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Chiarella E. Exploring the contribution of Zfp521/ZNF521 on primary hematopoietic stem/progenitor cells and leukemia progression. Cell Tissue Res 2024; 398:161-173. [PMID: 39436449 PMCID: PMC11614986 DOI: 10.1007/s00441-024-03926-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Accepted: 10/08/2024] [Indexed: 10/23/2024]
Abstract
Hematopoietic stem cells (HSCs) drive cellular turnover in the hematopoietic system by balancing self-renewal and differentiation. In the adult bone marrow (BM), these cells are regulated by a complex cellular microenvironment known as "niche," which involves dynamic interactions between diverse cellular and non-cellular elements. During blood cell maturation, lineage branching is guided by clusters of genes that interact or counteract each other, forming complex networks of lineage-specific transcription factors. Disruptions in these networks can lead to obstacles in differentiation, lineage reprogramming, and ultimately malignant transformation, including acute myeloid leukemia (AML). Zinc Finger Protein 521 (Znf521/Zfp521), a conserved transcription factor enriched in HSCs in both human and murine hematopoiesis, plays a pivotal role in regulating HSC self-renewal and differentiation. Its enforced expression preserves progenitor cell activity, while inhibition promotes differentiation toward the lymphoid and myeloid lineages. Transcriptomic analysis of human AML patient samples has revealed upregulation of ZNF521 in AMLs with the t(9;11) fusion gene MLL-AF9. In vitro studies have shown that ZNF521 collaborates with MLL-AF9 to enhance the growth of transformed leukemic cells, increase colony formation, and activate MLL target genes. Conversely, inhibition of ZNF521 using short-hairpin RNA (shRNA) results in decreased leukemia proliferation, reduced colony formation, and induction of cell cycle arrest in MLL-rearranged AML cell lines. In vivo experiments have demonstrated that mZFP521-deficient mice transduced with MLL-AF9 experience a delay in leukemia development. This review provides an overview of the regulatory network involving ZNF521, which plays a crucial role in controlling both HSC self-renewal and differentiation pathways. Furthermore, we examine the impact of ZNF521 on the leukemic phenotype and consider it a potential marker for MLL-AF9+ AML.
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Affiliation(s)
- Emanuela Chiarella
- Laboratory of Molecular Haematopoiesis and Stem Cell Biology, Department of Experimental and Clinical Medicine, University "Magna Græcia", 88100, Catanzaro, Italy.
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Alur V, Vastrad B, Raju V, Vastrad C, Kotturshetti S. The identification of key genes and pathways in polycystic ovary syndrome by bioinformatics analysis of next-generation sequencing data. MIDDLE EAST FERTILITY SOCIETY JOURNAL 2024; 29:53. [DOI: 10.1186/s43043-024-00212-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Accepted: 11/17/2024] [Indexed: 01/02/2025] Open
Abstract
Abstract
Background
Polycystic ovary syndrome (PCOS) is a reproductive endocrine disorder. The specific molecular mechanism of PCOS remains unclear. The aim of this study was to apply a bioinformatics approach to reveal related pathways or genes involved in the development of PCOS.
Methods
The next-generation sequencing (NGS) dataset GSE199225 was downloaded from the gene expression omnibus (GEO) database and NGS dataset analyzed is obtained from in vitro culture of PCOS patients’ muscle cells and muscle cells of healthy lean control women. Differentially expressed gene (DEG) analysis was performed using DESeq2. The g:Profiler was utilized to analyze the gene ontology (GO) and REACTOME pathways of the differentially expressed genes. A protein–protein interaction (PPI) network was constructed and module analysis was performed using HiPPIE and cytoscape. The miRNA-hub gene regulatory network and TF-hub gene regulatory network were constructed. The hub genes were validated by using receiver operating characteristic (ROC) curve analysis.
Results
We have identified 957 DEG in total, including 478 upregulated genes and 479 downregulated gene. GO terms and REACTOME pathways illustrated that DEG were significantly enriched in regulation of molecular function, developmental process, interferon signaling and platelet activation, signaling, and aggregation. The top 5 upregulated hub genes including HSPA5, PLK1, RIN3, DBN1, and CCDC85B and top 5 downregulated hub genes including DISC1, AR, MTUS2, LYN, and TCF4 might be associated with PCOS. The hub gens of HSPA5 and KMT2A, together with corresponding predicted miRNAs (e.g., hsa-mir-34b-5p and hsa-mir-378a-5p), and HSPA5 and TCF4 together with corresponding predicted TF (e.g., RCOR3 and TEAD4) were found to be significantly correlated with PCOS.
Conclusions
These study uses of bioinformatics analysis of NGS data to obtain hub genes and key signaling pathways related to PCOS and its associated complications. Also provides novel ideas for finding biomarkers and treatment methods for PCOS and its associated complications.
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Lee SY, Park JL, Kim K, Bae JS, Kim JY, Kim SY, Jung CK. Identification of NIFTP-Specific mRNA Markers for Reliable Molecular Diagnosis of Thyroid Tumors. Endocr Pathol 2023; 34:311-322. [PMID: 37658903 PMCID: PMC10511606 DOI: 10.1007/s12022-023-09781-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/03/2023] [Indexed: 09/05/2023]
Abstract
Non-invasive follicular thyroid neoplasm with papillary-like nuclear features (NIFTP) is a low-risk thyroid tumor with a favorable prognosis. Nonetheless, differentiating NIFTP from other thyroid tumors remains challenging, necessitating reliable diagnostic markers. This study is aimed at discovering NIFTP-specific mRNA markers through RNA sequencing analysis of thyroid tumor tissues. We performed mRNA expression profiling for 74 fresh frozen thyroid tissue samples, including NIFTP and benign and malignant follicular-cell-derived tumors. NIFTP/malignant tumors showed 255 downregulated genes and 737 upregulated genes compared to benign tumors. Venn diagram analysis revealed 19 significantly upregulated and 7 downregulated mRNAs in NIFTP. Akaike information criterion analysis allowed us to select OCLN, ZNF423, LYG1, and AQP5 mRNA markers. We subsequently developed a predictive model based on logistic regression analysis using these four mRNAs, which we validated in independent samples (n = 90) using a qRT-PCR assay. This model demonstrated high accuracy in predicting NIFTP in discovery dataset (AUC (area under the receiver operating characteristic) = 0.960) and the validation dataset (AUC = 0.757). Our results suggest that OCLN, ZNF423, LYG1, and AQP5 mRNA markers might serve as reliable molecular markers for identifying NIFTP among other thyroid tumors, ultimately aiding in accurate diagnosis and management of NIFTP patients.
