1
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Xiong L, Tan J, Zhang R, Long Q, Xiong R, Liu Y, Liu Y, Tang J, Li Y, Feng G, Song G, Liu K. LINC01305 recruits basonuclin 1 to act on G-protein pathway suppressor 1 to promote esophageal squamous cell carcinoma. Cancer Sci 2023; 114:4314-4328. [PMID: 37705202 PMCID: PMC10637064 DOI: 10.1111/cas.15963] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 08/20/2023] [Accepted: 08/27/2023] [Indexed: 09/15/2023] Open
Abstract
EsophageaL squamous cell carcinoma (ESCC) is one of the most common and lethal tumors, however, its underlying molecular mechanisms are not completely understood and new therapeutic targets are needed. Here, we found that the transcription factor basonuclin 1 (BNC1) was significantly upregulated and closely related to the differentiation and metastasis of ESCC. Furthermore, BNC1, LINC01305, and G-protein pathway suppressor 1 (GPS1) had significant oncogenic roles in ESCC. In addition, in vivo experiments showed that knockdown of BNC1 indeed significantly inhibited the proliferation and metastasis of ESCC. We also revealed the molecular mechanism by which LINC01305 recruits BNC1 to the promoter of GPS1, and then GPS1 could mediate the JNK signaling pathway to promote the proliferation and metastases of ESCC. Taken together, we discovered the novel molecular mechanism by which LINC01305/BNC1 upregulates GPS1 expression to promote the development of ESCC, providing a new therapeutic target for ESCC.
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Affiliation(s)
- Li Xiong
- Institute of Tissue Engineering and Stem Cells, Nanchong Central Hospital, The Second Clinical Medical CollegeNorth Sichuan Medical CollegeNanchongChina
- Department of Laboratory MedicineNorth Sichuan Medical CollegeNanchongChina
| | - Jinsong Tan
- Institute of Tissue Engineering and Stem Cells, Nanchong Central Hospital, The Second Clinical Medical CollegeNorth Sichuan Medical CollegeNanchongChina
- Institute of Basic Medicine and Forensic MedicineNorth Sichuan Medical CollegeNanchongChina
| | - Ruolan Zhang
- Institute of Tissue Engineering and Stem Cells, Nanchong Central Hospital, The Second Clinical Medical CollegeNorth Sichuan Medical CollegeNanchongChina
- Department of Laboratory MedicineNorth Sichuan Medical CollegeNanchongChina
| | - Qiongxian Long
- Institute of Tissue Engineering and Stem Cells, Nanchong Central Hospital, The Second Clinical Medical CollegeNorth Sichuan Medical CollegeNanchongChina
| | - Rong Xiong
- Institute of Tissue Engineering and Stem Cells, Nanchong Central Hospital, The Second Clinical Medical CollegeNorth Sichuan Medical CollegeNanchongChina
- Department of Laboratory MedicineNorth Sichuan Medical CollegeNanchongChina
| | - Yanqun Liu
- Institute of Tissue Engineering and Stem Cells, Nanchong Central Hospital, The Second Clinical Medical CollegeNorth Sichuan Medical CollegeNanchongChina
| | - Yun Liu
- Institute of Basic Medicine and Forensic MedicineNorth Sichuan Medical CollegeNanchongChina
| | - Jiancai Tang
- Institute of Basic Medicine and Forensic MedicineNorth Sichuan Medical CollegeNanchongChina
| | - Yan Li
- Department of Anatomy and Physiology, College of Basic Medical Science, Songjiang Research Institute and Songjiang HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Gang Feng
- Institute of Tissue Engineering and Stem Cells, Nanchong Central Hospital, The Second Clinical Medical CollegeNorth Sichuan Medical CollegeNanchongChina
| | - Guiqin Song
- Institute of Basic Medicine and Forensic MedicineNorth Sichuan Medical CollegeNanchongChina
| | - Kang Liu
- Institute of Tissue Engineering and Stem Cells, Nanchong Central Hospital, The Second Clinical Medical CollegeNorth Sichuan Medical CollegeNanchongChina
- Department of Laboratory MedicineNorth Sichuan Medical CollegeNanchongChina
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2
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Hurst CD, Cheng G, Platt FM, Alder O, Black EV, Burns JE, Brown J, Jain S, Roulson JA, Knowles MA. Molecular profile of pure squamous cell carcinoma of the bladder identifies major roles for OSMR and YAP signalling. JOURNAL OF PATHOLOGY CLINICAL RESEARCH 2022; 8:279-293. [PMID: 35289095 PMCID: PMC8977277 DOI: 10.1002/cjp2.261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/13/2022] [Accepted: 01/18/2022] [Indexed: 11/20/2022]
Abstract
Pure squamous cell carcinoma (SCC) is the most common pure variant form of bladder cancer, found in 2–5% of cases. It often presents late and is unresponsive to cisplatin‐based chemotherapy. The molecular features of these tumours have not been elucidated in detail. We carried out whole‐exome sequencing (WES), copy number, and transcriptome analysis of bladder SCC. Muscle‐invasive bladder cancer (MIBC) samples with no evidence of squamous differentiation (non‐SD) were used for comparison. To assess commonality of features with urothelial carcinoma with SD, we examined data from SD samples in The Cancer Genome Atlas (TCGA) study of MIBC. TP53 was the most commonly mutated gene in SCC (64%) followed by FAT1 (45%). Copy number analysis revealed complex changes in SCC, many differing from those in samples with SD. Gain of 5p and 7p was the most common feature, and focal regions on 5p included OSMR and RICTOR. In addition to 9p deletions, we found some samples with focal gain of 9p24 containing CD274 (PD‐L1). Loss of 4q35 containing FAT1 was found in many samples such that all but one sample analysed by WES had FAT1 mutation or deletion. Expression features included upregulation of oncostatin M receptor (OSMR), metalloproteinases, metallothioneins, keratinisation genes, extracellular matrix components, inflammatory response genes, stem cell markers, and immune response modulators. Exploration of differentially expressed transcription factors identified BNC1 and TFAP2A, a gene repressed by PPARG, as the most upregulated factors. Known urothelial differentiation factors were downregulated along with 72 Kruppel‐associated (KRAB) domain‐containing zinc finger family protein (KZFP) genes. Novel therapies are urgently needed for these tumours. In addition to upregulated expression of EGFR, which has been suggested as a therapeutic target in basal/squamous bladder cancer, we identified expression signatures that indicate upregulated OSMR and YAP/TAZ signalling. Preclinical evaluation of the effects of inhibition of these pathways alone or in combination is merited.
