Increased Promoter Activity Research Articles

Frequency of polymorphism of the <i>C-589T IL4</i> and <i>G-1082A IL10</i> genes in children with new coronavirus infection

Immune responses are involved in the initiation and development of COVID-19. Compared with mild COVID-19 cases, serum interleukins levels were significantly increased in severe and critical COVID-19 patients. Increases in IL-4 and IL-10 are associated with disease severity. The C-589T polymorphism of IL4 gene is associated with increased promoter activity of gene. Allelic variants GA and GG-1082 of IL10 gene have greater activity compared to the AA-1082 IL10. The purpose was to study the frequency of occurrence of polymorphic variants of the C-589T IL4 and G-1082A IL10 genes in children with a new coronavirus infection in the population of Crimea. Methods. Examined: 68 patients aged 0 to 14 years with a diagnosis of moderate and severe COVID-19, 100 adult patients (45.6±6.14 years). The frequency of occurrence of polymorphisms of the C-589T IL4 and G-1082A IL10 genes was analyzed. Results. The CC and CT variants of the C-589T IL4 in the group of children were more common than the TT C-589T IL4 variants. Statistically significant differences in the frequency of occurrence of the mutant CC genotype of the C-589T IL4 were shown between groups of children and adults. Statistical analysis did not reveal any genotype differences with disease in either children or adults. Analysis of the prevalence of G-1082A IL10 genotypes showed that in children the most common is GA. The same trend is typical for adults and control group. Conclusions. Analysis of the odds ratio showed that there was no pathogenetic significance between the polymorphism of the C-589T IL4 and G-1082A IL10 genes and the risk of developing a new coronavirus infection in the studied groups.

HiChIP-Based Epigenomic Footprinting Identifies a Promoter Variant of UXS1 That Confers Genetic Susceptibility to Gastroesophageal Cancer.

Genome-wide association studies (GWAS) have identified more than a hundred single nucleotide variants (SNV) associated with the risk of gastroesophageal cancer (GEC). The majority of the identified SNVs map to noncoding regions of the genome. Uncovering the causal SNVs and genes they modulate could help improve GEC prevention and treatment. Herein, we used HiChIP against histone 3 lysine 27 acetylation (H3K27ac) to simultaneously annotate active promoters and enhancers, identify the interactions between them, and detect nucleosome-free regions (NFR) harboring potential causal SNVs in a single assay. The application of H3K27ac HiChIP in GEC relevant models identified 61 potential functional SNVs that reside in NFRs and interact with 49 genes at 17 loci. The approach led to a 67% reduction in the number of SNVs in linkage disequilibrium at these 17 loci, and at 7 loci, a single putative causal SNV was identified. One SNV, rs147518036, located within the promoter of the UDP-glucuronate decarboxylase 1 (UXS1) gene, seemed to underlie the GEC risk association captured by the rs75460256 index SNV. The rs147518036 SNV creates a GABPA DNA recognition motif, resulting in increased promoter activity, and CRISPR-mediated inhibition of the UXS1 promoter reduced the viability of the GEC cells. These findings provide a framework that simplifies the identification of potentially functional regulatory SNVs and target genes underlying risk-associated loci. In addition, the study implicates increased expression of the enzyme UXS1 and activation of its metabolic pathway as a predisposition to gastric cancer, which highlights potential therapeutic avenues to treat this disease. Significance: Epigenomic footprinting using a histone posttranslational modification targeted 3D genomics methodology elucidates functional noncoding sequence variants and their target genes at cancer risk loci.

Elucidation of cellular signaling mechanism involved in Vibrio cholerae chitin-binding protein GbpA mediated IL-8 secretion in the intestinal cells

BackgroundVibrio cholerae N-acetylglucosamine-binding protein (GbpA) is a four-domain, secretory colonization factor which is essential for chitin utilization in the environment, as well as in adherence to intestinal cells. GbpA is also involved in inducing intestinal inflammation by enhancing mucin and interleukin-8 secretion. The underlying cell signaling mechanism involved in the induction of the pro-inflammatory response and IL-8 secretion has yet to be deciphered in detail. MethodsHerein, the process through which GbpA triggers the induction of IL-8 in intestinal cells was investigated by examining the role of GbpA in intestinal cell line HT 29. ResultsGbpA, specifically through the fourth domain, forms a binding connection with Toll-like receptor 2 (TLR2) and additionally, recruits TLR1 along with CD14 within a lipid raft micro-domain to initiate the signaling pathway. Notably, disruption of this micro-domain complex resulted in a reduction in IL-8 secretion. The lipid raft association served as the catalyst that invoked a downstream cellular inflammatory signaling pathway. This cascade involved the activation of various MAP kinases and NFκB and assembly of the AP-1 complex. This coordinated activation of signaling molecules eventually leads to enhanced IL-8 transcription via increased promoter activity. These findings suggested that GbpA is a crucial protein in V. cholerae, capable of inciting a pro-inflammatory response during infection by orchestrating the formation of the GbpA-TLR1/2-CD14 lipid raft complex. Activation of AP-1 and NFκB in the nucleus eventually enhanced IL-8 transcription through increased promoter activity. ConclusionsCollectively, these findings indicated that GbpA plays a pivotal role within V. cholerae by triggering a pro-inflammatory response during infection. This response is instrumented by the formation of the GbpA-TLR1/2-CD14 lipid raft complex.

