows genotyping of common and rare variants in AMD-associated genes. Polygenic risk scores (PRS) were applied to quantify AMD genetic risk, and may aid in predicting AMD progression. In conclusion, genomic studies represent a turning point in our exploration of AMD. The results of those studies now serve as a driving force for several clinical trials. Expanding to omics and systems genomics will further decipher function and causality from the associations that have been reported, and will enable the development of therapies that will lessen the burden of AMD. •The majority of AMD-associated loci have not yet been assessed in functional studies.•Single-cell sequencing studies have identified cell types that may be relevant for AMD pathogenesis.•eQTL studies and epigenomics have pinpointed potentially causal genes at AMD-associated loci.•Clinical trials targeting the AMD-associated GWAS hits CFH, HTRA1, C3, CFB and CFI are ongoing.•Polygenic risk scores may aid in risk prediction for AMD disease progression.