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Flemming JP, Wermuth PJ, Mahoney MG. Extracellular Vesicles in the Skin Microenvironment: Emerging Roles as Biomarkers and Therapeutic Tools in Dermatologic Health and Disease. J Invest Dermatol 2024; 144:225-233. [PMID: 37877931 DOI: 10.1016/j.jid.2023.08.024] [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: 08/01/2023] [Revised: 08/23/2023] [Accepted: 08/24/2023] [Indexed: 10/26/2023]
Abstract
The recent discovery of extracellular vesicles (EVs) carrying cargo consisting of various bioactive macromolecules that can modulate the phenotype of recipient target cells has revealed an important new mechanism through which cells can signal their neighbors and regulate their microenvironment. Because EV cargo and composition correlate with the physiologic state of their cell of origin, investigations into the role of EVs in disease pathogenesis and progression have become an area of intense study. The physiologic and pathologic effects of EVs on their microenvironment are incredibly diverse and include the modulation of molecular pathways involved in angiogenesis, inflammation, wound healing, epithelial-mesenchymal transition, proliferation, and immune escape. This review examines recent studies on the role of EVs in diseases of the skin and on how differences in EV composition and cargo can alter cell states and the surrounding microenvironment. We also discuss the potential clinical applications of EVs in skin disease diagnosis and management. We examine their value as an easily isolated source of biomarkers to predict disease prognosis or to monitor patient response to treatment. Given the ability of EVs to modulate disease-specific signaling pathways, we also assess their potential to serve as novel personalized precision therapeutic tools for dermatological diseases.
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Affiliation(s)
- Joseph P Flemming
- Department of Dermatology & Cutaneous Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA.
| | - Peter J Wermuth
- Department of Dermatology & Cutaneous Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA.
| | - Mỹ G Mahoney
- Department of Dermatology & Cutaneous Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA; Department of Pharmacology, Physiology, and Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA; Department of Otolaryngology - Head & Neck Surgery, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
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2
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Gouda MA, Zarzour MA, Vaporciyan AA, Kairemo K, Chuang HH, Subbiah V. Activity of pazopanib in EWSR1-NFATC2 translocation-associated bone sarcoma. Oncoscience 2023; 10:44-53. [PMID: 37736255 PMCID: PMC10511123 DOI: 10.18632/oncoscience.587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 08/21/2023] [Indexed: 09/23/2023] Open
Abstract
Pazopanib is a multi-kinase inhibitor that is currently approved for treatment of advanced renal cell carcinoma and chemotherapy-refractory soft tissue sarcoma. In this case report, we discuss the case of a patient with a EWSR1-NFATC2 fusion positive bone sarcoma who had exceptional tumor control through using pazopanib and surgery for an overall duration exceeding 5 years. We also review the literature on EWSR1-NFATC2 translocation-associated sarcomas and use of pazopanib in bone sarcomas.
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Affiliation(s)
- Mohamed A. Gouda
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Maria A. Zarzour
- Department of Sarcoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ara A. Vaporciyan
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kalevi Kairemo
- Department of Nuclear Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hubert H. Chuang
- Department of Nuclear Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Vivek Subbiah
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Sarah Cannon Research Institute, Nashville, TN 37203, USA
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3
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Benito-Martín A, Jasiulionis MG, García-Silva S. Extracellular vesicles and melanoma: New perspectives on tumor microenvironment and metastasis. Front Cell Dev Biol 2023; 10:1061982. [PMID: 36704194 PMCID: PMC9871288 DOI: 10.3389/fcell.2022.1061982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 12/27/2022] [Indexed: 01/11/2023] Open
Abstract
Secreted extracellular vesicles (EVs) are lipid bilayer particles without functional nucleus naturally released from cells which constitute an intercellular communication system. There is a broad spectrum of vesicles shed by cells based on their physical properties such as size (small EVs and large EVs), biogenesis, cargo and functions, which provide an increasingly heterogenous landscape. In addition, they are involved in multiple physiological and pathological processes. In cancer, EV release is opted by tumor cells as a beneficial process for tumor progression. Cutaneous melanoma is a cancer that originates from the melanocyte lineage and shows a favorable prognosis at early stages. However, when melanoma cells acquire invasive capacity, it constitutes the most aggressive and deadly skin cancer. In this context, extracellular vesicles have been shown their relevance in facilitating melanoma progression through the modulation of the microenvironment and metastatic spreading. In agreement with the melanosome secretory capacity of melanocytes, melanoma cells display an enhanced EV shedding activity that has contributed to the utility of melanoma models for unravelling EV cargo and functions within a cancer scenario. In this review, we provide an in-depth overview of the characteristics of melanoma-derived EVs and their role in melanoma progression highlighting key advances and remaining open questions in the field.
