Neovascularization of the macula, a common complication of many chorioretinal diseases such as neovascular age-related macular degeneration, polypoidal choroidal vasculopathy, and pathologic myopia, results from increased synthesis of vascular endothelial growth factor (VEGF) by the retinal pigment epithelium and/or Müller cells because of localized ischemia and inflammation. The Consensus on Neovascular AMD Nomenclature (CONAN) study group acknowledged that these vessels may originate from either the choriocapillaris or the retinal microvasculature, prompting them to propose the term 'macular neovascularization' (MNV) to include intraretinal, subretinal, and sub-pigment epithelial neovascularization localized to the macula. MNV frequently appears as a grey-green macular lesion with overlying intraretinal thickening and/or subretinal exudation, causing metamorphopsia, reduced central vision, relative central scotoma, decreased reading speed, and problems with color recognition. Multimodal imaging with optical coherence tomography (OCT), OCT angiography, dye-based angiographies, fundus autofluorescence, and multiwavelength photography help establish the diagnosis and aid in selecting an appropriate treatment. The standard of care for MNV is usually intravitreal anti-vascular endothelial growth factor injections, though thermal laser photocoagulation, verteporfin photodynamic therapy, and vitreoretinal surgery are occasionally used. We discuss the etiology and clinical features of MNV, the role of multimodal imaging in establishing the diagnosis, and the available therapeutic options.

Metabolomics is a rapidly evolving field focused on the comprehensive identification and quantification of small molecules in biological systems. As the final layer of the biological hierarchy following of the genome, transcriptome and proteome, it presents a dynamic snapshot of phenotype, influenced by genetic, environmental and physiological factors. Whilst the metabolome sits downstream of genes and proteins, there are multiple higher levels-tissues, organs, the entire organism, and interactions with other organisms, which need to be considered in order to fully comprehend organismal biology. Advances in metabolomics continue to expand its applications in plant biology, biotechnology, and natural product discovery unlocking many of nature's most beneficial colors, tastes, nutrients and medicines. Flavonoids and other specialized metabolites are essential for plant defense against oxidative stress and function as key phytonutrients for human health. Recent advancements in gene-editing and metabolic engineering have significantly improved the nutritional value and flavor of crop plants. Here we highlight how advanced metabolic analysis is driving improvements in crops uncovering genes that influence nutrient and flavor profile and plant derived compounds with medicinal potential.

Neovascular age-related macular degeneration (NVAMD) is a common retinal disease causing vision loss in the elderly. Neuroinflammation significantly contributes to NVAMD's etiology. This study explores the role of Programmed cell death ligand 1 (PD-L1), an immune checkpoint (ICP) in microglia, known for limiting neuroinflammation in neurodegenerative diseases, and its potential function in NVAMD. This work finds increased PD-L1 expression in retinal microglia following laser injury. PD-L1 knockout (KO) or inhibitory PD-L1 antibody treatment worsens vascular leakage and neoangiogenesis in a laser-induced NVAMD mouse model, effects reversible by microglia depletion with PLX5622. This study underscores that choroidal neovascularization (CNV) may be regulated by multiple mechanisms, with PD-L1 modulation representing one of these pathways. Blocking PD-L1 elevated proinflammatory factors and p-ERK levels, indicating microglial overactivation in NVAMD. Conversely, enhancing PD-L1 signaling reduced neuroinflammation and neovascularization via ERK. These findings highlight PD-L1's role in neoangiogenesis and neuroinflammation in NVAMD, suggesting its potential as a target for immunomodulatory treatment in NVAMD.

Age-related macular degeneration (AMD) is a leading cause of central vision loss, progressively impairing the retina and affecting millions worldwide. By 2040, global cases of AMD are projected to reach 300 million, posing a significant public health challenge. While early AMD may only cause mild visual impairment, advanced stages, particularly neovascular (wet) and non-neovascular (dry) AMD, can lead to severe vision loss or legal blindness, substantially affecting daily life. The introduction of anti-angiogenic therapies has revolutionized wet AMD treatment, offering a high probability of preserving or improving vision. However, these therapies do not halt AMD progression, and no definitive treatments exist for dry AMD. The limitations of current therapies, such as frequent injections and treatment resistance, underscore the urgent need for novel strategies. Gene therapy, which has shown success in treating other hereditary retinal diseases, offers a promising long-term solution for AMD by targeting retinal cells to produce therapeutic proteins. This review explores the potential of gene therapy for AMD, examining recent clinical trials and future treatment directions.

With the continuous advancements in high-throughput genome sequencing technologies and the development of innovative bioinformatics tools, bacterial genome-wide association studies (BGWAS) have emerged as a transformative approach for investigating the genetic variations underlying diverse bacterial phenotypes at the population genome level. This review provides a comprehensive overview of the application of BGWAS in elucidating genetic determinants of bacterial drug resistance, pathogenicity, host specificity, biofilm formation, and probiotic fermentation characteristics. We systematically summarize the BGWAS workflow, including study design, data analysis pipelines, and the bioinformatics software employed at various stages. Furthermore, we highlight specialized tools tailored for BGWAS and discuss their unique features and applications. We also discuss confounding factors that can influence the accuracy and reliability of BGWAS results, including population structure, linkage disequilibrium, and multiple testing. By incorporating recent advancements, this review serves as a comprehensive reference for researchers utilizing BGWAS to uncover the genetic basis of bacterial phenotypes.

Alzheimer's disease (AD) and age-related macular degeneration (AMD) represent the leading causes of dementia and vision impairment in the elderly, respectively. The retina is an extension of the brain, yet these two central nervous system (CNS) compartments are often studied separately. Despite affecting cognition vs. vision, AD and AMD share neuroinflammatory pathways. By comparing these diseases, we can identify converging immune mechanisms and potential cross-applicable therapies. Here, we review immune mechanisms highlighting the shared and distinct aspects of these two age-related neurodegenerative conditions, focusing on responses to hallmark disease manifestations, the opposite role of overlapping immune risk loci, and potential unified therapeutic approaches. We also discuss unique tissue requirements that may dictate different outcomes of conserved immune mechanisms and how we can reciprocally utilize lessons from AD therapeutics to AMD. Looking forward, we suggest promising directions for research, including the exploration of regenerative medicine, gene therapies, and innovative diagnostics.