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Affiliation(s)
- Carolyn D Hurst
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James's, St James's University Hospital, Leeds, UK
| | - Guo Cheng
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James's, St James's University Hospital, Leeds, UK
| | - Fiona M Platt
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James's, St James's University Hospital, Leeds, UK
| | - Olivia Alder
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James's, St James's University Hospital, Leeds, UK
| | - Emma Vi Black
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James's, St James's University Hospital, Leeds, UK
| | - Julie E Burns
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James's, St James's University Hospital, Leeds, UK
| | - Joanne Brown
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James's, St James's University Hospital, Leeds, UK
| | - Sunjay Jain
- Pyrah Department of Urology, St James's University Hospital, Leeds, UK
| | - Jo-An Roulson
- Department of Histopathology, St James's University Hospital, Leeds, UK
| | - Margaret A Knowles
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James's, St James's University Hospital, Leeds, UK
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3
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Liang ZQ, Zhong LY, Li J, Shen JH, Tu XY, Zhong ZH, Zeng JJ, Chen JH, Wei ZX, Dang YW, Huang SN, Chen G. Clinicopathological significance and underlying molecular mechanism of downregulation of basonuclin 1 expression in ovarian carcinoma. Exp Biol Med (Maywood) 2022; 247:106-119. [PMID: 34644201 PMCID: PMC8777474 DOI: 10.1177/15353702211052036] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
In this study, we aim to identify the clinical significance of basonuclin 1 (BNC1) expression in ovarian carcinoma (OV) and to explore its latent mechanisms. Via integrating in-house tissue microarrays, gene chips, and RNA-sequencing data, we explored the expression and clinical value of BNC1 in OV. Immunohistochemical staining was utilized to confirm the protein expression status of BNC1. A combined SMD of -2.339 (95% CI: -3.649 to -1.028, P < 0.001) identified that BNC1 was downregulated based on 1346 samples, and the sROC (AUC = 0.93) showed a favorable discriminatory ability of BNC1 in OV patients. We used univariate and multivariate Cox regulation to evaluate the prognostic role of BNC1 for OV patients, and a combined hazard ratio of 0.717 (95% CI: 0.445-0.989, P < 0.001) revealed that BNC1 was a protective factor for OV. Furthermore, the fraction of infiltrating naive B cells, memory B cells, and other immune cells showed statistical differences between the high- and low-BNC1 expression groups through cell-type identification by estimating relative subsets of RNA transcripts (CIBERSORT) algorithm. Enrichment analysis showed that BNC1 may have a relationship with immune-related items in OV. By predicting the potential regulatory transcription factors (TFs) of BNC1, friend leukemia virus integration 1 (FLI1) may be a potential upstream TF of BNC1. Corporately, a decreasing trend of BNC1 may serve as a tumor suppressor and prognostic biomarker in OV patients. Moreover, BNC1 may take part in immune-related pathways and influence the fraction of tumor-infiltrating immune cells.
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Affiliation(s)
- Zi-Qian Liang
- Department of Pathology, The First Affiliated Hospital of
Guangxi Medical University, Nanning 530021, P. R. China
| | - Lu-Yang Zhong
- Department of Pathology, The First Affiliated Hospital of
Guangxi Medical University, Nanning 530021, P. R. China
| | - Jie Li
- Department of Pathology, The First Affiliated Hospital of
Guangxi Medical University, Nanning 530021, P. R. China
| | - Jin-Hai Shen
- Department of Pathology, The First Affiliated Hospital of
Guangxi Medical University, Nanning 530021, P. R. China
| | - Xin-Yue Tu
- Department of Pathology, The First Affiliated Hospital of
Guangxi Medical University, Nanning 530021, P. R. China
| | - Zheng-Hong Zhong
- Department of Pathology, The First Affiliated Hospital of
Guangxi Medical University, Nanning 530021, P. R. China
| | - Jing-Jing Zeng
- Department of Pathology, The First Affiliated Hospital of
Guangxi Medical University, Nanning 530021, P. R. China
| | - Jun-Hong Chen
- Department of Pathology, Maternal and Child Health Hospital of
Guangxi Zhuang Autonomous Region, Nanning 530003, P. R. China
| | - Zhu-Xin Wei
- Department of Radiotherapy, The First Affiliated Hospital of
Guangxi Medical University, Nanning 530021, P. R. China
| | - Yi-Wu Dang
- Department of Pathology, The First Affiliated Hospital of
Guangxi Medical University, Nanning 530021, P. R. China
| | - Su-Ning Huang
- Department of Radiotherapy, Guangxi Medical University Cancer
Hospital, Nanning 530021, P.R. China
| | - Gang Chen
- Department of Pathology, The First Affiliated Hospital of
Guangxi Medical University, Nanning 530021, P. R. China
- Gang Chen.
