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Bagratuni T, Aktypi F, Theologi O, Sakkou M, Verrou KM, Mavrianou‐Koutsoukou N, Patseas D, Liacos C, Skourti S, Papadimou A, Taouxi K, Theodorakakou F, Kollias G, Sfikakis P, Terpos E, Dimopoulos MA, Kastritis E. Single-cell analysis of MYD88 L265P and MYD88 WT Waldenström macroglobulinemia patients. Hemasphere 2024; 8:e27. [PMID: 38435423 PMCID: PMC10878187 DOI: 10.1002/hem3.27] [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: 05/05/2023] [Accepted: 11/07/2023] [Indexed: 03/05/2024] Open
Abstract
Waldenström macroglobulinemia (WM) is characterized by the expansion of clonal lymphoplasmacytic cells; the MYD88L265P somatic mutation is found in >90% of patients, but malignant B cells may still display intra-clonal heterogeneity. To assess clonal heterogeneity in WM, we generated and performed single-cell RNA sequencing of CD19+ sorted cells from five patients with MYD88 L265P and two patients with MYD88 WT genotype as well as two healthy donors. We identified distinct transcriptional patterns in the clonal subpopulations not only between the two genetically distinct WM subgroups but also among MYD88 L265P patients, which affected the B cell composition in the different subgroups. Comparison of clonal and normal/polyclonal B cells within each patient sample enabled the identification of patient-specific transcriptional changes. We identified gene signatures active in a subset of MYD88L265P patients, while other signatures were active in MYD88 WT patients. Finally, gene expression analysis showed common transcriptional features between patients compared to the healthy control but also differentially expressed genes between MYD88 L265P and MYD88 WT patients involved in distinct pathways, including NFκΒ, BCL2, and BTK. Overall, our data highlight the intra-tumor clonal heterogeneity in WM with potential prognostic and therapeutic implications.
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Affiliation(s)
- Tina Bagratuni
- Department of Clinical Therapeutics, School of MedicineNational and Kapodistrian University of AthensAthensGreece
| | - Foteini Aktypi
- Department of Clinical Therapeutics, School of MedicineNational and Kapodistrian University of AthensAthensGreece
| | - Ourania Theologi
- Department of Clinical Therapeutics, School of MedicineNational and Kapodistrian University of AthensAthensGreece
| | - Maria Sakkou
- School of Medicine, Center of New Biotechnologies & Precision MedicineNational and Kapodistrian University of AthensAthensGreece
- Department of PhysiologyNational and Kapodistrian University of Athens Medical SchoolAthensGreece
- Biomedical Sciences Research Center (BSRC) ‘Alexander Fleming’Institute for BioinnovationVariGreece
| | - Kleio Maria Verrou
- School of Medicine, Center of New Biotechnologies & Precision MedicineNational and Kapodistrian University of AthensAthensGreece
- Joint Rheumatology ProgramNational and Kapodistrian University of Athens Medical SchoolAthensGreece
| | - Nefeli Mavrianou‐Koutsoukou
- Department of Clinical Therapeutics, School of MedicineNational and Kapodistrian University of AthensAthensGreece
| | - Dimitrios Patseas
- Department of Clinical Therapeutics, School of MedicineNational and Kapodistrian University of AthensAthensGreece
| | - Christine Liacos
- Department of Clinical Therapeutics, School of MedicineNational and Kapodistrian University of AthensAthensGreece
| | - Stamatia Skourti
- Department of Clinical Therapeutics, School of MedicineNational and Kapodistrian University of AthensAthensGreece
| | - Alexandra Papadimou
- Department of Clinical Therapeutics, School of MedicineNational and Kapodistrian University of AthensAthensGreece
| | - Kostantina Taouxi
- Department of Clinical Therapeutics, School of MedicineNational and Kapodistrian University of AthensAthensGreece
| | - Foteini Theodorakakou
- Department of Clinical Therapeutics, School of MedicineNational and Kapodistrian University of AthensAthensGreece
| | - Georgios Kollias
- School of Medicine, Center of New Biotechnologies & Precision MedicineNational and Kapodistrian University of AthensAthensGreece
- Department of PhysiologyNational and Kapodistrian University of Athens Medical SchoolAthensGreece
- Biomedical Sciences Research Center (BSRC) ‘Alexander Fleming’Institute for BioinnovationVariGreece
| | - Petros Sfikakis
- School of Medicine, Center of New Biotechnologies & Precision MedicineNational and Kapodistrian University of AthensAthensGreece
- Joint Rheumatology ProgramNational and Kapodistrian University of Athens Medical SchoolAthensGreece
| | - Evangelos Terpos
- Department of Clinical Therapeutics, School of MedicineNational and Kapodistrian University of AthensAthensGreece
| | - Meletios A. Dimopoulos
- Department of Clinical Therapeutics, School of MedicineNational and Kapodistrian University of AthensAthensGreece
| | - Efstathios Kastritis
- Department of Clinical Therapeutics, School of MedicineNational and Kapodistrian University of AthensAthensGreece
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Liu Z, Xu Y, Jin S, Liu X, Wang B. Construction of a Prognostic Model Based on Methylation-Related Genes in Patients with Colon Adenocarcinoma. Cancer Manag Res 2023; 15:1097-1110. [PMID: 37818334 PMCID: PMC10561619 DOI: 10.2147/cmar.s417897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 09/22/2023] [Indexed: 10/12/2023] Open
Abstract
Purpose Colon adenocarcinoma (COAD) is the second leading cause of death in the world, and the new incidence rate ranks third among all cancers. Abnormal DNA methylation is related to the occurrence and development of tumors. In this study, we aimed to identify genes associated with abnormal methylation in COAD. Methods COAD transcriptome data, methylation data and clinical information were downloaded from the TCGA database and GEO database. The differentially expressed genes (DEGs) and methylated genes (DMGs) were analyzed and identified in COAD. PCA analysis was applied to divide COAD into subtypes, and the survival and immune cell infiltration of each subtype were evaluated. Cox and LASSO analyses were performed to construct COAD risk model. GSEA was used to evaluate the enrichment pathways. The Kaplan-Meier was used to analyze the difference in survival. ROC curve was plotted to evaluate the accuracy of the model, and GSE17536 was used to verify the accuracy of the risk model. The risk model is combined with the clinicopathological characteristics of COAD patients to perform multivariate Cox regression analysis to obtain independent risk factors and draw nomograms. Results In total, 4564 DEGs and 1093 DMGs were screened, among which 298 were found to be overlapping genes. For 220 of these overlapping genes, the methylation was significantly negatively correlated to expression levels. An optimal signature from 4 methylated biomarkers was identified to construct the prognostic model. Conclusion Our study identified 4 methylated biomarkers in the COAD. Then, we constructed the risk model to provide a theoretical basis and reference value for the research and treatment of COAD.
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Affiliation(s)
- ZhenDong Liu
- Department of General Surgery, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, Hainan Province, People’s Republic of China
| | - YuYang Xu
- Department of General Surgery, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, Hainan Province, People’s Republic of China
| | - Shan Jin
- Department of Anesthesiology, Second Affiliated Hospital of Hainan Medical University, Haikou, Hainan Province, People’s Republic of China
| | - Xin Liu
- Department of General Surgery, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, Hainan Province, People’s Republic of China
| | - BaoChun Wang
- Department of General Surgery, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, Hainan Province, People’s Republic of China
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Bossi LE, Palumbo C, Trojani A, Melluso A, Di Camillo B, Beghini A, Sarnataro LM, Cairoli R. A Nine-Gene Expression Signature Distinguished a Patient with Chronic Lymphocytic Leukemia Who Underwent Prolonged Periodic Fasting. MEDICINA (KAUNAS, LITHUANIA) 2023; 59:1405. [PMID: 37629695 PMCID: PMC10456711 DOI: 10.3390/medicina59081405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/27/2023] [Accepted: 07/28/2023] [Indexed: 08/27/2023]
Abstract
Background and Objectives: This study aimed to investigate the causes of continuous deep fluctuations in the absolute lymphocyte count (ALC) in an untreated patient with Chronic Lymphocytic Leukemia (CLL), who has had a favorable prognosis since the time of diagnosis. Up until now, the patient has voluntarily chosen to adopt a predominantly vegetarian and fruitarian diet, along with prolonged periods of total fasting (ranging from 4 to 39 days) each year. Materials and Methods: For this purpose, we decided to analyze the whole transcriptome profiling of peripheral blood (PB) CD19+ cells from the patient (#1) at different time-points vs. the same cells of five other untreated CLL patients who followed a varied diet. Consequently, the CLL patients were categorized as follows: the 1st group comprised patient #1 at 20 different time-points (16 time-points during nutrition and 4 time-points during fasting), whereas the 2nd group included only one time point for each of the patients (#2, #3, #4, #5, and #6) as they followed a varied diet. We performed microarray experiments using a powerful tool, the Affymetrix Human Clariom™ D Pico Assay, to generate high-fidelity biomarker signatures. Statistical analysis was employed to identify differentially expressed genes and to perform sample clustering. Results: The lymphocytosis trend in patient #1 showed recurring fluctuations since the time of diagnosis. Interestingly, we observed that approximately 4-6 weeks after the conclusion of fasting periods, the absolute lymphocyte count was reduced by about half. The gene expression profiling analysis revealed that nine genes were statistically differently expressed between the 1st group and the 2nd group. Specifically, IGLC3, RPS26, CHPT1, and PCDH9 were under expressed in the 1st group compared to the 2nd group of CLL patients. Conversely, IGHV3-43, IGKV3D-20, PLEKHA1, CYBB, and GABRB2 were over-expressed in the 1st group when compared to the 2nd group of CLL patients. Furthermore, clustering analysis validated that all the samples from patient #1 clustered together, showing clear separation from the samples of the other CLL patients. Conclusions: This study unveiled a small gene expression signature consisting of nine genes that distinguished an untreated CLL patient who followed prolonged periods of total fasting, maintaining a gradual growth trend of lymphocytosis, compared to five untreated CLL patients with a varied diet. Future investigations focusing on patient #1 could potentially shed light on the role of prolonged periodic fasting and the implication of this specific gene signature in sustaining the lymphocytosis trend and the favorable course of the disease.
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Affiliation(s)
- Luca Emanuele Bossi
- Department of Hematology and Oncology ASST Grande Ospedale Metropolitano Niguarda, 20162 Milan, Italy; (A.T.); (A.M.); (L.M.S.); (R.C.)
| | - Cassandra Palumbo
- Department of Hematology and Oncology ASST Grande Ospedale Metropolitano Niguarda, 20162 Milan, Italy; (A.T.); (A.M.); (L.M.S.); (R.C.)
| | - Alessandra Trojani
- Department of Hematology and Oncology ASST Grande Ospedale Metropolitano Niguarda, 20162 Milan, Italy; (A.T.); (A.M.); (L.M.S.); (R.C.)
| | - Agostina Melluso
- Department of Hematology and Oncology ASST Grande Ospedale Metropolitano Niguarda, 20162 Milan, Italy; (A.T.); (A.M.); (L.M.S.); (R.C.)
| | - Barbara Di Camillo
- Department of Information Engineering, University of Padova, 35020 Padua, Italy;
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020 Padua, Italy
| | | | - Luca Maria Sarnataro
- Department of Hematology and Oncology ASST Grande Ospedale Metropolitano Niguarda, 20162 Milan, Italy; (A.T.); (A.M.); (L.M.S.); (R.C.)
| | - Roberto Cairoli
- Department of Hematology and Oncology ASST Grande Ospedale Metropolitano Niguarda, 20162 Milan, Italy; (A.T.); (A.M.); (L.M.S.); (R.C.)
