1
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Peng L, Wu T, Liu Y, Zhao D, He W, Yuan Y. OTUB1 accelerates hepatocellular carcinoma by stabilizing RACK1 via its non-canonical ubiquitination. Cell Oncol (Dordr) 2024; 47:987-1004. [PMID: 38315284 DOI: 10.1007/s13402-023-00913-7] [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] [Accepted: 12/23/2023] [Indexed: 02/07/2024] Open
Abstract
BACKGROUND Dysregulated ubiquitination modification occupies a pivotal role in hepatocellular carcinoma (HCC) tumorigenesis and progression. The ubiquitin aldehyde binding 1 (OTUB1) was aberrantly upregulated and exhibited the pro-tumorigenic function in HCC. However, the underlying mechanisms and responsible targets of OTUB1 remain unclear. METHODS First, bioinformatics analysis, western blot and immunohistochemistry staining were applied to analyze OTUB1 expression in HCC specimens. Then, immunoprecipitation assay-tandem mass spectrometry (MS) combined with the gene set enrichment analysis (GSEA) was used to explore the downstream target of OTUB1. Co-immunoprecipitation and ubiquitination assays were used to identify the mechanisms involved. Finally, we explored the regulatory effect of MAZ on OTUB1 through ChIP-qPCR and dual-luciferase reporter assay. RESULTS OTUB1 was broadly elevated in HCC tissues and promoted the proliferation and metastasis of HCC in vitro and in vivo. The receptor for activated C kinase 1 (RACK1) performed as a functional partner of OTUB1 and its hyperactivation was associated with aggressive development and other malignant features in HCC by activating oncogenes transcription. Mechanistically, OTUB1 directly bound to RACK1 at its C-terminal domain and decreased the K48-linked ubiquitination of RACK1 through its non-canonical suppression of ubiquitination activity, which stabilized RACK1 protein levels in HCC cells. Therefore, OTUB1 significantly increased multiple oncogenes expression and activated PI3K/AKT and FAK/ERK signaling in a RACK1-dependent manner in HCC. Moreover, the transcription factor MAZ upregulated OTUB1 expression through identifying a putative response element of OTUB1 promoter area. CONCLUSIONS Our findings might provide a new therapeutic strategy for HCC by modifying the MAZ-OTUB1-RACK1 axis.
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Affiliation(s)
- Liqun Peng
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary and Pancreatic Diseases of Hubei Province, Wuhan, China
| | - Tiangen Wu
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary and Pancreatic Diseases of Hubei Province, Wuhan, China
| | - Yingyi Liu
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary and Pancreatic Diseases of Hubei Province, Wuhan, China
| | - Dongli Zhao
- College of Life Sciences, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan, China
| | - Wenzhi He
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China.
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary and Pancreatic Diseases of Hubei Province, Wuhan, China.
- College of Life Sciences, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan, China.
| | - Yufeng Yuan
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China.
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary and Pancreatic Diseases of Hubei Province, Wuhan, China.
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2
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Zheng H, Liu M, Shi S, Huang H, Yang X, Luo Z, Song Y, Xu Q, Li T, Xue L, Lu F, Wang J. MAP4K4 and WT1 mediate SOX6-induced cellular senescence by synergistically activating the ATF2-TGFβ2-Smad2/3 signaling pathway in cervical cancer. Mol Oncol 2024; 18:1327-1346. [PMID: 38383842 PMCID: PMC11076992 DOI: 10.1002/1878-0261.13613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 01/18/2024] [Accepted: 02/04/2024] [Indexed: 02/23/2024] Open
Abstract
SRY-box transcription factor 6 (SOX6) is a member of the SOX gene family and inhibits the proliferation of cervical cancer cells by inducing cell cycle arrest. However, the final cell fate and significance of these cell-cycle-arrested cervical cancer cells induced by SOX6 remains unclear. Here, we report that SOX6 inhibits the proliferation of cervical cancer cells by inducing cellular senescence, which is mainly mediated by promoting transforming growth factor beta 2 (TGFB2) gene expression and subsequently activating the TGFβ2-Smad2/3-p53-p21WAF1/CIP1-Rb pathway. SOX6 promotes TGFB2 gene expression through the MAP4K4-MAPK (JNK/ERK/p38)-ATF2 and WT1-ATF2 pathways, which is dependent on its high-mobility group (HMG) domain. In addition, the SOX6-induced senescent cervical cancer cells are resistant to cisplatin treatment. ABT-263 (navitoclax) and ABT-199 (venetoclax), two classic senolytics, can specifically eliminate the SOX6-induced senescent cervical cancer cells, and thus significantly improve the chemosensitivity of cisplatin-resistant cervical cancer cells. This study uncovers that the MAP4K4/WT1-ATF2-TGFβ2 axis mediates SOX6-induced cellular senescence, which is a promising therapeutic target in improving the chemosensitivity of cervical cancer.
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Affiliation(s)
- Han Zheng
- Department of Microbiology and Infectious Disease Center, School of Basic Medical SciencesPeking University Health Science CenterBeijingChina
- NHC Key Laboratory of Medical ImmunologyPeking UniversityBeijingChina
| | - Mingchen Liu
- Department of Microbiology and Infectious Disease Center, School of Basic Medical SciencesPeking University Health Science CenterBeijingChina
| | - Shu Shi
- Department of Microbiology and Infectious Disease Center, School of Basic Medical SciencesPeking University Health Science CenterBeijingChina
| | - Hongxin Huang
- Department of Microbiology and Infectious Disease Center, School of Basic Medical SciencesPeking University Health Science CenterBeijingChina
| | - Xingwen Yang
- Department of Microbiology and Infectious Disease Center, School of Basic Medical SciencesPeking University Health Science CenterBeijingChina
- NHC Key Laboratory of Medical ImmunologyPeking UniversityBeijingChina
| | - Ziheng Luo
- Department of Microbiology and Infectious Disease Center, School of Basic Medical SciencesPeking University Health Science CenterBeijingChina
- NHC Key Laboratory of Medical ImmunologyPeking UniversityBeijingChina
| | - Yarong Song
- Department of Microbiology and Infectious Disease Center, School of Basic Medical SciencesPeking University Health Science CenterBeijingChina
- NHC Key Laboratory of Medical ImmunologyPeking UniversityBeijingChina
| | - Qiang Xu
- Department of Microbiology and Infectious Disease Center, School of Basic Medical SciencesPeking University Health Science CenterBeijingChina
| | - Tingting Li
- Department of Biomedical Informatics, School of Basic Medical SciencesPeking University Health Science CenterBeijingChina
| | - Lixiang Xue
- Department of Radiation OncologyCancer Center of Peking University Third Hospital, Peking University Third HospitalBeijingChina
| | - Fengmin Lu
- Department of Microbiology and Infectious Disease Center, School of Basic Medical SciencesPeking University Health Science CenterBeijingChina
| | - Jie Wang
- Department of Microbiology and Infectious Disease Center, School of Basic Medical SciencesPeking University Health Science CenterBeijingChina
- NHC Key Laboratory of Medical ImmunologyPeking UniversityBeijingChina
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3
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Song Z, Xue Z, Wang Y, Imran M, Assiri M, Fahad S. Insights into the roles of non-coding RNAs and angiogenesis in glioblastoma: An overview of current research and future perspectives. Biochim Biophys Acta Gen Subj 2024; 1868:130567. [PMID: 38242182 DOI: 10.1016/j.bbagen.2024.130567] [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: 06/21/2023] [Revised: 12/27/2023] [Accepted: 01/15/2024] [Indexed: 01/21/2024]
Abstract
Glioblastoma (GBM) is a highly aggressive type of primary brain cancer with a poor prognosis, and despite intensive research, survival rates have not significantly improved. Non-coding RNAs (ncRNAs) are emerging as critical regulators of GBM pathogenesis, including angiogenesis, which is essential for tumor growth and invasion. MicroRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) have been identified as regulators of angiogenesis in GBM. miRNAs such as miR-21, miR-10b, and miR-26a promote angiogenesis by targeting anti-angiogenic factors, while lncRNAs such as H19 and MALAT1 inhibit angiogenesis by regulating pro-angiogenic factors. CircRNAs, such as circSMARCA5 and circBACH2, also regulate angiogenesis through various mechanisms. Similarly, signaling pathways such as the vascular endothelial growth factor (VEGF) pathway play critical roles in angiogenesis and have been targeted for GBM therapy. However, resistance to anti-angiogenic therapies is a significant obstacle in clinical practice. Developing novel therapeutic strategies targeting ncRNAs and angiogenesis is a promising approach for GBM. Potential targets include miRNAs, lncRNAs, circRNAs, and downstream signaling pathways that regulate angiogenesis. This review highlights the critical roles of ncRNAs and angiogenesis in GBM pathogenesis and the potential for new therapeutic strategies targeting these pathways to improve the prognosis and quality of life for GBM patients.