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4
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Bispo S, Farias TDJ, de Araujo-Souza PS, Cintra R, Dos Santos HG, Jorge NAN, Castro MAA, Wajnberg G, Scherer NDM, Genta MLND, Carvalho JP, Villa LL, Sichero L, Passetti F. Dysregulation of Transcription Factor Networks Unveils Different Pathways in Human Papillomavirus 16-Positive Squamous Cell Carcinoma and Adenocarcinoma of the Uterine Cervix. Front Oncol 2021; 11:626187. [PMID: 34094909 PMCID: PMC8170088 DOI: 10.3389/fonc.2021.626187] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 02/17/2021] [Indexed: 12/24/2022] Open
Abstract
Squamous cell carcinoma (SCC) and adenocarcinoma (ADC) are the most common histological types of cervical cancer (CC). The worse prognosis of ADC cases highlights the need for better molecular characterization regarding differences between these CC types. RNA-Seq analysis of seven SCC and three ADC human papillomavirus 16-positive samples and the comparison with public data from non-tumoral human papillomavirus-negative cervical tissue samples revealed pathways exclusive to each histological type, such as the epithelial maintenance in SCC and the maturity-onset diabetes of the young (MODY) pathway in ADC. The transcriptional regulatory network analysis of cervical SCC samples unveiled a set of six transcription factor (TF) genes with the potential to positively regulate long non-coding RNA genes DSG1-AS1, CALML3-AS1, IGFL2-AS1, and TINCR. Additional analysis revealed a set of MODY TFs regulated in the sequence predicted to be repressed by miR-96-5p or miR-28-3p in ADC. These microRNAs were previously described to target LINC02381, which was predicted to be positively regulated by two MODY TFs upregulated in cervical ADC. Therefore, we hypothesize LINC02381 might act by decreasing the levels of miR-96-5p and miR-28-3p, promoting the MODY activation in cervical ADC. The novel TF networks here described should be explored for the development of more efficient diagnostic tools.
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Affiliation(s)
- Saloe Bispo
- Instituto Carlos Chagas, FIOCRUZ, Curitiba, Brazil
| | | | - Patricia Savio de Araujo-Souza
- Department of Immunobiology, Biology Institute, Universidade Federal Fluminense (UFF), Niterói, Brazil.,Laboratory of Immunogenetics and Histocompatibility, Department of Genetics, Universidade Federal do Paraná, Curitiba, Brazil
| | - Ricardo Cintra
- Department of Biochemistry, Instituto de Quimica, Universidade de São Paulo, São Paulo, Brazil
| | | | - Natasha Andressa Nogueira Jorge
- Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil.,Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, Leipzig University, Leipzig, Germany
| | | | - Gabriel Wajnberg
- Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil.,Atlantic Cancer Research Institute, Moncton, NB, Canada
| | - Nicole de Miranda Scherer
- Laboratory of Bioinformatics and Computational Biology, Division of Experimental and Translational Research, Brazilian National Cancer Institute (INCA), Rio de Janeiro, Brazil
| | - Maria Luiza Nogueira Dias Genta
- Discipline of Gynecology, Department of Obstetrics and Gynecology, Instituto do Cancer do Estado de São Paulo, Hospital das Clinicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Jesus Paula Carvalho
- Discipline of Gynecology, Department of Obstetrics and Gynecology, Instituto do Cancer do Estado de São Paulo, Hospital das Clinicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Luisa Lina Villa
- Department of Radiology and Oncology, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil.,Center for Translational Research in Oncology, Instituto do Cancer do Estado de São Paulo ICESP, Hospital das Clinicas da Faculdade de Medicina da Universidade de São Paulo FMUSP HC, São Paulo, Brazil
| | - Laura Sichero
- Center for Translational Research in Oncology, Instituto do Cancer do Estado de São Paulo ICESP, Hospital das Clinicas da Faculdade de Medicina da Universidade de São Paulo FMUSP HC, São Paulo, Brazil
| | - Fabio Passetti
- Instituto Carlos Chagas, FIOCRUZ, Curitiba, Brazil.,Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
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5
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Su P, Qiao Q, Ji G, Zhang Z. CircAMD1 regulates proliferation and collagen synthesis via sponging miR-27a-3p in P63-mutant human dermal fibroblasts. Differentiation 2021; 119:10-18. [PMID: 33991897 DOI: 10.1016/j.diff.2021.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 03/20/2021] [Accepted: 04/27/2021] [Indexed: 10/21/2022]
Abstract
Transcription factor p63 has critical functions in epidermal, hindgut/anorectal, and limb development. Human mutations in P63 correlate with congenital syndromes affecting the skin, anorectal, and limbs. Nevertheless, less are detected regarding networks and functions controlled by P63 mutations in dermal fibroblasts, which are closely related to skin physiology. To screen for new targets, we employed microarray technology to investigate the R226Q P63 mutation with regards to the resulting circular RNA (circRNA) profiles from P63 point mutations in human dermal fibroblasts (HDFs). In this study, we show that P63-mutant HDFs display reduced proliferation, collagen synthesis, and myofibroblast differentiation; circAMD1 was also downregulated in P63-mutant HDFs compared with wild-type HDFs. Furthermore, overexpressing circAMD1 rescued the functional and phenotypic alterations of p63-mutant HDFs. We as well determined that miR-27a-3p was circAMD1 target involved in effects of circAMD1 in P63-mutant HDFs. Collectively, our data show that circAMD1 functions as a miR-27a-3p sponge that inhibits the functional and phenotypical alteration of P63-mutant HDFs and may be a critical marker in pathogenesis regarding P63-associated traits.
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Affiliation(s)
- Pengjun Su
- Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Shenyang, China.
| | - Qi Qiao
- Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Gengfeng Ji
- Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Zhibo Zhang
- Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Shenyang, China
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6
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Napoli M, Flores ER. The p53 family reaches the final frontier: the variegated regulation of the dark matter of the genome by the p53 family in cancer. RNA Biol 2020; 17:1636-1647. [PMID: 31910062 PMCID: PMC7567494 DOI: 10.1080/15476286.2019.1710054] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The tumour suppressor p53 and its paralogues, p63 and p73, are essential to maintain cellular homoeostasis and the integrity of the cell's genetic material, thus meriting the title of 'guardians of the genome'. The p53 family members are transcription factors and fulfill their activities by controlling the expression of protein-coding and non-coding genes. Here, we review how the latter group transcended from the 'dark matter' of the transcriptome, providing unexpected and intriguing anti-cancer therapeutic strategies.