ENPP1 inhibits the transcription activity of the hepatitis B virus pregenomic promoter by upregulating the acetylation of LMNB1.

Current therapies for hepatitis B virus (HBV) infection can slow disease progression but cannot cure the infection, as it is difficult to eliminate or permanently silence HBV covalently closed circular DNA (cccDNA). The interaction between host factors and cccDNA is essential for their formation, stability, and transcriptional activity. Here, we focused on the regulatory role of the host factor ENPP1 and its interacting transcription factor LMNB1 in HBV replication and transcription to better understand the network of host factors that regulate HBV, which may facilitate the development of new antiviral drugs. Overexpression of ectonucleotide pyrophosphatase/phosphodiesterase 1(ENPP1) in Huh7 cells decreased HBV pregenomic RNA (pgRNA) and hepatitis B core antigen (HBcAg) expression levels, whereas knockdown of ENPP1 increased them. A series of HBV promoter and mutant plasmids were constructed, and a luciferase reporter assay showed that overexpression of ENPP1 caused inhibition of the HBV promoter and its mutants. A DNA pull-down assay showed that lamin B1 (LMNB1), but not ENPP1, interacts directly with the HBV enhancer II/basic core promoter(EnhII/BCP). ZDOCK and PyMOL software were used to predict the interaction of ENPP1 with LMNB1. Overexpression of LMNB1 inhibited the activity of the HBV promoter and its mutant. The acetylation levels at the amino acids 111K, 261K, and 483K of LMNB1 were reduced compared to the control, and an LMNB1 acetylation mutant containing 111R, 261Q, 261R, 483Q, and 483R showed increased promoter activity. In summary, ENPP1 together with LMNB1 increased the acetylation level at 111K and 261K, and LMNB1 inhibited the activity of HBV promoter and downregulated the expression of pregenomic RNA and HBcAg. Our follow-up studies will investigate the expression, clinical significance, and relevance of ENPP1 and LMNB1 in HBV patient tissues, explore the effect of LMNB1 on post-transcriptional progression, and examine whether ENPP1 can reduce cccDNA levels in the nucleus.

Association between mutations in a thyX-hsdS.1 region and para-aminosalicylic acid resistance in Mycobacterium tuberculosis clinical isolates

ABSTRACT Although para-aminosalicylic acid (PAS) has been used to treat tuberculosis agent for decades, its mechanisms of resistance are still not thoroughly understood. Previously, sporadic studies showed that certain mutations in the thyX-hsdS.1 region caused PAS resistance in M. tuberculosis, but a comprehensive analysis is lacking. Recently, we found a G–10A mutation in thyX-hsdS.1 in a PAS-resistant clinical isolate, but it did not cause PAS resistance. SNPs in thyX-hsdS.1 in 6550 clinical isolates were analyzed, and 153 SNPs were identified. C–16 T was the most common SNP identified (54.25%, 83/153), followed by C–4T (7.19%, 11/153) and G–9A (6.54%, 10/153). Subsequently, the effects of those SNPs on the promoter activity of thyX were tested, and the results showed that mutations C–1T, G–3A, C–4T, C–4G, G–7A, G–9A, C–16T, G–18C, and C–19G led to increased promoter activity compared with the wild-type sequence, but other mutations did not. Then, thyX and wild-type thyX-hsdS.1, or thyX-hsdS.1 containing specific SNPs, were overexpressed in M. tuberculosis H37Ra. The results showed that mutations resulting in increased promoter activity also caused PAS resistance. Moreover, the results of an electrophoretic mobility shift assay showed that thyX-hsdS.1 containing the C–16T mutation had a higher binding capacity to RNA polymerase than did the wild-type sequence. Taken together, our data demonstrated that among the SNPs identified in thyX-hsdS.1 of M. tuberculosis clinical isolates, only those able to increase the promoter activity of thyX caused PAS resistance and therefore can be considered as molecular markers for PAS resistance.

