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Mirhadi S, Zhang W, Pham NA, Karimzadeh F, Pintilie M, Tong J, Taylor P, Krieger J, Pitcher B, Sykes J, Wybenga-Groot L, Fladd C, Xu J, Wang T, Cabanero M, Li M, Weiss J, Sakashita S, Zaslaver O, Yu M, Caudy AA, St-Pierre J, Hawkins C, Kislinger T, Liu G, Shepherd FA, Tsao MS, Moran MF. Mitochondrial Aconitase ACO2 Links Iron Homeostasis with Tumorigenicity in Non-Small Cell Lung Cancer. Mol Cancer Res 2023; 21:36-50. [PMID: 36214668 PMCID: PMC9808373 DOI: 10.1158/1541-7786.mcr-22-0163] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 03/01/2022] [Revised: 08/08/2022] [Accepted: 10/03/2022] [Indexed: 02/03/2023]
Abstract
The ability of a patient tumor to engraft an immunodeficient mouse is the strongest known independent indicator of poor prognosis in early-stage non-small cell lung cancer (NSCLC). Analysis of primary NSCLC proteomes revealed low-level expression of mitochondrial aconitase (ACO2) in the more aggressive, engrafting tumors. Knockdown of ACO2 protein expression transformed immortalized lung epithelial cells, whereas upregulation of ACO2 in transformed NSCLC cells inhibited cell proliferation in vitro and tumor growth in vivo. High level ACO2 increased iron response element binding protein 1 (IRP1) and the intracellular labile iron pool. Impaired cellular proliferation associated with high level ACO2 was reversed by treatment of cells with an iron chelator, whereas increased cell proliferation associated with low level ACO2 was suppressed by treatment of cells with iron. Expression of CDGSH iron-sulfur (FeS) domain-containing protein 1 [CISD1; also known as mitoNEET (mNT)] was modulated by ACO2 expression level and inhibition of mNT by RNA interference or by treatment of cells with pioglitazone also increased iron and cell death. Hence, ACO2 is identified as a regulator of iron homeostasis and mNT is implicated as a target in aggressive NSCLC. IMPLICATIONS FeS cluster-associated proteins including ACO2, mNT (encoded by CISD1), and IRP1 (encoded by ACO1) are part of an "ACO2-Iron Axis" that regulates iron homeostasis and is a determinant of a particularly aggressive subset of NSCLC.
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Affiliation(s)
- Shideh Mirhadi
- Program in Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Wen Zhang
- Program in Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Nhu-An Pham
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | | | - Melania Pintilie
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Jiefei Tong
- Program in Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Paul Taylor
- Program in Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jonathan Krieger
- SPARC BioCentre, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Bethany Pitcher
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Jenna Sykes
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | | | - Christopher Fladd
- SPARC BioCentre, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jing Xu
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Tao Wang
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Michael Cabanero
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Ming Li
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Jessica Weiss
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Shingo Sakashita
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Olga Zaslaver
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Man Yu
- Program in Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Amy A. Caudy
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Julie St-Pierre
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Centre, McGill University, Montreal, Québec, Canada.,Department of Biochemistry, Microbiology, and Immunology and Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Cynthia Hawkins
- Program in Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Thomas Kislinger
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Geoffrey Liu
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Department of Medicine, Division of Medical Oncology, University of Toronto, Toronto, Ontario, Canada
| | - Frances A. Shepherd
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medicine, Division of Medical Oncology, University of Toronto, Toronto, Ontario, Canada
| | - Ming-Sound Tsao
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathology, University of Toronto, Toronto, Ontario, Canada.,Corresponding Authors: Michael F. Moran, Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada. Phone: 647-235-6435; E-mail: ; and Ming-Sound Tsao, Princess Margaret Cancer Research Tower, 101 College Street, Toronto, ON M5G 1L7, Canada. Phone: 416-340-4737; E-mail:
| | - Michael F. Moran
- Program in Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,SPARC BioCentre, Hospital for Sick Children, Toronto, Ontario, Canada.,Corresponding Authors: Michael F. Moran, Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada. Phone: 647-235-6435; E-mail: ; and Ming-Sound Tsao, Princess Margaret Cancer Research Tower, 101 College Street, Toronto, ON M5G 1L7, Canada. Phone: 416-340-4737; E-mail:
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2
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Ciereszko A, Dietrich MA, Słowińska M, Nynca J, Ciborowski M, Kaczmarek MM, Myszczyński K, Kiśluk J, Majewska A, Michalska-Falkowska A, Kodzik N, Reszeć J, Sierko E, Nikliński J. Application of two-dimensional difference gel electrophoresis to identify protein changes between center, margin, and adjacent non-tumor tissues obtained from non-small-cell lung cancer with adenocarcinoma or squamous cell carcinoma subtype. PLoS One 2022; 17:e0268073. [PMID: 35512017 PMCID: PMC9071164 DOI: 10.1371/journal.pone.0268073] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 01/13/2022] [Accepted: 04/21/2022] [Indexed: 12/12/2022] Open
Abstract
Lung cancer is responsible for the most cancer-related mortality worldwide and the mechanism of its development is poorly understood. Proteomics has become a powerful tool offering vital knowledge related to cancer development. Using a two-dimensional difference gel electrophoresis (2D-DIGE) approach, we sought to compare tissue samples from non-small-cell lung cancer (NSCLC) patients taken from the tumor center and tumor margin. Two subtypes of NSCLC, adenocarcinoma (ADC) and squamous cell carcinoma (SCC) were compared. Data are available via ProteomeXchange with identifier PXD032736 and PXD032962 for ADC and SCC, respectively. For ADC proteins, 26 significant canonical pathways were identified, including Rho signaling pathways, a semaphorin neuronal repulsive signaling pathway, and epithelial adherens junction signaling. For SCC proteins, nine significant canonical pathways were identified, including hypoxia-inducible factor-1α signaling, thyroid hormone biosynthesis, and phagosome maturation. Proteins differentiating the tumor center and tumor margin were linked to cancer invasion and progression, including cell migration, adhesion and invasion, cytoskeletal structure, protein folding, anaerobic metabolism, tumor angiogenesis, EMC transition, epithelial adherens junctions, and inflammatory responses. In conclusion, we identified several proteins that are important for the better characterization of tumor development and molecular specificity of both lung cancer subtypes. We also identified proteins that may be important as biomarkers and/or targets for anticancer therapy.