Liposomes are a well-established carrier and controlled release system in medicine and bioanalysis. Their biomimetic capabilities are harnessed for the development of a reliable homogeneous assay platform technology that lends itself to high-throughput screening and point-of-care applications since no wash or separation steps are needed. It was developed for fluorescent, chemiluminescent, and electrochemical detection strategies and applied to antibodies directed against small or polymeric molecules and peptides as model analytes. The simplicity of the approach is achieved as mere binding of analytes or analyte-associated entities to the liposome surface leads to the activation of the complement system, which in turn lyses the liposomes. Released encapsulated marker molecules are quantified and directly correlated to the analytes. Control over the liposome chemistry, including cholesterol content, surface chemistry, and encapsulants, was identified to be key to ensure their general serum and storage stability (more than 40 months at 4 °C and up to 4 weeks at 37 °C) and their efficient and specific response to complement activity. Additional assay conditions of relevance included the concentration of liposomes and their ratio to serum proteins, the amount of complement trigger per liposome, and the activity of complement proteins. Understanding and being able to control the liposomes enable various analysis strategies including the quantification of analytes, determination of complement activity, and evaluation of the therapeutic application potential of antibodies. A time-resolved version of the assay even allows the study of the complex actions of the complement system.

The chemokine system is associated with age-related macular degeneration (AMD), shown in previous studies. In this study, we investigate these chemokines and chemokine receptors and their association with treatment response in neovascular AMD (nAMD), and association to intermediate AMD (iAMD).

In this prospective cohort study, patients with nAMD, iAMD, and healthy controls were included. The initial and 1-year treatment response was evaluated in patients with nAMD. Plasma chemokine concentrations of CCL2, CCL3, CCL4, CCL20, CXCL8, and CXCL10 were measured with immunoassays. Chemokine receptor expression levels of CCR1, CCR2, CCR5, CCR6, CXCR2, CXCR3, and CX3CR1 on circulating T cells and monocytes were measured with flow cytometry. Correlation network analyses were performed of the chemokine system. Genotyping for CFH and ARMS2 risk polymorphisms was performed in patients with nAMD.

Patients with nAMD with poor initial treatment response had significantly lower proportions of CD4+CXCR3+, CCR5+ classical monocytes, and CCR2+ non-classical monocytes compared with good initial responders (all P < 0.05). Patients with nAMD with poor 1-year treatment response had significantly lower CD4+CXCR3+ and CCR2+ non-classical monocytes compared to good 1-year responders (both P < 0.05). Correlation networks revealed a more complex regulation in partial and poor initial treatment responders. Multiple chemokines and chemokine receptors significantly correlated with the risk genotypes of CFH and ARMS2.

Patients with nAMD with poor treatment response had dysregulation of the chemokine system. The chemokine system might be a potential target of novel treatment in nAMD. Further studies are needed to clarify the chemokine system's role in nAMD treatment response.

Age-related macular degeneration (AMD) is a leading cause of blindness among older adults worldwide, but treatment options are limited. Genetics studies have implicated the CFH locus, containing CFH and five CFHR genes, CFHR1-5, in AMD. While CFH has been robustly linked with AMD risk, potential additional roles for the CFHR genes remain unclear, obscured by strong linkage disequilibrium across the locus. Investigating rare coding variants can help to identify causal genes in such regions. We used whole-exome sequencing data from 406,952 UK Biobank participants to examine AMD associations with genes at the CFH locus. For each gene, we used burden testing to examine associations of rare (minor-allele frequency [MAF] < 1%) predicted loss-of-function (pLoF) and predicted damaging missense variants with AMD. We considered "broadly defined AMD" (ICD-10 35.3; ncases = 10,700) and "strictly defined AMD" (dry or wet AMD; ncases = 346). Adjusting for CFH-region variants known to independently associate with AMD, we find that CFHR5 rare variant burden significantly associates with a decreased risk of broadly defined AMD (odds ratio [OR] = 0.75, p = 7 × 10-4), with this association primarily driven by pLoF variants. Furthermore, the association of CFHR5 rare variants with AMD protection is estimated to be stronger for individuals with the CFH rs1061170 AMD risk allele (p.Tyr402His [p.Y402H]; interaction p = 0.04). Corresponding analyses of strict AMD were underpowered. However, we observe that thinning of the photoreceptor layer outer segment strongly predicts strict AMD and find that CFHR5 rare variant burden is significantly associated with increased thickness of this retinal layer (+0.34 SD, p = 4 × 10-4, n = 45,365). These findings suggest CFHR5 inhibition as a potential therapeutic approach for AMD.

Reduced kidney function is associated with increased risk of cardiovascular disease in addition to kidney disease progression. Kidney disease is considered an inflammatory state, based on elevated levels of C-reactive protein and inflammatory cytokines. A key mediator of cardiovascular and kidney disease progression in the setting of reduced kidney function is systemic and vascular inflammation. However, the exact pathways that link chronic kidney disease (CKD) with inflammation remain incompletely understood. For decades it has been known that factor D, the main activator of the alternative complement pathway, is increased in the plasma of patients with reduced kidney function. Recent biomarker evidence suggests alternative pathway activation in this setting. CKD, therefore, seems to alter the balance of alternative pathway proteins, promoting inflammation and potentially exacerbating complement-mediated diseases and CKD-associated complications. In this manuscript, we review the impact of reduced kidney function on biomarkers of the alternative complement pathway and the implications of alternative pathway activation on cardiovascular disease and kidney disease progression. Importantly, we highlight the need for ongoing research efforts that may lead to opportunities to target the alternative pathway of complement withx the goal of improving kidney and cardiovascular outcomes in persons with reduced kidney function.