RUNX1 Isoforms Regulate RUNX1 and Target-Genes Differentially in Platelets/Megakaryocytes: Association with Clinical Cardiovascular Events

RUNX1 is an essential transcription factor for hematopoiesis. Germline RUNX1 haplodeficiency is associated with thrombocytopenia, platelet dysfunction and predisposition to myeloid malignancies. Three major RUNX1 isoforms (A, B and C) are recognized and share a DNA binding RUNT domain; RUNX1A lacks the transactivation domain. Two distinct promoters regulate RUNX1 expression: distal P1 regulates RUNX1C; proximal P2 regulates RUNX1B and RUNX1A. Little is known regarding the differential effects of isoforms in RUNX1 autoregulation, target-gene regulation and association with clinical events. We performed studies in megakaryocytic HEL cells, HeLa cells (which do not express RUNX1) and in platelets of healthy subjects (n=74) and provide evidence for isoform-specific differential autoregulation and target-gene regulation by RUNX1. We show an association between expression of specific RUNX1-regulated genes in whole blood with cardiovascular events in patients. There are 5 RUNX1 consensus binding sites in P1 promoter and 1 in P2 promoter within ~1000 bp from ATG. Wild type RUNX1 P1 and P2 promoter regions were individually cloned into PGL4 luciferase promoter vector. ChIP studies using PMA-treated megakaryocytic HEL cells showed RUNX1 binding to chromatin regions encompassing the RUNX1 binding sites in both promoters. Mutations of 2 RUNX1 binding sites in intron region of P1 promoter reduced promoter activity; mutations of first 2 RUNX1 binding sites at the exon region of P1 promoter increased activity. Mutation of single RUNX1 binding site in P2 promoter increased promoter activity. Thus, RUNX1 binds to P1 and P2 promoters to regulate activities. To examine the RUNX1 autoregulation by individual isoforms, we co-transfected each isoform with P1 or P2 promoter vector in HeLa cells, which do not express endogenous RUNX1. In response to RUNX1B over-expression, both P1 and P2 promoters showed a dose-dependent decrease in promoter activity. RUNX1C over-expression increased P1 and P2 promoter activities. Thus, RUNX1B and RUNX1C regulate P1 and P2 promoters differentially. In HEL cells, which have endogenous RUNX1, RUNX1B overexpression decreased RUNX1C and RUNX1A mRNA/protein expression by ~50%. RUNX1C overexpression increased RUNX1B and RUNX1A mRNA/protein expression. Thus, RUNX1B decreases RUNX1C and RUNX1A expression; RUNX1C increases RUNX1B and RUNX1A. We studied the regulation by RUNX1 isoforms of target genes PCTP (phosphatidylcholine transfer protein), MYL9 (myosin light chain), PDE5A (phosphodiesterase 5A) and F13A (factor XIIIA) . In HeLa cells. RUNX1B overexpression increased PCTP, MYL9 and PDE5A (protein and mRNA); RUNX1C overexpression reduced PCTP and MYL9. In HEL cells RUNX1B increased PCTP, MYL9, PDE5A and F13A expression; RUNX1C reduced PCTP and MYL9 expression. To obtain evidence in vivo, we studied the relationships between RUNX1 isoforms and their relationships to RUNX1-target genes by RNAseq in leukocyte-poor platelets (74 healthy donors; ages 30-75 yrs). RUNX1B correlated negatively with RUNX1C (R= -0.413 and p=1.5e-06) and RUNX1A (R= -0.493 and p=0.00e+oo); RUNX1C correlated positively with RUNX1A (R=0.45, p<0.0001). RUNX1B correlated positively with PCTP, F131A, PDE5A and RAB1B, and negatively with MYL9 (Figure 1); no significant relationships were observed with RUNX1C or RUNX1A. To understand the relationships to cardiovascular events (MI or death), we explored whole blood gene expression using microarrays in 587 patients (2 cohorts, 190 and 397 patients) presenting to cardiac catherization for chest pain and followed for 3.8 years. In our previous studies RUNX1B transcripts were higher and RUNX1C lower in those with MI or death. We now found that higher expressions of F13A1(Figure 2) and RAB31, which have been shown by us to be RUNX1-targets, were associated with cardiovascular events. Conclusions: RUNX1 isoforms autoregulate RUNX1 expression differentially and regulate target genes in a differential manner, a pattern consistent with in vivo platelet gene expression. The relative expression of RUNX1B and RUNX1C isoforms and of their target genes associate with clinical cardiovascular events. RUNX1-isoform specific effects need to be considered in clinical scenarios where RUNX1 is involved and in its pharmacologic modulation.

