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Gress V, Roussy M, Boulianne L, Bilodeau M, Cardin S, El-Hachem N, Lisi V, Khakipoor B, Rouette A, Farah A, Théret L, Aubert L, Fatima F, Audemard É, Thibault P, Bonneil É, Chagraoui J, Laramée L, Gendron P, Jouan L, Jammali S, Paré B, Simpson SM, Tran TH, Duval M, Teira P, Bittencourt H, Santiago R, Barabé F, Sauvageau G, Smith MA, Hébert J, Roux PP, Gruber TA, Lavallée VP, Wilhelm BT, Cellot S. CBFA2T3::GLIS2 pediatric acute megakaryoblastic leukemia is sensitive to BCL-XL inhibition by navitoclax and DT2216. Blood Adv 2024; 8:112-129. [PMID: 37729615 PMCID: PMC10787250 DOI: 10.1182/bloodadvances.2022008899] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 07/25/2023] [Accepted: 09/02/2023] [Indexed: 09/22/2023] Open
Abstract
ABSTRACT Acute megakaryoblastic leukemia (AMKL) is a rare, developmentally restricted, and highly lethal cancer of early childhood. The paucity and hypocellularity (due to myelofibrosis) of primary patient samples hamper the discovery of cell- and genotype-specific treatments. AMKL is driven by mutually exclusive chimeric fusion oncogenes in two-thirds of the cases, with CBFA2T3::GLIS2 (CG2) and NUP98 fusions (NUP98r) representing the highest-fatality subgroups. We established CD34+ cord blood-derived CG2 models (n = 6) that sustain serial transplantation and recapitulate human leukemia regarding immunophenotype, leukemia-initiating cell frequencies, comutational landscape, and gene expression signature, with distinct upregulation of the prosurvival factor B-cell lymphoma 2 (BCL2). Cell membrane proteomic analyses highlighted CG2 surface markers preferentially expressed on leukemic cells compared with CD34+ cells (eg, NCAM1 and CD151). AMKL differentiation block in the mega-erythroid progenitor space was confirmed by single-cell profiling. Although CG2 cells were rather resistant to BCL2 genetic knockdown or selective pharmacological inhibition with venetoclax, they were vulnerable to strategies that target the megakaryocytic prosurvival factor BCL-XL (BCL2L1), including in vitro and in vivo treatment with BCL2/BCL-XL/BCL-W inhibitor navitoclax and DT2216, a selective BCL-XL proteolysis-targeting chimera degrader developed to limit thrombocytopenia in patients. NUP98r AMKL were also sensitive to BCL-XL inhibition but not the NUP98r monocytic leukemia, pointing to a lineage-specific dependency. Navitoclax or DT2216 treatment in combination with low-dose cytarabine further reduced leukemic burden in mice. This work extends the cellular and molecular diversity set of human AMKL models and uncovers BCL-XL as a therapeutic vulnerability in CG2 and NUP98r AMKL.
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Affiliation(s)
- Verena Gress
- Pediatric Hematology-Oncology Division, Charles-Bruneau Cancer Center, Centre Hospitalier Universitaire Sainte-Justine Research Center, Montréal, QC, Canada
- Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Mathieu Roussy
- Pediatric Hematology-Oncology Division, Charles-Bruneau Cancer Center, Centre Hospitalier Universitaire Sainte-Justine Research Center, Montréal, QC, Canada
- Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Luc Boulianne
- Pediatric Hematology-Oncology Division, Charles-Bruneau Cancer Center, Centre Hospitalier Universitaire Sainte-Justine Research Center, Montréal, QC, Canada
- Department of Pathology, McGill University, Montréal, QC, Canada
| | - Mélanie Bilodeau
- Pediatric Hematology-Oncology Division, Charles-Bruneau Cancer Center, Centre Hospitalier Universitaire Sainte-Justine Research Center, Montréal, QC, Canada
| | - Sophie Cardin
- Pediatric Hematology-Oncology Division, Charles-Bruneau Cancer Center, Centre Hospitalier Universitaire Sainte-Justine Research Center, Montréal, QC, Canada
| | - Nehme El-Hachem
- Pediatric Hematology-Oncology Division, Charles-Bruneau Cancer Center, Centre Hospitalier Universitaire Sainte-Justine Research Center, Montréal, QC, Canada
| | - Véronique Lisi
- Pediatric Hematology-Oncology Division, Charles-Bruneau Cancer Center, Centre Hospitalier Universitaire Sainte-Justine Research Center, Montréal, QC, Canada
| | - Banafsheh Khakipoor
- Pediatric Hematology-Oncology Division, Charles-Bruneau Cancer Center, Centre Hospitalier Universitaire Sainte-Justine Research Center, Montréal, QC, Canada
| | - Alexandre Rouette
- Molecular Diagnostic Laboratory, Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
| | - Azer Farah
- Pediatric Hematology-Oncology Division, Charles-Bruneau Cancer Center, Centre Hospitalier Universitaire Sainte-Justine Research Center, Montréal, QC, Canada
| | - Louis Théret
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
| | - Léo Aubert
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
| | - Furat Fatima
- Pediatric Hematology-Oncology Division, Charles-Bruneau Cancer Center, Centre Hospitalier Universitaire Sainte-Justine Research Center, Montréal, QC, Canada
- Department of Pathology, McGill University, Montréal, QC, Canada
| | - Éric Audemard
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
| | - Pierre Thibault
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
| | - Éric Bonneil
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
| | - Jalila Chagraoui
- Molecular Genetics of Stem Cells Laboratory, Institute for Research in Immunology and Cancer, Montréal, Québec, Canada
| | - Louise Laramée
- Pediatric Hematology-Oncology Division, Charles-Bruneau Cancer Center, Centre Hospitalier Universitaire Sainte-Justine Research Center, Montréal, QC, Canada
| | - Patrick Gendron
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
| | - Loubna Jouan
- Molecular Diagnostic Laboratory, Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
| | - Safa Jammali
- Pediatric Hematology-Oncology Division, Charles-Bruneau Cancer Center, Centre Hospitalier Universitaire Sainte-Justine Research Center, Montréal, QC, Canada
| | - Bastien Paré
- Pediatric Hematology-Oncology Division, Charles-Bruneau Cancer Center, Centre Hospitalier Universitaire Sainte-Justine Research Center, Montréal, QC, Canada
| | - Shawn M Simpson
- Pediatric Hematology-Oncology Division, Charles-Bruneau Cancer Center, Centre Hospitalier Universitaire Sainte-Justine Research Center, Montréal, QC, Canada
| | - Thai Hoa Tran
- Pediatric Hematology-Oncology Division, Charles-Bruneau Cancer Center, Centre Hospitalier Universitaire Sainte-Justine Research Center, Montréal, QC, Canada
- Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Michel Duval
- Pediatric Hematology-Oncology Division, Charles-Bruneau Cancer Center, Centre Hospitalier Universitaire Sainte-Justine Research Center, Montréal, QC, Canada
- Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Pierre Teira
- Pediatric Hematology-Oncology Division, Charles-Bruneau Cancer Center, Centre Hospitalier Universitaire Sainte-Justine Research Center, Montréal, QC, Canada
- Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Henrique Bittencourt
- Pediatric Hematology-Oncology Division, Charles-Bruneau Cancer Center, Centre Hospitalier Universitaire Sainte-Justine Research Center, Montréal, QC, Canada
- Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Raoul Santiago
- Division of Hematology-Oncology, Centre Hospitalier Universitaire de Québec-Université Laval, Québec City, QC, Canada
- Centre de recherche du Centre Hospitalier Universitaire de Québec-Université Laval, Québec City, QC, Canada
| | - Frédéric Barabé
- Centre de recherche du Centre Hospitalier Universitaire de Québec-Université Laval, Québec City, QC, Canada
- Department of Medicine, Faculty of Medicine, Université Laval, Québec City, QC, Canada
| | - Guy Sauvageau
- Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
- Molecular Genetics of Stem Cells Laboratory, Institute for Research in Immunology and Cancer, Montréal, Québec, Canada
- Division of Hematology, Maisonneuve-Rosemont Hospital, Montréal, QC, Canada
| | - Martin A Smith
- Pediatric Hematology-Oncology Division, Charles-Bruneau Cancer Center, Centre Hospitalier Universitaire Sainte-Justine Research Center, Montréal, QC, Canada
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Josée Hébert
- Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
- Division of Hematology-Oncology and Quebec Leukemia Cell Bank, Hôpital Maisonneuve-Rosemont, Montréal, QC, Canada
| | - Philippe P Roux
- Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
- Department of Pathology and Cell Biology, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Tanja A Gruber
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
| | - Vincent-Philippe Lavallée
- Pediatric Hematology-Oncology Division, Charles-Bruneau Cancer Center, Centre Hospitalier Universitaire Sainte-Justine Research Center, Montréal, QC, Canada
- Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Brian T Wilhelm
- Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
| | - Sonia Cellot
- Pediatric Hematology-Oncology Division, Charles-Bruneau Cancer Center, Centre Hospitalier Universitaire Sainte-Justine Research Center, Montréal, QC, Canada
- Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
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Salame N, Fooks K, El-Hachem N, Bikorimana JP, Mercier FE, Rafei M. Recent Advances in Cancer Drug Discovery Through the Use of Phenotypic Reporter Systems, Connectivity Mapping, and Pooled CRISPR Screening. Front Pharmacol 2022; 13:852143. [PMID: 35795568 PMCID: PMC9250974 DOI: 10.3389/fphar.2022.852143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 05/31/2022] [Indexed: 11/13/2022] Open
Abstract
Multi-omic approaches offer an unprecedented overview of the development, plasticity, and resistance of cancer. However, the translation from anti-cancer compounds identified in vitro to clinically active drugs have a notoriously low success rate. Here, we review how technical advances in cell culture, robotics, computational biology, and development of reporter systems have transformed drug discovery, enabling screening approaches tailored to clinically relevant functional readouts (e.g., bypassing drug resistance). Illustrating with selected examples of “success stories,” we describe the process of phenotype-based high-throughput drug screening to target malignant cells or the immune system. Second, we describe computational approaches that link transcriptomic profiling of cancers with existing pharmaceutical compounds to accelerate drug repurposing. Finally, we review how CRISPR-based screening can be applied for the discovery of mechanisms of drug resistance and sensitization. Overall, we explore how the complementary strengths of each of these approaches allow them to transform the paradigm of pre-clinical drug development.
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Affiliation(s)
- Natasha Salame
- Department of Biomedical Sciences, Université de Montréal, Montreal, QC, Canada
| | - Katharine Fooks
- Lady Davis Institute for Medical Research, Montreal, QC, Canada
- Department of Medicine, McGill University, Montreal, QC, Canada
| | - Nehme El-Hachem
- Department of Pharmacology and Physiology, Université de Montréal, Montreal, QC, Canada
| | - Jean-Pierre Bikorimana
- Department of Microbiology, Infectious Diseases and Immunology, Université de Montréal, Montreal, QC, Canada
| | - François E. Mercier
- Lady Davis Institute for Medical Research, Montreal, QC, Canada
- Department of Medicine, McGill University, Montreal, QC, Canada
- *Correspondence: François E. Mercier, ; Moutih Rafei,
| | - Moutih Rafei
- Department of Pharmacology and Physiology, Université de Montréal, Montreal, QC, Canada
- Department of Microbiology, Infectious Diseases and Immunology, Université de Montréal, Montreal, QC, Canada
- Molecular Biology Program, Université de Montréal, Montreal, QC, Canada
- *Correspondence: François E. Mercier, ; Moutih Rafei,
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Parisien M, Lima LV, Dagostino C, El-Hachem N, Drury GL, Grant AV, Huising J, Verma V, Meloto CB, Silva JR, Dutra GGS, Markova T, Dang H, Tessier PA, Slade GD, Nackley AG, Ghasemlou N, Mogil JS, Allegri M, Diatchenko L. Acute inflammatory response via neutrophil activation protects against the development of chronic pain. Sci Transl Med 2022; 14:eabj9954. [PMID: 35544595 DOI: 10.1126/scitranslmed.abj9954] [Citation(s) in RCA: 98] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The transition from acute to chronic pain is critically important but not well understood. Here, we investigated the pathophysiological mechanisms underlying the transition from acute to chronic low back pain (LBP) and performed transcriptome-wide analysis in peripheral immune cells of 98 participants with acute LBP, followed for 3 months. Transcriptomic changes were compared between patients whose LBP was resolved at 3 months with those whose LBP persisted. We found thousands of dynamic transcriptional changes over 3 months in LBP participants with resolved pain but none in those with persistent pain. Transient neutrophil-driven up-regulation of inflammatory responses was protective against the transition to chronic pain. In mouse pain assays, early treatment with a steroid or nonsteroidal anti-inflammatory drug (NSAID) also led to prolonged pain despite being analgesic in the short term; such a prolongation was not observed with other analgesics. Depletion of neutrophils delayed resolution of pain in mice, whereas peripheral injection of neutrophils themselves, or S100A8/A9 proteins normally released by neutrophils, prevented the development of long-lasting pain induced by an anti-inflammatory drug. Analysis of pain trajectories of human subjects reporting acute back pain in the UK Biobank identified elevated risk of pain persistence for subjects taking NSAIDs. Thus, despite analgesic efficacy at early time points, the management of acute inflammation may be counterproductive for long-term outcomes of LBP sufferers.
