Differentially Expressed Genes in Atopic Dermatitis: Bioinformatics analysis of pooled microarray gene expression datasets in Gene Expression Omnibus

Introduction: Atopic dermatitis (AD) is a chronic and refractory inflammatory skin disease characterized by relapsing eczematous and pruritic skin lesions. Understanding the specific gene expression patterns associated with AD is crucial for advancing diagnosis and targeted treatment development. Using bioinformatics methods, candidate genes and biological pathways involved in AD pathogenesis were identified based on gene expression profiles in the Gene Expression Omnibus (GEO) database. Materials and Methods: A comprehensive analysis of four pooled transcriptomic datasets obtained from the Gene Expression Omnibus (GEO) database were conducted. Differential gene expression analysis was performed using the GEO2R. The differentially expressed genes (DEGs) between lesion skin of AD patients and normal skin of individuals were analyzed using the Gene Ontology (GO) term enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, and protein-protein interaction (PPI) network to explore the functional roles of these genes. Results: Among the patient-level gene expression datasets, we identified 133 shared DEGs, consisting of 48 upregulated genes and 85 downregulated genes. GO analyses revealed these DEGs to be significantly enriched in biological processes including inflammatory responses, cytokine-mediated signaling pathway. These DEGs were also enriched in the KEGG pathway, including viral protein interaction with cytokine and cytokine receptor, C-type lectin receptor signaling pathway, cytokine-cytokine receptor interaction, JAK-STAT signaling pathway, and Adipocytokine signaling pathway. Conclusion: By comparing with other studies using the same method, we found that in addition to the already confirmed pathways such as inflammatory response, different studies have found changes in different hub genes and metabolic pathways, which prompts us to develop individualized treatments for AD

Differentially Expressed Genes in Atopic Dermatitis: Bioinformatics analysis of pooled microarray gene expression datasets in Gene Expression Omnibus

Introduction: Atopic dermatitis (AD) is a chronic and refractory inflammatory skin disease characterized by relapsing eczematous and pruritic skin lesions. Understanding the specific gene expression patterns associated with AD is crucial for advancing diagnosis and targeted treatment development. Using bioinformatics methods, candidate genes and biological pathways involved in AD pathogenesis were identified based on gene expression profiles in the Gene Expression Omnibus (GEO) database. Materials and Methods: A comprehensive analysis of four pooled transcriptomic datasets obtained from the Gene Expression Omnibus (GEO) database were conducted. Differential gene expression analysis was performed using the GEO2R. The differentially expressed genes (DEGs) between lesion skin of AD patients and normal skin of individuals were analyzed using the Gene Ontology (GO) term enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, and protein-protein interaction (PPI) network to explore the functional roles of these genes. Results: Among the patient-level gene expression datasets, we identified 133 shared DEGs, consisting of 48 upregulated genes and 85 downregulated genes. GO analyses revealed these DEGs to be significantly enriched in biological processes including inflammatory responses, cytokine-mediated signaling pathway. These DEGs were also enriched in the KEGG pathway, including viral protein interaction with cytokine and cytokine receptor, C-type lectin receptor signaling pathway, cytokine-cytokine receptor interaction, JAK-STAT signaling pathway, and Adipocytokine signaling pathway. Conclusion: By comparing with other studies using the same method, we found that in addition to the already confirmed pathways such as inflammatory response, different studies have found changes in different hub genes and metabolic pathways, which prompts us to develop individualized treatments for AD

CERKL regulates autophagy via the NAD-dependent deacetylase SIRT1

<p>Macroautophagy/autophagy is an important intracellular mechanism for the maintenance of cellular homeostasis. Here we show that the <i>CERKL</i> (ceramide kinase like) gene, a retinal degeneration (RD) pathogenic gene, plays a critical role in regulating autophagy by stabilizing SIRT1. <i>In vitro</i> and <i>in vivo</i>, suppressing CERKL results in impaired autophagy. SIRT1 is one of the main regulators of acetylation/deacetylation in autophagy. In CERKL-depleted retinas and cells, SIRT1 is downregulated. ATG5 and ATG7, 2 essential components of autophagy, show a higher degree of acetylation in CERKL-depleted cells. Overexpression of SIRT1 rescues autophagy in CERKL-depleted cells, whereas CERKL loses its function of regulating autophagy in SIRT1-depleted cells, and overexpression of CERKL upregulates SIRT1. Finally, we show that CERKL directly interacts with SIRT1, and may regulate its phosphorylation at Ser27 to stabilize SIRT1. These results show that CERKL is an important regulator of autophagy and it plays this role by stabilizing the deacetylase SIRT1.</p