Cardiolipin occupancy profiles of YidC paralogs reveal the significance of respective TM2 helix residues in determining paralog-specific phenotypes.

YidC belongs to an evolutionarily conserved family of insertases, YidC/Oxa1/Alb3, in bacteria, mitochondria, and chloroplasts, respectively. Unlike Gram-negative bacteria, Gram-positives including Streptococcus mutans harbor two paralogs of YidC. The mechanism for paralog-specific phenotypes of bacterial YidC1 versus YidC2 has been partially attributed to the differences in their cytoplasmic domains. However, we previously identified a W138R gain-of-function mutation in the YidC1 transmembrane helix 2. YidC1W138R mostly phenocopied YidC2, yet the mechanism remained unknown. Primary sequence comparison of streptococcal YidCs led us to identify and mutate the YidC1W138 analog, YidC2S152 to W/A, which resulted in a loss of YidC2- and acquisition of YidC1-like phenotype. The predicted lipid-facing side chains of YidC1W138/YidC2S152 led us to propose a role for membrane phospholipids in specific-residue dependent phenotypes of S. mutans YidC paralogs. Cardiolipin (CL), a prevalent phospholipid in the S. mutans cytoplasmic membrane during acid stress, is encoded by a single gene, cls. We show a concerted mechanism for cardiolipin and YidC2 under acid stress based on similarly increased promoter activities and similar elimination phenotypes. Using coarse grain molecular dynamics simulations with the Martini2.2 Forcefield, YidC1 and YidC2 wild-type and mutant interactions with CL were assessed in silico. We observed substantially increased CL interaction in dimeric versus monomeric proteins, and variable CL occupancy in YidC1 and YidC2 mutant constructs that mimicked characteristics of the other wild-type paralog. Hence, paralog-specific amino acid- CL interactions contribute to YidC1 and YidC2-associated phenotypes that can be exchanged by point mutation at positions 138 or 152, respectively.

A temperature dependent pilin promoter for production of thermostable enzymes in Thermus thermophilus

BackgroundEnzymes from thermophiles are of great interest for research and bioengineering due to their stability and efficiency. Thermophilic expression hosts such as Thermus thermophilus [T. thermophilus] can overcome specific challenges experienced with protein production in mesophilic expression hosts, such as leading to better folding, increased protein stability, solubility, and enzymatic activity. However, available inducible promoters for efficient protein production in T. thermophilus HB27 are limited.ResultsIn this study, we characterized the pilA4 promoter region and evaluated its potential as a tool for production of thermostable enzymes in T. thermophilus HB27. Reporter gene analysis using a promoterless β-glucosidase gene revealed that the pilA4 promoter is highly active under optimal growth conditions at 68 °C and downregulated during growth at 80 °C. Furthermore, growth in minimal medium led to significantly increased promoter activity in comparison to growth in complex medium. Finally, we proved the suitability of the pilA4 promoter for heterologous production of thermostable enzymes in T. thermophilus by producing a fully active soluble mannitol-1-phosphate dehydrogenase from Thermoanaerobacter kivui [T. kivui], which is used in degradation of brown algae that are rich in mannitol.ConclusionsOur results show that the pilA4 promoter is an efficient tool for gene expression in T. thermophilus with a high potential for use in biotechnology and synthetic biology applications.

FoxH1 Represses the Promoter Activity of cyp19a1a in the Ricefield Eel (Monopterus albus).

Forkhead box H1 (FoxH1) is a sexually dimorphic gene in Oreochromis niloticus, Oplegnathus fasciatus, and Acanthopagrus latus, indicating that it is essential for gonadal development. In the present study, the molecular characteristics and potential function of FoxH1 and the activation of the cyp19a1a promoter in vitro were evaluated in Monopterus albus. The levels of foxh1 in the ovaries were three times higher than those in the testes and were regulated by gonadotropins (Follicle-Stimulating Hormone and Human Chorionic Gonadotropin). FoxH1 colocalized with Cyp19a1a in the oocytes and granulosa cells of middle and late vitellogenic follicles. In addition, three FoxH1 binding sites were identified in the proximal promoter of cyp19a1a, namely, FH1 (-871/-860), FH2 (-535/-524), and FH3 (-218/-207). FoxH1 overexpression significantly attenuated the activity of the cyp19a1a promoter in CHO cells, and FH1/2 mutation increased promoter activity. Taken together, these results suggest that FoxH1 may act as an important regulator in the ovarian development of M. albus by repressing cyp19a1a promoter activity, which provides a foundation for the study of FoxH1 function in bony fish reproductive processes.