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Affiliation(s)
- Andrzej Ciereszko
- Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
- * E-mail:
| | - Mariola A. Dietrich
- Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | - Mariola Słowińska
- Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | - Joanna Nynca
- Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | - Michał Ciborowski
- Metabolomics Laboratory, Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
| | - Monika M. Kaczmarek
- Molecular Biology Laboratory, Institute of Animal Reproduction and Food Research Polish Academy of Sciences, Olsztyn, Poland
| | - Kamil Myszczyński
- Molecular Biology Laboratory, Institute of Animal Reproduction and Food Research Polish Academy of Sciences, Olsztyn, Poland
| | - Joanna Kiśluk
- Department of Clinical Molecular Biology, Medical University of Bialystok, Bialystok, Poland
| | - Anna Majewska
- Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | | | - Natalia Kodzik
- Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | - Joanna Reszeć
- Department of Medical Pathomorphology, Medical University of Bialystok, Bialystok, Poland
| | - Ewa Sierko
- Department of Oncology, Medical University of Bialystok, Bialystok, Poland
| | - Jacek Nikliński
- Department of Clinical Molecular Biology, Medical University of Bialystok, Bialystok, Poland
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3
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Zwicker F, Hauswald H, Weber KJ, Debus JÜ, Huber PE. In Vivo Evaluation of Combined CK2 Inhibition and Irradiation in Human WiDr Tumours. In Vivo 2021; 35:111-117. [PMID: 33402456 DOI: 10.21873/invivo.12238] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 10/17/2020] [Accepted: 10/21/2020] [Indexed: 11/10/2022]
Abstract
BACKGROUND/AIM Casein kinase 2 (CK2) which sustains multiple pro-survival functions in cellular DNA-damage response, is strictly regulated in normal cells but elevated in cancer. CK2 is considered as a potential therapeutic target, and its inhibition has been associated with radiosensitization in mammalian cells in vitro. Here, we investigated potential radiosensitization by CK2 inhibition in vivo. MATERIALS AND METHODS The effect of CK2 inhibition in vivo was investigated in human WiDr-xenograft tumours grown subcutaneously on BALB/c nu/nu mice with and without fractionated irradiation. CK2 inhibition was performed using the specific inhibitor tetra-bromobenzotriazole (TBB). Histological examinations included staining for apoptosis and double-strand breaks. RESULTS Both TBB treatment alone and radiation alone significantly reduced tumour growth, which was reflected by increased apoptosis rates. However, TBB treatment did not boost radiation-induced tumour growth suppression in combined treatment, although the apoptosis rate increased and repair of double-strand breaks was reduced. This was in stark contrast to previous data on in vitro radiosensitization. CONCLUSION The absence of radiosensitization by CK2 inhibition should be investigated in different tumour models.
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Affiliation(s)
- Felix Zwicker
- Department of Radiation Oncology, Heidelberg University Hospital, Heidelberg, Germany; .,Clinical Cooperation Unit Molecular Radiation Oncology, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Henrik Hauswald
- Department of Radiation Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Klaus-Josef Weber
- Department of Radiation Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - JÜrgen Debus
- Department of Radiation Oncology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Molecular Radiation Oncology, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Peter E Huber
- Department of Radiation Oncology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Molecular Radiation Oncology, German Cancer Research Centre (DKFZ), Heidelberg, Germany
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4
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Kurimchak AM, Kumar V, Herrera-Montávez C, Johnson KJ, Srivastava N, Davarajan K, Peri S, Cai KQ, Mantia-Smaldone GM, Duncan JS. Kinome Profiling of Primary Endometrial Tumors Using Multiplexed Inhibitor Beads and Mass Spectrometry Identifies SRPK1 as Candidate Therapeutic Target. Mol Cell Proteomics 2020; 19:2068-2090. [PMID: 32994315 PMCID: PMC7710141 DOI: 10.1074/mcp.ra120.002012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 09/15/2020] [Indexed: 12/11/2022] Open
Abstract
Endometrial carcinoma (EC) is the most common gynecologic malignancy in the United States, with limited effective targeted therapies. Endometrial tumors exhibit frequent alterations in protein kinases, yet only a small fraction of the kinome has been therapeutically explored. To identify kinase therapeutic avenues for EC, we profiled the kinome of endometrial tumors and normal endometrial tissues using Multiplexed Inhibitor Beads and Mass Spectrometry (MIB-MS). Our proteomics analysis identified a network of kinases overexpressed in tumors, including Serine/Arginine-Rich Splicing Factor Kinase 1 (SRPK1). Immunohistochemical (IHC) analysis of endometrial tumors confirmed MIB-MS findings and showed SRPK1 protein levels were highly expressed in endometrioid and uterine serous cancer (USC) histological subtypes. Moreover, querying large-scale genomics studies of EC tumors revealed high expression of SRPK1 correlated with poor survival. Loss-of-function studies targeting SRPK1 in an established USC cell line demonstrated SRPK1 was integral for RNA splicing, as well as cell cycle progression and survival under nutrient deficient conditions. Profiling of USC cells identified a compensatory response to SRPK1 inhibition that involved EGFR and the up-regulation of IGF1R and downstream AKT signaling. Co-targeting SRPK1 and EGFR or IGF1R synergistically enhanced growth inhibition in serous and endometrioid cell lines, representing a promising combination therapy for EC.
