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Miao L, Wu D, Zhao H, Xie A. TIMM17A overexpression in lung adenocarcinoma and its association with prognosis. Sci Rep 2024; 14:8840. [PMID: 38632467 PMCID: PMC11024209 DOI: 10.1038/s41598-024-59526-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 04/11/2024] [Indexed: 04/19/2024] Open
Abstract
Lung adenocarcinoma (LUAD), a leading cause of cancer-related mortality worldwide, demands a deeper understanding of its molecular mechanisms and the identification of reliable biomarkers for better diagnosis and targeted therapy. Leveraging data from the Cancer Genome Atlas (TCGA), the Clinical Proteomic Tumor Analysis Consortium (CPTAC), and the Human Protein Atlas (HPA), we investigated the mRNA and protein expression profiles of TIMM17A and assessed its prognostic significance through Kaplan-Meier survival curves and Cox regression analysis. Through Gene Set Enrichment Analysis, we explored the regulatory mechanisms of TIMM17A in LUAD progression and demonstrated its role in modulating the proliferative capacity of A549 cells, a type of LUAD cell, via in vitro experiments. Our results indicate that TIMM17A is significantly upregulated in LUAD tissues, correlating with clinical staging, lymph node metastasis, overall survival, and progression-free survival, thereby establishing it as a critical independent prognostic factor. The construction of a nomogram model further enhances our ability to predict patient outcomes. Knockdown of TIMM17A inhibited the growth of LUAD cells. The potential of TIMM17A as a biomarker and therapeutic target for LUAD presents a promising pathway for improving patient diagnosis and treatment strategies.
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Affiliation(s)
- Lili Miao
- Department of Respiration, YiZheng People's Hospital, YiZheng, Jiangsu, China
| | - Dejun Wu
- Department of Respiration, YiZheng People's Hospital, YiZheng, Jiangsu, China
| | - Hongyu Zhao
- Department of Respiration, YiZheng People's Hospital, YiZheng, Jiangsu, China
| | - Aiwei Xie
- Department of Nephrology, YiZheng People's Hospital, YiZheng, Jiangsu, China.
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2
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Czegle I, Huang C, Soria PG, Purkiss DW, Shields A, Wappler-Guzzetta EA. The Role of Genetic Mutations in Mitochondrial-Driven Cancer Growth in Selected Tumors: Breast and Gynecological Malignancies. Life (Basel) 2023; 13:996. [PMID: 37109525 PMCID: PMC10145875 DOI: 10.3390/life13040996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 03/15/2023] [Accepted: 03/31/2023] [Indexed: 04/29/2023] Open
Abstract
There is an increasing understanding of the molecular and cytogenetic background of various tumors that helps us better conceptualize the pathogenesis of specific diseases. Additionally, in many cases, these molecular and cytogenetic alterations have diagnostic, prognostic, and/or therapeutic applications that are heavily used in clinical practice. Given that there is always room for improvement in cancer treatments and in cancer patient management, it is important to discover new therapeutic targets for affected individuals. In this review, we discuss mitochondrial changes in breast and gynecological (endometrial and ovarian) cancers. In addition, we review how the frequently altered genes in these diseases (BRCA1/2, HER2, PTEN, PIK3CA, CTNNB1, RAS, CTNNB1, FGFR, TP53, ARID1A, and TERT) affect the mitochondria, highlighting the possible associated individual therapeutic targets. With this approach, drugs targeting mitochondrial glucose or fatty acid metabolism, reactive oxygen species production, mitochondrial biogenesis, mtDNA transcription, mitophagy, or cell death pathways could provide further tailored treatment.
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Affiliation(s)
- Ibolya Czegle
- Department of Internal Medicine and Haematology, Semmelweis University, H-1085 Budapest, Hungary
| | - Chelsea Huang
- Department of Pathology and Laboratory Medicine, Loma Linda University Health, Loma Linda, CA 92354, USA
| | - Priscilla Geraldine Soria
- Department of Pathology and Laboratory Medicine, Loma Linda University Health, Loma Linda, CA 92354, USA
| | - Dylan Wesley Purkiss
- Department of Pathology and Laboratory Medicine, Loma Linda University Health, Loma Linda, CA 92354, USA
| | - Andrea Shields
- Department of Pathology and Laboratory Medicine, Loma Linda University Health, Loma Linda, CA 92354, USA
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3
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Mitochondrial targeting theranostic nanomedicine and molecular biomarkers for efficient cancer diagnosis and therapy. Biomed Pharmacother 2022; 153:113451. [DOI: 10.1016/j.biopha.2022.113451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/12/2022] [Accepted: 07/18/2022] [Indexed: 01/10/2023] Open
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4
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Cai J, Chen J, Huang L, Wang C, Zhang W, Zhou Q, Sun Z. A TIMM17A Regulatory Network Contributing to Breast Cancer. Front Genet 2021; 12:658154. [PMID: 34421983 PMCID: PMC8375323 DOI: 10.3389/fgene.2021.658154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 06/15/2021] [Indexed: 01/11/2023] Open
Abstract
Background Translocase of inner mitochondrial membrane 17A (TIMM17A) is overexpressed in breast cancer (BRCA), and upregulation can increase the aggressiveness of BRCA cells. This study examined the influence of the TIMM17A gene network on BRCA outcome. Methods Expression levels of TIMM17A were compared between normal and tumor tissues from the OncomineTM database, and the association with patient survival was analyzed using Kaplan–Meier Plotter. Clinical factors influencing TIMM17A expression were studied by UALCAN. cBioPotal was then used to identify genes interacting with TIMM17A, and network relationships were assessed using the R clusterProfiler package. The association between TIMM17A mutation and mRNA expression in BRCA was examined using the LinkFinder application in LinkedOmics, and coexpressed genes were assessed for functional enrichment using the LinkInterpreter application. Furthermore, TIMM17A expression correlation with cell cycle phase distribution was performed by flow cytometry. Finally, the target networks of kinases, microRNAs (miRNAs), and transcription factors were identified using GeneMANIA. The expression and correlation of potential miRNAs and targets were further validated in BRCA cell lines by qRT-PCR. Results Expression of TIMM17A was significantly elevated in BRCA compared with normal tissue (p < 0.05), and overexpression was associated with both poor overall survival (OS) and shorter distant metastasis-free survival (DMFS) (p < 0.05). Expression of TIMM17A was not associated with age, sex, BRCA subclass, clinical stage, or patient ethnicity. The coexpressed TIMM17A network was enriched in genes targeted by cell cycle regulators such as CDK1, miR-331, and E2F family transcription factors (FDR < 0.001). Furthermore, flow cytometry revealed a strong association between higher TIMM17A expression and faster cell cycle progression in these BRCA cell lines. In addition, expression of TIMM17A protein was correlated with CDK1 protein expression in BRCA cell lines as measured by western blotting. Conclusion Elevated TIMM17A expression accelerates the progression of BRCA, thereby reducing OS and DMFS. The TIMM17A-associated networks identified here provide clues to the molecular pathogenesis of BRCA and potential targets for BRCA treatment.
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Affiliation(s)
- Jiajia Cai
- Department of Laboratory Medicine, General Hospital of Southern Theatre Command of PLA, Guangzhou, China
| | - Jianyun Chen
- Department of Laboratory Medicine, General Hospital of Southern Theatre Command of PLA, Guangzhou, China
| | - Ling Huang
- Department of Laboratory Medicine, General Hospital of Southern Theatre Command of PLA, Guangzhou, China.,The First College of Clinical Medical, South Medical University, Guangzhou, China
| | - Changxi Wang
- IT and Cloud Computing Center, Geneplus-Shenzhen, Shenzhen, China
| | - Weiyun Zhang
- Department of Laboratory Medicine, General Hospital of Southern Theatre Command of PLA, Guangzhou, China
| | - Quan Zhou
- Department of Laboratory Medicine, General Hospital of Southern Theatre Command of PLA, Guangzhou, China
| | - Zhaohui Sun
- Department of Laboratory Medicine, General Hospital of Southern Theatre Command of PLA, Guangzhou, China
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5
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Maity S, Chakrabarti O. Mitochondrial protein import as a quality control sensor. Biol Cell 2021; 113:375-400. [PMID: 33870508 DOI: 10.1111/boc.202100002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/04/2021] [Accepted: 04/09/2021] [Indexed: 12/17/2022]
Abstract
Mitochondria are organelles involved in various functions related to cellular metabolism and homoeostasis. Though mitochondria contain own genome, their nuclear counterparts encode most of the different mitochondrial proteins. These are synthesised as precursors in the cytosol and have to be delivered into the mitochondria. These organelles hence have elaborate machineries for the import of precursor proteins from cytosol. The protein import machineries present in both mitochondrial membrane and aqueous compartments show great variability in pre-protein recognition, translocation and sorting across or into it. Mitochondrial protein import machineries also interact transiently with other protein complexes of the respiratory chain or those involved in the maintenance of membrane architecture. Hence mitochondrial protein translocation is an indispensable part of the regulatory network that maintains protein biogenesis, bioenergetics, membrane dynamics and quality control of the organelle. Various stress conditions and diseases that are associated with mitochondrial import defects lead to changes in cellular transcriptomic and proteomic profiles. Dysfunction in mitochondrial protein import also causes over-accumulation of precursor proteins and their aggregation in the cytosol. Multiple pathways may be activated for buffering these harmful consequences. Here, we present a comprehensive picture of import machinery and its role in cellular quality control in response to defective mitochondrial import. We also discuss the pathological consequences of dysfunctional mitochondrial protein import in neurodegeneration and cancer.
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Affiliation(s)
- Sebabrata Maity
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, 700064, India.,Homi Bhabha National Institute, India
| | - Oishee Chakrabarti
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, 700064, India.,Homi Bhabha National Institute, India
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6
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Palmer CS, Anderson AJ, Stojanovski D. Mitochondrial protein import dysfunction: mitochondrial disease, neurodegenerative disease and cancer. FEBS Lett 2021; 595:1107-1131. [PMID: 33314127 DOI: 10.1002/1873-3468.14022] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/12/2020] [Accepted: 10/17/2020] [Indexed: 12/13/2022]
Abstract
The majority of proteins localised to mitochondria are encoded by the nuclear genome, with approximately 1500 proteins imported into mammalian mitochondria. Dysfunction in this fundamental cellular process is linked to a variety of pathologies including neuropathies, cardiovascular disorders, myopathies, neurodegenerative diseases and cancer, demonstrating the importance of mitochondrial protein import machinery for cellular function. Correct import of proteins into mitochondria requires the co-ordinated activity of multimeric protein translocation and sorting machineries located in both the outer and inner mitochondrial membranes, directing the imported proteins to the destined mitochondrial compartment. This dynamic process maintains cellular homeostasis, and its dysregulation significantly affects cellular signalling pathways and metabolism. This review summarises current knowledge of the mammalian mitochondrial import machinery and the pathological consequences of mutation of its components. In addition, we will discuss the role of mitochondrial import in cancer, and our current understanding of the role of mitochondrial import in neurodegenerative diseases including Alzheimer's disease, Huntington's disease and Parkinson's disease.