Lipid Metabolism Pathway Genes and Lung Cancer: ACADSB rs12220683G>C Is Associated with Better Survival Outcome in Patients with Non-Small Cell Lung Cancer

Introduction: Altered lipid metabolism has been reported to be associated with prognosis in multiple cancers. This study aimed to investigate the association of polymorphisms in lipid metabolism pathway genes with survival outcomes in patients with surgically resected non-small cell lung cancer (NSCLC). Methods: In total, 744 patients with surgically resected NSCLC (380 in the discovery cohort and 364 in the validation cohort) were included in this study. The association between 176 polymorphisms of lipid metabolism pathway genes and the clinical outcomes of NSCLC patients was analyzed. Results: Among the polymorphisms investigated, ACADSB rs10902859G>A was associated with significantly better overall survival (OS) in the discovery, validation, and combined cohorts. ACADSB rs10902859G>A was located in the repressed region and had strong linkage disequilibrium (D′ = 1.00 and r2 = 0.94), with rs12220683G>C located in the H3K4me3 peak region, which indicates the presence of active promoters. ACADSB rs12220683G>C was also associated with better OS in the discovery, validation, and combined cohorts (in a dominant model; adjusted hazard ratio [aHR] = 0.53, 95% confidence interval [CI] = 0.30–0.94, p = 0.03; aHR = 0.37, 95% CI = 0.15–0.89, p = 0.03; and aHR = 0.47, 95% CI = 0.29–0.75, p = 0.002, respectively). In vitro luciferase assay demonstrated that the promoter activity of ACADSB was significantly increased in the rs12220683 variant C allele compared with that in the wild G allele (p = 3 × 10−5). Conclusion: These results suggest that ACADSB rs12220683G>C increases promoter activity and that increased ACADSB expression may result in better OS in patients with surgically resected NSCLC.

Genetic variants in key necroptosis regulators predict prognosis of non-small cell lung cancer after surgical resection.

Necroptosis is a regulated inflammatory cell death which plays a significant role in cancer development and progression. In this study, we evaluated whether genetic variants in key regulators of necroptosis may affect survival outcome of non-small cell lung cancer (NSCLC) patients after surgical resection. A total of 674 patients who underwent curative surgery were included. Fifteen genetic variants in key regulators of necroptosis (RIPK1, RIPK3, and MLKL) were selected. The association of these variants with survival outcomes was evaluated. Two variants, RIPK1 rs17548629C > T and MLKL rs877375G > C, were associated with better overall survival and disease-free survival in multivariate analyses. When the patients were divided according to histology, the associations were significant only in adenocarcinoma, but not in squamous cell carcinoma. RIPK1 rs17548629 C-to-T change was associated with significantly increased luciferase activity by modulating the binding of miR-642a. Promoter assays showed a significantly increased promoter activity in MLKL rs877375C allele compared to G allele. Consistently, the mRNA expression level of RIPK1 and MLKL showed significant positive correlation with RIPK1 rs17548629C-to-T and MLKL rs877375G-to-C changes. Two genetic variants in key regulators in necroptosis, RIPK1 rs17548629C > T and MLKL rs877375G > C, may be used as biomarkers to predict survival outcomes in surgically resected NSCLC patients.

Transcription Factor E2F1 Regulates the Expression of ADRB2.

Adrenergic beta-2-receptor (ADRB2) is highly expressed in various tissue cells, affecting the susceptibility, development, and drug efficacy of diseases such as bronchial asthma and malignant tumor. However, the transcriptional regulatory mechanism of the human ADRB2 gene remains unclear. This study aimed to clarify whether E2F transcription factor 1 (E2F1) was involved in the transcriptional regulation of the human ADRB2 gene. First, the 5' flanking region of the human ADRB2 gene was cloned, and its activity was detected using A549 and BEAS-2B cells. Second, it was found that the overexpression of E2F1 could increase promoter activity by a dual-luciferase reporter gene assay. In contrast, treatment of knockdown of E2F1 significantly resulted in a decrease in its promoter activity. Moreover, mutation of the binding site of E2F1 greatly reduced the potential of human ADRB2 promoter transcriptional activity to be regulated by E2F1 overexpression and knockdown. Additionally, by real-time quantitative PCR and Western blot analysis, we demonstrated that overexpression of E2F1 elevated the ADRB2 mRNA expression and protein levels while si-E2F1 reduced its expression. Finally, the consequence of the chromatin immunoprecipitation assay showed that E2F1 was able to bind to the promoter region of ADRB2 in vivo. These results confirmed that E2F1 upregulated the expression of the human ADRB2 gene.

