Uticaj uklanjanja prvih serija izdanaka na vegetativni rast, prinos i kvalitet ploda kupine (Rubus fruticosus L.)

Paper presents results of the effect of removing the first flush primocanes on vegetative growth, yield and fruit quality of blackberry cultivar ‘Čačanska Bestrna’. Primocanes were removed on a single (10 of May) or double (10 of May and 1 of June) occasions. Removing the first flush primocanes had impact on number of fruiting branches developed in current year on floricanes, but no on their length. It was observed that treatments with removing primocanes had significantly higher yield per bush and per unit area. Increasing of yields was ranged from 11.4% (removal of primocanes twice) to 15.1% (removal of primocanes once). Fruit weight and soluble solids content in the blackberry fruits were not significantly different under the influence of various term of the removal of the first flush of primocanes. The aforementioned pomotechnical measure has significantly influenced the properties of newly developed blackberry primocanes.U radu su prikazani rezultati uticaja uklanjanja prvih serija izdanaka na vegetativni rast, prinos i kvalitet ploda kupine sorte ‘Čačanska bestrna’. Izdanci su uklanjani u jedan (10. maja) ili dva navrata (10. maja i 1. juna). Uklanjanje je uticalo na broj rodnih grančica razvijenih u tekućoj godini na dvogodišnjem izdanku kupine, ali ne i na njihovu dužinu. Prinos po žbunu i jedinici površine je bio značajno veći u varijantama uklanjanja prvih serija izdanaka nego kada oni nisu uklanjani. Povećanje prinosa se kretalo od 11,4% (uklanjanje izdanaka dva puta) pa do 15,1% (uklanjanje izdanaka jednom). Masa ploda i sadržaj rastvorljive suve materije u plodovima se nisu značajno razlikovali pod uticajem različitih varijanti uklanjanja prvih serija izdanaka kod kupine. Uklanjanje prvih serija izdanaka u toku vegetacije je značajno uticalo na osobine novorazvijenih izdanaka kupine

Genomic profiling of human vascular cells identifies TWIST1 as a causal gene for common vascular diseases

Genome-wide association studies have identified multiple novel genomic loci associated with vascular diseases. Many of these loci are common non-coding variants that affect the expression of disease-relevant genes within coronary vascular cells. To identify such genes on a genome-wide level, we performed deep transcriptomic analysis of genotyped primary human coronary artery smooth muscle cells (HCASMCs) and coronary endothelial cells (HCAECs) from the same subjects, including splicing Quantitative Trait Loci (sQTL), allele-specific expression (ASE), and colocalization analyses. We identified sQTLs for TARS2, YAP1, CFDP1, and STAT6 in HCASMCs and HCAECs, and 233 ASE genes, a subset of which are also GTEx eGenes in arterial tissues. Colocalization of GWAS association signals for coronary artery disease (CAD), migraine, stroke and abdominal aortic aneurysm with GTEx eGenes in aorta, coronary artery and tibial artery discovered novel candidate risk genes for these diseases. At the CAD and stroke locus tagged by rs2107595 we demonstrate colocalization with expression of the proximal gene TWIST1. We show that disrupting the rs2107595 locus alters TWIST1 expression and that the risk allele has increased binding of the NOTCH signaling protein RBPJ. Finally, we provide data that TWIST1 expression influences vascular SMC phenotypes, including proliferation and calcification, as a potential mechanism supporting a role for TWIST1 in CAD

Genomic profiling of human vascular cells identifies TWIST1 as a causal gene for common vascular diseases

Genome-wide association studies have identified multiple novel genomic loci associated with vascular diseases. Many of these loci are common non-coding variants that affect the expression of disease-relevant genes within coronary vascular cells. To identify such genes on a genome-wide level, we performed deep transcriptomic analysis of genotyped primary human coronary artery smooth muscle cells (HCASMCs) and coronary endothelial cells (HCAECs) from the same subjects, including splicing Quantitative Trait Loci (sQTL), allele-specific expression (ASE), and colocalization analyses. We identified sQTLs for TARS2, YAP1, CFDP1, and STAT6 in HCASMCs and HCAECs, and 233 ASE genes, a subset of which are also GTEx eGenes in arterial tissues. Colocalization of GWAS association signals for coronary artery disease (CAD), migraine, stroke and abdominal aortic aneurysm with GTEx eGenes in aorta, coronary artery and tibial artery discovered novel candidate risk genes for these diseases. At the CAD and stroke locus tagged by rs2107595 we demonstrate colocalization with expression of the proximal gene TWIST1. We show that disrupting the rs2107595 locus alters TWIST1 expression and that the risk allele has increased binding of the NOTCH signaling protein RBPJ. Finally, we provide data that TWIST1 expression influences vascular SMC phenotypes, including proliferation and calcification, as a potential mechanism supporting a role for TWIST1 in CAD