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Affiliation(s)
- So-Yeon Lee
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, 34141 Daejeon, Korea
- Graduate School of New Drug Discovery and Development, Chungnam National University, Daejeon, 34134 Korea
| | - Jong-Lyul Park
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, 34141 Daejeon, Korea
| | - Kwangsoon Kim
- Department of Surgery, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Ja Seong Bae
- Department of Surgery, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jae-Yoon Kim
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, 34141 Daejeon, Korea
| | - Seon-Young Kim
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, 34141 Daejeon, Korea
| | - Chan Kwon Jung
- Department of Hospital Pathology, College of Medicine, The Catholic University of Korea, Seoul, Korea
- College of Medicine, Cancer Research Institute, The Catholic University of Korea, Seoul, Korea
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Zhang J, Guo F, Li C, Wang Y, Wang J, Sun F, Zhou Y, Ma F, Zhang B, Qian H. Loss of TTC17 promotes breast cancer metastasis through RAP1/CDC42 signaling and sensitizes it to rapamycin and paclitaxel. Cell Biosci 2023; 13:50. [PMID: 36895029 PMCID: PMC9996991 DOI: 10.1186/s13578-023-01004-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 03/03/2023] [Indexed: 03/11/2023] Open
Abstract
BACKGROUND Breast cancer (BC) metastasis is the leading cause of poor prognosis and therapeutic failure. However, the mechanisms underlying cancer metastasis are far from clear. METHODS We screened candidate genes related to metastasis through genome-wide CRISPR screening and high-throughput sequencing of patients with metastatic BC, followed by a panel of metastatic model assays. The effects of tetratricopeptide repeat domain 17 (TTC17) on migration, invasion, and colony formation ability together with the responses to anticancer drugs were investigated in vitro and in vivo. The mechanism mediated by TTC17 was determined by RNA sequencing, Western blotting, immunohistochemistry, and immunofluorescence. The clinical significance of TTC17 was evaluated using BC tissue samples combined with clinicopathological data. RESULTS We identified the loss of TTC17 as a metastasis driver in BC, and its expression was negatively correlated with malignancy and positively correlated with patient prognosis. TTC17 loss in BC cells promoted their migration, invasion, and colony formation capacity in vitro and lung metastasis in vivo. Conversely, overexpressing TTC17 suppressed these aggressive phenotypes. Mechanistically, TTC17 knockdown in BC cells resulted in the activation of the RAP1/CDC42 pathway along with a disordered cytoskeleton in BC cells, and pharmacological blockade of CDC42 abolished the potentiation of motility and invasiveness caused by TTC17 silencing. Research on BC specimens demonstrated reduced TTC17 and increased CDC42 in metastatic tumors and lymph nodes, and low TTC17 expression was linked to more aggressive clinicopathologic characteristics. Through screening the anticancer drug library, the CDC42 inhibitor rapamycin and the microtubule-stabilizing drug paclitaxel showed stronger inhibition of TTC17-silenced BC cells, which was confirmed by more favorable efficacy in BC patients and tumor-bearing mice receiving rapamycin or paclitaxel in the TTC17Low arm. CONCLUSIONS TTC17 loss is a novel factor promoting BC metastasis, that enhances migration and invasion by activating RAP1/CDC42 signaling and sensitizes BC to rapamycin and paclitaxel, which may improve stratified treatment strategies under the concept of molecular phenotyping-based precision therapy of BC.
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Affiliation(s)
- Jingyao Zhang
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Fengzhu Guo
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.,Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Chunxiao Li
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.,Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Yang Wang
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Jinsong Wang
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Fangzhou Sun
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Yantong Zhou
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Fei Ma
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China. .,Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - Bailin Zhang
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - Haili Qian
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
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Linders DGJ, Bijlstra OD, Fallert LC, Hilling DE, Walker E, Straight B, March TL, Valentijn ARPM, Pool M, Burggraaf J, Basilion JP, Vahrmeijer AL, Kuppen PJK. Cysteine Cathepsins in Breast Cancer: Promising Targets for Fluorescence-Guided Surgery. Mol Imaging Biol 2023; 25:58-73. [PMID: 36002710 PMCID: PMC9971096 DOI: 10.1007/s11307-022-01768-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/10/2022] [Accepted: 08/12/2022] [Indexed: 12/24/2022]
Abstract
The majority of breast cancer patients is treated with breast-conserving surgery (BCS) combined with adjuvant radiation therapy. Up to 40% of patients has a tumor-positive resection margin after BCS, which necessitates re-resection or additional boost radiation. Cathepsin-targeted near-infrared fluorescence imaging during BCS could be used to detect residual cancer in the surgical cavity and guide additional resection, thereby preventing tumor-positive resection margins and associated mutilating treatments. The cysteine cathepsins are a family of proteases that play a major role in normal cellular physiology and neoplastic transformation. In breast cancer, the increased enzymatic activity and aberrant localization of many of the cysteine cathepsins drive tumor progression, proliferation, invasion, and metastasis. The upregulation of cysteine cathepsins in breast cancer cells indicates their potential as a target for intraoperative fluorescence imaging. This review provides a summary of the current knowledge on the role and expression of the most important cysteine cathepsins in breast cancer to better understand their potential as a target for fluorescence-guided surgery (FGS). In addition, it gives an overview of the cathepsin-targeted fluorescent probes that have been investigated preclinically and in breast cancer patients. The current review underscores that cysteine cathepsins are highly suitable molecular targets for FGS because of favorable expression and activity patterns in virtually all breast cancer subtypes. This is confirmed by cathepsin-targeted fluorescent probes that have been shown to facilitate in vivo breast cancer visualization and tumor resection in mouse models and breast cancer patients. These findings indicate that cathepsin-targeted FGS has potential to improve treatment outcomes in breast cancer patients.
