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Pastena P, Perera H, Martinino A, Kartsonis W, Giovinazzo F. Unraveling Biomarker Signatures in Triple-Negative Breast Cancer: A Systematic Review for Targeted Approaches. Int J Mol Sci 2024; 25:2559. [PMID: 38473804 PMCID: PMC10931553 DOI: 10.3390/ijms25052559] [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: 01/21/2024] [Revised: 02/16/2024] [Accepted: 02/18/2024] [Indexed: 03/14/2024] Open
Abstract
Triple-negative breast cancer (TNBC) is one of the most aggressive subtypes of breast cancer, marked by poor outcomes and dismal prognosis. Due to the absence of targetable receptors, chemotherapy still represents the main therapeutic option. Therefore, current research is now focusing on understanding the specific molecular pathways implicated in TNBC, in order to identify novel biomarker signatures and develop targeted therapies able to improve its clinical management. With the aim of identifying novel molecular features characterizing TNBC, elucidating the mechanisms by which these molecular biomarkers are implicated in the tumor development and progression, and assessing the impact on cancerous cells following their inhibition or modulation, we conducted a literature search from the earliest works to December 2023 on PubMed, Scopus, and Web Of Science. A total of 146 studies were selected. The results obtained demonstrated that TNBC is characterized by a heterogeneous molecular profile. Several biomarkers have proven not only to be characteristic of TNBC but also to serve as potential effective therapeutic targets, holding the promise of a new era of personalized treatments able to improve its prognosis. The pre-clinical findings that have emerged from our systematic review set the stage for further investigation in forthcoming clinical trials.
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Affiliation(s)
- Paola Pastena
- Department of Medicine, Stony Brook University, Stony Brook, Brookhaven, NY 11794, USA
| | - Hiran Perera
- Renaissance School of Medicine at Stony Brook University, Stony Brook, Brookhaven, NY 11794, USA
| | | | - William Kartsonis
- Renaissance School of Medicine at Stony Brook University, Stony Brook, Brookhaven, NY 11794, USA
| | - Francesco Giovinazzo
- Department of Surgery, Saint Camillus Hospital, 31100 Treviso, Italy
- Department of Surgery, UniCamillus-Saint Camillus International University of Health Sciences, 00131 Rome, Italy
- Department of Surgery, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
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2
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de Oliveira RC, Dos Reis SP, Cavalcante GC. Mutations in Structural Genes of the Mitochondrial Complex IV May Influence Breast Cancer. Genes (Basel) 2023; 14:1465. [PMID: 37510369 PMCID: PMC10379055 DOI: 10.3390/genes14071465] [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: 06/14/2023] [Revised: 07/13/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
Although it has gained more attention in recent years, the relationship between breast cancer (BC) and mitochondrial oxidative phosphorylation (OXPHOS) is still not well understood. Importantly, Complex IV or Cytochrome C Oxidase (COX) of OXPHOS is one of the key players in mitochondrial balance. An in silico investigation of mutations in structural genes of Complex IV was conducted in BC, comprising 2107 samples. Our findings show four variants (rs267606614, rs753969142, rs199476128 and rs267606884) with significant pathogenic potential. Moreover, we highlight nine genes (MT-CO1, MT-CO2, MT-CO3, CO4I2, COX5A, COX5B, COX6A2, COX6C and COX7B2) with a potential impact on BC.
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Affiliation(s)
- Ricardo Cunha de Oliveira
- Laboratory of Human and Medical Genetics, Graduate Program in Genetics and Molecular Biology, Federal University of Pará, Belém 66075-110, Brazil
| | - Sávio Pinho Dos Reis
- Center for Biological and Health Sciences, State University of Pará, Belém 66087-662, Brazil
| | - Giovanna C Cavalcante
- Laboratory of Human and Medical Genetics, Graduate Program in Genetics and Molecular Biology, Federal University of Pará, Belém 66075-110, Brazil
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3
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Geller C, Maddela J, Tuplano R, Runa F, Adamian Y, Güth R, Ortiz Soto G, Tomaneng L, Cantor J, Kelber JA. Fibronectin, DHPS and SLC3A2 Signaling Cooperate to Control Tumor Spheroid Growth, Subcellular eIF5A1/2 Distribution and CDK4/6 Inhibitor Resistance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.13.536765. [PMID: 37090582 PMCID: PMC10120696 DOI: 10.1101/2023.04.13.536765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Extracellular matrix (ECM) protein expression/deposition within and stiffening of the breast cancer microenvironment facilitates disease progression and correlates with poor patient survival. However, the mechanisms by which ECM components control tumorigenic behaviors and responses to therapeutic intervention remain poorly understood. Fibronectin (FN) is a major ECM protein controlling multiple processes. In this regard, we previously reported that DHPS-dependent hypusination of eIF5A1/2 is necessary for fibronectin-mediated breast cancer metastasis and epithelial to mesenchymal transition (EMT). Here, we explored the clinical significance of an interactome generated using hypusination pathway components and markers of intratumoral heterogeneity. Solute carrier 3A2 (SLC3A2 or CD98hc) stood out as an indicator of poor overall survival among patients with basal-like breast cancers that express elevated levels of DHPS. We subsequently discovered that blockade of DHPS or SLC3A2 reduced triple negative breast cancer (TNBC) spheroid growth. Interestingly, spheroids stimulated with exogenous fibronectin were less sensitive to inhibition of either DHPS or SLC3A2 - an effect that could be abrogated by dual DHPS/SLC3A2 blockade. We further discovered that a subset of TNBC cells responded to fibronectin by increasing cytoplasmic localization of eIF5A1/2. Notably, these fibronectin-induced subcellular localization phenotypes correlated with a G0/G1 cell cycle arrest. Fibronectin-treated TNBC cells responded to dual DHPS/SLC3A2 blockade by shifting eIF5A1/2 localization back to a nucleus-dominant state, suppressing proliferation and further arresting cells in the G2/M phase of the cell cycle. Finally, we observed that dual DHPS/SLC3A2 inhibition increased the sensitivity of both Rb-negative and -positive TNBC cells to the CDK4/6 inhibitor palbociclib. Taken together, these data identify a previously unrecognized mechanism through which extracellular fibronectin controls cancer cell tumorigenicity by modulating subcellular eIF5A1/2 localization and provides prognostic/therapeutic utility for targeting the cooperative DHPS/SLC3A2 signaling axis to improve breast cancer treatment responses.
