Local genetic ancestry in CDKN2B-AS1 is associated with primary open-angle glaucoma in an African American cohort extracted from de-identified electronic health records

Social Deprivation and the Risk of Screening Positive for Glaucoma in the MI-SIGHT Telemedicine-Based Glaucoma Detection Program

PURPOSE

To assess whether increased poverty is associated with increased risk of screening positive for glaucoma or suspected glaucoma in a large public screening and intervention program.

DESIGN

Cross-sectional study from 2020 to 2022.

PARTICIPANTS

Adults ≥ 18 years old without acute ocular symptoms.

METHODS

Michigan Screening and Intervention for Glaucoma and eye Health through Telemedicine (MI-SIGHT) program participants' sociodemographic characteristics and area deprivation index (ADI) values were summarized from the clinical sites, which included a free clinic and a Federally Qualified Health Center (FQHC). The ADI, a composite measure of neighborhood deprivation (range, 1-10; 10 is worst deprivation), was assigned on the basis of the participants' addresses. Group comparisons were performed via 2-sample t tests or Wilcoxon Mann-Whitney tests for continuous measures and chi-square tests or Fisher exact tests with Monte Carlo simulation for categorical measures; Holm adjustment was used for multiple comparisons.

MAIN OUTCOME MEASURES

Risk factors for screening positive for glaucoma or suspected glaucoma.

RESULTS

Of the 1171 enrolled participants, 1165 (99.5%) completed the screening: 34% at the free clinic and 66% at the FQHC. Participants were on average aged 55.1 ± 14.5 years, 62% were women, 54% self-reported as Black/African-American, 34% White, 10% Hispanic or Latino, and 70% earned < $30 000 annually. The mean ADI was 7.2 ± 3.1. The FQHC had higher (worse) ADI than the free clinic (free clinic: 4.5 ± 2.9, FQHC: 8.5 ± 2.1, P < 0.0001). One-quarter (24%) of participants screened positive for glaucoma or suspected glaucoma. Screening positive for glaucoma or suspected glaucoma was associated with being older (P = 0.01), identifying as Black/African-American (P = 0.0001), having an established eyecare clinician (P = 0.0005), and not driving a personal vehicle to the appointment (P = 0.001), which is a proxy for increased poverty. Participants who screened positive had worse ADI than those who screened negative (7.7 ± 2.8 vs. 7.0 ± 3.2, P = 0.002). A larger percentage of White participants screened positive at the FQHC compared with White participants at the free clinic (21.3% vs. 12.3%, P = 0.01). FQHC White participants had worse ADI than free clinic White participants (7.5 ± 2.5 vs. 3.7 ± 2.7, P < 0.0001).

CONCLUSIONS

Personal poverty, assessed as not driving a personal vehicle to the appointment, and neighborhood-level poverty were both associated with increased rates of screening positive for glaucoma or suspected glaucoma.

FINANCIAL DISCLOSURE(S)

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

Development and Evaluation of a Rules-based Algorithm for Primary Open-Angle Glaucoma in the VA Million Veteran Program

The availability of electronic health record (EHR)-linked biobank data for research presents opportunities to better understand complex ocular diseases. Developing accurate computable phenotypes for ocular diseases for which gold standard diagnosis includes imaging remains inaccessible in most biobank-linked EHRs. The objective of this study was to develop and validate a computable phenotype to identify primary open-angle glaucoma (POAG) through accessing the Department of Veterans Affairs (VA) Computerized Patient Record System (CPRS) and Million Veteran Program (MVP) biobank. Accessing CPRS clinical ophthalmology data from VA Medical Center Eye Clinic (VAMCEC) patients, we developed and iteratively refined POAG case and control algorithms based on clinical, prescription, and structured diagnosis data (ICD-CM codes). Refinement was performed via detailed chart review, initially at a single VAMCEC (n = 200) and validated at two additional VAMCECs (n = 100 each). Positive and negative predictive values (PPV, NPV) were computed as the proportion of CPRS patients correctly classified with POAG or without POAG, respectively, by the algorithms, validated by ophthalmologists and optometrists with access to gold-standard clinical diagnosis data. The final algorithms performed better than previously reported approaches in assuring the accuracy and reproducibility of POAG classification (PPV >83% and NPV >97%) with consistent performance in Black or African American and in White Veterans. Applied to the MVP to identify cases and controls, genetic analysis of a known POAG-associated locus further validated the algorithms. We conclude that ours is a viable approach to use combined EHR-genetic data to study patients with complex diseases that require imaging confirmation.