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Affiliation(s)
- Daan G. J. Linders
- Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Okker D. Bijlstra
- Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Laura C. Fallert
- Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Denise E. Hilling
- Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Ethan Walker
- Department of Biomedical Engineering, Case School of Engineering, Case Western Reserve University, Cleveland, OH 44106 USA
| | | | - Taryn L. March
- Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - A. Rob P. M. Valentijn
- Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
- Department of Clinical Pharmacy and Toxicology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Martin Pool
- Department of Clinical Pharmacy and Toxicology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Jacobus Burggraaf
- Centre for Human Drug Research, 2333 CL Leiden, The Netherlands
- Leiden Academic Center for Drug Research, 2333 AL Leiden, The Netherlands
| | - James P. Basilion
- Department of Biomedical Engineering, Case School of Engineering, Case Western Reserve University, Cleveland, OH 44106 USA
- Department of Radiology, Case School of Medicine, Case Western Reserve University, Cleveland, OH 44106 USA
| | | | - Peter J. K. Kuppen
- Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
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Poojari A, Dev K, Rabiee A. Lipedema: Insights into Morphology, Pathophysiology, and Challenges. Biomedicines 2022; 10:biomedicines10123081. [PMID: 36551837 PMCID: PMC9775665 DOI: 10.3390/biomedicines10123081] [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: 10/26/2022] [Revised: 11/26/2022] [Accepted: 11/28/2022] [Indexed: 12/02/2022] Open
Abstract
Lipedema is an adipofascial disorder that almost exclusively affects women. Lipedema leads to chronic pain, swelling, and other discomforts due to the bilateral and asymmetrical expansion of subcutaneous adipose tissue. Although various distinctive morphological characteristics, such as the hyperproliferation of fat cells, fibrosis, and inflammation, have been characterized in the progression of lipedema, the mechanisms underlying these changes have not yet been fully investigated. In addition, it is challenging to reduce the excessive fat in lipedema patients using conventional weight-loss techniques, such as lifestyle (diet and exercise) changes, bariatric surgery, and pharmacological interventions. Therefore, lipedema patients also go through additional psychosocial distress in the absence of permanent treatment. Research to understand the pathology of lipedema is still in its infancy, but promising markers derived from exosome, cytokine, lipidomic, and metabolomic profiling studies suggest a condition distinct from obesity and lymphedema. Although genetics seems to be a substantial cause of lipedema, due to the small number of patients involved in such studies, the extrapolation of data at a broader scale is challenging. With the current lack of etiology-guided treatments for lipedema, the discovery of new promising biomarkers could provide potential solutions to combat this complex disease. This review aims to address the morphological phenotype of lipedema fat, as well as its unclear pathophysiology, with a primary emphasis on excessive interstitial fluid, extracellular matrix remodeling, and lymphatic and vasculature dysfunction. The potential mechanisms, genetic implications, and proposed biomarkers for lipedema are further discussed in detail. Finally, we mention the challenges related to lipedema and emphasize the prospects of technological interventions to benefit the lipedema community in the future.
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Nurlaila I, Roh K, Yeom CH, Kang H, Lee S. Acquired lymphedema: Molecular contributors and future directions for developing intervention strategies. Front Pharmacol 2022; 13:873650. [PMID: 36386144 PMCID: PMC9640931 DOI: 10.3389/fphar.2022.873650] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 10/13/2022] [Indexed: 08/05/2023] Open
Abstract
Lymphedema is a debilitating chronic disease that mostly develops as an adverse reaction to cancer treatment modalities such as chemotherapy, surgery, and radiotherapy. Lymphedema also appears to be a deteriorating consequence of roundworm infections, as best represented by filariasis. According to its origin, lymphedema is classified as primary lymphedema and acquired lymphedema. The latter is an acquired condition that, hitherto, received a considerably low attention owing to the less number of fatal cases been reported. Notably, despite the low mortality rate in lymphedema, it has been widely reported to reduce the disease-free survival and thus the quality of life of affected patients. Hence, in this review, we focused on acquired lymphedema and orchestration of molecular interplays associated with either stimulation or inhibition of lymphedema development that were, in vast majority, clearly depicted in animal models with their specific and distinct technical approaches. We also discussed some recent progress made in phytochemical-based anti-lymphedema intervention strategies and the specific mechanisms underlying their anti-lymphedema properties. This review is crucial to understand not only the comprehensive aspects of the disease but also the future directions of the intervention strategies that can address the quality of life of affected patients rather than alleviating apparent symptoms only.
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Affiliation(s)
- Ika Nurlaila
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, South Korea
- Department of Vaccine and Drugs, The National Research and Innovation Agency, Jakarta, Indonesia
| | - Kangsan Roh
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
- Division of Cardiology and Corrigan Minehan Heart Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | | | - Hee Kang
- Humanitas College, Kyung Hee University, Yongin, South Korea
| | - Sukchan Lee
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, South Korea
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Nishi K, Fu W, Kiyama R. Novel estrogen-responsive genes (ERGs) for the evaluation of estrogenic activity. PLoS One 2022; 17:e0273164. [PMID: 35976950 PMCID: PMC9385026 DOI: 10.1371/journal.pone.0273164] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/03/2022] [Indexed: 11/19/2022] Open
Abstract
Estrogen action is mediated by various genes, including estrogen-responsive genes (ERGs). ERGs have been used as reporter-genes and markers for gene expression. Gene expression profiling using a set of ERGs has been used to examine statistically reliable transcriptomic assays such as DNA microarray assays and RNA sequencing (RNA-seq). However, the quality of ERGs has not been extensively examined. Here, we obtained a set of 300 ERGs that were newly identified by six sets of RNA-seq data from estrogen-treated and control human breast cancer MCF-7 cells. The ERGs exhibited statistical stability, which was based on the coefficient of variation (CV) analysis, correlation analysis, and examination of the functional association with estrogen action using database searches. A set of the top 30 genes based on CV ranking were further evaluated quantitatively by RT-PCR and qualitatively by a functional analysis using the GO and KEGG databases and by a mechanistic analysis to classify ERα/β-dependent or ER-independent types of transcriptional regulation. The 30 ERGs were characterized according to (1) the enzymes, such as metabolic enzymes, proteases, and protein kinases, (2) the genes with specific cell functions, such as cell-signaling mediators, tumor-suppressors, and the roles in breast cancer, (3) the association with transcriptional regulation, and (4) estrogen-responsiveness. Therefore, the ERGs identified here represent various cell functions and cell signaling pathways, including estrogen signaling, and thus, may be useful to evaluate estrogenic activity.
