1
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Alternative splicing liberates a cryptic cytoplasmic isoform of mitochondrial MECR that antagonizes influenza virus. PLoS Biol 2022; 20:e3001934. [PMID: 36542656 PMCID: PMC9815647 DOI: 10.1371/journal.pbio.3001934] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 01/05/2023] [Accepted: 11/29/2022] [Indexed: 12/24/2022] Open
Abstract
Viruses must balance their reliance on host cell machinery for replication while avoiding host defense. Influenza A viruses are zoonotic agents that frequently switch hosts, causing localized outbreaks with the potential for larger pandemics. The host range of influenza virus is limited by the need for successful interactions between the virus and cellular partners. Here we used immunocompetitive capture-mass spectrometry to identify cellular proteins that interact with human- and avian-style viral polymerases. We focused on the proviral activity of heterogenous nuclear ribonuclear protein U-like 1 (hnRNP UL1) and the antiviral activity of mitochondrial enoyl CoA-reductase (MECR). MECR is localized to mitochondria where it functions in mitochondrial fatty acid synthesis (mtFAS). While a small fraction of the polymerase subunit PB2 localizes to the mitochondria, PB2 did not interact with full-length MECR. By contrast, a minor splice variant produces cytoplasmic MECR (cMECR). Ectopic expression of cMECR shows that it binds the viral polymerase and suppresses viral replication by blocking assembly of viral ribonucleoprotein complexes (RNPs). MECR ablation through genome editing or drug treatment is detrimental for cell health, creating a generic block to virus replication. Using the yeast homolog Etr1 to supply the metabolic functions of MECR in MECR-null cells, we showed that specific antiviral activity is independent of mtFAS and is reconstituted by expressing cMECR. Thus, we propose a strategy where alternative splicing produces a cryptic antiviral protein that is embedded within a key metabolic enzyme.
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2
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Ju L, Dong Z, Yang J, Li M. Mechanism of intrinsic resistance of lung squamous cell carcinoma to epithelial growth factor receptor-tyrosine kinase inhibitors revealed by high-throughput RNA interference screening. Oncol Lett 2020; 20:363. [PMID: 33133263 PMCID: PMC7590427 DOI: 10.3892/ol.2020.12218] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 08/24/2020] [Indexed: 12/26/2022] Open
Abstract
Although targeted therapy has achieved a great breakthrough in the treatment of lung adenocarcinoma, there are still no effective targeted drugs for lung squamous cell carcinoma (SqCC). In addition, as immunotherapy can only prolong the overall survival (OS) of lung SqCC by ≤5 months, chemotherapy and radiotherapy are still the main types of therapy for advanced SqCC. The expression level of epithelial growth factor receptor (EGFR) in patients with lung SqCC is higher compared with those with adenocarcinoma, but the former group is intrinsically resistant to EGFR-tyrosine kinase inhibitors (EGFR-TKIs). Therefore, if the drug resistance in patients with lung SqCC could be reversed, the majority of patients may benefit from EGFR-TKIs. In the present study, the high-throughput RNA interference technology was used to screen the genes involved in the EGFR-TKI erlotinib resistance of lung SqCCs, and integrin-linked kinase (ILK) was identified to be the most effective. The role of ILK in erlotinib resistance was further studied in cell lines, and the expression of ILK was analyzed in patients with SqCC and adenocarcinoma. Finally, the mechanism of ILK in EGFR-TKIs resistance was analyzed using Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Ontology (GO) and ingenuity pathway analysis (IPA). The results demonstrated that the ILK gene knockdown could overcome erlotinib resistance by inhibiting cell proliferation, inducing apoptosis and blocking the cell cycle at the G2/M phase. The expression of ILK in patients with SqCC was significantly higher compared with those with adenocarcinoma with sensitizing EGFR mutations. In addition, the cell cycle pathway 'G2/M DNA damage and checkpoint regulation' was identified to be significantly inhibited by ILK knockdown in IPA, KEGG and GO analysis. The results of the present study may improve the understanding of EGFR-TKI resistance in lung SqCCs, thus promoting the development of potential targeted therapies for lung SqCCs.
