1
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Li L. Stimulating STING for cancer therapy: Taking the extracellular route. Cell Chem Biol 2024; 31:851-861. [PMID: 38723635 DOI: 10.1016/j.chembiol.2024.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 03/14/2024] [Accepted: 04/09/2024] [Indexed: 05/19/2024]
Abstract
Ten years ago, the second messenger cGAMP was discovered as the activator of the anti-cancer STING pathway. The characterization of cGAMP's paracrine action and dominant extracellular hydrolase ENPP1 cemented cGAMP as an intercellular immunotransmitter that coordinates the innate and adaptive immune systems to fight cancer. In this Perspective, I look back at a decade of discovery of extracellular cGAMP biology and drug development aiming to supply or preserve extracellular cGAMP for cancer treatment. Reviewing our understanding of the cell type-specific regulatory mechanisms of STING agonists, including their transporters and degradation enzymes, I explain on a molecular and cellular level the successes and challenges of direct STING agonists for cancer therapy. Based on what we know now, I propose new ways to stimulate the STING pathway in a manner that is not only cancer specific, but also cell type specific to fully harness the anti-cancer effect of cGAMP while avoiding collateral damage.
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Affiliation(s)
- Lingyin Li
- Arc Institute, Palo Alto, CA, 94304 USA; Department of Biochemistry and Sarafan ChEM-H Institute, Stanford University, Stanford, CA, 94305 USA.
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2
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Jia X, He X, Huang C, Li J, Dong Z, Liu K. Protein translation: biological processes and therapeutic strategies for human diseases. Signal Transduct Target Ther 2024; 9:44. [PMID: 38388452 PMCID: PMC10884018 DOI: 10.1038/s41392-024-01749-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 01/13/2024] [Accepted: 01/18/2024] [Indexed: 02/24/2024] Open
Abstract
Protein translation is a tightly regulated cellular process that is essential for gene expression and protein synthesis. The deregulation of this process is increasingly recognized as a critical factor in the pathogenesis of various human diseases. In this review, we discuss how deregulated translation can lead to aberrant protein synthesis, altered cellular functions, and disease progression. We explore the key mechanisms contributing to the deregulation of protein translation, including functional alterations in translation factors, tRNA, mRNA, and ribosome function. Deregulated translation leads to abnormal protein expression, disrupted cellular signaling, and perturbed cellular functions- all of which contribute to disease pathogenesis. The development of ribosome profiling techniques along with mass spectrometry-based proteomics, mRNA sequencing and single-cell approaches have opened new avenues for detecting diseases related to translation errors. Importantly, we highlight recent advances in therapies targeting translation-related disorders and their potential applications in neurodegenerative diseases, cancer, infectious diseases, and cardiovascular diseases. Moreover, the growing interest lies in targeted therapies aimed at restoring precise control over translation in diseased cells is discussed. In conclusion, this comprehensive review underscores the critical role of protein translation in disease and its potential as a therapeutic target. Advancements in understanding the molecular mechanisms of protein translation deregulation, coupled with the development of targeted therapies, offer promising avenues for improving disease outcomes in various human diseases. Additionally, it will unlock doors to the possibility of precision medicine by offering personalized therapies and a deeper understanding of the molecular underpinnings of diseases in the future.
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Affiliation(s)
- Xuechao Jia
- Department of Pathophysiology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, 450000, China
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, 450000, China
| | - Xinyu He
- Department of Pathophysiology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, 450000, China
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, 450000, China
| | - Chuntian Huang
- Department of Pathology and Pathophysiology, Henan University of Chinese Medicine, Zhengzhou, Henan, 450000, China
| | - Jian Li
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, 450000, China
| | - Zigang Dong
- Department of Pathophysiology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, 450000, China.
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, 450000, China.
- Tianjian Laboratory of Advanced Biomedical Sciences, Zhengzhou, Henan, 450052, China.
- Research Center for Basic Medicine Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450052, Henan, China.
- Provincial Cooperative Innovation Center for Cancer Chemoprevention, Zhengzhou University, Zhengzhou, Henan, 450000, China.
| | - Kangdong Liu
- Department of Pathophysiology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, 450000, China.
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, 450000, China.
- Tianjian Laboratory of Advanced Biomedical Sciences, Zhengzhou, Henan, 450052, China.
- Research Center for Basic Medicine Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450052, Henan, China.
- Provincial Cooperative Innovation Center for Cancer Chemoprevention, Zhengzhou University, Zhengzhou, Henan, 450000, China.
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, Henan, 450000, China.
- The Collaborative Innovation Center of Henan Province for Cancer Chemoprevention, Zhengzhou, Henan, 450000, China.
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3
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Wang S, Böhnert V, Joseph AJ, Sudaryo V, Skariah G, Swinderman JT, Yu FB, Subramanyam V, Wolf DM, Lyu X, Gilbert LA, van’t Veer LJ, Goodarzi H, Li L. ENPP1 is an innate immune checkpoint of the anticancer cGAMP-STING pathway in breast cancer. Proc Natl Acad Sci U S A 2023; 120:e2313693120. [PMID: 38117852 PMCID: PMC10756298 DOI: 10.1073/pnas.2313693120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 11/10/2023] [Indexed: 12/22/2023] Open
Abstract
Ectonucleotide pyrophosphatase/phosphodiesterase 1 (ENPP1) expression correlates with poor prognosis in many cancers, and we previously discovered that ENPP1 is the dominant hydrolase of extracellular cGAMP: a cancer-cell-produced immunotransmitter that activates the anticancer stimulator of interferon genes (STING) pathway. However, ENPP1 has other catalytic activities and the molecular and cellular mechanisms contributing to its tumorigenic effects remain unclear. Here, using single-cell RNA-seq, we show that ENPP1 in both cancer and normal tissues drives primary breast tumor growth and metastasis by dampening extracellular 2'3'-cyclic-GMP-AMP (cGAMP)-STING-mediated antitumoral immunity. ENPP1 loss-of-function in both cancer cells and normal tissues slowed primary tumor growth and abolished metastasis. Selectively abolishing the cGAMP hydrolysis activity of ENPP1 phenocopied ENPP1 knockout in a STING-dependent manner, demonstrating that restoration of paracrine cGAMP-STING signaling is the dominant anti-cancer mechanism of ENPP1 inhibition. Finally, ENPP1 expression in breast tumors deterministically predicated whether patients would remain free of distant metastasis after pembrolizumab (anti-PD-1) treatment followed by surgery. Altogether, ENPP1 blockade represents a strategy to exploit cancer-produced extracellular cGAMP for controlled local activation of STING and is therefore a promising therapeutic approach against breast cancer.
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Affiliation(s)
- Songnan Wang
- Department of Biochemistry, Stanford University, Stanford, CA94305
- ChEM-H Institute, Stanford University, Stanford, CA94305
- Arc Institute, Palo Alto, CA94304
| | - Volker Böhnert
- Department of Biochemistry, Stanford University, Stanford, CA94305
- ChEM-H Institute, Stanford University, Stanford, CA94305
| | - Alby J. Joseph
- Department of Biochemistry, Stanford University, Stanford, CA94305
- ChEM-H Institute, Stanford University, Stanford, CA94305
- Arc Institute, Palo Alto, CA94304
| | - Valentino Sudaryo
- Department of Biochemistry, Stanford University, Stanford, CA94305
- ChEM-H Institute, Stanford University, Stanford, CA94305
- Arc Institute, Palo Alto, CA94304
| | - Gemini Skariah
- Department of Biochemistry, Stanford University, Stanford, CA94305
- ChEM-H Institute, Stanford University, Stanford, CA94305
| | - Jason T. Swinderman
- Arc Institute, Palo Alto, CA94304
- Department of Urology, University of California, San Francisco, CA94143
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA94158
| | | | - Vishvak Subramanyam
- Department of Urology, University of California, San Francisco, CA94143
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA94158
- Department of Biophysics & Biochemistry, University of California, San Francisco, CA94143
- Baker Computational Health Science Institute, University of California, San Francisco, CA94143
| | - Denise M. Wolf
- Department of Laboratory Medicine, University of California, San Francisco, CA94115
| | - Xuchao Lyu
- ChEM-H Institute, Stanford University, Stanford, CA94305
- Department of Pathology, Stanford University School of Medicine, Stanford, CA94305
| | - Luke A. Gilbert
- Arc Institute, Palo Alto, CA94304
- Department of Urology, University of California, San Francisco, CA94143
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA94158
| | - Laura J. van’t Veer
- Department of Laboratory Medicine, University of California, San Francisco, CA94115
| | - Hani Goodarzi
- Department of Urology, University of California, San Francisco, CA94143
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA94158
- Department of Biophysics & Biochemistry, University of California, San Francisco, CA94143
- Baker Computational Health Science Institute, University of California, San Francisco, CA94143
| | - Lingyin Li
- Department of Biochemistry, Stanford University, Stanford, CA94305
- ChEM-H Institute, Stanford University, Stanford, CA94305
- Arc Institute, Palo Alto, CA94304
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4
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Bhattacharya S, Rathore AS. A novel filter-assisted protein precipitation (FAPP) based sample pre-treatment method for LC-MS peptide mapping for biosimilar characterization. J Pharm Biomed Anal 2023; 234:115527. [PMID: 37364451 DOI: 10.1016/j.jpba.2023.115527] [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: 03/02/2023] [Revised: 06/06/2023] [Accepted: 06/11/2023] [Indexed: 06/28/2023]
Abstract
Establishing analytical and functional comparability serves as the foundation of biosimilar development. A critical part of this exercise is sequence similarity search and categorization of post-translational modifications (PTMs), often by peptide mapping using liquid chromatography-mass spectrometry (LC-MS). When performing bottom-up proteomic sample preparation, efficient digestion of the protein and extraction of peptides for subsequent mass spectrometric analysis can be a challenge. Conventional sample preparation strategies face the risk of allowing interference of chemicals which are essential for extraction but are likely to interfere with digestion, resulting in complex chromatographic profiles due to semi-cleavages, insufficient peptide cleavages, and other unwanted reactions. Further, peptide cleanup through commonly used immobilized C-18 pipette tips can cause significant peptide loss as well as variability in individual peptide yields, thereby causing artifacts of various product-related modifications. In this study, we proposed a simple enzymatic digestion technique by incorporating different molecular weight filters and protein precipitation, with the objective to minimize interference of denaturing, reducing, and alkylating agents throughout overnight digestion. As a result, the need for peptide cleanup is significantly reduced and results in higher peptide yield. The proposed FAPP approach outperformed the conventional method across multiple metrics including, 30% more peptides, 8.19% more fully digested peptides, 14% higher sequence coverage rate, and 11.82% more site-specific alterations. Quantitative and qualitative repeatability of the proposed approach have been demonstrated. It can be concluded that the filter-assisted protein precipitation (FAPP) protocol proposed in this study offers an effective substitute for the traditional approach.
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Affiliation(s)
| | - Anurag S Rathore
- Chemical Engineering Department, Indian Institute of Technology Delhi, India.
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5
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Wang S, Böhnert V, Joseph AJ, Sudaryo V, Swinderman J, Yu FB, Lyu X, Skariah G, Subramanyam V, Gilbert LA, Goodarzi H, Lingyin L. ENPP1 is an innate immune checkpoint of the anticancer cGAMP-STING pathway. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.01.543353. [PMID: 37333273 PMCID: PMC10274658 DOI: 10.1101/2023.06.01.543353] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
ENPP1 expression correlates with poor prognosis in many cancers, and we previously discovered that ENPP1 is the dominant hydrolase of extracellular cGAMP: a cancer-cell-produced immunotransmitter that activates the anticancer STING pathway. However, ENPP1 has other catalytic activities and the molecular and cellular mechanisms contributing to its tumorigenic effects remain unclear. Here, using single cell RNA-seq (scRNA-seq), we show that ENPP1 overexpression drives primary breast tumor growth and metastasis by synergistically dampening extracellular cGAMP-STING mediated antitumoral immunity and activating immunosuppressive extracellular adenosine (eADO) signaling. In addition to cancer cells, stromal and immune cells in the tumor microenvironment (TME) also express ENPP1 that restrains their response to tumor-derived cGAMP. Enpp1 loss-of-function in both cancer cells and normal tissues slowed primary tumor initiation and growth and prevented metastasis in an extracellular cGAMP- and STING-dependent manner. Selectively abolishing the cGAMP hydrolysis activity of ENPP1 phenocopied total ENPP1 knockout, demonstrating that restoration of paracrine cGAMP-STING signaling is the dominant anti-cancer mechanism of ENPP1 inhibition. Strikingly, we find that breast cancer patients with low ENPP1 expression have significantly higher immune infiltration and improved response to therapeutics impacting cancer immunity upstream or downstream of the cGAMP-STING pathway, like PARP inhibitors and anti-PD1. Altogether, selective inhibition of ENPP1's cGAMP hydrolase activity alleviates an innate immune checkpoint to boost cancer immunity and is therefore a promising therapeutic approach against breast cancer that may synergize with other cancer immunotherapies.
