Expression of CXCL6 and BBS5 that may be glaucoma relevant genes is regulated by PITX2

CXCL6: A potential therapeutic target for inflammation and cancer

Chemokines were originally defined as cytokines that affect the movement of immune cells. In recent years, due to the increasing importance of immune cells in the tumor microenvironment (TME), the role of chemokines has changed from a single "chemotactic agent" to a key factor that can regulate TME and affect the tumor phenotype. CXCL6, also known as granulocyte chemoattractant protein-2 (GCP-2), can recruit neutrophils to complete non-specific immunity in the process of inflammation. Cancer-related genes and interleukin family can promote the abnormal secretion of CXCL6, which promotes tumor growth, metastasis, epithelial mesenchymal transformation (EMT) and angiogenesis in the TME. CXCL6 also has a role in promoting fibrosis and tissue damage repair. In this review, we focus on the regulatory network affecting CXCL6 expression, its role in the progress of inflammation and how it affects tumorigenesis and progression based on the TME, in an attempt to provide a potential target for the treatment of diseases such as inflammation and cancer.

Investigation of VGLL3 and sub-target genes in the aetiology of paediatric acute appendicitis: a prospective case-control study

PURPOSE

Vestigial like family member 3 (VGLL3) and its sub-target genes show considerable transcriptomic overlap in terms of several autoimmune and inflammatory diseases. Herein, we investigated the role of VGLL3 rs13074432 polymorphism and its sub-target genes in the aetiology of acute appendicitis (AA).

METHODS

In this prospective case-control study, we included 250 patients (age, 0-18 years) who underwent appendectomy with the diagnosis of AA (patient group; blood and appendix tissue samples) and 200 healthy children (control group; only blood samples) without appendectomy. ELISA method was used for protein-level detection of VGLL3 and sub-target genes expression change in obtained tissue samples, and real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR) was used for mRNA level detection. Genotyping analyses were performed on DNA samples isolated from blood using TaqMan SNP genotyping test.

RESULTS

The frequency of TT variant genotype (p < 0.001) and T allele (p = 0.002) showed a significant decrease in the patient group compared with the control group. No significant correlation was observed between the expression of VGLL3 in the appendiceal tissue and patient clinical and demographic data (p > 0.050).

CONCLUSION

This study revealed that the VGLL3 gene and its sub-target genes are associated with AA aetiology.

Insights into the regulatory molecules involved in glaucoma pathogenesis

Glaucoma is an important cause of irreversible blindness, characterized by optic nerve anomalies. Increased intraocular pressure (IOP) and aging are major risk factors. Retinal ganglion cells and trabecular meshwork cells are certainly involved in the etiology of glaucoma. Glaucoma is usually a complex disease, and various genes and functions may contribute to its etiology. Among these may be genes that encode regulatory molecules. In this review, regulatory molecules including 18 transcription factors (TFs), 195 microRNAs (miRNAs), 106 long noncoding RNAs (lncRNAs), and two circular RNAs (circRNAs) that are reasonable candidates for having roles in glaucoma pathogenesis are described. The targets of the regulators are reported. Glaucoma-related features including apoptosis, stress responses, immune functions, ECM properties, IOP, and eye development are affected by the targeted genes. The targeted genes that are frequently targeted by multiple regulators most often affect apoptosis and the related features of cell death and cell survival. BCL2, CDKN1A, and TP53 are among the frequent targets of three types of glaucoma-relevant regulators, TFs, miRNAs, and lncRNAs. TP53 was itself identified as a glaucoma-relevant TF. Several of the glaucoma-relevant TFs are themselves among frequent targets of regulatory molecules, which is consistent with existence of a complex network involved in glaucoma pathogenesis.

The Primary Cilium as a Therapeutic Target in Ocular Diseases

Primary cilia are microtubule-based cellular structures located on the surfaces of most mammalian cells and play important roles in detecting external stimuli, signal transduction, and cell cycle regulation. Primary cilia are also present in several structures of the eye, and their abnormal development or dysfunction can cause various ocular diseases. The rapid development of proteomics and metabolomics technologies have helped in the identification of many ocular disease-related proteins, some of which are dysregulated in primary cilia. This review focuses on ciliary dysregulation in a number of ocular diseases and discusses the potential of targeting primary cilia in gene and stem cell therapy for these diseases.