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Affiliation(s)
- Lixia Ju
- Department of Integrative Medicine, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University, Shanghai 200433, P.R. China
| | - Zhiyi Dong
- Department of Integrative Medicine, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University, Shanghai 200433, P.R. China
| | - Juan Yang
- Department of Emergency, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University, Shanghai 200433, P.R. China
| | - Minghua Li
- Department of Oncology, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shang University of Traditional Chinese Medicine, Shanghai 200071, P.R. China
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3
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Tabtimmai L, Srisook P, Kuaprasert B, Thumanu K, Choowongkomon K. FTIR spectra signatures reveal different cellular effects of EGFR inhibitors on nonsmall cell lung cancer cells. JOURNAL OF BIOPHOTONICS 2020; 13:e201960012. [PMID: 31595681 DOI: 10.1002/jbio.201960012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 08/25/2019] [Accepted: 10/02/2019] [Indexed: 06/10/2023]
Abstract
ATP-analogue inhibitors, Gefitinib (Iressa) and Erlotinib (Tarceva) had been approved for advanced and metastatic nonsmall cell lung cancer (NSCLC) cells against tyrosine kinase domain of epidermal growth factor receptor (EGFR). Many techniques have been developed to better understand the drug mechanism which is multistep, time-consuming and expensive. Herein, we performed Fourier-transform infrared (FTIR) microscopy for evaluating the biochemical change on NSCLC (A549) cells after treatment. At levels that produced equivalent effects, Gefitinib dramatically induced cell apoptosis via impaired mitochondrial transmembrane potential. Whereas, Erlotinib had a slight effect on A549. Principal component analysis was performed to distinguish the effect of EGFR inhibitors on A549. FTIR spectra regions were divided into three regions: lipids (3000-2800 cm-1 ), proteins (1700-1500 cm-1 ) and carbohydrates and nuclei acids (1200-1000 cm-1 ). Biochemical changes can be evaluated by these spectral regions. This work may be a novel concept for utilizing FTIR spectroscopy for high-throughput discriminative effects of a drug or compound and its derivatives on cells.
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Affiliation(s)
- Lueacha Tabtimmai
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Pimonwan Srisook
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Buabarn Kuaprasert
- Synchrotron Light Research Institute (Public Organization), Nakhon Ratchasrima, Thailand
| | - Kanjana Thumanu
- Synchrotron Light Research Institute (Public Organization), Nakhon Ratchasrima, Thailand
| | - Kiattawee Choowongkomon
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand
- Center for Advanced Studies in Nanotechnology for Chemical, Food and Agricultural Industries, KU Institute for Advanced Studies, Kasetsart University, Bangkok, Thailand
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4
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Sarcar B, Gimbrone NT, Wright G, Remsing Rix LL, Gordian ER, Rix U, Chiappori AA, Reuther GW, Santiago-Cardona PG, Muñoz-Antonia T, Cress WD. Characterization of epidermal growth factor receptor (EGFR) P848L, an unusual EGFR variant present in lung cancer patients, in a murine Ba/F3 model. FEBS Open Bio 2019; 9:1689-1704. [PMID: 31314158 PMCID: PMC6768113 DOI: 10.1002/2211-5463.12702] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 06/22/2019] [Accepted: 07/16/2019] [Indexed: 11/06/2022] Open
Abstract
Lung cancer patients with mutations in epidermal growth factor receptor (EGFR) benefit from treatments targeting tyrosine kinase inhibitors (TKIs). However, both intrinsic and acquired resistance of tumors to TKIs are common, and EGFR variants have been identified that are resistant to multiple TKIs. In the present study, we characterized selected EGFR variants previously observed in lung cancer patients and expressed in a murine bone marrow pro-B Ba/F3 cell model. Among these EGFR variants, we report that an exon 20 deletion/insertion mutation S768insVGH is resistant to erlotinib (a first-generation TKI), but sensitive to osimertinib (a third-generation TKI). We also characterized a rare exon 21 germline variant, EGFR P848L, which transformed Ba/F3 cells and conferred resistance to multiple EGFR-targeting TKIs. Our analysis revealed that P848L (a) does not bind erlotinib; (b) is turned over less rapidly than L858R (a common tumor-derived EGFR mutation); (c) is not autophosphorylated at Tyr 1045 [the major docking site for Cbl proto-oncogene (c-Cbl) binding]; and (d) does not bind c-Cbl. Using viability assays including 300 clinically relevant targeted compounds, we observed that Ba/F3 cells transduced with EGFR P848L, S768insVGH, or L858R have very different drug-sensitivity profiles. In particular, EGFR P848L, but not L858R or S768insVGH, was sensitive to multiple Janus kinase 1/2 inhibitors. In contrast, cells driven by L858R, but not by P848L, were sensitive to multikinase MAPK/extracellular-signal-regulated kinase (ERK) kinase and ERK inhibitors including EGFR-specific TKIs. These observations suggest that continued investigation of rare TKI-resistant EGFR variants is warranted to identify optimal treatments for cancer.
