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Tsuriel S, Hannes V, Hasona A, Raz M, Hershkovitz D. Digital PCR-Based Method for Detecting CDKN2A Loss in Brain Tumours. Mol Diagn Ther 2022; 26:689-698. [PMID: 36129665 DOI: 10.1007/s40291-022-00610-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/01/2022] [Indexed: 12/30/2022]
Abstract
INTRODUCTION CDKN2A is a key tumour suppressor gene and loss of CDKN2A can be found in many tumours. In astrocytoma grade IV, CDKN2A is deleted in more than 50% of tumours. In many instances, low-grade gliomas with homozygous loss of CDKN2A behave like high grade tumours. The available techniques for CDKN2A loss are laborious, expensive, unreliable, or unavailable in most pathology institutes. Therefore, although it is essential for accurate brain tumour diagnosis, the routine diagnosis does not include testing for CDKN2A deletion. METHODS We developed a digital polymerase chain reaction (dPCR) assay for CDKN2A loss detection. The assay is based on counting the copy number of CDKN2A gene and of a reference gene on the same chromosome. It was tested for the detection limit with regard to tumour content and minimal DNA quantity. It was then tested on 24 clinical samples with known CDKN2A status. Additionally, we tested 44 gliomas with unknown CDKN2A status. RESULTS We found that the newly developed assay is reliable in tissue with more than 50% tumour content and more than 0.4 ng of DNA. The validation cohort showed complete concordance, and we were able to detect homozygous loss in 16 gliomas with unknown CDKN2A status. DISCUSSION The method presented can give a fast, cost-effective, clinically reliable evaluation of CDKN2A loss in tissue with more than 50% tumour content. Its ability to work with old samples and with low amounts of DNA makes it the favoured assay in cases where other techniques fail.
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Affiliation(s)
- Shlomo Tsuriel
- Institute of Pathology, Tel-Aviv Sourasky Medical Center, 62431, Tel-Aviv, Israel.
| | - Victoria Hannes
- Institute of Pathology, Tel-Aviv Sourasky Medical Center, 62431, Tel-Aviv, Israel
| | - Asala Hasona
- Institute of Pathology, Tel-Aviv Sourasky Medical Center, 62431, Tel-Aviv, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, 69978, Tel-Aviv, Israel
| | - Michal Raz
- Institute of Pathology, Tel-Aviv Sourasky Medical Center, 62431, Tel-Aviv, Israel
| | - Dov Hershkovitz
- Institute of Pathology, Tel-Aviv Sourasky Medical Center, 62431, Tel-Aviv, Israel.
- Sackler Faculty of Medicine, Tel-Aviv University, 69978, Tel-Aviv, Israel.
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Minter-Dykhouse K, Nelson TJ, Folmes CD. Uncoupling of Proliferative Capacity from Developmental Stage During Directed Cardiac Differentiation of Pluripotent Stem Cells. Stem Cells Dev 2022; 31:521-528. [PMID: 35726436 PMCID: PMC9641990 DOI: 10.1089/scd.2022.0041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 06/17/2022] [Indexed: 11/13/2022] Open
Abstract
Lineage-specific differentiation of human-induced pluripotent stem cells (hiPSCs) into cardiomyocytes (CMs) offers a patient-specific model to dissect development and disease pathogenesis in a dish. However, challenges exist with this model system, such as the relative immaturity of iPSC-derived CMs, which evoke the question of whether this model faithfully recapitulates in vivo cardiac development. As in vivo cardiac developmental stage is intimately linked with the proliferative capacity (or maturation is inversely correlated to proliferative capacity), we sought to understand how proliferation is regulated during hiPSC CM differentiation and how it compares with in vivo mouse cardiac development. Using standard Chemically Defined Media 3 differentiation, gene expression profiles demonstrate that hiPSC-derived cardiomyocytes (hiPSC-CMs) do not progress past the equivalent of embryonic day 14.5 of murine cardiac development. Throughout differentiation, overall DNA synthesis rapidly declines with <5% of hiPSC-CMs actively synthesizing DNA at the end of the differentiation period despite their immaturity. Bivariate cell cycle analysis demonstrated that hiPSC-CMs have a cell cycle profile distinct from their non-cardiac counterparts from the same differentiation, with significantly fewer cells within G1 and a marked accumulation of cells in G2/M than their non-cardiac counterparts throughout differentiation. Pulse-chase analysis demonstrated that non-cardiac cells progressed completely through the cell cycle within a 24-h period, whereas hiPSC-CMs had restricted progression with only a small proportion of cells undergoing cytokinesis with the remainder stalling in late S-phase or G2/M. This cell cycle arrest phenotype is associated with abbreviated expression of cell cycle promoting genes compared with expression throughout murine embryonic cardiac development. In summary, directed differentiation of hiPSCs into CMs uncouples the developmental stage from cell cycle regulation compared with in vivo mouse cardiac development, leading to a premature exit of hiPSC-CMs from the cell cycle despite their relative immaturity.
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Affiliation(s)
- Katherine Minter-Dykhouse
- Stem Cell and Regenerative Metabolism Laboratory, Departments of Cardiovascular Diseases, Biochemistry and Molecular Biology, and Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Scottsdale, Arizona, USA
| | - Timothy J. Nelson
- Todd and Karen Wanek Family Program for Hypoplastic Left Heart Syndrome, Departments of General Internal Medicine and Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, USA
| | - Clifford D.L. Folmes
- Address correspondence to: Clifford D. L. Folmes, PhD, Stem Cell and Regenerative Metabolism Laboratory, Departments of Cardiovascular Diseases, Biochemistry and Molecular Biology, Mayo Clinic, 13400 E Shea Boulevard, Scottsdale, AZ 85259, USA
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Cardoso JC, Ribeiro IP, Caramelo F, Tellechea O, Barbosa de Melo J, Marques Carreira I. Basal cell carcinomas of the scalp after radiotherapy for tinea capitis in childhood: A genetic and epigenetic study with comparison with basal cell carcinomas evolving in chronically sun-exposed areas. Exp Dermatol 2021; 30:1126-1134. [PMID: 33205471 DOI: 10.1111/exd.14237] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 10/10/2020] [Accepted: 11/11/2020] [Indexed: 12/14/2022]
Abstract
BACKGROUND Basal cell carcinoma (BCC) has been mostly associated with sun exposure, but ionizing radiation is also a known risk factor. It is not clear if the pathogenesis of BCC, namely at a genomic and epigenetic level, differs according to the underlying triggering factors. OBJECTIVE The present study aims to compare genetic and epigenetic changes in BCCs related to ionizing radiation and chronic sun exposure. METHODS Tumor samples from BCCs of the scalp in patients submitted to radiotherapy to treat tinea capitis in childhood and BCCs from sun-exposed areas were analysed through array comparative genomic hybridization (array-CGH) and methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) to detect copy number alterations and methylation status of specific genes. RESULTS Genomic characterization of tumor samples revealed several copy number gains and losses in all chromosomes, with the most frequent gains observed at 2p, 6p, 12p, 14q, 15q, 18q, Xp and Yp, and the most frequent losses observed at 3q, 14q, 16p, 17q, 22q, Xp, Yp and Yq. We developed a statistical model, encompassing gains in 3p and 16p and losses in 14q and 20p, with potential to discriminate BCC samples with sporadic aetiology from BCC samples that evolve after radiotherapy in childhood for the treatment of tinea capitis, which presented statistical significance (P = 0.003). Few methylated genes were detected through MS-MLPA, most frequently RARB and CD44. CONCLUSIONS Our study represents a step forward in the understanding of the genetic mechanisms underlying the pathogenesis of BCC and suggests potential differences according to the underlying ris k factors.