Identification of genes involved in glaucoma pathogenesis using combined network analysis and empirical studies

Glaucoma is a leading cause of blindness. We aimed in this study to identify genes that may make subtle and cumulative contributions to glaucoma pathogenesis. To this end, we identified molecular interactions and pathways that include transcription factors (TFs) FOXC1, PITX2, PAX6 and NFKB1 and various microRNAs including miR-204 known to have relevance to trabecular meshwork (TM) functions and/or glaucoma. TM tissue is involved in glaucoma pathogenesis. In-house microarray transcriptome results and data sources were used to identify target genes of the regulatory molecules. Bioinformatics analyses were done to filter TM and glaucoma relevant genes. These were submitted to network-creating softwares to define interactions, pathways and a network that would include the genes. The network was stringently scrutinized and minimized, then expanded by addition of microarray data and data on TF and microRNA-binding sites. Selected features of the network were confirmed by empirical studies such as dual luciferase assays, real-time PCR and western blot experiments and apoptosis assays. MYOC, WDR36, LTPBP2, RHOA, CYP1B1, OPA1, SPARC, MEIS2, PLEKHG5, RGS5, BBS5, ALDH1A1, NOMO2, CXCL6, FMNL2, ADAMTS5, CLOCK and DKK1 were among the genes included in the final network. Pathways identified included those that affect ECM properties, IOP, ciliary body functions, retinal ganglion cell viability, apoptosis, focal adhesion and oxidative stress response. The identification of many genes potentially involved in glaucoma pathology is consistent with its being a complex disease. The inclusion of several known glaucoma-related genes validates the approach used.

Genetic association and differential expression of PITX2 with acute appendicitis

Appendicitis affects 9% of Americans and is the most common diagnosis requiring hospitalization of both children and adults. We performed a genome-wide association study of self-reported appendectomy with 18,773 affected adults and 114,907 unaffected adults of European American ancestry. A significant association with appendectomy was observed at 4q25 near the gene PITX2 (rs2129979, p value = 8.82 × 10-14) and was replicated in an independent sample of Caucasians (59 affected, 607 unaffected; p value = 0.005). Meta-analysis of the associated variant across our two cohorts and cohorts from Iceland and the Netherlands (in which this association had previously been reported) showed strong cumulative evidence of association (OR = 1.12; 95% CI 1.09-1.14; p value = 1.81 × 10-23) and some evidence for effect heterogeneity (p value = 0.03). Eight other loci were identified at suggestive significance in the discovery GWAS. Associations were followed up by measuring gene expression across resected appendices with varying levels of inflammation (N = 75). We measured expression of 27 genes based on physical proximity to the GWAS signals, evidence of being targeted by eQTLs near the signals according to RegulomeDB (score = 1), or both. Four of the 27 genes (including PITX2) showed significant evidence (p values < 0.0033) of differential expression across categories of appendix inflammation. An additional ten genes showed nominal evidence (p value < 0.05) of differential expression, which, together with the significant genes, is more than expected by chance (p value = 6.6 × 10-12). PITX2 impacts morphological development of intestinal tissue, promotes an anti-oxidant response, and its expression correlates with levels of intestinal bacteria and colonic inflammation. Further studies of the role of PITX2 in appendicitis are warranted.

Circular RNAs profiling in the cystathionine-β-synthase mutant mouse reveals novel gene targets for hyperhomocysteinemia induced ocular disorders

Cystathionine-β-synthase (CBS) gene encodes L-serine hydrolyase which catalyzes β-reaction to condense serine with homocysteine (Hcy) by pyridoxal-5'-phosphate helps to form cystathionine which in turn is converted to cysteine. CBS resides at the intersection of transmethylation, transsulfuration, and remethylation pathways, thus lack of CBS fundamentally blocks Hcy degradation; an essential step in glutathione synthesis. Redox homeostasis, free-radical detoxification and one-carbon metabolism (Methionine-Hcy-Folate cycle) require CBS and its deficiency leads to hyperhomocysteinemia (HHcy) causing retinovascular thromboembolism and eye-lens dislocation along with vascular cognitive impairment and dementia. HHcy results in retinovascular, coronary, cerebral and peripheral vessels' dysfunction and how it causes metabolic dysregulation predisposing patients to serious eye conditions remains unknown. HHcy orchestrates inflammation and redox imbalance via epigenetic remodeling leading to neurovascular pathologies. Although circular RNAs (circRNAs) are dominant players regulating their parental genes' expression dynamics, their importance in ocular biology has not been appreciated. Progress in gene-centered analytics via improved microarray and bioinformatics are enabling dissection of genomic pathways however there is an acute under-representation of circular RNAs in ocular disorders. This study undertook circRNAs' analysis in the eyes of CBS deficient mice identifying a pool of 12532 circRNAs, 74 exhibited differential expression profile, _∼27% were down-regulated while most were up-regulated (_∼73%). Findings also revealed several microRNAs that are specific to each circRNA suggesting their roles in HHcy induced ocular disorders. Further analysis of circRNAs helped identify novel parental genes that seem to influence certain eye disease phenotypes.

