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Navrazhina K, Garcet S, Williams SC, Gulati N, Kiecker F, Frew JW, Mitsui H, Krueger JG. Laser capture microdissection provides a novel molecular profile of human primary cutaneous melanoma. Pigment Cell Melanoma Res 2024; 37:81-89. [PMID: 37776566 PMCID: PMC10841058 DOI: 10.1111/pcmr.13121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 08/08/2023] [Accepted: 08/16/2023] [Indexed: 10/02/2023]
Abstract
Melanoma accounts for the majority of skin cancer-related mortality, highlighting the need to better understand melanoma initiation and progression. In-depth molecular analysis of neoplastic melanocytes in whole tissue biopsies may be diluted by inflammatory infiltration, which may obscure gene signatures specific to neoplastic cells. Thus, a method is needed to precisely uncover molecular changes specific to tumor cells from a limited sample of primary melanomas. Here, we performed laser capture microdissection (LCM) and gene expression profiling of patient-derived frozen sections of pigmented lesions and primary cutaneous melanoma. Compared to bulk tissue analysis, analysis of LCM-derived samples identified 9528 additional differentially expressed genes (DEGs) including melanocyte-specific genes like PMEL and TYR, with enriched of pathways related to cell proliferation. LCM methodology also identified potentially targetable kinases specific to melanoma cells that were not detected by bulk tissue analysis. Taken together, our data demonstrate that there are marked differences in gene expression profiles depending on the method of sample isolation. We found that LCM captured higher expression of melanoma-related genes while whole tissue biopsy identified a wider range of inflammatory markers. Taken together, our data demonstrate that LCM is a valid approach to identify melanoma-specific changes using a relatively small amount of primary patient-derived melanoma sample.
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Affiliation(s)
- Kristina Navrazhina
- Laboratory of Investigative Dermatology, The Rockefeller University, New York, NY, USA
- Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD program, New York, NY
| | - Sandra Garcet
- Laboratory of Investigative Dermatology, The Rockefeller University, New York, NY, USA
| | - Samuel C. Williams
- Laboratory of Investigative Dermatology, The Rockefeller University, New York, NY, USA
- Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD program, New York, NY
| | - Nicholas Gulati
- Laboratory of Investigative Dermatology, The Rockefeller University, New York, NY, USA
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Felix Kiecker
- Department of Dermatology and Allergy, Skin Cancer Center, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - John W. Frew
- Laboratory of Investigative Dermatology, The Rockefeller University, New York, NY, USA
| | - Hiroshi Mitsui
- Laboratory of Investigative Dermatology, The Rockefeller University, New York, NY, USA
- Department of Dermatology, Faculty of Medicine, University of Yamanashi, Yamanashi, Japan
| | - James G. Krueger
- Laboratory of Investigative Dermatology, The Rockefeller University, New York, NY, USA
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2
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Lapcik P, Sulc P, Janacova L, Jilkova K, Potesil D, Bouchalova P, Müller P, Bouchal P. Desmocollin-1 is associated with pro-metastatic phenotype of luminal A breast cancer cells and is modulated by parthenolide. Cell Mol Biol Lett 2023; 28:68. [PMID: 37620794 PMCID: PMC10464112 DOI: 10.1186/s11658-023-00481-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 07/27/2023] [Indexed: 08/26/2023] Open
Abstract
BACKGROUND Desmocollin-1 (DSC1) is a desmosomal transmembrane glycoprotein that maintains cell-to-cell adhesion. DSC1 was previously associated with lymph node metastasis of luminal A breast tumors and was found to increase migration and invasion of MCF7 cells in vitro. Therefore, we focused on DSC1 role in cellular and molecular mechanisms in luminal A breast cancer and its possible therapeutic modulation. METHODS Western blotting was used to select potential inhibitor decreasing DSC1 protein level in MCF7 cell line. Using atomic force microscopy we evaluated effect of DSC1 overexpression and modulation on cell morphology. The LC-MS/MS analysis of total proteome on Orbitrap Lumos and RNA-Seq analysis of total transcriptome on Illumina NextSeq 500 were performed to study the molecular mechanisms associated with DSC1. Pull-down analysis with LC-MS/MS detection was carried out to uncover DSC1 protein interactome in MCF7 cells. RESULTS Analysis of DSC1 protein levels in response to selected inhibitors displays significant DSC1 downregulation (p-value ≤ 0.01) in MCF7 cells treated with NF-κB inhibitor parthenolide. Analysis of mechanic cell properties in response to DSC1 overexpression and parthenolide treatment using atomic force microscopy reveals that DSC1 overexpression reduces height of MCF7 cells and conversely, parthenolide decreases cell stiffness of MCF7 cells overexpressing DSC1. The LC-MS/MS total proteome analysis in data-independent acquisition mode shows a strong connection between DSC1 overexpression and increased levels of proteins LACRT and IGFBP5, increased expression of IGFBP5 is confirmed by RNA-Seq. Pathway analysis of proteomics data uncovers enrichment of proliferative MCM_BIOCARTA pathway including CDK2 and MCM2-7 after DSC1 overexpression. Parthenolide decreases expression of LACRT, IGFBP5 and MCM_BIOCARTA pathway specifically in DSC1 overexpressing cells. Pull-down assay identifies DSC1 interactions with cadherin family proteins including DSG2, CDH1, CDH3 and tyrosine kinase receptors HER2 and HER3; parthenolide modulates DSC1-HER3 interaction. CONCLUSIONS Our systems biology data indicate that DSC1 is connected to mechanisms of cell cycle regulation in luminal A breast cancer cells, and can be effectively modulated by parthenolide.
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Affiliation(s)
- Petr Lapcik
- Department of Biochemistry, Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - Petr Sulc
- Department of Biochemistry, Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - Lucia Janacova
- Department of Biochemistry, Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - Katerina Jilkova
- Department of Biochemistry, Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - David Potesil
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Pavla Bouchalova
- Department of Biochemistry, Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - Petr Müller
- Masaryk Memorial Cancer Institute, RECAMO, Brno, Czech Republic
| | - Pavel Bouchal
- Department of Biochemistry, Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic.
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Azimi A, Patrick E, Teh R, Kim J, Fernandez-Penas P. Proteomic profiling of cutaneous melanoma explains the aggressiveness of distant organ metastasis. Exp Dermatol 2023. [PMID: 37082900 DOI: 10.1111/exd.14814] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 04/05/2023] [Accepted: 04/07/2023] [Indexed: 04/22/2023]
Abstract
Despite recent developments in managing metastatic melanomas, patients' overall survival remains low. Therefore, the current study aims to understand better the proteome-wide changes associated with melanoma metastasis that will assist with identifying targeted therapies. The latest development in mass spectrometry-based proteomics, together with extensive bioinformatics analysis, was used to investigate the molecular changes in 60 formalin-fixed and paraffin-embedded samples of primary and lymph nodes (LN) and distant organ metastatic melanomas. A total of 4631 proteins were identified, of which 72 and 453 were significantly changed between the LN and distant organ metastatic melanomas compared to the primary lesions (adj. p-value <0.05). An increase in proteins such as SLC9A3R1, CD20 and GRB2 and a decrease in CST6, SERPINB5 and ARG1 were associated with regional LN metastasis. By contrast, increased metastatic activities in distant organ metastatic melanomas were related to higher levels of CEACAM1, MC1R, AKT1 and MMP3-9 and decreased levels of CDKN2A, SDC1 and SDC4 proteins. Furthermore, machine learning analysis classified the lesions with up to 92% accuracy based on their metastatic status. The findings from this study provide up to date proteome-level information about the progression of melanomas to regional LN and distant organs, leading to the identification of protein signatures with potential for clinical translation.
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Affiliation(s)
- Ali Azimi
- Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
- Department of Dermatology, Westmead Hospital, Westmead, New South Wales, Australia
- Centre for Cancer Research, The Westmead Institute for Medical Research, The University of Sydney, Westmead, New South Wales, Australia
| | - Ellis Patrick
- Centre for Cancer Research, The Westmead Institute for Medical Research, The University of Sydney, Westmead, New South Wales, Australia
- School of Mathematics and Statistics, Faculty of Science, The University of Sydney, Camperdown, New South Wales, Australia
- Sydney Precision Data Science Centre, The University of Sydney, Camperdown, New South Wales, Australia
| | - Rachel Teh
- Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
- Department of Dermatology, Westmead Hospital, Westmead, New South Wales, Australia
- Centre for Cancer Research, The Westmead Institute for Medical Research, The University of Sydney, Westmead, New South Wales, Australia
| | - Jennifer Kim
- Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
- Centre for Cancer Research, The Westmead Institute for Medical Research, The University of Sydney, Westmead, New South Wales, Australia
- Department of Tissue Pathology and Diagnostic Oncology, Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, New South Wales, Australia
| | - Pablo Fernandez-Penas
- Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
- Department of Dermatology, Westmead Hospital, Westmead, New South Wales, Australia
- Centre for Cancer Research, The Westmead Institute for Medical Research, The University of Sydney, Westmead, New South Wales, Australia
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4
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Kitrell BM, Blue ED, Siller A, Lobl MB, Evans TD, Whitley MJ, Wysong A. Gene Expression Profiles in Cutaneous Oncology. Dermatol Clin 2022; 41:89-99. [DOI: 10.1016/j.det.2022.07.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Mutu DE, Avino A, Balcangiu‑Stroescu AE, Mehedințu M, Bălan D, Brîndușe L, Popescu AM, Ionescu D, Cristea BM, Tomescu L, Jecan CR, Răducu L. Histopathological evaluation of cutaneous malignant melanoma: A retrospective study. Exp Ther Med 2022; 23:402. [PMID: 35601077 PMCID: PMC9115627 DOI: 10.3892/etm.2022.11329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 11/05/2022] [Indexed: 11/11/2022] Open
Abstract
Malignant melanoma is a melanocytic neoplasm with a steadily increasing incidence worldwide. In order to define a proper diagnostic protocol and to establish an accurate prognostic method for the disease, specific biomarkers are of notable importance. Their contribution is also significant in the treatment of melanoma for the improvement of newer and more targeted therapeutic approaches. To emphasize the importance of specific immune markers in the diagnosis of melanoma, immunohistochemical analysis was performed on 56 formalin-fixed paraffin-embedded cutaneous melanomas. Besides the traditional prognostic factors, depth of invasion and mitotic rate, the markers tested in the present study were S100 protein family, Melan A, Ki67 and HMB-45. The present results indicated that immunocytochemistry represents a valuable test in the diagnosis and treatment of malignant melanoma and each biomarker had different associations with the progression and prognosis of the disease. Patients with S100 expression were 4.83 times (95% CI=1.2-20.8) more likely to suffer a relapse, whereas patients with a Ki67 expression of >30% had a 5.41-fold higher risk (95% CI=1.3-22.0). The correlation between S100 and the Breslow depth was statistically significant (r-value: 0.43; P=0.027). In addition, the importance of a multidisciplinary team including a plastic surgeon, anatomopathologist and oncologist was highlighted.
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Affiliation(s)
- Daniela-Elena Mutu
- Discipline of Anatomy, Faculty of Medicine, ‘Carol Davila’ University of Medicine and Pharmacy, Bucharest 020021, Romani
| | - Adelaida Avino
- Department of Plastic and Reconstructive Surgery, ‘Professor Dr Agrippa Ionescu’ Clinical Emergency Hospital, Bucharest 011356, Romania
| | - Andra-Elena Balcangiu‑Stroescu
- Discipline of Physiology, Faculty of Dental Medicine, ‘Carol Davila’ University of Medicine and Pharmacy, Bucharest 020021, Romania
| | - Mihai Mehedințu
- Department of Plastic and Reconstructive Surgery, ‘Professor Dr Agrippa Ionescu’ Clinical Emergency Hospital, Bucharest 011356, Romania
| | - Daniela Bălan
- Discipline of Physiology, Faculty of Dental Medicine, ‘Carol Davila’ University of Medicine and Pharmacy, Bucharest 020021, Romania
| | - Lăcrămioara Brîndușe
- Discipline of Public Health and Management, ‘Carol Davila’ University of Medicine and Pharmacy, Bucharest 020021, Romania
| | - Ana-Maria Popescu
- Department of Financial and Economic Analysis and Valuation, Faculty of Accounting and Management Information Systems, Bucharest University of Economic Studies, Bucharest 010731, Romania
| | - Dorin Ionescu
- Department of Medical Semiology, Discipline of Internal Medicine I and Nephrology, Faculty of Medicine, ‘Carol Davila’ University of Medicine and Pharmacy, Bucharest 020021, Romania
| | - Bogdan-Mihai Cristea
- Discipline of Anatomy, Faculty of Medicine, ‘Carol Davila’ University of Medicine and Pharmacy, Bucharest 020021, Romania
| | - Luminiţa Tomescu
- Department of Interventional Radiology, ‘Professor Dr Agrippa Ionescu’ Clinical Emergency Hospital, Bucharest 011356, Romania
| | - Cristian-Radu Jecan
- Department of Plastic and Reconstructive Surgery, ‘Professor Dr Agrippa Ionescu’ Clinical Emergency Hospital, Bucharest 011356, Romania
| | - Laura Răducu
- Department of Plastic and Reconstructive Surgery, ‘Professor Dr Agrippa Ionescu’ Clinical Emergency Hospital, Bucharest 011356, Romania
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Yoo S, Sinha A, Yang D, Altorki NK, Tandon R, Wang W, Chavez D, Lee E, Patel AS, Sato T, Kong R, Ding B, Schadt EE, Watanabe H, Massion PP, Borczuk AC, Zhu J, Powell CA. Integrative network analysis of early-stage lung adenocarcinoma identifies aurora kinase inhibition as interceptor of invasion and progression. Nat Commun 2022; 13:1592. [PMID: 35332150 PMCID: PMC8948234 DOI: 10.1038/s41467-022-29230-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 03/01/2022] [Indexed: 12/15/2022] Open
Abstract
Here we focus on the molecular characterization of clinically significant histological subtypes of early-stage lung adenocarcinoma (esLUAD), which is the most common histological subtype of lung cancer. Within lung adenocarcinoma, histology is heterogeneous and associated with tumor invasion and diverse clinical outcomes. We present a gene signature distinguishing invasive and non-invasive tumors among esLUAD. Using the gene signatures, we estimate an Invasiveness Score that is strongly associated with survival of esLUAD patients in multiple independent cohorts and with the invasiveness phenotype in lung cancer cell lines. Regulatory network analysis identifies aurora kinase as one of master regulators of the gene signature and the perturbation of aurora kinases in vitro and in a murine model of invasive lung adenocarcinoma reduces tumor invasion. Our study reveals aurora kinases as a therapeutic target for treatment of early-stage invasive lung adenocarcinoma.
