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Roseshter T, Klemantovich A, Cavallone L, Aguilar-Mahecha A, Lafleur J, Elebute OO, Jenna S, Boileau JF, Pelmus M, Basik M, Lan C. Abstract P2-11-26: The prognostic role of circulating tumor DNA after neoadjuvant chemotherapy in triple negative breast cancer with residual tumor. Cancer Res 2023. [DOI: 10.1158/1538-7445.sabcs22-p2-11-26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Abstract
Background The presence of residual tumour at surgery (non-pathological complete response or non-pCR) occurs in about half of TNBCs treated with neoadjuvant chemotherapy (NAC) and signals chemoresistance and poor prognosis. Although further adjuvant chemotherapy (Capecitabine/Xeloda) results in improved survival in patients with non-pCR, only about 15% of such patients do benefit. Circulating tumor DNA (ctDNA) is a plasma-based biomarker that can be used to reveal real-time data about the disease and treatment progression. We have previously shown that detection of ctDNA after NAC signals poor prognosis. To validate and extend our previous results using an academic hospital-based tumor bespoke assay, we performed ctDNA measurements in non-pCR TNBC patients at the pre-operative, post-operative, 3 and 6-month time points. Methods Whole exome sequencing (WES) was performed on residual tumors from 34 TNBC patients to identify tumour-specific mutations (5/patient). Digital droplet PCR (ddPCR) assays were developed for these mutations and performed as per our previous work. Patients with at least one detectable mutation were considered ctDNA positive for a given time point. The detection of ctDNA was correlated with relapse-free survival (RFS). Results The overall RFS was 44%, with 56 % of patients received adjuvant Xeloda. Detection of ctDNA at the end of NAC (T1) correlated with poor prognosis of RFS (n = 33, p-value = 0.009, HR = 0.29 (95% CI = 0.12 to 0.74)). Detection of ctDNA after surgery (T2) and while on Xeloda (T3) showed no significant prognostic value for RFS. However, ctDNA detection at the 6-month time point, after Xeloda treatment (T4), showed stronger prognostic value for RFS (n = 17, p-value = 0.004, HR = 0.12 (95% CI = 0.03 to 0.51)). When measuring changes in ctDNA detectability from T1 to T4, 4 patients initially positive became ctDNA negative after the 6-month interval, and only 1 of these 4 had a relapse, compared with 10 of 11 that remained positive at the 6-month time point (p = 0.01, Chi-squared test). 3 of the 4 patients that cleared their ctDNA had received Xeloda. In addition, 2 patients initially negative became ctDNA positive at the 6-month time point (T4) and both relapsed, compared with only 1 of 5 that remained negative at 6 months (p = 0.035, Chi-squared test). For patients who received adjuvant Xeloda ctDNA positivity at T1 was associated with a worse RFS (p-value = 0.028, HR = 3.3884 (95% CI = 1.160 to 13.00)). Conclusion ctDNA testing using ddPCR in an academic hospital-based context at the post-NAC time point as well as at 6 months after surgery identifies an excellent prognostic group in TNBC patients with non-pCR and changes in ctDNA during the adjuvant period have prognostic value. This personalized approach to treatment management is ready for prospective testing in patients who have undergone NAC and require additional chemotherapy.
Citation Format: Talia Roseshter, Anna Klemantovich, Luca Cavallone, Adriana Aguilar-Mahecha, Josiane Lafleur, Oluwadara O. Elebute, Sarah Jenna, Jean-Francois Boileau, Manuela Pelmus, Mark Basik, Cathy Lan. The prognostic role of circulating tumor DNA after neoadjuvant chemotherapy in triple negative breast cancer with residual tumor [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P2-11-26.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Manuela Pelmus
- 9Jewish General Hospital Segal Cancer Centre, McGill University, Montréal, Quebec, Canada
| | | | - Cathy Lan
- 11Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada
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Kapelanski-Lamoureux A, Tsamchoe M, Krzywon L, Bloom J, Cardin J, K Petrillo S, Gao ZH, Jenna S, Lazaris A, Metrakos P. AI-powered multi-omic signature to predict treatment response of patients with colorectal cancer liver metastasis. J Clin Oncol 2023. [DOI: 10.1200/jco.2023.41.4_suppl.252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
252 Background: Colorectal cancer (CRC) is the third leading cause of cancer-related deaths in North America with over 50% of CRC patients developing liver metastases (LM) and 90% will die from metastatic disease. CRCLM are categorized into two main histological growth patterns (HGP) lesions: Desmoplastic (DHGP) and Replacement (RHGP). We have previously published that HGPs display distinct patterns of vascularization, local invasion, growth and response to treatment. Resected CRCLM patients with predominantly DHGP metastasis (~45%) receiving anti-VEGF therapy and chemotherapy have more than double the 5-year overall survival compared to patients with RHGP (~55%) who have received the same treatment. We are therefore treating patients that will not respond and should in fact be managed differently. Currently, there are no available biomarkers or stratification tools that predict colorectal cancer liver metastasis response to therapy. Methods: In collaboration with My Intelligent Machines (MIMs’), we used a proprietary GI2 (Genetic Interaction Graph Inference) algorithm inferring genetic interactions. We developed an AI based pipeline to develop a multi-modality signature, based on blood test analysis, to identify CRCLM patients who will 1) respond to Angiogenic Inhibitor-based therapies and 2) monitor the development of drug resistance (non-responders). Results: We obtained transcriptomic (tumor tissue) as well as proteomic data (liquid biopsy: Extracellular vesicle cargo), linked to clinical data from 40 chemonaïve patients, and fed the data into MIMs platform (BioMark). The software was able to identify differentially expressed genes common to the top differentially enriched proteins leading to a robust liquid biopsy biomarker signature distinguishing DHGP and RHGP. Furthermore, our data demonstrates a unique multi-modality signature providing biological insight for therapeutic failures and/or success. Conclusions: We will use these signatures to not only predict response to treatment but also decipher the molecular mechanisms driving these two phenotypes and identify unique targets. It is expected that this knowledge will lead to optimization of current treatment strategies, allowing for a precision therapy approach to the management of metastatic disease and cost saving for the health care system.
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Affiliation(s)
| | - Migmar Tsamchoe
- Anatomy & Cell Biology Department, McGill University, Montreal, QC, Canada
| | - Lucyna Krzywon
- Experimental Surgery Department, McGill University, Montreal, QC, Canada
| | - Jessica Bloom
- Experimental Surgery Department, McGill University, Montreal, QC, Canada
| | - Julie Cardin
- Research Institute, McGill University Health Centre, Montreal, QC, Canada
| | | | - Zu-hua Gao
- Pathology & Laboratory Medicine department, University of British Columbia, Vancouver, BC, Canada
| | - Sarah Jenna
- My Intelligent Machines Inc., Montreal, QC, Canada
| | - Anthoula Lazaris
- Research Institute, McGill University Health Centre, Montreal, QC, Canada
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Jenna S, Boucher B, Dudragne L, Diallo AB. Abstract 6375: Augmented intelligence to define drug targets associated with triple negative breast cancer (TNBC) metabolic reprogramming. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-6375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction: Basal-like breast cancer (BLBC; TNBC) cells use aerobic glycolysis at a higher rate than Luminal A (LumA) cells. Metabolic reprogramming using aerobic glycolysis (Warburg effect), is correlated with increased aggressiveness of cancer cells and poor outcome in patients. Therefore, genes involved in this pathway are promising targets for developing cancer therapeutics.