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Affiliation(s)
- Alberto Benito-Martín
- Facultad de Medicina, Unidad de Investigación Biomédica, Universidad Alfonso X El Sabio (UAX), Villanueva de la Cañada, Spain,*Correspondence: Alberto Benito-Martín, ; Miriam Galvonas Jasiulionis, ; Susana García-Silva,
| | - Miriam Galvonas Jasiulionis
- Departamento de Farmacologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil,*Correspondence: Alberto Benito-Martín, ; Miriam Galvonas Jasiulionis, ; Susana García-Silva,
| | - Susana García-Silva
- Microenvironment and Metastasis Laboratory, Molecular Oncology Programme, Spanish National Cancer Research Center (CNIO), Madrid, Spain,*Correspondence: Alberto Benito-Martín, ; Miriam Galvonas Jasiulionis, ; Susana García-Silva,
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4
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Kohtamäki L, Arjama M, Mäkelä S, Ianevski P, Välimäki K, Juteau S, Ilmonen S, Ungureanu D, Kallioniemi O, Murumägi A, Hernberg M. High-throughput ex vivo drug testing identifies potential drugs and drug combinations for NRAS-positive malignant melanoma. Transl Oncol 2022; 15:101290. [PMID: 34837846 PMCID: PMC8633005 DOI: 10.1016/j.tranon.2021.101290] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 11/05/2021] [Accepted: 11/17/2021] [Indexed: 12/18/2022] Open
Abstract
Therapy options for patients with metastatic melanoma (MM) have considerably improved over the past decade. However, many patients still need effective therapy after unsuccessful immunotherapy, especially patients with BRAF-negative tumors who lack the option of targeted treatment second line. Therefore, the elucidation of efficient and personalized therapy options for these patients is required. In this study, three patient-derived cancer cells (PDCs) were established from NRAS Q61-positive MM patients. The response of PDCs and five established melanoma cell lines (two NRAS-positive, one wild type, and two BRAF V600-positive) was evaluated toward a panel of 527 oncology drugs using high-throughput drug sensitivity and resistance testing. The PDCs and cell lines displayed strong responses to MAPK inhibitors, as expected. Additionally, the PDCs and cell lines were responsive to PI3K/mTOR, mTOR, and PLK1 inhibitors among other effective drugs currently undergoing clinical trials. Combinations with a MEK inhibitor were tested with other targeted agents to identify effective synergies. MEK inhibitor showed synergy with multikinase inhibitor ponatinib, ABL inhibitor nilotinib, PI3K/mTOR inhibitor pictilisib, and pan-RAF inhibitor LY3009120. The application of the patients' cancer cells for functional drug testing ex vivo is one step further in the process of identifying potential agents and agent combinations to personalize treatment for patients with MM. Our preliminary study results suggest that this approach has the potential for larger-scale drug testing and personalized treatment applications in our expansion trial. Our results show that drug sensitivity and resistance testing may be implementable in the treatment planning of patients with MM.
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Affiliation(s)
- Laura Kohtamäki
- Helsinki University Hospital, Comprehensive Cancer Center, Department of Oncology, Helsinki and University of Helsinki, Finland.
| | - Mariliina Arjama
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), Helsinki, Finland and University of Helsinki, Finland
| | - Siru Mäkelä
- Helsinki University Hospital, Comprehensive Cancer Center, Department of Oncology, Helsinki and University of Helsinki, Finland
| | - Philipp Ianevski
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), Helsinki, Finland and University of Helsinki, Finland
| | - Katja Välimäki
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), Helsinki, Finland and University of Helsinki, Finland
| | - Susanna Juteau
- Department of Pathology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Suvi Ilmonen
- Helsinki University Hospital, Department of Surgery, Helsinki and University of Helsinki, Finland
| | - Daniela Ungureanu
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Olli Kallioniemi
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), Helsinki, Finland and University of Helsinki, Finland; Science for Life Laboratory (SciLifeLab), Department of Oncology and Pathology, Karolinska Institutet, Sweden
| | - Astrid Murumägi
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), Helsinki, Finland and University of Helsinki, Finland.
| | - Micaela Hernberg
- Helsinki University Hospital, Comprehensive Cancer Center, Department of Oncology, Helsinki and University of Helsinki, Finland
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Oliveira ÉAD, Chauhan J, Silva JRD, Carvalho LADC, Dias D, Carvalho DGD, Watanabe LRM, Rebecca VW, Mills G, Lu Y, da Silva ASF, Consolaro MEL, Herlyn M, Possik PA, Goding CR, Maria-Engler SS. TOP1 modulation during melanoma progression and in adaptative resistance to BRAF and MEK inhibitors. Pharmacol Res 2021; 173:105911. [PMID: 34560251 DOI: 10.1016/j.phrs.2021.105911] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 09/03/2021] [Accepted: 09/19/2021] [Indexed: 12/26/2022]
Abstract
In melanomas, therapy resistance can arise due to a combination of genetic, epigenetic and phenotypic mechanisms. Due to its crucial role in DNA supercoil relaxation, TOP1 is often considered an essential chemotherapeutic target in cancer. However, how TOP1 expression and activity might differ in therapy sensitive versus resistant cell types is unknown. Here we show that TOP1 expression is increased in metastatic melanoma and correlates with an invasive gene expression signature. More specifically, TOP1 expression is highest in cells with the lowest expression of MITF, a key regulator of melanoma biology. Notably, TOP1 and DNA Single-Strand Break Repair genes are downregulated in BRAFi- and BRAFi/MEKi-resistant cells and TOP1 inhibition decreases invasion markers only in BRAFi/MEKi-resistant cells. Thus, we show three different phenotypes related to TOP1 levels: i) non-malignant cells with low TOP1 levels; ii) metastatic cells with high TOP1 levels and high invasiveness; and iii) BRAFi- and BRAFi/MEKi-resistant cells with low TOP1 levels and high invasiveness. Together, these results highlight the potential role of TOP1 in melanoma progression and resistance.
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Affiliation(s)
- Érica Aparecida de Oliveira
- Skin Biology Group, Clinical Chemistry and Toxicology Department, School of Pharmaceutical Sciences, University of Sao Paulo, FCF/USP, Brazil; Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, UK
| | - Jagat Chauhan
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, UK
| | - Julia Rezende da Silva
- Skin Biology Group, Clinical Chemistry and Toxicology Department, School of Pharmaceutical Sciences, University of Sao Paulo, FCF/USP, Brazil
| | - Larissa Anastacio da Costa Carvalho
- Skin Biology Group, Clinical Chemistry and Toxicology Department, School of Pharmaceutical Sciences, University of Sao Paulo, FCF/USP, Brazil
| | - Diogo Dias
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, UK
| | | | - Luis Roberto Masao Watanabe
- Skin Biology Group, Clinical Chemistry and Toxicology Department, School of Pharmaceutical Sciences, University of Sao Paulo, FCF/USP, Brazil
| | - Vito W Rebecca
- Molecular and Cellular Oncogenesis Program and Melanoma Research Center, Wistar Institute, Philadelphia, PA, USA; Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | | | - Yiling Lu
- The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Aloisio Souza Felipe da Silva
- Department of Pathology, Anatomic Pathology Service, University Hospital, University of São Paulo, São Paulo, Brazil
| | | | - Meenhard Herlyn
- Molecular and Cellular Oncogenesis Program and Melanoma Research Center, Wistar Institute, Philadelphia, PA, USA
| | - Patricia A Possik
- Division of Cellular Biology, Brazilian National Cancer Institute, Brazil
| | - Colin R Goding
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, UK
| | - Silvya Stuchi Maria-Engler
- Skin Biology Group, Clinical Chemistry and Toxicology Department, School of Pharmaceutical Sciences, University of Sao Paulo, FCF/USP, Brazil.