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Affiliation(s)
- Seungyeul Yoo
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, New York, NY, USA
- Sema4, Stamford, CT, USA
| | - Abhilasha Sinha
- Division of Pulmonary, Critical Care and Sleep Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dawei Yang
- Division of Pulmonary, Critical Care and Sleep Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Nasser K Altorki
- Department of Cardiothoracic Surgery, Weill Cornell Medicine-New York Presbyterian Hospital, New York, NY, USA
| | - Radhika Tandon
- School of Medicine, St. George's University, West Indies, Grenada
| | - Wenhui Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, New York, NY, USA
| | - Deebly Chavez
- Division of Pulmonary, Critical Care and Sleep Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eunjee Lee
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, New York, NY, USA
- Sema4, Stamford, CT, USA
| | - Ayushi S Patel
- Division of Pulmonary, Critical Care and Sleep Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Vileck Institute of Graduate Biomedical Sciences, New York University School of Medicine, New York, NY, USA
| | - Takashi Sato
- Division of Pulmonary, Critical Care and Sleep Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
- Department of Respiratory Medicine, Kitasato University School of Medicine, Sagamihara, Japan
| | - Ranran Kong
- Division of Pulmonary, Critical Care and Sleep Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Thoracic Surgery, The Second Affiliated Hospital of Medical School, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Bisen Ding
- Division of Pulmonary, Critical Care and Sleep Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Key Laboratory of Birth Defects and Related Diseases of Women And Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, New York, NY, USA
- Sema4, Stamford, CT, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hideo Watanabe
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, New York, NY, USA
- Division of Pulmonary, Critical Care and Sleep Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Pierre P Massion
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Alain C Borczuk
- Department of Pathology, Weill Cornell Medicine, New York, NY, USA
| | - Jun Zhu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Icahn Institute for Data Science and Genomic Technology, New York, NY, USA.
- Sema4, Stamford, CT, USA.
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Charles A Powell
- Division of Pulmonary, Critical Care and Sleep Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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7
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Zhang W, Yang S, Chen D, Yuwen D, Zhang J, Wei X, Han X, Guan X. SOX2-OT induced by PAI-1 promotes triple-negative breast cancer cells metastasis by sponging miR-942-5p and activating PI3K/Akt signaling. Cell Mol Life Sci 2022; 79:59. [PMID: 34997317 PMCID: PMC11072091 DOI: 10.1007/s00018-021-04120-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 12/22/2021] [Accepted: 12/27/2021] [Indexed: 12/14/2022]
Abstract
Triple-negative breast cancer (TNBC) has an aggressive biological behavior and poor outcome. Our published study showed that PAI-1 could induce the migration and metastasis of TNBC cells. However, the underlying mechanism by which PAI-1 regulates TNBC metastasis has not been addressed. Here, we demonstrated that PAI-1 is high expressed in TNBC and promotes TNBC cells tumorigenesis. Using microarray analysis of lncRNA expression profiles, we identified a lncRNA SOX2-OT, which is induced by PAI-1 and could function as an oncogenic lncRNA in TNBC. Mechanistic analysis demonstrated that SOX2-OT acts as a molecular sponge for miR-942-5p to regulate the expression of PIK3CA, ultimately leading to activating PI3K/Akt signaling pathway and promoting TNBC metastasis. Taken together, our findings suggest that SOX2-OT regulates PAI-1-induced TNBC cell metastasis through miR-942-5p/PIK3CA signaling and illustrate the great potential of developing new SOX2-OT-targeting therapy for TNBC patients.
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Affiliation(s)
- Wenwen Zhang
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, 68 Changle Road, Nanjing, 210006, China.
| | - Shuofei Yang
- Department of Vascular Surgery, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Datian Chen
- Department of Oncology, Haimen People's Hospital, Nantong University, Nantong, China
| | - Daolu Yuwen
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, 68 Changle Road, Nanjing, 210006, China
| | - Juan Zhang
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, 68 Changle Road, Nanjing, 210006, China
| | - Xiaowei Wei
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, 68 Changle Road, Nanjing, 210006, China
| | - Xin Han
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China.
| | - Xiaoxiang Guan
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China.
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, Nanjing, China.
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8
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Clinical Study on the Increased Incidence of Nodular Melanoma Cases Compared to Superficial Melanoma. CURRENT HEALTH SCIENCES JOURNAL 2021; 47:298-305. [PMID: 34765252 PMCID: PMC8551895 DOI: 10.12865/chsj.47.02.22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 06/18/2021] [Indexed: 11/18/2022]
Abstract
Our study group was comprised of 67 patients with melanoma, admitted and operated in our clinic between 2010-2018. Only the patients with melanoma localized on the head, torso and upper limb were selected for our study. We attempted to establish a link between the clinical appearance, presence or absence of ulceration, presence or absence of regional lymphadenopathy or distant metastases, surgical technique, histopathological type, Clark level and Breslow depth, disease stage (TNM), adjuvant therapies and survival rates at 1, 3, 5 and 10 years.
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9
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Zhang M, Zhao Z, Pritykin Y, Hannum M, Scott AC, Kuo F, Sanghvi V, Chan TA, Seshan V, Wendel HG, Schietinger A, Sadelain M, Huse M. Ectopic activation of the miR-200c-EpCAM axis enhances antitumor T cell responses in models of adoptive cell therapy. Sci Transl Med 2021; 13:eabg4328. [PMID: 34524864 PMCID: PMC9374309 DOI: 10.1126/scitranslmed.abg4328] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Adoptive T cell therapy (ACT) is a promising strategy for treating cancer, but it often fails because of cell intrinsic regulatory programs that limit the degree or duration of T cell function. In this study, we found that ectopic expression of microRNA-200c (miR-200c) markedly enhanced the antitumor activity of CD8+ cytotoxic T lymphocytes (CTLs) during ACT in multiple mouse models. CTLs transduced with miR-200c exhibited reduced apoptosis during engraftment and enhanced in vivo persistence, accompanied by up-regulation of the transcriptional regulator T cell factor 1 (TCF1) and the inflammatory cytokine tumor necrosis factor (TNF). miR-200c elicited these changes by suppressing the transcription factor Zeb1 and thereby inducing genes characteristic of epithelial cells. Overexpression of one of these genes, Epcam, was sufficient to augment therapeutic T cell responses against both solid and liquid tumors. These results identify the miR-200c–EpCAM axis as an avenue for improving ACT and demonstrate that select genetic perturbations can produce phenotypically distinct T cells with advantageous therapeutic properties.
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Affiliation(s)
- Minggang Zhang
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Zeguo Zhao
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Yuri Pritykin
- Lewis-Sigler Institute for Integrative Genomics and Computer Science Department, Princeton University, Princeton, NJ 08540, USA
| | - Margaret Hannum
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Andrew C Scott
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Fengshen Kuo
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Viraj Sanghvi
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Timothy A Chan
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Venkatraman Seshan
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Hans-Guido Wendel
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Andrea Schietinger
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Michel Sadelain
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Morgan Huse
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
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10
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Bongiovanni L, Andriessen A, Silvestri S, Porcellato I, Brachelente C, de Bruin A. H2AFZ: A Novel Prognostic Marker in Canine Melanoma and a Predictive Marker for Resistance to CDK4/6 Inhibitor Treatment. Front Vet Sci 2021; 8:705359. [PMID: 34485433 PMCID: PMC8415453 DOI: 10.3389/fvets.2021.705359] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 07/19/2021] [Indexed: 11/13/2022] Open
Abstract
Uncontrolled proliferation is a key feature of tumor progression and malignancy. This suggests that cell-cycle related factors could be exploited as cancer biomarkers and that pathways specifically involved in the cell cycle, such as the Rb-E2F pathway, could be targeted as an effective anti-tumor therapy. We investigated 34 formalin-fixed paraffin-embedded (FFPE) tissue samples of canine cutaneous melanocytoma, cutaneous melanoma, and oral melanoma. Corresponding clinical follow-up data were used to determine the prognostic value of the mRNA expression levels of several cell cycle regulated E2F target genes (E2F1, DHFR, CDC6, ATAD2, MCM2, H2AFZ, GINS2, and survivin/BIRC5). Moreover, using four canine melanoma cell lines, we explored the possibility of blocking the Rb-E2F pathway by using a CDK4/6 inhibitor (Palbociclib) as a potential anti-cancer therapy. We investigated the expression levels of the same E2F target gene transcripts before and after treatment to determine the potential utility of these molecules as predictive markers. The E2F target gene H2AFZ was expressed in 91.43% of the primary tumors and H2AFZ expression was significantly higher in cases with unfavorable clinical outcome. Among the other tested genes, survivin/BIRC5 showed as well-promising results as a prognostic marker in canine melanoma. Three of the four tested melanoma cell lines were sensitive to the CDK4/6 inhibitor. The resistant cell line displayed higher expression levels of H2AFZ before treatment compared to the CDK4/6 inhibitor-sensitive cell lines. The present results suggest that CDK4/6 inhibitors could potentially be used as a new anti-cancer treatment for canine melanoma and that H2AFZ could serve as a prognostic and predictive marker for patient selection.
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Affiliation(s)
- Laura Bongiovanni
- Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Anneloes Andriessen
- Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | | | - Ilaria Porcellato
- Department of Veterinary Medicine, University of Perugia, Perugia, Italy
| | - Chiara Brachelente
- Department of Veterinary Medicine, University of Perugia, Perugia, Italy
| | - Alain de Bruin
- Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands.,Department of Pediatrics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
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11
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Vandyck HHLD, Hillen LM, Bosisio FM, van den Oord J, zur Hausen A, Winnepenninckx V. Rethinking the biology of metastatic melanoma: a holistic approach. Cancer Metastasis Rev 2021; 40:603-624. [PMID: 33870460 PMCID: PMC8213587 DOI: 10.1007/s10555-021-09960-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 03/29/2021] [Indexed: 02/06/2023]
Abstract
Over the past decades, melanoma-related mortality has remained nearly stable. The main reason is treatment failure of metastatic disease and the inherently linked knowledge gap regarding metastasis formation. In order to elicit invasion, melanoma cells manipulate the tumor microenvironment, gain motility, and adhere to the extracellular matrix and cancer-associated fibroblasts. Melanoma cells thereby express different cell adhesion molecules like laminins, integrins, N-cadherin, and others. Epithelial-mesenchymal transition (EMT) is physiological during embryologic development, but reactivated during malignancy. Despite not being truly epithelial, neural crest-derived malignancies like melanoma share similar biological programs that enable tumorigenesis, invasion, and metastasis. This complex phenomenon is termed phenotype switching and is intertwined with oncometabolism as well as dormancy escape. Additionally, it has been shown that primary melanoma shed exosomes that create a favorable premetastatic niche in the microenvironment of secondary organs and lymph nodes. Although the growing body of literature describes the aforementioned concepts separately, an integrative holistic approach is missing. Using melanoma as a tumor model, this review will shed light on these complex biological principles in an attempt to clarify the mechanistic metastatic pathways that dictate tumor and patient fate.
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Affiliation(s)
- Hendrik HLD Vandyck
- Department of Pathology, GROW-School for Oncology & Developmental Biology, Maastricht University Medical Center, MUMC+, PO Box 5800, 6202 AZ Maastricht, The Netherlands
| | - Lisa M Hillen
- Department of Pathology, GROW-School for Oncology & Developmental Biology, Maastricht University Medical Center, MUMC+, PO Box 5800, 6202 AZ Maastricht, The Netherlands
| | - Francesca M Bosisio
- Laboratory of Translational Cell and Tissue Research (TCTR), Department of Pathology, KU Leuven and UZ Leuven, Leuven, Belgium
| | - Joost van den Oord
- Laboratory of Translational Cell and Tissue Research (TCTR), Department of Pathology, KU Leuven and UZ Leuven, Leuven, Belgium
| | - Axel zur Hausen
- Department of Pathology, GROW-School for Oncology & Developmental Biology, Maastricht University Medical Center, MUMC+, PO Box 5800, 6202 AZ Maastricht, The Netherlands
| | - Véronique Winnepenninckx
- Department of Pathology, GROW-School for Oncology & Developmental Biology, Maastricht University Medical Center, MUMC+, PO Box 5800, 6202 AZ Maastricht, The Netherlands
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12
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Zhou JG, Liang B, Liu JG, Jin SH, He SS, Frey B, Gu N, Fietkau R, Hecht M, Ma H, Gaipl US. Identification of 15 lncRNAs Signature for Predicting Survival Benefit of Advanced Melanoma Patients Treated with Anti-PD-1 Monotherapy. Cells 2021; 10:cells10050977. [PMID: 33922038 PMCID: PMC8143567 DOI: 10.3390/cells10050977] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/14/2021] [Accepted: 04/17/2021] [Indexed: 02/07/2023] Open
Abstract
The blockade of programmed cell death protein 1 (PD-1) as monotherapy has been widely used in melanoma, but to identify melanoma patients with survival benefit from anti-PD-1 monotherapy is still a big challenge. There is an urgent need for prognostic signatures improving the prediction of immunotherapy responses of these patients. We analyzed transcriptomic data of pre-treatment tumor biopsies and clinical profiles in advanced melanoma patients receiving only anti-PD-1 monotherapy (nivolumab or pembrolizumab) from the PRJNA356761 and PRJEB23709 data sets as the training and validation cohort, respectively. Weighted gene co-expression network analysis was used to identify the key module, then least absolute shrinkage and selection operator was conducted to determine prognostic-related long noncoding RNAs (lncRNAs). Subsequently, the differentially expressed genes between different clusters were identified, and their function and pathway annotation were performed. In this investigation, 92 melanoma patients with complete survival information (51 from training cohort and 41 from validation cohort) were included in our analyses. We initiallyidentified the key module (skyblue) by weighted gene co-expression network analysis, and then identified a 15 predictive lncRNAs (AC010904.2, LINC01126, AC012360.1, AC024933.1, AL442128.2, AC022211.4, AC022211.2, AC127496.5, NARF-AS1, AP000919.3, AP005329.2, AC023983.1, AC023983.2, AC139100.1, and AC012615.4) signature in melanoma patients treated with anti-PD-1 monotherapy by least absolute shrinkage and selection operator in the training cohort. These results were then validated in the validation cohort. Finally, enrichment analysis showed that the functions of differentially expressed genes between two consensus clusters were mainly related to the immune process and treatment. In summary, the 15 lncRNAs signature is a novel effective predictor for prognosis in advanced melanoma patients treated with anti-PD-1 monotherapy.
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Affiliation(s)
- Jian-Guo Zhou
- Department of Oncology, The Second Affiliated Hospital of Zunyi Medical University, Zunyi 563000, China; (J.-G.Z.); (S.-S.H.)
- Department of Radiation Oncology, Universitätsklinikum Erlangen, 91054 Erlangen, Germany; (B.F.); (R.F.); (M.H.)
- Comprehensive Cancer Center Erlangen-EMN, 91054 Erlangen, Germany
| | - Bo Liang
- Nanjing University of Chinese Medicine, Nanjing 210029, China;
| | - Jian-Guo Liu
- Special Key Laboratory of Oral Diseases Research, Stomatological Hospital Affiliated to Zunyi Medical University, Zunyi 563000, China; (J.-G.L.); (S.-H.J.)
| | - Su-Han Jin
- Special Key Laboratory of Oral Diseases Research, Stomatological Hospital Affiliated to Zunyi Medical University, Zunyi 563000, China; (J.-G.L.); (S.-H.J.)
| | - Si-Si He
- Department of Oncology, The Second Affiliated Hospital of Zunyi Medical University, Zunyi 563000, China; (J.-G.Z.); (S.-S.H.)
| | - Benjamin Frey
- Department of Radiation Oncology, Universitätsklinikum Erlangen, 91054 Erlangen, Germany; (B.F.); (R.F.); (M.H.)