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Affiliation(s)
- José Carlos Cardoso
- Dermatology Department, Coimbra Hospital and University Centre, Coimbra, Portugal
| | - Ilda Patrícia Ribeiro
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, Coimbra, Portugal.,iCBR-CIMAGO - Center of Investigation on Environment, Genetics and Oncobiology - Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Francisco Caramelo
- Laboratory of Biostatistics and Medical Informatics, IBILI - Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Oscar Tellechea
- Dermatology Department, Coimbra Hospital and University Centre, Coimbra, Portugal
| | - Joana Barbosa de Melo
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, Coimbra, Portugal.,iCBR-CIMAGO - Center of Investigation on Environment, Genetics and Oncobiology - Faculty of Medicine, University of Coimbra, Coimbra, Portugal.,CNC, IBILI, Group of Aging and Brain Diseases: Advanced Diagnosis and Biomarkers, Coimbra, Portugal
| | - Isabel Marques Carreira
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, Coimbra, Portugal.,iCBR-CIMAGO - Center of Investigation on Environment, Genetics and Oncobiology - Faculty of Medicine, University of Coimbra, Coimbra, Portugal.,CNC, IBILI, Group of Aging and Brain Diseases: Advanced Diagnosis and Biomarkers, Coimbra, Portugal
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Gera R, Mokbel L, Jiang WG, Mokbel K. mRNA Expression of CDK2AP1 in Human Breast Cancer: Correlation with Clinical and Pathological Parameters. Cancer Genomics Proteomics 2018; 15:447-452. [PMID: 30343278 DOI: 10.21873/cgp.20103] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 09/11/2018] [Accepted: 09/13/2018] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Cyclin-dependent kinase 2-associated protein 1 (CDK2AP1) interacts with CDK2AP2, modulates the actions of transforming growth factor-B1, cyclin-dependent kinase 2 and retinoblastoma protein, and closely interacts with micro-RNA21 and micro-RNA25. Our objective was to determine if CDK2AP1 mRNA expression levels were consistent with tumour-suppressive functions in breast cancer. MATERIALS AND METHODS A total of 134 samples were analysed. CDK2AP1 mRNA levels were measured using quantitative polymerase chain reaction (RT-PCR) and normalised against glyceraldehyde 3-phosphate dehydrogenase mRNA. Levels in breast cancer and adjacent non-cancerous breast tissue were analysed against pathological and clinical parameters (TNM staging, survival over a 10-year follow-up period). RESULTS Normalised CDK2AP1 expression was 38-fold higher in adjacent non-cancerous breast tissue than in breast cancer. CDK2AP1 expression in disease-free patients at 10 years was more than threefold that of patients who died of breast cancer. However, neither of these differences in expression levels reached statistical significance. CDK2AP1 mRNA levels were higher in TNM1 compared to TNM3 (p=0.016) and with TNM4 (p=0.016). There were no significant associations between CDK2AP1 expression and estrogen receptor status, tumour grade and tumour type. There was no significant difference in overall survival between patients with high and those with low CDK2AP1 mRNA levels after a median follow-up of 10 years (Kaplan-Meier analysis, p=0.872). CONCLUSION To our knowledge, this is the first study in the literature to examine the mRNA expression of CDK2AP1 in human breast cancer over a long-term follow-up period. A compelling relationship exists between high CDK2AP1 mRNA expression and lower TNM classification of breast cancer, which is consistent with CDK2AP1 having a tumour-suppressive function.
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Affiliation(s)
- Ritika Gera
- The London Breast Institute, The Princess Grace Hospital, London, U.K
| | - Leon Mokbel
- The London Breast Institute, The Princess Grace Hospital, London, U.K
| | - Wen G Jiang
- Metastasis & Angiogenesis Research Group, University Department of Surgery, Cardiff University School of Medicine, Cardiff University, Cardiff, U.K
| | - Kefah Mokbel
- The London Breast Institute, The Princess Grace Hospital, London, U.K.
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Inhibition of MDM2 via Nutlin-3A: A Potential Therapeutic Approach for Pleural Mesotheliomas with MDM2-Induced Inactivation of Wild-Type P53. JOURNAL OF ONCOLOGY 2018; 2018:1986982. [PMID: 30112000 PMCID: PMC6077509 DOI: 10.1155/2018/1986982] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 05/23/2018] [Accepted: 06/11/2018] [Indexed: 12/12/2022]
Abstract
Previously, our group demonstrated that nuclear expression of E3 ubiquitin ligase (MDM2) in malignant pleural mesothelioma (MPM) is significantly associated with decreased overall survival. A possible explanation may be that overexpression of MDM2 leads to a proteasomal degradation of TP53 that eventually results in a loss of TP53-induced apoptosis and senescence. It is well known from other tumor entities that restoration of TP53 activity, e.g., by MDM2 inhibition, results in an instant TP53-induced stress and/or DNA damage response of cancer cells. Nutlin-3A (a cis-imidazoline analogue) has been described as a potent and selective MDM2 inhibitor preventing MDM2-TP53-interaction by specific binding to the hydrophobic TP53-binding pocket of MDM2. In the present study, the effects of MDM2 inhibition in MPM via Nutlin-3A and standard platinum based chemotherapeutic agents were comparatively tested in three MPM cell lines (NCI-H2052, MSTO-211H, and NCI-H2452) showing different expression profiles of TP53, MDM2, and its physiological inhibitor of MDM2—P14/ARF. Our in vitro experiments on MPM cell lines revealed that Nutlin-3A in combination with cisplatin resulted in up to 9.75 times higher induction of senescence (p=0.0050) and up to 5 times higher apoptosis rate (p=0.0067) compared to the commonly applied cisplatin and pemetrexed regimens. Thus Nutlin-3A, a potent inhibitor of MDM2, is associated with a significant induction of senescence and apoptosis in MPM cell lines, making Nutlin-3A a promising substance for a targeted therapy in the subgroup of MPM showing MDM2 overexpression.