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Affiliation(s)
- Catherine S Palmer
- Department of Biochemistry and Molecular Biology and The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Australia
| | - Alexander J Anderson
- Department of Biochemistry and Molecular Biology and The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Australia
| | - Diana Stojanovski
- Department of Biochemistry and Molecular Biology and The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Australia
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Wang J, Luo J, Sun Z, Sun F, Kong Z, Yu J. Identification of MTHFD2 as a novel prognosis biomarker in esophageal carcinoma patients based on transcriptomic data and methylation profiling. Medicine (Baltimore) 2020; 99:e22194. [PMID: 32925794 PMCID: PMC7489726 DOI: 10.1097/md.0000000000022194] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
DNA methylation is an important epigenetic regulatory mechanism in esophageal carcinoma (EC) and is associated with genomic instability and carcinogenesis. In the present study, we aimed to identify tumor biomarkers for predicting prognosis of EC patients.We downloaded mRNA expression profiles and DNA methylation profiles associated with EC from the Gene Expression Omnibus database. Differentially expressed and differentially methylated genes between tumor tissues and adjacent normal tissue samples were identified. Functional enrichment analyses were performed, followed by the construction of protein-protein interaction networks. Data were validated based on methylation profiles from The Cancer Genome Atlas. Candidate genes were further verified according to survival analysis and Cox regression analysis.We uncovered multiple genes with differential expression or methylation in tumor samples compared with normal samples. After taking the intersection of 3 differential gene sets, we obtained a total of 232 overlapping genes. Functional enrichment analysis revealed that these genes are related to pathways such as "glutathione metabolism," "p53 signaling pathway," and "focal adhesion." Furthermore, 8 hub genes with inversed expression and methylation correlation were identified as candidate genes. The abnormal expression levels of MSN, PELI1, and MTHFD2 were correlated with overall survival times in EC patients (P < .05). Only MTHFD2 was significantly associated with a pathologic stage according to univariate analysis (P = .037) and multivariate analysis (P = .043).Our study identified several novel EC biomarkers with prognostic value by integrated analysis of transcriptomic data and methylation profiles. MTHFD2 could serve as an independent biomarker for predicting prognosis and pathological stages of EC.
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Affiliation(s)
- Jianlin Wang
- Department of Radiotherapy, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University
- Center for Medical Physics, Nanjing Medical University, Changzhou, Jiangsu Province, China
| | - Judong Luo
- Department of Radiotherapy, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University
| | - Zhiqiang Sun
- Department of Radiotherapy, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University
| | - Fei Sun
- Department of Radiotherapy, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University
| | - Ze Kong
- Department of Radiotherapy, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University
| | - Jingping Yu
- Department of Radiotherapy, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University
- Center for Medical Physics, Nanjing Medical University, Changzhou, Jiangsu Province, China
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8
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González-Fernández MJ, Ortea I, Guil-Guerrero JL. α-Linolenic and γ-linolenic acids exercise differential antitumor effects on HT-29 human colorectal cancer cells. Toxicol Res (Camb) 2020; 9:474-483. [PMID: 32905142 DOI: 10.1093/toxres/tfaa046] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 05/30/2020] [Accepted: 06/03/2020] [Indexed: 12/19/2022] Open
Abstract
α-Linolenic acid (ALA, 18:3n-3) and γ-gamma linolenic acid (GLA, 18:3n-6) are polyunsaturated fatty acids (PUFA) that improve the human health. The present study focused on testing the in vitro antitumor actions of pure ALA and GLA on the HT-29 human colorectal cancer cell line. Cell viability was checked by MTT ((3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) test, cell membrane damage by the lactate dehydrogenase assay, apoptosis was tested by both caspase-3 activity trial and transmission electron microscopy images, and protein composition was analyzed by quantitative proteomics analysis. MTT test revealed IC50 values of 230 and 255 μM for ALA and GLA, respectively, at 72 h. After 24 h of incubation, both ALA and GLA induced apoptosis on HT-29 colorectal cancer cells according to the caspase-3 assay and microscopy images. SWATH/MS analysis evidenced that ALA significantly affected the mitochondrial protein import pathway and the citric acid cycle pathway, while GLA did not significantly affect any particular pathway. In summary, both ALA and GLA showed concentration-dependent inhibitory effects on HT-29 cells viability and induced cell death by apoptosis. ALA significantly affected cellular pathways, while GLA does not have specific actions on either pathway. Both n-3 and n-6 C18 PUFA are bioactive food components useful in the colorectal cancer prevention.
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Affiliation(s)
- María José González-Fernández
- Food Technology Division, Agrifood Campus of International Excellence, ceiA3, University of Almería, E-040120 Almería, Spain
| | - Ignacio Ortea
- Instituto de Investigación e Innovación Biomédica de Cádiz (INiBICA), Cádiz 11009, Spain
| | - José Luis Guil-Guerrero
- Food Technology Division, Agrifood Campus of International Excellence, ceiA3, University of Almería, E-040120 Almería, Spain
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9
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Heinemeyer T, Stemmet M, Bardien S, Neethling A. Underappreciated Roles of the Translocase of the Outer and Inner Mitochondrial Membrane Protein Complexes in Human Disease. DNA Cell Biol 2018; 38:23-40. [PMID: 30481057 DOI: 10.1089/dna.2018.4292] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Mitochondria are critical for cellular survival, and for their proper functioning, translocation of ∼1500 proteins across the mitochondrial membranes is required. The translocase of the outer (TOMM) and inner mitochondrial membrane (TIMM) complexes are major components of this translocation machinery. Through specific processes, preproteins and other molecules are imported, translocated, and directed to specific mitochondrial compartments for their function. In this study, we review the association of subunits of these complexes with human disease. Pathogenic mutations have been identified in the TIMM8A (DDP) and DNAJC19 (TIMM14) genes and are linked to Mohr-Tranebjærg syndrome and dilated cardiomyopathy syndrome (with and without ataxia), respectively. Polymorphisms in TOMM40 have been associated with Alzheimer's disease, frontotemporal lobar degeneration, Parkinson's disease with dementia, dementia with Lewy bodies, nonpathological cognitive aging, and various cardiovascular-related traits. Furthermore, reduced protein expression levels of several complex subunits have been associated with Parkinson's disease, Meniere's disease, and cardiovascular disorders. However, increased mRNA and protein levels of complex subunits are found in cancers. This review highlights the importance of the mitochondrial import machinery in human disease and stresses the need for further studies. Ultimately, this knowledge may prove to be critical for the development of therapeutic modalities for these conditions.
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Affiliation(s)
- Thea Heinemeyer
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University , Cape Town, South Africa
| | - Monique Stemmet
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University , Cape Town, South Africa
| | - Soraya Bardien
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University , Cape Town, South Africa
| | - Annika Neethling
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University , Cape Town, South Africa
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10
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Relator RT, Terada A, Sese J. Identifying statistically significant combinatorial markers for survival analysis. BMC Med Genomics 2018; 11:31. [PMID: 29697363 PMCID: PMC5918465 DOI: 10.1186/s12920-018-0346-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Background Survival analysis methods have been widely applied in different areas of health and medicine, spanning over varying events of interest and target diseases. They can be utilized to provide relationships between the survival time of individuals and factors of interest, rendering them useful in searching for biomarkers in diseases such as cancer. However, some disease progression can be very unpredictable because the conventional approaches have failed to consider multiple-marker interactions. An exponential increase in the number of candidate markers requires large correction factor in the multiple-testing correction and hide the significance. Methods We address the issue of testing marker combinations that affect survival by adapting the recently developed Limitless Arity Multiple-testing Procedure (LAMP), a p-value correction technique for statistical tests for combination of markers. LAMP cannot handle survival data statistics, and hence we extended LAMP for the log-rank test, making it more appropriate for clinical data, with newly introduced theoretical lower bound of the p-value. Results We applied the proposed method to gene combination detection for cancer and obtained gene interactions with statistically significant log-rank p-values. Gene combinations with orders of up to 32 genes were detected by our algorithm, and effects of some genes in these combinations are also supported by existing literature. Conclusion The novel approach for detecting prognostic markers presented here can identify statistically significant markers with no limitations on the order of interaction. Furthermore, it can be applied to different types of genomic data, provided that binarization is possible.
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Affiliation(s)
- Raissa T Relator
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Aika Terada
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan.,PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan.,Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan
| | - Jun Sese
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan. .,AIST-Tokyo Tech Real World Big-Data Computation Open Innovation Laboratory (RWBC-OIL), 2-12-1 Okayama, Meguro-ku, Tokyo, 152-8550, Japan.
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11
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Mao XY, Lee MJ, Zhu J, Zhu C, Law SM, Snijders AM. Genome-wide screen identifies a novel prognostic signature for breast cancer survival. Oncotarget 2017; 8:14003-14016. [PMID: 28122328 PMCID: PMC5355157 DOI: 10.18632/oncotarget.14776] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 12/31/2016] [Indexed: 12/17/2022] Open
Abstract
Large genomic datasets in combination with clinical data can be used as an unbiased tool to identify genes important in patient survival and discover potential therapeutic targets. We used a genome-wide screen to identify 587 genes significantly and robustly deregulated across four independent breast cancer (BC) datasets compared to normal breast tissue. Gene expression of 381 genes was significantly associated with relapse-free survival (RFS) in BC patients. We used a gene co-expression network approach to visualize the genetic architecture in normal breast and BCs. In normal breast tissue, co-expression cliques were identified enriched for cell cycle, gene transcription, cell adhesion, cytoskeletal organization and metabolism. In contrast, in BC, only two major co-expression cliques were identified enriched for cell cycle-related processes or blood vessel development, cell adhesion and mammary gland development processes. Interestingly, gene expression levels of 7 genes were found to be negatively correlated with many cell cycle related genes, highlighting these genes as potential tumor suppressors and novel therapeutic targets. A forward-conditional Cox regression analysis was used to identify a 12-gene signature associated with RFS. A prognostic scoring system was created based on the 12-gene signature. This scoring system robustly predicted BC patient RFS in 60 sampling test sets and was further validated in TCGA and METABRIC BC data. Our integrated study identified a 12-gene prognostic signature that could guide adjuvant therapy for BC patients and includes novel potential molecular targets for therapy.
