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Allum, F.; Shao, X.; Guénard, F.; Simon, M.M.; Busche, S.; Caron, M.; Lambourne, J.; Lessard, J.; Tandre, K.; Hedman, Å.K.; Kwan, T.; Ge, B.; Multiple, T.H.E.R.C.; Rönnblom, L.; McCarthy, M.I.; Deloukas, P.; Richmond, T.; Burgess, D.; Spector, T.D.; Tchernof, A.; Marceau, S.; Lathrop, M.; Vohl, M.C.; Pastinen, T.; Grundberg, E. |
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Title |
Characterization of functional methylomes by next-generation capture sequencing identifies novel disease-associated variants |
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2015 |
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Nat Commun |
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6 |
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7211 |
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Most genome-wide methylation studies (EWAS) of multifactorial disease traits use targeted arrays or enrichment methodologies preferentially covering CpG-dense regions, to characterize sufficiently large samples. To overcome this limitation, we present here a new customizable, cost-effective approach, methylC-capture sequencing (MCC-Seq), for sequencing functional methylomes, while simultaneously providing genetic variation information. To illustrate MCC-Seq, we use whole-genome bisulfite sequencing on adipose tissue (AT) samples and public databases to design AT-specific panels. We establish its efficiency for high-density interrogation of methylome variability by systematic comparisons with other approaches and demonstrate its applicability by identifying novel methylation variation within enhancers strongly correlated to plasma triglyceride and HDL-cholesterol, including at CD36. Our more comprehensive AT panel assesses tissue methylation and genotypes in parallel at ∼4 and ∼3 M sites, respectively. Our study demonstrates that MCC-Seq provides comparable accuracy to alternative approaches but enables more efficient cataloguing of functional and disease-relevant epigenetic and genetic variants for large-scale EWAS. |
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2041-1723 |
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UofT @ mathieu.lemaire @ |
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45631 |
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Ali, M.I.; Chen, X.; Didion, S.P. |
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Title |
Heterozygous eNOS deficiency is associated with oxidative stress and endothelial dysfunction in diet-induced obesity |
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Journal Article |
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2015 |
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Abbreviated Journal |
Physiol Rep |
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3 |
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12 |
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Heterozygous endothelial nitric oxide synthase (eNOS) deficiency is associated with normal endothelium-dependent responses, however, little is known regarding the mechanisms that maintain or impair endothelial function with heterozygous eNOS deficiency. The goals of this study were to (1) determine mechanism(s) which serve to maintain normal endothelial function in the absence of a single eNOS gene; and (2) to determine whether heterozygous eNOS deficiency predisposes blood vessels to endothelial dysfunction in response to a high-fat diet (HFD). Responses of carotid arteries were examined in wild-type (eNOS(+/+)) and heterozygous eNOS-deficient (eNOS(+/-)) treated with either vehicle (saline), N(G)-nitro-L-arginine (L-NNA, 100 μmol/L), an inhibitor of nitric oxide synthase, or 1H-[1,2,4]oxadiazolo[4,3-a]quinoxalin-1-one (ODQ, 1 μmol/L), an inhibitor of soluble guanylyl cyclase (sGC), and in eNOS(+/+) and eNOS(+/-) mice fed a control (10%) or a 45% HFD (kcal from fat). Responses to acetylcholine (ACh) were similar in vehicle-treated arteries from eNOS(+/+) and eNOS(+/-) mice, and were equally inhibited by L-NNA and ODQ. Phosphorylation of eNOS Ser1176, a site associated with increased eNOS activity, was significantly greater in eNOS(+/-) mice most likely as a compensatory response for the loss of a single eNOS gene. In contrast, responses to ACh were markedly impaired in carotid arteries from eNOS(+/-), but not eNOS(+/+), mice fed a HFD. Vascular superoxide levels as well as plasma levels of the pro-inflammatory cytokine interleukin-6 (IL-6) were selectively increased in HFD-fed eNOS(+/-) mice. In reconstitution experiments, IL-6 produced concentration-dependent impairment of endothelial responses as well as greater increases in NADPH-stimulated superoxide levels in arteries from eNOS(+/-) mice fed a control diet compared to eNOS(+/+) mice. Our findings of increased Ser1176-phosphorylation reveal a mechanism by which NOS- and sGC-dependent endothelial function can be maintained with heterozygous eNOS deficiency. In addition, heterozygous eNOS deficiency predisposes blood vessels to developing endothelial dysfunction in response to a HFD. The impairment produced by a HFD in eNOS(+/-) mice appears to be mediated by IL-6-induced increases in vascular superoxide. These findings serve as an important example of eNOS haploinsufficiency, one that may contribute to the development of carotid artery disease in obese humans. |
