Mutation screen of the cone-specific gene, CLUL1, in 376 patients with age-related macular degeneration

Genome-wide meta-analysis identifies novel loci associated with age-related macular degeneration

Age-related macular degeneration (AMD) is the leading cause of irreversible blindness among the elderly population. To accelerate the understanding of the genetics of AMD, we conducted a meta-analysis of genome-wide association studies (GWAS) combining data from the International AMD Genomics Consortium AMD-2016 GWAS (16,144 advanced AMD cases and 17,832 controls), AMD-2013 GWAS (17,181 cases and 60,074 controls), and new data on 4017 AMD cases and 14,984 controls from Genetic Epidemiology Research on Aging study. We identified 12 novel AMD loci near or within C4BPA-CD55, ZNF385B, ZBTB38, NFKB1, LINC00461, ADAM19, CPN1, ACSL5, CSK, RLBP1, CLUL1, and LBP. We then replicated the associations of the novel loci in independent cohorts, UK Biobank (5860 cases and 126,726 controls) and FinnGen (1266 cases and 47,560 control). In general, the concordance in effect sizes was very high (correlation in effect size estimates 0.89), 11 of 12 novel loci were in the expected direction, 5 were associated with AMD at a nominal significance level, and rs3825991 (near gene RLBP1) after Bonferroni correction. We identified an additional 21 novel genes using a gene-based test. Most of the novel genes are expressed in retinal tissue and could be involved in the pathogenesis of AMD (i.e., complement, inflammation, and lipid pathways). These findings enhance our understanding of the genetic architecture of AMD and shed light on the biological process underlying AMD pathogenesis.

Spatiotemporal transcriptomic divergence across human and macaque brain development

Human nervous system development is an intricate and protracted process that requires precise spatiotemporal transcriptional regulation. We generated tissue-level and single-cell transcriptomic data from up to 16 brain regions covering prenatal and postnatal rhesus macaque development. Integrative analysis with complementary human data revealed that global intraspecies (ontogenetic) and interspecies (phylogenetic) regional transcriptomic differences exhibit concerted cup-shaped patterns, with a late fetal-to-infancy (perinatal) convergence. Prenatal neocortical transcriptomic patterns revealed transient topographic gradients, whereas postnatal patterns largely reflected functional hierarchy. Genes exhibiting heterotopic and heterochronic divergence included those transiently enriched in the prenatal prefrontal cortex or linked to autism spectrum disorder and schizophrenia. Our findings shed light on transcriptomic programs underlying the evolution of human brain development and the pathogenesis of neuropsychiatric disorders.

Investigating the modulation of genetic effects on late AMD by age and sex: Lessons learned and two additional loci

Late-stage age-related macular degeneration (AMD) is the leading cause of visual impairment in the elderly with a complex etiology. The most important non-modifiable risk factors for onset and progression of late AMD are age and genetic risk factors, however, little is known about the interplay between genetics and age or sex. Here, we conducted a large-scale age- and sex-stratified genome-wide association study (GWAS) using 1000 Genomes imputed genome-wide and ExomeChip data (>12 million variants). The data were established by the International Age-related Macular Degeneration Genomics Consortium (IAMDGC) from 16,144 late AMD cases and 17,832 controls. Our systematic search for interaction effects yielded significantly stronger effects among younger individuals at two known AMD loci (near CFH and ARMS2/HTRA1). Accounting for age and gene-age interaction using a joint test identified two additional AMD loci compared to the previous main effect scan. One of these two is a novel AMD GWAS locus, near the retinal clusterin-like protein (CLUL1) gene, and the other, near the retinaldehyde binding protein 1 (RLBP1), was recently identified in a joint analysis of nuclear and mitochondrial variants. Despite considerable power in our data, neither sex-dependent effects nor effects with opposite directions between younger and older individuals were observed. This is the first genome-wide interaction study to incorporate age, sex and their interaction with genetic effects for late AMD. Results diminish the potential for a role of sex in the etiology of late AMD yet highlight the importance and existence of age-dependent genetic effects.

A family-based study of gene variants and maternal folate and choline in neuroblastoma: a report from the Children's Oncology Group

PURPOSE

Neuroblastoma is a childhood cancer of the sympathetic nervous system with embryonic origins. Previous epidemiologic studies suggest maternal vitamin supplementation during pregnancy reduces the risk of neuroblastoma. We hypothesized offspring and maternal genetic variants in folate-related and choline-related genes are associated with neuroblastoma and modify the effects of maternal intake of folate, choline, and folic acid.

