ABCG2 regulatory single-nucleotide polymorphisms alter in vivo enhancer activity and expression

Abstract Background Post-surgical infections due to Mycobacterium chimaera appeared as a novel nosocomial threat in 2015, with a worldwide outbreak due to contaminated heater-cooler units used in open chest surgery. We report the results of investigations conducted in France including whole genome sequencing comparison of patient and HCU isolates. Methods We sought M. chimaera infection cases from 2010 onwards through national epidemiological investigations in healthcare facilities performing cardiopulmonary bypass together with a survey on good practices and systematic heater-cooler unit microbial analyses. Clinical and HCU isolates were subjected to whole genome sequencing analyzed with regards to the reference outbreak strain Zuerich-1. Results Only two clinical cases were shown to be related to the outbreak, although 23% (41/175) heater-cooler units were declared positive for M. avium complex. Specific measures to prevent infection were applied in 89% (50/56) healthcare facilities although only 14% (8/56) of them followed the manufacturer maintenance recommendations. Whole genome sequencing comparison showed that the clinical isolates and 72% (26/36) of heater-cooler unit isolates belonged to the epidemic cluster. Within clinical isolates, 5 to 9 non-synonymous single nucleotide polymorphisms were observed, among which an in vivo mutation in a putative efflux pump gene observed in a clinical isolate obtained for one patient under antimicrobial treatment. Conclusions Cases of post-surgical M. chimaera infections were declared to be rare in France, although heater-cooler units were contaminated as in other countries. Genomic analyses confirmed the connection to the outbreak and identified specific single nucleotide polymorphisms, including one suggesting fitness evolution in vivo.

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The Implications of CaMK2A And MeCP2 Signalings In The Cognitive Ability of Adolescents

10.21203/rs.3.rs-506538/v1 ◽

2021 ◽

Author(s):

Li-Ching Lee ◽

Ming-Tsan Su ◽

Hsing-Ying Huang ◽

Ying-Chun Cho ◽

Ting-Kuang Yeh ◽

...

Keyword(s):

High School Students ◽

Single Nucleotide Polymorphisms ◽

Cognitive Ability ◽

Signaling Pathway ◽

Collective Effects ◽

Nucleotide Polymorphisms ◽

School Students ◽

Single Nucleotide ◽

Glutamatergic Signaling

Abstract The glutamatergic signaling pathway is involved in molecular learning and human cognitive ability. Specific single nucleotide polymorphisms (SNPs) in the genes encoding NMDA receptor subunits have been associated with neuropsychiatric disorders by altering glutamate transmission. But how these polymorphisms associated with cognition and brain psychological activities were rarely been explored in healthy adolescents. In this study, we screened SNPs of the glutamatergic signaling pathway to identify genetic variants associated with cognitive ability. We found that single nucleotide polymorphisms (SNPs) in subunits of ionotropic glutamate receptors, including GRIA1, GRINN1, GRIN2B, GRIN2C, GRIN3A, GRIN3B, and Calcium/ Calmodulin-dependent protein kinase II α (CaMK2A) associated with the cognitive function of students. Importantly, the plasma CaMK2A levels correlated positively with the cognitive ability of senior high school students in Taiwan. We demonstrated that the elevated CaMK2A increased its autophosphorylation at T286 and increased the expression of its downstream targets, including GRIA1 and phosphor GRIA1 in vivo. Additionally, the Methyl CpG binding protein 2 (MeCP2), a downstream target of CaMK2A, can activate the expression of CaMK2A, suggesting that MeCP2 and CaMK2A could form a positive feedback loop. In summary, we concluded that members of the glutamatergic signaling, CaMK2A, and MeCP2 were implicated in the cognitive ability of adolescents, and alternating in the CaMK2A expressing may have collective effects on the cognitive ability of youths.

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In vivo reporter assays uncover changes in enhancer activity caused by type 2 diabetes associated SNPs

10.2337/figshare.12906803 ◽

2020 ◽

Author(s):

Ada Admin ◽

Ana Eufrásio ◽

Chiara Perrod ◽

Marta Duque ◽

Fábio J.Ferreira ◽

...