- Comprehensive Cancer Center Erlangen-EMN, 91054 Erlangen, Germany
| | - Ning Gu
- Nanjing Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese Medicine, Nanjing 210029, China;
| | - Rainer Fietkau
- Department of Radiation Oncology, Universitätsklinikum Erlangen, 91054 Erlangen, Germany; (B.F.); (R.F.); (M.H.)
- Comprehensive Cancer Center Erlangen-EMN, 91054 Erlangen, Germany
| | - Markus Hecht
- Department of Radiation Oncology, Universitätsklinikum Erlangen, 91054 Erlangen, Germany; (B.F.); (R.F.); (M.H.)
- Comprehensive Cancer Center Erlangen-EMN, 91054 Erlangen, Germany
| | - Hu Ma
- Department of Oncology, The Second Affiliated Hospital of Zunyi Medical University, Zunyi 563000, China; (J.-G.Z.); (S.-S.H.)
- Correspondence: (H.M.); (U.S.G.); Tel.: +49-(0)9131-85-44258 (U.S.G.); Fax: +49-(0)9131-85-39335 (U.S.G.)
| | - Udo S. Gaipl
- Department of Radiation Oncology, Universitätsklinikum Erlangen, 91054 Erlangen, Germany; (B.F.); (R.F.); (M.H.)
- Comprehensive Cancer Center Erlangen-EMN, 91054 Erlangen, Germany
- Correspondence: (H.M.); (U.S.G.); Tel.: +49-(0)9131-85-44258 (U.S.G.); Fax: +49-(0)9131-85-39335 (U.S.G.)
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13
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Allais BS, Beatson M, Wang H, Shahbazi S, Bijelic L, Jang S, Venna S. Five-year survival in patients with nodular and superficial spreading melanomas in the US population. J Am Acad Dermatol 2021; 84:1015-1022. [PMID: 33253834 DOI: 10.1016/j.jaad.2020.11.047] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 11/03/2020] [Accepted: 11/19/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND Although superficial spreading melanomas (SSM) are diagnosed as thinner lesions, nodular melanomas (NM) have a more rapid growth rate and are biologically more aggressive compared with other histologic subtypes. OBJECTIVE To determine the difference in 5-year relative survival in patients with NM and SSM at the same Breslow depth and TNM stage. METHODS A population-based cross-sectional analysis compared the 5-year relative survival of patients with NM and SSM using data from the National Cancer Institute's Surveillance, Epidemiology, and End Results (SEER)∗Stat software (version 8.2.1-8.3.5). Chi-square tests compared the proportions, and Kaplan-Meier method with Z-score compared 5-year relative survival. RESULTS For patients receiving a diagnosis between 2004 and 2009, 5-year relative survival was lower in NM compared with SSM (53.7% vs 87.3%; Z score, -41.35; P < .001). Similarly, for patients receiving a diagnosis between 2010 and 2015, 5-year relative survival was lower in NM compared with SSM (61.5% vs 89.7%; Z score, -2.7078; P < .01). Subgroup analyses showed inferior survival in NM in T1b, and survival differences remained significant after excluding patients with nodal or distant metastases. CONCLUSIONS Five-year relative survival is worse in NM compared with SSM especially in T1b, T2a, and T2b melanomas. Melanoma subtype should be taken into consideration when making treatment recommendations.
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Affiliation(s)
- Blair S Allais
- Washington University Department of Dermatology, Washington, DC.
| | - Meghan Beatson
- Memorial Sloan Kettering Cancer Center Department of Medicine, New York, NY
| | - Hongkun Wang
- Georgetown University Departments of Biostatistics, Bioinformatics, and Biomathematics, Washington, DC
| | | | - Lana Bijelic
- Hospital de Sant Joan Despi Moises Broggi, Barcelona, Spain
| | - Sekwon Jang
- University of Virginia School of Medicine, Charlottesville, VA; Inova Melanoma and Skin Cancer Center, Inova Schar Cancer Institute, Fairfax, VA
| | - Suraj Venna
- University of Virginia School of Medicine, Charlottesville, VA; Inova Melanoma and Skin Cancer Center, Inova Schar Cancer Institute, Fairfax, VA
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14
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Yang L, Yan X, Chen J, Zhan Q, Hua Y, Xu S, Li Z, Wang Z, Dong Y, Zuo D, Xue M, Tang Y, Herschman HR, Lu S, Shi Q, Wei W. Hexokinase 2 discerns a novel circulating tumor cell population associated with poor prognosis in lung cancer patients. Proc Natl Acad Sci U S A 2021; 118:e2012228118. [PMID: 33836566 PMCID: PMC7980452 DOI: 10.1073/pnas.2012228118] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 02/09/2021] [Indexed: 12/11/2022] Open
Abstract
Unlike other epithelial cancer types, circulating tumor cells (CTCs) are less frequently detected in the peripheral blood of non-small cell lung cancer (NSCLC) patients using epithelial marker-based detection approaches despite the aggressive nature of NSCLC. Here, we demonstrate hexokinase-2 (HK2) as a metabolic function-associated marker for the detection of CTCs. In 59 NSCLC patients bearing cytokeratin-positive (CKpos) primary tumors, HK2 enables resolving cytokeratin-negative (HK2high/CKneg) CTCs as a prevalent population in about half of the peripheral blood samples with positive CTC counts. However, HK2high/CKneg tumor cells are a minority population in pleural effusions and cerebrospinal fluids. Single-cell analysis shows that HK2high/CKneg CTCs exhibit smaller sizes but consistent copy number variation profiles compared with CKpos counterparts. Single-cell transcriptome profiling reveals that CK expression levels of CTCs are independent of their epithelial-to-mesenchymal transition (EMT) status, challenging the long-standing association between CK expression and EMT. HK2high/CKneg CTCs display metastasis and EGFR inhibitor resistance-related molecular signatures and are selectively enriched in patients with EGFRL858R driver oncogene mutation as opposed to EGFR19Del , which is more frequently found in patients with prevalent CKpos CTCs in the blood. Consistently, treatment-naïve patients with a larger number or proportion of HK2high/CKneg CTCs in the blood exhibit poor therapy response and shorter progression-free survival. Collectively, our approach resolves a more complete spectrum of CTCs in NSCLC that can potentially be exploited to identify patient prognosis before therapy.
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Affiliation(s)
- Liu Yang
- Department of Orthopedics, Shanghai Bone Tumor Institute, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Xiaowei Yan
- Institute for Systems Biology, Seattle, WA 98109
| | - Jie Chen
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Qiong Zhan
- Department of Oncology, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Yingqi Hua
- Department of Orthopedics, Shanghai Bone Tumor Institute, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Shili Xu
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
| | - Ziming Li
- Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Zhuo Wang
- Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
- Key Laboratory of Whole-Period Monitoring and Precise Intervention of Digestive Cancer (SMHC), Minhang Hospital, Fudan University, Shanghai, 201199, China
| | - Yu Dong
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Dongqing Zuo
- Department of Orthopedics, Shanghai Bone Tumor Institute, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Min Xue
- Key Laboratory of Whole-Period Monitoring and Precise Intervention of Digestive Cancer (SMHC), Minhang Hospital, Fudan University, Shanghai, 201199, China
| | - Yin Tang
- Institute for Systems Biology, Seattle, WA 98109
| | - Harvey R Herschman
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
| | - Shun Lu
- Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, China;
| | - Qihui Shi
- Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China;
- Key Laboratory of Whole-Period Monitoring and Precise Intervention of Digestive Cancer (SMHC), Minhang Hospital, Fudan University, Shanghai, 201199, China
| | - Wei Wei
- Institute for Systems Biology, Seattle, WA 98109;
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
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15
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Wang H, Qi C, Wan D. MicroRNA-377-3p targeting MMP-16 inhibits ovarian cancer cell growth, invasion, and interstitial transition. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:124. [PMID: 33569426 PMCID: PMC7867897 DOI: 10.21037/atm-20-8027] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Background To evaluate role of microRNA (miRNA)-377-3p on the remission of ovarian cancer (OC) cell proliferation, invasion, and interstitial transition in vivo and vitro. Methods SKOV3 cells were used as the object of in vitro research and four-week-old immunodeficient BABL/c female nude mice were used to form the xenograft model. Cell models were constructed by transfecting NC mimics, miR-377 mimic, plasmid cloning DNA (pcDNA), pc-matrix metalloproteinase (MMP)-16, or co-transfecting miR-377 mimic and pc-MMP-16. TargetScan software was used to predict the targeting relationship between miRNA-377-3p and MMP-16 in OC cells. The combination of miRNA-377-3p and MMP-16 was detected by dual luciferase report experiment. miRNA expression levels of miRNA-377-3p and MMP-16 in each transfection group cells were detected by reverse transcription-polymerase chain reaction (RT-PCR). The proliferation of SKOV3 cells were assessed by 5-ethynyl-2'-deoxyuridine (EdU) staining and microtubule formation, while the invasion ability of SKOV3 cells was detected by Transwell assay. Protein expression levels of MMP-16, survivin, Ki67, vascular endothelial growth factor (VEGF), E-cadherin, and N-cadherin were detected by Western blot (WB), and the positive cells of Ki67 and VEGF were detected by immunohistochemistry (IHC). Results MMP-16 overexpression markedly increased the EDU-positive cell percentage, upregulated survivin and Ki67 levels, increased the number of invasive cells per field, and enhanced VEGF and N-cadherin expression. Importantly, co-transfection of miRNA-377-3p and MMP-16 reversed these abnormal phenomena. Xenotransplantation mouse models were formed by injecting SKOV-3 cells subcutaneously. Tumor size, tumor volume, and tumor weight were all reduced in the miR-377-3p mimic–transfected group. The results of IHC indicated that Ki67 and VEGF expression were decreased in the miR-377-3p mimic–transfected group. Conclusions These findings indicate that miR-377-3p could be a promising therapeutic agent for OC cell growth, invasion, and interstitial transition with MMP-16 being its likely target.
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Affiliation(s)
- Huabin Wang
- Department of Obstetrics and Gynecology, Eastern Hospital, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, China
| | - Changmin Qi
- Department of Cardiac Surgery Centre, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Dan Wan
- Department of Gynecology, Chongqing Hospital of Traditional Chinese Medicine, Chongqing, China
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16
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Martínez-Rodríguez M, Monteagudo C. CCL27 Signaling in the Tumor Microenvironment. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1302:113-132. [PMID: 34286445 DOI: 10.1007/978-3-030-62658-7_9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Chemokines are a group of small proteins which play an important role in leukocyte migration and invasion. They are also involved in the cellular proliferation and migration of tumor cells.Chemokine CCL27 (cutaneous T cell-attracting chemokine, CTACK) is mainly expressed by keratinocytes of the normal epidermis. It is well known that this chemokine plays an important role in several inflammatory diseases of the skin, such as atopic dermatitis, contact dermatitis, and psoriasis. Moreover, several studies have shown an association between CCL27 expression and a variety of neoplasms including skin cancer.In this chapter, we address the role of chemokine CCL27 in the tumor microenvironment in the most relevant cancers of the skin and other anatomical locations. We also make a brief comment on future perspectives and the potential relation of CCL27 with different immunotherapeutic modalities.
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Affiliation(s)
| | - Carlos Monteagudo
- Department of Pathology, University Clinic Hospital-INCLIVA, University of Valencia, Valencia, Spain.
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17
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Dai H, Guo L, Lin M, Cheng Z, Li J, Tang J, Huan X, Huang Y, Xu K. Comprehensive analysis and identification of key genes and signaling pathways in the occurrence and metastasis of cutaneous melanoma. PeerJ 2020; 8:e10265. [PMID: 33240619 PMCID: PMC7680623 DOI: 10.7717/peerj.10265] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 10/07/2020] [Indexed: 01/02/2023] Open
Abstract
Background Melanoma is a malignant tumor of melanocytes, and the incidence has increased faster than any other cancer over the past half century. Most primary melanoma can be cured by local excision, but metastatic melanoma has a poor prognosis. Cutaneous melanoma (CM) is prone to metastasis, so the research on the mechanism of melanoma occurrence and metastasis will be beneficial to diagnose early, improve treatment, and prolong life survival. In this study, we compared the gene expression of normal skin (N), primary cutaneous melanoma (PM) and metastatic cutaneous melanoma (MM) in the Gene Expression Omnibus (GEO) database. Then we identified the key genes and molecular pathways that may be involved in the development and metastasis of cutaneous melanoma, thus to discover potential markers or therapeutic targets. Methods Three gene expression profiles (GSE7553, GSE15605 and GSE46517) were downloaded from the GEO database, which contained 225 tissue samples. R software identified the differentially expressed genes (DEGs) between pairs of N, PM and MM samples in the three sets of data. Subsequently, we analyzed the gene ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway of the DEGs, and constructed a protein-protein interaction (PPI) network. MCODE was used to seek the most important modules in PPI network, and then the GO function and KEGG pathway of them were analyzed. Finally, the hub genes were calculated by the cytoHubba in Cytoscape software. The Cancer Genome Atlas (TCGA) data were analyzed using UALCAN and GEPIA to validate the hub genes and analyze the prognosis of patients. Results A total of 134, 317 and 147 DEGs were identified between N, PM and MM in pair. GO functions and KEGG pathways analysis results showed that the upregulated DEGs mainly concentrated in cell division, spindle microtubule, protein kinase activity and the pathway of transcriptional misregulation in cancer. The downregulated DEGs occurred in epidermis development, extracellular exosome, structural molecule activity, metabolic pathways and p53 signaling pathway. The PPI network obtained the most important module, whose GO function and KEGG pathway were enriched in oxidoreductase activity, cell division, cell exosomes, protein binding, structural molecule activity, and metabolic pathways. 14, 18 and 18 DEGs were identified respectively as the hub genes between N, PM and MM, and TCGA data confirmed the expression differences of hub genes. In addition, the overall survival curve of hub genes showed that the differences in these genes may lead to a significant decrease in overall survival of melanoma patients. Conclusions In this study, several hub genes were found from normal skin, primary melanoma and metastatic melanoma samples. These hub genes may play an important role in the production, invasion, recurrence or death of CM, and may provide new ideas and potential targets for its diagnosis or treatment.