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Affiliation(s)
- Songnan Wang
- Department of Biochemistry, Stanford University, Stanford 94305, USA
- ChEM-H Institute, Stanford University, Stanford 94305, USA
- Arc Institute, Palo Alto 94304, USA
| | - Volker Böhnert
- Department of Biochemistry, Stanford University, Stanford 94305, USA
- ChEM-H Institute, Stanford University, Stanford 94305, USA
| | - Alby J. Joseph
- Department of Biochemistry, Stanford University, Stanford 94305, USA
- ChEM-H Institute, Stanford University, Stanford 94305, USA
- Arc Institute, Palo Alto 94304, USA
| | - Valentino Sudaryo
- Department of Biochemistry, Stanford University, Stanford 94305, USA
- ChEM-H Institute, Stanford University, Stanford 94305, USA
- Arc Institute, Palo Alto 94304, USA
| | - Jason Swinderman
- Arc Institute, Palo Alto 94304, USA
- Department of Urology, University of California, San Francisco, San Francisco 94143, USA
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | | | - Xuchao Lyu
- ChEM-H Institute, Stanford University, Stanford 94305, USA
| | - Gemini Skariah
- Department of Biochemistry, Stanford University, Stanford 94305, USA
- ChEM-H Institute, Stanford University, Stanford 94305, USA
| | - Vishvak Subramanyam
- Department of Urology, University of California, San Francisco, San Francisco 94143, USA
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Biophysics & Biochemistry, University of California, San Francisco, San Francisco 94143, USA
- UCSF Baker Computational Health Science Institute, University of California, San Francisco, 94143, USA
| | - Luke A. Gilbert
- Arc Institute, Palo Alto 94304, USA
- Department of Urology, University of California, San Francisco, San Francisco 94143, USA
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Hani Goodarzi
- Department of Urology, University of California, San Francisco, San Francisco 94143, USA
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Biophysics & Biochemistry, University of California, San Francisco, San Francisco 94143, USA
- UCSF Baker Computational Health Science Institute, University of California, San Francisco, 94143, USA
| | - Li Lingyin
- Department of Biochemistry, Stanford University, Stanford 94305, USA
- ChEM-H Institute, Stanford University, Stanford 94305, USA
- Arc Institute, Palo Alto 94304, USA
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6
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Nisa MU, Farooq S, Ali S, Eachkoti R, Rehman MU, Hafiz S. Proteomics: A modern tool for identifying therapeutic targets in different types of carcinomas. Proteomics 2023. [DOI: 10.1016/b978-0-323-95072-5.00013-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
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7
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Chen W, Liang W, He Y, Liu C, Chen H, Lv P, Yao Y, Zhou H. Immune microenvironment-related gene mapping predicts immunochemotherapy response and prognosis in diffuse large B-cell lymphoma. Med Oncol 2022; 39:44. [PMID: 35092504 DOI: 10.1007/s12032-021-01642-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 12/23/2021] [Indexed: 01/01/2023]
Abstract
Diffuse large B-cell lymphoma (DLBCL) is the most common subtype of non-Hodgkin's lymphoma (NHL). The R-CHOP immunochemotherapy regimen is the first-line treatment option for DLBCL patients and has greatly improved the prognosis of DLBCL, making it a curable disease. However, drug resistance or relapse is the main challenge for current DLBCL treatment. Studies have shown that the tumor microenvironment plays an important role in the onset, development, and responsiveness to drugs in DLBCL. Here, we used the CIBERSORT algorithm to resolve the composition of the immune microenvironment of 471 DLBCL patients from the GEO database. We found that activated memory CD4+ T cells and γδ T cells were significantly associated with immunochemotherapy response. Weighted gene co-expression networks (WGCNA) were constructed using differentially expressed genes from immunochemotherapy responders and non-responders. The module most associated with these two types of T cells was defined as hub module. Enrichment analysis of the hub module showed that baseline immune status was significantly stronger in responders than in non-responders. A protein-protein interaction (PPI) network was constructed for hub module to identify hub genes. After survival analysis, five prognosis-related genes (CD3G, CD3D, GNB4, FCHO2, GPR183) were identified and all these genes were significantly negatively associated with PD1. Using our own patient cohort, we validated the efficacy of CD3G and CD3D in predicting immunochemotherapy response. Our study showed that CD3G, CD3D, GNB4, FCHO2, and GPR183 are involved in the regulation of the immune microenvironment of DLBCL. They can be used as biomarkers for predicting immunochemotherapy response and potential therapeutic targets in DLBCL.
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Affiliation(s)
- Wanjun Chen
- Department of Blood Transfusion, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Weijie Liang
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yongjian He
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Chixiang Liu
- Department of Blood Transfusion, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Hongtian Chen
- Department of Blood Transfusion, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Piao Lv
- Department of Blood Transfusion, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Yuan Yao
- Department of Blood Transfusion, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Huayou Zhou
- Department of Blood Transfusion, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
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8
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Saatci O, Huynh-Dam KT, Sahin O. Endocrine resistance in breast cancer: from molecular mechanisms to therapeutic strategies. J Mol Med (Berl) 2021; 99:1691-1710. [PMID: 34623477 PMCID: PMC8611518 DOI: 10.1007/s00109-021-02136-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/20/2021] [Accepted: 09/06/2021] [Indexed: 12/31/2022]
Abstract
Estrogen receptor-positive (ER +) breast cancer accounts for approximately 75% of all breast cancers. Endocrine therapies, including selective ER modulators (SERMs), aromatase inhibitors (AIs), and selective ER down-regulators (SERDs) provide substantial clinical benefit by reducing the risk of disease recurrence and mortality. However, resistance to endocrine therapies represents a major challenge, limiting the success of ER + breast cancer treatment. Mechanisms of endocrine resistance involve alterations in ER signaling via modulation of ER (e.g., ER downregulation, ESR1 mutations or fusions); alterations in ER coactivators/corepressors, transcription factors (TFs), nuclear receptors and epigenetic modulators; regulation of signaling pathways; modulation of cell cycle regulators; stress signaling; and alterations in tumor microenvironment, nutrient stress, and metabolic regulation. Current therapeutic strategies to improve outcome of endocrine-resistant patients in clinics include inhibitors against mechanistic target of rapamycin (mTOR), cyclin-dependent kinase (CDK) 4/6, and the phosphoinositide 3-kinase (PI3K) subunit, p110α. Preclinical studies reveal novel therapeutic targets, some of which are currently tested in clinical trials as single agents or in combination with endocrine therapies, such as ER partial agonists, ER proteolysis targeting chimeras (PROTACs), next-generation SERDs, AKT inhibitors, epidermal growth factor receptor 1 and 2 (EGFR/HER2) dual inhibitors, HER2 targeting antibody-drug conjugates (ADCs) and histone deacetylase (HDAC) inhibitors. In this review, we summarize the established and emerging mechanisms of endocrine resistance, alterations during metastatic recurrence, and discuss the approved therapies and ongoing clinical trials testing the combination of novel targeted therapies with endocrine therapy in endocrine-resistant ER + breast cancer patients.
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Affiliation(s)
- Ozge Saatci
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina, 715, Sumter Street, CLS609D, Columbia, SC, 29208, USA
| | - Kim-Tuyen Huynh-Dam
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina, 715, Sumter Street, CLS609D, Columbia, SC, 29208, USA
| | - Ozgur Sahin
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina, 715, Sumter Street, CLS609D, Columbia, SC, 29208, USA.
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9
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Chen TJ, Dehghanian SZ, Chan TC, He HL, Li WS, Abdollahi S, Chen NY, Li CF, Shiue YL. High G protein subunit beta 4 protein level is correlated to poor prognosis of urothelial carcinoma. Med Mol Morphol 2021; 54:356-367. [PMID: 34398348 DOI: 10.1007/s00795-021-00301-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 08/05/2021] [Indexed: 12/22/2022]
Abstract
Data mining on a public domain detected eight potential transcripts which were upregulated in advanced UBUCs, suggesting that they may take part in UC development or/and progression. Retrospectively, immunohistochemistry along with H-score recording was carried out to evaluate the GNB4 protein levels on tissues from UC patients. Correlations between GNB4 H-score and imperative clinicopathological factors, as well as the implication of GNB4 protein level on disease-specific and metastasis-free survivals were assessed. In UTUCs (n = 340) and UBUCs (n = 295), 170 (50.0%) and 148 (50.0%) cases, respectively, were identified to be of high GNB4 expression. The GNB4 protein levels were correlated to numerous clinicopathological features and patients' survivals. Upregulation of the GNB4 protein was significantly associated with primary tumor, nodal metastasis, histological grade, vascular invasion and mitotic rate. High GNB4 protein levels independently and significantly predicted poor disease-specific and metastasis-free in UTUC and UBUC, respectively. Ingenuity pathway analysis furthermore showed that multiple signaling pathways were enriched including 'Communication between Innate and Adaptive Immune Cells' and 'NFκB Signaling'. Our findings demonstrated that the upregulation of the GNB4 protein is an independent unfavorable prognosticator in UC. High GNB4 gene expression plays an important role in UC progression.
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Affiliation(s)
- Tzu-Ju Chen
- Department of Pathology, Chi Mei Medical Center, Tainan, Taiwan.,Department of Medical Technology, Chung Hwa University of Medical Technology, Tainan, Taiwan.,Institute of Biomedical Sciences, National Sun Yat-Sen University, 70 Lienhai Rd., 80424, Kaohsiung, Taiwan
| | - Seyedeh Zahra Dehghanian
- Institute of Biomedical Sciences, National Sun Yat-Sen University, 70 Lienhai Rd., 80424, Kaohsiung, Taiwan
| | - Ti-Chun Chan
- Department of Medical Research, Chi Mei Medical Center, 901 Zhanghua Rd, 71004, Tainan, Taiwan.,National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan
| | - Hong-Lin He
- Department of Pathology, Chi Mei Medical Center, Tainan, Taiwan.,Department of Optometry, Chung Hwa University of Medical Technology, Tainan, Taiwan
| | - Wan-Shan Li
- Department of Pathology, Chi Mei Medical Center, Tainan, Taiwan.,Department of Medical Technology, Chung Hwa University of Medical Technology, Tainan, Taiwan
| | - Sina Abdollahi
- Department of Computer Science and Information Engineering, National Cheng-Kung University, Tainan, Taiwan
| | - Nai-Yu Chen
- Institute of Precision Medicine, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Chien-Feng Li
- Department of Pathology, Chi Mei Medical Center, Tainan, Taiwan. .,Department of Medical Research, Chi Mei Medical Center, 901 Zhanghua Rd, 71004, Tainan, Taiwan. .,National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan. .,Department of Pathology, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.
| | - Yow-Ling Shiue
- Institute of Biomedical Sciences, National Sun Yat-Sen University, 70 Lienhai Rd., 80424, Kaohsiung, Taiwan. .,Institute of Precision Medicine, National Sun Yat-Sen University, Kaohsiung, Taiwan.
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10
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Quantitative proteomics characterization of cancer biomarkers and treatment. MOLECULAR THERAPY-ONCOLYTICS 2021; 21:255-263. [PMID: 34095463 PMCID: PMC8142045 DOI: 10.1016/j.omto.2021.04.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Cancer accounted for 16% of all death worldwide in 2018. Significant progress has been made in understanding tumor occurrence, progression, diagnosis, treatment, and prognosis at the molecular level. However, genomics changes cannot truly reflect the state of protein activity in the body due to the poor correlation between genes and proteins. Quantitative proteomics, capable of quantifying the relatively different protein abundance in cancer patients, has been increasingly adopted in cancer research. Quantitative proteomics has great application potentials, including cancer diagnosis, personalized therapeutic drug selection, real-time therapeutic effects and toxicity evaluation, prognosis and drug resistance evaluation, and new therapeutic target discovery. In this review, the development, testing samples, and detection methods of quantitative proteomics are introduced. The biomarkers identified by quantitative proteomics for clinical diagnosis, prognosis, and drug resistance are reviewed. The challenges and prospects of quantitative proteomics for personalized medicine are also discussed.
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11
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Morris C, Durand S, Jalinot P. Decreased expression of the translation factor eIF3e induces senescence in breast cancer cells via suppression of PARP1 and activation of mTORC1. Oncotarget 2021; 12:649-664. [PMID: 33868586 PMCID: PMC8021025 DOI: 10.18632/oncotarget.27923] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 03/08/2021] [Indexed: 12/28/2022] Open
Abstract
Altered expression of the translation factor eIF3e is associated with breast cancer occurrence. We have previously shown that eIF3e deficiency leads to an impaired DNA damage response with a marked decrease in DNA repair by homologous recombination. Here, we explored the possibility to exploit this DNA repair defect in targeted cancer therapy using PARP inhibitors. Surprisingly, eIF3e-deficient breast cancer cells are resistant to these drugs, in contrast to BRCA1-deficient cells. Studying this, we found that eIF3e-depleted cells synthesize lowered amounts of PARP1 protein, due to a weakened translation of the corresponding mRNA, associated with a strong decrease in cellular poly(ADP-ribosyl)ation. Additionally, we discovered that the mTORC1 signaling pathway is aberrantly activated in response to eIF3e suppression. Together, these PARP1 and mTORC1 dysfunctions upon eIF3e depletion are causally linked to induction of cellular senescence associated with a pro-inflammatory secretory phenotype. This study provides mechanistic insights into how eIF3e protects against breast cancer, with potential novel cancer therapeutic opportunities. While PARP inhibitors appear as inappropriate drugs for eIF3e-deficient breast tumors, our findings suggest that such cancers may benefit from senolytic drugs or mTORC1 inhibitors.
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Affiliation(s)
- Christelle Morris
- University Lyon, ENS de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5239, INSERM U1210, LBMC, Lyon, France
| | - Sébastien Durand
- University Lyon, ENS de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5239, INSERM U1210, LBMC, Lyon, France.,University Lyon, Cancer Research Center of Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS UMR 5286, Centre Léon Bérard, Cancer Cell Plasticity Department, Equipe 'Transcriptome Diversity in Stem Cells', Lyon, France
| | - Pierre Jalinot
- University Lyon, ENS de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5239, INSERM U1210, LBMC, Lyon, France
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12
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Patent highlights August-September 2020. Pharm Pat Anal 2021; 10:1-7. [PMID: 33441018 DOI: 10.4155/ppa-2020-0032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A snapshot of noteworthy recent developments in the patent literature of relevance to pharmaceutical and medical research and development.