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Affiliation(s)
- Marc Parisien
- Faculty of Dental Medicine and Oral Health Sciences, Department of Anesthesia, Faculty of Medicine, Alan Edwards Centre for Research on Pain, McGill University, Montreal, Quebec H3A 1G1, Canada
| | - Lucas V Lima
- Department of Psychology, Faculty of Science, Alan Edwards Centre for Research on Pain, McGill University, Montreal, Quebec H3A 1G1, Canada
| | - Concetta Dagostino
- Department of Medicine and Surgery, University of Parma, Parma 43126, Italy
| | - Nehme El-Hachem
- Faculty of Dental Medicine and Oral Health Sciences, Department of Anesthesia, Faculty of Medicine, Alan Edwards Centre for Research on Pain, McGill University, Montreal, Quebec H3A 1G1, Canada
| | - Gillian L Drury
- Faculty of Dental Medicine and Oral Health Sciences, Department of Anesthesia, Faculty of Medicine, Alan Edwards Centre for Research on Pain, McGill University, Montreal, Quebec H3A 1G1, Canada
| | - Audrey V Grant
- Faculty of Dental Medicine and Oral Health Sciences, Department of Anesthesia, Faculty of Medicine, Alan Edwards Centre for Research on Pain, McGill University, Montreal, Quebec H3A 1G1, Canada
| | - Jonathan Huising
- Department of Anesthesiology, Pain and Palliative Medicine, Radboudumc, Nijmegen 6525, Netherlands
| | - Vivek Verma
- Faculty of Dental Medicine and Oral Health Sciences, Department of Anesthesia, Faculty of Medicine, Alan Edwards Centre for Research on Pain, McGill University, Montreal, Quebec H3A 1G1, Canada
| | - Carolina B Meloto
- Faculty of Dental Medicine and Oral Health Sciences, Department of Anesthesia, Faculty of Medicine, Alan Edwards Centre for Research on Pain, McGill University, Montreal, Quebec H3A 1G1, Canada
| | - Jaqueline R Silva
- Departments of Anesthesiology and Perioperative Medicine and Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Gabrielle G S Dutra
- Department of Psychology, Faculty of Science, Alan Edwards Centre for Research on Pain, McGill University, Montreal, Quebec H3A 1G1, Canada
| | - Teodora Markova
- Department of Psychology, Faculty of Science, Alan Edwards Centre for Research on Pain, McGill University, Montreal, Quebec H3A 1G1, Canada
| | - Hong Dang
- Cystic Fibrosis Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Philippe A Tessier
- Department of Microbiology and Immunology, Faculty of Medicine, Laval University, Quebec City, Quebec G1V 0A6, Canada
| | - Gary D Slade
- Center for Pain Research and Innovation, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Andrea G Nackley
- Center for Translational Pain Medicine and Departments of Anesthesiology and Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Nader Ghasemlou
- Departments of Anesthesiology and Perioperative Medicine and Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Jeffrey S Mogil
- Department of Psychology, Faculty of Science, Alan Edwards Centre for Research on Pain, McGill University, Montreal, Quebec H3A 1G1, Canada
| | - Massimo Allegri
- Pain Therapy Service, Policlinico of Monza Hospital, Monza 20900, Italy.,Pain Management and Neuromodulation Centre, Ensemble Hospitalier de la Côte, Morges 1110, Switzerland
| | - Luda Diatchenko
- Faculty of Dental Medicine and Oral Health Sciences, Department of Anesthesia, Faculty of Medicine, Alan Edwards Centre for Research on Pain, McGill University, Montreal, Quebec H3A 1G1, Canada
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Bikorimana JP, Abusarah J, Salame N, El-Hachem N, Shammaa R, Rafei M. Humoral Immunity to Allogeneic Immunoproteasome-Expressing Mesenchymal Stromal Cells Requires Efferocytosis by Endogenous Phagocytes. Cells 2022; 11:cells11040596. [PMID: 35203247 PMCID: PMC8869887 DOI: 10.3390/cells11040596] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/07/2022] [Accepted: 02/08/2022] [Indexed: 02/05/2023] Open
Abstract
The extensive use of mesenchymal stromal cells (MSCs) over the last decade has revolutionized modern medicine. From the delivery of pharmacological proteins to regenerative medicine and immune modulation, these cells have proven to be highly pleiotropic and responsive to their surrounding environment. Nevertheless, their role in promoting inflammation has been fairly limited by the questionable use of interferon-gamma, as this approach has also been proven to enhance the cells' immune-suppressive abilities. Alternatively, we have previously shown that de novo expression of the immunoproteasome (IPr) complex instills potent antigen cross-presentation capabilities in MSCs. Interestingly, these cells were found to express the major histocompatibility class (MHC) II protein, which prompted us to investigate their ability to stimulate humoral immunity. Using a series of in vivo studies, we found that administration of allogeneic ovalbumin (OVA)-pulsed MSC-IPr cells elicits a moderate antibody titer, which was further enhanced by the combined use of pro-inflammatory cytokines. The generated antibodies were functional as they blocked CD4 T-cell activation following their co-culture with OVA-pulsed MSC-IPr and mitigated E.G7 tumor growth in vivo. The therapeutic potency of MSC-IPr was, however, dependent on efferocytosis, as phagocyte depletion prior to vaccination abrogated MSC-IPr-induced humoral responses while promoting their survival in the host. In contrast, antibody-mediated neutralization of CD47, a potent "do not eat me signal", enhanced antibody titer levels. These observations highlight the major role played by myeloid cells in supporting antibody production by MSC-IPr and suggest that the immune outcome is dictated by a net balance between efferocytosis-stimulating and -inhibiting signals.
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Affiliation(s)
- Jean-Pierre Bikorimana
- Department of Microbiology, Infectious Diseases and Immunology, Université de Montréal, Montreal, QC H3T 1A8, Canada;
| | - Jamilah Abusarah
- Department of Pharmacology and Physiology, Université de Montréal, Montreal, QC H3T 1A8, Canada; (J.A.); (N.E.-H.)
| | - Natasha Salame
- Department of Biomedical Sciences, Université de Montréal, Montreal, QC H3T 1A8, Canada;
| | - Nehme El-Hachem
- Department of Pharmacology and Physiology, Université de Montréal, Montreal, QC H3T 1A8, Canada; (J.A.); (N.E.-H.)
- Pediatric Hematology-Oncology Division, Centre Hospitalier Universitaire Sainte-Justine Research Centre, Montreal, QC H3T 1C5, Canada
| | - Riam Shammaa
- Canadian Centers for Regenerative Therapy, Toronto, ON M5R 1A8, Canada;
- IntelliStem Technologies Inc., Toronto, ON M5R 3N5, Canada
| | - Moutih Rafei
- Department of Microbiology, Infectious Diseases and Immunology, Université de Montréal, Montreal, QC H3T 1A8, Canada;
- Department of Pharmacology and Physiology, Université de Montréal, Montreal, QC H3T 1A8, Canada; (J.A.); (N.E.-H.)
- Molecular Biology Program, Université de Montréal, Montreal, QC H3T 1A8, Canada
- Correspondence:
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5
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Salame N, Bikorimana JP, El-Hachem N, Saad W, Kurdi M, Zhao J, Eliopoulos N, Shammaa R, Rafei M. UM171A-induced ROS promote antigen cross-presentation of immunogenic peptides by bone marrow-derived mesenchymal stromal cells. Stem Cell Res Ther 2022; 13:16. [PMID: 35012668 PMCID: PMC8751335 DOI: 10.1186/s13287-021-02693-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 12/24/2021] [Indexed: 12/20/2022] Open
Abstract
Background Mesenchymal stromal cells (MSCs) have been extensively used in the clinic due to their exquisite tissue repair capacity. However, they also hold promise in the field of cellular vaccination as they can behave as conditional antigen presenting cells in response to interferon (IFN)-gamma treatment under a specific treatment regimen. This suggests that the immune function of MSCs can be pharmacologically modulated. Given the capacity of the agonist pyrimido-indole derivative UM171a to trigger the expression of various antigen presentation-related genes in human hematopoietic progenitor cells, we explored the potential use of UM171a as a means to pharmacologically instill and/or promote antigen presentation by MSCs. Methods Besides completing a series of flow-cytometry-based phenotypic analyses, several functional antigen presentation assays were conducted using the SIINFEKL-specific T-cell clone B3Z. Anti-oxidants and electron transport chain inhibitors were also used to decipher UM171a’s mode of action in MSCs. Finally, the potency of UM171a-treated MSCs was evaluated in the context of therapeutic vaccination using immunocompetent C57BL/6 mice with pre-established syngeneic EG.7T-cell lymphoma. Results Treatment of MSCs with UM171a triggered potent increase in H2-Kb cell surface levels along with the acquisition of antigen cross-presentation abilities. Mechanistically, such effects occurred in response to UM171a-mediated production of mitochondrial-derived reactive oxygen species as their neutralization using anti-oxidants or Antimycin-A mitigated MSCs’ ability to cross-present antigens. Processing and presentation of the immunogenic ovalbumin-derived SIINFEKL peptide was caused by de novo expression of the Psmb8 gene in response to UM171a-triggered oxidative stress. When evaluated for their anti-tumoral properties in the context of therapeutic vaccination, UM171a-treated MSC administration to immunocompetent mice with pre-established T-cell lymphoma controlled tumor growth resulting in 40% survival without the need of additional supportive therapy and/or standard-of-care. Conclusions Altogether, our findings reveal a new immune-related function for UM171a and clearly allude to a direct link between UM171a-mediated ROS induction and antigen cross-presentation by MSCs. The fact that UM171a treatment modulates MSCs to become antigen-presenting cells without the use of IFN-gamma opens-up a new line of investigation to search for additional agents capable of converting immune-suppressive MSCs to a cellular tool easily adaptable to vaccination. Graphical abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13287-021-02693-z.
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Affiliation(s)
- Natasha Salame
- Department of Biomedical Sciences, Université de Montréal, Montreal, QC, Canada
| | - Jean-Pierre Bikorimana
- Department of Microbiology, Infectious Diseases and Immunology, Université de Montréal, Montreal, QC, Canada
| | - Nehme El-Hachem
- Department of Pharmacology and Physiology, Université de Montréal, Montreal, QC, Canada.,Pediatric Hematology-Oncology Division, Centre Hospitalier Universitaire Sainte-Justine Research Centre, Montreal, QC, Canada
| | - Wael Saad
- Laboratory of Experimental and Clinical Pharmacology, Department of Chemistry and Biochemistry, Faculty of Sciences, Lebanese University, Hadat, Lebanon
| | - Mazen Kurdi
- Laboratory of Experimental and Clinical Pharmacology, Department of Chemistry and Biochemistry, Faculty of Sciences, Lebanese University, Hadat, Lebanon
| | - Jing Zhao
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada
| | - Nicoletta Eliopoulos
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada.,Department of Surgery, McGill University, Montreal, QC, Canada
| | - Riam Shammaa
- Department of Family and Community Medicine, University of Toronto, Toronto, ON, Canada.,Canadian Centers for Regenerative Therapy, Toronto, ON, Canada.,IntelliStem Technologies Inc., Toronto, ON, Canada
| | - Moutih Rafei
- Department of Microbiology, Infectious Diseases and Immunology, Université de Montréal, Montreal, QC, Canada. .,Department of Pharmacology and Physiology, Université de Montréal, Montreal, QC, Canada. .,Molecular Biology Program, Université de Montréal, Montreal, QC, Canada. .,Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada.
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6
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Abusarah J, Khodayarian F, El-Hachem N, Salame N, Olivier M, Balood M, Roversi K, Talbot S, Bikorimana JP, Chen J, Jolicoeur M, Trudeau LE, Kamyabiazar S, Annabi B, Robert F, Pelletier J, El-Kadiry AEH, Shammaa R, Rafei M. Engineering immunoproteasome-expressing mesenchymal stromal cells: A potent cellular vaccine for lymphoma and melanoma in mice. Cell Rep Med 2021; 2:100455. [PMID: 35028603 PMCID: PMC8714858 DOI: 10.1016/j.xcrm.2021.100455] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 08/30/2021] [Accepted: 10/22/2021] [Indexed: 11/29/2022]
Abstract
Dendritic cells (DCs) excel at cross-presenting antigens, but their effectiveness as cancer vaccine is limited. Here, we describe a vaccination approach using mesenchymal stromal cells (MSCs) engineered to express the immunoproteasome complex (MSC-IPr). Such modification instills efficient antigen cross-presentation abilities associated with enhanced major histocompatibility complex class I and CD80 expression, de novo production of interleukin-12, and higher chemokine secretion. This cross-presentation capacity of MSC-IPr is highly dependent on their metabolic activity. Compared with DCs, MSC-IPr hold the ability to cross-present a vastly different epitope repertoire, which translates into potent re-activation of T cell immunity against EL4 and A20 lymphomas and B16 melanoma tumors. Moreover, therapeutic vaccination of mice with pre-established tumors efficiently controls cancer growth, an effect further enhanced when combined with antibodies targeting PD-1, CTLA4, LAG3, or 4-1BB under both autologous and allogeneic settings. Therefore, MSC-IPr constitute a promising subset of non-hematopoietic antigen-presenting cells suitable for designing universal cell-based cancer vaccines.
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Affiliation(s)
- Jamilah Abusarah
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Fatemeh Khodayarian
- Department of Pharmacology and Physiology, Université de Montréal, Montreal, QC, Canada
| | - Nehme El-Hachem
- Department of Pharmacology and Physiology, Université de Montréal, Montreal, QC, Canada
| | - Natasha Salame
- Department of Biomedical Sciences, Université de Montréal, Montreal, QC, Canada
| | - Martin Olivier
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Mohammad Balood
- Department of Pharmacology and Physiology, Université de Montréal, Montreal, QC, Canada
| | - Katiane Roversi
- Department of Pharmacology and Physiology, Université de Montréal, Montreal, QC, Canada
| | - Sebastien Talbot
- Department of Pharmacology and Physiology, Université de Montréal, Montreal, QC, Canada
| | - Jean-Pierre Bikorimana
- Department of Microbiology, Infectious Diseases and Immunology, Université de Montréal, Montreal, QC, Canada
| | - Jingkui Chen
- Research Laboratory in Applied Metabolic Engineering, Department of Chemical Engineering, Polytechnique Montréal, Montreal, QC, Canada
| | - Mario Jolicoeur
- Research Laboratory in Applied Metabolic Engineering, Department of Chemical Engineering, Polytechnique Montréal, Montreal, QC, Canada
| | - Louis-Eric Trudeau
- Department of Pharmacology and Physiology, Université de Montréal, Montreal, QC, Canada
| | - Samaneh Kamyabiazar
- Department of Chemistry, Université du Québec à Montréal, Montreal, QC, Canada
| | - Borhane Annabi
- Department of Chemistry, Université du Québec à Montréal, Montreal, QC, Canada
| | - Francis Robert
- Department of Biochemistry, McGill University, Montreal, QC, Canada
| | - Jerry Pelletier
- Department of Biochemistry, McGill University, Montreal, QC, Canada
| | | | - Riam Shammaa
- Department of Family and Community Medicine, University of Toronto, Toronto, ON, Canada
- Canadian Centers for Regenerative Therapy, Toronto, ON, Canada
- IntelliStem Technologies Inc., Toronto, ON, Canada
| | - Moutih Rafei
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
- Department of Pharmacology and Physiology, Université de Montréal, Montreal, QC, Canada
- Department of Microbiology, Infectious Diseases and Immunology, Université de Montréal, Montreal, QC, Canada
- Molecular Biology Program, Université de Montréal, Montreal, QC, Canada
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7
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Al Khoury C, Nemer G, Humber R, El-Hachem N, Guillot J, Chehab R, Noujeim E, El Khoury Y, Skaff W, Estephan N, Nemer N. Bioexploration and Phylogenetic Placement of Entomopathogenic Fungi of the Genus Beauveria in Soils of Lebanon Cedar Forests. J Fungi (Basel) 2021; 7:924. [PMID: 34829214 PMCID: PMC8622946 DOI: 10.3390/jof7110924] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 11/17/2022] Open
Abstract
The cedar forests of Lebanon have been threatened by the outbreak caused by climate change of a web-spinning sawfly, Cephalcia tannourinensis (Hymenoptera: Pamphiliidae), which negatively impacted the survival of one of the oldest tree species on earth. In this study, we investigated the occurrence of naturally soil-inhabiting entomopathogenic fungi for their role in containing the massive outbreak of this insect. We used a combination of fungal bioexploration methods, including insect bait and selective media. Morphological features and multilocus phylogeny-based on Sanger sequencing of the transcripts encoding the translation elongation factor 1-alpha (TEF-α), RNA polymerase II second largest subunit (RBP2), and the nuclear intergenic region (Bloc) were used for species identification. The occurrence rate of entomopathogenic fungi (EPF) varied with location, soil structure, forest structure, and isolation method. From 15 soil samples positive for fungal occurrence, a total of 249 isolates was obtained from all locations using different isolation methods. The phylogenetic analysis confirmed the existence of two novel indigenous species: Beauveria tannourinensis sp. nov. and Beauveria ehdenensis sp. nov. In conclusion, the present survey was successful (1) in optimizing the isolation methods for EPF, (2) investigating the natural occurrence of Beauveria spp. in outbreak areas of C. tannourinensis, and (3) in characterizing the presence of new Beauveria species in Lebanese cedar forest soil.