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Affiliation(s)
- Hanying Dai
- Department of Laboratory Medicine, the Third Xiangya Hospital, Central South University, ChangSha, HuNan, People's Republic of China.,Department of Laboratory Medicine, Xiangya School of Medicine, Central South University, ChangSha, HuNan, People's Republic of China
| | - Lihuang Guo
- Department of Laboratory Medicine, the Third Xiangya Hospital, Central South University, ChangSha, HuNan, People's Republic of China.,Department of Laboratory Medicine, Xiangya School of Medicine, Central South University, ChangSha, HuNan, People's Republic of China
| | - Mingyue Lin
- Department of Laboratory Medicine, the Third Xiangya Hospital, Central South University, ChangSha, HuNan, People's Republic of China.,Department of Laboratory Medicine, Xiangya School of Medicine, Central South University, ChangSha, HuNan, People's Republic of China
| | - Zhenbo Cheng
- Department of Laboratory Medicine, the Third Xiangya Hospital, Central South University, ChangSha, HuNan, People's Republic of China.,Department of Laboratory Medicine, Xiangya School of Medicine, Central South University, ChangSha, HuNan, People's Republic of China
| | - Jiancheng Li
- Department of Laboratory Medicine, the Third Xiangya Hospital, Central South University, ChangSha, HuNan, People's Republic of China.,Department of Laboratory Medicine, Xiangya School of Medicine, Central South University, ChangSha, HuNan, People's Republic of China
| | - Jinxia Tang
- Department of Laboratory Medicine, the Third Xiangya Hospital, Central South University, ChangSha, HuNan, People's Republic of China.,Department of Laboratory Medicine, Xiangya School of Medicine, Central South University, ChangSha, HuNan, People's Republic of China
| | - Xisha Huan
- Department of Laboratory Medicine, the Third Xiangya Hospital, Central South University, ChangSha, HuNan, People's Republic of China.,Department of Laboratory Medicine, Xiangya School of Medicine, Central South University, ChangSha, HuNan, People's Republic of China
| | - Yue Huang
- Department of Laboratory Medicine, the Third Xiangya Hospital, Central South University, ChangSha, HuNan, People's Republic of China.,Department of Laboratory Medicine, Xiangya School of Medicine, Central South University, ChangSha, HuNan, People's Republic of China
| | - Keqian Xu
- Department of Laboratory Medicine, the Third Xiangya Hospital, Central South University, ChangSha, HuNan, People's Republic of China.,Department of Laboratory Medicine, Xiangya School of Medicine, Central South University, ChangSha, HuNan, People's Republic of China
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18
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Li M, Zhang C, Zhou L, Li S, Cao YJ, Wang L, Xiang R, Shi Y, Piao Y. Identification and validation of novel DNA methylation markers for early diagnosis of lung adenocarcinoma. Mol Oncol 2020; 14:2744-2758. [PMID: 32688456 PMCID: PMC7607165 DOI: 10.1002/1878-0261.12767] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 06/07/2020] [Accepted: 07/16/2020] [Indexed: 12/15/2022] Open
Abstract
Lung cancer has the highest mortality of all cancers worldwide. Epigenetic alterations have emerged as potential biomarkers for early diagnosis of various cancer tissue types. To identify methylation markers for early diagnosis of lung adenocarcinoma, we aimed to integrate genome‐wide DNA methylation and gene expression data from The Cancer Genome Atlas. To this end, we first examined the global DNA methylation pattern of lung adenocarcinoma and investigated the relationship between DNA methylation subtypes and clinical features. We then extracted differentially methylated and expressed genes, and adopted feature selection techniques to determine the final methylation markers. The performance of the markers in predicting lung adenocarcinoma was evaluated on three independent datasets from Gene Expression Omnibus. Protein levels of marker genes were validated by immunohistochemistry, and their biological function was further verified in vivo. We identified three novel methylation markers in lung adenocarcinoma including cg08032924, cg14823851, and cg19161124, mapping to CMTM2, TBX4, and DPP6, respectively. Validating these results on three independent datasets indicated that the three markers can achieve extremely high sensitivity and specificity in distinguishing lung adenocarcinoma from normal samples. Immunohistochemistry quantification results confirmed that markers are weakly expressed in human lung adenocarcinoma, and CMTM2 decreased tumor growth of mouse Lewis lung carcinoma in vivo. Overall, our study identified three novel methylation markers in lung adenocarcinoma which may contribute toward an improved diagnosis potentially leading to a better outcome for patients with lung adenocarcinoma.
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Affiliation(s)
- Miao Li
- School of Medicine, Nankai University, Tianjin, China
| | - Chen Zhang
- School of Medicine, Nankai University, Tianjin, China
| | - Lijun Zhou
- School of Medicine, Nankai University, Tianjin, China
| | - Siyu Li
- School of Medicine, Nankai University, Tianjin, China
| | - Yuan Jie Cao
- Department of Radiation and Oncology, National Clinical Research Center for Cancer and Tianjin Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Longlong Wang
- School of Medicine, Nankai University, Tianjin, China.,Tianjin Key Laboratory of Human Development and Reproductive Regulation, Nankai University Affiliated Hospital of Obstetrics and Gynecology, Tianjin, China
| | - Rong Xiang
- School of Medicine, Nankai University, Tianjin, China
| | - Yi Shi
- School of Medicine, Nankai University, Tianjin, China.,Tianjin Key Laboratory of Human Development and Reproductive Regulation, Nankai University Affiliated Hospital of Obstetrics and Gynecology, Tianjin, China
| | - Yongjun Piao
- School of Medicine, Nankai University, Tianjin, China.,Tianjin Key Laboratory of Human Development and Reproductive Regulation, Nankai University Affiliated Hospital of Obstetrics and Gynecology, Tianjin, China
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19
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Roedig H, Damiescu R, Zeng-Brouwers J, Kutija I, Trebicka J, Wygrecka M, Schaefer L. Danger matrix molecules orchestrate CD14/CD44 signaling in cancer development. Semin Cancer Biol 2020; 62:31-47. [PMID: 31412297 DOI: 10.1016/j.semcancer.2019.07.026] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 07/29/2019] [Accepted: 07/30/2019] [Indexed: 02/06/2023]
Abstract
The tumor matrix together with inflammation and autophagy are crucial regulators of cancer development. Embedded in the tumor stroma are numerous proteoglycans which, in their soluble form, act as danger-associated molecular patterns (DAMPs). By interacting with innate immune receptors, the Toll-like receptors (TLRs), DAMPs autonomously trigger aseptic inflammation and can regulate autophagy. Biglycan, a known danger proteoglycan, can regulate the cross-talk between inflammation and autophagy by evoking a switch between pro-inflammatory CD14 and pro-autophagic CD44 co-receptors for TLRs. Thus, these novel mechanistic insights provide some explanation for the plethora of reports indicating that the same matrix-derived DAMP acts either as a promoter or suppressor of tumor growth. In this review we will summarize and critically discuss the role of the matrix-derived DAMPs biglycan, hyaluronan, and versican in regulating the TLR-, CD14- and CD44-signaling dialogue between inflammation and autophagy with particular emphasis on cancer development.
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Affiliation(s)
- Heiko Roedig
- Pharmazentrum Frankfurt, Institut für Allgemeine Pharmakologie und Toxikologie, Goethe University, Frankfurt am Main, Germany
| | - Roxana Damiescu
- Pharmazentrum Frankfurt, Institut für Allgemeine Pharmakologie und Toxikologie, Goethe University, Frankfurt am Main, Germany
| | - Jinyang Zeng-Brouwers
- Pharmazentrum Frankfurt, Institut für Allgemeine Pharmakologie und Toxikologie, Goethe University, Frankfurt am Main, Germany
| | - Iva Kutija
- Pharmazentrum Frankfurt, Institut für Allgemeine Pharmakologie und Toxikologie, Goethe University, Frankfurt am Main, Germany
| | - Jonel Trebicka
- Translational Hepatology, Department of Internal Medicine I, University Clinic Frankfurt, Germany
| | - Malgorzata Wygrecka
- Department of Biochemistry, Faculty of Medicine, Universities of Giessen and Marburg Lung Center, Giessen, Germany
| | - Liliana Schaefer
- Pharmazentrum Frankfurt, Institut für Allgemeine Pharmakologie und Toxikologie, Goethe University, Frankfurt am Main, Germany.
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20
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Lattanzi M, Lee Y, Simpson D, Moran U, Darvishian F, Kim RH, Hernando E, Polsky D, Hanniford D, Shapiro R, Berman R, Pavlick AC, Wilson MA, Kirchhoff T, Weber JS, Zhong J, Osman I. Primary Melanoma Histologic Subtype: Impact on Survival and Response to Therapy. J Natl Cancer Inst 2020; 111:180-188. [PMID: 29912415 PMCID: PMC7962783 DOI: 10.1093/jnci/djy086] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 02/28/2018] [Accepted: 04/11/2018] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Two primary histologic subtypes, superficial spreading melanoma (SSM) and nodular melanoma (NM), comprise the majority of all cutaneous melanomas. NM is associated with worse outcomes, which have been attributed to increased thickness at presentation, and it is widely expected that NM and SSM would exhibit similar behavior once metastasized. Herein, we tested the hypothesis that primary histologic subtype is an independent predictor of survival and may impact response to treatment in the metastatic setting. METHODS We examined the most recent Surveillance, Epidemiology, and End Results (SEER) cohort (n = 118 508) and the New York University (NYU) cohort (n = 1621) with available protocol-driven follow-up. Outcomes specified by primary histology were studied in both the primary and metastatic settings with respect to BRAF-targeted therapy and immunotherapy. We characterized known driver mutations and examined a 140-gene panel in a subset of NM and SSM cases using next-generation sequencing. All statistical tests were two-sided. RESULTS NM was an independent risk factor for death in both the SEER (hazard ratio [HR] = 1.55, 95% confidence interval [CI] = 1.41 to 1.70, P < .001) and NYU (HR = 1.47, 95% CI = 1.05, 2.07, P = .03) cohorts, controlling for thickness, ulceration, stage, and other variables. In the metastatic setting, NM remained an independent risk factor for death upon treatment with BRAF-targeted therapy (HR = 3.33, 95% CI = 1.06 to 10.47, P = .04) but showed no statistically significant difference with immune checkpoint inhibition. NM was associated with a higher rate of NRAS mutation (P < .001), and high-throughput sequencing revealed NM-specific genomic alterations in NOTCH4, ANK3, and ZNF560, which were independently validated. CONCLUSIONS Our data reveal distinct clinical and biological differences between NM and SSM that support revisiting the prognostic and predictive impact of primary histology subtype in the management of cutaneous melanoma.
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Affiliation(s)
- Michael Lattanzi
- Department of Medicine.,Interdisciplinary Melanoma Cooperative Group
| | - Yesung Lee
- Interdisciplinary Melanoma Cooperative Group.,The Ronald O. Perelman Department of Dermatology
| | - Danny Simpson
- Interdisciplinary Melanoma Cooperative Group.,Department of Population Health
| | - Una Moran
- Interdisciplinary Melanoma Cooperative Group.,The Ronald O. Perelman Department of Dermatology
| | - Farbod Darvishian
- Interdisciplinary Melanoma Cooperative Group.,Department of Pathology
| | - Randie H Kim
- Interdisciplinary Melanoma Cooperative Group.,The Ronald O. Perelman Department of Dermatology
| | - Eva Hernando
- Interdisciplinary Melanoma Cooperative Group.,Department of Pathology
| | - David Polsky
- Interdisciplinary Melanoma Cooperative Group.,The Ronald O. Perelman Department of Dermatology.,Department of Pathology
| | - Doug Hanniford
- Interdisciplinary Melanoma Cooperative Group.,Department of Pathology
| | - Richard Shapiro
- Interdisciplinary Melanoma Cooperative Group.,Department of Surgery, NYU School of Medicine, New York, NY
| | - Russell Berman
- Interdisciplinary Melanoma Cooperative Group.,Department of Surgery, NYU School of Medicine, New York, NY
| | - Anna C Pavlick
- Department of Medicine.,Interdisciplinary Melanoma Cooperative Group.,The Ronald O. Perelman Department of Dermatology
| | - Melissa A Wilson
- Department of Medicine.,Interdisciplinary Melanoma Cooperative Group
| | - Tomas Kirchhoff
- Interdisciplinary Melanoma Cooperative Group.,Department of Population Health
| | - Jeffrey S Weber
- Department of Medicine.,Interdisciplinary Melanoma Cooperative Group.,The Ronald O. Perelman Department of Dermatology
| | - Judy Zhong
- Interdisciplinary Melanoma Cooperative Group.,Department of Population Health
| | - Iman Osman
- Department of Medicine.,Interdisciplinary Melanoma Cooperative Group.,The Ronald O. Perelman Department of Dermatology
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21
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Zhang Z, Lin E, Zhuang H, Xie L, Feng X, Liu J, Yu Y. Construction of a novel gene-based model for prognosis prediction of clear cell renal cell carcinoma. Cancer Cell Int 2020; 20:27. [PMID: 32002016 PMCID: PMC6986036 DOI: 10.1186/s12935-020-1113-6] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 01/17/2020] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Clear cell renal cell carcinoma (ccRCC) comprises the majority of kidney cancer death worldwide, whose incidence and mortality are not promising. Identifying ideal biomarkers to construct a more accurate prognostic model than conventional clinical parameters is crucial. METHODS Raw count of RNA-sequencing data and clinicopathological data were acquired from The Cancer Genome Atlas (TCGA). Tumor samples were divided into two sets. Differentially expressed genes (DEGs) were screened in the whole set and prognosis-related genes were identified from the training set. Their common genes were used in LASSO and best subset regression which were performed to identify the best prognostic 5 genes. The gene-based risk score was developed based on the Cox coefficient of the individual gene. Time-dependent receiver operating characteristic (ROC) and Kaplan-Meier (KM) survival analysis were used to assess its prognostic power. GSE29609 dataset from GEO (Gene Expression Omnibus) database was used to validate the signature. Univariate and multivariate Cox regression were performed to screen independent prognostic parameters to construct a nomogram. The predictive power of the nomogram was revealed by time-dependent ROC curves and the calibration plot and verified in the validation set. Finally, Functional enrichment analysis of DEGs and 5 novel genes were performed to suggest the potential biological pathways. RESULTS PADI1, ATP6V0D2, DPP6, C9orf135 and PLG were screened to be significantly related to the prognosis of ccRCC patients. The risk score effectively stratified the patients into high-risk group with poor overall survival (OS) based on survival analysis. AJCC-stage, age, recurrence and risk score were regarded as independent prognostic parameters by Cox regression analysis and were used to construct a nomogram. Time-dependent ROC curves showed the nomogram performed best in 1-, 3- and 5-year survival predictions compared with AJCC-stage and risk score in validation sets. The calibration plot showed good agreement of the nomogram between predicted and observed outcomes. Functional enrichment analysis suggested several enriched biological pathways related to cancer. CONCLUSIONS In our study, we constructed a gene-based model integrating clinical prognostic parameters to predict prognosis of ccRCC well, which might provide a reliable prognosis assessment tool for clinician and aid treatment decision-making in the clinic.
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Affiliation(s)
- Zedan Zhang
- Department of Urology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Shantou University Medical College, Shantou, China
| | - Enyu Lin
- Department of Urology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Shantou University Medical College, Shantou, China
| | - Hongkai Zhuang
- Department of Urology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Shantou University Medical College, Shantou, China
| | - Lu Xie
- Department of Urology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Xiaoqiang Feng
- Department of Immunology, School of Basic Medical Science, Southern Medical University, Guangzhou, China
| | - Jiumin Liu
- Department of Urology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yuming Yu
- Department of Urology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
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22
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Aderhold K, Wilson M, Berger AC, Levi S, Bennett J. Precision Medicine in the Treatment of Melanoma. Surg Oncol Clin N Am 2020; 29:1-13. [DOI: 10.1016/j.soc.2019.08.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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23
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Imrédi E, Liszkay G, Kenessey I, Plotár V, Gödény M, Tóth B, Fedorcsák I, Tímár J. Aquaporin-1 Protein Expression of the Primary Tumor May Predict Cerebral Progression of Cutaneous Melanoma. Pathol Oncol Res 2020; 26:405-410. [PMID: 30378011 DOI: 10.1007/s12253-018-0513-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 10/17/2018] [Indexed: 01/27/2023]
Abstract
Brain metastasis is a frequent complication of the progression of malignant melanoma. In a previous study aquaporin 1 (AQP1) protein expression was found to be associated with increased mortality and decreased progression free survival in cutaneous melanoma. To explore further the potential of this marker we studied the AQP1 protein expression in 67 metastatic melanoma patients using immunohistochemistry. Primary tumor samples were acquired from patients with brain (BR) (n = 44) and extra-cranial (EC) (n = 23) metastases, while brain metastatic samples were collected during neurosurgical resection (n = 5). Patients with brain metastases had shorter overall survival (p = 0.02) and significantly higher AQP1 expression in the primary tumors (median H-score = 250 vs. 140, p = 0.044) as compared to patients of the EC metastasis group. AQP1 expression was found to be significantly lower in the brain metastases compared to the corresponding primary tumors (median H-score = 35 vs. 300 p = 0.01). However, in brain metastases AQP1 expression was heterogenous, AQP1 protein was more abundant in the melanoma cells far away from the capillaries as compared to tumor cells adjacent to vessels indicating a hypoxia-driven expression of AQP1. We suggest that AQP1 expression could well be a prognostic marker of brain metastatic potential of human cutaneous melanoma.