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13
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Jiang SL, Mo JL, Peng J, Lei L, Yin JY, Zhou HH, Liu ZQ, Hong WX. Targeting translation regulators improves cancer therapy. Genomics 2020; 113:1247-1256. [PMID: 33189778 DOI: 10.1016/j.ygeno.2020.11.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 10/14/2020] [Accepted: 11/11/2020] [Indexed: 02/07/2023]
Abstract
Deregulation of protein synthesis may be involved in multiple aspects of cancer, such as gene expression, signal transduction and drive specific cell biological responses, resulting in promoting cancer growth, invasion and metastasis. Study the molecular mechanisms about translational control may help us to find more effective anti-cancer drugs and develop novel therapeutic opportunities. Recently, the researchers had focused on targeting translational machinery to overcome cancer, and various small molecular inhibitors targeting translation factors or pathways have been tested in clinical trials and exhibited improving outcomes in several cancer types. There is no doubt that an insight into the class of translation regulation protein would provide new target for pharmacologic intervention and further provide opportunities to develop novel anti-tumor therapeutic interventions. In this review, we summarized the developments of translational control in cancer survival and progression et al, and highlighted the therapeutic approach targeted translation regulation to overcome the cancer.
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Affiliation(s)
- Shi-Long Jiang
- Department of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, and National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, PR China; Institute of Clinical Pharmacology, Engineering Research Center for applied Technology of Pharmacogenomics of Ministry of Education, Central South University, Changsha 410078, PR China
| | - Jun-Luan Mo
- Department of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, and National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, PR China; Institute of Clinical Pharmacology, Engineering Research Center for applied Technology of Pharmacogenomics of Ministry of Education, Central South University, Changsha 410078, PR China; Shenzhen Center for Chronic Disease Control and Prevention, Shenzhen 518020, PR China
| | - Ji Peng
- Shenzhen Center for Chronic Disease Control and Prevention, Shenzhen 518020, PR China
| | - Lin Lei
- Shenzhen Center for Chronic Disease Control and Prevention, Shenzhen 518020, PR China
| | - Ji-Ye Yin
- Department of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, and National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, PR China; Institute of Clinical Pharmacology, Engineering Research Center for applied Technology of Pharmacogenomics of Ministry of Education, Central South University, Changsha 410078, PR China
| | - Hong-Hao Zhou
- Department of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, and National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, PR China; Institute of Clinical Pharmacology, Engineering Research Center for applied Technology of Pharmacogenomics of Ministry of Education, Central South University, Changsha 410078, PR China
| | - Zhao-Qian Liu
- Department of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, and National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, PR China; Institute of Clinical Pharmacology, Engineering Research Center for applied Technology of Pharmacogenomics of Ministry of Education, Central South University, Changsha 410078, PR China.
| | - Wen-Xu Hong
- Shenzhen Center for Chronic Disease Control and Prevention, Shenzhen 518020, PR China.
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Abstract
The activation of the cGAS-STING pathway has tremendous potential to improve anti-tumor immunity by generating type I interferons. In recent decades, we have witnessed that producing dsDNA upon various stimuli is an initiative factor, triggering the cGAS-SING pathway for a defensive host. The understanding of both intracellular cascade reaction and the changes of molecular components gains insight into type I IFNs and adaptive immunity. Based on the immunological study, the STING-cGAS pathway is coupled to cancer biotherapy. The most challenging problem is the limited therapeutic effect. Therefore, people view 5, 6-dimethylxanthenone-4-acetic acid, cyclic dinucleotides and various derivative as cGAS-STING pathway agonists. Even so, these agonists have flaws in decreasing biotherapeutic efficacy. Subsequently, we exploited agonist delivery systems (nanocarriers, microparticles and hydrogels). The article will discuss the activation of the cGAS-STING pathway and underlying mechanisms, with an introduction of cGAS-STING agonists, related clinical trials and agonist delivery systems.
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15
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Gao J, Yu T, Xuan Y, Zhu Z. High expression of GNB4 predicts poor prognosis in patients with Helicobacter pylori-positive advanced gastric cancer. Transl Cancer Res 2020; 9:4224-4238. [PMID: 35117790 PMCID: PMC8798254 DOI: 10.21037/tcr-19-2914] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Accepted: 06/03/2020] [Indexed: 12/16/2022]
Abstract
Background Helicobacter pylori (H. pylori) is recognized as the most evident etiologic factor of infection-related gastric cancer (GC) and its involvement in GC initiation and progression has been well investigated. However, only a limited number of studies were performed to identify prognostic biomarkers and evaluate their clinical significance in GC patients infected with H. pylori. This study was conducted to investigate the clinical significance as well as its potential prognostic value of GNB4 in H. pylori-positive GC patients receiving standard treatment. Methods Retrospective statistical analysis was performed on 448 H. pylori-positive GC patients, with 137 early gastric cancer (EGC) patients undergoing radical gastrectomy alone and 311 advanced gastric cancer (AGC) patients receiving the same surgical procedure followed by fluorouracil-based chemotherapy. GNB4 expression was detected by immunohistochemistry staining on patient samples. H. pylori infection was routinely examined on endoscopic biopsy and/or surgical specimen of GC patients. Results High expression of GNB4 was 65.7% (90/137) in EGC and 62.7% (195/311) in AGC patients infected with H. pylori, respectively. In EGC patients, GNB4 expression was not associated with either clinicopathological parameters or 5-year overall survival (OS). In AGC patients however, high expression of GNB4 was significantly associated with patient’s pathological stage (P=0.047). Univariate analysis showed that tumor invasion depth (P=0.001), lymph node metastasis (P<0.001), pathological stage (P<0.001) as well as high expression of GNB4 (P=0.002) were significantly associated with 5-year OS. Multivariate analysis further identified lymph node metastasis (P=0.013) and GNB4 high expression (P=0.020) as independent prognostic factors for long-term outcome of H. pylori-positive AGC patients. Conclusions This study demonstrates that high expression of GNB4 is significantly associated with pathological stage of AGC patients with H. pylori infection. GNB4 expression independently predicts the 5-year OS of H. pylori-positive AGC patients undergoing radical gastrectomy and adjuvant chemotherapy.
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Affiliation(s)
- Jianpeng Gao
- Department of Gastric Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Teng Yu
- Department of Pathology, Ruijin hospital affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yi Xuan
- Department of Gastric Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhenglun Zhu
- Department of Gastrointestinal Surgery, Ruijin hospital affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
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16
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Carozza JA, Böhnert V, Nguyen KC, Skariah G, Shaw KE, Brown JA, Rafat M, von Eyben R, Graves EE, Glenn JS, Smith M, Li L. Extracellular cGAMP is a cancer cell-produced immunotransmitter involved in radiation-induced anti-cancer immunity. NATURE CANCER 2020; 1:184-196. [PMID: 33768207 PMCID: PMC7990037 DOI: 10.1038/s43018-020-0028-4] [Citation(s) in RCA: 162] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 01/15/2020] [Indexed: 12/18/2022]
Abstract
2'3'-cyclic GMP-AMP (cGAMP) is an intracellular second messenger that is synthesized in response to cytosolic double-stranded DNA and activates the innate immune STING pathway. Our previous discovery of its extracellular hydrolase ENPP1 hinted at the existence of extracellular cGAMP. Here, we detected that cGAMP is continuously exported but then efficiently cleared by ENPP1, explaining why it has previously escaped detection. By developing potent, specific, and cell impermeable ENPP1 inhibitors, we found that cancer cells continuously export cGAMP in culture at steady state and at higher levels when treated with ionizing radiation (IR). In mouse tumors, depletion of extracellular cGAMP decreased tumor-associated immune cell infiltration and abolished the curative effect of IR. Boosting extracellular cGAMP with ENPP1 inhibitors synergized with IR to delay tumor growth. In conclusion, extracellular cGAMP is an anti-cancer immunotransmitter that could be harnessed to treat cancers with low immunogenicity.
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Affiliation(s)
- Jacqueline A Carozza
- Department of Chemistry, Stanford University, Stanford, CA, USA
- Stanford ChEM-H, Stanford University, Stanford, CA, USA
| | - Volker Böhnert
- Stanford ChEM-H, Stanford University, Stanford, CA, USA
- Department of Biochemistry, Stanford University, School of Medicine, Stanford, CA, USA
| | - Khanh C Nguyen
- Departments of Medicine and Microbiology & Immunology, Stanford University, School of Medicine, Stanford, CA, USA
| | - Gemini Skariah
- Stanford ChEM-H, Stanford University, Stanford, CA, USA
- Department of Biochemistry, Stanford University, School of Medicine, Stanford, CA, USA
| | - Kelsey E Shaw
- Stanford ChEM-H, Stanford University, Stanford, CA, USA
- Department of Biochemistry, Stanford University, School of Medicine, Stanford, CA, USA
| | - Jenifer A Brown
- Stanford ChEM-H, Stanford University, Stanford, CA, USA
- Biophysics Program, Stanford University, Stanford, CA, USA
| | - Marjan Rafat
- Department of Radiation Oncology, Stanford University, School of Medicine, Stanford, CA, USA
| | - Rie von Eyben
- Department of Radiation Oncology, Stanford University, School of Medicine, Stanford, CA, USA
| | - Edward E Graves
- Department of Radiation Oncology, Stanford University, School of Medicine, Stanford, CA, USA
| | - Jeffrey S Glenn
- Departments of Medicine and Microbiology & Immunology, Stanford University, School of Medicine, Stanford, CA, USA
| | - Mark Smith
- Stanford ChEM-H, Stanford University, Stanford, CA, USA
| | - Lingyin Li
- Stanford ChEM-H, Stanford University, Stanford, CA, USA.
- Department of Biochemistry, Stanford University, School of Medicine, Stanford, CA, USA.
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17
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Fujimoto Y, Inoue N, Morimoto K, Watanabe T, Hirota S, Imamura M, Matsushita Y, Katagiri T, Okamura H, Miyoshi Y. Significant association between high serum CCL5 levels and better disease-free survival of patients with early breast cancer. Cancer Sci 2019; 111:209-218. [PMID: 31724785 PMCID: PMC6942441 DOI: 10.1111/cas.14234] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 10/10/2019] [Accepted: 10/25/2019] [Indexed: 12/26/2022] Open
Abstract
Analysis of anticancer immunity aids in assessing the prognosis of patients with breast cancer. From 250 operated breast cancers, we focused on serum levels of C‐C motif chemokine ligand 5 (CCL5), which is involved in cancer immune reactions. Serum levels of CCL5 were measured using a cytometric bead‐based immunoassay kit and CCL5 expression in cancer cells was determined using immunohistochemical staining. In addition, mRNA in cancer and stromal cells was analyzed by microdissection and comparison with the public dataset. Disease‐free survival (DFS) of patients with high CCL5 levels (cut‐off, 13.87 ng/mL; n = 192) was significantly better than those with low CCL5 levels (n = 58; hazard ratio, 0.20; 95% confidence interval, 0.10‐0.39; P < .0001). An improved overall survival was observed in patients with high CCL5 levels compared to those with low CCL5 levels (P = .024). On the contrary, high immunohistochemical expression of CCL5 in cancer cells was significantly associated with decreased DFS. As serum CCL5 levels did not correlate with CCL5 expression in cancer cells and the relative expression of mRNA CCL5 was elevated in stromal cells in relation to cancer cells, serum CCL5 might be derived not from cancer cells, but from stromal cells. Expression of CCL5 in serum, but not in cancer cells, might contribute to improved patient prognosis mediating through not only immune reaction, but through other mechanisms. Determination of circulating CCL5 levels could be useful for predicting patient prognosis.
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Affiliation(s)
- Yukie Fujimoto
- Division of Breast and Endocrine Surgery, Department of Surgery, Hyogo College of Medicine, Nishinomiya, Japan
| | - Natsuko Inoue
- Division of Breast and Endocrine Surgery, Department of Surgery, Hyogo College of Medicine, Nishinomiya, Japan
| | - Koji Morimoto
- Osaka Ryokuryo High School, Fujiidera, Japan.,Department of Surgery, National Hospital Organization Osaka National Hospital, Osaka, Japan.,Biofunctional Synthetic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Japan
| | - Takahiro Watanabe
- Department of Surgical Pathology, Hyogo College of Medicine, Nishinomiya, Japan
| | - Seiichi Hirota
- Department of Surgical Pathology, Hyogo College of Medicine, Nishinomiya, Japan
| | - Michiko Imamura
- Division of Breast and Endocrine Surgery, Department of Surgery, Hyogo College of Medicine, Nishinomiya, Japan
| | - Yosuke Matsushita
- Division of Genome Medicine, Institute for Genome Research, Tokushima University, Tokushima, Japan
| | - Toyomasa Katagiri
- Division of Genome Medicine, Institute for Genome Research, Tokushima University, Tokushima, Japan
| | - Haruki Okamura
- Laboratory of Tumor Immunology and Cell Therapy, Hyogo College of Medicine, Nishinomiya, Japan
| | - Yasuo Miyoshi
- Division of Breast and Endocrine Surgery, Department of Surgery, Hyogo College of Medicine, Nishinomiya, Japan
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Russo R, Matrone N, Belli V, Ciardiello D, Valletta M, Esposito S, Pedone PV, Ciardiello F, Troiani T, Chambery A. Macrophage Migration Inhibitory Factor Is a Molecular Determinant of the Anti-EGFR Monoclonal Antibody Cetuximab Resistance in Human Colorectal Cancer Cells. Cancers (Basel) 2019; 11:cancers11101430. [PMID: 31557914 PMCID: PMC6826402 DOI: 10.3390/cancers11101430] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 09/16/2019] [Accepted: 09/18/2019] [Indexed: 12/12/2022] Open
Abstract
Background: The clinical impact of the monoclonal antibody cetuximab targeting the EGFR in colorectal cancer (CRC) is widely recognized. Nevertheless, the onset of cetuximab resistance is a serious issue that limits the effectiveness of this drug in targeted therapies. Unraveling the molecular players involved in cancer resistance is the first step towards the identification of alternative signaling pathways that can be targeted to circumvent resistance mechanisms restoring the efficacy of therapeutic treatments in a tailored manner. Methods: By applying a nanoLC-MS/MS TMT isobaric labeling-based approach, we have delineated a molecular hallmark of cetuximab-resistance in CRC. Results: We identified macrophage migration inhibitory factor (MIF) as a molecular determinant capable of triggering cancer resistance in sensitive human CRC cells. Blocking the MIF axis in resistant cells by a selective MIF inhibitor restores cell sensitivity to cetuximab. The combined treatment with cetuximab and the MIF inhibitor further enhanced cell growth inhibition in CRC resistant cell lines with a synergistic effect depending on inhibition of key downstream effectors of the MAPK and AKT signaling pathways. Conclusions: Collectively, our results suggest the association of MIF signaling and its dysregulation to cetuximab drug resistance, paving the way to the development of personalized combination therapies targeting the MIF axis.