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Hu Y, Fan S, Zhu Y, Xie X. A novel circadian cycle-related gene signature for prognosis prediction of patients with breast cancer. Medicine (Baltimore) 2023; 102:e33718. [PMID: 37144994 PMCID: PMC10158864 DOI: 10.1097/md.0000000000033718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 04/18/2023] [Indexed: 05/06/2023] Open
Abstract
The extensive and intricate relationships between circadian rhythm and cancer have been reported in numerous studies. However, in breast cancer (BC), the potential role of circadian clock-related genes (CCRGs) in prognosis prediction has not been fully clarified. The transcriptome data and clinical information were downloaded from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus databases. A CCRGs-based risk signature was established by differential expression analysis, univariate, Lasso and multivariate Cox regression analyses. we conducted a gene set enrichment analysis (GSEA) between groups. A nomogram integrating independent clinical factors and risk score was generated and evaluated by calibration curves and decision curve analysis (DCA). Differentially expression analysis revealed 80 differentially expressed CCRGs, and 27 of them were significantly associated with the overall survival (OS) of BC. BC can be classified into 4 molecular subtypes with significant differences in prognosis based on the 27 CCRGs. Three prognostic CCRGs, including desmocollin 1 (DSC1), LEF1, and protocadherin 9 (PCDH9), were identified to be independent risk factors of BC prognosis and were used to construct a risk score model. BC patients were divided into high- and low-risk groups, and there were significant differences in prognosis between the 2 groups both in the training and validation cohorts. It was found that patients in different groups of race, status, or T stage had significant levels of risk score. Furthermore, patients of different risk levels exhibit varying degrees of sensitivity to vinorelbine, lapatinib, metformin, and vinblastine. GSEA showed that in the high-risk group, immune response-related activities were dramatically repressed whereas cilium-related processes were significantly stimulated. Cox regression analysis demonstrated that age, N stage, radiotherapy and the risk score were independent prognostic risk factors of BC, and a nomogram was established based on these variables. The nomogram exerted a favorable concordance index (0.798) as well as calibration performance, which strongly supports the clinical application of the nomogram. Our study indicated the disruption of the expression of CCRGs in BC and built a favorable prognostic risk model based on 3 independent prognostic CCRGs. These genes may be applied as candidate molecular targets for the diagnosis and therapy of BC.
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Affiliation(s)
- Yuanyuan Hu
- Department of Breast Surgery, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, Zhejiang, China
| | - Shuyao Fan
- Department of Breast Surgery, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, Zhejiang, China
| | - Yiwan Zhu
- The First Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Xiaohong Xie
- Department of Breast Surgery, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, Zhejiang, China
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Zhang J, Yang HZ, Liu S, Islam MO, Zhu Y, Wang Z, Chen R. PCDH9 suppresses melanoma proliferation and cell migration. Front Oncol 2022; 12:903554. [DOI: 10.3389/fonc.2022.903554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 10/12/2022] [Indexed: 11/16/2022] Open
Abstract
BackgroundMelanoma has dramatically increased during last 30 years with low 5-year survival and prognosis rate.MethodsMelanoma cells (A375 and G361) were chosen as the in vitro model. The immunohistochemical (IHC) analysis and bioinformatics mining exhibited the suppression of PCDH9 on melanoma. The interference and overexpression of PCDH9 were infected by lentivirus. The effects of PCDH9 on melanoma cells were assessed in terms of alteration of PCDH9 such as cell viability, apoptosis, cell cycle, and wound-healing assay. Moreover, expressions of PCDH9 with other genes (MMP2, MMP9, CCND1, and RAC1) were also assessed by PCR.ResultsThe alteration of PCDH9 has a negative correlation with MMP2, MMP9, and RAC1 but had a positive correlation with CCND1 (Cyclin D1) and apoptosis. Increase of PCDH9 could suppress melanoma cells and inhibit migration but not exert significant effects on cell cycle. IHC showed lower PCDH9 expression in melanoma tissue with main expression in cytoplasm.ConclusionOverexpressed PCDH9 suppressed melanoma cells, and PCDH9 can be considered as an independent prognostic factor for melanoma; even re-expression of PCDH9 can serve as a potential therapeutic strategy for melanoma treatment.
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Cai G, Zou R, yang H, Xie J, Chen X, Zheng C, Luo S, Wei N, Liu S, Chen R. Circ_0084043-miR-134-5p axis regulates PCDH9 to suppress melanoma. Front Oncol 2022; 12:891476. [PMID: 36387162 PMCID: PMC9641620 DOI: 10.3389/fonc.2022.891476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 09/20/2022] [Indexed: 11/29/2022] Open
Abstract
The low survival rates, poor responses, and drug resistance of patients with melanoma make it urgent to find new therapeutic targets. This study investigated whether the circ_0084043-miR-134-5p axis regulates the antitumor effect of protocadherin 9 (PCDH9) in melanoma. Ectopic expression or knock down (KD) of PCDH9 with a lentivirus vector, we explored its effects on the proliferation, invasion, and apoptosis of melanoma and verified its regulatory effect on ras-related C3 botulinum toxin substrate 1 (RAC1), proline-rich tyrosine kinase 2 (Pyk2), Cyclin D1, matrix metalloproteinase 2 (MMP2), and MMP9. We further observed the effect of KD circ_0084043 on the malignant behavior of melanoma and studied whether circ_0084043 sponged miR-134-5p and regulated PCDH9. We found that circ_0084043 was overexpressed in melanoma and associated with the malignant phenotype. PCDH9 was poorly expressed in human melanoma tissues, and overexpression of PCDH9 inhibited melanoma progression. Quantitative real-time PCR and Western blotting results showed that overexpression of PCDH9 could downregulate RAC1, MMP2, and MMP9 and upregulate Pyk2 and Cyclin D1. Circ_0084043 KD inhibited invasion and promoted apoptosis in melanoma cells. Circ_0084043 could sponge miR-134-5p and thus indirectly regulate PCDH9. Furthermore, we discovered that inhibiting circ_0084043 had an anti–PD-Ll effect. In vivo, PCDH9 overexpression inhibited melanoma tumor growth, but PCDH9 KD promoted it. In conclusion, PCDH9, which is regulated by the circ 0084043-miR-134-5p axis, can suppress malignant biological behavior in melanoma and influence the expression levels of Pyk2, RAC1, Cyclin D1, MMP2, and MMP9.
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Affiliation(s)
- Guiyue Cai
- Dermatology Department, Dermatology Hospital, Southern Medical University, Guangzhou, China
- Clinical School, Guangdong Medical University, Zhanjiang, China
| | - Ruitao Zou
- Dermatology Department, Dermatology Hospital, Southern Medical University, Guangzhou, China
- Clinical School, Guangdong Medical University, Zhanjiang, China
| | - Huizhi yang
- Dermatology Department, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jiahao Xie
- Dermatology Department, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xiaoxuan Chen
- Clinical School, Guangdong Medical University, Zhanjiang, China
| | - Chunchan Zheng
- Dermatology Department, Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Sujun Luo
- Dermatology Department, Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Na Wei
- Dermatology Department, Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Shuang Liu
- Dermatology Department, Dermatology Hospital, Southern Medical University, Guangzhou, China
- *Correspondence: Shuang Liu, ; Rongyi Chen,
| | - Rongyi Chen
- Dermatology Department, Dermatology Hospital, Southern Medical University, Guangzhou, China
- Clinical School, Guangdong Medical University, Zhanjiang, China
- *Correspondence: Shuang Liu, ; Rongyi Chen,
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Ning Y, Deng C, Li C, Peng W, Yan C, Ran J, Chen W, Liu Y, Xia J, Ye L, Wei Z, Xiang T. PCDH20 inhibits esophageal squamous cell carcinoma proliferation and migration by suppression of the mitogen-activated protein kinase 9/AKT/β-catenin pathway. Front Oncol 2022; 12:937716. [PMID: 36248995 PMCID: PMC9555239 DOI: 10.3389/fonc.2022.937716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 09/02/2022] [Indexed: 11/13/2022] Open
Abstract
Aberrant protocadherins (PCDHs) expression trigger tumor invasion and metastasis. PCDH20 anti-tumor functions in various tumor have been identified. Tumor suppression is due to Wnt/β-catenin pathway antagonism and may be suppressed caused by PCDH20 downregulation through promotor methylation, whereas PCDH20 effects and regulation mechanism in esophageal squamous cell carcinoma (ESCC) remains elusive. We analyzed PCDH20 effects on ESCC and underlying action mechanisms for PCDH20. We test PCDH20 expression in ESCC tissues and cells by semi-quantitative PCR (RT-PCR) and q-PCR (real-time quantitative polymerase chain reaction). MSP (methylation-specific PCR) was carried out to assess the methylation of PCDH20 in ESCC cells and tissues. Anti-tumor effects of PCDH20 in vitro were assessed by clone formation assay, CCK8 assay, Transwell assay, and flow cytometry. Nude mice tumorigenicity was used to assess PCDH20 anti-tumor effect in vivo. Online database, qPCR, and Western blotting were used to identify the downregulation of MAP3K9 by PCDH20, associated with AKT/β-catenin signaling inactivation. We found that PCDH20 expression was dramatically attenuated in esophageal cancer tissues and cells, maybe due to promotor methylation, and ectopic PCDH20 expression suppressed ESCC malignant biological phenotypes. PCDH20 exerted anti-tumor effects by MAP3K9 downregulation, which suppressed AKT/β-catenin signaling in ESCC cells.ConclusionPCDH20 was a tumor suppressor gene, which antagonized AKT/β-catenin signaling pathway in ESCC by decreasing MAP3K9.
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Affiliation(s)
- Yijiao Ning
- Gastrointestinal Surgical Unit, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Chaoqun Deng
- Gastrointestinal Surgical Unit, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Chunhong Li
- Department of Oncology, Suining Central Hospital, Suining, China
- *Correspondence: Tingxiu Xiang, ; Chunhong Li,
| | - Weiyan Peng
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Chun Yan
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jing Ran
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing, China
| | - Weihong Chen
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yujia Liu
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jiuyi Xia
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Lin Ye
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Zhengqiang Wei
- Gastrointestinal Surgical Unit, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Tingxiu Xiang
- Gastrointestinal Surgical Unit, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- *Correspondence: Tingxiu Xiang, ; Chunhong Li,
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Paszkiewicz-Kozik E, Kluska A, Piątkowska M, Bałabas A, Żeber-Lubecka N, Karczmarski J, Goryca K, Kulecka M, Wojciechowska-Lampka E, Osiadacz W, Romejko-Jarosińska J, Świerkowska M, Paziewska A, Ambrożkiewicz F, Walewski J, Mikula M, Ostrowski J. Genetic associations with lymphomas in Polish patients: A pooled-DNA genome-wide association analysis. Int J Immunogenet 2022; 49:353-363. [PMID: 36036752 DOI: 10.1111/iji.12596] [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: 05/16/2022] [Revised: 07/26/2022] [Accepted: 08/10/2022] [Indexed: 11/29/2022]
Abstract
Several single nucleotide polymorphisms (SNPs) associated with susceptibility to Hodgkin lymphoma (HL) and diffuse large B-cell lymphoma (DLBCL) have been identified. The aim of this study was to identify susceptibility loci for HL and DLBCL in Polish patients. Altogether, DLBCL (n = 218 and HL patients (n = 224) and healthy individuals (n = 1181) were recruited. Lymphoma diagnosis was based on standard criteria. Genome-wide association study (GWAS) was performed using pooled-DNA samples on llumina Infinium Omni2.5 Exome-8 v1.3, and selected loci were replicated by TaqMan SNP genotyping of individuals. GWAS detected thirteen and seven SNPs associated with DLBCL and HL, respectively. In the replication study, six and seven SNPs reached significance after correction for multiple testing in the DLBCL and HL cohorts, respectively. One and four SNPs associated with DLBCL and HL, respectively, were localized within, and two SNPs-near the major histocompatibility complex (MHC) region. In conclusion, the majority of loci associated with HL and DLBCL aetiology in previous studies have potential roles in immune function. Our pooled-DNA GWAS enabled the identification of several susceptibility loci for DLBCL and HL in the Polish population; some of them were mapped within or adjacent to the MHC, and other associated SNPs were located outside the MHC.