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Affiliation(s)
- E Imrédi
- 2nd Department of Pathology, Semmelweis University, Üllői Str 93, Budapest, H-1091, Hungary
- National Institute of Oncology, Budapest, Hungary
| | - G Liszkay
- National Institute of Oncology, Budapest, Hungary
| | - I Kenessey
- 2nd Department of Pathology, Semmelweis University, Üllői Str 93, Budapest, H-1091, Hungary
| | - V Plotár
- National Institute of Oncology, Budapest, Hungary
| | - M Gödény
- National Institute of Oncology, Budapest, Hungary
| | - B Tóth
- Department of Dermatology, Venerology and Dermato-Oncology, Budapest, Hungary
| | - I Fedorcsák
- National Institute of Clinical Neuroscience, Budapest, Hungary
| | - József Tímár
- 2nd Department of Pathology, Semmelweis University, Üllői Str 93, Budapest, H-1091, Hungary.
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24
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Grossman D, Kim CC, Hartman RI, Berry E, Nelson KC, Okwundu N, Curiel-Lewandrowski C, Leachman SA, Swetter SM. Prognostic gene expression profiling in melanoma: necessary steps to incorporate into clinical practice. Melanoma Manag 2019; 6:MMT32. [PMID: 31871621 PMCID: PMC6920745 DOI: 10.2217/mmt-2019-0016] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Prognostic gene expression profiling (GEP) tests for cutaneous melanoma (CM) are not recommended in current guidelines outside of a clinical trial. However, their use is becoming more prevalent and some practitioners are using GEP tests to guide patient management. Thus, there is an urgent need to bridge this gap between test usage and clinical guideline recommendations by obtaining high-quality evidence to guide us toward best practice use of GEP testing in CM patients. We focus here on the opportunities and uncertainties associated with prognostic GEP testing in CM, review how GEP testing was incorporated into clinical care guidelines for uveal melanoma and breast cancer and discuss the role of clinical trials to determine best use in patients with CM.
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Affiliation(s)
- Douglas Grossman
- Dermatology, Huntsman Cancer Institute & University of Utah Health Sciences Center, Salt Lake City, UT 84112, USA
| | - Caroline C Kim
- Dermatology, Tufts Medical Center, Boston & Newton Wellesley Hospital, Wellesley, MA 02111, USA
| | - Rebecca I Hartman
- Dermatology, Brigham & Women's Hospital, Harvard Medical School, & Veterans Affairs Boston Healthcare System, Boston, MA 02446, USA
| | - Elizabeth Berry
- Dermatology, Oregon Health & Sciences University & Knight Cancer Institute, Portland, OR 97239, USA
| | - Kelly C Nelson
- Dermatology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Nwanneka Okwundu
- Dermatology, Huntsman Cancer Institute & University of Utah Health Sciences Center, Salt Lake City, UT 84112, USA
| | | | - Sancy A Leachman
- Dermatology, Oregon Health & Sciences University & Knight Cancer Institute, Portland, OR 97239, USA
| | - Susan M Swetter
- Dermatology, Stanford University Medical Center & Veterans Affairs Palo Alto Health Care System, Palo Alto, CA 94305, USA
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25
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Modelling of Protein Kinase Signaling Pathways in Melanoma and Other Cancers. Cancers (Basel) 2019; 11:cancers11040465. [PMID: 30987166 PMCID: PMC6520749 DOI: 10.3390/cancers11040465] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 03/26/2019] [Accepted: 03/30/2019] [Indexed: 12/18/2022] Open
Abstract
Melanoma is a highly aggressive tumor with a strong dependence on intracellular signaling pathways. Almost half of all melanomas are driven by mutations in the v-Raf murine sarcoma viral oncogene homolog B (BRAF) with BRAFV600E being the most prevalent mutation. Recently developed targeted treatment directed against mutant BRAF and downstream mitogen-activated protein kinase (MAPK) MAP2K1 (also termed MEK1) have improved overall survival of melanoma patients. However, the MAPK signaling pathway is far more complex than a single chain of consecutively activated MAPK enzymes and it contains nested-, inherent feedback mechanisms, crosstalk with other signaling pathways, epigenetic regulatory mechanisms, and interacting small non-coding RNAs. A more complete understanding of this pathway is needed to better understand melanoma development and mechanisms of treatment resistance. Network reconstruction, analysis, and modelling under the systems biology paradigm have been used recently in different malignant tumors including melanoma to analyze and integrate 'omics' data, formulate mechanistic hypotheses on tumorigenesis, assess and personalize anticancer therapy, and propose new drug targets. Here we review the current knowledge of network modelling approaches in cancer with a special emphasis on melanoma.
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26
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Rabbie R, Ferguson P, Molina‐Aguilar C, Adams DJ, Robles‐Espinoza CD. Melanoma subtypes: genomic profiles, prognostic molecular markers and therapeutic possibilities. J Pathol 2019; 247:539-551. [PMID: 30511391 PMCID: PMC6492003 DOI: 10.1002/path.5213] [Citation(s) in RCA: 124] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 11/27/2018] [Accepted: 11/30/2018] [Indexed: 12/24/2022]
Abstract
Melanoma is characterised by its ability to metastasise at early stages of tumour development. Current clinico-pathologic staging based on the American Joint Committee on Cancer criteria is used to guide surveillance and management in early-stage disease, but its ability to predict clinical outcome has limitations. Herein we review the genomics of melanoma subtypes including cutaneous, acral, uveal and mucosal, with a focus on the prognostic and predictive significance of key molecular aberrations. © 2018 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Roy Rabbie
- Experimental Cancer GeneticsThe Wellcome Sanger InstituteHinxtonUK
- Cambridge Cancer CentreCambridge University Hospitals NHS Foundation TrustCambridgeUK
| | - Peter Ferguson
- Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred HospitalSydneyAustralia
- Melanoma Institute Australia, The University of SydneySydneyAustralia
| | - Christian Molina‐Aguilar
- Laboratorio Internacional de Investigación sobre el Genoma HumanoUniversidad Nacional Autónoma de MéxicoSantiago de QuerétaroMexico
| | - David J Adams
- Experimental Cancer GeneticsThe Wellcome Sanger InstituteHinxtonUK
| | - Carla D Robles‐Espinoza
- Experimental Cancer GeneticsThe Wellcome Sanger InstituteHinxtonUK
- Laboratorio Internacional de Investigación sobre el Genoma HumanoUniversidad Nacional Autónoma de MéxicoSantiago de QuerétaroMexico
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27
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Cui T, Yang L, Ma Y, Petersen I, Chen Y. Desmocollin 3 has a tumor suppressive activity through inhibition of AKT pathway in colorectal cancer. Exp Cell Res 2019; 378:124-130. [PMID: 30857973 DOI: 10.1016/j.yexcr.2019.03.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 03/07/2019] [Accepted: 03/08/2019] [Indexed: 01/01/2023]
Abstract
Desmocollin 3 (DSC3) is a transmembrane adhesion protein of desmosomes and involved in carcinogenesis in various cancer types. Downregulation of DSC3 has been reported in colorectal cancer (CRC). However, the function of DSC3 in CRC has not yet been elucidated. In this study, we performed cell-based functional analysis after DSC3 overexpression by stable transfection and knockdown by siRNA in CRC cells. It turned out that overexpression of DSC3 reduced cell proliferation, colony forming ability, induced G0/G1 cell cycle arrest and promoted apoptosis. Further pathway analysis showed that overexpression of DSC3 significantly inhibited the activity of AKT pathway and increased the expression of E-cadherin as well as p53 and p21. In contrast, siRNA-mediated knockdown of DSC3 increased cell proliferation and colony formation, activated the AKT pathway and decreased the expression of E-cadherin as well as p53 and p21. Additionally, in primary CRC patient samples, the expression of DSC3 protein was significantly related to the expression of desmocollin 1 (DSC1) and desmocollin 2 (DSC2) as well as E-cadherin (p < 0.001 respectively). Taken together, our data reveal that DSC3 suppresses CRC cell growth through inhibition of AKT pathway and regulation of E-cadherin. DSC3 may serve as a novel therapeutic target for CRC.
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Affiliation(s)
- Tiantain Cui
- Section Pathology of the Institute of Forensic Medicine, University Hospital Jena, Friedrich Schiller University Jena, Am Klinikum 1, 07747 Jena, Germany; Department of Radiation Oncology, Arthur G. James Hospital/Ohio State Comprehensive Cancer Center, Columbus, OH, 43210, USA
| | - Linlin Yang
- Section Pathology of the Institute of Forensic Medicine, University Hospital Jena, Friedrich Schiller University Jena, Am Klinikum 1, 07747 Jena, Germany; Department of Radiation Oncology, Arthur G. James Hospital/Ohio State Comprehensive Cancer Center, Columbus, OH, 43210, USA
| | - Yunxia Ma
- Section Pathology of the Institute of Forensic Medicine, University Hospital Jena, Friedrich Schiller University Jena, Am Klinikum 1, 07747 Jena, Germany
| | - Iver Petersen
- Section Pathology of the Institute of Forensic Medicine, University Hospital Jena, Friedrich Schiller University Jena, Am Klinikum 1, 07747 Jena, Germany; Institute of Pathology, SRH Wald-Klinikum Gera, Germany
| | - Yuan Chen
- Section Pathology of the Institute of Forensic Medicine, University Hospital Jena, Friedrich Schiller University Jena, Am Klinikum 1, 07747 Jena, Germany.
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28
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Klapperich ME, Bowen GM, Grossman D. Current controversies in early-stage melanoma: Questions on management and surveillance. J Am Acad Dermatol 2019; 80:15-25. [PMID: 30553299 DOI: 10.1016/j.jaad.2018.03.054] [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] [Received: 01/31/2018] [Revised: 03/12/2018] [Accepted: 03/18/2018] [Indexed: 12/24/2022]
Abstract
There are a number of controversies and uncertainties relating to the management and surveillance of patients with early-stage, localized (ie, stage 0, I, and II) cutaneous melanoma. While tumor stage is a critical predictor of clinical outcome and guides treatment, accurate determination of stage may be affected by the biopsy technique used and the method of sectioning before histologic review. A new molecular prognostic test is available but has not been formally incorporated into staging or treatment guidelines. There are no randomized controlled clinical trials to support guidelines for surveillance following the treatment of early-stage melanoma. In the second article in this continuing medical education series, we review the controversies and uncertainties relating to these issues. The questions we address are controversial because they speak to clinical scenarios for which there are no evidence-based guidelines or randomized clinical trials with the consequence of considerable variability in clinical practice. Our goal is to provide the clinician with up-to-date contextual knowledge to appreciate the multiple sides of each controversy and to suggest pathways to resolution.
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Affiliation(s)
- Marki E Klapperich
- University of Wisconsin-Madison School of Medicine and Public Health, Madison, Wisconsin
| | - Glen M Bowen
- Department of Dermatology, University of Utah Health Sciences Center, Salt Lake City, Utah; Huntsman Cancer Institute, University of Utah Health Sciences Center, Salt Lake City, Utah
| | - Douglas Grossman
- Department of Dermatology, University of Utah Health Sciences Center, Salt Lake City, Utah; Huntsman Cancer Institute, University of Utah Health Sciences Center, Salt Lake City, Utah.
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29
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Kappel S, Borgström A, Stokłosa P, Dörr K, Peinelt C. Store-operated calcium entry in disease: Beyond STIM/Orai expression levels. Semin Cell Dev Biol 2019; 94:66-73. [PMID: 30630032 DOI: 10.1016/j.semcdb.2019.01.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 11/29/2018] [Accepted: 01/05/2019] [Indexed: 12/19/2022]
Abstract
Precise intracellular calcium signaling is crucial to numerous cellular functions. In non-excitable cells, store-operated calcium entry (SOCE) is a key step in the generation of intracellular calcium signals. Tight regulation of SOCE is important, and dysregulation is involved in several pathophysiological cellular malfunctions. The current underlying SOCE, calcium release-activated calcium current (ICRAC), was first discovered almost three decades ago. Since its discovery, the molecular components of ICRAC, Orai1 and stromal interaction molecule 1 (STIM1), have been extensively investigated. Several regulatory mechanisms and proteins contribute to alterations in SOCE and cellular malfunctions in cancer, immune and neurodegenerative diseases, inflammation, and neuronal disorders. This review summarizes these regulatory mechanisms, including glycosylation, pH sensing, and the regulatory proteins golli, α-SNAP, SARAF, ORMDL3, CRACR2A, and TRPM4 channels.
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Affiliation(s)
- Sven Kappel
- Institute of Biochemistry and Molecular Medicine, National Center of Competence in Research NCCR TransCure, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland
| | - Anna Borgström
- Institute of Biochemistry and Molecular Medicine, National Center of Competence in Research NCCR TransCure, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland
| | - Paulina Stokłosa
- Institute of Biochemistry and Molecular Medicine, National Center of Competence in Research NCCR TransCure, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland
| | | | - Christine Peinelt
- Institute of Biochemistry and Molecular Medicine, National Center of Competence in Research NCCR TransCure, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland.
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30
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Hyams DM, Cook RW, Buzaid AC. Identification of risk in cutaneous melanoma patients: Prognostic and predictive markers. J Surg Oncol 2019; 119:175-186. [PMID: 30548543 PMCID: PMC6590387 DOI: 10.1002/jso.25319] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 11/15/2018] [Indexed: 12/23/2022]
Abstract
New therapeutic modalities for melanoma promise benefit in selected individuals. Efficacy appears greater in patients with lower tumor burden, suggesting an important role for risk-stratified surveillance. Robust predictive markers might permit optimization of agent to patient, while low-risk prognostic markers might guide more conservative management. This review evaluates protein, gene, and multiplexed marker panels that may contribute to better risk assessment and improved management of patients with cutaneous melanoma.
