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Gerby B.,University of Montreal | Tremblay C.S.,University of Montreal | Tremblay C.S.,Monash University | Tremblay M.,University of Montreal | And 9 more authors.
PLoS Genetics | Year: 2014

The molecular determinants that render specific populations of normal cells susceptible to oncogenic reprogramming into self-renewing cancer stem cells are poorly understood. Here, we exploit T-cell acute lymphoblastic leukemia (T-ALL) as a model to define the critical initiating events in this disease. First, thymocytes that are reprogrammed by the SCL and LMO1 oncogenic transcription factors into self-renewing pre-leukemic stem cells (pre-LSCs) remain non-malignant, as evidenced by their capacities to generate functional T cells. Second, we provide strong genetic evidence that SCL directly interacts with LMO1 to activate the transcription of a self-renewal program coordinated by LYL1. Moreover, LYL1 can substitute for SCL to reprogram thymocytes in concert with LMO1. In contrast, inhibition of E2A was not sufficient to substitute for SCL, indicating that thymocyte reprogramming requires transcription activation by SCL-LMO1. Third, only a specific subset of normal thymic cells, known as DN3 thymocytes, is susceptible to reprogramming. This is because physiological NOTCH1 signals are highest in DN3 cells compared to other thymocyte subsets. Consistent with this, overexpression of a ligand-independent hyperactive NOTCH1 allele in all immature thymocytes is sufficient to sensitize them to SCL-LMO1, thereby increasing the pool of self-renewing cells. Surprisingly, hyperactive NOTCH1 cannot reprogram thymocytes on its own, despite the fact that NOTCH1 is activated by gain of function mutations in more than 55% of T-ALL cases. Rather, elevating NOTCH1 triggers a parallel pathway involving Hes1 and Myc that dramatically enhances the activity of SCL-LMO1 We conclude that the acquisition of self-renewal and the genesis of pre-LSCs from thymocytes with a finite lifespan represent a critical first event in T-ALL. Finally, LYL1 and LMO1 or LMO2 are co-expressed in most human T-ALL samples, except the cortical T subtype. We therefore anticipate that the self-renewal network described here may be relevant to a majority of human T-ALL. © 2014 Gerby et al. Source


Faraj M.,University of Montreal | Faraj M.,Clinical Research Institute of Montreal IRCM | Lavoie M.-E.,University of Montreal | Messier L.,University of Montreal | And 2 more authors.
Atherosclerosis | Year: 2010

Objective: Large inter-individual variations exist in changes in inflammation and insulin resistance (IR) in response to hypocaloric-interventions in obese subjects that are not explained by weight-loss per se. We identified the number of serum apoB-lipoproteins (serum apoB) as the primary predictor of inflammatory markers in post-menopausal overweight/obese women. As apoB-lipoproteins are related to inflammation and inflammation promotes IR, we hypothesized that the reduction in inflammation and IR following hypocaloric-interventions is associated with the reduction in serum apoB. Methods/results: After a 6-month hypocaloric-dietary-intervention in 56 overweight/obese post-menopausal women, there was a significant reduction in weight, total, subcutaneous abdominal and visceral abdominal fat mass, apoB, Lp(a), hsCRP, orosomucoid, haptoglobin and IR (increased M clamp) and an increase in LDL-C/apoB ratio. In regression analysis, % change in apoB was the primary predictor of % changes in hsCRP (R 2=0.22), orosomucoid (R 2=0.35), haptoglobin (R 2=0.43) and M clamp (R 2=0.17). When the study population was split around baseline median apoB (0.97g/L), women who were above median apoB (N=27) had significant reduction in apoB (-17%), hsCRP (-24%), orosomucoid (-8%), haptoglobin (-18%) and IR (M clamp +14%). On the other hand, women below median apoB (N=29) had no significant changes in these parameters despite equivalent reduction in weight and fat depots in the two groups. Conclusion: Reduction in apoB associated strongly and independently with the reduction in inflammatory markers and IR following a hypocaloric-diet in overweight/obese women. We hypothesize that the elevated apoB phenotype may be key therapeutic target to reduce obesity-associated inflammation and IR maximally by hypocaloric-dietary-interventions. © 2010 Elsevier Ireland Ltd. Source


Zhang X.,University of British Columbia | Robertson G.,Cancer Agency Genome science Center | Krzywinski M.,Cancer Agency Genome science Center | Ning K.,University of British Columbia | And 5 more authors.
Biometrics | Year: 2011