<i>TCF21</i> and the environmental sensor aryl-hydrocarbon receptor cooperate to activate a pro-inflammatory gene expression program in coronary artery smooth muscle cells

<div><p>Both environmental factors and genetic loci have been associated with coronary artery disease (CAD), however gene-gene and gene-environment interactions that might identify molecular mechanisms of risk are not easily studied by human genetic approaches. We have previously identified the transcription factor <i>TCF21</i> as the causal CAD gene at 6q23.2 and characterized its downstream transcriptional network that is enriched for CAD GWAS genes. Here we investigate the hypothesis that TCF21 interacts with a downstream target gene, the aryl hydrocarbon receptor (AHR), a ligand-activated transcription factor that mediates the cellular response to environmental contaminants, including dioxin and polycyclic aromatic hydrocarbons (e.g., tobacco smoke). Perturbation of <i>TCF21</i> expression in human coronary artery smooth muscle cells (HCASMC) revealed that TCF21 promotes expression of <i>AHR</i>, its heterodimerization partner <i>ARNT</i>, and cooperates with these factors to upregulate a number of inflammatory downstream disease related genes including <i>IL1A</i>, <i>MMP1</i>, and <i>CYP1A1</i>. TCF21 was shown to bind in <i>AHR</i>, <i>ARNT</i> and downstream target gene loci, and co-localization was noted for AHR-ARNT and TCF21 binding sites genome-wide in regions of HCASMC open chromatin. These regions of co-localization were found to be enriched for GWAS signals associated with cardio-metabolic as well as chronic inflammatory disease phenotypes. Finally, we show that similar to TCF21, AHR gene expression is increased in atherosclerotic lesions in mice in vivo using laser capture microdissection, and AHR protein is localized in human carotid atherosclerotic lesions where it is associated with protein kinases with a critical role in innate immune response. These data suggest that TCF21 can cooperate with AHR to activate an inflammatory gene expression program that is exacerbated by environmental stimuli, and may contribute to the overall risk for CAD.</p></div

Gene Mutation Profiles in Primary Diffuse Large B Cell Lymphoma of Central Nervous System: Next Generation Sequencing Analyses

The existence of a potential primary central nervous system lymphoma-specific genomic signature that differs from the systemic form of diffuse large B cell lymphoma (DLBCL) has been suggested, but is still controversial. We investigated 19 patients with primary DLBCL of central nervous system (DLBCL CNS) using the TruSeq Amplicon Cancer Panel (TSACP) for 48 cancer-related genes. Next generation sequencing (NGS) analyses have revealed that over 80% of potentially protein-changing mutations were located in eight genes (CTNNB1, PIK3CA, PTEN, ATM, KRAS, PTPN11, TP53 and JAK3), pointing to the potential role of these genes in lymphomagenesis. TP53 was the only gene harboring mutations in all 19 patients. In addition, the presence of mutated TP53 and ATM genes correlated with a higher total number of mutations in other analyzed genes. Furthermore, the presence of mutated ATM correlated with poorer event-free survival (EFS) (p = 0.036). The presence of the mutated SMO gene correlated with earlier disease relapse (p = 0.023), inferior event-free survival (p = 0.011) and overall survival (OS) (p = 0.017), while mutations in the PTEN gene were associated with inferior OS (p = 0.048). Our findings suggest that the TP53 and ATM genes could be involved in the molecular pathophysiology of primary DLBCL CNS, whereas mutations in the PTEN and SMO genes could affect survival regardless of the initial treatment approach

Gene Mutation Profiles in Primary Diffuse Large B Cell Lymphoma of Central Nervous System: Next Generation Sequencing Analyses

The existence of a potential primary central nervous system lymphoma-specific genomic signature that differs from the systemic form of diffuse large B cell lymphoma (DLBCL) has been suggested, but is still controversial. We investigated 19 patients with primary DLBCL of central nervous system (DLBCL CNS) using the TruSeq Amplicon Cancer Panel (TSACP) for 48 cancer-related genes. Next generation sequencing (NGS) analyses have revealed that over 80% of potentially protein-changing mutations were located in eight genes (CTNNB1, PIK3CA, PTEN, ATM, KRAS, PTPN11, TP53 and JAK3), pointing to the potential role of these genes in lymphomagenesis. TP53 was the only gene harboring mutations in all 19 patients. In addition, the presence of mutated TP53 and ATM genes correlated with a higher total number of mutations in other analyzed genes. Furthermore, the presence of mutated ATM correlated with poorer event-free survival (EFS) (p = 0.036). The presence of the mutated SMO gene correlated with earlier disease relapse (p = 0.023), inferior event-free survival (p = 0.011) and overall survival (OS) (p = 0.017), while mutations in the PTEN gene were associated with inferior OS (p = 0.048). Our findings suggest that the TP53 and ATM genes could be involved in the molecular pathophysiology of primary DLBCL CNS, whereas mutations in the PTEN and SMO genes could affect survival regardless of the initial treatment approach

Functional regulatory mechanism of smooth muscle cell-restricted LMOD1 coronary artery disease locus.