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Affiliation(s)
- Xuan Y Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Matthew J Lee
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Jeffrey Zhu
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Carissa Zhu
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Sindy M Law
- Department of Psychiatry, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, California, USA
| | - Antoine M Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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12
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Gu Y, Si J, Xiao X, Tian Y, Yang S. miR-92a Inhibits Proliferation and Induces Apoptosis by Regulating Methylenetetrahydrofolate Dehydrogenase 2 (MTHFD2) Expression in Acute Myeloid Leukemia. Oncol Res 2017; 25:1069-1079. [PMID: 28059050 PMCID: PMC7841081 DOI: 10.3727/096504016x14829256525028] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Aberrant expression of microRNA-92a (miR-92a) has been investigated in various cancers. However, the function and mechanism of miR-92a in acute myeloid leukemia (AML) remain to be elucidated. Our data showed that miR-92a was evidently downregulated and methylenetetrahydrofolate dehydrogenase 2 (MTHFD2) was remarkably upregulated in AML cell lines HL-60 and THP-1. Dual luciferase reporter assay revealed that MTHFD2 was a direct target of miR-92a. Gain- and loss-of-function analysis demonstrated that MTHFD2 knockdown or miR-92a overexpression notably inhibited proliferation and promoted apoptosis of AML cell lines. Restoration of MTHFD2 expression reversed proliferation inhibition and apoptosis induction of AML cells triggered by miR-92a. Moreover, an implanted tumor model in mice indicated that miR-92a overexpression dramatically decreased tumor growth and MTHFD2 expression in vivo. Taken together, our results suggest that miR-92a inhibits proliferation and induces apoptosis by directly regulating MTHFD2 expression in AML. miR-92a may act as a tumor suppressor in AML, providing a promising therapeutic target for AML patients.
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Affiliation(s)
- Yueli Gu
- *Department of Hematology, Shangqiu First People’s Hospital, Shangqiu, P.R. China
| | - Jinchun Si
- †Department of Surgery Teaching and Research Section, Shangqiu Medical College, Shangqiu, P.R. China
| | - Xichun Xiao
- *Department of Hematology, Shangqiu First People’s Hospital, Shangqiu, P.R. China
| | - Ying Tian
- *Department of Hematology, Shangqiu First People’s Hospital, Shangqiu, P.R. China
| | - Shuo Yang
- *Department of Hematology, Shangqiu First People’s Hospital, Shangqiu, P.R. China
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13
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Kang Y, Fielden LF, Stojanovski D. Mitochondrial protein transport in health and disease. Semin Cell Dev Biol 2017; 76:142-153. [PMID: 28765093 DOI: 10.1016/j.semcdb.2017.07.028] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 07/18/2017] [Accepted: 07/19/2017] [Indexed: 01/17/2023]
Abstract
Mitochondria are fundamental structures that fulfil important and diverse functions within cells, including cellular respiration and iron-sulfur cluster biogenesis. Mitochondrial function is reliant on the organelles proteome, which is maintained and adjusted depending on cellular requirements. The majority of mitochondrial proteins are encoded by nuclear genes and must be trafficked to, and imported into the organelle following synthesis in the cytosol. These nuclear-encoded mitochondrial precursors utilise dynamic and multimeric translocation machines to traverse the organelles membranes and be partitioned to the appropriate mitochondrial subcompartment. Yeast model systems have been instrumental in establishing the molecular basis of mitochondrial protein import machines and mechanisms, however unique players and mechanisms are apparent in higher eukaryotes. Here, we review our current knowledge on mitochondrial protein import in human cells and how dysfunction in these pathways can lead to disease.
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Affiliation(s)
- Yilin Kang
- Department of Biochemistry and Molecular Biology and The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Laura F Fielden
- Department of Biochemistry and Molecular Biology and The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Diana Stojanovski
- Department of Biochemistry and Molecular Biology and The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, 3010, Australia.
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14
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Role of Tim17 Transmembrane Regions in Regulating the Architecture of Presequence Translocase and Mitochondrial DNA Stability. Mol Cell Biol 2017; 37:MCB.00491-16. [PMID: 27994013 DOI: 10.1128/mcb.00491-16] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 12/11/2016] [Indexed: 12/11/2022] Open
Abstract
Mitochondrial life cycle and protein import are intricate cellular processes, which require precise coordination between the transport machineries of outer and inner mitochondrial membranes. Presequence translocase performs the indispensable function of translocating preproteins having N-terminal targeting sequences across the inner membrane. Tim23 forms the core of the voltage-gated import channel, while Tim17 is presumed to maintain the stoichiometry of the translocase. However, mechanistic insights into how Tim17 coordinates these regulatory events within the complex remained elusive. We demonstrate that Tim17 harbors conserved G/AXXXG/A motifs within its transmembrane regions and plays an imperative role in the translocase assembly through interaction with Tim23. Tandem motifs are highly essential, as most of the amino acid substitutions lead to nonviability due to the complete destabilization of the TIM23 channel. Importantly, Tim17 transmembrane regions regulate the dynamic assembly of translocase to form either the TIM23 (PAM)-complex or TIM23 (SORT)-complex by recruiting the presequence translocase-associated motor (PAM) machinery or Tim21, respectively. To a greater significance, tim17 mutants displayed mitochondrial DNA (mtDNA) instability, membrane potential loss, and defective import, resulting in organellar dysfunction. We conclude that the integrity of Tim17 transmembrane regions is critical for mitochondrial function and protein turnover.
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15
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Fryknäs M, Zhang X, Bremberg U, Senkowski W, Olofsson MH, Brandt P, Persson I, D'Arcy P, Gullbo J, Nygren P, Schughart LK, Linder S, Larsson R. Iron chelators target both proliferating and quiescent cancer cells. Sci Rep 2016; 6:38343. [PMID: 27924826 PMCID: PMC5141479 DOI: 10.1038/srep38343] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 11/08/2016] [Indexed: 12/21/2022] Open
Abstract
Poorly vascularized areas of solid tumors contain quiescent cell populations that are resistant to cell cycle-active cancer drugs. The compound VLX600 was recently identified to target quiescent tumor cells and to inhibit mitochondrial respiration. We here performed gene expression analysis in order to characterize the cellular response to VLX600. The compound-specific signature of VLX600 revealed a striking similarity to signatures generated by compounds known to chelate iron. Validation experiments including addition of ferrous and ferric iron in excess, EXAFS measurements, and structure activity relationship analyses showed that VLX600 chelates iron and supported the hypothesis that the biological effects of this compound is due to iron chelation. Compounds that chelate iron possess anti-cancer activity, an effect largely attributed to inhibition of ribonucleotide reductase in proliferating cells. Here we show that iron chelators decrease mitochondrial energy production, an effect poorly tolerated by metabolically stressed tumor cells. These pleiotropic features make iron chelators an attractive option for the treatment of solid tumors containing heterogeneous populations of proliferating and quiescent cells.
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Affiliation(s)
- Mårten Fryknäs
- Department of Medical Sciences, Division of Cancer Pharmacology and Computational Medicine, Uppsala University, SE-751 85 Uppsala, Sweden
| | - Xiaonan Zhang
- Department of Medical and Health Sciences, Linköping University, SE-58183 Linköping, Sweden.,Cancer Center Karolinska, Department of Oncology and Pathology, Karolinska Institute, SE-171 76 Stockholm, Sweden
| | | | - Wojciech Senkowski
- Department of Medical Sciences, Division of Cancer Pharmacology and Computational Medicine, Uppsala University, SE-751 85 Uppsala, Sweden
| | - Maria Hägg Olofsson
- Cancer Center Karolinska, Department of Oncology and Pathology, Karolinska Institute, SE-171 76 Stockholm, Sweden
| | - Peter Brandt
- Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry, Uppsala University, SE-751 23 Uppsala, Sweden
| | - Ingmar Persson
- Department of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, P.O. Box 7015, SE-756 51 Uppsala, Sweden
| | - Padraig D'Arcy
- Department of Medical and Health Sciences, Linköping University, SE-58183 Linköping, Sweden
| | - Joachim Gullbo
- Department of Medical Sciences, Division of Cancer Pharmacology and Computational Medicine, Uppsala University, SE-751 85 Uppsala, Sweden.,Department of Immunology, Genetics and Pathology, Section of Oncology, Uppsala University, SE-75185, Uppsala, Sweden
| | - Peter Nygren
- Department of Immunology, Genetics and Pathology, Section of Oncology, Uppsala University, SE-75185, Uppsala, Sweden
| | - Leoni Kunz Schughart
- OncoRay-National Center for Radiation Research in Oncology, TU Dresden, D-01307 Dresden, Germany
| | - Stig Linder
- Department of Medical and Health Sciences, Linköping University, SE-58183 Linköping, Sweden.,Cancer Center Karolinska, Department of Oncology and Pathology, Karolinska Institute, SE-171 76 Stockholm, Sweden
| | - Rolf Larsson
- Department of Medical Sciences, Division of Cancer Pharmacology and Computational Medicine, Uppsala University, SE-751 85 Uppsala, Sweden
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Gustafsson R, Jemth AS, Gustafsson NMS, Färnegårdh K, Loseva O, Wiita E, Bonagas N, Dahllund L, Llona-Minguez S, Häggblad M, Henriksson M, Andersson Y, Homan E, Helleday T, Stenmark P. Crystal Structure of the Emerging Cancer Target MTHFD2 in Complex with a Substrate-Based Inhibitor. Cancer Res 2016; 77:937-948. [PMID: 27899380 DOI: 10.1158/0008-5472.can-16-1476] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 09/23/2016] [Accepted: 11/04/2016] [Indexed: 11/16/2022]
Abstract
To sustain their proliferation, cancer cells become dependent on one-carbon metabolism to support purine and thymidylate synthesis. Indeed, one of the most highly upregulated enzymes during neoplastic transformation is MTHFD2, a mitochondrial methylenetetrahydrofolate dehydrogenase and cyclohydrolase involved in one-carbon metabolism. Because MTHFD2 is expressed normally only during embryonic development, it offers a disease-selective therapeutic target for eradicating cancer cells while sparing healthy cells. Here we report the synthesis and preclinical characterization of the first inhibitor of human MTHFD2. We also disclose the first crystal structure of MTHFD2 in complex with a substrate-based inhibitor and the enzyme cofactors NAD+ and inorganic phosphate. Our work provides a rationale for continued development of a structural framework for the generation of potent and selective MTHFD2 inhibitors for cancer treatment. Cancer Res; 77(4); 937-48. ©2017 AACR.