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2051-817x |
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UofT @ mathieu.lemaire @ |
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45799 |
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Al-Awqati, Q. |
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Title |
Kidney growth and hypertrophy: the role of mTOR and vesicle trafficking |
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Journal Article |
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2015 |
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J Clin Invest |
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125 |
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6 |
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2267-2270 |
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The kidney, like other organs, grows in constant proportion to the rest of the body. When one kidney is removed, the remaining one hypertrophies. In a comprehensive series of studies, Chen et al. show that growth during maturation is mediated by the mTORC1 signaling pathway, which is induced by EGF-like peptides, and requires PI3K, PDK, AKT, mTORC2, and activation of mTORC1 through the combined effects of TSC and RHEB as part of a multiprotein complex localized on lysosomes. However, compensatory growth is mediated by amino acids, which act on mTORC1 independently of the previous pathway, and requires a class III PI3K (VPS34) that is known to be involved in vesicle trafficking to the lysosomes. |
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0021-9738 |
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UofT @ mathieu.lemaire @ |
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45804 |
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Akchurin, O.; Reidy, K.J. |
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Title |
Genetic causes of proteinuria and nephrotic syndrome: impact on podocyte pathobiology |
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Journal Article |
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2015 |
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Pediatr Nephrol |
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30 |
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2 |
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221-233 |
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In the past 20 years, multiple genetic mutations have been identified in patients with congenital nephrotic syndrome (CNS) and both familial and sporadic focal segmental glomerulosclerosis (FSGS). Characterization of the genetic basis of CNS and FSGS has led to the recognition of the importance of podocyte injury to the development of glomerulosclerosis. Genetic mutations induce injury due to effects on the podocyte’s structure, actin cytoskeleton, calcium signaling, and lysosomal and mitochondrial function. Transgenic animal studies have contributed to our understanding of podocyte pathobiology. Podocyte endoplasmic reticulum stress response, cell polarity, and autophagy play a role in maintenance of podocyte health. Further investigations related to the effects of genetic mutations on podocytes may identify new pathways for targeting therapeutics for nephrotic syndrome. |
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0931-041x |
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UofT @ mathieu.lemaire @ |
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45820 |
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Amendola, L.M.; Dorschner, M.O.; Robertson, P.D.; Salama, J.S.; Hart, R.; Shirts, B.H.; Murray, M.L.; Tokita, M.J.; Gallego, C.J.; Kim, D.S.; Bennett, J.T.; Crosslin, D.R.; Ranchalis, J.; Jones, K.L.; Rosenthal, E.A.; Jarvik, E.R.; Itsara, A.; Turner, E.H.; Herman, D.S.; Schleit, J.; Burt, A.; Jamal, S.M.; Abrudan, J.L.; Johnson, A.D.; Conlin, L.K.; Dulik, M.C.; Santani, A.; Metterville, D.R.; Kelly, M.; Foreman, A.K.; Lee, K.; Taylor, K.D.; Guo, X.; Crooks, K.; Kiedrowski, L.A.; Raffel, L.J.; Gordon, O.; Machini, K.; Desnick, R.J.; Biesecker, L.G.; Lubitz, S.A.; Mulchandani, S.; Cooper, G.M.; Joffe, S.; Richards, C.S.; Yang, Y.; Rotter, J.I.; Rich, S.S.; O’Donnell, C.J.; Berg, J.S.; Spinner, N.B.; Evans, J.P.; Fullerton, S.M.; Leppig, K.A.; Bennett, R.L.; Bird, T.; Sybert, V.P.; Grady, W.M.; Tabor, H.K.; Kim, J.H.; Bamshad, M.J.; Wilfond, B.; Motulsky, A.G.; Scott, C.R.; Pritchard, C.C.; Walsh, T.D.; Burke, W.; Raskind, W.H.; Byers, P.; Hisama, F.M.; Rehm, H.; Nickerson, D.A.; Jarvik, G.P. |
