scholarly journals Increased gene copy number of DEFA1/DEFA3 worsens sepsis by inducing endothelial pyroptosis

2019 ◽  
Vol 116 (8) ◽  
pp. 3161-3170 ◽  
Author(s):  
QiXing Chen ◽  
Yang Yang ◽  
JinChao Hou ◽  
Qiang Shu ◽  
YiXuan Yin ◽  
...  
Keyword(s):  
Endothelial Cell ◽  
Copy Number ◽  
Treatment Options ◽  
Gene Copy Number ◽  
High Copy Number ◽  
Gene Copy ◽  
Dependent Manner ◽  
Barrier Dysfunction ◽  
Specific Expression

Sepsis claims an estimated 30 million episodes and 6 million deaths per year, and treatment options are rather limited. Human neutrophil peptides 1–3 (HNP1–3) are the most abundant neutrophil granule proteins but their neutrophil content varies because of unusually extensive gene copy number polymorphism. A genetic association study found that increased copy number of the HNP-encoding gene DEFA1/DEFA3 is a risk factor for organ dysfunction during sepsis development. However, direct experimental evidence demonstrating that these risk alleles are pathogenic for sepsis is lacking because the genes are present only in some primates and humans. Here, we generate DEFA1/DEFA3 transgenic mice with neutrophil-specific expression of the peptides. We show that mice with high copy number of DEFA1/DEFA3 genes have more severe sepsis-related vital organ damage and mortality than mice with low copy number of DEFA1/DEFA3 or wild-type mice, resulting from more severe endothelial barrier dysfunction and endothelial cell pyroptosis after sepsis challenge. Mechanistically, HNP-1 induces endothelial cell pyroptosis via P2X7 receptor-mediating canonical caspase-1 activation in a NLRP3 inflammasome-dependent manner. Based on these findings, we engineered a monoclonal antibody against HNP-1 to block the interaction with P2X7 and found that the blocking antibody protected mice carrying high copy number of DEFA1/DEFA3 from lethal sepsis. We thus demonstrate that DEFA1/DEFA3 copy number variation strongly modulates sepsis development in vivo and explore a paradigm for the precision treatment of sepsis tailored by individual genetic information.

MET Gene High Copy Number (Amplification/Polysomy) Identified in Melanoma for Potential Targeted Therapy

2021 ◽  
Author(s):  
Nisha S Ramani ◽  
Ajaykumar C Morani ◽  
Shengle Zhang
Keyword(s):  
Targeted Therapy ◽  
Gene Amplification ◽  
Copy Number ◽  
Kinase Inhibitors ◽  
Gene Copy Number ◽  
Tissue Microarrays ◽  
High Copy Number ◽  
Gene Copy ◽  
Aberrant Expression ◽  
Mesenchymal Epithelial Transition Factor

Abstract Objectives Aberrant expression of the mesenchymal epithelial transition factor (MET) gene has been observed in several malignancies, and drugs targeting the MET gene have been implicated in clinical trials with promising results. Hence, MET is a potentially targetable oncogenic driver. We explored the frequency of MET gene high copy number in melanomas and carcinomas. Methods The study group included 135 patients. Tissue microarrays were constructed with 19 melanomas and 116 carcinomas diagnosed from 2010 to 2012. We screened MET gene copy number by fluorescence in situ hybridization analysis using probes for MET gene and CEP7 as control. Results We found MET gene amplification in 2 (11%) of 19 melanoma cases, whereas 5 (26%) of 19 melanoma cases showed polysomy. For carcinomas, there was no MET gene amplification identified. However, 8 (7%) of 116 cases showed polysomy. Conclusions In our study, MET gene amplification was identified in 11% of melanomas and is relatively concordant with few reported studies. However, about 26% of the additional melanoma cases showed MET gene polysomy, which has not been reported as per our knowledge. If these results are validated with further orthogonal studies, more of the melanoma cases could potentially benefit from targeted therapy with MET tyrosine kinase inhibitors.

scholarly journals Ceftazidime-Avibactam Resistance Associated with Increased blaKPC-3 Gene Copy Number Mediated by pKpQIL Plasmid Derivatives in Sequence Type 258 Klebsiella pneumoniae