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Basal Cell Carcinoma With Matrical Differentiation: Clinicopathologic, Immunohistochemical, and Molecular Biological Study of 22 Cases. Am J Surg Pathol 2017; 41:738-749. [PMID: 28368926 DOI: 10.1097/pas.0000000000000841] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Basal cell carcinoma (BCC) with matrical differentiation is a fairly rare neoplasm, with about 30 cases documented mainly as isolated case reports. We studied a series of this neoplasm, including cases with an atypical matrical component, a hitherto unreported feature. Lesions coded as BCC with matrical differentiation were reviewed; 22 cases were included. Immunohistochemical studies were performed using antibodies against BerEp4, β-catenin, and epithelial membrane antigen (EMA). Molecular genetic studies using Ion AmpliSeq Cancer Hotspot Panel v2 by massively parallel sequencing on Ion Torrent PGM were performed in 2 cases with an atypical matrical component (1 was previously subjected to microdissection to sample the matrical and BCC areas separately). There were 13 male and 9 female patients, ranging in age from 41 to 89 years. Microscopically, all lesions manifested at least 2 components, a BCC area (follicular germinative differentiation) and areas with matrical differentiation. A BCC component dominated in 14 cases, whereas a matrical component dominated in 4 cases. Matrical differentiation was recognized as matrical/supramatrical cells (n=21), shadow cells (n=21), bright red trichohyaline granules (n=18), and blue-gray corneocytes (n=18). In 2 cases, matrical areas manifested cytologic atypia, and a third case exhibited an infiltrative growth pattern, with the tumor metastasizing to a lymph node. BerEP4 labeled the follicular germinative cells, whereas it was markedly reduced or negative in matrical areas. The reverse pattern was seen with β-catenin. EMA was negative in BCC areas but stained a proportion of matrical/supramatrical cells. Genetic studies revealed mutations of the following genes: CTNNB1, KIT, CDKN2A, TP53, SMAD4, ERBB4, and PTCH1, with some differences between the matrical and BCC components. It is concluded that matrical differentiation in BCC in most cases occurs as multiple foci. Rare neoplasms manifest atypia in the matrical areas. Immunohistochemical analysis for BerEP4, EMA, and β-catenin can be helpful in limited biopsy specimens. From a molecular biological prospective, BCC and matrical components appear to share some of the gene mutations but have differences in others, but this observation must be validated in a large series.
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D'Arcangelo D, Tinaburri L, Dellambra E. The Role of p16 INK4a Pathway in Human Epidermal Stem Cell Self-Renewal, Aging and Cancer. Int J Mol Sci 2017; 18:ijms18071591. [PMID: 28737694 PMCID: PMC5536078 DOI: 10.3390/ijms18071591] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 07/13/2017] [Accepted: 07/19/2017] [Indexed: 12/31/2022] Open
Abstract
The epidermis is a self-renewing tissue. The balance between proliferation and differentiation processes is tightly regulated to ensure the maintenance of the stem cell (SC) population in the epidermis during life. Aging and cancer may be considered related endpoints of accumulating damages within epidermal self-renewing compartment. p16INK4a is a potent inhibitor of the G1/S-phase transition of the cell cycle. p16INK4a governs the processes of SC self-renewal in several tissues and its deregulation may result in aging or tumor development. Keratinocytes are equipped with several epigenetic enzymes and transcription factors that shape the gene expression signatures of different epidermal layers and allow dynamic and coordinated expression changes to finely balance keratinocyte self-renewal and differentiation. These factors converge their activity in the basal layer to repress p16INK4a expression, protecting cells from senescence, and preserving epidermal homeostasis and regeneration. Several stress stimuli may activate p16INK4a expression that orchestrates cell cycle exit and senescence response. In the present review, we discuss the role of p16INK4a regulators in human epidermal SC self-renewal, aging and cancer.
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Affiliation(s)
- Daniela D'Arcangelo
- Laboratory of Vascular Pathology, Istituto Dermopatico dell'Immacolata, Istituto di Ricovero e Cura a Carattere Scientifico (IDI-IRCCS), Fondazione Luigi Maria Monti (FLMM), via Monti di Creta 104, 00167 Rome, Italy.
| | - Lavinia Tinaburri
- Molecular and Cell Biology Laboratory, Istituto Dermopatico dell'Immacolata, Istituto di Ricovero e Cura a Carattere Scientifico (IDI-IRCCS), Fondazione Luigi Maria Monti (FLMM), via Monti di Creta 104, 00167 Rome, Italy.
| | - Elena Dellambra
- Molecular and Cell Biology Laboratory, Istituto Dermopatico dell'Immacolata, Istituto di Ricovero e Cura a Carattere Scientifico (IDI-IRCCS), Fondazione Luigi Maria Monti (FLMM), via Monti di Creta 104, 00167 Rome, Italy.
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Mairinger FD, Werner R, Flom E, Schmeller J, Borchert S, Wessolly M, Wohlschlaeger J, Hager T, Mairinger T, Kollmeier J, Christoph DC, Schmid KW, Walter RFH. miRNA regulation is important for DNA damage repair and recognition in malignant pleural mesothelioma. Virchows Arch 2017; 470:627-637. [PMID: 28466156 DOI: 10.1007/s00428-017-2133-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 04/10/2017] [Accepted: 04/13/2017] [Indexed: 01/06/2023]
Abstract
Platin-containing regimes are currently considered as state-of-the-art therapies in malignant pleural mesotheliomas (MPM) but show dissatisfying response rates ranging from 6 to 16% only. Still, the reasons for the rather poor efficacy remain largely unknown. A clear stratification of patients based on new biomarkers seems to be a promising approach to enhance clinical management, which would be a long-needed improvement for MPM patients but does not seem likely soon unless new biomarkers can be validated. Twenty-four formalin-fixed, paraffin-embedded (FFPE) tumour specimens were subjected to a miRNA expression screening of 800 important miRNAs using digital quantification via the nCounter technique (NanoString). We defined a small subset of miRNAs regulating the key enzymes involved in the repair of platin-associated DNA damage. Particularly, the TP53 pathway network for DNA damage recognition as well as genes related to the term "BRCAness" are the main miRNA targets within this context. The TP53 pathway network for DNA damage recognition as well as genes related to the term "BRCAness" are the main players for risk stratification in patients suffering from this severe disease. Taking the specific molecular profile of the tumour into account can help to enhance the clinical management prospectively and to smooth the way to better response prediction.