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Affiliation(s)
- Cameron Geller
- Department of Biology, California State University Northridge, Northridge, CA & Department of Biology, Baylor University, Waco, TX
| | - Joanna Maddela
- Department of Biology, California State University Northridge, Northridge, CA & Department of Biology, Baylor University, Waco, TX
| | - Ranel Tuplano
- Department of Biology, California State University Northridge, Northridge, CA & Department of Biology, Baylor University, Waco, TX
| | - Farhana Runa
- Department of Biology, California State University Northridge, Northridge, CA & Department of Biology, Baylor University, Waco, TX
| | - Yvess Adamian
- Department of Biology, California State University Northridge, Northridge, CA & Department of Biology, Baylor University, Waco, TX
| | - Robert Güth
- Department of Biology, California State University Northridge, Northridge, CA & Department of Biology, Baylor University, Waco, TX
| | - Gabriela Ortiz Soto
- Department of Biology, California State University Northridge, Northridge, CA & Department of Biology, Baylor University, Waco, TX
| | - Luke Tomaneng
- Department of Biology, California State University Northridge, Northridge, CA & Department of Biology, Baylor University, Waco, TX
| | - Joseph Cantor
- BD Biosciences, 1077 N Torrey Pines Rd, La Jolla, CA
| | - Jonathan A. Kelber
- Department of Biology, California State University Northridge, Northridge, CA & Department of Biology, Baylor University, Waco, TX
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4
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Zhang S, Liu X, Abdulmomen Ali Mohammed S, Li H, Cai W, Guan W, Liu D, Wei Y, Rong D, Fang Y, Haider F, Lv H, Jin Z, Chen X, Mo Z, Li L, Yang S, Wang H. Adaptor SH3BGRL drives autophagy-mediated chemoresistance through promoting PIK3C3 translation and ATG12 stability in breast cancers. Autophagy 2021; 18:1822-1840. [PMID: 34870550 PMCID: PMC9450985 DOI: 10.1080/15548627.2021.2002108] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Acquired chemotherapy resistance is one of the main culprits in the relapse of breast cancer. But the underlying mechanism of chemotherapy resistance remains elusive. Here, we demonstrate that a small adaptor protein, SH3BGRL, is not only elevated in the majority of breast cancer patients but also has relevance with the relapse and poor prognosis of breast cancer patients. Functionally, SH3BGRL upregulation enhances the chemoresistance of breast cancer cells to the first-line doxorubicin treatment through macroautophagic/autophagic protection. Mechanistically, SH3BGRL can unexpectedly bind to ribosomal subunits to enhance PIK3C3 translation efficiency and sustain ATG12 stability. Therefore, inhibition of autophagy or silence of PIK3C3 or ATG12 can effectively block the driving effect of SH3BGRL on doxorubicin resistance of breast cancer cells in vitro and in vivo. We also validate that SH3BGRL expression is positively correlated with that of PIK3C3 or ATG12, as well as the constitutive occurrence of autophagy in clinical breast cancer tissues. Taken together, our data reveal that SH3BGRL upregulation would be a key driver to the acquired chemotherapy resistance through autophagy enhancement in breast cancer while targeting SH3BGRL could be a potential therapeutic strategy against breast cancer. Abbreviations: ABCs: ATP-binding cassette transporters; Act D: actinomycin D; ACTB/β-actin: actin beta; ATG: autophagy-related; Baf A1: bafilomycin A1; CASP3: caspase 3; CHX: cycloheximide; CQ: chloroquine; Dox: doxorubicin; FBS: fetal bovine serum; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; GEO: gene expression omnibus; GFP: green fluorescent protein; G6PD: glucose-6-phosphate dehydrogenase; GSEA: gene set enrichment analysis; IHC: immunochemistry; KEGG: Kyoto Encyclopedia of Genes and Genomes; MAP1LC3B/LC3B: microtubule-associated protein 1 light chain 3 beta; 3-MA: 3-methyladenine; mRNA: messenger RNA; PIK3C3: phosphatidylinositol 3-kinase catalytic subunit type 3; SH3BGRL: SH3 domain binding glutamate-rich protein-like; SQSTM1/p62: sequestosome 1; ULK1: unc-51 like autophagy activating kinase 1
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Affiliation(s)
- Shaoyang Zhang
- Centers for Translational Medicine Centre, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Xiufeng Liu
- Centers for Translational Medicine Centre, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | | | - Hui Li
- Reproductive Medical Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Wanhua Cai
- Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Wen Guan
- Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
| | - Daiyun Liu
- Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Yanli Wei
- Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Dade Rong
- Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Ying Fang
- Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Farhan Haider
- Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Haimei Lv
- Centers for Translational Medicine Centre, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ziwei Jin
- Centers for Translational Medicine Centre, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Xiaomin Chen
- Department of Hematology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Zhuomao Mo
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory of Ministry of Education, Sun Yat-sen University, Guangzhou, China
| | - Lujie Li
- Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Shulan Yang
- Centers for Translational Medicine Centre, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Haihe Wang
- Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Center for Stem Cell Biology and Tissue Engineering, Key Laboratory of Ministry of Education, Sun Yat-sen University, Guangzhou, China
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5
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Adaptor SH3BGRL promotes breast cancer metastasis through PFN1 degradation by translational STUB1 upregulation. Oncogene 2021; 40:5677-5690. [PMID: 34331014 DOI: 10.1038/s41388-021-01970-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 07/11/2021] [Accepted: 07/19/2021] [Indexed: 02/07/2023]
Abstract
Metastatic recurrence is still a major challenge in breast cancer treatment, but the underlying mechanisms remain unclear. Here, we report that a small adaptor protein, SH3BGRL, is upregulated in the majority of breast cancer patients, especially elevated in those with metastatic relapse, indicating it as a marker for the poor prognosis of breast cancer. Physiologically, SH3BGRL can multifunctionally promote breast cancer cell tumorigenicity, migration, invasiveness, and efficient lung colonization in nude mice. Mechanistically, SH3BGRL downregulates the acting-binding protein profilin 1 (PFN1) by accelerating the translation of the PFN1 E3 ligase, STUB1 via SH3BGRL interaction with ribosomal proteins, or/and enhancing the interaction of PFN1 with STUB1 to accelerate PFN1 degradation. Loss of PFN1 consequently contributes to downstream multiple activations of AKT, NF-kB, and WNT signaling pathways. In contrast, the forced expression of compensatory PFN1 in SH3BGRL-high cells efficiently neutralizes SH3BGRL-induced metastasis and tumorigenesis with PTEN upregulation and PI3K-AKT signaling inactivation. Clinical analysis validates that SH3BGRL expression is negatively correlated with PFN1 and PTEN levels, but positively to the activations of AKT, NF-kB, and WNT signaling pathways in breast patient tissues. Our results thus suggest that SH3BGRL is a valuable prognostic factor and a potential therapeutic target for preventing breast cancer progression and metastasis.