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Affiliation(s)
- Rosita Russo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Università degli studi della Campania "Luigi Vanvitelli", 81100 Caserta, Italy.
| | - Nunzia Matrone
- Department of Precision Medicine, Università degli studi della Campania "Luigi Vanvitelli", 80131 Naples, Italy.
| | - Valentina Belli
- Department of Precision Medicine, Università degli studi della Campania "Luigi Vanvitelli", 80131 Naples, Italy.
| | - Davide Ciardiello
- Department of Precision Medicine, Università degli studi della Campania "Luigi Vanvitelli", 80131 Naples, Italy.
| | - Mariangela Valletta
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Università degli studi della Campania "Luigi Vanvitelli", 81100 Caserta, Italy.
| | - Sabrina Esposito
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Università degli studi della Campania "Luigi Vanvitelli", 81100 Caserta, Italy.
| | - Paolo Vincenzo Pedone
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Università degli studi della Campania "Luigi Vanvitelli", 81100 Caserta, Italy.
| | - Fortunato Ciardiello
- Department of Precision Medicine, Università degli studi della Campania "Luigi Vanvitelli", 80131 Naples, Italy.
| | - Teresa Troiani
- Department of Precision Medicine, Università degli studi della Campania "Luigi Vanvitelli", 80131 Naples, Italy.
| | - Angela Chambery
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Università degli studi della Campania "Luigi Vanvitelli", 81100 Caserta, Italy.
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An Y, Zhou L, Huang Z, Nice EC, Zhang H, Huang C. Molecular insights into cancer drug resistance from a proteomics perspective. Expert Rev Proteomics 2019; 16:413-429. [PMID: 30925852 DOI: 10.1080/14789450.2019.1601561] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
INTRODUCTION Resistance to chemotherapy and development of specific and effective molecular targeted therapies are major obstacles facing current cancer treatment. Comparative proteomic approaches have been employed for the discovery of putative biomarkers associated with cancer drug resistance and have yielded a number of candidate proteins, showing great promise for both novel drug target identification and personalized medicine for the treatment of drug-resistant cancer. Areas covered: Herein, we review the recent advances and challenges in proteomics studies on cancer drug resistance with an emphasis on biomarker discovery, as well as understanding the interconnectivity of proteins in disease-related signaling pathways. In addition, we highlight the critical role that post-translational modifications (PTMs) play in the mechanisms of cancer drug resistance. Expert opinion: Revealing changes in proteome profiles and the role of PTMs in drug-resistant cancer is key to deciphering the mechanisms of treatment resistance. With the development of sensitive and specific mass spectrometry (MS)-based proteomics and related technologies, it is now possible to investigate in depth potential biomarkers and the molecular mechanisms of cancer drug resistance, assisting the development of individualized therapeutic strategies for cancer patients.
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Affiliation(s)
- Yao An
- a West China School of Basic Medical Sciences & Forensic Medicine , Sichuan University , Chengdu , PR China.,b Department of Oncology , The Second Affiliated Hospital of Hainan Medical University , Haikou , P.R. China
| | - Li Zhou
- a West China School of Basic Medical Sciences & Forensic Medicine , Sichuan University , Chengdu , PR China
| | - Zhao Huang
- a West China School of Basic Medical Sciences & Forensic Medicine , Sichuan University , Chengdu , PR China
| | - Edouard C Nice
- c Department of Biochemistry and Molecular Biology , Monash University , Clayton , Australia
| | - Haiyuan Zhang
- b Department of Oncology , The Second Affiliated Hospital of Hainan Medical University , Haikou , P.R. China
| | - Canhua Huang
- a West China School of Basic Medical Sciences & Forensic Medicine , Sichuan University , Chengdu , PR China.,b Department of Oncology , The Second Affiliated Hospital of Hainan Medical University , Haikou , P.R. China
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20
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Huang M, Wang Y. Roles of Small GTPases in Acquired Tamoxifen Resistance in MCF-7 Cells Revealed by Targeted, Quantitative Proteomic Analysis. Anal Chem 2018; 90:14551-14560. [PMID: 30431262 DOI: 10.1021/acs.analchem.8b04526] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Development of tamoxifen resistance remains a tremendous challenge for the treatment of estrogen-receptor (ER)-positive breast cancer. Small GTPases of the Ras superfamily play crucial roles in intracellular trafficking and cell signaling, and aberrant small-GTPase signaling is implicated in many types of cancer. In this study, we employed a targeted, quantitative proteomic approach that relies on stable-isotope labeling by amino acids in cell culture (SILAC), gel fractionation, and scheduled multiple-reaction-monitoring (MRM) analysis, to assess the differential expression of small GTPases in MCF-7 and the paired tamoxifen-resistant breast cancer cells. The method displayed superior sensitivity and reproducibility over the shotgun-proteomic approach, and it facilitated the quantification of 96 small GTPases. Among them, 13 and 10 proteins were significantly down- and up-regulated (with >1.5-fold change), respectively, in the tamoxifen-resistant line relative to in the parental line. In particular, we observed a significant down-regulation of RAB31 in tamoxifen-resistant cells, which, in combination with bioinformatic analysis and downstream validation experiments, supported a role for RAB31 in tamoxifen resistance in ER-positive breast-cancer cells. Together, our results demonstrated that the targeted proteomic method constituted a powerful approach for revealing the role of small GTPases in therapeutic resistance.
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Dou M, Zhu Y, Liyu A, Liang Y, Chen J, Piehowski PD, Xu K, Zhao R, Moore RJ, Atkinson MA, Mathews CE, Qian WJ, Kelly RT. Nanowell-mediated two-dimensional liquid chromatography enables deep proteome profiling of <1000 mammalian cells. Chem Sci 2018; 9:6944-6951. [PMID: 30210768 PMCID: PMC6124911 DOI: 10.1039/c8sc02680g] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 07/15/2018] [Indexed: 12/14/2022] Open
Abstract
Multidimensional peptide separations can greatly increase the depth of coverage in proteome profiling. However, a major challenge for multidimensional separations is the requirement of large biological samples, often containing milligram amounts of protein. We have developed nanowell-mediated two-dimensional (2D) reversed-phase nanoflow liquid chromatography (LC) separations for in-depth proteome profiling of low-nanogram samples. Peptides are first separated using high-pH LC and the effluent is concatenated into 4 or 12 nanowells. The contents of each nanowell are reconstituted in LC buffer and collected for subsequent separation and analysis by low-pH nanoLC-MS/MS. The nanowell platform minimizes peptide losses to surfaces in offline 2D LC fractionation, enabling >5800 proteins to be confidently identified from just 50 ng of HeLa digest. Furthermore, in combination with a recently developed nanowell-based sample preparation workflow, we demonstrated deep proteome profiling of >6000 protein groups from small populations of cells, including ∼650 HeLa cells and 10 single human pancreatic islet thin sections (∼1000 cells) from a pre-symptomatic type 1 diabetic donor.
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Affiliation(s)
- Maowei Dou
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , WA 99354 , USA .
| | - Ying Zhu
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , WA 99354 , USA .
| | - Andrey Liyu
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , WA 99354 , USA .
| | - Yiran Liang
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , WA 99354 , USA .
| | - Jing Chen
- Department of Pathology , Immunology and Laboratory Medicine , University of Florida , Gainesville , FL 32611 , USA
| | - Paul D Piehowski
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , WA 99354 , USA
| | - Kerui Xu
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , WA 99354 , USA .
| | - Rui Zhao
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , WA 99354 , USA .
| | - Ronald J Moore
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , WA 99354 , USA
| | - Mark A Atkinson
- Department of Pathology , Immunology and Laboratory Medicine , University of Florida , Gainesville , FL 32611 , USA
| | - Clayton E Mathews
- Department of Pathology , Immunology and Laboratory Medicine , University of Florida , Gainesville , FL 32611 , USA
| | - Wei-Jun Qian
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , WA 99354 , USA
| | - Ryan T Kelly
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , WA 99354 , USA .
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22
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Wang B, Li D, Rodriguez-Juarez R, Farfus A, Storozynsky Q, Malach M, Carpenter E, Filkowski J, Lykkesfeldt AE, Kovalchuk O. A suppressive role of guanine nucleotide-binding protein subunit beta-4 inhibited by DNA methylation in the growth of anti-estrogen resistant breast cancer cells. BMC Cancer 2018; 18:817. [PMID: 30103729 PMCID: PMC6090602 DOI: 10.1186/s12885-018-4711-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 07/31/2018] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Breast cancer is the most common malignancy in women worldwide. Although the endocrine therapy that targets estrogen receptor α (ERα) signaling has been well established as an effective adjuvant treatment for patients with ERα-positive breast cancers, long-term exposure may eventually lead to the development of acquired resistance to the anti-estrogen drugs, such as fulvestrant and tamoxifen. A better understanding of the mechanisms underlying antiestrogen resistance and identification of the key molecules involved may help in overcoming antiestrogen resistance in breast cancer. METHODS The whole-genome gene expression and DNA methylation profilings were performed using fulvestrant-resistant cell line 182R-6 and tamoxifen-resistant cell line TAMR-1 as a model system. In addition, qRT-PCR and Western blot analysis were performed to determine the levels of mRNA and protein molecules. MTT, apoptosis and cell cycle analyses were performed to examine the effect of either guanine nucleotide-binding protein beta-4 (GNB4) overexpression or knockdown on cell proliferation, apoptosis and cell cycle. RESULTS Among 9 candidate genes, GNB4 was identified and validated by qRT-PCR as a potential target silenced by DNA methylation via DNA methyltransferase 3B (DNMT3B). We generated stable 182R-6 and TAMR-1 cell lines that are constantly expressing GNB4 and determined the effect of the ectopic GNB4 on cell proliferation, cell cycle, and apoptosis of the antiestrogen-resistant cells in response to either fulvestrant or tamoxifen. Ectopic expression of GNB4 in two antiestrogen resistant cell lines significantly promoted cell growth and shortened cell cycle in the presence of either fulvestrant or tamoxifen. The ectopic GNB4 induced apoptosis in 182R-6 cells, whereas it inhibited apoptosis in TAMR-1 cells. Many regulators controlling cell cycle and apoptosis were aberrantly expressed in two resistant cell lines in response to the enforced GNB4 expression, which may contribute to GNB4-mediated biologic and/or pathologic processes. Furthermore, knockdown of GNB4 decreased growth of both antiestrogen resistant and sensitive breast cancer cells. CONCLUSION GNB4 is important for growth of breast cancer cells and a potential target for treatment.
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Affiliation(s)
- Bo Wang
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB Canada
- Department of Biochemistry, Qiqihar Medical University, Qiqihar, People’s Republic of China
| | - Dongping Li
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB Canada
- Department of Biochemistry, Qiqihar Medical University, Qiqihar, People’s Republic of China
| | | | - Allison Farfus
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB Canada
| | - Quinn Storozynsky
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB Canada
| | - Megan Malach
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB Canada
| | - Emily Carpenter
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB Canada
| | - Jody Filkowski
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB Canada
| | - Anne E. Lykkesfeldt
- Breast Cancer Group, Cell Death and Metabolism, Danish Cancer Society Research Center, Strandboulevarden, Copenhagen, Denmark
| | - Olga Kovalchuk
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB Canada
- Hepler Hall, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4 Canada
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23
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Bevilacqua C, Ducos B. Laser microdissection: A powerful tool for genomics at cell level. Mol Aspects Med 2017; 59:5-27. [PMID: 28927943 DOI: 10.1016/j.mam.2017.09.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 09/13/2017] [Indexed: 12/18/2022]
Abstract
Laser microdissection (LM) has become widely democratized over the last fifteen years. Instruments have evolved to offer more powerful and efficient lasers as well as new options for sample collection and preparation. Technological evolutions have also focused on the post-microdissection analysis capabilities, opening up investigations in all disciplines of experimental and clinical biology, thanks to the advent of new high-throughput methods of genome analysis, including RNAseq and proteomics, now globally known as microgenomics, i.e. analysis of biomolecules at the cell level. In spite of the advances these rapidly developing methods have allowed, the workflow for sampling and collection by LM remains a critical step in insuring sample integrity in terms of histology (accurate cell identification) and biochemistry (reliable analyzes of biomolecules). In this review, we describe the sample processing as well as the strengths and limiting factors of LM applied to the specific selection of one or more cells of interest from a heterogeneous tissue. We will see how the latest developments in protocols and methods have made LM a powerful and sometimes essential tool for genomic and proteomic analyzes of tiny amounts of biomolecules extracted from few cells isolated from a complex tissue, in their physiological context, thus offering new opportunities for understanding fundamental physiological and/or patho-physiological processes.