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Affiliation(s)
- Charbel Al Khoury
- Department of Natural Sciences, Byblos Campus, School of Arts and Sciences, Lebanese American University, Byblos P.O. Box 36, Lebanon
| | - Georges Nemer
- Division of Genomics and Translational Biomedicine, College of Health and Life Sciences, Hamad Bin Khalifa University, Doha P.O. Box 34110, Qatar;
- Department of Biochemistry and Molecular Genetics, American University of Beirut, Beirut P.O. Box 110236, Lebanon;
| | - Richard Humber
- Robert W. Holley Center for Agriculture and Health, USDA-ARS Emerging Pests and Pathogens Research Unit, 538 Tower Road, Ithaca, NY 14853-2901, USA;
| | - Nehme El-Hachem
- Department of Biochemistry and Molecular Genetics, American University of Beirut, Beirut P.O. Box 110236, Lebanon;
| | - Jacques Guillot
- Department of Dermatology Parasitology and Mycology, Oniris, Ecole Nationale Vétérinaire, Agroalimentaire et de l’Alimentation, P.O. Box 44307 Nantes, France;
| | - Racha Chehab
- Department of Agriculture and Food Engineering, Holy Spirit University of Kaslik, Jounieh P.O. Box 446, Lebanon;
| | - Elise Noujeim
- National Center for Marine Sciences, National Council for Scientific Research—CNRS, Beirut P.O. Box 11-8281, Lebanon; (E.N.); (Y.E.K.)
| | - Yara El Khoury
- National Center for Marine Sciences, National Council for Scientific Research—CNRS, Beirut P.O. Box 11-8281, Lebanon; (E.N.); (Y.E.K.)
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti (Di.S.S.P.A.), Università degli Studi di Bari “Aldo Moro”, P.O. Box 70126 Bari, Italy
| | - Wadih Skaff
- Ecole Supérieure d’Ingénieurs d’Agronomie Méditerranéenne, Université Saint Joseph, Taanayel, Zahlé P.O. Box 159, Lebanon;
| | - Nathalie Estephan
- Department of Chemistry and Biochemistry, Faculty of Arts and Sciences, Holy Spirit University of Kaslik, Jounieh P.O. Box 446, Lebanon;
| | - Nabil Nemer
- Department of Agriculture and Food Engineering, Holy Spirit University of Kaslik, Jounieh P.O. Box 446, Lebanon;
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8
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El-Hachem N, Fardoun MM, Slika H, Baydoun E, Eid AH. Repurposing Cilostazol for Raynaud's Phenomenon. Curr Med Chem 2021; 28:2409-2417. [PMID: 32881655 DOI: 10.2174/0929867327666200903114154] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/16/2020] [Accepted: 07/21/2020] [Indexed: 11/22/2022]
Abstract
Raynaud 's Phenomenon (RP) results from exaggerated cold-induced vasoconstriction. RP patients suffer from vasospastic attacks and compromised digital blood perfusion leading to a triple color change at the level the fingers. Severe RP may cause ulcers and threaten tissue viability. Many drugs have been used to alleviate the symptoms of RP. These include calcium-channel blockers, cGMP-specific phosphodiesterase type 5 inhibitors, prostacyclin analogs, and angiotensin receptor blockers. Despite their variety, these drugs do not treat RP but rather alleviate its symptoms. To date, no drug for RP has been yet approved by the U.S Food and Drugs Administration. Cilostazol is a selective inhibitor of phosphodiesterase-III, originally prescribed to treat intermittent claudication. Owing to its antiplatelet and vasodilating properties, cilostazol is being repurposed as a potential drug for RP. This review focuses on the different lines of action of cilostazol serving to enhance blood perfusion in RP patients.
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Affiliation(s)
- Nehme El-Hachem
- Laboratory of Medical Genetics, Institute of Experimental Cardiology, National Medical Research Center of Cardiology, Beirut, Lebanon
| | - Manal M Fardoun
- Department of Biology, American University of Beirut, Beirut, Lebanon
| | - Hasan Slika
- Department of Pharmacology and Toxicology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Elias Baydoun
- Department of Biology, American University of Beirut, Beirut, Lebanon
| | - Ali H Eid
- Department of Pharmacology and Toxicology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
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9
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Bikorimana JP, El-Hachem N, El-Kadiry AEH, Abusarah J, Salame N, Shammaa R, Rafei M. Thymoproteasome-Expressing Mesenchymal Stromal Cells Confer Protective Anti-Tumor Immunity via Cross-Priming of Endogenous Dendritic Cells. Front Immunol 2021; 11:596303. [PMID: 33542714 PMCID: PMC7853649 DOI: 10.3389/fimmu.2020.596303] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 12/14/2020] [Indexed: 12/01/2022] Open
Abstract
Proteasomes are complex macromolecular structures existing in various forms to regulate a myriad of cellular processes. Besides degrading unwanted or misfolded proteins (proteostasis), distinct immune functions were ascribed for the immunoproteasome and thymoproteasome (TPr) complexes. For instance, antigen degradation during ongoing immune responses mainly relies on immunoproteasome activity, whereas intrathymic CD8 T-cell development requires peptide generation by the TPr complex. Despite these substantial differences, the functional contribution of the TPr to peripheral T-cell immunity remains ill-defined. We herein explored whether the use of mesenchymal stromal cells (MSCs) engineered to exhibit altered proteasomal activity through de novo expression of the TPr complex can be exploited as a novel anti-cancer vaccine capable of triggering potent CD8 T-cell activation. Phenotypic and molecular characterization of MSC-TPr revealed a substantial decrease in MHCI (H2-Kb and H2-Dd) expression along with elevated secretion of various chemokines (CCL2, CCL9, CXCL1, LIX, and CX3CL1). In parallel, transcriptomic analysis pinpointed the limited ability of MSC-TPr to present endogenous antigens, which is consistent with their low expression levels of the peptide-loading proteins TAP, CALR, and PDAI3. Nevertheless, MSC-TPr cross-presented peptides derived from captured soluble proteins. When tested for their protective capacity, MSC-TPr triggered modest anti-tumoral responses despite efficient generation of effector memory CD4 and CD8 T cells. In contrast, clodronate administration prior to vaccination dramatically enhanced the MSC-TPr-induced anti-tumoral immunity clearly highlighting a refractory role mediated by phagocytic cells. Thus, our data elute to a DC cross-priming-dependant pathway in mediating the therapeutic effect of MSC-TPr.
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Affiliation(s)
- Jean-Pierre Bikorimana
- Department of Microbiology, Infectious Diseases and Immunology, Université de Montréal, Montreal, QC, Canada
| | - Nehme El-Hachem
- Centre Hospitalier Universitaire (CHU) Ste-Justine Research Center, Université de Montréal, Montreal, QC, Canada.,Genomics Institute of Precision Medicine, American University of Beirut, Beirut, Lebanon
| | | | - Jamilah Abusarah
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Natasha Salame
- Department of Biomedical Sciences, Université de Montréal, Montreal, QC, Canada
| | - Riam Shammaa
- Department of Family and Community Medicine, University of Toronto, Toronto, ON, Canada.,Canadian Centers for Regenerative Therapy, Toronto, ON, Canada.,Intellistem Technologies Inc., Toronto, ON, Canada
| | - Moutih Rafei
- Department of Microbiology, Infectious Diseases and Immunology, Université de Montréal, Montreal, QC, Canada.,Department of Pharmacology and Physiology, Université de Montréal, Montreal, QC, Canada.,Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada.,Molecular Biology Program, Université de Montréal, Montreal, QC, Canada
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10
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El-Hachem N, Eid E, Nemer G, Dbaibo G, Abbas O, Rubeiz N, Zeineldine S, Matar GM, Bikorimana JP, Shammaa R, Haibe-Kains B, Kurban M, Rafei M. Integrative Transcriptome Analyses Empower the Anti-COVID-19 Drug Arsenal. iScience 2020; 23:101697. [PMID: 33103068 PMCID: PMC7571421 DOI: 10.1016/j.isci.2020.101697] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 09/14/2020] [Accepted: 10/14/2020] [Indexed: 02/06/2023] Open
Abstract
The beginning of the 21st century has been marked by three distinct waves of zoonotic coronavirus outbreaks into the human population. The COVID-19 (coronavirus disease 2019) pandemic is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and emerged as a global threat endangering the livelihoods of millions worldwide. Currently, and despite collaborative efforts, diverse therapeutic strategies from ongoing clinical trials are still debated. To address the need for such an immediate call of action, we leveraged the largest dataset of drug-induced transcriptomic perturbations, public SARS-CoV-2 transcriptomic datasets, and expression profiles from normal lung transcriptomes. Most importantly, our unbiased systems biology approach prioritized more than 50 repurposable drug candidates (e.g., corticosteroids, Janus kinase and Bruton kinase inhibitors). Further clinical investigation of these FDA-approved candidates as monotherapy or in combination with an antiviral regimen (e.g., remdesivir) could lead to promising outcomes in patients with COVID-19.
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Affiliation(s)
- Nehme El-Hachem
- Faculty of Medicine, Division of Genomics Innovation, American University of Beirut, Lebanon
- CHU Sainte-Justine Research Centre, Montreal, Canada
| | - Edward Eid
- Department of Dermatology, American University of Beirut, Lebanon
| | - Georges Nemer
- Division of Genomics and Translational Biomedicine, College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Ghassan Dbaibo
- Center for Infectious Diseases Research, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
- Department of Pediatrics and Adolescent Medicine, Faculty of Medicine, American University of Beirut Medical Center, Beirut, Lebanon
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Ossama Abbas
- Department of Dermatology, American University of Beirut, Lebanon
| | - Nelly Rubeiz
- Department of Dermatology, American University of Beirut, Lebanon
| | - Salah Zeineldine
- American University of Beirut, Department of Internal Medicine, Faculty of Medicine, Beirut, Lebanon
| | - Ghassan M. Matar
- Department of Experimental Pathology, Immunology and Microbiology, Center for Infectious Diseases Research, WHO Collaborating Center for Reference & Research on Bacterial Pathogens, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Jean-Pierre Bikorimana
- Department of Microbiology, Infectious Diseases and Immunology, Université de Montréal, Montreal, QC, Canada
| | - Riam Shammaa
- Department of Family and Community Medicine, University of Toronto, Toronto, ON, Canada
- Canadian Centers for Regenerative Therapy, Toronto, ON, Canada
- IntelliStem Technologies Inc., Toronto, ON, Canada
| | - Benjamin Haibe-Kains
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Vector Institute, Toronto, ON, Canada
| | - Mazen Kurban
- Department of Dermatology, American University of Beirut, Lebanon
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Moutih Rafei
- Department of Pharmacology and Physiology, Université de Montréal, Montreal, QC, Canada
- Department of Microbiology, Infectious Diseases and Immunology, Université de Montréal, Montreal, QC, Canada
- Molecular Biology Program, Université de Montréal, Montreal, QC, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
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11
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Abusarah J, Cui Y, El-Hachem N, El-Kadiry AEH, Hammond-Martel I, Wurtele H, Beaudry A, Raynal NJM, Robert F, Pelletier J, Jankovic M, Mercier F, Kamyabiazar S, Annabi B, Rafei M. TACIMA-218: A Novel Pro-Oxidant Agent Exhibiting Selective Antitumoral Activity. Mol Cancer Ther 2020; 20:37-49. [PMID: 33087510 DOI: 10.1158/1535-7163.mct-20-0333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/28/2020] [Accepted: 10/08/2020] [Indexed: 11/16/2022]
Abstract
We report the discovery, via a unique high-throughput screening strategy, of a novel bioactive anticancer compound: Thiol Alkylating Compound Inducing Massive Apoptosis (TACIMA)-218. We demonstrate that this molecule engenders apoptotic cell death in genetically diverse murine and human cancer cell lines, irrespective of their p53 status, while sparing normal cells. TACIMA-218 causes oxidative stress in the absence of protective antioxidants normally induced by Nuclear factor erythroid 2-related factor 2 activation. As such, TACIMA-218 represses RNA translation and triggers cell signaling cascade alterations in AKT, p38, and JNK pathways. In addition, TACIMA-218 manifests thiol-alkylating properties resulting in the disruption of redox homeostasis along with key metabolic pathways. When administered to immunocompetent animals as a monotherapy, TACIMA-218 has no apparent toxicity and induces complete regression of pre-established lymphoma and melanoma tumors. In sum, TACIMA-218 is a potent oxidative stress inducer capable of selective cancer cell targeting.
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Affiliation(s)
- Jamilah Abusarah
- The Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
| | - Yun Cui
- The Department of Pharmacology and Physiology, Université de Montréal, Montréal, Québec, Canada
| | - Nehme El-Hachem
- Department of Pediatric Hematology-Oncology, Centre Hospitalier Universitaire (CHU) Sainte-Justine Research Center, Montréal, Québec, Canada.,Medical Genomics, Institute of Precision Medicine, American University of Beirut, Beirut, Lebanon
| | - Abed El-Hakim El-Kadiry
- The Department of Pharmacology and Physiology, Université de Montréal, Montréal, Québec, Canada
| | - Ian Hammond-Martel
- Maisonneuve-Rosemont Hospital Research Center, Montréal, Québec, Canada.,Molecular Biology Program, Université de Montréal, Montréal, Québec, Canada
| | - Hugo Wurtele
- Maisonneuve-Rosemont Hospital Research Center, Montréal, Québec, Canada.,Department of Medicine, Université de Montréal, Montréal, Québec, Canada
| | - Annie Beaudry
- The Department of Pharmacology and Physiology, Université de Montréal, Montréal, Québec, Canada
| | - Noël J-M Raynal
- The Department of Pharmacology and Physiology, Université de Montréal, Montréal, Québec, Canada
| | - Francis Robert
- Department of Biochemistry, McGill University, Montréal, Québec, Canada
| | - Jerry Pelletier
- Department of Biochemistry, McGill University, Montréal, Québec, Canada
| | - Maja Jankovic
- Lady Davis Institute for Medical Research, Segal Cancer Centre, Jewish General Hospital, Montréal, Québec, Canada.,Division of Experimental Medicine, McGill University, Montréal, Québec, Canada
| | - Francois Mercier
- Lady Davis Institute for Medical Research, Segal Cancer Centre, Jewish General Hospital, Montréal, Québec, Canada.,Division of Experimental Medicine, McGill University, Montréal, Québec, Canada
| | - Samaneh Kamyabiazar
- Department of Chemistry, Université du Québec à Montréal, Montréal, Québec, Canada
| | - Borhane Annabi
- Department of Chemistry, Université du Québec à Montréal, Montréal, Québec, Canada
| | - Moutih Rafei
- The Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada. .,The Department of Pharmacology and Physiology, Université de Montréal, Montréal, Québec, Canada.,Molecular Biology Program, Université de Montréal, Montréal, Québec, Canada.,The Department of Microbiology, Infectious Diseases and Immunology, Université de Montréal, Montréal, Québec, Canada
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12
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Ahmad A, Ibrahim Z, Sakr G, El-Bizri A, Masri L, Elhajj IH, El-Hachem N, Isma'eel H. A comparison of artificial intelligence-based algorithms for the identification of patients with depressed right ventricular function from 2-dimentional echocardiography parameters and clinical features. Cardiovasc Diagn Ther 2020; 10:859-868. [PMID: 32968641 DOI: 10.21037/cdt-20-471] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Background Recognizing low right ventricular (RV) function from 2-dimentiontial echocardiography (2D-ECHO) is challenging when parameters are contradictory. We aim to develop a model to predict low RV function integrating the various 2D-ECHO parameters in reference to cardiac magnetic resonance (CMR)-the gold standard. Methods We retrospectively identified patients who underwent a 2D-ECHO and a CMR within 3 months of each other at our institution (American University of Beirut Medical Center). We extracted three parameters (TAPSE, S' and FACRV) that are classically used to assess RV function. We have assessed the ability of 2D-ECHO derived parameters and clinical features to predict RV function measured by the gold standard CMR. We compared outcomes from four machine learning algorithms, widely used in the biomedical community to solve classification problems. Results One hundred fifty-five patients were identified and included in our study. Average age was 43±17.1 years old and 52/156 (33.3%) were females. According to CMR, 21 patients were identified to have RV dysfunction, with an RVEF of 34.7%±6.4%, as opposed to 54.7%±6.7% in the normal RV population (P<0.0001). The Random Forest model was able to detect low RV function with an AUC =0.80, while general linear regression performed poorly in our population with an AUC of 0.62. Conclusions In this study, we trained and validated an ML-based algorithm that could detect low RV function from clinical and 2D-ECHO parameters. The algorithm has two advantages: first, it performed better than general linear regression, and second, it integrated the various 2D-ECHO parameters.
