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Zhao Z, Song Z, Wang Z, Zhang F, Ding Z, Zhao Z, Liu L, Fan T. Retinol dehydrogenase 10 promotes epithelial-mesenchymal transition in spinal cord gliomas via PI3K/AKT pathway. Int J Immunopathol Pharmacol 2024; 38:3946320241276336. [PMID: 39180753 PMCID: PMC11344904 DOI: 10.1177/03946320241276336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 07/30/2024] [Indexed: 08/26/2024] Open
Abstract
Background: Spinal cord glioma (SCG), a rare subset of central nervous system (CNS) glioma, represents a complex challenge in neuro-oncology. There has been research showing that Retinol Dehydrogenase 10 (RDH10) may be a tumor promoting factor in brain glioma, but the biological effects of RDH10 remain undefined in SCG. Methods: We performed gene set enrichment analysis (GSEA) and unsupervised clustering analysis to investigate the roles of EMT (epithelial-mesenchymal transition) in glioma. DEG (differently expressed gene) screening and correlation analysis were conducted to filter the candidate genes which were closely associated with EMT process in SCG. Enrichment analysis and GSVA (Gene Set Variation Analysis) were conducted to investigate the potential mechanism of RDH10 for SCG. Trans-well and healing assay were performed to explore the role of RDH10 in the invasion of SCG. Western blotting was performed to evaluate the levels of markers in PI3K-AKT and EMT pathway. In vivo tests were conducted to verify the role of RDH10 in EMT process. Results: Bioinformatic analysis demonstrated the EMT pathway was associated with dismal prognosis of glioma. Further analysis demonstrated that RDH10 showed the strongest correlation with the EMT process. Retinol Dehydrogenase 10 expression was significantly increased in SCG tissues, correlating with advanced tumor grade and unfavorable prognosis. Functional analysis indicated that decreasing RDH10 levels impeded the invasive and migratory abilities of SCG cells, whereas increasing RDH10 levels augmented them. Enrichment analysis and western blot revealed that RDH10 regulated EMT process of SCG by PI3K-AKT pathway. We observed that the enhanced invasion ability and increased EMT-related protein induced by RDH10 overexpression can be suppressed by PI3K-AKT pathway inhibitor (LY294002). Conclusion: Our research found that RDH10 was an effective biomarker associated with tumor grade and prognosis of SCG. RDH10 could regulate EMT process of SCG through PI3K-AKT pathway.
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Affiliation(s)
- Zijun Zhao
- Spine Center, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Zihan Song
- Department of Neurosurgery, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Zairan Wang
- Department of Neurosurgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Fan Zhang
- Spine Center, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Ze Ding
- Spine Center, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Zongmao Zhao
- Department of Neurosurgery, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Liqiang Liu
- Department of Neurosurgery, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Tao Fan
- Spine Center, Sanbo Brain Hospital, Capital Medical University, Beijing, China
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Oldak L, Lukaszewski Z, Leśniewska A, Goławski K, Laudański P, Gorodkiewicz E. Development of an SPRi Test for the Quantitative Detection of Cadherin 12 in Human Plasma and Peritoneal Fluid. Int J Mol Sci 2023; 24:16894. [PMID: 38069216 PMCID: PMC10706750 DOI: 10.3390/ijms242316894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 11/24/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
A new method for the determination of cadherin 12 (CDH12)-an adhesive protein that has a significant impact on the development, growth, and movement of cancer cells-was developed and validated. The method is based on a biosensor using surface plasmon resonance imaging (SPRi) detection. A quartz crystal microbalance was used to analyze the characteristics of the formation of successive layers of the biosensor, from the linker monolayer to the final capture of CDH12 from solution. The association equilibrium constant (KA = 1.66 × 1011 dm3 mol-1) and the dissociation equilibrium constant (KD = 7.52 × 10-12 mol dm-3) of the anti-CDH12 antibody-CDH12 protein complex were determined. The determined analytical parameters, namely the values determining the accuracy, precision, and repeatability of the method, do not exceed the permissible 20% deviations specified by the aforementioned institutions. The proposed method is also selective with respect to possible potential interferents, occurring in up to 100-fold excess concentration relative to the CDH12 concentration. The determined Limit of Quantification (LOQ = 4.92 pg mL-1) indicates the possibility of performing quantitative analysis in human plasma or peritoneal fluid without the need to concentrate the samples; however, particular attention should be paid to their storage conditions, as the analyte does not exhibit high stability. The Passing-Bablok regression model revealed good agreement between the reference method and the SPRi biosensor, with ρSpearman values of 0.961 and 0.925.
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Affiliation(s)
- Lukasz Oldak
- Bioanalysis Laboratory, Faculty of Chemistry, University of Bialystok, Ciolkowskiego 1K, 15-245 Bialystok, Poland (E.G.)
| | - Zenon Lukaszewski
- Faculty of Chemical Technology, Poznan University of Technology, pl. Sklodowskiej-Curie 5, 60-965 Poznan, Poland
| | - Anna Leśniewska
- Bioanalysis Laboratory, Faculty of Chemistry, University of Bialystok, Ciolkowskiego 1K, 15-245 Bialystok, Poland (E.G.)
| | - Ksawery Goławski
- 1st Department of Obstetrics and Gynecology, Medical University of Warsaw, 02-091 Warsaw, Poland
| | - Piotr Laudański
- Department of Obstetrics, Gynecology and Gynecological Oncology, Medical University of Warsaw, 02-091 Warsaw, Poland
- OVIklinika Infertility Center, 01-377 Warsaw, Poland
- Women’s Health Research Institute, Calisia University, 62-800 Kalisz, Poland
| | - Ewa Gorodkiewicz
- Bioanalysis Laboratory, Faculty of Chemistry, University of Bialystok, Ciolkowskiego 1K, 15-245 Bialystok, Poland (E.G.)
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Šafanda A, Kendall Bártů M, Michálková R, Stružinská I, Drozenová J, Fabián P, Hausnerová J, Laco J, Matěj R, Škapa P, Švajdler M, Špůrková Z, Méhes G, Dundr P, Němejcová K. Immunohistochemical expression of PRAME in 485 cases of epithelial tubo-ovarian tumors. Virchows Arch 2023; 483:509-516. [PMID: 37610627 DOI: 10.1007/s00428-023-03629-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/21/2023] [Accepted: 08/14/2023] [Indexed: 08/24/2023]
Abstract
Preferentially expressed antigen of melanoma (PRAME) is a cancer/testis antigen selectively expressed in somatic tissues and various solid malignant tumors and is associated with poor prognostic outcome. Our research aimed to comprehensively compare its expression in a large cohort of tubo-ovarian epithelial tumors and examine its correlation with our clinico-pathologic data, as well as to assess its potential use in diagnostics and therapy.We examined 485 cases of epithelial tubo-ovarian tumors including 107 clear cell carcinomas (CCC), 52 endometroid carcinomas (EC), 103 high grade serous carcinomas (HGSC), 119 low grade serous carcinomas (LGSC)/micropapillary variant of serous borderline tumors (mSBT), and 104 cases of mucinous carcinomas (MC)/mucinous borderline tumors (MBT). The immunohistochemical analysis was performed using TMAs.The highest levels of expression were seen in EC (60%), HGSC (62%), and CCC (56%), while expression in LGSC/mSBT (4%) and MC/MBT (2%) was rare. The clinico-pathologic correlations and survival analysis showed no prognostic significance.The results of our study showed that PRAME is neither prognostic nor a suitable ancillary marker in the differential diagnosis of tubo-ovarian epithelial tumors. Nevertheless, knowledge about the PRAME expression may be important concerning its potential predictive significance, because targeting PRAME as a potential therapeutic option is currently under investigation.
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Affiliation(s)
- Adam Šafanda
- Department of Pathology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Studničkova 2, 12800, Prague 2, Czech Republic
| | - Michaela Kendall Bártů
- Department of Pathology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Studničkova 2, 12800, Prague 2, Czech Republic
| | - Romana Michálková
- Department of Pathology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Studničkova 2, 12800, Prague 2, Czech Republic
| | - Ivana Stružinská
- Department of Pathology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Studničkova 2, 12800, Prague 2, Czech Republic
| | - Jana Drozenová
- Department of Pathology, 3rd Faculty of Medicine, Charles University, University Hospital Kralovske Vinohrady, 10034, Prague, Czech Republic
| | - Pavel Fabián
- Department of Oncological Pathology, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Jitka Hausnerová
- Department of Pathology, University Hospital Brno and Medical Faculty, Masaryk University, Brno, Czech Republic
| | - Jan Laco
- The Fingerland Department of Pathology, Charles University Faculty of Medicine in Hradec Králové and University Hospital Hradec Králové, Hradec Králové, Czech Republic
| | - Radoslav Matěj
- Department of Pathology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Studničkova 2, 12800, Prague 2, Czech Republic
- Department of Pathology, 3rd Faculty of Medicine, Charles University, University Hospital Kralovske Vinohrady, 10034, Prague, Czech Republic
- Department of Pathology and Molecular Medicine, Third Faculty of Medicine, Charles University, Thomayer University Hospital, Prague, Czech Republic
| | - Petr Škapa
- Department of Pathology and Molecular Medicine, Second Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Marián Švajdler
- Šikl's Department of Pathology, The Faculty of Medicine and Faculty Hospital in Pilsen, Charles University, Pilsen, Czech Republic
| | - Zuzana Špůrková
- Department of Pathology, Bulovka Hospital, Prague, Czech Republic
| | - Gábor Méhes
- Department of Pathology, Faculty of Medicine, University of Debrecen, 4032, Debrecen, Hungary
| | - Pavel Dundr
- Department of Pathology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Studničkova 2, 12800, Prague 2, Czech Republic
| | - Kristýna Němejcová
- Department of Pathology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Studničkova 2, 12800, Prague 2, Czech Republic.
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Li Y, Kan X. Mendelian randomization analysis to analyze the genetic causality between different levels of obesity and different allergic diseases. BMC Pulm Med 2023; 23:352. [PMID: 37723557 PMCID: PMC10508031 DOI: 10.1186/s12890-023-02636-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 09/06/2023] [Indexed: 09/20/2023] Open
Abstract
BACKGROUND The causal relationship between obesity and different allergic diseases remains controversial. METHODS The Two Sample MR package and Phenoscanner database were used to obtain and filter Genome-Wide Association Study (GWAS) data from the Open GWAS database. Mendelian randomization (MR) analysis was used to study the causal relationship between different levels of obesity and different allergic diseases. The data sets related to obesity and asthma were obtained from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were screened by the limma package. Cluster Profiler and GO plot packages were used for enrichment analysis to verify the results of MR analysis. RESULTS Two-sample MR analysis showed a causal relationship between obesity and childhood allergy (age < 16), allergic asthma and atopic dermatitis (P < 0.05). In addition, there was also a causal relationship between allergic asthma and obesity (P < 0.05), while there was no genetic causal relationship between obesity and allergic rhinitis, eczema, lactose intolerance and so on (P > 0.05). Subgroup analysis revealed a causal relationship between both class 1 and class 2 obesity and childhood allergy (age < 16) (P < 0.05). Obesity class 1 was associated with allergic asthma, while obesity class 3 was associated with atopic dermatitis (P < 0.05). Bioinformatics analysis shows that there were common DEGs between obesity and allergic asthma. CONCLUSION Obesity is a risk factor for childhood allergy (age < 16), allergic asthma and atopic dermatitis, while allergic asthma is also a risk factor for obesity. Class 1 and class 2 obesity are both causally associated with childhood allergy (age < 16). In addition, there is a causal relationship between milder obesity and allergic asthma, while heavier obesity is causally related to atopic dermatitis.
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Affiliation(s)
- Yujian Li
- Department of Pediatrics, General Hospital of Tianjin Medical University, No. 154, Anshan Road, Heping District, 300052, Tianjin, China
| | - Xuan Kan
- Department of Pediatrics, General Hospital of Tianjin Medical University, No. 154, Anshan Road, Heping District, 300052, Tianjin, China.
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Ponomaryova AA, Schegoleva AA, Gervas PA, Pancova OV, Gerashchenko TS, Zarubin AA, Perelmuter VM, Cherdyntseva NV, Denisov EV. DNA methylome analysis reveals potential alterations contributing to the progression of bronchial hyperplasia. Mol Biol Rep 2023; 50:7941-7947. [PMID: 37480511 DOI: 10.1007/s11033-023-08571-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/31/2023] [Indexed: 07/24/2023]
Abstract
BACKGROUND Squamous cell lung cancer (SCLC) arises from bronchial changes: basal cell hyperplasia (BCH), squamous metaplasia (SM), and dysplasia. However, the premalignant process preceding SCLC is not inevitable; it can stop at any of the bronchial lesions. Previously, we hypothesized that combinations of premalignant lesions observed in the small bronchi of SCLC patients can reflect the different "scenarios" of the premalignant process: BCHi-the stoppage at the stage of hyperplasia and BCHSM-the progression of hyperplasia to metaplasia. METHODS AND RESULTS In this study, using whole-genome bisulfite sequencing we analyzed the DNA methylome of two forms of BCH: isolated BCH (BCHi) and BCH co-occurred with SM (BCHSM) in the small bronchi of SCLC patients. It was shown that BCHi harbored differentially methylated regions (DMRs) affecting genes associated with regulating phosphatase activity. In BCHSM, DMRs were found in genes involved in PI3K-Akt and AMPK signaling pathways. DMRs were also found to affect specific miRNA genes: miR-34a and miR-3648 in BCHi and miR-924 and miR-100 in BCHSM. CONCLUSIONS Thus, this study demonstrated the significant changes in DNA methylome between the isolated BCH and BCH combined with SM. The identified epigenetic alterations may underlie different "scenarios" of the premalignant process in the bronchial epithelium.
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Affiliation(s)
- A A Ponomaryova
- Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia.
| | - A A Schegoleva
- Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia
- National Research Tomsk State University, Tomsk, Russia
| | - P A Gervas
- Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia
| | - O V Pancova
- Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia
| | - T S Gerashchenko
- Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia
| | - A A Zarubin
- Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia
| | - V M Perelmuter
- Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia
| | - N V Cherdyntseva
- Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia
- National Research Tomsk State University, Tomsk, Russia
| | - E V Denisov
- Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia
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D MO, C TZ, R SP. Human orphan cytochromes P450: An update. Curr Drug Metab 2022; 23:CDM-EPUB-128186. [PMID: 36503398 DOI: 10.2174/1389200224666221209153032] [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: 08/05/2022] [Revised: 10/25/2022] [Accepted: 11/11/2022] [Indexed: 12/14/2022]
Abstract
Orphan cytochromes P450 (CYP) are enzymes whose biological functions and substrates are unknown. However, the use of new experimental strategies has allowed obtaining more information about their relevance in the metabolism of endogenous and exogenous compounds. Likewise, the modulation of their expression and activity has been associated with pathogenesis and prognosis in different diseases. In this work, we review the regulatory pathways and the possible role of orphan CYP to provide evidence that allow us to stop considering some of them as orphan enzymes and to propose them as possible therapeutic targets in the design of new strategies for the treatment of diseases associated with CYP-mediated metabolism.
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Affiliation(s)
- Molina-Ortiz D
- Laboratorio de Toxicología Genética, Instituto Nacional de Pediatría, Coyoacán, Mexico City, México, 04530
| | - Torres-Zárate C
- Laboratorio de Toxicología Genética, Instituto Nacional de Pediatría, Coyoacán, Mexico City, México, 04530
| | - Santes-Palacios R
- Laboratorio de Toxicología Genética, Instituto Nacional de Pediatría, Coyoacán, Mexico City, México, 04530
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Decreased TSPAN14 Expression Contributes to NSCLC Progression. Life (Basel) 2022; 12:life12091291. [PMID: 36143328 PMCID: PMC9506201 DOI: 10.3390/life12091291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/08/2022] [Accepted: 08/18/2022] [Indexed: 11/18/2022] Open
Abstract
Tspan14 is a transmembrane protein of the tetraspanin (Tspan) protein family. Different members of the Tspan family can promote or suppress tumor progression. The exact role of Tspan14 in tumor cells is unknown. Earlier, mutational inactivation of the TSPAN14 gene has been proposed to coincide with a low survival rate in NSCLC patients. This study aimed to investigate the correlation of TSPAN14 lack of function with clinicopathological features of NSCLC patients, and to elucidate the role TSPAN14 might have in NSCLC progression. TSPAN14 expression was lower in tumor cells than non-tumor cells in NSCLC patients’ samples. The decreased gene expression was correlated with a low survival rate of patients and was more frequent in patients with aggressive, invasive tumor types. Additionally, the role of decreased TSPAN14 expression in the metastatic potential of cancer cells was confirmed in NSCLC cell lines. The highly invasive NSCLC cell line (NCI-H661) had the lowest TSPAN14 gene and protein expression, whereas the NSCLC cell line with the highest TSPAN14 expression (NCI-H460) had no significant metastatic potential. Finally, silencing of TSPAN14 in these non-metastatic cancer cells caused an increased expression of matrix-degrading enzymes MMP-2 and MMP-9, followed by an elevated capacity of cancer cells to degrade gelatin. The results of this study propose TSPAN14 expression as an indicator of NSCLC metastatic potential and progression.