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Affiliation(s)
- Bhaswati Sarcar
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Nicholas T Gimbrone
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Gabriela Wright
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Lily L Remsing Rix
- Department of Drug Discovery, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Edna R Gordian
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Uwe Rix
- Department of Drug Discovery, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Alberto A Chiappori
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA.,Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Gary W Reuther
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | | | - Teresita Muñoz-Antonia
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - William Douglas Cress
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA.,Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
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5
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Tabtimmai L, Suphakun P, Srisook P, Kiriwan D, Phanthong S, Kiatwuthinon P, Chaicumpa W, Choowongkomon K. Cell-penetrable nanobodies (transbodies) that inhibit the tyrosine kinase activity of EGFR leading to the impediment of human lung adenocarcinoma cell motility and survival. J Cell Biochem 2019; 120:18077-18087. [PMID: 31172597 DOI: 10.1002/jcb.29111] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 05/02/2019] [Accepted: 05/07/2019] [Indexed: 12/30/2022]
Abstract
Most patients suffering from non-small cell lung cancer (NSCLC) have epidermal growth factor receptor (EGFR) overexpression. Currently, EGFR tyrosine kinase inhibitors (TKIs) that act as the ATP-analogs and monoclonal antibodies (MAbs) to EGFR-ectodomain that block intracellular signaling are used for the treatment of advanced NSCLC. Unfortunately, adverse effects due to the TKI off-target and drug resistance occur in a significant number of the treated patients while some NSCLC genotypes do not respond to the therapeutic MAbs. Thus, a more effective remedy for the treatment of EGFR-overexpressed cancers is deemed necessary. In this study, VH/VH H displayed-phage clones that are bound to recombinant EGFR-TK were fished-out from a humanized-camel VH/VH H phage display library. VH/VH H of three phage-infected Escherichia coli clones (VH18, VH H35, and VH36) were linked molecularly to nonaarginine (R9) for making them cell penetrable. R9-VH18, R9-VH H35, and R9-VH36 were cytotoxic to human adenocarcinomic alveolar basal epithelial cells (A549) at the fifty percent inhibitory concentration (IC50 ) 0.181 ± 0.132, 0.00961 ± 0.00516, and 0.00996 ± 0.00752 μM, respectively, which were approximately 1000-fold more effective than small molecular TKIs. R9-VH18 and R9-VH36 also delayed cancer cell migration in a scratch-wound assay. Computerized homology modeling and intermolecular docking revealed that VH18 and VH H35 used CDR3 to interact with EGFR-TK residues close to the catalytic site, which might sterically hinder the ATP-binding of the TK; VH36 used CDR2 to bind at the asymmetric dimerization surface, which might disrupt EGFR dimerization leading to inhibition of intracellular signaling. The humanized-cell penetrable nanobodies have a high potential for developing further towards a clinical application.
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Affiliation(s)
- Lueacha Tabtimmai
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Praphasri Suphakun
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Pimonwan Srisook
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Duangnapa Kiriwan
- Genetic Engineering Interdisciplinary Program, Graduate School, Kasetsart University, Bangkok, Thailand
| | - Siratcha Phanthong
- Department of Parasitology, Faculty of Medicine Siriraj Hospital, Center of Research Excellence on Therapeutic Proteins and Antibody Engineering, Mahidol University, Bangkok, Thailand
| | - Pichamon Kiatwuthinon
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Wanpen Chaicumpa
- Department of Parasitology, Faculty of Medicine Siriraj Hospital, Center of Research Excellence on Therapeutic Proteins and Antibody Engineering, Mahidol University, Bangkok, Thailand
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6
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HtrA1 Mediated Intracellular Effects on Tubulin Using a Polarized RPE Disease Model. EBioMedicine 2017; 27:258-274. [PMID: 29269042 PMCID: PMC5828370 DOI: 10.1016/j.ebiom.2017.12.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 12/08/2017] [Accepted: 12/11/2017] [Indexed: 12/18/2022] Open
Abstract
Age-related macular degeneration (AMD) is the leading cause of irreversible vision loss. The protein HtrA1 is enriched in retinal pigment epithelial (RPE) cells isolated from AMD patients and in drusen deposits. However, it is poorly understood how increased levels of HtrA1 affect the physiological function of the RPE at the intracellular level. Here, we developed hfRPE (human fetal retinal pigment epithelial) cell culture model where cells fully differentiated into a polarized functional monolayer. In this model, we fine-tuned the cellular levels of HtrA1 by targeted overexpression. Our data show that HtrA1 enzymatic activity leads to intracellular degradation of tubulin with a corresponding reduction in the number of microtubules, and consequently to an altered mechanical cell phenotype. HtrA1 overexpression further leads to impaired apical processes and decreased phagocytosis, an essential function for photoreceptor survival. These cellular alterations correlate with the AMD phenotype and thus highlight HtrA1 as an intracellular target for therapeutic interventions towards AMD treatment.
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7
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Binding to SMN2 pre-mRNA-protein complex elicits specificity for small molecule splicing modifiers. Nat Commun 2017; 8:1476. [PMID: 29133793 PMCID: PMC5684323 DOI: 10.1038/s41467-017-01559-4] [Citation(s) in RCA: 134] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 09/27/2017] [Indexed: 01/28/2023] Open
Abstract
Small molecule splicing modifiers have been previously described that target the general splicing machinery and thus have low specificity for individual genes. Several potent molecules correcting the splicing deficit of the SMN2 (survival of motor neuron 2) gene have been identified and these molecules are moving towards a potential therapy for spinal muscular atrophy (SMA). Here by using a combination of RNA splicing, transcription, and protein chemistry techniques, we show that these molecules directly bind to two distinct sites of the SMN2 pre-mRNA, thereby stabilizing a yet unidentified ribonucleoprotein (RNP) complex that is critical to the specificity of these small molecules for SMN2 over other genes. In addition to the therapeutic potential of these molecules for treatment of SMA, our work has wide-ranging implications in understanding how small molecules can interact with specific quaternary RNA structures. Small molecules correcting the splicing deficit of the survival of motor neuron 2 (SMN2) gene have been identified as having therapeutic potential. Here, the authors provide evidence that SMN2 mRNA forms a ribonucleoprotein complex that can be specifically targeted by these small molecules.
