A genome-wide association study reveals a substantial genetic basis underlying the Ebbinghaus illusion.

The Ebbinghaus illusion (EI) is an optical illusion of relative size perception that reflects the contextual integration ability in the visual modality. The current study investigated the genetic basis of two subtypes of EI, EI overestimation, and EI underestimation in humans, using quantitative genomic analyses. A total of 2825 Chinese adults were tested on their magnitudes of EI overestimation and underestimation using the method of adjustment, a standard psychophysical protocol. Heritability estimation based on common single nucleotide polymorphisms (SNPs) revealed a moderate heritability (34.3%) of EI overestimation but a nonsignificant heritability of EI underestimation. A meta-analysis of two phases (phase 1: n = 1986, phase 2: n = 839) of genome-wide association study (GWAS) discovered 1969 and 58 SNPs reaching genome-wide significance for EI overestimation and EI underestimation, respectively. Among these SNPs, 55 linkage-disequilibrium-independent SNPs were associated with EI overestimation in phase 1 with genome-wide significance and their associations could be confirmed in phase 2 cohort. Gene-based analyses found seven genes to be associated with EI overestimation at the genome-wide level, two from meta-analysis, and five from classical two-stage analysis. Overall, this study provided consistent evidence for a substantial genetic basis of the Ebbinghaus illusion.

Genomic Analyses of Visual Cognition: Perceptual Rivalry and Top-Down Control.

Visual cognition in humans has traditionally been studied with cognitive behavioral methods and brain imaging, but much less with genetic methods. Perceptual rivalry, an important phenomenon in visual cognition, is the spontaneous perceptual alternation that occurs between two distinct interpretations of a physically constant visual stimulus (e.g., binocular rivalry stimuli) or a perceptually ambiguous stimulus (e.g., the Necker cube). The switching rate varies dramatically across individuals and can be voluntarily modulated by observers. Here, we adopted a genomic approach to systematically investigate the genetics underlying binocular rivalry, Necker cube rivalry and voluntary modulation of Necker cube rivalry in young Chinese adults (Homo sapiens, 81% female, 20 ± 1 years old) at multiple levels, including common single nucleotide polymorphism (SNP)-based heritability estimation, SNP-based genome-wide association study (GWAS), gene-based analysis, and pathway analysis. We performed a pilot GWAS in 2441 individuals and replicated it in an independent cohort of 943 individuals. Common SNP-based heritability was estimated to be 25% for spontaneous perceptual rivalry. SNPs rs184765639 and rs75595941 were associated with voluntary modulation, and imaging data suggested genotypic difference of rs184765639 in the surface area of the left caudal-middle frontal cortex. Additionally, converging evidence from multilevel analyses associated genes such as PRMT1 with perceptual switching rate, and MIR1178 with voluntary modulation strength. In summary, this study discovered specific genetic contributions to perceptual rivalry and its voluntary modulation in human beings. These findings may promote our understanding of psychiatric disorders, as perceptual rivalry is a potential psychiatric biomarker.SIGNIFICANCE STATEMENT Perceptual rivalry is an important visual phenomenon in which our perception of a physically constant visual input spontaneously switches between two different states. There are individual variations in perceptual switching rate and voluntary modulation strength. Our genomic analyses reveal several loci associated with these two kinds of variation. Because perceptual rivalry is thought to be relevant to and potentially an endophenotype for psychiatric disorders, these results may help understand not only visual cognition, but also psychiatric disorders.

Nature vs. nurture in human sociality: multi-level genomic analyses of social conformity.

Social conformity is fundamental to human societies and has been studied for more than six decades, but our understanding of its mechanisms remains limited. Individual differences in conformity have been attributed to social and cultural environmental influences, but not to genes. Here we demonstrate a genetic contribution to conformity after analyzing 1,140 twins and single-nucleotide polymorphism (SNP)-based studies of 2,130 young adults. A two-step genome-wide association study (GWAS) revealed replicable associations in 9 genomic loci, and a meta-analysis of three GWAS with a sample size of ~2,600 further confirmed one locus, corresponding to the NAV3 (Neuron Navigator 3) gene which encodes a protein important for axon outgrowth and guidance. Further multi-level (haplotype, gene, pathway) GWAS strongly associated genes including NAV3, PTPRD (protein tyrosine phosphatase receptor type D), ARL10 (ADP ribosylation factor-like GTPase 10), and CTNND2 (catenin delta 2), with conformity. Magnetic resonance imaging of 64 subjects shows correlation of activation or structural features of brain regions with the SNPs of these genes, supporting their functional significance. Our results suggest potential moderate genetic influence on conformity, implicate several specific genetic elements in conformity and will facilitate further research on cellular and molecular mechanisms underlying human conformity.

