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Kalinauskiene R, Brazdziunaite D, Burokiene N, Dirsė V, Morkuniene A, Utkus A, Preiksaitiene E. A De Novo 8q22.2q22.3 Interstitial Microdeletion in a Girl with Developmental Delay and Congenital Defects. MEDICINA (KAUNAS, LITHUANIA) 2023; 59:1156. [PMID: 37374360 DOI: 10.3390/medicina59061156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 05/18/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023]
Abstract
Background and Objectives: Only nine patients with interstitial de novo 8q22.2q22.3 microdeletions have been reported to date. The objective of this report is to present clinical features of a new patient with an 8q22.2q22.3 microdeletion, to compare her phenotype to other previously reported patients, and to further expand the phenotype associated with this microdeletion. Materials and Methods: We describe an 8½-year-old girl with developmental delay, congenital hip dysplasia, a bilateral foot deformity, bilateral congenital radioulnar synostosis, a congenital heart defect, and minor facial anomalies. Results: Chromosomal microarray analysis revealed a 4.9 Mb deletion in the 8q22.2q22.3 region. De novo origin was confirmed by real-time PCR analysis. Conclusions: Microdeletions in the 8q22.2q22.3 region are characterized by moderate to severe intellectual disability, seizures, distinct facial features and skeletal abnormalities. In addition to one already reported individual with an 8q22.2q22.3 microdeletion and unilateral radioulnar synostosis, this report of a child with bilateral radioulnar synostosis provides additional evidence, that radioulnar synostosis is not an incidental finding in individuals with an 8q22.2q22.3 microdeletion. Additional patients with similar microdeletions would be of a great importance for more accurate phenotypic description and further analysis of the genotypic-phenotypic relationship.
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Affiliation(s)
| | - Deimante Brazdziunaite
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, 01513 Vilnius, Lithuania
| | - Neringa Burokiene
- Clinic of Internal Diseases and Family Medicine, Institute of Clinical Medicine, Faculty of Medicine, Vilnius University, 01513 Vilnius, Lithuania
| | - Vaidas Dirsė
- Hematology, Oncology and Transfusion Medicine Center, Vilnius University Hospital Santaros Klinikos, 01513 Vilnius, Lithuania
| | - Ausra Morkuniene
- Centre for Medical Genetics, Vilnius University Hospital Santaros Klinikos, 01513 Vilnius, Lithuania
| | - Algirdas Utkus
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, 01513 Vilnius, Lithuania
| | - Egle Preiksaitiene
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, 01513 Vilnius, Lithuania
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Song K, Artibani M. The role of DNA methylation in ovarian cancer chemoresistance: A narrative review. Health Sci Rep 2023; 6:e1235. [PMID: 37123549 PMCID: PMC10140645 DOI: 10.1002/hsr2.1235] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 04/07/2023] [Accepted: 04/10/2023] [Indexed: 05/02/2023] Open
Abstract
Background and Aims Ovarian cancer (OC) is the most lethal gynecological cancer. In 2018, it was responsible for over 180,000 deaths worldwide. The high mortality rate is the culmination of a lack of early diagnosis and high rates of chemotherapy resistance, which is synonymous with disease recurrence. Over the last two decades, an increasingly significant role of epigenetic mechanisms, in particular DNA methylation, has emerged. This review will discuss several of the most significant genes whose hypo/hypermethylation profiles are associated with chemoresistance. Aside from functionally elucidating and evaluating these epimutations, this review will discuss recent trials of DNA methyltransferase inhibitors (DNMTi). Finally, we will propose future directions that could enhance the feasibility of utilizing these candidate epimutations as clinical biomarkers. Methods To perform this review, a comprehensive literature search based on our keywords was conducted across the online databases PubMed and Google Scholar for identifying relevant studies published up until August 2022. Results Epimutations affecting MLH1, MSH2, and Ras-association domain family 1 isoform A (DNA damage repair and apoptosis); ATP-binding cassette subfamily B member 1 and methylation-controlled J (drug export); secreted frizzled-related proteins (Wnt/β-catenin signaling), neurocalcin delta (calcium and G protein-coupled receptor signaling), and zinc finger protein 671 all have potential as biomarkers for chemoresistance. However, specific uncertainties relating to these epimutations include histotype-specific differences, intrinsic versus acquired chemoresistance, and the interplay with complete surgical debulking. DNMTi for chemoresistant OC patients has shown some promise; however, issues surrounding their efficacy and dose-limiting toxicities remain; a personalized approach is required to maximize their effectiveness. Conclusion Establishing a panel of aberrantly methylated chemoresistance-related genes to predict chemoresponsiveness and patients' suitability to DNMTi could significantly reduce OC recurrence, while improving DNMTi therapy viability. To achieve this, a large-scale prospective genome-wide DNA methylation profile study that spans different histotypes, includes paired samples (before and after chemotherapy), and integrates transcriptomic and methylomic analysis, is warranted.
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Affiliation(s)
- Kaiyang Song
- Green Templeton CollegeUniversity of OxfordOxfordUK
| | - Mara Artibani
- Ovarian Cancer Cell Laboratory, Medical Research Council (MRC) Weatherall Institute of Molecular MedicineUniversity of OxfordOxfordUK
- Nuffield Department of Women's & Reproductive HealthUniversity of OxfordOxfordUK
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Zhu Y, Zhang J, Yu L, Xu S, Chen L, Wu K, Kong L, Lin W, Xue J, Wang Q, Lin Y, Chen X. SENP3 promotes tumor progression and is a novel prognostic biomarker in triple-negative breast cancer. Front Oncol 2023; 12:972969. [PMID: 36698419 PMCID: PMC9868814 DOI: 10.3389/fonc.2022.972969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 12/14/2022] [Indexed: 01/12/2023] Open
Abstract
Background The clinical outcome of triple-negative breast cancer (TNBC) is poor. Finding more targets for the treatment of TNBC is an urgent need. SENPs are SUMO-specific proteins that play an important role in SUMO modification. Among several tumor types, SENPs have been identified as relevant biomarkers for progression and prognosis. The role of SENPs in TNBC is not yet clear. Methods The expression and prognosis of SENPs in TNBC were analyzed by TCGA and GEO data. SENP3 coexpression regulatory networks were determined by weighted gene coexpression network analysis (WGCNA). Least absolute shrinkage and selection operator (LASSO) and Cox univariate analyses were used to develop a risk signature based on genes associated with SENP3. A time-dependent receiver operating characteristic (ROC) analysis was employed to evaluate a risk signature's predictive accuracy and sensitivity. Moreover, a nomogram was constructed to facilitate clinical application. Results The prognostic and expression effects of SENP family genes were validated using the TCGA and GEO databases. SENP3 was found to be the only gene in the SENP family that was highly expressed and associated with an unfavorable prognosis in TNBC patients. Cell functional experiments showed that knockdown of SENP3 leads to growth, invasion, and migration inhibition of TNBC cells in vitro. By using WGCNA, 273 SENP3-related genes were identified. Finally, 11 SENP3-related genes were obtained from Cox univariate analysis and LASSO regression. Based on this, a prognostic risk prediction model was established. The risk signature of SENP3-related genes was verified as an independent prognostic marker for TNBC patients. Conclusion Among SENP family genes, we found that SENP3 was overexpressed in TNBC and associated with a worse prognosis. SENP3 knockdown can inhibit tumor proliferation, invasion, and migration. In TNBC patients, a risk signature based on the expression of 11 SENP3-related genes may improve prognosis prediction. The established risk markers may be promising prognostic biomarkers that can guide the individualized treatment of TNBC patients.