Genetic association studies have focused on testing additive models in cohorts with European ancestry. Little is known about recessive effects on common diseases, specifically for non-European ancestry. Genes & Health is a cohort of British Pakistani and Bangladeshi individuals with elevated rates of consanguinity and endogamy, making it suitable to study recessive effects. We imputed variants into a genotyped dataset (n = 44,190) by using two reference panels: a set of 4,982 whole-exome sequences from within the cohort and the Trans-Omics for Precision Medicine (TOPMed-r2) panel. We performed association testing with 898 diseases from electronic health records. 185 independent loci reached genome-wide significance (p < 5 × 10-8) under the recessive model, with p values lower than under the additive model, and >40% of these were novel. 140 loci demonstrated nominally significant (p < 0.05) dominance deviation p values, confirming a recessive association pattern. Sixteen loci in three clusters were significant at a Bonferroni threshold, accounting for multiple phenotypes tested (p < 5.4 × 10-12). In FinnGen, we replicated 44% of the expected number of Bonferroni-significant loci we were powered to replicate, at least one from each cluster, including an intronic variant in patatin-like phospholipase domain-containing protein 3 (PNPLA3; rs66812091) and non-alcoholic fatty liver disease, a previously reported additive association. We present evidence suggesting that the association is recessive instead (odds ratio [OR] = 1.3, recessive p = 2 × 10-12, additive p = 2 × 10-11, dominance deviation p = 3 × 10-2, and FinnGen recessive OR = 1.3 and p = 6 × 10-12). We identified a novel protective recessive association between a missense variant in SGLT4 (rs61746559), a sodium-glucose transporter with a possible role in the renin-angiotensin-aldosterone system, and hypertension (OR = 0.2, p = 3 × 10-8, dominance deviation p = 7 × 10-6). These results motivate interrogating recessive effects on common diseases more widely.

There are no effective therapies for patients with dry age-related macular degeneration (AMD) or C3 glomerulonephritis (C3G). Unfortunately, past efforts to treat C3G using exogenous human complement factor H (CFH) found limited success due to immune rejection of a foreign protein response. AMD research has also faced myriad challenges, including the absence of an ideal therapeutic target and difficulties with treatment delivery in certain preclinical models. In pursuit of an AMD therapy to overcome these obstacles, we ultimately capitalized on parallels in complement dysregulation between AMD and C3G. Here, we investigate the potential for CFH supplementation as a strategy to rescue C3G. Our findings demonstrate restored inhibition of complement's alternative pathway and long-term reversal of disease without immune rejection using adeno-associated virus (AAV)-mediated delivery of truncated CFH (tCFH) in a Cfh-/- mouse model of C3G. We tested three different tCFH vectors and found significant differences in their relative transduction efficiency and therapeutic efficacy. These discoveries motivate the development of AAV-mediated tCFH replacement therapy for patients with C3G while simultaneously demonstrating proof of concept for AAV-mediated tCFH gene augmentation therapy for patients with AMD.

Gene therapy is an innovative medical approach that offers new treatment options for congenital and acquired diseases by transferring, correcting, inactivating or regulating genes to supplement, replace or modify a gene function. The approval of voretigene neparvovec (Luxturna), a gene therapy for RPE65-associated retinopathy, has marked a milestone for the field of retinal gene therapy, but has also helped to accelerate the development of gene therapies for genetic diseases affecting other organs. Voretigene neparvovec is a vector based on adeno-associated virus (AAV) that delivers a functional copy of RPE65 to supplement the missing function of this gene. The AAV-based gene delivery has proven to be versatile and safe for the transfer of genetic material to retinal cells. However, challenges remain in treating additional inherited as well as acquired retinopathies with this technology. Despite the high level of activity in this field, no other AAV gene therapy for retinal diseases has been approved since voretigene neparvovec. Ongoing research focuses on overcoming the current restraints through innovative strategies like AAV capsid engineering, dual-AAV vector systems, or CRISPR/Cas-mediated genome editing. Additionally, AAV gene therapy is being explored for the treatment of complex acquired diseases like age-related macular degeneration (AMD) and diabetic retinopathy (DR) by targeting molecules involved in the pathobiology of the degenerative processes. This review outlines the current state of retinal gene therapy, highlighting ongoing challenges and future directions.

Circular RNAs (circRNAs) are a large class of widely expressed RNAs with covalently closed continuous structures. However, it is currently unknown if circRNAs shows allele-specific expression, as are the consequences of genetic variation on their circularization efficiency and subsequent biological function. Here, we propose a novel pipeline, ASE-circRNA, to accurately quantify both circRNA and their related linear RNA for each allele, and then assess the allele-specificity of the expression of a circular RNA. We identified and analyzed allele-specific circRNAs from human tissue, as well as brains from reciprocal crosses between pairs of highly divergent strains of both mice and pigs by next generation sequencing. Droplet digital PCR (ddPCR) was used to confirm the circularization efficiency measured by next generation sequencing. We found that variation in intron sequences affect the circularization efficiency of circRNAs. Furthermore, we demonstrate that a circRNA, circHK1, regulates the expression of POLR2A to influence the rate of cell proliferation. Our study provides new insight into the molecular mechanisms impacted by variation in genome sequence in the origin of human disease and phenotype.

The Bruch's membrane (BM) is an acellular, extracellular matrix that lies between the choroid and retinal pigment epithelium (RPE). The BM plays a critical role in retinal health, performing various functions including biomolecule diffusion and RPE support. The BM is also involved in many retinal diseases, and insights into BM dysfunction allow for further understanding of the pathophysiology of various chorioretinal pathologies. Thus, characterization of the BM serves as an important area of research to further understand its involvement in retinal disease. In this article, we provide a review of various advancements in characterizing and visualizing the BM. We provide an overview of the BM in retinal health, as well as changes observed in aging and disease. We then describe current state-of-the-art imaging modalities and advances to further visualize the BM including various types of optical coherence tomography imaging, near-infrared reflectance (NIR), and autofluorescence imaging and tissue matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI-IMS). Following advances in imaging of the BM, we describe animal, cellular, and synthetic models that have been developed to further visualize the BM. Following this section, we provide an overview of deep learning in retinal imaging and describe advances in computational and artificial intelligence (AI) techniques to provide automated segmentation of the BM and BM opening. We conclude this section considering the clinical implications of these segmentation techniques. Ultimately, the diverse advances aimed to further characterize the BM may allow for deeper insights into the involvement of this critical structure in retinal health and disease.

