Below you will find scientific publications authored by our members or those enabled by our platform services.
2020
Morfin, Nuria; Goodwin, Paul H; Guzman-Novoa, Ernesto
In: PLOS ONE, vol. 15, no. 2, pp. e0229030, 2020, ISSN: 1932-6203, (Publisher: Public Library of Science).
Abstract | Links | BibTeX | Tags: Bees, Behavior, Gene expression, Honey bees, Insecticides, Invertebrate genomics, Mites, Parasitism
@article{morfin_interaction_2020,
title = {Interaction of field realistic doses of clothianidin and Varroa destructor parasitism on adult honey bee (Apis mellifera L.) health and neural gene expression, and antagonistic effects on differentially expressed genes},
author = {Nuria Morfin and Paul H Goodwin and Ernesto Guzman-Novoa},
url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0229030},
doi = {10.1371/journal.pone.0229030},
issn = {1932-6203},
year = {2020},
date = {2020-01-01},
urldate = {2021-05-26},
journal = {PLOS ONE},
volume = {15},
number = {2},
pages = {e0229030},
abstract = {While many studies have examined the effects of neonicotinoid insecticides and the parasitic mite Varroa destructor on honey bees (Apis mellifera), more information on the combined effects of such stressors on gene expression, including neural related genes, and their impact on biological pathways is needed. This study analyzed the effects of field realistic concentrations of the neonicotinoid clothianidin on adult bees infested and not infested with V. destructor over 21 consecutive days and then determined bee survivorship, weight, deformed wing virus (DWV) levels and gene expression. V. destructor parasitism with or without clothianidin exposure was significantly associated with decreased survivorship, weight loss and higher DWV levels, while clothianidin exposure was only associated with higher levels of DWV. Expression analysis of the neural genes AmNlg-1, BlCh and AmAChE-2 showed that V. destructor caused a significant down-regulation of all of them, whereas clothianidin caused a significant down-regulation of only AmNrx-1 and BlCh. An interaction was only detected for AmNrx-1 expression. RNAseq analysis showed that clothianidin exposure resulted in 6.5 times more up-regulated differentially expressed genes (DEGs) than V. destructor alone and 123 times more than clothianidin combined with V. destructor. Similar results were obtained with down-regulated DEGs, except for a higher number of DEGs shared between V. destructor and the combined stressors. KEGG (Kyoto Encyclopedia of Genes and Genomes) biological pathway analysis of the DEGs showed that the stressor linked to the highest number of KEGG pathways was clothianidin, followed by V. destructor, and then considerably fewer number of KEGG pathways with the combined stressors. The reduced numbers of DEGs and KEGG pathways associated with the DEGs for the combined stressors compared to the stressors alone indicates that the interaction of the stressors is not additive or synergistic, but antagonistic. The possible implications of the antagonistic effect on the number of DEGs are discussed.},
note = {Publisher: Public Library of Science},
keywords = {Bees, Behavior, Gene expression, Honey bees, Insecticides, Invertebrate genomics, Mites, Parasitism},
pubstate = {published},
tppubtype = {article}
}
Zhuang, Qinwei Kim-Wee; Galvez, Jose Hector; Xiao, Qian; AlOgayil, Najla; Hyacinthe, Jeffrey; Taketo, Teruko; Bourque, Guillaume; Naumova, Anna K
Sex Chromosomes and Sex Phenotype Contribute to Biased DNA Methylation in Mouse Liver Journal Article
In: Cells, vol. 9, no. 6, pp. 1436, 2020, (Number: 6 Publisher: Multidisciplinary Digital Publishing Institute).
