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Zhao Q, Yao Z, Chen L, He Y, Xie Z, Zhang H, Lin W, Chen F, Xie Q, Zhang X. Transcriptome-Wide Dynamics of m6A Methylation in Tumor Livers Induced by ALV-J Infection in Chickens. Front Immunol 2022; 13:868892. [PMID: 35529873 PMCID: PMC9072629 DOI: 10.3389/fimmu.2022.868892] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 03/28/2022] [Indexed: 11/26/2022] Open
Abstract
Avian Leukosis Virus Subgroup J (ALV-J) is a tumorigenic virus with high morbidity and rapid transmission. N6-methyladenosine (m6A) is a common epigenetic modification that may be closely related to the pathogenicity of ALV-J. Currently, there are no reports on whether m6A modification is related to ALV-J induced tumor formation. In this study, we used methylated RNA immunoprecipitation sequencing (MeRIP-seq) and RNA sequencing (RNA-seq) to examine the differences in m6A methylation and gene expression in normal livers and ALV-J-induced tumor livers systematically, with functional enrichment and co-expression analysis. The results identified 6,541 m6A methylated peaks, mainly enriched in CDS, and more than 83% of the transcripts contained 1-2 m6A peaks. For RNA-seq, 1,896 and 1,757 differentially expressed mRNAs and lncRNAs were identified, respectively. Gene enrichment analysis indicated that they may be involved in biological processes and pathways such as immunology-related and apoptosis. Moreover, we identified 17 lncRNAs, commonly existing in differently expressed methylome and transcriptome. Through co-expression analysis, 126 differentially expressed lncRNAs, and 18 potentially m6A-related methyltransferases were finally identified and connected, suggesting that m6A modifications might affect gene expression of lncRNAs and play a role in ALV-J induced tumor formation. This study provides the first comprehensive description of the m6A expression profile in tumor livers induced by ALV-J infection in chickens, which provides a basis for studying the role of m6A modification in ALV-J induced tumorigenesis. This study provides clues for studying the epigenetic etiology and pathogenesis of ALV-J.
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Affiliation(s)
- Qiqi Zhao
- Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology & Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding & Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
- South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, China
| | - Ziqi Yao
- Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology & Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding & Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
- South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, China
| | - Liyi Chen
- Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology & Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding & Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
- South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, China
| | - Yaai He
- Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology & Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding & Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
- South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, China
| | - Zi Xie
- Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology & Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding & Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
- South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, China
- Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou, China
| | - Huanmin Zhang
- United States Department of Agriculture (USDA), Agriculture Research Service, Avian Disease and Oncology Laboratory, East Lansing, MI, United States
| | - Wencheng Lin
- Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology & Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding & Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
- South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, China
- Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou, China
| | - Feng Chen
- Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology & Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding & Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
- South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, China
- Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou, China
| | - Qingmei Xie
- Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology & Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding & Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
- South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, China
- Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou, China
- *Correspondence: Qingmei Xie, ; Xinheng Zhang,
| | - Xinheng Zhang
- Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology & Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding & Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
- South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, China
- Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou, China
- *Correspondence: Qingmei Xie, ; Xinheng Zhang,
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2
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Vigneswara V, Kong A. Predictive biomarkers and EGFR inhibitors in squamous cell carcinoma of head and neck (SCCHN). Ann Oncol 2019; 29:794-796. [PMID: 29444313 DOI: 10.1093/annonc/mdy065] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- V Vigneswara
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - A Kong
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK.