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Zhang Z, Wang L, Zhao L, Wang Q, Yang C, Zhang M, Wang B, Jiang K, Ye Y, Wang S, Shen Z. N6-methyladenosine demethylase ALKBH5 suppresses colorectal cancer progression potentially by decreasing PHF20 mRNA methylation. Clin Transl Med 2022; 12:e940. [PMID: 35979628 PMCID: PMC9386323 DOI: 10.1002/ctm2.940] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 05/30/2022] [Accepted: 06/06/2022] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND As the most widespread mRNAs modification, N6-methyladenosine (m6 A) is dynamically and reversibly modulated by methyltransferases and demethylases. ALKBH5 is a major demethylase, and plays vital roles in the progression of cancers. However, the role and mechanisms of ALKBH5 in colorectal cancer (CRC) is unclear. RESULTS Herein, we discovered that in CRC, downregulated ALKBH5 was closely related to poor prognosis of CRC patients. Functionally, our results demonstrated that knockdown of ALKBH5 enhanced the proliferation, migration and invasion of LOVO and RKO in vitro, while overexpression of ALKBH5 inhibited the functions of these cells. The results also demonstrated that knockdown of ALKBH5 promoted subcutaneous tumorigenesis of LOVO in vivo, while overexpression of ALKBH5 suppressed this ability. Mechanistically, results from joint analyses of MeRIP-seq and RNA-seq indicated that PHF20 mRNA was a key molecule that was regulated by ALKBH5-mediated m6 A modification. Further experiments indicated that ALKBH5 may inhibit stability of PHF20 mRNA by removing the m6 A modification of PHF20 mRNA 3'UTR. CONCLUSIONS ALKBH5 suppresses CRC progression by decreasing PHF20 mRNA methylation. ALKBH5-mediated m6 A modification of PHF20 mRNA can serve as a hopeful strategy for the intervention and treatment of CRC.
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Affiliation(s)
- Zhen Zhang
- Department of Gastroenterological SurgeryPeking University People's HospitalBeijingChina
- Laboratory of Surgical OncologyBeijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment ResearchPeking University People's HospitalBeijingChina
| | - Ling Wang
- Department of Medical OncologyAffiliated Hangzhou First People's HospitalZhejiang University School of MedicineHangzhouChina
| | - Long Zhao
- Department of Gastroenterological SurgeryPeking University People's HospitalBeijingChina
- Laboratory of Surgical OncologyBeijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment ResearchPeking University People's HospitalBeijingChina
| | - Quan Wang
- Department of Gastroenterological SurgeryPeking University People's HospitalBeijingChina
- Laboratory of Surgical OncologyBeijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment ResearchPeking University People's HospitalBeijingChina
| | - Changjiang Yang
- Department of Gastroenterological SurgeryPeking University People's HospitalBeijingChina
- Laboratory of Surgical OncologyBeijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment ResearchPeking University People's HospitalBeijingChina
| | - Mengmeng Zhang
- Department of Gastroenterological SurgeryPeking University People's HospitalBeijingChina
- Laboratory of Surgical OncologyBeijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment ResearchPeking University People's HospitalBeijingChina
| | - Bo Wang
- Department of Gastroenterological SurgeryPeking University People's HospitalBeijingChina
- Laboratory of Surgical OncologyBeijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment ResearchPeking University People's HospitalBeijingChina
| | - Kewei Jiang
- Department of Gastroenterological SurgeryPeking University People's HospitalBeijingChina
- Laboratory of Surgical OncologyBeijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment ResearchPeking University People's HospitalBeijingChina
| | - Yingjiang Ye
- Department of Gastroenterological SurgeryPeking University People's HospitalBeijingChina
- Laboratory of Surgical OncologyBeijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment ResearchPeking University People's HospitalBeijingChina
| | - Shan Wang
- Department of Gastroenterological SurgeryPeking University People's HospitalBeijingChina
- Laboratory of Surgical OncologyBeijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment ResearchPeking University People's HospitalBeijingChina
| | - Zhanlong Shen
- Department of Gastroenterological SurgeryPeking University People's HospitalBeijingChina
- Laboratory of Surgical OncologyBeijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment ResearchPeking University People's HospitalBeijingChina
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Herrera‐Luis E, Ortega VE, Ampleford EJ, Sio YY, Granell R, de Roos E, Terzikhan N, Vergara E, Hernandez‐Pacheco N, Perez‐Garcia J, Martin‐Gonzalez E, Lorenzo‐Diaz F, Hashimoto S, Brinkman P, Jorgensen AL, Yan Q, Forno E, Vijverberg SJ, Lethem R, Espuela‐Ortiz A, Gorenjak M, Eng C, González‐Pérez R, Hernández‐Pérez JM, Poza‐Guedes P, Sardón O, Corcuera P, Hawkins G, Marsico A, Bahmer T, Rabe KF, Hansen G, Kopp MV, Rios R, Cruz M, González‐Barcala F, Olaguibel JM, Plaza V, Quirce S, Canino G, Cloutier M, del Pozo V, Rodriguez‐Santana JR, Korta‐Murua J, Villar J, Potočnik U, Figueiredo C, Kabesch M, Mukhopadhyay S, Pirmohamed M, Hawcutt D, Melén E, Palmer CN, Turner S, Maitland‐van der Zee AH, von Mutius E, Celedón JC, Brusselle G, Chew FT, Bleecker E, Meyers D, Burchard EG, Pino‐Yanes M. Multi-ancestry genome-wide association study of asthma exacerbations. Pediatr Allergy Immunol 2022; 33:e13802. [PMID: 35754128 PMCID: PMC9671132 DOI: 10.1111/pai.13802] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 05/01/2022] [Accepted: 05/04/2022] [Indexed: 12/11/2022]
Abstract
BACKGROUND Asthma exacerbations are a serious public health concern due to high healthcare resource utilization, work/school productivity loss, impact on quality of life, and risk of mortality. The genetic basis of asthma exacerbations has been studied in several populations, but no prior study has performed a multi-ancestry meta-analysis of genome-wide association studies (meta-GWAS) for this trait. We aimed to identify common genetic loci associated with asthma exacerbations across diverse populations and to assess their functional role in regulating DNA methylation and gene expression. METHODS A meta-GWAS of asthma exacerbations in 4989 Europeans, 2181 Hispanics/Latinos, 1250 Singaporean Chinese, and 972 African Americans analyzed 9.6 million genetic variants. Suggestively associated variants (p ≤ 5 × 10-5 ) were assessed for replication in 36,477 European and 1078 non-European asthma patients. Functional effects on DNA methylation were assessed in 595 Hispanic/Latino and African American asthma patients and in publicly available databases. The effect on gene expression was evaluated in silico. RESULTS One hundred and twenty-six independent variants were suggestively associated with asthma exacerbations in the discovery phase. Two variants independently replicated: rs12091010 located at vascular cell adhesion molecule-1/exostosin like glycosyltransferase-2 (VCAM1/EXTL2) (discovery: odds ratio (ORT allele ) = 0.82, p = 9.05 × 10-6 and replication: ORT allele = 0.89, p = 5.35 × 10-3 ) and rs943126 from pantothenate kinase 1 (PANK1) (discovery: ORC allele = 0.85, p = 3.10 × 10-5 and replication: ORC allele = 0.89, p = 1.30 × 10-2 ). Both variants regulate gene expression of genes where they locate and DNA methylation levels of nearby genes in whole blood. CONCLUSIONS This multi-ancestry study revealed novel suggestive regulatory loci for asthma exacerbations located in genomic regions participating in inflammation and host defense.
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Affiliation(s)
- Esther Herrera‐Luis
- Genomics and Health GroupDepartment of Biochemistry, Microbiology, Cell Biology and GeneticsUniversidad de La Laguna (ULL)San Cristóbal de La Laguna, TenerifeSpain
| | - Victor E. Ortega
- Division of Respiratory MedicineDepartment of Internal MedicineMayo ClinicScottsdaleArizonaUSA
| | - Elizabeth J. Ampleford
- Department of Internal MedicineCenter for Precision MedicineWake Forest School of MedicineWinston‐SalemNorth CarolinaUSA
| | - Yang Yie Sio
- Department of Biological SciencesNational University of SingaporeSingapore CitySingapore
| | - Raquel Granell
- MRC Integrative Epidemiology Unit (IEU)Population Health SciencesBristol Medical SchoolUniversity of BristolBristolUK
| | - Emmely de Roos
- Department of EpidemiologyErasmus University Medical CenterRotterdamThe Netherlands
- Department of Respiratory MedicineGhent University HospitalGhentBelgium
| | - Natalie Terzikhan
- Department of EpidemiologyErasmus University Medical CenterRotterdamThe Netherlands
- Department of Respiratory MedicineGhent University HospitalGhentBelgium
| | - Ernesto Elorduy Vergara
- Institute of Computation BiologyHelmholtz Zentrum MünchenGerman Research Center for Environmental HealthMunichGermany
| | - Natalia Hernandez‐Pacheco
- Department of Clinical Sciences and EducationSödersjukhusetKarolinska InstitutetStockholmSweden
- CIBER de Enfermedades Respiratorias (CIBERES)MadridSpain
| | - Javier Perez‐Garcia
- Genomics and Health GroupDepartment of Biochemistry, Microbiology, Cell Biology and GeneticsUniversidad de La Laguna (ULL)San Cristóbal de La Laguna, TenerifeSpain
| | - Elena Martin‐Gonzalez
- Genomics and Health GroupDepartment of Biochemistry, Microbiology, Cell Biology and GeneticsUniversidad de La Laguna (ULL)San Cristóbal de La Laguna, TenerifeSpain
| | - Fabian Lorenzo‐Diaz
- Genomics and Health GroupDepartment of Biochemistry, Microbiology, Cell Biology and GeneticsUniversidad de La Laguna (ULL)San Cristóbal de La Laguna, TenerifeSpain
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias (IUETSPC)Universidad de La Laguna (ULL)San Cristóbal de La Laguna, TenerifeSpain
| | - Simone Hashimoto
- Department of Respiratory MedicineAmsterdam University Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands
| | - Paul Brinkman
- Department of Respiratory MedicineAmsterdam University Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands
| | | | - Andrea L. Jorgensen
- Department of Health Data ScienceInstitute of Population HealthUniversity of LiverpoolLiverpoolUK
| | - Qi Yan
- Department of Obstetrics and GynecologyColumbia University Irving Medical CenterNew YorkNew YorkUSA
| | - Erick Forno
- Division of Pediatric Pulmonary MedicineUPMC Children's Hospital of PittsburghUniversity of PittsburghPittsburghPennsylvaniaUSA
| | - Susanne J. Vijverberg
- Department of Respiratory MedicineAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
- Division of Pharmacoepidemiology and Clinical PharmacologyFaculty of ScienceUtrecht UniversityUtrechtThe Netherlands
- Department of Paediatric Respiratory Medicine and AllergyEmma's Children HospitalAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
| | - Ryan Lethem
- MRC Integrative Epidemiology Unit (IEU)Population Health SciencesBristol Medical SchoolUniversity of BristolBristolUK
| | - Antonio Espuela‐Ortiz
- Genomics and Health GroupDepartment of Biochemistry, Microbiology, Cell Biology and GeneticsUniversidad de La Laguna (ULL)San Cristóbal de La Laguna, TenerifeSpain
| | - Mario Gorenjak
- Center for Human Molecular Genetics and PharmacogenomicsFaculty of MedicineUniversity of MariborMariborSlovenia
| | - Celeste Eng
- Department of MedicineUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Ruperto González‐Pérez
- Allergy DepartmentHospital Universitario de CanariasSanta Cruz de TenerifeTenerifeSpain
- Severe Asthma Unit, Allergy DepartmentHospital Universitario de CanariasSanta Cruz de TenerifeTenerifeSpain
| | - José M. Hernández‐Pérez
- Pulmonary MedicineHospital Universitario de N.S de CandelariaSanta Cruz de TenerifeSpain
- Pulmonary MedicineHospital General de La PalmaLa Palma, Santa Cruz de TenerifeSpain
| | - Paloma Poza‐Guedes
- Allergy DepartmentHospital Universitario de CanariasSanta Cruz de TenerifeTenerifeSpain
- Severe Asthma Unit, Allergy DepartmentHospital Universitario de CanariasSanta Cruz de TenerifeTenerifeSpain
| | - Olaia Sardón
- Division of Pediatric Respiratory MedicineHospital Universitario DonostiaSan SebastiánSpain
- Department of PediatricsUniversity of the Basque Country (UPV/EHU)San SebastiánSpain
| | - Paula Corcuera
- Division of Pediatric Respiratory MedicineHospital Universitario DonostiaSan SebastiánSpain
| | - Greg A. Hawkins
- Department of BiochemistryWake Forest School of MedicineWinston‐SalemNorth CarolinaUSA
| | - Annalisa Marsico
- Computational Health CenterHelmholtz Zentrum MünchenGerman Research Center for Environmental HealthMunichGermany
| | - Thomas Bahmer
- LungenClinic Grosshansdorf, PneumologyGrosshansdorfGermany
- Airway Research Center North (ARCN)Members of the Germany Center for Lung Research (DZL)GrosshansdorfGermany
| | - Klaus F. Rabe
- LungenClinic Grosshansdorf, PneumologyGrosshansdorfGermany
- Airway Research Center North (ARCN)Members of the Germany Center for Lung Research (DZL)GrosshansdorfGermany
| | - Gesine Hansen
- Department of Pediatric Pneumology, Allergology and NeonatologyHannover Medical SchoolHannoverGermany
| | - Matthias Volkmar Kopp
- Division of Pediatric Pneumology & AllergologyUniversity Medical Center Schleswig‐HolsteinLübeckGermany
- Airway Research Center North (ARCN)Members of the Germany Center for Lung Research (DZL)LübeckGermany
- Department of Paediatric Respiratory MedicineInselspitalUniversity Children's Hospital of BernUniversity of BernBernSwitzerland
| | - Raimon Rios
- Programa de Pós Graduação em Imunologia (PPGIm)Instituto de Ciências da SaúdeUniversidade Federal da Bahia (UFBA)SalvadorBrazil
| | - Maria Jesus Cruz
- CIBER de Enfermedades Respiratorias (CIBERES)MadridSpain
- Servicio de NeumologíaHospital Vall d’HebronBarcelonaSpain
| | | | - José María Olaguibel
- CIBER de Enfermedades Respiratorias (CIBERES)MadridSpain
- Servicio de AlergologíaComplejo Hospitalario de NavarraPamplonaNavarraSpain
| | - Vicente Plaza
- CIBER de Enfermedades Respiratorias (CIBERES)MadridSpain
- Departamento de Medicina RespiratoriaHospital de la Santa Creu i Sant PauInstituto de Investigación Biomédica Sant Pau (IIB Sant Pau)BarcelonaSpain
| | - Santiago Quirce
- CIBER de Enfermedades Respiratorias (CIBERES)MadridSpain
- Department of AllergyLa Paz University HospitalIdiPAZMadridSpain
| | - Glorisa Canino
- Behavioral Sciences Research InstituteUniversity of Puerto RicoSan JuanPuerto Rico
| | - Michelle Cloutier
- Department of PediatricsUniversity of ConnecticutFarmingtonConnecticutUSA
| | - Victoria del Pozo
- CIBER de Enfermedades Respiratorias (CIBERES)MadridSpain
- Immunology DepartmentInstituto de Investigación Sanitaria Hospital Universitario Fundación Jiménez DíazMadridSpain
| | | | - Javier Korta‐Murua
- Department of PediatricsUniversity of the Basque Country (UPV/EHU)San SebastiánSpain
| | - Jesús Villar
- CIBER de Enfermedades Respiratorias (CIBERES)MadridSpain
- Multidisciplinary Organ Dysfunction Evaluation Research NetworkResearch UnitHospital Universitario Dr. NegrínLas Palmas de Gran CanariaSpain
| | - Uroš Potočnik
- Laboratory for Biochemistry, Molecular Biology and GenomicsFaculty for Chemistry and Chemical EngineeringUniversity of MariborMariborSlovenia
| | - Camila Figueiredo
- Instituto de Ciências da SaúdeUniversidade Federal da BahiaSalvadorBrazil
| | - Michael Kabesch
- Department of Paediatric Pneumology and AllergyUniversity Children's Hospital Regensburg (KUNO)RegensburgGermany
| | - Somnath Mukhopadhyay
- Academic Department of PaediatricsBrighton and Sussex Medical School, Royal Alexandra Children's HospitalBrightonUK
- Population Pharmacogenetics GroupBiomedical Research InstituteNinewells Hospital and Medical SchoolUniversity of DundeeDundeeUK
| | - Munir Pirmohamed
- Department of Pharmacology and TherapeuticsInstitute of Systems, Molecular and Integrative BiologyUniversity of LiverpoolLiverpoolUK
| | - Daniel B. Hawcutt
- Department of Women's and Children's HealthUniversity of LiverpoolLiverpoolUK
- Alder Hey Children's HospitalLiverpoolUK
- NIHR Alder Hey Clinical Research FacilityAlder Hey Children's HospitalLiverpoolUK
| | - Erik Melén
- Department of Clinical Sciences and EducationSödersjukhusetKarolinska InstitutetStockholmSweden
- Sachs’ Children’s HospitalSouth General HospitalStockholmSweden
| | - Colin N. Palmer
- Population Pharmacogenetics GroupBiomedical Research InstituteNinewells Hospital and Medical SchoolUniversity of DundeeDundeeUK
| | | | - Anke H. Maitland‐van der Zee
- Department of Respiratory MedicineAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
- Division of Pharmacoepidemiology and Clinical PharmacologyFaculty of ScienceUtrecht UniversityUtrechtThe Netherlands
- Department of Paediatric Respiratory Medicine and AllergyEmma's Children HospitalAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
| | - Erika von Mutius
- Institute for Asthma and Allergy PreventionHelmholtz Zentrum MünchenGerman Research Center for Environmental HealthMunichGermany
- Dr von Hauner Children's HospitalLudwig‐Maximilians‐UniversitätMunichGermany
- Comprehensive Pneumology Center Munich (CPC‐M)Member of the German Center for Lung ResearchMunichGermany
| | - Juan C. Celedón
- Division of Pediatric Pulmonary MedicineUPMC Children's Hospital of PittsburghUniversity of PittsburghPittsburghPennsylvaniaUSA
| | - Guy Brusselle
- Department of EpidemiologyErasmus University Medical CenterRotterdamThe Netherlands
- Department of Respiratory MedicineGhent University HospitalGhentBelgium
- Department of Respiratory MedicineErasmus University Medical CenterRotterdamThe Netherlands
| | - Fook Tim Chew
- Department of Biological SciencesNational University of SingaporeSingapore CitySingapore
| | - Eugene Bleecker
- Division of Genetics, Genomics, and Precision MedicineDepartment of Internal MedicineUniversity of Arizona College of MedicineTucsonArizonaUSA
| | - Deborah Meyers
- Division of Genetics, Genomics, and Precision MedicineDepartment of Internal MedicineUniversity of Arizona College of MedicineTucsonArizonaUSA
| | - Esteban G. Burchard
- Severe Asthma Unit, Allergy DepartmentHospital Universitario de CanariasSanta Cruz de TenerifeTenerifeSpain
- Department of Bioengineering and Therapeutic SciencesUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Maria Pino‐Yanes
- Genomics and Health GroupDepartment of Biochemistry, Microbiology, Cell Biology and GeneticsUniversidad de La Laguna (ULL)San Cristóbal de La Laguna, TenerifeSpain
- CIBER de Enfermedades Respiratorias (CIBERES)MadridSpain
- Instituto de Tecnologías Biomédicas (ITB)Universidad de La Laguna (ULL)San Cristóbal de La Laguna, TenerifeSpain
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10
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Li F, Wan B, Li XQ. Expression Profile and Prognostic Values of CDH Family Members in Lung Adenocarcinoma. DISEASE MARKERS 2022; 2022:9644466. [PMID: 35242247 PMCID: PMC8886772 DOI: 10.1155/2022/9644466] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 12/12/2022]
Abstract
Many studies have confirmed that the classical cadherin (CDH) gene family may be involved in the development and progression of various tumors. However, the comprehensive assays of CDH family members in lung adenocarcinoma (LUAD) were rarely reported. In this study, our group analyzed TCGA datasets and identified 18 dysregulated CDH members in LUAD specimens. Several CDH members exhibited an increased level in LUAD specimens, such as CDH1, CDH2, CDH3, CDH4, CDH5, CDH15, CDH16, CDH17, CDH18, CDH24, and CDH26. However, some others exhibited decreased levels in LUAD specimens. Correlation analysis revealed that most CDH members were negatively regulated by the methylation of CDH genes, leading to their low expression in LUAD tissues. Survival assays identified 16 survival-related CDH members in LUAD patients. More importantly, we further performed multivariate analysis to determine the prognostic value of the above CDH family members and found that the expression levels of CDH17, CDH19, and CDH24 were an independent prognostic biomarker of the LUAD outcome. Finally, the results of functional enrichments revealed that CDH members participated in several tumor-related pathways. Collectively, our findings suggest that CDH Family members functioned as oncogenes or antioncogenes in LUAD and may be a potential biomarker for this malignancy.