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Affiliation(s)
- Zhengfei Song
- Department of Neurosurgery, SIR Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Zhaoliang Xue
- Department of Neurosurgery, SIR Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yirong Wang
- Department of Neurosurgery, SIR Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China.
| | - Muhammad Imran
- Department of Chemistry, Faculty of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
| | - Mohammed Assiri
- Department of Chemistry, Faculty of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
| | - Shah Fahad
- Department of Agronomy, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa 23200, Pakistan; Department of Natural Sciences, Lebanese American University, Byblos, Lebanon.
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4
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Wang W, Li D, Xu Q, Cheng J, Yu Z, Li G, Qiao S, Pan J, Wang H, Shi J, Zheng T, Sui G. G-quadruplexes promote the motility in MAZ phase-separated condensates to activate CCND1 expression and contribute to hepatocarcinogenesis. Nat Commun 2024; 15:1045. [PMID: 38316778 PMCID: PMC10844655 DOI: 10.1038/s41467-024-45353-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 01/22/2024] [Indexed: 02/07/2024] Open
Abstract
G-quadruplexes (G4s) can recruit transcription factors to activate gene expression, but detailed mechanisms remain enigmatic. Here, we demonstrate that G4s in the CCND1 promoter propel the motility in MAZ phase-separated condensates and subsequently activate CCND1 transcription. Zinc finger (ZF) 2 of MAZ is a responsible for G4 binding, while ZF3-5, but not a highly disordered region, is critical for MAZ condensation. MAZ nuclear puncta overlaps with signals of G4s and various coactivators including BRD4, MED1, CDK9 and active RNA polymerase II, as well as gene activation histone markers. MAZ mutants lacking either G4 binding or phase separation ability did not form nuclear puncta, and showed deficiencies in promoting hepatocellular carcinoma cell proliferation and xenograft tumor formation. Overall, we unveiled that G4s recruit MAZ to the CCND1 promoter and facilitate the motility in MAZ condensates that compartmentalize coactivators to activate CCND1 expression and subsequently exacerbate hepatocarcinogenesis.
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Affiliation(s)
- Wenmeng Wang
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Dangdang Li
- College of Life Science, Northeast Forestry University, Harbin, 150040, China.
| | - Qingqing Xu
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Jiahui Cheng
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Zhiwei Yu
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, 150081, China
| | - Guangyue Li
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Shiyao Qiao
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Jiasong Pan
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Hao Wang
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Jinming Shi
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Tongsen Zheng
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, 150081, China
- Key Laboratory of Molecular Oncology of Heilongjiang Province, Harbin, China
| | - Guangchao Sui
- College of Life Science, Northeast Forestry University, Harbin, 150040, China.
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5
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Malik S, Pradeep SP, Kumar V, Xiao Y, Deng Y, Fan R, Vasquez JC, Singh V, Bahal R. Antitumor efficacy of a sequence-specific DNA-targeted γPNA-based c-Myc inhibitor. Cell Rep Med 2024; 5:101354. [PMID: 38183981 PMCID: PMC10829792 DOI: 10.1016/j.xcrm.2023.101354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 09/21/2023] [Accepted: 12/11/2023] [Indexed: 01/08/2024]
Abstract
Targeting oncogenes at the genomic DNA level can open new avenues for precision medicine. Significant efforts are ongoing to target oncogenes using RNA-targeted and protein-targeted platforms, but no progress has been made to target genomic DNA for cancer therapy. Here, we introduce a gamma peptide nucleic acid (γPNA)-based genomic DNA-targeted platform to silence oncogenes in vivo. γPNAs efficiently invade the mixed sequences of genomic DNA with high affinity and specificity. As a proof of concept, we establish that γPNA can inhibit c-Myc transcription in multiple cell lines. We evaluate the in vivo efficacy and safety of genomic DNA targeting in three pre-clinical models. We also establish that anti-transcription γPNA in combination with histone deacetylase inhibitors and chemotherapeutic drugs results in robust antitumor activity in cell-line- and patient-derived xenografts. Overall, this strategy offers a unique therapeutic platform to target genomic DNA to inhibit oncogenes for cancer therapy.
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Affiliation(s)
- Shipra Malik
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT 06269, USA
| | - Sai Pallavi Pradeep
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT 06269, USA
| | - Vikas Kumar
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT 06269, USA
| | - Yong Xiao
- Department of Biomedical Engineering, Yale University, New Haven, CT 06510, USA; Department of Neurosurgery, Nanjing Brain Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Yanxiang Deng
- Department of Biomedical Engineering, Yale University, New Haven, CT 06510, USA; Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Rong Fan
- Department of Biomedical Engineering, Yale University, New Haven, CT 06510, USA; Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA; Human and Translational Immunology, Yale School of Medicine, New Haven, CT 06520, USA; Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Juan C Vasquez
- Department of Pediatrics, Yale School of Medicine, New Haven, CT 06520, USA
| | - Vijender Singh
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
| | - Raman Bahal
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT 06269, USA.
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6
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Romano F, Di Porzio A, Iaccarino N, Riccardi G, Di Lorenzo R, Laneri S, Pagano B, Amato J, Randazzo A. G-quadruplexes in cancer-related gene promoters: from identification to therapeutic targeting. Expert Opin Ther Pat 2023; 33:745-773. [PMID: 37855085 DOI: 10.1080/13543776.2023.2271168] [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: 06/26/2023] [Accepted: 10/11/2023] [Indexed: 10/20/2023]
Abstract
INTRODUCTION Guanine-rich DNA sequences can fold into four-stranded noncanonical secondary structures called G-quadruplexes (G4s) which are widely distributed in functional regions of the human genome, such as telomeres and gene promoter regions. Compelling evidence suggests their involvement in key genome functions such as gene expression and genome stability. Notably, the abundance of G4-forming sequences near transcription start sites suggests their potential involvement in regulating oncogenes. AREAS COVERED This review provides an overview of current knowledge on G4s in human oncogene promoters. The most representative G4-binding ligands have also been documented. The objective of this work is to present a comprehensive overview of the most promising targets for the development of novel and highly specific anticancer drugs capable of selectively impacting the expression of individual or a limited number of genes. EXPERT OPINION Modulation of G4 formation by specific ligands has been proposed as a powerful new tool to treat cancer through the control of oncogene expression. Actually, most of G4-binding small molecules seem to simultaneously target a range of gene promoter G4s, potentially influencing several critical driver genes in cancer, thus producing significant therapeutic benefits.