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Affiliation(s)
- Robert Gustafsson
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Ann-Sofie Jemth
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Nina M S Gustafsson
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Katarina Färnegårdh
- Drug Discovery and Development Platform, Science for Life Laboratory, Department of Organic Chemistry, Stockholm University, Solna, Sweden
| | - Olga Loseva
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Elisée Wiita
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Nadilly Bonagas
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Leif Dahllund
- Drug Discovery and Development Platform, Science for Life Laboratory, School of Biotechnology, Royal Institute of Technology, Solna, Sweden
| | - Sabin Llona-Minguez
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Maria Häggblad
- Biochemical and Cellular Screening, Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Martin Henriksson
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Yasmin Andersson
- Drug Discovery and Development Platform, Science for Life Laboratory, School of Biotechnology, Royal Institute of Technology, Solna, Sweden
| | - Evert Homan
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Thomas Helleday
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
| | - Pål Stenmark
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
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17
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Lin CC, Fang CL, Sun DP, Hseu YC, Uen YH, Lin KY, Lin YC. High expression of mitochondrial intermembrane chaperone TIMM9 represents a negative prognostic marker in gastric cancer. J Formos Med Assoc 2016; 116:476-483. [PMID: 27720672 DOI: 10.1016/j.jfma.2016.08.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 07/26/2016] [Accepted: 08/03/2016] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND/PURPOSE Gastric cancer (GC) is one of the most common malignant cancers worldwide. However, little is known about the molecular process underlying this disease and its progression. This study investigated correlations between the expression of a mitochondrial inner membrane protein translocase of inner mitochondrial membrane 9 homolog (TIMM9) and various clinicopathologic parameters as well as patients' survival. METHODS Gastric tissue samples were obtained from 140 patients with GC and expression levels of TIMM9 were analyzed through immunohistochemistry. Paired t tests were used to analyze the differences in the expression levels of TIMM9 in both tumor and nontumor tissues for each patient. Two-tailed χ2 tests were performed to determine whether the differences in TIMM9 expression and clinicopathologic parameters were significant. Time-to-event endpoints for clinicopathologic parameters were plotted using the Kaplan-Meier method, and statistical significance was determined using univariate log-rank tests. Cox proportional hazard model was used for multivariate analysis to determine the independence of prognostic effects of TIMM9 expression. RESULTS A borderline association was found between overexpression of TIMM9 and vascular invasion (p = 0.0887). Patients with high expression levels of TIMM9 achieved a significantly lower disease-free survival rate compared with those with low expression levels (p = 0.005). Multivariate Cox regression analysis showed that overexpression of TIMM9 was an independent prognostic marker for GC (p = 0.011). CONCLUSION Overexpression of TIMM9 can be used as a marker to predict the outcome of patients with GC.
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Affiliation(s)
- Chih-Chan Lin
- Department of Medical Research, Chi Mei Medical Center, Tainan, Taiwan; Department of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Chia-Lang Fang
- Department of Pathology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan; Department of Pathology, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
| | - Ding-Ping Sun
- Department of Surgery, Chi Mei Medical Center, Tainan, Taiwan; Department of Food Science and Technology, Chia Nan University of Pharmacy and Science, Tainan, Taiwan
| | - You-Cheng Hseu
- Department of Cosmeceutics, China Medical University, Taichung, Taiwan; Department of Health and Nutrition Biotechnology, Asia University, Taichung, Taiwan
| | - Yih-Huei Uen
- Department of Medical Research, Chi Mei Medical Center, Tainan, Taiwan; The Superintendent's Office, Chi Mei Hospital Chiali, Tainan, Taiwan
| | - Kai-Yuan Lin
- Department of Medical Research, Chi Mei Medical Center, Tainan, Taiwan; Department of Biotechnology, Chia Nan University of Pharmacy and Science, Tainan, Taiwan.
| | - Yung-Chang Lin
- Department of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan.
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18
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Gao SP, Sun HF, Jiang HL, Li LD, Hu X, Xu XE, Jin W. Loss of COX5B inhibits proliferation and promotes senescence via mitochondrial dysfunction in breast cancer. Oncotarget 2016; 6:43363-74. [PMID: 26506233 PMCID: PMC4791237 DOI: 10.18632/oncotarget.6222] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 10/14/2015] [Indexed: 11/25/2022] Open
Abstract
COX5B, a peripheral subunit of the cytochrome c oxidase complex, has previously been reported to maintain the stability of this complex. However, its functions and mechanisms involved in breast cancer progression remain unclear. Here, by performing SILAC assays in breast cancer cell models and detecting COX5B expression in tissues, we found that COX5B expression was elevated in breast cancer. Down-regulation of COX5B in breast cancer cell lines can suppress cell proliferation and induced cell senescence which was accompanied by elevating production of IL-8 and other cytokines. Interestingly, conditioned medium from COX5B knockdown cells could promote breast cancer cell migration. Mechanistic studies reveal that COX5B silence induces an increase in production of ROS, depolarization of MMP and a decrease in ATP. What's more, silence of COX5B leads to metabolic disorders, such as increased glucose uptake and decreased lactate secretion. Collectively, our study shows that loss of COX5B induces mitochondrial dysfunction and subsequently leads to cell growth suppression and cell senescence. Cytokines such as IL-8 secreted by senescent cells may in turn alter the microenvironment which could enhance cell migration. These findings may provide a novel paradigm for the treatment which combined anti-cancer drugs with particular cytokine inhibitors such as IL-8 blockers.
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Affiliation(s)
- Shui-Ping Gao
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Collaborative Innovation Center for Cancer Medicine, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - He-Fen Sun
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Collaborative Innovation Center for Cancer Medicine, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Hong-Lin Jiang
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Collaborative Innovation Center for Cancer Medicine, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Liang-Dong Li
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Collaborative Innovation Center for Cancer Medicine, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xin Hu
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Collaborative Innovation Center for Cancer Medicine, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Xiao-En Xu
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Collaborative Innovation Center for Cancer Medicine, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wei Jin
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Collaborative Innovation Center for Cancer Medicine, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
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19
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Demishtein-Zohary K, Azem A. The TIM23 mitochondrial protein import complex: function and dysfunction. Cell Tissue Res 2016; 367:33-41. [DOI: 10.1007/s00441-016-2486-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 08/05/2016] [Indexed: 01/16/2023]
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20
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Kang Y, Baker MJ, Liem M, Louber J, McKenzie M, Atukorala I, Ang CS, Keerthikumar S, Mathivanan S, Stojanovski D. Tim29 is a novel subunit of the human TIM22 translocase and is involved in complex assembly and stability. eLife 2016; 5. [PMID: 27554484 PMCID: PMC5016092 DOI: 10.7554/elife.17463] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 08/14/2016] [Indexed: 12/14/2022] Open
Abstract
The TIM22 complex mediates the import of hydrophobic carrier proteins into the mitochondrial inner membrane. While the TIM22 machinery has been well characterised in yeast, the human complex remains poorly characterised. Here, we identify Tim29 (C19orf52) as a novel, metazoan-specific subunit of the human TIM22 complex. The protein is integrated into the mitochondrial inner membrane with it's C-terminus exposed to the intermembrane space. Tim29 is required for the stability of the TIM22 complex and functions in the assembly of hTim22. Furthermore, Tim29 contacts the Translocase of the Outer Mitochondrial Membrane, TOM complex, enabling a mechanism for transport of hydrophobic carrier substrates across the aqueous intermembrane space. Identification of Tim29 highlights the significance of analysing mitochondrial import systems across phylogenetic boundaries, which can reveal novel components and mechanisms in higher organisms.
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Affiliation(s)
- Yilin Kang
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Melbourne, Australia.,The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Australia
| | - Michael James Baker
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Melbourne, Australia.,The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Australia
| | - Michael Liem
- Department of Biochemistry and Genetics, La Trobe University, Melbourne, Australia.,La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Jade Louber
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Melbourne, Australia.,The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Australia
| | - Matthew McKenzie
- Centre for Genetic Diseases, Hudson Institute of Medical Research, Melbourne, Australia
| | - Ishara Atukorala
- Department of Biochemistry and Genetics, La Trobe University, Melbourne, Australia.,La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Ching-Seng Ang
- The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Australia
| | - Shivakumar Keerthikumar
- Department of Biochemistry and Genetics, La Trobe University, Melbourne, Australia.,La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Suresh Mathivanan
- Department of Biochemistry and Genetics, La Trobe University, Melbourne, Australia.,La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Diana Stojanovski
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Melbourne, Australia.,The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Australia
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21
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Wang H, Shi T, Qian WJ, Liu T, Kagan J, Srivastava S, Smith RD, Rodland KD, Camp DG. The clinical impact of recent advances in LC-MS for cancer biomarker discovery and verification. Expert Rev Proteomics 2015; 13:99-114. [PMID: 26581546 DOI: 10.1586/14789450.2016.1122529] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mass spectrometry (MS) -based proteomics has become an indispensable tool with broad applications in systems biology and biomedical research. With recent advances in liquid chromatography (LC) and MS instrumentation, LC-MS is making increasingly significant contributions to clinical applications, especially in the area of cancer biomarker discovery and verification. To overcome challenges associated with analyses of clinical samples (for example, a wide dynamic range of protein concentrations in bodily fluids and the need to perform high throughput and accurate quantification of candidate biomarker proteins), significant efforts have been devoted to improve the overall performance of LC-MS-based clinical proteomics platforms. Reviewed here are the recent advances in LC-MS and its applications in cancer biomarker discovery and quantification, along with the potentials, limitations and future perspectives.
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Affiliation(s)
- Hui Wang
- a Biological Sciences Division , Pacific Northwest National Laboratory , Richland , WA , USA
| | - Tujin Shi
- a Biological Sciences Division , Pacific Northwest National Laboratory , Richland , WA , USA
| | - Wei-Jun Qian
- a Biological Sciences Division , Pacific Northwest National Laboratory , Richland , WA , USA
| | - Tao Liu
- a Biological Sciences Division , Pacific Northwest National Laboratory , Richland , WA , USA
| | - Jacob Kagan
- b Division of Cancer Prevention , National Cancer Institute (NCI) , Rockville , MD , USA
| | - Sudhir Srivastava
- b Division of Cancer Prevention , National Cancer Institute (NCI) , Rockville , MD , USA
| | - Richard D Smith
- a Biological Sciences Division , Pacific Northwest National Laboratory , Richland , WA , USA
| | - Karin D Rodland
- a Biological Sciences Division , Pacific Northwest National Laboratory , Richland , WA , USA
| | - David G Camp
- a Biological Sciences Division , Pacific Northwest National Laboratory , Richland , WA , USA
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22
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Targeting Mitochondrial Function to Treat Quiescent Tumor Cells in Solid Tumors. Int J Mol Sci 2015; 16:27313-26. [PMID: 26580606 PMCID: PMC4661878 DOI: 10.3390/ijms161126020] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 10/20/2015] [Accepted: 11/02/2015] [Indexed: 12/12/2022] Open
Abstract
The disorganized nature of tumor vasculature results in the generation of microenvironments characterized by nutrient starvation, hypoxia and accumulation of acidic metabolites. Tumor cell populations in such areas are often slowly proliferating and thus refractory to chemotherapeutical drugs that are dependent on an active cell cycle. There is an urgent need for alternative therapeutic interventions that circumvent growth dependency. The screening of drug libraries using multicellular tumor spheroids (MCTS) or glucose-starved tumor cells has led to the identification of several compounds with promising therapeutic potential and that display activity on quiescent tumor cells. Interestingly, a common theme of these drug screens is the recurrent identification of agents that affect mitochondrial function. Such data suggest that, contrary to the classical Warburg view, tumor cells in nutritionally-compromised microenvironments are dependent on mitochondrial function for energy metabolism and survival. These findings suggest that mitochondria may represent an “Achilles heel” for the survival of slowly-proliferating tumor cells and suggest strategies for the development of therapy to target these cell populations.