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Affiliation(s)
- Marco Napoli
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL, USA.,Cancer Biology and Evolution Program, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL, USA
| | - Elsa R Flores
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL, USA.,Cancer Biology and Evolution Program, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL, USA
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7
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Ni Y, Zhang X, Wan Y, Dun Tang K, Xiao Y, Jing Y, Song Y, Huang X, Punyadeera C, Hu Q. Relationship between p16 expression and prognosis in different anatomic subsites of OSCC. Cancer Biomark 2019; 26:375-383. [PMID: 31594213 DOI: 10.3233/cbm-192402] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Yanhong Ni
- Central Laboratory, Nanjing Stomatological Hospital, Medical School, Nanjing University, Nanjing, Jiangsu, China
- Department of Oral and Maxillofacial Surgery, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, China
- Central Laboratory, Nanjing Stomatological Hospital, Medical School, Nanjing University, Nanjing, Jiangsu, China
| | - Xiaoxin Zhang
- Central Laboratory, Nanjing Stomatological Hospital, Medical School, Nanjing University, Nanjing, Jiangsu, China
- Central Laboratory, Nanjing Stomatological Hospital, Medical School, Nanjing University, Nanjing, Jiangsu, China
| | - Yunxia Wan
- The School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD, Australia and the Translational Research Institute, Brisbane, Australia
| | - Kai Dun Tang
- The School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD, Australia and the Translational Research Institute, Brisbane, Australia
| | - Yin Xiao
- The School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD, Australia and the Translational Research Institute, Brisbane, Australia
| | - Yue Jing
- Central Laboratory, Nanjing Stomatological Hospital, Medical School, Nanjing University, Nanjing, Jiangsu, China
| | - Yuxian Song
- Central Laboratory, Nanjing Stomatological Hospital, Medical School, Nanjing University, Nanjing, Jiangsu, China
| | - Xiaofeng Huang
- Central Laboratory, Nanjing Stomatological Hospital, Medical School, Nanjing University, Nanjing, Jiangsu, China
| | - Chamindie Punyadeera
- The School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD, Australia and the Translational Research Institute, Brisbane, Australia
| | - Qingang Hu
- Central Laboratory, Nanjing Stomatological Hospital, Medical School, Nanjing University, Nanjing, Jiangsu, China
- Department of Oral and Maxillofacial Surgery, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, China
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8
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García-Díez I, Hernández-Muñoz I, Hernández-Ruiz E, Nonell L, Puigdecanet E, Bódalo-Torruella M, Andrades E, Pujol RM, Toll A. Transcriptome and cytogenetic profiling analysis of matched in situ/invasive cutaneous squamous cell carcinomas from immunocompetent patients. Genes Chromosomes Cancer 2019; 58:164-174. [DOI: 10.1002/gcc.22712] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 11/01/2018] [Accepted: 11/22/2018] [Indexed: 12/17/2022] Open
Affiliation(s)
- Irene García-Díez
- Department of Dermatology; Hospital del Mar, Universitat Autònoma de Barcelona (UAB); Barcelona Spain
- Group of Inflammatory and Neoplastic Dermatological Diseases, IMIM (Hospital del Mar Medical Research Institute); Barcelona Spain
| | - Inmaculada Hernández-Muñoz
- Group of Inflammatory and Neoplastic Dermatological Diseases, IMIM (Hospital del Mar Medical Research Institute); Barcelona Spain
| | - Eugenia Hernández-Ruiz
- Department of Dermatology; Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB); Barcelona Spain
| | - Lara Nonell
- Microarray Analysis Service, IMIM (Hospital del Mar Medical Research Institute); Barcelona Spain
| | - Eulàlia Puigdecanet
- Microarray Analysis Service, IMIM (Hospital del Mar Medical Research Institute); Barcelona Spain
| | - Marta Bódalo-Torruella
- Microarray Analysis Service, IMIM (Hospital del Mar Medical Research Institute); Barcelona Spain
| | - Evelyn Andrades
- Group of Inflammatory and Neoplastic Dermatological Diseases, IMIM (Hospital del Mar Medical Research Institute); Barcelona Spain
| | - Ramon M. Pujol
- Department of Dermatology; Hospital del Mar, Universitat Autònoma de Barcelona (UAB); Barcelona Spain
- Group of Inflammatory and Neoplastic Dermatological Diseases, IMIM (Hospital del Mar Medical Research Institute); Barcelona Spain
| | - Agustí Toll
- Department of Dermatology; Hospital del Mar, Universitat Autònoma de Barcelona (UAB); Barcelona Spain
- Group of Inflammatory and Neoplastic Dermatological Diseases, IMIM (Hospital del Mar Medical Research Institute); Barcelona Spain
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9
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Joly F, Deret S, Gamboa B, Menigot C, Fogel P, Mounier C, Reiniche P, Sidou F, Aubert J, Lear J, Fryer AA, Zolezzi F, Voegel JJ. Photodynamic therapy corrects abnormal cancer-associated gene expression observed in actinic keratosis lesions and induces a remodeling effect in photodamaged skin. J Dermatol Sci 2018; 91:S0923-1811(17)30775-2. [PMID: 29779986 DOI: 10.1016/j.jdermsci.2018.05.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 04/13/2018] [Accepted: 05/07/2018] [Indexed: 10/16/2022]
Abstract
BACKGROUND Actinic keratoses (AK) are proliferations of neoplastic keratinocytes in the epidermis resulting from cumulative exposure to ultraviolet radiation (UVR), which are liable to transform into squamous cell carcinoma (SCC). Organ Transplant Recipients (OTR) have an increased risk of developing SCC as a consequence of long-term immunosuppressive therapy. The aim of this study was to determine the molecular signature of AKs from OTR prior to treatment with methyl aminolevulinate-photodynamic therapy (MAL-PDT), and to assess what impact the treatment has on promoting remodeling of the photo-damaged skin. METHODS Seven patients were enrolled on a clinical trial to assess the effect of MAL-PDT with biopsies taken at screening prior to the first treatment session (week 1), and six weeks after completion of final treatment (week 18). Whole-genome gene expression analysis was carried out on skin biopsies isolated from an AK lesion, an area surrounding the lesion, and a non-sun exposed region of the body. Quantitative PCR was utilized to confirm the differential expression of key genes. RESULTS MAL-PDT treatment corrected abnormal proliferation-related gene profiles, corrected aberrantly expressed cancer-associated genes and induced expression of dermal extracellular matrix genes in photo-exposed skin. CONCLUSION The efficacy of the MAL-PDT on AK lesions was confirmed at whole-genome gene expression level. A transcriptional signature of remodeling, identified through assessing the effect of MAL-PDT on photodamaged skin, supports the use of MAL-PDT for treating photodamaged skin and field cancerized areas.