Impaired Autophagy Causes Severe Corneal Neovascularization.

PURPOSE: To investigate the role of macrophage autophagy in the process of corneal neovascularization (CNV). METHODS: In vivo, mice CNV was induced by alkali injury and compared with rapamycin-treated alkaline burn mice. Western blot was used to determine the autophagic status of the macrophages. We quantified the levels of macrophage polarization markers (CD86, INOS, CD163, CD206) by RT-qPCR and measured inflammatory factors through ELISA (IL-6 and TNF-α) in the early phase after injury. In vitro, the human umbilical vein endothelial cells (HUVECs) were co-cultured with macrophage-conditioned medium (MCM) induced by the THP-1 cell line to simulate the neovascular microenvironment. The vascularization capacity of HUVECs was examined using the CCK-8 assay kit, tube formation assay, and scratch wound-healing assay. RESULTS: In vivo, the mRNA expression of Beclin-1 and ATG5 was increased, together with the upregulation of M1 macrophage markers (CD86 and INOS) in corneas after early alkali injury. The area of CNV is effectively relieved in the rapamycin-treated mice. In vitro, upregulation of autophagy level by pretreatment with 3-methyladenine (3-MA) could increase the mRNA expression of the M1 markers. Macrophage-conditioned medium with impaired autophagy contains more IL-6 and TNF-α compared to the M1 macrophage-conditioned medium, promoting HUVEC proliferation, migration, and tube formation capacity. Enhancing the autophagy level with rapamycin (RAPA) could reverse this phenomenon. CONCLUSIONS: Impaired autophagy promoted macrophage polarization toward M1 type and increased the expression of IL-6 and TNF-α, which led to severe CNV. Using the autophagy activator (RAPA) could effectively alleviate CNV by promoting autophagy.

Potential Factors of Corneal Endothelial Cells for Progression in Children with Uveitis.

OBJECTIVE: To observe the morphological changes and abnormal structure of corneal endothelial cells in children with uveitis, to analyze the related factors affecting the morphological changes of corneal endothelial cells, and to explore the clinical application of a corneal endothelial microscope in children with uveitis. METHODS: The corneal endothelial cells of 70 patients with uveitis were photographed with the Topcon SP-3000 noncontact corneal endothelial microscope, and the corneal endothelial cell density (CD), average cell area (AVE), coefficient of variation of the cell area (CV), and percentage of hexagonal cells (PHC) were measured with the IMAGEnet system. Twenty-eight patients (56 eyes) with monocular uveitis were selected, with the affected eyes (28 eyes) as the experimental group and the contralateral healthy eyes (28 eyes) as the control group. The corneal endothelial cell parameters between the two groups were statistically analyzed. The parameters of corneal endothelial cells in 70 children with uveitis were compared, and the effects of the course of the disease, inflammatory cells in the anterior chamber, and posterior corneal deposition (KP) on the parameters of corneal endothelial cells were analyzed. RESULTS: There are four abnormal forms of the corneal endothelium in children with uveitis: enlarged cell area gap, irregular cell shape, blurred intercellular space, and cell loss. KP showed irregular high reflective white spots in the corneal endothelial microscope images, surrounded by dark areas, and existed in all the eyes with dusty KP found in slit lamp examination and a small number of eyes without obvious KP. Comparing the corneal endothelial cell parameters between the experimental group and the control group, it was found that the corneal endothelial CD and PHC of the former were lower than those of the latter, and the difference was statistically significant (P < 0.001 and P = 0.018, respectively). The AVE and CA of the former were higher than those of the latter (P = 0.013 and P = 0.046, respectively). The corneal endothelial cell density of the eyes with a course of the disease of more than 1 year was lower than that of the eyes with a course of the disease less than 1 year, the coefficient of variation of the corneal endothelial cell area of the eyes with KP was higher than that of the eyes without KP, and the difference was statistically significant (P = 0.003 and P = 0.030, respectively). CONCLUSION: Corneal endothelial microscopy is one of the important methods for the detection of uveitis with high sensitivity. The change of morphological parameters of corneal endothelial cells is one of the important indexes to assist in the diagnosis of uveitis and can be further promoted in ophthalmological examination.

[VEGF short hairpin RNA expression plasmid blocks VEGF expression in rat vascular endothelial cell and inhibits rat corneal neovascularization].