Characterization and engineering of the xylose-inducible xylP promoter for use in mold fungal species

Conditional promoters allowing both induction and silencing of gene expression are indispensable for basic and applied research. The xylP promoter (pxylP) from Penicillium chrysogenum was demonstrated to function in various mold species including Aspergillus fumigatus. pxylP allows high induction by xylan or its degradation product xylose with low basal activity in the absence of an inducer. Here we structurally characterized and engineered pxylP in A. fumigatus to optimize its application. Mutational analysis demonstrated the importance of the putative TATA-box and a pyrimidine-rich region in the core promoter, both copies of a largely duplicated 91-bp sequence (91bpDS), as well as putative binding sites for the transcription factor XlnR and a GATA motif within the 91bpDS. In agreement, pxylP activity was found to depend on XlnR, while glucose repression appeared to be indirect. Truncation of the originally used 1643-bp promoter fragment to 725 bp largely preserved the promoter activity and the regulatory pattern. Integration of a third 91bpDS significantly increased promoter activity particularly under low inducer concentrations. Truncation of pxylP to 199 bp demonstrated that the upstream region including the 91bpDSs mediates not only inducer-dependent activation but also repression in the absence of inducer. Remarkably, the 1579-bp pxylP was found to act bi-bidirectionally with a similar regulatory pattern by driving expression of the upstream-located arabinofuranosidase gene. The latter opens the possibility of dual bidirectional use of pxylP. Comparison with a doxycycline-inducible TetOn system revealed a significantly higher dynamic range of pxylP. Taken together, this study identified functional elements of pxylP and opened new methodological opportunities for its application.

Differential RUNX1-Isoform Specific Autoregulation of RUNX1 and Regulation of Target Genes (PCTP, MYL9) in Megakaryocytic Cells

RUNX1 is an essential transcription factor for hematopoiesis. Human germline RUNX1 haplodeficiency is associated with impaired megakaryocyte differentiation, thrombocytopenia, platelet dysfunction and predisposition to myeloid malignancies. The two major RUNX1 isoforms RUNX1C and RUNX1B differ at N-terminus by 14AA, and are regulated by two distinct promoters P1 and P2, respectively. RUNX1B and RUNX1C have distinct roles and tissue expression. Little is known regarding the differential effects of RUNX1 isoforms in RUNX1 autoregulation, and on their regulation of target genes. There are 5 RUNX1 consensus binding sites located in P1 promoter and one RUNX1 site in P2 promoter. To study RUNX1 promoters, both WT RUNX1 P1 and P2 promoter regions were individually cloned into PGL4 luciferase promoter vector. ChIP studies using PMA-treated megakaryocytic HEL cells showed RUNX1 binding to chromatin regions encompassing the RUNX1 binding sites in both promoters. Mutations of 2 RUNX1 binding sites in intron region of P1 promoter reduced promoter activity; mutations of first 2 RUNX1 binding sites in at the exon region of P1 promoter increased activity. Mutation of single RUNX1 binding site in P2 promoter increased promoter activity. Thus, RUNX1 binds to P1 and P2 promoters to regulate their activities. To examine the RUNX1 autoregulation by individual isoforms, we co-transfected each isoform with P1 or P2 promoter vector in HeLa cells, which express negligible endogenous RUNX1. In response to RUNX1B, P1 promoter showed a dose-dependent decrease in promoter activity. RUNX1C expression, increased P1 promoter activity in a dose-dependent manner. With constant RUNX1C expression, increase in RUNX1B co-expression led to a dose-dependent decrease in P1 promoter activity. In HeLa cells RUNX1B decreased P2 promoter activity in a dose-dependent manner. With constant RUNX1B expression, an increase in RUNX1C increased RUNX1 P2 promoter activity. Thus, RUNX1B and RUNX1C regulate both P1 and P2 promoters in a distinct manner. In studies in megakaryocytic HEL cells, which express endogenous RUNX1, RUNX1B overexpression decreased RUNX1C expression by 50%. RUNX1C overexpression increased by 2-fold RUNX1B protein. In studies using RUNX1C-specific antibody, and expression plasmids for hemagglutinin-tagged-RUNX1B and c-Myc-tagged RUNX1C, RUNX1B overexpression decreased RUNX1C; RUNX1C overexpression increased RUNX1B. These studies indicate that RUNX1 isoforms autoregulate in a differential manner at the protein level. We studied the effects of RUNX1 isoforms on two established downstream RUNX1 target genes PCTP (phosphatidylcholine transfer protein) and MYL9(myosin light chain) in HeLa cells. RUNX1B overexpression increased both PCTP and MYL9 protein on immunoblotting, while RUNX1C overexpression reduced both proteins. This suggests RUNX1B and RUNX1C have differential effects in regulating downstream genes. These findings are in line with our studies in whole blood from a large cohort of patients with CAD showing a positive correlation between PCTP (Circulation 2017136(10):927-939) with RUNX1B transcript levels and a negative relationship with those for RUNX1C. Conclusions: RUNX1 isoforms autoregulate RUNX1 expression differentially in an isoform-specific manner. Moreover, they regulate target genes (MYL9 and PCTP) in a differential manner. These RUNX1 isoform-specific effects may be important in understanding the consequences of germline RUNX1 haplodeficiency and in modulating RUNX1 levels for therapeutic purposes.