Abstract | Links | BibTeX | Tags: DNA methylation, Gene expression, mouse liver, sex-chromosome complement, sexual dimorphism, whole genome bisulfite sequencing
@article{zhuang_sex_2020,
title = {Sex Chromosomes and Sex Phenotype Contribute to Biased DNA Methylation in Mouse Liver},
author = {Qinwei Kim-Wee Zhuang and Jose Hector Galvez and Qian Xiao and Najla AlOgayil and Jeffrey Hyacinthe and Teruko Taketo and Guillaume Bourque and Anna K Naumova},
url = {https://www.mdpi.com/2073-4409/9/6/1436},
doi = {10.3390/cells9061436},
year = {2020},
date = {2020-01-01},
urldate = {2021-05-26},
journal = {Cells},
volume = {9},
number = {6},
pages = {1436},
abstract = {Sex biases in the genome-wide distribution of DNA methylation and gene expression levels are some of the manifestations of sexual dimorphism in mammals. To advance our understanding of the mechanisms that contribute to sex biases in DNA methylation and gene expression, we conducted whole genome bisulfite sequencing (WGBS) as well as RNA-seq on liver samples from mice with different combinations of sex phenotype and sex-chromosome complement. We compared groups of animals with different sex phenotypes, but the same genetic sexes, and vice versa, same sex phenotypes, but different sex-chromosome complements. We also compared sex-biased DNA methylation in mouse and human livers. Our data show that sex phenotype, X-chromosome dosage, and the presence of Y chromosome shape the differences in DNA methylation between males and females. We also demonstrate that sex bias in autosomal methylation is associated with sex bias in gene expression, whereas X-chromosome dosage-dependent methylation differences are not, as expected for a dosage-compensation mechanism. Furthermore, we find partial conservation between the repertoires of mouse and human genes that are associated with sex-biased methylation, an indication that gene function is likely to be an important factor in this phenomenon.},
note = {Number: 6
Publisher: Multidisciplinary Digital Publishing Institute},
keywords = {DNA methylation, Gene expression, mouse liver, sex-chromosome complement, sexual dimorphism, whole genome bisulfite sequencing},
pubstate = {published},
tppubtype = {article}
}
2019
Chang, Matthew L; Moussette, Sanny; Gamero-Estevez, Enrique; Gálvez, José Héctor; Chiwara, Victoria; Gupta, Indra R; Ryan, Aimee K; Naumova, Anna K
Regulatory interaction between the ZPBP2-ORMDL3/Zpbp2-Ormdl3 region and the circadian clock Journal Article
In: PLOS ONE, vol. 14, no. 9, pp. e0223212, 2019, ISSN: 1932-6203, (Publisher: Public Library of Science).
Abstract | Links | BibTeX | Tags: Asthma, Circadian oscillators, Circadian rhythms, Gene expression, Gene regulation, Genetic oscillators, Ileum, Transcriptional control
@article{chang_regulatory_2019,
title = {Regulatory interaction between the ZPBP2-ORMDL3/Zpbp2-Ormdl3 region and the circadian clock},
author = {Matthew L Chang and Sanny Moussette and Enrique Gamero-Estevez and José Héctor Gálvez and Victoria Chiwara and Indra R Gupta and Aimee K Ryan and Anna K Naumova},
url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0223212},
doi = {10.1371/journal.pone.0223212},
issn = {1932-6203},
year = {2019},
date = {2019-01-01},
urldate = {2021-05-26},
journal = {PLOS ONE},
volume = {14},
number = {9},
pages = {e0223212},
abstract = {Genome-wide association study (GWAS) loci for several immunity-mediated diseases (early onset asthma, inflammatory bowel disease (IBD), primary biliary cholangitis, and rheumatoid arthritis) map to chromosomal region 17q12-q21. The predominant view is that association between 17q12-q21 alleles and increased risk of developing asthma or IBD is due to regulatory variants. ORM sphingolipid biosynthesis regulator (ORMDL3) residing in this region is the most promising gene candidate for explaining association with disease. However, the relationship between 17q12-q21 alleles and disease is complex suggesting contributions from other factors, such as trans-acting genetic and environmental modifiers