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Affiliation(s)
- Claudia Bevilacqua
- GABI, Plateforme @BRIDGE, INRA, AgroParisTech, Université Paris-Saclay, Domaine de Vilvert, 78350 Jouy en Josas, France.
| | - Bertrand Ducos
- LPS-ENS, CNRS UMR 8550, UPMC, Université Denis Diderot, PSL Research University, 24 Rue Lhomond, 75005 Paris France; High Throughput qPCR Core Facility, IBENS, 46 Rue d'Ulm, 75005 Paris France; Laser Microdissection Facility of Montagne Sainte Geneviève, CIRB Collège de France, Place Marcellin Berthelot, 75005 Paris France.
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24
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Braakman RBH, Stingl C, Tilanus-Linthorst MMA, van Deurzen CHM, Timmermans MAM, Smid M, Foekens JA, Luider TM, Martens JWM, Umar A. Proteomic characterization of microdissected breast tissue environment provides a protein-level overview of malignant transformation. Proteomics 2017; 17. [PMID: 28058811 PMCID: PMC5347865 DOI: 10.1002/pmic.201600213] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 11/23/2016] [Accepted: 01/03/2017] [Indexed: 01/26/2023]
Abstract
Both healthy and cancerous breast tissue is heterogeneous, which is a bottleneck for proteomics‐based biomarker analysis, as it obscures the cellular origin of a measured protein. We therefore aimed at obtaining a protein‐level interpretation of malignant transformation through global proteome analysis of a variety of laser capture microdissected cells originating from benign and malignant breast tissues. We compared proteomic differences between these tissues, both from cells of epithelial origin and the stromal environment, and performed string analysis. Differences in protein abundances corresponded with several hallmarks of cancer, including loss of cell adhesion, transformation to a migratory phenotype, and enhanced energy metabolism. Furthermore, despite enriching for (tumor) epithelial cells, many changes to the extracellular matrix were detected in microdissected cells of epithelial origin. The stromal compartment was heterogeneous and richer in the number of fibroblast and immune cells in malignant sections, compared to benign tissue sections. Furthermore, stroma could be clearly divided into reactive and nonreactive based on extracellular matrix disassembly proteins. We conclude that proteomics analysis of both microdissected epithelium and stroma gives an additional layer of information and more detailed insight into malignant transformation.
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Affiliation(s)
- René B H Braakman
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands.,Postgraduate School of Molecular Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Christoph Stingl
- Department of Neurology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | | | | | - Mieke A M Timmermans
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Marcel Smid
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - John A Foekens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands.,Postgraduate School of Molecular Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Theo M Luider
- Department of Neurology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands.,Postgraduate School of Molecular Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Arzu Umar
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands.,Postgraduate School of Molecular Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands
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25
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Renda F, Pellacani C, Strunov A, Bucciarelli E, Naim V, Bosso G, Kiseleva E, Bonaccorsi S, Sharp DJ, Khodjakov A, Gatti M, Somma MP. The Drosophila orthologue of the INT6 onco-protein regulates mitotic microtubule growth and kinetochore structure. PLoS Genet 2017; 13:e1006784. [PMID: 28505193 PMCID: PMC5448806 DOI: 10.1371/journal.pgen.1006784] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 05/30/2017] [Accepted: 04/27/2017] [Indexed: 12/01/2022] Open
Abstract
INT6/eIF3e is a highly conserved component of the translation initiation complex that interacts with both the 26S proteasome and the COP9 signalosome, two complexes implicated in ubiquitin-mediated protein degradation. The INT6 gene was originally identified as the insertion site of the mouse mammary tumor virus (MMTV), and later shown to be involved in human tumorigenesis. Here we show that depletion of the Drosophila orthologue of INT6 (Int6) results in short mitotic spindles and deformed centromeres and kinetochores with low intra-kinetochore distance. Poleward flux of microtubule subunits during metaphase is reduced, although fluorescence recovery after photobleaching (FRAP) demonstrates that microtubules remain dynamic both near the kinetochores and at spindle poles. Mitotic progression is delayed during metaphase due to the activity of the spindle assembly checkpoint (SAC). Interestingly, a deubiquitinated form of the kinesin Klp67A (a putative orthologue of human Kif18A) accumulates near the kinetochores in Int6-depleted cells. Consistent with this finding, Klp67A overexpression mimics the Int6 RNAi phenotype. Furthermore, simultaneous depletion of Int6 and Klp67A results in a phenotype identical to RNAi of just Klp67A, which indicates that Klp67A deficiency is epistatic over Int6 deficiency. We propose that Int6-mediated ubiquitination is required to control the activity of Klp67A. In the absence of this control, excess of Klp67A at the kinetochore suppresses microtubule plus-end polymerization, which in turn results in reduced microtubule flux, spindle shortening, and centromere/kinetochore deformation. INT6 is an evolutionarily conserved gene originally identified as the insertion site of the mouse mammary tumor virus that causes tumors in mice. INT6 is downregulated in many human cancers, suggesting that it acts as tumor suppressor gene. The INT6 protein is involved in several biological processes, including translation and ubiquitin-mediated protein degradation. We performed RNA interference (RNAi) against the Drosophila homologue of INT6 (Int6) and analyzed the effects of Int6 depletion on mitotic cell division. We found that loss of Int6 results in short spindles, delayed progression though metaphase and abnormally shaped centromeres/kinetochores. We also found that Int6-depleted cells fail to degrade the kinesin Klp67A. This protein, known to attenuate polymerization of microtubule (MTs) plus ends, accumulated at the kinetochores in Int6-depleted cells. We propose that this condition affects MT growth at the kinetochore, which in turn results in centromere/kinetochore deformation and delays satisfaction of the mitotic checkpoint.
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Affiliation(s)
- Fioranna Renda
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza, Università di Roma, Roma, Italy
- Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | - Claudia Pellacani
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza, Università di Roma, Roma, Italy
- Istituto di Biologia e Patologia Molecolari (IBPM) del CNR, Roma, Italy
| | - Anton Strunov
- Institute of Molecular and Cellular Biology, Siberian Branch of RAS, Novosibirsk, Russia
- Institute of Cytology and Genetics, Siberian Branch of RAS, Novosibirsk, Russia
| | | | - Valeria Naim
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza, Università di Roma, Roma, Italy
| | - Giuseppe Bosso
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza, Università di Roma, Roma, Italy
| | - Elena Kiseleva
- Institute of Molecular and Cellular Biology, Siberian Branch of RAS, Novosibirsk, Russia
- Institute of Cytology and Genetics, Siberian Branch of RAS, Novosibirsk, Russia
| | - Silvia Bonaccorsi
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza, Università di Roma, Roma, Italy
| | - David J. Sharp
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Alexey Khodjakov
- Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | - Maurizio Gatti
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza, Università di Roma, Roma, Italy
- Istituto di Biologia e Patologia Molecolari (IBPM) del CNR, Roma, Italy
- Institute of Molecular and Cellular Biology, Siberian Branch of RAS, Novosibirsk, Russia
- * E-mail: (MPS); (MG)
| | - Maria Patrizia Somma
- Istituto di Biologia e Patologia Molecolari (IBPM) del CNR, Roma, Italy
- * E-mail: (MPS); (MG)
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26
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Faria SS, Morris CFM, Silva AR, Fonseca MP, Forget P, Castro MS, Fontes W. A Timely Shift from Shotgun to Targeted Proteomics and How It Can Be Groundbreaking for Cancer Research. Front Oncol 2017; 7:13. [PMID: 28265552 PMCID: PMC5316539 DOI: 10.3389/fonc.2017.00013] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 01/17/2017] [Indexed: 01/10/2023] Open
Abstract
The fact that cancer is a leading cause of death all around the world has naturally sparked major efforts in the pursuit of novel and more efficient biomarkers that could better serve as diagnostic tools, prognostic predictors, or therapeutical targets in the battle against this type of disease. Mass spectrometry-based proteomics has proven itself as a robust and logical alternative to the immuno-based methods that once dominated the field. Nevertheless, intrinsic limitations of classic proteomic approaches such as the natural gap between shotgun discovery-based methods and clinically applicable results have called for the implementation of more direct, hypothesis-based studies such as those made available through targeted approaches, that might be able to streamline biomarker discovery and validation as a means to increase survivability of affected patients. In fact, the paradigm shifting potential of modern targeted proteomics applied to cancer research can be demonstrated by the large number of advancements and increasing examples of new and more useful biomarkers found during the course of this review in different aspects of cancer research. Out of the many studies dedicated to cancer biomarker discovery, we were able to devise some clear trends, such as the fact that breast cancer is the most common type of tumor studied and that most of the research for any given type of cancer is focused on the discovery diagnostic biomarkers, with the exception of those that rely on samples other than plasma and serum, which are generally aimed toward prognostic markers. Interestingly, the most common type of targeted approach is based on stable isotope dilution-selected reaction monitoring protocols for quantification of the target molecules. Overall, this reinforces that notion that targeted proteomics has already started to fulfill its role as a groundbreaking strategy that may enable researchers to catapult the number of viable, effective, and validated biomarkers in cancer clinical practice.
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Affiliation(s)
- Sara S Faria
- Mastology Program, Federal University of Uberlandia (UFU) , Uberlandia , Brazil
| | - Carlos F M Morris
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, Institute of Biology, University of Brasilia , Brasília , Brazil
| | - Adriano R Silva
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, Institute of Biology, University of Brasilia , Brasília , Brazil
| | - Micaella P Fonseca
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, Institute of Biology, University of Brasilia, Brasília, Brazil; Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Patrice Forget
- Department of Anesthesiology and Perioperative Medicine, Universitair Ziekenhuis Brussel, Vrije Universiteit of Brussel , Brussels , Belgium
| | - Mariana S Castro
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, Institute of Biology, University of Brasilia , Brasília , Brazil
| | - Wagner Fontes
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, Institute of Biology, University of Brasilia , Brasília , Brazil
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27
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de Graaf EL, Pellegrini D, McDonnell LA. Set of Novel Automated Quantitative Microproteomics Protocols for Small Sample Amounts and Its Application to Kidney Tissue Substructures. J Proteome Res 2016; 15:4722-4730. [PMID: 27809536 DOI: 10.1021/acs.jproteome.6b00889] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Here we assessed the ability of an automated sample preparation device equipped with disposable microcolumns to prepare mass-limited samples for high-sensitivity quantitative proteomics, using both label-free and isobaric labeling approaches. First, we compared peptide label-free quantification reproducibility for 1.5-150 μg of cell lysates and found that labware preconditioning was essential for reproducible quantification of <7.5 μg digest. Second, in-solution and on-column tandem mass tag (TMT) labeling protocols were compared and optimized for 1 μg of sample. Surprisingly, standard methods for in-solution and on-column labeling showed poor TMT labeling (50-85%); however, novel optimized and automated protocols restored efficient labeling to >98%. Third, compared with a single long gradient experiment, a simple robotized high-pH fractionation protocol using only 6 μg of starting material doubled the number of unique peptides and increased proteome coverage 1.43-fold. To facilitate the analysis of heterogeneous tissue samples, such as those obtained from laser capture microdissection, a modified BCA protein assay was developed that consumes and detects down to 15 ng of protein. As a proof-of-principle, the modular automated workflow was applied to 0.5 and 1 mm2 mouse kidney cortex and medulla microdissections to show the method's potential for real-life small sample sources and to create kidney substructure-specific proteomes.
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Affiliation(s)
| | - Davide Pellegrini
- Fondazione Pisana per la Scienza ONLUS , Pisa 56121, Italy.,NEST, Scuola Normale Superiore , Pisa 56127, Italy
| | - Liam A McDonnell
- Fondazione Pisana per la Scienza ONLUS , Pisa 56121, Italy.,Leiden University Medical Center , Leiden 2333 ZA, The Netherlands
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28
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Morris C, Tomimatsu N, Burma S, Jalinot P. INT6/EIF3E Controls the RNF8-Dependent Ubiquitylation Pathway and Facilitates DNA Double-Strand Break Repair in Human Cells. Cancer Res 2016; 76:6054-6065. [PMID: 27550454 DOI: 10.1158/0008-5472.can-16-0723] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 07/27/2016] [Indexed: 11/16/2022]
Abstract
Unrepaired DNA double-strand breaks (DSB) are the most destructive chromosomal lesions driving genomic instability, a core hallmark of cancer. Here, we identify the antioncogenic breast cancer factor INT6/EIF3E as an essential regulator of DSB repair that promotes homologous recombination (HR)-mediated repair and, to a lesser extent, nonhomologous end-joining repair. INT6 silencing impaired the accrual of the ubiquitin ligase RNF8 at DSBs and the formation of ubiquitin conjugates at DSB sites, especially Lys63-linked polyubiquitin chains, resulting in impaired recruitment of BRCA1, BRCA2, and RAD51, which are all involved in HR repair. In contrast, INT6 deficiency did not affect the accumulation of RNF168, 53BP1, or RPA at DSBs. In INT6-silenced cells, there was also an alteration in DNA damage-induced localization of MDC1, a key target for ATM phosphorylation, which is a prerequisite for RNF8 recruitment. The attenuated DNA damage localization of RNF8 resulting from INT6 depletion could be attributed to the defective retention of ATM previously reported by us. Our findings deepen insights into how INT6 protects against breast cancer by showing how it functions in DSB repair, with potential clinical implications for cancer therapy. Cancer Res; 76(20); 6054-65. ©2016 AACR.
