LncRNA VEAL2 regulates PRKCB2 to modulate endothelial permeability in diabetic retinopathy

Long non‐coding RNAs (lncRNAs) are emerging as key regulators of endothelial cell function. Here, we investigated the role of a novel vascular endothelial‐associated lncRNA (VEAL2) in regulating endothelial permeability. Precise editing of veal2 loci in zebrafish (veal2 ^gib005Δ8/+) induced cranial hemorrhage. In vitro and in vivo studies revealed that veal2 competes with diacylglycerol for interaction with protein kinase C beta‐b (Prkcbb) and regulates its kinase activity. Using PRKCB2 as bait, we identified functional ortholog of veal2 in humans from HUVECs and named it as VEAL2. Overexpression and knockdown of VEAL2 affected tubulogenesis and permeability in HUVECs. VEAL2 was differentially expressed in choroid tissue in eye and blood from patients with diabetic retinopathy, a disease where PRKCB2 is known to be hyperactivated. Further, VEAL2 could rescue the effects of PRKCB2‐mediated turnover of endothelial junctional proteins thus reducing hyperpermeability in hyperglycemic HUVEC model of diabetic retinopathy. Based on evidence from zebrafish and hyperglycemic HUVEC models and diabetic retinopathy patients, we report a hitherto unknown VEAL2 lncRNA‐mediated regulation of PRKCB2, for modulating junctional dynamics and maintenance of endothelial permeability.     

A branched histidine/lysine peptide, H2K4b, in complex with plasmids encoding antitumor proteins inhibits tumor xenografts

BACKGROUND: In this study we investigated whether a particular branched HK polymer, H2K4b, was an effective in vivo carrier of plasmids expressing the antiangiogenic kringle 1-5 or the tumor suppressor p53. METHODS: H2K4b was synthesized on a solid-phase peptide synthesizer. Distribution, optimization and time course studies were done in tumor-bearing nude mice by systemically administering H2K4b in complex with a luciferase-expressing plasmid. We examined the amount of tumor angiogenesis in C6 with MDA-MB-435 xenografts utilizing the carmine dye. The ability of H2K4b to carry luciferase plasmids to different tissues was compared with several liposomal carriers. Medium from cells transfected with mKr1-5 was tested for its capacity to inhibit angiogenesis with an in vivo Matrigel assay. We then determined if systemically delivered H2K4b in complex with plasmid encoding mKr1-5 inhibited tumor growth; we also compared the antitumor activity of HK polyplexes containing hKr1-5, mKr1-5, and p53 plasmids. RESULTS: H2K4b carried the luciferase-expressing plasmid in order of descending efficacy to these tissues: lung, spleen, tumor, and liver. Compared to DOTAP-containing liposomes, H2K4b was a more effective carrier of a luciferase-containing plasmid to extrapulmonary tissues. We then determined that mKr1-5 in complex with H2K4b reduced MDA-MB-435 tumor growth by approximately 50% compared to the control group (P < 0.01). Similarly, H2K4b/mKr1-5 polyplexes reduced the growth of C6 xenografts. In MDA-MB-435 xenografts, p53- and Kr1-5-expressing plasmids in complex with H2K4b had comparable antitumor activity. CONCLUSION: H2K4b demonstrates potential as a carrier of plasmids encoding antiangiogenic and/or tumor suppressor proteins in a tumor-bearing mouse model.     

Antibiotic Resistance Genes Online (ARGO): a Database on vancomycin and beta-lactam resistance genes

Vancomycin and beta-lactams are antibiotics that inhibit gram positive bacteria by interfering with cell wall synthesis. However, continuous use of antibiotics results in the emergence of multi-drug resistant (MDR) bacterial strains. Here, we describe ARGO, a database containing gene sequences conferring resistance to these two classes of antibiotics. It is designed as a resource to enhance research on the prevalence and spread of antibiotic resistance genes. ARGO is the first attempt to compile the resistance gene sequence data with state specific information. AVAILABILITY: AGRO is available for free at http://www.argodb.org/     

Comparative Whole-Genome Analysis of Clinical Isolates Reveals Characteristic Architecture of Mycobacterium tuberculosis Pangenome

The tubercle complex consists of closely related mycobacterium species which appear to be variants of a single species. Comparative genome analysis of different strains could provide useful clues and insights into the genetic diversity of the species. We integrated genome assemblies of 96 strains from Mycobacterium tuberculosis complex (MTBC), which included 8 Indian clinical isolates sequenced and assembled in this study, to understand its pangenome architecture. We predicted genes for all the 96 strains and clustered their respective CDSs into homologous gene clusters (HGCs) to reveal a hard-core, soft-core and accessory genome component of MTBC. The hard-core (HGCs shared amongst 100% of the strains) was comprised of 2,066 gene clusters whereas the soft-core (HGCs shared amongst at least 95% of the strains) comprised of 3,374 gene clusters. The change in the core and accessory genome components when observed as a function of their size revealed that MTBC has an open pangenome. We identified 74 HGCs that were absent from reference strains H37Rv and H37Ra but were present in most of clinical isolates. We report PCR validation on 9 candidate genes depicting 7 genes completely absent from H37Rv and H37Ra whereas 2 genes shared partial homology with them accounting to probable insertion and deletion events. The pangenome approach is a promising tool for studying strain specific genetic differences occurring within species. We also suggest that since selecting appropriate target genes for typing purposes requires the expected target gene be present in all isolates being typed, therefore estimating the core-component of the species becomes a subject of prime importance.