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Affiliation(s)
- Youzhi Zhu
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Jiasheng Zhang
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Liangfei Yu
- Department of Breast Surgery, the First Hospital of Fuzhou, Fuzhou, China
| | - Sunwang Xu
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Ling Chen
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Kunlin Wu
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Lingjun Kong
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Wei Lin
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Jiajie Xue
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Qingshui Wang
- Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China,*Correspondence: Xiangjin Chen, ; Yao Lin, ; Qingshui Wang,
| | - Yao Lin
- Central Laboratory at The Second Affiliated Hospital of Fujian Traditional Chinese Medical University, Innovation and Transformation Center, Fujian University of Traditional Chinese Medicine, Fuzhou, China,*Correspondence: Xiangjin Chen, ; Yao Lin, ; Qingshui Wang,
| | - Xiangjin Chen
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China,*Correspondence: Xiangjin Chen, ; Yao Lin, ; Qingshui Wang,
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Konrad SM, Schwamborn K, Krüger A, Honert K, Schmitt M, Hellmann D, Schmalfeldt B, Meindl A, Kiechle M, Quante AS, Brambs C, Grill S, Ramser J. NCALD as a potential predictive biomarker for the efficacy of platinum-based chemotherapy in ovarian cancer. Biomark Med 2022; 16:1029-1041. [PMID: 36444691 DOI: 10.2217/bmm-2021-0781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Aim: Since reliable response predictors to platinum-based chemotherapy in ovarian cancer (OC) are scarce, we characterize NCALD as a predictive biomarker. Materials & methods: NCALD mRNA (n = 100) and protein (n = 102) expression was analyzed in OC samples and associated with patient outcome. A stable OC cell line knockdown was generated and cellular response to platinum was explored. Results: High NCALD mRNA and protein expression was significantly associated with longer overall patient survival (p = 0.037/0.002). Knockdown experiments revealed a significant association between cisplatin sensitivity and NCALD expression. Conclusion: Low NCALD expression was associated with reduced sensitivity to platinum-based chemotherapy. NCALD may be a new biomarker candidate to identify patients who might benefit from platinum-based chemotherapy.
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Affiliation(s)
- Sarah M Konrad
- Department of Gynecology & Obstetrics, University Hospital rechts der Isar, Technical University of Munich, Munich, 81675, Germany.,German Cancer Consortium (DKTK), partner site München, & German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
| | - Kristina Schwamborn
- Institute of Pathology, School of Medicine, Technical University of Munich, Munich, 81675, Germany
| | - Achim Krüger
- Institute of Experimental Oncology & Therapy Research, School of Medicine, Technical University of Munich, Munich, 81675, Germany
| | - Katja Honert
- Institute of Experimental Oncology & Therapy Research, School of Medicine, Technical University of Munich, Munich, 81675, Germany
| | - Manfred Schmitt
- Department of Gynecology & Obstetrics, University Hospital rechts der Isar, Technical University of Munich, Munich, 81675, Germany
| | - Daniela Hellmann
- Department of Gynecology & Obstetrics, University Hospital rechts der Isar, Technical University of Munich, Munich, 81675, Germany
| | - Barbara Schmalfeldt
- Department of Gynecology & Obstetrics, University Hospital rechts der Isar, Technical University of Munich, Munich, 81675, Germany.,Department of Gynecology & Gynecologic Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, 20251, Germany
| | - Alfons Meindl
- Department of Gynecology & Obstetrics, University Hospital rechts der Isar, Technical University of Munich, Munich, 81675, Germany.,Department of Gynecology & Obstetrics, University Hospital Munich, Ludwig-Maximilians-Universität München, Munich, 81377, Germany
| | - Marion Kiechle
- Department of Gynecology & Obstetrics, University Hospital rechts der Isar, Technical University of Munich, Munich, 81675, Germany
| | - Anne S Quante
- Department of Gynecology & Obstetrics, University Hospital rechts der Isar, Technical University of Munich, Munich, 81675, Germany.,Institute of Human Genetics, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, 79106, Germany
| | - Christine Brambs
- Department of Gynecology & Obstetrics, Cantonal Hospital of Lucerne, Lucerne, 6000, Switzerland
| | - Sabine Grill
- Department of Gynecology & Obstetrics, University Hospital rechts der Isar, Technical University of Munich, Munich, 81675, Germany
| | - Juliane Ramser
- Department of Gynecology & Obstetrics, University Hospital rechts der Isar, Technical University of Munich, Munich, 81675, Germany
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Zhang XT, Zhang Y, Zhang YX, Jiang ZY, Yang H, Jiang L, Yang B, Tong JC. Helicid Reverses the Effect of Overexpressing NCALD, Which Blocks the sGC/cGMP/PKG Signaling Pathway in the CUMS-Induced Rat Model. JOURNAL OF HEALTHCARE ENGINEERING 2021; 2021:7168397. [PMID: 34931140 PMCID: PMC8684516 DOI: 10.1155/2021/7168397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 11/23/2021] [Accepted: 11/26/2021] [Indexed: 12/02/2022]
Abstract
Background Increasing evidence has shown that apoptosis in the hippocampus is closely related to depressive-like behavior. We previously reported that helicid had good antidepressant activities, which manifested as the alleviation of depression-like behaviors and the reversal of the high expression of neurocalcin delta (NCALD) in chronic unpredictable mild stress (CUMS) rats. The aim of this study was, therefore, to characterize the antidepressant-like effects and underlying mechanism of helicid on CUMS rats by silencing NCALD and using rescue experiments. Methods We developed the CUMS rat model using CUMS stimulation from week 0 to week 6. The rats were treated with helicid, or NCALD silenced, then we overexpressed NCALD using adeno-associated virus. We also measured the protein levels of sGCα1, sGCβ1, PKG1/2, and cleaved caspase-3 in hippocampal tissues using western blotting and measured cGMP using an ELISA. Results Treating CUMS rats by silencing NCALD or by the administration of helicid improved the depressive-like behavior. The levels of proteins, including sGC, PKG, cleaved caspase-3, and cGMP, in hippocampus all decreased. NCALD overexpression reversed these decreases and reversed the alleviation of depression-like behaviors in CUMS rats. Limitation. We only detected the antidepressant effects of helicid in the hippocampus; therefore, other parts of brain should also be studied. Conclusions Inhibition of NCALD, as well as helicid administration, alleviated antidepressant-like behavior by regulating the expressions of apoptotic cytokines and the sGC/cGMP/PKG signaling pathway. Overexpressing NCALD reversed the amelioration effects of silenced NCALD and helicid administration.