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3
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Momeny M, Zarrinrad G, Moghaddaskho F, Poursheikhani A, Sankanian G, Zaghal A, Mirshahvaladi S, Esmaeili F, Eyvani H, Barghi F, Sabourinejad Z, Alishahi Z, Yousefi H, Ghasemi R, Dardaei L, Bashash D, Chahardouli B, Dehpour AR, Tavakkoly-Bazzaz J, Alimoghaddam K, Ghavamzadeh A, Ghaffari SH. Dacomitinib, a pan-inhibitor of ErbB receptors, suppresses growth and invasive capacity of chemoresistant ovarian carcinoma cells. Sci Rep 2017. [PMID: 28646172 PMCID: PMC5482808 DOI: 10.1038/s41598-017-04147-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Epithelial ovarian cancer (EOC) is the most lethal gynaecological malignancy worldwide. Development of chemoresistance and peritoneal dissemination of EOC cells are the major reasons for low survival rate. Targeting signal transduction pathways which promote therapy resistance and metastatic dissemination is the key to successful treatment. Members of the ErbB family of receptors are over-expressed in EOC and play key roles in chemoresistance and invasiveness. Despite this, single-targeted ErbB inhibitors have demonstrated limited activity in chemoresistant EOC. In this report, we show that dacomitinib, a pan-ErbB receptor inhibitor, diminished growth, clonogenic potential, anoikis resistance and induced apoptotic cell death in therapy-resistant EOC cells. Dacominitib inhibited PLK1-FOXM1 signalling pathway and its down-stream targets Aurora kinase B and survivin. Moreover, dacomitinib attenuated migration and invasion of the EOC cells and reduced expression of epithelial-to-mesenchymal transition (EMT) markers ZEB1, ZEB2 and CDH2 (which encodes N-cadherin). Conversely, the anti-tumour activity of single-targeted ErbB agents including cetuximab (a ligand-blocking anti-EGFR mAb), transtuzumab (anti-HER2 mAb), H3.105.5 (anti-HER3 mAb) and erlotinib (EGFR small-molecule tyrosine kinase inhibitor) were marginal. Our results provide a rationale for further investigation on the therapeutic potential of dacomitinib in treatment of the chemoresistant EOC.
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Affiliation(s)
- Majid Momeny
- Haematology/Oncology and Stem Cell Transplantation Research Centre, Shariati Hospital, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Ghazaleh Zarrinrad
- Haematology/Oncology and Stem Cell Transplantation Research Centre, Shariati Hospital, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Farima Moghaddaskho
- Haematology/Oncology and Stem Cell Transplantation Research Centre, Shariati Hospital, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Arash Poursheikhani
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Ghazaleh Sankanian
- Haematology/Oncology and Stem Cell Transplantation Research Centre, Shariati Hospital, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Azam Zaghal
- Haematology/Oncology and Stem Cell Transplantation Research Centre, Shariati Hospital, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Shahab Mirshahvaladi
- Department of Molecular Systems Biology, Cell Science Research Centre, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Fatemeh Esmaeili
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Haniyeh Eyvani
- Haematology/Oncology and Stem Cell Transplantation Research Centre, Shariati Hospital, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Farinaz Barghi
- Haematology/Oncology and Stem Cell Transplantation Research Centre, Shariati Hospital, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Zahra Sabourinejad
- Haematology/Oncology and Stem Cell Transplantation Research Centre, Shariati Hospital, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Zivar Alishahi
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Hassan Yousefi
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Reza Ghasemi
- Section of Stem Cell Biology, Division of Oncology, Department of Medicine, Washington University in Saint Louis, Saint Louis, MO, USA
| | - Leila Dardaei
- Massachusetts General Hospital Cancer Centre, Charlestown, MA, USA
| | - Davood Bashash
- Department of Haematology and Blood Banking, Faculty of Allied Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Bahram Chahardouli
- Haematology/Oncology and Stem Cell Transplantation Research Centre, Shariati Hospital, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Ahmad R Dehpour
- Experimental Medicine Research Centre, Tehran University of Medical Sciences, Tehran, Iran.,Department of Pharmacology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Javad Tavakkoly-Bazzaz
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Kamran Alimoghaddam
- Haematology/Oncology and Stem Cell Transplantation Research Centre, Shariati Hospital, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Ardeshir Ghavamzadeh