Genome-wide association studies (GWAS) are computationally intensive, requiring significant time and resources with computational complexity scaling at least linearly with sample size. Here, we present an accurate and resource-efficient pipeline for GWAS that mitigates the impact of sample size on computational demands. Our approach involves (1) randomly partitioning the cohort into equally sized sub-cohorts, (2) conducting independent GWAS within each sub-cohort, and (3) integrating the results using a novel meta-analysis technique that accounts for population structure and other confounders between sub-cohorts. Importantly, we demonstrate through simulations and real-data examples in humans that our approach effectively manages analyzing related individuals, a critical factor in real datasets, while controlling for inflated effect sizes, a phenomenon known as winner's curse. We show that our method achieves the same discovery levels as standard approaches but with significantly reduced computational costs. Additionally, it is well-suited for incremental GWAS as new samples are added over time. Our implementation within a bioinformatics workflow management system enhances reproducibility and scalability.

In plant genetics, most modern association analyses are performed on panels that bring together individuals from several populations, including admixed individuals whose genomes comprise chromosomal regions from different populations. These panels can identify quantitative trait loci (QTLs) with population-specific effects and epistatic interactions between QTLs and polygenic backgrounds. However, analyzing a diverse panel constitutes a challenge for statistical analysis. The statistical model must account for possible interactions between a QTL and the panel structure while strictly controlling the detection error rate. Although models to detect population-specific QTLs have already been developed, they rely on prior information about the population structure. In practice, this prior information may be missing as many genome-wide association study (GWAS) panels exhibit complex population structures. The present study introduces 2 new models for detecting QTLs interacting with complex population structures. Both incorporate an interaction term between single nucleotide polymorphism/haplotype block and genetic background into conventional GWAS models. The proposed models were compared with state-of-the-art models through simulation studies that considered QTLs with different levels of interaction with their genetic backgrounds. Results showed that models matching simulation settings were most effective for detecting corresponding QTLs while the proposed models outperformed classical models in detecting QTLs interacting with polygenes. Additionally, when applied to a soybean dataset, one of our models identified putative associated QTLs that conventional models failed to detect. The new models, implemented in the RAINBOWR package available on CRAN, are expected to help uncover complex trait genetic architectures.

AMD is a multifactorial progressive disease of the central retina that leads to severe vision loss among the elderly. Genome-wide association studies in AMD patients and preclinical data have identified a dysregulated complement system and aberrant microglia responses in the pathogenesis of AMD. Specifically, a genetic variant in the complement factor H (CFH) gene, an important inhibitor of the alternative complement pathway, confers the strongest risk for AMD. Here, we investigated whether moss-derived recombinant human CFH proteins, termed CPV-101 and CPV-104, can modulate microglia reactivity and limit retinal degeneration in a murine light damage paradigm mimicking important features of AMD.

Two glycosylated human recombinant CFH proteins CPV101, and CPV-104 were produced in moss suspension cultures. In addition, glycans of the CPV-104 variant are sialylated, an optimization that makes CPV-104 an analog of human CFH. BALB/cJ mice received intravitreal injections of 5 µg CPV-101 and CPV-104 or vehicle, starting 1 day prior to exposure to 10,000 lx white light for 30 min. The effects of CPV-101 and CPV-104 treatment on mononuclear phagocyte and Müller cell reactivity were analyzed by immunostainings of retinal sections and flat mounts. Gene expression of microglia markers was analyzed using quantitative real-time PCR (qRT-PCR). Optical coherence tomography (OCT); Blue Peak Autofluorescence (BAF); terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) staining, and morphometric analyses were used to quantify the extent of retinal degeneration and photoreceptor apoptosis.

Light-exposed mice treated with moss-derived recombinant human full-length CFH showed reduced complement activation and MAC deposition in the retina. Concomitantly, mononuclear phagocyte and Müller cell reactivity in light-exposed retinas were also ameliorated upon CFH substitution. Moreover, attenuated light-induced retinal degeneration was detected in mice that received moss-derived CFH.

Modulating the alternative complement pathway using moss-derived recombinant human full-length CFH variant CPV-101 and CPV-104 counter-regulate gliosis and attenuates light-induced retinal degeneration, highlighting a promising concept for the treatment of AMD patients.

Understanding the mechanisms by which genes control and regulate complex quantitative traits during periods of fluctuating resources remains a challenging and uncertain task in photosynthesis studies. Most studies have focused on the structure of photosynthesis, the photosynthetic response under stress, or the genetic mechanisms involved in photosynthetic effects and neglected the interactive genetic mechanism that governs various traits through significant quantitative trait loci (QTLs). In this study, we have developed a differential dynamic system that enables the identification of QTLs based on the photosynthetic phenotypic and genotypic data under varying levels of light intensity gradients. The framework not only allows for the assessment of the direct effects of QTLs on phenotypes but also captures how they influence interactions among phenotypes as light intensities change. We have analyzed the genetic effects and genetic variance, visualized the genetic network associated with photosynthesis interactions, and validated the effectiveness and stability of the DDS framework. Pivotal pleiotropic QTLs were identified individually to uncover the process and pattern of interaction. Through functional annotation, we made an intriguing discovery that seemingly unimportant QTLs can still have significant genetic effects on phenotypic changes through their regulation with other QTLs. This finding emphasizes the significance of considering the interactive genetic architecture when seeking to understand the genetic interaction mechanism of photosynthesis in natural populations of woody plants. Moreover, our research provides a novel framework that can be extended to explore the interactive genetic architecture among organisms, contributing to a deeper understanding of stress resistance mechanisms in woody plants.

Age-related macular degeneration (AMD) is a multifactorial disease, and studies have implicated the role of gut microbiota in its pathogenesis. However, characterization of microbiome dysbiosis and associated microbial-derived metabolomic profiles across AMD stages remains unknown. In this pilot study, we explored how gut microbiome composition and gut-derived metabolites differ in AMD.