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Affiliation(s)
- Feng Li
- Department of Oncology, The Chongqing Hospital of Traditional Chinese Medicine, Jiangbei District, Chongqing, China
| | - Bin Wan
- Physical Examination Center, The Chongqing Hospital of Traditional Chinese Medicine, Jiangbei District, Chongqing, China
| | - Xiao-qing Li
- Department of Oncology, The Chongqing Hospital of Traditional Chinese Medicine, Jiangbei District, Chongqing, China
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11
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Van HT, Harkins PR, Patel A, Jain AK, Lu Y, Bedford MT, Santos MA. Methyl-lysine readers PHF20 and PHF20L1 define two distinct gene expression-regulating NSL complexes. J Biol Chem 2022; 298:101588. [PMID: 35033534 PMCID: PMC8867114 DOI: 10.1016/j.jbc.2022.101588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 01/06/2022] [Accepted: 01/08/2022] [Indexed: 11/16/2022] Open
Abstract
The methyl-lysine readers plant homeodomain finger protein 20 (PHF20) and its homolog PHF20-like protein 1 (PHF20L1) are known components of the nonspecific lethal (NSL) complex that regulates gene expression through its histone acetyltransferase activity. In the current model, both PHF homologs coexist in the same NSL complex, although this was not formally tested; nor have the functions of PHF20 and PHF20L1 regarding NSL complex integrity and transcriptional regulation been investigated. Here, we perform an in-depth biochemical and functional characterization of PHF20 and PHF20L1 in the context of the NSL complex. Using mass spectrometry, genome-wide chromatin analysis, and protein-domain mapping, we identify the existence of two distinct NSL complexes that exclusively contain either PHF20 or PHF20L1. We show that the C-terminal domains of PHF20 and PHF20L1 are essential for complex formation with NSL, and the Tudor 2 domains are required for chromatin binding. The genome-wide chromatin landscape of PHF20–PHF20L1 shows that these proteins bind mostly to the same genomic regions, at promoters of highly expressed/housekeeping genes. Yet, deletion of PHF20 and PHF20L1 does not abrogate gene expression or impact the recruitment of the NSL complex to those target gene promoters, suggesting the existence of an alternative mechanism that compensates for the transcription of genes whose sustained expression is important for critical cellular functions. This work shifts the current paradigm and lays the foundation for studies on the differential roles of PHF20 and PHF20L1 in regulating NSL complex activity in physiological and diseases states.
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Affiliation(s)
- Hieu T Van
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA; Graduate Program in Genetics & Epigenetics, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, Texas, USA
| | - Peter R Harkins
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Avni Patel
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Abhinav K Jain
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Yue Lu
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Mark T Bedford
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Margarida A Santos
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.
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12
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Martinez-Pastor B, Silveira GG, Clarke TL, Chung D, Gu Y, Cosentino C, Davidow LS, Mata G, Hassanieh S, Salsman J, Ciccia A, Bae N, Bedford MT, Megias D, Rubin LL, Efeyan A, Dellaire G, Mostoslavsky R. Assessing kinetics and recruitment of DNA repair factors using high content screens. Cell Rep 2021; 37:110176. [PMID: 34965416 PMCID: PMC8763642 DOI: 10.1016/j.celrep.2021.110176] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 10/08/2021] [Accepted: 12/04/2021] [Indexed: 11/30/2022] Open
Abstract
Repair of genetic damage is coordinated in the context of chromatin, so cells dynamically modulate accessibility at DNA breaks for the recruitment of DNA damage response (DDR) factors. The identification of chromatin factors with roles in DDR has mostly relied on loss-of-function screens while lacking robust high-throughput systems to study DNA repair. In this study, we have developed two high-throughput systems that allow the study of DNA repair kinetics and the recruitment of factors to double-strand breaks in a 384-well plate format. Using a customized gain-of-function open-reading frame library ("ChromORFeome" library), we identify chromatin factors with putative roles in the DDR. Among these, we find the PHF20 factor is excluded from DNA breaks, affecting DNA repair by competing with 53BP1 recruitment. Adaptable for genetic perturbations, small-molecule screens, and large-scale analysis of DNA repair, these resources can aid our understanding and manipulation of DNA repair.
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Affiliation(s)
- Barbara Martinez-Pastor
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114, USA; Molecular Oncology Program, Spanish National Cancer Research Center (CNIO), Madrid 28029, Spain.
| | - Giorgia G Silveira
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114, USA; The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Thomas L Clarke
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114, USA; The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Dudley Chung
- Department of Pathology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Yuchao Gu
- School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Claudia Cosentino
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114, USA
| | - Lance S Davidow
- Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Gadea Mata
- Confocal Microscopy Unit, Spanish National Cancer Research Center (CNIO), Madrid 28029, Spain
| | - Sylvana Hassanieh
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114, USA
| | - Jayme Salsman
- Department of Pathology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Alberto Ciccia
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA
| | - Narkhyun Bae
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
| | - Mark T Bedford
- Department of Epigenetics & Molecular Carcinogenesis, M.D.Anderson Cancer Center, University of Texas, Smithville, TX 78957, USA
| | - Diego Megias
- Confocal Microscopy Unit, Spanish National Cancer Research Center (CNIO), Madrid 28029, Spain
| | - Lee L Rubin
- Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Alejo Efeyan
- Molecular Oncology Program, Spanish National Cancer Research Center (CNIO), Madrid 28029, Spain
| | - Graham Dellaire
- Department of Pathology, Dalhousie University, Halifax, NS B3H 4R2, Canada; Beatrice Hunter Cancer Research Institute, Halifax, NS B3H 4R2, Canada.
| | - Raul Mostoslavsky
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114, USA; The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
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13
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Guo B, Qi M, Huang S, Zhuo R, Zhang W, Zhang Y, Xu M, Liu M, Guan T, Liu Y. Cadherin-12 Regulates Neurite Outgrowth Through the PKA/Rac1/Cdc42 Pathway in Cortical Neurons. Front Cell Dev Biol 2021; 9:768970. [PMID: 34820384 PMCID: PMC8606577 DOI: 10.3389/fcell.2021.768970] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 10/11/2021] [Indexed: 12/22/2022] Open
Abstract
Cadherins play an important role in tissue homeostasis, as they are responsible for cell-cell adhesion during embryogenesis, tissue morphogenesis, and differentiation. In this study, we identified Cadherin-12 (CDH12), which encodes a type II classical cadherin, as a gene that promotes neurite outgrowth in an in vitro model of neurons with differentiated intrinsic growth ability. First, the effects of CDH12 on neurons were evaluated via RNA interference, and the results indicated that the knockdown of CDH12 expression restrained the axon extension of E18 neurons. The transcriptome profile of neurons with or without siCDH12 treatment revealed a set of pathways positively correlated with the effect of CDH12 on neurite outgrowth. We further revealed that CDH12 affected Rac1/Cdc42 phosphorylation in a PKA-dependent manner after testing using H-89 and 8-Bromo-cAMP sodium salt. Moreover, we investigated the expression of CDH12 in the brain, spinal cord, and dorsal root ganglia (DRG) during development using immunofluorescence staining. After that, we explored the effects of CDH12 on neurite outgrowth in vivo. A zebrafish model of CDH12 knockdown was established using the NgAgo-gDNA system, and the vital role of CDH12 in peripheral neurogenesis was determined. In summary, our study is the first to report the effect of CDH12 on axonal extension in vitro and in vivo, and we provide a preliminary explanation for this mechanism.
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Affiliation(s)
- Beibei Guo
- Key Laboratory of Neuroregeneration of Jiangsu Province and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China
| | - Mengwei Qi
- Key Laboratory of Neuroregeneration of Jiangsu Province and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China
| | - Shuai Huang
- Key Laboratory of Neuroregeneration of Jiangsu Province and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China
| | - Run Zhuo
- Key Laboratory of Neuroregeneration of Jiangsu Province and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China
| | - Wenxue Zhang
- Key Laboratory of Neuroregeneration of Jiangsu Province and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China
| | - Yufang Zhang
- Key Laboratory of Neuroregeneration of Jiangsu Province and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China
| | - Man Xu
- Key Laboratory of Neuroregeneration of Jiangsu Province and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China
| | - Mei Liu
- Key Laboratory of Neuroregeneration of Jiangsu Province and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China
| | - Tuchen Guan
- Key Laboratory of Neuroregeneration of Jiangsu Province and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China
| | - Yan Liu
- Key Laboratory of Neuroregeneration of Jiangsu Province and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China
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14
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Torii K, Okada Y, Morita A. Determining the immune environment of cutaneous T-cell lymphoma lesions through the assessment of lesional blood drops. Sci Rep 2021; 11:19629. [PMID: 34608214 PMCID: PMC8490448 DOI: 10.1038/s41598-021-98804-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 09/14/2021] [Indexed: 12/28/2022] Open
Abstract
Detailed analysis of the cells that infiltrate lesional skin cannot be performed in skin biopsy specimens using immunohistochemistry or cell separation techniques because enzyme treatments applied during the isolation step can destroy small amounts of protein and minor cell populations in the biopsy specimen. Here, we describe a method for isolating T cells from drops of whole blood obtained from lesions during skin biopsy in patients with cutaneous T-cell lymphoma. Lesional blood is assumed to contain lesional resident cells, cells from capillary vessels, and blood overflowing from capillary vessels into the lesion area. The lesional blood showed substantial increases in distinct cell populations, chemokines, and the expression of various genes. The proportion of CD8+CD45RO+ T cells in the lesional blood negatively correlated with the modified severity-weighted assessment tool scores. CD4+CD45RO+ T cells in the lesional blood expressed genes associated with the development of cancer and progression of cutaneous T-cell lymphoma. In addition, CD8+CD45RO+ T cells in lesional blood had unique T-cell receptor repertoires in lesions of each stage. Assessment of lesional blood drops might provide new insight into the pathogenesis of mycosis fungoides and facilitate evaluation of the treatment efficacy for mycosis fungoides as well as other skin inflammatory diseases.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Biomarkers, Tumor/blood
- Disease Management
- Disease Susceptibility
- Female
- Humans
- Immunohistochemistry
- Immunophenotyping
- Lymphocyte Count
- Lymphocytes, Tumor-Infiltrating/immunology
- Lymphocytes, Tumor-Infiltrating/metabolism
- Lymphocytes, Tumor-Infiltrating/pathology
- Lymphoma, T-Cell, Cutaneous/blood
- Lymphoma, T-Cell, Cutaneous/diagnosis
- Lymphoma, T-Cell, Cutaneous/etiology
- Male
- Middle Aged
- Neoplasm Staging
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/metabolism
- T-Lymphocyte Subsets/immunology
- T-Lymphocyte Subsets/metabolism
- T-Lymphocyte Subsets/pathology
- Tumor Microenvironment/immunology
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Affiliation(s)
- Kan Torii
- Department of Geriatric and Environmental Dermatology, Nagoya City University Graduate School of Medical Sciences, Mizuho-Ku, Nagoya, 467-8601, Japan
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan
| | - Akimichi Morita
- Department of Geriatric and Environmental Dermatology, Nagoya City University Graduate School of Medical Sciences, Mizuho-Ku, Nagoya, 467-8601, Japan.
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15
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Chen P, Wu S, Yu J, Tang X, Dai C, Qi H, Zhu J, Li W, Chen B, Zhu J, Wang H, Zhao S, Liu H, Kuang P, He Y. mRNA Network: Solution for Tracking Chemotherapy Insensitivity in Small-Cell Lung Cancer. JOURNAL OF HEALTHCARE ENGINEERING 2021; 2021:2105176. [PMID: 34621500 PMCID: PMC8492269 DOI: 10.1155/2021/2105176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/14/2021] [Accepted: 08/05/2021] [Indexed: 12/25/2022]
Abstract
Background Small-cell lung cancer (SCLC) has poor prognosis and is prone to drug resistance. It is necessary to search for possible influencing factors for SCLC chemotherapy insensitivity. Therefore, we proposed an mRNA network to track the chemotherapy insensitivity in SCLC. Methods Six samples of patients with SCLC were recruited for RNA sequencing. TopHat2 and Cufflinks were used to make differential analysis. Functional analysis was applied as well. Finally, multidimensional validation was applied for verifying the results we obtained by experiment. Results This study was a trial of drug resistance in 6 SCLC patients after first-line chemotherapy. The top 10 downregulated genes differentially expressed in the chemo-insensitive group were SERPING1, DRD5, PARVG, PRAME, NKX1-1, MCTP2, PID1, PLEKHA4, SPP1, and SLN. Cell-cell signaling by Wnt (p=6.98E - 21) was the most significantly enriched GO term in biological process, while systemic lupus erythematosus (p=6.97E - 10), alcoholism (p=1.01E - 09), and transcriptional misregulation in cancer (p=0.00227988) were the top three ones of KEGG pathways. In multiple public databases, we also highlighted and verified the vital role of glycolysis/gluconeogenesis pathway and corresponding genes in chemo-insensitivity in SCLC. Conclusion Our study confirmed some SCLC chemotherapy insensitivity-related genes, biological processes, and pathways, thus constructing the chemotherapy-insensitive network for SCLC.