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8
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Jung HJ. Chemical Proteomic Approaches Targeting Cancer Stem Cells: A Review of Current Literature. Cancer Genomics Proteomics 2017; 14:315-327. [PMID: 28870999 PMCID: PMC5611518 DOI: 10.21873/cgp.20042] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 07/18/2017] [Accepted: 07/20/2017] [Indexed: 12/24/2022] Open
Abstract
Cancer stem cells (CSCs) have been proposed as central drivers of tumor initiation, progression, recurrence, and therapeutic resistance. Therefore, identifying stem-like cells within cancers and understanding their properties is crucial for the development of effective anticancer therapies. Recently, chemical proteomics has become a powerful tool to efficiently determine protein networks responsible for CSC pathophysiology and comprehensively elucidate molecular mechanisms of drug action against CSCs. This review provides an overview of major methodologies utilized in chemical proteomic approaches. In addition, recent successful chemical proteomic applications targeting CSCs are highlighted. Future direction of potential CSC research by integrating chemical genomic and proteomic data obtained from a single biological sample of CSCs are also suggested in this review.
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Affiliation(s)
- Hye Jin Jung
- Department of BT-Convergent Pharmaceutical Engineering, Sun Moon University, Asan, Republic of Korea
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9
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Lugert S, Kremer T, Jagasia R, Herrmann A, Aigner S, Giachino C, Mendez-David I, Gardier AM, Carralot JP, Meistermann H, Augustin A, Saxe MD, Lamerz J, Duran-Pacheco G, Ducret A, Taylor V, David DJ, Czech C. Glypican-2 levels in cerebrospinal fluid predict the status of adult hippocampal neurogenesis. Sci Rep 2017; 7:46543. [PMID: 28440309 PMCID: PMC5404329 DOI: 10.1038/srep46543] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 03/17/2017] [Indexed: 12/20/2022] Open
Abstract
Adult hippocampal neurogenesis is a remarkable form of brain plasticity through which new neurons are generated throughout life. Despite its important roles in cognition and emotion and its modulation in various preclinical disease models, the functional importance of adult hippocampal neurogenesis in human health has not been revealed because of a lack of tools for monitoring adult neurogenesis in vivo. Therefore, we performed an unbiased proteomics screen to identify novel proteins expressed during neuronal differentiation using a human neural stem cell model, and we identified the proteoglycan Glypican-2 (Gpc2) as a putative secreted marker of immature neurons. Exogenous Gpc2 binds to FGF2 and inhibits FGF2-induced neural progenitor cell proliferation. Gpc2 is enriched in neurogenic regions of the adult brain. Its expression is increased by physiological stimuli that increase hippocampal neurogenesis and decreased in transgenic models in which neurogenesis is selectively ablated. Changes in neurogenesis also result in changes in Gpc2 protein level in cerebrospinal fluid (CSF). Gpc2 is detectable in adult human CSF, and first pilot experiments with a longitudinal cohort indicate a decrease over time. Thus, Gpc2 may serve as a potential marker to monitor adult neurogenesis in both animal and human physiology and disease, warranting future studies.