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Affiliation(s)
| | - Sophie Deret
- GALDERMA R&D, 06902 Sophia Antipolis Cedex, France
| | | | | | - Paul Fogel
- Independent Consultant, Paris 75006, France
| | | | | | | | | | - John Lear
- Manchester Academic Health Science Centre, MAHSC, Manchester University and Salford Royal NHS Trust, Manchester, UK
| | - Anthony A Fryer
- Institute for Applied Clinical Sciences, Keele University, Guy Hilton Research Centre, Thornburrow Drive, Hartshill, Stoke-on-Trent Staffordshire, ST4 7QB, UK
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10
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Stefen H, Suchowerska AK, Chen BJ, Brettle M, Kuschelewski J, Gunning PW, Janitz M, Fath T. Tropomyosin isoforms have specific effects on the transcriptome of undifferentiated and differentiated B35 neuroblastoma cells. FEBS Open Bio 2018; 8:570-583. [PMID: 29632810 PMCID: PMC5881551 DOI: 10.1002/2211-5463.12386] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 01/10/2018] [Accepted: 01/16/2018] [Indexed: 12/14/2022] Open
Abstract
Tropomyosins, a family of actin‐associated proteins, bestow actin filaments with distinct biochemical and physical properties which are important for determining cell shape and regulating many cellular processes in eukaryotic cells. Here, we used RNA‐seq to investigate the effect of four tropomyosin isoforms on gene expression in undifferentiated and differentiated rat B35 neuroblastoma cells. In undifferentiated cells, overexpression of tropomyosin isoforms Tpm1.12, Tpm2.1, Tpm3.1, and Tpm4.2 differentially regulates a vast number of genes, clustering into several gene ontology terms. In differentiated cells, tropomyosin overexpression exerts a much weaker influence on overall gene expression. Our findings are particularly compelling because they demonstrate that tropomyosin‐dependent changes are attenuated once the cells are induced to follow a defined path of differentiation. Database Sequence data for public availability are deposited in the European Nucleotide Archive under the accession number PRJEB24136.
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Affiliation(s)
- Holly Stefen
- Neurodegenerative and Repair Unit School of Medical Science UNSW Sydney NSW Australia
| | | | - Bei Jun Chen
- School of Biotechnology and Biomolecular Sciences UNSW Sydney NSW Australia
| | - Merryn Brettle
- Neurodegenerative and Repair Unit School of Medical Science UNSW Sydney NSW Australia
| | - Jennifer Kuschelewski
- Neurodegenerative and Repair Unit School of Medical Science UNSW Sydney NSW Australia
| | - Peter William Gunning
- Cellular and Genetic Medicine Unit School of Medical Sciences UNSW Sydney NSW Australia
| | - Michael Janitz
- School of Biotechnology and Biomolecular Sciences UNSW Sydney NSW Australia
| | - Thomas Fath
- Neurodegenerative and Repair Unit School of Medical Science UNSW Sydney NSW Australia
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Wu Y, Zhang X, Liu Y, Lu F, Chen X. Decreased Expression of BNC1 and BNC2 Is Associated with Genetic or Epigenetic Regulation in Hepatocellular Carcinoma. Int J Mol Sci 2016; 17:ijms17020153. [PMID: 26821013 PMCID: PMC4783887 DOI: 10.3390/ijms17020153] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 01/08/2016] [Accepted: 01/19/2016] [Indexed: 01/05/2023] Open
Abstract
The aberrant expression of transcription factor Basonuclin (BNC) had been reported in different kinds of tumors. Here, we investigated the expression and methylation status of two Basonuclin homologs, BNC1 and BNC2 in hepatocellular carcinoma (HCC). We found that the expression levels of both BNC1 and BNC2 were down-regulated in HCC cell lines and primary HCC tissues. The frequency and intensity of BNC1 promoter hypermethylation in tumor tissues was significantly higher than that in adjacent non-tumor tissues. 5-Aza-2’-Deoxycytidine treatment could significantly increase the BNC1 expression in the methylated HCC cell lines, which implicated that epigenetic modification contributed to the down-regulation of BNC1. In addition, BNC1 hypermethylation in tumor tissues was more likely to happen in female patients. No methylation of the BNC2 promoter was found in HCC tumor tissues. However, a frequent deletion of the BNC2 gene was observed, which indicated that the chromosomal loss of the BNC2 gene might be one important reason for its lower expression level in HCC. Our results suggested that BNC1 and BNC2 were down-regulated in HCC which may provide new insight into the tumorigenesis of HCC.