METHODS

The Neuroblastoma Epidemiology in North America (NENA) study recruited 563 affected children and their parents through the Children's Oncology Group's Childhood Cancer Research Network. We used questionnaires to ascertain pre-pregnancy supplementation and estimate usual maternal dietary intake of folate, choline, and folic acid. We genotyped 955 genetic variants related to folate or choline using DNA extracted from saliva samples and used a log-linear model to estimate both child and maternal risk ratios and stratum-specific risk ratios for gene-environment interactions.

RESULTS

Overall, no maternal or offspring genotypic results met criteria for a false discovery rate (FDR) Q-value <0.2. Associations were also null for gene-environment interaction with pre-pregnancy vitamin supplementation, dietary folic acid, and folate. FDR-significant gene-choline interactions were found for offspring SNPs rs10489810 and rs9966612 located in MTHFD1L and TYMS, respectively, with maternal choline dietary intake dichotomized at the first quartile.

CONCLUSION

These results suggest that variants related to one-carbon metabolism are not strongly associated with neuroblastoma. Choline-related variants may play a role; however, the functional consequences of the interacting variants are unknown and require independent replication.

Mutation screen of beta-crystallin genes in 274 patients with age-related macular degeneration

PURPOSE

The crystallin family of proteins comprise the main structural proteins of the vertebrate lens and have been classified into alpha-, beta-, and gamma- families. Several of the beta-crystallin proteins have been detected in the retina where they are each localized to different compartments of rod and cone photoreceptors. Functionally, beta-crystallins have been implicated in the protection of the retina from intense light exposure. Two members of the beta-crystallins, CRYBB1 and CRYBB2, have been identified in drusen preparations isolated from the retina of donor eyes of patients with age-related macular degeneration (AMD), the leading cause of blindness in the elderly population of developed countries. We therefore investigated CRYBB1 and CRYBB2 as candidate genes for AMD in 274 unrelated patients.

RESULTS

A mutation screen of the entire coding region of the CRYBB1gene uncovered eight sequence variations, including three missense changes, two intronic changes and three isocoding changes. A mutation screen of the entire coding region of the CRYBB2 gene uncovered three sequence variations, one isocoding change and two intronic changes.

CONCLUSIONS

Although variant alleles of the CRYBB1 and CRYBB2 genes were found, none are considered pathogenic.

Protective effects of myricetin and related flavonols against A2E and light mediated-cell death in bovine retinal primary cell culture

The present study was performed to investigate the effect of flavonols, namely myricetin and structurally related quercetin and kaempferol against A2E and blue light-induced photoreceptors death in primary retinal cell cultures. Primary retinal cell cultures were prepared from bovine retinas. Fourteen-day-old cultures were pretreated with different concentrations of myricetin, quercetin, kaempferol (1-40 microM) for 24 h, then treated with 30 microM of A2E or exposed to blue-actinic light for 20 h. Green nucleic acid stain assay was used to evaluate cell death. Photoreceptor and bipolar cells were immunolabeled with specific antibodies and were counted using automated microscope imaging and image-based cell counting software. Twenty hours exposure to blue light induced approximately 75% death of photoreceptors in bovine retinal cell cultures. Myricetin protected 100% of photoreceptors against blue-light-mediated damage with an EC(50) of 9+/-0.7 microM. Quercetin resulted in a maximum of 15% protection against light damage, and kaempferol was inactive. A2E induced photoreceptor and bipolar cell death in a concentration-dependent manner with EC(50) of 25 microM for photoreceptors and 31 microM for bipolar cells. Myricetin, quercetin and kaempferol protected against A2E-induced photoreceptors and bipolar cells death with EC(50) values of 2+/-0.3 microM, 2+/-0.3 microM, 5+/-0.09 microM and 0.8+/-0.07 microM, 0.44+/-0.06 microM, 1+/-0.4 microM, respectively. Caspase-3 inhibitor (Z-DEVD-fmk) protected 42% photoreceptors and 57% bipolar cells from A2E toxicity. In contrast, this inhibitor had no effect against light-induced photoreceptor damage. Despite the poor activity of quercetin and the inactivity of kaempferol against blue light, myricetin, quercetin and kaempferol exhibited approximately 100% protection against A2E toxicity. This suggests that light- and A2E-induced cell deaths are mediated through different pathways. These results suggest that myricetin functions as potent and effective neuroprotective agent for photoreceptor cells against A2E and light damage.