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Affiliation(s)
- S Lugert
- Roche Pharmaceutical Research and Early Development, NORD Discovery &Translational Area, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - T Kremer
- Roche Pharmaceutical Research and Early Development, NORD Discovery &Translational Area, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - R Jagasia
- Roche Pharmaceutical Research and Early Development, NORD Discovery &Translational Area, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - A Herrmann
- Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - S Aigner
- Roche Pharmaceutical Research and Early Development, NORD Discovery &Translational Area, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - C Giachino
- Embryology and Stem Cell Biology, Department of Biomedicine, University of Basel, Mattenstrasse 28, CH-4058 Basel, Switzerland
| | - I Mendez-David
- CESP/UMR-S 1178, Univ. Paris-Sud, Fac. Pharmacie, INSERM, Université Paris-Saclay, Chatenay Malabry, 92290, France
| | - A M Gardier
- CESP/UMR-S 1178, Univ. Paris-Sud, Fac. Pharmacie, INSERM, Université Paris-Saclay, Chatenay Malabry, 92290, France
| | - J P Carralot
- Roche Pharmaceutical Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - H Meistermann
- Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - A Augustin
- Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - M D Saxe
- Roche Pharmaceutical Research and Early Development, NORD Discovery &Translational Area, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - J Lamerz
- Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - G Duran-Pacheco
- Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - A Ducret
- Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - V Taylor
- Embryology and Stem Cell Biology, Department of Biomedicine, University of Basel, Mattenstrasse 28, CH-4058 Basel, Switzerland
| | - D J David
- CESP/UMR-S 1178, Univ. Paris-Sud, Fac. Pharmacie, INSERM, Université Paris-Saclay, Chatenay Malabry, 92290, France
| | - C Czech
- Roche Pharmaceutical Research and Early Development, NORD Discovery &Translational Area, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070 Basel, Switzerland
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10
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Yang Z, Hackshaw A, Feng Q, Fu X, Zhang Y, Mao C, Tang J. Comparison of gefitinib, erlotinib and afatinib in non-small cell lung cancer: A meta-analysis. Int J Cancer 2017; 140:2805-2819. [PMID: 28295308 DOI: 10.1002/ijc.30691] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 02/18/2017] [Accepted: 02/28/2017] [Indexed: 12/21/2022]
Abstract
Gefitinib, erlotinib and afatinib are three widely used epidermal growth factor receptor tyrosine kinase inhibitors (EGFR TKIs) for treating advanced non-small cell lung cancer (NSCLC) with proven efficacy. We undertook a systematic review and meta-analysis to synthesize existing studies with direct comparisons of EGFR TKIs in NSCLC in terms of both efficacy and safety. Eight randomized trials and 82 cohort studies with a total of 17,621 patients were included for analysis. Gefitinib and erlotinib demonstrated comparable effects on progression-free survival (hazard ratio [HR], 1.00; 95% confidence interval [CI], 0.95 to 1.04), overall survival (HR, 0.99; 95% CI, 0.93 to 1.06), overall response rate (risk ratio [RR], 1.05; 95% CI, 1.00 to 1.11), and disease control rate (RR, 0.98; 95% CI, 0.96 to 1.01), which did not vary considerably with EGFR mutation status, ethnicity, line of treatment, and baseline brain metastasis status. Gefitinib was associated with more grade 3/4 liver dysfunction, but tended to cause lower rates of dose reduction, treatment discontinuation, total grade 3/4 adverse events (RR, 0.78; 95% CI 0.65 to 0.94), and a number of specific adverse events such as rash and diarrhea. No solid evidence was found that afatinib had greater efficacy than gefitinib or erlotinib in first-line treatment of EGFR-mutant NSCLC. However, afatinib was more effective than erlotinib as second-line treatment of patients with advanced squamous cell carcinoma. The grade 3/4 adverse events rate of afatinib was comparable to that of erlotinib but higher than that of gefitinib.
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Affiliation(s)
- Zuyao Yang
- Division of Epidemiology, the Jockey Club School of Public Health and Primary Care, the Chinese University of Hong Kong, Hong Kong, China.,The Hong Kong Branch of the Chinese Cochrane Centre, the Chinese University of Hong Kong, Hong Kong, China
| | - Allan Hackshaw
- Cancer Research UK and University College London Cancer Trials Centre, 90 Tottenham Court Rd, London, W1T 4TJ, United Kingdom
| | - Qi Feng
- Division of Epidemiology, the Jockey Club School of Public Health and Primary Care, the Chinese University of Hong Kong, Hong Kong, China
| | - Xiaohong Fu
- Division of Epidemiology, the Jockey Club School of Public Health and Primary Care, the Chinese University of Hong Kong, Hong Kong, China
| | - Yuelun Zhang
- Division of Epidemiology, the Jockey Club School of Public Health and Primary Care, the Chinese University of Hong Kong, Hong Kong, China
| | - Chen Mao
- Division of Epidemiology, the Jockey Club School of Public Health and Primary Care, the Chinese University of Hong Kong, Hong Kong, China.,Shenzhen Key Laboratory for Health Risk Analysis, Shenzhen Research Institute of the Chinese University of Hong Kong, Shenzhen, Guangdong Province, China
| | - Jinling Tang
- Division of Epidemiology, the Jockey Club School of Public Health and Primary Care, the Chinese University of Hong Kong, Hong Kong, China.,The Hong Kong Branch of the Chinese Cochrane Centre, the Chinese University of Hong Kong, Hong Kong, China.,Shenzhen Key Laboratory for Health Risk Analysis, Shenzhen Research Institute of the Chinese University of Hong Kong, Shenzhen, Guangdong Province, China
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11
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Sakellakis M, Koutras A, Pittaka M, Tsitsopoulos E, Kalofonou F, Kalofonos HP. Long-term disease stabilization following treatment with erlotinib in heavily pretreated patients with wild-type epidermal growth factor receptor non-small-cell lung carcinoma: Two case reports. Mol Clin Oncol 2017; 5:803-806. [PMID: 28105360 DOI: 10.3892/mco.2016.1036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 07/25/2016] [Indexed: 11/06/2022] Open
Abstract
Lung adenocarcinomas carrying epidermal growth factor receptor (EGFR) mutations have been identified as a unique group of entities that depend on EGFR for their proliferation and metastasis. The introduction of reversible EGFR tyrosine kinase inhibitors, such as erlotinib, has significantly affected the management of metastatic disease in this subset of patients. Interestingly, although erlotinib is highly effective in patients with EGFR mutations, it may occasionally prove useful, even in the absence of mutations. We herein present the course of two heavily pretreated patients who achieved remarkable disease stabilization over several years, despite harbouring no EGFR mutations. Our cases underscore the fact that further research is required to identify which subset of patients will benefit the most from this treatment, as a substantial minority may present with favourable outcomes.