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23
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Butvilovskaya VI, Tsybulskaya MV, Tikhonov AA, Talibov VO, Belousov PV, Sazykin AY, Schwartz AM, Surzhikov SA, Stomakhin AA, Solopova ON, Rubina AY. Preparation of recombinant serpins B3 and B4 and investigation of their specific interactions with antibodies using hydrogel-based microarrays. Mol Biol 2015. [DOI: 10.1134/s0026893315050040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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24
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An Optimization-Driven Analysis Pipeline to Uncover Biomarkers and Signaling Paths: Cervix Cancer. MICROARRAYS 2015; 4:287-310. [PMID: 26388997 PMCID: PMC4573573 DOI: 10.3390/microarrays4020287] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Establishing how a series of potentially important genes might relate to each other is relevant to understand the origin and evolution of illnesses, such as cancer. High-throughput biological experiments have played a critical role in providing information in this regard. A special challenge, however, is that of trying to conciliate information from separate microarray experiments to build a potential genetic signaling path. This work proposes a two-step analysis pipeline, based on optimization, to approach meta-analysis aiming to build a proxy for a genetic signaling path.
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25
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Loss of TIM50 suppresses proliferation and induces apoptosis in breast cancer. Tumour Biol 2015; 37:1279-87. [DOI: 10.1007/s13277-015-3878-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 07/30/2015] [Indexed: 10/23/2022] Open
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26
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Establishment of a new OSCC cell line derived from OLK and identification of malignant transformation-related proteins by differential proteomics approach. Sci Rep 2015; 5:12668. [PMID: 26234610 PMCID: PMC4522661 DOI: 10.1038/srep12668] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 06/29/2015] [Indexed: 12/12/2022] Open
Abstract
Oral squamous cell carcinoma (OSCC) is usually preceded by the oral premalignant lesions, mainly oral leukoplakia (OLK) after repeated insults of carcinogens, tobacco. B(a)P and DMBA are key carcinogens in tobacco smoke. In the present study, for the first time we established the cancerous cell line OSCC-BD induced by B(a)P/DMBA mixture and transformed from dysplastic oral leukoplakia cell line DOK. Cell morphology, proliferation ability, migration ability, colony formation, and tumorigenicity were studied and confirmed the malignant characteristics of OSCC-BD cells. We further identified the differential proteins between DOK and OSCC-BD cells by stable isotope dimethyl labeling based quantitative proteomic method, which showed 18 proteins up-regulated and 16 proteins down-regulated with RSD < 8%. Differential proteins are mainly related to cell cycle, cell proliferation, DNA replication, RNA splicing and apoptosis. Abberant binding function, catalysis activity and transportor activity of differential proteins might contribute to the malignant transformation of OLK. Of the 34 identified differential proteins with RSD < 8%, 13 novel cancer-related proteins were reported in the present study. This study might provide a new insight into the mechanism of OLK malignant transformation and the potent biomarkers for early diagnosis, meanwhile further facilitate the application of the quantification proteomics to carcinogenesis research.
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27
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Calderón-González KG, Valero Rustarazo ML, Labra-Barrios ML, Bazán-Méndez CI, Tavera-Tapia A, Herrera-Aguirre ME, Sánchez del Pino MM, Gallegos-Pérez JL, González-Márquez H, Hernández-Hernández JM, León-Ávila G, Rodríguez-Cuevas S, Guisa-Hohenstein F, Luna-Arias JP. Determination of the protein expression profiles of breast cancer cell lines by quantitative proteomics using iTRAQ labelling and tandem mass spectrometry. J Proteomics 2015; 124:50-78. [PMID: 25918110 DOI: 10.1016/j.jprot.2015.04.018] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 04/11/2015] [Accepted: 04/13/2015] [Indexed: 02/06/2023]
Abstract
UNLABELLED Breast cancer is the principal cancer in women worldwide. Although there are serum tumor markers such as CEA and HER2, they are detected in advanced stages of the disease and used as progression and recurrence markers. Therefore, there is a necessity for the identification of new markers that might lead to an early detection and also provide evidence of an effective treatment. The aim of this work was to determine the differential protein expression profiles of four breast cancer cell lines in comparison to a normal control cell line by iTRAQ labelling and tandem mass spectrometry, in order to identify putative biomarkers of the disease. We identified 1,020 iTRAQ-labelled polypeptides with at least one peptide identified with more than 95% in confidence. Overexpressed polypeptides in all cancer cell lines were 78, whilst the subexpressed were 128. We categorised them with PANTHER program into biological processes, being the metabolic pathways the most affected. We detected six groups of proteins with the STRING program involved in DNA topology, glycolysis, translation initiation, splicing, pentose pathway, and proteasome degradation. The main subexpressed protein network included mitochondrial proteins involved in oxidative phosphorylation. We propose BAG6, DDX39, ANXA8 and COX4 as putative biomarkers in breast cancer. BIOLOGICAL SIGNIFICANCE We report a set of differentially expressed proteins in the MCF7 and T47D (Luminal A), MDA-MB-231 (Claudin low) and SK-BR-3 (HER2(+)) breast cancer cell lines that have not been previously reported in breast cancer disease. From these proteins, we propose BAG6, DDX39, ANXA8 and COX4 as putative biomarkers in breast cancer. On the other hand, we propose sets of unique polypeptides in each breast cancer cell line that can be useful in the classification of different subtypes of breast cancer.
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Affiliation(s)
- Karla Grisel Calderón-González
- Doctorado en Ciencias Biológicas, División de Ciencias Biológicas y de la Salud, Universidad Autónoma Metropolitana, Unidad Iztapalapa, Av. San Rafael Atlixco No. 186, Col. Vicentina, Iztapalapa, C.P. 09340, México, D. F., México.
| | - Ma Luz Valero Rustarazo
- Unidad de Proteómica, Centro de Investigación Príncipe Felipe, C/Rambla del Saler 16, 46012 Valencia, España.
| | - Maria Luisa Labra-Barrios
- Departmento de Biología Celular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, Gustavo A. Madero, C.P. 07360, México, D. F., México.
| | - César Isaac Bazán-Méndez
- Departmento de Biología Celular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, Gustavo A. Madero, C.P. 07360, México, D. F., México.
| | - Alejandra Tavera-Tapia
- Departmento de Biología Celular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, Gustavo A. Madero, C.P. 07360, México, D. F., México.
| | - Maria Esther Herrera-Aguirre
- Departmento de Biología Celular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, Gustavo A. Madero, C.P. 07360, México, D. F., México.
| | - Manuel M Sánchez del Pino
- Unidad de Proteómica, Centro de Investigación Príncipe Felipe, C/Rambla del Saler 16, 46012 Valencia, España.
| | | | - Humberto González-Márquez
- Doctorado en Ciencias Biológicas, División de Ciencias Biológicas y de la Salud, Universidad Autónoma Metropolitana, Unidad Iztapalapa, Av. San Rafael Atlixco No. 186, Col. Vicentina, Iztapalapa, C.P. 09340, México, D. F., México.
| | - Jose Manuel Hernández-Hernández
- Departmento de Biología Celular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, Gustavo A. Madero, C.P. 07360, México, D. F., México.
| | - Gloria León-Ávila
- Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Col. Santo Tomás, Miguel Hidalgo, C.P. 11340, México, D. F., México.
| | - Sergio Rodríguez-Cuevas
- Instituto de Enfermedades de la Mama, Fundación del Cáncer de Mama (FUCAM A.C.), Av. Bordo No. 100, Col. Viejo Ejido de Santa Ursula Coapa, Coyoacán, C.P. 04980, México, D. F., México.
| | - Fernando Guisa-Hohenstein
- Instituto de Enfermedades de la Mama, Fundación del Cáncer de Mama (FUCAM A.C.), Av. Bordo No. 100, Col. Viejo Ejido de Santa Ursula Coapa, Coyoacán, C.P. 04980, México, D. F., México.
| | - Juan Pedro Luna-Arias
- Departmento de Biología Celular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, Gustavo A. Madero, C.P. 07360, México, D. F., México.