Complete mitochondrial genomes of Callospermophilus lateralis and Urocitellus richardsonii (Rodentia: Sciuridae)

The complete mitochondrial genomes of Callospermophilus lateralis and Urocitellus richardsonii (Rodentia: Sciuridae) were sequenced to analyze the gene arrangement and discuss the phylogenetic relationship of species within the Xerinae. The genomes are circular molecules of 16,457 bp and 16,460 bp in length, respectively, including the 37 genes typically found in other squirrels. The AT content of the overall base composition is 63.2% for both species. The length of control region for C. lateralis is 1009 bp with 62.8% AT content; the corresponding values for U. richardsonii are 1012 bp and 62.0% AT content. In BI and ML phylogenetic trees, the monophyly of the family Sciuridae and subfamilies Callosciurinae and Sciurinae are well supported, but the monophyly of Xerinae is not supported. Within the Xerinae, the relationship of (Tamias sibiricus+(Callospermophilus lateralis+(Marmota himalayana+(Urocitellus richardsonii+(Ictidomys tridecemlineatus+(Cynomys leucurus+Cynomys ludovicianus)))))) is well supported. However, Tamiops swinhoei (Xerinae) within the subfamily Callosciurinae is a clade sister to Dremomys rufigenis (Callosciurinae). Spermophilus dauricus (Xerinae) within subfamily Sciurinae is a sister clade to Sciurus vulgaris (Sciurinae). The monophyly of Xerinae is failed to support in this study

Tulp1 deficiency causes early-onset retinal degeneration through affecting ciliogenesis and activating ferroptosis in zebrafish

Mutations in TUB-like protein 1 (TULP1) are associated with severe early-onset retinal degeneration in humans. However, the pathogenesis remains largely unknown. There are two homologous genes of TULP1 in zebrafish, namely tulp1a and tulp1b. Here, we generated the single knockout (tulp1a(−/−) and tulp1b(−/−)) and double knockout (tulp1-dKO) models in zebrafish. Knockout of tulp1a resulted in the mislocalization of UV cone opsins and the degeneration of UV cones specifically, while knockout of tulp1b resulted in mislocalization of rod opsins and rod-cone degeneration. In the tulp1-dKO zebrafish, mislocalization of opsins was present in all types of photoreceptors, and severe degeneration was observed at a very early age, mimicking the clinical manifestations of TULP1 patients. Photoreceptor cilium length was significantly reduced in the tulp1-dKO retinas. RNA-seq analysis showed that the expression of tektin2 (tekt2), a ciliary and flagellar microtubule structural component, was downregulated in the tulp1-dKO zebrafish. Dual-luciferase reporter assay suggested that Tulp1a and Tulp1b transcriptionally activate the promoter of tekt2. In addition, ferroptosis might be activated in the tulp1-dKO zebrafish, as suggested by the up-regulation of genes related to the ferroptosis pathway, the shrinkage of mitochondria, reduction or disappearance of mitochondria cristae, and the iron and lipid droplet deposition in the retina of tulp1-dKO zebrafish. In conclusion, our study establishes an appropriate zebrafish model for TULP1-associated retinal degeneration and proposes that loss of TULP1 causes defects in cilia structure and opsin trafficking through the downregulation of tekt2, which further increases the death of photoreceptors via ferroptosis. These findings offer insight into the pathogenesis and clinical treatment of early-onset retinal degeneration

Rod genesis driven by mafba in an nrl knockout zebrafish model with altered photoreceptor composition and progressive retinal degeneration