A metabolic regulatory network for the Caenorhabditis elegans intestine

SummaryMetabolic perturbations can affect gene expression, for instance to rewire metabolism. While numerous efforts have measured gene expression in response to individual metabolic perturbations, methods that determine all metabolic perturbations that affect the expression for a given gene or set of genes have not been available. Here, we use a gene-centered approach to derive a first-pass metabolic regulatory network for Caenorhabditis elegans by performing RNAi of more than 1,400 metabolic genes with a set of 19 promoter reporter strains that express a fluorescent protein in the animal’s intestine. We find that metabolic perturbations generally increase promoter activity, which contrasts with transcription factor (TF) RNAi, which tends to repress promoter activity. We identify several TFs that modulate promoter activity in response to perturbations of the electron transport chain and explore complex genetic interactions among metabolic pathways. This work provides a blueprint for a systems-level understanding of how metabolism affects gene expression.

The suppressive role of phytochemical-induced glutathione S-transferase Mu 2 in human urothelial carcinoma cells

Glutathione S-transferases (GSTs) belong to one class of phase 2 detoxification enzymes which are important in metabolism and/or detoxification of various electrophilic endogenous metabolites and xenobiotics. From the available database, we found that GSTM2 gene expression is lower in high stages of bladder urothelial carcinoma than in stage 1 and normal bladder tissue. GSTM2 overexpression retards invasion, migration and tumor sphere formation of bladder cancer cells. Analysis of GSTM2 promoter activity shows that one SP1 site located at − 48 to − 40 bp is important for GSTM2 gene expression in BFTC 905 cells. An SP1 inhibitor, mithramycin A, inhibits GSTM2 promoter activity and protein expression. SP1 overexpression also increases GSTM2 expression in BFTC 905 and 5637 cells. Eight potential phytochemicals were analyzed for GSTM2 promoter activation, and results indicated that baicalein, berberrubine, chalcone, curcumin, resveratrol, and wogonin can increase promoter activity. In endogenous GSTM2 expression, berberrubine and resveratrol activated GSTM2 mRNA and protein expression the most. A DNA methylation inhibitor, 5-aza-deoxycytidine, can decrease GSTM2 gene methylation level and then increase its gene expression; 50 μM berberrubine decreased the GSTM2 gene methylation level, providing a mechanism for activating GSTM2 gene expression. Berberrubine and resveratrol also increased SP1 protein expression as one of the mechanisms for GSTM2 gene expression. In summary, berberrubine and resveratrol activates GSTM2 expression which inhibits cell proliferation, migration, and invasion of bladder cancer cells. The GSTM2 expression mechanism is partially via SP1 activation, and the effect of berberrubine is also partly via DNA CpG demethylation.

VCAM1, HMOX1 and NOS3 differential endothelial expression may impact sickle cell anemia vasculopathy

Endothelial dysfunction plays a major role in sickle cell anemia (SCA) systemic vasculopathy, with upregulation of adhesion molecules (e.g., VCAM-1), decreased nitric oxide bioavailability, and oxidative stress. We aimed to assess the modulation role of pro-inflammatory and pro-oxidative stimuli on endothelial VCAM1, NOS3, and HMOX1 expression. We also evaluated the effect of the main SCA therapeutic agent, hydroxyurea, on that modulation.Our results showed that two VCAM1 promoter haplotypes, we previously associated with pediatric cerebral vasculopathy and severe hemolysis in SCA, increased promoter activity in TNF-α-stimulated transfected EA.hy926 and HBEC cell lines, consistent with a higher VCAM1 expression in macro and microvascular settings. In non-transfected cells, we also observed TNF-α-induced VCAM1 overexpression as well as heme-induced overexpression of HMOX1 in both cell models. Heme did not affect VCAM1 nor NOS3 expression and the latter was also not affected by TNF-α stimulus. Hydroxyurea treatment lowered TNF-induced VCAM1 and NOS3 expression but did not affect heme-induced HMOX1 expression.These data further indicate that VCAM1 haplotypes we studied lead to higher VCAM1 expression affecting not only cerebral but also systemic vasculopathy risk. The differential endothelial expression of VCAM1, NOS3, and HMOX1 also confirms their genetic modulation role in SCA systemic vasculopathy.