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Affiliation(s)
- Alison M Kurimchak
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
| | - Vikas Kumar
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
| | | | - Katherine J Johnson
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
| | - Nishi Srivastava
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
| | - Karthik Davarajan
- Biostatistics and Bioinformatics Facility, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
| | - Suraj Peri
- Biostatistics and Bioinformatics Facility, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
| | - Kathy Q Cai
- Histopathology Facility, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
| | - Gina M Mantia-Smaldone
- Division of Gynecologic Oncology, Department of Surgical Oncology, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
| | - James S Duncan
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA.
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5
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Zhuo H, Zhao Y, Cheng X, Xu M, Wang L, Lin L, Lyu Z, Hong X, Cai J. Tumor endothelial cell-derived cadherin-2 promotes angiogenesis and has prognostic significance for lung adenocarcinoma. Mol Cancer 2019; 18:34. [PMID: 30832661 PMCID: PMC6399986 DOI: 10.1186/s12943-019-0987-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [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: 02/26/2019] [Indexed: 12/31/2022] Open
Abstract
In lung cancer, antiangiogenic strategies targeting tumor-derived endothelial cells (TECs) afford a survival advantage, but the characteristics of TECs have not been comprehensively elucidated. Herein, high-purity (> 98%) TECs were obtained, and these cells retained expression of EC markers and exhibited high viability. ITRAQ-2DLC-MS/MS was performed to profile the proteome and the heterogeneity of ECs. Only 31 of 1820 identified proteins were differentially expressed between adenocarcinoma (ADC)- and squamous cell carcinoma (SCC)-derived TECs (TEC-A and TEC-S, respectively), and cadherin-2 (CDH2) was the most significantly upregulated protein in TEC-A samples. Positive immunostaining for CDH2 (score > 3) was significantly more frequent in the endothelium of ADC tissues than in that of SCC tissues. Loss- or gain-of-function analysis showed that CDH2 significantly promoted in vitro and in vivo angiogenesis and sensitivity to the antagonist exherin. The MAPK/ERK and MAPK/JNK signaling pathways may play crucial roles in CDH2-induced HIF-1α/VEGF-mediated angiogenesis. Moreover, high CDH2 expression in TECs was significantly associated with tumor stage, visceral pleural metastasis, and decreased overall survival in patients with ADC but not SCC. Together, these data indicate the importance of CDH2 in angiogenesis and highlight its potential both for antiangiogenic therapy and as a candidate prognostic marker for ADC.
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Affiliation(s)
- Huiqin Zhuo
- Department of Gastrointestinal Surgery, The Affiliated Zhongshan Hospital, Xiamen University, Xiamen, 361004, Fujian, China. .,Institute of Gastrointestinal Oncology, School of Medicine, Xiamen University, Xiamen, 361004, Fujian, China.
| | - Yan Zhao
- Central Laboratory, The First Hospital Affiliated to Xiamen University, Xiamen University, Xiamen, 361004, Fujian, China
| | - Xiao Cheng
- Respiratory Department, The Affiliated Zhongshan Hospital, Xiamen University, Xiamen, 361004, Fujian, China
| | - Mao Xu
- Department of Gastrointestinal Surgery, The Affiliated Zhongshan Hospital, Xiamen University, Xiamen, 361004, Fujian, China.,Institute of Gastrointestinal Oncology, School of Medicine, Xiamen University, Xiamen, 361004, Fujian, China
| | - Lin Wang
- Department of Gastrointestinal Surgery, The Affiliated Zhongshan Hospital, Xiamen University, Xiamen, 361004, Fujian, China.,Institute of Gastrointestinal Oncology, School of Medicine, Xiamen University, Xiamen, 361004, Fujian, China
| | - Lingyun Lin
- Department of Gastrointestinal Surgery, The Affiliated Zhongshan Hospital, Xiamen University, Xiamen, 361004, Fujian, China.,Institute of Gastrointestinal Oncology, School of Medicine, Xiamen University, Xiamen, 361004, Fujian, China
| | - Zhi Lyu
- Respiratory Department, The Affiliated Zhongshan Hospital, Xiamen University, Xiamen, 361004, Fujian, China
| | - Xuehui Hong
- Department of Gastrointestinal Surgery, The Affiliated Zhongshan Hospital, Xiamen University, Xiamen, 361004, Fujian, China. .,Institute of Gastrointestinal Oncology, School of Medicine, Xiamen University, Xiamen, 361004, Fujian, China.
| | - Jianchun Cai
- Department of Gastrointestinal Surgery, The Affiliated Zhongshan Hospital, Xiamen University, Xiamen, 361004, Fujian, China. .,Institute of Gastrointestinal Oncology, School of Medicine, Xiamen University, Xiamen, 361004, Fujian, China.
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6
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Abstract
Objective: The main objective in studying large-scale cancer omics is to identify molecular mechanisms of cancer and discover novel biomedical targets. This work not only discovers the cancer subtypes in genome scale data by using clustering and classification but also measures their accuracy. Methods: Initially, candidate cancer subtypes are recognized by max-flow/min-cut graph clustering. Finally, prognosis-enhanced neural network classifier is proposed for classification. We analyzed the heterogeneity and identified the subtypes of glioblastoma multiforme, an aggressive adult brain tumor, from 215 samples with microRNA expression (12 042 genes). The samples were classified into 4 different classes such as mesenchymal, classical, proneural, and neural subtypes owing to mutations and gene expression. The results are measured using the metrics such as silhouette width, biological stability index, clustering accuracy, precision, recall, and f-measure. Results: Max-flow/min-cut clustering produces higher clustering accuracy of 88.93% for 215 samples. The proposed prognosis-enhanced neural network classifier algorithm produces higher accuracy results of 89.2% for 215 samples efficiently. Conclusion: From the experimental results, the proposed prognosis-enhanced neural network classifier is seen as an alternative, which is full of promise for cancer subtype prediction in genome scale data.