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Affiliation(s)
- Ewa Paszkiewicz-Kozik
- Department of Lymphoproliferative Diseases, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Anna Kluska
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Magdalena Piątkowska
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Aneta Bałabas
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Natalia Żeber-Lubecka
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - Jakub Karczmarski
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Krzysztof Goryca
- Genomics Core Facility, Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Maria Kulecka
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland.,Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - Elżbieta Wojciechowska-Lampka
- Department of Lymphoproliferative Diseases, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Włodzimierz Osiadacz
- Department of Lymphoproliferative Diseases, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Joanna Romejko-Jarosińska
- Department of Lymphoproliferative Diseases, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Monika Świerkowska
- Department of Lymphoproliferative Diseases, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Agnieszka Paziewska
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland.,Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - Filip Ambrożkiewicz
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Jan Walewski
- Department of Lymphoproliferative Diseases, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Michał Mikula
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Jerzy Ostrowski
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland.,Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, Warsaw, Poland
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Protocadherin Gamma C3 (PCDHGC3) Is Strongly Expressed in Glioblastoma and Its High Expression Is Associated with Longer Progression-Free Survival of Patients. Int J Mol Sci 2022; 23:ijms23158101. [PMID: 35897674 PMCID: PMC9330298 DOI: 10.3390/ijms23158101] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/11/2022] [Accepted: 07/20/2022] [Indexed: 12/03/2022] Open
Abstract
Protocadherins (PCDHs) belong to the cadherin superfamily and represent the largest subgroup of calcium-dependent adhesion molecules. In the genome, most PCDHs are arranged in three clusters, α, β, and γ on chromosome 5q31. PCDHs are highly expressed in the central nervous system (CNS). Several PCDHs have tumor suppressor functions, but their individual role in primary brain tumors has not yet been elucidated. Here, we examined the mRNA expression of PCDHGC3, a member of the PCDHγ cluster, in non-cancerous brain tissue and in gliomas of different World Health Organization (WHO) grades and correlated it with the clinical data of the patients. We generated a PCDHGC3 knockout U343 cell line and examined its growth rate and migration in a wound healing assay. We showed that PCDHGC3 mRNA and protein were significantly overexpressed in glioma tissue compared to a non-cancerous brain specimen. This could be confirmed in glioma cell lines. High PCDHGC3 mRNA expression correlated with longer progression-free survival (PFS) in glioma patients. PCDHGC3 knockout in U343 resulted in a slower growth rate but a significantly faster migration rate in the wound healing assay and decreased the expression of several genes involved in WNT signaling. PCDHGC3 expression should therefore be further investigated as a PFS-marker in gliomas. However, more studies are needed to elucidate the molecular mechanisms underlying the PCDHGC3 effects.
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10
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Wu Q, Shi X, Pan Y, Liao X, Xu J, Gu X, Yu W, Chen Y, Yu G. The Chemopreventive Role of β-Elemene in Cholangiocarcinoma by Restoring PCDH9 Expression. Front Oncol 2022; 12:874457. [PMID: 35903688 PMCID: PMC9314746 DOI: 10.3389/fonc.2022.874457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 05/26/2022] [Indexed: 11/17/2022] Open
Abstract
Background β-Elemene, an effective anticancer component isolated from the Chinese herbal medicine Rhizoma Zedoariae, has been proved to have therapeutic potential against multiple cancers by extensive clinical trials and experimental research. However, its preventive role in cholangiocarcinoma (CCA) and the mechanisms of action of β-elemene on CCA need to be further investigated. Methods A thioacetamide (TAA)-induced pre-CCA animal model was well-established, and a low dosage of β-elemene was intragastrically (i.g.) administered for 6 months. Livers were harvested and examined histologically by a deep-learning convolutional neural network (CNN). cDNA array was used to analyze the genetic changes of CCA cells following β-elemene treatment. Immunohistochemical methods were applied to detect β-elemene-targeted protein PCDH9 in CCA specimens, and its predictive role was analyzed. β-Elemene treatment at the cellular or animal level was performed to test the effect of this traditional Chinese medicine on CCA cells. Results In the rat model of pre-CCA, the ratio of cholangiolar proliferation lesions was 0.98% ± 0.72% in the control group, significantly higher than that of the β-elemene (0. 47% ± 0.30%) groups (p = 0.0471). Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that the top 10 pathways affected by β-elemene treatment were associated with energy metabolism, and one was associated with the cell cycle. β-Elemene inactivated a number of oncogenes and restored the expression of multiple tumor suppressors. PCDH9 is a target of β-elemene and displays an important role in predicting tumor recurrence in CCA patients. Conclusions These findings proved that long-term use of β-elemene has the potential to interrupt the progression of CCA and improve the life quality of rats. Moreover, β-elemene exerted its anticancer potential partially by restoring the expression of PCDH9.
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Affiliation(s)
- Qing Wu
- Department of Oncology, Longhua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xintong Shi
- Department of Biliary Tract Surgery, Shanghai Eastern Hepatobiliary Surgery Hospital, Naval Medical University, Shanghai, China
| | - Yating Pan
- Department of Oncology, Longhua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xinyi Liao
- Department of Oncology, Longhua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Jiahua Xu
- Department of Oncology, Longhua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xiaoqiang Gu
- Department of Oncology, Longhua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Wenlong Yu
- Department of Biliary Tract Surgery, Shanghai Eastern Hepatobiliary Surgery Hospital, Naval Medical University, Shanghai, China
| | - Ying Chen
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai, China
- *Correspondence: Guanzhen Yu, ; Ying Chen,
| | - Guanzhen Yu
- Department of Oncology, Longhua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
- *Correspondence: Guanzhen Yu, ; Ying Chen,
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11
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Guan B, Xu T, Zhao Y, Li Y, Dong X. A random grouping-based self-regulating artificial bee colony algorithm for interactive feature detection. Knowl Based Syst 2022. [DOI: 10.1016/j.knosys.2022.108434] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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12
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COP1 Acts as a Ubiquitin Ligase for PCDH9 Ubiquitination and Degradation in Human Glioma. Mol Neurobiol 2022; 59:2378-2388. [PMID: 35084653 DOI: 10.1007/s12035-021-02634-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 11/02/2021] [Indexed: 10/19/2022]
Abstract
Constitutive photomorphogenic 1 (COP1, also known as RFWD2), a ring-finger-type E3 ubiquitin ligase, has been reported to play a pivotal role in the regulation of cell growth, apoptosis, and DNA repair. Accumulating evidence has suggested that COP1 plays a role in tumorigenesis by triggering the ubiquitination and degradation of its substrates, but the potential mechanism remains unclear. In this study, COP1 was used as a bait in a yeast two-hybrid experiment to screen COP1-interacting proteins in a human brain cDNA library, and the results indicated that protocadherin 9 (PCDH9) was a potential binding protein of COP1. The interaction between and colocalization of COP1 and PCDH9 was further confirmed by coimmunoprecipitation (co-IP) assay and immunofluorescent staining. Subsequently, we demonstrated that COP1 acted as an E3 ligase to promote the ubiquitination and degradation of PCDH9 through the proteasome pathway in glioma cells. Furthermore, we identified that the type of COP1 mediated PCDH9 ubiquitination was Lys48-linked polyubiquitination. Finally, we found that the COP1 protein level was inversely correlated with the PCDH9 protein level in human glioma tissues. Taken together, our results suggest that COP1 is an E3 ubiquitin ligase for PCDH9 and reveal an important mechanism for PCDH9 regulation in human glioma.
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13
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Mehrotra R, Stanaway IB, Jarvik GP, Lambie M, Morelle J, Perl J, Himmelfarb J, Heimburger O, Johnson DW, Imam TH, Robinson B, Stenvinkel P, Devuyst O, Davies SJ. A genome-wide association study suggests correlations of common genetic variants with peritoneal solute transfer rates in patients with kidney failure receiving peritoneal dialysis. Kidney Int 2021; 100:1101-1111. [PMID: 34197840 PMCID: PMC8545920 DOI: 10.1016/j.kint.2021.05.037] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 05/19/2021] [Accepted: 05/27/2021] [Indexed: 12/17/2022]
Abstract
Movement of solutes across the peritoneum allows for the use of peritoneal dialysis to treat kidney failure. However, there is a large inter-individual variability in the peritoneal solute transfer rate (PSTR). Here, we tested the hypothesis that common genetic variants are associated with variability in PSTR. Of the 3561 participants from 69 centers in six countries, 2850 with complete data were included in a genome-wide association study. PSTR was defined as the four-hour dialysate/plasma creatinine ratio from the first peritoneal equilibration test after starting PD. Heritability of PSTR was estimated using genomic-restricted maximum-likelihood analysis, and the association of PSTR with a genome-wide polygenic risk score was also tested. The mean four-hour dialysate/plasma creatinine ratio in participants was 0.70. In 2212 participants of European ancestry, no signal reached genome-wide significance but 23 single nucleotide variants at four loci demonstrated suggestive associations with PSTR. Meta-analysis of ancestry-stratified regressions in 2850 participants revealed five single-nucleotide variants at four loci with suggestive correlations with PSTR. Association across ancestry strata was consistent for rs28644184 at the KDM2B locus. The estimated heritability of PSTR was 19%, and a permuted model polygenic risk score was significantly associated with PSTR. Thus, this genome-wide association study of patients receiving peritoneal dialysis bolsters evidence for a genetic contribution to inter-individual variability in PSTR.