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Affiliation(s)
- Kentaro Nishi
- Department of Life Science, Faculty of Life Science, Kyushu Sangyo University Matsukadai, Higashi-ku, Fukuoka, Japan
| | - Wenqiang Fu
- Department of Life Science, Faculty of Life Science, Kyushu Sangyo University Matsukadai, Higashi-ku, Fukuoka, Japan
| | - Ryoiti Kiyama
- Department of Life Science, Faculty of Life Science, Kyushu Sangyo University Matsukadai, Higashi-ku, Fukuoka, Japan
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Sivadas A, Kok VC, Ng KL. Multi-omics analyses provide novel biological insights to distinguish lobular ductal types of invasive breast cancers. Breast Cancer Res Treat 2022; 193:361-379. [PMID: 35348974 DOI: 10.1007/s10549-022-06567-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 03/12/2022] [Indexed: 02/07/2023]
Abstract
BACKGROUND Invasive lobular carcinoma (ILC) treatment is similar to invasive ductal carcinoma (IDC; now invasive carcinoma-no special type, IBC-NST), based on its intrinsic subtype. However, further investigation is required for an integrative understanding of differentially perturbed molecular patterns and pathways in these histotypes. METHODS A dataset of 780 IDC and 201 ILC samples from the TCGA-BRCA project for cross-platform multi-omics was analyzed. We leveraged a consensus approach integrating different bioinformatic algorithms to analyze mutations, CNAs, mRNA, miRNA abundance, methylation, and protein abundance to understand the complex crosstalks that distinguish ILC and IDC samples. A histotype-matched comparison was performed. We performed Cox survival analyses for prognosis based on our identified 53 histotype-specific and four discordant genes. RESULTS Approximately 90% of ILC cases were of the luminal subtype. Somatic mutations in CDH1 were higher in ILC than in IDC (FDR-adjusted p < 0.01). Fifty-three significant oncogenic or tumor-suppressive DEGs were identified in a single histotype. PPAR signaling and lipolysis regulation in adipocytes were significantly enriched in ILC tumors. CDH1 protein had the highest differential abundance (AUC: 0.85). Moreover, BTG2, GSTA2, GPR37L1, and PGBD5 amplification was associated with poorer OS in ILC compared with no alteration. RIMS2, NACA4P, MYC, ZFPM2, and POU5F1B amplification showed a lower overall survival in patients with IDC. miR-195 showed an IDC-specific downregulation, causing overexpression of CCNE1. Integrative multi-omics supervised analysis identified 296 differentially expressed genes that successfully distinguished IDC and ILC histotypes. CONCLUSIONS Our findings identify novel molecular candidates that potentially drive and modify the disease differentially among these histotypes.
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Affiliation(s)
- Ambily Sivadas
- Division of Nutrition, St. John's Research Institute, St. John's National Academy of Health Sciences, Bangalore, India
| | - Victor C Kok
- Division of Medical Oncology, Kuang Tien General Hospital Cancer Center, 117 Shatien Rd Shalu Dist, Taichung, 43303, Taiwan.
- Department of Bioinformatics and Medical Engineering, Asia University Taiwan, Taichung, 40354, Taiwan.
| | - Ka-Lok Ng
- Department of Bioinformatics and Medical Engineering, Asia University Taiwan, Taichung, 40354, Taiwan
- Department of Medical Research, China Medical University Hospital, China Medical University, Taichung, Taiwan
- Center for Artificial Intelligence and Precision Medicine Research, Asia University, Taichung, 40354, Taiwan
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10
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Wang S, Hu H, Li X. A systematic study of motif pairs that may facilitate enhancer-promoter interactions. J Integr Bioinform 2022; 19:jib-2021-0038. [PMID: 35130376 PMCID: PMC9069648 DOI: 10.1515/jib-2021-0038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 01/20/2022] [Indexed: 01/06/2023] Open
Abstract
Pairs of interacting transcription factors (TFs) have previously been shown to bind to enhancers and promoters and contribute to their physical interactions. However, to date, we have limited knowledge about such TF pairs. To fill this void, we systematically studied the co-occurrence of TF-binding motifs in interacting enhancer-promoter (EP) pairs in seven human cell lines. We discovered 423 motif pairs that significantly co-occur in enhancers and promoters of interacting EP pairs. We demonstrated that these motif pairs are biologically meaningful and significantly enriched with motif pairs of known interacting TF pairs. We also showed that the identified motif pairs facilitated the discovery of the interacting EP pairs. The developed pipeline, EPmotifPair, together with the predicted motifs and motif pairs, is available at https://doi.org/10.6084/m9.figshare.14192000. Our study provides a comprehensive list of motif pairs that may contribute to EP physical interactions, which facilitate generating meaningful hypotheses for experimental validation.
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Affiliation(s)
- Saidi Wang
- Department of Computer Science, University of Central Florida, Orlando, FL, 32816, USA
| | - Haiyan Hu
- Department of Computer Science, University of Central Florida, Orlando, FL, 32816, USA
| | - Xiaoman Li
- Burnett school of Biomedical Science, College of Medicine, University of Central Florida, Orlando, FL, 32816, USA
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11
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Regulatory Role of microRNAs Targeting the Transcription Co-Factor ZNF521 in Normal Tissues and Cancers. Int J Mol Sci 2021; 22:ijms22168461. [PMID: 34445164 PMCID: PMC8395128 DOI: 10.3390/ijms22168461] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 08/02/2021] [Accepted: 08/03/2021] [Indexed: 12/13/2022] Open
Abstract
Powerful bioinformatics tools have provided a wealth of novel miRNA–transcription factor networks crucial in controlling gene regulation. In this review, we focus on the biological functions of miRNAs targeting ZNF521, explaining the molecular mechanisms by which the dysregulation of this axis contributes to malignancy. ZNF521 is a stem cell-associated co-transcription factor implicated in the regulation of hematopoietic, neural, and mesenchymal stem cells. The aberrant expression of ZNF521 transcripts, frequently associated with miRNA deregulation, has been detected in several tumors including pancreatic, hepatocellular, gastric, bladder transitional cell carcinomas as well as in breast and ovarian cancers. miRNA expression profiling tools are currently identifying a multitude of miRNAs, involved together with oncogenes and TFs in the regulation of oncogenesis, including ZNF521, which may be candidates for diagnostic and prognostic biomarkers of cancer.