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Affiliation(s)
- Minas Sakellakis
- Division of Oncology, Department of Medicine, University Hospital, Patras Medical School, 26504 Patras, Greece
| | - Angelos Koutras
- Division of Oncology, Department of Medicine, University Hospital, Patras Medical School, 26504 Patras, Greece
| | - Maria Pittaka
- Department of Radiation Oncology, University Hospital, Patras Medical School, 26504 Patras, Greece
| | | | - Fotini Kalofonou
- Division of Oncology, Department of Medicine, University Hospital, Patras Medical School, 26504 Patras, Greece
| | - Haralabos P Kalofonos
- Division of Oncology, Department of Medicine, University Hospital, Patras Medical School, 26504 Patras, Greece
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12
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Knezevic CE, Wright G, Rix LLR, Kim W, Kuenzi BM, Luo Y, Watters JM, Koomen JM, Haura EB, Monteiro AN, Radu C, Lawrence HR, Rix U. Proteome-wide Profiling of Clinical PARP Inhibitors Reveals Compound-Specific Secondary Targets. Cell Chem Biol 2016; 23:1490-1503. [PMID: 27866910 DOI: 10.1016/j.chembiol.2016.10.011] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 08/11/2016] [Accepted: 10/20/2016] [Indexed: 01/02/2023]
Abstract
Poly(ADP-ribose) polymerase (PARP) inhibitors (PARPi) are a promising class of targeted cancer drugs, but their individual target profiles beyond the PARP family, which could result in differential clinical use or toxicity, are unknown. Using an unbiased, mass spectrometry-based chemical proteomics approach, we generated a comparative proteome-wide target map of the four clinical PARPi, olaparib, veliparib, niraparib, and rucaparib. PARPi as a class displayed high target selectivity. However, in addition to the canonical targets PARP1, PARP2, and several of their binding partners, we also identified hexose-6-phosphate dehydrogenase (H6PD) and deoxycytidine kinase (DCK) as previously unrecognized targets of rucaparib and niraparib, respectively. Subsequent functional validation suggested that inhibition of DCK by niraparib could have detrimental effects when combined with nucleoside analog pro-drugs. H6PD silencing can cause apoptosis and further sensitize cells to PARPi, suggesting that H6PD may be, in addition to its established role in metabolic disorders, a new anticancer target.
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Affiliation(s)
- Claire E Knezevic
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Gabriela Wright
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Lily L Remsing Rix
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Woosuk Kim
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA.,Ahmanson Translational Imaging Division, University of California, Los Angeles, Los Angeles, CA, USA
| | - Brent M Kuenzi
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA.,Cancer Biology Ph.D. Program, University of South Florida, Tampa, FL, USA
| | - Yunting Luo
- Chemical Biology Core, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - January M Watters
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA.,Cancer Biology Ph.D. Program, University of South Florida, Tampa, FL, USA
| | - John M Koomen
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Eric B Haura
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Alvaro N Monteiro
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Caius Radu
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA.,Ahmanson Translational Imaging Division, University of California, Los Angeles, Los Angeles, CA, USA
| | - Harshani R Lawrence
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA.,Chemical Biology Core, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Uwe Rix
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
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13
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Sarin H. Conserved molecular mechanisms underlying the effects of small molecule xenobiotic chemotherapeutics on cells. Mol Clin Oncol 2015; 4:326-368. [PMID: 26998284 DOI: 10.3892/mco.2015.714] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 12/08/2015] [Indexed: 12/14/2022] Open
Abstract
For proper determination of the apoptotic potential of chemoxenobiotics in synergism, it is important to understand the modes, levels and character of interactions of chemoxenobiotics with cells in the context of predicted conserved biophysical properties. Chemoxenobiotic structures are studied with respect to atom distribution over molecular space, the predicted overall octanol-to-water partition coefficient (Log OWPC; unitless) and molecular size viz a viz van der Waals diameter (vdWD). The Log OWPC-to-vdWD (nm-1 ) parameter is determined, and where applicable, hydrophilic interacting moiety/core-to-vdWD (nm-1 ) and lipophilic incorporating hydrophobic moiety/core-to-vdWD (nm-1 ) parameters of their part-structures are determined. The cellular and sub-cellular level interactions of the spectrum of xenobiotic chemotherapies have been characterized, for which a classification system has been developed based on predicted conserved biophysical properties with respect to the mode of chemotherapeutic effect. The findings of this study are applicable towards improving the effectiveness of existing combination chemotherapy regimens and the predictive accuracy of personalized cancer treatment algorithms as well as towards the selection of appropriate novel xenobiotics with the potential to be potent chemotherapeutics for dendrimer nanoparticle-based effective transvascular delivery.