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The ATO/miRNA-885-5p/MTPN axis induces reversal of drug-resistance in cholangiocarcinoma. Cell Oncol (Dordr) 2021; 44:907-916. [PMID: 34170484 DOI: 10.1007/s13402-021-00610-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/13/2021] [Indexed: 10/21/2022] Open
Abstract
PURPOSE Cholangiocarcinoma (CCA) is the second most malignant tumor of the hepatobiliary system. Due to its cumbersome early diagnosis and rapid progression, chemotherapy has become the main treatment option. Primary drug resistance is a major cause of the poor efficacy of chemotherapeutic drugs. Therefore, it is considered urgent to explore new drugs to overcome primary drug resistance of CCA. METHODS Western blot and qRT-PCR assays were used to assess the expression of myotrophin (MTPN) and microRNA-885-5p (miR-885-5p) in CCA tissues and cells. The viability of CCA cells treated with arsenic trioxide (ATO), 5-fluorouracil (5-Fu) and cisplatin (CDDP) was analyzed using a CCK-8 assay. A luciferase reporter assay was used to assess the interaction between miR-885-5p and MTPN. Kaplan-Meier analyses were used for survival assessments. RESULT We found that ATO can reduce the resistance of CCA cells to 5-Fu and CDDP and promote the killing effect of 5-Fu and CDDP. Low-dose ATO showed an anti-drug-resistance effect through up-regulation of the expression of miR-885-5p. Combined with sequencing results and database predictions, we found that MTPN may serve as a direct target of miR-885-5p. After MTPN knockdown, the sensitivity of CCA cells to 5-FU and CDDP was increased. Finally, we found that ATO can reverse chemotherapy resistance induced by overexpression of MTPN. CONCLUSION Our data indicate that the ATO/miR-885-5p/MTPN axis may serve as a target for improving the sensitivity of CCA cells to chemotherapy.
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7
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Liu J, Zhang H, Zhang J, Bing Z, Wang Y, Li Q, Yang K. Identification of robust diagnostic and prognostic gene signatures in different grades of gliomas: a retrospective study. PeerJ 2021; 9:e11350. [PMID: 34026352 PMCID: PMC8121073 DOI: 10.7717/peerj.11350] [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: 10/20/2020] [Accepted: 04/05/2021] [Indexed: 12/23/2022] Open
Abstract
Background Gliomas are the most common primary tumors of the central nervous system. The complexity and heterogeneity of the tumor makes it difficult to obtain good biomarkers for drug development. In this study, through The Cancer Genome Atlas (TCGA) and Chinese Glioma Genome Atlas (CGGA), we analyze the common diagnostic and prognostic moleculer markers in Caucasian and Asian populations, which can be used as drug targets in the future. Methods The RNA-seq data from Genotype-Tissue Expression (GTEx) and The Cancer Genome Atlas (TCGA) were analyzed to identify signatures. Based on the signatures, the prognosis index (PI) of every patient was constructed to predict the prognostic risk. Also, gene ontology (GO) functional enrichment analysis and KEGG analysis were conducted to investigate the biological functions of these mRNAs. Glioma patients’ data in the CGGA database were introduced to validate the effectiveness of the signatures among Chinese populations. Excluding the previously reported prognostic markers of gliomas from this study, the expression of HSPA5 and MTPN were examined by qRT-PCR and immunohistochemical assay. Results In total, 20 mRNAs were finally selected to build PI for patients from TCGA, including 16 high-risk genes and four low-risk genes. For Chinese patients, the log-rank test p values of PI were both less than 0.0001 in two independent datasets. And the AUCs were 0.831 and 0.907 for 3 years of two datasets, respectively. Moreover, among these 20 mRNAs, 10 and 15 mRNAs also had a significant predictive effect via univariate COX analysis in CGGA_693 and CGGA_325, respectively. qRT-PCR and Immunohistochemistry assay indicated that HSPA5 and MTPN over-expressed in Glioma samples compared to normal samples. Conclusion The 20-gene signature can forecast the risk of Glioma in TCGA effectively, moreover it can also predict the risks of Chinese patients through validation in the CGGA database. HSPA5 and MTPN are possible biomarkers of gliomas suitable for all populations to improve the prognosis of these patients.