LTBP2 knockdown and oxidative stress affect glaucoma features including TGFβ pathways, ECM genes expression and apoptosis in trabecular meshwork cells

Glaucoma is the leading cause of irreversible blindness worldwide. Although the etiology of glaucoma is incompletely understood, it is known that the extracellular matrix (ECM) of the trabecular meshwork, oxidative stress, TGFβ signaling pathways, and apoptosis are important components of glaucoma pathogenesis. These components appear to be interrelated, but knowledge on their interactions remains incomplete. Relevant to this gap in knowledge, LTBP2, glaucoma causing gene, may also be related to the mentioned components of glaucoma pathogenesis because of its putative roles in TGFβ signaling and ECM functions. This background prompted us to further query interactions among some molecules and pathways thought to be important in glaucoma etiology, with emphasis on oxidative stress and LTBP2. To this end, effects of LTBP2 siRNA knockdown, oxidative stress induction, TGFβ2 and gremlin exposures on canonical TGFβ and BMP signaling pathways, expression of ECM related genes, and apoptosis were assayed in primary human trabecular meshwork cell cultures. We found that oxidative stress induction and LTBP2 knockdown both affected all the processes queried, and that their affects paralleled one another. We suggest that effects of both oxidative stress and LTBP2 knockdown on the ECM and apoptosis may be mediated by TGFβ and BMP signaling pathway activation.

Research progress on human genes involved in the pathogenesis of glaucoma (Review)

Glaucoma is the leading cause of irreversible blindness globally. It is known that the incidence of glaucoma is closely associated with inheritance. A large number of studies have suggested that genetic factors are involved in the occurrence and development of glaucoma, and even affect the drug sensitivity and prognosis of glaucoma. In the present review, 22 loci of glaucoma are presented, including the relevant genes (myocilin, interleukin 20 receptor subunit B, optineurin, ankyrin repeat- and SOCS box-containing protein 10, WD repeat-containing protein 36, EGF-containing fibulin-like extracellular matrix protein 1, neurotrophin 4, TANK-binding kinase 1, cytochrome P450 subfamily I polypeptide 1, latent transforming growth factor β binding protein 2 and TEK tyrosine kinase endothelial) and 74 other genes (including toll-like receptor 4, sine oculis homeobox Drosophila homolog of 1, doublecortin-like kinase 1, RE repeats-encoding gene, retinitis pigmentosa GTPase regulator-interacting protein, lysyl oxidase-like protein 1, heat-shock 70-kDa protein 1A, baculoviral IAP repeat-containing protein 6, 5,10-methylenetetrahydrofolate reductase and nitric oxide synthase 3 and nanophthalmos 1) that are more closely associated with glaucoma. The pathogenesis of these glaucoma-associated genes, glaucomatous genetics and genetic approaches, as well as glaucomatous risk factors, including increasing age, glaucoma family history, high myopia, diabetes, ocular trauma, smoking, intraocular pressure increase and/or fluctuation were also discussed.

Molecular Insights into Pathogenesis and Infection with Aspergillus Fumigatus

The virulence of fungi is dependent on multiple factors, including the immune status of patients and biological features of fungi. In particular, the virulence of Aspergillus fumigatus is due to the complex interaction among various molecules involved in thermotolerance (such as ribosomal biogenesis proteins, α-mannosyltransferase and heat shock proteins), pigment production (DHN-melanin), immune evasion (like melanin and hydrophobin) and nutrient uptake (such as siderophores and zinc transporters). Other molecules also play important roles in the virulence of A. fumigatus, including cell wall components and those which maintain its integrity (for instance β-1-3 glucan, α-1-3 glucan, chitin, galactomannan and mannoproteins) and adhesion (such as hydrophobins), as well as various hydrolytic enzymes (such as serine and aspartic protease, phospholipases, metalloproteinase and dipeptidyl peptidases). Signalling molecules (including G-protein, cAMP, Ras protein and calcineurin) also increase the virulence through altering the metabolic response to stress conditions and toxins (such as gliotoxin, fumitremorgins, fumagatin and helvolic acid).