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Affiliation(s)
- David M. Hyams
- Desert Surgical Oncology, Eisenhower Medical CenterRancho MirageCalifornia
| | - Robert W. Cook
- R&D and Medical Affairs, Castle Biosciences, IncFriendswoodTexas
| | - Antonio C. Buzaid
- Oncology Center, Hospital Israelita Albert EinsteinSão PauloBrazil
- Centro Oncológico Antonio Ermírio de Moraes, Beneficência Portuguesa de São PauloSão PauloBrazil
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31
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Schmidt L, Møller M, Haldrup C, Strand SH, Vang S, Hedegaard J, Høyer S, Borre M, Ørntoft T, Sørensen KD. Exploring the transcriptome of hormone-naive multifocal prostate cancer and matched lymph node metastases. Br J Cancer 2018; 119:1527-1537. [PMID: 30449885 PMCID: PMC6288156 DOI: 10.1038/s41416-018-0321-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 10/09/2018] [Accepted: 10/09/2018] [Indexed: 11/09/2022] Open
Abstract
Background The current inability to predict whether a primary prostate cancer (PC) will progress to metastatic disease leads to overtreatment of indolent PCs as well as undertreatment of aggressive PCs. Here, we explored the transcriptional changes associated with metastatic progression of multifocal hormone-naive PC. Methods Using total RNA-sequencing, we analysed laser micro-dissected primary PC foci (n = 23), adjacent normal prostate tissue samples (n = 23) and lymph node metastases (n = 9) from ten hormone-naive PC patients. Genes important for PC progression were identified using differential gene expression and clustering analysis. From these, two multi-gene-based expression signatures (models) were developed, and their prognostic potential was evaluated using Cox-regression and Kaplan–Meier analyses in three independent radical prostatectomy (RP) cohorts (>650 patients). Results We identified several novel PC-associated transcripts deregulated during PC progression, and these transcripts were used to develop two novel gene-expression-based prognostic models. The models showed independent prognostic potential in three RP cohorts (n = 405, n = 107 and n = 91), using biochemical recurrence after RP as the primary clinical endpoint. Conclusions We identified several transcripts deregulated during PC progression and developed two new prognostic models for PC risk stratification, each of which showed independent prognostic value beyond routine clinicopathological factors in three independent RP cohorts.
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Affiliation(s)
- Linnéa Schmidt
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Mia Møller
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Christa Haldrup
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Siri H Strand
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Søren Vang
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Jakob Hedegaard
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Søren Høyer
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
| | - Michael Borre
- Department of Urology, Aarhus University Hospital, Aarhus, Denmark
| | - Torben Ørntoft
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
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32
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RNA-seq analysis identifies different transcriptomic types and developmental trajectories of primary melanomas. Oncogene 2018; 37:6136-6151. [PMID: 29995873 DOI: 10.1038/s41388-018-0385-y] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 05/30/2018] [Accepted: 05/31/2018] [Indexed: 12/13/2022]
Abstract
Recent studies revealed trajectories of mutational events in early melanomagenesis, but the accompanying changes in gene expression are far less understood. Therefore, we performed a comprehensive RNA-seq analysis of laser-microdissected melanocytic nevi (n = 23) and primary melanoma samples (n = 57) and characterized the molecular mechanisms of early melanoma development. Using self-organizing maps, unsupervised clustering, and analysis of pseudotime (PT) dynamics to identify evolutionary trajectories, we describe here two transcriptomic types of melanocytic nevi (N1 and N2) and primary melanomas (M1 and M2). N1/M1 lesions are characterized by pigmentation-type and MITF gene signatures, and a high prevalence of NRAS mutations in M1 melanomas. N2/M2 lesions are characterized by inflammatory-type and AXL gene signatures with an equal distribution of wild-type and mutated BRAF and low prevalence of NRAS mutations in M2 melanomas. Interestingly, N1 nevi and M1 melanomas and N2 nevi and M2 melanomas, respectively, cluster together, but there is no clustering in a stage-dependent manner. Transcriptional signatures of M1 melanomas harbor signatures of BRAF/MEK inhibitor resistance and M2 melanomas harbor signatures of anti-PD-1 antibody treatment resistance. Pseudotime dynamics of nevus and melanoma samples are suggestive for a switch-like immune-escape mechanism in melanoma development with downregulation of immune genes paralleled by an increasing expression of a cell cycle signature in late-stage melanomas. Taken together, the transcriptome analysis identifies gene signatures and mechanisms underlying development of melanoma in early and late stages with relevance for diagnostics and therapy.
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33
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Bracalente C, Ibañez IL, Berenstein A, Notcovich C, Cerda MB, Klamt F, Chernomoretz A, Durán H. Reprogramming human A375 amelanotic melanoma cells by catalase overexpression: Upregulation of antioxidant genes correlates with regression of melanoma malignancy and with malignant progression when downregulated. Oncotarget 2018; 7:41154-41171. [PMID: 27206673 PMCID: PMC5173049 DOI: 10.18632/oncotarget.9273] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 04/02/2016] [Indexed: 12/18/2022] Open
Abstract
Reactive oxygen species (ROS) are implicated in tumor transformation. The antioxidant system (AOS) protects cells from ROS damage. However, it is also hijacked by cancers cells to proliferate within the tumor. Thus, identifying proteins altered by redox imbalance in cancer cells is an attractive prognostic and therapeutic tool. Gene expression microarrays in A375 melanoma cells with different ROS levels after overexpressing catalase were performed. Dissimilar phenotypes by differential compensation to hydrogen peroxide scavenging were generated. The melanotic A375-A7 (A7) upregulated TYRP1, CNTN1 and UCHL1 promoting melanogenesis. The metastatic A375-G10 (G10) downregulated MTSS1 and TIAM1, proteins absent in metastasis. Moreover, differential coexpression of AOS genes (EPHX2, GSTM3, MGST1, MSRA, TXNRD3, MGST3 and GSR) was found in A7 and G10. Their increase in A7 improved its AOS ability and therefore, oxidative stress response, resembling less aggressive tumor cells. Meanwhile, their decrease in G10 revealed a disruption in the AOS and therefore, enhanced its metastatic capacity. These gene signatures, not only bring new insights into the physiopathology of melanoma, but also could be relevant in clinical prognostic to classify between non aggressive and metastatic melanomas.
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Affiliation(s)
- Candelaria Bracalente
- Departamento de Micro y Nanotecnología, Comisión Nacional de Energía Atómica, San Martín, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Tecnológicas, Buenos Aires, Argentina
| | - Irene L Ibañez
- Departamento de Micro y Nanotecnología, Comisión Nacional de Energía Atómica, San Martín, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Tecnológicas, Buenos Aires, Argentina
| | - Ariel Berenstein
- Fundación Instituto Leloir and Departamento de Física, Facultad Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Cintia Notcovich
- Departamento de Micro y Nanotecnología, Comisión Nacional de Energía Atómica, San Martín, Buenos Aires, Argentina
| | - María B Cerda
- Departamento de Micro y Nanotecnología, Comisión Nacional de Energía Atómica, San Martín, Buenos Aires, Argentina
| | - Fabio Klamt
- Laboratório de Bioquímica Celular, Departamento de Bioquímica, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brasil
| | - Ariel Chernomoretz
- Fundación Instituto Leloir and Departamento de Física, Facultad Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Hebe Durán
- Departamento de Micro y Nanotecnología, Comisión Nacional de Energía Atómica, San Martín, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Tecnológicas, Buenos Aires, Argentina.,Escuela de Ciencia y Tecnología, Universidad Nacional de San Martín, San Martín, Buenos Aires, Argentina
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Metri R, Mohan A, Nsengimana J, Pozniak J, Molina-Paris C, Newton-Bishop J, Bishop D, Chandra N. Identification of a gene signature for discriminating metastatic from primary melanoma using a molecular interaction network approach. Sci Rep 2017; 7:17314. [PMID: 29229936 PMCID: PMC5725601 DOI: 10.1038/s41598-017-17330-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 11/10/2017] [Indexed: 01/15/2023] Open
Abstract
Understanding the biological factors that are characteristic of metastasis in melanoma remains a key approach to improving treatment. In this study, we seek to identify a gene signature of metastatic melanoma. We configured a new network-based computational pipeline, combined with a machine learning method, to mine publicly available transcriptomic data from melanoma patient samples. Our method is unbiased and scans a genome-wide protein-protein interaction network using a novel formulation for network scoring. Using this, we identify the most influential, differentially expressed nodes in metastatic as compared to primary melanoma. We evaluated the shortlisted genes by a machine learning method to rank them by their discriminatory capacities. From this, we identified a panel of 6 genes, ALDH1A1, HSP90AB1, KIT, KRT16, SPRR3 and TMEM45B whose expression values discriminated metastatic from primary melanoma (87% classification accuracy). In an independent transcriptomic data set derived from 703 primary melanomas, we showed that all six genes were significant in predicting melanoma specific survival (MSS) in a univariate analysis, which was also consistent with AJCC staging. Further, 3 of these genes, HSP90AB1, SPRR3 and KRT16 remained significant predictors of MSS in a joint analysis (HR = 2.3, P = 0.03) although, HSP90AB1 (HR = 1.9, P = 2 × 10-4) alone remained predictive after adjusting for clinical predictors.
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Affiliation(s)
- Rahul Metri
- IISc Mathematics Initiative (IMI), Indian Institute of Science, Bangalore, Karnataka, India
| | - Abhilash Mohan
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka, India
| | - Jérémie Nsengimana
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Joanna Pozniak
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Carmen Molina-Paris
- Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds, UK
| | - Julia Newton-Bishop
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - David Bishop
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Nagasuma Chandra
- IISc Mathematics Initiative (IMI), Indian Institute of Science, Bangalore, Karnataka, India.
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka, India.
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35
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Theocharis AD, Karamanos NK. Proteoglycans remodeling in cancer: Underlying molecular mechanisms. Matrix Biol 2017; 75-76:220-259. [PMID: 29128506 DOI: 10.1016/j.matbio.2017.10.008] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 10/23/2017] [Accepted: 10/24/2017] [Indexed: 02/07/2023]
Abstract
Extracellular matrix is a highly dynamic macromolecular network. Proteoglycans are major components of extracellular matrix playing key roles in its structural organization and cell signaling contributing to the control of numerous normal and pathological processes. As multifunctional molecules, proteoglycans participate in various cell functions during morphogenesis, wound healing, inflammation and tumorigenesis. Their interactions with matrix effectors, cell surface receptors and enzymes enable them with unique properties. In malignancy, extensive remodeling of tumor stroma is associated with marked alterations in proteoglycans' expression and structural variability. Proteoglycans exert diverse functions in tumor stroma in a cell-specific and context-specific manner and they mainly contribute to the formation of a permissive provisional matrix for tumor growth affecting tissue organization, cell-cell and cell-matrix interactions and tumor cell signaling. Proteoglycans also modulate cancer cell phenotype and properties, the development of drug resistance and tumor stroma angiogenesis. This review summarizes the proteoglycans remodeling and their novel biological roles in malignancies with particular emphasis to the underlying molecular mechanisms.
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Affiliation(s)
- Achilleas D Theocharis
- Biochemistry, Biochemical Analysis & Matrix Pathobiochemistry Research Group, Laboratory of Biochemistry, Department of Chemistry, University of Patras, 26500 Patras, Greece.
| | - Nikos K Karamanos
- Biochemistry, Biochemical Analysis & Matrix Pathobiochemistry Research Group, Laboratory of Biochemistry, Department of Chemistry, University of Patras, 26500 Patras, Greece.
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36
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The convergent roles of the nuclear factor I transcription factors in development and cancer. Cancer Lett 2017; 410:124-138. [PMID: 28962832 DOI: 10.1016/j.canlet.2017.09.015] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 09/11/2017] [Accepted: 09/16/2017] [Indexed: 02/07/2023]
Abstract
The nuclear factor I (NFI) transcription factors play important roles during normal development and have been associated with developmental abnormalities in humans. All four family members, NFIA, NFIB, NFIC and NFIX, have a homologous DNA binding domain and function by regulating cell proliferation and differentiation via the transcriptional control of their target genes. More recently, NFI genes have also been implicated in cancer based on genomic analyses and studies of animal models in a variety of tumours across multiple organ systems. However, the association between their functions in development and in cancer is not well described. In this review, we summarise the evidence suggesting a converging role for the NFI genes in development and cancer. Our review includes all cancer types in which the NFI genes are implicated, focusing predominantly on studies demonstrating their oncogenic or tumour-suppressive potential. We conclude by presenting the challenges impeding our understanding of NFI function in cancer biology, and demonstrate how a developmental perspective may contribute towards overcoming such hurdles.
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37
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Leachman SA, Mengden Koon S, Korcheva VB, White KP. Assessing Genetic Expression Profiles in Melanoma Diagnosis. Dermatol Clin 2017; 35:537-544. [PMID: 28886810 DOI: 10.1016/j.det.2017.06.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Most melanocytic tumors can be characterized as a benign nevus or a melanoma by a trained pathologist using traditional histopathological methods. However, a minority demonstrates ambiguous features and continues to be a diagnostic challenge. Genetic expression profiling (GEP) assays have been developed in an effort to resolve this dilemma. These assays measure mRNA levels of specified genes using reverse transcription quantitative polymerase chain reaction technology. The development of GEP assays, methodology, challenges associated with GEP validation and testing, and the suitability of a currently available GEP test for clinical use are reviewed.
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Affiliation(s)
- Sancy A Leachman
- Melanoma and Skin Cancer Program, Department of Dermatology, OHSU Knight Cancer Institute, Oregon Health & Science University, 3303 SW Bond Avenue, Portland, OR 97239, USA.
| | - Stephanie Mengden Koon
- Department of Dermatology, Oregon Health & Science University, 3303 SW Bond Avenue, Portland, OR 97239, USA
| | - Veselina B Korcheva
- Department of Dermatology, Oregon Health & Science University, 3303 SW Bond Avenue, Portland, OR 97239, USA
| | - Kevin P White
- Department of Dermatology, Oregon Health & Science University, 3303 SW Bond Avenue, Portland, OR 97239, USA
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38
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Hsueh EC, DeBloom JR, Lee J, Sussman JJ, Covington KR, Middlebrook B, Johnson C, Cook RW, Slingluff CL, McMasters KM. Interim analysis of survival in a prospective, multi-center registry cohort of cutaneous melanoma tested with a prognostic 31-gene expression profile test. J Hematol Oncol 2017; 10:152. [PMID: 28851416 PMCID: PMC5576286 DOI: 10.1186/s13045-017-0520-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 08/18/2017] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND A 31-gene expression profile (GEP) test that provides risk classification of cutaneous melanoma (CM) patients has been validated in several retrospective studies. The objective of the reported study was a prospective evaluation of the GEP performance in patients enrolled in two clinical registries. METHODS Three-hundred twenty two CM patients enrolled in the EXPAND (NCT02355587) and INTEGRATE (NCT02355574) registries met the criteria of age ≥ 16 years, successful GEP result and ≥1 follow-up visit for inclusion in this interim analysis. Primary endpoints were recurrence-free (RFS), distant metastasis-free (DMFS), and overall survival (OS). RESULTS Median follow-up was 1.5 years for event-free patients. Median age for subjects was 58 years (range 18-87) and median Breslow thickness was 1.2 mm (range 0.2-12.0). Eighty-eight percent (282/322) of cases had stage I/II disease and 74% (237/322) had a SLN biopsy. Seventy-seven percent (248/322) had class 1 molecular profiles. 1.5-year RFS, DMFS, and OS rates were 97 vs. 77%, 99 vs. 89%, and 99 vs. 92% for class 1 vs. class 2, respectively (p < 0.0001 for each). Multivariate Cox regression showed Breslow thickness, mitotic rate, and GEP class to significantly predict recurrence (p < 0.01), while tumor thickness was the only significant predictor of distant metastasis and overall survival in this interim analysis. CONCLUSIONS Interim analysis of patient outcomes from a combined prospective cohort supports the 31-gene GEP's ability to stratify early-stage CM patients into two groups with significantly different metastatic risk. RFS outcomes in this real-world cohort are consistent with previously published analyses with retrospective specimens. GEP testing complements current clinicopathologic features and increases identification of high-risk patients. TRIAL REGISTRATION ClinicalTrials.gov, NCT02355574 and NCT02355587.