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Affiliation(s)
- Rajnish Mehrotra
- Kidney Research Institute, Division of Nephrology, Department of Medicine, University of Washington, Seattle, Washington, USA.
| | - Ian B Stanaway
- Kidney Research Institute, Division of Nephrology, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Gail P Jarvik
- Department of Medicine (Medical Genetics), University of Washington, Seattle, Washington, USA; Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Mark Lambie
- School of Medicine, Faculty of Medicine and Health Sciences, Keele University, Keele, UK
| | - Johann Morelle
- Division of Nephrology, Cliniques Universitaires Saint-Luc, Brussels, Belgium; Institut de Recherche Experimentale et Clinique, UClouvain, Brussels, Belgium
| | - Jeffrey Perl
- Division of Nephrology, St. Michael's Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Jonathan Himmelfarb
- Kidney Research Institute, Division of Nephrology, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Olof Heimburger
- Division of Renal Medicine, Department of Clinical Science, Intervention, and Technology, Karolinska Institute, Stockholm, Sweden
| | - David W Johnson
- Australasian Trials Network, University of Queensland, Brisbane, Australia
| | - Talha H Imam
- Department of Nephrology, Kaiser Permanente, Fontana, California, USA
| | - Bruce Robinson
- Arbor Research Collaborative for Health, Ann Arbor, Michigan, USA
| | - Peter Stenvinkel
- Division of Renal Medicine, Department of Clinical Science, Intervention, and Technology, Karolinska Institute, Stockholm, Sweden
| | - Olivier Devuyst
- Division of Nephrology, Cliniques Universitaires Saint-Luc, Brussels, Belgium; Institut de Recherche Experimentale et Clinique, UClouvain, Brussels, Belgium
| | - Simon J Davies
- School of Medicine, Faculty of Medicine and Health Sciences, Keele University, Keele, UK
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Zhang L, Meng X, Li D, Han X. piR-001773 and piR-017184 promote prostate cancer progression by interacting with PCDH9. Cell Signal 2020; 76:109780. [PMID: 32949716 DOI: 10.1016/j.cellsig.2020.109780] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 09/10/2020] [Accepted: 09/10/2020] [Indexed: 12/25/2022]
Abstract
Prostate cancer is one of the most common malignancies and the major cause of cancer-related death in men. Increasing evidence has revealed that P-element-induced wimpy (piwi)-interacting RNAs (piRNAs) play an important role in tumor progression. Few studies have been explored the functional mechanism of piRNAs in prostate cancer progression. In the present study, we demonstrated that piR-001773 and piR-017184 were increased in prostate cancer tissues. Protocadherin 9 (PCDH9) was downregulated and acted as a tumor suppressor in prostate cancer cells. PCDH9 could bind to p85α, the regulatory subunit of PI3K. The downregulation of PCDH9 in PCa cells resulted in an increase in AKT phosphorylation and activity. PCDH9 was posttranscriptionally regulated by piR-001773 and piR-017184. The upregulation of piR-001773 and piR-017184 promoted tumor growth both in vitro and in vivo. In addition, the downregulation of piR-001773 and piR-017184 markedly inhibited tumor growth. In conclusion, these results indicated that piR-001773 and piR-017184 are oncogenic RNAs and thus might be therapeutic targets in prostate cancer.
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Affiliation(s)
- Ling Zhang
- Immunology and Reproduction Biology Laboratory & State Key Laboratory of Analytical Chemistry for Life Science, Medical School, Nanjing University, Nanjing, Jiangsu 210093, China; Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, Jiangsu 210093, China
| | - Xiannan Meng
- Immunology and Reproduction Biology Laboratory & State Key Laboratory of Analytical Chemistry for Life Science, Medical School, Nanjing University, Nanjing, Jiangsu 210093, China; Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, Jiangsu 210093, China
| | - Dongmei Li
- Immunology and Reproduction Biology Laboratory & State Key Laboratory of Analytical Chemistry for Life Science, Medical School, Nanjing University, Nanjing, Jiangsu 210093, China; Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, Jiangsu 210093, China.
| | - Xiaodong Han
- Immunology and Reproduction Biology Laboratory & State Key Laboratory of Analytical Chemistry for Life Science, Medical School, Nanjing University, Nanjing, Jiangsu 210093, China; Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, Jiangsu 210093, China.
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15
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Clinical relevance and functional significance of cell-free microRNA-1260b expression profiles in infiltrative myxofibrosarcoma. Sci Rep 2020; 10:9414. [PMID: 32523124 PMCID: PMC7287053 DOI: 10.1038/s41598-020-66120-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 05/13/2020] [Indexed: 12/24/2022] Open
Abstract
Infiltrative tumor growth into adjacent soft tissues is a major cause of the frequent recurrence and tumor-related death of myxofibrosarcoma (MFS), but no useful biomarkers reflecting tumor burden and infiltrative growth are available. While emerging evidence suggests a diagnostic and functional role of extracellular/circulating microRNA (miRNA) in various malignant diseases, their significance in MFS patients remains unknown. Global miRNA profiling identified four upregulated miRNAs in MFS patient sera and culture media of MFS cells. Among these, serum miR-1260b level was significantly upregulated in patient serum discriminating from healthy individuals and closely correlated with clinical status and tumor dynamics in MFS-bearing mice. In addition, high miR-1260b expression in serum was correlated with radiological tail-like patterns, characteristic of the infiltrative MFS. The extracellular miR-1260b was embedded in tumor-derived extracellular vesicles (EVs) and promoted cellular invasion of MFS through the downregulation of PCDH9 in the adjacent normal fibroblasts. Collectively, circulating miR-1260b expression may represent a novel diagnostic target for tumor monitoring of this highly aggressive sarcoma. Moreover, EV-miR-1260b could act as a transfer messenger to adjacent cells and mediate the infiltrative growth of MFS, providing new insights into the mechanism of infiltrative nature via crosstalk between tumor cells and their microenvironment.
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16
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Ding X, Tian X, Liu W, Li Z. CDHR5 inhibits proliferation of hepatocellular carcinoma and predicts clinical prognosis. Ir J Med Sci 2019; 189:439-447. [PMID: 31482521 DOI: 10.1007/s11845-019-02092-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 08/27/2019] [Indexed: 01/03/2023]
Abstract
BACKGROUND As one of the most prevalent malignancies, hepatocellular carcinoma (HCC) ranks the third leading cause of cancer death worldwide. Due to the lack of biomarkers for early diagnosis, the clinical outcome of HCC remains unsatisfied with the current common therapeutic approaches, including surgery and chemotherapies. Thus, sensitive biomarkers and targeted therapies are in great need. AIMS In this study, we explored and verified whether CDHR5 (cadherin-related family member 5), a cadherin family protein, could serve as the potential biomarkers for HCC in the clinic. METHODS A retrospective study which contained 154 HCC patients was performed. Chi-square was utilized to analyze the relationship between CDHR5 expression and the clinicopathological features of HCC patients. The Kaplan-Meier method and Cox regression analyses were then used to evaluate the survival of HCC patients. In addition, cell proliferation assay and colony formation assay were performed to examine the effects of CDHR5 on the progression of HepG2 and Huh7 cells. RESULTS IHC and RT-qPCR revealed that CDHR5 was downregulated in HCC tissues compared with adjacent liver tissues. In addition, CDHR5 expression was significantly correlated with tumor numbers, tumor size, and TNM stage. CDHR5 expression was then shown to be an independent risk factor for survival of HCC patients by survival analysis. In vitro experiments showed that CDHR5 suppressed the proliferation capacity of HCC cells. CONCLUSIONS Taken together, our study not only identified CDHR5 as a novel prognostic biomarker in HCC but also provided evidence that CDHR5 can inhibit HCC cell proliferation.
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Affiliation(s)
- Xue Ding
- Department of Cardiology, Yidu Central Hospital of Weifang, Weifang, 262500, Shandong, China
| | - Xiaomin Tian
- Department of Cardiology, Yidu Central Hospital of Weifang, Weifang, 262500, Shandong, China
| | - Wei Liu
- Department of Cardiology, Yidu Central Hospital of Weifang, Weifang, 262500, Shandong, China
| | - Zijia Li
- Department of Immunology and Rheumatology, Gansu Provincial Hospital, Lanzhou, 730000, Gansu, China.
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17
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Cesarini V, Silvestris DA, Tassinari V, Tomaselli S, Alon S, Eisenberg E, Locatelli F, Gallo A. ADAR2/miR-589-3p axis controls glioblastoma cell migration/invasion. Nucleic Acids Res 2019; 46:2045-2059. [PMID: 29267965 PMCID: PMC5829642 DOI: 10.1093/nar/gkx1257] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 12/05/2017] [Indexed: 12/26/2022] Open
Abstract
Recent studies have reported the emerging role of microRNAs (miRNAs) in human cancers. We systematically characterized miRNA expression and editing in the human brain, which displays the highest number of A-to-I RNA editing sites among human tissues, and in de novo glioblastoma brain cancer. We identified 299 miRNAs altered in their expression and 24 miRNAs differently edited in human brain compared to glioblastoma tissues. We focused on the editing site within the miR-589–3p seed. MiR-589–3p is a unique miRNA almost fully edited (∼100%) in normal brain and with a consistent editing decrease in glioblastoma. The edited version of miR-589–3p inhibits glioblastoma cell proliferation, migration and invasion, while the unedited version boosts cell proliferation and motility/invasion, thus being a potential cancer-promoting factor. We demonstrated that the editing of this miRNA is mediated by ADAR2, and retargets miR-589–3p from the tumor-suppressor PCDH9 to ADAM12, which codes for the metalloproteinase 12 promoting glioblastoma invasion. Overall, our study dissects the role of a unique brain-specific editing site within miR-589–3p, with important anticancer features, and highlights the importance of RNA editing as an essential player not only for diversifying the genomic message but also for correcting not-tolerable/critical genomic coding sites.
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Affiliation(s)
- Valeriana Cesarini
- RNA Editing Laboratory, Oncohaematology Department, IRCCS Ospedale Pediatrico Bambino Gesù, Viale di San Paolo, 15, 00146 Rome, Italy
| | - Domenico A Silvestris
- RNA Editing Laboratory, Oncohaematology Department, IRCCS Ospedale Pediatrico Bambino Gesù, Viale di San Paolo, 15, 00146 Rome, Italy
| | - Valentina Tassinari
- RNA Editing Laboratory, Oncohaematology Department, IRCCS Ospedale Pediatrico Bambino Gesù, Viale di San Paolo, 15, 00146 Rome, Italy
| | - Sara Tomaselli
- RNA Editing Laboratory, Oncohaematology Department, IRCCS Ospedale Pediatrico Bambino Gesù, Viale di San Paolo, 15, 00146 Rome, Italy
| | - Shahar Alon
- Media Laboratory and McGovern Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Eli Eisenberg
- Raymond and Beverly Sackler School of Physics and Astronomy, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Franco Locatelli
- RNA Editing Laboratory, Oncohaematology Department, IRCCS Ospedale Pediatrico Bambino Gesù, Viale di San Paolo, 15, 00146 Rome, Italy.,Department of Pediatric Science, University of Pavia, 27100 Pavia, Italy
| | - Angela Gallo
- RNA Editing Laboratory, Oncohaematology Department, IRCCS Ospedale Pediatrico Bambino Gesù, Viale di San Paolo, 15, 00146 Rome, Italy
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18
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Xia Z, Huang M, Zhu Q, Li Y, Ma Q, Wang Y, Chen X, Li J, Qiu L, Zhang J, Zheng J, Lu B. Cadherin Related Family Member 2 Acts As A Tumor Suppressor By Inactivating AKT In Human Hepatocellular Carcinoma. J Cancer 2019; 10:864-873. [PMID: 30854092 PMCID: PMC6400803 DOI: 10.7150/jca.27663] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 01/02/2019] [Indexed: 02/06/2023] Open
Abstract
Cadherin related family member 2 (CDHR2) belongs to the protocadherin family and is abundant in normal liver, kidney, and colon tissues, but weakly expressed in cancers arising from these tissues. In this study, we demonstrated that CDHR2 was highly expressed in para-cancer tissues of human hepatocellular carcinoma (HCC), but significantly downregulated or silenced in 85.7% (6/7) of HCC cell lines by both semi-quantitative PCR and western blot, and 79.1% (19/24) and 80.2% (89/111) of tumor tissues from patients with HCC by semi-quantitative PCR, and immunohistochemistry, respectively. Interestingly, CpG islands in the promoter of CDHR2 gene were hypermethylated in HCC cell lines and tissues compared with the para-cancer tissues by methylation-specific PCR analysis, leading to transcriptional repression and silencing of CDHR2 in HCC. In addition, CDHR2 overexpression by lentiviral vectors had suppressive effects on HCC cell growth and proliferation, as evidenced by prolonged cell doubling time and reduced colony-forming ability in vitro, as well as by decreased tumorigenicity in vivo. Mechanistically, CDHR2 overexpression resulted in AKT dephosphorylation along with downregulation of cyclooxygenase-2 (COX2), a downstream target of AKT. This effect was reversed by myristoylated AKT, a constitutively active form of AKT, suggesting an involvement of CDHR2-AKT-COX2 axis in the suppression of HCC growth. Taken together, our study identified CDHR2 as a novel tumor suppressor in HCC and provided a new therapeutic target for HCC.