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12
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Pavanelli AC, Mangone FR, Barros LRC, Machado-Rugolo J, Capelozzi VL, Nagai MA. Abnormal Long Non-Coding RNAs Expression Patterns Have the Potential Ability for Predicting Survival and Treatment Response in Breast Cancer. Genes (Basel) 2021; 12:genes12070996. [PMID: 34209776 PMCID: PMC8305383 DOI: 10.3390/genes12070996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/11/2021] [Accepted: 06/23/2021] [Indexed: 12/09/2022] Open
Abstract
Abnormal long non-coding RNAs (lncRNAs) expression has been documented to have oncogene or tumor suppressor functions in the development and progression of cancer, emerging as promising independent biomarkers for molecular cancer stratification and patients’ prognosis. Examining the relationship between lncRNAs and the survival rates in malignancies creates new scenarios for precision medicine and targeted therapy. Breast cancer (BRCA) is a heterogeneous malignancy. Despite advances in its molecular classification, there are still gaps to explain in its multifaceted presentations and a substantial lack of biomarkers that can better predict patients’ prognosis in response to different therapeutic strategies. Here, we performed a re-analysis of gene expression data generated using cDNA microarrays in a previous study of our group, aiming to identify differentially expressed lncRNAs (DELncRNAs) with a potential predictive value for response to treatment with taxanes in breast cancer patients. Results revealed 157 DELncRNAs (90 up- and 67 down-regulated). We validated these new biomarkers as having prognostic and predictive value for breast cancer using in silico analysis in public databases. Data from TCGA showed that compared to normal tissue, MIAT was up-regulated, while KCNQ1OT1, LOC100270804, and FLJ10038 were down-regulated in breast tumor tissues. KCNQ1OT1, LOC100270804, and FLJ10038 median levels were found to be significantly higher in the luminal subtype. The ROC plotter platform results showed that reduced expression of these three DElncRNAs was associated with breast cancer patients who did not respond to taxane treatment. Kaplan–Meier survival analysis revealed that a lower expression of the selected lncRNAs was significantly associated with worse relapse-free survival (RFS) in breast cancer patients. Further validation of the expression of these DELncRNAs might be helpful to better tailor breast cancer prognosis and treatment.
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Affiliation(s)
- Ana Carolina Pavanelli
- Discipline of Oncology, Department of Radiology and Oncology, Faculty of Medicine, University of São Paulo, São Paulo 01246-903, Brazil; (A.C.P.); (F.R.M.); (L.R.C.B.)
- Center for Translational Research in Oncology, Cancer Institute of São Paulo, São Paulo 01246-903, Brazil
| | - Flavia Rotea Mangone
- Discipline of Oncology, Department of Radiology and Oncology, Faculty of Medicine, University of São Paulo, São Paulo 01246-903, Brazil; (A.C.P.); (F.R.M.); (L.R.C.B.)
- Center for Translational Research in Oncology, Cancer Institute of São Paulo, São Paulo 01246-903, Brazil
| | - Luciana R. C. Barros
- Discipline of Oncology, Department of Radiology and Oncology, Faculty of Medicine, University of São Paulo, São Paulo 01246-903, Brazil; (A.C.P.); (F.R.M.); (L.R.C.B.)
- Center for Translational Research in Oncology, Cancer Institute of São Paulo, São Paulo 01246-903, Brazil
| | - Juliana Machado-Rugolo
- Department of Pathology, University of São Paulo Medical School (USP), São Paulo 01246-903, Brazil; (J.M.-R.); (V.L.C.)
- Health Technology Assessment Center (NATS), Clinical Hospital (HCFMB), Medical School of São Paulo State University (UNESP), Botucatu, São Paulo 01246-903, Brazil
| | - Vera L. Capelozzi
- Department of Pathology, University of São Paulo Medical School (USP), São Paulo 01246-903, Brazil; (J.M.-R.); (V.L.C.)
| | - Maria A. Nagai
- Discipline of Oncology, Department of Radiology and Oncology, Faculty of Medicine, University of São Paulo, São Paulo 01246-903, Brazil; (A.C.P.); (F.R.M.); (L.R.C.B.)
- Center for Translational Research in Oncology, Cancer Institute of São Paulo, São Paulo 01246-903, Brazil
- Correspondence:
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13
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Chiarella E, Lombardo N, Lobello N, Aloisio A, Aragona T, Pelaia C, Scicchitano S, Bond HM, Mesuraca M. Nasal Polyposis: Insights in Epithelial-Mesenchymal Transition and Differentiation of Polyp Mesenchymal Stem Cells. Int J Mol Sci 2020; 21:E6878. [PMID: 32961745 PMCID: PMC7555226 DOI: 10.3390/ijms21186878] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/11/2020] [Accepted: 09/17/2020] [Indexed: 12/17/2022] Open
Abstract
Chronic rhinosinusitis is a common inflammatory disease of paranasal sinuses, which causes rhinorrhea, nasal congestion, and hyposmia. The genetic predisposition or the exposure to irritants can sustain the inflammatory response and the development of nasal polyposis. Nasal polyps are benign and teardrop-shaped growths that project in the nasal cavities, and originate from the ethmoid sinuses. This inflammatory process is associated with high expression of IL-4, IL-5 and IL-13 and IgE. Antibodies targeting these cytokines or receptors represent a therapeutic strategy in the treatment of nasal polyposis in combination with corticosteroids. The molecular pathogenesis of nasal polyps in chronic rhinosinusitis (CRS) patients is associated with remodeling transition, a process in which epithelial cells lose their typical phenotype, acquiring a mesenchymal-like aspect. TGFβ/SMAD, ERK, and Wnt/β-catenin pathways are altered during the nasal tissue remodeling. miRNA and inhibitor molecules targeting these signaling pathways are able to interfere with the process; which could lead to alternative therapies. Nasal polyps are an alternative source of mesenchymal stem cells, which can be isolated from surgical biopsies. A molecular understanding of the biology of PO-MSCs will contribute to the delineating inflammatory process underlying the development of nasal polyps.