or circadian rhythms. Circadian rhythms regulate expression levels of thousands of genes and their dysregulation is implicated in the etiology of several common chronic inflammatory diseases. However, their role in the regulation of the 17q12-q21 genes has not been investigated. Moreover, the core clock gene nuclear receptor subfamily 1, group D, member 1 (NR1D1) resides about 200 kb distal to the GWAS region. We hypothesized that circadian rhythms influenced gene expression levels in 17q12-q21 region and conversely, regulatory elements in this region influenced transcription of the core clock gene NR1D1 in cis. To test these hypotheses, we examined the diurnal expression profiles of zona pellucida binding protein 2 (ZPBP2/Zpbp2), gasdermin B (GSDMB), and ORMDL3/Ormdl3 in human and mouse tissues and analyzed the impact of genetic variation in the ZPBP2/Zpbp2 region on NR1D1/Nr1d1 expression. We found that Ormdl3 and Zpbp2 were controlled by the circadian clock in a tissue-specific fashion. We also report that deletion of the Zpbp2 region altered the expression profile of Nr1d1 in lungs and ileum in a time-dependent manner. In liver, the deletion was associated with enhanced expression of Ormdl3. We provide the first evidence that disease-associated genes Zpbp2 and Ormdl3 are regulated by circadian rhythms and the Zpbp2 region influences expression of the core clock gene Nr1d1.},
note = {Publisher: Public Library of Science},
keywords = {Asthma, Circadian oscillators, Circadian rhythms, Gene expression, Gene regulation, Genetic oscillators, Ileum, Transcriptional control},
pubstate = {published},
tppubtype = {article}
}
2018
Lewin, Jeremy; Ghoraie, Laleh Soltan; Bedard, Philippe L; Hamilton, Robert J; Chung, Peter; Moore, Malcolm; Jewett, Michael A S; Anson‐Cartwright, Lynn; Virtanen, Carl; Winegarden, Neil; Tsao, Julie; Warde, Padraig; Sweet, Joan; Haibe‐Kains, Benjamin; Hansen, Aaron R
Gene expression signatures prognostic for relapse in stage I testicular germ cell tumours Journal Article
In: BJU International, vol. 122, no. 5, pp. 814–822, 2018, ISSN: 1464-410X, (_eprint: https://bjui-journals.onlinelibrary.wiley.com/doi/pdf/10.1111/bju.14372).
Abstract | Links | BibTeX | Tags: #TesticularCancer, #tscsm, Gene expression, germ cell tumour, relapse, surveillance, testicular neoplasm
@article{lewin_gene_2018,
title = {Gene expression signatures prognostic for relapse in stage I testicular germ cell tumours},
author = {Jeremy Lewin and Laleh Soltan Ghoraie and Philippe L Bedard and Robert J Hamilton and Peter Chung and Malcolm Moore and Michael A S Jewett and Lynn Anson‐Cartwright and Carl Virtanen and Neil Winegarden and Julie Tsao and Padraig Warde and Joan Sweet and Benjamin Haibe‐Kains and Aaron R Hansen},
url = {https://bjui-journals.onlinelibrary.wiley.com/doi/abs/10.1111/bju.14372},
doi = {https://doi.org/10.1111/bju.14372},
issn = {1464-410X},
year = {2018},
date = {2018-01-01},
urldate = {2021-05-19},
journal = {BJU International},
volume = {122},
number = {5},
pages = {814--822},
abstract = {Objectives To identify differentially expressed genes between relapsed and non-relapsed clinical stage I testicular germ cell tumours (TGCTs). Materials and Methods We reviewed patients with clinical stage I non-seminoma and seminoma from an institutional database (2000–2012) who were managed by active surveillance. Patients with non-relapsed non-seminoma and non-relapsed seminoma were defined as being relapse-free after 2 and 3 years of surveillance, respectively. RNA extraction and gene expression analysis was performed on archival primary tumour samples and gene-set enrichment analysis (GSEA) was conducted in order to identify differentiating biological pathways. Results A total of 57 patients (relapsed non-seminoma},
note = {_eprint: https://bjui-journals.onlinelibrary.wiley.com/doi/pdf/10.1111/bju.14372},
keywords = {#TesticularCancer, #tscsm, Gene expression, germ cell tumour, relapse, surveillance, testicular neoplasm},
pubstate = {published},
tppubtype = {article}
}