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Affiliation(s)
- Jieting Liu
- The First Clinical Medical College, Lanzhou University, Lanzhou, China.,Department of Anesthesiology, Lanzhou University Second Hospital, Lanzhou, China.,Evidence-based Medicine Center, Lanzhou University, Lanzhou, China
| | - Hongrui Zhang
- College of Pharmacy, Lanzhou University, Lanzhou, China
| | - Jingyun Zhang
- School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhitong Bing
- Department of Computational Physics, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,School of Nuclear Science and Technology, University of Chinese Academy of Sciences, Lanzhou, China
| | - Yingbin Wang
- Department of Anesthesiology, Lanzhou University Second Hospital, Lanzhou, China
| | - Qiao Li
- Department of Neurosurgery, Lanzhou University Second Hospital, Lanzhou, China
| | - Kehu Yang
- The First Clinical Medical College, Lanzhou University, Lanzhou, China.,Evidence-based Medicine Center, Lanzhou University, Lanzhou, China
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Pavelić SK, Markova-Car E, Klobučar M, Sappe L, Spaventi R. Technological Advances in Preclinical Drug Evaluation: The Role of -Omics Methods. Curr Med Chem 2020; 27:1337-1349. [PMID: 31296156 DOI: 10.2174/0929867326666190711122819] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 06/03/2019] [Accepted: 06/11/2019] [Indexed: 12/11/2022]
Abstract
Preclinical drug development is an essential step in the drug development process where the evaluation of new chemical entities occurs. In particular, preclinical drug development phases include deep analysis of drug candidates' interactions with biomolecules/targets, their safety, toxicity, pharmacokinetics, metabolism by use of assays in vitro and in vivo animal assays. Legal aspects of the required procedures are well-established. Herein, we present a comprehensive summary of current state-of-the art approaches and techniques used in preclinical studies. In particular, we will review the potential of new, -omics methods and platforms for mechanistic evaluation of drug candidates and speed-up of the preclinical evaluation steps.
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Affiliation(s)
- Sandra Kraljević Pavelić
- Department of Biotechnology, Centre for High-Throughput Technologies, University of Rijeka, 51000 Rijeka, Croatia
| | - Elitza Markova-Car
- Department of Biotechnology, Centre for High-Throughput Technologies, University of Rijeka, 51000 Rijeka, Croatia
| | - Marko Klobučar
- Department of Biotechnology, Centre for High-Throughput Technologies, University of Rijeka, 51000 Rijeka, Croatia
| | - Lana Sappe
- Department of Biotechnology, Centre for High-Throughput Technologies, University of Rijeka, 51000 Rijeka, Croatia.,Novartis Oncology Region Europe Headquarter, Largo Umberto Boccioni 1, 21040 Origgio, Italia
| | - Radan Spaventi
- Triadelta Partners d.o.o., Međimurska 19/2, Zagreb, Croatia
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Moriggi M, Giussani M, Torretta E, Capitanio D, Sandri M, Leone R, De Palma S, Vasso M, Vozzi G, Tagliabue E, Gelfi C. ECM Remodeling in Breast Cancer with Different Grade: Contribution of 2D-DIGE Proteomics. Proteomics 2019; 18:e1800278. [PMID: 30353998 DOI: 10.1002/pmic.201800278] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 09/24/2018] [Indexed: 01/05/2023]
Abstract
Tumor extracellular matrix (ECM) plays a pivotal role in outcome of breast cancer (BC) patients. Overexpression of 58 genes, encoding 43 structural ECM proteins, has been identified to determine a specific cluster of BC with accelerated metastatic potential only in the undifferentiated (grade III) phenotype. The scope of this study is to characterize protein repertoire able to predict patient outcome in BC according to ECM gene expression pattern and histological grade. The differential proteomic analysis is based on 2D-differential gel electrophoresis, MALDI-MS, bioinformatics, and immunoblotting. Results suggest a relationship among ECM remodeling, signal mechanotransduction, and metabolic rewiring in BCs characterized by a specific mRNA ECM signature and identified a set of dysregulated proteins characteristic of hormone receptors expression as fibrinogen-β chain, collagen α-1(VI) chain, and α-1B-glycoprotein. Furthermore, in triple negative tumors with ECM signature, the FGG and α5β1/αvβ3 integrins increase whereas detyrosinated α-tubulin and mimecan decrease leading to unorganized integrin presentation involving focal adhesion kinase, activation of Rho GTPases associated to epithelial mesenchymal transition. In hormone receptors negative BCs characterized by a specific ECM gene cluster, the differentially regulated proteins, identified in the present study, can be potentially relevant to predict patient's outcome.
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Affiliation(s)
- Manuela Moriggi
- Department of Biomedical Sciences for Health, University of Milan, Milan 20129, Italy
| | - Marta Giussani
- Molecular Targeting Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan 20133, Italy
| | - Enrica Torretta
- Department of Biomedical Sciences for Health, University of Milan, Milan 20129, Italy
| | - Daniele Capitanio
- Department of Biomedical Sciences for Health, University of Milan, Milan 20129, Italy.,IRCCS Istituto Ortopedico Galeazzi, Milano 20161, Italy
| | - Marco Sandri
- Molecular Targeting Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan 20133, Italy
| | - Roberta Leone
- Department of Biomedical Sciences for Health, University of Milan, Milan 20129, Italy
| | - Sara De Palma
- Institute of Bioimaging and Molecular Physiology, National Research Council (CNR), Segrate-Cefalù 20090, Italy
| | - Michele Vasso
- Institute of Bioimaging and Molecular Physiology, National Research Council (CNR), Segrate-Cefalù 20090, Italy
| | - Giovanni Vozzi
- Research Center BE. Piaggio, University of Pisa, Pisa 56122, Italy.,Dipartimento di Ingegneria dell'Informazione (DII), University of Pisa, Pisa 56122, Italy
| | - Elda Tagliabue
- Molecular Targeting Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan 20133, Italy
| | - Cecilia Gelfi
- Department of Biomedical Sciences for Health, University of Milan, Milan 20129, Italy.,IRCCS Istituto Ortopedico Galeazzi, Milano 20161, Italy
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10
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Eremina L, Pashintseva N, Kovalev L, Kovaleva M, Shishkin S. Proteomics of mammalian mitochondria in health and malignancy: From protein identification to function. Anal Biochem 2018; 552:4-18. [DOI: 10.1016/j.ab.2017.03.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 03/07/2017] [Accepted: 03/23/2017] [Indexed: 12/28/2022]
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11
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Ma L, Liang Z, Zhou H, Qu L. Applications of RNA Indexes for Precision Oncology in Breast Cancer. GENOMICS, PROTEOMICS & BIOINFORMATICS 2018; 16:108-119. [PMID: 29753129 PMCID: PMC6112337 DOI: 10.1016/j.gpb.2018.03.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 03/25/2018] [Accepted: 03/30/2018] [Indexed: 12/11/2022]
Abstract
Precision oncology aims to offer the most appropriate treatments to cancer patients mainly based on their individual genetic information. Genomics has provided numerous valuable data on driver mutations and risk loci; however, it remains a formidable challenge to transform these data into therapeutic agents. Transcriptomics describes the multifarious expression patterns of both mRNAs and non-coding RNAs (ncRNAs), which facilitates the deciphering of genomic codes. In this review, we take breast cancer as an example to demonstrate the applications of these rich RNA resources in precision medicine exploration. These include the use of mRNA profiles in triple-negative breast cancer (TNBC) subtyping to inform corresponding candidate targeted therapies; current advancements and achievements of high-throughput RNA interference (RNAi) screening technologies in breast cancer; and microRNAs as functional signatures for defining cell identities and regulating the biological activities of breast cancer cells. We summarize the benefits of transcriptomic analyses in breast cancer management and propose that unscrambling the core signaling networks of cancer may be an important task of multiple-omic data integration for precision oncology.