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Zebrowska A, Widlak P, Whiteside T, Pietrowska M. Signaling of Tumor-Derived sEV Impacts Melanoma Progression. Int J Mol Sci 2020; 21:ijms21145066. [PMID: 32709086 PMCID: PMC7404104 DOI: 10.3390/ijms21145066] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/14/2020] [Accepted: 07/15/2020] [Indexed: 12/12/2022] Open
Abstract
Small extracellular vesicles (sEV or exosomes) are nanovesicles (30–150 nm) released both in vivo and in vitro by most cell types. Tumor cells produce sEV called TEX and disperse them throughout all body fluids. TEX contain a cargo of proteins, lipids, and RNA that is similar but not identical to that of the “parent” producer cell (i.e., the cargo of exosomes released by melanoma cells is similar but not identical to exosomes released by melanocytes), possibly due to selective endosomal packaging. TEX and their role in cancer biology have been intensively investigated largely due to the possibility that TEX might serve as key component of a “liquid tumor biopsy.” TEX are also involved in the crosstalk between cancer and immune cells and play a key role in the suppression of anti-tumor immune responses, thus contributing to the tumor progression. Most of the available information about the TEX molecular composition and functions has been gained using sEV isolated from supernatants of cancer cell lines. However, newer data linking plasma levels of TEX with cancer progression have focused attention on TEX in the patients’ peripheral circulation as potential biomarkers of cancer diagnosis, development, activity, and response to therapy. Here, we consider the molecular cargo and functions of TEX as potential biomarkers of one of the most fatal malignancies—melanoma. Studies of TEX in plasma of patients with melanoma offer the possibility of an in-depth understanding of the melanoma biology and response to immune therapies. This review features melanoma cell-derived exosomes (MTEX) with special emphasis on exosome-mediated signaling between melanoma cells and the host immune system.
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Affiliation(s)
- Aneta Zebrowska
- Maria Sklodowska-Curie National Research Institute of Oncology, Gliwice Branch, 44-100 Gliwice, Poland; (A.Z.); (P.W.)
| | - Piotr Widlak
- Maria Sklodowska-Curie National Research Institute of Oncology, Gliwice Branch, 44-100 Gliwice, Poland; (A.Z.); (P.W.)
| | - Theresa Whiteside
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15213, USA;
- Department of Pathology, University of Pittsburgh School of Medicine Pittsburgh, Pittsburgh, PA 15261, USA
| | - Monika Pietrowska
- Maria Sklodowska-Curie National Research Institute of Oncology, Gliwice Branch, 44-100 Gliwice, Poland; (A.Z.); (P.W.)
- Correspondence: ; Tel.: +48-32-278-9627
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Ha JH, Lee C, Lee KS, Pak CS, Sun CH, Koh Y, Chang H. The molecular pathogenesis of Trichilemmal carcinoma. BMC Cancer 2020; 20:516. [PMID: 32493317 PMCID: PMC7271408 DOI: 10.1186/s12885-020-07009-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 05/27/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Trichilemmal carcinoma (TC) is an extremely rare hair follicle tumor. We aimed to explore the genetic abnormalities involved in TC to gain insight into its molecular pathogenesis. METHODS Data from patients diagnosed with TC within a 12-year period were retrospectively reviewed. Genomic DNA isolated from a formalin-fixed paraffin-embedded (FFPE) tumor tissue block was sequenced and explored for a panel of cancer genes. RESULTS DNA was extracted from the FFPE tissue of four patients (50% female; mean age, 51.5 years) diagnosed with TC for analysis. The tumor was located in the head and neck of three patients and in the shoulder of one patient. TP53 mutations (p.Arg213*, p.Arg249Trp, and p.Arg248Gln) were found in three patients. Fusions previously identified in melanoma were detected in two patients (TACC3-FGFR3 and ROS1-GOPC fusions). Other mutations found included NF1-truncating mutation (Arg1362*), NRAS mutation (p.Gln61Lys), TOP1 amplification, and PTEN deletion. Overall, genetic changes found in TC resemble that of other skin cancers, suggesting similar pathogenesis. All patients with TP53 mutations had aggressive clinical course, two who died (OS 93 and 36 months), and one who experienced recurrent relapse. CONCLUSIONS We reported the genomic variations found in TC, which may give insight into the molecular pathogenesis. Overall, genetic changes found in TC resembled that of other skin cancers, suggesting similar pathogenesis. TP53 mutations was were identified in patients who had an aggressive clinical course. Genetic alterations identified may further suggest the potential treatment options of TC.