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Affiliation(s)
- Emanuela Chiarella
- Laboratory of Molecular Haematopoiesis and Stem Cell Biology, Department of Experimental and Clinical Medicine, University “Magna Græcia”, 88100 Catanzaro, Italy; (E.C.); (A.A.); (S.S.)
| | - Nicola Lombardo
- Otolaryngology Head and Neck Surgery, Department Medical and Surgical Sciences, University “Magna Græcia”, 88100 Catanzaro, Italy; (N.L.); (N.L.)
| | - Nadia Lobello
- Otolaryngology Head and Neck Surgery, Department Medical and Surgical Sciences, University “Magna Græcia”, 88100 Catanzaro, Italy; (N.L.); (N.L.)
| | - Annamaria Aloisio
- Laboratory of Molecular Haematopoiesis and Stem Cell Biology, Department of Experimental and Clinical Medicine, University “Magna Græcia”, 88100 Catanzaro, Italy; (E.C.); (A.A.); (S.S.)
| | - Teodoro Aragona
- Otolaryngology, A.O.U. Ospedali Riuniti, 60123 Ancona, Italy;
| | - Corrado Pelaia
- Department of Health Sciences, University “Magna Græcia” of Catanzaro, 88100 Catanzaro, Italy;
| | - Stefania Scicchitano
- Laboratory of Molecular Haematopoiesis and Stem Cell Biology, Department of Experimental and Clinical Medicine, University “Magna Græcia”, 88100 Catanzaro, Italy; (E.C.); (A.A.); (S.S.)
| | - Heather Mandy Bond
- Laboratory of Molecular Haematopoiesis and Stem Cell Biology, Department of Experimental and Clinical Medicine, University “Magna Græcia”, 88100 Catanzaro, Italy; (E.C.); (A.A.); (S.S.)
| | - Maria Mesuraca
- Laboratory of Molecular Haematopoiesis and Stem Cell Biology, Department of Experimental and Clinical Medicine, University “Magna Græcia”, 88100 Catanzaro, Italy; (E.C.); (A.A.); (S.S.)
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14
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Milutin Gašperov N, Sabol I, Božinović K, Dediol E, Mravak-Stipetić M, Licastro D, Dal Monego S, Grce M. DNA Methylome Distinguishes Head and Neck Cancer from Potentially Malignant Oral Lesions and Healthy Oral Mucosa. Int J Mol Sci 2020; 21:ijms21186853. [PMID: 32961999 PMCID: PMC7554960 DOI: 10.3390/ijms21186853] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/14/2020] [Accepted: 09/15/2020] [Indexed: 12/15/2022] Open
Abstract
There is a strong need to find new, good biomarkers of head and neck squamous cell carcinoma (HNSCC) because of the bad prognoses and high mortality rates. The aim of this study was to identify the potential biomarkers in HNSCC that have differences in their DNA methylome and potentially premalignant oral lesions, in comparison to healthy oral mucosa. In this study, 32 oral samples were tested: nine healthy oral mucosae, 13 HNSCC, and 10 oral lesions for DNA methylation by the Infinium MethylationEPIC BeadChip. Our findings showed that a panel of genes significantly hypermethylated in their promoters or specific sites in HNSCC samples in comparison to healthy oral samples, which are mainly oncogenes, receptor, and transcription factor genes, or genes included in cell cycle, transformation, apoptosis, and autophagy. A group of hypomethylated genes in HNSCC, in comparison to healthy oral mucosa, are mainly involved in the host immune response and transcriptional regulation. The results also showed significant differences in gene methylation between HNSCC and potentially premalignant oral lesions, as well as differently methylated genes that discriminate between oral lesions and healthy mucosa. The given methylation panels point to novel potential biomarkers for early diagnostics of HNSCC, as well as potentially premalignant oral lesions.
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Affiliation(s)
- Nina Milutin Gašperov
- Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (I.S.); (K.B.)
- Correspondence: (N.M.G.); (M.G.)
| | - Ivan Sabol
- Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (I.S.); (K.B.)
| | - Ksenija Božinović
- Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (I.S.); (K.B.)
| | - Emil Dediol
- Department of Maxillofacial Surgery, School of Medicine, Clinical Hospital Dubrava, University of Zagreb, 10000 Zagreb, Croatia;
| | - Marinka Mravak-Stipetić
- Department of Oral Medicine, School of Dental Medicine, University of Zagreb, 10000 Zagreb, Croatia;
| | - Danilo Licastro
- ARGO Open Lab Platform for Genome sequencing, AREA Science Park, Padriciano, 99, 34149 Trieste, Italy; (D.L.); (S.D.M.)
| | - Simeone Dal Monego
- ARGO Open Lab Platform for Genome sequencing, AREA Science Park, Padriciano, 99, 34149 Trieste, Italy; (D.L.); (S.D.M.)
| | - Magdalena Grce
- Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (I.S.); (K.B.)
- Correspondence: (N.M.G.); (M.G.)