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Affiliation(s)
- Fabian Dominik Mairinger
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Hufelandstraße 55, 45147, Essen, Germany.
| | - Robert Werner
- Institute of Pathology, Helios Klinikum Emil von Behring, Berlin, Germany
| | - Elena Flom
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Hufelandstraße 55, 45147, Essen, Germany
| | - Jan Schmeller
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Hufelandstraße 55, 45147, Essen, Germany
| | - Sabrina Borchert
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Hufelandstraße 55, 45147, Essen, Germany
| | - Michael Wessolly
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Hufelandstraße 55, 45147, Essen, Germany
| | - Jeremias Wohlschlaeger
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Hufelandstraße 55, 45147, Essen, Germany
| | - Thomas Hager
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Hufelandstraße 55, 45147, Essen, Germany
| | - Thomas Mairinger
- Institute of Pathology, Helios Klinikum Emil von Behring, Berlin, Germany
| | - Jens Kollmeier
- Institute of Pneumology, Helios Klinikum Emil von Behring, Berlin, Germany
| | - Daniel Christian Christoph
- Department of Medical Oncology, West German Cancer Centre, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Kurt Werner Schmid
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Hufelandstraße 55, 45147, Essen, Germany
| | - Robert Fred Henry Walter
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Hufelandstraße 55, 45147, Essen, Germany.,Ruhrlandklinik, West German Lung Centre, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
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Differing tumor-suppressor functions of Arf and p53 in murine basal cell carcinoma initiation and progression. Oncogene 2017; 36:3772-3780. [PMID: 28263978 DOI: 10.1038/onc.2017.12] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 01/15/2017] [Accepted: 01/18/2017] [Indexed: 12/21/2022]
Abstract
Human basal cell carcinomas (BCCs) very frequently carry p53 mutations, and p53 loss markedly accelerates murine BCC carcinogenesis. We report here our studies of the mechanism by which p53 is activated to suppress BCC carcinogenesis. We find that aberrant hedgehog signaling in microscopic BCCs activates p53 in part via Arf (that is, the oncogene-induced stress pathway) but not via the DNA damage response pathway. However, Arf loss and p53 loss produce differing outcomes-loss of p53 promotes both tumor initiation and progression; loss of Arf promotes tumor progression but not initiation. Intriguingly, increased expression of Arf in tumor stromal cells, as in tumor keratinocytes themselves, contributes to suppression of BCC carcinogenesis.
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Walter RFH, Vollbrecht C, Werner R, Wohlschlaeger J, Christoph DC, Schmid KW, Mairinger FD. microRNAs are differentially regulated between MDM2-positive and negative malignant pleural mesothelioma. Oncotarget 2017; 7:18713-21. [PMID: 26918730 PMCID: PMC4951323 DOI: 10.18632/oncotarget.7666] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 02/02/2016] [Indexed: 12/14/2022] Open
Abstract
Background Malignant pleural mesothelioma (MPM) is a highly aggressive tumour first-line treated with a combination of cisplatin and pemetrexed. MDM2 and P14/ARF (CDKN2A) are upstream regulators of TP53 and may contribute to its inactivation. In the present study, we now aimed to define the impact of miRNA expression on this mechanism. Material and Methods 24 formalin-fixed paraffin-embedded (FFPE) tumour specimens were used for miRNA expression analysis of the 800 most important miRNAs using the nCounter technique (NanoString). Significantly deregulated miRNAs were identified before a KEGG-pathway analysis was performed. Results 17 miRNAs regulating TP53, 18 miRNAs regulating MDM2, and 11 miRNAs directly regulating CDKN2A are significantly downregulated in MDM2-expressing mesotheliomas. TP53 is downregulated in MDM2-negative tumours through miRNAs with a miSVR prediction score of 11.67, RB1 with a prediction score of 8.02, MDM2 with a prediction score of 4.50 and CDKN2A with a prediction score of 1.27. Conclusion MDM2 expression seems to impact miRNA expression levels in MPM. Especially, miRNAs involved in TP53-signaling are strongly decreased in MDM2-positive mesotheliomas. A better understanding of its tumour biology may open the chance for new therapeutic approaches and thereby augment patients' outcome.
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Affiliation(s)
- Robert Fred Henry Walter
- Ruhrlandklinik, West German Lung Centre, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.,Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Claudia Vollbrecht
- Institute of Pathology, University Hospital Cologne, Germany.,Institute of Pathology, Division of Molecular Pathology, Charité, Berlin, Germany
| | - Robert Werner
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Jeremias Wohlschlaeger
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Daniel Christian Christoph
- Department of Medical Oncology, West German Cancer Centre, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Kurt Werner Schmid
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Fabian Dominik Mairinger
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.,Institute of Pathology, Division of Molecular Pathology, Charité, Berlin, Germany
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Vand-Rajabpour F, Sadeghipour N, Saee-Rad S, Fathi H, Noormohammadpour P, Yaseri M, Hesari KK, Bagherpour Z, Tabrizi M. Differential BMI1, TWIST1, SNAI2 mRNA expression pattern correlation with malignancy type in a spectrum of common cutaneous malignancies: basal cell carcinoma, squamous cell carcinoma, and melanoma. Clin Transl Oncol 2016; 19:489-497. [PMID: 27718152 DOI: 10.1007/s12094-016-1555-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Accepted: 09/22/2016] [Indexed: 02/01/2023]
Abstract
PURPOSE Melanoma, squamous cell carcinoma (SCC), and basal cell carcinoma (BCC) can be used as a unique model to identify molecular mechanisms to distinguish rarely metastatic (BCC), often metastatic (SCC) and most metastatic (melanoma) cancer. It is known that epithelial-mesenchymal transition and stemness transcription factors (TWIST1, SNAI2/SLUG, and BMI1) play an important role in metastasis and their dysregulation has been demonstrated in metastatic cancers. We hypothesized that this spectrum of cutaneous cancers (BCC, SCC, and melanoma) would be a unique cancer model system to elucidate steps toward cancer invasion and metastasis. METHODS We evaluated the mRNA expression level of BMI1, TWIST1, and SNAI2/SLUG and studied clinicopathological features in 170 skin cancers along with normal tissue samples. RESULTS We demonstrate downregulation of BMI1 mRNA expression in BCC samples compared with controls (p = 0.0001), SCC (p = 0.001), and melanoma (p = 0.0001) samples. Downregulation of TWIST1 mRNA expression is seen in only BCC samples compared with controls (p = 0.031). High SNAI2 mRNA expression is represented in melanoma samples compared with controls (p = 0.022) and SCC samples (p = 0.031). High mRNA expression of TWIST1 is seen in patients with positive history of cancers. Extremely low mRNA expression of BMI1 is detected in patients with positive history of cancers other than skin cancer. CONCLUSIONS These findings provide support for the hypothesis that the spectrum of cutaneous cancers could be better understood as a series of gene dosage-dependent entities with distinct molecular events. Oncogene-induced senescence, mechanism of which is still unclear, could be one explanation for these results.