OBJECTIVE: To investigate RNA interference in rat corneal neovascularization and vascular endothelial cells of vascular endothelial growth factor expression and its mechanism. METHODS: In empirical study short hairpin RNA (shRNA) targeting VEGF mRNA was designed and synthesized and VEGF shRNA eukaryotic plasmids were transfected into EC with Lipofectamine 2000 transfection system. Expression of VEGF mRNA and protein in transfected cells was detected by RT-PCR and Western blot. Twenty SD rats were randomized into two groups by randomly Design, experimental group were 10 and 10 in the control group. CNV was induced in vivo by alkaline cauterization of the central cornea, the rats received subconjunctival injection of VEGF shRNA3 plasmid. Then corneal neovascularization was evaluated with microscope. After seven days, VEGF mRNA and protein was determined by RT-PCR and Western blot respectively. RESULTS: VEGF shRNA expression plasmids were successfully constructed and identified by restriction enzyme and sequence analysis. VEGF expression was down regulated by VEGF shRNA1, 2, 3 plasmids, and VEGF shRNA3 plasmid showed stronger inhibitory effect. The inhibitory effects of VEGF mRNA and protein are 68.92% and 66.22%. At the 3, 5 and 7 days after alkali cauterization, the CNV length of the experimental group was obviously decreased comparing with the control group, the difference between two groups has statistics meaning (F=402.700, P=0.000); the CNV area of the experimental group was also obviously decreased comparing with the control group, the difference between two groups has statistics meaning (F=402.700, P=0.000); the VEGF mRNA and protein in corneas was also decreased, the inhibitory effects of which are 41.84% and 41.86%. CONCLUSIONS: RNAi significantly suppresses expression of VEGF in rat EC in vitro. In vivo, subconjunctival delivery of VEGF shRNA3 plasmid suppresses injury-induced VEGF expression and CNV.

Heritability of human visual contour integration-an integrated genomic study.

Contour integration, a key visual function to deal with occlusion and discontinuity in natural scenes, is essential to human survival. However, individuals are not equally well equipped with this ability. In particular, contour integration deficiencies are commonly detected in patients with mental disorders, especially schizophrenia. To understand the underlying sources of these individual differences, the current study investigated the genetic basis of contour integration in humans. A total of 2619 normal participants were tested on their ability to detect continuous contours embedded in a cluttered background. Quantitative genomic analysis was performed, involving heritability estimation based on single nucleotide polymorphisms (SNPs) and association testing at SNP, gene, and pathway levels. Heritability estimation showed that common SNPs contributed 49.5% (standard error of the mean = 15.6%) of overall phenotypic variation, indicating moderate heritability of contour integration. Two-stage genome-wide association analysis (GWAS) detected four SNPs reaching genome-wide significance in the discovery test (N = 1931) but not passing the replication test (N = 688). Gene-level analysis further revealed a significant genome-wide association of a microRNA-encoding gene MIR1178 in both the discovery and replication cohorts. Another gene poly(A)-binding protein nuclear 1 like, cytoplasmic (PABPN1L) showed suggestive significance in the discovery cohort (p < 1 × 10-4) and was replicated in the replication cohort (p = 0.009). The pathway analysis did not detect any significant pathway. Taken together, this study identified significant gene associations with contour integration and provided support for a genetic transmission of the ability to perceive continuous contours in the environment.

Multi-level genomic analyses suggest new genetic variants involved in human memory.

Development of high-throughput genotyping platforms provides an opportunity to identify new genetic elements related to complex cognitive functions. Taking advantage of multi-level genomic analysis, here we studied the genetic basis of human short-term (STM, n = 1623) and long-term (LTM, n = 1522) memory functions. Heritability estimation based on single nucleotide polymorphism showed moderate (61%, standard error 35%) heritability of short-term memory but almost zero heritability of long-term memory. We further performed a two-step genome-wide association study, but failed to find any SNPs that could pass genome-wide significance and survive replication at the same time. However, suggestive significance for rs7011450 was found in the shared component of the two STM tasks. Further inspections on its nearby gene zinc finger and at-hook domain containing and SNPs around this gene showed suggestive association with STM. In LTM, a polymorphism within branched chain amino acid transaminase 2 showed suggestive significance in the discovery cohort and has been replicated in another independent population of 1862. Furthermore, we performed a pathway analysis based on the current genomic data and found pathways including mTOR signaling and axon guidance significantly associated with STM capacity. These findings warrant further replication in other larger populations.