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Affiliation(s)
- Francesca Romano
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Anna Di Porzio
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Nunzia Iaccarino
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | | | | | - Sonia Laneri
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Bruno Pagano
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Jussara Amato
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
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7
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Mafi A, Mannani R, Khalilollah S, Hedayati N, Salami R, Rezaee M, Dehmordi RM, Ghorbanhosseini SS, Alimohammadi M, Akhavan-Sigari R. The Significant Role of microRNAs in Gliomas Angiogenesis: A Particular Focus on Molecular Mechanisms and Opportunities for Clinical Application. Cell Mol Neurobiol 2023; 43:3277-3299. [PMID: 37414973 DOI: 10.1007/s10571-023-01385-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 06/25/2023] [Indexed: 07/08/2023]
Abstract
MicroRNAs (miRNAs) are non-coding RNAs with only 20-22 nucleic acids that inhibit gene transcription and translation by binding to mRNA. MiRNAs have a diverse set of target genes and can alter most physiological processes, including cell cycle checkpoints, cell survival, and cell death mechanisms, affecting the growth, development, and invasion of various cancers, including gliomas. So optimum management of miRNA expression is essential for preserving a normal biological environment. Due to their small size, stability, and capability of specifically targeting oncogenes, miRNAs have emerged as a promising marker and new biopharmaceutical targeted therapy for glioma patients. This review focuses on the most common miRNAs associated with gliomagenesis and development by controlling glioma-determining markers such as angiogenesis. We also summarized the recent research about miRNA effects on signaling pathways, their mechanistic role and cellular targets in the development of gliomas angiogenesis. Strategies for miRNA-based therapeutic targets, as well as limitations in clinical applications, are also discussed.
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Affiliation(s)
- Alireza Mafi
- Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
- Nutrition and Food Security Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Reza Mannani
- Department of Surgery, Faculty of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Shayan Khalilollah
- Department of Neurosurgery, Faculty of Medicine, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Neda Hedayati
- School of Medicine, Iran University of Medical Science, Tehran, Iran
| | - Raziyeh Salami
- Department of Clinical Biochemistry, School of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Malihe Rezaee
- Department of Pharmacology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Tehran Heart Center, Cardiovascular Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Rohollah Mousavi Dehmordi
- Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
- Department of Clinical Biochemistry, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Seyedeh Sara Ghorbanhosseini
- Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mina Alimohammadi
- Student Research Committee, Department of Immunology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Reza Akhavan-Sigari
- Department of Neurosurgery, University Medical Center Tuebingen, Tübingen, Germany
- Department of Health Care Management and Clinical Research, Collegium Humanum Warsaw Management University Warsaw, Warsaw, Poland
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8
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Zhong S, Borlak J. Sex disparities in non-small cell lung cancer: mechanistic insights from a cRaf transgenic disease model. EBioMedicine 2023; 95:104763. [PMID: 37625265 PMCID: PMC10470261 DOI: 10.1016/j.ebiom.2023.104763] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 07/10/2023] [Accepted: 08/03/2023] [Indexed: 08/27/2023] Open
Abstract
BACKGROUND Women are at greater risk of developing non-small cell lung cancer (NSCLC), yet the underlying causes remain unclear. METHODS We performed whole genome scans in lung tumours of cRaf transgenic mice and identified miRNA, transcription factor and hormone receptor dependent gene regulations. We confirmed hormone receptors by immunohistochemistry and constructed regulatory gene networks by considering experimentally validated miRNA-gene and transcription factor-miRNA/gene targets. Bioinformatics, genomic foot-printing and gene enrichment analysis established sex-specific circuits of lung tumour growth. Translational research involved a large cohort of NSCLC patients. We evaluated commonalities in sex-specific NSCLC gene regulations between mice and humans and determined their prognostic value in Kaplan-Meier survival statistics and COX proportional hazard regression analysis. FINDINGS Overexpression of the cRaf kinase elicited an extraordinary 8-fold increase in tumour growth among females, and nearly 70% of the 112 differentially expressed genes (DEGs) were female specific. We identified oncogenes, oncomirs, tumour suppressors, cell cycle regulators and MAPK/EGFR signalling molecules, which prompted sex-based differences in NSCLC, and we deciphered a regulatory gene-network, which protected males from accelerated tumour growth. Strikingly, 41% of DEGs are targets of hormone receptors, and the majority (85%) are oestrogen receptor (ER) dependent. We confirmed the role of ER in a large cohort of NSCLC patients and validated 40% of DEGs induced by cRaf in clinical tumour samples. INTERPRETATION We report the molecular wiring that prompted sex disparities in tumour growth. This allowed us to propose the development of molecular targeted therapies by jointly blocking ER, CDK1 and arginase 2 in NSCLC. FUNDING We gratefully acknowledge the financial support of the Lower Saxony Ministry of Culture and Sciences and Volkswagen Foundation, Germany to JB (25A.5-7251-99-3/00) and of the Chinese Scholarship Council to SZ (202008080022). This publication is funded by the Deutsche Forschungsgemeinschaft (DFG) as part of the "Open Access Publikationskosten" program.
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Affiliation(s)
- Shen Zhong
- Centre for Pharmacology and Toxicology, Hannover Medical School, Carl-Neuberg-Str. 1, Hannover 30625, Germany
| | - Jürgen Borlak
- Centre for Pharmacology and Toxicology, Hannover Medical School, Carl-Neuberg-Str. 1, Hannover 30625, Germany.
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Ren X, Yang H, Nierenberg JL, Sun Y, Chen J, Beaman C, Pham T, Nobuhara M, Takagi MA, Narayan V, Li Y, Ziv E, Shen Y. High throughput PRIME editing screens identify functional DNA variants in the human genome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.12.548736. [PMID: 37502948 PMCID: PMC10370011 DOI: 10.1101/2023.07.12.548736] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Despite tremendous progress in detecting DNA variants associated with human disease, interpreting their functional impact in a high-throughput and base-pair resolution manner remains challenging. Here, we develop a novel pooled prime editing screen method, PRIME, which can be applied to characterize thousands of coding and non-coding variants in a single experiment with high reproducibility. To showcase its applications, we first identified essential nucleotides for a 716 bp MYC enhancer via PRIME-mediated saturation mutagenesis. Next, we applied PRIME to functionally characterize 1,304 non-coding variants associated with breast cancer and 3,699 variants from ClinVar. We discovered that 103 non-coding variants and 156 variants of uncertain significance are functional via affecting cell fitness. Collectively, we demonstrate PRIME capable of characterizing genetic variants at base-pair resolution and scale, advancing accurate genome annotation for disease risk prediction, diagnosis, and therapeutic target identification.