Our pilot study analyzed fasted stool samples that were collected from 22 patients at a tertiary academic center. Subjects were classified as control, intermediate AMD, or advanced AMD based on clinical presentation. 16S rRNA amplicon sequencing and standard chromatography-mass spectrometry methods were used to identify bacterial taxonomy composition and abundance of short-chain fatty acids (SCFAs) and bile acids (BAs), respectively. Genetic testing was used to investigate the frequency of 14 high-risk single nucleotide polymorphisms (SNPs) associated with AMD in the AMD cohort.

Forty-three differentially abundant genera were present among the control, intermediate, and advanced groups. Taxa with known roles in immunologic pathways, such as Desulfovibrionales (q = 0.10) and Terrisporobacter (q = 1.16e-03), were in greater abundance in advanced AMD patients compared to intermediate. Advanced AMD patients had decreased abundance of 12 SCFAs, including acetate (P = 0.002), butyrate (P = 0.04), and propionate (P = 0.01), along with 12 BAs, including taurocholic acid (P = 0.02) and tauroursodeoxycholic acid (P = 0.04). Frequencies of high-risk SNPs were not significantly different between the intermediate and advanced AMD groups.

This pilot study identifies distinct gut microbiome compositions and metabolomic profiles associated with AMD and its stages, providing preliminary evidence of a potential link between gut microbiota and AMD pathogenesis. To validate these findings and elucidate the underlying mechanisms, future research with larger cohorts and more comprehensive sampling is strongly recommended.

Age-related macular degeneration (AMD) poses a significant threat to visual health among the elderly, necessitating urgent preventive measures as the global population ages. Extensive research has implicated oxidative stress (OS)-induced retinal damage as a primary contributor to AMD pathogenesis, prompting investigations into potential therapeutic interventions. Among the various nutrients studied for their potential in AMD risk reduction, antioxidants have shown promise, with initial findings from the Age-Related Eye Disease Study suggesting a correlation between antioxidant supplementation and decreased AMD progression. This article explores the scientific foundation supporting the therapeutic efficacy of tocotrienol-rich fraction (TRF) as a viable candidate for slowing AMD progression, based on interventional studies. AMD is characterized by OS, inflammation, dysregulated lipid metabolism, and angiogenesis, all of which TRF purportedly addresses through its potent anti-inflammatory, lipid-lowering, antiangiogenic, and antioxidant properties. The review underscores TRF's promising attributes, aiming to deepen understanding of AMD pathogenesis and advocate for TRF-based pharmacological interventions to enhance therapeutic outcomes. Given the pressing need for effective AMD treatments, TRF represents a promising avenue for intervention, offering hope for improved vision outcomes and enhanced quality of life for individuals affected by this debilitating condition.

Complement is activated through the three different pathways, which are the classical (CP), lectin (LP), and alternative pathways (AP). Complement activation functions to eliminate invading pathogens, whereas dysregulation of complement activation can induce inflammatory disorders such as age-related macular degeneration (AMD). In retinal degeneration induced by sodium iodate (NaIO3), a murine model of dry AMD (also called atrophic AMD), it has been suggested that the AP and CP are involved in the disease development. On the other hand, the role of the LP in the development of AMD remains unclear. In the current study, we generated murine dry AMD model with NaIO3 using mice deficient for mannose-binding lectin-associated serine protease (MASP)-1 and/or MASP-3, which are required for the LP and AP activation, respectively. Wild-type (WT) C57BL/6J mice showed retinal degeneration, including depigmentation and disruption of the retinal pigment epithelium (RPE), atrophy of the photoreceptor layer (PL), and thinning of the outer nuclear layer (ONL) after NaIO3 injection. In contrast, those pathological changes after NaIO3 injection were significantly attenuated in MASP-1-deficient (MASP-1-/-), MASP-3-deficient (MASP-3-/-), and MASP-1/3-double deficient (MASP-1/3-/-) mice. These results indicate that both MASP-1 and MASP-3 play a role in photoreceptor degeneration in the NaIO3-induced murine dry AMD model. In addition, photoreceptor cell death and retinal C3 activation were observed in NaIO3-injected WT mice, whereas those pathological changes were significantly attenuated in NaIO3-injected MASP-3-/- and MASP-1/3-/- mice. On the other hand, those pathological changes in NaIO3-injected MASP-1-/- mice were comparable to those in NaIO3-injected WT mice. Taken together, our results indicate that MASP-3 plays a pivotal role in C3 activation in the retina most likely via activation of the AP leading to the development of retinal degeneration in the NaIO3-induced murine dry AMD model. Our results also indicate that MASP-1 plays a role in the development of NaIO3-induced retinal degeneration in this murine model, although it remains unclear whether its role in the retinal degeneration is through the LP activation.

In civilizations, individuals are born into or sorted into different levels of socio-economic status (SES). SES clusters in families and geographically, and is robustly associated with genetic effects. Here we first review the history of scientific research on the relationship between SES and heredity. We then discuss recent findings in genomics research in light of the hypothesis that SES is a dynamic social construct that involves genetically influenced traits that help in achieving or retaining a socio-economic position, and can affect the distribution of genes associated with such traits. Social stratification results in people with differing traits being sorted into strata with different environmental exposures, which can result in evolutionary selection pressures through differences in mortality, reproduction and non-random mating. Genomics research is revealing previously concealed genetic consequences of the way society is organized, yielding insights that should be approached with caution in pursuit of a fair and functional society.

Genetic information will be increasingly integrated into clinical eye care within the current generation of ophthalmologists. For monogenic diseases such as retinoblastoma, genetic studies have been relatively straightforward as these conditions result from pathogenic variants in a single gene resulting in large physiological effects. However, most eye diseases result from the cumulative effects of multiple genetic variants and environmental factors. In such diseases, because each variant usually has an individually small effect, genetic studies for complex diseases are comparatively more challenging. This article aims to provide an overview of three genetic epidemiology methods for polygenic (or complex) diseases: genome-wide association studies (GWAS), Polygenic Risk Scores (PRS) and Mendelian randomisation (MR). A GWAS systematically conducts association analyses of a trait of interest against millions of genetic variants, usually in the form of single nucleotide polymorphisms, across the genome. GWAS findings can then be used for PRS construction and MR analyses. To construct a PRS, the cumulative effect of many genetic variants associated with a trait from a prior GWAS is calculated and taken as a quantitative representation of an individual's genetic risk of a complex disease. MR studies analyse an outcome measure against the genetic variants of an exposure, and are particularly useful in investigating causal relations between two traits where randomised controlled trials are not possible or ethical. In addition to explaining the principles of these three genetic epidemiology concepts, this article provides a minimally technical description of their basic methodology that is accessible to the non-expert reader.