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Affiliation(s)
| | - Thangamani Murugesan
- 2 Department of Computer Science and Engineering, Kongu Engineering College, Perundurai, Tamilnadu, India
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7
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Zeng Y, Wang S, Gao S, Soares F, Ahmed M, Guo H, Wang M, Hua JT, Guan J, Moran MF, Tsao MS, He HH. Refined RIP-seq protocol for epitranscriptome analysis with low input materials. PLoS Biol 2018; 16:e2006092. [PMID: 30212448 PMCID: PMC6136692 DOI: 10.1371/journal.pbio.2006092] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 08/01/2018] [Indexed: 11/18/2022] Open
Abstract
N6-Methyladenosine (m6A) accounts for approximately 0.2% to 0.6% of all adenosine in mammalian mRNA, representing the most abundant internal mRNA modifications. m6A RNA immunoprecipitation followed by high-throughput sequencing (MeRIP-seq) is a powerful technique to map the m6A location transcriptome-wide. However, this method typically requires 300 μg of total RNA, which limits its application to patient tumors. In this study, we present a refined m6A MeRIP-seq protocol and analysis pipeline that can be applied to profile low-input RNA samples from patient tumors. We optimized the key parameters of m6A MeRIP-seq, including the starting amount of RNA, RNA fragmentation, antibody selection, MeRIP washing/elution conditions, methods for RNA library construction, and the bioinformatics analysis pipeline. With the optimized immunoprecipitation (IP) conditions and a postamplification rRNA depletion strategy, we were able to profile the m6A epitranscriptome using 500 ng of total RNA. We identified approximately 12,000 m6A peaks with a high signal-to-noise (S/N) ratio from 2 lung adenocarcinoma (ADC) patient tumors. Through integrative analysis of the transcriptome, m6A epitranscriptome, and proteome data in the same patient tumors, we identified dynamics at the m6A level that account for the discordance between mRNA and protein levels in these tumors. The refined m6A MeRIP-seq method is suitable for m6A epitranscriptome profiling in a limited amount of patient tumors, setting the ground for unraveling the dynamics of the m6A epitranscriptome and the underlying mechanisms in clinical settings. N6-Methyladenosine (m6A) is one of the most abundant and conserved mRNA modifications. It has been reported to influence multiple steps of RNA life cycle and play an important role in the initiation and progression of human cancers. m6A RNA immunoprecipitation followed by high-throughput sequencing (MeRIP-seq) is a powerful technique to map the m6A location transcriptome-wide. However, this method typically requires 300 μg of total RNA, which limits its application to patient tumors. In this study, we presented an optimized MeRIP-seq protocol that allows us to profile m6A epitranscriptiome using as low as 500 ng of total RNA. By applying our refined protocol to 2 lung cancer patient tumors and integrating with proteomic data, we identified dynamics at the m6A level that account for the discordance between mRNA and protein levels in these tumors.
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Affiliation(s)
- Yong Zeng
- Princess Margaret Cancer Centre/University Health Network, Toronto, Ontario, Canada
| | - Shiyan Wang
- Princess Margaret Cancer Centre/University Health Network, Toronto, Ontario, Canada
| | - Shanshan Gao
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong
| | - Fraser Soares
- Princess Margaret Cancer Centre/University Health Network, Toronto, Ontario, Canada
| | - Musadeqque Ahmed
- Princess Margaret Cancer Centre/University Health Network, Toronto, Ontario, Canada
| | - Haiyang Guo
- Princess Margaret Cancer Centre/University Health Network, Toronto, Ontario, Canada
| | - Miranda Wang
- Princess Margaret Cancer Centre/University Health Network, Toronto, Ontario, Canada
| | - Junjie Tony Hua
- Princess Margaret Cancer Centre/University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Jiansheng Guan
- Princess Margaret Cancer Centre/University Health Network, Toronto, Ontario, Canada
- College of Electrical Engineering and Automation, Xiamen University of Technology, Xiamen, China
| | - Michael F. Moran
- Princess Margaret Cancer Centre/University Health Network, Toronto, Ontario, Canada
- Program in Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Ming Sound Tsao
- Princess Margaret Cancer Centre/University Health Network, Toronto, Ontario, Canada
- Campbell Family Institute for Cancer Research, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Housheng Hansen He
- Princess Margaret Cancer Centre/University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- * E-mail:
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8
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Stewart PA, Fang B, Slebos RJC, Zhang G, Borne AL, Fellows K, Teer JK, Chen YA, Welsh E, Eschrich SA, Haura EB, Koomen JM. Relative protein quantification and accessible biology in lung tumor proteomes from four LC-MS/MS discovery platforms. Proteomics 2017; 17. [PMID: 28195392 DOI: 10.1002/pmic.201600300] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Revised: 01/31/2017] [Accepted: 02/03/2017] [Indexed: 01/01/2023]
Abstract
Discovery proteomics experiments include many options for sample preparation and MS data acquisition, which are capable of creating datasets for quantifying thousands of proteins. To define a strategy that would produce a dataset with sufficient content while optimizing required resources, we compared (1) single-sample LC-MS/MS with data-dependent acquisition to single-sample LC-MS/MS with data-independent acquisition and (2) peptide fractionation with label-free (LF) quantification to peptide fractionation with relative quantification of chemically labeled peptides (sixplex tandem mass tags (TMT)). These strategies were applied to the same set of four frozen lung squamous cell carcinomas and four adjacent tissues, and the overall outcomes of each experiment were assessed. We identified 6656 unique protein groups with LF, 5535 using TMT, 3409 proteins from single-sample analysis with data-independent acquisition, and 2219 proteins from single-sample analysis with data-dependent acquisition. Pathway analysis indicated the number of proteins per pathway was proportional to the total protein identifications from each method, suggesting limited biological bias between experiments. The results suggest the use of single-sample experiments as a rapid tissue assessment tool and digestion quality control or as a technique to maximize output from limited samples and use of TMT or LF quantification as methods for larger amounts of tumor tissue with the selection being driven mainly by instrument time limitations. Data are available via ProteomeXchange with identifiers PXD004682, PXD004683, PXD004684, and PXD005733.