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Affiliation(s)
- Yali Wu
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Science, Peking University Health Science Center, Beijing 100191, China.
| | - Xiaolei Zhang
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Science, Peking University Health Science Center, Beijing 100191, China.
| | - Yongzhen Liu
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Science, Peking University Health Science Center, Beijing 100191, China.
| | - Fengmin Lu
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Science, Peking University Health Science Center, Beijing 100191, China.
| | - Xiangmei Chen
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Science, Peking University Health Science Center, Beijing 100191, China.
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12
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Sulahian R, Chen J, Arany Z, Jadhav U, Peng S, Rustgi AK, Bass AJ, Srivastava A, Hornick JL, Shivdasani RA. SOX15 governs transcription in human stratified epithelia and a subset of esophageal adenocarcinomas. Cell Mol Gastroenterol Hepatol 2015; 1:598-609.e6. [PMID: 26516633 PMCID: PMC4620585 DOI: 10.1016/j.jcmgh.2015.07.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND & AIMS Intestinal metaplasia (Barrett's esophagus, BE) is the principal risk factor for esophageal adenocarcinoma (EAC). Study of the basis for BE has centered on intestinal factors, but loss of esophageal identity likely also reflects absence of key squamous-cell factors. As few determinants of stratified epithelial cell-specific gene expression are characterized, it is important to identify the necessary transcription factors. METHODS We tested regional expression of mRNAs for all putative DNA-binding proteins in the mouse digestive tract and verified esophagus-specific factors in human tissues and cell lines. Integration of diverse data defined a human squamous esophagus-specific transcriptome. We used chromatin immunoprecipitation (ChIP-seq) to locate transcription factor binding sites, computational approaches to profile transcripts in cancer datasets, and immunohistochemistry to reveal protein expression. RESULTS The transcription factor SOX15 is restricted to esophageal and other murine and human stratified epithelia. SOX15 mRNA levels are attenuated in BE and its depletion in human esophageal cells reduced esophageal transcripts significantly and specifically. SOX15 binding is highly enriched near esophagus-expressed genes, indicating direct transcriptional control. SOX15 and hundreds of genes co-expressed in squamous cells are reactivated in up to 30% of EAC specimens. Genes normally confined to the esophagus or intestine appear in different cells within the same malignant glands. CONCLUSIONS These data identify a novel transcriptional regulator of stratified epithelial cells and a subtype of EAC with bi-lineage gene expression. Broad activation of squamous-cell genes may shed light on whether EACs arise in the native stratified epithelium or in ectopic columnar cells.
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Affiliation(s)
- Rita Sulahian
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts,Department of Medicine, Harvard Medical School, Harvard University, Boston, Massachusetts
| | - Justina Chen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Zoltan Arany
- Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Unmesh Jadhav
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts,Department of Medicine, Harvard Medical School, Harvard University, Boston, Massachusetts
| | - Shouyong Peng
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Anil K. Rustgi
- Division of Gastroenterology, Departments of Medicine and Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Adam J. Bass
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts,Department of Medicine, Harvard Medical School, Harvard University, Boston, Massachusetts
| | - Amitabh Srivastava
- Department of Pathology, Brigham & Women’s Hospital, and Department of Pathology, Harvard Medical School, Harvard University, Boston, Massachusetts
| | - Jason L. Hornick
- Department of Pathology, Brigham & Women’s Hospital, and Department of Pathology, Harvard Medical School, Harvard University, Boston, Massachusetts
| | - Ramesh A. Shivdasani
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts,Department of Medicine, Harvard Medical School, Harvard University, Boston, Massachusetts,Correspondence Address correspondence to: Ramesh A. Shivdasani, MD, PhD, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215. fax: (617) 582-7198.Dana-Farber Cancer Institute450 Brookline AvenueBostonMassachusetts 02215
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13
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Expression of p16 in squamous cell carcinoma of the mobile tongue is independent of HPV infection despite presence of the HPV-receptor syndecan-1. Br J Cancer 2015; 113:321-6. [PMID: 26057450 PMCID: PMC4506391 DOI: 10.1038/bjc.2015.207] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 05/07/2015] [Accepted: 05/13/2015] [Indexed: 02/03/2023] Open
Abstract
Background: Tongue squamous cell carcinoma (TSCC) is increasing in incidence, especially among young patients and preferably females. Infection with human papilloma virus (HPV) has been suggested as a cause of SCC in the head and neck, and the proportion of oropharyngeal cancers caused by HPV has steadily increased. Methods: Samples from 109 patients with primary TSCC were analysed for the presence of HPV16 by in situ hybridisation and for expression of its surrogate marker p16 and the HPV receptor syndecan-1 by immunhistochemistry. Results: No evidence of HPV16 DNA was observed in the tumours, although one-third showed p16 staining. There was no difference in the expression of the primary HPV receptor, syndecan-1, between TSCC and a group of tonsil SCC. Conclusion: Whereas p16 is expressed in some TSCCs, HPV16 is undetectable, therefore, p16 cannot be used as a surrogate marker for high-risk HPV-infection in this tumour. Despite presence of the HPV-receptor syndecan-1 in TSCC, HPV prefers the tonsillar environment. Lack of p16 associates with worse prognosis primarily in patients aged ⩽40 years with tongue SCC. The improved prognosis seen in p16-positive TSCC can be due to induction of a senescent phenotype or an inherent radiosensitivity due to the ability of p16 to inhibit homologous recombination repair.