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Affiliation(s)
- Christelle Morris
- Laboratory of Biology and Modelling of the Cell, CNRS UMR 5239, INSERM U1210, ENS de Lyon, University of Lyon, Lyon, France
| | - Nozomi Tomimatsu
- Division of Molecular Radiation Biology, Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Sandeep Burma
- Division of Molecular Radiation Biology, Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Pierre Jalinot
- Laboratory of Biology and Modelling of the Cell, CNRS UMR 5239, INSERM U1210, ENS de Lyon, University of Lyon, Lyon, France.
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29
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De Marchi T, Foekens JA, Umar A, Martens JWM. Endocrine therapy resistance in estrogen receptor (ER)-positive breast cancer. Drug Discov Today 2016; 21:1181-8. [PMID: 27233379 DOI: 10.1016/j.drudis.2016.05.012] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 04/25/2016] [Accepted: 05/18/2016] [Indexed: 12/20/2022]
Abstract
Estrogen receptor (ER)-positive breast cancer represents the majority (∼70%) of all breast malignancies. In this subgroup of breast cancers, endocrine therapies are effective both in the adjuvant and recurrent settings, although resistance remains a major issue. Several high-throughput approaches have been used to elucidate mechanisms of resistance and to derive potential predictive markers or alternative therapies. In this review, we cover the state-of-the-art of endocrine-resistance biomarker discovery with regard to the latest technological developments, and discuss current opportunities and restrictions for their implementation into a clinical setting.
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Affiliation(s)
- Tommaso De Marchi
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - John A Foekens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands.
| | - Arzu Umar
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
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30
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Zheng Q, Liu H, Ye J, Zhang H, Jia Z, Cao J. Nuclear distribution of eIF3g and its interacting nuclear proteins in breast cancer cells. Mol Med Rep 2016; 13:2973-80. [PMID: 26935993 PMCID: PMC4805062 DOI: 10.3892/mmr.2016.4935] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 01/11/2016] [Indexed: 12/11/2022] Open
Abstract
Eukaryotic translation initiation factor 3 subunit g (eIF3g) is a core subunit of the eukaryotic translation initiation factor 3 complex, and is important in the initiation of translation. It is also involved in caspase-mediated apoptosis, and is upregulated in multidrug-resistant cancer cells. In the present study, the nuclear distribution of eIF3g was determined by performing co-immunoprecipitation of proteins that potentially interact with eIF3g in the nucleus. Mass spectrometry characterization showed that three proteins, heterogeneous nuclear ribonucleoprotein U/scaffold attachment factor A, HSZFP36/zinc finger protein 823 and β-actin, were among the candidate eIF3g-interacting proteins in the nucleus. The protein-protein interaction was further confirmed by cross-linking and a glutathione S-transferase pull-down assay, followed by western blotting. The co-localization of these proteins was determined by confocal microscopy. These findings provide novel insight into the possible functions of eIF3g in the nucleus and serves as an important first step for further investigation of the roles of eIF3g in cancer development.
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Affiliation(s)
- Qiaoli Zheng
- Clinical Research Center, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310009, P.R. China
| | - Hao Liu
- Institute of Occupational Diseases, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang 310007, P.R. China
| | - Jingjia Ye
- Clinical Research Center, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310009, P.R. China
| | - Hui Zhang
- Department of Clinical Laboratory, Hangzhou First People's Hospital, Hangzhou, Zhejiang 310006, P.R. China
| | - Zhenyu Jia
- Institute of Occupational Diseases, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang 310007, P.R. China
| | - Jiang Cao
- Clinical Research Center, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310009, P.R. China
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31
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Fields AP, Justilien V, Murray NR. The chromosome 3q26 OncCassette: A multigenic driver of human cancer. Adv Biol Regul 2015; 60:47-63. [PMID: 26754874 DOI: 10.1016/j.jbior.2015.10.009] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 10/28/2015] [Accepted: 10/29/2015] [Indexed: 02/06/2023]
Abstract
Recurrent copy number variations (CNVs) are genetic alterations commonly observed in human tumors. One of the most frequent CNVs in human tumors involves copy number gains (CNGs) at chromosome 3q26, which is estimated to occur in >20% of human tumors. The high prevalence and frequent occurrence of 3q26 CNG suggest that it drives the biology of tumors harboring this genetic alteration. The chromosomal region subject to CNG (the 3q26 amplicon) spans from chromosome 3q26 to q29, a region containing ∼200 protein-encoding genes. The large number of genes within the amplicon makes it difficult to identify relevant oncogenic target(s). Whereas a number of genes in this region have been linked to the transformed phenotype, recent studies indicate a high level of cooperativity among a subset of frequently amplified 3q26 genes. Here we use a novel bioinformatics approach to identify potential driver genes within the recurrent 3q26 amplicon in lung squamous cell carcinoma (LSCC). Our analysis reveals a set of 35 3q26 amplicon genes that are coordinately amplified and overexpressed in human LSCC tumors, and that also map to a major LSCC susceptibility locus identified on mouse chromosome 3 that is syntenic with human chromosome 3q26. Pathway analysis reveals that 21 of these genes exist within a single predicted network module. Four 3q26 genes, SOX2, ECT2, PRKCI and PI3KCA occupy the hub of this network module and serve as nodal genes around which the network is organized. Integration of available genetic, genomic, biochemical and functional data demonstrates that SOX2, ECT2, PRKCI and PIK3CA are cooperating oncogenes that function within an integrated cell signaling network that drives a highly aggressive, stem-like phenotype in LSCC tumors harboring 3q26 amplification. Based on the high level of genomic, genetic, biochemical and functional integration amongst these 4 3q26 nodal genes, we propose that they are the key oncogenic targets of the 3q26 amplicon and together define a "3q26 OncCassette" that mediates 3q26 CNG-driven tumorigenesis. Genomic analysis indicates that the 3q26 OncCassette also operates in other major tumor types that exhibit frequent 3q26 CNGs, including head and neck squamous cell carcinoma (HNSCC), ovarian serous cancer and cervical cancer. Finally, we discuss how the 3q26 OncCassette represents a tractable target for development of novel therapeutic intervention strategies that hold promise for improving treatment of 3q26-driven cancers.
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Affiliation(s)
- Alan P Fields
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, FL, United States.
| | - Verline Justilien
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, FL, United States
| | - Nicole R Murray
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, FL, United States
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32
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Wu X, Zahari MS, Renuse S, Nirujogi RS, Kim MS, Manda SS, Stearns V, Gabrielson E, Sukumar S, Pandey A. Phosphoproteomic Analysis Identifies Focal Adhesion Kinase 2 (FAK2) as a Potential Therapeutic Target for Tamoxifen Resistance in Breast Cancer. Mol Cell Proteomics 2015; 14:2887-900. [PMID: 26330541 DOI: 10.1074/mcp.m115.050484] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Indexed: 01/13/2023] Open
Abstract
Tamoxifen, an estrogen receptor-α (ER) antagonist, is an important agent for the treatment of breast cancer. However, this therapy is complicated by the fact that a substantial number of patients exhibit either de novo or acquired resistance. To characterize the signaling mechanisms underlying this resistance, we treated the MCF7 breast cancer cell line with tamoxifen for over six months and showed that this cell line acquired resistance to tamoxifen in vitro and in vivo. We performed SILAC-based quantitative phosphoproteomic profiling on the tamoxifen resistant and vehicle-treated sensitive cell lines to quantify the phosphorylation alterations associated with tamoxifen resistance. From >5600 unique phosphopeptides identified, 1529 peptides exhibited hyperphosphorylation and 409 peptides showed hypophosphorylation in the tamoxifen resistant cells. Gene set enrichment analysis revealed that focal adhesion pathway was one of the most enriched signaling pathways activated in tamoxifen resistant cells. Significantly, we showed that the focal adhesion kinase FAK2 was not only hyperphosphorylated but also transcriptionally up-regulated in tamoxifen resistant cells. FAK2 suppression by specific siRNA knockdown or a small molecule inhibitor repressed cellular proliferation in vitro and tumor formation in vivo. More importantly, our survival analysis revealed that high expression of FAK2 is significantly associated with shorter metastasis-free survival in estrogen receptor-positive breast cancer patients treated with tamoxifen. Our studies suggest that FAK2 is a potential therapeutic target for the management of hormone-refractory breast cancers.
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Affiliation(s)
- Xinyan Wu
- From the ‡McKusick-Nathans Institute of Genetic Medicine and Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Muhammad Saddiq Zahari
- From the ‡McKusick-Nathans Institute of Genetic Medicine and Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Santosh Renuse
- §Institute of Bioinformatics, International Technology Park, Bangalore, 560066 India
| | - Raja Sekhar Nirujogi
- §Institute of Bioinformatics, International Technology Park, Bangalore, 560066 India
| | - Min-Sik Kim
- From the ‡McKusick-Nathans Institute of Genetic Medicine and Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Srikanth S Manda
- §Institute of Bioinformatics, International Technology Park, Bangalore, 560066 India
| | | | - Edward Gabrielson
- ‖Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231
| | | | - Akhilesh Pandey
- From the ‡McKusick-Nathans Institute of Genetic Medicine and Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205; ¶Department of Oncology; ‖Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231
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Sjöström M, Ossola R, Breslin T, Rinner O, Malmström L, Schmidt A, Aebersold R, Malmström J, Niméus E. A Combined Shotgun and Targeted Mass Spectrometry Strategy for Breast Cancer Biomarker Discovery. J Proteome Res 2015; 14:2807-18. [DOI: 10.1021/acs.jproteome.5b00315] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | | | | | | | | | - Ruedi Aebersold
- Department
of Biology, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule, 8092 Zurich, Switzerland
| | | | - Emma Niméus
- Division
of Surgery, Skåne University Hospital, 221 85 Lund, Sweden
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34
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Johansson J, Tabor V, Wikell A, Jalkanen S, Fuxe J. TGF-β1-Induced Epithelial-Mesenchymal Transition Promotes Monocyte/Macrophage Properties in Breast Cancer Cells. Front Oncol 2015; 5:3. [PMID: 25674539 PMCID: PMC4306317 DOI: 10.3389/fonc.2015.00003] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 01/08/2015] [Indexed: 12/21/2022] Open
Abstract
Breast cancer progression toward metastatic disease is linked to re-activation of epithelial–mesenchymal transition (EMT), a latent developmental process. Breast cancer cells undergoing EMT lose epithelial characteristics and gain the capacity to invade the surrounding tissue and migrate away from the primary tumor. However, less is known about the possible role of EMT in providing cancer cells with properties that allow them to traffic to distant sites. Given the fact that pro-metastatic cancer cells share a unique capacity with immune cells to traffic in-and-out of blood and lymphatic vessels we hypothesized that tumor cells undergoing EMT may acquire properties of immune cells. To study this, we performed gene-profiling analysis of mouse mammary EpRas tumor cells that had been allowed to adopt an EMT program after long-term treatment with TGF-β1 for 2 weeks. As expected, EMT cells acquired traits of mesenchymal cell differentiation and migration. However, in addition, we found another cluster of induced genes, which was specifically enriched in monocyte-derived macrophages, mast cells, and myeloid dendritic cells, but less in other types of immune cells. Further studies revealed that this monocyte/macrophage gene cluster was enriched in human breast cancer cell lines displaying an EMT or a Basal B profile, and in human breast tumors with EMT and undifferentiated (ER−/PR−) characteristics. The results identify an EMT-induced monocyte/macrophage gene cluster, which may play a role in breast cancer cell dissemination and metastasis.
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Affiliation(s)
- Joel Johansson
- Department of Medical Biochemistry and Biophysics, Division of Vascular Biology, Karolinska Institute , Stockholm , Sweden
| | - Vedrana Tabor
- Department of Medical Biochemistry and Biophysics, Division of Vascular Biology, Karolinska Institute , Stockholm , Sweden
| | - Anna Wikell
- Department of Medical Biochemistry and Biophysics, Division of Vascular Biology, Karolinska Institute , Stockholm , Sweden
| | - Sirpa Jalkanen
- MediCity Research Laboratory, University of Turku , Turku , Finland
| | - Jonas Fuxe
- Department of Medical Biochemistry and Biophysics, Division of Vascular Biology, Karolinska Institute , Stockholm , Sweden
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35
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Use of universal stable isotope labeling by amino acids in cell culture (SILAC)-based selected reaction monitoring (SRM) approach for verification of breast cancer-related protein markers. Methods Mol Biol 2014. [PMID: 24791998 DOI: 10.1007/978-1-4939-0685-7_21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Mass spectrometry-based proteomics facilitates high-throughput discovery of protein markers for diagnosis and treatment of breast cancer patients. Hundreds of putative prognostic and predictive markers are being identified every year, but only a very small proportion of them can be validated as clinically relevant markers. A quantitative and cost-efficient verification method is highly desirable to pick up real "nuggets" from the "sand." To fulfill these criteria, we previously introduced a stable isotope labeling by amino acids in cell culture (SILAC)-based selected reaction monitoring (SRM) approach for studying breast cancer-related protein markers. Here we describe a hands-on protocol of using this SILAC-SRM method for verification of breast cancer-related markers, which can also be used for verification of protein markers in other types of solid tumor tissues.