ChIP-seq combines chromatin immunoprecipitation with massively parallel short-read sequencing. While it can profile genome-wide in vivo transcription factor-DNA association with higher sensitivity, specificity, and spatial resolution than ChIP-chip, it poses new challenges for statistical analysis that derive from the complexity of the biological systems characterized and from variability and biases in its sequence data. We propose a method called PICS (Probabilistic Inference for ChIP-seq) for identifying regions bound by transcription factors from aligned reads. PICS identifies binding event locations by modeling local concentrations of directional reads, and uses DNA fragment length prior information to discriminate closely adjacent binding events via a Bayesian hierarchicalt-mixture model. It uses precalculated, whole-genome read mappability profiles and a truncatedt-distribution to adjust binding event models for reads that are missing due to local genome repetitiveness. It estimates uncertainties in model parameters that can be used to define confidence regions on binding event locations and to filter estimates. Finally, PICS calculates a per-event enrichment score relative to a control sample, and can use a control sample to estimate a false discovery rate. Using published GABP and FOXA1 data from human cell lines, we show that PICS' predicted binding sites were more consistent with computationally predicted binding motifs than the alternative methods MACS, QuEST, CisGenome, and USeq. We then use a simulation study to confirm that PICS compares favorably to these methods and is robust to model misspecification. © 2010, The International Biometric Society. Source


Bridge S.H.,Northumbria University | Sheridan D.A.,Northumbria University | Sheridan D.A.,University of Plymouth | Felmlee D.J.,Northumbria University | And 16 more authors.
Journal of Hepatology | Year: 2015

Background & Aims Hepatitis C virus (HCV) associates with lipoproteins to form "lipoviral particles" (LVPs) that can facilitate viral entry into hepatocytes. Initial attachment occurs via heparan sulphate proteoglycans and low-density lipoprotein receptor (LDLR); CD81 then mediates a post-attachment event. Proprotein convertase subtilisin kexin type 9 (PCSK9) enhances the degradation of the LDLR and modulates liver CD81 levels. We measured LVP and PCSK9 in patients chronically infected with HCV genotype (G)3. PCSK9 concentrations were also measured in HCV-G1 to indirectly examine the role of LDLR in LVP clearance. Methods HCV RNA, LVP (d <1.07 g/ml) and non-LVP (d >1.07 g/ml) fractions, were quantified in patients with HCV-G3 (n = 39) by real time RT-PCR and LVP ratios (LVPr; LVP/(LVP + non-LVP)) were calculated. Insulin resistance (IR) was assessed using the homeostasis model assessment of IR (HOMA-IR). Plasma PCSK9 concentrations were measured by ELISA in HCV-G3 and HCV-G1 (n = 51). Results In HCV-G3 LVP load correlated inversely with HDL-C (r = -0.421; p = 0.008), and apoE (r = -0.428; p = 0.013). The LVPr varied more than 35-fold (median 0.286; range 0.027 to 0.969); PCSK9 was the strongest negative predictor of LVPr (R2 = 16.2%; p = 0.012). HOMA-IR was not associated with LVP load or LVPr. PCSK9 concentrations were significantly lower in HCV-G3 compared to HCV-G1 (p <0.001). PCSK9 did not correlate with LDL-C in HCV-G3 or G1. Conclusions The inverse correlation of LVP with apoE in HCV-G3, compared to the reverse in HCV-G1 suggests HCV genotype-specific differences in apoE mediated viral entry. Lower PCSK9 and LDL concentrations imply upregulated LDLR activity in HCV-G3. © 2014 European Association for the Study of the Liver. Source


Rousselet E.,Clinical Research Institute of Montreal IRCM | Marcinkiewicz J.,Clinical Research Institute of Montreal IRCM | Kriz J.,Laval University | Zhou A.,Robert S Dow Neurobiology Laboratories | And 3 more authors.
Journal of Lipid Research | Year: 2011

Proprotein convertase subtilisin/kexin type 9 (PCSK9) plays a major role in cholesterol homeostasis through enhanced degradation of the LDL receptor (LDLR) in liver. As novel inhibitors/silencers of PCSK9 are now being tested in clinical trials to treat hypercholesterolemia, it is crucial to define the physiological consequences of the lack of PCSK9 in various organs. LDLR regulation by PCSK9 has not been extensively described during mouse brain development and injury. Herein, we show that PCSK9 and LDLR are co-expressed in mouse brain during development and at adulthood. Although the protein levels of LDLR and apolipoprotein E (apoE) in the adult brain of Pcsk9 -/- mice are similar to those of wild-type (WT) mice, LDLR levels increased and were accompanied by a reduction of apoE levels during development. This suggests that the upregulation of LDLR protein levels in Pcsk9-/- mice enhances apoE degradation. Upon ischemic stroke, PCSK9 was expressed in the dentate gyrus between 24 h and 72 h following brain reperfusion. Although mouse behavior and lesion volume were similar, LDLR protein levels dropped ∼2-fold less in the Pcsk9-/--lesioned hippocampus, without affecting apoE levels and neurogenesis. Thus, PCSK9 downregulates LDLR levels during brain development and following transient ischemic stroke in adult mice. Copyright © 2011 by the American Society for Biochemistry and Molecular Biology, Inc. Source

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