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Affiliation(s)
- Xiao-Tong Zhang
- The First Affiliated Hospital of Wannan Medical College, Yijishan Hospital, Wuhu 241001, Anhui, China
- Wannan Medical College, Wuhu 241002, Anhui, China
| | - Yuan Zhang
- The First Affiliated Hospital of Wannan Medical College, Yijishan Hospital, Wuhu 241001, Anhui, China
- Wannan Medical College, Wuhu 241002, Anhui, China
| | | | - Zhen-Yi Jiang
- The First Affiliated Hospital of Wannan Medical College, Yijishan Hospital, Wuhu 241001, Anhui, China
- Wannan Medical College, Wuhu 241002, Anhui, China
| | - Hui Yang
- Key Laboratory of Non-Coding RNA Transformation Research of Anhui Higher Education Institution (Wannan Medical College), Wuhu, China
- Central Laboratory, Yijishan Hospital, The First Affiliated Hospital of Wannan Medical College, Wuhu, China
| | - Lan Jiang
- Key Laboratory of Non-Coding RNA Transformation Research of Anhui Higher Education Institution (Wannan Medical College), Wuhu, China
- Central Laboratory, Yijishan Hospital, The First Affiliated Hospital of Wannan Medical College, Wuhu, China
| | - Bin Yang
- Department of Clinical Pharmacy, The First Affiliated Hospital of Wannan Medical College, Yijishan Hospital, Wuhu 241001, Anhui, China
| | - Jiu-Cui Tong
- The First Affiliated Hospital of Wannan Medical College, Yijishan Hospital, Wuhu 241001, Anhui, China
- Wannan Medical College, Wuhu 241002, Anhui, China
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6
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Feng LY, Li L. Low expression of NCALD is associated with chemotherapy resistance and poor prognosis in epithelial ovarian cancer. J Ovarian Res 2020; 13:35. [PMID: 32228639 PMCID: PMC7106630 DOI: 10.1186/s13048-020-00635-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 03/12/2020] [Indexed: 12/13/2022] Open
Abstract
Background Low expression of NCALD(neurocalcin delta) in peripheral blood of ovarian cancer patients predicts poor prognosis. However, the molecular mechanism of NCALD in ovarian cancer and its relationship with chemotherapy outcomes is unclear. The aim of this study was to investigate the potential signaling pathways of NCALD and to evaluate its ability to predict chemotherapy outcomes and prognosis. Methods High-throughput RNA sequencing data were downloaded from TCGA. GSEA explored the potential signaling pathways of NCALD. The expression of NCALD in chemotherapy sensitive and chemotherapy resistant ovarian cancer patients was detected by TCGA data and clinical samples. ROC analysis confirmed the ability of NCALD to predict chemotherapy outcomes. The association between NCALD expression and prognosis in ovarian cancer patients was assessed using Kaplan-Meier plotter. Results In patients with NCALD overexpression, genes expression related to ERK1 / 2 signaling pathway, NF-kappaB signaling pathway, TGF-β signaling pathway and immune response pathway was increased, especially ERK1 / 2 signaling pathway. The expression of NCALD in chemoresistant patients was significantly lower than chemosensitive patients. In TCGA data and immunohistochemical samples, the AUC of NCALD expression predicting chemotherapy outcome was 0.59 and 0.64, respectively. In clinical samples, low expression of NCALD was associated with poor OS and PFS. Conclusions NCALD may activate the ERK1 / 2 signaling pathway in ovarian cancer. As a new biomarker of chemotherapy sensitivity, NCALD was significantly down-regulated in chemotherapy resistance ovarian cancer patients. Low expression of NCALD in ovarian cancer is associated with poor OS and PFS. In the future, further research will be needed on the potential mechanism and clinical application value of NCALD in ovarian cancer.
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Affiliation(s)
- Li-Yuan Feng
- Department of Gynecologic oncology, Guangxi Medical University Cancer Hospital, 71 Hedi Road, Nanning, Guangxi, 530021, P.R. China
| | - Li Li
- Department of Gynecologic oncology, Guangxi Medical University Cancer Hospital, 71 Hedi Road, Nanning, Guangxi, 530021, P.R. China.