Common causes of visual impairment in the elderly

Background

Aging is not a disease; rather, it is a process. As people age, visual impairment (VI) becomes more common. In 2010, the overall prevalence rate of vision impairment in all races was 25.66% in individuals aged ≥ 80 years, according to the estimate of the National Eye Institute at the National Institutes of Health. This review aimed to address the common causes of VI in the elderly.

Methods

In this narrative review, an electronic search of the PubMed/MEDLINE database was conducted using "visual impairment" and "elderly" for the period between January 2010 and April 2021, to include randomized clinical trials and observational studies concerning VI in the elderly. The selected time period was chosen to provide an updated review.

Results

The search yielded 2955 articles published over the period of more than 11 years. The relevant randomized clinical trials or observational studies were included and reviewed. Cataracts, refractive errors, open-angle glaucoma, age-related macular degeneration, and diabetic retinopathy were the most common age-related ocular disorders leading to VI if untreated in the elderly. The loss of visual acuity can adversely affect quality of life in the elderly. Difficulty with activities of daily living related to VI can lead to social isolation, depression, and anxiety. Loss of vision in the elderly is linked to an increased risk of falls, hip fracture, depression, and poor quality of life.

Conclusions

The most common causes of VI in the elderly are cataracts and refractive errors. VI in most ocular diseases is more prevalent in women than in men due to longer lifespan. The overall prevalence of the main causes of VI in the elderly is expected to increase; therefore, health policymakers should consider this when planning for the health-enhancement program of the population.

Significance of the lncRNAs MALAT1 and ANRIL in occurrence and development of glaucoma

Background

Primary open‐angle glaucoma (POAG) is the commonest form of glaucoma which is estimated to cause bilaterally blind within 11.1 million people by 2020. Therefore, the primary objectives of this study were to investigate the clinical significance of single‐nucleotide polymorphisms (SNPs) in the lncRNAs MALAT1 and ANRIL in a Chinese Han POAG cohort.

Methods

Three hundred and forty‐six glaucoma patients and 263 healthy controls were recruited, and totally 14 SNPs in MALAT1 and ANRIL were genotyped between the two populations.

Results

The MALAT1 SNPs rs619586 (A>G), rs3200401 (C>T), and rs664589 (C>G) were associated with POAG risk, and the ANRIL SNPs rs2383207 (A>G), rs564398 (A>G), rs2157719 (A>G), rs7865618 (G>A), and rs4977574 (A>G) were associated with POAG (p < 0.05). The MALAT1 haplotypes ACG and ATC, comprised rs619586, rs3200401, and rs664589, increased POAG risk, and the ANRIL haplotype AAGAA, made up of rs2383207, rs7865618, rs4977574, rs564398, and rs2157719, show a significantly increased risk of POAG. In addition, rs619586 (A>G) of MALAT1 and rs564398/rs2157719 of ANRIL were associated with a smaller vertical cup‐to‐disc ratio, while rs619586 of MALAT1 and rs2383207/rs4977574 of ANRIL were associated with higher intraocular pressure in the POAG population.

Conclusion

Single‐nucleotide polymorphisms and haplotypes in ANRIL and MALAT1 were associated with POAG onset in our study population, which provide more possibilities to POAG diagnosis and treatment.

Potential Therapeutic Targeting of lncRNAs in Cholesterol Homeostasis

Maintaining cholesterol homeostasis is essential for normal cellular and systemic functions. Long non-coding RNAs (lncRNAs) represent a mechanism to fine-tune numerous biological processes by controlling gene expression. LncRNAs have emerged as important regulators in cholesterol homeostasis. Dysregulation of lncRNAs expression is associated with lipid-related diseases, suggesting that manipulating the lncRNAs expression could be a promising therapeutic approach to ameliorate liver disease progression and cardiovascular disease (CVD). However, given the high-abundant lncRNAs and the poor genetic conservation between species, much work is required to elucidate the specific role of lncRNAs in regulating cholesterol homeostasis. In this review, we highlighted the latest advances in the pivotal role and mechanism of lncRNAs in regulating cholesterol homeostasis. These findings provide novel insights into the underlying mechanisms of lncRNAs in lipid-related diseases and may offer potential therapeutic targets for treating lipid-related diseases.