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Affiliation(s)
- Paul A Stewart
- Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Bin Fang
- Proteomics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Robbert J C Slebos
- Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Guolin Zhang
- Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Adam L Borne
- Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Katherine Fellows
- Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Jamie K Teer
- Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Y Ann Chen
- Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Eric Welsh
- Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Steven A Eschrich
- Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Eric B Haura
- Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - John M Koomen
- Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
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9
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Adlung L, Kar S, Wagner MC, She B, Chakraborty S, Bao J, Lattermann S, Boerries M, Busch H, Wuchter P, Ho AD, Timmer J, Schilling M, Höfer T, Klingmüller U. Protein abundance of AKT and ERK pathway components governs cell type-specific regulation of proliferation. Mol Syst Biol 2017; 13:904. [PMID: 28123004 PMCID: PMC5293153 DOI: 10.15252/msb.20167258] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [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] [Indexed: 11/18/2022] Open
Abstract
Signaling through the AKT and ERK pathways controls cell proliferation. However, the integrated regulation of this multistep process, involving signal processing, cell growth and cell cycle progression, is poorly understood. Here, we study different hematopoietic cell types, in which AKT and ERK signaling is triggered by erythropoietin (Epo). Although these cell types share the molecular network topology for pro‐proliferative Epo signaling, they exhibit distinct proliferative responses. Iterating quantitative experiments and mathematical modeling, we identify two molecular sources for cell type‐specific proliferation. First, cell type‐specific protein abundance patterns cause differential signal flow along the AKT and ERK pathways. Second, downstream regulators of both pathways have differential effects on proliferation, suggesting that protein synthesis is rate‐limiting for faster cycling cells while slower cell cycles are controlled at the G1‐S progression. The integrated mathematical model of Epo‐driven proliferation explains cell type‐specific effects of targeted AKT and ERK inhibitors and faithfully predicts, based on the protein abundance, anti‐proliferative effects of inhibitors in primary human erythroid progenitor cells. Our findings suggest that the effectiveness of targeted cancer therapy might become predictable from protein abundance.
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Affiliation(s)
- Lorenz Adlung
- Division of Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sandip Kar
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,BioQuant Center, University of Heidelberg, Heidelberg, Germany.,Department of Chemistry, Indian Institute of Technology, Mumbai, India
| | - Marie-Christine Wagner
- Division of Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Bin She
- Division of Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sajib Chakraborty
- Division of Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jie Bao
- Systems Biology of the Cellular Microenvironment Group, IMMZ, ALU, Freiburg, Germany
| | - Susen Lattermann
- Division of Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Melanie Boerries
- Systems Biology of the Cellular Microenvironment Group, IMMZ, ALU, Freiburg, Germany.,German Cancer Consortium (DKTK), Freiburg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hauke Busch
- Systems Biology of the Cellular Microenvironment Group, IMMZ, ALU, Freiburg, Germany.,German Cancer Consortium (DKTK), Freiburg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Patrick Wuchter
- Department of Medicine V, University of Heidelberg, Heidelberg, Germany.,Institute for Transfusion Medicine and Immunology, University of Heidelberg, Mannheim, Germany
| | - Anthony D Ho
- Department of Medicine V, University of Heidelberg, Heidelberg, Germany
| | - Jens Timmer
- Center for Biological Signaling Studies (BIOSS), Institute of Physics, University of Freiburg, Freiburg, Germany
| | - Marcel Schilling
- Division of Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Thomas Höfer
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany .,BioQuant Center, University of Heidelberg, Heidelberg, Germany
| | - Ursula Klingmüller
- Division of Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), Heidelberg, Germany .,Translational Lung Research Center (TLRC), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
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10
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Korrodi-Gregório L, Soto-Cerrato V, Vitorino R, Fardilha M, Pérez-Tomás R. From Proteomic Analysis to Potential Therapeutic Targets: Functional Profile of Two Lung Cancer Cell Lines, A549 and SW900, Widely Studied in Pre-Clinical Research. PLoS One 2016; 11:e0165973. [PMID: 27814385 DOI: 10.1371/journal.pone.0165973] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 10/20/2016] [Indexed: 12/18/2022] Open
Abstract
Lung cancer is a serious health problem and the leading cause of cancer death worldwide. The standard use of cell lines as in vitro pre-clinical models to study the molecular mechanisms that drive tumorigenesis and access drug sensitivity/effectiveness is of undisputable importance. Label-free mass spectrometry and bioinformatics were employed to study the proteomic profiles of two representative lung cancer cell lines and to unravel the specific biological processes. Adenocarcinoma A549 cells were enriched in proteins related to cellular respiration, ubiquitination, apoptosis and response to drug/hypoxia/oxidative stress. In turn, squamous carcinoma SW900 cells were enriched in proteins related to translation, apoptosis, response to inorganic/organic substances and cytoskeleton organization. Several proteins with differential expression were related to cancer transformation, tumor resistance, proliferation, migration, invasion and metastasis. Combined analysis of proteome and interactome data highlighted key proteins and suggested that adenocarcinoma might be more prone to PI3K/Akt/mTOR and topoisomerase IIα inhibitors, and squamous carcinoma to Ck2 inhibitors. Moreover, ILF3 overexpression in adenocarcinoma, and PCNA and NEDD8 in squamous carcinoma shows them as promising candidates for therapeutic purposes. This study highlights the functional proteomic differences of two main subtypes of lung cancer models and hints several targeted therapies that might assist in this type of cancer.