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Affiliation(s)
- F Vand-Rajabpour
- Medical Genetics Department, School of Medicine, Tehran University of Medical Sciences, P.O. Box 14155-6447, Tehran, 14176-13151, Iran
| | - N Sadeghipour
- Medical Genetics Department, School of Medicine, Tehran University of Medical Sciences, P.O. Box 14155-6447, Tehran, 14176-13151, Iran
| | - S Saee-Rad
- Dietary Supplements and Probiotic Research Center, Alborz University of Medical Sciences, Karaj, Iran
| | - H Fathi
- Plastic, Reconstructive and Aesthetic Surgery Department, Imam Khomeini Hospital, Tehran University of Medical Sciences, Tehran, Iran.,Tumor Clinic, Pathology Department and the Department of Plastic and Reconstructive Surgery, Razi Dermatology Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - P Noormohammadpour
- Tumor Clinic, Pathology Department and the Department of Plastic and Reconstructive Surgery, Razi Dermatology Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - M Yaseri
- Epidemiology and Biostatistics Department, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - K K Hesari
- Tumor Clinic, Pathology Department and the Department of Plastic and Reconstructive Surgery, Razi Dermatology Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Z Bagherpour
- Medical Genetics Department, School of Medicine, Tehran University of Medical Sciences, P.O. Box 14155-6447, Tehran, 14176-13151, Iran
| | - M Tabrizi
- Medical Genetics Department, School of Medicine, Tehran University of Medical Sciences, P.O. Box 14155-6447, Tehran, 14176-13151, Iran.
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12
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Walter RFH, Vollbrecht C, Werner R, Mairinger T, Schmeller J, Flom E, Wohlschlaeger J, Barbetakis N, Paliouras D, Chatzinikolaou F, Adamidis V, Tsakiridis K, Zarogoulidis P, Trakada G, Christoph DC, Schmid KW, Mairinger FD. Screening of Pleural Mesotheliomas for DNA-damage Repair Players by Digital Gene Expression Analysis Can Enhance Clinical Management of Patients Receiving Platin-Based Chemotherapy. J Cancer 2016; 7:1915-1925. [PMID: 27698933 PMCID: PMC5039377 DOI: 10.7150/jca.16390] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Accepted: 08/14/2016] [Indexed: 12/23/2022] Open
Abstract
Background: Malignant pleural mesothelioma (MPM) is a rare, predominantly asbestos-related and biologically highly aggressive tumour leading to a dismal prognosis. Multimodality therapy consisting of platinum-based chemotherapy is the treatment of choice. The reasons for the rather poor efficacy of platinum compounds remain largely unknown. Material and Methods: For this exploratory mRNA study, 24 FFPE tumour specimens were screened by digital gene expression analysis. Based on data from preliminary experiments and recent literature, a total of 366 mRNAs were investigated using a Custom CodeSet from NanoString. All statistical analyses were calculated with the R i386 statistical programming environment. Results: CDC25A and PARP1 gene expression were correlated with lymph node spread, BRCA1 and TP73 expression levels with higher IMIG stage. NTHL1 and XRCC3 expression was associated with TNM stage. CHECK1 as well as XRCC2 expression levels were correlated with tumour progression in the overall cohort of patients. CDKN2A and MLH1 gene expression influenced overall survival in this collective. In the adjuvant treated cohort only, CDKN2A, CHEK1 as well as ERCC1 were significantly associated with overall survival. Furthermore, TP73 expression was associated with progression in this subgroup. Conclusion: DNA-damage response plays a crucial role in response to platin-based chemotherapeutic regimes. In particular, CHEK1, XRCC2 and TP73 are strongly associated with tumour progression. ERCC1, MLH1, CDKN2A and most promising CHEK1 are prognostic markers for OS in MPM. TP73, CDKN2A, CHEK1 and ERCC1 seem to be also predictive markers in adjuvant treated MPMs. After a prospective validation, these markers may improve clinical and pathological practice, finally leading to a patients' benefit by an enhanced clinical management.
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Affiliation(s)
- Robert Fred Henry Walter
- Ruhrlandklinik, West German Lung Centre, University Hospital Essen, University of Duisburg-Essen, Essen, Germany;; Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Claudia Vollbrecht
- Institute of Pathology, Division of Molecular Pathology, Charité, Berlin, Germany
| | - Robert Werner
- Department of Pathology, Helios Klinikum Emil von Behring, Berlin Germany
| | - Thomas Mairinger
- Department of Pathology, Helios Klinikum Emil von Behring, Berlin Germany
| | - Jan Schmeller
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Elena Flom
- Ruhrlandklinik, West German Lung Centre, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Jeremias Wohlschlaeger
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany;; Institute of Pathology, Ev.-Luth. Diakonissenkrankenhaus Flensburg, Flensburg, Germany
| | - Nikolaos Barbetakis
- Thoracic Surgery Department, Theagenio Cancer Hospital, Thessaloniki, Greece
| | - Dimitrios Paliouras
- Thoracic Surgery Department, Theagenio Cancer Hospital, Thessaloniki, Greece
| | | | - Vasilis Adamidis
- Pulmonary Department-Oncology Unit, "G. Papanikolaou" General Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Kosmas Tsakiridis
- Pulmonary Department-Oncology Unit, "G. Papanikolaou" General Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Paul Zarogoulidis
- Pulmonary Department-Oncology Unit, "G. Papanikolaou" General Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Georgia Trakada
- Division of Pulmonology, Department of Clinical Therapeutics, National and Kapodistrian University of Athens School of Medicine, Alexandra Hospital, Athens, Greece
| | | | - Kurt Werner Schmid
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
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13
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Chan WH, Mohamad MS, Deris S, Zaki N, Kasim S, Omatu S, Corchado JM, Al Ashwal H. Identification of informative genes and pathways using an improved penalized support vector machine with a weighting scheme. Comput Biol Med 2016; 77:102-15. [PMID: 27522238 DOI: 10.1016/j.compbiomed.2016.08.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 08/03/2016] [Accepted: 08/03/2016] [Indexed: 01/03/2023]
Abstract
Incorporation of pathway knowledge into microarray analysis has brought better biological interpretation of the analysis outcome. However, most pathway data are manually curated without specific biological context. Non-informative genes could be included when the pathway data is used for analysis of context specific data like cancer microarray data. Therefore, efficient identification of informative genes is inevitable. Embedded methods like penalized classifiers have been used for microarray analysis due to their embedded gene selection. This paper proposes an improved penalized support vector machine with absolute t-test weighting scheme to identify informative genes and pathways. Experiments are done on four microarray data sets. The results are compared with previous methods using 10-fold cross validation in terms of accuracy, sensitivity, specificity and F-score. Our method shows consistent improvement over the previous methods and biological validation has been done to elucidate the relation of the selected genes and pathway with the phenotype under study.