Little is known about sialic acids of the human retina, despite their integral role in self/non-self-discrimination by complement factor H (CFH), the alternative complement pathway inhibitor.

A custom sialoglycan microarray was used to characterize the sialic acid-binding specificity of native CFH or recombinant molecules where IgG Fc was fused to CFH domains 16-20 (contains a sialic acid-binding site), domains 6-7 (contains a glycosaminoglycan-binding site) or the CFH-related proteins (CFHRs) 1 and 3. We analyzed macular and peripheral retinal tissue from post-mortem ocular globes for amount, type, and presentation (glycosidic linkage type) of sialic acid in individuals with age-related macular degeneration (AMD) and age-matched controls using fluorescent lectins and antibodies to detect sialic acid and endogenous CFH. Released sialic acids from neural retina, retinal pigmented epithelium (RPE) cells and the Bruch's membrane (BrM) were labelled with 1,2-diamino-4,5-methylenedioxybenzene-2HCl (DMB), separated and quantified by high-performance liquid chromatography (DMB-HPLC).

Both native CFH and the recombinant CFH domains 16-20 recognized Neu5Ac and Neu5Gc that is α2-3-linked to the underlying galactose. 4-O-Actylation of sialic acid and sulfation of GlcNAc did not inhibit binding. Different linkage types of sialic acid were localized at different layers of the retina. The greatest density of α2-3-sialic acid, which is the preferred ligand of CFH, did not colocalize with endogenous CFH. The level of sialic acids at the BrM/choroid interface of macula and peripheral retina of individuals with AMD were significantly reduced.

The sialome of the human retina is altered in AMD. This can affect CFH binding and consequently, alternative complement pathway regulation.

Variant calling is hindered in segmental duplications by sequence homology. We developed Paraphase, a HiFi-based informatics method that resolves highly similar genes by phasing all haplotypes of paralogous genes together. We applied Paraphase to 160 long (>10 kb) segmental duplication regions across the human genome with high (>99%) sequence similarity, encoding 316 genes. Analysis across five ancestral populations revealed highly variable copy numbers of these regions. We identified 23 paralog groups with exceptionally low within-group diversity, where extensive gene conversion and unequal crossing over contribute to highly similar gene copies. Furthermore, our analysis of 36 trios identified 7 de novo SNVs and 4 de novo gene conversion events, 2 of which are non-allelic. Finally, we summarized extensive genetic diversity in 9 medically relevant genes previously considered challenging to genotype. Paraphase provides a framework for resolving gene paralogs, enabling accurate testing in medically relevant genes and population-wide studies of previously inaccessible genes.

Complement-associated disorders are caused by the dysregulation and disbalance of the complement system, especially excessive activation. Most drugs that target the complement system are designed to inhibit the complement pathway at either the proximal or terminal levels. The use of a natural complement regulator such as factor H (FH) could provide a superior treatment option by restoring balance to an overactive complement system. We recently reported the moss-based production of an analog of human FH with an optimized glycan profile (CPV-104), which showed in vitro and in vivo characteristics comparable to its human counterpart. Here, we follow up our previous work, focusing in more detail on the time course and long-term efficacy of CPV-104 treatment in FH-deficient (FH -/-) mice. The analysis of long-term treatment effects following multiple injections of human FH into mice was previously hindered by the immune response, so we developed a protocol for the sustained depletion of CD20+ B-cells and CD4+ T-cells, preventing antibody formation without influencing the C3G phenotype. Using this dual-depletion method, we were able to complete dosing interval experiments in FH -/- mice, administering up to three injections of CPV-104 at different intervals. Repeated CPV-104 administration was able to lastingly resolve C3 deposits, offering additional rationale for the clinical testing of CPV-104 in human C3G patients. Moreover, our novel dual-depletion method has the potential for adaptation to different mouse models, allowing the testing of multiple doses of other therapeutic proteins.

Myeloid cells are heterogeneous cells that are critical for spontaneous choroidal neovascularization (CNV) in the Vldlr-/- mouse model. However, the specific myeloid cell subtype necessary for CNV remains unknown.

To investigate the role of monocytes, we bred Ccr2-/- and Nr4a1-/- mice into the Vldlr-/- background. We found that Ccr2 and Nr4a1 deficiency had no effect upon macrophage counts, CNV lesion number, or total CNV area. Next, we investigated the role of microglia by generating Vldlr-/-Tmem119CreER/+Rosa26DTR/+ mice. Diphtheria toxin (DT) treatment reduced macrophage counts at CNV lesions and CNV lesion number, but did not affect total CNV lesion area. To target microglia via a second strategy, we generated Vldlr-/-Cx3cr1CreERCsf1riDTR mice and treated them with a single low dose of tamoxifen to target microglia without affecting choroidal macrophages. DT treatment in Vldlr-/-Cx3cr1CreERCsf1riDTR mice decreased macrophage counts at CNV lesions and CNV lesion number but again had no effect upon total CNV lesion area. To target choroidal macrophages and microglia, we treated Vldlr-/-Cx3cr1CreERCsf1riDTR mice with 9 tamoxifen treatments. DT-treated mice showed dramatic reductions in macrophage counts, CNV number, and total lesion area.

These data suggest that monocytes and monocyte-derived macrophages are dispensable, microglia are likely initiators for CNV development, and choroidal macrophages are potential key contributors to CNV growth and/or maintenance in the Vldlr-/- model.