Method: MIMs has developed a unique platform of augmented intelligence that combines bioinformatics, systems biology and artificial intelligence. It integrates multi-layered omics data with a knowledge-base that aggregates structured data from more than 140 databases as well as unstructured data from the scientific literature. Using this approach a genetic interaction graph (GI-Graph) is inferred per patient, capturing functional relationships between genes in the specific context of the tumor. The GI-Graphs are subsequently used to train supervised machine learning algorithms for predicting gene functionality and potential as a target. Preliminary analysis was performed on transcriptomic data from 321 LumA and 162 TNBC samples, from the TCGA Data Portal and a predictive model was developed using two GI-Graphs from the two subgroups. Briefly, subgraphs, containing genes with functional interactions with the known genes in OXPHOS and glycolysis pathways, were used to extract gene attributes, and to build an algorithm that predicts involvement of a gene in the Warburg effect. Using a testing gene set extracted from the literature the performance of the model was assessed, which showed a true positive rate of 18% and a false positive rate of 0.36%, and outperformed 5-times the classical bioinformatics tools.
Results: This model predicted 108 genes as the top 1% genes being involved in the metabolic reprogramming of TNBC. Additional information from MIMs’ platform, including differential gene expression between LumA and TNBC, gene pleiotropy and essentiality and the topological metrics, enabled the life scientists to further refine the gene lists, based on the expected characteristics of a good target in oncology. Following this process, 30 genes were selected as potential targets controlling the metabolic reprogramming of TNBC, among which 4 genes were already evaluated in TNBC clinical trials.
Conclusion: Our preliminary data strongly supports that the predictive model based on the GI-Graphs has the potential to identify promising therapeutic targets for TNBC.
Citation Format: Sarah Jenna, Benjamin Boucher, Liebaut Dudragne, Abdoulaye Baniré Diallo. Augmented intelligence to define drug targets associated with triple negative breast cancer (TNBC) metabolic reprogramming [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6375.
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Affiliation(s)
- Sarah Jenna
- 1My Intelligent Machines, Montreal, Quebec, Canada
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Aguilar-Mahecha A, Majedi Y, Elebute O, Lafleur J, Papadakis A, Lan C, Pelmus M, Rashid T, Jenna S, Basik M. Abstract 4011: Prognostic value of transcriptomic analysis in residual post neo-adjuvant triple negative breast cancer tumors. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-4011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Triple negative breast cancer is the most aggressive type of breast cancer. Approximately 50% of TNBC patients respond to pre-operative neo-adjuvant chemotherapy (NAC), however those patients with residual disease (non-pathological complete response or non-pCR) have a very poor prognosis. Recently, the use of capecitabine in the adjuvant setting was shown to increase disease-free survival in non-pCR patients. However, there are no biomarkers to identify patients who may benefit from adjuvant capecitabine. Moreover, novel therapeutic targets are needed to treat patients with non-pCR.
Methods: RNA extracted from 32 Formalin Fixed Paraffin Embedded (FFPE) residual post-NAC tumor samples underwent NanoString nCounter gene expression analysis using the BC360 panel as well as RNAseq.
Results: Comparison of tumors from poor (RFS<2 yrs) and good prognosis (RFS>2 yrs) patients showed 65 genes differentially expressed (≥1.5 fold change and p<0.05) by nCounter. 40 of these genes had differential expression also validated by RNAseq (R2= 0.96) and were selected for further pathway analysis. Gene Set Enrichment Analysis (GSEA) showed an enrichment for biological pathways involved in cell cycle, with all genes in this set upregulated in the poor prognosis group. GSEA analysis of 310 upregulated genes identified by RNAseq showed an enrichment for biological pathways associated with cell population proliferation and skin development. Interestingly, one of the upregulated genes identified was TYMS, encoding thymidylate synthase, the target of capecitabine, which showed 2-fold increased expression in the poor prognosis group (p≤0.005).
Conclusion: Our results suggest that residual tumors from TNBC patients who relapse within two years of surgery show transcriptomic evidence of increased proliferation and that expression levels of TYMS may be a potential biomarker to select patients for capecitabine in the adjuvant setting.
Citation Format: Adriana Aguilar-Mahecha, Yasamin Majedi, Oluwadara Elebute, Josiane Lafleur, Andreas Papadakis, Cathy Lan, Manuela Pelmus, Touhidur Rashid, Sarah Jenna, Mark Basik. Prognostic value of transcriptomic analysis in residual post neo-adjuvant triple negative breast cancer tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 4011.
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Affiliation(s)
- Adriana Aguilar-Mahecha
- 1Lady Davis Institute, Segal Cancer Center, Jewish General Hospital, Montreal, Quebec, Canada
| | - Yasamin Majedi
- 1Lady Davis Institute, Segal Cancer Center, Jewish General Hospital, Montreal, Quebec, Canada
| | | | - Josiane Lafleur
- 1Lady Davis Institute, Segal Cancer Center, Jewish General Hospital, Montreal, Quebec, Canada
| | - Andreas Papadakis
- 1Lady Davis Institute, Segal Cancer Center, Jewish General Hospital, Montreal, Quebec, Canada
| | - Cathy Lan
- 1Lady Davis Institute, Segal Cancer Center, Jewish General Hospital, Montreal, Quebec, Canada
| | | | | | - Sarah Jenna
- 2My Intelligent Machines, Montreal, Quebec, Canada
| | - Mark Basik
- 1Lady Davis Institute, Segal Cancer Center, Jewish General Hospital, Montreal, Quebec, Canada
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Jenna S, Lemaçon A, Dehghani M, Renaut S, Baniré Diallo A. Inference of sample-specific genetic interactions to increase accuracy of indication prioritization in oncology clinical trials and facilitate exploration of combined therapy opportunities. J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.16_suppl.3123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
3123 Background: Precision oncology is growing rapidly in parallel with advances in high throughput sequencing. Development of new anti-cancer therapies is, however, still associated with low efficacy issues, leading to phase II and III clinical trial failures. Improved methodologies are required to identify clinical and molecular patient profiles associated with good drug response to inform decisions on indication prioritization. Methods: We used a sample-specific Genetic Interaction Graph Inference (ssGI2) algorithm, integrating bulk tumor transcriptomic data as well as data collected from 120 public databases and scientific literature in oncology, to infer genetic interactions (GI). More than 10,000 genes from 17,000 samples, covering 195 oncology ICD10 codes, were used to infer GIs for each individual sample. GIs involving a given drug target are selected from a compendium of 17,000 networks of 2M GIs each, and ranked based on their prevalence in the patient cohort and data-support. The mean Z-scored expression of genes from the top ranked GIs were subsequently used to predict drug response for each patient and to calculate the response rate for each indication. Detailed information on each drug target’s genetic interactors was used to characterize the drug’s mechanisms of action and explore opportunities for combined therapies. We investigated our method's ability to predict good responders using four FDA approved immune and targeted therapies (pembrolizumab, nivolumab, ipilimumab and sorafenib) across seven clinical studies. Importantly this methodology is suitable for drugs with no clinical studies available. Results: Our results show that the prediction of good responders can be achieved with Precision-Recall AUC on average 13% higher than predictions based on drug target expression level solely, in five out of seven studies. Also, for each drug target, between 30 to 140 genetic interactors with good performance (Precision=0.92; Recall=0.61) were identified, suggesting potential synergistic effects of drugs, some of which have already been confirmed by clinical studies on combined therapies. Conclusions: Our ssGI2-derived signatures are powerful predictors of good response to a drug even without available clinical data. Applying this methodology at a pre-clinical stage will significantly de-risk clinical trials, particularly for novel therapies, and could also support investigation of new combined therapies.