Recent genome-wide association studies (GWAS) have identified multiple new loci which appear to alter coronary artery disease (CAD) risk via arterial wall-specific mechanisms. One of the annotated genes encodes LMOD1 (Leiomodin 1), a member of the actin filament nucleator family that is highly enriched in smooth muscle-containing tissues such as the artery wall. However, it is still unknown whether LMOD1 is the causal gene at this locus and also how the associated variants alter LMOD1 expression/function and CAD risk. Using epigenomic profiling we recently identified a non-coding regulatory variant, rs34091558, which is in tight linkage disequilibrium (LD) with the lead CAD GWAS variant, rs2820315. Herein we demonstrate through expression quantitative trait loci (eQTL) and statistical fine-mapping in GTEx, STARNET, and human coronary artery smooth muscle cell (HCASMC) datasets, rs34091558 is the top regulatory variant for LMOD1 in vascular tissues. Position weight matrix (PWM) analyses identify the protective allele rs34091558-TA to form a conserved Forkhead box O3 (FOXO3) binding motif, which is disrupted by the risk allele rs34091558-A. FOXO3 chromatin immunoprecipitation and reporter assays show reduced FOXO3 binding and LMOD1 transcriptional activity by the risk allele, consistent with effects of FOXO3 downregulation on LMOD1. LMOD1 knockdown results in increased proliferation and migration and decreased cell contraction in HCASMC, and immunostaining in atherosclerotic lesions in the SMC lineage tracing reporter mouse support a key role for LMOD1 in maintaining the differentiated SMC phenotype. These results provide compelling functional evidence that genetic variation is associated with dysregulated LMOD1 expression/function in SMCs, together contributing to the heritable risk for CAD

AHR expression in HCASMC is mediated by an eQTL that modulates <i>TCF21</i> binding.

<p>(a) The downstream region of the <i>AHR</i> gene on chr7 (located on >20kb distance from the transcription end site) contains a strong open chromatin region and enhancer in HCASMC marked by ATAC-Seq, H3K27ac tracks and binding of AP1 transcription factors, JUN and JUND, as well as TCF21. Enhanced view shows that SNP rs10265174 directly overlaps the ATAC-Seq open chromatin, H3K27ac enhancer mark, JUN and JUND ChIP-Seq peaks, and is within a broad TCF21 ChIP-Seq peak. (b) The LocusZoom plot shows <i>AHR</i> gene eQTL distribution in HCASMC across 1Mb (16.9–17.9Mb) on chr7 encompassing <i>AHR</i> gene, with SNP rs10265174 being the top eQTL in the locus. (c) rs10265174 alters the position weight matrix scores for AP1 and TCF4 transcription factors (data from Haploreg). (d) TCF21 ChIP-qPCR shows enrichment at the <i>AHR</i> upstream genomic region compared to IgG control (p<0.05).</p

Schematic representation of AHR-TCF21 interactions that may modulate the effect of environmental stimuli on the progression of inflammation and atherosclerotic plaque formation.

<p>Environmental toxins, including dioxin and tobacco, as well as endogenous activators such as ox-LDL activate the AHR pathway, leading to increased inflammatory burden in the plaque. TCF21 can further increase the burden by increasing AHR expression as well as interacting with AHR at its downstream genes.</p

<i>TCF21</i> overexpression perturbs expression of chronic inflammatory genes and genes linked to vascular disease pathophysiology.

<p><b>(</b>a). Representation of GO categories that are significantly altered by the <i>TCF21</i> overexpression. Red text indicates immune related GO terms, black text indicates other categories. CTRL, control cell growth conditions; <i>TCF21</i>, <i>TCF21</i> over-expression. (b) Selected DAVID GO ontology analysis restricted to genes that show significant up- or down- regulation with <i>TCF21</i> overexpression in HCASMC. Upregulated GO clusters colored in blue, downregulated in red. (c) Co-expression modules of <i>TCF21</i> and <i>AHR-ARNT</i> show a high degree of connectivity. <i>TCF21</i> and <i>AHR</i> co-expression modules were defined using 4164 human microarray datasets through GeneFriends and visualized with Cytoscape. A few representative genes are identified by gene symbol. (d) Co-expression network of 77 CAD GWAS related genes was built using GeneFriends:Microarray, and visualized with Cytoscape. Transcription modules identify three primary clusters of CAD GWAS genes, with <i>TCF21</i> and <i>AHR</i> appearing in the same cluster. Genes <i>PDGFD</i>, <i>SMAD3</i> and <i>COL4A1</i> also appear in this cluster. A second cluster is composed primarily of lipid-related genes, such as APOA1, APOA5, APOB, LPA, etc.</p