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11
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Kriegsmann M, Casadonte R, Kriegsmann J, Dienemann H, Schirmacher P, Hendrik Kobarg J, Schwamborn K, Stenzinger A, Warth A, Weichert W. Reliable Entity Subtyping in Non-small Cell Lung Cancer by Matrix-assisted Laser Desorption/Ionization Imaging Mass Spectrometry on Formalin-fixed Paraffin-embedded Tissue Specimens. Mol Cell Proteomics 2016; 15:3081-3089. [PMID: 27473201 PMCID: PMC5054336 DOI: 10.1074/mcp.m115.057513] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 07/27/2016] [Indexed: 12/24/2022] Open
Abstract
Histopathological subtyping of non-small cell lung cancer (NSCLC) into adenocarcinoma (ADC), and squamous cell carcinoma (SqCC) is of utmost relevance for treatment stratification. However, current immunohistochemistry (IHC) based typing approaches on biopsies are imperfect, therefore novel analytical methods for reliable subtyping are needed. We analyzed formalin-fixed paraffin-embedded tissue cores of NSCLC by Matrix-assisted laser desorption/ionization (MALDI) imaging on tissue microarrays to identify and validate discriminating MALDI imaging profiles for NSCLC subtyping. 110 ADC and 98 SqCC were used to train a Linear Discriminant Analysis (LDA) model. Results were validated on a separate set of 58 ADC and 60 SqCC. Selected differentially expressed proteins were identified by tandem mass spectrometry and validated by IHC. The LDA classification model incorporated 339 m/z values. In the validation cohort, in 117 cases (99.1%) MALDI classification on tissue cores was in accordance with the pathological diagnosis made on resection specimen. Overall, three cases in the combined cohorts were discordant, after reevaluation two were initially misclassified by pathology whereas one was classified incorrectly by MALDI. Identification of differentially expressed peptides detected well-known IHC discriminators (CK5, CK7), but also less well known differentially expressed proteins (CK15, HSP27). In conclusion, MALDI imaging on NSCLC tissue cores as small biopsy equivalents is capable to discriminate lung ADC and SqCC with a very high accuracy. In addition, replacing multislide IHC by an one-slide MALDI approach may also save tissue for subsequent predictive molecular testing. We therefore advocate to pursue routine diagnostic implementation strategies for MALDI imaging in solid tumor typing.
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Affiliation(s)
- Mark Kriegsmann
- From the ‡Institute of Pathology, University Heidelberg, 69120 Heidelberg, Germany;
| | | | - Jörg Kriegsmann
- §Proteopath GmbH, 54296 Trier, Germany; ¶Center for Histology, Cytology and Molecular Diagnostics, 54296 Trier, Germany
| | - Hendrik Dienemann
- ‖Department of Thoracic Surgery, Thoraxklinik at Heidelberg University, 69126 Heidelberg, Germany
| | - Peter Schirmacher
- From the ‡Institute of Pathology, University Heidelberg, 69120 Heidelberg, Germany
| | | | - Kristina Schwamborn
- ‡‡Institute of Pathology, Technical University Munich (TUM), 81675 Munich, Germany
| | - Albrecht Stenzinger
- From the ‡Institute of Pathology, University Heidelberg, 69120 Heidelberg, Germany; §§German Cancer Consortium (DKTK)
| | - Arne Warth
- From the ‡Institute of Pathology, University Heidelberg, 69120 Heidelberg, Germany; ¶¶Translational Lung Research Centre Heidelberg, Member of the German Centre for Lung Research
| | - Wilko Weichert
- From the ‡Institute of Pathology, University Heidelberg, 69120 Heidelberg, Germany; ‡‡Institute of Pathology, Technical University Munich (TUM), 81675 Munich, Germany; §§German Cancer Consortium (DKTK); ‖‖National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany
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12
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Marrugal Á, Ojeda L, Paz-Ares L, Molina-Pinelo S, Ferrer I. Proteomic-Based Approaches for the Study of Cytokines in Lung Cancer. Dis Markers 2016; 2016:2138627. [PMID: 27445423 DOI: 10.1155/2016/2138627] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 06/12/2016] [Indexed: 02/06/2023]
Abstract
Proteomic techniques are currently used to understand the biology of different human diseases, including studies of the cell signaling pathways implicated in cancer progression, which is important in knowing the roles of different proteins in tumor development. Due to its poor prognosis, proteomic approaches are focused on the identification of new biomarkers for the early diagnosis, prognosis, and targeted treatment of lung cancer. Cytokines are proteins involved in inflammatory processes and have been proposed as lung cancer biomarkers and therapeutic targets because it has been reported that some cytokines play important roles in tumor development, invasion, and metastasis. In this review, we aim to summarize the different proteomic techniques used to discover new lung cancer biomarkers and therapeutic targets. Several cytokines have been identified as important players in lung cancer using these techniques. We underline the most important cytokines that are useful as biomarkers and therapeutic targets. We also summarize some of the therapeutic strategies targeted for these cytokines in lung cancer.