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Affiliation(s)
- Jeong Hyun Ha
- Department of Plastic and Reconstructive Surgery, Seoul Metropolitan Government-Seoul National University Boramae Medical Center, Seoul, Korea
| | - Cheol Lee
- Department of Pathology, Seoul National University Hospital, Seoul, Korea
| | - Kyu Sang Lee
- Department of Pathology, Seoul National University Bundang Hospital, Gyeonggi, Korea
| | - Chang-sik Pak
- Department of Plastic and Reconstructive Surgery, Asan Medical Center, Seoul, Korea
| | | | - Youngil Koh
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
- Center for Medical Innovation, Seoul National University Hospital, Seoul, Korea
| | - Hak Chang
- Department of Plastic and Reconstructive Surgery, Seoul National University College of Medicine, Seoul, Korea
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Oliveira ÉAD, Lima DSD, Cardozo LE, Souza GFD, de Souza N, Alves-Fernandes DK, Faião-Flores F, Quincoces JAP, Barros SBDM, Nakaya HI, Monteiro G, Maria-Engler SS. Toxicogenomic and bioinformatics platforms to identify key molecular mechanisms of a curcumin-analogue DM-1 toxicity in melanoma cells. Pharmacol Res 2017; 125:178-187. [PMID: 28882690 DOI: 10.1016/j.phrs.2017.08.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 07/31/2017] [Accepted: 08/30/2017] [Indexed: 12/17/2022]
Abstract
Melanoma is a highly invasive and metastatic cancer with high mortality rates and chemoresistance. Around 50% of melanomas are driven by activating mutations in BRAF that has led to the development of potent anti-BRAF inhibitors. However resistance to anti-BRAF therapy usually develops within a few months and consequently there is a need to identify alternative therapies that will bypass BRAF inhibitor resistance. The curcumin analogue DM-1 (sodium 4-[5-(4-hydroxy-3-methoxy-phenyl)-3-oxo-penta-1,4-dienyl]-2-methoxy-phenolate) has substantial anti-tumor activity in melanoma, but its mechanism of action remains unclear. Here we use a synthetic lethal genetic screen in Saccharomyces cerevisiae to identify 211 genes implicated in sensitivity to DM-1 toxicity. From these 211 genes, 74 had close human orthologues implicated in oxidative phosphorylation, insulin signaling and iron and RNA metabolism. Further analysis identified 7 target genes (ADK, ATP6V0B, PEMT, TOP1, ZFP36, ZFP36L1, ZFP36L2) with differential expression during melanoma progression implicated in regulation of tumor progression, cell differentiation, and epithelial-mesenchymal transition. Of these TOP1 and ADK were regulated by DM-1 in treatment-naïve and vemurafenib-resistant melanoma cells respectively. These data reveal that the anticancer effect of curcumin analogues is likely to be mediated via multiple targets and identify several genes that represent candidates for combinatorial targeting in melanoma.
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Affiliation(s)
- Érica Aparecida de Oliveira
- Skin Biology Group, Clinical Chemistry and Toxicology Department, School of Pharmaceutical Sciences, University of Sao Paulo, FCF/USP, Sao Paulo, Brazil
| | - Diogenes Saulo de Lima
- Computational Systems Biology Laboratory, School of Pharmaceutical Sciences, University of Sao Paulo, FCF/USP, Sao Paulo, Brazil
| | - Lucas Esteves Cardozo
- Computational Systems Biology Laboratory, School of Pharmaceutical Sciences, University of Sao Paulo, FCF/USP, Sao Paulo, Brazil
| | | | - Nayane de Souza
- Skin Biology Group, Clinical Chemistry and Toxicology Department, School of Pharmaceutical Sciences, University of Sao Paulo, FCF/USP, Sao Paulo, Brazil
| | - Debora Kristina Alves-Fernandes
- Skin Biology Group, Clinical Chemistry and Toxicology Department, School of Pharmaceutical Sciences, University of Sao Paulo, FCF/USP, Sao Paulo, Brazil
| | - Fernanda Faião-Flores
- Skin Biology Group, Clinical Chemistry and Toxicology Department, School of Pharmaceutical Sciences, University of Sao Paulo, FCF/USP, Sao Paulo, Brazil
| | | | - Silvia Berlanga de Moraes Barros
- Skin Biology Group, Clinical Chemistry and Toxicology Department, School of Pharmaceutical Sciences, University of Sao Paulo, FCF/USP, Sao Paulo, Brazil
| | - Helder I Nakaya
- Computational Systems Biology Laboratory, School of Pharmaceutical Sciences, University of Sao Paulo, FCF/USP, Sao Paulo, Brazil
| | - Gisele Monteiro
- Biochemical Pharmaceutical Technology Department, School of Pharmaceutical Sciences, University of Sao Paulo, FCF/USP, Sao Paulo, Brazil
| | - Silvya Stuchi Maria-Engler
- Skin Biology Group, Clinical Chemistry and Toxicology Department, School of Pharmaceutical Sciences, University of Sao Paulo, FCF/USP, Sao Paulo, Brazil.