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Affiliation(s)
- Ziyuan Xia
- Department of Biochemical Pharmacy, School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Meijin Huang
- Department of Oncology, 920th Hospital of PLA Joint Logistics support Force, Yunnan, China
| | - Qiangqiang Zhu
- Department of Biochemical Pharmacy, School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Yinghua Li
- Department of Biochemical Pharmacy, School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Qian Ma
- Department of Pathology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Yang Wang
- Department of Pathology, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xia Chen
- Yangpu Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jianzhong Li
- Department of Biochemical Pharmacy, School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Lei Qiu
- Department of Biochemical Pharmacy, School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Junping Zhang
- Department of Biochemical Pharmacy, School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Jiaoyang Zheng
- Department of Endocrinology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Bin Lu
- Department of Biochemical Pharmacy, School of Pharmacy, Second Military Medical University, Shanghai, China
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Świerczewska M, Klejewski A, Brązert M, Kaźmierczak D, Iżycki D, Nowicki M, Zabel M, Januchowski R. New and Old Genes Associated with Primary and Established Responses to Paclitaxel Treatment in Ovarian Cancer Cell Lines. Molecules 2018; 23:molecules23040891. [PMID: 29649113 PMCID: PMC6017641 DOI: 10.3390/molecules23040891] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 04/04/2018] [Accepted: 04/10/2018] [Indexed: 01/10/2023] Open
Abstract
Development of drug resistance is the main reason for low chemotherapy effectiveness in treating ovarian cancer. Paclitaxel (PAC) is a chemotherapeutic drug used in the treatment of this cancer. We analysed the development of PAC resistance in two ovarian cancer cell lines. Exposure of drug-sensitive cell lines (A2780 and W1) to PAC was used to determine the primary response. An established response was determined in PAC-resistant sublines of the A2780 and W1 cell lines. qRT-PCR was performed to measure the expression levels of specific genes. We observed decreased expression of the PCDH9, NSBP1, MCTP1 and SEMA3A genes in the PAC-resistant cell lines. Short-term exposure to PAC led to increased expression of the MDR1 and BCRP genes in the A2780 and W1 cell lines. In the A2780 cell line, we also observed increased expression of the C4orf18 gene and decreased expression of the PCDH9 and SEMA3A genes after PAC treatment. In the W1 cell line, short-term treatment with PAC upregulated the expression of the ALDH1A1 gene, a marker of Cancer stem cells (CSCs). Our results suggest that downregulation of the PCDH9, NSBP1, MCTP1 and SEMA3A genes and upregulation of the MDR1, BCRP, C4orf18 and ALDH1A1 genes may be related to PAC resistance.
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Affiliation(s)
- Monika Świerczewska
- Department of Histology and Embryology, Poznan University of Medical Sciences, Święcickiego 6 St., 61-781 Poznań, Poland.
| | - Andrzej Klejewski
- Department of Nursing, Poznan University of Medical Sciences, Smoluchowskiego 11 St., 60-179 Poznan, Poland.
- Department of Obstetrics and Women's Diseases, Poznan University of Medical Sciences, Smoluchowskiego 11 St., 60-179 Poznan, Poland.
| | - Maciej Brązert
- Division of Infertility and Reproductive Endocrinology, Department of Gynecology, Obstetrics and Gynecological Oncology, Poznan University of Medical Sciences, Polna 33 St., 60-535 Poznań, Poland.
| | - Dominika Kaźmierczak
- Department of Histology and Embryology, Poznan University of Medical Sciences, Święcickiego 6 St., 61-781 Poznań, Poland.
| | - Dariusz Iżycki
- Department of Cancer Immunology, Poznan University of Medical Sciences, Garbary 15 St., 61-866 Poznań, Poland.
| | - Michał Nowicki
- Department of Histology and Embryology, Poznan University of Medical Sciences, Święcickiego 6 St., 61-781 Poznań, Poland.
| | - Maciej Zabel
- Department of Histology and Embryology, Poznan University of Medical Sciences, Święcickiego 6 St., 61-781 Poznań, Poland.
| | - Radosław Januchowski
- Department of Histology and Embryology, Poznan University of Medical Sciences, Święcickiego 6 St., 61-781 Poznań, Poland.
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20
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Li M, Sun Q, Wang X. Transcriptional landscape of human cancers. Oncotarget 2018; 8:34534-34551. [PMID: 28427185 PMCID: PMC5470989 DOI: 10.18632/oncotarget.15837] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Accepted: 02/08/2017] [Indexed: 12/21/2022] Open
Abstract
The homogeneity and heterogeneity in somatic mutations, copy number alterations and methylation across different cancer types have been extensively explored. However, the related exploration based on transcriptome data is lacking. In this study we explored gene expression profiles across 33 human cancer types using The Cancer Genome Atlas (TCGA) data. We identified consistently upregulated genes (such as E2F1, EZH2, FOXM1, MYBL2, PLK1, TTK, AURKA/B and BUB1) and consistently downregulated genes (such as SCARA5, MYOM1, NKAPL, PEG3, USP2, SLC5A7 and HMGCLL1) across various cancers. The dysregulation of these genes is likely to be associated with poor clinical outcomes in cancer. The dysregulated pathways commonly in cancers include cell cycle, DNA replication, repair, and recombination, Notch signaling, p53 signaling, Wnt signaling, TGFβ signaling, immune response etc. We also identified genes consistently upregulated or downregulated in highly-advanced cancers compared to lowly-advanced cancers. The highly (low) expressed genes in highly-advanced cancers are likely to have higher (lower) expression levels in cancers than in normal tissue, indicating that common gene expression perturbations drive cancer initiation and cancer progression. In addition, we identified a substantial number of genes exclusively dysregulated in a single cancer type or inconsistently dysregulated in different cancer types, demonstrating the intertumor heterogeneity. More importantly, we found a number of genes commonly dysregulated in various cancers such as PLP1, MYOM1, NKAPL and USP2 which were investigated in few cancer related studies, and thus represent our novel findings. Our study provides comprehensive portraits of transcriptional landscape of human cancers.
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Affiliation(s)
- Mengyuan Li
- School of Science, China Pharmaceutical University, Nanjing 211198, China
| | - Qingrong Sun
- School of Science, China Pharmaceutical University, Nanjing 211198, China
| | - Xiaosheng Wang
- Department of Basic Medicine, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China
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21
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Wang C, Chen Q, Li S, Li S, Zhao Z, Gao H, Wang X, Li B, Zhang W, Yuan Y, Ming L, He H, Tao B, Zhong J. Dual inhibition of PCDH9 expression by miR-215-5p up-regulation in gliomas. Oncotarget 2018; 8:10287-10297. [PMID: 28055966 PMCID: PMC5354659 DOI: 10.18632/oncotarget.14396] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 12/12/2016] [Indexed: 12/25/2022] Open
Abstract
The clinical prognosis of malignant gliomas is poor and PCDH9 down-regulation is strongly associated with its poor prognosis. But the mechanism of PCDH9 down-regulation is unknown. Abnormal miRNAs profiles regulate tumor phenotypes through inhibiting their target genes and miRNAs could inhibit target genes more efficiently by binding to both the promoter and 3′UTR of target genes. In this study, to search the dual inhibitory miRNAs which suppress PCDH9 expression in gliomas, we performed an integrative analysis of databases including miRDB, TargetScan, microPIR and miRCancer. We identified three candidate miRNAs which were predicted to bind both the promoter and 3′UTR of PCDH9 and up-regulated in gliomas. Then, we validated miR-215-5p up-regulation and PCDH9 down-regulation in glioma samples and demonstrated that miR-215-5p could inhibit the mRNA and protein levels of PCDH9 in glioma cell lines by targeting its promoter and 3′ UTR at the same time. Moreover, miR-215-5p could increase glioma cell proliferation, clone formation, in-vitro migration and reduce apoptosis via inhibiting PCDH9 expression. Our study provides evidence for a novel dual inhibition of PCDH9 by miR-215-5p in gliomas and suggests that miR-215-5p might be a therapeutic target for the treatment of gliomas.
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Affiliation(s)
- Chunlin Wang
- Department of Neurosurgery, The 105th Hospital of PLA, Hefei, Anhui 230000, China
| | - Qi Chen
- Department of Anesthesiology, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 200003, China
| | - Shu Li
- Department of Pathophysiology, Wannan Medical College, Wuhu 241002, China; Department of Neurosurgery, Wuxi Second People's Hospital, Wuxi, Jiangsu, 214002, China
| | - Shiting Li
- Department of Neurosurgery, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 200003, China
| | - Zhenyu Zhao
- Department of Neurosurgery, Chinese PLA General Hospital, Beijing 100003, China
| | - Hongliang Gao
- Department of Pathophysiology, Wannan Medical College, Wuhu 241002, China; Department of Neurosurgery, Wuxi Second People's Hospital, Wuxi, Jiangsu, 214002, China
| | - Xiaoqiang Wang
- Department of Neurosurgery, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 200003, China
| | - Bin Li
- Department of Neurosurgery, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 200003, China
| | - Wenchuan Zhang
- Department of Neurosurgery, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 200003, China
| | - Yan Yuan
- Department of Neurosurgery, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 200003, China
| | - Linzhao Ming
- Department of Neurosurgery, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 200003, China
| | - Hua He
- Department of Neurosurgery, Changzheng Hospital, The Second Hospital affiliated with The Second Military Medical University, Shanghai 200003, China
| | - Bangbao Tao
- Department of Neurosurgery, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 200003, China
| | - Jun Zhong
- Department of Neurosurgery, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 200003, China
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22
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van Dongen J, Bonder MJ, Dekkers KF, Nivard MG, van Iterson M, Willemsen G, Beekman M, van der Spek A, van Meurs JBJ, Franke L, Heijmans BT, van Duijn CM, Slagboom PE, Boomsma DI. DNA methylation signatures of educational attainment. NPJ SCIENCE OF LEARNING 2018; 3:7. [PMID: 30631468 PMCID: PMC6220239 DOI: 10.1038/s41539-018-0020-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 11/18/2017] [Accepted: 02/09/2018] [Indexed: 05/09/2023]
Abstract
Educational attainment is a key behavioural measure in studies of cognitive and physical health, and socioeconomic status. We measured DNA methylation at 410,746 CpGs (N = 4152) and identified 58 CpGs associated with educational attainment at loci characterized by pleiotropic functions shared with neuronal, immune and developmental processes. Associations overlapped with those for smoking behaviour, but remained after accounting for smoking at many CpGs: Effect sizes were on average 28% smaller and genome-wide significant at 11 CpGs after adjusting for smoking and were 62% smaller in never smokers. We examined sources and biological implications of education-related methylation differences, demonstrating correlations with maternal prenatal folate, smoking and air pollution signatures, and associations with gene expression in cis, dynamic methylation in foetal brain, and correlations between blood and brain. Our findings show that the methylome of lower-educated people resembles that of smokers beyond effects of their own smoking behaviour and shows traces of various other exposures.