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Affiliation(s)
- Peixin Chen
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
- Medical School, Tongji University, Shanghai 200433, China
| | - Shengyu Wu
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
- Medical School, Tongji University, Shanghai 200433, China
| | - Jia Yu
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
- Medical School, Tongji University, Shanghai 200433, China
| | - Xuzhen Tang
- Oncology and Immunology BU, Research Service Division, WuXi Apptec, Shanghai, China
| | - Chunlei Dai
- Oncology and Immunology BU, Research Service Division, WuXi Apptec, Shanghai, China
| | - Hui Qi
- Oncology and Immunology BU, Research Service Division, WuXi Apptec, Shanghai, China
| | - Junjie Zhu
- Department of Surgery, Shanghai Pulmonary Hospital, Tongji University, Tongji University School of Medicine, Shanghai 200433, China
| | - Wei Li
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
- Medical School, Tongji University, Shanghai 200433, China
| | - Bin Chen
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
- Medical School, Tongji University, Shanghai 200433, China
| | - Jun Zhu
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
- Medical School, Tongji University, Shanghai 200433, China
| | - Hao Wang
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
- Medical School, Tongji University, Shanghai 200433, China
| | - Sha Zhao
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
- Medical School, Tongji University, Shanghai 200433, China
| | - Hongcheng Liu
- Department of Surgery, Shanghai Pulmonary Hospital, Tongji University, Tongji University School of Medicine, Shanghai 200433, China
| | - Peng Kuang
- Department of Medical Oncology, The First Affiliated Hospital of Nanchang University, Nanchang 330006, China
| | - Yayi He
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
- Medical School, Tongji University, Shanghai 200433, China
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16
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Liu X, Zhang Z, Kan S, Lv Z, Zhou S, Liu X, Jing P, Xu W. PHF20 inhibition promotes apoptosis and cisplatin chemosensitivity via the OCT4‑p‑STAT3‑MCL1 signaling pathway in hypopharyngeal squamous cell carcinoma. Int J Oncol 2021; 59:38. [PMID: 33982773 PMCID: PMC8121096 DOI: 10.3892/ijo.2021.5218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 04/12/2021] [Indexed: 12/13/2022] Open
Abstract
Cisplatin is a widely used platinum‑based chemotherapeutic agent for hypopharyngeal squamous cell carcinoma (HSCC). However, resistance to cisplatin limits its use for the treatment of HSCC, and the underlying molecular mechanism requires further investigation. The present study performed functional assays to determine whether the expression of plant homeodomain finger protein 20 (PHF20) may be involved in the apoptosis and cisplatin resistance of HSCC. The expression levels of PHF20 were higher in cisplatin‑resistant HSCC cells compared with those in cisplatin‑sensitive cells. The inhibition of PHF20 suppressed cell viability but did not affect the migratory and invasive abilities of HSCC cells compared with those of negative control‑transfected cells. Furthermore, PHF20 inhibition reduced cell viability by enhancing apoptosis compared with those in the control cells in vitro. Notably, the inhibition of PHF20 sensitized HSCC cells to cisplatin, thus increasing apoptosis via the signal transducer and activator of transcription 3 (STAT3)‑myeloid cell leukemia‑1 (MCL1) pathway. Octamer‑binding transcription factor 4 (OCT4) overexpression restored phosphorylated STAT3‑MCL1‑mediated apoptosis induced by PHF20 inhibition. In vivo experiments confirmed that PHF20 silencing induced tumor growth and increased apoptosis in HSCC cells compared with those in the control cells. Thus, PHF20 inhibition may promote apoptosis and improve cisplatin chemosensitivity via the OCT4‑p‑STAT3‑MCL1 signaling pathway in HSCC.
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Affiliation(s)
- Xiuxiu Liu
- Department of Otorhinolaryngology, Head and Neck Surgery, Shandong Provincial ENT Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, P.R. China
- Shandong Provincial Key Laboratory of Otology, Jinan, Shandong 250022, P.R. China
| | - Zhancheng Zhang
- Department of Otorhinolaryngology, Head and Neck Surgery, Shandong Provincial ENT Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, P.R. China
- Department of Otorhinolaryngology, The Fourth Hospital of Jinan, Jinan, Shandong 250031, P.R. China
| | - Shifeng Kan
- Department of Otorhinolaryngology, Head and Neck Surgery, Shandong Provincial ENT Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, P.R. China
- Shandong Provincial Key Laboratory of Otology, Jinan, Shandong 250022, P.R. China
| | - Zhenghua Lv
- Department of Otorhinolaryngology, Head and Neck Surgery, Shandong Provincial ENT Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, P.R. China
- Shandong Provincial Key Laboratory of Otology, Jinan, Shandong 250022, P.R. China
| | - Shengli Zhou
- Department of Otorhinolaryngology, Head and Neck Surgery, Shandong Provincial ENT Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, P.R. China
- Shandong Provincial Key Laboratory of Otology, Jinan, Shandong 250022, P.R. China
| | - Xianfang Liu
- Department of Otorhinolaryngology, Head and Neck Surgery, Shandong Provincial ENT Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, P.R. China
- Shandong Provincial Key Laboratory of Otology, Jinan, Shandong 250022, P.R. China
| | - Peihang Jing
- Department of Otorhinolaryngology, Head and Neck Surgery, Shandong Provincial ENT Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, P.R. China
| | - Wei Xu
- Department of Otorhinolaryngology, Head and Neck Surgery, Shandong Provincial ENT Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, P.R. China
- Shandong Provincial Key Laboratory of Otology, Jinan, Shandong 250022, P.R. China
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17
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van der Zanden LFM, van Rooij IALM, Quaedackers JSLT, Nijman RJM, Steffens M, de Wall LLL, Bongers EMHF, Schaefer F, Kirchner M, Behnisch R, Bayazit AK, Caliskan S, Obrycki L, Montini G, Duzova A, Wuttke M, Jennings R, Hanley NA, Milmoe NJ, Winyard PJD, Renkema KY, Schreuder MF, Roeleveld N, Feitz WFJ. CDH12 as a Candidate Gene for Kidney Injury in Posterior Urethral Valve Cases: A Genome-wide Association Study Among Patients with Obstructive Uropathies. EUR UROL SUPPL 2021; 28:26-35. [PMID: 34337522 PMCID: PMC8317879 DOI: 10.1016/j.euros.2021.04.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/08/2021] [Indexed: 02/01/2023] Open
Abstract
Background Posterior urethral valves (PUVs) and ureteropelvic junction obstruction (UPJO) are congenital obstructive uropathies that may impair kidney development. Objective To identify genetic variants associated with kidney injury in patients with obstructive uropathy. Design, setting, and participants We included 487 patients born in 1981 or later who underwent pyeloplasty or valve resection before 18 yr of age in the discovery phase, 102 PUV patients in a first replication phase, and 102 in a second replication phase. Outcome measurements and statistical analysis Signs of kidney injury were defined as dialysis, nephrectomy, kidney transplantation, estimated glomerular filtration rate (eGFR) <60 ml/min/1.73 m2, high blood pressure, antihypertensive medication use, proteinuria, and/or one kidney functioning at <45%. We used χ2 tests to calculate p values and odds ratios for >600 000 single-nucleotide polymorphisms (SNPs) in the discovery sample comparing patients with and without signs of kidney injury within 5 yr after surgery. We performed stratified analyses for PUV and UPJO and Kaplan-Meier and Cox regression analyses in the discovery and two replication samples for the associated SNPs, and RNA and protein expression analyses for the associated gene in fetal tissues. Results and limitations Despite the small and nonhomogeneous sample, we observed suggestive associations for six SNPs in three loci, of which rs6874819 in the CDH12 gene was the most clear (p = 7.5 × 10–7). This SNP also seemed to be associated with time to kidney injury in the PUV discovery and replication samples. RNA expression analyses showed clear CDH12 expression in fetal kidneys, which was confirmed by protein immunolocalization. Conclusions This study identified CDH12 as a candidate gene for kidney injury in PUV. Patient summary We found that variants of the CDH12 gene increase the risk of kidney injury in patients with extra flaps of tissue in the urethra (posterior urethral valves). This is the first report on this gene in this context. Our study provides interesting new information about the pathways involved and important leads for further research for this condition.
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Affiliation(s)
- Loes F M van der Zanden
- Radboud Institute for Health Sciences, Department for Health Evidence, Radboud university medical center, Nijmegen, The Netherlands
| | - Iris A L M van Rooij
- Radboud Institute for Health Sciences, Department for Health Evidence, Radboud university medical center, Nijmegen, The Netherlands
| | | | - Rien J M Nijman
- Department of Urology, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Liesbeth L L de Wall
- Radboud Institute for Molecular Life Sciences, Division of Pediatric Urology, Department of Urology, Radboudumc Amalia Children's Hospital, Nijmegen, The Netherlands
| | - Ernie M H F Bongers
- Radboud Institute for Molecular Life Sciences, Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Franz Schaefer
- Center for Pediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Marietta Kirchner
- Institute of Medical Biometry and Informatics, University of Heidelberg, Heidelberg, Germany
| | - Rouven Behnisch
- Institute of Medical Biometry and Informatics, University of Heidelberg, Heidelberg, Germany
| | - Aysun K Bayazit
- Department of Pediatric Nephrology, Faculty of Medicine, Cukurova University, Adana, Turkey
| | - Salim Caliskan
- Department of Pediatric Nephrology, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Lukasz Obrycki
- Department of Nephrology, Kidney Transplantation and Hypertension, Children's Memorial Health Institute, Warsaw, Poland
| | - Giovanni Montini
- Pediatric Nephrology, Dialysis and Transplant Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico di Milano, Milan, Italy.,Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Ali Duzova
- Division of Pediatric Nephrology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Matthias Wuttke
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Rachel Jennings
- Faculty of Biology, Medicine and Health, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, UK.,Endocrinology Department, Manchester University NHS Foundation Trust, Manchester, UK
| | - Neil A Hanley
- Faculty of Biology, Medicine and Health, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, UK.,Endocrinology Department, Manchester University NHS Foundation Trust, Manchester, UK
| | - Natalie J Milmoe
- Nephro-Urology Research Group, Developmental Biology and Cancer Programme, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Paul J D Winyard
- Nephro-Urology Research Group, Developmental Biology and Cancer Programme, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Kirsten Y Renkema
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Michiel F Schreuder
- Radboud Institute for Molecular Life Sciences, Department of Pediatric Nephrology, Radboudumc Amalia Children's Hospital, Nijmegen, The Netherlands
| | - Nel Roeleveld
- Radboud Institute for Health Sciences, Department for Health Evidence, Radboud university medical center, Nijmegen, The Netherlands
| | - Wout F J Feitz
- Radboud Institute for Molecular Life Sciences, Division of Pediatric Urology, Department of Urology, Radboudumc Amalia Children's Hospital, Nijmegen, The Netherlands
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18
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Discovery of a novel potent cytochrome P450 CYP4Z1 inhibitor. Eur J Med Chem 2021; 215:113255. [PMID: 33611185 DOI: 10.1016/j.ejmech.2021.113255] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 01/27/2021] [Accepted: 01/29/2021] [Indexed: 02/08/2023]
Abstract
Human cytochrome P450 enzyme CYP4Z1 represents a promising target for the treatment of a multitude of malignancies including breast cancer. The most active known non-covalent inhibitor (1-benzylimidazole) only shows low micromolar affinity to CYP4Z1. We report a new, highly active inhibitor for CYP4Z1 showing confirmed binding in an enzymatic assay and an IC50 value of 63 ± 19 nM in stably transfected MCF-7 cells overexpressing CYP4Z1. The new inhibitor was identified by a systematically developed virtual screening protocol. Binding was rationalized using a carefully elaborated 3D pharmacophore hypothesis and thoroughly characterized using extensive molecular dynamics simulations and dynamic 3D pharmacophore (dynophore) analyses. This novel inhibitor represents a valuable pharmacological tool to accelerate characterization of the still understudied CYP4Z1 and might pave the way for a new treatment strategy in CYP4Z1-associated malignancies. The presented in silico model for predicting CYP4Z1 interaction provides novel mechanistic insights and revealed that the drug ozagrel interacts with CYP4Z1.
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19
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Marakhonov AV, Přechová M, Konovalov FA, Filatova AY, Zamkova MA, Kanivets IV, Solonichenko VG, Semenova NA, Zinchenko RA, Treisman R, Skoblov MY. Mutation in PHACTR1 associated with multifocal epilepsy with infantile spasms and hypsarrhythmia. Clin Genet 2021; 99:673-683. [PMID: 33463715 PMCID: PMC8629116 DOI: 10.1111/cge.13926] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 01/07/2021] [Accepted: 01/13/2021] [Indexed: 11/28/2022]
Abstract
A young boy with multifocal epilepsy with infantile spasms and hypsarrhythmia with minimal organic lesions of brain structures underwent DNA diagnosis using whole‐exome sequencing. A heterozygous amino‐acid substitution p.L519R in a PHACTR1 gene was identified. PHACTR1 belongs to a protein family of G‐actin binding protein phosphatase 1 (PP1) cofactors and was not previously associated with a human disease. The missense single nucleotide variant in the proband was shown to occur de novo in the paternal allele. The mutation was shown in vitro to reduce the affinity of PHACTR1 for G‐actin, and to increase its propensity to form complexes with the catalytic subunit of PP1. These properties are associated with altered subcellular localization of PHACTR1 and increased ability to induce cytoskeletal rearrangements. Although the molecular role of the PHACTR1 in neuronal excitability and differentiation remains to be defined, PHACTR1 has been previously shown to be involved in Slack channelopathy pathogenesis, consistent with our findings. We conclude that this activating mutation in PHACTR1 causes a severe type of sporadic multifocal epilepsy in the patient.
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Affiliation(s)
- Andrey V Marakhonov
- Laboratory of Genetic Epidemiology, Laboratory of Functional Genomics, Department of Genetic Counseling, Research Centre for Medical Genetics, Moscow, Russia
| | - Magdalena Přechová
- Laboratory of Integrative Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic.,Signalling and Transcription Laboratory, Francis Crick Institute, London, UK
| | | | - Alexandra Yu Filatova
- Laboratory of Genetic Epidemiology, Laboratory of Functional Genomics, Department of Genetic Counseling, Research Centre for Medical Genetics, Moscow, Russia
| | - Maria A Zamkova
- Laboratory of Regulatory Mechanisms in Immunity, Institute of Carcinogenesis, N.N. Blokhin Russian Cancer Research Center, Moscow, Russia
| | - Ilya V Kanivets
- Laboratory of Molecular Pathology, Genomed Ltd., Moscow, Russia.,Medical Genetic Centre, Filatov Moscow Pediatric Clinical Hospital, Moscow, Russia
| | | | - Natalia A Semenova
- Laboratory of Genetic Epidemiology, Laboratory of Functional Genomics, Department of Genetic Counseling, Research Centre for Medical Genetics, Moscow, Russia
| | - Rena A Zinchenko
- Laboratory of Genetic Epidemiology, Laboratory of Functional Genomics, Department of Genetic Counseling, Research Centre for Medical Genetics, Moscow, Russia.,N.A. Semashko National Research Institute of Public Health, Moscow, Russia
| | - Richard Treisman
- Signalling and Transcription Laboratory, Francis Crick Institute, London, UK
| | - Mikhail Yu Skoblov
- Laboratory of Genetic Epidemiology, Laboratory of Functional Genomics, Department of Genetic Counseling, Research Centre for Medical Genetics, Moscow, Russia
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20
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Ma Q, Long W, Xing C, Jiang C, Su J, Wang HY, Liu Q, Wang RF. PHF20 Promotes Glioblastoma Cell Malignancies Through a WISP1/ BGN-Dependent Pathway. Front Oncol 2020; 10:573318. [PMID: 33117706 PMCID: PMC7574681 DOI: 10.3389/fonc.2020.573318] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 09/04/2020] [Indexed: 12/20/2022] Open
Abstract
Glioblastoma (GBM) stem cells are resistant to cancer therapy, and therefore responsible for tumor progression and recurrence after conventional therapy. However, the molecular mechanisms driving the maintenance of stemness and dedifferentiation are poorly understood. In this study, we identified plant homeodomain finger-containing protein 20 (PHF20) as a crucial epigenetic regulator for sustaining the stem cell-like phenotype of GBM. It is highly expressed in GBM and tightly associated with high levels of aggressiveness of tumors and potential poor prognosis in GBM patients. Knockout of PHF20 inhibits GBM cell proliferation, as well as its invasiveness and stem cell-like traits. Mechanistically, PHF20 interacts with WDR5 and binds to the promoter regions of WISP1 for its expression. Subsequently, WISP1 and BGN act in concert to regulate the degradation of β-Catenin. Our findings have identified PHF20 as a key driver of GBM malignant behaviors, and provided a potential target for developing prognosis and therapy.
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Affiliation(s)
- Qianquan Ma
- Department of Neurosurgery in Xiangya Hospital, Central South University, Changsha, China.,Department of Neurosurgery in the Third Hospital of Peking University, Peking University, Beijing, China.,Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, TX, United States
| | - Wenyong Long
- Department of Neurosurgery in Xiangya Hospital, Central South University, Changsha, China
| | - Changsheng Xing
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Chongming Jiang
- Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, TX, United States
| | - Jun Su
- Department of Neurosurgery in Xiangya Hospital, Central South University, Changsha, China
| | - Helen Y Wang
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Qing Liu
- Department of Neurosurgery in Xiangya Hospital, Central South University, Changsha, China
| | - Rong-Fu Wang
- Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, TX, United States.,Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States.,Department of Pediatrics, Children's Hospital of Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States.,Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
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21
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Identification of novel bioactive molecules from garlic bulbs: A special effort to determine the anticancer potential against lung cancer with targeted drugs. Saudi J Biol Sci 2020; 27:3274-3289. [PMID: 33304133 PMCID: PMC7715046 DOI: 10.1016/j.sjbs.2020.09.041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 09/14/2020] [Accepted: 09/20/2020] [Indexed: 12/12/2022] Open
Abstract
Garlic (Allium sativum L.), is a predominant spice, which is used as an herbal medicine and flavoring agent, since ancient times. It has a rich source of various secondary metabolites such as flavonoids, terpenoids and alkaloids, which have various pharmacological properties. Garlic is used in the treatment of various ailments such as cancer, diabetes and cardiovascular diseases. The present study aims to explore the plausible mechanisms of the selected phytocompounds as potential inhibitors against the known drug targets of non-small-cell lung cancer (NSCLC). The phytocompounds of garlic were identified by gas chromatography-mass spectrometry (GC–MS) technique. Subsequently, the identified phytocompounds were subjected to molecular docking to predict the binding with the drug targets, epidermal growth factor receptor (EGFR), human epidermal growth factor receptor 2 (HER2), echinoderm microtubule-associated protein-like 4-anaplastic lymphoma kinase (EML4-ALK) and group IIa secretory phospholipase A2 (sPLA2-IIA). Molecular dynamics is used to predict the stability of the identified phytocompounds against NSCLC drug targets by refining the intermolecular interactions formed between them. Among the 12 phytocompounds of garlic, three compounds[1,4-dimethyl-7-(1-methylethyl)-2-azulenyl]phenylmethanone, 2,4-bis(1-phenylethyl)-phenol and 4,5–2 h-oxazole-5-one,4-[3,5-di-t-butyl-4-methoxyphenyl] methylene-2-phenyl were identified as potential inhibitors, which might be suitable for targeting the different clinical forms of EGFR and dual inhibition of the studied drug targets to combat NSCLC. The result of this study suggest that these identified phytocompounds from garlic would serve as promising leads for the development of lead molecules to design new multi-targeting drugs to address the different clinical forms of NSCLC.