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Palshof JA, Høgdall EVS, Poulsen TS, Linnemann D, Jensen BV, Pfeiffer P, Tarpgaard LS, Brünner N, Stenvang J, Yilmaz M, Nielsen DL. Topoisomerase I copy number alterations as biomarker for irinotecan efficacy in metastatic colorectal cancer. BMC Cancer 2017; 17:48. [PMID: 28077117 PMCID: PMC5225543 DOI: 10.1186/s12885-016-3001-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 12/14/2016] [Indexed: 12/18/2022] Open
Abstract
Background No biomarker exists to guide the optimal choice of chemotherapy for patients with metastatic colorectal cancer. We examined the copy numbers (CN) of topoisomerase I (TOP1) as well as the ratios of TOP1/CEN-20 and TOP1/CEN-2 as biomarkers for irinotecan efficacy in patients with metastatic colorectal cancer. Methods From a national cohort, we identified 163 patients treated every third week with irinotecan 350 mg/m2 as second-line therapy. Among these 108 were eligible for analyses and thus entered the study. Primary tumors samples were collected and tissue microarray (TMA) blocks were produced. FISH analysis was performed using two probe-mixes: TOP1/CEN-20 and TOP1/CEN-2. Only samples harboring all three signals (TOP1, CEN-20 and CEN-2) using FISH were included in the analyses. Results In the TOP1/CEN-20 probe-mix the median TOP1- and CEN-20 CN were 4.46 (range: 1.5–9.5) and 2.00 (range: 0.55–4.55), respectively. The median TOP1- and CEN-2 CN in the TOP1/CEN-2 probe-mix, were 4.57 (range: 1.82–10.43) and 1.98 (range: 1.22–6.14), respectively. The median TOP1/CEN-20 ratio and TOP1/CEN-2 ratio were 1.25 (range: 0.92–2.90) and 2.05 (range: 1.00–6.00), respectively. None of the markers TOP1 CN, TOP1/CEN-20-ratio or TOP1/CEN-2-ratio were associated with progression free survival, overall survival or baseline characteristics. Yet, we observed a borderline association for a stepwise increase of the TOP1 CN in relation to objective response as hazard ratio were 1.35 (95% CI 0.96–1.90; p = 0.081). Conclusions We verified a borderline significant association between increasing TOP1 CN and objective response as previously reported. Applying the probes representing CEN-20 and CEN-2, in order to investigate the ratios of TOP1/CEN-20 and TOP1/CEN-2 provided no further information in search of a biomarker driven patient stratification. Other biomarkers to be paired with TOP1 CN are therefore highly warranted.
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Affiliation(s)
- Jesper Andreas Palshof
- Department of Oncology, Herlev Hospital, University of Copenhagen, Herlev Ringvej 75, DK-2730, Herlev, Denmark.
| | - Estrid Vilma Solyom Høgdall
- Department of Pathology, Herlev Hospital, University of Copenhagen, Herlev Ringvej 75, DK-2730, Herlev, Denmark
| | - Tim Svenstrup Poulsen
- Department of Pathology, Herlev Hospital, University of Copenhagen, Herlev Ringvej 75, DK-2730, Herlev, Denmark
| | - Dorte Linnemann
- Department of Pathology, Herlev Hospital, University of Copenhagen, Herlev Ringvej 75, DK-2730, Herlev, Denmark
| | - Benny Vittrup Jensen
- Department of Oncology, Herlev Hospital, University of Copenhagen, Herlev Ringvej 75, DK-2730, Herlev, Denmark
| | - Per Pfeiffer
- Department of Oncology, Odense University Hospital, Sdr. Boulevard 29, 5000, Odense C, Denmark
| | - Line Schmidt Tarpgaard
- Department of Oncology, Odense University Hospital, Sdr. Boulevard 29, 5000, Odense C, Denmark
| | - Nils Brünner
- Faculty of Health and Medical Sciences, Department of Veterinary Disease Biology, Section for Molecular Disease Biology and Sino-Danish Breast Cancer Research Centre, University of Copenhagen, Copenhagen, Denmark
| | - Jan Stenvang
- Faculty of Health and Medical Sciences, Department of Veterinary Disease Biology, Section for Molecular Disease Biology and Sino-Danish Breast Cancer Research Centre, University of Copenhagen, Copenhagen, Denmark
| | - Mette Yilmaz
- Department of Oncology, Aalborg University Hospital, Hobrovej 18-22, 9100, Aalborg, Denmark
| | - Dorte Lisbet Nielsen
- Department of Oncology, Herlev Hospital, University of Copenhagen, Herlev Ringvej 75, DK-2730, Herlev, Denmark
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Lee YC, Lee CH, Tsai HP, An HW, Lee CM, Wu JC, Chen CS, Huang SH, Hwang J, Cheng KT, Leiw PL, Chen CL, Lin CM. Targeting of Topoisomerase I for Prognoses and Therapeutics of Camptothecin-Resistant Ovarian Cancer. PLoS One 2015. [PMID: 26207989 PMCID: PMC4514822 DOI: 10.1371/journal.pone.0132579] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
DNA topoisomerase I (TOP1) levels of several human neoplasms are higher than those of normal tissues. TOP1 inhibitors are widely used in treating conventional therapy-resistant ovarian cancers. However, patients may develop resistance to TOP1 inhibitors, hampering chemotherapy success. In this study, we examined the mechanisms associated with the development of camptothecin (CPT) resistance in ovarian cancers and identified evodiamine (EVO), a natural product with TOP1 inhibiting activity that overcomes the resistance. The correlations among TOP1 levels, cancer staging, and overall survival (OS) were analyzed. The effect of EVO on CPT-resistant ovarian cancer was evaluated in vitro and in vivo. TOP1 was associated with poor prognosis in ovarian cancers (p = 0.024). EVO induced apoptosis that was detected using flow cytometry and terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) assay. The tumor size decreased significantly in the EVO treatment group compared with the control group (p < 0.01) in a xenograft mouse model. Effects of drugs targeting TOP1 for prognosis and therapy in CPT-resistant ovarian cancer are anticipated. EVO with TOP1 can be developed as an antiproliferative agent for overcoming CPT resistance in ovarian cancers.