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Affiliation(s)
- Liming Ma
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Zirui Liang
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Hui Zhou
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Lianghu Qu
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
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12
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Larson NB, Fogarty ZC, Larson MC, Kalli KR, Lawrenson K, Gayther S, Fridley BL, Goode EL, Winham SJ. An integrative approach to assess X-chromosome inactivation using allele-specific expression with applications to epithelial ovarian cancer. Genet Epidemiol 2017; 41:898-914. [PMID: 29119601 PMCID: PMC5726546 DOI: 10.1002/gepi.22091] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 09/06/2017] [Accepted: 09/27/2017] [Indexed: 01/05/2023]
Abstract
X-chromosome inactivation (XCI) epigenetically silences transcription of an X chromosome in females; patterns of XCI are thought to be aberrant in women's cancers, but are understudied due to statistical challenges. We develop a two-stage statistical framework to assess skewed XCI and evaluate gene-level patterns of XCI for an individual sample by integration of RNA sequence, copy number alteration, and genotype data. Our method relies on allele-specific expression (ASE) to directly measure XCI and does not rely on male samples or paired normal tissue for comparison. We model ASE using a two-component mixture of beta distributions, allowing estimation for a given sample of the degree of skewness (based on a composite likelihood ratio test) and the posterior probability that a given gene escapes XCI (using a Bayesian beta-binomial mixture model). To illustrate the utility of our approach, we applied these methods to data from tumors of ovarian cancer patients. Among 99 patients, 45 tumors were informative for analysis and showed evidence of XCI skewed toward a particular parental chromosome. For 397 X-linked genes, we observed tumor XCI patterns largely consistent with previously identified consensus states based on multiple normal tissue types. However, 37 genes differed in XCI state between ovarian tumors and the consensus state; 17 genes aberrantly escaped XCI in ovarian tumors (including many oncogenes), whereas 20 genes were unexpectedly inactivated in ovarian tumors (including many tumor suppressor genes). These results provide evidence of the importance of XCI in ovarian cancer and demonstrate the utility of our two-stage analysis.
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MESH Headings
- Adult
- Alleles
- Bayes Theorem
- Carcinoma, Ovarian Epithelial
- Chromosomes, Human, X
- Female
- Genes, X-Linked
- Genotype
- Humans
- Models, Genetic
- Neoplasms, Glandular and Epithelial/genetics
- Neoplasms, Glandular and Epithelial/pathology
- Ovarian Neoplasms/genetics
- Ovarian Neoplasms/pathology
- Polymorphism, Single Nucleotide
- RNA, Neoplasm/chemistry
- RNA, Neoplasm/isolation & purification
- RNA, Neoplasm/metabolism
- Sequence Analysis, RNA
- X Chromosome Inactivation
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Affiliation(s)
- Nicholas B. Larson
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Zachary C. Fogarty
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Melissa C. Larson
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | | | - Kate Lawrenson
- Women’s Cancer Program, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Center for Bioinformatics and Functional Genomics, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Simon Gayther
- Center for Bioinformatics and Functional Genomics, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Brooke L. Fridley
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, USA
| | - Ellen L. Goode
- Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Stacey J. Winham
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
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13
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Dehghan-Nayeri N, Eshghi P, Pour KG, Rezaei-Tavirani M, Omrani MD, Gharehbaghian A. Differential expression pattern of protein markers for predicting chemosensitivity of dexamethasone-based chemotherapy of B cell acute lymphoblastic leukemia. Cancer Chemother Pharmacol 2017; 80:177-185. [PMID: 28585036 DOI: 10.1007/s00280-017-3347-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 05/29/2017] [Indexed: 02/06/2023]
Abstract
Dexamethasone is considered as a direct chemotherapeutic agent in the treatment of pediatric acute lymphoblastic leukemia (ALL). Beside the advantages of the drug, some problems arising from the dose-related side effects are challenging issues during the treatment. Accordingly, the classification of patients to dexamethasone sensitive and resistance groups can help to select optimizing the therapeutic dose with the lowest adverse effects particularly in sensitive cases. For this purpose, we investigated inhibited proliferation and induced cytotoxicity in NALM-6 cells, as sensitive cells, after dexamethasone treatment. In addition, comparative protein expression analysis using the 2DE-MALDI-TOF MS technique was performed to identify the specific altered proteins. In addition, we evaluated mRNA expression levels of the identified proteins in bone-marrow samples from pediatric ALL patients using the real-time q-PCR method. Eventually, proteomic analysis revealed a combination of biomarkers, including capping proteins (CAPZA1 and CAPZB), chloride channel (CLIC1), purine nucleoside phosphorylase (PNP), and proteasome activator (PSME1), in response to the dexamethasone treatment. In addition, our results indicated low expression of identified proteins at both the mRNA and protein expression levels after drug treatment. Moreover, quantitative real-time PCR data analysis indicated that independent of the molecular subtypes of the leukemia, CAPZA1, CAPZB, CLIC1, and PNP expression levels were lower in ALL samples than normal samples, although PSME1 expression level was higher in ALL samples than normal samples. Furthermore, the expression level of all proteins (except PSME1) was different between high-risk and standard-risk patients that suggesting the prognostic value of them. In conclusion, our study suggests a panel of biomarkers comprising CAPZA1, CAPZB, CLIC1, PNP, and PSME1 as early diagnosis and treatment evaluation markers that may differentiate cancer cells which are presumably to benefit from dexamethasone-based chemotherapy and may facilitate the prediction of clinical outcome.