Construction of a Porcine Skeletal Muscle-Specific Promoter by Inducing the Seed Region of miR-208a.

Transgenic promoter systems are of great interest for their potential use in gene therapy or production due to their high activity, long term, and cell specificity. Here, in order to obtain promoters with high activity and expressed specifically in skeletal muscle, the MYOD1, MYF5, and MCK were selected as the candidate genes. The truncated promoters were amplified and their activity was verified through dual-luciferase reporter gene test. We used genetic engineering techniques to improve promoter activity by tandemly linking enhancers and promoters or two promoters. Furthermore, synthetic promoter was the most active when two eMCK enhancers and pMCK promoter were cascaded. To improve the tissue specificity of the promoter, the seed region of translational repressor miR-208a was inserted into the downstream of the promoter (pGL3-2eMCK-pMCK-T208-mCherry-EGFP). The results showed that the expression level of target genes decreased significantly (P < 0.05) in myocardium rather than in skeletal muscle. The results of in vivo transfection indicated that tandem transcriptional regulatory elements can increase promoter activity in mice. This work laid the foundation for future research on genetically modified pigs.

Epigenetic readers and lung cancer: the rs2427964C>T variant of the bromodomain and extraterminal domain gene BRD3 is associated with poorer survival outcome in NSCLC.

Bromodomain and extraterminal domain (BET) proteins are epigenetic readers that regulate gene expression. We investigated whether variants in BET genes are associated with survival outcomes for lung cancer. To do this, the associations between 77 variants in BET family genes and survival outcomes were analyzed in 773 non‐small‐cell lung cancer (NSCLC) patients who underwent surgery (349 and 424 patients in the discovery and validation cohorts, respectively). We found that six variants were significantly associated with overall survival (OS) in the discovery cohort, and one variant (rs2506711C>T) was replicated in the validation cohort. BRD3 rs2506711C>T is located in the repressed area and has a strong linkage disequilibrium with rs2427964C>T in the promoter region. BRD3 rs2427964C>T was significantly associated with worse OS in the discovery cohort, validation cohort, and combined analysis. In a luciferase assay, promoter activity in the BRD3 rs2427964 T allele was significantly higher than that in the BRD3 rs2427964 C allele, which selectively bound with the transcriptional repressor SIN3A. Knockdown of BRD3 with BRD3‐specific siRNA decreased the proliferation and migration of lung cancer cells while also increasing the rate of apoptosis. These results suggest that BRD3 rs2427964C>T increases BRD3 expression through increased promoter activity, which is associated with poor prognosis for lung cancer.

WITHDRAWN: Genetic polymorphisms and promoter methylation of miR-9-3 in the modulation of breast cancer risk in a Chinese population

<h2>Abstract</h2><h3>Background</h3> <b>:</b> Genome-wide association study has discovered some susceptibility loci of breast cancer (BC), such as 1q32.1, 5q14.3, and 15q26.1. miR-9-3, located on 15q26.1, was down-regulated in BC, involving in estrogen receptor-α signaling pathway and p53-related apoptotic pathway. We aimed to investigate the role of genetic polymorphisms and promoter methylation of miR-9-3 in the modulation of BC risk. <h3>Materials and Methods</h3> <b>:</b> The rs4335754 and rs4932217 in the promoter of miR-9-3 were genotyped using the Taqman assay. The relative expression levels of miR-9-3 and <i>CDH1</i> were measured by qRT-PCR. miR-9-3 promoter methylation was examined by bisulfate genomic sequencing and transcriptional activity was evaluated by dual-luciferase reporter assay. <h3>Results</h3> <b>:</b> The rs4335754 GG, AG/GG genotypes, and G allele were associated with a reduced risk of BC (GG vs. AA: adjusted OR = 0.46, 95 % CI, 0.26-0.79, <i>p</i> = 0.004; AG/GG vs. AA: adjusted OR = 0.72, 95 % CI, 0.56-0.92, <i>p</i> = 0.009; G vs. A: adjusted OR = 0.73, 95 % CI, 0.60-0.89, <i>p</i> = 0.002, respectively). The rs4335754 AG/GG carriers displayed high levels of miR-9-3 and the rs4335754 G allele increased promoter activity. Moreover, miR-9-3 promoter hypermethylation can also reduce the expression of miR-9-3. Ectopic expression of miR-9-3 inhibited cell proliferation through targeting <i>CDH1.</i> <h3>Conclusion</h3> <b>:</b> These findings indicate that rs4335754 as well as CpGs methylation in the promoter of miR-9-3 altered its expression, and ultimately affected individual's susceptibility for the development of BC.