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Affiliation(s)
- Yu-Chieh Lee
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Chii-Hong Lee
- Department of Pathology, Taipei Medical University-Shuang Ho Hospital, New Taipei City, Taiwan
| | - Hsiang-Ping Tsai
- Department of Biochemistry, School of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Herng-Wei An
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Chi-Ming Lee
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Jen-Chine Wu
- Center for Stem Cells and Translational Cancer Research, Chang Gung Memorial Hospital, Gueishan, Taoyuan County, Taiwan
| | - Chien-Shu Chen
- School of Pharmacy, China Medical University, Taichung, Taiwan
| | - Shih-Hao Huang
- Department of Food and Beverage Management, Taipei College of Maritime Technology, Taipei, Taiwan
| | - Jaulang Hwang
- Department of Biochemistry, School of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Kur-Ta Cheng
- Department of Biochemistry, School of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Phui-Ly Leiw
- Department of Pathology, Taipei Medical University-Shuang Ho Hospital, New Taipei City, Taiwan
| | - Chi-Long Chen
- Department of Pathology, College of Medicine, Taipei Medical University, Taipei, Taiwan; Department of Pathology, Taipei Medical University Hospital, Taipei, Taiwan
| | - Chun-Mao Lin
- Department of Biochemistry, School of Medicine, Taipei Medical University, Taipei, Taiwan
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11
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van den Hurk K, Balint B, Toomey S, O'Leary PC, Unwin L, Sheahan K, McDermott EW, Murphy I, van den Oord JJ, Rafferty M, FitzGerald DM, Moran J, Cummins R, MacEneaney O, Kay EW, O'Brien CP, Finn SP, Heffron CCBB, Murphy M, Yela R, Power DG, Regan PJ, McDermott CM, O'Keeffe A, Orosz Z, Donnellan PP, Crown JP, Hennessy BT, Gallagher WM. High-throughput oncogene mutation profiling shows demographic differences in BRAF mutation rates among melanoma patients. Melanoma Res 2015; 25:189-99. [PMID: 25746038 DOI: 10.1097/cmr.0000000000000149] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Because of advances in targeted therapies, the clinical evaluation of cutaneous melanoma is increasingly based on a combination of traditional histopathology and molecular pathology. Therefore, it is necessary to expand our knowledge of the molecular events that accompany the development and progression of melanoma to optimize clinical management. The central objective of this study was to increase our knowledge of the mutational events that complement melanoma progression. High-throughput genotyping was adapted to query 159 known single nucleotide mutations in 33 cancer-related genes across two melanoma cohorts from Ireland (n=94) and Belgium (n=60). Results were correlated with various clinicopathological characteristics. A total of 23 mutations in 12 genes were identified, that is--BRAF, NRAS, MET, PHLPP2, PIK3R1, IDH1, KIT, STK11, CTNNB1, JAK2, ALK, and GNAS. Unexpectedly, we discovered significant differences in BRAF, MET, and PIK3R1 mutations between the cohorts. That is, cases from Ireland showed significantly lower (P<0.001) BRAF(V600E) mutation rates (19%) compared with the mutation frequency observed in Belgian patients (43%). Moreover, MET mutations were detected in 12% of Irish cases, whereas none of the Belgian patients harbored these mutations, and Irish patients significantly more often (P=0.027) had PIK3R1-mutant (33%) melanoma versus 17% of Belgian cases. The low incidence of BRAF(V600E)(-) mutant melanoma among Irish patients was confirmed in five independent Irish cohorts, and in total, only 165 of 689 (24%) Irish cases carried mutant BRAF(V600E). Together, our data show that melanoma-driving mutations vary by demographic area, which has important implications for the clinical management of this disease.
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Affiliation(s)
- Karin van den Hurk
- aOncoMark Ltd, NovaUCD bDepartment of Medical Oncology, Royal College of Surgeons cUCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin Departments of dPathology eSurgery fMedical Oncology, St Vincent's University Hospital gDepartment of Histopathology, Royal College of Surgeons in Ireland Education and Research Centre, Beaumont Hospital hDepartment of Histopathology, St James's Hospital iDepartment of Histopathology, Trinity College, Dublin jDepartment of Pathology, Cork University Hospital, Cork Departments of kSurgery lMedical Oncology, University Hospital Galway mDepartment of Medicine, National University of Ireland Galway nDepartment of Histopathology, University Hospital Galway, Galway, Ireland oDepartment of Pathology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, Maastricht, The Netherlands pLaboratory of Morphology and Molecular Pathology, Katholieke Universiteit Leuven, Leuven, Belgium
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12
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Abstract
The majority of melanocytic neoplasms can be correctly diagnosed using routine histopathologic analysis. However, a significant minority of tumors have ambiguous histopathologic attributes that overlap between melanocytic nevi and melanoma. Ancillary tests that assist in distinguishing potentially lethal melanomas from benign melanocytic nevi with atypical histopathologic features are available, but still need refining.Most melanomas have chromosomal copy number aberrations, frequently involving multiple chromosomes. With rare exceptions, such anomalies are not found in melanocytic nevi. This difference formed the basis to develop assays that can help distinguish melanoma from nevi by fluorescence in situ hybridization (FISH) and comparative genomic hybridization (CGH). FISH can detect chromosomal copy number changes of a limited number of loci within individual cells. By contrast, CGH assesses copy number across the entire genome, but typically is performed on bulk cell populations so that copy number changes in individual cells or subpopulations of cells can go undetected. Both FISH and CGH have been used to provide genomic information in histopathologically ambiguous melanocytic tumors that can assist pathologists make correct diagnoses.