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Affiliation(s)
- Xingjie Ren
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Han Yang
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Jovia L. Nierenberg
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Yifan Sun
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Jiawen Chen
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Cooper Beaman
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Thu Pham
- Pharmaceutical Sciences and Pharmacogenomics Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Mai Nobuhara
- Pharmaceutical Sciences and Pharmacogenomics Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Maya Asami Takagi
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Vivek Narayan
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Yun Li
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
- Department of Computer Science, University of North Carolina, Chapel Hill, NC, USA
| | - Elad Ziv
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
- Division of General Internal Medicine, Department of Medicine, and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Yin Shen
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
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10
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Zhu M, Zhang RN, Zhang H, Qu CB, Zhang XC, Ren LX, Yang Z, Gu JF. PCGF6/MAX/KDM5D facilitates MAZ/CDK4 axis expression and pRCC progression by hypomethylation of the DNA promoter. Epigenetics Chromatin 2023; 16:9. [PMID: 36890610 PMCID: PMC9996882 DOI: 10.1186/s13072-023-00483-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 03/01/2023] [Indexed: 03/10/2023] Open
Abstract
Polycomb group RING finger protein 6 (PCGF6) plays an important role as a regulator of transcription in a variety of cellular processes, including tumorigenesis. However, the function and expression of PCGF6 in papillary RCC (pRCC) remain unclear. In the present study, we found that PCGF6 expression was significantly elevated in pRCC tissues, and high expression of PCGF6 was associated with poor survival of patients with pRCC. The overexpression of PCGF6 promoted while depletion of PCGF6 depressed the proliferation of pRCC cells in vitro. Interestingly, myc-related zinc finger protein (MAZ), a downstream molecular of PCGF6, was upregulated in pRCC with hypomethylation promoter. Mechanically, PCGF6 promoted MAZ expression by interacting with MAX and KDM5D to form a complex, and MAX recruited PCGF6 and KDM5D to the CpG island of the MAZ promoter and facilitated H3K4 histone demethylation. Furthermore, CDK4 was a downstream molecule of MAZ that participated in PCGF6/MAZ-regulated progression of pRCC. These results indicated that the upregulation of PCGF6 facilitated MAZ/CDK4 axis expression and pRCC progression by hypomethylation of the MAZ promoter. The PCGF6/MAZ/CDK4 regulatory axis may be a potential target for the treatment of ccRCC.
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Affiliation(s)
- Meng Zhu
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping West Road, Shijiazhuang, 050000, China
| | - Ruo-Nan Zhang
- School of Chinese Integrative Medicine, Hebei Medical University, Shijiazhuang, Hebei, China
| | - Hong Zhang
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping West Road, Shijiazhuang, 050000, China
| | - Chang-Bao Qu
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping West Road, Shijiazhuang, 050000, China
| | | | - Li-Xin Ren
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping West Road, Shijiazhuang, 050000, China
| | - Zhan Yang
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping West Road, Shijiazhuang, 050000, China
- Molecular Biology Laboratory, Talent and Academic Exchange Center, The Second Hospital of Hebei Medical University, Shijiazhang, China
| | - Jun-Fei Gu
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping West Road, Shijiazhuang, 050000, China.
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11
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Ruthig VA, Lamb DJ. Modeling development of genitourinary birth defects to understand disruption due to changes in gene dosage. AMERICAN JOURNAL OF CLINICAL AND EXPERIMENTAL UROLOGY 2022; 10:412-424. [PMID: 36636694 PMCID: PMC9831917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 12/25/2022] [Indexed: 01/14/2023]
Abstract
Genitourinary development is a delicately orchestrated process that begins in the embryo. Once complete, the genitourinary system is a collection of functionally disparate organs spread throughout the abdominal and pelvic regions. These distinct organs are interconnected through an elaborate duct system which aggregates the organs' products to a common exit point. The complicated nature of the genitourinary system makes it highly susceptible to developmental disruptions that produce anomalies. In fact, genitourinary anomalies are among the most common class of human birth defects. Aside from congenital anomalies of the kidney and urinary tract (CAKUT), for males, these birth defects can also occur in the penis (hypospadias) and testis (cryptorchism), which impact male fertility and male mental health. As genetic technology has advanced, it has become clear that a subset of cases of genitourinary birth defects are due to gene variation causing dosage changes in critical regulatory genes. Here we first review the parallels between human and mouse genitourinary development. We then demonstrate how translational research leverages mouse models of human gene variation cases to advance mechanistic understanding of causation in genitourinary birth defects. We close with a view to the future highlighting upcoming technologies that will provide a deeper understanding of gene variation affecting regulation of genitourinary development, which should ultimately advance treatment options for patients.
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Affiliation(s)
- Victor A Ruthig
- Department of Urology, Weill Cornell MedicineNew York, NY, USA,Sexual Medicine Laboratory, Weill Cornell MedicineNew York, NY, USA
| | - Dolores J Lamb
- Department of Urology, Weill Cornell MedicineNew York, NY, USA,Center for Reproductive Genomics, Weill Cornell MedicineNew York, NY, USA,Englander Institute for Precision Medicine, Weill Cornell MedicineNew York, NY, USA
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12
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Song J, Nabeel-Shah S, Pu S, Lee H, Braunschweig U, Ni Z, Ahmed N, Marcon E, Zhong G, Ray D, Ha KCH, Guo X, Zhang Z, Hughes TR, Blencowe BJ, Greenblatt JF. Regulation of alternative polyadenylation by the C2H2-zinc-finger protein Sp1. Mol Cell 2022; 82:3135-3150.e9. [PMID: 35914531 DOI: 10.1016/j.molcel.2022.06.031] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 04/09/2022] [Accepted: 06/28/2022] [Indexed: 11/18/2022]
Abstract
Alternative polyadenylation (APA) enhances gene regulatory potential by increasing the diversity of mRNA transcripts. 3' UTR shortening through APA correlates with enhanced cellular proliferation and is a widespread phenomenon in tumor cells. Here, we show that the ubiquitously expressed transcription factor Sp1 binds RNA in vivo and is a common repressor of distal poly(A) site usage. RNA sequencing identified 2,344 genes (36% of the total mapped mRNA transcripts) with lengthened 3' UTRs upon Sp1 depletion. Sp1 preferentially binds the 3' UTRs of such lengthened transcripts and inhibits cleavage at distal sites by interacting with the subunits of the core cleavage and polyadenylation (CPA) machinery. The 3' UTR lengths of Sp1 target genes in breast cancer patient RNA-seq data correlate with Sp1 expression levels, implicating Sp1-mediated APA regulation in modulating tumorigenic properties. Taken together, our findings provide insights into the mechanism for dynamic APA regulation by unraveling a previously unknown function of the DNA-binding transcription factor Sp1.
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Affiliation(s)
- Jingwen Song
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Syed Nabeel-Shah
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
| | - Shuye Pu
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Hyunmin Lee
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada; Department of Computer Science, University of Toronto, 10 King's College Road, Toronto, ON M5S 3G4, Canada
| | - Ulrich Braunschweig
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Zuyao Ni
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Nujhat Ahmed
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
| | - Edyta Marcon
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Guoqing Zhong
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Debashish Ray
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Kevin C H Ha
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
| | - Xinghua Guo
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Zhaolei Zhang
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada; Department of Computer Science, University of Toronto, 10 King's College Road, Toronto, ON M5S 3G4, Canada
| | - Timothy R Hughes
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
| | - Benjamin J Blencowe
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
| | - Jack F Greenblatt
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada.