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36
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Dabydeen SA, Kang K, Díaz-Cruz ES, Alamri A, Axelrod ML, Bouker KB, Al-Kharboosh R, Clarke R, Hennighausen L, Furth PA. Comparison of tamoxifen and letrozole response in mammary preneoplasia of ER and aromatase overexpressing mice defines an immune-associated gene signature linked to tamoxifen resistance. Carcinogenesis 2014; 36:122-32. [PMID: 25421723 DOI: 10.1093/carcin/bgu237] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Response to breast cancer chemoprevention can depend upon host genetic makeup and initiating events leading up to preneoplasia. Increased expression of aromatase and estrogen receptor (ER) is found in conjunction with breast cancer. To investigate response or resistance to endocrine therapy, mice with targeted overexpression of Esr1 or CYP19A1 to mammary epithelial cells were employed, representing two direct pathophysiological interventions in estrogen pathway signaling. Both Esr1 and CYP19A1 overexpressing mice responded to letrozole with reduced hyperplastic alveolar nodule prevalence and decreased mammary epithelial cell proliferation. CYP19A1 overexpressing mice were tamoxifen sensitive but Esr1 overexpressing mice were tamoxifen resistant. Increased ER expression occurred with tamoxifen resistance but no consistent changes in progesterone receptor, pSTAT3, pSTAT5, cyclin D1 or cyclin E levels in association with response or resistance were found. RNA-sequencing (RNA-seq) was employed to seek a transcriptome predictive of tamoxifen resistance using these models and a second tamoxifen-resistant model, BRCA1 deficient/Trp53 haploinsufficient mice. Sixty-eight genes associated with immune system processing were upregulated in tamoxifen-resistant Esr1- and Brca1-deficient mice, whereas genes related to aromatic compound metabolic process were upregulated in tamoxifen-sensitive CYP19A1 mice. Interferon regulatory factor 7 was identified as a key transcription factor regulating these 68 immune processing genes. Two loci encoding novel transcripts with high homology to human immunoglobulin lambda-like polypeptide 1 were uniquely upregulated in the tamoxifen-resistant models. Letrozole proved to be a successful alternative to tamoxifen. Further study of transcriptional changes associated with tamoxifen resistance including immune-related genes could expand our mechanistic understanding and lead to biomarkers predictive of escape or response to endocrine therapies.
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Affiliation(s)
- Sarah A Dabydeen
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA
| | - Keunsoo Kang
- Laboratory Genetics and Physiology, NIDDK, NIH, Bethesda, MD 20892, USA Department of Microbiology, Dankook University, Cheonan 330-714, Republic of Korea
| | - Edgar S Díaz-Cruz
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA, Department of Pharmaceutical, Social, & Administrative Sciences, Belmont University College of Pharmacy, Nashville, TN 37212, USA
| | - Ahmad Alamri
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA, Clinical Laboratories Sciences, College of Applied Medical Sciences, King Khalid University, Abha 62529, Saudi Arabia and
| | - Margaret L Axelrod
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA
| | - Kerrie B Bouker
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA
| | - Rawan Al-Kharboosh
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA
| | - Robert Clarke
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA
| | | | - Priscilla A Furth
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA, Department of Medicine, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA
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Prediction of individual response to anticancer therapy: historical and future perspectives. Cell Mol Life Sci 2014; 72:729-57. [PMID: 25387856 PMCID: PMC4309902 DOI: 10.1007/s00018-014-1772-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Revised: 10/23/2014] [Accepted: 10/27/2014] [Indexed: 02/06/2023]
Abstract
Since the introduction of chemotherapy for cancer treatment in the early 20th century considerable efforts have been made to maximize drug efficiency and at the same time minimize side effects. As there is a great interpatient variability in response to chemotherapy, the development of predictive biomarkers is an ambitious aim for the rapidly growing research area of personalized molecular medicine. The individual prediction of response will improve treatment and thus increase survival and life quality of patients. In the past, cell cultures were used as in vitro models to predict in vivo response to chemotherapy. Several in vitro chemosensitivity assays served as tools to measure miscellaneous endpoints such as DNA damage, apoptosis and cytotoxicity or growth inhibition. Twenty years ago, the development of high-throughput technologies, e.g. cDNA microarrays enabled a more detailed analysis of drug responses. Thousands of genes were screened and expression levels were correlated to drug responses. In addition, mutation analysis became more and more important for the prediction of therapeutic success. Today, as research enters the area of -omics technologies, identification of signaling pathways is a tool to understand molecular mechanism underlying drug resistance. Combining new tissue models, e.g. 3D organoid cultures with modern technologies for biomarker discovery will offer new opportunities to identify new drug targets and in parallel predict individual responses to anticancer therapy. In this review, we present different currently used chemosensitivity assays including 2D and 3D cell culture models and several -omics approaches for the discovery of predictive biomarkers. Furthermore, we discuss the potential of these assays and biomarkers to predict the clinical outcome of individual patients and future perspectives.
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38
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Hydrolysis of 2'3'-cGAMP by ENPP1 and design of nonhydrolyzable analogs. Nat Chem Biol 2014; 10:1043-8. [PMID: 25344812 PMCID: PMC4232468 DOI: 10.1038/nchembio.1661] [Citation(s) in RCA: 307] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2014] [Accepted: 08/28/2014] [Indexed: 12/13/2022]
Abstract
Agonists of mouse STING (TMEM173) shrink and even cure solid tumor by activating innate immunity; human STING agonists are needed to test this therapeutic hypothesis in man. The endogenous STING agonist is 2′3′-cGAMP, a 2nd messenger that signals the presence of cytosolic dsDNA. We report activity-guided partial purification and identification of ENPP1 as the dominant 2′3′-cGAMP hydrolyzing activity in cultured cells. The hydrolysis activity of ENPP1 was confirmed using recombinant protein and was depleted in tissue extracts and plasma from Enpp1-/- mice. We synthesized a hydrolysis-resistant bis-phosphothioate analog of 2′3′-cGAMP (2′3′-cGsAsMP) with similar affinity for human STING in vitro and 10 times more potent at inducing IFN-β secretion from human THP1 monocytes. Studies in mouse Enpp1-/- lung fibroblasts indicate that resistance to hydrolysis contributes significantly to its higher potency. 2′3′-cGsAsMP is therefore improved over natural 2′3′-cGAMP as a model agonist, and has potential as a vaccine adjuvant and cancer therapeutic.
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39
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LaPorta E, Welsh J. Modeling vitamin D actions in triple negative/basal-like breast cancer. J Steroid Biochem Mol Biol 2014; 144 Pt A:65-73. [PMID: 24239860 PMCID: PMC4021002 DOI: 10.1016/j.jsbmb.2013.10.022] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 10/21/2013] [Accepted: 10/23/2013] [Indexed: 10/26/2022]
Abstract
Breast cancer is a heterogeneous disease with six molecularly defined subtypes, the most aggressive of which are triple negative breast cancers that lack expression of estrogen receptor (ER) and progesterone receptor (PR) and do not exhibit amplification of the growth factor receptor HER2. Triple negative breast cancers often exhibit basal-like gene signatures and are enriched for CD44+ cancer stem cells. In this report we have characterized the molecular actions of the VDR in a model of triple negative breast cancer. Estrogen independent, invasive mammary tumor cell lines established from wild-type (WT) and VDR knockout (VDRKO) mice were used to demonstrate that VDR is necessary for 1,25-dihydroxyvitamin D3 (1,25D) mediated anti-cancer actions in vitro and to identify novel targets of this receptor. Western blotting confirmed differential VDR expression and demonstrated the lack of ER, PR and Her2 in these cell lines. Re-introduction of human VDR (hVDR) into VDRKO cells restored the anti-proliferative actions of 1,25D. Genomic profiling demonstrated that 1,25D failed to alter gene expression in KO240 cells whereas major changes were observed in WT145 cells and in KO clones stably expressing hVDR (KO(hVDR) cells). With a 2-fold cutoff, 117 transcripts in WT145 cells and 197 transcripts in the KO(hVDR) clones were significantly altered by 1,25D. Thirty-five genes were found to be commonly regulated by 1,25D in all VDR-positive cell lines. Of these, we identified a cohort of four genes (Plau, Hbegf, Postn, Has2) that are known to drive breast cancer invasion and metastasis whose expression was markedly down regulated by 1,25D. These data support a model whereby 1,25D coordinately suppresses multiple proteins that are required for survival of triple-negative/basal-like breast cancer cells. Since studies have demonstrated a high prevalence of vitamin D deficiency in women with basal-like breast cancer, correction of vitamin D deficiency in these women represents a reasonable, but as yet untested, strategy to delay recurrence and extend survival. This article is part of a Special Issue entitled '16th Vitamin D Workshop'.
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Affiliation(s)
- Erika LaPorta
- Cancer Research Center, University at Albany, USA; Department of Biomedical Sciences, University at Albany, USA
| | - JoEllen Welsh
- Cancer Research Center, University at Albany, USA; Department of Environmental Health Sciences, University at Albany, USA.
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40
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Longuespée R, Fléron M, Pottier C, Quesada-Calvo F, Meuwis MA, Baiwir D, Smargiasso N, Mazzucchelli G, De Pauw-Gillet MC, Delvenne P, De Pauw E. Tissue Proteomics for the Next Decade? Towards a Molecular Dimension in Histology. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2014; 18:539-52. [DOI: 10.1089/omi.2014.0033] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Rémi Longuespée
- Mass Spectrometry Laboratory, GIGA-Research, Department of Chemistry, University of Liège, Liège, Belgium
| | - Maximilien Fléron
- Mammalian Cell Culture Laboratory, GIGA-Research, Department of Biomedical and Preclinical Sciences, University of Liège, Liège, Belgium
| | - Charles Pottier
- Laboratory of Experimental Pathology, GIGA-Cancer, Department of Pathology, University of Liège, Liège, Belgium
| | - Florence Quesada-Calvo
- Hepato-Gastroenterology and Digestive Oncology Department, Liège University Hospital, University of Liège, Liège, Belgium
| | - Marie-Alice Meuwis
- Hepato-Gastroenterology and Digestive Oncology Department, Liège University Hospital, University of Liège, Liège, Belgium
| | - Dominique Baiwir
- GIGA-R, GIGA Proteomic Facilities, University of Liège, Liège, Belgium
| | - Nicolas Smargiasso
- Mass Spectrometry Laboratory, GIGA-Research, Department of Chemistry, University of Liège, Liège, Belgium
| | - Gabriel Mazzucchelli
- Mass Spectrometry Laboratory, GIGA-Research, Department of Chemistry, University of Liège, Liège, Belgium
| | - Marie-Claire De Pauw-Gillet
- Mammalian Cell Culture Laboratory, GIGA-Research, Department of Biomedical and Preclinical Sciences, University of Liège, Liège, Belgium
| | - Philippe Delvenne
- Laboratory of Experimental Pathology, GIGA-Cancer, Department of Pathology, University of Liège, Liège, Belgium
| | - Edwin De Pauw
- Mass Spectrometry Laboratory, GIGA-Research, Department of Chemistry, University of Liège, Liège, Belgium
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41
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Chakrabarty AM, Bernardes N, Fialho AM. Bacterial proteins and peptides in cancer therapy: today and tomorrow. Bioengineered 2014; 5:234-42. [PMID: 24875003 PMCID: PMC4140868 DOI: 10.4161/bioe.29266] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Cancer is one of the most deadly diseases worldwide. In the last three decades many efforts have been made focused on understanding how cancer grows and responds to drugs. The dominant drug-development paradigm has been the "one drug, one target." Based on that, the two main targeted therapies developed to combat cancer include the use of tyrosine kinase inhibitors and monoclonal antibodies. Development of drug resistance and side effects represent the major limiting factors for their use in cancer treatment. Nowadays, a new paradigm for cancer drug discovery is emerging wherein multi-targeted approaches gain ground in cancer therapy. Therefore, to overcome resistance to therapy, it is clear that a new generation of drugs is urgently needed. Here, regarding the concept of multi-targeted therapy, we discuss the challenges of using bacterial proteins and peptides as a new generation of effective anti-cancer drugs.
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Affiliation(s)
- Ananda M Chakrabarty
- Department of Microbiology & Immunology; University of Illinois College of Medicine; Chicago, IL USA
| | - Nuno Bernardes
- Institute for Biotechnology & Bioengineering; Department of Bioengineering; Instituto Superior Técnico; Universidade de Lisboa; Lisbon, Portugal
| | - Arsenio M Fialho
- Institute for Biotechnology & Bioengineering; Department of Bioengineering; Instituto Superior Técnico; Universidade de Lisboa; Lisbon, Portugal
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42
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Pavlou MP, Dimitromanolakis A, Martinez-Morillo E, Smid M, Foekens JA, Diamandis EP. Integrating Meta-Analysis of Microarray Data and Targeted Proteomics for Biomarker Identification: Application in Breast Cancer. J Proteome Res 2014; 13:2897-909. [DOI: 10.1021/pr500352e] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Maria P. Pavlou
- Department
of Laboratory Medicine and Pathobiology, University of Toronto, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
- Department
of Pathology and Laboratory Medicine, Mount Sinai Hospital, 60 Murray
Street, Toronto, ON M5T 3L9, Canada
| | - Apostolos Dimitromanolakis
- Department
of Pathology and Laboratory Medicine, Mount Sinai Hospital, 60 Murray
Street, Toronto, ON M5T 3L9, Canada
| | - Eduardo Martinez-Morillo
- Lunenfeld-Tanenbaum
Research Institute, Joseph and Wolf Lebovic Health Complex, Mount Sinai Hospital, 60 Murray Street, Toronto, ON M5T 3L9, Canada
| | - Marcel Smid
- Department
of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Groene Hilledijk 301, 3075 EA Rotterdam, The Netherlands
| | - John A. Foekens
- Department
of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Groene Hilledijk 301, 3075 EA Rotterdam, The Netherlands
| | - Eleftherios P. Diamandis
- Department
of Laboratory Medicine and Pathobiology, University of Toronto, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
- Department
of Pathology and Laboratory Medicine, Mount Sinai Hospital, 60 Murray
Street, Toronto, ON M5T 3L9, Canada
- Lunenfeld-Tanenbaum
Research Institute, Joseph and Wolf Lebovic Health Complex, Mount Sinai Hospital, 60 Murray Street, Toronto, ON M5T 3L9, Canada
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43
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Akcakanat A, Hong DS, Meric-Bernstam F. Targeting translation initiation in breast cancer. ACTA ACUST UNITED AC 2014; 2:e28968. [PMID: 26779407 PMCID: PMC4705830 DOI: 10.4161/trla.28968] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 04/09/2014] [Accepted: 04/22/2014] [Indexed: 12/23/2022]
Abstract
Over the past 20 years, a better understanding of cancer biology, screening for early detection, improved adjuvant treatment, and targeted therapies have decreased the rate of breast cancer deaths. However, resistance to treatment is common, and new approaches are needed. Deregulation of translation initiation is associated with the commencement and progression of cancer. Often, translation initiation factors are overexpressed and the related signaling pathways activated in human tumors. Recently, a significant number of inhibitors that target translation factors and pathways have become available. These inhibitors are being tested alone or in combination with chemotherapeutic agents in clinical trials. The results are varied, and it is not yet clear which drug treatments most effectively inhibit tumor growth. This review highlights the pathways and downstream effects of the activation of translation and discusses targeting the control of translation initiation as a therapeutic approach in cancer, focusing on breast cancer clinical trials.