2020 ◽  
Vol 64 (4) ◽  
Author(s):  
Marco Coppi ◽  
Vincenzo Di Pilato ◽  
Francesco Monaco ◽  
Tommaso Giani ◽  
Pier Giulio Conaldi ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Copy Number ◽  
Acquired Resistance ◽  
Gene Copy Number ◽  
Gene Copy ◽  
Content Type ◽  
Outer Membrane Porins ◽  
Long Read ◽  
Multiple Copies

ABSTRACT This study reports on the characterization of two ceftazidime-avibactam (CZA)-resistant KPC-producing Klebsiella pneumoniae strains (KP-14159 and KP-8788) sequentially isolated from infections occurred in a patient never treated with CZA. Whole-genome sequencing characterization using a combined short- and long-read sequencing approach showed that both isolates belonged to the same ST258 strain, had altered outer membrane porins (a truncated OmpK35 and an Asp137Thr138 duplication in the L3 loop of OmpK36), and carried novel pKpQIL plasmid derivatives (pIT-14159 and pIT-8788, respectively) harboring two copies of the Tn4401a KPC-3-encoding transposon. Plasmid pIT-8788 was a cointegrate of pIT-14159 with a ColE replicon (that was also present in KP-14159) apparently evolved in vivo during infection. pIT-8788 was maintained at a higher copy number than pIT-14159 and, upon transfer to Escherichia coli DH10B, was able to increase the CZA MIC by 32-fold. The present findings provide novel insights about the mechanisms of acquired resistance to CZA, underscoring the role that the evolution of broadly disseminated pKpQIL plasmid derivatives may have in increasing the blaKPC gene copy number and KPC-3 expression in bacterial hosts. Although not self-transferable, similar elements, with multiple copies of Tn4401 and maintained at a high copy number, could mediate transferable CZA resistance upon mobilization.

Confirmation of Glyphosate-Resistant Kochia (Kochia scoparia) from Sugar Beet Fields in Idaho and Oregon

2017 ◽  
Vol 32 (1) ◽  
pp. 27-33 ◽  
Author(s):  
Vipan Kumar ◽  
Joel Felix ◽  
Don Morishita ◽  
Prashant Jha
Keyword(s):  
Sugar Beet ◽  
Copy Number ◽  
Cropping Systems ◽  
Gene Copy Number ◽  
Glyphosate Resistance ◽  
Gene Copy ◽  
Resistance Level ◽  
Control Programs ◽  
Gene Copies

AbstractGlyphosate-resistant (GR) kochia is an increasing management concern in major cropping systems of the northwestern US. In 2014, we investigated four putative GR kochia accessions (designated as ALA, VAL, WIL, DB) collected from sugar beet fields in eastern Oregon and southwestern Idaho to characterize the level of evolved glyphosate resistance and determine the relationship between the 5-enol-pyruvylshikimate-3-phospate synthase (EPSPS) gene copy number and level of glyphosate resistance. TheEPSPSgene copy number was used as a molecular marker to detect GR kochia in subsequent surveys in 2015 and 2016. Based on LD50values from a whole-plant dose-response study, the four putative GR kochia populations were 2.0- to 9.6-fold more resistant to glyphosate than the glyphosate-susceptible (GS) accession. In anin vivoleaf-disk shikimate assay, leaf disks of GS kochia plants treated with 100-μM glyphosate accumulated 2.4- to 4.0-fold higher amounts of shikimate than the GR plants. The four GR accessions had 2.7 to 9.1 relativeEPSPSgene copies compared with the GS accession (<1EPSPSgene copies), and there was a linear relationship betweenEPSPSgene copy number and glyphosate resistance level (LD50values). The 2015 and 2016 GR kochia survey results indicated that about half of the collected populations from sugar beet fields in eastern Oregon had developed resistance to glyphosate whereas only one population from the Idaho collection was confirmed glyphosate resistant. This is the first confirmation of GR kochia in sugar beet fields in eastern Oregon and southwestern Idaho. Diversified weed control programs will be required to prevent further development and spread of GR kochia in sugar beet-based rotations in this region.

Gene amplification in a leukemic patient treated with methotrexate.