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Affiliation(s)
- Weng Howe Chan
- Artificial Intelligence and Bioinformatics Research Group, Faculty of Computing, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia
| | - Mohd Saberi Mohamad
- Artificial Intelligence and Bioinformatics Research Group, Faculty of Computing, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia.
| | - Safaai Deris
- Faculty of Creative Technology & Heritage, Universiti Malaysia Kelantan, Locked Bag 01, Bachok, 16300 Kota Bharu, Kelantan, Malaysia
| | - Nazar Zaki
- College of Information Technology, United Arab Emirate University, Al Ain 15551, United Arab Emirates
| | - Shahreen Kasim
- Faculty of Computer Science and Information Technology, Universiti Tun Hussein Onn Malaysia, 86400 Batu Pahat, Malaysia
| | - Sigeru Omatu
- Department of Electronics, Information and Communication Engineering, Osaka Institute of Technology, Osaka 535-8585, Japan
| | - Juan Manuel Corchado
- Biomedical Research Institute of Salamanca/BISITE Research Group, University of Salamanca, Salamanca, Spain
| | - Hany Al Ashwal
- College of Information Technology, United Arab Emirate University, Al Ain 15551, United Arab Emirates
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14
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Expression Analysis of Genes Involved in the RB/E2F Pathway in Astrocytic Tumors. PLoS One 2015; 10:e0137259. [PMID: 26317630 PMCID: PMC4552853 DOI: 10.1371/journal.pone.0137259] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 08/13/2015] [Indexed: 02/08/2023] Open
Abstract
Astrocytic gliomas, which are derived from glial cells, are considered the most common primary neoplasias of the central nervous system (CNS) and are histologically classified as low grade (I and II) or high grade (III and IV). Recent studies have shown that astrocytoma formation is the result of the deregulation of several pathways, including the RB/E2F pathway, which is commonly deregulated in various human cancers via genetic or epigenetic mechanisms. On the basis of the assumption that the study of the mechanisms controlling the INK4/ARF locus can help elucidate the molecular pathogenesis of astrocytic tumors, identify diagnostic and prognostic markers, and help select appropriate clinical treatments, the present study aimed to evaluate and compare methylation patterns using bisulfite sequencing PCR and evaluate the gene expression profile using real-time PCR in the genes CDKN2A, CDKN2B, CDC6, Bmi-1, CCND1, and RB1 in astrocytic tumors. Our results indicate that all the evaluated genes are not methylated independent of the tumor grade. However, the real-time PCR results indicate that these genes undergo progressive deregulation as a function of the tumor grade. In addition, the genes CDKN2A, CDKN2B, and RB1 were underexpressed, whereas CDC6, Bmi-1, and CCND1 were overexpressed; the increase in gene expression was significantly associated with decreased patient survival. Therefore, we propose that the evaluation of the expression levels of the genes involved in the RB/E2F pathway can be used in the monitoring of patients with astrocytomas in clinical practice and for the prognostic indication of disease progression.
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15
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Abstract
Human papilloma virus (HPV)-associated head and neck carcinoma is quite heterogeneous and most of the tumors arise in the oral cavity, oropharynx, hypopharynx and larynx. HPV was just recently recognized as an emerging risk factor for oropharyngeal squamous cell carcinoma (OSCC). HPV(+) tumors represent 5-20% of all head and neck squamous-cell carcinomas (HNSCCs) and 40-90% of those arising from the oropharynx, with widely variable rates depending on the geographic area, population, relative prevalence of environment-related SCC and detection assay. Different carcinogenic mechanisms are most likely implicated in cervical and oropharyngeal carcinogenesis. The most certain carcinogenic genotype for the head and neck region and the most common high-risk HPV genotype, HPV-16, is frequently detected in OSCC. A combination of p16INK4A expression and molecular detection of HPV DNA is the gold standard for the viral identification in tissue and exfoliated cell samples. Differences in the biology of HPV(+) and HPV(-) OSCC may have implications for the management of patients. New immunotherapy drugs based on the release of the co-inhibitory receptors, cytotoxic T-lymphocyte-associated antigen 4 (CTLA-4) and programmed-death 1 (PD-1) have currently emerged. The goal of therapeutic cancer vaccination is inculcation of a persistent, tumor antigen-specific T cell response which kills tumor cells. The efficacy of the current HPV vaccines, Cervarix and Gardasil, in preventing HPV-related HNSCC is at present unknown. Treatment de-escalation is recommended as the current management of HPV-induced HNSCCs.
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Affiliation(s)
- Apostolos Zaravinos
- Molecular Medicine Research Center and Laboratory of Molecular and Medical Genetics, Department of Biological Sciences, University of Cyprus, 1678 Nicosia, Cyprus. Division of Clinical Immunology and Transfusion Medicine, Department of Laboratory Medicine, Karolinska Institutet, 14145 Huddinge, Sweden
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16
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Walter RFH, Mairinger FD, Ting S, Vollbrecht C, Mairinger T, Theegarten D, Christoph DC, Schmid KW, Wohlschlaeger J. MDM2 is an important prognostic and predictive factor for platin-pemetrexed therapy in malignant pleural mesotheliomas and deregulation of P14/ARF (encoded by CDKN2A) seems to contribute to an MDM2-driven inactivation of P53. Br J Cancer 2015; 112:883-90. [PMID: 25668009 PMCID: PMC4453955 DOI: 10.1038/bjc.2015.27] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 01/01/2015] [Accepted: 01/12/2015] [Indexed: 12/28/2022] Open
Abstract
Background: Malignant pleural mesothelioma (MPM) is a highly aggressive tumour that is
first-line treated with a combination of cisplatin and pemetrexed. Until
now, predictive and prognostic biomarkers are lacking, making it a
non-tailored therapy regimen with unknown outcome. P53 is frequently
inactivated in MPM, but mutations are extremely rare. MDM2 and P14/ARF
are upstream regulators of P53 that may contribute to P53 inactivation. Methods: A total of 72 MPM patients were investigated. MDM2 immunoexpression was
assessed in 65 patients. MDM2 and P14/ARF mRNA
expression was analysed in 48 patients of the overall collective. The
expression results were correlated to overall survival (OS) and
progression-free survival (PFS). Results: OS and PFS correlated highly significantly with MDM2 mRNA and protein
expression, showing a dismal prognosis for patients with elevated MDM2
expression (for OS: Score (logrank) test: P⩽0.002, and for PFS:
Score (logrank) test; P<0.007). MDM2 was identified as robust
prognostic and predictive biomarker for MPM on the mRNA and protein level.
