Gene expression in response to optical defocus of opposite signs reveals bidirectional mechanism of visually guided eye growth
Fig 3
Myopic optical defocus induces large-scale changes in gene expression and signaling pathways in the retina.
RNA-seq analysis of differential gene expression in two groups of marmosets exposed to +5D-lens-imposed myopic defocus for 10 days or 5 weeks. (A and E) Volcano plots showing differentially expressed genes. (B and F) Hierarchical clustering results showing that differentially expressed genes are organized into two clusters, i.e., genes that are down-regulated and genes that are up-regulated in the retina exposed to defocus. Right, +5D-lens-treated eye. Left, plano-lens-treated control eye. Letters and numbers above each column of the hierarchical clustering results indicate animal IDs. (C and G) Gene ontology analysis results showing biological processes affected by the differentially expressed genes. Vertical yellow line indicates P = 0.05. (D and H) Canonical signaling pathways affected by the differentially expressed genes. Vertical yellow line indicates P = 0.05. Z-score shows activation or suppression of the corresponding pathways. See S3, S4, S7, S8, S11, S12, S15, and S16 Tables for details. CNTF, ciliary neurotrophic factor; CREB, cAMP responsive element binding protein; EIF2, eukaryotic translation initiation factor 2; eIF4, eukaryotic initiation factor 4; ERK, extracellular signal-regulated kinase; iNOS, inducible nitric oxide synthase; JAK, Janus kinase; JNK, c-Jun N-terminal kinase; MAPK, mitogen-activated protein kinase; mTOR, mammalian target of rapamycin; NAD, nicotinamide adenine dinucleotide; NGF, nerve growth factor; p70S6K, ribosomal protein S6 kinase; RANK, receptor activator of nuclear factor kappa-B; RNA-seq, massive parallel RNA sequencing; SAPK, stress-activated protein kinase; Stat, signal transducer and activator of transcription protein.