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Title |
Actionable exomic incidental findings in 6503 participants: challenges of variant classification |
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Journal Article |
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2015 |
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Abbreviated Journal |
Genome Res |
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25 |
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3 |
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305-315 |
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Recommendations for laboratories to report incidental findings from genomic tests have stimulated interest in such results. In order to investigate the criteria and processes for assigning the pathogenicity of specific variants and to estimate the frequency of such incidental findings in patients of European and African ancestry, we classified potentially actionable pathogenic single-nucleotide variants (SNVs) in all 4300 European- and 2203 African-ancestry participants sequenced by the NHLBI Exome Sequencing Project (ESP). We considered 112 gene-disease pairs selected by an expert panel as associated with medically actionable genetic disorders that may be undiagnosed in adults. The resulting classifications were compared to classifications from other clinical and research genetic testing laboratories, as well as with in silico pathogenicity scores. Among European-ancestry participants, 30 of 4300 (0.7%) had a pathogenic SNV and six (0.1%) had a disruptive variant that was expected to be pathogenic, whereas 52 (1.2%) had likely pathogenic SNVs. For African-ancestry participants, six of 2203 (0.3%) had a pathogenic SNV and six (0.3%) had an expected pathogenic disruptive variant, whereas 13 (0.6%) had likely pathogenic SNVs. Genomic Evolutionary Rate Profiling mammalian conservation score and the Combined Annotation Dependent Depletion summary score of conservation, substitution, regulation, and other evidence were compared across pathogenicity assignments and appear to have utility in variant classification. This work provides a refined estimate of the burden of adult onset, medically actionable incidental findings expected from exome sequencing, highlights challenges in variant classification, and demonstrates the need for a better curated variant interpretation knowledge base. |
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1088-9051 |
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UofT @ mathieu.lemaire @ |
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45831 |
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Andrade-Oliveira, V.; Amano, M.T.; Correa-Costa, M.; Castoldi, A.; Felizardo, R.J.; de Almeida, D.C.; Bassi, E.J.; Moraes-Vieira, P.M.; Hiyane, M.I.; Rodas, A.C.; Peron, J.P.; Aguiar, C.F.; Reis, M.A.; Ribeiro, W.R.; Valduga, C.J.; Curi, R.; Vinolo, M.A.; Ferreira, C.M.; Câmara, N.O. |
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Title |
Gut Bacteria Products Prevent AKI Induced by Ischemia-Reperfusion |
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Journal Article |
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2015 |
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J Am Soc Nephrol |
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26 |
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8 |
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1877-1888 |
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Short-chain fatty acids (SCFAs) are fermentation end products produced by the intestinal microbiota and have anti-inflammatory and histone deacetylase-inhibiting properties. Recently, a dual relationship between the intestine and kidneys has been unraveled. Therefore, we evaluated the role of SCFA in an AKI model in which the inflammatory process has a detrimental role. We observed that therapy with the three main SCFAs (acetate, propionate, and butyrate) improved renal dysfunction caused by injury. This protection was associated with low levels of local and systemic inflammation, oxidative cellular stress, cell infiltration/activation, and apoptosis. However, it was also associated with an increase in autophagy. Moreover, SCFAs inhibited histone deacetylase activity and modulated the expression levels of enzymes involved in chromatin modification. In vitro analyses showed that SCFAs modulated the inflammatory process, decreasing the maturation of dendritic cells and inhibiting the capacity of these cells to induce CD4(+) and CD8(+) T cell proliferation. Furthermore, SCFAs ameliorated the effects of hypoxia in kidney epithelial cells by improving mitochondrial biogenesis. Notably, mice treated with acetate-producing bacteria also had better outcomes after AKI. Thus, we demonstrate that SCFAs improve organ function and viability after an injury through modulation of the inflammatory process, most likely via epigenetic modification. |