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Affiliation(s)
- Jenny van Dongen
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Marc Jan Bonder
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Koen F. Dekkers
- Molecular Epidemiology section, Leiden University Medical Center, Leiden, The Netherlands
| | - Michel G. Nivard
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Maarten van Iterson
- Molecular Epidemiology section, Leiden University Medical Center, Leiden, The Netherlands
| | - Gonneke Willemsen
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Marian Beekman
- Molecular Epidemiology section, Leiden University Medical Center, Leiden, The Netherlands
| | - Ashley van der Spek
- Department of Epidemiology, Genetic Epidemiology Unit, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Lude Franke
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Bastiaan T. Heijmans
- Molecular Epidemiology section, Leiden University Medical Center, Leiden, The Netherlands
| | - Cornelia M. van Duijn
- Department of Epidemiology, Genetic Epidemiology Unit, Erasmus Medical Center, Rotterdam, The Netherlands
| | - P. Eline Slagboom
- Molecular Epidemiology section, Leiden University Medical Center, Leiden, The Netherlands
| | - Dorret I. Boomsma
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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23
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Ren S, Wei GH, Liu D, Wang L, Hou Y, Zhu S, Peng L, Zhang Q, Cheng Y, Su H, Zhou X, Zhang J, Li F, Zheng H, Zhao Z, Yin C, He Z, Gao X, Zhau HE, Chu CY, Wu JB, Collins C, Volik SV, Bell R, Huang J, Wu K, Xu D, Ye D, Yu Y, Zhu L, Qiao M, Lee HM, Yang Y, Zhu Y, Shi X, Chen R, Wang Y, Xu W, Cheng Y, Xu C, Gao X, Zhou T, Yang B, Hou J, Liu L, Zhang Z, Zhu Y, Qin C, Shao P, Pang J, Chung LWK, Xu J, Wu CL, Zhong W, Xu X, Li Y, Zhang X, Wang J, Yang H, Wang J, Huang H, Sun Y. Whole-genome and Transcriptome Sequencing of Prostate Cancer Identify New Genetic Alterations Driving Disease Progression. Eur Urol 2017; 73:322-339. [PMID: 28927585 DOI: 10.1016/j.eururo.2017.08.027] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 08/24/2017] [Indexed: 01/25/2023]
Abstract
BACKGROUND Global disparities in prostate cancer (PCa) incidence highlight the urgent need to identify genomic abnormalities in prostate tumors in different ethnic populations including Asian men. OBJECTIVE To systematically explore the genomic complexity and define disease-driven genetic alterations in PCa. DESIGN, SETTING, AND PARTICIPANTS The study sequenced whole-genome and transcriptome of tumor-benign paired tissues from 65 treatment-naive Chinese PCa patients. Subsequent targeted deep sequencing of 293 PCa-relevant genes was performed in another cohort of 145 prostate tumors. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS The genomic alteration landscape in PCa was analyzed using an integrated computational pipeline. Relationships with PCa progression and survival were analyzed using nonparametric test, log-rank, and multivariable Cox regression analyses. RESULTS AND LIMITATIONS We demonstrated an association of high frequency of CHD1 deletion with a low rate of TMPRSS2-ERG fusion and relatively high percentage of mutations in androgen receptor upstream activator genes in Chinese patients. We identified five putative clustered deleted tumor suppressor genes and provided experimental and clinical evidence that PCDH9, deleted/loss in approximately 23% of tumors, functions as a novel tumor suppressor gene with prognostic potential in PCa. Furthermore, axon guidance pathway genes were frequently deregulated, including gain/amplification of PLXNA1 gene in approximately 17% of tumors. Functional and clinical data analyses showed that increased expression of PLXNA1 promoted prostate tumor growth and independently predicted prostate tumor biochemical recurrence, metastasis, and poor survival in multi-institutional cohorts of patients with PCa. A limitation of this study is that other genetic alterations were not experimentally investigated. CONCLUSIONS There are shared and salient genetic characteristics of PCa in Chinese and Caucasian men. Novel genetic alterations in PCDH9 and PLXNA1 were associated with disease progression. PATIENT SUMMARY We reported the first large-scale and comprehensive genomic data of prostate cancer from Asian population. Identification of these genetic alterations may help advance prostate cancer diagnosis, prognosis, and treatment.
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Affiliation(s)
- Shancheng Ren
- Department of Urology, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Gong-Hong Wei
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Dongbing Liu
- BGI-Shenzhen, Shenzhen, China; China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Liguo Wang
- Division of Biomedical Statistics and Informatics, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Yong Hou
- BGI-Shenzhen, Shenzhen, China; China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen, China; State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Shida Zhu
- BGI-Shenzhen, Shenzhen, China; China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen, China; Division of Genomics and Bioinformatics, CUHK-BGI Innovation Institute of Trans-Omics, The Chinese University of Hong Kong, Hong Kong, China
| | - Lihua Peng
- BGI-Shenzhen, Shenzhen, China; China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen, China; BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Qin Zhang
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Yanbing Cheng
- BGI-Shenzhen, Shenzhen, China; Division of Genomics and Bioinformatics, CUHK-BGI Innovation Institute of Trans-Omics, The Chinese University of Hong Kong, Hong Kong, China
| | - Hong Su
- BGI-Shenzhen, Shenzhen, China; China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Xiuqing Zhou
- BGI-Shenzhen, Shenzhen, China; China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | | | - Fuqiang Li
- BGI-Shenzhen, Shenzhen, China; China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | | | - Zhikun Zhao
- BGI-Shenzhen, Shenzhen, China; China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen, China; School of Biological Science and Medical Engineering, Southeast University, Nanjing, China; State Key Laboratory of Bioelectronics, Southeast University, Nanjing, China
| | - Changjun Yin
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | | | - Xin Gao
- Department of Urology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Haiyen E Zhau
- Uro-Oncology Research Program, Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Chia-Yi Chu
- Uro-Oncology Research Program, Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jason Boyang Wu
- Uro-Oncology Research Program, Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Colin Collins
- Vancouver Prostate Centre and Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Stanislav V Volik
- Vancouver Prostate Centre and Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Robert Bell
- Vancouver Prostate Centre and Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Jiaoti Huang
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Kui Wu
- BGI-Shenzhen, Shenzhen, China; China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Danfeng Xu
- Department of Urology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Dingwei Ye
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Yongwei Yu
- Department of Pathology, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Lianhui Zhu
- Department of Urology, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Meng Qiao
- Department of Urology, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Hang-Mao Lee
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Yuehong Yang
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Yasheng Zhu
- Department of Urology, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Xiaolei Shi
- Department of Urology, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Rui Chen
- Department of Urology, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Yang Wang
- Department of Pathology, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Weidong Xu
- Department of Urology, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Yanqiong Cheng
- Department of Urology, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Chuanliang Xu
- Department of Urology, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Xu Gao
- Department of Urology, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Tie Zhou
- Department of Urology, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Bo Yang
- Department of Urology, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Jianguo Hou
- Department of Urology, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Li Liu
- BGI-Shenzhen, Shenzhen, China
| | - Zhensheng Zhang
- Department of Urology, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Yao Zhu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Chao Qin
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Pengfei Shao
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jun Pang
- Department of Urology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Leland W K Chung
- Uro-Oncology Research Program, Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jianfeng Xu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China; Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, IL, USA
| | - Chin-Lee Wu
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Weide Zhong
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, China; China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | | | | | - Jian Wang
- BGI-Shenzhen, Shenzhen, China; James D. Watson Institute of Genome Sciences, Hangzhou, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, China; James D. Watson Institute of Genome Sciences, Hangzhou, China
| | - Jun Wang
- BGI-Shenzhen, Shenzhen, China; Department of Biology, University of Copenhagen, Copenhagen, Denmark; The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark; King Abdulaziz University, Jeddah, Saudi Arabia
| | - Haojie Huang
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Yinghao Sun
- Department of Urology, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China.
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24
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Lv J, Zhu P, Zhang X, Zhang L, Chen X, Lu F, Yu Z, Liu S. PCDH9 acts as a tumor suppressor inducing tumor cell arrest at G0/G1 phase and is frequently methylated in hepatocellular carcinoma. Mol Med Rep 2017; 16:4475-4482. [PMID: 28791409 PMCID: PMC5647006 DOI: 10.3892/mmr.2017.7193] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Accepted: 05/26/2017] [Indexed: 12/17/2022] Open
Abstract
Tumor suppressor genes (TSGs) are frequently involved in the pathogenesis of hepatocellular carcinoma (HCC). The epigenetic and genetic alterations of a novel TSG-protocadherin 9 (PCDH9) and its functions in the pathogenesis of HCC were investigated. The methylation status of the PCDH9 promoter was quantitatively analyzed, and the PCDH9 expression was analyzed in HCC cell lines treated with 5-azacytidine. The effects of PCDH9 re-expression and knockdown on growth, proliferation and tumorigenic potential were determined. The results indicated that expression of PCDH9 mRNA was restored in hypermethylation HCC cells following treatment with the DNA de-methylation reagent 5′-Aza. Methylation of the PCDH9 promoter was observed in 22% primary HCC tissues (24/111 tumors). Among the primary HCC cases, the methylated PCDH9 appeared to be associated with a larger tumor size (≥5 cm; P=0.0139) and a more pronounced intrahepatic dissemination (P=0.0312). In addition, it was observed that restored PCDH9 expression could inhibit tumor cell proliferation and xenograft tumor formation. Furthermore, restored PCDH9 expression could inhibit cell proliferation of HCC cell lines via inducing cell cycle arrest at G0/G1 phase. Thus, it is suggested that PCDH9 may act as a novel tumor suppressor candidate gene in HCC pathogenesis.
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Affiliation(s)
- Jun Lv
- Department of Infectious Disease, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Pengfei Zhu
- Department of Microbiology & Infectious Disease Center, Peking University Health Science Center, Beijing 100191, P.R. China
| | - Xiaolei Zhang
- Department of Microbiology & Infectious Disease Center, Peking University Health Science Center, Beijing 100191, P.R. China
| | - Ling Zhang
- Department of Hepatobiliary Surgery, Henan Cancer Hospital, Zhengzhou, Henan 450008, P.R. China
| | - Xiangmei Chen
- Department of Microbiology & Infectious Disease Center, Peking University Health Science Center, Beijing 100191, P.R. China
| | - Fengmin Lu
- Department of Microbiology & Infectious Disease Center, Peking University Health Science Center, Beijing 100191, P.R. China
| | - Zujiang Yu
- Department of Infectious Disease, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Shuang Liu
- Beijing Artificial Liver Treatment & Training Center, Beijing Youan Hospital Capital Medical University, Beijing 100069, P.R. China
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25
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Januchowski R, Sterzyńska K, Zawierucha P, Ruciński M, Świerczewska M, Partyka M, Bednarek-Rajewska K, Brązert M, Nowicki M, Zabel M, Klejewski A. Microarray-based detection and expression analysis of new genes associated with drug resistance in ovarian cancer cell lines. Oncotarget 2017; 8:49944-49958. [PMID: 28611294 PMCID: PMC5564819 DOI: 10.18632/oncotarget.18278] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 04/24/2017] [Indexed: 12/24/2022] Open
Abstract
PURPOSE The present study is to discover a new genes associated with drug resistance development in ovarian cancer. METHODS We used microarray analysis to determine alterations in the level of expression of genes in cisplatin- (CisPt), doxorubicin- (Dox), topotecan- (Top), and paclitaxel- (Pac) resistant variants of W1 and A2780 ovarian cancer cell lines. Immunohistochemistry assay was used to determine protein expression in ovarian cancer patients. RESULTS We observed alterations in the expression of 22 genes that were common to all three cell lines that were resistant to the same cytostatic drug. The level of expression of 13 genes was upregulated and that of nine genes was downregulated. In the CisPt-resistant cell line, we observed downregulated expression of ABCC6, BST2, ERAP2 and MCTP1; in the Pac-resistant cell line, we observe upregulated expression of ABCB1, EPHA7 and RUNDC3B and downregulated expression of LIPG, MCTP1, NSBP1, PCDH9, PTPRK and SEMA3A. The expression levels of three genes, ABCB1, ABCB4 and IFI16, were upregulated in the Dox-resistant cell lines. In the Top-resistant cell lines, we observed increased expression levels of ABCG2, HERC5, IFIH1, MYOT, S100A3, SAMD4A, SPP1 and TGFBI and decreased expression levels of MCTP1 and PTPRK. The expression of EPHA7, IFI16, SPP1 and TGFBI was confirmed at protein level in analyzed ovarian cancer patients.. CONCLUSIONS The expression profiles of the investigated cell lines indicated that new candidate genes are related to the development of resistance to the cytostatic drugs that are used in first- and second-line chemotherapy of ovarian cancer.