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Affiliation(s)
- Hemant Sarin
- Freelance Investigator in Translational Science and Medicine, Charleston, WV 25314, USA
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14
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Cutler P, Voshol H. Proteomics in pharmaceutical research and development. Proteomics Clin Appl 2015; 9:643-50. [PMID: 25763573 DOI: 10.1002/prca.201400181] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 02/10/2015] [Accepted: 03/09/2015] [Indexed: 01/07/2023]
Abstract
In the 20 years since its inception, the evolution of proteomics in pharmaceutical industry has mirrored the developments within academia and indeed other industries. From initial enthusiasm and subsequent disappointment in global protein expression profiling, pharma research saw the biggest impact when relating to more focused approaches, such as those exploring the interaction between proteins and drugs. Nowadays, proteomics technologies have been integrated in many areas of pharmaceutical R&D, ranging from the analysis of therapeutic proteins to the monitoring of clinical trials. Here, we review the development of proteomics in the drug discovery process, placing it in a historical context as well as reviewing the current status in light of the contributions to this special issue, which reflect some of the diverse demands of the drug and biomarker pipelines.
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Affiliation(s)
- Paul Cutler
- Translational Technologies and Bioinformatics, Pharmaceutical Sciences, Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Basel, Switzerland
| | - Hans Voshol
- Novartis Institutes for BioMedical Research, Analytical Sciences and Imaging, Basel, Switzerland
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15
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Abstract
Small molecule inhibitors of protein kinases are key tools for signal transduction research and represent a major class of targeted drugs. Recent developments in quantitative proteomics enable an unbiased view on kinase inhibitor selectivity and modes of action in the biological context. While chemical proteomics techniques utilizing quantitative mass spectrometry interrogate both target specificity and affinity in cellular extracts, proteome-wide phosphorylation analyses upon kinase inhibitor treatment identify signal transduction pathway and network regulation in an unbiased manner. Thus, critical information is provided to promote new insights into mechanisms of kinase signaling and their relevance for kinase inhibitor drug discovery.
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Affiliation(s)
- Henrik Daub
- Evotec (München) GmbH, Am Klopferspitz
19a, 82152 Martinsried, Germany
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16
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Gridling M, Ficarro SB, Breitwieser FP, Song L, Parapatics K, Colinge J, Haura EB, Marto JA, Superti-Furga G, Bennett KL, Rix U. Identification of kinase inhibitor targets in the lung cancer microenvironment by chemical and phosphoproteomics. Mol Cancer Ther 2014; 13:2751-62. [PMID: 25189542 PMCID: PMC4221415 DOI: 10.1158/1535-7163.mct-14-0152] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A growing number of gene mutations, which are recognized as cancer drivers, can be successfully targeted with drugs. The redundant and dynamic nature of oncogenic signaling networks and complex interactions between cancer cells and the microenvironment, however, can cause drug resistance. While these challenges can be addressed by developing drug combinations or polypharmacology drugs, this benefits greatly from a detailed understanding of the proteome-wide target profiles. Using mass spectrometry-based chemical proteomics, we report the comprehensive characterization of the drug-protein interaction networks for the multikinase inhibitors dasatinib and sunitinib in primary lung cancer tissue specimens derived from patients. We observed in excess of 100 protein kinase targets plus various protein complexes involving, for instance, AMPK, TBK1 (sunitinib), and ILK (dasatinib). Importantly, comparison with lung cancer cell lines and mouse xenografts thereof showed that most targets were shared between cell lines and tissues. Several targets, however, were only present in tumor tissues. In xenografts, most of these proteins were of mouse origin suggesting that they originate from the tumor microenvironment. Furthermore, intersection with subsequent global phosphoproteomic analysis identified several activated signaling pathways. These included MAPK, immune, and integrin signaling, which were affected by these drugs in both cancer cells and the microenvironment. Thus, the combination of chemical and phosphoproteomics can generate a systems view of proteins, complexes, and signaling pathways that are simultaneously engaged by multitargeted drugs in cancer cells and the tumor microenvironment. This may allow for the design of novel anticancer therapies that concurrently target multiple tumor compartments.
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Affiliation(s)
- Manuela Gridling
- Research Center for Molecular Medicine of the Austrian Academy of Sciences (CeMM), Vienna, Austria
| | - Scott B Ficarro
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts. Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, Massachusetts. Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts
| | - Florian P Breitwieser
- Research Center for Molecular Medicine of the Austrian Academy of Sciences (CeMM), Vienna, Austria
| | - Lanxi Song
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Katja Parapatics
- Research Center for Molecular Medicine of the Austrian Academy of Sciences (CeMM), Vienna, Austria
| | - Jacques Colinge
- Research Center for Molecular Medicine of the Austrian Academy of Sciences (CeMM), Vienna, Austria
| | - Eric B Haura
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Jarrod A Marto
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts. Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, Massachusetts. Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts
| | - Giulio Superti-Furga
- Research Center for Molecular Medicine of the Austrian Academy of Sciences (CeMM), Vienna, Austria
| | - Keiryn L Bennett
- Research Center for Molecular Medicine of the Austrian Academy of Sciences (CeMM), Vienna, Austria
| | - Uwe Rix
- Research Center for Molecular Medicine of the Austrian Academy of Sciences (CeMM), Vienna, Austria. Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida.