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Metabolic control via the mitochondrial protein import machinery. Curr Opin Cell Biol 2015; 33:42-8. [DOI: 10.1016/j.ceb.2014.11.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 11/16/2014] [Indexed: 12/19/2022]
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29
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Groessl M, Slany A, Bileck A, Gloessmann K, Kreutz D, Jaeger W, Pfeiler G, Gerner C. Proteome Profiling of Breast Cancer Biopsies Reveals a Wound Healing Signature of Cancer-Associated Fibroblasts. J Proteome Res 2014; 13:4773-82. [DOI: 10.1021/pr500727h] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Michael Groessl
- Department
of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Währingerstr. 38, Vienna A-1090, Austria
| | - Astrid Slany
- Department
of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Währingerstr. 38, Vienna A-1090, Austria
| | - Andrea Bileck
- Department
of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Währingerstr. 38, Vienna A-1090, Austria
| | - Kerstin Gloessmann
- Department
of Medicine I, Comprehensive Cancer Center, Institute of Cancer Research, Medical University of Vienna, Spitalgasse 23, Vienna A-1090, Austria
| | - Dominique Kreutz
- Department
of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Währingerstr. 38, Vienna A-1090, Austria
| | - Walter Jaeger
- Department
of Clinical Pharmacy and Diagnostics, University of Vienna, Althanstrasse
14, Vienna A-1090, Austria
| | - Georg Pfeiler
- Division
of Special Gynaecology, Department of Obstetrics and Gynecology, Medical University of Vienna, Währinger Gürtel 18-20, Vienna A-1090, Austria
| | - Christopher Gerner
- Department
of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Währingerstr. 38, Vienna A-1090, Austria
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30
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Chen SX, Xu XE, Wang XQ, Cui SJ, Xu LL, Jiang YH, Zhang Y, Yan HB, Zhang Q, Qiao J, Yang PY, Liu F. Identification of colonic fibroblast secretomes reveals secretory factors regulating colon cancer cell proliferation. J Proteomics 2014; 110:155-71. [PMID: 25118038 DOI: 10.1016/j.jprot.2014.07.031] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Revised: 07/14/2014] [Accepted: 07/29/2014] [Indexed: 01/01/2023]
Abstract
UNLABELLED Stromal microenvironment influences tumor cell proliferation and migration. Fibroblasts represent the most abundant stromal constituents. Here, we established two pairs of normal fibroblast (NF) and cancer-associated fibroblast (CAF) cultures from colorectal adenocarcinoma tissues and the normal counterparts. The NFs and CAFs were stained positive for typical fibroblast markers and inhibited colon cancer (CC) cell proliferation in in vitro cocultures and in xenograft mouse models. The fibroblast conditioned media were analyzed using LC-MS and 227 proteins were identified at a false discovery rate of 1.3%, including 131 putative secretory and 20 plasma membrane proteins. These proteins were enriched for functional categories of extracellular matrix, adhesion, cell motion, inflammatory response, redox homeostasis and peptidase inhibitor. Secreted protein acidic and rich in cysteine, transgelin, follistatin-related protein 1 (FSTL1) and decorin was abundant in the fibroblast secretome as confirmed by Western blot. Silencing of FSTL1 and transgelin in colonic fibroblast cell line CCD-18Co induced an accelerated proliferation of CC cells in cocultures. Exogenous FSTL1 attenuates CC cell proliferation in a negative fashion. FSTL1 was upregulated in CC patient plasma and cancerous tissues but had no implication in prognosis. Our results provided novel insights into the molecular signatures and modulatory role of CC associated fibroblasts. BIOLOGICAL SIGNIFICANCE In this study, a label-free LC-MS was performed to analyze the secretomes of two paired primary fibroblasts, which were isolated from fresh surgical specimen of colorectal adenocarcinoma and adjacent normal colonic tissues and exhibited negative modulatory activity for colon cancer cell growth in in vitro cocultures and in vivo xenograph mouse models. Follistatin-related protein 1 was further revealed to be one of the stroma-derived factors of potential suppression role for colon cancer cell proliferation. Our results provide novel insights into the molecular signatures and the modulatory role of colon cancer associated fibroblasts, and establish a valuable resource for the development of therapeutic agents or novel clinic biomarker.
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Affiliation(s)
- Sun-Xia Chen
- Department of Medical Systems Biology of School of Basic Medical Sciences and Institutes of Biomedical Sciences, Fudan University, 131 Dongan Road, Shanghai 200032, China
| | - Xiao-En Xu
- Department of Medical Systems Biology of School of Basic Medical Sciences and Institutes of Biomedical Sciences, Fudan University, 131 Dongan Road, Shanghai 200032, China
| | - Xiao-Qing Wang
- Department of Medical Systems Biology of School of Basic Medical Sciences and Institutes of Biomedical Sciences, Fudan University, 131 Dongan Road, Shanghai 200032, China; Department of Chemistry, Fudan University, 220 Handan Road, Shanghai 200433, China
| | - Shu-Jian Cui
- College of Bioscience and Biotechnology, Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
| | - Lei-Lei Xu
- Department of Medical Systems Biology of School of Basic Medical Sciences and Institutes of Biomedical Sciences, Fudan University, 131 Dongan Road, Shanghai 200032, China
| | - Ying-Hua Jiang
- Department of Medical Systems Biology of School of Basic Medical Sciences and Institutes of Biomedical Sciences, Fudan University, 131 Dongan Road, Shanghai 200032, China
| | - Yang Zhang
- Department of Medical Systems Biology of School of Basic Medical Sciences and Institutes of Biomedical Sciences, Fudan University, 131 Dongan Road, Shanghai 200032, China
| | - Hai-Bo Yan
- Department of Medical Systems Biology of School of Basic Medical Sciences and Institutes of Biomedical Sciences, Fudan University, 131 Dongan Road, Shanghai 200032, China
| | - Qian Zhang
- Department of Medical Systems Biology of School of Basic Medical Sciences and Institutes of Biomedical Sciences, Fudan University, 131 Dongan Road, Shanghai 200032, China
| | - Jie Qiao
- Department of Medical Systems Biology of School of Basic Medical Sciences and Institutes of Biomedical Sciences, Fudan University, 131 Dongan Road, Shanghai 200032, China
| | - Peng-Yuan Yang
- Department of Medical Systems Biology of School of Basic Medical Sciences and Institutes of Biomedical Sciences, Fudan University, 131 Dongan Road, Shanghai 200032, China; Department of Chemistry, Fudan University, 220 Handan Road, Shanghai 200433, China.
| | - Feng Liu
- Department of Medical Systems Biology of School of Basic Medical Sciences and Institutes of Biomedical Sciences, Fudan University, 131 Dongan Road, Shanghai 200032, China.
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31
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Increased MTHFD2 expression is associated with poor prognosis in breast cancer. Tumour Biol 2014; 35:8685-90. [PMID: 24870594 DOI: 10.1007/s13277-014-2111-x] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 05/15/2014] [Indexed: 02/01/2023] Open
Abstract
The aim of this study was to investigate the expression levels of methylenetetrahydrofolate dehydrogenase (NADP + -dependent) 2 (MTHFD2) and the associated clinical implications in breast cancer. MTHFD2 expression was measured by Western blot and immunohistochemistry in 698 tissue sections taken from breast cancer patients. The relationship between MTHFD2 expression, clinicopathological parameters, and the prognosis of breast cancer was subsequently determined. In comparison with para-carcinoma tissue specimens, an enhanced expression of MTHFD2 was observed in breast cancer tissue specimens (P < 0.05). In total, 41.12 % (287/698) of breast cancer tissue specimens had high levels of MTHFD2. After universal and Spearman regression correlation analyses, MTHFD2 expression was found to correlate with tumor size, histological grade, lymph node metastasis, and distant metastases (P = 0.001, 0.002, 0.001, and 0.001, respectively). Furthermore, patients with MTHFD2-expressing tumors had a significantly poorer prognosis than those with no or low MTHFD2 expression. (P = 0.002). Using the Cox regression test, MTHFD2 was identified as an independent prognostic factor (P = 0.001). MTHFD2 was differentially expressed in breast cancer tissue. Therefore, this protein may be an independent prognostic factor and a potential therapeutic target for future breast cancer treatments.
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32
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Cava C, Bertoli G, Ripamonti M, Mauri G, Zoppis I, Rosa PAD, Gilardi MC, Castiglioni I. Integration of mRNA expression profile, copy number alterations, and microRNA expression levels in breast cancer to improve grade definition. PLoS One 2014; 9:e97681. [PMID: 24866763 PMCID: PMC4035288 DOI: 10.1371/journal.pone.0097681] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 04/23/2014] [Indexed: 12/20/2022] Open
Abstract
Defining the aggressiveness and growth rate of a malignant cell population is a key step in the clinical approach to treating tumor disease. The correct grading of breast cancer (BC) is a fundamental part in determining the appropriate treatment. Biological variables can make it difficult to elucidate the mechanisms underlying BC development. To identify potential markers that can be used for BC classification, we analyzed mRNAs expression profiles, gene copy numbers, microRNAs expression and their association with tumor grade in BC microarray-derived datasets. From mRNA expression results, we found that grade 2 BC is most likely a mixture of grade 1 and grade 3 that have been misclassified, being described by the gene signature of either grade 1 or grade 3. We assessed the potential of the new approach of integrating mRNA expression profile, copy number alterations, and microRNA expression levels to select a limited number of genomic BC biomarkers. The combination of mRNA profile analysis and copy number data with microRNA expression levels led to the identification of two gene signatures of 42 and 4 altered genes (FOXM1, KPNA4, H2AFV and DDX19A) respectively, the latter obtained through a meta-analytical procedure. The 42-based gene signature identifies 4 classes of up- or down-regulated microRNAs (17 microRNAs) and of their 17 target mRNA, and the 4-based genes signature identified 4 microRNAs (Hsa-miR-320d, Hsa-miR-139-5p, Hsa-miR-567 and Hsa-let-7c). These results are discussed from a biological point of view with respect to pathological features of BC. Our identified mRNAs and microRNAs were validated as prognostic factors of BC disease progression, and could potentially facilitate the implementation of assays for laboratory validation, due to their reduced number.
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Affiliation(s)
- Claudia Cava
- Institute of Molecular Bioimaging and Physiology (IBFM), National Research Council (CNR), Milan, Italy
| | - Gloria Bertoli
- Institute of Molecular Bioimaging and Physiology (IBFM), National Research Council (CNR), Milan, Italy
| | - Marilena Ripamonti
- Institute of Molecular Bioimaging and Physiology (IBFM), National Research Council (CNR), Milan, Italy
| | - Giancarlo Mauri
- Department of Informatics, Systems and Communications, University of Milan–Bicocca, Milan, Italy
| | - Italo Zoppis
- Department of Informatics, Systems and Communications, University of Milan–Bicocca, Milan, Italy
| | | | - Maria Carla Gilardi
- Institute of Molecular Bioimaging and Physiology (IBFM), National Research Council (CNR), Milan, Italy
| | - Isabella Castiglioni
- Institute of Molecular Bioimaging and Physiology (IBFM), National Research Council (CNR), Milan, Italy
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33
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Mitochondrial protein translocases for survival and wellbeing. FEBS Lett 2014; 588:2484-95. [DOI: 10.1016/j.febslet.2014.05.028] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 05/15/2014] [Accepted: 05/15/2014] [Indexed: 11/20/2022]
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34
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Kočevar N, Grazio SF, Komel R. Two-dimensional gel electrophoresis of gastric tissue in an alkaline pH range. Proteomics 2014; 14:311-21. [PMID: 24293252 DOI: 10.1002/pmic.201200574] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Revised: 10/09/2013] [Accepted: 11/13/2013] [Indexed: 12/17/2022]
Abstract
2DE in combination with MS has facilitated the discovery of several proteins with altered abundance in gastric cancer. While acidic and wide pH ranges have been widely investigated, analysis in the alkaline pH range has not been specifically performed in gastric cancer to date. In the present study, we initially optimized the 2DE in alkaline pH range (pH 7-11) for gastric tissue samples. Using a modified lysis buffer, we analyzed pooled nontumor and tumor samples for proteins with altered abundance in gastric adenocarcinoma. We successfully identified 38 silver-stained spots as 24 different proteins. Four of these were chosen for investigation with immunoblotting on individual paired samples to determine whether the changes seen in 2DE represent the overall abundance of the protein or possibly only a single form. While mitochondrial trifunctional protein (MTP) subunits were decreased in 2DE gels, immunoblotting identified their overall abundance as being differently dysregulated: in the gastric tumor samples, the MTP-α subunit was decreased, and the MTP-β subunit was increased. On the other hand, heterogenous nuclear ribonucleoprotein M and galectin-4 were increased in the gastric tumor samples in both 2DE and immunoblotting.