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Dong C, Yin F, Zhu D, Cai X, Chen C, Liu X. NCALD affects drug resistance and prognosis by acting as a ceRNA of CX3CL1 in ovarian cancer. J Cell Biochem 2020; 121:4470-4483. [PMID: 32030795 DOI: 10.1002/jcb.29670] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 01/10/2020] [Indexed: 01/01/2023]
Abstract
Drug resistance, an impenetrable barrier in the treatment of ovarian cancer (OC), is often associated with poor outcomes. Hence, it is urgent to discover new factors controlling drug resistance and survival. The association between neurocalcin delta (NCALD) and cancer drug resistance is poorly understood. Here, we reveal that NCALD messenger RNA expression, probably regulated by DNA methylation and microRNAs, was significantly downregulated in at least three independent microarrays covering 633 ovarian carcinomas and 16 normal controls, which includes the Cancer Genome Atlas (TCGA) ovarian cohort. In the sub-groups of the TCGA cohort, NCALD was suppressed in 90 platinum-resistant tissues vs in 197 sensitive tissues. It is consistent with the quantitative reverse transcription polymerase chain reaction results revealing gene downregulation in carboplatin-resistant SKOV3 and HeyA8 OC cells as compared with that in controls. Low expression of NCALD predicted poor overall survival (OS) in sub-groups of 1656 patients, progression-free survival (PFS) in 1435 patients, and post-progression survival (PPS) in 782 patients according to Kaplan-Meier plotter covering 1815 OC patients. Comprehensive bioinformatic analyses strongly implicated NCALD in the regulation of drug resistance, probably via competing for endogenous RNA (ceRNA) interactions with CX3CL1 and tumor immune-microenvironment. NCALD acted as a ceRNA for CX3CL1 in 21 different cancers includes OC according to Starbase. These two genes negatively correlated with tumor purity and positively correlated with infiltration levels of neutrophils and dendritic cells in OC. The combined low expression of NCALD and CX3CL1 showed better prognosis potential for OS, PFS, and PPS in the 1815 OC patients than any of the individually tested genes. In summary, NCALD acts as a ceRNA for CX3CL1, and its downregulation may affect drug resistance and prognosis in OC. Thus, NCALD could be a new therapeutic target for anticancer therapy and a new biomarker for survival prediction in OC.
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Affiliation(s)
- Caihua Dong
- Key Laboratory of Longevity and Ageing-Related Disease of Chinese Ministry of Education, Centre for Translational Medicine and School of Preclinical Medicine, Guangxi Medical University, Nanning, Guangxi, China
| | - Fuqiang Yin
- Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi, China.,Key Laboratory of High-Incidence-Tumor Prevention and Treatment (Guangxi Medical University), Ministry of Education, Nanning, Guangxi, China
| | - Dan Zhu
- Pharmaceutical College, Guangxi Medical University, Nanning, Guangxi, China
| | - Xiangxue Cai
- Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi, China
| | - Cuilan Chen
- Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi, China
| | - Xia Liu
- Key Laboratory of Longevity and Ageing-Related Disease of Chinese Ministry of Education, Centre for Translational Medicine and School of Preclinical Medicine, Guangxi Medical University, Nanning, Guangxi, China
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Song Y, Zhang W, He X, Liu X, Yang P, Wang J, Hu K, Liu W, Zhang X, Jing H, Yuan X. High NCALD expression predicts poor prognosis of cytogenetic normal acute myeloid leukemia. J Transl Med 2019; 17:166. [PMID: 31109331 PMCID: PMC6528257 DOI: 10.1186/s12967-019-1904-5] [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: 11/27/2018] [Accepted: 05/03/2019] [Indexed: 12/22/2022] Open
Abstract
Background Acute myeloid leukemia (AML) is a heterogeneous disease in terms of genetic basis, clinical, biological and prognostic, and is a malignant clonal disease of leukemia stem cells (LSCs). Nearly half of adult AML patients exhibit a cytogenetic normal acute myeloid leukemia (CN-AML). The expression level of NCALD gene was associated with the prognosis of ovarian cancer and non-small cell lung cancer (NSCLC). The expression level of NCALD gene is still unclear in the prognosis of patients with AML. Method We integrated 5 independent datasets totally 665 AML patients (497 CN-AML patients) to analyzed relation between NCALD gene expression and the clinical FAB classification, gene mutation, therapy, prognosis of CN-AML. We analyzed the NCALD gene expression with the prognosis and LSC of 165 AML patients from The Cancer Genome Atlas (TCGA) dataset and 78 AML patients from GEO dataset. Results High NCALD-expressing CN-AML patients were associated with poor event-free survival (EFS) and overall survival (OS) compared to low NCALD expression (EFS, P < 0.0001, OS, P < 0.0001). In AML patients of allogeneic hematopoietic stem cell transplantation (allo-HSCT), high NCALD expression was associated with poor survival prognosis in EFS and OS (EFS, P < 0.0051, OS, P = 0.028). Post-chemotherapy in AML patients, high NCALD expression led a worse prognosis in EFS and OS (EFS, P = 0.011; OS, P = 0.0056). In multivariate analysis, high NCALD expression was an independent prognostic factor that predicts shorter EFS and OS (EFS, P = 3.84E−05, OS, P = 8.53E−05) of CN-AML. Conclusion Our results indicate that high expression of NCALD gene is a poor prognostic factor for CN-AML. NCALD can be considered as independent predictors of CN-AML patients and can be used as a biomarker for the prognosis of CN-AML. Electronic supplementary material The online version of this article (10.1186/s12967-019-1904-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ying Song
- The First Clinical College of Gannan Medical University, Ganzhou, 341000, China
| | - Weilong Zhang
- Department of Hematology, Lymphoma Research Center, Peking University Third Hospital, No. 49 North Garden Road, Haidian District, Beijing, 100191, People's Republic of China
| | - Xue He
- Department of Pathology, Beijing Tiantan Hospital Affiliated With Capital Medical University, No. 6 Tiantan Xili, Beijing, 100050, China
| | - Xiaoni Liu
- Department of Respiratory Medicine, The First Affiliated Hospital of Gannan Medical University, No. 23 Qingnian Road, Zhanggong District, Ganzhou, 341000, China
| | - Ping Yang
- Department of Hematology, Lymphoma Research Center, Peking University Third Hospital, No. 49 North Garden Road, Haidian District, Beijing, 100191, People's Republic of China
| | - Jing Wang
- Department of Hematology, Lymphoma Research Center, Peking University Third Hospital, No. 49 North Garden Road, Haidian District, Beijing, 100191, People's Republic of China
| | - Kai Hu
- Department of Hematology, Lymphoma Research Center, Peking University Third Hospital, No. 49 North Garden Road, Haidian District, Beijing, 100191, People's Republic of China
| | - Weiyou Liu
- Department of Respiratory Medicine, The First Affiliated Hospital of Gannan Medical University, No. 23 Qingnian Road, Zhanggong District, Ganzhou, 341000, China
| | - Xiuru Zhang
- Department of Pathology, Beijing Tiantan Hospital Affiliated With Capital Medical University, No. 6 Tiantan Xili, Beijing, 100050, China.
| | - Hongmei Jing
- Department of Hematology, Lymphoma Research Center, Peking University Third Hospital, No. 49 North Garden Road, Haidian District, Beijing, 100191, People's Republic of China.
| | - Xiaoliang Yuan
- Department of Respiratory Medicine, The First Affiliated Hospital of Gannan Medical University, No. 23 Qingnian Road, Zhanggong District, Ganzhou, 341000, China.