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1046-6673 |
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UofT @ mathieu.lemaire @ |
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45839 |
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Al-Nouri, Z.L.; Reese, J.A.; Terrell, D.R.; Vesely, S.K.; George, J.N. |
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Drug-induced thrombotic microangiopathy: a systematic review of published reports |
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Journal Article |
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2015 |
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Blood |
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125 |
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4 |
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616-618 |
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Many patients with syndromes of thrombotic microangiopathy (TMA), including thrombotic thrombocytopenic purpura and hemolytic-uremic syndrome, have been reported to have a drug-induced etiology, and many different drugs have been suspected as a cause of TMA. We established criteria to assess the strength of evidence for a causal association of a drug with TMA and systematically searched for all published reports of drug-induced TMA. We identified 1569 articles: 604 were retrieved for review, 344 reported evaluable data for 586 individual patients, 43 reported evaluable data on 46 patient groups. Seventy-eight drugs were described; 22 had evidence supporting a definite causal association with TMA. Three drugs accounted for 61 of the 104 patient reports with definite evidence (quinine, 34; cyclosporine, 15; tacrolimus, 12). Twenty additional drugs had evidence supporting a probable association with TMA. These criteria and data can provide support for clinicians evaluating patients with suspected TMA. |
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0006-4971 |
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UofT @ mathieu.lemaire @ |
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45847 |
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Albers, J.; Danzer, C.; Rechsteiner, M.; Lehmann, H.; Brandt, L.P.; Hejhal, T.; Catalano, A.; Busenhart, P.; Gonçalves, A.F.; Brandt, S.; Bode, P.K.; Bode-Lesniewska, B.; Wild, P.J.; Frew, I.J. |
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Title |
A versatile modular vector system for rapid combinatorial mammalian genetics |
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Journal Article |
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Year |
2015 |
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Abbreviated Journal |
J Clin Invest |
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Volume |
125 |
Issue |
4 |
Pages |
1603-1619 |
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Animals; Apoptosis; Caspase 9; Cells, Cultured; Cloning, Molecular; Clustered Regularly Interspaced Short Palindromic Repeats; Doxycycline; Drug Resistance; Gene Deletion; Gene Knockdown Techniques; Genetic Vectors; Humans; Hypoxia-Inducible Factor 1, alpha Subunit; Lentivirus; Mice; Mice, SCID; PTEN Phosphohydrolase; Recombination, Genetic; research support, non-u.s. gov’t; Retinoblastoma Protein; RNA, Small Interfering; Sarcoma, Experimental; Transduction, Genetic; Tumor Suppressor Protein p53; Xenograft Model Antitumor Assays; Cas9/CRIPSR; Journal club |
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Here, we describe the multiple lentiviral expression (MuLE) system that allows multiple genetic alterations to be introduced simultaneously into mammalian cells. We created a toolbox of MuLE vectors that constitute a flexible, modular system for the rapid engineering of complex polycistronic lentiviruses, allowing combinatorial gene overexpression, gene knockdown, Cre-mediated gene deletion, or CRISPR/Cas9-mediated (where CRISPR indicates clustered regularly interspaced short palindromic repeats) gene mutation, together with expression of fluorescent or enzymatic reporters for cellular assays and animal imaging. Examples of tumor engineering were used to illustrate the speed and versatility of performing combinatorial genetics using the MuLE system. By transducing cultured primary mouse cells with single MuLE lentiviruses, we engineered tumors containing up to 5 different genetic alterations, identified genetic dependencies of molecularly defined