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Gil S, Goetgheluck J, Paci A, Broutin S, Friard S, Couderc L, Ayoubi J, Picone O, Tcherakian C. Efficacy and safety of gefitinib during pregnancy: Case report and literature review. Lung Cancer 2014; 85:481-4. [DOI: 10.1016/j.lungcan.2014.06.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 05/27/2014] [Accepted: 06/08/2014] [Indexed: 11/28/2022]
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18
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Meistermann H, Gao J, Golling S, Lamerz J, Le Pogam S, Tzouros M, Sankabathula S, Gruenbaum L, Nájera I, Langen H, Klumpp K, Augustin A. A novel immuno-competitive capture mass spectrometry strategy for protein-protein interaction profiling reveals that LATS kinases regulate HCV replication through NS5A phosphorylation. Mol Cell Proteomics 2014; 13:3040-8. [PMID: 25044019 DOI: 10.1074/mcp.m113.028977] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mapping protein-protein interactions is essential to fully characterize the biological function of a protein and improve our understanding of diseases. Affinity purification coupled to mass spectrometry (AP-MS) using selective antibodies against a target protein has been commonly applied to study protein complexes. However, one major limitation is a lack of specificity as a substantial part of the proposed binders is due to nonspecific interactions. Here, we describe an innovative immuno-competitive capture mass spectrometry (ICC-MS) method to allow systematic investigation of protein-protein interactions. ICC-MS markedly increases the specificity of classical immunoprecipitation (IP) by introducing a competition step between free and capturing antibody prior to IP. Instead of comparing only one experimental sample with a control, the methodology generates a 12-concentration antibody competition profile. Label-free quantitation followed by a robust statistical analysis of the data is then used to extract the cellular interactome of a protein of interest and to filter out background proteins. We applied this new approach to specifically map the interactome of hepatitis C virus (HCV) nonstructural protein 5A (NS5A) in a cellular HCV replication system and uncovered eight new NS5A-interacting protein candidates along with two previously validated binding partners. Follow-up biological validation experiments revealed that large tumor suppressor homolog 1 and 2 (LATS1 and LATS2, respectively), two closely related human protein kinases, are novel host kinases responsible for NS5A phosphorylation at a highly conserved position required for optimal HCV genome replication. These results are the first illustration of the value of ICC-MS for the analysis of endogenous protein complexes to identify biologically relevant protein-protein interactions with high specificity.
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Affiliation(s)
- Hélène Meistermann
- From the ‡Pharma Research and Early Development Department, F. Hoffmann-La Roche Ltd, Basel 4070, Switzerland and
| | - Junjun Gao
- the ¶Pharma Research and Early Development Department, F. Hoffmann-La Roche Ltd, Nutley, NJ, 07110-1199
| | - Sabrina Golling
- From the ‡Pharma Research and Early Development Department, F. Hoffmann-La Roche Ltd, Basel 4070, Switzerland and
| | - Jens Lamerz
- From the ‡Pharma Research and Early Development Department, F. Hoffmann-La Roche Ltd, Basel 4070, Switzerland and
| | - Sophie Le Pogam
- the ¶Pharma Research and Early Development Department, F. Hoffmann-La Roche Ltd, Nutley, NJ, 07110-1199
| | - Manuel Tzouros
- From the ‡Pharma Research and Early Development Department, F. Hoffmann-La Roche Ltd, Basel 4070, Switzerland and
| | - Sailaja Sankabathula
- the ¶Pharma Research and Early Development Department, F. Hoffmann-La Roche Ltd, Nutley, NJ, 07110-1199
| | - Lore Gruenbaum
- the ¶Pharma Research and Early Development Department, F. Hoffmann-La Roche Ltd, Nutley, NJ, 07110-1199
| | - Isabel Nájera
- the ¶Pharma Research and Early Development Department, F. Hoffmann-La Roche Ltd, Nutley, NJ, 07110-1199
| | - Hanno Langen
- From the ‡Pharma Research and Early Development Department, F. Hoffmann-La Roche Ltd, Basel 4070, Switzerland and
| | - Klaus Klumpp
- the ¶Pharma Research and Early Development Department, F. Hoffmann-La Roche Ltd, Nutley, NJ, 07110-1199
| | - Angélique Augustin
- From the ‡Pharma Research and Early Development Department, F. Hoffmann-La Roche Ltd, Basel 4070, Switzerland and
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