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Upadhyay A, Hosseinibarkooie S, Schneider S, Kaczmarek A, Torres-Benito L, Mendoza-Ferreira N, Overhoff M, Rombo R, Grysko V, Kye MJ, Kononenko NL, Wirth B. Neurocalcin Delta Knockout Impairs Adult Neurogenesis Whereas Half Reduction Is Not Pathological. Front Mol Neurosci 2019; 12:19. [PMID: 30853885 PMCID: PMC6396726 DOI: 10.3389/fnmol.2019.00019] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 01/21/2019] [Indexed: 12/22/2022] Open
Abstract
Neurocalcin delta (NCALD) is a brain-enriched neuronal calcium sensor and its reduction acts protective against spinal muscular atrophy (SMA). However, the physiological function of NCALD and implications of NCALD reduction are still elusive. Here, we analyzed the ubiquitous Ncald knockout in homozygous (NcaldKO/KO) and heterozygous (NcaldKO/WT) mice to unravel the physiological role of NCALD in the brain and to study whether 50% NCALD reduction is a safe option for SMA therapy. We found that NcaldKO/KO but not NcaldKO/WT mice exhibit significant changes in the hippocampal morphology, likely due to impaired generation and migration of newborn neurons in the dentate gyrus (DG). To understand the mechanism behind, we studied the NCALD interactome and identified mitogen-activated protein kinase kinase kinase 10 (MAP3K10) as a novel NCALD interacting partner. MAP3K10 is an upstream activating kinase of c-Jun N-terminal kinase (JNK), which regulates adult neurogenesis. Strikingly, the JNK activation was significantly upregulated in the NcaldKO/KO brains. Contrary, neither adult neurogenesis nor JNK activation were altered by heterozygous Ncald deletion. Taken together, our study identifies a novel link between NCALD and adult neurogenesis in the hippocampus, possibly via a MAP3K10-JNK pathway and emphasizes the safety of using NCALD reduction as a therapeutic option for SMA.
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Affiliation(s)
- Aaradhita Upadhyay
- Institute of Human Genetics, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany.,Institute for Genetics, University of Cologne, Cologne, Germany
| | - Seyyedmohsen Hosseinibarkooie
- Institute of Human Genetics, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany.,Institute for Genetics, University of Cologne, Cologne, Germany
| | - Svenja Schneider
- Institute of Human Genetics, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany.,Institute for Genetics, University of Cologne, Cologne, Germany
| | - Anna Kaczmarek
- Institute of Human Genetics, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany.,Institute for Genetics, University of Cologne, Cologne, Germany
| | - Laura Torres-Benito
- Institute of Human Genetics, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany.,Institute for Genetics, University of Cologne, Cologne, Germany
| | - Natalia Mendoza-Ferreira
- Institute of Human Genetics, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany.,Institute for Genetics, University of Cologne, Cologne, Germany
| | - Melina Overhoff
- Institute for Genetics, University of Cologne, Cologne, Germany.,Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Roman Rombo
- Institute of Human Genetics, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany.,Institute for Genetics, University of Cologne, Cologne, Germany
| | - Vanessa Grysko
- Institute of Human Genetics, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany.,Institute for Genetics, University of Cologne, Cologne, Germany
| | - Min Jeong Kye
- Institute of Human Genetics, University of Cologne, Cologne, Germany
| | - Natalia L Kononenko
- Institute for Genetics, University of Cologne, Cologne, Germany.,Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Brunhilde Wirth
- Institute of Human Genetics, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany.,Institute for Genetics, University of Cologne, Cologne, Germany.,Center for Rare Diseases Cologne, University Hospital of Cologne, Cologne, Germany
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10
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Chen CP, Chang TY, Hung FY, Chern SR, Wu PS, Chen SW, Lai ST, Chuang TY, Lee CC, Wang W. Prenatal diagnosis of an 8q22.2-q23.3 deletion associated with bilateral cleft lip and palate and intrauterine growth restriction on fetal ultrasound. Taiwan J Obstet Gynecol 2018; 56:843-846. [PMID: 29241932 DOI: 10.1016/j.tjog.2017.10.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/17/2017] [Indexed: 12/20/2022] Open
Abstract
OBJECTIVE We present prenatal diagnosis of an interstitial 8q22.2-q23.3 deletion associated with bilateral cleft lip and palate and intrauterine growth restriction (IUGR) on fetal ultrasound. CASE REPORT A 29-year-old, primigravid woman underwent elective amniocentesis at 17 weeks of gestation because of anxiety. Amniocentesis revealed a karyotype of 46, XX. However, level II ultrasound at 21 weeks of gestation revealed a fetus with IUGR and bilateral cleft lip and palate. Repeat amniocentesis was performed at 21 weeks of gestation, and array comparative genomic hybridization using uncultured amniocytes revealed a 13.5-Mb interstitial deletion of 8q22.2-q23.3 encompassing 37 Online Mendelian Inheritance of in Man (OMIM) genes including SPAG1, GRHL2, NCALD, RRM2B and ZFPM2. Polymorphic DNA marker analysis determined a paternal origin of the deletion. The pregnancy was subsequently terminated, and a malformed fetus was delivered with a depressed nose and bilateral cleft lip and palate. CONCLUSION Prenatal diagnosis of facial cleft with IUGR should raise a suspicion of subtle chromosome deletions.