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Affiliation(s)
- Ali Ahmad
- Vascular Medicine Program, Division of Cardiology, American University of Beirut, Beirut, Lebanon.,Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Zahi Ibrahim
- Vascular Medicine Program, Division of Cardiology, American University of Beirut, Beirut, Lebanon
| | - Georges Sakr
- Department of Computer Engineering, St Joseph University of Beirut, Beirut, Lebanon
| | - Abdallah El-Bizri
- Department of Internal Medicine, American University of Beirut, Beirut, Lebanon
| | - Lara Masri
- Vascular Medicine Program, Division of Cardiology, American University of Beirut, Beirut, Lebanon
| | - Imad H Elhajj
- Department of Electrical and Computer Engineering, American University of Beirut, Beirut, Lebanon
| | - Nehme El-Hachem
- Department of Electrical and Computer Engineering, American University of Beirut, Beirut, Lebanon
| | - Hussain Isma'eel
- Vascular Medicine Program, Division of Cardiology, American University of Beirut, Beirut, Lebanon.,Department of Internal Medicine, American University of Beirut, Beirut, Lebanon
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13
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Nemer G, El-Hachem N, Eid E, Hamie L, Bardawil T, Khalil S, El-Rassy I, Safi R, Khalil A, Abbas O, Shimomura Y, Kurban M. A novel TRAF3IP2 variant causing familial scarring alopecia with mixed features of discoid lupus erythematosus and folliculitis decalvans. Clin Genet 2020; 98:116-125. [PMID: 32350852 DOI: 10.1111/cge.13767] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 04/21/2020] [Accepted: 04/22/2020] [Indexed: 12/22/2022]
Abstract
Discoid lupus erythematosus (DLE) is an autoimmune disorder with a poorly defined etiology. Despite epidemiologic gender and ethnic biases, a clear genetic basis for DLE remains elusive. In this study, we used exome and RNA sequencing technologies to characterize a consanguineous Lebanese family with four affected individuals who presented with classical scalp DLE and generalized folliculitis. Our results unraveled a novel biallelic variant c.1313C > A leading to a missense substitution p.(Thr438Asn) in TRAF3IP2(NM_147200.3). Expression studies in cultured cells revealed mis-localization of the mutated protein. Functional characterization of the mutated protein showed significant reduction in the physical interaction with the interleukin 17-A receptor (IL17RA), while interaction with TRAF6 was unaffected. By conducting a differential genome-wide transcriptomics analysis between affected and non-affected individuals, we showed that the hair follicle differentiation pathway is drastically suppressed, whereas cytokine and inflammation responses are significantly upregulated. Furthermore, our results were highly concordant with molecular signatures in patients with DLE from a public dataset. In conclusion, this is the first report on a new putative role for TRAF3IP2 in the etiology of DLE. The identified molecular features associated with this gene could pave the way for better DLE-targeted treatment.
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Affiliation(s)
- Georges Nemer
- Department of Biochemistry and Molecular Genetics, American University of Beirut, Beirut, Lebanon
| | - Nehme El-Hachem
- Department of Biochemistry and Molecular Genetics, American University of Beirut, Beirut, Lebanon
- Pillar Genomics Institute of Precision Medicine, American University of Beirut, Beirut, Lebanon
| | - Edward Eid
- Dermatology, American University of Beirut, Beirut, Lebanon
| | - Lamiaa Hamie
- Dermatology, American University of Beirut, Beirut, Lebanon
| | - Tara Bardawil
- Dermatology, American University of Beirut, Beirut, Lebanon
| | - Samar Khalil
- Dermatology, American University of Beirut, Beirut, Lebanon
| | - Inaam El-Rassy
- Pillar Genomics Institute of Precision Medicine, American University of Beirut, Beirut, Lebanon
| | - Remi Safi
- Dermatology, American University of Beirut, Beirut, Lebanon
| | - Athar Khalil
- Department of Biochemistry and Molecular Genetics, American University of Beirut, Beirut, Lebanon
| | - Ossama Abbas
- Dermatology, American University of Beirut, Beirut, Lebanon
| | - Yutaka Shimomura
- Department of Dermatology, Yamaguchi University, Yamaguchi, Japan
| | - Mazen Kurban
- Department of Biochemistry and Molecular Genetics, American University of Beirut, Beirut, Lebanon
- Dermatology, American University of Beirut, Beirut, Lebanon
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14
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El-Kadiry AEH, Abusarah J, Cui YE, El-Hachem N, Hammond-Martel I, Wurtele H, Thomas S, Ahmadi M, Balood M, Talbot S, Rafei M. A Novel Sulfonyl-Based Small Molecule Exhibiting Anti-cancer Properties. Front Pharmacol 2020; 11:237. [PMID: 32231565 PMCID: PMC7081885 DOI: 10.3389/fphar.2020.00237] [Citation(s) in RCA: 2] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 02/21/2020] [Indexed: 11/13/2022] Open
Abstract
Phenotypic screening is an ideal strategy for the discovery of novel bioactive molecules. Using a customized high-throughput screening (HTS) assay employing primary T lymphocytes, we screened a small library of 4,398 compounds with unknown biological function/target to identify compounds eliciting immunomodulatory properties and discovered a sulfonyl-containing hit, we named InhiTinib. This compound inhibited interferon (IFN)-gamma production and proliferation of primary CD3+ T cells without inducing cell death. In contrast, InhiTinib triggered apoptosis in several murine and human cancer cell lines. Besides, the compound was well tolerated by immunocompetent mice, triggered tumor regression in animals with pre-established EL4 T-cell lymphomas, and prolonged the overall survival of mice harboring advanced tumors. Altogether, our data demonstrate the anti-cancer properties of InhiTinib, which can henceforth bridge to wider-scale biochemical and clinical tests following further in-depth pharmacodynamic studies.
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Affiliation(s)
- Abed El-Hakim El-Kadiry
- Department of Biomedical Sciences, Université de Montréal, Montreal, QC, Canada.,Department of Pharmacology and Physiology, Université de Montréal, Montreal, QC, Canada
| | - Jamilah Abusarah
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Yun Emma Cui
- Department of Pharmacology and Physiology, Université de Montréal, Montreal, QC, Canada
| | - Nehme El-Hachem
- Department of Pharmacology and Physiology, Université de Montréal, Montreal, QC, Canada.,Genomics Institute of Precision Medicine, American University of Beirut, Beirut, Lebanon
| | - Ian Hammond-Martel
- Department of Medicine, Université de Montréal, Montreal, QC, Canada.,Maisonneuve-Rosemont Hospital Research Center, Montreal, QC, Canada
| | - Hugo Wurtele
- Department of Medicine, Université de Montréal, Montreal, QC, Canada.,Maisonneuve-Rosemont Hospital Research Center, Montreal, QC, Canada
| | - Sini Thomas
- Department of Pharmacology and Physiology, Université de Montréal, Montreal, QC, Canada
| | - Maryam Ahmadi
- Department of Pharmacology and Physiology, Université de Montréal, Montreal, QC, Canada
| | - Mohammad Balood
- Department of Pharmacology and Physiology, Université de Montréal, Montreal, QC, Canada
| | - Sébastien Talbot
- Department of Pharmacology and Physiology, Université de Montréal, Montreal, QC, Canada
| | - Moutih Rafei
- Department of Pharmacology and Physiology, Université de Montréal, Montreal, QC, Canada.,Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada.,Molecular Biology Program, Université de Montréal, Montreal, QC, Canada.,Department of Microbiology, Infectious Diseases and Immunology, Université de Montréal, Montreal, QC, Canada
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15
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Ayoub AJ, Hariss L, El-Hachem N, El-Achkar GA, Ghayad SE, Dagher OK, Borghol N, Grée R, Badran B, Hachem A, Hamade E, Habib A. gem-Difluorobisarylic derivatives: design, synthesis and anti-inflammatory effect. BMC Chem 2019; 13:124. [PMID: 31696161 PMCID: PMC6824041 DOI: 10.1186/s13065-019-0640-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 10/03/2019] [Indexed: 11/10/2022] Open
Abstract
Introduction New fluorinated diaryl ethers and bisarylic ketones were designed and evaluated for their anti-inflammatory effects in primary macrophages. Methods The synthesis of the designed molecules started from easily accessible and versatile gem-difluoro propargylic derivatives. The desired aromatic systems were obtained using Diels-Alder/aromatization sequences and this was followed by Pd-catalyzed coupling reactions and, when required, final functionalization steps. Both direct inhibitory effects on cyclooxygenase-1 or -2 activities, protein expression of cyclooxygenase-2 and nitric oxide synthase-II and the production of prostaglandin E2, the pro-inflammatory nitric oxide and interleukin-6 were evaluated in primary murine bone marrow-derived macrophages in response to lipopolysaccharide. Docking of the designed molecules in cyclooxygenase-1 or -2 was performed. Results Only fluorinated compounds exerted anti-inflammatory activities by lowering the secretion of interleukin-6, nitric oxide, and prostaglandin E2, and decreasing the protein expression of inducible nitric oxide synthase and cyclooxygenase-2 in mouse primary macrophages exposed to lipopolysaccharide, as well as cyclooxygenase activity for some inhibitors with different efficiencies depending on the R-groups. Docking observation suggested an inhibitory role of cyclooxygenase-1 or -2 for compounds A3, A4 and A5 in addition to their capacity to inhibit nitrite, interleukin-6, and nitric oxide synthase-II and cyclooxygenase-2 expression. Conclusion The new fluorinated diaryl ethers and bisarylic ketones have anti-inflammatory effects in macrophages. These fluorinated compounds have improved potential anti-inflammatory properties due to the fluorine residues in the bioactive molecules.
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Affiliation(s)
- Abeer J Ayoub
- 1Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon.,2Laboratory of Cancer Biology and Molecular Immunology, Faculty of Sciences I, Lebanese University, Hadath, Beirut, Lebanon
| | - Layal Hariss
- 3Laboratory for Medicinal Chemistry and Natural Products, Faculty of Sciences I and PRASE-EDST Lebanese University, Beirut, Lebanon
| | - Nehme El-Hachem
- 4Integrative Systems Biology, Institut de Recherches Cliniques de Montréal, Montreal, QC Canada.,8Present Address: Department of Electrical and Computer Engineering, American University of Beirut, Beirut, Lebanon
| | - Ghewa A El-Achkar
- 1Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Sandra E Ghayad
- 5Department of Biology, Faculty of Sciences II, EDST, Lebanese University, Fanar, Lebanon
| | - Oula K Dagher
- 1Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Nada Borghol
- 2Laboratory of Cancer Biology and Molecular Immunology, Faculty of Sciences I, Lebanese University, Hadath, Beirut, Lebanon
| | - René Grée
- 6Université de Rennes, CNRS, ISCR (Institut des Sciences Chimiques de Rennes) UMR 6226, 35000 Rennes, France
| | - Bassam Badran
- 2Laboratory of Cancer Biology and Molecular Immunology, Faculty of Sciences I, Lebanese University, Hadath, Beirut, Lebanon
| | - Ali Hachem
- 3Laboratory for Medicinal Chemistry and Natural Products, Faculty of Sciences I and PRASE-EDST Lebanese University, Beirut, Lebanon
| | - Eva Hamade
- 2Laboratory of Cancer Biology and Molecular Immunology, Faculty of Sciences I, Lebanese University, Hadath, Beirut, Lebanon
| | - Aida Habib
- 1Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon.,Université de Paris, Centre de Recherche sur l'Inflammation (CRI), INSERM, UMR1149, CNRS, ERL 8252, 75018 Paris, France
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16
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Madani Tonekaboni SA, Manem VSK, El-Hachem N, Haibe-Kains B. SIGN: similarity identification in gene expression. Bioinformatics 2019; 35:4830-4833. [PMID: 31198954 DOI: 10.1093/bioinformatics/btz485] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 04/12/2019] [Accepted: 06/10/2019] [Indexed: 12/12/2022] Open
Abstract
MOTIVATION High-throughput molecular profiles of human cells have been used in predictive computational approaches for stratification of healthy and malignant phenotypes and identification of their biological states. In this regard, pathway activities have been used as biological features in unsupervised and supervised learning schemes. RESULTS We developed SIGN (Similarity Identification in Gene expressioN), a flexible open-source R package facilitating the use of pathway activities and their expression patterns to identify similarities between biological samples. We defined a new measure, the transcriptional similarity coefficient, which captures similarity of gene expression patterns, instead of quantifying overall activity, in biological pathways between the samples. To demonstrate the utility of SIGN in biomedical research, we establish that SIGN discriminates subtypes of breast tumors and patients with good or poor overall survival. SIGN outperforms the best models in DREAM challenge in predicting survival of breast cancer patients using the data from the Molecular Taxonomy of Breast Cancer International Consortium. In summary, SIGN can be used as a new tool for interrogating pathway activity and gene expression patterns in unsupervised and supervised learning schemes to improve prognostic risk estimation for cancer patients by the biomedical research community. AVAILABILITY AND IMPLEMENTATION An open-source R package is available (https://cran.r-project.org/web/packages/SIGN/).