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13
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Yang R, Zuo L, Ma H, Zhou Y, Zhou P, Wang L, Wang M, Latif M, Kong L. Downregulation of nc886 contributes to prostate cancer cell invasion and TGFβ1-induced EMT. Genes Dis 2022; 9:1086-1098. [PMID: 35685460 PMCID: PMC9170576 DOI: 10.1016/j.gendis.2020.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 12/09/2020] [Accepted: 12/24/2020] [Indexed: 11/16/2022] Open
Abstract
Epithelial-to-mesenchymal transition (EMT) activation is important in cancer progression and metastasis. Evidence indicates that nc886 is a representative Pol III gene that processes microRNA products via Dicer and further downregulates its target gene transforming growth factor- β1 (TGF-β1), which is the most prominent inducer of EMT in prostate cancer (PC). Consistent with the previous literature, we found that nc886 downregulation was strongly associated with metastatic behavior and showed worse outcomes in PC patients. However, little is known about the association between nc886 and the EMT signaling pathway. We developed a PC cell model with stable overexpression of nc886 and found that nc886 changed cellular morphology and drove MET. The underlying mechanism may be related to its promotion of SNAIL protein degradation via ubiquitination, but not to its neighboring genes, TGFβ-induced protein (TGFBI) and SMAD5, which are Pol II-transcribed. TGF-β1 also override nc886 promotion of MET via transient suppression the transcription of nc886, promotion of TGFBI or increase in SMAD5 phosphorylation. Both nc886 inhibition and TGFBI activation occur regardless of their methylation status. The literature suggests that MYC inhibition by TGF-β1 is attributed to nc886 downregulation. We incidentally identified MYC-associated zinc finger protein (MAZ) as a suppressive transcription factor of TGFBI, which is controlled by TGF-β1. We elucidate a new mechanism of TGF-β1 differential control of Pol II and the transcription of its neighboring Pol III gene and identify a new EMT unit consisting of nc886 and its neighboring genes.
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Affiliation(s)
- Ronghui Yang
- Department of Biochemistry and Molecular Biology, Capital Medical University, Beijing 100069, PR China
| | - Lingkun Zuo
- Department of Biochemistry and Molecular Biology, Capital Medical University, Beijing 100069, PR China
| | - Hui Ma
- Department of Biochemistry and Molecular Biology, Capital Medical University, Beijing 100069, PR China
| | - Ying Zhou
- Department of Biochemistry and Molecular Biology, Capital Medical University, Beijing 100069, PR China
| | - Ping Zhou
- Biomedical Engineering Institute of Capital Medical University, Capital Medical University, Beijing 100069, PR China
| | - Liyong Wang
- Department of Biochemistry and Molecular Biology, Capital Medical University, Beijing 100069, PR China
| | - Miao Wang
- Department of Pathology, Beijing Friendship Hospital, The Second Clinical Medical College of Capital Medical University, Beijing 100050, PR China
| | - Mahrukh Latif
- Department of Nuclear Medicine, Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei 050010, PR China
| | - Lu Kong
- Department of Biochemistry and Molecular Biology, Capital Medical University, Beijing 100069, PR China
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14
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Eltager M, Abdelaal T, Mahfouz A, Reinders MJT. scMoC: single-cell multi-omics clustering. BIOINFORMATICS ADVANCES 2022; 2:vbac011. [PMID: 36699396 PMCID: PMC9710707 DOI: 10.1093/bioadv/vbac011] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 01/27/2022] [Accepted: 02/11/2022] [Indexed: 01/28/2023]
Abstract
Motivation Single-cell multi-omics assays simultaneously measure different molecular features from the same cell. A key question is how to benefit from the complementary data available and perform cross-modal clustering of cells. Results We propose Single-Cell Multi-omics Clustering (scMoC), an approach to identify cell clusters from data with comeasurements of scRNA-seq and scATAC-seq from the same cell. We overcome the high sparsity of the scATAC-seq data by using an imputation strategy that exploits the less-sparse scRNA-seq data available from the same cell. Subsequently, scMoC identifies clusters of cells by merging clusterings derived from both data domains individually. We tested scMoC on datasets generated using different protocols with variable data sparsity levels. We show that scMoC (i) is able to generate informative scATAC-seq data due to its RNA-guided imputation strategy and (ii) results in integrated clusters based on both RNA and ATAC information that are biologically meaningful either from the RNA or from the ATAC perspective. Availability and implementation The data used in this manuscript is publicly available, and we refer to the original manuscript for their description and availability. For convience sci-CAR data is available at NCBI GEO under the accession number of GSE117089. SNARE-seq data is available at NCBI GEO under the accession number of GSE126074. The 10X multiome data is available at the following link https://www.10xgenomics.com/resources/datasets/pbmc-from-a-healthy-donor-no-cell-sorting-3-k-1-standard-2-0-0. Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
- Mostafa Eltager
- Delft Bioinformatics Lab, Delft University of Technology, Delft 2628XE, The Netherlands
| | - Tamim Abdelaal
- Delft Bioinformatics Lab, Delft University of Technology, Delft 2628XE, The Netherlands,Leiden Computational Biology Center, Leiden University Medical Center, Leiden 2333ZC, The Netherlands,Division of Image Processing, Department of Radiology, Leiden University Medical Center, Leiden, 2333ZC, The Netherlands
| | - Ahmed Mahfouz
- Delft Bioinformatics Lab, Delft University of Technology, Delft 2628XE, The Netherlands,Leiden Computational Biology Center, Leiden University Medical Center, Leiden 2333ZC, The Netherlands,Department of Human Genetics, Leiden University Medical Center, Leiden 2333ZC, The Netherlands
| | - Marcel J T Reinders
- Delft Bioinformatics Lab, Delft University of Technology, Delft 2628XE, The Netherlands,Leiden Computational Biology Center, Leiden University Medical Center, Leiden 2333ZC, The Netherlands,To whom correspondence should be addressed.
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15
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Ortabozkoyun H, Huang PY, Cho H, Narendra V, LeRoy G, Gonzalez-Buendia E, Skok JA, Tsirigos A, Mazzoni EO, Reinberg D. CRISPR and biochemical screens identify MAZ as a cofactor in CTCF-mediated insulation at Hox clusters. Nat Genet 2022; 54:202-212. [PMID: 35145304 PMCID: PMC8837555 DOI: 10.1038/s41588-021-01008-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 12/22/2021] [Indexed: 12/14/2022]
Abstract
CCCTC-binding factor (CTCF) is critical to three-dimensional genome organization. Upon differentiation, CTCF insulates active and repressed genes within Hox gene clusters. We conducted a genome-wide CRISPR knockout (KO) screen to identify genes required for CTCF-boundary activity at the HoxA cluster, complemented by biochemical approaches. Among the candidates, we identified Myc-associated zinc-finger protein (MAZ) as a cofactor in CTCF insulation. MAZ colocalizes with CTCF at chromatin borders and, similar to CTCF, interacts with the cohesin subunit RAD21. MAZ KO disrupts gene expression and local contacts within topologically associating domains. Similar to CTCF motif deletions, MAZ motif deletions lead to derepression of posterior Hox genes immediately after CTCF boundaries upon differentiation, giving rise to homeotic transformations in mouse. Thus, MAZ is a factor contributing to appropriate insulation, gene expression and genomic architecture during development.