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Affiliation(s)
- Sarah Jenna
- My Intelligent Machines Inc., Montreal, QC, Canada
| | | | | | | | - Abdoulaye Baniré Diallo
- Université du Québec à Montréal (UQAM) - Department of Computer Science, Montreal, QC, Canada
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Abstract
Autophagy is the process where cytosolic components are digested by the cell. This process is required for cell survival in stressful conditions. It was also shown to control cell division and more recently, cell morphology and migration. We characterized signalling pathways enabling embryonic epidermal cells of the nematode Caenorhabditis elegans to elongate along their antero-posterior axis. Previous studies revealed that epidermal cells can adopt either a RhoA-like or a Rac1-like morphogenic program. We show here that the AMP-activated protein kinase (AMPK) and genes controlling autophagy are required for proper elongation of epidermal cells following the RhoA-like program and are dispensable for other cells. This suggests that AMPK-autophagy is used by the embryo to fuel the most energy-demanding morphogenic processes promoting early elongation.
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Affiliation(s)
- Emmanuel Martin
- Integrative Genomics and cell signaling laboratory, Chemistry-Biochemistry Department, Université du Québec à Montréal (UQAM), Montreal, Canada
| | - Grégoire Bonnamour
- Integrative Genomics and cell signaling laboratory, Chemistry-Biochemistry Department, Université du Québec à Montréal (UQAM), Montreal, Canada
| | - Sarah Jenna
- Integrative Genomics and cell signaling laboratory, Chemistry-Biochemistry Department, Université du Québec à Montréal (UQAM), Montreal, Canada
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7
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Caruso ME, Jenna S, Baillie DL, Bossé R, Simpson JC, Chevet E, Taouji S. Systematic functional analysis of the Ras GTPase family unveils a conserved network required for anterograde protein trafficking. Proteomics 2016; 17. [PMID: 27957805 DOI: 10.1002/pmic.201600302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 11/24/2016] [Accepted: 12/07/2016] [Indexed: 11/05/2022]
Abstract
Phylogeny is often used to compare entire families of genes/proteins. We previously showed that classification of Caenorhabditis elegans Rho GTPases on the basis of their enzymatic properties was significantly different from sequence alignments. To further develop this concept, we have developed an integrated approach to classify C. elegans small GTPases based on functional data comprising affinity for GTP, sub-cellular localization, tissue distribution and silencing impact. This analysis led to establish a novel functional classification for small GTPases. To test the relevance of this classification in mammals, we focused our attention on the human orthologs of small GTPases from a specific group comprising arf-1.2, evl-20, arl-1, Y54E10BR.2, unc-108 and rab-7. We then tested their involvement in protein secretion and membrane traffic in mammalian systems. Using this approach we identify a novel network containing 18 GTPases, and 23 functionally interacting proteins, conserved between C. elegans and mammals, which is involved in membrane traffic and protein secretion.
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Affiliation(s)
| | - Sarah Jenna
- Department of Surgery, McGill University, Montreal, QC, Canada
| | - David L Baillie
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | | | - Jeremy C Simpson
- School of Biology & Environmental Science and Conway Institute of Biomolecular & Biomedical Research, University College Dublin (UCD), Dublin, Ireland
| | - Eric Chevet
- Department of Surgery, McGill University, Montreal, QC, Canada.,INSERM U1242, COSS, Université de Rennes-1, CLCC Eugene Marquis, Rennes, France.,BMYscreen, Bordeaux, France
| | - Saïd Taouji
- BMYscreen, Bordeaux, France.,INSERM U1218, CLCC Institut Bergonié, Bordeaux, France
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8
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Perreault S, de Denus S, White M, White-Guay B, Bouvier M, Dorais M, Dubé MP, Rouleau JL, Tardif JC, Jenna S, Haibe-Kains B, Leduc R, Deblois D. Older adults with heart failure treated with carvedilol, bisoprolol, or metoprolol tartrate: risk of mortality. Pharmacoepidemiol Drug Saf 2016; 26:81-90. [PMID: 27859924 DOI: 10.1002/pds.4132] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 10/04/2016] [Accepted: 10/17/2016] [Indexed: 11/12/2022]
Abstract
PURPOSE The long-term use of β-blockers has been shown to improve clinical outcomes among patients with heart failure (HF). However, a lack of data persists in assessing whether carvedilol or bisoprolol are superior to metoprolol tartrate in clinical practice. We endeavored to compare the effectiveness of β-blockers among older adults following a primary hospital admission for HF. METHODS We conducted a cohort study using Quebec administrative databases to identify patients who were using β-blockers, carvedilol, bisoprolol, or metoprolol tartrate after the diagnosis of HF. We characterized the patients by the type of β-blocker prescribed at discharge of their first HF hospitalization. An adjusted multivariate Cox proportional hazards model was used to compare the primary outcome of all-cause mortality. We also conducted analyses by matching for a propensity score for initiation of β-blocker therapy and assessed the effect on primary outcome. RESULTS Among 3197 patients with HF with a median follow-up of 2.8 years, the crude annual mortality rates (per 100 person-years) were at 16, 14.9, and 17.7 for metoprolol tartrate, carvedilol, and bisoprolol, respectively. Adjusted hazard ratios of carvedilol (hazard ratio 0.92; 0.78-1.09) and bisoprolol (hazard ratio 1.04; 0.93-1.16) were not significantly different from that of metoprolol tartrate in improving survival. After matching for propensity score, carvedilol and bisoprolol showed no additional benefit with respect to all-cause mortality compared with metoprolol tartrate. CONCLUSIONS Our evidence suggests no differential effect of β-blockers on all-cause mortality among older adults with HF. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Sylvie Perreault
- Faculty of Pharmacy, University of Montreal, Montreal, Quebec, Canada.,University of Montreal, Montreal, Quebec, Canada
| | - Simon de Denus
- Faculty of Pharmacy, University of Montreal, Montreal, Quebec, Canada.,University of Montreal, Montreal, Quebec, Canada.,Montreal Heart Institute, Montreal, Quebec, Canada
| | - Michel White
- Faculty of Medicine, University of Montreal, Montreal, Quebec, Canada.,University of Montreal, Montreal, Quebec, Canada.,Montreal Heart Institute, Montreal, Quebec, Canada
| | - Brian White-Guay
- Faculty of Pharmacy, University of Montreal, Montreal, Quebec, Canada.,Faculty of Medicine, University of Montreal, Montreal, Quebec, Canada.,University of Montreal, Montreal, Quebec, Canada
| | - Michel Bouvier
- Faculty of Medicine, University of Montreal, Montreal, Quebec, Canada.,University of Montreal, Montreal, Quebec, Canada
| | - Marc Dorais
- Stats Sciences, University of Montreal, Montreal, Quebec, Canada
| | - Marie-Pierre Dubé
- Faculty of Medicine, University of Montreal, Montreal, Quebec, Canada.,University of Montreal, Montreal, Quebec, Canada.,Montreal Heart Institute, Montreal, Quebec, Canada
| | - Jean-Lucien Rouleau
- Faculty of Medicine, University of Montreal, Montreal, Quebec, Canada.,University of Montreal, Montreal, Quebec, Canada.,Montreal Heart Institute, Montreal, Quebec, Canada
| | - Jean-Claude Tardif
- Faculty of Medicine, University of Montreal, Montreal, Quebec, Canada.,University of Montreal, Montreal, Quebec, Canada.,Montreal Heart Institute, Montreal, Quebec, Canada
| | - Sarah Jenna
- University of Quebec in Montreal, Montreal, Quebec, Canada
| | - Benjamin Haibe-Kains
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Canada.,Department of Computer Science, University of Toronto, Toronto, Canada
| | - Richard Leduc
- University of Sherbrooke, Montreal, Quebec, Canada.,Faculty of Medicine, University of Sherbrooke, Quebec, Canada
| | - Denis Deblois
- Faculty of Pharmacy, University of Montreal, Montreal, Quebec, Canada.,University of Montreal, Montreal, Quebec, Canada
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Martin E, Ouellette MH, Jenna S. Rac1/RhoA antagonism defines cell-to-cell heterogeneity during epidermal morphogenesis in nematodes. J Cell Biol 2016; 215:483-498. [PMID: 27821782 PMCID: PMC5119937 DOI: 10.1083/jcb.201604015] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 07/29/2016] [Accepted: 10/19/2016] [Indexed: 01/13/2023] Open
Abstract
Antagonism between the GTPases Rac1 and RhoA controls different morphogenetic processes during embryonic development. Martin et al. use quantitative imaging analyses to demonstrate that cell-autonomous antagonism between the RhoA- and Rac1-like pathways defines cell-to-cell heterogeneity during epidermal morphogenesis in Caenorhabditis elegans. The antagonism between the GTPases Rac1 and RhoA controls cell-to-cell heterogeneity in isogenic populations of cells in vitro and epithelial morphogenesis in vivo. Its involvement in the regulation of cell-to-cell heterogeneity during epidermal morphogenesis has, however, never been addressed. We used a quantitative cell imaging approach to characterize epidermal morphogenesis at a single-cell level during early elongation of Caenorhabditis elegans embryos. This study reveals that a Rac1-like pathway, involving the Rac/Cdc42 guanine-exchange factor β-PIX/PIX-1 and effector PAK1/PAK-1, and a RhoA-like pathway, involving ROCK/LET-502, control the remodeling of apical junctions and the formation of basolateral protrusions in distinct subsets of hypodermal cells. In these contexts, protrusions adopt lamellipodia or an amoeboid morphology. We propose that lamella formation may reduce tension building at cell–cell junctions during morphogenesis. Cell-autonomous antagonism between these pathways enables cells to switch between Rac1- and RhoA-like morphogenetic programs. This study identifies the first case of cell-to-cell heterogeneity controlled by Rac1/RhoA antagonism during epidermal morphogenesis.