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Affiliation(s)
- Seyed Ali Madani Tonekaboni
- Princess Margaret Cancer Centre, University of Toronto, Toronto, ON M5G 1L7, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Venkata Satya Kumar Manem
- Princess Margaret Cancer Centre, University of Toronto, Toronto, ON M5G 1L7, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada.,Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval, QC G1V 4G5, Canada
| | - Nehme El-Hachem
- Integrative Systems Biology, Institut de Recherches Cliniques de Montréal, Montréal, QC, Canada.,Department of Medicine, University of Montreal, Montréal, QC, Canada
| | - Benjamin Haibe-Kains
- Princess Margaret Cancer Centre, University of Toronto, Toronto, ON M5G 1L7, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada.,Department of Computer Science, University of Toronto, Toronto, ON M5T 3A1, Canada.,Ontario Institute of Cancer Research, Toronto, ON M5G 1L7, Canada.,Vector Institute, Toronto, ON M5G 1L7, Canada
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17
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Smirnov P, Kofia V, Maru A, Freeman M, Ho C, El-Hachem N, Adam GA, Ba-Alawi W, Safikhani Z, Haibe-Kains B. PharmacoDB: an integrative database for mining in vitro anticancer drug screening studies. Nucleic Acids Res 2019; 46:D994-D1002. [PMID: 30053271 PMCID: PMC5753377 DOI: 10.1093/nar/gkx911] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [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: 08/15/2017] [Accepted: 09/27/2017] [Indexed: 12/18/2022] Open
Abstract
Recent cancer pharmacogenomic studies profiled large panels of cell lines against hundreds of approved drugs and experimental chemical compounds. The overarching goal of these screens is to measure sensitivity of cell lines to chemical perturbations, correlate these measures to genomic features, and thereby develop novel predictors of drug response. However, leveraging these valuable data is challenging due to the lack of standards for annotating cell lines and chemical compounds, and quantifying drug response. Moreover, it has been recently shown that the complexity and complementarity of the experimental protocols used in the field result in high levels of technical and biological variation in the in vitro pharmacological profiles. There is therefore a need for new tools to facilitate rigorous comparison and integrative analysis of large-scale drug screening datasets. To address this issue, we have developed PharmacoDB (pharmacodb.pmgenomics.ca), a database integrating the largest cancer pharmacogenomic studies published to date. Here, we describe how the curation of cell line and chemical compound identifiers maximizes the overlap between datasets and how users can leverage such data to compare and extract robust drug phenotypes. PharmacoDB provides a unique resource to mine a compendium of curated cancer pharmacogenomic datasets that are otherwise disparate and difficult to integrate.
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Affiliation(s)
- Petr Smirnov
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Victor Kofia
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Alexander Maru
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Mark Freeman
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Chantal Ho
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Nehme El-Hachem
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - George-Alexandru Adam
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Wail Ba-Alawi
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Zhaleh Safikhani
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Benjamin Haibe-Kains
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.,Ontario Institute of Cancer Research, Toronto, Ontario, Canada
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18
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Yao F, Madani Tonekaboni SA, Safikhani Z, Smirnov P, El-Hachem N, Freeman M, Manem VSK, Haibe-Kains B. Tissue specificity of in vitro drug sensitivity. J Am Med Inform Assoc 2019; 25:158-166. [PMID: 29016819 DOI: 10.1093/jamia/ocx062] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 05/22/2017] [Indexed: 12/11/2022] Open
Abstract
Objectives We sought to investigate the tissue specificity of drug sensitivities in large-scale pharmacological studies and compare these associations to those found in drug clinical indications. Materials and Methods We leveraged the curated cell line response data from PharmacoGx and applied an enrichment algorithm on drug sensitivity values' area under the drug dose-response curves (AUCs) with and without adjustment for general level of drug sensitivity. Results We observed tissue specificity in 63% of tested drugs, with 8% of total interactions deemed significant (false discovery rate <0.05). By restricting the drug-tissue interactions to those with AUC > 0.2, we found that in 52% of interactions, the tissue was predictive of drug sensitivity (concordance index > 0.65). When compared with clinical indications, the observed overlap was weak (Matthew correlation coefficient, MCC = 0.0003, P > .10). Discussion While drugs exhibit significant tissue specificity in vitro, there is little overlap with clinical indications. This can be attributed to factors such as underlying biological differences between in vitro models and patient tumors, or the inability of tissue-specific drugs to bring additional benefits beyond gold standard treatments during clinical trials. Conclusion Our meta-analysis of pan-cancer drug screening datasets indicates that most tested drugs exhibit tissue-specific sensitivities in a large panel of cancer cell lines. However, the observed preclinical results do not translate to the clinical setting. Our results suggest that additional research into showing parallels between preclinical and clinical data is required to increase the translational potential of in vitro drug screening.
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Affiliation(s)
- Fupan Yao
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Seyed Ali Madani Tonekaboni
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Zhaleh Safikhani
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Petr Smirnov
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Nehme El-Hachem
- Integrative Systems Biology, Institut de Recherches Cliniques de Montréal, Montreal, Quebec, Canada.,Department of Medicine, University of Montreal, Montréal, Quebec, Canada
| | - Mark Freeman
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Venkata Satya Kumar Manem
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Benjamin Haibe-Kains
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.,Ontario Institute of Cancer Research, Toronto, Ontario, Canada
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19
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Goyette MA, Cusseddu R, Elkholi I, Abu-Thuraia A, El-Hachem N, Haibe-Kains B, Gratton JP, Côté JF. AXL knockdown gene signature reveals a drug repurposing opportunity for a class of antipsychotics to reduce growth and metastasis of triple-negative breast cancer. Oncotarget 2019; 10:2055-2067. [PMID: 31007848 PMCID: PMC6459349 DOI: 10.18632/oncotarget.26725] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 02/15/2019] [Indexed: 11/25/2022] Open
Abstract
Triple-Negative Breast Cancer (TNBC) is an aggressive cancer subtype that is associated with a poor prognosis due to its propensity to form metastases. The receptor tyrosine kinase AXL plays a role in tumor cell dissemination and its expression in breast cancers correlates with poor patient survival. Here, we explored whether already used drugs might elicit a gene signature similar to that seen with AXL knockdown in TNBC cells and which could, therefore, offer an opportunity for drug repurposing. To this end, we queried the Connectivity Map with an AXL gene signature which revealed a class of dopamine receptors antagonists named phenothiazines (Thioridazine, Fluphenazine and Trifluoperazine) typically used as anti-psychotics. We next tested if these drugs, similarly to AXL depletion, were able to limit growth and metastatic progression of TNBC cells and found that phenothiazines are able to reduce cell invasion, proliferation, viability and increase apoptosis of TNBC cells in vitro. Mechanistically, these drugs did not affect AXL activity but instead reduced PI3K/AKT/mTOR and ERK signaling. When administered to mice bearing TNBC xenografts, phenothiazines were able to reduce tumor growth and metastatic burden. Collectively, these results suggest that these antipsychotics display anti-tumor and anti-metastatic activity and that they could potentially be repurposed, in combination with standard chemotherapy, for the treatment of TNBC.
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Affiliation(s)
- Marie-Anne Goyette
- Montreal Clinical Research Institute (IRCM), Montréal, QC, H2W 1R7, Canada.,Molecular Biology Programs, Université de Montréal, Montréal, QC, H3T 1J4, Canada
| | - Rebecca Cusseddu
- Montreal Clinical Research Institute (IRCM), Montréal, QC, H2W 1R7, Canada.,Molecular Biology Programs, Université de Montréal, Montréal, QC, H3T 1J4, Canada
| | - Islam Elkholi
- Montreal Clinical Research Institute (IRCM), Montréal, QC, H2W 1R7, Canada.,Molecular Biology Programs, Université de Montréal, Montréal, QC, H3T 1J4, Canada
| | - Afnan Abu-Thuraia
- Montreal Clinical Research Institute (IRCM), Montréal, QC, H2W 1R7, Canada.,Molecular Biology Programs, Université de Montréal, Montréal, QC, H3T 1J4, Canada
| | - Nehme El-Hachem
- Montreal Clinical Research Institute (IRCM), Montréal, QC, H2W 1R7, Canada
| | - Benjamin Haibe-Kains
- Princess Margaret Cancer Centre, Toronto, University Health Network, ON M5G 1L7, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada.,Department of Computer Science, University of Toronto, Toronto, ON M5T 3A1, Canada.,Ontario Institute for Cancer Research, Toronto, ON M5G 1L7, Canada.,Vector Institute, Toronto, ON M5G 1L7, Canada
| | - Jean-Philippe Gratton
- Department of Pharmacology and Physiology, Université de Montréal, Montréal, QC, H3C 3J7, Canada
| | - Jean-François Côté
- Montreal Clinical Research Institute (IRCM), Montréal, QC, H2W 1R7, Canada.,Molecular Biology Programs, Université de Montréal, Montréal, QC, H3T 1J4, Canada.,Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC, H3C 3J7, Canada.,Department of Anatomy and Cell Biology, McGill University, Montréal, QC, H3A 0C7, Canada
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20
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Parisien M, Samoshkin A, Tansley SN, Piltonen MH, Martin LJ, El-Hachem N, Dagostino C, Allegri M, Mogil JS, Khoutorsky A, Diatchenko L. Genetic pathway analysis reveals a major role for extracellular matrix organization in inflammatory and neuropathic pain. Pain 2019; 160:932-944. [DOI: 10.1097/j.pain.0000000000001471] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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21
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Khalil A, Dekmak B, Boulos F, Kantrowitz J, Spira A, Fujimoto J, Kadara H, El-Hachem N, Nemer G. Transcriptomic Alterations in Lung Adenocarcinoma Unveil New Mechanisms Targeted by the TBX2 Subfamily of Tumor Suppressor Genes. Front Oncol 2018; 8:482. [PMID: 30425966 PMCID: PMC6218583 DOI: 10.3389/fonc.2018.00482] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 10/09/2018] [Indexed: 12/22/2022] Open
Abstract
T-box (TBX) transcription factors are evolutionary conserved genes and master transcriptional regulators. In mammals, TBX2 subfamily (TBX2, TBX3, TBX4, and TBX5) genes are expressed in the developing lung bud and tracheae. Our group previously showed that the expression of TBX2 subfamily was significantly high in human normal lungs, but markedly suppressed in lung adenocarcinoma (LUAD). To further elucidate their role in LUAD pathogenesis, we first confirmed abundant expression of protein products of the four members by immunostaining in adult human normal lung tissues. We also found overall suppressed expression of these genes and their corresponding proteins in a panel of human LUAD cell lines. Transient over-expression of each of the genes in human (NCI-H1299), and mouse (MDA-F471) derived lung cancer cells was found to significantly inhibit growth and proliferation as well as induce apoptosis. Genome-wide transcriptomic analyses on NCI-H1299 cells, overexpressing TBX2 gene subfamily, unraveled novel regulatory pathways. These included, among others, inhibition of cell cycle progression but more importantly activation of the histone demethylase pathway. When using a pattern-matching algorithm, we showed that TBX's overexpression mimic molecular signatures from azacitidine treated NCI-H1299 cells which in turn are inversely correlated to expression profiles of both human and murine lung tumors relative to matched normal lung. In conclusion, we showed that the TBX2 subfamily genes play a critical tumor suppressor role in lung cancer pathogenesis through regulating its methylating pattern, making them putative candidates for epigenetic therapy in LUAD.
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Affiliation(s)
- Athar Khalil
- Departments of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Batoul Dekmak
- Departments of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Fouad Boulos
- Department of Pathology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Jake Kantrowitz
- Section of Computational Biomedicine, Boston University, Boston, MA, United States
| | - Avrum Spira
- Section of Computational Biomedicine, Boston University, Boston, MA, United States
| | - Junya Fujimoto
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Humam Kadara
- Departments of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon.,Division of Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Nehme El-Hachem
- Faculty of Medicine and Genome Innovation Centre, McGill University, Montreal, QC, Canada
| | - Georges Nemer
- Departments of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
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22
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Khalil A, El-Hachem N, Dekmak B, Kadara H, Nemer G. Abstract 5513: Role of the evolutionarily conserved TBX2 subfamily of transcription factors in the molecular pathogenesis of human lung adenocarcinoma. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-5513] [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
T-box (TBX) transcription factors are evolutionary conserved genes and master regulators of transcription repression and activation. In mammals, 18 members were described functionally and structurally, of which the TBX2 subfamily (TBX2, TBX3, TBX4, TBX5) genes were shown to be expressed early on in the developing lung bud and tracheae. Despite these insights into the role of the TBX2 subfamily in normal lung organogenesis, little is known about the role of these genes in pathological pulmonary conditions in humans; particularly lung cancer, an aggressive malignancy that is the leading cause of cancer-deaths worldwide. To fill this void, our group previously surveyed the expression of TBX2 subfamily in various publicly available datasets and found that all four members were preferentially and highly expressed in human normal lung, but markedly and consistently suppressed in lung adenocarcinoma (LUAD) the most common histological subtype of lung cancer. We also showed that the subfamily was also suppressed in preneoplastic lesions preceding the development of LUADs. Following the above and to further elucidate the role of the TBX2 subfamily in LUAD pathogenesis, we first probed and confirmed abundant expression of protein products of the four members by immunostaining in adult human normal lung tissues. On the other hand, quantitative real-time PCR and western blotting analyses demonstrated overall suppressed expression of the genes and corresponding proteins in a panel of human LUAD cell lines. Transient over-expression of each of the four genes in human LUAD cell lines (H1299 and H1944) was found to overall significantly inhibit cancer cell growth and proliferation. Additionally, over-expression of the four genes induced apoptosis, evidenced by sub-G0/G1 accumulation following cell cycle analysis, in both cell lines (ranging from 40% to 90% compared to control). To understand genome-wide effects of TBX2 subfamily in LUAD, we interrogated global expression programs downstream of these transcription factors by RNA-Seq in H1299 cells engineered to over-express the four members separately. We unraveled novel signaling cues signifying canonical pathways found in our analysis to be directly regulated by members of the TBX2 subfamily. These included, among others, inhibition of cell cycle progression and glycolysis, suppression of pathways mediated by epidermal growth factor (EGFR) and WNT signaling and activation of the major anti-tumor immune marker interferon gamma (IFNG). All in all, our findings point to tumor suppressor roles for TBX2 subfamily in human LUAD pathogenesis and suggest “oncophenotypes” downstream of these factors as putative targets for lung cancer therapy.
Citation Format: Athar Khalil, Nehme El-Hachem, Batoul Dekmak, Humam Kadara, Georges Nemer. Role of the evolutionarily conserved TBX2 subfamily of transcription factors in the molecular pathogenesis of human lung adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5513.
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Affiliation(s)
| | - Nehme El-Hachem
- 2Institut de Recherches Cliniques de Montréal, Quebec, Canada
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23
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Kamar A, Fahed AC, Shibbani K, El-Hachem N, Bou-Slaiman S, Arabi M, Kurban M, Seidman JG, Seidman CE, Haidar R, Baydoun E, Nemer G, Bitar F. A Novel Role for CSRP1 in a Lebanese Family with Congenital Cardiac Defects. Front Genet 2017; 8:217. [PMID: 29326753 PMCID: PMC5741687 DOI: 10.3389/fgene.2017.00217] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 12/04/2017] [Indexed: 12/12/2022] Open
Abstract
Despite an obvious role for consanguinity in congenital heart disease (CHD), most studies fail to document a monogenic model of inheritance except for few cases. We hereby describe a first-degree cousins consanguineous Lebanese family with 7 conceived children: 2 died in utero of unknown causes, 3 have CHD, and 4 have polydactyly. The aim of the study is to unveil the genetic variant(s) causing these phenotypes using next generation sequencing (NGS) technology. Targeted exome sequencing identified a heterozygous duplication in CSRP1 which leads to a potential frameshift mutation at position 154 of the protein. This mutation is inherited from the father, and segregates only with the CHD phenotype. The in vitro characterization demonstrates that the mutation dramatically abrogates its transcriptional activity over cardiac promoters like NPPA. In addition, it differentially inhibits the physical association of CSRP1 with SRF, GATA4, and with the newly described partner herein TBX5. Whole exome sequencing failed to show any potential variant linked to polydactyly, but revealed a novel missense mutation in TRPS1. This mutation is inherited from the healthy mother, and segregating only with the cardiac phenotype. Both TRPS1 and CSRP1 physically interact, and the mutations in each abrogate their partnership. Our findings add fundamental knowledge into the molecular basis of CHD, and propose the di-genic model of inheritance as responsible for such malformations.