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14
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Marcel V, Catez F, Diaz JJ. p53, a translational regulator: contribution to its tumour-suppressor activity. Oncogene 2015; 34:5513-23. [DOI: 10.1038/onc.2015.25] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 01/08/2015] [Accepted: 01/12/2015] [Indexed: 12/14/2022]
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Abstract
The introduction of novel technologies that can be applied to the investigation of the molecular underpinnings of human cancer has allowed for new insights into the mechanisms associated with tumor development and progression. They have also advanced the diagnosis, prognosis and treatment of cancer. These technologies include microarray and other analysis methods for the generation of large-scale gene expression data on both mRNA and miRNA, next-generation DNA sequencing technologies utilizing a number of platforms to perform whole genome, whole exome, or targeted DNA sequencing to determine somatic mutational differences and gene rearrangements, and a variety of proteomic analysis platforms including liquid chromatography/mass spectrometry (LC/MS) analysis to survey alterations in protein profiles in tumors. One other important advancement has been our current ability to survey the methylome of human tumors in a comprehensive fashion through the use of sequence-based and array-based methylation analysis (Bock et al., Nat Biotechnol 28:1106-1114, 2010; Harris et al., Nat Biotechnol 28:1097-1105, 2010). The focus of this chapter is to present and discuss the evidence for key genes involved in prostate tumor development, progression, or resistance to therapy that are regulated by methylation-induced silencing.
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Affiliation(s)
- Tawnya C McKee
- Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, Diagnostic Biomarkers and Technology Branch, National Cancer Institute, Bethesda, MD, 20892-7430, USA
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16
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Feuerborn A, Mathow D, Srivastava PK, Gretz N, Gröne HJ. Basonuclin-1 modulates epithelial plasticity and TGF-β1-induced loss of epithelial cell integrity. Oncogene 2014; 34:1185-95. [PMID: 24662832 DOI: 10.1038/onc.2014.54] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2012] [Revised: 01/03/2014] [Accepted: 01/06/2014] [Indexed: 02/06/2023]
Abstract
Transforming growth factor-β1 (TGF-β1) is a multifunctional cytokine and critically involved in the progression of a variety of cancers. TGF-β1 signaling can impair tumor development by its anti-proliferative and pro-apoptotic features. In contrast, it may actively promote tumor progression and cancer cell dissemination by inducing a gradual switch from epithelial towards mesenchymal-like cell features (EMT-like), including decreased intercellular adhesion. Here, we show that expression of the transcription factor Basonuclin-1 (Bnc1) modulates TGF-β1-induced epithelial dedifferentiation of mammary epithelial cells. RNAi-mediated repression of Bnc1 resulted in enhanced intercellular adhesion and strongly impaired TGF-β1-dependent sheet disintegration and cell scattering. In contrast, forced expression of Bnc1 modifies plasma membrane/cytoskeletal dynamics and seemingly interferes with the initiation of sustainable cell-cell contacts. Follow-up analyses revealed that Bnc1 affects the expression of numerous TGF-β1-responsive genes including distinct EMT-related transcription factors, some of which modulate the expression of Bnc1 themselves. These results suggest that Bnc1 is part of a transcription factor network related to epithelial plasticity with reciprocal feedback-loop connections on which Smad-factors integrate TGF-β1 signaling. Our study demonstrates that Bnc1 regulates epithelial plasticity of mammary epithelial cells and influences outcome of TGF-β1 signaling.
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Affiliation(s)
- A Feuerborn
- Department of Cellular and Molecular Pathology, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - D Mathow
- Department of Cellular and Molecular Pathology, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - P K Srivastava
- Physiological Genomics and Medicine, MRC Clinical Sciences, Imperial College, London, UK
| | - N Gretz
- Department of Medical Research, Faculty of Medicine, Medical Research Centre (ZMF), University of Heidelberg, Mannheim, Germany
| | - H-J Gröne
- Department of Cellular and Molecular Pathology, German Cancer Research Centre (DKFZ), Heidelberg, Germany
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17
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Ricketts CJ, Hill VK, Linehan WM. Tumor-specific hypermethylation of epigenetic biomarkers, including SFRP1, predicts for poorer survival in patients from the TCGA Kidney Renal Clear Cell Carcinoma (KIRC) project. PLoS One 2014; 9:e85621. [PMID: 24454902 PMCID: PMC3893219 DOI: 10.1371/journal.pone.0085621] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 12/05/2013] [Indexed: 01/08/2023] Open
Abstract
The recent publication of the TCGA Kidney Renal Clear Cell Carcinoma (KIRC) project has provided an immense wealth and breadth of data providing an invaluable tool for confirmation and expansion upon previous observations in a large data set containing multiple data types including DNA methylation, somatic mutation, and clinical information. In clear cell renal cell carcinoma (CCRCC) many genes have been demonstrated to be epigenetically inactivated by promoter hypermethylated and in a small number of cases to be associated with clinical outcome. This study created two cohorts based on the Illumina BeadChip array used to confirm the frequency of tumor-specific hypermethylation of these published hypermethylated genes, assess the impact of somatic mutation or chromosomal loss and provide the most comprehensive assessment to date of the association of this hypermethylation with patient survival. Hypermethylation of the Fibrillin 2 (FBN2) gene was the most consistent epigenetic biomarker for CCRCC across both cohorts in 40.2% or 52.5% of tumors respectively. Hypermethylation of the secreted frizzled-related protein 1 (SFRP1) gene and the basonuclin 1 (BNC1) gene were both statistically associated with poorer survival in both cohorts (SFRP1 - p = <0.0001 or 0.0010 and BNC1 - p = <0.0001 or 0.0380) and represented better independent markers of survival than tumor stage, grade or dimension in one cohort and tumor stage or dimension in the other cohort. Loss of the SFRP1 protein can potentially activate the WNT pathway and this analysis highlighted hypermethylation of several other WNT pathway regulating genes and demonstrated a poorer survival outcome for patients with somatic mutation of these genes. The success of demethylating drugs in hematological malignances and the current trials in solid tumors suggest that the identification of clinically relevant hypermethylated genes combined with therapeutic advances may improve the effectiveness and usefulness of such drugs in clear cell renal cell carcinoma.