Keyword(s):

Type 2 Diabetes ◽

Nucleotide Polymorphisms ◽

Enhancer Activity ◽

Single Nucleotide ◽

Increased Risk ◽

Nucleotide Mutation ◽

Reporter Assays ◽

Coding Snp

Many single nucleotide polymorphisms (SNPs) associated to type 2 diabetes overlap with putative endocrine pancreatic enhancers, suggesting that these SNPs modulate enhancer activity and consequently, gene expression. We performed in vivo mosaic transgenesis assays in zebrafish to quantitatively test the enhancer activity of type 2 diabetes-associated loci. Six out of ten tested sequences are endocrine pancreatic enhancers. The risk variant of two sequences decreased enhancer activity, while in another two incremented it. One of the latter (rs13266634) locates in a SLC30A8 exon, encoding a tryptophan-to-arginine substitution that decreases SLC30A8 function, being the canonical explanation for type 2 diabetes risk association. However, other type 2 diabetes associated SNPs that truncate SLC30A8, confer protection to this disease, contradicting this explanation. Here, we clarify this incongruence showing that rs13266634 boosts the activity of an overlapping enhancer, suggesting a SLC30A8 gain-of-function as the cause for the increased risk for the disease. We further dissected the functionality of this enhancer finding a single nucleotide mutation sufficient to impair its activity. Overall, this work assesses in vivo the importance of disease-associated SNPs in the activity of endocrine pancreatic enhancers, including a poorly explored case where a coding SNP modulates the activity of an enhancer.

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In vivo reporter assays uncover changes in enhancer activity caused by type 2 diabetes associated SNPs

10.2337/figshare.12906803.v1 ◽

2020 ◽

Author(s):

Ada Admin ◽

Ana Eufrásio ◽

Chiara Perrod ◽

Marta Duque ◽

Fábio J.Ferreira ◽

...

Keyword(s):

Type 2 Diabetes ◽

Nucleotide Polymorphisms ◽

Enhancer Activity ◽

Single Nucleotide ◽

Increased Risk ◽

Nucleotide Mutation ◽

Reporter Assays ◽

Coding Snp

Many single nucleotide polymorphisms (SNPs) associated to type 2 diabetes overlap with putative endocrine pancreatic enhancers, suggesting that these SNPs modulate enhancer activity and consequently, gene expression. We performed in vivo mosaic transgenesis assays in zebrafish to quantitatively test the enhancer activity of type 2 diabetes-associated loci. Six out of ten tested sequences are endocrine pancreatic enhancers. The risk variant of two sequences decreased enhancer activity, while in another two incremented it. One of the latter (rs13266634) locates in a SLC30A8 exon, encoding a tryptophan-to-arginine substitution that decreases SLC30A8 function, being the canonical explanation for type 2 diabetes risk association. However, other type 2 diabetes associated SNPs that truncate SLC30A8, confer protection to this disease, contradicting this explanation. Here, we clarify this incongruence showing that rs13266634 boosts the activity of an overlapping enhancer, suggesting a SLC30A8 gain-of-function as the cause for the increased risk for the disease. We further dissected the functionality of this enhancer finding a single nucleotide mutation sufficient to impair its activity. Overall, this work assesses in vivo the importance of disease-associated SNPs in the activity of endocrine pancreatic enhancers, including a poorly explored case where a coding SNP modulates the activity of an enhancer.