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Affiliation(s)
- Chih-Ping Chen
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan; Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan; Department of Biotechnology, Asia University, Taichung, Taiwan; School of Chinese Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan; Institute of Clinical and Community Health Nursing, National Yang-Ming University, Taipei, Taiwan; Department of Obstetrics and Gynecology, School of Medicine, National Yang-Ming University, Taipei, Taiwan.
| | | | - Fang-Yu Hung
- Department of Obstetrics and Gynecology, Hsinchu MacKay Memorial Hospital, Hsinchu, Taiwan
| | - Schu-Rern Chern
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
| | | | - Shin-Wen Chen
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Shih-Ting Lai
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Tzu-Yun Chuang
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Chen-Chi Lee
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Wayseen Wang
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan; Department of Bioengineering, Tatung University, Taipei, Taiwan
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11
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Shi X, Ma C, Zhu Q, Yuan D, Sun M, Gu X, Wu G, Lv T, Song Y. Upregulation of long intergenic noncoding RNA 00673 promotes tumor proliferation via LSD1 interaction and repression of NCALD in non-small-cell lung cancer. Oncotarget 2018; 7:25558-75. [PMID: 27027352 PMCID: PMC5041926 DOI: 10.18632/oncotarget.8338] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 03/07/2016] [Indexed: 12/31/2022] Open
Abstract
Despite improvements in diagnostics and treatment of non-small cell lung cancer (NSCLC), it remains the leading causes of cancer-related mortality worldwide. In more recent years, mutiple lines of evidence have highlighted long noncoding RNAs (lncRNAs) serve as novel class of regulators of cancer biological processes, including proliferation, apoptosis and metastasis. LncRNAs serve as a novel class of regulators of cancer biological processes in cancer, but little is known of their expression and potential functions in NSCLC. We identified an oncogene, linc00673, whose expression level was upregulated by bioinformatics analyses and qRT-PCR analyses in NSCLC. The effects of linc00673 on tumor progression were investigated in vitro and in vivo. Linc00673 knockdown significantly inhibited cell proliferation and colony-forming ability, and suppressed S-phase entry in vitro and shRNA linc00673 mediated knockdown significantly inhibit tumor growth in vivo, meanwhile, linc00673 overexpression increased tumor cell growth. Analysis of RNAseq data revealed linc00673 could modulate the transcription of a large amount of genes including oncogene and tumor suppressor gene, so we investigated the role and regulatory mechanism of linc00673 in NSCLC proliferation. Further mechanistic analyses indicated that the oncogenic activity of linc00673 is partially attributable to its repression of NCALD through association with the epigenetic repressor LSD1. Taken together, these findings suggested that linc00673 could play crucial role in NSCLC progression and might be a potential therapeutic target for patients with NSCLC.
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Affiliation(s)
- Xuefei Shi
- Department of Respiratory Medicine, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China.,Department of Respiratory Medicine, Huzhou Central Hospital, Huzhou, China
| | - Chenhui Ma
- Department of Respiratory Medicine, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Qingqing Zhu
- Department of Respiratory Medicine, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Dongmei Yuan
- Department of Respiratory Medicine, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Ming Sun
- Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing, China
| | - Xiaoling Gu
- Department of Respiratory Medicine, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Guannan Wu
- Department of Respiratory Medicine, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Tangfeng Lv
- Department of Respiratory Medicine, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Yong Song
- Department of Respiratory Medicine, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
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12
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Sinajon P, Gofine T, Ingram J, So J. Microdeletion 8q22.2-q22.3 in a 40-year-old male. Eur J Med Genet 2015; 58:569-72. [DOI: 10.1016/j.ejmg.2015.10.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Revised: 10/01/2015] [Accepted: 10/03/2015] [Indexed: 10/22/2022]
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13
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Mabuchi M, Shimizu T, Ueda M, Mitamura K, Ikegawa S, Tanaka A. Improvement of solid material for affinity resins by application of long PEG spacers to capture the whole target complex of FK506. Bioorg Med Chem Lett 2015; 25:2788-92. [PMID: 26025877 DOI: 10.1016/j.bmcl.2015.05.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2015] [Revised: 04/12/2015] [Accepted: 05/07/2015] [Indexed: 11/20/2022]
Abstract
Solid materials for affinity resins bearing long PEG spacers between a functional group used for immobilization of a bio-active compound and the solid surface were synthesized to capture not only small target proteins but also large and/or complex target proteins. Solid materials with PEG1000 or PEG2000 as spacers, which bear a benzenesulfonamide derivative, exhibited excellent selectivity between the specific binding protein carbonic anhydrase type II (CAII) and non-specific ones. These materials also exhibited efficacy in capturing a particular target at a maximal amount. Affinity resins using solid materials with PEG1000 or PEG2000 spacers, bear a FK506 derivative, successfully captured the whole target complex of specific binding proteins at the silver staining level, while all previously known affinity resins with solid materials failed to achieve this objective. These novel affinity resins captured other specific binding proteins such as dynamin and neurocalcin δ as well.
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Affiliation(s)
- Miyuki Mabuchi
- Department of Pharmacy, Hyogo University of Health Sciences, 1-3-6 Minatojima, Chuo-ku, Kobe 650-8530, Japan; KOBE Chemical Genetics., Inc. 2-2-2 Minatojima-nakamachi, Chuo-ku, Kobe 650-8530, Japan
| | - Tadashi Shimizu
- Department of Pharmacy, Hyogo University of Health Sciences, 1-3-6 Minatojima, Chuo-ku, Kobe 650-8530, Japan
| | - Masahiro Ueda
- Department of Pharmacy, Hyogo University of Health Sciences, 1-3-6 Minatojima, Chuo-ku, Kobe 650-8530, Japan
| | - Kuniko Mitamura
- Faculty of Pharmaceutical Sciences, Kinki University, 3-4-1 Kowakae, Higashi-Osaka 577-8502, Japan
| | - Shigeo Ikegawa
- Faculty of Pharmaceutical Sciences, Kinki University, 3-4-1 Kowakae, Higashi-Osaka 577-8502, Japan
| | - Akito Tanaka
- Department of Pharmacy, Hyogo University of Health Sciences, 1-3-6 Minatojima, Chuo-ku, Kobe 650-8530, Japan; KOBE Chemical Genetics., Inc. 2-2-2 Minatojima-nakamachi, Chuo-ku, Kobe 650-8530, Japan.