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15
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Scicchitano S, Giordano M, Lucchino V, Montalcini Y, Chiarella E, Aloisio A, Codispoti B, Zoppoli P, Melocchi V, Bianchi F, De Smaele E, Mesuraca M, Morrone G, Bond HM. The stem cell-associated transcription co-factor, ZNF521, interacts with GLI1 and GLI2 and enhances the activity of the Sonic hedgehog pathway. Cell Death Dis 2019; 10:715. [PMID: 31558698 PMCID: PMC6763495 DOI: 10.1038/s41419-019-1946-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 08/17/2019] [Accepted: 08/29/2019] [Indexed: 01/18/2023]
Abstract
ZNF521 is a transcription co-factor with recognized regulatory functions in haematopoietic, osteo-adipogenic and neural progenitor cells. Among its diverse activities, ZNF521 has been implicated in the regulation of medulloblastoma (MB) cells, where the Hedgehog (HH) pathway, has a key role in the development of normal cerebellum and of a substantial fraction of MBs. Here a functional cross-talk is shown for ZNF521 with the HH pathway, where it interacts with GLI1 and GLI2, the major HH transcriptional effectors and enhances the activity of HH signalling. In particular, ZNF521 cooperates with GLI1 and GLI2 in the transcriptional activation of GLI (glioma-associated transcription factor)-responsive promoters. This synergism is dependent on the presence of the N-terminal, NuRD-binding motif in ZNF521, and is sensitive to HDAC (histone deacetylase) and GLI inhibitors. Taken together, these results highlight the role of ZNF521, and its interaction with the NuRD complex, in determining the HH response at the level of transcription. This may be of particular relevance in HH-driven diseases, especially regarding the MBs belonging to the SHH (sonic HH) subgroup where a high expression of ZNF521 is correlated with that of HH pathway components.
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Affiliation(s)
- Stefania Scicchitano
- Laboratory of Molecular Haematopoiesis and Stem Cell Biology, Department of Experimental and Clinical Medicine, University Magna Græcia, 88100, Catanzaro, Italy
| | - Marco Giordano
- Unit of Gynecological Oncology Research, European Institute of Oncology IRCCS, Via G. Ripamonti 435, 20141, Milano, Italy
| | - Valeria Lucchino
- Laboratory of Molecular Haematopoiesis and Stem Cell Biology, Department of Experimental and Clinical Medicine, University Magna Græcia, 88100, Catanzaro, Italy.,German Center for Neurodegenerative Diseases (DZNE), 53127, Bonn, Germany
| | - Ylenia Montalcini
- Laboratory of Molecular Haematopoiesis and Stem Cell Biology, Department of Experimental and Clinical Medicine, University Magna Græcia, 88100, Catanzaro, Italy
| | - Emanuela Chiarella
- Laboratory of Molecular Haematopoiesis and Stem Cell Biology, Department of Experimental and Clinical Medicine, University Magna Græcia, 88100, Catanzaro, Italy
| | - Annamaria Aloisio
- Laboratory of Molecular Haematopoiesis and Stem Cell Biology, Department of Experimental and Clinical Medicine, University Magna Græcia, 88100, Catanzaro, Italy
| | - Bruna Codispoti
- Tecnologica Research Institute-Marrelli Hospital, 88900, Crotone, Italy
| | - Pietro Zoppoli
- Laboratory of Pre-clinical and Translational Research, IRCCS-CROB, Referral Cancer Center of Basilicata, Rionero in Vulture, Italy
| | - Valentina Melocchi
- Fondazione IRCCS - Casa Sollievo della Sofferenza, Laboratory of Cancer Biomarkers, San Giovanni Rotondo, 71013, (FG), Italy
| | - Fabrizio Bianchi
- Fondazione IRCCS - Casa Sollievo della Sofferenza, Laboratory of Cancer Biomarkers, San Giovanni Rotondo, 71013, (FG), Italy
| | - Enrico De Smaele
- Department of Experimental Medicine, University La Sapienza, 00161, Rome, Italy
| | - Maria Mesuraca
- Laboratory of Molecular Haematopoiesis and Stem Cell Biology, Department of Experimental and Clinical Medicine, University Magna Græcia, 88100, Catanzaro, Italy.
| | - Giovanni Morrone
- Laboratory of Molecular Haematopoiesis and Stem Cell Biology, Department of Experimental and Clinical Medicine, University Magna Græcia, 88100, Catanzaro, Italy
| | - Heather M Bond
- Laboratory of Molecular Haematopoiesis and Stem Cell Biology, Department of Experimental and Clinical Medicine, University Magna Græcia, 88100, Catanzaro, Italy.
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16
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Baker E, Sims R, Leonenko G, Frizzati A, Harwood JC, Grozeva D, Morgan K, Passmore P, Holmes C, Powell J, Brayne C, Gill M, Mead S, Bossù P, Spalletta G, Goate AM, Cruchaga C, Maier W, Heun R, Jessen F, Peters O, Dichgans M, FröLich L, Ramirez A, Jones L, Hardy J, Ivanov D, Hill M, Holmans P, Allen ND, Morgan BP, Seshadri S, Schellenberg GD, Amouyel P, Williams J, Escott-Price V. Gene-based analysis in HRC imputed genome wide association data identifies three novel genes for Alzheimer's disease. PLoS One 2019; 14:e0218111. [PMID: 31283791 PMCID: PMC6613773 DOI: 10.1371/journal.pone.0218111] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 05/27/2019] [Indexed: 12/17/2022] Open
Abstract
Late onset Alzheimer's disease is the most common form of dementia for which about 30 susceptibility loci have been reported. The aim of the current study is to identify novel genes associated with Alzheimer's disease using the largest up-to-date reference single nucleotide polymorphism (SNP) panel, the most accurate imputation software and a novel gene-based analysis approach which tests for patterns of association within genes, in the powerful genome-wide association dataset of the International Genomics of Alzheimer's Project Consortium, comprising over 7 million genotypes from 17,008 Alzheimer's cases and 37,154 controls. In addition to earlier reported genes, we detected three novel gene-wide significant loci PPARGC1A (p = 2.2 × 10-6), RORA (p = 7.4 × 10-7) and ZNF423 (p = 2.1 × 10-6). PPARGC1A and RORA are involved in circadian rhythm; circadian disturbances are one of the earliest symptoms of Alzheimer's disease. PPARGC1A is additionally linked to energy metabolism and the generation of amyloid beta plaques. RORA is involved in a variety of functions apart from circadian rhythm, such as cholesterol metabolism and inflammation. The ZNF423 gene resides in an Alzheimer's disease-specific protein network and is likely involved with centrosomes and DNA damage repair.