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Affiliation(s)
- Emmanuel Martin
- Department of Chemistry, Pharmaqam, Université du Québec à Montréal, Montreal, QC H3C 3P8, Canada
| | - Marie-Hélène Ouellette
- Department of Chemistry, Pharmaqam, Université du Québec à Montréal, Montreal, QC H3C 3P8, Canada
| | - Sarah Jenna
- Department of Chemistry, Pharmaqam, Université du Québec à Montréal, Montreal, QC H3C 3P8, Canada
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Martin E, Rocheleau-Leclair O, Jenna S. Novel Metrics to Characterize Embryonic Elongation of the Nematode Caenorhabditis elegans. J Vis Exp 2016:e53712. [PMID: 27077374 DOI: 10.3791/53712] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Dissecting the signaling pathways that control the alteration of morphogenic processes during embryonic development requires robust and sensitive metrics. Embryonic elongation of the nematode Caenorhabditis elegans is a late developmental stage consisting of the elongation of the embryo along its longitudinal axis. This developmental stage is controlled by intercellular communication between hypodermal cells and underlying body-wall muscles. These signaling mechanisms control the morphology of hypodermal cells by remodeling the cytoskeleton and the cell-cell junctions. Measurement of embryonic lethality and developmental arrest at larval stages as well as alteration of cytoskeleton and cell-cell adhesion structures in hypodermal and muscle cells are classical phenotypes that have been used for more than 25 years to dissect these signaling pathways. Recent studies required the development of novel metrics specifically targeting either early or late elongation and characterizing morphogenic defects along the antero-posterior axis of the embryo. Here, we provide detailed protocols enabling the accurate measurement of the length and the width of the elongating embryos as well as the length of synchronized larvae. These methods constitute useful tools to identify genes controlling elongation, to assess whether these genes control both early and late phases of this stage and are required evenly along the antero-posterior axis of the embryo.
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Affiliation(s)
- Emmanuel Martin
- Department of Chemistry, Pharmaqam, Université du Québec à Montréal
| | | | - Sarah Jenna
- Department of Chemistry, Pharmaqam, Université du Québec à Montréal;
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11
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Ouellette MH, Martin E, Lacoste-Caron G, Hamiche K, Jenna S. Spatial control of active CDC-42 during collective migration of hypodermal cells in Caenorhabditis elegans. J Mol Cell Biol 2015; 8:313-27. [PMID: 26578656 DOI: 10.1093/jmcb/mjv062] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 08/12/2015] [Indexed: 12/11/2022] Open
Abstract
Collective epithelial cell migration requires the maintenance of cell-cell junctions while enabling the generation of actin-rich protrusions at the leading edge of migrating cells. Ventral enclosure of Caenorhabditis elegans embryos depends on the collective migration of anterior-positioned leading hypodermal cells towards the ventral midline where they form new junctions with their contralateral neighbours. In this study, we characterized the zygotic function of RGA-7/SPV-1, a CDC-42/Cdc42 and RHO-1/RhoA-specific Rho GTPase-activating protein, which controls the formation of actin-rich protrusions at the leading edge of leading hypodermal cells and the formation of new junctions between contralateral cells. We show that RGA-7 controls these processes in an antagonistic manner with the CDC-42's effector WSP-1/N-WASP and the CDC-42-binding proteins TOCA-1/2/TOCA1. RGA-7 is recruited to spatially distinct locations at junctions between adjacent leading cells, where it promotes the accumulation of clusters of activated CDC-42. It also inhibits the spreading of these clusters towards the leading edge of the junctions and regulates their accumulation and distribution at new junctions formed between contralateral leading cells. Our study suggests that RGA-7 controls collective migration and junction formation between epithelial cells by spatially restricting active CDC-42 within cell-cell junctions.
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Affiliation(s)
- Marie-Hélène Ouellette
- Department of Chemistry, Pharmaqam, Biomed, Université du Québec à Montréal, Montréal, Québec, Canada
| | - Emmanuel Martin
- Department of Chemistry, Pharmaqam, Biomed, Université du Québec à Montréal, Montréal, Québec, Canada
| | - Germain Lacoste-Caron
- Department of Chemistry, Pharmaqam, Biomed, Université du Québec à Montréal, Montréal, Québec, Canada
| | - Karim Hamiche
- Department of Chemistry, Pharmaqam, Biomed, Université du Québec à Montréal, Montréal, Québec, Canada
| | - Sarah Jenna
- Department of Chemistry, Pharmaqam, Biomed, Université du Québec à Montréal, Montréal, Québec, Canada
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Martin E, Harel S, Nkengfac B, Hamiche K, Neault M, Jenna S. pix-1 controls early elongation in parallel with mel-11 and let-502 in Caenorhabditis elegans. PLoS One 2014; 9:e94684. [PMID: 24732978 PMCID: PMC3986101 DOI: 10.1371/journal.pone.0094684] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 03/17/2014] [Indexed: 12/17/2022] Open
Abstract
Cell shape changes are crucial for metazoan development. During Caenorhabditis elegans embryogenesis, epidermal cell shape changes transform ovoid embryos into vermiform larvae. This process is divided into two phases: early and late elongation. Early elongation involves the contraction of filamentous actin bundles by phosphorylated non-muscle myosin in a subset of epidermal (hypodermal) cells. The genes controlling early elongation are associated with two parallel pathways. The first one involves the rho-1/RHOA-specific effector let-502/Rho-kinase and mel-11/myosin phosphatase regulatory subunit. The second pathway involves the CDC42/RAC-specific effector pak-1. Late elongation is driven by mechanotransduction in ventral and dorsal hypodermal cells in response to body-wall muscle contractions, and involves the CDC42/RAC-specific Guanine-nucleotide Exchange Factor (GEF) pix-1, the GTPase ced-10/RAC and pak-1. In this study, pix-1 is shown to control early elongation in parallel with let-502/mel-11, as previously shown for pak-1. We show that pix-1, pak-1 and let-502 control the rate of elongation, and the antero-posterior morphology of the embryos. In particular, pix-1 and pak-1 are shown to control head, but not tail width, while let-502 controls both head and tail width. This suggests that let-502 function is required throughout the antero-posterior axis of the embryo during early elongation, while pix-1/pak-1 function may be mostly required in the anterior part of the embryo. Supporting this hypothesis we show that low pix-1 expression level in the dorsal-posterior hypodermal cells is required to ensure high elongation rate during early elongation.