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Affiliation(s)
- Nina Kočevar
- Medical Centre for Molecular Biology, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
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35
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Lehtinen L, Ketola K, Mäkelä R, Mpindi JP, Viitala M, Kallioniemi O, Iljin K. High-throughput RNAi screening for novel modulators of vimentin expression identifies MTHFD2 as a regulator of breast cancer cell migration and invasion. Oncotarget 2013; 4:48-63. [PMID: 23295955 PMCID: PMC3702207 DOI: 10.18632/oncotarget.756] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Vimentin is an intermediate filament protein, with a key role in the epithelial to mesenchymal transition as well as cell invasion, and it is often upregulated during cancer progression. However, relatively little is known about its regulation in cancer cells. Here, we performed an RNA interference screen followed by protein lysate microarray analysis in bone metastatic MDA-MB-231(SA) breast cancer cells to identify novel regulators of vimentin expression. Out of the 596 genes investigated, three novel vimentin regulators EPHB4, WIPF2 and MTHFD2 were identified. The reduced vimentin expression in response to EPHB4, WIPF2 and MTHFD2 silencing was observed at mRNA and protein levels. Bioinformatic analysis of gene expression data across cancers indicated overexpression of EPHB4 and MTHFD2 in breast cancer and high expression associated with poor clinical characteristics. Analysis of 96 cDNA samples derived from both normal and malignant human tissues suggested putative association with metastatic disease. MTHFD2 knockdown resulted in impaired cell migration and invasion into extracellular matrix as well as decreased the fraction of cells with a high CD44 expression, a marker of cancer stem cells. Furthermore, MTHFD2 expression was induced in response to TGF-β stimulation in breast cancer cells. Our results show that MTHFD2 is overexpressed in breast cancer, associates with poor clinical characteristics and promotes cellular features connected with metastatic disease, thus implicating MTHFD2 as a potential drug target to block breast cancer cell migration and invasion.
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Affiliation(s)
- Laura Lehtinen
- Medical Biotechnology, VTT Technical Research Centre of Finland and Turku Centre for Biotechnology, University of Turku, Turku, Finland.
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36
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Chen J, Ma M, Shen N, Xi JJ, Tian W. Integration of cancer gene co-expression network and metabolic network to uncover potential cancer drug targets. J Proteome Res 2013; 12:2354-64. [PMID: 23590569 DOI: 10.1021/pr400162t] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Cell metabolism is critical for cancer cell transformation and progression. In this study, we have developed a novel method, named Met-express, that integrates a cancer gene co-expression network with the metabolic network to predict key enzyme-coding genes and metabolites in cancer cell metabolism. Met-express successfully identified a group of key enzyme-coding genes and metabolites in lung, leukemia, and breast cancers. Literature reviews suggest that approximately 33-53% of the predicted genes are either known or suggested anti-cancer drug targets, while 22% of the predicted metabolites are known or high-potential drug compounds in therapeutic use. Furthermore, experimental validations prove that 90% of the selected genes and 70% of metabolites demonstrate the significant anti-cancer phenotypes in cancer cells, implying that they may play important roles in cancer metabolism. Therefore, Met-express is a powerful tool for uncovering novel therapeutic biomarkers.
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Affiliation(s)
- Jingqi Chen
- State Key Laboratory of Genetic Engineering, Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University, Shanghai, China
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37
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Mass spectrometry-based proteomics in molecular diagnostics: discovery of cancer biomarkers using tissue culture. BIOMED RESEARCH INTERNATIONAL 2013; 2013:783131. [PMID: 23586059 PMCID: PMC3613068 DOI: 10.1155/2013/783131] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 01/30/2013] [Indexed: 12/14/2022]
Abstract
Accurate diagnosis and proper monitoring of cancer patients remain a key obstacle for successful cancer treatment and prevention. Therein comes the need for biomarker discovery, which is crucial to the current oncological and other clinical practices having the potential to impact the diagnosis and prognosis. In fact, most of the biomarkers have been discovered utilizing the proteomics-based approaches. Although high-throughput mass spectrometry-based proteomic approaches like SILAC, 2D-DIGE, and iTRAQ are filling up the pitfalls of the conventional techniques, still serum proteomics importunately poses hurdle in overcoming a wide range of protein concentrations, and also the availability of patient tissue samples is a limitation for the biomarker discovery. Thus, researchers have looked for alternatives, and profiling of candidate biomarkers through tissue culture of tumor cell lines comes up as a promising option. It is a rich source of tumor cell-derived proteins, thereby, representing a wide array of potential biomarkers. Interestingly, most of the clinical biomarkers in use today (CA 125, CA 15.3, CA 19.9, and PSA) were discovered through tissue culture-based system and tissue extracts. This paper tries to emphasize the tissue culture-based discovery of candidate biomarkers through various mass spectrometry-based proteomic approaches.
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38
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Sánchez-Peña ML, Isaza CE, Pérez-Morales J, Rodríguez-Padilla C, Castro JM, Cabrera-Ríos M. Identification of potential biomarkers from microarray experiments using multiple criteria optimization. Cancer Med 2013; 2:253-65. [PMID: 23634293 PMCID: PMC3639664 DOI: 10.1002/cam4.69] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Revised: 01/23/2013] [Accepted: 01/24/2013] [Indexed: 12/14/2022] Open
Abstract
Microarray experiments are capable of determining the relative expression of tens of thousands of genes simultaneously, thus resulting in very large databases. The analysis of these databases and the extraction of biologically relevant knowledge from them are challenging tasks. The identification of potential cancer biomarker genes is one of the most important aims for microarray analysis and, as such, has been widely targeted in the literature. However, identifying a set of these genes consistently across different experiments, researches, microarray platforms, or cancer types is still an elusive endeavor. Besides the inherent difficulty of the large and nonconstant variability in these experiments and the incommensurability between different microarray technologies, there is the issue of the users having to adjust a series of parameters that significantly affect the outcome of the analyses and that do not have a biological or medical meaning. In this study, the identification of potential cancer biomarkers from microarray data is casted as a multiple criteria optimization (MCO) problem. The efficient solutions to this problem, found here through data envelopment analysis (DEA), are associated to genes that are proposed as potential cancer biomarkers. The method does not require any parameter adjustment by the user, and thus fosters repeatability. The approach also allows the analysis of different microarray experiments, microarray platforms, and cancer types simultaneously. The results include the analysis of three publicly available microarray databases related to cervix cancer. This study points to the feasibility of modeling the selection of potential cancer biomarkers from microarray data as an MCO problem and solve it using DEA. Using MCO entails a new optic to the identification of potential cancer biomarkers as it does not require the definition of a threshold value to establish significance for a particular gene and the selection of a normalization procedure to compare different experiments is no longer necessary.
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Affiliation(s)
- Matilde L Sánchez-Peña
- Bio IE Lab, Industrial Engineering Department, University of Puerto Rico at Mayaguez, Mayagüez, Puerto Rico
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39
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Yang LS, Xu XE, Liu XP, Jin H, Chen ZQ, Liu XH, Wang Y, Huang FP, Shi Q. iTRAQ-based quantitative proteomic analysis for identification of oligodendroglioma biomarkers related with loss of heterozygosity on chromosomal arm 1p. J Proteomics 2012; 77:480-91. [DOI: 10.1016/j.jprot.2012.09.028] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Revised: 08/11/2012] [Accepted: 09/24/2012] [Indexed: 11/25/2022]
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40
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Sotgia F, Whitaker-Menezes D, Martinez-Outschoorn UE, Salem AF, Tsirigos A, Lamb R, Sneddon S, Hulit J, Howell A, Lisanti MP. Mitochondria "fuel" breast cancer metabolism: fifteen markers of mitochondrial biogenesis label epithelial cancer cells, but are excluded from adjacent stromal cells. Cell Cycle 2012; 11:4390-401. [PMID: 23172368 DOI: 10.4161/cc.22777] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Here, we present new genetic and morphological evidence that human tumors consist of two distinct metabolic compartments. First, re-analysis of genome-wide transcriptional profiling data revealed that > 95 gene transcripts associated with mitochondrial biogenesis and/or mitochondrial translation were significantly elevated in human breast cancer cells, as compared with adjacent stromal tissue. Remarkably, nearly 40 of these upregulated gene transcripts were mitochondrial ribosomal proteins (MRPs), functionally associated with mitochondrial translation of protein components of the OXPHOS complex. Second, during validation by immunohistochemistry, we observed that antibodies directed against 15 markers of mitochondrial biogenesis and/or mitochondrial translation (AKAP1, GOLPH3, GOLPH3L, MCT1, MRPL40, MRPS7, MRPS15, MRPS22, NRF1, NRF2, PGC1-α, POLRMT, TFAM, TIMM9 and TOMM70A) selectively labeled epithelial breast cancer cells. These same mitochondrial markers were largely absent or excluded from adjacent tumor stromal cells. Finally, markers of mitochondrial lipid synthesis (GOLPH3) and mitochondrial translation (POLRMT) were associated with poor clinical outcome in human breast cancer patients. Thus, we conclude that human breast cancers contain two distinct metabolic compartments-a glycolytic tumor stroma, which surrounds oxidative epithelial cancer cells-that are mitochondria-rich. The co-existence of these two compartments is indicative of metabolic symbiosis between epithelial cancer cells and their surrounding stroma. As such, epithelial breast cancer cells should be viewed as predatory metabolic "parasites," which undergo anabolic reprogramming to amplify their mitochondrial "power." This notion is consistent with the observation that the anti-malarial agent chloroquine may be an effective anticancer agent. New anticancer therapies should be developed to target mitochondrial biogenesis and/or mitochondrial translation in human cancer cells.
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Affiliation(s)
- Federica Sotgia
- Jefferson Stem Cell Biology and Regenerative Medicine Center; Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA USA.
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41
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De Paepe B. Mitochondrial Markers for Cancer: Relevance to Diagnosis, Therapy, and Prognosis and General Understanding of Malignant Disease Mechanisms. ACTA ACUST UNITED AC 2012. [DOI: 10.5402/2012/217162] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Cancer cells display changes that aid them to escape from cell death, sustain their proliferative powers, and shift their metabolism toward glycolytic energy production. Mitochondria are key organelles in many metabolic and biosynthetic pathways, and the adaptation of mitochondrial function has been recognized as crucial to the changes that occur in cancer cells. This paper zooms in on the pathologic evaluation of mitochondrial markers for diagnosing and staging of human cancer and determining the patients’ prognoses.