- Haematology/Oncology and Stem Cell Transplantation Research Centre, Shariati Hospital, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Seyed H Ghaffari
- Haematology/Oncology and Stem Cell Transplantation Research Centre, Shariati Hospital, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
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EGFR signaling pathways are wired differently in normal 184A1L5 human mammary epithelial and MDA-MB-231 breast cancer cells. J Cell Commun Signal 2017; 11:341-356. [PMID: 28357710 DOI: 10.1007/s12079-017-0389-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 03/22/2017] [Indexed: 01/10/2023] Open
Abstract
Because of differences in the downstream signaling patterns of its pathways, the role of the human epidermal growth factor family of receptors (HER) in promoting cell growth and survival is cell line and context dependent. Using two model cell lines, we have studied how the regulatory interaction network among the key proteins of HER signaling pathways may be rewired upon normal to cancerous transformation. We in particular investigated how the transcription factor STAT3 and several key kinases' involvement in cancer-related signaling processes differ between normal 184A1L5 human mammary epithelial (HME) and MDA-MB-231 breast cancer epithelial cells. Comparison of the responses in these cells showed that normal-to-cancerous cellular transformation causes a major re-wiring of the growth factor initiated signaling. In particular, we found that: i) regulatory interactions between Erk, p38, JNK and STAT3 are triangulated and tightly coupled in 184A1L5 HME cells, and ii) STAT3 is only weakly associated with the Erk-p38-JNK pathway in MDA-MB-231 cells. Utilizing the concept of pathway substitution, we predicted how the observed differences in the regulatory interactions may affect the proliferation/survival and motility responses of the 184A1L5 and MDA-MB-231 cells when exposed to various inhibitors. We then validated our predictions experimentally to complete the experiment-computation-experiment iteration loop. Validated differences in the regulatory interactions of the 184A1L5 and MDA-MB-231 cells indicated that instead of inhibiting STAT3, which has severe toxic side effects, simultaneous inhibition of JNK together with Erk or p38 could be a more effective strategy to impose cell death selectively to MDA-MB-231 cancer cells while considerably lowering the side effects to normal epithelial cells. Presented analysis establishes a framework with examples that would enable cell signaling researchers to identify the signaling network structures which can be used to predict the phenotypic responses in particular cell lines of interest.
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5
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Analysis of the interplay between methylation and expression reveals its potential role in cancer aetiology. Funct Integr Genomics 2016; 17:53-68. [PMID: 27819121 DOI: 10.1007/s10142-016-0533-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 09/07/2016] [Accepted: 10/17/2016] [Indexed: 12/31/2022]
Abstract
With ongoing developments in technology, changes in DNA methylation levels have become prevalent to study cancer biology. Previous studies report that DNA methylation affects gene expression in a direct manner, most probably by blocking gene regulatory regions. In this study, we have studied the interplay between methylation and expression to improve our knowledge of cancer aetiology. For this purpose, we have investigated which genomic regions are of higher importance; hence, first exon, 5'UTR and 200 bp near the transcription start sites are proposed as being more crucial compared to other genomic regions. Furthermore, we have searched for a valid methylation level change threshold, and as a result, 25 % methylation change in previously determined genomic regions showed the highest inverse correlation with expression data. As a final step, we have examined the commonly affected genes and pathways by integrating methylation and expression information. Remarkably, the GPR115 gene and ErbB signalling pathway were found to be significantly altered for all cancer types in our analysis. Overall, combining methylation and expression information and identifying commonly affected genes and pathways in a variety of cancer types revealed new insights of cancer disease mechanisms. Moreover, compared to previous methylation-based studies, we have identified more important genomic regions and have defined a methylation change threshold level in order to obtain more reliable results. In addition to the novel analysis framework that involves the analysis of four different cancer types, our study exposes essential information regarding the contribution of methylation changes and its impact on cancer disease biology, which may facilitate the identification of new drug targets.