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Affiliation(s)
- Amina Kamar
- Department of Biology, American University of Beirut, Beirut, Lebanon
| | - Akl C Fahed
- Department of Genetics, Harvard Medical School, Boston, MA, United States.,Department of Medicine, Massachusetts General Hospital, Boston, MA, United States.,Division of Cardiology, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA, United States
| | - Kamel Shibbani
- Department of Biochemistry and Molecular Genetics, American University of Beirut, Beirut, Lebanon
| | - Nehme El-Hachem
- Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Salim Bou-Slaiman
- Department of Biochemistry and Molecular Genetics, American University of Beirut, Beirut, Lebanon
| | - Mariam Arabi
- Department of Pediatrics and Adolescent Medicine, American University of Beirut, Beirut, Lebanon
| | - Mazen Kurban
- Department of Biochemistry and Molecular Genetics, American University of Beirut, Beirut, Lebanon.,Department of Dermatology, American University of Beirut, Beirut, Lebanon.,Department of Dermatology, Columbia University, New York, NY, United States
| | - Jonathan G Seidman
- Department of Genetics, Harvard Medical School, Boston, MA, United States
| | - Christine E Seidman
- Department of Genetics, Harvard Medical School, Boston, MA, United States.,Division of Cardiology, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA, United States
| | - Rachid Haidar
- Department of Surgery, American University of Beirut, Beirut, Lebanon
| | - Elias Baydoun
- Department of Biology, American University of Beirut, Beirut, Lebanon
| | - Georges Nemer
- Department of Medicine, Massachusetts General Hospital, Boston, MA, United States
| | - Fadi Bitar
- Department of Pediatrics and Adolescent Medicine, American University of Beirut, Beirut, Lebanon
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24
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Safikhani Z, Smirnov P, Thu KL, Silvester J, El-Hachem N, Quevedo R, Lupien M, Mak TW, Cescon D, Haibe-Kains B. Gene isoforms as expression-based biomarkers predictive of drug response in vitro. Nat Commun 2017; 8:1126. [PMID: 29066719 PMCID: PMC5655668 DOI: 10.1038/s41467-017-01153-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [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: 08/30/2016] [Accepted: 08/23/2017] [Indexed: 01/09/2023] Open
Abstract
Next-generation sequencing technologies have recently been used in pharmacogenomic studies to characterize large panels of cancer cell lines at the genomic and transcriptomic levels. Among these technologies, RNA-sequencing enable profiling of alternatively spliced transcripts. Given the high frequency of mRNA splicing in cancers, linking this feature to drug response will open new avenues of research in biomarker discovery. To identify robust transcriptomic biomarkers for drug response across studies, we develop a meta-analytical framework combining the pharmacological data from two large-scale drug screening datasets. We use an independent pan-cancer pharmacogenomic dataset to test the robustness of our candidate biomarkers across multiple cancer types. We further analyze two independent breast cancer datasets and find that specific isoforms of IGF2BP2, NECTIN4, ITGB6, and KLHDC9 are significantly associated with AZD6244, lapatinib, erlotinib, and paclitaxel, respectively. Our results support isoform expressions as a rich resource for biomarkers predictive of drug response.
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Affiliation(s)
- Zhaleh Safikhani
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Toronto, ON, Canada, M5G1L7
- Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON, Canada, M5G1L7
| | - Petr Smirnov
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Toronto, ON, Canada, M5G1L7
| | - Kelsie L Thu
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Toronto, ON, Canada, M5G1L7
- Institut de Recherches Cliniques de Montréal, 110 Pine Avenue West, Montreal, QC, Canada, H2W 1R7
| | - Jennifer Silvester
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Toronto, ON, Canada, M5G1L7
- Institut de Recherches Cliniques de Montréal, 110 Pine Avenue West, Montreal, QC, Canada, H2W 1R7
| | - Nehme El-Hachem
- Institut de Recherches Cliniques de Montréal, 110 Pine Avenue West, Montreal, QC, Canada, H2W 1R7
| | - Rene Quevedo
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Toronto, ON, Canada, M5G1L7
- Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON, Canada, M5G1L7
| | - Mathieu Lupien
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Toronto, ON, Canada, M5G1L7
- Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON, Canada, M5G1L7
| | - Tak W Mak
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Toronto, ON, Canada, M5G1L7
- Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON, Canada, M5G1L7
- Campbell Family Institute for Breast Cancer Research, 620 University Avenue, Toronto, ON, Canada, M5G2C1
| | - David Cescon
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Toronto, ON, Canada, M5G1L7
- Campbell Family Institute for Breast Cancer Research, 620 University Avenue, Toronto, ON, Canada, M5G2C1
- Division of Medical Oncology and Hematology, Department of Medicine, University of Toronto, 27 King's College Circle, Toronto, ON, Canada, M5S 1A1
| | - Benjamin Haibe-Kains
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Toronto, ON, Canada, M5G1L7.
- Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON, Canada, M5G1L7.
- Department of Computer Science, University of Toronto, 10 King's College Road, Toronto, ON, Canada, M5S 3G4.
- Ontario Institute of Cancer Research, 661 University Avenue, Suite 510, Toronto, ON, Canada, M5G 0A3.
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25
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El-Hachem N, Ba-Alawi W, Smith I, Mer AS, Haibe-Kains B. Integrative cancer pharmacogenomics to establish drug mechanism of action: drug repurposing. Pharmacogenomics 2017; 18:1469-1472. [PMID: 29057710 DOI: 10.2217/pgs-2017-0132] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Nehme El-Hachem
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Wail Ba-Alawi
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Ian Smith
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Arvind Singh Mer
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Benjamin Haibe-Kains
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.,Ontario Institute of Cancer Research, Toronto, Ontario, Canada
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26
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Grossmann P, Stringfield O, El-Hachem N, Bui MM, Rios Velazquez E, Parmar C, Leijenaar RT, Haibe-Kains B, Lambin P, Gillies RJ, Aerts HJ. Defining the biological basis of radiomic phenotypes in lung cancer. eLife 2017; 6:23421. [PMID: 28731408 PMCID: PMC5590809 DOI: 10.7554/elife.23421] [Citation(s) in RCA: 209] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2016] [Accepted: 07/17/2017] [Indexed: 02/06/2023] Open
Abstract
Medical imaging can visualize characteristics of human cancer noninvasively. Radiomics is an emerging field that translates these medical images into quantitative data to enable phenotypic profiling of tumors. While radiomics has been associated with several clinical endpoints, the complex relationships of radiomics, clinical factors, and tumor biology are largely unknown. To this end, we analyzed two independent cohorts of respectively 262 North American and 89 European patients with lung cancer, and consistently identified previously undescribed associations between radiomic imaging features, molecular pathways, and clinical factors. In particular, we found a relationship between imaging features, immune response, inflammation, and survival, which was further validated by immunohistochemical staining. Moreover, a number of imaging features showed predictive value for specific pathways; for example, intra-tumor heterogeneity features predicted activity of RNA polymerase transcription (AUC = 0.62, p=0.03) and intensity dispersion was predictive of the autodegration pathway of a ubiquitin ligase (AUC = 0.69, p<10-4). Finally, we observed that prognostic biomarkers performed highest when combining radiomic, genetic, and clinical information (CI = 0.73, p<10-9) indicating complementary value of these data. In conclusion, we demonstrate that radiomic approaches permit noninvasive assessment of both molecular and clinical characteristics of tumors, and therefore have the potential to advance clinical decision-making by systematically analyzing standard-of-care medical images. DOI:http://dx.doi.org/10.7554/eLife.23421.001 Medical imaging covers a wide range of techniques that are used to look inside the body, including X-rays, MRI scans and ultrasound. A process called radiomics uses computer algorithms to process the data collected by these techniques to identify and precisely measure a large number of features that would not otherwise be quantifiable by human experts. By doing so, radiomics can automatically measure the radiographic characteristics of a tumor. For example, radiomics can establish the size, shape and texture of a tumor to help to diagnose cancer and guide its treatment. Research has suggested that radiomics can predict certain clinical characteristics of cancer, such as how far through the body the cancer has spread, how likely it is to respond to treatment, and how likely a patient is to survive. However, these radiomic characteristics have not yet been precisely linked to the biological processes that drive how cancer develops and spreads. Cancers develop as a result of genetic changes that activate “molecular pathways” in the cells and trigger processes such as cell division and inflammation. To work out exactly which changes are behind a particular tumor, a sample of the tumor from biopsy or surgery is analyzed using genomics techniques. Linking radiomics features to the molecular processes active in a tumor can generate further information that can complement the molecular data. Images are routinely collected on all cancer patients yet molecular data is not. Hence, in some cases, the images can be used to infer the molecular underpinnings of cancer in individual patients. Grossmann et al. have now analyzed radiomic, genomic and clinical data collected from approximately 350 patients with lung cancer. The analysis revealed links between biological processes normally detected by genomics – in particular, inflammatory responses – and radiomics features. Furthermore, these features could also be associated with clinical characteristics, such as tumor type and patient survival rates. These results were further validated by using a technique called immunohistochemical staining on tumor tissue obtained by surgery. Further investigation revealed that certain radiomics features can predict the state of molecular pathways that are key to cancer development (such as the inflammatory response). Furthermore, Grossmann et al. found that combining data from radiomics, genomics and clinical parameters predicts how the cancer will progress better than any of these parameters can predict on their own. These results demonstrate the complementary value of radiomic data to genomic and clinical data. There are many different algorithms that can be used to process images for radiomics. Before radiomics can be used clinically to assess the biological processes underlying the tumors of patients, a specific algorithm needs to be decided upon and then tested in prospective clinical trials. DOI:http://dx.doi.org/10.7554/eLife.23421.002
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Affiliation(s)
- Patrick Grossmann
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, United States.,Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, United States
| | - Olya Stringfield
- Department of Cancer Imaging and Metabolism, H. Lee Moffitt Cancer Center and Research Institute, Tampa, United States
| | - Nehme El-Hachem
- Integrative systems biology, Institut de recherches cliniques de Montreal, Montreal, Canada
| | - Marilyn M Bui
- Department of Anatomic Pathology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, United States
| | - Emmanuel Rios Velazquez
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, United States
| | - Chintan Parmar
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, United States.,Department of Radiation Oncology, Research Institute GROW, Maastricht University, Maastricht, Netherlands
| | - Ralph Th Leijenaar
- Department of Radiation Oncology, Research Institute GROW, Maastricht University, Maastricht, Netherlands
| | - Benjamin Haibe-Kains
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Canada.,Medical Biophysics Department, University of Toronto, Toronto, Canada
| | - Philippe Lambin
- Department of Radiation Oncology, Research Institute GROW, Maastricht University, Maastricht, Netherlands
| | - Robert J Gillies
- Department of Cancer Imaging and Metabolism, H. Lee Moffitt Cancer Center and Research Institute, Tampa, United States
| | - Hugo Jwl Aerts
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, United States.,Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, United States.,Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, United States
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27
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El-Hachem N, Gendoo DMA, Ghoraie LS, Safikhani Z, Smirnov P, Chung C, Deng K, Fang A, Birkwood E, Ho C, Isserlin R, Bader GD, Goldenberg A, Haibe-Kains B. Integrative Cancer Pharmacogenomics to Infer Large-Scale Drug Taxonomy. Cancer Res 2017; 77:3057-3069. [PMID: 28314784 DOI: 10.1158/0008-5472.can-17-0096] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 02/27/2017] [Accepted: 03/13/2017] [Indexed: 11/16/2022]
Abstract
Identification of drug targets and mechanism of action (MoA) for new and uncharacterized anticancer drugs is important for optimization of treatment efficacy. Current MoA prediction largely relies on prior information including side effects, therapeutic indication, and chemoinformatics. Such information is not transferable or applicable for newly identified, previously uncharacterized small molecules. Therefore, a shift in the paradigm of MoA predictions is necessary toward development of unbiased approaches that can elucidate drug relationships and efficiently classify new compounds with basic input data. We propose here a new integrative computational pharmacogenomic approach, referred to as Drug Network Fusion (DNF), to infer scalable drug taxonomies that rely only on basic drug characteristics toward elucidating drug-drug relationships. DNF is the first framework to integrate drug structural information, high-throughput drug perturbation, and drug sensitivity profiles, enabling drug classification of new experimental compounds with minimal prior information. DNF taxonomy succeeded in identifying pertinent and novel drug-drug relationships, making it suitable for investigating experimental drugs with potential new targets or MoA. The scalability of DNF facilitated identification of key drug relationships across different drug categories, providing a flexible tool for potential clinical applications in precision medicine. Our results support DNF as a valuable resource to the cancer research community by providing new hypotheses on compound MoA and potential insights for drug repurposing. Cancer Res; 77(11); 3057-69. ©2017 AACR.
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Affiliation(s)
- Nehme El-Hachem
- Integrative Computational Systems Biology, Institut de Recherches Cliniques de Montréal, Montreal, Quebec, Canada.,Department of Biomedical Sciences. Université de Montréal, Montreal, Quebec, Canada
| | - Deena M A Gendoo
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Laleh Soltan Ghoraie
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Zhaleh Safikhani
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Petr Smirnov
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Christina Chung
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Kenan Deng
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Ailsa Fang
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Erin Birkwood
- School of Computer Science, McGill University, Montreal, Quebec, Canada
| | - Chantal Ho
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Ruth Isserlin
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Gary D Bader
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.,The Donnelly Centre, Toronto, Ontario, Canada.,The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Anna Goldenberg
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.,Hospital for Sick Children, Toronto, Ontario, Canada
| | - Benjamin Haibe-Kains
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada. .,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.,Ontario Institute of Cancer Research, Toronto, Ontario, Canada
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28
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El-Hachem N, Haibe-Kains B, Khalil A, Kobeissy FH, Nemer G. AutoDock and AutoDockTools for Protein-Ligand Docking: Beta-Site Amyloid Precursor Protein Cleaving Enzyme 1(BACE1) as a Case Study. Methods Mol Biol 2017; 1598:391-403. [PMID: 28508374 DOI: 10.1007/978-1-4939-6952-4_20] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Computational docking and scoring techniques have revolutionized structural bioinformatics by providing unprecedented insights on key aspects of ligand-receptor interaction. Docking is used for optimizing known drugs and for identifying novel binders by predicting their binding mode and affinity. AutoDock and AutoDockTools are free of charge techniques that have been extensively cited in the literature as essential tools in structure-based drug design. Moreover, these methods are fast enough to permit virtual screening of ligand libraries containing tens of thousands of compounds. However using Autodock requires some knowledge in programming which creates a limitation for biologists and makes them prone for commercial applications. Here, we selected a relevant target involved in the progression of Alzheimer disease and provided a fully reproducible docking protocol. This example will show how docking techniques would be an important asset to identify new BACE1 inhibitors. The following friendly user tutorial targets both undergraduate and graduate students, allowing them to understand docking as a computational tool for structure-based drug design.