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Affiliation(s)
- Emmanuel Martin
- Department of Chemistry, Pharmaqam, Biomed, Université du Québec à Montréal (UQÀM), Montréal, Québec, Canada
| | - Sharon Harel
- Department of Chemistry, Pharmaqam, Biomed, Université du Québec à Montréal (UQÀM), Montréal, Québec, Canada
| | - Bernard Nkengfac
- Department of Chemistry, Pharmaqam, Biomed, Université du Québec à Montréal (UQÀM), Montréal, Québec, Canada
| | - Karim Hamiche
- Department of Chemistry, Pharmaqam, Biomed, Université du Québec à Montréal (UQÀM), Montréal, Québec, Canada
| | - Mathieu Neault
- Department of Chemistry, Pharmaqam, Biomed, Université du Québec à Montréal (UQÀM), Montréal, Québec, Canada
| | - Sarah Jenna
- Department of Chemistry, Pharmaqam, Biomed, Université du Québec à Montréal (UQÀM), Montréal, Québec, Canada
- * E-mail:
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Abstract
A genetic interaction (GI) between two genes generally indicates that the phenotype of a double mutant differs from what is expected from each individual mutant. In the last decade, genome scale studies of quantitative GIs were completed using mainly synthetic genetic array technology and RNA interference in yeast and Caenorhabditis elegans. These studies raised questions regarding the functional interpretation of GIs, the relationship of genetic and molecular interaction networks, the usefulness of GI networks to infer gene function and co-functionality, the evolutionary conservation of GI, etc. While GIs have been used for decades to dissect signaling pathways in genetic models, their functional interpretations are still not trivial. The existence of a GI between two genes does not necessarily imply that these two genes code for interacting proteins or that the two genes are even expressed in the same cell. In fact, a GI only implies that the two genes share a functional relationship. These two genes may be involved in the same biological process or pathway; or they may also be involved in compensatory pathways with unrelated apparent function. Considering the powerful opportunity to better understand gene function, genetic relationship, robustness and evolution, provided by a genome-wide mapping of GIs, several in silico approaches have been employed to predict GIs in unicellular and multicellular organisms. Most of these methods used weighted data integration. In this article, we will review the later knowledge acquired on GI networks in metazoans by looking more closely into their relationship with pathways, biological processes and molecular complexes but also into their modularity and organization. We will also review the different in silico methods developed to predict GIs and will discuss how the knowledge acquired on GI networks can be used to design predictive tools with higher performances.
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Affiliation(s)
- Benjamin Boucher
- Laboratory of Integrative Genomics and Cell Signalling, Pharmaqam, Biomed, Department of Chemistry, Université du Québec à Montréal Montréal, QC, Canada
| | - Sarah Jenna
- Laboratory of Integrative Genomics and Cell Signalling, Pharmaqam, Biomed, Department of Chemistry, Université du Québec à Montréal Montréal, QC, Canada
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Abstract
Mental retardation (MR) occurs in 2 to 3 % of the general population and is still not therapeutically addressed. Milder forms of MR result from deficient synaptogenesis and/or impaired synaptic plasticity during childhood. These alterations would result from disequilibrium in signalling pathways regulating the balance between long term potentiation (LTP) and long term depression (LTD) in certain neurons such as hippocampus neurons. To provide mentally retarded children with increased cognitive abilities, novel experimental approaches are currently being developed to characterize signalling status associated with MR and to identify therapeutic targets that would restore lost equilibrium. Several studies also highlighted the major role played by molecular switches like kinases, phosphatases, small G proteins and their regulators in the coordination and integration of signalling pathways associated with synaptic plasticity. These proteins may therefore constitute promising therapeutic targets for a number of cognitive deficiencies.
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Affiliation(s)
- Sharon Harel
- Université du Québec à Montréal, Département de chimie, Pharmaqam, Biomed, CP 8888, Succursale Centre-ville, Montréal, Québec H3C3P8, Canada
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Chartrand É, Arnold AA, Gravel A, Jenna S, Marcotte I. Potential role of the membrane in hERG channel functioning and drug-induced long QT syndrome. Biochimica et Biophysica Acta (BBA) - Biomembranes 2010; 1798:1651-62. [DOI: 10.1016/j.bbamem.2010.05.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2009] [Revised: 04/21/2010] [Accepted: 05/17/2010] [Indexed: 11/16/2022]
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Lee AY, Perreault R, Harel S, Boulier EL, Suderman M, Hallett M, Jenna S. Searching for signaling balance through the identification of genetic interactors of the Rab guanine-nucleotide dissociation inhibitor gdi-1. PLoS One 2010; 5:e10624. [PMID: 20498707 PMCID: PMC2869356 DOI: 10.1371/journal.pone.0010624] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2009] [Accepted: 03/22/2010] [Indexed: 12/27/2022] Open
Abstract
Background The symptoms of numerous diseases result from genetic mutations that disrupt the homeostasis maintained by the appropriate integration of signaling gene activities. The relationships between signaling genes suggest avenues through which homeostasis can be restored and disease symptoms subsequently reduced. Specifically, disease symptoms caused by loss-of-function mutations in a particular gene may be reduced by concomitant perturbations in genes with antagonistic activities. Methodology/Principal Findings Here we use network-neighborhood analyses to predict genetic interactions in Caenorhabditis elegans towards mapping antagonisms and synergisms between genes in an animal model. Most of the predicted interactions are novel, and the experimental validation establishes that our approach provides a gain in accuracy compared to previous efforts. In particular, we identified genetic interactors of gdi-1, the orthologue of GDI1, a gene associated with mental retardation in human. Interestingly, some gdi-1 interactors have human orthologues with known neurological functions, and upon validation of the interactions in mammalian systems, these orthologues would be potential therapeutic targets for GDI1-associated neurological disorders. We also observed the conservation of a gdi-1 interaction between different cellular systems in C. elegans, suggesting the involvement of GDI1 in human muscle degeneration. Conclusions/Significance We developed a novel predictor of genetic interactions that may have the ability to significantly streamline the identification of therapeutic targets for monogenic disorders involving genes conserved between human and C. elegans.