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Affiliation(s)
- Emily Baker
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, United Kingdom
- UK Dementia Research Institute at Cardiff University, Cardiff, United Kingdom
| | - Rebecca Sims
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, United Kingdom
| | - Ganna Leonenko
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, United Kingdom
| | - Aura Frizzati
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, United Kingdom
| | - Janet C. Harwood
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, United Kingdom
| | - Detelina Grozeva
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, United Kingdom
| | | | | | | | | | | | - Kevin Morgan
- Human Genetics, School of Life Sciences, Life Sciences Building A27, University Park, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
| | - Peter Passmore
- Centre for Public Health, School of Medicine, Dentistry and Biomedical Sciences, Queens University, Belfast, United Kingdom
| | - Clive Holmes
- Division of Clinical Neurosciences, School of Medicine, University of Southampton, Southampton, United Kingdom
| | - John Powell
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, Kings College London, London, United Kingdom
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Carol Brayne
- Institute of Public Health, University of Cambridge, Cambridge, United Kingdom
| | - Michael Gill
- Mercer’s Institute for Research on Ageing, St. James’ Hospital, Dublin, Ireland
- James Hospital and Trinity College, Dublin, Ireland
| | - Simon Mead
- MRC Prion Unit at UCL, Institute of Prion Diseases, London, United Kingdom
| | - Paola Bossù
- Experimental Neuropsychobiology Laboratory, IRCCS Santa Lucia Foundation, Department of Clinical and Behavioral Neurology, Rome, Italy
| | | | - Alison M. Goate
- Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Hope Center Program on Protein Aggregation and Neurodegeneration, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Carlos Cruchaga
- Hope Center Program on Protein Aggregation and Neurodegeneration, Washington University School of Medicine, St Louis, Missouri, United States of America
- Department of Psychiatry, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Wolfgang Maier
- German Centre for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany
| | - Reinhard Heun
- Department of Psychiatry and Psychotherapy, University of Bonn, 53127, Bonn, Germany
| | - Frank Jessen
- German Centre for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany
- Department of Psychiatry and Psychotherapy, University of Cologne, 50937 Cologne, Germany
| | - Oliver Peters
- Department of Psychiatry and Psychotherapy, Charité Berlin, Berlin, Germany
- German Center for Neurodegenerative Diseases (DZNE), Berlin, Germany
| | - Martin Dichgans
- Institute for Stroke and Dementia Research, Klinikum der Universität München, Munich, Germany
- German Center for Neurodegenerative Diseases (DZNE, Munich), Munich, 80336, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Lutz FröLich
- Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Heidelberg, Germany
| | - Alfredo Ramirez
- Department of Psychiatry and Psychotherapy, University of Cologne, 50937 Cologne, Germany
- Department for Neurodegenerative Diseases and Geriatric Psychiatry, University Hospital Bonn, Bonn, Germany
| | - Lesley Jones
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, United Kingdom
| | - John Hardy
- Department of Molecular Neuroscience, UCL, Institute of Neurology, London, United Kingdom
| | - Dobril Ivanov
- UK Dementia Research Institute at Cardiff University, Cardiff, United Kingdom
| | - Matthew Hill
- UK Dementia Research Institute at Cardiff University, Cardiff, United Kingdom
| | - Peter Holmans
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, United Kingdom
| | - Nicholas D. Allen
- UK Dementia Research Institute at Cardiff University, Cardiff, United Kingdom
| | - B. Paul Morgan
- UK Dementia Research Institute at Cardiff University, Cardiff, United Kingdom
| | - Sudha Seshadri
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Gerard D. Schellenberg
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Philippe Amouyel
- Univ. Lille, Inserm, CHU Lille University Hospital, Institut Pasteur de Lille, LabEx DISTALZ-UMR1167 - RID-AGE - Risk factors and molecular determinants of aging-related, F-59000 Lille, France
| | - Julie Williams
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, United Kingdom
- UK Dementia Research Institute at Cardiff University, Cardiff, United Kingdom
| | - Valentina Escott-Price
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, United Kingdom
- UK Dementia Research Institute at Cardiff University, Cardiff, United Kingdom
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17
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Chaiprasert T, Armartmuntree N, Techasen A, Sakonsinsiri C, Pinlaor S, Ungarreevittaya P, Khuntikeo N, Namwat N, Thanan R. Roles of Zinc Finger Protein 423 in Proliferation and Invasion of Cholangiocarcinoma through Oxidative Stress. Biomolecules 2019; 9:biom9070263. [PMID: 31284679 PMCID: PMC6681239 DOI: 10.3390/biom9070263] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 06/26/2019] [Accepted: 07/03/2019] [Indexed: 12/21/2022] Open
Abstract
Zinc finger protein 423 (ZNF423) is a transcriptional factor involved in the development and progression of cancers but has not yet been examined in cholangiocarcinoma (CCA), an oxidative stress-driven cancer of biliary epithelium. In this study, we hypothesized that oxidative stress mediated ZNF423 expression regulates its downstream genes resulting in CCA genesis. ZNF423 protein expression patterns and 8-oxodG (an oxidative stress marker) formation in CCA tissues were investigated using immunohistochemical analysis. The results showed that ZNF423 was overexpressed in CCA cells compared to normal bile duct cells adjacent of the tumor. Notably, ZNF423 expression was positively correlated with 8-oxodG formation. Moreover, ZNF423 expression in an immortalized cholangiocyte cell line (MMNK1) was increased by hydrogen peroxide-treatment, suggesting that oxidative stress induces ZNF423 expression. To investigate the roles of ZNF423 in CCA progression, ZNF423 mRNA was silenced using specific siRNA in CCA cell lines, KKU-100 and KKU-213. Silencing of ZNF423 significantly inhibits cell proliferation and invasion of both CCA cell lines. Taking all these results together, the present study denoted that ZNF423 is an oxidative stress-responsive gene with an oncogenic property contributing to the regulation of CCA genesis.
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Affiliation(s)
- Timpika Chaiprasert
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Napat Armartmuntree
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Anchalee Techasen
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand
- Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Chadamas Sakonsinsiri
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Somchai Pinlaor
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand
- Department of Parasitology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Piti Ungarreevittaya
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand
- Department of Pathology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Narong Khuntikeo
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand
- Department of Surgery, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Nisana Namwat
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Raynoo Thanan
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand.
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand.
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