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Affiliation(s)
- Radosław Januchowski
- Department of Histology and Embryology, Poznań University of Medical Sciences, Poznań, 60-781, Poland
| | - Karolina Sterzyńska
- Department of Histology and Embryology, Poznań University of Medical Sciences, Poznań, 60-781, Poland
| | - Piotr Zawierucha
- Department of Histology and Embryology, Poznań University of Medical Sciences, Poznań, 60-781, Poland
- Department of Anatomy, Poznań University of Medical Sciences, Poznań, 60-781, Poland
| | - Marcin Ruciński
- Department of Histology and Embryology, Poznań University of Medical Sciences, Poznań, 60-781, Poland
| | - Monika Świerczewska
- Department of Histology and Embryology, Poznań University of Medical Sciences, Poznań, 60-781, Poland
| | - Małgorzata Partyka
- Department of Histology and Embryology, Poznań University of Medical Sciences, Poznań, 60-781, Poland
| | | | - Maciej Brązert
- Division of Infertility and Reproductive Endocrinology, Department of Gynecology, Obstetrics and Gynecological Oncology, Poznań University of Medical Sciences, Poznań, 60-535, Poland
| | - Michał Nowicki
- Department of Histology and Embryology, Poznań University of Medical Sciences, Poznań, 60-781, Poland
| | - Maciej Zabel
- Department of Histology and Embryology, Poznań University of Medical Sciences, Poznań, 60-781, Poland
- Department of Histology and Embryology, Wrocław Medical University, Wrocław, 50-368, Poland
| | - Andrzej Klejewski
- Department of Nursing, Poznań University of Medical Sciences, Poznań, 60-179, Poland
- Departament of Obstetrics and Womens Dieseases, Poznań University of Medical Sciences, Poznań, 60-535, Poland
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26
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LeBlanc VG, Firme M, Song J, Chan SY, Lee MH, Yip S, Chittaranjan S, Marra MA. Comparative transcriptome analysis of isogenic cell line models and primary cancers links capicua (CIC) loss to activation of the MAPK signalling cascade. J Pathol 2017; 242:206-220. [PMID: 28295365 PMCID: PMC5485162 DOI: 10.1002/path.4894] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 02/27/2017] [Accepted: 03/09/2017] [Indexed: 01/30/2023]
Abstract
CIC encodes a transcriptional repressor, capicua (CIC), whose disrupted activity appears to be involved in several cancer types, including type I low‐grade gliomas (LGGs) and stomach adenocarcinomas (STADs). To explore human CIC's transcriptional network in an isogenic background, we developed novel isogenic CIC knockout cell lines as model systems, and used these in transcriptome analyses to study the consequences of CIC loss. We also compared our results with analyses of transcriptome data from TCGA for type I LGGs and STADs. We identified 39 candidate targets of CIC transcriptional regulation, and confirmed seven of these as direct targets. We showed that, although many CIC targets appear to be context‐specific, the effects of CIC loss converge on the dysregulation of similar biological processes in different cancer types. For example, we found that CIC deficiency was associated with disruptions in the expression of genes involved in cell–cell adhesion, and in the development of several cell and tissue types. We also showed that loss of CIC leads to overexpression of downstream members of the mitogen‐activated protein kinase (MAPK) signalling cascade, indicating that CIC deficiency may present a novel mechanism for activation of this oncogenic pathway. © 2017 The Authors. Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Veronique G LeBlanc
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada.,Genome Science and Technology Program, University of British Columbia, Vancouver, BC, Canada
| | - Marlo Firme
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada
| | - Jungeun Song
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada
| | - Susanna Y Chan
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada
| | - Min Hye Lee
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada
| | - Stephen Yip
- Department of Pathology and Laboratory Medicine, University of British Columbia, BC, Canada
| | - Suganthi Chittaranjan
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
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Liu R, Wang G, Liu C, Qiu J, Yan L, Li X, Wang X. Gene expression profile analysis of dbpA knockdown in colorectal cancer cells. Cell Biol Int 2016; 40:1280-1293. [PMID: 27569444 DOI: 10.1002/cbin.10670] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 08/20/2016] [Indexed: 12/20/2022]
Affiliation(s)
- Ruiting Liu
- Department of General Surgery, Shaanxi Provincial People's Hospital; The Third Affiliated Hospital, Medical College, Xi'an Jiao Tong University; Xi'an 710068 China
| | - Guorong Wang
- Department of General Surgery, Shaanxi Provincial People's Hospital; The Third Affiliated Hospital, Medical College, Xi'an Jiao Tong University; Xi'an 710068 China
| | - Chang Liu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital, Medical College; Xi'an Jiao Tong University; Xi'an 710061 China
| | - Jian Qiu
- Department of General Surgery, Shaanxi Provincial People's Hospital; The Third Affiliated Hospital, Medical College, Xi'an Jiao Tong University; Xi'an 710068 China
| | - Likun Yan
- Department of General Surgery, Shaanxi Provincial People's Hospital; The Third Affiliated Hospital, Medical College, Xi'an Jiao Tong University; Xi'an 710068 China
| | - Xiaojun Li
- Department of General Surgery, Shaanxi Provincial People's Hospital; The Third Affiliated Hospital, Medical College, Xi'an Jiao Tong University; Xi'an 710068 China
| | - Xiaoqiang Wang
- Department of General Surgery, Shaanxi Provincial People's Hospital; The Third Affiliated Hospital, Medical College, Xi'an Jiao Tong University; Xi'an 710068 China
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28
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Yu G, Yu W, Jin G, Xu D, Chen Y, Xia T, Yu A, Fang W, Zhang X, Li Z, Xie K. PKM2 regulates neural invasion of and predicts poor prognosis for human hilar cholangiocarcinoma. Mol Cancer 2015; 14:193. [PMID: 26576639 PMCID: PMC4650283 DOI: 10.1186/s12943-015-0462-6] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 10/22/2015] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND The therapeutic and prognostic value of the glycolytic enzymes hexokinase, phosphofructokinase, and pyruvate kinase (PK) has been implicated in a variety of cancers, while their roles in treatment of and prognosis for hilar cholangiocarcinoma (HC) remain unclear. In this study, we determined the expression of PKM2 in and its impact on biology and clinical outcome of human HC. METHODS The regulation and function of PKM2 in HC pathogenesis was evaluated using human tissues, molecular and cell biology, and animal models, and its prognostic significance was determined according to its impact on patient survival. RESULTS We found that expression of hexokinase 1 and the M2 splice isoform of PK (PKM2) was upregulated in HC tissues and that this expression correlated with tumor recurrence and outcome. PKM2 expression was increased in HC cases with chronic cholangitis as demonstrated by isobaric tags for relative and absolute quantification. High PKM2 expression was highly correlated with high syndecan 2 (SDC2) expression and neural invasion. PKM2 downregulation led to a decrease in SDC2 expression. Treatment with metformin markedly suppressed PKM2 and SDC2 expression at both the transcriptional and posttranscriptional levels and inhibited HC cell proliferation and tumor growth. CONCLUSIONS PKM2 regulates neural invasion of HC cells at least in part via regulation of SDC2. Inhibition of PKM2 and SDC2 expression contributes to the therapeutic effect of metformin on HC. Therefore, PKM2 is an independent prognostic factor and potential therapeutic target for human HC.
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Affiliation(s)
- Guanzhen Yu
- Department of Oncology, East Hospital, Tongji University School of Medicine, Shanghai, 200120, People's Republic of China.
- Department of Gastroenterology, Hepatology and Nutrition, Unit 1466, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA.
| | - Wenlong Yu
- Department of Surgery, Eastern Hepatobiliary Hospital, Shanghai, People's Republic of China
| | - Guangzhi Jin
- Department of Pathology, Eastern Hepatobiliary Hospital, Shanghai, People's Republic of China
| | - Dongyun Xu
- Department of Oncology, East Hospital, Tongji University School of Medicine, Shanghai, 200120, People's Republic of China
| | - Ying Chen
- Department of Pathology, Changhai Hospital, Shanghai, People's Republic of China
| | - Tian Xia
- Department of Gastroenterology, Changhai Hospital, Shanghai, 200433, People's Republic of China
- Department of Gastroenterology, Hepatology and Nutrition, Unit 1466, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Allan Yu
- Department of Gastroenterology, Hepatology and Nutrition, Unit 1466, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Wenzheng Fang
- Department of Oncology, East Hospital, Tongji University School of Medicine, Shanghai, 200120, People's Republic of China
| | - Xiaoli Zhang
- Department of Pathology, Chinese People's Liberation Army, No 411 Hospital, Shanghai, People's Republic of China
| | - Zhaosheng Li
- Department of Gastroenterology, Changhai Hospital, Shanghai, 200433, People's Republic of China.
| | - Keping Xie
- Department of Gastroenterology, Hepatology and Nutrition, Unit 1466, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA.
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29
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Westland R, Verbitsky M, Vukojevic K, Perry BJ, Fasel DA, Zwijnenburg PJG, Bökenkamp A, Gille JJP, Saraga-Babic M, Ghiggeri GM, D'Agati VD, Schreuder MF, Gharavi AG, van Wijk JAE, Sanna-Cherchi S. Copy number variation analysis identifies novel CAKUT candidate genes in children with a solitary functioning kidney. Kidney Int 2015; 88:1402-1410. [PMID: 26352300 PMCID: PMC4834924 DOI: 10.1038/ki.2015.239] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 05/28/2015] [Accepted: 06/12/2015] [Indexed: 12/29/2022]
Abstract
Copy number variations associate with different developmental phenotypes and represent a major cause of congenital anomalies of the kidney and urinary tract (CAKUT). Because rare pathogenic copy number variations are often large and contain multiple genes, identification of the underlying genetic drivers has proven to be difficult. Here we studied the role of rare copy number variations in 80 patients from the KIMONO-study cohort for which pathogenic mutations in three genes commonly implicated in CAKUT were excluded. In total, 13 known or novel genomic imbalances in 11 of 80 patients were absent or extremely rare in 23,362 population controls. To identify the most likely genetic drivers for the CAKUT phenotype underlying these rare copy number variations, we used a systematic in silico approach based on frequency in a large dataset of controls, annotation with publicly available databases for developmental diseases, tolerance and haploinsufficiency scores, and gene expression profile in the developing kidney and urinary tract. Five novel candidate genes for CAKUT were identified that showed specific expression in the human and mouse developing urinary tract. Among these genes, DLG1 and KIF12 are likely novel susceptibility genes for CAKUT in humans. Thus, there is a significant role of genomic imbalance in the determination of kidney developmental phenotypes. Additionally, we defined a systematic strategy to identify genetic drivers underlying rare copy number variations.