tumors, conducted genetic interaction screens, and induced the simultaneous CRISPR/Cas9-mediated knockout of 3 tumor-suppressor genes. Intramuscular injection of MuLE viruses expressing oncogenic H-RasG12V together with combinations of knockdowns of the tumor suppressors cyclin-dependent kinase inhibitor 2A (Cdkn2a), transformation-related protein 53 (Trp53), and phosphatase and tensin homolog (Pten) allowed the generation of 3 murine sarcoma models, demonstrating that genetically defined autochthonous tumors can be rapidly generated and quantitatively monitored via direct injection of polycistronic MuLE lentiviruses into mouse tissues. Together, our results demonstrate that the MuLE system provides genetic power for the systematic investigation of the molecular mechanisms that underlie human diseases. |
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0021-9738 |
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UofT @ mathieu.lemaire @ |
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45848 |
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Afshinnekoo, E.; Meydan, C.; Chowdhury, S.; Jaroudi, D.; Boyer, C.; Bernstein, N.; Maritz, J.M.; Reeves, D.; Gandara, J.; Chhangawala, S.; Ahsanuddin, S.; Simmons, A.; Nessel, T.; Sundaresh, B.; Pereira, E.; Jorgensen, E.; Kolokotronis, S.O.; Kirchberger, N.; Garcia, I.; Gandara, D.; Dhanraj, S.; Nawrin, T.; Saletore, Y.; Alexander, N.; Vijay, P.; Hénaff, E.M.; Zumbo, P.; Walsh, M.; O’Mullan, G.D.; Tighe, S.; Dudley, J.T.; Dunaif, A.; Ennis, S.; O’Halloran, E.; Magalhaes, T.R.; Boone, B.; Jones, A.L.; Muth, T.R.; Paolantonio, K.S.; Alter, E.; Schadt, E.E.; Garbarino, J.; Prill, R.J.; Carlton, J.M.; Levy, S.; Mason, C.E. |
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Title |
Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics |
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Journal Article |
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2015 |
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Abbreviated Journal |
Cell Syst |
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1 |
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72-87 |
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Aop |
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The panoply of microorganisms and other species present in our environment influence human health and disease, especially in cities, but have not been profiled with metagenomics at a city-wide scale. We sequenced DNA from surfaces across the entire New York City (NYC) subway system, the Gowanus Canal, and public parks. Nearly half of the DNA (48%) does not match any known organism; identified organisms spanned 1,688 bacterial, viral, archaeal, and eukaryotic taxa, which were enriched for harmless genera associated with skin (e.g., Acinetobacter). Predicted ancestry of human DNA left on subway surfaces can recapitulate U.S. Census demographic data, and bacterial signatures can reveal a station’s history, such as marine-associated bacteria in a hurricane-flooded station. Some evidence of pathogens was found (Bacillus anthracis), but a lack of reported cases in NYC suggests that the pathogens represent a normal, urban microbiome. This baseline metagenomic map of NYC could help long-term disease surveillance, bioterrorism threat mitigation, and health management in the built environment of cities. |
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2405-4712 |
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UofT @ mathieu.lemaire @ |
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45849 |
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Alkuraya, F.S. |
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Natural human knockouts and the era of genotype to phenotype |
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Journal Article |
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2015 |
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Abbreviated Journal |
Genome Med |
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7 |
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1 |
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48 |
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Complete loss of gene function in humans by naturally occurring biallelic loss-of-function mutations (human knockout) is not a new concept. However, the recent identification of human knockouts along the entire spectrum of health and disease by next-generation sequencing promises to unlock their full potential to accelerate the medical and functional annotation of the human genome. |
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1756-994x |
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UofT @ mathieu.lemaire @ |
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45850 |
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