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13
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Lazar C, Gatto L, Ferro M, Bruley C, Burger T. Accounting for the Multiple Natures of Missing Values in Label-Free Quantitative Proteomics Data Sets to Compare Imputation Strategies. J Proteome Res 2016; 15:1116-25. [DOI: 10.1021/acs.jproteome.5b00981] [Citation(s) in RCA: 232] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Cosmin Lazar
- Univ. Grenoble Alpes, iRTSV-BGE, F-38000 Grenoble, France
- CEA, iRTSV-BGE, F-38000 Grenoble, France
- INSERM, BGE, F-38000 Grenoble, France
| | - Laurent Gatto
- Computational Proteomics Unit, Cambridge CB2 1GA, United Kingdom
- Cambridge Center for Proteomics, Cambridge CB2 1GA, United Kingdom
| | - Myriam Ferro
- Univ. Grenoble Alpes, iRTSV-BGE, F-38000 Grenoble, France
- CEA, iRTSV-BGE, F-38000 Grenoble, France
- INSERM, BGE, F-38000 Grenoble, France
| | - Christophe Bruley
- Univ. Grenoble Alpes, iRTSV-BGE, F-38000 Grenoble, France
- CEA, iRTSV-BGE, F-38000 Grenoble, France
- INSERM, BGE, F-38000 Grenoble, France
| | - Thomas Burger
- Univ. Grenoble Alpes, iRTSV-BGE, F-38000 Grenoble, France
- CNRS, iRTSV-BGE, F-38000 Grenoble, France
- CEA, iRTSV-BGE, F-38000 Grenoble, France
- INSERM, BGE, F-38000 Grenoble, France
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14
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Pozniak Y, Balint-lahat N, Rudolph J, Lindskog C, Katzir R, Avivi C, Pontén F, Ruppin E, Barshack I, Geiger T. System-wide Clinical Proteomics of Breast Cancer Reveals Global Remodeling of Tissue Homeostasis. Cell Syst 2016; 2:172-84. [DOI: 10.1016/j.cels.2016.02.001] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 11/24/2015] [Accepted: 01/30/2016] [Indexed: 12/30/2022]
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15
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Abstract
High-throughput genomic and proteomic studies have generated near-comprehensive catalogs of biological constituents within many model systems. Nevertheless, static catalogs are often insufficient to fully describe the dynamic processes that drive biology. Quantitative proteomic techniques address this need by providing insight into closely related biological states such as the stages of a therapeutic response or cellular differentiation. The maturation of quantitative proteomics in recent years has brought about a variety of technologies, each with their own strengths and weaknesses. It can be difficult for those unfamiliar with this evolving landscape to match the experiment at hand with the best tool for the job. Here, we outline quantitative methods for proteomic mass spectrometry and discuss their benefits and weaknesses from the perspective of the biologist aiming to generate meaningful data and address mechanistic questions.
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Affiliation(s)
- Corey E Bakalarski
- From the Departments of ‡Protein Chemistry and §Bioinformatics and Computational Biology, Genentech, Inc., South San Francisco, California 94080
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16
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Stewart PA, Parapatics K, Welsh EA, Müller AC, Cao H, Fang B, Koomen JM, Eschrich SA, Bennett KL, Haura EB. A Pilot Proteogenomic Study with Data Integration Identifies MCT1 and GLUT1 as Prognostic Markers in Lung Adenocarcinoma. PLoS One 2015; 10:e0142162. [PMID: 26539827 PMCID: PMC4634858 DOI: 10.1371/journal.pone.0142162] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [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: 07/29/2015] [Accepted: 10/19/2015] [Indexed: 11/19/2022] Open
Abstract
We performed a pilot proteogenomic study to compare lung adenocarcinoma to lung squamous cell carcinoma using quantitative proteomics (6-plex TMT) combined with a customized Affymetrix GeneChip. Using MaxQuant software, we identified 51,001 unique peptides that mapped to 7,241 unique proteins and from these identified 6,373 genes with matching protein expression for further analysis. We found a minor correlation between gene expression and protein expression; both datasets were able to independently recapitulate known differences between the adenocarcinoma and squamous cell carcinoma subtypes. We found 565 proteins and 629 genes to be differentially expressed between adenocarcinoma and squamous cell carcinoma, with 113 of these consistently differentially expressed at both the gene and protein levels. We then compared our results to published adenocarcinoma versus squamous cell carcinoma proteomic data that we also processed with MaxQuant. We selected two proteins consistently overexpressed in squamous cell carcinoma in all studies, MCT1 (SLC16A1) and GLUT1 (SLC2A1), for further investigation. We found differential expression of these same proteins at the gene level in our study as well as in other public gene expression datasets. These findings combined with survival analysis of public datasets suggest that MCT1 and GLUT1 may be potential prognostic markers in adenocarcinoma and druggable targets in squamous cell carcinoma. Data are available via ProteomeXchange with identifier PXD002622.