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Affiliation(s)
- Eddy C. Hsueh
- Dept. of Surgery, St. Louis University, St. Louis, MO USA
| | | | - Jonathan Lee
- Northside Melanoma and Sarcoma Specialists of Georgia, Atlanta, GA USA
| | - Jeffrey J. Sussman
- Dept. of Surgery, University of Cincinnati Cancer Institute, Cincinnati, OH USA
| | - Kyle R. Covington
- Castle Biosciences, Inc., 820 S. Friendswood Drive Suite 201, Friendswood, TX USA
| | - Brooke Middlebrook
- Castle Biosciences, Inc., 820 S. Friendswood Drive Suite 201, Friendswood, TX USA
| | - Clare Johnson
- Castle Biosciences, Inc., 820 S. Friendswood Drive Suite 201, Friendswood, TX USA
| | - Robert W. Cook
- Castle Biosciences, Inc., 820 S. Friendswood Drive Suite 201, Friendswood, TX USA
| | - Craig L. Slingluff
- Dept. of Surgery and Cancer Center, University of Virginia School of Medicine, Charlottesville, VA USA
| | - Kelly M. McMasters
- Dept. of Surgical Oncology, James Graham Brown Cancer Center, University of Louisville School of Medicine, Louisville, KY USA
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39
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Nagarajan S, Bedi U, Budida A, Hamdan FH, Mishra VK, Najafova Z, Xie W, Alawi M, Indenbirken D, Knapp S, Chiang CM, Grundhoff A, Kari V, Scheel CH, Wegwitz F, Johnsen SA. BRD4 promotes p63 and GRHL3 expression downstream of FOXO in mammary epithelial cells. Nucleic Acids Res 2017; 45:3130-3145. [PMID: 27980063 PMCID: PMC5389510 DOI: 10.1093/nar/gkw1276] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Accepted: 12/09/2016] [Indexed: 12/12/2022] Open
Abstract
Bromodomain-containing protein 4 (BRD4) is a member of the bromo- and extraterminal (BET) domain-containing family of epigenetic readers which is under intensive investigation as a target for anti-tumor therapy. BRD4 plays a central role in promoting the expression of select subsets of genes including many driven by oncogenic transcription factors and signaling pathways. However, the role of BRD4 and the effects of BET inhibitors in non-transformed cells remain mostly unclear. We demonstrate that BRD4 is required for the maintenance of a basal epithelial phenotype by regulating the expression of epithelial-specific genes including TP63 and Grainy Head-like transcription factor-3 (GRHL3) in non-transformed basal-like mammary epithelial cells. Moreover, BRD4 occupancy correlates with enhancer activity and enhancer RNA (eRNA) transcription. Motif analyses of cell context-specific BRD4-enriched regions predicted the involvement of FOXO transcription factors. Consistently, activation of FOXO1 function via inhibition of EGFR-AKT signaling promoted the expression of TP63 and GRHL3. Moreover, activation of Src kinase signaling and FOXO1 inhibition decreased the expression of FOXO/BRD4 target genes. Together, our findings support a function for BRD4 in promoting basal mammary cell epithelial differentiation, at least in part, by regulating FOXO factor function on enhancers to activate TP63 and GRHL3 expression.
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Affiliation(s)
- Sankari Nagarajan
- Department of General, Visceral and Pediatric Surgery, Göttingen Center for Molecular Biosciences, University Medical Center Göttingen, 37077 Göttingen, Germany
| | - Upasana Bedi
- Institute of Molecular Oncology, University Medical Center Göttingen, 37077 Göttingen, Germany.,Institute of Tumor Biology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Anusha Budida
- Department of General, Visceral and Pediatric Surgery, Göttingen Center for Molecular Biosciences, University Medical Center Göttingen, 37077 Göttingen, Germany
| | - Feda H Hamdan
- Department of General, Visceral and Pediatric Surgery, Göttingen Center for Molecular Biosciences, University Medical Center Göttingen, 37077 Göttingen, Germany
| | - Vivek Kumar Mishra
- Department of General, Visceral and Pediatric Surgery, Göttingen Center for Molecular Biosciences, University Medical Center Göttingen, 37077 Göttingen, Germany
| | - Zeynab Najafova
- Department of General, Visceral and Pediatric Surgery, Göttingen Center for Molecular Biosciences, University Medical Center Göttingen, 37077 Göttingen, Germany
| | - Wanhua Xie
- Department of General, Visceral and Pediatric Surgery, Göttingen Center for Molecular Biosciences, University Medical Center Göttingen, 37077 Göttingen, Germany
| | - Malik Alawi
- Bioinformatics Core, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany.,Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, 20251 Hamburg, Germany
| | - Daniela Indenbirken
- Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, 20251 Hamburg, Germany
| | - Stefan Knapp
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK.,Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, UK.,Institute for Pharmaceutical Chemistry, Goethe University Frankfurt 60323, Germany
| | - Cheng-Ming Chiang
- University of Texas Southwestern Medical Center, Simmons Comprehensive Cancer Center, Dallas, TX 75235, USA
| | - Adam Grundhoff
- Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, 20251 Hamburg, Germany
| | - Vijayalakshmi Kari
- Department of General, Visceral and Pediatric Surgery, Göttingen Center for Molecular Biosciences, University Medical Center Göttingen, 37077 Göttingen, Germany
| | - Christina H Scheel
- Institute of Stem Cell Research, Helmholtz Center for Health and Environmental Research Munich, 85764 Neuherberg, Germany
| | - Florian Wegwitz
- Department of General, Visceral and Pediatric Surgery, Göttingen Center for Molecular Biosciences, University Medical Center Göttingen, 37077 Göttingen, Germany
| | - Steven A Johnsen
- Department of General, Visceral and Pediatric Surgery, Göttingen Center for Molecular Biosciences, University Medical Center Göttingen, 37077 Göttingen, Germany
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Genome-wide screen for differentially methylated long noncoding RNAs identifies Esrp2 and lncRNA Esrp2-as regulated by enhancer DNA methylation with prognostic relevance for human breast cancer. Oncogene 2017; 36:6446-6461. [PMID: 28759043 PMCID: PMC5701091 DOI: 10.1038/onc.2017.246] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Revised: 06/05/2017] [Accepted: 06/08/2017] [Indexed: 12/14/2022]
Abstract
The majority of long noncoding RNAs (lncRNAs) is still poorly characterized with respect to function, interactions with protein-coding genes, and mechanisms that regulate their expression. As for protein-coding RNAs, epigenetic deregulation of lncRNA expression by alterations in DNA methylation might contribute to carcinogenesis. To provide genome-wide information on lncRNAs aberrantly methylated in breast cancer we profiled tumors of the C3(1) SV40TAg mouse model by MCIp-seq (Methylated CpG Immunoprecipitation followed by sequencing). This approach detected 69 lncRNAs differentially methylated between tumor tissue and normal mammary glands, with 26 located in antisense orientation of a protein-coding gene. One of the hypomethylated lncRNAs, 1810019D21Rik (now called Esrp2-antisense (as)) was identified in proximity to the epithelial splicing regulatory protein 2 (Esrp2) that is significantly elevated in C3(1) tumors. ESRPs were shown previously to have a dual role in carcinogenesis. Both gain and loss have been associated with poor prognosis in human cancers, but the mechanisms regulating expression are not known. In-depth analyses indicate that coordinate overexpression of Esrp2 and Esrp2-as inversely correlates with DNA methylation. Luciferase reporter gene assays support co-expression of Esrp2 and the major short Esrp2-as variant from a bidirectional promoter, and transcriptional regulation by methylation of a proximal enhancer. Ultimately, this enhancer-based regulatory mechanism provides a novel explanation for tissue-specific expression differences and upregulation of Esrp2 during carcinogenesis. Knockdown of Esrp2-as reduced Esrp2 protein levels without affecting mRNA expression and resulted in an altered transcriptional profile associated with extracellular matrix (ECM), cell motility and reduced proliferation, whereas overexpression enhanced proliferation. Our findings not only hold true for the murine tumor model, but led to the identification of an unannotated human homolog of Esrp2-as which is significantly upregulated in human breast cancer and associated with poor prognosis.
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41
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Brachelente C, Cappelli K, Capomaccio S, Porcellato I, Silvestri S, Bongiovanni L, De Maria R, Verini Supplizi A, Mechelli L, Sforna M. Transcriptome Analysis of Canine Cutaneous Melanoma and Melanocytoma Reveals a Modulation of Genes Regulating Extracellular Matrix Metabolism and Cell Cycle. Sci Rep 2017; 7:6386. [PMID: 28743863 PMCID: PMC5526991 DOI: 10.1038/s41598-017-06281-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 06/12/2017] [Indexed: 12/16/2022] Open
Abstract
Interactions between tumor cells and tumor microenvironment are considered critical in carcinogenesis, tumor invasion and metastasis. To examine transcriptome changes and to explore the relationship with tumor microenvironment in canine cutaneous melanocytoma and melanoma, we extracted RNA from formalin-fixed, paraffin-embedded (FFPE) specimens and analyzed them by means of RNA-seq for transcriptional analysis. Melanocytoma and melanoma samples were compared to detect differential gene expressions and significant enriched pathways were explored to reveal functional relations between differentially expressed genes. The study demonstrated a differential expression of 60 genes in melanomas compared to melanocytomas. The differentially expressed genes cluster in the extracellular matrix-receptor interaction, protein digestion and absorption, focal adhesion and PI3K-Akt (phosphoinositide 3-kinase/protein kinase B) signaling pathways. Genes encoding for several collagen proteins were more commonly differentially expressed. Results of the RNA-seq were validated by qRT-PCR and protein expression of some target molecules was investigated by means of immunohistochemistry. We hypothesize that the developing melanoma actively promotes collagen metabolism and extracellular matrix remodeling as well as enhancing cell proliferation and survival contributing to disease progression and metastasis. In this study, we also detected unidentified genes in human melanoma expression studies and uncover new candidate drug targets for further testing in canine melanoma.
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Affiliation(s)
| | - Katia Cappelli
- Department of Veterinary Medicine, 06126, Perugia, Italy
| | | | | | | | - Laura Bongiovanni
- Faculty of Veterinary Medicine, 64100, Teramo, Italy
- Department of Pathobiology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | | | | | - Luca Mechelli
- Department of Veterinary Medicine, 06126, Perugia, Italy
| | - Monica Sforna
- Department of Veterinary Medicine, 06126, Perugia, Italy
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Wouters J, Vizoso M, Martinez-Cardus A, Carmona FJ, Govaere O, Laguna T, Joseph J, Dynoodt P, Aura C, Foth M, Cloots R, van den Hurk K, Balint B, Murphy IG, McDermott EW, Sheahan K, Jirström K, Nodin B, Mallya-Udupi G, van den Oord JJ, Gallagher WM, Esteller M. Comprehensive DNA methylation study identifies novel progression-related and prognostic markers for cutaneous melanoma. BMC Med 2017; 15:101. [PMID: 28578692 PMCID: PMC5458482 DOI: 10.1186/s12916-017-0851-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 04/03/2017] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Cutaneous melanoma is the deadliest skin cancer, with an increasing incidence and mortality rate. Currently, staging of patients with primary melanoma is performed using histological biomarkers such as tumor thickness and ulceration. As disruption of the epigenomic landscape is recognized as a widespread feature inherent in tumor development and progression, we aimed to identify novel biomarkers providing additional clinical information over current factors using unbiased genome-wide DNA methylation analyses. METHODS We performed a comprehensive DNA methylation analysis during all progression stages of melanoma using Infinium HumanMethylation450 BeadChips on a discovery cohort of benign nevi (n = 14) and malignant melanoma from both primary (n = 33) and metastatic (n = 28) sites, integrating the DNA methylome with gene expression data. We validated the discovered biomarkers in three independent validation cohorts by pyrosequencing and immunohistochemistry. RESULTS We identified and validated biomarkers for, and pathways involved in, melanoma development (e.g., HOXA9 DNA methylation) and tumor progression (e.g., TBC1D16 DNA methylation). In addition, we determined a prognostic signature with potential clinical applicability and validated PON3 DNA methylation and OVOL1 protein expression as biomarkers with prognostic information independent of tumor thickness and ulceration. CONCLUSIONS Our data underscores the importance of epigenomic regulation in triggering metastatic dissemination through the inactivation of central cancer-related pathways. Inactivation of cell-adhesion and differentiation unleashes dissemination, and subsequent activation of inflammatory and immune system programs impairs anti-tumoral defense pathways. Moreover, we identify several markers of tumor development and progression previously unrelated to melanoma, and determined a prognostic signature with potential clinical utility.
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Affiliation(s)
- Jasper Wouters
- Translational Cell and Tissue Research, KU Leuven (University of Leuven), Leuven, Belgium
- OncoMark Ltd, NovaUCD, Dublin 4, Ireland
- Laboratory of Computational Biology, VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven (University of Leuven), Leuven, Belgium
| | - Miguel Vizoso
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain
| | - Anna Martinez-Cardus
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain
| | - F Javier Carmona
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain
| | - Olivier Govaere
- Translational Cell and Tissue Research, KU Leuven (University of Leuven), Leuven, Belgium
| | - Teresa Laguna
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain
- Institute of Molecular Biology (IMB), Mainz, Germany
| | | | | | - Claudia Aura
- Translational Cell and Tissue Research, KU Leuven (University of Leuven), Leuven, Belgium
| | - Mona Foth
- OncoMark Ltd, NovaUCD, Dublin 4, Ireland
- Cancer Research UK, Beatson Institute, Glasgow, G61 1BD, UK
| | - Roy Cloots
- OncoMark Ltd, NovaUCD, Dublin 4, Ireland
- Department of Pathology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Karin van den Hurk
- OncoMark Ltd, NovaUCD, Dublin 4, Ireland
- Department of Pathology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Balazs Balint
- OncoMark Ltd, NovaUCD, Dublin 4, Ireland
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain
| | - Ian G Murphy
- Department of Surgery, St. Vincent's University Hospital, Dublin 4, Ireland
| | - Enda W McDermott
- Department of Surgery, St. Vincent's University Hospital, Dublin 4, Ireland
| | - Kieran Sheahan
- Department of Pathology and Laboratory Medicine, St. Vincent's University Hospital, Dublin 4, Ireland
| | - Karin Jirström
- Department of Clinical Sciences, Division of Pathology, Lund University, Skåne University Hospital, 221 85, Lund, Sweden
| | - Bjorn Nodin
- Department of Clinical Sciences, Division of Pathology, Lund University, Skåne University Hospital, 221 85, Lund, Sweden
| | | | - Joost J van den Oord
- Translational Cell and Tissue Research, KU Leuven (University of Leuven), Leuven, Belgium
| | - William M Gallagher
- OncoMark Ltd, NovaUCD, Dublin 4, Ireland.