Due to the slowly progressing nature of age-related macular degeneration (AMD) and critical differences in ocular anatomy between humans and animals, it has been difficult to model disease progression, hampering the development of novel therapeutics aimed at impacting drusen biogenesis. To determine whether "drusen-in-a-dish" model systems are of utility in screening potential therapeutics aimed at early-intermediate dry AMD, we developed a detailed characterization of the protein, glycoprotein, and lipid composition of sub-retinal pigment epithelium (RPE) deposits grown by monolayers of ex vivo porcine RPE with human drusen in AMD globes.

Immunohistochemistry and imaging mass spectrometry (IMS) were performed on 20-week aged monolayers of porcine RPE and human donor globes recovered from an 81-year-old non-transplant donor with confirmed diagnosis of bilateral dry AMD. The presence of major protein, glycoprotein, and lipid species was compared between porcine sub-RPE deposits and human drusen with reference to macular/peripheral eccentricity.

The protein and glycoprotein composition of porcine sub-RPE deposits closely mimics human drusen identified in donor globes with dry AMD, including the presence of major complement components (C9, CFH, CHI), apolipoproteins (ApoE, ApoJ), extracellular matrix proteins (vitronectin, collagen VI), and calcification (hydroxyapatite). Sub-RPE deposits were additionally rich in long-chain ceramide species (Cer, CerPE, PI), which have only recently been described in human drusen.

Due to their compositional similarity to human drusen, ex vivo "drusen-in-a-dish" systems represent a potentially robust and cost-effective model for both studying the pathobiology of drusen biogenesis and screening novel therapeutics aimed at limiting drusen formation.

Human genetic diversity in today's world has been shaped by evolutionary history, demographic shifts and environmental exposures, influencing complex traits, disease susceptibility and drug responses. Capturing this diversity is essential for advancing precision medicine and promoting equitable healthcare. Despite the great progress achieved with initiatives such as the human Pangenome and large biobanks that aim for a better representation of human diversity, important challenges remain. In this Perspective, we discuss the importance of diversity in clinical genomics through an evolutionary lens. We highlight progress and challenges and outline key clinical applications of diverse genetic data. We argue that diversifying both datasets and methodologies-integrating ancestral and environmental factors-is crucial for fully understanding the genetic basis of human health and disease.

Decades of genetic association testing in human cohorts have provided important insights into the genetic architecture and biological underpinnings of complex traits and diseases. However, for certain traits, genome-wide association studies (GWAS) for common SNPs are approaching signal saturation, which underscores the need to explore other types of genetic variation to understand the genetic basis of traits and diseases. Copy number variation (CNV) is an important source of heritability that is well known to functionally affect human traits. Recent technological and computational advances enable the large-scale, genome-wide evaluation of CNVs, with implications for downstream applications such as polygenic risk scoring and drug target identification. Here, we review the current state of CNV-GWAS, discuss current limitations in resource infrastructure that need to be overcome to enable the wider uptake of CNV-GWAS results, highlight emerging opportunities and suggest guidelines and standards for future GWAS for genetic variation beyond SNPs at scale.

This scoping review aims to summarize the current state of knowledge on the potential involvement of infections in age-related macular degeneration (AMD).

Age-related macular degeneration is a multifactorial disease and the leading cause of vision loss among older adults in developed countries. Clarifying whether certain infections participate in its onset or progression seems essential, given the potential implications for treatment and prevention.

Using the PubMed database, we searched for articles in English, published until June 1, 2023, whose title and/or abstract contained terms related to AMD and infections. All types of study design, infectious agents, AMD diagnostic methods, and AMD stages were considered. Articles dealing with the oral and gut microbiota were not included but we provide a brief summary of high-quality literature reviews recently published on the subject.

Two investigators independently screened the 868 articles obtained by our algorithm and the reference lists of selected studies. In total, 40 articles were included, among which 30 on human data, 9 animal studies, 6 in vitro experiments, and 1 hypothesis paper (sometimes with several data types in the same article). Of these, 27 studies were published after 2010, highlighting a growing interest in recent years. A wide range of infectious agents has been investigated, including various microbiota (nasal, pharyngeal), 8 bacteria, 6 viral species, and 1 yeast. Among them, most have been investigated anecdotally. Only Chlamydia pneumoniae, Cytomegalovirus, and hepatitis B virus received more attention with 17, 6, and 4 studies, respectively. Numerous potential pathophysiological mechanisms have been discussed, including (1) an indirect role of infectious agents (i.e. a role of infections located distant from the eye, mainly through their interactions with the immune system) and (2) a direct role of some infectious agents implying potential infection of various cells types within AMD-related tissues.

Overall, this review highlights the diversity of possible interactions between infectious agents and AMD and suggests avenues of research to enrich the data currently available, which provide an insufficient level of evidence to conclude whether or not infectious agents are involved in this pathology.

Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.

Age-related Macular degeneration (AMD) is a major cause of vision loss and is linked to several predisposing single nucleotide polymorphisms (SNPs). CRISPR-mediated genome editing offers the potential to target negatively associated SNPs in an allele-specific manner, necessitating the need for a relevant cell model. The ARPE-19 cell line, with its stable monolayer growth and retinal pigment epithelium (RPE) characteristics, serves as an ideal model for AMD studies. Chronic inflammation and complement system dysregulation are implicated in AMD pathogenesis. Most genetic variations associated with AMD are in complement genes, suggesting their regulatory role. In this study, we conducted targeted PCRs to identify AMD-related SNPs in ARPE-19 cells and used CRISPR constructs to assess allele-specific activity. Guide RNA sequences were cloned into an EF-1-driven SpCas9 vector and packaged into lentivirus. Targeting efficiencies were evaluated with TIDE analysis, and allele-specificity was measured with NGS analysis 30 days post-transduction. Our results showed varying targeting efficiencies depending on guide RNA efficacy. For example, TIDE analysis of CFH SNPs rs1061170 and rs1410996 revealed efficiencies of 35.5% and 33.8%, respectively. CFB SNP rs4541862 showed efficiencies from 3% to 36.7%, and rs641153 ranged from 3.4% to 23.8%. Additionally, allele-specific targeting of AMD-related SNPs rs1061170, rs1410996, rs4541862, and rs641153 ranged from 48% to 52% in heterozygous differentiated ARPE-19 cells. These findings demonstrate the potential to manipulate the complement system in an AMD model by targeting disease-associated SNPs in an allele-specific manner, offering a promising therapeutic approach.