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Affiliation(s)
- Paul A. Stewart
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America 33612
| | - Katja Parapatics
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090 Vienna, Austria
| | - Eric A. Welsh
- Cancer Informatics Core Facility, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America 33612
| | - André C. Müller
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090 Vienna, Austria
| | - Haoyun Cao
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America 33612
| | - Bin Fang
- Proteomics Core Facility, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America 33612
| | - John M. Koomen
- Proteomics Core Facility, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America 33612
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America 33612
| | - Steven A. Eschrich
- Cancer Informatics Core Facility, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America 33612
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America 33612
| | - Keiryn L. Bennett
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090 Vienna, Austria
| | - Eric B. Haura
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America 33612
- * E-mail:
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17
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Chen X, Wei S, Ji Y, Guo X, Yang F. Quantitative proteomics using SILAC: Principles, applications, and developments. Proteomics 2015; 15:3175-92. [DOI: 10.1002/pmic.201500108] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 04/24/2015] [Accepted: 06/08/2015] [Indexed: 12/21/2022]
Affiliation(s)
- Xiulan Chen
- Key Laboratory of Protein and Peptide Pharmaceuticals and Laboratory of Proteomics; Institute of Biophysics; Chinese Academy of Sciences; Beijing P. R. China
| | - Shasha Wei
- Key Laboratory of Protein and Peptide Pharmaceuticals and Laboratory of Proteomics; Institute of Biophysics; Chinese Academy of Sciences; Beijing P. R. China
| | - Yanlong Ji
- Key Laboratory of Protein and Peptide Pharmaceuticals and Laboratory of Proteomics; Institute of Biophysics; Chinese Academy of Sciences; Beijing P. R. China
- University of Chinese Academy of Sciences; Beijing P. R. China
| | - Xiaojing Guo
- Key Laboratory of Protein and Peptide Pharmaceuticals and Laboratory of Proteomics; Institute of Biophysics; Chinese Academy of Sciences; Beijing P. R. China
| | - Fuquan Yang
- Key Laboratory of Protein and Peptide Pharmaceuticals and Laboratory of Proteomics; Institute of Biophysics; Chinese Academy of Sciences; Beijing P. R. China
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18
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Koh HWL, Swa HLF, Fermin D, Ler SG, Gunaratne J, Choi H. EBprot: Statistical analysis of labeling-based quantitative proteomics data. Proteomics 2015; 15:2580-91. [PMID: 25913743 DOI: 10.1002/pmic.201400620] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 02/26/2015] [Accepted: 04/14/2015] [Indexed: 11/07/2022]
Abstract
Labeling-based proteomics is a powerful method for detection of differentially expressed proteins (DEPs). The current data analysis platform typically relies on protein-level ratios, which is obtained by summarizing peptide-level ratios for each protein. In shotgun proteomics, however, some proteins are quantified with more peptides than others, and this reproducibility information is not incorporated into the differential expression (DE) analysis. Here, we propose a novel probabilistic framework EBprot that directly models the peptide-protein hierarchy and rewards the proteins with reproducible evidence of DE over multiple peptides. To evaluate its performance with known DE states, we conducted a simulation study to show that the peptide-level analysis of EBprot provides better receiver-operating characteristic and more accurate estimation of the false discovery rates than the methods based on protein-level ratios. We also demonstrate superior classification performance of peptide-level EBprot analysis in a spike-in dataset. To illustrate the wide applicability of EBprot in different experimental designs, we applied EBprot to a dataset for lung cancer subtype analysis with biological replicates and another dataset for time course phosphoproteome analysis of EGF-stimulated HeLa cells with multiplexed labeling. Through these examples, we show that the peptide-level analysis of EBprot is a robust alternative to the existing statistical methods for the DE analysis of labeling-based quantitative datasets. The software suite is freely available on the Sourceforge website http://ebprot.sourceforge.net/. All MS data have been deposited in the ProteomeXchange with identifier PXD001426 (http://proteomecentral.proteomexchange.org/dataset/PXD001426/).
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Affiliation(s)
- Hiromi W L Koh
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore
| | - Hannah L F Swa
- Institute of Molecular and Cell Biology, A*STAR, Singapore
| | - Damian Fermin
- Department of Pathology, Yale University, New Haven, CT, USA
| | - Siok Ghee Ler
- Institute of Molecular and Cell Biology, A*STAR, Singapore
| | - Jayantha Gunaratne
- Institute of Molecular and Cell Biology, A*STAR, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Hyungwon Choi
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore.,Institute of Molecular and Cell Biology, A*STAR, Singapore
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19
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Abstract
Large-scale transcriptome and epigenome analyses have been widely utilized to discover gene alterations implicated in cancer development at the genetic level. However, mapping of signaling dynamics at the protein level is likely to be more insightful and needed to complement massive genomic data. Stable isotope labeling with amino acids in cell culture (SILAC)-based proteomic analysis represents one of the most promising comparative quantitative methods that has been extensively employed in proteomic research. This technology allows for global, robust and confident identification and quantification of signal perturbations important for the progress of human diseases, particularly malignancies. The present review summarizes the latest applications of in vitro and in vivo SILAC-based proteomics in identifying global proteome/phosphoproteome and genome-wide protein-protein interactions that contribute to oncogenesis, highlighting the recent advances in dissecting signaling dynamics in cancer.
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Affiliation(s)
- Hua Zhang
- Department of Surgery and Cancer, Division of Cancer, Imperial College London, Hammersmith Hospital Campus, ICTEM Building, Du Cane Road, London, W12 ONN, UK
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20
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Li L, Wei Y, To C, Zhu CQ, Tong J, Pham NA, Taylor P, Ignatchenko V, Ignatchenko A, Zhang W, Wang D, Yanagawa N, Li M, Pintilie M, Liu G, Muthuswamy L, Shepherd FA, Tsao MS, Kislinger T, Moran MF. Integrated Omic analysis of lung cancer reveals metabolism proteome signatures with prognostic impact. Nat Commun 2014; 5:5469. [DOI: 10.1038/ncomms6469] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Accepted: 10/03/2014] [Indexed: 11/09/2022] Open
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21
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Haenen S, Clynen E, Nemery B, Hoet PH, Vanoirbeek JA. Biomarker discovery in asthma and COPD: Application of proteomics techniques in human and mice. EuPA Open Proteomics 2014. [DOI: 10.1016/j.euprot.2014.04.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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22
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Hollenberg MD. KLKs and their hormone-like signaling actions: a new life for the PSA-KLK family. Biol Chem 2014; 395:915-29. [DOI: 10.1515/hsz-2014-0123] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 04/23/2014] [Indexed: 11/15/2022]
Abstract
Abstract
Human kallikrein-related peptidases (KLKs), including the well-known prostate cancer biomarker, prostate-specific antigen (PSA-KLK3), along with 14 other serine proteinase KLK family members are now known to regulate cells by cleaving and activating members of the G-protein-coupled proteinase-activated receptor (PAR) family. This hormone-like signaling action of the KLKs has provided a new perspective for understanding the biological roles that KLKs may play in normal and pathophysiological settings. This overview summarizes the circumstances leading up to the discovery of this action of the KLKs and provides an overview of the diverse impact on tissue function that may result from KLK-triggered PAR activation.
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