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6
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Koumakis L, Kanterakis A, Kartsaki E, Chatzimina M, Zervakis M, Tsiknakis M, Vassou D, Kafetzopoulos D, Marias K, Moustakis V, Potamias G. MinePath: Mining for Phenotype Differential Sub-paths in Molecular Pathways. PLoS Comput Biol 2016; 12:e1005187. [PMID: 27832067 PMCID: PMC5104320 DOI: 10.1371/journal.pcbi.1005187] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 10/10/2016] [Indexed: 01/04/2023] Open
Abstract
Pathway analysis methodologies couple traditional gene expression analysis with knowledge encoded in established molecular pathway networks, offering a promising approach towards the biological interpretation of phenotype differentiating genes. Early pathway analysis methodologies, named as gene set analysis (GSA), view pathways just as plain lists of genes without taking into account either the underlying pathway network topology or the involved gene regulatory relations. These approaches, even if they achieve computational efficiency and simplicity, consider pathways that involve the same genes as equivalent in terms of their gene enrichment characteristics. Most recent pathway analysis approaches take into account the underlying gene regulatory relations by examining their consistency with gene expression profiles and computing a score for each profile. Even with this approach, assessing and scoring single-relations limits the ability to reveal key gene regulation mechanisms hidden in longer pathway sub-paths. We introduce MinePath, a pathway analysis methodology that addresses and overcomes the aforementioned problems. MinePath facilitates the decomposition of pathways into their constituent sub-paths. Decomposition leads to the transformation of single-relations to complex regulation sub-paths. Regulation sub-paths are then matched with gene expression sample profiles in order to evaluate their functional status and to assess phenotype differential power. Assessment of differential power supports the identification of the most discriminant profiles. In addition, MinePath assess the significance of the pathways as a whole, ranking them by their p-values. Comparison results with state-of-the-art pathway analysis systems are indicative for the soundness and reliability of the MinePath approach. In contrast with many pathway analysis tools, MinePath is a web-based system (www.minepath.org) offering dynamic and rich pathway visualization functionality, with the unique characteristic to color regulatory relations between genes and reveal their phenotype inclination. This unique characteristic makes MinePath a valuable tool for in silico molecular biology experimentation as it serves the biomedical researchers' exploratory needs to reveal and interpret the regulatory mechanisms that underlie and putatively govern the expression of target phenotypes.
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Affiliation(s)
- Lefteris Koumakis
- Computational BioMedicine Laboratory (CBML), Institute of Computers Science (ICS), Foundation for Research and Technology-Hellas (FORTH), Heraklion, Crete, Greece
| | - Alexandros Kanterakis
- Computational BioMedicine Laboratory (CBML), Institute of Computers Science (ICS), Foundation for Research and Technology-Hellas (FORTH), Heraklion, Crete, Greece
| | - Evgenia Kartsaki
- Computational BioMedicine Laboratory (CBML), Institute of Computers Science (ICS), Foundation for Research and Technology-Hellas (FORTH), Heraklion, Crete, Greece
| | - Maria Chatzimina
- Computational BioMedicine Laboratory (CBML), Institute of Computers Science (ICS), Foundation for Research and Technology-Hellas (FORTH), Heraklion, Crete, Greece
| | - Michalis Zervakis
- School of Electrical and Computer Engineering, Technical University of Crete, Greece
| | - Manolis Tsiknakis
- Computational BioMedicine Laboratory (CBML), Institute of Computers Science (ICS), Foundation for Research and Technology-Hellas (FORTH), Heraklion, Crete, Greece
- Department of Informatics Engineering, Technological Educational Institute of Crete, Greece
| | - Despoina Vassou
- Institute of Molecular Biology & Biotechnology, FORTH, Heraklion, Crete, Greece
| | | | - Kostas Marias
- Computational BioMedicine Laboratory (CBML), Institute of Computers Science (ICS), Foundation for Research and Technology-Hellas (FORTH), Heraklion, Crete, Greece
| | - Vassilis Moustakis
- School of Production Engineering & Management, Technical University of Crete, Greece
| | - George Potamias
- Computational BioMedicine Laboratory (CBML), Institute of Computers Science (ICS), Foundation for Research and Technology-Hellas (FORTH), Heraklion, Crete, Greece
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7
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Calvo E, Soria JC, Ma WW, Wang T, Bahleda R, Tolcher AW, Gernhardt D, O'Connell J, Millham R, Giri N, Wick MJ, Adjei AA, Hidalgo M. A Phase I Clinical Trial and Independent Patient-Derived Xenograft Study of Combined Targeted Treatment with Dacomitinib and Figitumumab in Advanced Solid Tumors. Clin Cancer Res 2016; 23:1177-1185. [PMID: 27733479 DOI: 10.1158/1078-0432.ccr-15-2301] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 08/24/2016] [Accepted: 09/15/2016] [Indexed: 11/16/2022]