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22
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Lai B, Lai Y, Zhang Y, Zhou M, Sheng L, OuYang G. The Solute Carrier Family 2 Genes Are Potential Prognostic Biomarkers in Acute Myeloid Leukemia. Technol Cancer Res Treat 2020; 19:1533033819894308. [PMID: 31918632 PMCID: PMC7099669 DOI: 10.1177/1533033819894308] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Aims: The solute carrier family 2 (SLC2) genes are comprised of 14 members which are essential for the maintenance of glucose uptake and survival of tumour cells. This study was performed to investigate the associations of SLC2 family gene expression with mortality in acute myeloid leukemia (AML). Methods: Clinical features and SLC2 family gene expression data were obtained from The Cancer Genome Atlas and Gene Expression Omnibus database. The associations between SLC2 family gene expression and clinicopathologic features were analyzed using linear regression model. Kaplan-Meier survival, univariate, multivariate survival analyses and validation analysis were performed to analyze the associations between SLC2 family gene expression and patients’ overall survival. Results: Patient mortality was positively associated with age and cytogenetic risk in AML patients. Kaplan-Meier survival analysis suggested that patients with high SLC2A5 and SLC2A10 expression showed poorer survival than those with low SLC2A5 and SLC2A10 expression. In contrast, patients with high SLC2A13 expression exhibited better prognosis than those with low SLC2A13 expression (P < 0.05 for all cases, log rank test). Multivariate survival analysis and validation analysis confirmed that high expression of SLC2A5 and SLC2A10 and low expression of SLC2A13 were associated with increased mortality (P = 0.00, Odd ratio [OR]:4.05, 95% Confidence Interval [CI]: 1.73-10.22; P = 0.00, OR: 3.66, 95% CI: 1.54-9.25; and P = 0.01, OR: 0.26, 95% CI: 0.09-0.68, respectively). Conclusion: SLC family gene expression, such as SLC2A5, SLC2A10 and SLC2A13, was significantly associated with prognosis of AML patients, their expression levels might become useful prognostic biomarkers in AML.
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Affiliation(s)
- Binbin Lai
- Department of Hematology, Ningbo First Hospital, Ningbo, Zhejiang Province, China
| | - Yanli Lai
- Department of Hematology, Ningbo First Hospital, Ningbo, Zhejiang Province, China
| | - Yanli Zhang
- Department of Hematology, Ningbo First Hospital, Ningbo, Zhejiang Province, China
| | - Miao Zhou
- Department of Hematology, Ningbo First Hospital, Ningbo, Zhejiang Province, China
| | - Lixia Sheng
- Department of Hematology, Ningbo First Hospital, Ningbo, Zhejiang Province, China
| | - Guifang OuYang
- Department of Hematology, Ningbo First Hospital, Ningbo, Zhejiang Province, China
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23
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Yang L, Dao FT, Chang Y, Wang YZ, Li LD, Chen WM, Long LY, Liu YR, Lu J, Liu KY, Qin YZ. Both Methylation and Copy Number Variation Participated in the Varied Expression of PRAME in Multiple Myeloma. Onco Targets Ther 2020; 13:7545-7553. [PMID: 32801773 PMCID: PMC7402861 DOI: 10.2147/ott.s240979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 07/03/2020] [Indexed: 11/24/2022] Open
Abstract
Purpose The cancer-testis antigen, which is a preferentially expressed antigen of melanoma (PRAME), is an ideal target for immunotherapy and cancer vaccines. Since the expression of this antigen is relevant to therapy responses, the heterogeneity in its expression and the underlying mechanism need to be investigated. Patients and Methods Plasma cell sorting was performed in 48 newly diagnosed multiple myeloma (MM) patients. Real-time quantitative PCR was performed to examine the PRAME transcript levels and gene copy numbers. Bisulfate clone sequencing of the PRAME promoter and exon 1b regions was performed in 4 patients. Quantitative methylation-specific PCR of the +287 CpG site was performed for all patients. The human MM cell lines RPMI8226, LP-1 and MOLP-2 were treated with 5-azacytidine. Results The median PRAME transcript level was 3.1% (range: 0–298.3%) in the plasma cells sorted from the 48 MM patients. Eleven (22.9%) and 37 (77.1%) patients were individually categorized into the PRAME low- and high-expression groups according to the cut-off value of 0.05%. The methylation ratios of the promoter and the 3ʹ region of exon 1b region were both negatively related to the transcript levels. The degrees of methylation at the +287 CpG site were significantly negatively related to the transcript levels in all 48 patients (r=−0.44, P=0.0018), and those in the high-expression group (r=−0.69, P<0.0001) but not those in the low-expression group (r=−0.27, P=0.43). All 5 patients with homozygous deletions were categorized into the low-expression group. There were no significant differences in the PRAME transcript levels between the hemizygous deletion (n=8) and no deletion (n=35) groups (P=0.40). Furthermore, the PRAME transcript levels significantly increased in the MM cell lines after treatment with 5-azacytidine. Conclusion Both methylation and copy number variation may participate in the regulation of PRAME expression in MM; in patients with no homozygous deletion, PRAME expression is mainly controlled by methylation, and a proportion of fairly low expression is caused by homozygous deletion.
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Affiliation(s)
- Lu Yang
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing, People's Republic of China
| | - Feng-Ting Dao
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing, People's Republic of China
| | - Yan Chang
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing, People's Republic of China
| | - Ya-Zhe Wang
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing, People's Republic of China
| | - Ling-Di Li
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing, People's Republic of China
| | - Wen-Min Chen
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing, People's Republic of China
| | - Ling-Yu Long
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing, People's Republic of China
| | - Yan-Rong Liu
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing, People's Republic of China
| | - Jin Lu
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing, People's Republic of China
| | - Kai-Yan Liu
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing, People's Republic of China
| | - Ya-Zhen Qin
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing, People's Republic of China
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Retinol dehydrogenase 10 promotes metastasis of glioma cells via the transforming growth factor-β/SMAD signaling pathway. Chin Med J (Engl) 2020; 132:2430-2437. [PMID: 31613821 PMCID: PMC6831065 DOI: 10.1097/cm9.0000000000000478] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Background: Glioma is the most common primary malignant tumor in the central nervous system. Because of the resistance of glioma to chemoradiotherapy and its aggressive growth, the survival rate of patients with glioma has not improved. This study aimed to disclose the effect of retinol dehydrogenase 10 (RDH10) on the migration and invasion of glioma cells, and to explore the potential mechanism. Methods: Reverse transcription-polymerase chain reaction (RT-PCR) was used to determine the expression levels of RDH10 in healthy glial cells and glioma cells. Human glioma cell strains, U87 and U251, were infected with negative control or RDH10-interfering lentiviruses. RT-PCR and Western blotting were performed to determine the knockdown efficiency. Scratch and transwell assays were used to assess cell migration and invasion after RDH10 knockdown. Finally, changes in transforming growth factor-β (TGF-β)/SMAD signaling pathway-related expression were examined by Western blotting. Differences between groups were analyzed by one-way analysis of variance. Results: RDH10 was highly expressed in glioma cells. Compared with the control group, RDH10 knockdown significantly reduced RDH10 messenger RNA and protein expression levels in U87 and U251 glioma cells (U87: 1.00 ± 0.08 vs. 0.22 ± 0.02, t = 16.55, P < 0.001; U251: 1.00 ± 0.17 vs. 0.39 ± 0.01, t = 6.30, P < 0.001). The scratch assay indicated that compared with the control group, RDH10 knockdown significantly inhibited the migration of glioma cells (U87: 1.00% ± 0.04% vs. 2.00% ± 0.25%, t = 6.08, P < 0.01; U251: 1.00% ± 0.11% vs. 2.48% ± 0.31%, t = 5.79, P < 0.01). Furthermore, RDH10 knockdown significantly inhibited the invasive capacity of glioma cells (U87: 97.30 ± 7.01 vs. 13.70 ± 0.58, t = 20.36, P < 0.001; U251: 96.20 ± 7.10 vs. 18.30 ± 2.08, t = 18.51, P < 0.001). Finally, Western blotting demonstrated that compared with the control group, downregulation of RDH10 significantly inhibited TGF-β expression, phosphorylated SMAD2, and phosphorylated SMAD3 (TGF-β: 1.00 ± 0.10 vs. 0.53 ± 0.06, t = 7.05, P < 0.01; phosphorylated SMAD2: 1.00 ± 0.20 vs. 0.42 ± 0.17, t = 4.01, P < 0.01; phosphorylated SMAD3: 1.00 ± 0.18 vs. 0.41 ± 0.12, t = 4.12, P < 0.01). Conclusion: RDH10 knockdown might inhibit metastasis of glioma cells via the TGF-β/SMAD signaling pathway.
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Abstract
Generation of the autacoid all-trans-retinoic acid (ATRA) from retinol (vitamin A) relies on a complex metabolon that includes retinol binding-proteins and enzymes from the short-chain dehydrogenase/reductase and aldehyde dehydrogenase gene families. Serum retinol binding-protein delivers all-trans-retinol (vitamin A) from blood to cells through two membrane receptors, Stra6 and Rbpr2. Stra6 and Rbpr2 convey retinol to cellular retinol binding-protein type 1 (Crbp1). Holo-Crbp1 delivers retinol to lecithin: retinol acyl transferase (Lrat) for esterification and storage. Lrat channels retinol directly into its active site from holo-Crbp1 by protein-protein interaction. The ratio apo-Crbp1/holo-Crbp1 directs flux of retinol into and out of retinyl esters, through regulating esterification vs ester hydrolysis. Multiple retinol dehydrogenases (Rdh1, Rdh10, Dhrs9, Rdhe2, Rdhe2s) channel retinol from holo-Crbp1 to generate retinal for ATRA biosynthesis. β-Carotene oxidase type 1 generates retinal from carotenoids, delivered by the scavenger receptor-B1. Retinal reductases (Dhrs3, Dhrs4, Rdh11) reduce retinal into retinol, thereby restraining ATRA biosynthesis. Retinal dehydrogenases (Raldh1, 2, 3) dehydrogenate retinal irreversibly into ATRA. ATRA regulates its own concentrations by inducing Lrat and ATRA degradative enzymes. ATRA exhibits hormesis. Its effects relate to its concentration as an inverted J-shaped curve, transitioning from beneficial in the "goldilocks" zone to toxicity, as concentrations increase. Hormesis has distorted understanding physiological effects of ATRA post-nataly using chow-diet fed, ATRA-dosed animal models. Cancer, immune deficiency and metabolic abnormalities result from mutations and/or insufficiency in Crbp1 and retinoid metabolizing enzymes.
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Affiliation(s)
- Joseph L Napoli
- Graduate Program in Metabolic Biology, Nutritional Sciences and Toxicology, University of California, Berkeley, CA, United States.
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Xu Y, Zou R, Wang J, Wang ZW, Zhu X. The role of the cancer testis antigen PRAME in tumorigenesis and immunotherapy in human cancer. Cell Prolif 2020; 53:e12770. [PMID: 32022332 PMCID: PMC7106952 DOI: 10.1111/cpr.12770] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 01/01/2020] [Accepted: 01/15/2020] [Indexed: 12/24/2022] Open
Abstract
Preferentially expressed antigen in melanoma (PRAME), which belongs to the cancer/testis antigen (CTA) gene family, plays a pivotal role in multiple cellular processes and immunotherapy response in human cancers. PRAME is highly expressed in different types of cancers and is involved in cell proliferation, apoptosis, differentiation and metastasis as well as the outcomes of patients with cancer. In this review article, we discuss the potential roles and physiological functions of PRAME in various types of cancers. Moreover, this review highlights immunotherapeutic strategies that target PRAME in human malignancies. Therefore, the modulation of PRAME might be useful for the treatment of patients with cancer.
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Affiliation(s)
- Yichi Xu
- Departmant of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Ruanmin Zou
- Departmant of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Jing Wang
- Departmant of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Zhi-Wei Wang
- Departmant of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.,Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Xueqiong Zhu
- Departmant of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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Ahmed F. Integrated Network Analysis Reveals FOXM1 and MYBL2 as Key Regulators of Cell Proliferation in Non-small Cell Lung Cancer. Front Oncol 2019; 9:1011. [PMID: 31681566 PMCID: PMC6804573 DOI: 10.3389/fonc.2019.01011] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 09/20/2019] [Indexed: 12/21/2022] Open
Abstract
Background: Loss of control on cell division is an important factor for the development of non-small cell lung cancer (NSCLC), however, its molecular mechanism and gene regulatory network are not clearly understood. This study utilized the systems bioinformatics approach to reveal the “driver-network” involve in tumorigenic processes in NSCLC. Methods: A meta-analysis of gene expression data of NSCLC was integrated with protein-protein interaction (PPI) data to construct an NSCLC network. MCODE and iRegulone were used to identify the local clusters and its upstream transcription regulators involve in NSCLC. Pair-wise gene expression correlation was performed using GEPIA. The survival analysis was performed by the Kaplan-Meier plot. Results: This study identified a local “driver-network” with highest MCODE score having 26 up-regulated genes involved in the process of cell proliferation in NSCLC. Interestingly, the “driver-network” is under the regulation of TFs FOXM1 and MYBL2 as well as miRNAs. Furthermore, the overexpression of member genes in “driver-network” and the TFs are associated with poor overall survival (OS) in NSCLC patients. Conclusion: This study identified a local “driver-network” and its upstream regulators responsible for the cell proliferation in NSCLC, which could be promising biomarkers and therapeutic targets for NSCLC treatment.
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Affiliation(s)
- Firoz Ahmed
- Department of Biochemistry, University of Jeddah, Jeddah, Saudi Arabia.,University of Jeddah Center for Scientific and Medical Research, University of Jeddah, Jeddah, Saudi Arabia
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Long W, Zhao W, Ning B, Huang J, Chu J, Li L, Ma Q, Xing C, Wang HY, Liu Q, Wang RF. PHF20 collaborates with PARP1 to promote stemness and aggressiveness of neuroblastoma cells through activation of SOX2 and OCT4. J Mol Cell Biol 2019; 10:147-160. [PMID: 29452418 DOI: 10.1093/jmcb/mjy007] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 02/09/2018] [Indexed: 12/22/2022] Open
Abstract
The differentiation status of neuroblastoma (NB) strongly correlates with its clinical outcomes; however, the molecular mechanisms driving maintenance of stemness and differentiation remain poorly understood. Here, we show that plant homeodomain finger-containing protein 20 (PHF20) functions as a critical epigenetic regulator in sustaining stem cell-like phenotype of NB by using CRISPR/Cas9-based targeted knockout (KO) for high-throughput screening of gene function in NB cell differentiation. The expression of PHF20 in NB was significantly associated with high aggressiveness of the tumor and poor outcomes for NB patients. Deletion of PHF20 inhibited NB cell proliferation, invasive migration, and stem cell-like traits. Mechanistically, PHF20 interacts with poly(ADP-ribose) polymerase 1 (PARP1) and directly binds to promoter regions of octamer-binding transcription factor 4 (OCT4) and sex determining region Y-box 2 (SOX2) to modulate a histone mark associated with active transcription, trimethylation of lysine 4 on histone H3 protein subunit (H3K4me3). Overexpression of OCT4 and SOX2 restored growth and progression of PHF20 KO tumor cells. Consistently, OCT4 and SOX2 protein levels in clinical NB specimens were positively correlated with PHF20 expression. Our results establish PHF20 as a key driver of NB stem cell-like properties and aggressive behaviors, with implications for prognosis and therapy.