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Affiliation(s)
- Anna Y. Lee
- McGill Centre for Bioinformatics, McGill University, Montréal, Québec, Canada
- School of Computer Science, McGill University, Montréal, Québec, Canada
| | - Richard Perreault
- Department of Chemistry, Université du Québec à Montréal, Montréal, Québec, Canada
| | - Sharon Harel
- Department of Chemistry, Université du Québec à Montréal, Montréal, Québec, Canada
| | - Elodie L. Boulier
- Department of Chemistry, Université du Québec à Montréal, Montréal, Québec, Canada
| | - Matthew Suderman
- McGill Centre for Bioinformatics, McGill University, Montréal, Québec, Canada
| | - Michael Hallett
- McGill Centre for Bioinformatics, McGill University, Montréal, Québec, Canada
- School of Computer Science, McGill University, Montréal, Québec, Canada
- Rosalind and Morris Goodman Cancer Centre, McGill University, Montréal, Québec, Canada
| | - Sarah Jenna
- Department of Chemistry, Université du Québec à Montréal, Montréal, Québec, Canada
- Pharmaqam, Université du Québec à Montréal, Montréal, Québec, Canada
- Biomed, Université du Québec à Montréal, Montréal, Québec, Canada
- * E-mail:
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17
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Chartrand E, Arnold AA, Convenant S, Jenna S, Marcotte I. NMR Study of the Interaction of Cardiotoxic Drugs with the Extracellular Segment Ile583 - Tyr597 from the hERG Channel. Biophys J 2009. [DOI: 10.1016/j.bpj.2008.12.2287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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18
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Emadali A, Muscatelli-Groux B, Delom F, Jenna S, Boismenu D, Sacks DB, Metrakos PP, Chevet E. Proteomic analysis of ischemia-reperfusion injury upon human liver transplantation reveals the protective role of IQGAP1. Mol Cell Proteomics 2006; 5:1300-13. [PMID: 16622255 DOI: 10.1074/mcp.m500393-mcp200] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Ischemia-reperfusion injury (IRI) represents a major determinant of liver transplantation. IRI-induced graft dysfunction is related to biliary damage, partly due to a loss of bile canaliculi (BC) integrity associated with a dramatic remodeling of actin cytoskeleton. However, the molecular mechanisms associated with these events remain poorly characterized. Using liver biopsies collected during the early phases of organ procurement (ischemia) and transplantation (reperfusion), we characterized the global patterns of expression and phosphorylation of cytoskeleton-related proteins during hepatic IRI. This targeted functional proteomic approach, which combined protein expression pattern profiling and phosphoprotein enrichment followed by mass spectrometry analysis, allowed us to identify IQGAP1, a Cdc42/Rac1 effector, as a potential regulator of actin cytoskeleton remodeling and maintenance of BC integrity. Cell fractionation and immunohistochemistry revealed that IQGAP1 expression and localization were affected upon IRI and related to actin reorganization. Furthermore using an IRI model in human hepatoma cells, we demonstrated that IQGAP1 silencing decreased the basal level of actin polymerization at BC periphery, reflecting a defect in BC structure coincident with reduced cellular resistance to IRI. In summary, this study uncovered new mechanistic insights into the global regulation of IRI-induced cytoskeleton remodeling and led to the identification of IQGAP1 as a regulator of BC structure. IQGAP1 therefore represents a potential target for the design of new organ preservation strategies to improve transplantation outcome.
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Affiliation(s)
- Anouk Emadali
- Organelle Signalling Laboratory, Hepato-Biliary and Transplant Research Group, Department of Surgery, McGill University, Montreal, Quebec, Canada
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19
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Tzimas GN, Chevet E, Jenna S, Nguyên DT, Khatib AM, Marcus V, Zhang Y, Chrétien M, Seidah N, Metrakos P. Abnormal expression and processing of the proprotein convertases PC1 and PC2 in human colorectal liver metastases. BMC Cancer 2005; 5:149. [PMID: 16293189 PMCID: PMC1310616 DOI: 10.1186/1471-2407-5-149] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2005] [Accepted: 11/17/2005] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The family of proprotein convertases has been recently implicated in tumorigenesis and metastasis in animal models. However, these studies have not yet been completely corroborated in human tumors. METHODS Using RT PCR, immunoblot and immunohistochemistry we assessed the presence and the processing patterns of the convertases PC1 and PC2 as well as the PC2 specific chaperone 7B2 in human liver metastases originating from colorectal cancer and compared them to unaffected and normal liver. Furthermore, we assessed the presence and processing profiles of PC1, PC2 and 7B2 in primary colon cancers. RESULTS mRNA, protein expression, and protein cleavage profiles of proprotein convertases 1 and 2 are altered in liver colorectal metastasis, compared to unaffected and normal liver. Active PC1 protein is overexpressed in tumor, correlating with its mRNA profile. Moreover, the enhanced PC2 processing pattern in tumor correlates with the overexpression of its specific binding protein 7B2. These results were corroborated by immunohistochemistry. The specific and uniform convertase pattern observed in the metastases was present only in a fraction of primary colon cancers. CONCLUSION The uniformly altered proprotein convertase profile in liver metastases is observed only in a fraction of primary colon cancers, suggesting possible selection processes involving PCs during metastasis as well as an active role of PCs in liver metastasis. In addition, the exclusive presence of 7B2 in metastatic tumors may represent a new target for early diagnosis, prognosis and/or treatment.
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Affiliation(s)
- George N Tzimas
- Transplant and Hepato-pancreatobiliary Research Group, McGill University Health Center, McGill University, 687 Pine Avenue West, S.10.26, Montreal, Canada H3A1A1
- Department of Surgical Services, Kypselis General Hospital, 24 Drossopoulou Street, Athens 11257, Greece
- Organelle Signaling Laboratory, Department of Surgery, McGill University Health Center, McGill University, 687 Pine Avenue West, S.10.26, Montreal, Canada H3A1A1
| | - Eric Chevet
- Organelle Signaling Laboratory, Department of Surgery, McGill University Health Center, McGill University, 687 Pine Avenue West, S.10.26, Montreal, Canada H3A1A1
| | - Sarah Jenna
- Organelle Signaling Laboratory, Department of Surgery, McGill University Health Center, McGill University, 687 Pine Avenue West, S.10.26, Montreal, Canada H3A1A1
| | - Duc Thang Nguyên
- Organelle Signaling Laboratory, Department of Surgery, McGill University Health Center, McGill University, 687 Pine Avenue West, S.10.26, Montreal, Canada H3A1A1
| | - Abdel M Khatib
- Ottawa Health Research Institute, University of Ottawa, Ottawa, Canada Y1K 4K9
| | - Victoria Marcus
- Department of Pathology, McGill University Health Center, McGill University, 1650 Cedar Avenue, Montreal, Canada H3G 1A4
| | - Yi Zhang
- Department of Pathology, McGill University Health Center, McGill University, 1650 Cedar Avenue, Montreal, Canada H3G 1A4
| | - Michel Chrétien
- Ottawa Health Research Institute, University of Ottawa, Ottawa, Canada Y1K 4K9
| | - Nabil Seidah
- Laboratory of Biochemical Neuroendocrinology, Clinical Research Institute of Montreal, University of Montreal, Montreal, Canada H2W 1R7, QC
| | - Peter Metrakos
- Transplant and Hepato-pancreatobiliary Research Group, McGill University Health Center, McGill University, 687 Pine Avenue West, S.10.26, Montreal, Canada H3A1A1
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Tcherkezian J, Danek EI, Jenna S, Triki I, Lamarche-Vane N. Extracellular signal-regulated kinase 1 interacts with and phosphorylates CdGAP at an important regulatory site. Mol Cell Biol 2005; 25:6314-29. [PMID: 16024771 PMCID: PMC1190322 DOI: 10.1128/mcb.25.15.6314-6329.2005] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rho GTPases regulate multiple cellular processes affecting both cell proliferation and cytoskeletal dynamics. Their cycling between inactive GDP- and active GTP-bound states is tightly regulated by guanine nucleotide exchange factors and GTPase-activating proteins (GAPs). We have previously identified CdGAP (for Cdc42 GTPase-activating protein) as a specific GAP for Rac1 and Cdc42. CdGAP consists of an N-terminal RhoGAP domain and a C-terminal proline-rich region. In addition, CdGAP is a member of the impressively large number of mammalian RhoGAP proteins that is well conserved among both vertebrates and invertebrates. In mice, we find two predominant isoforms of CdGAP differentially expressed in specific tissues. We report here that CdGAP is highly phosphorylated in vivo on serine and threonine residues. We find that CdGAP is phosphorylated downstream of the MEK-extracellular signal-regulated kinase (ERK) pathway in response to serum or platelet-derived growth factor stimulation. Furthermore, CdGAP interacts with and is phosphorylated by ERK-1 and RSK-1 in vitro. A putative DEF (docking for ERK FXFP) domain located in the proline-rich region of CdGAP is required for efficient binding and phosphorylation by ERK1/2. We identify Thr776 as an in vivo target site of ERK1/2 and as an important regulatory site of CdGAP activity. Together, these data suggest that CdGAP is a novel substrate of ERK1/2 and mediates cross talk between the Ras/mitogen-activated protein kinase pathway and regulation of Rac1 activity.