1984 ◽  
Vol 2 (1) ◽  
pp. 2-7 ◽  
Author(s):  
R C Horns ◽  
W J Dower ◽  
R T Schimke
Keyword(s):  
Gene Amplification ◽  
Copy Number ◽  
Blast Crisis ◽  
Gene Copy Number ◽  
Leukemia Cells ◽  
Gene Copy ◽  
Dhfr Gene ◽  
Before And After ◽  
Cloned Cdna

Resistance to methotrexate (MTX) has been shown in mouse, hamster, and human cell lines grown in sequentially increased MTX concentrations to be due to increased dihydrofolate reductase (DHFR) synthesis and a proportional increase in DHFR gene copy number. Leukemia cells of a patient were studied to assess change in DHFR gene copy number after MTX treatment. The patient presented with chronic myeloid leukemia which rapidly evolved into blast crisis; 90% of peripheral white cells were lymphoblasts. Treatment included intrathecal and intravenous MTX; the lymphoblasts were reduced to undetectable levels. Three months later a second blast crisis occurred; 90% of peripheral white cells were lymphoblasts. Cells from each blast crisis were obtained by leukapheresis and stored for study. Quantification of DHFR gene copy number in DNA from lymphoblasts before and after MTX treatment was done: a radiolabeled cloned cDNA constituting the mouse DHFR coding sequence was used to probe high molecular weight pretreatment and posttreatment DNA bound to nitrocellulose filters. Posttreatment DNA contained two- to three-fold more DHFR gene sequences than pretreatment DNA. Quantitative Southern blotting of EcoRI-digested pretreatment and posttreatment DNA confirmed amplification of the DHFR gene. Karyotype analysis showed no double minute chromosomes or homogeneously staining regions. This is the first study demonstrating DHFR gene amplification in leukemia cells sampled in vivo from a patient treated with MTX.

scholarly journals EZH2 facilitates BMI1-dependent hepatocarcinogenesis through epigenetically silencing microRNA-200c

Oncogenesis ◽  
2020 ◽  
Vol 9 (11) ◽  
Author(s):  
Leibo Xu ◽  
Junlong Lin ◽  
Wanyu Deng ◽  
Weixin Luo ◽  
Yipei Huang ◽  
...  
Keyword(s):  
Copy Number ◽  
Gene Copy Number ◽  
Copy Number Gain ◽  
Gene Copy ◽  
Promoting Effect ◽  
Downstream Target ◽  
Bmi1 Expression ◽  
Hcc Cells

Abstract EZH2, a histone methyltransferase, has been shown to involve in cancer development and progression via epigenetic regulation of tumor suppressor microRNAs, whereas BMI1, a driver of hepatocellular carcinoma (HCC), is a downstream target of these microRNAs. However, it remains unclear whether EZH2 can epigenetically regulate microRNA expression to modulate BMI1-dependent hepatocarcinogenesis. Here, we established that high EZH2 expression correlated with enhanced tumor size, elevated metastasis, increased relapse, and poor prognosis in HCC patients. Further clinical studies revealed that EZH2 overexpression was positively correlated to its gene copy number gain/amplification in HCC. Mechanistically, EZH2 epigenetically suppressed miR-200c expression both in vitro and in vivo, and more importantly, miR-200c post-transcriptionally regulated BMI1 expression by binding to the 3′-UTR region of its mRNA. Furthermore, miR-200c overexpression inhibits the growth of HCC cells in vivo. Silencing miR-200c rescued the tumorigenicity of EZH2-depleted HCC cells, whereas knocking down BMI1 reduced the promoting effect of miR-200c depletion on HCC cell migration. Finally, combination treatment of EZH2 and BMI1 inhibitors further inhibited the viability of HCC cells compared with the cells treated with EZH2 or BMI1 inhibitor alone. Our findings demonstrated that alteration of EZH2 gene copy number status induced BMI1-mediated hepatocarcinogenesis via epigenetically silencing miR-200c, providing novel therapeutic targets for HCC treatment.

scholarly journals The influence of antibiotics on transitory resistome during gut colonization with CTX-M-15 and OXA-162 producing Klebsiella pneumoniae ST15