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Affiliation(s)
- Havva Ortabozkoyun
- Howard Hughes Medical Institute, NYU Grossman School of Medicine, New York, NY, USA.,Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA
| | - Pin-Yao Huang
- Howard Hughes Medical Institute, NYU Grossman School of Medicine, New York, NY, USA.,Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA
| | - Hyunwoo Cho
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA.,Applied Bioinformatics Laboratories, NYU Grossman School of Medicine, New York, NY, USA.,Department of Radiation Oncology, NYU Grossman School of Medicine, New York, NY, USA
| | - Varun Narendra
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gary LeRoy
- Howard Hughes Medical Institute, NYU Grossman School of Medicine, New York, NY, USA.,Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA
| | - Edgar Gonzalez-Buendia
- Howard Hughes Medical Institute, NYU Grossman School of Medicine, New York, NY, USA.,Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA
| | - Jane A Skok
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA
| | - Aristotelis Tsirigos
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA.,Applied Bioinformatics Laboratories, NYU Grossman School of Medicine, New York, NY, USA.,Institute for Computational Medicine, NYU Grossman School of Medicine, New York, NY, USA
| | | | - Danny Reinberg
- Howard Hughes Medical Institute, NYU Grossman School of Medicine, New York, NY, USA. .,Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA.
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16
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Zheng C, Wu H, Jin S, Li D, Tan S, Zhu X. Roles of Myc-associated zinc finger protein in malignant tumors. Asia Pac J Clin Oncol 2022; 18:506-514. [PMID: 35098656 DOI: 10.1111/ajco.13748] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 12/04/2021] [Indexed: 11/30/2022]
Abstract
As an important transcription factor that is widely expressed in most tissues of the human body, Myc-associated zinc finger protein (MAZ) has been reported highly expressed in many malignant tumors and thought to be a promising therapeutic target for cancer treatment. In this review, we aim to offer a comprehensive understanding of MAZ regulation in malignant tumors. The carboxy terminal of MAZ protein contains six C2H2 zinc fingers, and its regulation of transcription is based on the interaction between the GC-rich DNA binding sites of target genes and its carboxy-terminal zinc finger motifs. MAZ protein has been found to activate or inhibit the transcriptional initiation process of many target genes, as well as play an important role in the transcriptional termination process of some target genes, so MAZ poses dual regulatory functions in the initiation and termination process of gene transcription. Through the transcriptional regulation of c-myc and Ras gene family, MAZ poses an important role in the occurrence and development of breast cancer, pancreatic cancer, prostate cancer, glioblastoma, neuroblastoma, and other malignant tumors. Our review shows a vital role of MAZ in many malignant tumors and provides novel insight for cancer diagnosis and treatment.
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Affiliation(s)
- Chuanjun Zheng
- Department of Epidemiology and Statistics, School of Public Health, Guilin Medical University, Guilin, China
| | - Hongmei Wu
- Department of Epidemiology and Statistics, School of Public Health, Guilin Medical University, Guilin, China
| | - Song Jin
- Department of Epidemiology and Statistics, School of Public Health, Guilin Medical University, Guilin, China
| | - Di Li
- Department of Epidemiology and Statistics, School of Public Health, Guilin Medical University, Guilin, China
| | - Shengkui Tan
- Department of Epidemiology and Statistics, School of Public Health, Guilin Medical University, Guilin, China
| | - Xiaonian Zhu
- Department of Epidemiology and Statistics, School of Public Health, Guilin Medical University, Guilin, China
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17
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Oncogenic Truncations of ASXL1 Enhance a Motif for BRD4 ET-Domain Binding. J Mol Biol 2021; 433:167242. [PMID: 34536441 DOI: 10.1016/j.jmb.2021.167242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 09/04/2021] [Accepted: 09/07/2021] [Indexed: 11/23/2022]
Abstract
Proper regulation of gene-expression relies on specific protein-protein interactions between a myriad of epigenetic regulators. As such, mutation of genes encoding epigenetic regulators often drive cancer and developmental disorders. Additional sex combs-like protein 1 (ASXL1) is a key example, where mutations frequently drive haematological cancers and can cause developmental disorders. It has been reported that nonsense mutations in ASXL1 promote an interaction with BRD4, another central epigenetic regulator. Here we provide a molecular mechanism for the BRD4-ASXL1 interaction, demonstrating that a motif near to common truncation breakpoints of ASXL1 contains an epitope that binds the ET domain within BRD4. Binding-studies show that this interaction is analogous to common ET-binding modes of BRD4-interactors, and that all three ASX-like protein orthologs (ASXL1-3) contain a functional ET domain-binding epitope. Crucially, we observe that BRD4-ASXL1 binding is markedly increased in the prevalent ASXL1Y591X truncation that maintains the BRD4-binding epitope, relative to full-length ASXL1 or truncated proteins that delete the epitope. Together, these results show that ASXL1 truncation enhances BRD4 recruitment to transcriptional complexes via its ET domain, which could misdirect regulatory activity of either BRD4 or ASXL1 and may inform potential therapeutic interventions.
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18
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Balandeh E, Mohammadshafie K, Mahmoudi Y, Hossein Pourhanifeh M, Rajabi A, Bahabadi ZR, Mohammadi AH, Rahimian N, Hamblin MR, Mirzaei H. Roles of Non-coding RNAs and Angiogenesis in Glioblastoma. Front Cell Dev Biol 2021; 9:716462. [PMID: 34646821 PMCID: PMC8502969 DOI: 10.3389/fcell.2021.716462] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 08/24/2021] [Indexed: 12/12/2022] Open
Abstract
One of the significant hallmarks of cancer is angiogenesis. It has a crucial function in tumor development and metastasis. Thus, angiogenesis has become one of the most exciting targets for drug development in cancer treatment. Here we discuss the regulatory effects on angiogenesis in glioblastoma (GBM) of non-coding RNAs (ncRNAs), including long ncRNA (lncRNA), microRNA (miRNA), and circular RNA (circRNA). These ncRNAs may function in trans or cis forms and modify gene transcription by various mechanisms, including epigenetics. NcRNAs may also serve as crucial regulators of angiogenesis-inducing molecules. These molecules include, metalloproteinases, cytokines, several growth factors (platelet-derived growth factor, vascular endothelial growth factor, fibroblast growth factor, hypoxia-inducible factor-1, and epidermal growth factor), phosphoinositide 3-kinase, mitogen-activated protein kinase, and transforming growth factor signaling pathways.