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MESH Headings
- Antineoplastic Agents, Hormonal/administration & dosage
- Antineoplastic Agents, Hormonal/pharmacology
- Biomarkers, Tumor/metabolism
- Cell Line, Tumor
- Cell Proliferation/drug effects
- Child
- Child, Preschool
- Dexamethasone/administration & dosage
- Dexamethasone/pharmacology
- Drug Resistance, Neoplasm
- Female
- Gene Expression Regulation, Neoplastic
- Humans
- Infant
- Male
- Precursor B-Cell Lymphoblastic Leukemia-Lymphoma/drug therapy
- Precursor B-Cell Lymphoblastic Leukemia-Lymphoma/genetics
- Precursor B-Cell Lymphoblastic Leukemia-Lymphoma/pathology
- Prognosis
- Proteomics
- RNA, Messenger/metabolism
- Real-Time Polymerase Chain Reaction
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods
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Affiliation(s)
- Nasrin Dehghan-Nayeri
- Proteomics Research Center, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Peyman Eshghi
- Pediatric Congenital Hematologic Disorders Research Center, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Kourosh Goudarzi Pour
- Pediatric Congenital Hematologic Disorders Research Center, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mostafa Rezaei-Tavirani
- Proteomics Research Center, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mir Davood Omrani
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ahmad Gharehbaghian
- Pediatric Congenital Hematologic Disorders Research Center, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
- Department of Hematology and Blood Bank, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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14
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Abdullah MI, Lee CC, Mat Junit S, Ng KL, Hashim OH. Tissue and serum samples of patients with papillary thyroid cancer with and without benign background demonstrate different altered expression of proteins. PeerJ 2016; 4:e2450. [PMID: 27672505 PMCID: PMC5028788 DOI: 10.7717/peerj.2450] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 08/16/2016] [Indexed: 01/08/2023] Open
Abstract
Background Papillary thyroid cancer (PTC) is mainly diagnosed using fine-needle aspiration biopsy. This most common form of well-differentiated thyroid cancer occurs with or without a background of benign thyroid goiter (BTG). Methods In the present study, a gel-based proteomics analysis was performed to analyse the expression of proteins in tissue and serum samples of PTC patients with (PTCb; n = 6) and without a history of BTG (PTCa; n = 8) relative to patients with BTG (n = 20). This was followed by confirmation of the levels of proteins which showed significant altered abundances of more than two-fold difference (p < 0.01) in the tissue and serum samples of the same subjects using ELISA. Results The data of our study showed that PTCa and PTCb distinguish themselves from BTG in the types of tissue and serum proteins of altered abundance. While higher levels of alpha-1 antitrypsin (A1AT) and heat shock 70 kDa protein were associated with PTCa, lower levels of A1AT, protein disulfide isomerase and ubiquitin-conjugating enzyme E2 N seemed apparent in the PTCb. In case of the serum proteins, higher abundances of A1AT and alpha 1-beta glycoprotein were detected in PTCa, while PTCb was associated with enhanced apolipoprotein A-IV and alpha 2-HS glycoprotein (AHSG). The different altered expression of tissue and serum A1AT as well as serum AHSG between PTCa and PTCb patients were also validated by ELISA. Discussion The distinctive altered abundances of the tissue and serum proteins form preliminary indications that PTCa and PTCb are two distinct cancers of the thyroid that are etiologically and mechanistically different although it is currently not possible to rule out that they may also be due other reasons such as the different stages of the malignant disease. These proteins stand to have a potential use as tissue or serum biomarkers to discriminate the three different thyroid neoplasms although this requires further validation in clinically representative populations.
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Affiliation(s)
- Mardiaty Iryani Abdullah
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya , Kuala Lumpur , Malaysia
| | - Ching Chin Lee
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya , Kuala Lumpur , Malaysia
| | - Sarni Mat Junit
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia; University of Malaya Centre for Proteomics Research, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Khoon Leong Ng
- Department of Surgery, Faculty of Medicine, University of Malaya , Kuala Lumpur , Malaysia
| | - Onn Haji Hashim
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia; University of Malaya Centre for Proteomics Research, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
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15
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QuIN: A Web Server for Querying and Visualizing Chromatin Interaction Networks. PLoS Comput Biol 2016; 12:e1004809. [PMID: 27336171 PMCID: PMC4919057 DOI: 10.1371/journal.pcbi.1004809] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 05/12/2016] [Indexed: 01/30/2023] Open
Abstract
Recent studies of the human genome have indicated that regulatory elements (e.g. promoters and enhancers) at distal genomic locations can interact with each other via chromatin folding and affect gene expression levels. Genomic technologies for mapping interactions between DNA regions, e.g., ChIA-PET and HiC, can generate genome-wide maps of interactions between regulatory elements. These interaction datasets are important resources to infer distal gene targets of non-coding regulatory elements and to facilitate prioritization of critical loci for important cellular functions. With the increasing diversity and complexity of genomic information and public ontologies, making sense of these datasets demands integrative and easy-to-use software tools. Moreover, network representation of chromatin interaction maps enables effective data visualization, integration, and mining. Currently, there is no software that can take full advantage of network theory approaches for the analysis of chromatin interaction datasets. To fill this gap, we developed a web-based application, QuIN, which enables: 1) building and visualizing chromatin interaction networks, 2) annotating networks with user-provided private and publicly available functional genomics and interaction datasets, 3) querying network components based on gene name or chromosome location, and 4) utilizing network based measures to identify and prioritize critical regulatory targets and their direct and indirect interactions. AVAILABILITY: QuIN’s web server is available at http://quin.jax.org QuIN is developed in Java and JavaScript, utilizing an Apache Tomcat web server and MySQL database and the source code is available under the GPLV3 license available on GitHub: https://github.com/UcarLab/QuIN/.