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Affiliation(s)
- Joseph Tcherkezian
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada
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Caruso ME, Jenna S, Beaulne S, Lee EH, Bergeron A, Chauve C, Roby P, Rual JF, Hill DE, Vidal M, Bossé R, Chevet E. Biochemical clustering of monomeric GTPases of the Ras superfamily. Mol Cell Proteomics 2005; 4:936-44. [PMID: 15814614 DOI: 10.1074/mcp.m500025-mcp200] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
To date phylogeny has been used to compare entire families of proteins based on their nucleotide or amino acid sequence. Here we developed a novel analytical platform allowing a systematic comparison of protein families based on their biochemical properties. This approach was validated on the Rho subfamily of GTPases. We used two high throughput methods, referred to as AlphaScreen and FlashPlate, to measure nucleotide binding capacity, exchange, and hydrolysis activities of small monomeric GTPases. These two technologies have the characteristics to be very sensitive and to allow homogenous and high throughput assays. To analyze and integrate the data obtained, we developed an algorithm that allows the classification of GTPases according to their enzymatic activities. Integration and hierarchical clustering of these results revealed unexpected features of the small Rho GTPases when compared with primary sequence-based trees. Hence we propose a novel phylobiochemical classification of the Ras superfamily of GTPases.
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Affiliation(s)
- Marie-Elaine Caruso
- Organelle Signaling Laboratory, Department of Surgery and Montreal Proteomics Network, McGill University, Montreal, Quebec H3A 2B2, Canada
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Jenna S, Caruso ME, Emadali A, Nguyên DT, Dominguez M, Li S, Roy R, Reboul J, Vidal M, Tzimas GN, Bossé R, Chevet E. Regulation of membrane trafficking by a novel Cdc42-related protein in Caenorhabditis elegans epithelial cells. Mol Biol Cell 2005; 16:1629-39. [PMID: 15659649 PMCID: PMC1073647 DOI: 10.1091/mbc.e04-08-0760] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2004] [Accepted: 01/11/2005] [Indexed: 12/23/2022] Open
Abstract
Rho GTPases are mainly known for their implication in cytoskeleton remodeling. They have also been recently shown to regulate various aspects of membrane trafficking. Here, we report the identification and the characterization of a novel Caenorhabditis elegans Cdc42-related protein, CRP-1, that shows atypical enzymatic characteristics in vitro. Expression in mouse fibroblasts revealed that, in contrast with CDC-42, CRP-1 was unable to reorganize the actin cytoskeleton and mainly localized to trans-Golgi network and recycling endosomes. This subcellular localization, as well as its expression profile restricted to a subset of epithelial-like cells in C. elegans, suggested a potential function for this protein in polarized membrane trafficking. Consistent with this hypothesis, alteration of CRP-1 expression affected the apical trafficking of CHE-14 in vulval and rectal epithelial cells and sphingolipids (C(6)-NBD-ceramide) uptake and/or trafficking in intestinal cells. However, it did not affect basolateral trafficking of myotactin in the pharynx and the targeting of IFB-2 and AJM-1, two cytosolic apical markers of intestine epithelial cells. Hence, our data demonstrate a function for CRP-1 in the regulation of membrane trafficking in a subset of cells with epithelial characteristics.
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Affiliation(s)
- S Jenna
- Organelle Signaling Laboratory, Department of Surgery, McGill University, Montreal, Quebec, Canada
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Nguyên DT, Kebache S, Fazel A, Wong HN, Jenna S, Emadali A, Lee EH, Bergeron JJM, Kaufman RJ, Larose L, Chevet E. Nck-dependent activation of extracellular signal-regulated kinase-1 and regulation of cell survival during endoplasmic reticulum stress. Mol Biol Cell 2004; 15:4248-60. [PMID: 15201339 PMCID: PMC515356 DOI: 10.1091/mbc.e03-11-0851] [Citation(s) in RCA: 132] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2003] [Revised: 05/21/2004] [Accepted: 06/07/2004] [Indexed: 11/11/2022] Open
Abstract
In response to stress, the endoplasmic reticulum (ER) signaling machinery triggers the inhibition of protein synthesis and up-regulation of genes whose products are involved in protein folding, cell cycle exit, and/or apoptosis. We demonstrate that the misfolding agents azetidine-2-carboxylic acid (Azc) and tunicamycin initiate signaling from the ER, resulting in the activation of Jun-N-terminal kinase, p44(MAPK)/extracellular signal-regulated kinase-1 (ERK-1), and p38(MAPK) through IRE1alpha-dependent mechanisms. To characterize the ER proximal signaling events involved, immuno-isolated ER membranes from rat fibroblasts treated with ER stress inducers were used to reconstitute the activation of the stress-activated protein kinase/mitogen-activate protein kinase (MAPK) pathways in vitro. This allowed us to demonstrate a role for the SH2/SH3 domain containing adaptor Nck in ERK-1 activation after Azc treatment. We also show both in vitro and in vivo that under basal conditions ER-associated Nck represses ERK-1 activation and that upon ER stress this pool of Nck dissociates from the ER membrane to allow ERK-1 activation. Moreover, under the same conditions, Nck-null cells elicit a stronger ERK-1 activation in response to Azc stress, thus, correlating with an enhanced survival phenotype. These data delineate a novel mechanism for the regulation of ER stress signaling to the MAPK pathway and demonstrate a critical role for Nck in ER stress and cell survival.
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Affiliation(s)
- Duc Thang Nguyên
- Department of Surgery, McGill University, Montreal, Quebec, H3A 1A1 Canada
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Reboul J, Vaglio P, Rual JF, Lamesch P, Martinez M, Armstrong CM, Li S, Jacotot L, Bertin N, Janky R, Moore T, Hudson JR, Hartley JL, Brasch MA, Vandenhaute J, Boulton S, Endress GA, Jenna S, Chevet E, Papasotiropoulos V, Tolias PP, Ptacek J, Snyder M, Huang R, Chance MR, Lee H, Doucette-Stamm L, Hill DE, Vidal M. C. elegans ORFeome version 1.1: experimental verification of the genome annotation and resource for proteome-scale protein expression. Nat Genet 2003; 34:35-41. [PMID: 12679813 DOI: 10.1038/ng1140] [Citation(s) in RCA: 310] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2003] [Accepted: 03/14/2003] [Indexed: 11/08/2022]
Abstract
To verify the genome annotation and to create a resource to functionally characterize the proteome, we attempted to Gateway-clone all predicted protein-encoding open reading frames (ORFs), or the 'ORFeome,' of Caenorhabditis elegans. We successfully cloned approximately 12,000 ORFs (ORFeome 1.1), of which roughly 4,000 correspond to genes that are untouched by any cDNA or expressed-sequence tag (EST). More than 50% of predicted genes needed corrections in their intron-exon structures. Notably, approximately 11,000 C. elegans proteins can now be expressed under many conditions and characterized using various high-throughput strategies, including large-scale interactome mapping. We suggest that similar ORFeome projects will be valuable for other organisms, including humans.