Gestational diabetes mellitus (GDM) is a common pregnancy complication characterized by hyperglycemia and insulin resistance, with unclear genetic mechanisms. The specific involvement of proinflammatory cytokines, including IL-17A, and the immuno-tolerogenic HLA-G remains poorly understood in GDM. We aimed to explore the associations of three polymorphisms, IL-17A -197G>A (rs2275913), IL-17RA -947A>G (rs4819554), and HLA-G 14-bp insertion/deletion (indel), with GDM risk in a Brazilian population. We conducted a case-control study (79 GDM cases and 79 controls). Genetic polymorphisms were analyzed using PCR-RFLP, with DNA extracted using the Salting-out procedure. Significant associations were identified between -197G>A rs2275913 and HLA-G 14-bp indel polymorphisms in both codominant and recessive models. The IL-17A rs2275913 AA genotype was associated with a nearly ten-fold increased risk of GDM in both the codominant (p = 0.021, OR 9.89, 95% CI: 1.63-59.92) and recessive models (p = 0.006, OR 9.33, 95% CI: 1.57-55.38). Similarly, the HLA-G 14-bp Ins/Ins genotype was associated with an increased risk in both the codominant (p = 0.026, OR 3.34, 95% CI: 0.98-11.41) and recessive models (p = 0.010, OR 4.20, 95% CI: 1.36-12.96). IL-17RA polymorphism showed no significant associations. The study findings highlight the potential genetic and immune factors associated with GDM, particularly the -197G>A rs2275913 and HLA-G 14-bp indel polymorphisms. Further functional characterization is warranted to uncover the mechanism of genotype-phenotype association.

Understanding the relationship between genotypes and phenotypes is crucial for advancing personalized medicine. Expression quantitative trait loci (eQTL) mapping plays a significant role by correlating genetic variants to gene expression levels. Despite the progress made by large-scale projects, eQTL mapping still faces challenges in statistical power and privacy concerns. Multi-site studies can increase sample sizes but are hindered by privacy issues. We present privateQTL, a novel framework leveraging secure multi-party computation for secure and federated eQTL mapping. When tested in a real-world scenario with data from different studies, privateQTL outperformed meta-analysis by accurately correcting for covariates and batch effect and retaining higher accuracy and precision for both eGene-eVariant mapping and effect size estimation. In addition, privateQTL is modular and scalable, making it adaptable for other molecular phenotypes and large-scale studies. Our results indicate that privateQTL is a practical solution for privacy-preserving collaborative eQTL mapping.

This research examined whether educational polygenic scores were associated with physical limitations among older adults with European or African ancestry. In the European ancestry sample, we found that education polygenic scores were significantly associated with physical limitations, net of age, sex, and current socioeconomic status. In the African ancestry sample, education polygenic scores were not associated with physical limitations in any of the models. Observed educational attainment was a robust predictor of physical limitations in both samples. This research demonstrates the inequalities in the predictive capacity of educational polygenic scores for physical health. We hypothesize that this disparity is a result of structural barriers to educational attainment by race, selection bias, and/or racial inequities in data collection. All of these explanations stem from structural racism and highlight the limited usefulness of polygenic scores for clinical decision-making.

The rapid advancements in the field of genetics have significantly propelled the development of gene therapies, paving the way for innovative treatments of various hereditary disorders. This review focuses on the genetics of ophthalmologic conditions, highlighting the currently approved ophthalmic gene therapy and exploring emerging therapeutic strategies under development. Inherited retinal dystrophies represent a heterogeneous group of genetic disorders that manifest across a broad spectrum from infancy to late middle age. Key clinical features include nyctalopia (night blindness), constriction of the visual field, impairments in color perception, reduced central visual acuity, and rapid eye movements. Recent technological advancements, such as multimodal imaging, psychophysical assessments, and electrophysiological testing, have greatly enhanced our ability to understand disease progression and establish genotype-phenotype correlations. Additionally, the integration of molecular diagnostics into clinical practice is revolutionizing patient stratification and the design of targeted interventions, underscoring the transformative potential of personalized medicine in ophthalmology. The review also covers the challenges and opportunities in developing gene therapies for other ophthalmic conditions, such as age-related macular degeneration and optic neuropathies. We discuss the viral and non-viral vector systems used in ocular gene therapy, highlighting their advantages and limitations. Additionally, we explore the potential of emerging technologies like CRISPR/Cas9 in treating genetic eye diseases. We briefly address the regulatory landscape, concerns, challenges, and future directions of gene therapy in ophthalmology. We emphasize the need for long-term safety and efficacy data as these innovative treatments move from bench to bedside.

Dogs have played an outsized role in the field of behavioral genetics since its earliest days. Their unique evolutionary history and ubiquity in the modern world make them a potentially powerful model system for discovering how genetic changes lead to changes in behavior. Genomic technology has supercharged this potential by enabling scientists to sequence the DNA of thousands of dogs and test for correlations with behavioral traits. However, fractures in the early history of animal behavior between biological and psychological subfields may be impeding progress. In addition, canine behavioral genetics has included almost exclusively dogs from modern breeds, who represent just a small fraction of all dog diversity. By expanding the scope of dog behavior studies, and incorporating an evolutionary perspective on canine behavioral genetics, we can move beyond associations to understanding the complex interactions between genes and environment that lead to dog behavior.

The last 15 years have seen unprecedent advancement in genomics techniques such as dense single nucleotide variants (SNVs) arrays or next generation Sequencing. In parallel, new analytical methodologies have been developed to streamline data understanding and integration. These advances have been instrumental in identifying common genetic variants associated with pancreatic ductal adenocarcinoma (PDAC) risk. The role of the individual variants is rather small, and they have no clinical utility for screening or early detection. However, their combined effect computed though polygenic risk scores (PGS) are showing promising potentiality in PDAC risk prediction. There still caveats, and limitations that need to be properly addressed however it is foreseeable that the genetic background will become a powerful tool in PDAC prediction, leveraging the advantage that it has compared to other biomarkers: germline genetics is invariable from birth to death.