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Affiliation(s)
- Ebrahim Balandeh
- Department of Clinical Psychology, School of Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | | | - Yaser Mahmoudi
- Department of Anatomical Sciences, Yasuj University of Medical Sciences, Yasuj, Iran
| | | | - Ali Rajabi
- Razi Drug Research Center, Iran University of Medical Sciences, Tehran, Iran
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | - Zahra Razaghi Bahabadi
- Razi Drug Research Center, Iran University of Medical Sciences, Tehran, Iran
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | - Amir Hossein Mohammadi
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
| | - Neda Rahimian
- Endocrine Research Center, Institute of Endocrinology and Metabolism, Iran University of Medical Sciences, Tehran, Iran
| | - Michael R. Hamblin
- Laser Research Centre, Faculty of Health Science, University of Johannesburg, Doornfontein, South Africa
| | - Hamed Mirzaei
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
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19
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Punjani N, Kang C, Lamb DJ, Schlegel PN. Current updates and future perspectives in the evaluation of azoospermia: A systematic review. Arab J Urol 2021; 19:206-214. [PMID: 34552771 PMCID: PMC8451618 DOI: 10.1080/2090598x.2021.1954415] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Objectives: To provide a summary of the current evaluation of azoospermia and insights into future perspectives in the evaluation and counselling of men with azoospermia. Methods: A search of PubMed, Cochrane Reviews and Web of Science databases was performed for full-text English-language articles published between 1943 and 2020 focussing on ‘future perspectives’, ‘azoospermia’ and ‘evaluation’. Results: Azoospermia represents a severe form of male infertility characterised by sperm production so impaired that there are no sperm present in the ejaculate. The current evaluation of azoospermia focusses on patient history and physical examination with selected adjunctive laboratory investigations including serum hormones, a karyotype and screening for Y chromosome microdeletions. Future diagnostics are focussed on identifying the underlying genetic aetiologies for azoospermia, as well as a greater emphasis on screening for systemic illness that men with severe infertility may be predisposed to develop. Conclusion: Azoospermia represents an extreme form of male infertility, and evaluation relies heavily on history and physical examination, as genetic evaluations for these individuals remain limited. Future evaluation will focus on next-generation sequencing and more rigorous evaluation for possible co-existing and future risk of systemic disease. ABBREVIATIONS: ADGRG2, adhesion G protein-coupled receptor G2; ASRM: American Society of Reproductive Medicine; AZF: azoospermia factor; CBAVD: congenital bilateral absence of the vas deferens; CFTR: cystic fibrosis transmembrane conductance regulator; CRKL: CRK-like proto-oncogene; E2F1: E2F transcription factor 1; HAUS7: HAUS augmin-like complex subunit 7; HR: hazard ratio; KS: Klinefelter syndrome; MAZ, MYC-associated zinc finger protein; NGS: next-generation sequencing; NOA: non-obstructive azoospermia; OA: obstructive azoospermia; RHOX: reproductive homeobox on the X chromosome; SH2: SRC homology 2; TAF7L: TATA-box binding protein associated factor 7-like; TEX11: testis-expressed 11; WES: whole-exome sequencing
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Affiliation(s)
- Nahid Punjani
- Department of Urology, Weill Cornell Medical College, New York, NY, USA
| | - Caroline Kang
- Department of Urology, Weill Cornell Medical College, New York, NY, USA
| | - Dolores J Lamb
- Department of Urology, Weill Cornell Medical College, New York, NY, USA.,Englander Institute for Precision Medicine, Weill Cornell Medical College, New York, NY, USA.,Center for Reproductive Genomics, Weill Cornell Medical College, New York, NY, USA
| | - Peter N Schlegel
- Department of Urology, Weill Cornell Medical College, New York, NY, USA.,Center for Reproductive Genomics, Weill Cornell Medical College, New York, NY, USA
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20
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Abstract
CXXC5 is a member of the zinc-finger CXXC family that binds to unmethylated CpG dinucleotides. CXXC5 modulates gene expressions resulting in diverse cellular events mediated by distinct signaling pathways. However, the mechanism responsible for CXXC5 expression remains largely unknown. We found here that of the 14 annotated CXXC5 transcripts with distinct 5' untranslated regions encoding the same protein, transcript variant 2 with the highest expression level among variants represents the main transcript in cell models. The DNA segment in and at the immediate 5'-sequences of the first exon of variant 2 contains a core promoter within which multiple transcription start sites are present. Residing in a region with high G-C nucleotide content and CpG repeats, the core promoter is unmethylated, deficient in nucleosomes, and associated with active RNA polymerase-II. These findings suggest that a CpG island promoter drives CXXC5 expression. Promoter pull-down revealed the association of various transcription factors (TFs) and transcription co-regulatory proteins, as well as proteins involved in histone/chromatin, DNA, and RNA processing with the core promoter. Of the TFs, we verified that ELF1 and MAZ contribute to CXXC5 expression. Moreover, the first exon of variant 2 may contain a G-quadruplex forming region that could modulate CXXC5 expression.
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21
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Wang Y, Shi FY, Liang Y, Gao G. REVA as A Well-curated Database for Human Expression-modulating Variants. GENOMICS PROTEOMICS & BIOINFORMATICS 2021; 19:590-601. [PMID: 34224878 PMCID: PMC9040024 DOI: 10.1016/j.gpb.2021.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 06/22/2021] [Accepted: 06/25/2021] [Indexed: 10/25/2022]
Abstract
More than 90% of disease- and trait-associated human variants are noncoding. By systematically screening multiple large-scale studies, we compiled REVA, a manually curated database for over 11.8 million experimentally tested noncoding variants with expression-modulating potentials. We provided 2424 functional annotations that could be used to pinpoint the plausible regulatory mechanism of these variants. We further benchmarked multiple state-of-the-art computational tools and found their limited sensitivity remains a serious challenge for effective large-scale analysis. REVA provides high-quality experimentally tested expression-modulating variants with extensive functional annotations, which will be useful for users in the noncoding variants community. REVA is available at http://reva.gao-lab.org.
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Affiliation(s)
- Yu Wang
- Biomedical Pioneering Innovation Center (BIOPIC) & Beijing Advanced Innovation Center for Genomics (ICG), Center for Bioinformatics (CBI) and State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Fang-Yuan Shi
- Biomedical Pioneering Innovation Center (BIOPIC) & Beijing Advanced Innovation Center for Genomics (ICG), Center for Bioinformatics (CBI) and State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Yu Liang
- Human Aging Research Institute, School of Life Sciences, Nanchang University, Nanchang 330031, China
| | - Ge Gao
- Biomedical Pioneering Innovation Center (BIOPIC) & Beijing Advanced Innovation Center for Genomics (ICG), Center for Bioinformatics (CBI) and State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China.
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22
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Abstract
Male factor infertility is a common problem. Evidence is emerging regarding the spectrum of systemic disease and illness harbored by infertile men who otherwise appear healthy. In this review, we present evidence that infertile men have poor overall health and increased morbidity and mortality, increased rates of both genitourinary and non-genitourinary malignancy, and greater risks of systemic disease. The review also highlights numerous genetic conditions associated with male infertility as well as emerging translational evidence of genitourinary birth defects and their impact on male infertility. Finally, parallels to the overall health of infertile women are presented. This review highlights the importance of a comprehensive health evaluation of men who present for an infertility assessment.