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Dublin 4, Ireland.
| | - Manel Esteller
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain.
- Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Catalonia, Spain.
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain.
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Kani K, Garri C, Tiemann K, Malihi PD, Punj V, Nguyen AL, Lee J, Hughes LD, Alvarez RM, Wood DM, Joo AY, Katz JE, Agus DB, Mallick P. JUN-Mediated Downregulation of EGFR Signaling Is Associated with Resistance to Gefitinib in EGFR-mutant NSCLC Cell Lines. Mol Cancer Ther 2017; 16:1645-1657. [PMID: 28566434 DOI: 10.1158/1535-7163.mct-16-0564] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 03/08/2017] [Accepted: 05/08/2017] [Indexed: 12/27/2022]
Abstract
Mutations or deletions in exons 18-21 in the EGFR) are present in approximately 15% of tumors in patients with non-small cell lung cancer (NSCLC). They lead to activation of the EGFR kinase domain and sensitivity to molecularly targeted therapeutics aimed at this domain (gefitinib or erlotinib). These drugs have demonstrated objective clinical response in many of these patients; however, invariably, all patients acquire resistance. To examine the molecular origins of resistance, we derived a set of gefitinib-resistant cells by exposing lung adenocarcinoma cell line, HCC827, with an activating mutation in the EGFR tyrosine kinase domain, to increasing gefitinib concentrations. Gefitinib-resistant cells acquired an increased expression and activation of JUN, a known oncogene involved in cancer progression. Ectopic overexpression of JUN in HCC827 cells increased gefitinib IC50 from 49 nmol/L to 8 μmol/L (P < 0.001). Downregulation of JUN expression through shRNA resensitized HCC827 cells to gefitinib (IC50 from 49 nmol/L to 2 nmol/L; P < 0.01). Inhibitors targeting JUN were 3-fold more effective in the gefitinib-resistant cells than in the parental cell line (P < 0.01). Analysis of gene expression in patient tumors with EGFR-activating mutations and poor response to erlotinib revealed a similar pattern as the top 260 differentially expressed genes in the gefitinib-resistant cells (Spearman correlation coefficient of 0.78, P < 0.01). These findings suggest that increased JUN expression and activity may contribute to gefitinib resistance in NSCLC and that JUN pathway therapeutics merit investigation as an alternate treatment strategy. Mol Cancer Ther; 16(8); 1645-57. ©2017 AACR.
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Affiliation(s)
- Kian Kani
- Lawrence J. Ellison Institute for Transformative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California.
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California Keck School of Medicine, Los Angeles, California
| | - Carolina Garri
- Lawrence J. Ellison Institute for Transformative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Katrin Tiemann
- Lawrence J. Ellison Institute for Transformative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Paymaneh D Malihi
- Lawrence J. Ellison Institute for Transformative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Vasu Punj
- Division of Hematology, Department of Medicine, University of Southern California, Los Angeles, California
| | - Anthony L Nguyen
- Lawrence J. Ellison Institute for Transformative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Janet Lee
- Lawrence J. Ellison Institute for Transformative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Lindsey D Hughes
- Lawrence J. Ellison Institute for Transformative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Ruth M Alvarez
- Lawrence J. Ellison Institute for Transformative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Damien M Wood
- Lawrence J. Ellison Institute for Transformative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Ah Young Joo
- Lawrence J. Ellison Institute for Transformative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Jonathan E Katz
- Lawrence J. Ellison Institute for Transformative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - David B Agus
- Lawrence J. Ellison Institute for Transformative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California Keck School of Medicine, Los Angeles, California
| | - Parag Mallick
- Lawrence J. Ellison Institute for Transformative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California.
- Department of Radiology, Stanford University, Stanford, California
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44
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Ko JS, Matharoo-Ball B, Billings SD, Thomson BJ, Tang JY, Sarin KY, Cai E, Kim J, Rock C, Kimbrell HZ, Flake DD, Warf MB, Nelson J, Davis T, Miller C, Rushton K, Hartman AR, Wenstrup RJ, Clarke LE. Diagnostic Distinction of Malignant Melanoma and Benign Nevi by a Gene Expression Signature and Correlation to Clinical Outcomes. Cancer Epidemiol Biomarkers Prev 2017; 26:1107-1113. [DOI: 10.1158/1055-9965.epi-16-0958] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 11/18/2016] [Accepted: 03/09/2017] [Indexed: 11/16/2022] Open
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Hothem Z, Bayci A, Thibodeau BJ, Ketelsen BE, Fortier LE, Uzieblo AF, Cosner D, Totoraitis K, Keidan RD, Wilson GD. Using global gene expression to discriminate thin melanomas with poor outcomes. Mol Cell Oncol 2017; 4:e1253527. [PMID: 28197532 DOI: 10.1080/23723556.2016.1253527] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 10/21/2016] [Accepted: 10/21/2016] [Indexed: 12/15/2022]
Abstract
Most melanomas present as thin lesions (≤1.0 mm) with a good prognosis; however, a small percentage of patients with thin lesions experience recurrence or metastasis. The aim of our study was to identify a distinct pattern of gene expression within thin melanomas known to have eventually metastasized to regional lymph nodes or distant sites compared with those that followed the typical course with good response to wide local excision alone. Patients who were disease-free for a minimum of 10 y served as controls (n = 10) to the experimental group who developed metastasis (n = 9). Laser capture microdissection was used to specifically isolate cancer cells from formalin-fixed paraffin-embedded tissue with subsequent gene expression analysis on Affymetrix Human Transcriptome Array 2.0 Arrays. Although gene expression differences were observed between the patients with thin melanoma with poor clinical outcome and those with good clinical outcome, neither the number of genes nor the magnitude of the fold difference was very substantial or significant. Cluster analysis with this subset of genes could definitively separate a subset of the poor responders from the good responders, but there remained a mixed group of tumors that could not be predicted from gene expression alone. Pathway analysis identified cellular processes that were regulated based on the response, including categories commonly associated with melanoma progression. Ultimately, we concluded that there were very few differences between these groups. Future research will be required and investigation of the mutational landscape may be another strategy to uncover genomic changes that drive recurrence and metastasis in thin melanoma.
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Affiliation(s)
- Zachary Hothem
- Department of Surgery, William Beaumont Hospital , Royal Oak, MI, USA
| | - Andrew Bayci
- Department of Surgery, William Beaumont Hospital , Royal Oak, MI, USA
| | | | | | - Laura E Fortier
- Beaumont BioBank, William Beaumont Hospital , Royal Oak, MI, USA
| | - Alison F Uzieblo
- Department of Anatomic Pathology, William Beaumont Hospital , Royal Oak, MI, USA
| | - Diane Cosner
- Department of Anatomic Pathology, William Beaumont Hospital , Royal Oak, MI, USA
| | - Kristin Totoraitis
- Oakland University William Beaumont School of Medicine , Rochester, MI, USA
| | - Richard D Keidan
- Department of Surgery, William Beaumont Hospital , Royal Oak, MI, USA
| | - George D Wilson
- Beaumont BioBank, William Beaumont Hospital , Royal Oak, MI, USA
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46
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Zainulabadeen A, Yao P, Zare H. Underexpression of Specific Interferon Genes Is Associated with Poor Prognosis of Melanoma. PLoS One 2017; 12:e0170025. [PMID: 28114321 PMCID: PMC5256985 DOI: 10.1371/journal.pone.0170025] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 12/26/2016] [Indexed: 01/30/2023] Open
Abstract
Because the prognosis of melanoma is challenging and inaccurate when using current clinical approaches, clinicians are seeking more accurate molecular markers to improve risk models. Accordingly, we performed a survival analysis on 404 samples from The Cancer Genome Atlas (TCGA) cohort of skin cutaneous melanoma. Using our recently developed gene network model, we identified biological signatures that confidently predict the prognosis of melanoma (p-value < 10-5). Our model predicted 38 cases as low-risk and 54 cases as high-risk. The probability of surviving at least 5 years was 64% for low-risk and 14% for high-risk cases. In particular, we found that the overexpression of specific genes in the mitotic cell cycle pathway and the underexpression of specific genes in the interferon pathway are both associated with poor prognosis. We show that our predictive model assesses the risk more accurately than the traditional Clark staging method. Therefore, our model can help clinicians design treatment strategies more effectively. Furthermore, our findings shed light on the biology of melanoma and its prognosis. This is the first in vivo study that demonstrates the association between the interferon pathway and the prognosis of melanoma.
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Affiliation(s)
- Aamir Zainulabadeen
- Department of Computer Science, Texas State University, San Marcos, Texas, United States of America
- Department of Computer Science, Princeton University, Princeton, New Jersey, United States of America
| | - Philip Yao
- Department of Computer Science, Texas State University, San Marcos, Texas, United States of America
- Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Habil Zare
- Department of Computer Science, Texas State University, San Marcos, Texas, United States of America
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47
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Lu YT, Chen TL, Chang KS, Chang CM, Wei TY, Liu JW, Hsiao CA, Shih TL. Synthesis of novel C4-benzazole naphthalimide derivatives with potent anti-tumor properties against murine melanoma. Bioorg Med Chem 2017; 25:789-794. [DOI: 10.1016/j.bmc.2016.11.057] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 11/29/2016] [Indexed: 01/08/2023]
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48
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Martinez-Rodriguez M, Thompson AK, Monteagudo C. High CCL27 immunoreactivity in 'supratumoral' epidermis correlates with better prognosis in patients with cutaneous malignant melanoma. J Clin Pathol 2017; 70:15-19. [PMID: 27325798 DOI: 10.1136/jclinpath-2015-203537] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 04/12/2016] [Accepted: 04/30/2016] [Indexed: 02/04/2023]
Abstract
AIMS It has been proposed that the expression of chemokines and chemokine receptors by melanoma cells may have a role in tumour immune escape. Chemokine CCL27 is reported to be expressed specifically on the epidermal keratinocytes. The implication of CCL27 in cutaneous melanomas is currently unresolved. It has been suggested that CCL27 expression in melanomas can induce antitumoral immunity, and that CCL27 may suppress tumour growth probably due to the local lymphocyte recruitment. METHODS We studied CCL27 chemokine expression in three different concentric epidermal areas covering the primary cutaneous melanoma in patients with a long clinical follow-up. Our study included 91 cases of primary melanomas of the skin diagnosed during the 10-year period 1992-2002, and a minimum clinical follow-up of 10 years. RESULTS We evaluated three different concentric and easily reproducible areas in the epidermis: the area covering melanoma (which we called 'supratumoral'), the area adjacent to the tumour ('peritumoral') and the most peripheral epidermal area ('peripheral'). Only CCL27 expression in supratumoral epidermis correlated with clinical outcome. CONCLUSIONS Our study showed that a higher immunostaining of CCL27 in supratumoral epidermis is associated with longer progression-free interval and melanoma-specific survival.
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Affiliation(s)
- Miguel Martinez-Rodriguez
- Department of Pathology, Hospital Clínico Universitario-INCLIVA, University of Valencia, Valencia, Spain
- Department of Pathology, Telemark Hospital, Skien, Norway
| | - Alec K Thompson
- Department of Dermatopathology and Ocular Pathology, Ullevål University Hospital, University of Oslo Medical Center, Oslo, Norway
| | - Carlos Monteagudo
- Department of Pathology, Hospital Clínico Universitario-INCLIVA, University of Valencia, Valencia, Spain
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49
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Schaefer L, Tredup C, Gubbiotti MA, Iozzo RV. Proteoglycan neofunctions: regulation of inflammation and autophagy in cancer biology. FEBS J 2017; 284:10-26. [PMID: 27860287 PMCID: PMC5226885 DOI: 10.1111/febs.13963] [Citation(s) in RCA: 120] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 10/27/2016] [Accepted: 11/11/2016] [Indexed: 12/18/2022]
Abstract
Inflammation and autophagy have emerged as prominent issues in the context of proteoglycan signaling. In particular, two small, leucine-rich proteoglycans, biglycan and decorin, play pivotal roles in the regulation of these vital cellular pathways and, as such, are intrinsically involved in cancer initiation and progression. In this minireview, we will address novel functions of biglycan and decorin in inflammation and autophagy, and analyze new emerging signaling events triggered by these proteoglycans, which directly or indirectly modulate these processes. We will critically discuss the dual role of proteoglycan-driven inflammation and autophagy in tumor biology, and delineate the potential mechanisms through which soluble extracellular matrix constituents affect the microenvironment associated with inflammatory and neoplastic diseases.
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Affiliation(s)
- Liliana Schaefer
- Pharmazentrum Frankfurt/ZAFES, Institut für Allgemeine Pharmakologie und Toxikologie, Klinikum der Goethe-Universität Frankfurt am Main, Frankfurt am Main, Germany
| | - Claudia Tredup
- Pharmazentrum Frankfurt/ZAFES, Institut für Allgemeine Pharmakologie und Toxikologie, Klinikum der Goethe-Universität Frankfurt am Main, Frankfurt am Main, Germany
| | - Maria A. Gubbiotti
- Department of Pathology, Anatomy and Cell Biology, and the Cancer Cell Biology and Signaling Program, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, USA
| | - Renato V. Iozzo
- Department of Pathology, Anatomy and Cell Biology, and the Cancer Cell Biology and Signaling Program, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, USA
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50
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Xi T, Zhang G. Epigenetic regulation on the gene expression signature in esophagus adenocarcinoma. Pathol Res Pract 2016; 213:83-88. [PMID: 28049580 DOI: 10.1016/j.prp.2016.12.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 12/13/2016] [Accepted: 12/15/2016] [Indexed: 10/20/2022]
Abstract
BACKGROUND Understanding the molecular mechanisms represents an important step in the development of diagnostic and therapeutic measures of esophagus adenocarcinoma (NOS). The objective of this study is to identify the epigenetic regulation on gene expression in NOS, shedding light on the molecular mechanisms of NOS. METHODS In this study, 78 patients with NOS were included and the data of mRNA, miRNA and DNA methylation of were downloaded from The Cancer Genome Atlas (TCGA). Differential analysis between NOS and controls was performed in terms of gene expression, miRNA expression, and DNA methylation. Bioinformatic analysis was followed to explore the regulation mechanisms of miRNA and DNA methylationon gene expression. RESULTS Totally, up to 1320 differentially expressed genes (DEGs) and 32 differentially expressed miRNAs were identified. 240 DEGs that were not only the target genes but also negatively correlated with the screened differentially expressed miRNAs. 101 DEGs were found to be highlymethylated in CpG islands. Then, 8 differentially methylated genes (DMGs) were selected, which showed down-regulated expression in NOS. Among of these genes, 6 genes including ADHFE1, DPP6, GRIA4, CNKSR2, RPS6KA6 and ZNF135 were target genes of differentially expressed miRNAs (hsa-mir-335, hsa-mir-18a, hsa-mir-93, hsa-mir-106b and hsa-mir-21). CONCLUSIONS The identified altered miRNA, genes and DNA methylation site may be applied as biomarkers for diagnosis and prognosis of NOS.
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Affiliation(s)
- Ting Xi
- Department of Gastroenterology, People's Hospital of Liaocheng of Shandong Province, China.
| | - Guizhi Zhang
- Department of Gastroenterology, Second People's Hospital of Liaocheng of Shandong Province, China.
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