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Affiliation(s)
- Christopher J. Ricketts
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Victoria K. Hill
- Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - W. Marston Linehan
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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Brady PD, DeKoninck P, Fryns JP, Devriendt K, Deprest JA, Vermeesch JR. Identification of dosage-sensitive genes in fetuses referred with severe isolated congenital diaphragmatic hernia. Prenat Diagn 2013; 33:1283-92. [PMID: 24122781 DOI: 10.1002/pd.4244] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Revised: 09/09/2013] [Accepted: 09/21/2013] [Indexed: 01/08/2023]
Abstract
OBJECTIVE Congenital diaphragmatic hernia (CDH) is a fetal abnormality affecting diaphragm and lung development with a high mortality rate despite advances in fetal and neonatal therapy. CDH may occur either as an isolated defect or in syndromic form for which the prognosis is worse. Although conventional karyotyping and, more recently, chromosomal microarrays support a substantial role for genetic factors, causal genes responsible for isolated CDH remain elusive. We propose that chromosomal microarray analysis will identify copy number variations (CNVs) associated with isolated CDH. METHODS We perform a prospective genome-wide screen for CNVs using chromosomal microarrays on 75 fetuses referred with apparently isolated CDH, six of which were later reclassified as non-isolated CDH. RESULTS The results pinpoint haploinsufficiency of NR2F2 as a cause of CDH and cardiovascular malformations. In addition, the 15q25.2 and 16p11.2 recurrent microdeletions are associated with isolated CDH. By using gene prioritisation and network analysis, we provide strong evidence for several novel dosage-sensitive candidate genes associated with CDH. CONCLUSIONS Chromosomal microarray analysis detects submicroscopic CNVs associated with isolated CDH or CDH with cardiovascular malformations.
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Affiliation(s)
- P D Brady
- Centre for Human Genetics, KU Leuven/University Hospital Leuven, Leuven, Belgium
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19
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Devaney JM, Wang S, Funda S, Long J, Taghipour DJ, Tbaishat R, Furbert-Harris P, Ittmann M, Kwabi-Addo B. Identification of novel DNA-methylated genes that correlate with human prostate cancer and high-grade prostatic intraepithelial neoplasia. Prostate Cancer Prostatic Dis 2013; 16:292-300. [PMID: 23896626 DOI: 10.1038/pcan.2013.21] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Revised: 06/24/2013] [Accepted: 06/27/2013] [Indexed: 02/06/2023]
Abstract
BACKGROUND Prostate cancer (PCa) harbors a myriad of genomic and epigenetic defects. Cytosine methylation of CpG-rich promoter DNA is an important mechanism of epigenetic gene inactivation in PCa. There is considerable amount of data to suggest that DNA methylation-based biomarkers may be useful for the early detection and diagnosis of PCa. In addition, candidate gene-based studies have shown an association between specific gene methylation and alterations and clinicopathologic indicators of poor prognosis in PCa. METHODS To more comprehensively identify DNA methylation alterations in PCa initiation and progression, we examined the methylation status of 485 577 CpG sites from regions with a broad spectrum of CpG densities, interrogating both gene-associated and non-associated regions using the recently developed Illumina 450K methylation platform. RESULTS In all, we selected 33 promoter-associated novel CpG sites that were differentially methylated in high-grade prostatic intraepithelial neoplasia and PCa in comparison with benign prostate tissue samples (false discovery rate-adjusted P-value <0.05; β-value 0.2; fold change >1.5). Of the 33 genes, hierarchical clustering analysis demonstrated BNC1, FZD1, RPL39L, SYN2, LMX1B, CXXC5, ZNF783 and CYB5R2 as top candidate novel genes that are frequently methylated and whose methylation was associated with inactivation of gene expression in PCa cell lines. Pathway analysis of the genes with altered methylation patterns identified the involvement of a cancer-related network of genes whose activity may be regulated by TP53, MYC, TNF, IL1 and 6, IFN-γ and FOS in prostate pathogenesis. CONCLUSION Our genome-wide methylation profile shows epigenetic dysregulation of important regulatory signals in prostate carcinogenesis.
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Affiliation(s)
- J M Devaney
- Children's National Medical Center, Center for Genetic Medicine Research, Washington, DC, USA
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Loljung L, Coates PJ, Nekulova M, Laurell G, Wahlgren M, Wilms T, Widlöf M, Hansel A, Nylander K. High expression of p63 is correlated to poor prognosis in squamous cell carcinoma of the tongue. J Oral Pathol Med 2013; 43:14-9. [PMID: 23607508 DOI: 10.1111/jop.12074] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/04/2013] [Indexed: 01/09/2023]
Abstract
BACKGROUND p63 proteins are important in formation of the oral mucosa. Normal oral mucosa shows a balance between the six protein isoforms, whereas an imbalance between them is seen in squamous cell carcinomas (SCC). There is controversy over the clinical impact of p63 in SCC, which may relate to different expression in different areas. In addition, p63 isoforms can act as p53-like molecules (TAp63) or can inhibit p53 functions (ΔNp63) and expression of these isoforms varies in different tumours. Here, we chose to concentrate on the most common intra-oral sub-site, SCC of the mobile tongue. METHODS Total p63, ΔNp63 and TAp63 were analysed separately using immunohistochemistry. The percentage of cells and intensity of expression of different isoforms of p63 was evaluated using a quick score method and correlated with clinical data in a group of 87 patients with tongue SCC. RESULTS All tumours expressed p63 in at least 60% of the cells when using two different antibodies detecting all 6 isoforms. p63 expression correlated significantly with 2-year survival (P = 0.018), with fewer patients surviving 2 years if their tumours expressed p63 with strong intensity in at least 80% of the cells (quick score 18). Looking at 5-year survival, this was even more emphasized. ΔNp63 was expressed in all tumours, whereas expression of TAp63 was seen only in 59/87 patients, usually at very low levels. CONCLUSIONS Based on the present data, we recommend using expression of p63 as an additional factor contributing prognostic information in analysis of SCC in the tongue.
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Affiliation(s)
- Lotta Loljung
- Department of Medical Biosciences/Pathology, Umeå University, Umeå, Sweden
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