Neural retina leucine zipper (NRL) is an essential gene for the fate determination and differentiation of the precursor cells into rod photoreceptors in mammals. Mutations in NRL are associated with the autosomal recessive enhanced S-cone syndrome and autosomal dominant retinitis pigmentosa. However, the exact role of Nrl in regulating the development and maintenance of photoreceptors in the zebrafish (Danio rerio), a popular animal model used for retinal degeneration and regeneration studies, has not been fully determined. In this study, we generated an nrl knockout zebrafish model via the CRISPR-Cas9 technology and observed a surprising phenotype characterized by a reduced number, but not the total loss, of rods and over-growth of green cones. We discovered two waves of rod genesis, nrl-dependent and -independent at the embryonic and post-embryonic stages, respectively, in zebrafish by monitoring the rod development. Through bulk and single-cell RNA sequencing, we characterized the gene expression profiles of the whole retina and each retinal cell type from the wild type and nrl knockout zebrafish. The over-growth of green cones and mis-expression of green-cone-specific genes in rods in nrl mutants suggested that there are rod/green-cone bipotent precursors, whose fate choice between rod versus green-cone is controlled by nrl. Besides, we identified the mafba gene as a novel regulator of the nrl-independent rod development, based on the cell-type-specific expression patterns and the retinal phenotype of nrl/mafba double-knockout zebrafish. Gene collinearity analysis revealed the evolutionary origin of mafba and suggested that the function of mafba in rod development is specific to modern fishes. Furthermore, the altered photoreceptor composition and abnormal gene expression in nrl mutants caused progressive retinal degeneration and subsequent regeneration. Accordingly, this study revealed a novel function of the mafba gene in rod development and established a working model for the developmental and regulatory mechanisms regarding the rod and green-cone photoreceptors in zebrafish

StateLens: A Reverse Engineering Solution for Making Existing Dynamic Touchscreens Accessible

Blind people frequently encounter inaccessible dynamic touchscreens in their everyday lives that are difficult, frustrating, and often impossible to use independently. Touchscreens are often the only way to control everything from coffee machines and payment terminals, to subway ticket machines and in-flight entertainment systems. Interacting with dynamic touchscreens is difficult non-visually because the visual user interfaces change, interactions often occur over multiple different screens, and it is easy to accidentally trigger interface actions while exploring the screen. To solve these problems, we introduce StateLens - a three-part reverse engineering solution that makes existing dynamic touchscreens accessible. First, StateLens reverse engineers the underlying state diagrams of existing interfaces using point-of-view videos found online or taken by users using a hybrid crowd-computer vision pipeline. Second, using the state diagrams, StateLens automatically generates conversational agents to guide blind users through specifying the tasks that the interface can perform, allowing the StateLens iOS application to provide interactive guidance and feedback so that blind users can access the interface. Finally, a set of 3D-printed accessories enable blind people to explore capacitive touchscreens without the risk of triggering accidental touches on the interface. Our technical evaluation shows that StateLens can accurately reconstruct interfaces from stationary, hand-held, and web videos; and, a user study of the complete system demonstrates that StateLens successfully enables blind users to access otherwise inaccessible dynamic touchscreens.Comment: ACM UIST 201

The splicing factor DHX38 enables retinal development through safeguarding genome integrity

DEAH-Box Helicase 38 (DHX38) is a pre-mRNA splicing factor and also a disease-causing gene of autosomal recessive retinitis pigmentosa (arRP). The role of DHX38 in the development and maintenance of the retina remains largely unknown. In this study, by using the dhx38 knockout zebrafish model, wedemonstrated that Dhx38 deficiency causes severe differentiation defects and apoptosis of retinal progenitor cells (RPCs) through disrupted mitosis and increased DNA damage. Furthermore, we found a significant accumulation of R-loops in the dhx38-deficient RPCs and human cell lines. Finally, we found that DNA replication stress is the prerequisite for R-loop-induced DNA damage in the DHX38 knockdown cells. Taken together, our study demonstrates a necessary role of DHX38 in the development of retina and reveals a DHX38/R-loop/replication stress/DNA damage regulatory axis that is relatively independent of the known functions of DHX38 in mitosis control