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Balázs Stercz ◽  
Ferenc B. Farkas ◽  
Ákos Tóth ◽  
Márió Gajdács ◽  
Judit Domokos ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Resistance Gene ◽  
Copy Number ◽  
Gene Copy Number ◽  
Gene Copy ◽  
Antibiotic Administration ◽  
Mice Model ◽  
Gut Colonization ◽  
Colonization Rates

AbstractGreat efforts have been made to limit the transmission of carbapenemase-producing Enterobacteriaceae (CPE), however, the intestinal reservoir of these strains and its modulation by various antibiotics remain largely unexplored. Our aim was to assess the effects of antibiotic administration (ampicillin, ceftazidime, ciprofloxacin) on the establishment and elimination of intestinal colonization with a CTX-M-15 ESBL and OXA-162 carbapenemase producing Klebsiella pneumoniae ST15 (KP5825) in a murine (C57BL/6 male mice) model. Whole genome sequencing of KP5825 strain was performed on an Illumina MiSeq platform. Conjugation assays were carried out by broth mating method. In colonization experiments, 5 × 106 CFU of KP5825 was administered to the animals by orogastric gavage, and antibiotics were administered in their drinking water for two weeks and were changed every day. The gut colonization rates with KP5825 were assessed by cultivation and qPCR. In each of the stool samples, the gene copy number of blaOXA-162 and blaCTX-M-15 were determined by qPCR. Antibiotic concentrations in the stool were determined by high pressure liquid chromatography and a bioanalytical method. The KP5825 contained four different plasmid replicon types, namely IncFII(K), IncL, IncFIB and ColpVC. IncL (containing the blaOXA-162 resistance gene within a Tn1991.2 genetic element) and IncFII(K) (containing the blaCTX-M-15 resistance gene) plasmids were successfully conjugated. During ampicillin and ceftazidime treatments, colonization rate of KP5825 increased, while, ciprofloxacin treatments in both concentrations (0.1 g/L and 0.5 g/L) led to significantly decreased colonization rates. The gene copy number blaOXA-162 correlated with K. pneumoniae in vivo, while a major elevation was observed in the copy number of blaCTX-M-15 from the first day to the fifteenth day in the 0.5 g/L dose ceftazidime treatment group. Our results demonstrate that commonly used antibiotics may have diverse impacts on the colonization rates of intestinally-carried CPE, in addition to affecting the gene copy number of their resistance genes, thus facilitating their stable persistance and dissemination.

scholarly journals No Impact of Increased EPSPS Gene Copy Number on Growth and Fecundity of Glyphosate-Resistant Kochia (Bassia scoparia)

Weed Science ◽  
2018 ◽  
Vol 67 (1) ◽  
pp. 22-28 ◽  
Author(s):  
O. Adewale Osipitan ◽  
J. Anita Dille
Keyword(s):  
Weed Management ◽  
Copy Number ◽  
Plant Biomass ◽  
Management Strategies ◽  
Gene Copy Number ◽  
Glyphosate Resistance ◽  
Gene Copy ◽  
Competitive Response ◽  
Epsps Gene

AbstractThe level of glyphosate resistance in kochia [Bassia scoparia(L.) A. J. Scott] was reported to be due to an increase in 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene copy number. A field study was conducted near Manhattan, KS, in 2014 and 2015 to evaluate the relationship between EPSPS gene copy number and growth and fecundity variables ofB. scopariaindividuals within suspected glyphosate-resistant (GR) populations from western Kansas. Initial assays of EPSPS gene copy and in vivo shikimate accumulation showed thatB. scopariapopulations from Finney (FN-R), Scott (SC-R), and Thomas (TH-R) counties were segregating for glyphosate resistance, with some individuals still being glyphosate susceptible (GS). A target-neighborhood competition approach was used to evaluate the competitive response of individual target plants with relatively low (classified as GS) and high (classified as GR) EPSPS gene copy number within the populations. There was no relationship observed between EPSPS gene copy number and vegetative or fecundity variables. There was no differential competitive response of target plant biomass to increasing neighbor density between individuals with low and high EPSPS gene copy number within each population. Lack of associated vegetative growth and fecundity cost to the increased EPSPS gene copy in the GRB. scopariaplants suggests that the plants are likely to persist in field populations, except when effective weed management strategies are adopted that would prevent their growth and seed production.

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