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Resistência anti-helmíntica em nematoides gastrintestinais de pequenos ruminantes: avanços e limitações para seu diagnóstico

Pesquisa Veterinária Brasileira ◽

10.1590/s0100-736x2013001200001 ◽

2013 ◽

Vol 33 (12) ◽

pp. 1391-1402 ◽

Cited By ~ 17

Author(s):

Fernanda S. Fortes ◽

Marcelo B. Molento

Keyword(s):

Single Nucleotide Polymorphisms ◽

Nucleotide Polymorphisms ◽

Single Nucleotide

A seleção e a crescente disseminação de nematoides resistentes aos anti-helmínticos mais comumente utilizados, benzimidazóis (BZs), imidazotiazóis e lactonas macrocíclicas (LMs), constituem um sério entrave na produção de pequenos ruminantes em todo o mundo. O uso de métodos eficientes e sensíveis para a detecção e o monitoramento da resistência anti-helmíntica no campo torna-se urgente, especialmente para os grupos de BZs e LMs, devido aos constantes relatos de resistência. A obtenção de um diagnóstico preciso e precoce da resistência é extremamente importante para auxiliar a tomada de decisão em programas de controle parasitário, com o objetivo de preservar a vida útil dos produtos e limitar o desenvolvimento da resistência nas populações de nematoides. Os testes in vivo e, mais recentemente, os testes in vitro têm sido desenvolvidos para a detecção de nematoides resistentes aos principais grupos de anti-helmínticos. No entanto, a disponibilidade de testes in vitro validados e o seu uso prático ainda são muito limitados. Embora o teste de redução na contagem de ovos nas fezes (TRCOF, in vivo - indireto) seja o principal método de escolha para a detecção de resistência no campo, vem recebendo críticas quanto à validade dos resultados, e passa por significativas modificações. Além disso, o desenvolvimento de técnicas moleculares a partir de alterações genômicas gerou avanços consideráveis nessa área de investigação, com o uso de mutações nos códons 167, 198 e 200 do gene da β-tubulina como principais SNPs (polimorfismos de nucleotídeo único; do inglês Single Nucleotide Polymorphisms) associados à resistência aos BZs. A presente revisão tem o objetivo de discutir os métodos de diagnóstico disponíveis para a detecção de resistência anti-helmíntica em nematoides de pequenos ruminantes, destacando progressos e obstáculos para seu uso na rotina laboratorial e no campo.

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Imidazopyridine Compounds Inhibit Mycobacterial Growth by Depleting ATP Levels

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.02439-17 ◽

2018 ◽

Vol 62 (6) ◽

Cited By ~ 11

Author(s):

Theresa O'Malley ◽

Torey Alling ◽

Julie V. Early ◽

Heather A. Wescott ◽

Anuradha Kumar ◽

...

Keyword(s):

Single Nucleotide Polymorphisms ◽

Bacterial Species ◽

Cross Resistance ◽

Nucleotide Polymorphisms ◽

Ph Homeostasis ◽

Single Nucleotide ◽

Atp Generation ◽

Resistant Mutants

ABSTRACT The imidazopyridines are a promising new class of antitubercular agents with potent activity in vitro and in vivo . We isolated mutants of Mycobacterium tuberculosis resistant to a representative imidazopyridine; the mutants had large shifts (>20-fold) in MIC. Whole-genome sequencing revealed mutations in Rv1339, a hypothetical protein of unknown function. We isolated mutants resistant to three further compounds from the series; resistant mutants isolated from two of the compounds had single nucleotide polymorphisms in Rv1339 and resistant mutants isolated from the third compound had single nucleotide polymorphisms in QcrB, the proposed target for the series. All the strains were resistant to two compounds, regardless of the mutation, and a strain carrying the QcrB T313I mutation was resistant to all of the imidazopyridine derivatives tested, confirming cross-resistance. By monitoring pH homeostasis and ATP generation, we confirmed that compounds from the series were targeting QcrB; imidazopyridines disrupted pH homeostasis and depleted ATP, providing further evidence of an effect on the electron transport chain. A representative compound was bacteriostatic against replicating bacteria, consistent with a mode of action against QcrB. The series had a narrow inhibitory spectrum, with no activity against other bacterial species. No synergy or antagonism was seen with other antituberculosis drugs under development. In conclusion, our data support the hypothesis that the imidazopyridine series functions by reducing ATP generation via inhibition of QcrB.

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