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14
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Rudkowska I, Pérusse L, Bellis C, Blangero J, Després JP, Bouchard C, Vohl MC. Interaction between Common Genetic Variants and Total Fat Intake on Low-Density Lipoprotein Peak Particle Diameter: A Genome-Wide Association Study. JOURNAL OF NUTRIGENETICS AND NUTRIGENOMICS 2015; 8:44-53. [PMID: 26112879 DOI: 10.1159/000431151] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 02/05/2015] [Indexed: 11/19/2022]
Abstract
BACKGROUND/AIM Total fat intake has an important impact on the low-density lipoprotein (LDL) peak particle diameter (LDL-PPD) and may interact with nutrient-sensitive single nucleotide polymorphisms (SNPs). The objective was to examine whether there is suggestive evidence of SNP × dietary fat intake interaction effects influencing the LDL-PPD in the Quebec Family Study (QFS) in order to generate hypotheses to be tested in larger studies. METHODS SNPs from a genome-wide association study (GWAS) using Illumina Human610-Quad BeadChip, total fat intake derived from a 3-day weighted food record, and SNP × total fat intake interaction effects were examined on LDL-PPD in 541 QFS subjects. RESULTS The GWAS analyses 29 identified independent SNP × total fat intake interaction effects on the LDL-PPD at p < 10(-5), including SNPs in the following genes: ABCG2, CPA3, FNBP1, KCNQ3, NBAS, NCALD, OPRL1, NKAIN2, SH3BGRL2, SOX5, and SUSD4. CONCLUSIONS This observational study suggests that multiple SNPs interact with dietary fat intake to influence variation in the LDL-PPD.
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Affiliation(s)
- Iwona Rudkowska
- Institute of Nutrition and Functional Foods (INAF), Laval University, Québec, Qué., Canada
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15
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Isaksson HS, Sorbe B, Nilsson TK. Whole genome expression profiling of blood cells in ovarian cancer patients -prognostic impact of the CYP1B1, MTSS1, NCALD, and NOP14. Oncotarget 2015; 5:4040-9. [PMID: 24961659 PMCID: PMC4147304 DOI: 10.18632/oncotarget.1938] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Ovarian cancer patients with different tumor stages and cell differentiation might be distinguished from each other by gene expression profiles in whole blood cell mRNA by the Affymetrix Human Gene 1.0 ST Array. We also examined if there is any association with other clinical variables, response to therapy, and residual tumor burden after surgery. Patients were divided into two groups, one with poor prognosis, advanced stage and poorly differentiated tumors (n = 22), and one group with good prognosis, early stage and well- to medium differentiated tumors (n = 11). Six genes were found to be differentially expressed: the PDIA3, LYAR, NOP14, NCALD and MTSS1 genes were down-regulated and the CYP1B1 gene expression was up-regulated in the poor prognosis group, all with p value <0.05, adjusted for mass comparison. In survival analyses, CYP1B1, MTSS1, NCALD and NOP14 remained significantly different (p<0.05). Patient groups did not differ in any transcript related to acute phase or immune responses. This minimal gene expression signature of prognostic ovarian cancer-related genes opens up an avenue for more practicable monitoring of ovarian cancer patients by simple peripheral blood tests, which may evolve into a tool to guide selection of curative and postoperative supportive therapies.
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Affiliation(s)
| | | | - Torbjörn K Nilsson
- Department of Medical Biosciences/Clinical Chemistry, Umeå University,Umeå, Sweden
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16
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Kuroda Y, Ohashi I, Saito T, Nagai JI, Ida K, Naruto T, Iai M, Kurosawa K. Refinement of the deletion in 8q22.2-q22.3: The minimum deletion size at 8q22.3 related to intellectual disability and epilepsy. Am J Med Genet A 2014; 164A:2104-8. [DOI: 10.1002/ajmg.a.36604] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 04/04/2014] [Indexed: 11/06/2022]
Affiliation(s)
- Yukiko Kuroda
- Division of Medical Genetics; Kanagawa Children's Medical Center; Yokohama Japan
| | - Ikuko Ohashi
- Division of Medical Genetics; Kanagawa Children's Medical Center; Yokohama Japan
| | - Toshiyuki Saito
- Department of Clinical Laboratory; Kanagawa Children's Medical Center; Yokohama Japan
| | - Jun-ichi Nagai
- Department of Clinical Laboratory; Kanagawa Children's Medical Center; Yokohama Japan
| | - Kazumi Ida
- Division of Medical Genetics; Kanagawa Children's Medical Center; Yokohama Japan
| | - Takuya Naruto
- Division of Medical Genetics; Kanagawa Children's Medical Center; Yokohama Japan
| | - Mizue Iai
- Division of Pediatric Neurology; Kanagawa Children's Medical Center; Yokohama Japan
| | - Kenji Kurosawa
- Division of Medical Genetics; Kanagawa Children's Medical Center; Yokohama Japan
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17
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Kamiyama M, Kobayashi M, Araki SI, Iida A, Tsunoda T, Kawai K, Imanishi M, Nomura M, Babazono T, Iwamoto Y, Kashiwagi A, Kaku K, Kawamori R, Ng DPK, Hansen T, Gaede P, Pedersen O, Nakamura Y, Maeda S. Polymorphisms in the 3' UTR in the neurocalcin delta gene affect mRNA stability, and confer susceptibility to diabetic nephropathy. Hum Genet 2007; 122:397-407. [PMID: 17671797 DOI: 10.1007/s00439-007-0414-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2007] [Accepted: 07/24/2007] [Indexed: 10/23/2022]
Abstract
Using a large-scale genotyping analysis of gene-based single nucleotide polymorphisms (SNPs) in Japanese type 2 diabetic patients, we have identified a gene encoding neurocalcin delta (NCALD) as a candidate for a susceptibility gene to diabetic nephropathy; the landmark SNP was found in the 3' UTR of NCALD (rs1131863: exon 4 +1340 A vs. G, P = 0.00004, odds ratio = 1.59, 95% CI 1.27-1.98). We also discovered two other SNPs in exon 4 of this gene (+999 T/A, +1307 A/G) that showed absolute linkage disequilibrium to the landmark SNP. Subsequent in vitro functional analysis revealed that synthetic mRNA corresponding to the disease susceptible haplotype (exon 4 +1340 G, +1307 G, +999 A) was degraded faster than mRNA corresponding to the major haplotype (exon 4 +1340 A, +1307 A, +999 T), and allelic mRNA expression of the disease susceptibility allele was significantly lower than that of the major allele in normal kidney tissues. In an experiment using a short interfering RNA targeting NCALD, we found that silencing of the NCALD led to a considerable enhancement of cell migration, accompanied by a significant reduction in E-cadherin expression, and by an elevation of alpha smooth muscle actin expression in cultured renal proximal tubular epithelial cells. We also identified the association of the landmark SNP with the progression of diabetic nephropathy in a 8-year prospective study (A vs. G, P = 0.03, odds ratio = 1.91, 95% CI 1.07-3.42). These results suggest that the NCALD gene is a likely candidate for conferring susceptibility to diabetic nephropathy.