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Affiliation(s)
- Wenyong Long
- Department of Neurosurgery in Xiangya Hospital, Central South University, Changsha 410008, China.,Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Wei Zhao
- Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, TX 77030, USA.,Key Laboratory of Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Bo Ning
- Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, TX 77030, USA.,Institute Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Jing Huang
- Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Junjun Chu
- Key Laboratory of Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Linfeng Li
- Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Qianquan Ma
- Department of Neurosurgery in Xiangya Hospital, Central South University, Changsha 410008, China.,Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Changsheng Xing
- Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Helen Y Wang
- Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Qing Liu
- Department of Neurosurgery in Xiangya Hospital, Central South University, Changsha 410008, China
| | - Rong-Fu Wang
- Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, TX 77030, USA.,Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA.,Institute of Biosciences and Technology, Texas A&M University Health Science Center, Houston, TX 77030, USA
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Transcriptional E2F1/2/5/8 as potential targets and transcriptional E2F3/6/7 as new biomarkers for the prognosis of human lung carcinoma. Aging (Albany NY) 2019; 10:973-987. [PMID: 29754146 PMCID: PMC5990399 DOI: 10.18632/aging.101441] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 04/28/2018] [Indexed: 12/20/2022]
Abstract
E2F is a group of genes that encode a family of transcription factors (TFs) in higher eukaryotes and participate in cell cycle regulation and DNA synthesis in mammalian cells. Evidence from cell lines, mouse models, and human tissues indicates that TFs are implicated in lung cancer (LC) tumorigenesis. However, the diverse expression patterns and prognostic values of eight E2Fs have yet to be elucidated. In the current study, we examined the transcriptional and survival data of E2Fs in patients with LC from ONCOMINE, GEPIA, Kaplan-Meier Plotter, and cBioPortal databases. We found that the expression levels of E2F1/2/3/5/6/7/8 were higher in lung adenocarcinoma and squamous cell lung carcinoma tissues than in lung tissues, whereas the expression level of E2F4 was lower in the former than in the latter. The expression levels of E2F2/4/5/7/8 were correlated with advanced tumor stage. Survival analysis using the Kaplan-Meier Plotter database revealed that the high transcription levels of E2F1/2/4/5/7/8 were associated with low relapse-free survival (RFS) in all of the patients with LC. Conversely, high E2F3/6 levels predicted high RFS in these patients. This study implied that E2F3/6/7 are potential targets of precision therapy for patients with LC and that E2F1/2/4/5/8 are new biomarkers for the prognosis of LC.
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Al-Khadairi G, Decock J. Cancer Testis Antigens and Immunotherapy: Where Do We Stand in the Targeting of PRAME? Cancers (Basel) 2019; 11:cancers11070984. [PMID: 31311081 PMCID: PMC6678383 DOI: 10.3390/cancers11070984] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 07/04/2019] [Accepted: 07/10/2019] [Indexed: 02/07/2023] Open
Abstract
PRAME or PReferentially expressed Antigen in Melanoma is a testis-selective cancer testis antigen (CTA) with restricted expression in somatic tissues and re-expression in various cancers. It is one of the most widely studied CTAs and has been associated with the outcome and risk of metastasis. Although little is known about its pathophysiological function, PRAME has gained interest as a candidate target for immunotherapy. This review provides an update on our knowledge on PRAME expression and function in healthy and malignant cells and the current immunotherapeutic strategies targeting PRAME with their specific challenges and opportunities. We also highlight some of the features that position PRAME as a unique cancer testis antigen to target.
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Affiliation(s)
- Ghaneya Al-Khadairi
- College of Health and Life Sciences (CHLS), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha P.O. Box 34110, Qatar
| | - Julie Decock
- College of Health and Life Sciences (CHLS), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha P.O. Box 34110, Qatar.
- Cancer Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha P.O. Box 34110, Qatar.
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31
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Yang W, Liu H, Duan B, Xu X, Carmody D, Luo S, Walsh KM, Abbruzzese JL, Zhang X, Chen X, Wei Q. Three novel genetic variants in NRF2 signaling pathway genes are associated with pancreatic cancer risk. Cancer Sci 2019; 110:2022-2032. [PMID: 30972876 PMCID: PMC6550126 DOI: 10.1111/cas.14017] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 03/06/2019] [Accepted: 04/07/2019] [Indexed: 12/12/2022] Open
Abstract
Pancreatic cancer (PanC) is one of the most lethal solid malignancies, and metastatic PanC is often present at the time of diagnosis. Although several high- and low-penetrance genes have been implicated in PanC, their roles in carcinogenesis remain only partially elucidated. Because the nuclear factor erythroid2-related factor2 (NRF2) signaling pathway is involved in human cancers, we hypothesize that genetic variants in NRF2 pathway genes are associated with PanC risk. To test this hypothesis, we assessed associations between 31 583 common single nucleotide polymorphisms (SNP) in 164 NRF2-related genes and PanC risk using three published genome-wide association study (GWAS) datasets, which included 8474 cases and 6944 controls of European descent. We also carried out expression quantitative trait loci (eQTL) analysis to assess the genotype-phenotype correlation of the identified significant SNP using publicly available data in the 1000 Genomes Project. We found that three novel SNP (ie, rs3124761, rs17458086 and rs1630747) were significantly associated with PanC risk (P = 5.17 × 10-7 , 5.61 × 10-4 and 5.52 × 10-4 , respectively). Combined analysis using the number of unfavorable genotypes (NUG) of these three SNP suggested that carriers of two to three NUG had an increased risk of PanC (P < 0.0001), compared with those carrying zero to one NUG. Furthermore, eQTL analysis showed that both rs3124761 T and rs17458086 C alleles were associated with increased mRNA expression levels of SLC2A6 and SLC2A13, respectively (P < 0.05). In conclusion, genetic variants in NRF2 pathway genes could play a role in susceptibility to PanC, and further functional exploration of the underlying molecular mechanisms is warranted.
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Affiliation(s)
- Wenjun Yang
- Key Laboratory of Fertility Preservation and MaintenanceSchool of Basic Medicine and the General HospitalNingxia Medical UniversityYinchuanChina
- Cancer Research ProgramJulius L. Chambers Biomedical Biotechnology Research InstituteNorth Carolina Central UniversityDurham
| | - Hongliang Liu
- Duke Cancer InstituteDuke University Medical CenterDurham
- Department of Population Health SciencesDuke University School of MedicineDurham
| | - Bensong Duan
- Duke Cancer InstituteDuke University Medical CenterDurham
- Department of Population Health SciencesDuke University School of MedicineDurham
| | - Xinyuan Xu
- Duke Cancer InstituteDuke University Medical CenterDurham
- Department of Population Health SciencesDuke University School of MedicineDurham
| | - Dennis Carmody
- Duke Cancer InstituteDuke University Medical CenterDurham
- Department of Population Health SciencesDuke University School of MedicineDurham
| | - Sheng Luo
- Department of Biostatistics and BioinformaticsDuke University School of MedicineDurham
| | - Kyle M. Walsh
- Duke Cancer InstituteDuke University Medical CenterDurham
- Department of NeurosurgeryDuke University School of MedicineDurham
| | - James L. Abbruzzese
- Duke Cancer InstituteDuke University Medical CenterDurham
- Department of Medicine, Population Health SciencesDuke University School of MedicineDurham
| | - Xuefeng Zhang
- Duke Cancer InstituteDuke University Medical CenterDurham
- Department of PathologyDuke University School of MedicineDurham
| | - Xiaoxin Chen
- Cancer Research ProgramJulius L. Chambers Biomedical Biotechnology Research InstituteNorth Carolina Central UniversityDurham
| | - Qingyi Wei
- Duke Cancer InstituteDuke University Medical CenterDurham
- Department of Population Health SciencesDuke University School of MedicineDurham
- Department of Medicine, Population Health SciencesDuke University School of MedicineDurham
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Dragoj M, Bankovic J, Podolski-Renic A, Buric SS, Pesic M, Tanic N, Stankovic T. Association of Overexpressed MYC Gene with Altered PHACTR3 and E2F4 Genes Contributes to Non-small Cell Lung Carcinoma Pathogenesis. J Med Biochem 2019; 38:188-195. [PMID: 30867647 PMCID: PMC6410994 DOI: 10.2478/jomb-2018-0022] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Accepted: 06/02/2018] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND C-Myc is one of the major cellular oncogenes overexpressed in non-small cell lung carcinoma (NSCLC). Its deregulated expression is necessary but not sufficient for malignant transformation. We evaluated expression of MYC gene in NSCLC patients and its association with alterations in the genes previously identified to be related to NSCLC pathogenesis, PHACTR3 and E2F4. METHODS We analyzed MYC gene expression by qRT-PCR in 30 NSCLC patients' samples and paired normal lung tissue. MYC expression was further statistically evaluated in relation to histopathological parameters, PHACTR3 and E2F4 gene alterations and survival. Alterations in aforementioned genes were previously detected and identified based on AP-PCR profiles of paired normal and tumor DNA samples, selection of DNA bands with altered mobility in tumor samples and their characterization by the reamplification, cloning and sequencing. RESULTS MYC expression was significantly increased in NSCLC samples and its overexpression significantly associated with squamous cell carcinoma subtype. Most importantly, MYC overexpression significantly coincided with mutations in PHACTR3 and E2F4 genes, in group of all patients and in squamous cell carcinoma subtype. Moreover, patients with jointly overexpressed MYC and altered PHACTR3 or E2F4 showed trend of shorter survival. CONCLUSIONS Overall, MYC is frequently overexpressed in NSCLC and it is associated with mutated PHACTR3 gene, as well as mutated E2F4 gene. These joint gene alterations could be considered as potential molecular markers of NSCLC and its specific subtypes.
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Affiliation(s)
- Miodrag Dragoj
- Department of Neurobiology, Institute for Biological Research »Sinisa Stankovic«, University of Belgrade, Belgrade, Serbia
| | - Jasna Bankovic
- Department of Neurobiology, Institute for Biological Research »Sinisa Stankovic«, University of Belgrade, Belgrade, Serbia
| | - Ana Podolski-Renic
- Department of Neurobiology, Institute for Biological Research »Sinisa Stankovic«, University of Belgrade, Belgrade, Serbia
| | - Sonja Stojkovic Buric
- Department of Neurobiology, Institute for Biological Research »Sinisa Stankovic«, University of Belgrade, Belgrade, Serbia
| | - Milica Pesic
- Department of Neurobiology, Institute for Biological Research »Sinisa Stankovic«, University of Belgrade, Belgrade, Serbia
| | - Nikola Tanic
- Department of Neurobiology, Institute for Biological Research »Sinisa Stankovic«, University of Belgrade, Belgrade, Serbia
| | - Tijana Stankovic
- Department of Neurobiology, Institute for Biological Research »Sinisa Stankovic«, University of Belgrade, Belgrade, Serbia
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Xu X, Gu H, Wang Y, Wang J, Qin P. Autoencoder Based Feature Selection Method for Classification of Anticancer Drug Response. Front Genet 2019; 10:233. [PMID: 30972101 PMCID: PMC6445890 DOI: 10.3389/fgene.2019.00233] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Accepted: 03/04/2019] [Indexed: 12/14/2022] Open
Abstract
Anticancer drug responses can be varied for individual patients. This difference is mainly caused by genetic reasons, like mutations and RNA expression. Thus, these genetic features are often used to construct classification models to predict the drug response. This research focuses on the feature selection issue for the classification models. Because of the vast dimensions of the feature space for predicting drug response, the autoencoder network was first built, and a subset of inputs with the important contribution was selected. Then by using the Boruta algorithm, a further small set of features was determined for the random forest, which was used to predict drug response. Two datasets, GDSC and CCLE, were used to illustrate the efficiency of the proposed method.
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Affiliation(s)
- Xiaolu Xu
- Faculty of Electronic Information and Electrical Engineering, Dalian University of Technology, Dalian, China
| | - Hong Gu
- Faculty of Electronic Information and Electrical Engineering, Dalian University of Technology, Dalian, China
| | - Yang Wang
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Jia Wang
- Department of Breast Surgery, Institute of Breast Disease, Second Hospital of Dalian Medical University, Dalian, China
| | - Pan Qin
- Faculty of Electronic Information and Electrical Engineering, Dalian University of Technology, Dalian, China
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Jing Y, Zhang L, Xu Z, Chen H, Ju S, Ding J, Guo Y, Tian H. Phosphatase Actin Regulator-1 (PHACTR-1) Knockdown Suppresses Cell Proliferation and Migration and Promotes Cell Apoptosis in the bEnd.3 Mouse Brain Capillary Endothelial Cell Line. Med Sci Monit 2019; 25:1291-1300. [PMID: 30772888 PMCID: PMC6391858 DOI: 10.12659/msm.912586] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 11/05/2018] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND The phosphatase actin regulator-1 (PHACTR-1) gene on chromosome 6 encodes an actin and protein phosphatase 1 (PP1) binding protein, Phactr-1, which is highly expressed in brain tissues. Phactr-1 expression is involved in physiological and pathological cerebral microvascular events. This study aimed to investigate the role of expression of Phactr-1 in a mouse brain capillary endothelial cell line, bEnd.3, by knockdown the PHACTR-1 gene. MATERIAL AND METHODS Three bEnd.3 cell groups were studied, CON (normal control cells), NC (control scramble transfected cells), and KD (cells with PHACTR-1 gene knockdown). The PHACTR-1 gene was knocked down using transfection with small hairpin RNA (shRNA). In the three cell groups cell proliferation, migration, and apoptosis were studied by MTT and colony formation assays, transwell and scratch assays, and flow cytometry. The related cell pathways of associated with Phactr-1 knockdown were studied by Western blot. RESULTS Phactr-1 knockdown suppressed bEnd.3 cell proliferation and migration, promoted cell apoptosis, and downregulated the expressions of migration-associated proteins, including matrix metalloproteinase (MMP)-2 and MMP-9 and upregulated apoptosis-associated proteins, including Bax, Bcl-2, cleaved caspase-3, and caspase-3. CONCLUSIONS Phactr-1 was shown to have a role in the inhibition of endothelial cell proliferation and migration, promoted cell apoptosis, and regulated matrix metalloproteinases and apoptosis-associated proteins. These findings indicate that the expression of the Phactr-1 should be studied further in the cerebral microvasculature, both in vitro and in vivo, regarding its potential as a diagnostic and therapeutic target for cerebral microvascular disease.
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35
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Cavic M, Spasic J, Krivokuca A, Boljevic I, Kuburovic M, Radosavljevic D, Jankovic R. TP53 and DNA-repair gene polymorphisms genotyping as a low-cost lung adenocarcinoma screening tool. J Clin Pathol 2018; 72:75-80. [PMID: 30467244 DOI: 10.1136/jclinpath-2018-205553] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 11/01/2018] [Accepted: 11/02/2018] [Indexed: 12/16/2022]
Abstract
AIM TP53 and DNA repair polymorphisms have been proposed as cancer risk factors. This study evaluated the usability of TP53 Arg72Pro single-nucleotide polymorphism, X RCC1 Arg399Gln and RAD51 G135C as a low-cost lung adenocarcinoma screening tool. PATIENTS AND METHODS This case-control study included 78 atients with lung adenocarcinoma and 79 healthy matched controls. TP53, XRCC1 and RAD51 genotyping was done by PCR followed by restriction length polymorphism. Descriptive analyses included genotype and allelic frequencies and deviations of the frequencies from those expected under Hardy-Weinberg equilibrium were assessed using the χ2 test. The OR and 95% CIs were calculated as an estimate of relative risk, with significance set at p value <0.05. RESULTS The TP53 codon 72 Pro allele and the XRCC1 codon 399 Arg allele in a homozygous state were associated with lung adenocarcinoma (p=0.037; OR (95% CI) 2.42 (1.10 to 5.31)), that is, p=0.037; OR (95% CI) 2.16 (1.08 to 4.33), respectively. Also, carriers of the TP53 codon 72 Pro allele and the XRCC1 codon 399 ArgArg genotype older than 50 showed an even higher risk of developing lung adenocarcinoma (p=0.03 in both cases). CONCLUSIONS The TP53 codon 72 Arg allele and XRCC1 codon 399 Gln allele are likely to have a protective effect against lung adenocarcinoma, especially in individuals older than 50 years of age. XRCC1 and TP53 genotyping might be a useful low-cost tool for evaluating individual lung cancer risk, leading to earlier detection and management of this disease.
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Affiliation(s)
- Milena Cavic
- Department of Experimental Oncology, Institute for Oncology and Radiology of Serbia, Belgrade, Serbia
| | - Jelena Spasic
- Clinic for Medical Oncology, Institute for Oncology and Radiology of Serbia, Belgrade, Serbia
| | - Ana Krivokuca
- Department of Experimental Oncology, Institute for Oncology and Radiology of Serbia, Belgrade, Serbia
| | - Ivana Boljevic
- Department of Experimental Oncology, Institute for Oncology and Radiology of Serbia, Belgrade, Serbia
| | - Mira Kuburovic
- Department of Experimental Oncology, Institute for Oncology and Radiology of Serbia, Belgrade, Serbia
| | - Davorin Radosavljevic
- Clinic for Medical Oncology, Institute for Oncology and Radiology of Serbia, Belgrade, Serbia
| | - Radmila Jankovic
- Department of Experimental Oncology, Institute for Oncology and Radiology of Serbia, Belgrade, Serbia
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Altered hepatic genes related to retinol metabolism and plasma retinol in patients with non-alcoholic fatty liver disease. PLoS One 2018; 13:e0205747. [PMID: 30379862 PMCID: PMC6209208 DOI: 10.1371/journal.pone.0205747] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 10/01/2018] [Indexed: 02/07/2023] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD), especially non-alcoholic steatohepatitis (NASH) is a chronic liver disease commonly associated with hepatic fibrosis. NASH patients have an increased risk for hepatocellular carcinoma (HCC). An altered retinol metabolism is one of the pathways involved in the process of hepatic fibrosis, and enzymes involved in retinol metabolism have been associated with HCC. We aimed to determine the association between plasma retinol levels and hepatic expression of genes related to retinol metabolism, as well as to assess the hepatic expression of transcription factors regulated by retinoic acid in patients with NAFLD. Cross-sectional study where hepatic gene expression (Illumina microarray) and plasma retinol levels (HPLC) were measured in 17 patients with simple steatosis (SS), 15 with NASH, and 22 living liver donors (LD) as controls. Plasma retinol levels were higher in SS (1.53 ± 0.44 μmol/L) and NASH (1.51 ± 0.56 μmol/L) compared to LD (1.21 ± 0.38 μmol/L; p<0.05). AKR1B10 was highly overexpressed in NASH compared to SS (+6.2-fold) and LD (+9.9-fold; p = 4.89E-11). Retinaldehyde dehydrogenase 1 family, member A2 (ALDH1A2) and retinaldehyde dehydrogenase 1 family, member A3 (ALDH1A3), key enzymes for retinoic acid synthesis, were underexpressed in SS (-1.48 and -2.3-fold, respectively) and NASH (-1.47 and -2.6-fold, respectively) versus LD. In NASH, hepatic ALDH1A2 and ALDH1A3 were underexpressed and inversely correlated with plasma retinol levels, which may reduce retinoic acid in the liver. This, in addition to changes in expression of other genes involved in retinol metabolism, suggests a role for altered retinol homeostasis in NASH.