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16
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Tong F, Zhang M, Guo X, Shi H, Li L, Guan W, Wang H, Yang S. Expression patterns of SH3BGR family members in zebrafish development. Dev Genes Evol 2016; 226:287-95. [DOI: 10.1007/s00427-016-0552-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Accepted: 05/20/2016] [Indexed: 11/25/2022]
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17
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Davalieva K, Kostovska IM, Kiprijanovska S, Markoska K, Kubelka-Sabit K, Filipovski V, Stavridis S, Stankov O, Komina S, Petrusevska G, Polenakovic M. Proteomics analysis of malignant and benign prostate tissue by 2D DIGE/MS reveals new insights into proteins involved in prostate cancer. Prostate 2015; 75:1586-600. [PMID: 26074449 DOI: 10.1002/pros.23034] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 05/18/2015] [Indexed: 12/25/2022]
Abstract
BACKGROUND The key to a more effective diagnosis, prognosis, and therapeutic management of prostate cancer (PCa) could lie in the direct analysis of cancer tissue. In this study, by comparative proteomics analysis of PCa and benign prostate hyperplasia (BPH) tissues we attempted to elucidate the proteins and regulatory pathways involved in this disease. METHODS The samples used in this study were fresh surgical tissues with clinically and histologically confirmed PCa (n = 19) and BPH (n = 33). We used two dimensional difference in gel electrophoresis (2D DIGE) coupled with mass spectrometry (MS) and bioinformatics analysis. RESULTS Thirty-nine spots with statistically significant 1.8-fold variation or more in abundance, corresponding to 28 proteins were identified. The IPA analysis pointed out to 3 possible networks regulated within MAPK, ERK, TGFB1, and ubiquitin pathways. Thirteen of the identified proteins, namely, constituents of the intermediate filaments (KRT8, KRT18, DES), potential tumor suppressors (ARHGAP1, AZGP1, GSTM2, and MFAP4), transport and membrane organization proteins (FABP5, GC, and EHD2), chaperons (FKBP4 and HSPD1) and known cancer marker (NME1) have been associated with prostate and other cancers by numerous proteomics, genomics or functional studies. We evidenced for the first time the dysregulation of 9 proteins (CSNK1A1, ARID5B, LYPLA1, PSMB6, RABEP1, TALDO1, UBE2N, PPP1CB, and SERPINB1) that may have role in PCa. The UBE2N, PSMB6, and PPP1CB, involved in cell cycle regulation and progression were evaluated by Western blot analysis which confirmed significantly higher abundances of UBE2N and PSMB6 and significantly lower abundance of PPP1CB in PCa. CONCLUSION In addition to the identification of substantial number of proteins with known association with PCa, the proteomic approach in this study revealed proteins not previously clearly related to PCa, providing a starting point for further elucidation of their function in disease initiation and progression.
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Affiliation(s)
- Katarina Davalieva
- Research Centre for Genetic Engineering and Biotechnology "Georgi D Efremov", Macedonian Academy of Sciences and Arts, Skopje, Republic of Macedonia
| | - Ivana Maleva Kostovska
- Research Centre for Genetic Engineering and Biotechnology "Georgi D Efremov", Macedonian Academy of Sciences and Arts, Skopje, Republic of Macedonia
| | - Sanja Kiprijanovska
- Research Centre for Genetic Engineering and Biotechnology "Georgi D Efremov", Macedonian Academy of Sciences and Arts, Skopje, Republic of Macedonia
| | - Katerina Markoska
- Research Centre for Genetic Engineering and Biotechnology "Georgi D Efremov", Macedonian Academy of Sciences and Arts, Skopje, Republic of Macedonia
| | - Katerina Kubelka-Sabit
- Labaratory for Histopathology, Clinical Hospital "Sistina", Skopje, Republic of Macedonia
| | - Vanja Filipovski
- Labaratory for Histopathology, Clinical Hospital "Sistina", Skopje, Republic of Macedonia
| | - Sotir Stavridis
- University Clinic for Urology, University Clinical Centre "Mother Theresa", Skopje, Republic of Macedonia
| | - Oliver Stankov
- University Clinic for Urology, University Clinical Centre "Mother Theresa", Skopje, Republic of Macedonia
| | - Selim Komina
- Institute of Pathology, Medical Faculty, University "St. Cyril and Methodius", Skopje, Republic of Macedonia
| | - Gordana Petrusevska
- Institute of Pathology, Medical Faculty, University "St. Cyril and Methodius", Skopje, Republic of Macedonia
| | - Momir Polenakovic
- Research Centre for Genetic Engineering and Biotechnology "Georgi D Efremov", Macedonian Academy of Sciences and Arts, Skopje, Republic of Macedonia
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18
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Flores-Pérez A, Marchat LA, Sánchez LL, Romero-Zamora D, Arechaga-Ocampo E, Ramírez-Torres N, Chávez JD, Carlos-Reyes Á, Astudillo-de la Vega H, Ruiz-García E, González-Pérez A, López-Camarillo C. Differential proteomic analysis reveals that EGCG inhibits HDGF and activates apoptosis to increase the sensitivity of non-small cells lung cancer to chemotherapy. Proteomics Clin Appl 2015; 10:172-82. [PMID: 26175166 DOI: 10.1002/prca.201500008] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 06/11/2015] [Accepted: 07/09/2015] [Indexed: 12/29/2022]
Abstract
PURPOSE To search for regulated proteins in response to green tea (-)-epigallocatechin-3-gallate (EGCG) in A549 lung cancer cells. EXPERIMENTAL DESIGN 2DE and ESI/multistage MS (ESI-MS/MS) were performed to identify modulated proteins in A549 cells treated with EGCG. Cell migration was evaluated by transwell assays. RNA interference was used to silence the hepatoma-derived growth factor (HDGF). Caspase-3, caspase-9, and HDGF were immunodetected by Western blot assays. Flow cytometry was used for detection of mitochondrial membrane potential and apoptosis. RESULTS We found that HDGF expression was threefold suppressed by EGCG treatment. Downregulation of HDGF by EGCG was confirmed using anti-HDGF antibodies in three lung cancer cell lines. EGCG treatment and HDGF abrogation by RNA interference resulted in a decreased migration of A549 cells. In addition, EGCG induced a marked synergistic effect with cisplatin in cell death. Consistently, an enhanced cytotoxicity in HDGF-silenced cells was also found. Cell death was associated to increased apoptosis, disruption of the mitochondrial membrane potential, and activation of caspase-3 and caspase-9. CONCLUSION AND CLINICAL RELEVANCE Our data suggest for the first time that abrogation of HDGF by EGCG enhances cisplatin-induced apoptosis and sensitize A549 cells to chemotherapy. Therefore, we propose that decreasing the HDGF levels by using EGCG may represent a novel strategy in lung cancer therapy.