P14/ARF mRNA expression reached no statistical
significance, but Kaplan–Meier curves distinguished patients with low
P14/ARF expression and hence shorter survival from patients
with higher expression and prolonged survival. Conclusions: MDM2 is a prognostic and predictive marker for a platin–pemetrexed
therapy of patients with MPMs. Downregulation of P14/ARF expression
seems to contribute to MDM2-overexpression-mediated P53 inactivation in MPM
patients.
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Affiliation(s)
- R F H Walter
- 1] Ruhrlandklinik, West German Lung Center, University Hospital Essen, University of Duisburg-Essen, Tüschener Weg 40, Essen D-45239, Germany [2] Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - F D Mairinger
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - S Ting
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - C Vollbrecht
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
| | - T Mairinger
- Department of Pathology, Helios Klinikum Emil von Behring, Berlin, Germany
| | - D Theegarten
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
| | - D C Christoph
- 1] Department of Medical Oncology, West German Cancer Center, University Hospital Essen, University of Duisburg-Essen, Essen, Germany [2] Department of Medicine, Division of Medical Oncology, University of Colorado Denver, Aurora, CO, USA
| | - K W Schmid
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - J Wohlschlaeger
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
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17
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Zhang A, Gao C, Han X, Wang L, Yu C, Zeng X, Chen L, Li D, Chen W. Inactivation of p15 INK4b in chronic arsenic poisoning cases. Toxicol Rep 2014; 1:692-698. [PMID: 28962283 PMCID: PMC5598098 DOI: 10.1016/j.toxrep.2014.08.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Revised: 07/30/2014] [Accepted: 08/13/2014] [Indexed: 11/27/2022] Open
Abstract
Arsenic exposure from burning high arsenic-containing coal has been associated with human skin lesion and cancer. However, the mechanisms of arsenic-related carcinogenesis are not fully understood. Inactivation of critical tumor suppression genes by epigenetic regulation or genetic modification might contribute to arsenic-induced carcinogenicity. This study aims to clarify the correlation between arsenic pollution and functional defect of p15INK4b gene in arsenic exposure residents from a region of Guizhou Province, China. To this end, 103 arsenic exposure residents and 105 control subjects were recruited in this study. The results showed that the exposure group exhibited higher levels of urinary and hair arsenic compared with the control group (55.28 vs 28.87 μg/L, 5.16 vs 1.36 μg/g). Subjects with higher arsenic concentrations are more likely to have p15INK4b methylation and gene deletion (χ2 = 4.28, P = 0.04 and χ2 = 4.31, P = 0.04). We also found that the degree of p15INK4b hypermethylation and gene deletion occurred at higher incidence in the poisoning cases with skin cancer (3.7% and 14.81% in non-skin cancer group, 41.18% and 47.06 in skin cancer group), and were significantly associated with the stage of skin lesions (χ2 = 12.82, P < 0.01 and χ2 = 7.835, P = 0.005). These observations indicate that inactivation of p15INK4b through genetic alteration or epigenetic modification is a common event that is associated with arsenic exposure and the development of arsenicosis.
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Affiliation(s)
- Aihua Zhang
- Department of Toxicology, School of Public Health, Guiyang Medical University, Guiyang 550004, China
| | - Chen Gao
- Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Xue Han
- Department of Toxicology, School of Public Health, Guiyang Medical University, Guiyang 550004, China
| | - Lifang Wang
- Department of Toxicology, School of Public Health, Guiyang Medical University, Guiyang 550004, China
| | - Chun Yu
- Department of Toxicology, School of Public Health, Guiyang Medical University, Guiyang 550004, China
| | - Xiaowen Zeng
- Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Liping Chen
- Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Daochuan Li
- Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Wen Chen
- Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
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18
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Kraft S, Granter SR. Molecular pathology of skin neoplasms of the head and neck. Arch Pathol Lab Med 2014; 138:759-87. [PMID: 24878016 DOI: 10.5858/arpa.2013-0157-ra] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT Skin neoplasms include the most common malignancies affecting humans. Many show an ultraviolet (UV)-induced pathogenesis and often affect the head and neck region. OBJECTIVE To review literature on cutaneous neoplasms that show a predilection for the head and neck region and that are associated with molecular alterations. DATA SOURCES Literature review. CONCLUSIONS Common nonmelanoma skin cancers, such as basal and squamous cell carcinomas, show a UV-induced pathogenesis. Basal cell carcinomas are characterized by molecular alterations of the Hedgehog pathway, affecting patched and smoothened genes. While squamous cell carcinomas show UV-induced mutations in several genes, driver mutations are only beginning to be identified. In addition, certain adnexal neoplasms also predominantly affect the head and neck region and show interesting, recently discovered molecular abnormalities, or are associated with hereditary conditions whose molecular genetic pathogenesis is well understood. Furthermore, recent advances have led to an increased understanding of the molecular pathogenesis of melanoma. Certain melanoma subtypes, such as lentigo maligna melanoma and desmoplastic melanoma, which are more often seen on the chronically sun-damaged skin of the head and neck, show differences in their molecular signature when compared to the other more common subtypes, such as superficial spreading melanoma, which are more prone to occur at sites with acute intermittent sun damage. In summary, molecular alterations in cutaneous neoplasms of the head and neck are often related to UV exposure. Their molecular footprint often reflects the histologic tumor type, and familiarity with these changes will be increasingly necessary for diagnostic and therapeutic considerations.
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Affiliation(s)
- Stefan Kraft
- From the Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts (Dr Kraft); and the Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts (Dr Granter)
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19
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Zaravinos A, Pieri M, Mourmouras N, Anastasiadou N, Zouvani I, Delakas D, Deltas C. Altered metabolic pathways in clear cell renal cell carcinoma: A meta-analysis and validation study focused on the deregulated genes and their associated networks. Oncoscience 2014; 1:117-31. [PMID: 25594006 PMCID: PMC4278286 DOI: 10.18632/oncoscience.13] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2013] [Accepted: 12/27/2013] [Indexed: 12/16/2022] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is the predominant subtype of renal cell carcinoma (RCC). It is one of the most therapy-resistant carcinomas, responding very poorly or not at all to radiotherapy, hormonal therapy and chemotherapy. A more comprehensive understanding of the deregulated pathways in ccRCC can lead to the development of new therapies and prognostic markers. We performed a meta- analysis of 5 publicly available gene expression datasets and identified a list of co- deregulated genes, for which we performed extensive bioinformatic analysis coupled with experimental validation on the mRNA level. Gene ontology enrichment showed that many proteins are involved in response to hypoxia/oxygen levels and positive regulation of the VEGFR signaling pathway. KEGG analysis revealed that metabolic pathways are mostly altered in ccRCC. Similarly, Ingenuity Pathway Analysis showed that the antigen presentation, inositol metabolism, pentose phosphate, glycolysis/gluconeogenesis and fructose/mannose metabolism pathways are altered in the disease. Cellular growth, proliferation and carbohydrate metabolism, were among the top molecular and cellular functions of the co-deregulated genes. qRT-PCR validated the deregulated expression of several genes in Caki-2 and ACHN cell lines and in a cohort of ccRCC tissues. NNMT and NR3C1 increased expression was evident in ccRCC biopsies from patients using immunohistochemistry. ROC curves evaluated the diagnostic performance of the top deregulated genes in each dataset. We show that metabolic pathways are mostly deregulated in ccRCC and we highlight those being most responsible in its formation. We suggest that these genes are candidate predictive markers of the disease.