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Affiliation(s)
- Nehme El-Hachem
- Integrative Computational Systems Biology, Institut de Recherches Cliniques de Montreal, Montreal, QC, Canada
| | | | - Athar Khalil
- Department of Biochemistry and Molecular Genetics, American University of Beirut, DTS4-19A, Bliss Street, Riad El Solh, Beirut, 1107 2020, Lebanon
| | - Firas H Kobeissy
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
- Department of Psychiatry, Center for Neuroproteomics and Biomarkers Research, University of Florida, Gainesville, FL, USA
| | - Georges Nemer
- Department of Biochemistry and Molecular Genetics, American University of Beirut, DTS4-19A, Bliss Street, Riad El Solh, Beirut, 1107 2020, Lebanon.
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Safikhani Z, El-Hachem N, Smirnov P, Freeman M, Goldenberg A, Birkbak NJ, Beck AH, Aerts HJWL, Quackenbush J, Haibe-Kains B. Safikhani et al. reply. Nature 2016; 540:E2-E4. [PMID: 27905430 DOI: 10.1038/nature19839] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Zhaleh Safikhani
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Nehme El-Hachem
- Institut de recherches cliniques de Montréal, Montreal, Quebec H2W 1R7, Canada
| | - Petr Smirnov
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada
| | - Mark Freeman
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada
| | - Anna Goldenberg
- Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada.,Department of Computer Science, University of Toronto, Toronto, Ontario M5S 2E4, Canada
| | - Nicolai J Birkbak
- The Francis Crick Institute, University College London, London NW1 1AT, UK.University College London Cancer Institute, London, WC1E 6BT, UK
| | - Andrew H Beck
- Beth Israel Deaconess Medical Center, Boston, Massachusetts 02215, USA.,Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Hugo J W L Aerts
- Harvard Medical School, Boston, Massachusetts 02115, USA.,Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA.,Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - John Quackenbush
- Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA.,Harvard School of Public Health, Boston, Massachusetts 02115, USA
| | - Benjamin Haibe-Kains
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada.,Department of Computer Science, University of Toronto, Toronto, Ontario M5S 2E4, Canada.,Ontario Institute of Cancer Research, Toronto, Ontario M5G 1L7, Canada
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30
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Safikhani Z, El-Hachem N, Smirnov P, Freeman M, Goldenberg A, Birkbak NJ, Beck AH, Aerts HJWL, Quackenbush J, Haibe-Kains B. Safikhani et al. reply. Nature 2016; 540:E6-E8. [PMID: 27905416 DOI: 10.1038/nature20172] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Zhaleh Safikhani
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Nehme El-Hachem
- Institut de recherches cliniques de Montréal, Montreal, Quebec H2W 1R7, Canada
| | - Petr Smirnov
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada
| | - Mark Freeman
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada
| | - Anna Goldenberg
- Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada.,Department of Computer Science, University of Toronto, Toronto, Ontario M5S 2E4, Canada
| | - Nicolai J Birkbak
- The Francis Crick Institute, London NW1 1AT, UK.,University College London Cancer Institute, London WC1E 6BT, UK
| | - Andrew H Beck
- Beth Israel Deaconess Medical Center, Boston, Massachusetts 02215, USA.,Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Hugo J W L Aerts
- Harvard Medical School, Boston, Massachusetts 02115, USA.,Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA.,Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - John Quackenbush
- Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA.,Harvard TH Chan School of Public Health, Boston, Massachusetts 02115, USA
| | - Benjamin Haibe-Kains
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada.,Department of Computer Science, University of Toronto, Toronto, Ontario M5S 2E4, Canada.,Ontario Institute of Cancer Research, Toronto, Ontario M5G 1L7, Canada
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31
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Safikhani Z, Smirnov P, Freeman M, El-Hachem N, She A, Rene Q, Goldenberg A, Birkbak NJ, Hatzis C, Shi L, Beck AH, Aerts HJ, Quackenbush J, Haibe-Kains B. Revisiting inconsistency in large pharmacogenomic studies. F1000Res 2016; 5:2333. [PMID: 28928933 PMCID: PMC5580432 DOI: 10.12688/f1000research.9611.3] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/11/2017] [Indexed: 01/30/2023] Open
Abstract
In 2013, we published a comparative analysis of mutation and gene expression profiles and drug sensitivity measurements for 15 drugs characterized in the 471 cancer cell lines screened in the Genomics of Drug Sensitivity in Cancer (GDSC) and Cancer Cell Line Encyclopedia (CCLE). While we found good concordance in gene expression profiles, there was substantial inconsistency in the drug responses reported by the GDSC and CCLE projects. We received extensive feedback on the comparisons that we performed. This feedback, along with the release of new data, prompted us to revisit our initial analysis. We present a new analysis using these expanded data, where we address the most significant suggestions for improvements on our published analysis - that targeted therapies and broad cytotoxic drugs should have been treated differently in assessing consistency, that consistency of both molecular profiles and drug sensitivity measurements should be compared across cell lines, and that the software analysis tools provided should have been easier to run, particularly as the GDSC and CCLE released additional data. Our re-analysis supports our previous finding that gene expression data are significantly more consistent than drug sensitivity measurements. Using new statistics to assess data consistency allowed identification of two broad effect drugs and three targeted drugs with moderate to good consistency in drug sensitivity data between GDSC and CCLE. For three other targeted drugs, there were not enough sensitive cell lines to assess the consistency of the pharmacological profiles. We found evidence of inconsistencies in pharmacological phenotypes for the remaining eight drugs. Overall, our findings suggest that the drug sensitivity data in GDSC and CCLE continue to present challenges for robust biomarker discovery. This re-analysis provides additional support for the argument that experimental standardization and validation of pharmacogenomic response will be necessary to advance the broad use of large pharmacogenomic screens.
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Affiliation(s)
- Zhaleh Safikhani
- Department of Medical Biophysics, University of Toronto, Toronto, M5G 1L7, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, M5G 1L7, Canada
| | - Petr Smirnov
- Princess Margaret Cancer Centre, University Health Network, Toronto, M5G 1L7, Canada
| | - Mark Freeman
- Princess Margaret Cancer Centre, University Health Network, Toronto, M5G 1L7, Canada
| | - Nehme El-Hachem
- Institut de Recherches Cliniques de Montréal, Montréal, H2W 1R7, Canada
| | - Adrian She
- Princess Margaret Cancer Centre, University Health Network, Toronto, M5G 1L7, Canada
| | - Quevedo Rene
- Department of Medical Biophysics, University of Toronto, Toronto, M5G 1L7, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, M5G 1L7, Canada
| | - Anna Goldenberg
- Department of Computer Science, University of Toronto, Toronto, M5S 2E4, Canada
- Hospital for Sick Children, Toronto, M5G 1X8, Canada
| | | | - Christos Hatzis
- Yale Cancer Center, Yale University, New Haven, CT, 06510, USA
- Section of Medical Oncology, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Leming Shi
- University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
- Fudan University, Shanghai City, 200135, China
| | - Andrew H. Beck
- Department of Pathology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, 02215, USA
| | - Hugo J.W.L. Aerts
- Department of Biostatistics and Computational Biology and Center for Cancer Computational Biology, Boston, MA, 02215, USA
- Department of Radiation Oncology and Radiology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA
| | - John Quackenbush
- Department of Biostatistics and Computational Biology and Center for Cancer Computational Biology, Boston, MA, 02215, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Benjamin Haibe-Kains
- Department of Medical Biophysics, University of Toronto, Toronto, M5G 1L7, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, M5G 1L7, Canada
- Department of Computer Science, University of Toronto, Toronto, M5S 2E4, Canada
- Ontario Institute of Cancer Research, Toronto, M5G 1L7, Canada
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32
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Safikhani Z, Smirnov P, Freeman M, El-Hachem N, She A, Rene Q, Goldenberg A, Birkbak NJ, Hatzis C, Shi L, Beck AH, Aerts HJ, Quackenbush J, Haibe-Kains B. Revisiting inconsistency in large pharmacogenomic studies. F1000Res 2016; 5:2333. [PMID: 28928933 PMCID: PMC5580432 DOI: 10.12688/f1000research.9611.2] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/21/2017] [Indexed: 11/13/2023] Open
Abstract
In 2013, we published a comparative analysis of mutation and gene expression profiles and drug sensitivity measurements for 15 drugs characterized in the 471 cancer cell lines screened in the Genomics of Drug Sensitivity in Cancer (GDSC) and Cancer Cell Line Encyclopedia (CCLE). While we found good concordance in gene expression profiles, there was substantial inconsistency in the drug responses reported by the GDSC and CCLE projects. We received extensive feedback on the comparisons that we performed. This feedback, along with the release of new data, prompted us to revisit our initial analysis. We present a new analysis using these expanded data, where we address the most significant suggestions for improvements on our published analysis - that targeted therapies and broad cytotoxic drugs should have been treated differently in assessing consistency, that consistency of both molecular profiles and drug sensitivity measurements should be compared across cell lines, and that the software analysis tools provided should have been easier to run, particularly as the GDSC and CCLE released additional data. Our re-analysis supports our previous finding that gene expression data are significantly more consistent than drug sensitivity measurements. Using new statistics to assess data consistency allowed identification of two broad effect drugs and three targeted drugs with moderate to good consistency in drug sensitivity data between GDSC and CCLE. For three other targeted drugs, there were not enough sensitive cell lines to assess the consistency of the pharmacological profiles. We found evidence of inconsistencies in pharmacological phenotypes for the remaining eight drugs. Overall, our findings suggest that the drug sensitivity data in GDSC and CCLE continue to present challenges for robust biomarker discovery. This re-analysis provides additional support for the argument that experimental standardization and validation of pharmacogenomic response will be necessary to advance the broad use of large pharmacogenomic screens.
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Affiliation(s)
- Zhaleh Safikhani
- Department of Medical Biophysics, University of Toronto, Toronto, M5G 1L7, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, M5G 1L7, Canada
| | - Petr Smirnov
- Princess Margaret Cancer Centre, University Health Network, Toronto, M5G 1L7, Canada
| | - Mark Freeman
- Princess Margaret Cancer Centre, University Health Network, Toronto, M5G 1L7, Canada
| | - Nehme El-Hachem
- Institut de Recherches Cliniques de Montréal, Montréal, H2W 1R7, Canada
| | - Adrian She
- Princess Margaret Cancer Centre, University Health Network, Toronto, M5G 1L7, Canada
| | - Quevedo Rene
- Department of Medical Biophysics, University of Toronto, Toronto, M5G 1L7, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, M5G 1L7, Canada
| | - Anna Goldenberg
- Department of Computer Science, University of Toronto, Toronto, M5S 2E4, Canada
- Hospital for Sick Children, Toronto, M5G 1X8, Canada
| | | | - Christos Hatzis
- Yale Cancer Center, Yale University, New Haven, CT, 06510, USA
- Section of Medical Oncology, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Leming Shi
- University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
- Fudan University, Shanghai City, 200135, China
| | - Andrew H. Beck
- Department of Pathology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, 02215, USA
| | - Hugo J.W.L. Aerts
- Department of Biostatistics and Computational Biology and Center for Cancer Computational Biology, Boston, MA, 02215, USA
- Department of Radiation Oncology and Radiology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA
| | - John Quackenbush
- Department of Biostatistics and Computational Biology and Center for Cancer Computational Biology, Boston, MA, 02215, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Benjamin Haibe-Kains
- Department of Medical Biophysics, University of Toronto, Toronto, M5G 1L7, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, M5G 1L7, Canada
- Department of Computer Science, University of Toronto, Toronto, M5S 2E4, Canada
- Ontario Institute of Cancer Research, Toronto, M5G 1L7, Canada
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Safikhani Z, Smirnov P, Freeman M, El-Hachem N, She A, Rene Q, Goldenberg A, Birkbak NJ, Hatzis C, Shi L, Beck AH, Aerts HJ, Quackenbush J, Haibe-Kains B. Revisiting inconsistency in large pharmacogenomic studies. F1000Res 2016; 5:2333. [PMID: 28928933 PMCID: PMC5580432 DOI: 10.12688/f1000research.9611.1] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/15/2016] [Indexed: 01/22/2023] Open
Abstract
In 2013, we published a comparative analysis mutation and gene expression profiles and drug sensitivity measurements for 15 drugs characterized in the 471 cancer cell lines screened in the Genomics of Drug Sensitivity in Cancer (GDSC) and Cancer Cell Line Encyclopedia (CCLE). While we found good concordance in gene expression profiles, there was substantial inconsistency in the drug responses reported by the GDSC and CCLE projects. We received extensive feedback on the comparisons that we performed. This feedback, along with the release of new data, prompted us to revisit our initial analysis. Here we present a new analysis using these expanded data in which we address the most significant suggestions for improvements on our published analysis - that targeted therapies and broad cytotoxic drugs should have been treated differently in assessing consistency, that consistency of both molecular profiles and drug sensitivity measurements should both be compared across cell lines, and that the software analysis tools we provided should have been easier to run, particularly as the GDSC and CCLE released additional data. Our re-analysis supports our previous finding that gene expression data are significantly more consistent than drug sensitivity measurements. The use of new statistics to assess data consistency allowed us to identify two broad effect drugs and three targeted drugs with moderate to good consistency in drug sensitivity data between GDSC and CCLE. For three other targeted drugs, there were not enough sensitive cell lines to assess the consistency of the pharmacological profiles. We found evidence of inconsistencies in pharmacological phenotypes for the remaining eight drugs. Overall, our findings suggest that the drug sensitivity data in GDSC and CCLE continue to present challenges for robust biomarker discovery. This re-analysis provides additional support for the argument that experimental standardization and validation of pharmacogenomic response will be necessary to advance the broad use of large pharmacogenomic screens.
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Affiliation(s)
- Zhaleh Safikhani
- Department of Medical Biophysics, University of Toronto, Toronto, M5G 1L7, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, M5G 1L7, Canada
| | - Petr Smirnov
- Princess Margaret Cancer Centre, University Health Network, Toronto, M5G 1L7, Canada
| | - Mark Freeman
- Princess Margaret Cancer Centre, University Health Network, Toronto, M5G 1L7, Canada
| | - Nehme El-Hachem
- Institut de Recherches Cliniques de Montréal, Montréal, H2W 1R7, Canada
| | - Adrian She
- Princess Margaret Cancer Centre, University Health Network, Toronto, M5G 1L7, Canada
| | - Quevedo Rene
- Department of Medical Biophysics, University of Toronto, Toronto, M5G 1L7, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, M5G 1L7, Canada
| | - Anna Goldenberg
- Department of Computer Science, University of Toronto, Toronto, M5S 2E4, Canada
- Hospital for Sick Children, Toronto, M5G 1X8, Canada
| | | | - Christos Hatzis
- Yale Cancer Center, Yale University, New Haven, CT, 06510, USA
- Section of Medical Oncology, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Leming Shi
- University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
- Fudan University, Shanghai City, 200135, China
| | - Andrew H. Beck
- Department of Pathology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, 02215, USA
| | - Hugo J.W.L. Aerts
- Department of Biostatistics and Computational Biology and Center for Cancer Computational Biology, Boston, MA, 02215, USA
- Department of Radiation Oncology and Radiology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA
| | - John Quackenbush
- Department of Biostatistics and Computational Biology and Center for Cancer Computational Biology, Boston, MA, 02215, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Benjamin Haibe-Kains
- Department of Medical Biophysics, University of Toronto, Toronto, M5G 1L7, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, M5G 1L7, Canada
- Department of Computer Science, University of Toronto, Toronto, M5S 2E4, Canada
- Ontario Institute of Cancer Research, Toronto, M5G 1L7, Canada
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Safikhani Z, El-Hachem N, Quevedo R, Smirnov P, Goldenberg A, Juul Birkbak N, Mason C, Hatzis C, Shi L, Aerts HJWL, Quackenbush J, Haibe-Kains B. Assessment of pharmacogenomic agreement. F1000Res 2016; 5:825. [PMID: 27408686 PMCID: PMC4926729 DOI: 10.12688/f1000research.8705.1] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/03/2016] [Indexed: 11/20/2022] Open
Abstract
In 2013 we published an analysis demonstrating that drug response data and gene-drug associations reported in two independent large-scale pharmacogenomic screens, Genomics of Drug Sensitivity in Cancer (GDSC) and Cancer Cell Line Encyclopedia (CCLE), were inconsistent. The GDSC and CCLE investigators recently reported that their respective studies exhibit reasonable agreement and yield similar molecular predictors of drug response, seemingly contradicting our previous findings. Reanalyzing the authors' published methods and results, we found that their analysis failed to account for variability in the genomic data and more importantly compared different drug sensitivity measures from each study, which substantially deviate from our more stringent consistency assessment. Our comparison of the most updated genomic and pharmacological data from the GDSC and CCLE confirms our published findings that the measures of drug response reported by these two groups are not consistent. We believe that a principled approach to assess the reproducibility of drug sensitivity predictors is necessary before envisioning their translation into clinical settings.