Abstract
Purpose: This phase I, open-label, single-arm trial assessed the safety and tolerability of dacomitinib-figitumumab combination therapy in patients with advanced solid tumors.Experimental Design: A standard 3 + 3 dose escalation/de-escalation design was utilized. Starting doses were figitumumab 20 mg/kg administered intravenously once every 3 weeks and dacomitinib 30 mg administered orally once daily. We also performed an independent study of the combination in patient-derived xenograft (avatar mouse) models of adenoid cystic carcinoma.Results: Of the 74 patients enrolled, the most common malignancies were non-small cell lung cancer (24.3%) and colorectal cancer (14.9%). The most common treatment-related adverse events in the 71 patients who received treatment across five dose levels were diarrhea (59.2%), mucosal inflammation (47.9%), and fatigue and acneiform dermatitis (45.1% each). The most common dose-limiting toxicity was mucosal inflammation. Dosing schedules of dacomitinib 10 or 15 mg daily plus figitumumab 20 mg/kg every 3 weeks after a figitumumab loading dose were tolerated by patients over multiple cycles and considered recommended doses for further evaluation. Objective responses were seen in patients with adenoid cystic carcinoma, ovarian carcinoma, and salivary gland cancer. Pharmacokinetic analysis did not show any significant drug-drug interaction. In the adenoid cystic carcinoma xenograft model, figitumumab exerted significant antitumor activity, whereas dacomitinib did not. Figitumumab-sensitive tumors showed downregulation of genes in the insulin-like growth factor receptor 1 pathway.Conclusions: Dacomitinib-figitumumab combination therapy was tolerable with significant dose reductions of both agents to less than the recommended single-agent phase II dose of each drug. Preliminary clinical activity was demonstrated in the potential target tumor adenoid cystic carcinoma. Clin Cancer Res; 23(5); 1177-85. ©2016 AACRSee related commentary by Sundar et al., p. 1123.
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Affiliation(s)
- Emiliano Calvo
- START Madrid, Centro Integral Oncológico Clara Campal, Madrid, Spain.
| | | | - Wen Wee Ma
- Roswell Park Cancer Institute, Buffalo, New York
| | - Tao Wang
- Pfizer Inc., Groton, Connecticut
| | | | | | | | | | | | | | | | - Alex A Adjei
- Roswell Park Cancer Institute, Buffalo, New York
| | - Manuel Hidalgo
- START Madrid, Centro Integral Oncológico Clara Campal, Madrid, Spain
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8
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Chen HR, Sherr DH, Hu Z, DeLisi C. A network based approach to drug repositioning identifies plausible candidates for breast cancer and prostate cancer. BMC Med Genomics 2016; 9:51. [PMID: 27475327 PMCID: PMC4967295 DOI: 10.1186/s12920-016-0212-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 07/20/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The high cost and the long time required to bring drugs into commerce is driving efforts to repurpose FDA approved drugs-to find new uses for which they weren't intended, and to thereby reduce the overall cost of commercialization, and shorten the lag between drug discovery and availability. We report on the development, testing and application of a promising new approach to repositioning. METHODS Our approach is based on mining a human functional linkage network for inversely correlated modules of drug and disease gene targets. The method takes account of multiple information sources, including gene mutation, gene expression, and functional connectivity and proximity of within module genes. RESULTS The method was used to identify candidates for treating breast and prostate cancer. We found that (i) the recall rate for FDA approved drugs for breast (prostate) cancer is 20/20 (10/11), while the rates for drugs in clinical trials were 131/154 and 82/106; (ii) the ROC/AUC performance substantially exceeds that of comparable methods; (iii) preliminary in vitro studies indicate that 5/5 candidates have therapeutic indices superior to that of Doxorubicin in MCF7 and SUM149 cancer cell lines. We briefly discuss the biological plausibility of the candidates at a molecular level in the context of the biological processes that they mediate. CONCLUSIONS Our method appears to offer promise for the identification of multi-targeted drug candidates that can correct aberrant cellular functions. In particular the computational performance exceeded that of other CMap-based methods, and in vitro experiments indicate that 5/5 candidates have therapeutic indices superior to that of Doxorubicin in MCF7 and SUM149 cancer cell lines. The approach has the potential to provide a more efficient drug discovery pipeline.