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TSPAN15 interacts with BTRC to promote oesophageal squamous cell carcinoma metastasis via activating NF-κB signaling. Nat Commun 2018; 9:1423. [PMID: 29650964 PMCID: PMC5897412 DOI: 10.1038/s41467-018-03716-9] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 03/07/2018] [Indexed: 01/01/2023] Open
Abstract
Beta-transducin repeat containing E3 ubiquitin protein ligase (BTRC) is crucial for the degradation of IκBα. Our previous transcriptome sequencing analysis revealed that tetraspanin 15 (TSPAN15) was significantly upregulated in clinical oesophageal squamous cell carcinoma (OSCC) tissues. Here, we show that high TSPAN15 expression in OSCC tissues is significantly associated with lymph node and distant metastasis, advanced clinical stage, and poor prognosis. Elevated TSPAN15 expression is, in part, caused by the reduction of miR-339-5p. Functional studies demonstrate that TSPAN15 promotes metastatic capabilities of OSCC cells. We further show that TSPAN15 specifically interacts with BTRC to promote the ubiquitination and proteasomal degradation of p-IκBα, and thereby triggers NF-κB nuclear translocation and subsequent activation of transcription of several metastasis-related genes, including ICAM1, VCAM1, uPA, MMP9, TNFα, and CCL2. Collectively, our findings indicate that TSPAN15 may serve as a new biomarker and/or provide a novel therapeutic target to OSCC patients. BTRC can activate NF-κB signaling through the ubiquitination and degradation of IκB-α. Here the authors show that TSPAN15 promotes metastasis of oesophageal squamous cell cancer by enhancing BTRC induced degradation of IκB-α and subsequent activation of NF-κB.
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Ito H, Mizuno M, Noguchi K, Morishita R, Iwamoto I, Hara A, Nagata KI. Expression analyses of Phactr1 (phosphatase and actin regulator 1) during mouse brain development. Neurosci Res 2018; 128:50-57. [DOI: 10.1016/j.neures.2017.08.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 08/03/2017] [Accepted: 08/07/2017] [Indexed: 12/18/2022]
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Klein BJ, Wang X, Cui G, Yuan C, Botuyan MV, Lin K, Lu Y, Wang X, Zhao Y, Bruns CJ, Mer G, Shi X, Kutateladze TG. PHF20 Readers Link Methylation of Histone H3K4 and p53 with H4K16 Acetylation. Cell Rep 2017; 17:1158-1170. [PMID: 27760318 DOI: 10.1016/j.celrep.2016.09.056] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 09/05/2016] [Accepted: 09/16/2016] [Indexed: 01/06/2023] Open
Abstract
PHF20 is a core component of the lysine acetyltransferase complex MOF (male absent on the first)-NSL (non-specific lethal) that generates the major epigenetic mark H4K16ac and is necessary for transcriptional regulation and DNA repair. The role of PHF20 in the complex remains elusive. Here, we report on functional coupling between methylation readers in PHF20. We show that the plant homeodomain (PHD) finger of PHF20 recognizes dimethylated lysine 4 of histone H3 (H3K4me2) and represents an example of a native reader that selects for this modification. Biochemical and structural analyses help to explain this selectivity and the preference of Tudor2, another reader in PHF20, for dimethylated p53. Binding of the PHD finger to H3K4me2 is required for histone acetylation, accumulation of PHF20 at target genes, and transcriptional activation. Together, our findings establish a unique PHF20-mediated link between MOF histone acetyltransferase (HAT), p53, and H3K4me2, and suggest a model for rapid spreading of H4K16ac-enriched open chromatin.
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Affiliation(s)
- Brianna J Klein
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Xiaoyan Wang
- Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Faculty of Medicine, Ludwig Maximilian University of Munich, Munich 80336, Germany
| | - Gaofeng Cui
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Chao Yuan
- Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | | | - Kevin Lin
- Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yue Lu
- Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xiaolu Wang
- Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yue Zhao
- Department of General, Visceral and Tumor Surgery, University Clinic Cologne, Cologne 50931, Germany
| | - Christiane J Bruns
- Faculty of Medicine, Ludwig Maximilian University of Munich, Munich 80336, Germany; Department of General, Visceral and Tumor Surgery, University Clinic Cologne, Cologne 50931, Germany
| | - Georges Mer
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA.
| | - Xiaobing Shi
- Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA.
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Guan F, Wang L, Hao S, Wu Z, Bai J, Kang Z, Zhou Q, Chang H, Yin H, Li D, Tian K, Ma J, Zhang G, Zhang J. Retinol dehydrogenase-10 promotes development and progression of human glioma via the TWEAK-NF-κB axis. Oncotarget 2017; 8:105262-105275. [PMID: 29285249 PMCID: PMC5739636 DOI: 10.18632/oncotarget.22166] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 09/25/2017] [Indexed: 12/03/2022] Open
Abstract
Retinol dehydrogenase-10 (RDH10) is a member of the short-chain dehydrogenase/reductase family, which plays an important role in retinoic acid (RA) synthesis. Here, we show that RDH10 is highly expressed in human gliomas, and its expression correlates with tumor grade and patient survival times. In vitro, lentivirus-mediated shRNA knockdown of RDH10 suppressed glioma cell proliferation, survival, and invasiveness and cell cycle progression. In vivo, RDH10 knockdown reduced glioma growth in nude mice. Microarray analysis revealed that RDH10 silencing reduces expression of TNFRSF12A (Fn14), TNFSF12 (TWEAK), TRAF3, IKBKB (IKK-β), and BMPR2, while it increases expression of TRAF1, NFKBIA (IκBα), NFKBIE (IκBε), and TNFAIP3. This suggests that RDH10 promotes glioma cell proliferation and survival by regulating the TWEAK-NF-κB axis, and that it could potentially serve as a novel target for human glioma treatment.
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Affiliation(s)
- Feng Guan
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Liang Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Shuyu Hao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Zhen Wu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Jian Bai
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Zhuang Kang
- Department of Glioma, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Quan Zhou
- Department of Pathology, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Hong Chang
- Department of Pathology, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Hui Yin
- Department of Social Medicine and Health Education, School of Public Health, Peking University, Beijing, China
| | - Da Li
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Kaibin Tian
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Junpeng Ma
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Guijun Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Junting Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
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Liu T, Zhang T, Zhou F, Wang J, Zhai X, Mu N, Park J, Liu M, Liu W, Shang P, Ding Y, Wen A, Li Y. Identification of genes and pathways potentially related to PHF20 by gene expression profile analysis of glioblastoma U87 cell line. Cancer Cell Int 2017; 17:87. [PMID: 29033691 PMCID: PMC5628484 DOI: 10.1186/s12935-017-0459-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Accepted: 09/27/2017] [Indexed: 01/01/2023] Open
Abstract
Background Glioblastoma is the most common and aggressive brain tumor associated with a poor prognosis. Plant homeodomain finger protein 20 (PHF20) is highly expressed in primary human gliomas and its expression is associated with tumor grade. However, the molecular mechanism by which PHF20 regulates glioblastoma remains poorly understood. Methods Genome wide gene expression analysis was performed to identify differentially expressed genes (DEGs) in U87 cells with PHF20 gene knockdown. Gene ontology (GO) and pathway enrichment analyses were performed to investigate the functions and pathways of DEGs. Pathway-net and signal-net analyses were conducted to identify the key genes and pathways related to PHF20. Results Expression of 540 genes, including FEN1 and CCL3, were significantly altered upon PHF20 gene silencing. GO analysis results showed that DEGs were significantly enriched in small molecule metabolic and apoptotic processes. Pathway analysis indicated that DEGs were mainly involved in cancer and metabolic pathways. The MAPK, apoptosis and p53 signaling pathways were identified as the hub pathways in the pathway network, while PLCB1, NRAS and PIK3 s were hub genes in the signaling network. Conclusions Our findings indicated that PHF20 is a pivotal upstream regulator. It affects the occurrence and development of glioma by regulating a series of tumor-related genes, such as FEN1, CCL3, PLCB1, NRAS and PIK3s, and activation of apoptosis signaling pathways. Therefore, PHF20 might be a novel biomarker for early diagnosis, and a potential target for glioblastoma therapies. Electronic supplementary material The online version of this article (doi:10.1186/s12935-017-0459-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tianlong Liu
- Department of Pharmacy, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Tiejun Zhang
- Department of Neurosurgery, The First Affiliated Hospital of SooChow University, Suzhou, China
| | - Feng Zhou
- Department of Neurosurgery, The First Affiliated Hospital of SooChow University, Suzhou, China
| | - Jitao Wang
- Department of Pharmacy, The First Affiliated Hospital of SooChow University, Suzhou, China
| | - Xiaohu Zhai
- Department of Pharmacy, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Nan Mu
- State Key Laboratory of Cancer Biology, Department of Biopharmaceutics, School of Pharmacy, Fourth Military Medical University, Xi'an, China
| | - Jongsun Park
- Department of Pharmacology, Chungnam National University, Daejon, South Korea
| | - Minna Liu
- Department of Nephrology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Wenxing Liu
- Department of Pharmacy, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Peijin Shang
- Department of Pharmacy, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Yi Ding
- Department of Pharmacy, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Aidong Wen
- Department of Pharmacy, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Yuwen Li
- Department of Pharmacy, Xijing Hospital, Fourth Military Medical University, Xi'an, China.,Department of Pharmacy, The First Affiliated Hospital of SooChow University, Suzhou, China
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Clawson GA, Matters GL, Xin P, McGovern C, Wafula E, dePamphilis C, Meckley M, Wong J, Stewart L, D’Jamoos C, Altman N, Imamura Kawasawa Y, Du Z, Honaas L, Abraham T. "Stealth dissemination" of macrophage-tumor cell fusions cultured from blood of patients with pancreatic ductal adenocarcinoma. PLoS One 2017; 12:e0184451. [PMID: 28957348 PMCID: PMC5619717 DOI: 10.1371/journal.pone.0184451] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 08/24/2017] [Indexed: 12/12/2022] Open
Abstract
Here we describe isolation and characterization of macrophage-tumor cell fusions (MTFs) from the blood of pancreatic ductal adenocarcinoma (PDAC) patients. The MTFs were generally aneuploidy, and immunophenotypic characterizations showed that the MTFs express markers characteristic of PDAC and stem cells, as well as M2-polarized macrophages. Single cell RNASeq analyses showed that the MTFs express many transcripts implicated in cancer progression, LINE1 retrotransposons, and very high levels of several long non-coding transcripts involved in metastasis (such as MALAT1). When cultured MTFs were transplanted orthotopically into mouse pancreas, they grew as obvious well-differentiated islands of cells, but they also disseminated widely throughout multiple tissues in "stealth" fashion. They were found distributed throughout multiple organs at 4, 8, or 12 weeks after transplantation (including liver, spleen, lung), occurring as single cells or small groups of cells, without formation of obvious tumors or any apparent progression over the 4 to 12 week period. We suggest that MTFs form continually during PDAC development, and that they disseminate early in cancer progression, forming "niches" at distant sites for subsequent colonization by metastasis-initiating cells.
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Affiliation(s)
- Gary A. Clawson
- Gittlen Cancer Research Laboratories and the Department of Pathology, Hershey Medical Center (HMC), Pennsylvania State University (PSU), Hershey, PA, United States of America
| | - Gail L. Matters
- Department of Biochemistry & Molecular Biology, HMC, PSU, Hershey, PA, United States of America
| | - Ping Xin
- Gittlen Cancer Research Laboratories and the Department of Pathology, Hershey Medical Center (HMC), Pennsylvania State University (PSU), Hershey, PA, United States of America
| | - Christopher McGovern
- Department of Biochemistry & Molecular Biology, HMC, PSU, Hershey, PA, United States of America
| | - Eric Wafula
- Department of Biology, Eberly College, University Park (UP), Pennsylvania State University, University Park, PA, United States of America
| | - Claude dePamphilis
- Department of Biology, Eberly College, University Park (UP), Pennsylvania State University, University Park, PA, United States of America
| | - Morgan Meckley
- Gittlen Cancer Research Laboratories and the Department of Pathology, Hershey Medical Center (HMC), Pennsylvania State University (PSU), Hershey, PA, United States of America
| | - Joyce Wong
- Department of Surgery, HMC, PSU, Hershey, PA, United States of America
| | - Luke Stewart
- Applications Support, Fluidigm Corporation, South San Francisco, CA, United States of America
| | - Christopher D’Jamoos
- Applications Support, Fluidigm Corporation, South San Francisco, CA, United States of America
| | - Naomi Altman
- Department of Statistics, Eberly College, UP, PSU, University Park, PA, United States of America
| | - Yuka Imamura Kawasawa
- Department of Pharmacology and Biochemistry & Molecular Biology, Institute for Personalized Medicine, HMC, PSU, Hershey, PA, United States of America
| | - Zhen Du
- Gittlen Cancer Research Laboratories and the Department of Pathology, Hershey Medical Center (HMC), Pennsylvania State University (PSU), Hershey, PA, United States of America
| | - Loren Honaas
- Department of Biology, Eberly College, University Park (UP), Pennsylvania State University, University Park, PA, United States of America
| | - Thomas Abraham
- Department of Neural & Behavioral Sciences and Microscopy Imaging Facility, HMC, PSU, Hershey, PA, United States of America
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Efficient substrate screening and inhibitor testing of human CYP4Z1 using permeabilized recombinant fission yeast. Biochem Pharmacol 2017; 146:174-187. [PMID: 28951277 DOI: 10.1016/j.bcp.2017.09.011] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 09/21/2017] [Indexed: 01/09/2023]
Abstract
We have established a protocol for the preparation of permeabilized fission yeast cells (enzyme bags) that recombinantly express human cytochrome P450 enzymes (CYPs). A direct comparison of CYP3A4 activity gave an eightfold higher space-time yield for enzyme bag-catalyzed biotransformation as compared to whole-cell biotransformation, even though the total number of cells employed was lower by a factor of 150. Biotransformation of the luminogenic substrate Luciferin-H using CYP2C9-containing enzyme bags proceeded efficiently and stably for 24h. CYP4Z1 is of interest because it is strongly overexpressed both in breast cancer cells and in breast cancer metastases; however, current knowledge about its catalytic properties is very limited. Screening of CYP4Z1-containing enzyme bags with 15 luminogenic substrates enabled us to identify two new hydroxylations and eleven ether cleavage reactions that are catalyzed by CYP4Z1. By far the best substrate found in this study was Luciferin benzyl ether (Luciferin-BE). On the basis of the recently published crystal structure of CYP4B1 we created a new homology model of CYP4Z1 and performed molecular docking experiments, which indicate that all active substrates show a highly similar binding geometry compared to the endogenous substrates. The model predicts that Ser113, Ser222, Asn381, and Ser383 are key hydrogen bonding residues. We also identified five new inhibitors of CYP4Z1: miconazole, econazole, aminobenzotriazole, tolazoline, and 1-benzylimidazole respectively, with the last compound being the most potent giving an IC50 value of 180nM in our test system.
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Zhang J, Shao J, Zhu L, Zhao R, Xing J, Wang J, Guo X, Tu S, Han B, Yu K. Molecular profiling identifies prognostic markers of stage IA lung adenocarcinoma. Oncotarget 2017; 8:74846-74855. [PMID: 29088828 PMCID: PMC5650383 DOI: 10.18632/oncotarget.20420] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 06/16/2017] [Indexed: 12/29/2022] Open
Abstract
We previously showed that different pathologic subtypes were associated with different prognostic values in patients with stage IA lung adenocarcinoma (AC). We hypothesize that differential gene expression profiles of different subtypes may be valuable factors for prognosis in stage IA lung adenocarcinoma. We performed microarray gene expression profiling on tumor tissues micro-dissected from patients with acinar and solid predominant subtypes of stage IA lung adenocarcinoma. These patients had undergone a lobectomy and mediastinal lymph node dissection at the Shanghai Chest Hospital, Shanghai, China in 2012. No patient had preoperative treatment. We performed the Gene Set Enrichment Analysis (GSEA) analysis to look for gene expression signatures associated with tumor subtypes. The histologic subtypes of all patients were classified according to the 2015 WHO lung Adenocarcinoma classification. We found that patients with the solid predominant subtype are enriched for genes involved in RNA polymerase activity as well as inactivation of the p53 pathway. Further, we identified a list of genes that may serve as prognostic markers for stage IA lung adenocarcinoma. Validation in the TCGA database shows that these genes are correlated with survival, suggesting that they are novel prognostic factors for stage IA lung adenocarcinoma. In conclusion, we have uncovered novel prognostic factors for stage IA lung adenocarcinoma using gene expression profiling in combination with histopathology subtyping.