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Affiliation(s)
- Apostolos Zaravinos
- Molecular Medicine Research Center and Laboratory of Molecular and Medical Genetics, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Myrtani Pieri
- Molecular Medicine Research Center and Laboratory of Molecular and Medical Genetics, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Nikos Mourmouras
- Department of Urology, Asklipieio General Hospital, Athens, Greece
| | | | - Ioanna Zouvani
- Department of Nephrology, Nicosia General Hospital, Nicosia, Cyprus
| | - Dimitris Delakas
- Department of Urology, Asklipieio General Hospital, Athens, Greece
| | - Constantinos Deltas
- Molecular Medicine Research Center and Laboratory of Molecular and Medical Genetics, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
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20
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Zhang JC, Gao B, Yu ZT, Liu XB, Lu J, Xie F, Luo HJ, Li HP. Promoter hypermethylation of p14 (ARF) , RB, and INK4 gene family in hepatocellular carcinoma with hepatitis B virus infection. Tumour Biol 2013; 35:2795-802. [PMID: 24254306 DOI: 10.1007/s13277-013-1372-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Accepted: 10/28/2013] [Indexed: 01/14/2023] Open
Abstract
Both hepatitis B virus (HBV) and gene methylation play important roles in hepatocarcinogenesis. However, their association between HBV infection and gene methylation is not fully understood. Cell cycle control involving RB1 gene-related cell inhibitors is one of the main regulatory pathways were reported to be altered in hepatocellular carcinoma (HCC). The purpose of this research is to assess the methylation status of p14 (ARF) and INK4 gene family (p14 (ARF) , p15 (INK4B) , p16 (INK4A) , and p18 (INK4C) ) in HCC with HBV infection and HCC without it, and discuss possible role of HBV-induced hypermethylation in the mechanism of hepatocarcinogenesis. Methylation status of RB, p14 (ARF) , and INK4 gene family in 64 case of HCC with HBV infection and 24 cases without it were detected by methylation-specific polymerase chain reaction, and HBV-DNA of the plasma were detected by quantitative real-time polymerase chain reaction. p14 (ARF) , p15 (INK4B) , p16 (INK4A) , and RB hypermethylation were observed in 30 (34.1%), 50 (56.8%), 62 (70.5%), and 24(27.3%) of 88 hepatocellular carcinomas, respectively. Methylation frequencies of them between HCC with HBV infection and HCC without it were 43.8% versus 8.3 % (p14 (ARF) ), 68.9% versus 25% (p15 (INK4B) ), 90.6% versus 16.7% ( p16 (INK4A) ), and 28.1 % versus 25% (RB), respectively. In HBV-associated HCC, the numbers of methylated genes were also more than HCC without virus infection, more than two methylated genes were seen in 48 of 64 (75 %) cases; more than three methylated genes were found in 32 of 64 (50%); correspondently, no one case has more than two genes methylated. p18 (INK4C) methylation product was not found in cancerous or non-cancerous tissues of 88 HCC. HBV infection is associated with p14 (ARF) , p15 (INK4B) , p16 (INK4A) , and RB gene methylation (P = 0.048, 0.035, 0.02); HBV-DNA replication is associated with p14 (ARF) , p15 (INK4B) , p16 (INK4A) , and RB gene methylation (P = 0.048, 0.035, 0.02); high rate of p14 (ARF) , p15 (INK4B) , and p16 (INK4A) in HCC with HBV infection suggests that HBV-induced hypermethylation may be one of the mechanisms of HBV involved in hepatocellular carcinogenesis.
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Affiliation(s)
- Ji-Cai Zhang
- Department of Laboratory Medicine, Taihe Hospital Affiliated to Hubei University of Medicine, Shiyan, 442000, People's Republic of China
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21
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22
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Chen IP, Henning S, Faust A, Boukamp P, Volkmer B, Greinert R. UVA-induced epigenetic regulation of P16(INK4a) in human epidermal keratinocytes and skin tumor derived cells. Photochem Photobiol Sci 2011; 11:180-90. [PMID: 21986889 DOI: 10.1039/c1pp05197k] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
UVA-radiation (315-400 nm) has been demonstrated to be capable of inducing DNA damage and is regarded as a carcinogen. While chromosomal aberrations found in UVA-irradiated cells and skin tumors provided evidence of the genetic involvement in UVA-carcinogenesis, its epigenetic participation is still illusive. We thus analysed the epigenetic patterns of 5 specific genes that are involved in stem cell fate (KLF4, NANOG), telomere maintenance (hTERT) and tumor suppression in cell cycle control (P16(INK4a), P21(WAFI/CIPI)) in chronically UVA-irradiated HaCaT human keratinocytes. A striking reduction of the permissive histone mark H3K4me3 has been detected in the promoter of P16(INK4a) (4-fold and 9-fold reduction for 10 and 15 weeks UVA-irradiated cells, respectively), which has often been found deregulated in skin cancers. This alteration in histone modification together with a severe promoter hypermethylation strongly impaired the transcription of P16(INK4a) (20-fold and 40-fold for 10 weeks and 15 weeks UVA-irradiation, respectively). Analysis of the skin tumor-derived cells revealed the same severe impairment of the P16(INK4a) transcription attributed to promoter hypermethylation and enrichment of the heterochromatin histone mark H3K9me3 and the repressive mark H3K27me3. Less pronounced UVA-induced epigenetic alterations were also detected for the other genes, demonstrating for the first time that UVA is able to modify transcription of skin cancer associated genes by means of epigenetic DNA and histone alterations.
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Affiliation(s)
- I-Peng Chen
- Dept. Mol. Cell Biology, Center of Dermatology, Elbekliniken, Stade/Buxtehude, Germany
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