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Affiliation(s)
- Boel De Paepe
- Laboratories for Neuropathology & Mitochondrial Disorders, Ghent University Hospital, Building K5 3rd Floor, De Pintelaan 185, 9000 Ghent, Belgium
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42
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Alberghina L, Gaglio D, Gelfi C, Moresco RM, Mauri G, Bertolazzi P, Messa C, Gilardi MC, Chiaradonna F, Vanoni M. Cancer cell growth and survival as a system-level property sustained by enhanced glycolysis and mitochondrial metabolic remodeling. Front Physiol 2012; 3:362. [PMID: 22988443 PMCID: PMC3440026 DOI: 10.3389/fphys.2012.00362] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Accepted: 08/23/2012] [Indexed: 12/14/2022] Open
Abstract
Systems Biology holds that complex cellular functions are generated as system-level properties endowed with robustness, each involving large networks of molecular determinants, generally identified by “omics” analyses. In this paper we describe four basic cancer cell properties that can easily be investigated in vitro: enhanced proliferation, evasion from apoptosis, genomic instability, and inability to undergo oncogene-induced senescence. Focusing our analysis on a K-ras dependent transformation system, we show that enhanced proliferation and evasion from apoptosis are closely linked, and present findings that indicate how a large metabolic remodeling sustains the enhanced growth ability. Network analysis of transcriptional profiling gives the first indication on this remodeling, further supported by biochemical investigations and metabolic flux analysis (MFA). Enhanced glycolysis, down-regulation of TCA cycle, decoupling of glucose and glutamine utilization, with increased reductive carboxylation of glutamine, so to yield a sustained production of growth building blocks and glutathione, are the hallmarks of enhanced proliferation. Low glucose availability specifically induces cell death in K-ras transformed cells, while PKA activation reverts this effect, possibly through at least two mitochondrial targets. The central role of mitochondria in determining the two investigated cancer cell properties is finally discussed. Taken together the findings reported herein indicate that a system-level property is sustained by a cascade of interconnected biochemical pathways that behave differently in normal and in transformed cells.
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Affiliation(s)
- Lilia Alberghina
- SysBio Centre for Systems Biology Milano and Rome, Italy ; Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza Milano, Italy
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Selcuklu SD, Donoghue MTA, Rehmet K, de Souza Gomes M, Fort A, Kovvuru P, Muniyappa MK, Kerin MJ, Enright AJ, Spillane C. MicroRNA-9 inhibition of cell proliferation and identification of novel miR-9 targets by transcriptome profiling in breast cancer cells. J Biol Chem 2012; 287:29516-28. [PMID: 22761433 DOI: 10.1074/jbc.m111.335943] [Citation(s) in RCA: 154] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Although underexpression of miR-9 in cancer cells is reported in many cancer types, it is currently difficult to classify miR-9 as a tumor suppressor or an oncomir. We demonstrate that miR-9 expression is down-regulated in MCF-7 and MDA-MB-231 breast cancer cells compared with MCF-10-2A normal breast cell line. Increasing miR-9 expression levels in breast cancer cells induced anti-proliferative, anti-invasive, and pro-apoptotic activity. In addition, microarray profiling of the transcriptome of MCF-7 cells overexpressing miR-9 identified six novel direct miR-9 targets (AP3B1, CCNG1, LARP1, MTHFD1L, MTHFD2, and SRPK1). Among these, MTHFD2 was identified as a miR-9 target gene that affects cell proliferation. Knockdown of MTHFD2 mimicked the effect observed when miR-9 was overexpressed by decreasing cell viability and increasing apoptotic activity. Despite variable effects on different cell lines, proliferative and anti-apoptotic activity of MTHFD2 was demonstrated whereby it could escape from miR-9-directed suppression (by overexpression of MTHFD2 with mutated miR-9 binding sites). Furthermore, endogenous expression levels of miR-9 and MTHFD2 displayed inverse expression profiles in primary breast tumor samples compared with normal breast samples; miR-9 was down-regulated, and MTHFD2 was up-regulated. These results indicate anti-proliferative and pro-apoptotic activity of miR-9 and that direct targeting of MTHFD2 can contribute to tumor suppressor-like activity of miR-9 in breast cancer cells.
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Affiliation(s)
- S Duygu Selcuklu
- Genetics and Biotechnology Laboratory, Centre for Chromosome Biology, National University of Ireland, Galway, Ireland
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Warmoes M, Jaspers JE, Pham TV, Piersma SR, Oudgenoeg G, Massink MPG, Waisfisz Q, Rottenberg S, Boven E, Jonkers J, Jimenez CR. Proteomics of mouse BRCA1-deficient mammary tumors identifies DNA repair proteins with potential diagnostic and prognostic value in human breast cancer. Mol Cell Proteomics 2012; 11:M111.013334. [PMID: 22366898 DOI: 10.1074/mcp.m111.013334] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Breast cancer 1, early onset (BRCA1) hereditary breast cancer, a type of cancer with defects in the homology-directed DNA repair pathway, would benefit from the identification of proteins for diagnosis, which might also be of potential use as screening, prognostic, or predictive markers. Sporadic breast cancers with defects in the BRCA1 pathway might also be diagnosed. We employed proteomics based on one-dimensional gel electrophoresis in combination with nano-LC-MS/MS and spectral counting to compare the protein profiles of mammary tumor tissues of genetic mouse models either deficient or proficient in BRCA1. We identified a total of 3,545 proteins, of which 801 were significantly differentially regulated between the BRCA1-deficient and -proficient breast tumors. Pathway and protein complex analysis identified DNA repair and related functions as the major processes associated with the up-regulated proteins in the BRCA1-deficient tumors. In addition, by selecting highly connected nodes, we identified a BRCA1 deficiency signature of 45 proteins that enriches for homology-directed DNA repair deficiency in human gene expression breast cancer data sets. This signature also exhibits prognostic power across multiple data sets, with optimal performance in a data set enriched in tumors deficient in homology-directed DNA repair. In conclusion, by comparing mouse proteomes from BRCA1-proficient and -deficient mammary tumors, we were able to identify several markers associated with BRCA1 deficiency and a prognostic signature for human breast cancer deficient in homology-directed DNA repair.
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Affiliation(s)
- Marc Warmoes
- Oncoproteomics Laboratory, Department of Medical Oncology, VU University Medical Center, De Boelelaan 1117, 1081HV, Amsterdam, The Netherlands
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Shortening of 3'UTRs correlates with poor prognosis in breast and lung cancer. PLoS One 2012; 7:e31129. [PMID: 22347440 PMCID: PMC3275581 DOI: 10.1371/journal.pone.0031129] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2011] [Accepted: 01/03/2012] [Indexed: 02/06/2023] Open
Abstract
A major part of the post-transcriptional regulation of gene expression is affected by trans-acting elements, such as microRNAs, binding the 3' untraslated region (UTR) of their target mRNAs. Proliferating cells partly escape this type of negative regulation by expressing shorter 3' UTRs, depleted of microRNA binding sites, compared to non-proliferating cells. Using large-scale gene expression datasets, we show that a similar phenomenon takes place in breast and lung cancer: tumors expressing shorter 3' UTRs tend to be more aggressive and to result in shorter patient survival. Moreover, we show that a gene expression signature based only on the expression ratio of alternative 3' UTRs is a strong predictor of survival in both tumors. Genes undergoing 3'UTR shortening in aggressive tumors of the two tissues significantly overlap, and several of them are known to be involved in tumor progression. However the pattern of 3' UTR shortening in aggressive tumors in vivo is clearly distinct from analogous patterns involved in proliferation and transformation.
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CHO WCS, 南 娟. [Proteomics and translational medicine: molecular biomarkers for cancer diagnosis, prognosis and prediction of therapy outcome]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2011; 14:C6-9. [PMID: 23676997 PMCID: PMC6134426 DOI: 10.3779/j.issn.1009-3419.2011.08.12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- William CS CHO
- Department of Clinical Oncology, Queen Elizabeth Hospital, Hong Kong,William CS Cho, PhD, FIBMS, Chartered Scientist.. Department of Clinical Oncology, Queen Elizabeth Hospital, 30 Gascoigne Road, Kowloon, Hong Kong Tel: +852 2958 5441; Fax: +852 2958 5455; E-mail:
| | - 娟 南
- 天津医科大学总医院,天津市肺癌研究所,天津市肺癌转移与肿瘤微环境重点实验室
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Tran LM, Zhang B, Zhang Z, Zhang C, Xie T, Lamb JR, Dai H, Schadt EE, Zhu J. Inferring causal genomic alterations in breast cancer using gene expression data. BMC SYSTEMS BIOLOGY 2011; 5:121. [PMID: 21806811 PMCID: PMC3162519 DOI: 10.1186/1752-0509-5-121] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Accepted: 08/01/2011] [Indexed: 12/29/2022]
Abstract
BACKGROUND One of the primary objectives in cancer research is to identify causal genomic alterations, such as somatic copy number variation (CNV) and somatic mutations, during tumor development. Many valuable studies lack genomic data to detect CNV; therefore, methods that are able to infer CNVs from gene expression data would help maximize the value of these studies. RESULTS We developed a framework for identifying recurrent regions of CNV and distinguishing the cancer driver genes from the passenger genes in the regions. By inferring CNV regions across many datasets we were able to identify 109 recurrent amplified/deleted CNV regions. Many of these regions are enriched for genes involved in many important processes associated with tumorigenesis and cancer progression. Genes in these recurrent CNV regions were then examined in the context of gene regulatory networks to prioritize putative cancer driver genes. The cancer driver genes uncovered by the framework include not only well-known oncogenes but also a number of novel cancer susceptibility genes validated via siRNA experiments. CONCLUSIONS To our knowledge, this is the first effort to systematically identify and validate drivers for expression based CNV regions in breast cancer. The framework where the wavelet analysis of copy number alteration based on expression coupled with the gene regulatory network analysis, provides a blueprint for leveraging genomic data to identify key regulatory components and gene targets. This integrative approach can be applied to many other large-scale gene expression studies and other novel types of cancer data such as next-generation sequencing based expression (RNA-Seq) as well as CNV data.
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Hu H, Deng C, Yang T, Dong Q, Chen Y, Nice EC, Huang C, Wei Y. Proteomics revisits the cancer metabolome. Expert Rev Proteomics 2011; 8:505-533. [DOI: 10.1586/epr.11.31] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
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Cho WCS. Proteomics and translational medicine: molecular biomarkers for cancer diagnosis, prognosis and prediction of therapy outcome. Expert Rev Proteomics 2011; 8:1-4. [PMID: 21329422 DOI: 10.1586/epr.10.108] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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50
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Long X, Zhang J, Zhang Y, Yao J, Cai Z, Yang P. Nano-LC-MS/MS based proteomics of hepatocellular carcinoma cells compared to Chang liver cells and tanshinone IIA induction. MOLECULAR BIOSYSTEMS 2011; 7:1728-41. [DOI: 10.1039/c0mb00343c] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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