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Affiliation(s)
- Rik Westland
- Division of Nephrology, Columbia University, New York, New York, USA.,Department of Pediatric Nephrology, VU University Medical Center, Amsterdam, The Netherlands
| | - Miguel Verbitsky
- Division of Nephrology, Columbia University, New York, New York, USA
| | - Katarina Vukojevic
- Division of Nephrology, Columbia University, New York, New York, USA.,Department of Anatomy, Histology, and Embryology, School of Medicine, University of Split, Split, Croatia
| | - Brittany J Perry
- Division of Nephrology, Columbia University, New York, New York, USA
| | - David A Fasel
- Division of Nephrology, Columbia University, New York, New York, USA
| | - Petra J G Zwijnenburg
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Arend Bökenkamp
- Department of Pediatric Nephrology, VU University Medical Center, Amsterdam, The Netherlands
| | - Johan J P Gille
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Mirna Saraga-Babic
- Department of Anatomy, Histology, and Embryology, School of Medicine, University of Split, Split, Croatia
| | - Gian Marco Ghiggeri
- Division of Nephrology, Dialysis, Transplantation, and Laboratory on Pathophysiology of Uremia, Istituto G. Gaslini, Genoa, Italy
| | - Vivette D D'Agati
- Department of Pathology, Columbia University, New York, New York, USA
| | - Michiel F Schreuder
- Department of Pediatric Nephrology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ali G Gharavi
- Division of Nephrology, Columbia University, New York, New York, USA
| | - Joanna A E van Wijk
- Department of Pediatric Nephrology, VU University Medical Center, Amsterdam, The Netherlands
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30
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Thompson MJ, Rubbi L, Dawson DW, Donahue TR, Pellegrini M. Pancreatic cancer patient survival correlates with DNA methylation of pancreas development genes. PLoS One 2015; 10:e0128814. [PMID: 26039411 PMCID: PMC4454596 DOI: 10.1371/journal.pone.0128814] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 04/30/2015] [Indexed: 02/07/2023] Open
Abstract
DNA methylation is an epigenetic mark associated with regulation of transcription and genome structure. These markers have been investigated in a variety of cancer settings for their utility in differentiating normal tissue from tumor tissue. Here, we examine the direct correlation between DNA methylation and patient survival. We find that changes in the DNA methylation of key pancreatic developmental genes are strongly associated with patient survival.
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Affiliation(s)
- Michael J. Thompson
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California, 90095, United States of America
| | - Liudmilla Rubbi
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California, 90095, United States of America
| | - David W. Dawson
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California, 90095, United States of America
- Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, California, 90095, United States of America
| | - Timothy R. Donahue
- Department of Surgery, University of California Los Angeles, Los Angeles, California, 90095, United States of America
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, California, 90095, United States of America
- Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, California, 90095, United States of America
| | - Matteo Pellegrini
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California, 90095, United States of America
- * E-mail:
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31
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Loss of PCDH9 is associated with the differentiation of tumor cells and metastasis and predicts poor survival in gastric cancer. Clin Exp Metastasis 2015; 32:417-28. [DOI: 10.1007/s10585-015-9712-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 03/05/2015] [Indexed: 12/23/2022]
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32
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Protocadherin 9 inhibits epithelial-mesenchymal transition and cell migration through activating GSK-3β in hepatocellular carcinoma. Biochem Biophys Res Commun 2014; 452:567-74. [PMID: 25172662 DOI: 10.1016/j.bbrc.2014.08.101] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Accepted: 08/21/2014] [Indexed: 11/21/2022]
Abstract
Protocadherin 9 (PCDH9) was found frequently lost in hepatocellular carcinoma (HCC). Here we investigated the role of PCDH9 in the development of HCC. We confirmed that PCDH9 was down-regulated in HCC tissues and cell lines compared with the adjacent non-tumor tissues. PCDH9 downregulation was significantly associated with malignant portal vein invasion of HCC patients. Gain- and loss-of-function studies revealed that downregulation of PCDH9 facilitated tumor cell migration and epithelial-mesenchymal transition (EMT). We identified PCDH9 as a novel regulator of EMT by increasing the activity of GSK-3β and inhibiting Snail1, indicating its potential therapeutic value for reducing metastasis of HCC.
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33
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Integrated exome and transcriptome sequencing reveals ZAK isoform usage in gastric cancer. Nat Commun 2014; 5:3830. [PMID: 24807215 PMCID: PMC4024760 DOI: 10.1038/ncomms4830] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 04/07/2014] [Indexed: 02/06/2023] Open
Abstract
Gastric cancer is the second leading cause of worldwide cancer mortality, yet the underlying genomic alterations remain poorly understood. Here we perform exome and transcriptome sequencing and SNP array assays to characterize 51 primary gastric tumours and 32 cell lines. Meta-analysis of exome data and previously published data sets reveals 24 significantly mutated genes in microsatellite stable (MSS) tumours and 16 in microsatellite instable (MSI) tumours. Over half the patients in our collection could potentially benefit from targeted therapies. We identify 55 splice site mutations accompanied by aberrant splicing products, in addition to mutation-independent differential isoform usage in tumours. ZAK kinase isoform TV1 is preferentially upregulated in gastric tumours and cell lines relative to normal samples. This pattern is also observed in colorectal, bladder and breast cancers. Overexpression of this particular isoform activates multiple cancer-related transcription factor reporters, while depletion of ZAK in gastric cell lines inhibits proliferation. These results reveal the spectrum of genomic and transcriptomic alterations in gastric cancer, and identify isoform-specific oncogenic properties of ZAK. The genetic basis of gastric cancer, the fourth most common cancer worldwide, remains poorly understood. Here, the authors sequence and analyse the exomes and transcriptomes of primary gastric tumours and cell lines, and identify a ZAK kinase isoform that may have an oncogenic role in gastric cancer.
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34
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Abstract
Loss of cadherin 1 (CDH1; also known as epithelial cadherin (E-cadherin)) is used for the diagnosis and prognosis of epithelial cancers. However, it should not be ignored that the superfamily of transmembrane cadherin proteins encompasses more than 100 members in humans, including other classical cadherins, numerous protocadherins and cadherin-related proteins. Elucidation of their roles in suppression versus initiation or progression of various tumour types is a young but fascinating field of molecular cancer research. These cadherins are very diverse in both structure and function, and their mutual interactions seem to influence biological responses in complex and versatile ways.
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Affiliation(s)
- Frans van Roy
- Department of Biomedical Molecular Biology, Ghent University, B-9052 Ghent, Belgium.The Inflammation Research Center, VIB, B-9052 Ghent, Belgium
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35
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Hirabayashi T, Yagi T. Protocadherins in neurological diseases. ADVANCES IN NEUROBIOLOGY 2014; 8:293-314. [PMID: 25300142 DOI: 10.1007/978-1-4614-8090-7_13] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cadherins were originally isolated as calcium-dependent cell adhesion molecules and are characterized by their cadherin motifs in the extracellular domain. In vertebrates, including humans, there are more than 100 different cadherin-related genes, which constitute the cadherin superfamily. The protocadherin (Pcdh) family comprises a large subgroup within the cadherin superfamily. The Pcdhs are divided into clustered and non-clustered Pcdhs, based on their genomic structure. Almost all the Pcdh genes are expressed widely in the brain and play important roles in brain development and in the regulation of brain function. This chapter presents an overview of Pcdh family members with regard to their functions, knockout mouse phenotypes, and association with neurological diseases and tumors.
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36
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Lin J, Wang C, Redies C. Expression of multiple delta-protocadherins during feather bud formation. Gene Expr Patterns 2013; 13:57-65. [DOI: 10.1016/j.gep.2013.01.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 12/30/2012] [Accepted: 01/03/2013] [Indexed: 12/31/2022]
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37
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Kahr I, Vandepoele K, van Roy F. Delta-protocadherins in health and disease. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2013; 116:169-92. [PMID: 23481195 DOI: 10.1016/b978-0-12-394311-8.00008-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The protocadherin family comprises clustered and nonclustered protocadherin genes. The nonclustered genes encode mainly δ-protocadherins, which deviate markedly from classical cadherins. They can be subdivided phylogenetically into δ0-protocadherins (protocadherin-20), δ1-protocadherins (protocadherin-1, -7, -9, and -11X/Y), and δ2-protocadherins (protocadherin-8, -10, -17, -18, and -19). δ-Protocadherins share a similar gene structure and are expressed as multiple alternative splice forms differing mostly in their cytoplasmic domains (CDs). Some δ-protocadherins reportedly show cell-cell adhesion properties. Individual δ-protocadherins appear to be involved in specific signaling pathways, as they interact with proteins such as TAF1/Set, TAO2β, Nap1, and the Frizzled-7 receptor. The spatiotemporally restricted expression of δ-protocadherins in various tissues and species and their functional analysis suggest that they play multiple, tightly regulated roles in vertebrate development. Furthermore, several δ-protocadherins have been implicated in neurological disorders and in cancers, highlighting the importance of scrutinizing their properties and their dysregulation in various pathologies.
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Affiliation(s)
- Irene Kahr
- Department for Molecular Biomedical Research, VIB, Ghent, Belgium
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38
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Novotny GW, Belling KC, Bramsen JB, Nielsen JE, Bork-Jensen J, Almstrup K, Sonne SB, Kjems J, Rajpert-De Meyts E, Leffers H. MicroRNA expression profiling of carcinoma in situ cells of the testis. Endocr Relat Cancer 2012; 19:365-79. [PMID: 22420006 DOI: 10.1530/erc-11-0271] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Testicular germ cell tumours, seminoma (SE) and non-seminoma (NS), of young adult men develop from a precursor cell, carcinoma in situ (CIS), which resembles foetal gonocytes and retains embryonic pluripotency. We used microarrays to analyse microRNA (miRNA) expression in 12 human testis samples with CIS cells and compared it with miRNA expression profiles of normal adult testis, testis with Sertoli-cell-only that lacks germ cells, testis tumours (SE and embryonal carcinoma (EC), an undifferentiated component of NS) and foetal male and female gonads. Principal components analysis revealed distinct miRNA expression profiles characteristic for each of the different tissue types. We identified several miRNAs that were unique to testis with CIS cells, foetal gonads and testis tumours. These included miRNAs from the hsa-miR-371-373 and -302-367 clusters that have previously been reported in germ cell tumours and three miRNAs (hsa-miR-96, -141 and -200c) that were also expressed in human epididymis. We found several miRNAs that were upregulated in testis tumours: hsa-miR-9, -105 and -182-183-96 clusters were highly expressed in SE, while the hsa-miR-515-526 cluster was high in EC. We conclude that the miRNA expression profile changes during testis development and that the miRNA profile of adult testis with CIS cells shares characteristic similarities with the expression in foetal gonocytes.
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Affiliation(s)
- Guy Wayne Novotny
- Department of Growth and Reproduction, Rigshospitalet, Blegdamsvej 9, 2100 Copenhagen, Denmark
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