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Affiliation(s)
- Jeffrey P North
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
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13
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Stenvang J, Kümler I, Nygård SB, Smith DH, Nielsen D, Brünner N, Moreira JMA. Biomarker-guided repurposing of chemotherapeutic drugs for cancer therapy: a novel strategy in drug development. Front Oncol 2013; 3:313. [PMID: 24400218 PMCID: PMC3872326 DOI: 10.3389/fonc.2013.00313] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2013] [Accepted: 12/10/2013] [Indexed: 12/29/2022] Open
Abstract
Cancer is a leading cause of mortality worldwide and matters are only set to worsen as its incidence continues to rise. Traditional approaches to combat cancer include improved prevention, early diagnosis, optimized surgery, development of novel drugs, and honing regimens of existing anti-cancer drugs. Although discovery and development of novel and effective anti-cancer drugs is a major research area, it is well known that oncology drug development is a lengthy process, extremely costly and with high attrition rates. Furthermore, those drugs that do make it through the drug development mill are often quite expensive, laden with severe side-effects and unfortunately, to date, have only demonstrated minimal increases in overall survival. Therefore, a strong interest has emerged to identify approved non-cancer drugs that possess anti-cancer activity, thus shortcutting the development process. This research strategy is commonly known as drug repurposing or drug repositioning and provides a faster path to the clinics. We have developed and implemented a modification of the standard drug repurposing strategy that we review here; rather than investigating target-promiscuous non-cancer drugs for possible anti-cancer activity, we focus on the discovery of novel cancer indications for already approved chemotherapeutic anti-cancer drugs. Clinical implementation of this strategy is normally commenced at clinical phase II trials and includes pre-treated patients. As the response rates to any non-standard chemotherapeutic drug will be relatively low in such a patient cohort it is a pre-requisite that such testing is based on predictive biomarkers. This review describes our strategy of biomarker-guided repurposing of chemotherapeutic drugs for cancer therapy, taking the repurposing of topoisomerase I (Top1) inhibitors and Top1 as a potential predictive biomarker as case in point.
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Affiliation(s)
- Jan Stenvang
- Faculty of Health and Medical Sciences, Department of Veterinary Disease Biology, Section for Molecular Disease Biology and Sino-Danish Breast Cancer Research Centre, University of Copenhagen , Copenhagen , Denmark ; Danish Centre for Translational Breast Cancer Research , Copenhagen , Denmark
| | - Iben Kümler
- Department of Oncology, Center for Cancer Research, Herlev Hospital, University of Copenhagen , Copenhagen , Denmark
| | - Sune Boris Nygård
- Faculty of Health and Medical Sciences, Department of Veterinary Disease Biology, Section for Molecular Disease Biology and Sino-Danish Breast Cancer Research Centre, University of Copenhagen , Copenhagen , Denmark
| | - David Hersi Smith
- Faculty of Health and Medical Sciences, Department of Veterinary Disease Biology, Section for Molecular Disease Biology and Sino-Danish Breast Cancer Research Centre, University of Copenhagen , Copenhagen , Denmark ; DAKO A/S , Glostrup , Denmark
| | - Dorte Nielsen
- Department of Oncology, Center for Cancer Research, Herlev Hospital, University of Copenhagen , Copenhagen , Denmark
| | - Nils Brünner
- Faculty of Health and Medical Sciences, Department of Veterinary Disease Biology, Section for Molecular Disease Biology and Sino-Danish Breast Cancer Research Centre, University of Copenhagen , Copenhagen , Denmark ; Danish Centre for Translational Breast Cancer Research , Copenhagen , Denmark
| | - José M A Moreira
- Faculty of Health and Medical Sciences, Department of Veterinary Disease Biology, Section for Molecular Disease Biology and Sino-Danish Breast Cancer Research Centre, University of Copenhagen , Copenhagen , Denmark ; Danish Centre for Translational Breast Cancer Research , Copenhagen , Denmark
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14
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Smith DH, Christensen IJ, Jensen NF, Markussen B, Rømer MU, Nygård SB, Müller S, Nielsen HJ, Brünner N, Nielsen KV. Mechanisms of topoisomerase I (TOP1) gene copy number increase in a stage III colorectal cancer patient cohort. PLoS One 2013; 8:e60613. [PMID: 23577133 PMCID: PMC3618421 DOI: 10.1371/journal.pone.0060613] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 02/28/2013] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Topoisomerase I (Top1) is the target of Top1 inhibitor chemotherapy. The TOP1 gene, located at 20q12-q13.1, is frequently detected at elevated copy numbers in colorectal cancer (CRC). The present study explores the mechanism, frequency and prognostic impact of TOP1 gene aberrations in stage III CRC and how these can be detected by fluorescent in situ hybridization (FISH). METHODS Nine CRC cell line metaphase spreads were analyzed by FISH with a TOP1 probe in combination with a reference probe covering either the centromeric region of chromosome 20 (CEN-20) or chromosome 2 (CEN-2). Tissue sections from 154 chemonaive stage III CRC patients, previously studied with TOP1/CEN-20, were analyzed with TOP1/CEN-2. Relationships between biomarker status and overall survival (OS), time to recurrence (TTR) in CRC and time to local recurrence (LR; rectal cancer only) were determined. RESULTS TOP1 aberrations were observed in four cell line metaphases. In all cell lines CEN-2 was found to reflect chromosomal ploidy levels and therefore the TOP1/CEN-2 probe combination was selected to identify TOP1 gene gains (TOP1/CEN-2≥1.5). One hundred and three patients (68.2%) had TOP1 gain, of which 15 patients (14.6%) harbored an amplification (TOP1/CEN-20≥2.0). TOP1 gene gain did not have any association with clinical endpoints, whereas TOP1 amplification showed a non-significant trend towards longer TTR (multivariate HR: 0.50, p = 0.08). Once amplified cases were segregated from other cases of gene gain, non-amplified gene increases (TOP1/CEN-2≥1.5 and TOP1/CEN-20<2.0) showed a trend towards shorter TTR (univariate HR: 1.57, p = 0.07). CONCLUSIONS TOP1 gene copy number increase occurs frequently in stage III CRC in a mechanism that often includes CEN-20. Using CEN-2 as a measurement for tumor ploidy levels, we were able to discriminate between different mechanisms of gene gain, which appeared to differ in prognostic impact. TOP1 FISH guidelines have been updated.