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Affiliation(s)
- Jie Zhang
- Shanghai Chest Hospital, Shanghai JiaoTong University, Department of Pathology, Shanghai, China
| | - Jinchen Shao
- Shanghai Chest Hospital, Shanghai JiaoTong University, Department of Pathology, Shanghai, China
| | - Lei Zhu
- Shanghai Chest Hospital, Shanghai JiaoTong University, Department of Pathology, Shanghai, China
| | - Ruiying Zhao
- Shanghai Chest Hospital, Shanghai JiaoTong University, Department of Pathology, Shanghai, China
| | - Jie Xing
- Shanghai Chest Hospital, Shanghai JiaoTong University, Department of Pathology, Shanghai, China
| | - Jun Wang
- Tumor Initiation & Maintenance Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla
| | - Xiaohui Guo
- Bioinformatics Core, Sanford Burnham Prebys Medical Discovery Institute, La Jolla
| | - Shichun Tu
- Allele Biotechnology & Pharmaceuticals, Inc., Nancy Ridge Drive, San Diego, USA
| | - Baohui Han
- Shanghai Chest Hospital, Shanghai JiaoTong University, Department of Pulmonary Medicine, Shanghai, China
| | - Keke Yu
- Shanghai Chest Hospital, Shanghai JiaoTong University, Department of Pathology, Shanghai, China.,Shanghai Chest Hospital, Shanghai JiaoTong University, Department of Biobank, Shanghai, China
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Avian and Mammalian Facilitative Glucose Transporters. MICROARRAYS 2017; 6:microarrays6020007. [PMID: 28379195 PMCID: PMC5487954 DOI: 10.3390/microarrays6020007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 03/15/2017] [Accepted: 03/15/2017] [Indexed: 12/17/2022]
Abstract
The GLUT members belong to a family of glucose transporter proteins that facilitate glucose transport across the cell membrane. The mammalian GLUT family consists of thirteen members (GLUTs 1-12 and H⁺-myo-inositol transporter (HMIT)). Humans have a recently duplicated GLUT member, GLUT14. Avians express the majority of GLUT members. The arrangement of multiple GLUTs across all somatic tissues signifies the important role of glucose across all organisms. Defects in glucose transport have been linked to metabolic disorders, insulin resistance and diabetes. Despite the essential importance of these transporters, our knowledge regarding GLUT members in avians is fragmented. It is clear that there are no chicken orthologs of mammalian GLUT4 and GLUT7. Our examination of GLUT members in the chicken revealed that some chicken GLUT members do not have corresponding orthologs in mammals. We review the information regarding GLUT orthologs and their function and expression in mammals and birds, with emphasis on chickens and humans.
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46
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Clarke LE, Flake DD, Busam K, Cockerell C, Helm K, McNiff J, Reed J, Tschen J, Kim J, Barnhill R, Elenitsas R, Prieto VG, Nelson J, Kimbrell H, Kolquist KA, Brown KL, Warf MB, Roa BB, Wenstrup RJ. An independent validation of a gene expression signature to differentiate malignant melanoma from benign melanocytic nevi. Cancer 2017; 123:617-628. [PMID: 27768230 PMCID: PMC5324582 DOI: 10.1002/cncr.30385] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 08/22/2016] [Accepted: 09/19/2016] [Indexed: 12/18/2022]
Abstract
BACKGROUND Recently, a 23-gene signature was developed to produce a melanoma diagnostic score capable of differentiating malignant and benign melanocytic lesions. The primary objective of this study was to independently assess the ability of the gene signature to differentiate melanoma from benign nevi in clinically relevant lesions. METHODS A set of 1400 melanocytic lesions was selected from samples prospectively submitted for gene expression testing at a clinical laboratory. Each sample was tested and subjected to an independent histopathologic evaluation by 3 experienced dermatopathologists. A primary diagnosis (benign or malignant) was assigned to each sample, and diagnostic concordance among the 3 dermatopathologists was required for inclusion in analyses. The sensitivity and specificity of the score in differentiating benign and malignant melanocytic lesions were calculated to assess the association between the score and the pathologic diagnosis. RESULTS The gene expression signature differentiated benign nevi from malignant melanoma with a sensitivity of 91.5% and a specificity of 92.5%. CONCLUSIONS These results reflect the performance of the gene signature in a diverse array of samples encountered in routine clinical practice. Cancer 2017;123:617-628. © 2016 American Cancer Society.
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Affiliation(s)
| | | | - Klaus Busam
- Memorial Sloan Kettering Cancer CenterNew YorkNew York
| | - Clay Cockerell
- The University of Texas Southwestern Medical CenterDallasTexas
| | - Klaus Helm
- Penn State Hershey DermatologyHersheyPennsylvania
| | | | - Jon Reed
- CellNetix Pathology and Laboratories LLCSeattleWashington
| | | | - Jinah Kim
- Department of PathologyStanford School of MedicineStanfordCalifornia
| | - Raymond Barnhill
- Department of PathologyUniversity of California Los AngelesLos AngelesCalifornia
| | - Rosalie Elenitsas
- Department of DermatologyUniversity of PennsylvaniaPhiladelphiaPennsylvania
| | - Victor G. Prieto
- Department of PathologyThe University of Texas MD Anderson Cancer CenterHoustonTexas
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Huang Q, Wei H, Wu Z, Li L, Yao L, Sun Z, Li L, Lin Z, Xu W, Han S, Cao W, Xu Y, Song D, Yang X, Xiao J. Preferentially Expressed Antigen of Melanoma Prevents Lung Cancer Metastasis. PLoS One 2016; 11:e0149640. [PMID: 27391090 PMCID: PMC4938541 DOI: 10.1371/journal.pone.0149640] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 02/03/2016] [Indexed: 12/28/2022] Open
Abstract
Lung cancer is the most common cause of cancer death worldwide. The poor survival rate is largely due to the extensive local invasion and metastasis. However, the mechanisms underlying the invasion and metastasis of lung cancer cells remain largely elusive. In this study, we examined the role of preferentially expressed antigen of melanoma (PRAME) in lung cancer metastasis. Our results show that PRAME is downregulated in lung adenocarcinoma and lung bone metastasis compared with normal human lung. Knockdown of PRAME decreases the expression of E-Cadherin and promotes the proliferation, invasion, and metastasis of lung cancer cells by regulating multiple critical genes, most of which are related to cell migration, including MMP1, CCL2, CTGF, and PLAU. Clinical data analysis reveals that the expression of MMP1 correlates with the clinical features and outcome of lung adenocarcinoma. Taken together, our data demonstrate that PRAME plays a role in preventing the invasion and metastasis of lung adenocarcinoma and novel diagnostic or therapeutic strategies can be developed by targeting PRAME.
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Affiliation(s)
- Quan Huang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
- Department of Orthopedic Oncology, Changzheng Hospital, The Second Military Medical University, No. 415 Fengyang Road, Shanghai, 200003, China
| | - Haifeng Wei
- Department of Orthopedic Oncology, Changzheng Hospital, The Second Military Medical University, No. 415 Fengyang Road, Shanghai, 200003, China
- * E-mail: (YFX); (DWS); (HFW); (XHY); (JRX)
| | - Zhipeng Wu
- Department of Orthopedic Oncology, Changzheng Hospital, The Second Military Medical University, No. 415 Fengyang Road, Shanghai, 200003, China
| | - Lin Li
- Department of Orthopedic Oncology, Changzheng Hospital, The Second Military Medical University, No. 415 Fengyang Road, Shanghai, 200003, China
| | - Liangfang Yao
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Zhengwang Sun
- Department of Orthopedic Oncology, Changzheng Hospital, The Second Military Medical University, No. 415 Fengyang Road, Shanghai, 200003, China
| | - Lei Li
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
- Department of Orthopedic Oncology, Changzheng Hospital, The Second Military Medical University, No. 415 Fengyang Road, Shanghai, 200003, China
| | - Zaijun Lin
- Department of Orthopedic Oncology, Changzheng Hospital, The Second Military Medical University, No. 415 Fengyang Road, Shanghai, 200003, China
| | - Wei Xu
- Department of Orthopedic Oncology, Changzheng Hospital, The Second Military Medical University, No. 415 Fengyang Road, Shanghai, 200003, China
| | - Shuai Han
- Department of Orthopedic Oncology, Changzheng Hospital, The Second Military Medical University, No. 415 Fengyang Road, Shanghai, 200003, China
| | - Wenjiao Cao
- The International Peace Maternity& Child Health Hospital of China welfare institute (IPMCH), Shanghai, China
| | - Yunfei Xu
- Urology Department, Tenth People's Hospital of Tongji University, Shanghai, PR China
- * E-mail: (YFX); (DWS); (HFW); (XHY); (JRX)
| | - Dianwen Song
- Department of Orthopedic Oncology, Changzheng Hospital, The Second Military Medical University, No. 415 Fengyang Road, Shanghai, 200003, China
- * E-mail: (YFX); (DWS); (HFW); (XHY); (JRX)
| | - Xinghai Yang
- Department of Orthopedic Oncology, Changzheng Hospital, The Second Military Medical University, No. 415 Fengyang Road, Shanghai, 200003, China
- * E-mail: (YFX); (DWS); (HFW); (XHY); (JRX)
| | - Jianru Xiao
- Department of Orthopedic Oncology, Changzheng Hospital, The Second Military Medical University, No. 415 Fengyang Road, Shanghai, 200003, China
- * E-mail: (YFX); (DWS); (HFW); (XHY); (JRX)
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Huang Q, Li L, Lin Z, Xu W, Han S, Zhao C, Li L, Cao W, Yang X, Wei H, Xiao J. Identification of Preferentially Expressed Antigen of Melanoma as a Potential Tumor Suppressor in Lung Adenocarcinoma. Med Sci Monit 2016; 22:1837-42. [PMID: 27241212 PMCID: PMC4913835 DOI: 10.12659/msm.895642] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Background Preferentially expressed antigen of melanoma (PRAME) is known as a tumor-associated antigen that is altered in a variety of malignancies, including lung cancer. However, the role of PRAME in lung cancer remains unclear. Material/Methods We analyzed the expression of PRAME in human lung adenocarcinomas and studied the function of PRAME using small interfering RNA (siRNA)-induced gene knockdown in lung cancer cell lines PC9 and A549. Results We found that PRAME expression is down-regulated in lung adenocarcinomas. Knockdown of PRAME promoted proliferation and suppressed apoptosis of PC9 and A549 cells. Conclusions In line with its roles in controlling cell growth, RPAME regulates multiple critical cell-growth related genes, including IGF1R oncogene. IGF1R up-regulation contributes to increase of cell growth upon the knockdown of PRAME. Taken together, our results suggest that PRAME has inhibitory roles in lung cancer.
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Affiliation(s)
- Quan Huang
- Department of Orthopedic Oncology, Changzheng Hospital, The Second Military Medical University, Shanghai, China (mainland)
| | - Lin Li
- Department of Orthopedic Oncology, Changzheng Hospital, The Second Military Medical University, Shanghai, China (mainland)
| | - Zaijun Lin
- Department of Orthopedic Oncology, Changzheng Hospital, The Second Military Medical University, Shanghai, China (mainland)
| | - Wei Xu
- , The International Peace Maternity & Child Health Hospital of China Welfare Institute (IPMCH), Shanghai, China (mainland)
| | - Shuai Han
- Department of Orthopedic Oncology, Changzheng Hospital, The Second Military Medical University, Shanghai, China (mainland)
| | - Chenglong Zhao
- Department of Orthopedic Oncology, Changzheng Hospital, The Second Military Medical University, Shanghai, China (mainland)
| | - Lei Li
- Department of Orthopedic Oncology, Changzheng Hospital, The Second Military Medical University, Shanghai, China (mainland)
| | - Wenjiao Cao
- , The International Peace Maternity & Child Health Hospital of China Welfare Institute (IPMCH), Shanghai, China (mainland)
| | - Xinghai Yang
- Department of Orthopedic Oncology, Changzheng Hospital, The Second Military Medical University, Shanghai, China (mainland)
| | - Haifeng Wei
- Department of Orthopedic Oncology, Changzheng Hospital, The Second Military Medical University, Shanghai, China (mainland)
| | - Jianru Xiao
- Department of Orthopedic Oncology, Changzheng Hospital, The Second Military Medical University, Shanghai, China (mainland)
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49
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Ma J, Zhao J, Lu J, Wang P, Feng H, Zong Y, Ou B, Zheng M, Lu A. Cadherin-12 enhances proliferation in colorectal cancer cells and increases progression by promoting EMT. Tumour Biol 2016; 37:9077-88. [PMID: 26762412 PMCID: PMC4990612 DOI: 10.1007/s13277-015-4555-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Accepted: 11/30/2015] [Indexed: 12/17/2022] Open
Abstract
Cadherin-12 (CDH12) is a subtype of N-cadherin family. In this study, we investigated the expression of CDH12 and the role of CDH12 in prognosis of colorectal cancer (CRC) patients. In addition, we observed the influence of CDH12 on proliferation and progression of CRC cell lines. By using immunohistochemical staining, we analyzed CRC samples and adjacent non-tumor tissues collected from 78 patients who underwent laparoscopic surgery in Shanghai Minimally Invasive Center, China. Statistical analyses were used to analyze relationship between CDH12 and tumor features. Kaplan-Meier method was used to analyze patients' survival. Proliferation ability of CRC cells was tested by CCK-8 assay, and transwell assays were performed to detect migration and invasion ability. Western blot assay was performed to investigate epithelial-mesenchymal transition (EMT) variants. We found that expression of CDH12 in tumor tissue was higher than in adjacent normal tissue. High expression of CDH12 was associated with tumor invasion depth and predicts poor prognosis of CRC patients. Ectopic/repressing expression of CDH12 increased/decreased the proliferation and migration ability of CRC cells. CDH12 is able to increase cancer cell migration and invasion via promoting EMT by targeting transcriptional factor Snail. These findings may conclude that CDH12 may act as a predictor in CRC patients' prognosis and an oncogene in CRC cell proliferation and migration. CDH12 may influence CRC cell progression through promoting EMT by targeting Snail. In addition, CDH12 is promoted by MCP1 through induction of MCPIP.
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Affiliation(s)
- Junjun Ma
- Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China
| | - Jingkun Zhao
- Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China.,Shanghai Institute of Digestive Surgery, Shanghai, People's Republic of China
| | - Jun Lu
- Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China.,Department of General Surgery, Hangzhou First People's Hospital, Hangzhou, Zhejiang, People's Republic of China
| | - Puxiongzhi Wang
- Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China.,Shanghai Institute of Digestive Surgery, Shanghai, People's Republic of China
| | - Hao Feng
- Department of Surgery, Munich University, Munich, Germany
| | - Yaping Zong
- Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China
| | - Baochi Ou
- Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China.,Shanghai Institute of Digestive Surgery, Shanghai, People's Republic of China
| | - Minhua Zheng
- Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China.
| | - Aiguo Lu
- Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China.
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50
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Lemjabbar-Alaoui H, Hassan OU, Yang YW, Buchanan P. Lung cancer: Biology and treatment options. BIOCHIMICA ET BIOPHYSICA ACTA 2015; 1856:189-210. [PMID: 26297204 PMCID: PMC4663145 DOI: 10.1016/j.bbcan.2015.08.002] [Citation(s) in RCA: 456] [Impact Index Per Article: 50.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Revised: 07/30/2015] [Accepted: 08/16/2015] [Indexed: 12/25/2022]
Abstract
Lung cancer remains the leading cause of cancer mortality in men and women in the U.S. and worldwide. About 90% of lung cancer cases are caused by smoking and the use of tobacco products. However, other factors such as radon gas, asbestos, air pollution exposures, and chronic infections can contribute to lung carcinogenesis. In addition, multiple inherited and acquired mechanisms of susceptibility to lung cancer have been proposed. Lung cancer is divided into two broad histologic classes, which grow and spread differently: small-cell lung carcinomas (SCLCs) and non-small cell lung carcinomas (NSCLCs). Treatment options for lung cancer include surgery, radiation therapy, chemotherapy, and targeted therapy. Therapeutic-modalities recommendations depend on several factors, including the type and stage of cancer. Despite the improvements in diagnosis and therapy made during the past 25 years, the prognosis for patients with lung cancer is still unsatisfactory. The responses to current standard therapies are poor except for the most localized cancers. However, a better understanding of the biology pertinent to these challenging malignancies, might lead to the development of more efficacious and perhaps more specific drugs. The purpose of this review is to summarize the recent developments in lung cancer biology and its therapeutic strategies, and discuss the latest treatment advances including therapies currently under clinical investigation.
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Affiliation(s)
- Hassan Lemjabbar-Alaoui
- Department of Surgery, Thoracic Oncology Division, University of CA, San Francisco 94143, USA
| | - Omer Ui Hassan
- Department of Surgery, Thoracic Oncology Division, University of CA, San Francisco 94143, USA
| | - Yi-Wei Yang
- Department of Surgery, Thoracic Oncology Division, University of CA, San Francisco 94143, USA
| | - Petra Buchanan
- Department of Surgery, Thoracic Oncology Division, University of CA, San Francisco 94143, USA
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