New findings in the roles of Cyclin-dependent Kinase inhibitors 2B Antisense RNA 1 (CDKN2B-AS1) rs1333049 G/C and rs4977574 A/G variants on the risk to coronary heart disease

The relationship between Cyclin-Dependent Kinase Inhibitors 2B Antisense RNA 1 (CDKN2B-AS1) variants rs1333049 G/C and rs4977574 A/G and the risk of coronary heart disease is unclear. We conducted an update analysis incorporating odds ratios and 95% confidence intervals to assess the correlation. Furthermore, we used in silico analysis to investigate the genes and proteins that interact with CDKN2B. Fifty case-control studies with a sample size of 35,915 cases and 48,873 controls were involved. We revealed that the rs1333049 C allele could increase the risk of coronary heart disease in the overall analysis (allele comparison, OR = 1.13, 95%CI = 1.05–1.21, P = 0.001; homozygous contrast, OR = 1.29, 95%CI = 1.11–1.49, P = 0.001; dominant comparison, OR = 1.14, 95%CI = 1.03–1.27, P = 0.011; recessive comparison, OR = 1.21, 95%CI = 1.10–1.34, P < 0.001). In subgroup analysis, positive correlations were detected in studies involving West and East Asians and in population-based control studies. The rs4977574 G allele was also a risk factor for coronary heart disease (allelic comparison, P = 0.001; heterozygous comparison, P = 0.003; homozygous comparison, P < 0.001; dominant comparison, P = 0.001). These results indicate correlation of CDKN2B-AS1 rs1333049 G/C and rs4977574 A/G variants may be correlated with the risk of coronary heart disease.

Abbreviations CDK: Cyclin Dependent Kinase; CCND: G1/S-specific cyclin-D; CDKN: Cyclin Dependent Kinase Inhibitor; GWAS: Genome-wide association study; CDKN2B-AS1: Cyclin-Dependent Kinase Inhibitors 2B Antisense RNA 1; CHD: Coronary heart disease; MAF: minor allele frequencies; HWE: Hardy-Weinberg equilibrium of controls; CI: confidence interval; COL8A2: Collagen type VIII alpha 2 chain; HB: Hospital-based; ORs: odds ratios; ITGA11: Integrin subunit alpha 11; LTBP: Latent transforming factor beta binding protein; PB: Population-based; IBC: Itmat Broad Care; NA: Not applicable; PCR-RFLP: polymerase chain reaction-restriction fragment length polymorphism; MI: Myocardial Infarction; SNP: single nucleotide polymorphism; SMAD: Mothers against decapentaplegic homolog; RT-PCR: Real-time polymerase chain reaction; UK: United Kingdom

Molecular Genetics and Functional Analysis Implicate CDKN2BAS1-CDKN2B Involvement in POAG Pathogenesis

The genes in the 9p21 locus (CDKN2B-AS1 & CDKN2B) are widely associated with Primary open-angle glaucoma (POAG). However, the functional importance of this locus in POAG pathogenesis is still unexplored. This study investigated the role of CDKN2BAS1-CDKN2B axis in POAG. We observed significant association of CDKN2B-AS1 SNP rs4977756 with POAG and its endophenotypic traits (vertical cup-disc ratio (p = 0.033) and central corneal thickness (p = 0.008)) by screening African American POAG cases (n = 1567) and controls (n = 1600). A luciferase reporter assay in Human embryonic kidney 293T (HEK293T) cells revealed that the region surrounding rs4977756 likely serves as a transcriptional repressor. siRNA-mediated knockdown of CDKN2B-AS1 in HEK293T cells and trabecular meshwork (TM) cells resulted in significantly increased expression of CDKN2B, which was also observed in human POAG ocular tissues. Pathway focused qRT-PCR gene expression analysis showed increased cellular senescence, TGFβ signaling and ECM deposition in TM cells after CDKN2B-AS1 suppression. In conclusion, we report that CDKN2B-AS1 may act as a regulator, and it could function by modulating the expression of CDKN2B. In addition, increase in CDKN2B levels due to CDKN2B-AS1 suppression may result in the senescence of trabecular meshwork cells leading to POAG pathogenesis.