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Affiliation(s)
- Masumi Kamiyama
- Laboratory for Diabetic Nephropathy, SNP Research Centre, Institute of Physical and Chemical Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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18
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Veney SL, Peabody C, Smith GW, Wade J. Sexually dimorphic neurocalcin expression in the developing zebra finch telencephalon. JOURNAL OF NEUROBIOLOGY 2003; 56:372-86. [PMID: 12918021 DOI: 10.1002/neu.10246] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Differential display RT-PCR was used on RNA isolated from the zebra finch telencephalon to identify gene products potentially involved in its development, including the sexually dimorphic nuclei responsible for song learning and production. A cDNA identified only in juvenile females was cloned and sequenced. It shares homology with neurocalcin, a calcium binding protein. Northern blots indicated three neurocalcin species. A 10.6 kb transcript was present in males and most females throughout development and in adulthood. Smaller 6.2 and 3.3 kb species were detected almost exclusively in females and primarily between posthatching days 18-25. In situ hybridization, using a probe that identified all three mRNA species, indicated a broad distribution in the telencephalon of both sexes, with particularly high levels in the song nucleus RA. Across regions examined, neurocalcin expression was enhanced in females compared to males, probably reflecting the presence of the two smaller transcripts. However, within RA, neurocalcin expression was statistically equivalent between the sexes. These data indicate that calcium signaling via neurocalcin may be involved in telencephalic development, but suggest that sexually dimorphic expression of this gene exists on a level too general to specifically regulate masculine or feminine development of song control regions. Neurocalcin might: broadly influence functional differentiation, including areas that are not morphologically distinct between the sexes; be a benign consequence of general dimorphisms, such as those due to sex chromosomes; or involve a compensatory mechanism, which allows function of the juvenile female telencephalon to equal that of males, despite fundamental physiological differences.
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Affiliation(s)
- Sean L Veney
- Neuroscience Program, Michigan State University, East Lansing, Michigan 48824, USA.
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19
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Huminiecki L, Lloyd AT, Wolfe KH. Congruence of tissue expression profiles from Gene Expression Atlas, SAGEmap and TissueInfo databases. BMC Genomics 2003; 4:31. [PMID: 12885301 PMCID: PMC183867 DOI: 10.1186/1471-2164-4-31] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2003] [Accepted: 07/29/2003] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Extracting biological knowledge from large amounts of gene expression information deposited in public databases is a major challenge of the postgenomic era. Additional insights may be derived by data integration and cross-platform comparisons of expression profiles. However, database meta-analysis is complicated by differences in experimental technologies, data post-processing, database formats, and inconsistent gene and sample annotation. RESULTS We have analysed expression profiles from three public databases: Gene Expression Atlas, SAGEmap and TissueInfo. These are repositories of oligonucleotide microarray, Serial Analysis of Gene Expression and Expressed Sequence Tag human gene expression data respectively. We devised a method, Preferential Expression Measure, to identify genes that are significantly over- or under-expressed in any given tissue. We examined intra- and inter-database consistency of Preferential Expression Measures. There was good correlation between replicate experiments of oligonucleotide microarray data, but there was less coherence in expression profiles as measured by Serial Analysis of Gene Expression and Expressed Sequence Tag counts. We investigated inter-database correlations for six tissue categories, for which data were present in the three databases. Significant positive correlations were found for brain, prostate and vascular endothelium but not for ovary, kidney, and pancreas. CONCLUSION We show that data from Gene Expression Atlas, SAGEmap and TissueInfo can be integrated using the UniGene gene index, and that expression profiles correlate relatively well when large numbers of tags are available or when tissue cellular composition is simple. Finally, in the case of brain, we demonstrate that when PEM values show good correlation, predictions of tissue-specific expression based on integrated data are very accurate.
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Affiliation(s)
- Lukasz Huminiecki
- Department of Genetics, Smurfit Institute, University of Dublin Trinity College, Dublin 2, Ireland
| | - Andrew T Lloyd
- Department of Genetics, Smurfit Institute, University of Dublin Trinity College, Dublin 2, Ireland
| | - Kenneth H Wolfe
- Department of Genetics, Smurfit Institute, University of Dublin Trinity College, Dublin 2, Ireland
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Spilker C, Gundelfinger ED, Braunewell KH. Evidence for different functional properties of the neuronal calcium sensor proteins VILIP-1 and VILIP-3: from subcellular localization to cellular function. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1600:118-27. [PMID: 12445467 DOI: 10.1016/s1570-9639(02)00452-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The visinin-like-proteins VILIP-1 and -3 are EF-hand calcium-binding proteins and belong to the family of neuronal calcium sensor (NCS) proteins. Members of this family are involved in the calcium-dependent regulation of signal transduction cascades mainly in the nervous system. VILIP-1 and VILIP-3 are expressed in different populations of neuronal cells. To gain insights into the different functional characteristics of VILIP-1 and -3, we have compared the localization of the proteins in intact cells and the calcium-dependent membrane association in subcellular fractions. Furthermore, we have investigated the different functional properties of the two proteins in activating cGMP signal pathways and have defined different sets of protein interaction partners. Our data indicate that VILIP-3, which is mainly expressed in Purkinje cells, and VILIP-1, which is expressed in granule cells in the cerebellum, show a different calcium-dependent subcellular localization, may activate different cellular signaling pathways, and thus have signaling functions which seem to be cell-type specific.
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Affiliation(s)
- C Spilker
- Signal Transduction Research Group, Leibniz Institute for Neurobiology, Germany
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