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15
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Xiao D, Ohlendorf J, Chen Y, Taylor DD, Rai SN, Waigel S, Zacharias W, Hao H, McMasters KM. Identifying mRNA, microRNA and protein profiles of melanoma exosomes. PLoS One 2012; 7:e46874. [PMID: 23056502 PMCID: PMC3467276 DOI: 10.1371/journal.pone.0046874] [Citation(s) in RCA: 209] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Accepted: 09/10/2012] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Exosomes are small membranous vesicles secreted into body fluids by multiple cell types, including tumor cells, and in various disease conditions. Tumor exosomes contain intact and functional mRNAs, small RNAs (including miRNAs), and proteins that can alter the cellular environment to favor tumor growth. Molecular profiling may increase our understanding of the role of exosomes in melanoma progression and may lead to discovery of useful biomarkers. METHODOLOGY/PRINCIPAL FINDINGS In the present study, we used mRNA array profiling to identify thousands of exosomal mRNAs associated with melanoma progression and metastasis. Similarly, miRNA array profiling identified specific miRNAs, such as hsa-miR-31, -185, and -34b, involved in melanoma invasion. We also used proteomic analysis and discovered differentially expressed melanoma exosomal proteins, including HAPLN1, GRP78, syntenin-1, annexin A1, and annexin A2. Importantly, normal melanocytes acquired invasion ability through molecules transported in melanoma cell-derived exosomes. CONCLUSIONS/SIGNIFICANCE Our results indicate that melanoma-derived exosomes have unique gene expression signatures, miRNA and proteomics profiles compared to exosomes from normal melanocytes. To the best of our knowledge, this is the first in-depth screening of the whole transcriptome/miRNome/proteome expression in melanoma exosomes. These results provide a starting point for future more in-depth studies of tumor-derived melanoma exosomes, which will aid our understanding of melanoma biogenesis and new drug-targets that may be translated into clinical applications, or as non-invasive biomarkers for melanoma.
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Affiliation(s)
- Deyi Xiao
- Department of Surgery, University of Louisville School of Medicine, Louisville, Kentucky, United States of America
| | - Joanna Ohlendorf
- Department of Surgery, University of Louisville School of Medicine, Louisville, Kentucky, United States of America
| | - Yinlu Chen
- Microarray facility, University of Louisville School of Medicine, Louisville, Kentucky, United States of America
| | - Douglas D. Taylor
- Department of Obstetrics, Gynecology, and Women’s Health, University of Louisville School of Medicine, Louisville, Kentucky, United States of America
| | - Shesh N. Rai
- Department of Bioinformatics and Biostatistics, University of Louisville School of Medicine, Louisville, Kentucky, United States of America
| | - Sabine Waigel
- Microarray facility, University of Louisville School of Medicine, Louisville, Kentucky, United States of America
| | - Wolfgang Zacharias
- Microarray facility, University of Louisville School of Medicine, Louisville, Kentucky, United States of America
- Department of Medicine and Department of Pharmacology and Toxicology, James Graham Brown Cancer Center, University of Louisville School of Medicine, Louisville, Kentucky, United States of America
| | - Hongying Hao
- Department of Surgery, University of Louisville School of Medicine, Louisville, Kentucky, United States of America
- * E-mail: (HH); (KMM)
| | - Kelly M. McMasters
- Department of Surgery, University of Louisville School of Medicine, Louisville, Kentucky, United States of America
- * E-mail: (HH); (KMM)
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16
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Prassas I, Chrystoja CC, Makawita S, Diamandis EP. Bioinformatic identification of proteins with tissue-specific expression for biomarker discovery. BMC Med 2012; 10:39. [PMID: 22515324 PMCID: PMC3378448 DOI: 10.1186/1741-7015-10-39] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Accepted: 04/19/2012] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND There is an important need for the identification of novel serological biomarkers for the early detection of cancer. Current biomarkers suffer from a lack of tissue specificity, rendering them vulnerable to non-disease-specific increases. The present study details a strategy to rapidly identify tissue-specific proteins using bioinformatics. METHODS Previous studies have focused on either gene or protein expression databases for the identification of candidates. We developed a strategy that mines six publicly available gene and protein databases for tissue-specific proteins, selects proteins likely to enter the circulation, and integrates proteomic datasets enriched for the cancer secretome to prioritize candidates for further verification and validation studies. RESULTS Using colon, lung, pancreatic and prostate cancer as case examples, we identified 48 candidate tissue-specific biomarkers, of which 14 have been previously studied as biomarkers of cancer or benign disease. Twenty-six candidate biomarkers for these four cancer types are proposed. CONCLUSIONS We present a novel strategy using bioinformatics to identify tissue-specific proteins that are potential cancer serum biomarkers. Investigation of the 26 candidates in disease states of the organs is warranted.
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Affiliation(s)
- Ioannis Prassas
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
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17
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Pontén F, Schwenk JM, Asplund A, Edqvist PHD. The Human Protein Atlas as a proteomic resource for biomarker discovery. J Intern Med 2011; 270:428-46. [PMID: 21752111 DOI: 10.1111/j.1365-2796.2011.02427.x] [Citation(s) in RCA: 191] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The analysis of tissue-specific expression at both the gene and protein levels is vital for understanding human biology and disease. Antibody-based proteomics provides a strategy for the systematic generation of antibodies against all human proteins to combine with protein profiling in tissues and cells using tissue microarrays, immunohistochemistry and immunofluorescence. The Human Protein Atlas project was launched in 2003 with the aim of creating a map of protein expression patterns in normal cells, tissues and cancer. At present, 11,200 unique proteins corresponding to over 50% of all human protein-encoding genes have been analysed. All protein expression data, including underlying high-resolution images, are published on the free and publically available Human Protein Atlas portal (http://www.proteinatlas.org). This database provides an important source of information for numerous biomedical research projects, including biomarker discovery efforts. Moreover, the global analysis of how our genome is expressed at the protein level has provided basic knowledge on the ubiquitous expression of a large proportion of our proteins and revealed the paucity of cell- and tissue-type-specific proteins.
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Affiliation(s)
- F Pontén
- Department of Genetics and Pathology, Uppsala University, Uppsala, Sweden.
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