The Genetic and Endoplasmic Reticulum-Mediated Molecular Mechanisms of Primary Open-Angle Glaucoma

Glaucoma is a heterogenous, chronic, progressive group of eye diseases, which results in irreversible loss of vision. There are several types of glaucoma, whereas the primary open-angle glaucoma (POAG) constitutes the most common type of glaucoma, accounting for three-quarters of all glaucoma cases. The pathological mechanisms leading to POAG pathogenesis are multifactorial and still poorly understood, but it is commonly known that significantly elevated intraocular pressure (IOP) plays a crucial role in POAG pathogenesis. Besides, genetic predisposition and aggregation of abrogated proteins within the endoplasmic reticulum (ER) lumen and subsequent activation of the protein kinase RNA-like endoplasmic reticulum kinase (PERK)-dependent unfolded protein response (UPR) signaling pathway may also constitute important factors for POAG pathogenesis at the molecular level. Glaucoma is commonly known as a ‘silent thief of sight’, as it remains asymptomatic until later stages, and thus its diagnosis is frequently delayed. Thereby, detailed knowledge about the glaucoma pathophysiology is necessary to develop both biochemical and genetic tests to improve its early diagnosis as well as develop a novel, ground-breaking treatment strategy, as currently used medical therapies against glaucoma are limited and may evoke numerous adverse side-effects in patients.

Clinical implications of recent advances in primary open-angle glaucoma genetics

Over the last decade, genetic studies, including genome-wide association studies (GWAS), have accelerated the discovery of genes and genomic regions contributing to primary open-angle glaucoma (POAG), a leading cause of irreversible vision loss. Here, we review the findings of genetic studies of POAG published in English prior to September 2019. In total, 74 genomic regions have been associated at a genome-wide level of significance with POAG susceptibility. Recent POAG GWAS provide not only insight into global and ethnic-specific genetic risk factors for POAG susceptibility across populations of diverse ancestry, but also important functional insights underlying biological mechanisms of glaucoma pathogenesis. In this review, we also summarize the genetic overlap between POAG, glaucoma endophenotypes, such as intraocular pressure and vertical cup-disc ratio (VCDR), and other eye disorders. We also discuss approaches recently developed to increase power for POAG locus discovery and to predict POAG risk. Finally, we discuss the recent development of POAG gene-based therapies and future strategies to treat glaucoma effectively. Understanding the genetic architecture of POAG is essential for an earlier diagnosis of this common eye disorder, predictive testing of at-risk patients, and design of gene-based targeted medical therapies none of which are currently available.

A Social Determinant of Health May Modify Genetic Associations for Blood Pressure: Evidence From a SNP by Education Interaction in an African American Population

African Americans experience the highest burden of hypertension in the United States compared with other groups. Genetic contributions to this complex condition are now emerging in this as well as other populations through large-scale genome-wide association studies (GWAS) and meta-analyses. Despite these recent discovery efforts, relatively few large-scale studies of blood pressure have considered the joint influence of genetics and social determinants of health despite extensive evidence supporting their impact on hypertension. To identify these expected interactions, we accessed a subset of the Vanderbilt University Medical Center (VUMC) biorepository linked to de-identified electronic health records (EHRs) of adult African Americans genotyped using the Illumina Metabochip (n = 2,577). To examine potential interactions between education, a recognized social determinant of health, and genetic variants contributing to blood pressure, we used linear regression models to investigate two-way interactions for systolic and diastolic blood pressure (DBP). We identified a two-way interaction between rs6687976 and education affecting DBP (p = 0.052). Individuals homozygous for the minor allele and having less than a high school education had higher DBP compared with (1) individuals homozygous for the minor allele and high school education or greater and (2) individuals not homozygous for the minor allele and less than a high school education. To our knowledge, this is the first EHR -based study to suggest a gene-environment interaction for blood pressure in African Americans, supporting the hypothesis that genetic contributions to hypertension may be modulated by social factors.