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Affiliation(s)
- Hsiao-Rong Chen
- Bioinformatics Program, College of Engineering, Boston University, Boston, MA, USA.,Graduate Program in Translational Molecular Medicine, Boston University School of Medicine, Boston, MA, USA
| | - David H Sherr
- Department of Environmental Health, Boston University School of Public Health, Boston, MA, USA
| | - Zhenjun Hu
- Bioinformatics Program, College of Engineering, Boston University, Boston, MA, USA
| | - Charles DeLisi
- Bioinformatics Program, College of Engineering, Boston University, Boston, MA, USA. .,Department of Biomedical Engineering, Boston University, Boston, MA, USA.
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9
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Shao X, Liu Y, Li Y, Xian M, Zhou Q, Yang B, Ying M, He Q. The HER2 inhibitor TAK165 Sensitizes Human Acute Myeloid Leukemia Cells to Retinoic Acid-Induced Myeloid Differentiation by activating MEK/ERK mediated RARα/STAT1 axis. Sci Rep 2016; 6:24589. [PMID: 27074819 PMCID: PMC4830980 DOI: 10.1038/srep24589] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 04/01/2016] [Indexed: 12/21/2022] Open
Abstract
The success of all-trans retinoic acid (ATRA) in differentiation therapy for patients with acute promyelocytic leukemia (APL) highly encourages researches to apply this therapy to other types of acute myeloid leukemia (AML). However, AML, with the exception of APL, fails to respond to differentiation therapy. Therefore, research strategies to further sensitize cells to retinoids and to extend the range of AMLs that respond to retinoids beyond APLs are urgently needed. In this study, we showed that TAK165, a HER2 inhibitor, exhibited a strong synergy with ATRA to promote AML cell differentiation. We observed that TAK165 sensitized the AML cells to ATRA-induced cell growth inhibition, G0/G1 phase arrest, CD11b expression, mature morphologic changes, NBT reduction and myeloid regulator expression. Unexpectedly, HER2 pathway might not be essential for TAK165-enhanced differentiation when combined with ATRA, while the enhanced differentiation was dependent on the activation of the RARα/STAT1 axis. Furthermore, the MEK/ERK cascade regulated the activation of STAT1. Taken together, our study is the first to evaluate the synergy of TAK165 and ATRA in AML cell differentiation and to assess new opportunities for the combination of TAK165 and ATRA as a promising approach for future differentiation therapy.
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Affiliation(s)
- Xuejing Shao
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, School of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yujia Liu
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, School of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yangling Li
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, School of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Miao Xian
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, School of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Qian Zhou
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, School of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Bo Yang
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, School of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Meidan Ying
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, School of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Qiaojun He
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, School of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
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10
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Horn L, Sandler A. Epidermal growth factor receptor inhibitors and antiangiogenic agents for the treatment of non-small cell lung cancer. Clin Cancer Res 2009; 15:5040-8. [PMID: 19671872 PMCID: PMC3528182 DOI: 10.1158/1078-0432.ccr-09-0520] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Non-small cell lung cancer (NSCLC) is a major global health problem and represents the leading cause of cancer-related deaths worldwide. The majority of patients with NSCLC are diagnosed with advanced-stage disease, and the prognosis for such patients is poor. The currently approved cytotoxic chemotherapy is associated with substantial limitations in both efficacy and safety. The availability of agents targeted against the epidermal growth factor receptor (EGFR), as well as the antiangiogenic agent bevacizumab, have provided some clinical benefit. Nonetheless, the efficacy of these agents is also inadequate, and resistance has emerged as a clinical problem. Numerous novel targeted therapies are now in clinical development and may have potential for overcoming the limitations associated with currently available agents. In this article we review clinical data for molecular-targeted therapies in NSCLC, with emphasis on EGFR inhibitors and antiangiogenic agents.