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Affiliation(s)
- Zhaleh Safikhani
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 1L7, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, M5G 1L7, Canada
| | - Nehme El-Hachem
- Institut de recherches cliniques de Montréal, Montreal, Quebec, H2W 1R7, Canada
| | - Rene Quevedo
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 1L7, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, M5G 1L7, Canada
| | - Petr Smirnov
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 1L7, Canada
| | - Anna Goldenberg
- Hospital for Sick Children, Toronto, Ontario, M5G 1X8, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, M5S 2E4, Canada
| | | | - Christopher Mason
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, 10065, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, 10021, USA
- The Feil Family Brain and Mind Research Institute (BMRI), New York, NY, 10065, USA
| | - Christos Hatzis
- Section of Medical Oncology, Yale School of Medicine, New Haven, CT, 06520, USA
- Yale Cancer Center, Yale University, New Haven, CT, 06510, USA
| | - Leming Shi
- Fudan University, Shanghai City, 200135, China
- University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Hugo JWL Aerts
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Radiation Oncology and Radiology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02215, USA
| | - John Quackenbush
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Biostatistics and Computational Biology and Center for Cancer Computational Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Benjamin Haibe-Kains
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 1L7, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, M5G 1L7, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, M5S 2E4, Canada
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El-Hachem N, Grossmann P, Blanchet-Cohen A, Bateman AR, Bouchard N, Archambault J, Aerts HJ, Haibe-Kains B. Characterization of Conserved Toxicogenomic Responses in Chemically Exposed Hepatocytes across Species and Platforms. Environ Health Perspect 2016; 124:313-20. [PMID: 26173225 PMCID: PMC4786983 DOI: 10.1289/ehp.1409157] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 07/09/2015] [Indexed: 05/03/2023]
Abstract
BACKGROUND Genome-wide expression profiling is increasingly being used to identify transcriptional changes induced by drugs and environmental stressors. In this context, the Toxicogenomics Project-Genomics Assisted Toxicity Evaluation system (TG-GATEs) project generated transcriptional profiles from rat liver samples and human/rat cultured primary hepatocytes exposed to more than 100 different chemicals. OBJECTIVES To assess the capacity of the cell culture models to recapitulate pathways induced by chemicals in vivo, we leveraged the TG-GATEs data set to compare the early transcriptional responses observed in the liver of rats treated with a large set of chemicals with those of cultured rat and human primary hepatocytes challenged with the same compounds in vitro. METHODS We developed a new pathway-based computational pipeline that efficiently combines gene set enrichment analysis (GSEA) using pathways from the Reactome database with biclustering to identify common modules of pathways that are modulated by several chemicals in vivo and in vitro across species. RESULTS We found that some chemicals induced conserved patterns of early transcriptional responses in in vitro and in vivo settings, and across human and rat genomes. These responses involved pathways of cell survival, inflammation, xenobiotic metabolism, oxidative stress, and apoptosis. Moreover, our results support the transforming growth factor beta receptor (TGF-βR) signaling pathway as a candidate biomarker associated with exposure to environmental toxicants in primary human hepatocytes. CONCLUSIONS Our integrative analysis of toxicogenomics data provides a comprehensive overview of biochemical perturbations affected by a large panel of chemicals. Furthermore, we show that the early toxicological response occurring in animals is recapitulated in human and rat primary hepatocyte cultures at the molecular level, indicating that these models reproduce key pathways in response to chemical stress. These findings expand our understanding and interpretation of toxicogenomics data from human hepatocytes exposed to environmental toxicants.
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Affiliation(s)
- Nehme El-Hachem
- Integrative systems biology, Institut de Recherches Cliniques de Montréal, Montreal, Quebec, Canada
- Department of Medicine, University of Montreal, Montréal, Quebec, Canada
| | - Patrick Grossmann
- Department of Biostatistics & Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Alain R. Bateman
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Nicolas Bouchard
- Department of Medicine, University of Montreal, Montréal, Quebec, Canada
- Molecular Biology of Neural Development, Institut de Recherches Cliniques de Montréal, Montreal, Canada
| | - Jacques Archambault
- Laboratory of Molecular Virology, Institut de Recherches Cliniques de Montréal, Montreal, Quebec, Canada
| | - Hugo J.W.L. Aerts
- Department of Biostatistics & Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Radiology, Dana-Farber Cancer Institute, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Address correspondence to B. Haibe-Kains, Princess Margaret Cancer Centre, University Health Network, 101 College St., Toronto, ON, M5G 1L7, Canada. Telephone: 1 (416) 581-7628. E-mail: , or to H.J.W.L. Aerts, Department of Radiology, Dana-Farber Cancer Institute, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115 USA. E-mail:
| | - Benjamin Haibe-Kains
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Medical Biophysics Department, University of Toronto, Toronto, Ontario, Canada
- Address correspondence to B. Haibe-Kains, Princess Margaret Cancer Centre, University Health Network, 101 College St., Toronto, ON, M5G 1L7, Canada. Telephone: 1 (416) 581-7628. E-mail: , or to H.J.W.L. Aerts, Department of Radiology, Dana-Farber Cancer Institute, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115 USA. E-mail:
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Smirnov P, Safikhani Z, El-Hachem N, Wang D, She A, Olsen C, Freeman M, Selby H, Gendoo DMA, Grossmann P, Beck AH, Aerts HJWL, Lupien M, Goldenberg A, Haibe-Kains B. PharmacoGx: an R package for analysis of large pharmacogenomic datasets. Bioinformatics 2015; 32:1244-6. [PMID: 26656004 DOI: 10.1093/bioinformatics/btv723] [Citation(s) in RCA: 165] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 12/06/2015] [Indexed: 11/14/2022] Open
Abstract
UNLABELLED Pharmacogenomics holds great promise for the development of biomarkers of drug response and the design of new therapeutic options, which are key challenges in precision medicine. However, such data are scattered and lack standards for efficient access and analysis, consequently preventing the realization of the full potential of pharmacogenomics. To address these issues, we implemented PharmacoGx, an easy-to-use, open source package for integrative analysis of multiple pharmacogenomic datasets. We demonstrate the utility of our package in comparing large drug sensitivity datasets, such as the Genomics of Drug Sensitivity in Cancer and the Cancer Cell Line Encyclopedia. Moreover, we show how to use our package to easily perform Connectivity Map analysis. With increasing availability of drug-related data, our package will open new avenues of research for meta-analysis of pharmacogenomic data. AVAILABILITY AND IMPLEMENTATION PharmacoGx is implemented in R and can be easily installed on any system. The package is available from CRAN and its source code is available from GitHub. CONTACT bhaibeka@uhnresearch.ca or benjamin.haibe.kains@utoronto.ca SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Petr Smirnov
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Zhaleh Safikhani
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada, Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Nehme El-Hachem
- Institut De Recherches Cliniques De Montréal, Montreal, QC, Canada
| | - Dong Wang
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Adrian She
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Catharina Olsen
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada, Interuniversity Institute of Bioinformatics in Brussels (IB)2, Brussels, Belgium, Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Mark Freeman
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Heather Selby
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA, Department of Bioinformatics, Boston University, Boston, MA, USA
| | - Deena M A Gendoo
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada, Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Patrick Grossmann
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Andrew H Beck
- Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Hugo J W L Aerts
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Mathieu Lupien
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada, Machine Learning Group (MLG), Department d'Informatique, Université libre de Bruxelles (ULB), Brussels, Belgium, Ontario Institute of Cancer Research, Toronto, ON, Canada
| | - Anna Goldenberg
- Hospital for Sick Children, Toronto, ON, Canada and Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | - Benjamin Haibe-Kains
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada, Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
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37
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Kannan L, Ramos M, Re A, El-Hachem N, Safikhani Z, Gendoo DM, Davis S, Gomez-Cabrero D, Castelo R, Hansen KD, Carey VJ, Morgan M, Culhane AC, Haibe-Kains B, Waldron L. Public data and open source tools for multi-assay genomic investigation of disease. Brief Bioinform 2015; 17:603-15. [PMID: 26463000 PMCID: PMC4945830 DOI: 10.1093/bib/bbv080] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Indexed: 01/07/2023] Open
Abstract
Molecular interrogation of a biological sample through DNA sequencing, RNA and microRNA profiling, proteomics and other assays, has the potential to provide a systems level approach to predicting treatment response and disease progression, and to developing precision therapies. Large publicly funded projects have generated extensive and freely available multi-assay data resources; however, bioinformatic and statistical methods for the analysis of such experiments are still nascent. We review multi-assay genomic data resources in the areas of clinical oncology, pharmacogenomics and other perturbation experiments, population genomics and regulatory genomics and other areas, and tools for data acquisition. Finally, we review bioinformatic tools that are explicitly geared toward integrative genomic data visualization and analysis. This review provides starting points for accessing publicly available data and tools to support development of needed integrative methods.
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38
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Grossmann P, Grove O, El-Hachem N, Velazquez ER, Parmar C, Leijenaar R, Haibe-Kains B, Lambin P, Gillies R, Aerts H. TU-CD-BRB-02: BEST IN PHYSICS (JOINT IMAGING-THERAPY): Identification of Molecular Phenotypes by Integrating Radiomics and Genomics. Med Phys 2015. [DOI: 10.1118/1.4925587] [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: 11/07/2022] Open
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39
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Bateman AR, El-Hachem N, Beck AH, Aerts HJWL, Haibe-Kains B. Importance of collection in gene set enrichment analysis of drug response in cancer cell lines. Sci Rep 2014; 4:4092. [PMID: 24522610 PMCID: PMC3923229 DOI: 10.1038/srep04092] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [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: 09/25/2013] [Accepted: 01/29/2014] [Indexed: 12/27/2022] Open
Abstract
Gene set enrichment analysis (GSEA) associates gene sets and phenotypes, its use is predicated on the choice of a pre-defined collection of sets. The defacto standard implementation of GSEA provides seven collections yet there are no guidelines for the choice of collections and the impact of such choice, if any, is unknown. Here we compare each of the standard gene set collections in the context of a large dataset of drug response in human cancer cell lines. We define and test a new collection based on gene co-expression in cancer cell lines to compare the performance of the standard collections to an externally derived cell line based collection. The results show that GSEA findings vary significantly depending on the collection chosen for analysis. Henceforth, collections should be carefully selected and reported in studies that leverage GSEA.
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Affiliation(s)
- Alain R Bateman
- Bioinformatics and Computational Genomics Laboratory, Institut de Recherches Cliniques de Montréal, University of Montreal, Montreal, Quebec, Canada
| | - Nehme El-Hachem
- Bioinformatics and Computational Genomics Laboratory, Institut de Recherches Cliniques de Montréal, University of Montreal, Montreal, Quebec, Canada
| | - Andrew H Beck
- Department of Pathology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
| | - Hugo J W L Aerts
- 1] Department of Biostatistics and Computational Biology and Center for Cancer Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA [2] Department of Radiation Oncology & Radiology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA [3] Department of Radiation Oncology, Maastricht University, Maastricht, The Netherlands
| | - Benjamin Haibe-Kains
- 1] Bioinformatics and Computational Genomics Laboratory, Institut de Recherches Cliniques de Montréal, University of Montreal, Montreal, Quebec, Canada [2] Ontario Cancer Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
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40
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De Jay N, Papillon-Cavanagh S, Olsen C, El-Hachem N, Bontempi G, Haibe-Kains B. mRMRe: an R package for parallelized mRMR ensemble feature selection. Bioinformatics 2013; 29:2365-8. [DOI: 10.1093/bioinformatics/btt383] [Citation(s) in RCA: 134] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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41
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Hirz T, Khalaf A, El-Hachem N, Mrad MF, Abdallah H, Créminon C, Grée R, Merhi RA, Habib A, Hachem A, Hamade E. New analogues of 13-hydroxyocatdecadienoic acid and 12-hydroxyeicosatetraenoic acid block human blood platelet aggregation and cyclooxygenase-1 activity. Chem Cent J 2012; 6:152. [PMID: 23228056 PMCID: PMC3582601 DOI: 10.1186/1752-153x-6-152] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [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: 09/24/2012] [Accepted: 12/03/2012] [Indexed: 12/05/2022] Open
Abstract
Background Thromboxane A2 is derived from arachidonic acid through the action of cyclooxygenases and thromboxane synthase. It is mainly formed in blood platelets upon activation and plays an important role in aggregation. Aspirin is effective in reducing the incidence of complications following acute coronary syndrome and stroke. The anti-thrombotic effect of aspirin is obtained through the irreversible inhibition of cyclooxygenases. Analogues of 12-hydroxyeicosatetraenoic acid and 13-hydroxyocatdecadienoic acid were shown previously to modulate platelet activation and to block thromboxane receptors. Results and discussion We synthesized 10 compounds based on the structures of analogues of 12-hydroxyeicosatetraenoic acid and 13-hydroxyocatdecadienoic acid and evaluated their effect on platelet aggregation triggered by arachidonic acid. The structure activity relationship was evaluated. Five compounds showed a significant inhibition of platelet aggregation and highlighted the importance of the lipidic hydrophobic hydrocarbon chain and the phenol group. Their IC50 ranged from 7.5 ± 0.8 to 14.2 ± 5.7 μM (Mean ± S.E.M.). All five compounds decreased platelet aggregation and thromboxane synthesis in response to collagen whereas no modification of platelet aggregation in response to thromboxane receptor agonist, U46619, was observed. Using COS-7 cells overexpressing human cyclooxygenase-1, we showed that these compounds are specific inhibitors of cyclooxygenase-1 with IC50 ranging from 1.3 to 12 μM. Docking observation of human recombinant cyclooxygenase-1 supported a role of the phenol group in the fitting of cyclooxygenase-1, most likely related to hydrogen bonding with the Tyr 355 of cyclooxygenase-1. Conclusions In conclusion, the compounds we synthesized at first based on the structures of analogues of 12 lipoxygenase metabolites showed a role of the phenol group in the anti-platelet and anti-cyclooxygenase-1 activities. These compounds mediate their effects via blockade of cyclooxygenase-1.
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Affiliation(s)
- Taghreed Hirz
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, AUB, Beirut, POBox 11-236, Lebanon.
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