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Affiliation(s)
- Argun Akcakanat
- Department of Investigational Cancer Therapeutics; Houston, TX USA
| | - David S Hong
- Department of Investigational Cancer Therapeutics; Houston, TX USA
| | - Funda Meric-Bernstam
- Department of Investigational Cancer Therapeutics; Houston, TX USA; Department of Surgical Oncology; The University of Texas MD Anderson Cancer Center; Houston, TX USA
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44
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Liu NQ, De Marchi T, Timmermans AM, Beekhof R, Trapman-Jansen AMAC, Foekens R, Look MP, van Deurzen CHM, Span PN, Sweep FCGJ, Brask JB, Timmermans-Wielenga V, Debets R, Martens JWM, Foekens JA, Umar A. Ferritin heavy chain in triple negative breast cancer: a favorable prognostic marker that relates to a cluster of differentiation 8 positive (CD8+) effector T-cell response. Mol Cell Proteomics 2014; 13:1814-27. [PMID: 24742827 PMCID: PMC4083117 DOI: 10.1074/mcp.m113.037176] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Ferritin heavy chain (FTH1) is a 21-kDa subunit of the ferritin complex, known for its role in iron metabolism, and which has recently been identified as a favorable prognostic protein for triple negative breast cancer (TNBC) patients. Currently, it is not well understood how FTH1 contributes to an anti-tumor response. Here, we explored whether expression and cellular compartmentalization of FTH1 correlates to an effective immune response in TNBC patients. Analysis of the tumor tissue transcriptome, complemented with in silico pathway analysis, revealed that FTH1 was an integral part of an immunomodulatory network of cytokine signaling, adaptive immunity, and cell death. These findings were confirmed using mass spectrometry (MS)-derived proteomic data, and immunohistochemical staining of tissue microarrays. We observed that FTH1 is localized in both the cytoplasm and/or nucleus of cancer cells. However, high cytoplasmic (c) FTH1 was associated with favorable prognosis (Log-rank p = 0.001), whereas nuclear (n) FTH1 staining was associated with adverse prognosis (Log-rank p = 0.019). cFTH1 staining significantly correlated with total FTH1 expression in TNBC tissue samples, as measured by MS analysis (Rs = 0.473, p = 0.0007), but nFTH1 staining did not (Rs = 0.197, p = 0.1801). Notably, IFN γ-producing CD8+ effector T cells, but not CD4+ T cells, were preferentially enriched in tumors with high expression of cFTH1 (p = 0.02). Collectively, our data provide evidence toward new immune regulatory properties of FTH1 in TNBC, which may facilitate development of novel therapeutic targets.
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Affiliation(s)
- Ning Qing Liu
- From the ‡Department of Medical Oncology, Erasmus MC Cancer Institute, ‡‡Netherlands Proteomics Centre, Utrecht, The Netherlands; §§Postgraduate School of Molecular Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands; ¶¶Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen, 6525 GA, Nijmegen, The Netherlands
| | - Tommaso De Marchi
- From the ‡Department of Medical Oncology, Erasmus MC Cancer Institute, §§Postgraduate School of Molecular Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | - Robin Beekhof
- From the ‡Department of Medical Oncology, Erasmus MC Cancer Institute
| | | | - Renée Foekens
- From the ‡Department of Medical Oncology, Erasmus MC Cancer Institute
| | - Maxime P Look
- From the ‡Department of Medical Oncology, Erasmus MC Cancer Institute
| | | | | | - Fred C G J Sweep
- ‖Department of Laboratory Medicine, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Julie Benedicte Brask
- **Department of Pathology, the Centre of Diagnostic Investigations, Copenhagen University Hospital, Copenhagen, Denmark
| | - Vera Timmermans-Wielenga
- **Department of Pathology, the Centre of Diagnostic Investigations, Copenhagen University Hospital, Copenhagen, Denmark
| | - Reno Debets
- From the ‡Department of Medical Oncology, Erasmus MC Cancer Institute
| | - John W M Martens
- From the ‡Department of Medical Oncology, Erasmus MC Cancer Institute, ‡‡Netherlands Proteomics Centre, Utrecht, The Netherlands
| | - John A Foekens
- From the ‡Department of Medical Oncology, Erasmus MC Cancer Institute, ‡‡Netherlands Proteomics Centre, Utrecht, The Netherlands
| | - Arzu Umar
- From the ‡Department of Medical Oncology, Erasmus MC Cancer Institute, ‡‡Netherlands Proteomics Centre, Utrecht, The Netherlands;
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Gromov P, Moreira JMA, Gromova I. Proteomic analysis of tissue samples in translational breast cancer research. Expert Rev Proteomics 2014; 11:285-302. [DOI: 10.1586/14789450.2014.899469] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Int6/eIF3e is essential for proliferation and survival of human glioblastoma cells. Int J Mol Sci 2014; 15:2172-90. [PMID: 24481065 PMCID: PMC3958844 DOI: 10.3390/ijms15022172] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2013] [Revised: 12/25/2013] [Accepted: 01/23/2014] [Indexed: 12/15/2022] Open
Abstract
Glioblastomas (GBM) are very aggressive and malignant brain tumors, with frequent relapses despite an appropriate treatment combining surgery, chemotherapy and radiotherapy. In GBM, hypoxia is a characteristic feature and activation of Hypoxia Inducible Factors (HIF-1α and HIF-2α) has been associated with resistance to anti-cancer therapeutics. Int6, also named eIF3e, is the “e” subunit of the translation initiation factor eIF3, and was identified as novel regulator of HIF-2α. Eukaryotic initiation factors (eIFs) are key factors regulating total protein synthesis, which controls cell growth, size and proliferation. The functional significance of Int6 and the effect of Int6/EIF3E gene silencing on human brain GBM has not yet been described and its role on the HIFs is unknown in glioma cells. In the present study, we show that Int6/eIF3e suppression affects cell proliferation, cell cycle and apoptosis of various GBM cells. We highlight that Int6 inhibition induces a diminution of proliferation through cell cycle arrest and increased apoptosis. Surprisingly, these phenotypes are independent of global cell translation inhibition and are accompanied by decreased HIF expression when Int6 is silenced. In conclusion, we demonstrate here that Int6/eIF3e is essential for proliferation and survival of GBM cells, presumably through modulation of the HIFs.
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Legres LG, Janin A, Masselon C, Bertheau P. Beyond laser microdissection technology: follow the yellow brick road for cancer research. Am J Cancer Res 2014; 4:1-28. [PMID: 24482735 PMCID: PMC3902229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 10/25/2013] [Indexed: 06/03/2023] Open
Abstract
Normal biological tissues harbour different populations of cells with intricate spacial distribution patterns resulting in heterogeneity of their overall cellular composition. Laser microdissection involving direct viewing and expertise by a pathologist, enables access to defined cell populations or specific region on any type of tissue sample, thus selecting near-pure populations of targeted cells. It opens the way for molecular methods directed towards well-defined populations, and provides also a powerful tool in studies focused on a limited number of cells. Laser microdissection has wide applications in oncology (diagnosis and research), cellular and molecular biology, biochemistry and forensics for tissue selection, but other areas have been gradually opened up to these new methodological approaches, such as cell cultures and cytogenetics. In clinical oncology trials, molecular profiling of microdissected samples can yield global "omics" information which, together, with the morphological analysis of cells, can provide the basis for diagnosis, prognosis and patient-tailored treatments. This remarkable technology has brought new insights in the understanding of DNA, RNA, and the biological functions and regulation of proteins to identify molecular disease signatures. We review herein the different applications of laser microdissection in a variety of fields, and we particularly focus attention on the pre-analytical steps that are crucial to successfully perform molecular-level investigations.
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Affiliation(s)
- Luc G Legres
- Inserm UMR_S1165, Institut Universitaire d’HématologieParis
- Université Paris-DiderotParis
| | - Anne Janin
- Inserm UMR_S1165, Institut Universitaire d’HématologieParis
- Université Paris-DiderotParis
- AP-HP, Hôpital Saint-Louis, Service de PathologieParis
| | - Christophe Masselon
- CEA, iRTSV/Laboratoire de Biologie à Grande EchelleGrenoble
- Inserm UMR_S 1038Grenoble
| | - Philippe Bertheau
- Inserm UMR_S1165, Institut Universitaire d’HématologieParis
- Université Paris-DiderotParis
- AP-HP, Hôpital Saint-Louis, Service de PathologieParis
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Liu NQ, Stingl C, Look MP, Smid M, Braakman RBH, De Marchi T, Sieuwerts AM, Span PN, Sweep FCGJ, Linderholm BK, Mangia A, Paradiso A, Dirix LY, Van Laere SJ, Luider TM, Martens JWM, Foekens JA, Umar A. Comparative proteome analysis revealing an 11-protein signature for aggressive triple-negative breast cancer. J Natl Cancer Inst 2014; 106:djt376. [PMID: 24399849 PMCID: PMC3952199 DOI: 10.1093/jnci/djt376] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Background Clinical outcome of patients with triple-negative breast cancer (TNBC) is highly variable. This study aims to identify and validate a prognostic protein signature for TNBC patients to reduce unnecessary adjuvant systemic therapy. Methods Frozen primary tumors were collected from 126 lymph node–negative and adjuvant therapy–naive TNBC patients. These samples were used for global proteome profiling in two series: an in-house training (n = 63) and a multicenter test (n = 63) set. Patients who remained free of distant metastasis for a minimum of 5 years after surgery were defined as having good prognosis. Cox regression analysis was performed to develop a prognostic signature, which was independently validated. All statistical tests were two-sided. Results An 11-protein signature was developed in the training set (median follow-up for good-prognosis patients = 117 months) and subsequently validated in the test set (median follow-up for good-prognosis patients = 108 months) showing 89.5% sensitivity (95% confidence interval [CI] = 69.2% to 98.1%), 70.5% specificity (95% CI = 61.7% to 74.2%), 56.7% positive predictive value (95% CI = 43.8% to 62.1%), and 93.9% negative predictive value (95% CI = 82.3% to 98.9%) for poor-prognosis patients. The predicted poor-prognosis patients had higher risk to develop distant metastasis than the predicted good-prognosis patients in univariate (hazard ratio [HR] = 13.15; 95% CI = 3.03 to 57.07; P = .001) and multivariable (HR = 12.45; 95% CI = 2.67 to 58.11; P = .001) analysis. Furthermore, the predicted poor-prognosis group had statistically significantly more breast cancer–specific mortality. Using our signature as guidance, more than 60% of patients would have been exempted from unnecessary adjuvant chemotherapy compared with conventional prognostic guidelines. Conclusions We report the first validated proteomic signature to assess the natural course of clinical TNBC.
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Affiliation(s)
- Ning Qing Liu
- Affiliations of authors: Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands (NQL, MPL, MS, RBHB, TDM, AMS, JWMM, JAF, AU); Department of Neurology (CS, TML) and Postgraduate School of Molecular Medicine (NQL, RBHB, TDM, AMS, JWMM, JAF, AU), Erasmus University Medical Center, Rotterdam, The Netherlands; Department of Radiation Oncology (PNS) and Department of Laboratory Medicine (FCGJS), Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands; Department of Oncology, Sahlgrenska University Hospital, Gothenburg, Sweden (BKL); Department of Oncology/Pathology, Karolinska Institute, Stockholm, Sweden (BKL); Clinical Experimental Oncology Laboratory, National Cancer Centre Giovanni Paolo II, Bari, Italy (AM, AP); Translational Cancer Research Unit, Oncology Center, GZA Hospitals St-Augustinus, Antwerp, Belgium (LYD, SJVL); Netherlands Proteomics Centre, Utrecht, The Netherlands (NQL, AU); Cancer Genomics Centre, Utrecht, The Netherlands (MS, AMS, JWMM, JAF, AU); Center for Translational Molecular Medicine, Eindhoven, The Netherlands (RBHB, JAF, AU)
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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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Majidzadeh-A K, Gharechahi J. Plasma proteomics analysis of tamoxifen resistance in breast cancer. Med Oncol 2013; 30:753. [DOI: 10.1007/s12032-013-0753-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 10/15/2013] [Indexed: 02/08/2023]
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