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Affiliation(s)
- Leora Horn
- Vanderbilt Ingram Cancer Centre, Division of Hematology/Oncology, Nashville, Tennessee, USA
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Becker JC, Muller-Tidow C, Serve H, Domschke W, Pohle T. Role of receptor tyrosine kinases in gastric cancer: New targets for a selective therapy. World J Gastroenterol 2006; 12:3297-305. [PMID: 16733844 PMCID: PMC4087885 DOI: 10.3748/wjg.v12.i21.3297] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Receptor tyrosine kinases (RTKs) such as the epidermal growth factor receptor family participate in several steps of tumor formation including proliferation and metastatic spread. Several known RTKs are upregulated in gastric cancer being prime targets of a tailored therapy. Only preliminary data exist, however, on the use of the currently clinically available drugs such as trastuzumab, cetuximab, bevacizumab, gefitinib, erlotinib, and imatinib in the setting of gastric cancer. Preclinical data suggest a potential benefit of their use, especially in combination with “conventional” cytostatic therapy. This review summarizes the current knowledge about their use in cancer therapy as well as new approaches and drugs to optimize treatment success.
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Shigematsu H, Takahashi T, Nomura M, Majmudar K, Suzuki M, Lee H, Wistuba II, Fong KM, Toyooka S, Shimizu N, Fujisawa T, Minna JD, Gazdar AF. Somatic mutations of the HER2 kinase domain in lung adenocarcinomas. Cancer Res 2005; 65:1642-6. [PMID: 15753357 DOI: 10.1158/0008-5472.can-04-4235] [Citation(s) in RCA: 510] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Mutations in the epidermal growth factor receptor gene (EGFR) in lung cancers predict for sensitivity to EGFR kinase inhibitors. HER2 (also known as NEU, EGFR2, or ERBB2) is a member of the EGFR family of receptor tyrosine kinases and plays important roles in the pathogenesis of certain human cancers, and mutations have recently been reported in lung cancers. We sequenced the tyrosine kinase domain of HER2 in 671 primary non-small cell lung cancers (NSCLC), 80 NSCLC cell lines, and 55 SCLCs and other neuroendocrine lung tumors as well as 85 other epithelial cancers (breast, bladder, prostate, and colorectal cancers) and compared the mutational status with clinicopathologic features and the presence of EGFR or KRAS mutations. HER2 mutations were present in 1.6% (11 of 671) of NSCLC and were absent in other types of cancers. Only one adenocarcinoma cell line (NCI-H1781) had a mutation. All HER2 mutations were in-frame insertions in exon 20 and target the identical corresponding region as did EGFR insertions. HER2 mutations were significantly more frequent in never smokers (3.2%, 8 of 248; P=0.02) and adenocarcinoma histology (2.8%, 11 of 394; P=0.003). In 394 adenocarcinoma cases, HER2 mutations preferentially targeted Oriental ethnicity (3.9%) compared with other ethnicities (0.7%), female gender (3.6%) compared with male gender (1.9%) and never smokers (4.1%) compared with smokers (1.4%). Mutations in EGFR, HER2, and KRAS genes were never present together in individual tumors and cell lines. The remarkable similarities of mutations in EGFR and HER2 genes involving tumor type and subtype, mutation type, gene location, and specific patient subpopulations targeted are unprecedented and suggest similar etiologic factors. EGFR, HER2, and KRAS mutations are mutually exclusive, suggesting different pathways to lung cancer in smokers and never smokers.
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Affiliation(s)
- Hisayuki Shigematsu
- Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, Texas 75390-8593, USA
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