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Affiliation(s)
- Ali Flores-Pérez
- Genomics Sciences Program, Autonomous University of Mexico City, Mexico City, Mexico
| | - Laurence A Marchat
- Molecular Biomedicine Program, National School of Medicine and Homeopathy, National Polytechnic Institute, Mexico.,Biotechnology Program, National School of Medicine and Homeopathy, National Polytechnic Institute, Mexico
| | - Lidia López Sánchez
- Genomics Sciences Program, Autonomous University of Mexico City, Mexico City, Mexico
| | - Diana Romero-Zamora
- Genomics Sciences Program, Autonomous University of Mexico City, Mexico City, Mexico
| | | | - Nayeli Ramírez-Torres
- Genomics Sciences Program, Autonomous University of Mexico City, Mexico City, Mexico
| | - José Díaz Chávez
- Oncogenomics Laboratory, National Institute of Cancerology, Mexico
| | | | - Horacio Astudillo-de la Vega
- Laboratory of Translational Cancer Research and Cellular Therapy, Oncology Hospital, Medical Center Siglo XXI, Mexico
| | - Erika Ruiz-García
- Translational Medicine Laboratory, National Institute of Cancerology, Mexico
| | | | - César López-Camarillo
- Genomics Sciences Program, Autonomous University of Mexico City, Mexico City, Mexico
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19
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Campone M, Valo I, Jézéquel P, Moreau M, Boissard A, Campion L, Loussouarn D, Verriele V, Coqueret O, Guette C. Prediction of Recurrence and Survival for Triple-Negative Breast Cancer (TNBC) by a Protein Signature in Tissue Samples. Mol Cell Proteomics 2015. [PMID: 26209610 DOI: 10.1074/mcp.m115.048967] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
To date, there is no available targeted therapy for patients who are diagnosed with triple-negative breast cancers (TNBC). The aim of this study was to identify a new specific target for specific treatments. Frozen primary tumors were collected from 83 adjuvant therapy-naive TNBC patients. These samples were used for global proteome profiling by iTRAQ-OFFGEL-LC-MS/MS approach in two series: a training cohort (n = 42) and a test set (n = 41). Patients who remains free of local or distant metastasis for a minimum of 5 years after surgery were classified in the no-relapse group; the others were in the relapse group. OPLS and Kaplan-Meier analyses were performed to select candidate markers, which were validated by immunohistochemistry. Three proteins were identified in the training set and validated in the test set by Kaplan-Meier method and immunohistochemistry (IHC): TrpRS as a good prognostic markers and DP and TSP1 as bad prognostic markers. We propose the establishment of an IHC test to calculate the score of TrpRS, DP, and TSP1 in TNBC tumors to evaluate the degree of aggressiveness of the tumors. Finally, we propose that DP and TSP1 could provide therapeutic targets for specific treatments.
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Affiliation(s)
- Mario Campone
- ‡René Gauducheau ICO Cancer Center, Inserm U892, CNRS 6299, Bd J. Monod, 44805 Saint Herblain Cedex, France; §Paul Papin ICO Cancer Center, Inserm U892, CNRS 6299, 2 rue Moll, 49933 Angers Cedex 9, France
| | - Isabelle Valo
- §Paul Papin ICO Cancer Center, Inserm U892, CNRS 6299, 2 rue Moll, 49933 Angers Cedex 9, France
| | - Pascal Jézéquel
- ‡René Gauducheau ICO Cancer Center, Inserm U892, CNRS 6299, Bd J. Monod, 44805 Saint Herblain Cedex, France
| | - Marie Moreau
- ¶Angers University, 4 Boulevard de Lavoisier, Angers, 49000, France
| | - Alice Boissard
- §Paul Papin ICO Cancer Center, Inserm U892, CNRS 6299, 2 rue Moll, 49933 Angers Cedex 9, France
| | - Loic Campion
- ‡René Gauducheau ICO Cancer Center, Inserm U892, CNRS 6299, Bd J. Monod, 44805 Saint Herblain Cedex, France
| | - Delphine Loussouarn
- ‖INSERM U892, CNRS 6299, IRT-UN, 8 quai Moncousu, 44007 Nantes Cedex, France
| | - Véronique Verriele
- §Paul Papin ICO Cancer Center, Inserm U892, CNRS 6299, 2 rue Moll, 49933 Angers Cedex 9, France
| | - Olivier Coqueret
- §Paul Papin ICO Cancer Center, Inserm U892, CNRS 6299, 2 rue Moll, 49933 Angers Cedex 9, France; ¶Angers University, 4 Boulevard de Lavoisier, Angers, 49000, France
| | - Catherine Guette
- §Paul Papin ICO Cancer Center, Inserm U892, CNRS 6299, 2 rue Moll, 49933 Angers Cedex 9, France;
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