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Affiliation(s)
- Jérôme Reboul
- Dana-Farber Cancer Institute and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
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Jenna S, Hussain NK, Danek EI, Triki I, Wasiak S, McPherson PS, Lamarche-Vane N. The activity of the GTPase-activating protein CdGAP is regulated by the endocytic protein intersectin. J Biol Chem 2002; 277:6366-73. [PMID: 11744688 DOI: 10.1074/jbc.m105516200] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Rho GTPases RhoA, Rac1, and Cdc42 play a major role in regulating the reorganization of the actin cytoskeleton. We recently identified CdGAP, a novel GTPase-activating protein with activity toward Rac1 and Cdc42. CdGAP consists of a N-terminal GAP domain, a central domain, and a C-terminal proline-rich domain. Here we show that through a subset of its Src homology 3 domains, the endocytic protein intersectin interacts with CdGAP. In platelet-derived growth factor-stimulated Swiss 3T3 cells, intersectin co-localizes with CdGAP and inhibits its GAP activity toward Rac1. Intersectin-Src homology 3 also inhibits CdGAP activity in GAP assays in vitro. Although the C-terminal proline-rich domain of CdGAP is required for the regulation of its GAP activity by intersectin both in vivo and in vitro, it is not necessary for CdGAP-intersectin interaction. Our data suggest that the central domain of CdGAP is required for CdGAP-intersectin interaction. Thus, we propose a model in which intersectin binding results in a change of CdGAP conformation involving the proline-rich domain that leads to the inhibition of its GAP activity. These observations provide the first demonstration of a direct regulation of RhoGAP activity through a protein-protein interaction and suggest a function for intersectin in Rac1 regulation and actin dynamics.
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Affiliation(s)
- Sarah Jenna
- Department of Anatomy and Cell Biology, McGill University, Montreal, QC H3A 2B2, Canada
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Hussain NK, Jenna S, Glogauer M, Quinn CC, Wasiak S, Guipponi M, Antonarakis SE, Kay BK, Stossel TP, Lamarche-Vane N, McPherson PS. Endocytic protein intersectin-l regulates actin assembly via Cdc42 and N-WASP. Nat Cell Biol 2001; 3:927-32. [PMID: 11584276 DOI: 10.1038/ncb1001-927] [Citation(s) in RCA: 277] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Intersectin-s is a modular scaffolding protein regulating the formation of clathrin-coated vesicles. In addition to the Eps15 homology (EH) and Src homology 3 (SH3) domains of intersectin-s, the neuronal variant (intersectin-l) also has Dbl homology (DH), pleckstrin homology (PH) and C2 domains. We now show that intersectin-l functions through its DH domain as a guanine nucleotide exchange factor (GEF) for Cdc42. In cultured cells, expression of DH-domain-containing constructs cause actin rearrangements specific for Cdc42 activation. Moreover, in vivo studies reveal that stimulation of Cdc42 by intersectin-l accelerates actin assembly via N-WASP and the Arp2/3 complex. N-WASP binds directly to intersectin-l and upregulates its GEF activity, thereby generating GTP-bound Cdc42, a critical activator of N-WASP. These studies reveal a role for intersectin-l in a novel mechanism of N-WASP activation and in regulation of the actin cytoskeleton.
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Affiliation(s)
- N K Hussain
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Quebec, H3A 2B4, Canada
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Prakash SK, Paylor R, Jenna S, Lamarche-Vane N, Armstrong DL, Xu B, Mancini MA, Zoghbi HY. Functional analysis of ARHGAP6, a novel GTPase-activating protein for RhoA. Hum Mol Genet 2000; 9:477-88. [PMID: 10699171 DOI: 10.1093/hmg/9.4.477] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Microphthalmia with linear skin defects (MLS) is an X-linked dominant, male-lethal syndrome characterized by microphthalmia, aplastic skin and agenesis of the corpus callosum, and is caused by the deletion of a 500 kb critical region in Xp22.3. Our laboratory isolated a novel rho GTPase-activating protein (rhoGAP) gene named ARHGAP6 from the MLS region. ARHGAP6 contains 14 exons encoding a 974 amino acid protein with three putative SH3-binding domains. Because exons 2-14 are deleted in all MLS patients, we hypothesized that ARHGAP6 may be responsible for some of the phenotypic features of MLS. We pursued two approaches to study the function of ARHGAP6 and its role in the pathogenesis of MLS: gene targeting of the rhoGAP domain in mouse embryonic stem cells and in vitro expression studies. Surprisingly, loss of the rhoGAP function of Arhgap6 does not cause any detectable phenotypic or behavioral abnormalities in the mutant mice. Transfected mammalian cells expressing ARHGAP6 lose their actin stress fibers, retract from the growth surface and extend thin, branching processes resembling filopodia. The ARHGAP6 protein co-localizes with actin filaments through an N-terminal domain and recruits F-actin into the growing processes. Mutation of a conserved arginine residue in the rhoGAP domain prevents the loss of stress fibers but has little effect on process outgrowth. These results suggest that ARHGAP6 has two independent functions: one as a GAP with specificity for RhoA and the other as a cytoskeletal protein that promotes actin remodeling.
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Affiliation(s)
- S K Prakash
- Departments of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
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Jenna S, Sureau C. Mutations in the carboxyl-terminal domain of the small hepatitis B virus envelope protein impair the assembly of hepatitis delta virus particles. J Virol 1999; 73:3351-8. [PMID: 10074189 PMCID: PMC104099 DOI: 10.1128/jvi.73.4.3351-3358.1999] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The carboxyl-terminal domain of the small (S) envelope protein of hepatitis B virus was subjected to mutagenesis to identify sequences important for the envelopment of the nucleocapsid during morphogenesis of hepatitis delta virus (HDV) virions. The mutations consisted of carboxyl-terminal truncations of 4 to 64 amino acid residues and small combined deletions and insertions spanning the entire hydrophobic domain between residues 163 and 224. Truncation of as few as 14 residues partially inhibited glycosylation and secretion of S and prevented assembly or stability of HDV virions. Short internal combined deletions and insertions were tolerated for secretion of subviral particles with the exceptions of those affecting residues 164 to 173 and 219 to 223. However, mutants competent for subviral particle secretion had a reduced capacity for HDV assembly compared to that of the wild type. One exception was a mutant carrying a deletion of residues 214 to 218, which exhibited a twofold increase in HDV assembly (or stability), whereas deletions of residues 179 to 183, 194 to 198, and 199 to 203 were the most inhibitory. Substitutions of single amino acids between residues 194 and 198 demonstrated that HDV assembly deficiency could be assigned to the replacement of the tryptophan residue at position 196. We concluded that assembly of stable HDV particles requires a specific function of the carboxyl terminus of S which is mediated at least in part by Trp-196.
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Affiliation(s)
- S Jenna
- Laboratoire de Virologie, Institut de Biologie, 34060 Montpellier, France
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Abstract
The gene coding for the small (S) envelope protein of hepatitis B virus was mutated to identify sequences important for the envelopment of the nucleocapsid during morphogenesis of hepatitis delta virus (HDV) virions. This study was focused on a domain of the S protein that is exposed in the cytoplasm during synthesis and thereby represented a good candidate for interaction with the viral nucleocapsid during virion assembly. The mutations consisted of deletion/insertions spanning the entire cytosolic domain of S between amino acid residues 24 and 80. Although the expression of mutants clustered between residues 59 and 80 could not be obtained, we demonstrated that a large part of the cytosolic loop, from residues 29-47 and 49-59, does not contain motifs essential for production of hepatitis B virus subviral particles or HDV virions. However, deletion of residues 24-28 led to the synthesis of S protein mutant, which was competent for secretion of subviral particles but deficient for production of HDV. We concluded that the sequence between Arg-24 and Ile-28 located at the carboxyl boundary of the transmembrane signal I for S contains residue or residues important for HDV particle assembly.
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Affiliation(s)
- S Jenna
- Laboratoire de Virologie, Institut de Biologie, 2 Boulevard Henri IV, Montpellier, 34060, France
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