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Affiliation(s)
- Nahid Punjani
- James Buchanan Brady Foundation Institute of Urology, Weill Cornell Medical College, New York, NY 10065, USA;
| | - Dolores J Lamb
- James Buchanan Brady Foundation Institute of Urology, Weill Cornell Medical College, New York, NY 10065, USA; .,Englander Institute for Precision Medicine, Weill Cornell Medical College, New York, NY 10021, USA.,Center for Reproductive Genomics, Weill Cornell Medical College, New York, NY 10065, USA
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23
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Ren LX, Qi JC, Zhao AN, Shi B, Zhang H, Wang DD, Yang Z. Myc-associated zinc-finger protein promotes clear cell renal cell carcinoma progression through transcriptional activation of the MAP2K2-dependent ERK pathway. Cancer Cell Int 2021; 21:323. [PMID: 34183010 PMCID: PMC8240279 DOI: 10.1186/s12935-021-02020-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 06/10/2021] [Indexed: 12/29/2022] Open
Abstract
Background The dysfunction of myc-related zinc finger protein (MAZ) has been proven to contribute to tumorigenesis and development of multiple cancer types. However, the biological roles and clinical significance of MAZ in clear cell renal carcinoma (ccRCC) remain unclear. Methods MAZ expression was examined in ccRCC and normal kidney tissue by quantitative real-time PCR and Western blot. Statistical analysis was used to evaluate the clinical correlation between MAZ expression and clinicopathological characteristics to determine the relationship between MAZ expression and the survival of ccRCC patients. The biological roles of MAZ in cells were investigated in vitro using MTT and colony assays. Luciferase reporter assays and chromatin immunoprecipitation (ChIP) were used to investigate the relationship between MAZ and its potential downstream signaling molecules. Results MAZ expression is elevated in ccRCC tissues, and higher levels of MAZ were correlated with poor survival of patients with ccRCC. MAZ upregulation elevates the proliferation ability of ccRCC cells in vitro, whereas silencing MAZ represses this ability. Our results further reveal that MAZ promotes cell growth, which is dependent on ERK signaling. Importantly, we found that MAZ positively regulates MAP2K2 expression in ccRCC cells. Mechanistically, MAZ binds to the MAP2K2 promoter and increases MAP2K2 transcription. Furthermore, MAP2K2 levels were shown to be increased in ccRCC tissues and to be associated with a poor prognosis of ccRCC patients. MAP2K2 upregulation activates the ERK signaling pathway and promotes ccRCC progression. Conclusion These results reveal that the MAZ/MAP2K2/ERK signaling axis plays a crucial role in promoting ccRCC progression, which suggests the potential therapeutic utility of MAZ in ccRCC. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-021-02020-9.
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Affiliation(s)
- Li-Xin Ren
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping West Road, Shijiazhuang, 050000, China
| | - Jin-Chun Qi
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping West Road, Shijiazhuang, 050000, China
| | - An-Ning Zhao
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping West Road, Shijiazhuang, 050000, China
| | - Bei Shi
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping West Road, Shijiazhuang, 050000, China
| | - Hong Zhang
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping West Road, Shijiazhuang, 050000, China
| | - Dan-Dan Wang
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping West Road, Shijiazhuang, 050000, China
| | - Zhan Yang
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping West Road, Shijiazhuang, 050000, China.
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24
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Long X, Yang Z, Li Y, Sun Q, Li X, Kuang E. BRLF1-dependent viral and cellular transcriptomes and transcriptional regulation during EBV primary infection in B lymphoma cells. Genomics 2021; 113:2591-2604. [PMID: 34087421 DOI: 10.1016/j.ygeno.2021.05.039] [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: 09/02/2020] [Revised: 02/17/2021] [Accepted: 05/30/2021] [Indexed: 12/11/2022]
Abstract
The immediate-early protein BRLF1 plays important roles in lytic infection of Epstein-Barr virus (EBV), in which it activates lytic viral transcription and replication. However, knowledge of the influence of BRLF1 on cellular gene expression and transcriptional reprogramming during the early lytic cycle remains limited. In the present study, deep RNA-sequencing analysis identified all differentially expressed genes (DEGs) and alternative splicing in B lymphoma cells subjected to wild-type and BRLF1-deficient EBV primary infection. The BRLF1-dependent cellular DEGs were annotated, and major differentially enriched pathways were related to DNA replication and transcription, immune and inflammatory responses, cytokine-receptor interactions and chemokine signaling and metabolic processes. Furthermore, analysis of BRLF1-binding proteins by mass spectrometry shows that BRLF1 binds to and cooperates with several transcription factors and components of the spliceosome and then influences both RNA polymerase II-dependent transcription and pre-mRNA splicing. The RTA-binding RRE motifs or specific motifs of unique cooperative transcription factors in viral and cellular DEG promoter regions indicate that BRLF1 employs different strategies for regulating viral and cellular transcription. Thus, our study characterized BRLF1-dependent cellular and viral transcriptional profile during primary infection and then revealed the comprehensive virus-cell interaction and alterations of transcription during EBV primary infection and lytic replication.
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Affiliation(s)
- Xubing Long
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong 510080, China
| | - Ziwei Yang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong 510080, China
| | - Yang Li
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong 510080, China
| | - Qinqin Sun
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong 510080, China
| | - Xiaojuan Li
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong 510080, China.
| | - Ersheng Kuang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong 510080, China; Key Laboratory of Tropical Disease Control (Sun Yat-Sen University), Ministry of Education, Guangzhou, Guangdong 510080, China.
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25
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Cha M, Zheng H, Talukder A, Barham C, Li X, Hu H. A two-stream convolutional neural network for microRNA transcription start site feature integration and identification. Sci Rep 2021; 11:5625. [PMID: 33707582 PMCID: PMC7952457 DOI: 10.1038/s41598-021-85173-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 02/24/2021] [Indexed: 12/31/2022] Open
Abstract
MicroRNAs (miRNAs) play important roles in post-transcriptional gene regulation and phenotype development. Understanding the regulation of miRNA genes is critical to understand gene regulation. One of the challenges to study miRNA gene regulation is the lack of condition-specific annotation of miRNA transcription start sites (TSSs). Unlike protein-coding genes, miRNA TSSs can be tens of thousands of nucleotides away from the precursor miRNAs and they are hard to be detected by conventional RNA-Seq experiments. A number of studies have been attempted to computationally predict miRNA TSSs. However, high-resolution condition-specific miRNA TSS prediction remains a challenging problem. Recently, deep learning models have been successfully applied to various bioinformatics problems but have not been effectively created for condition-specific miRNA TSS prediction. Here we created a two-stream deep learning model called D-miRT for computational prediction of condition-specific miRNA TSSs ( http://hulab.ucf.edu/research/projects/DmiRT/ ). D-miRT is a natural fit for the integration of low-resolution epigenetic features (DNase-Seq and histone modification data) and high-resolution sequence features. Compared with alternative computational models on different sets of training data, D-miRT outperformed all baseline models and demonstrated high accuracy for condition-specific miRNA TSS prediction tasks. Comparing with the most recent approaches on cell-specific miRNA TSS identification using cell lines that were unseen to the model training processes, D-miRT also showed superior performance.
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Affiliation(s)
- Mingyu Cha
- Department of Computer Science, University of Central Florida, Orlando, FL, USA
| | - Hansi Zheng
- Department of Computer Science, University of Central Florida, Orlando, FL, USA
| | - Amlan Talukder
- Department of Computer Science, University of Central Florida, Orlando, FL, USA
| | - Clayton Barham
- Department of Computer Science, University of Central Florida, Orlando, FL, USA
| | - Xiaoman Li
- Burnett School of Biomedical Science, College of Medicine, University of Central Florida, Orlando, FL, USA.
| | - Haiyan Hu
- Department of Computer Science, University of Central Florida, Orlando, FL, USA.
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26
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Bartas M, Červeň J, Guziurová S, Slychko K, Pečinka P. Amino Acid Composition in Various Types of Nucleic Acid-Binding Proteins. Int J Mol Sci 2021; 22:ijms22020922. [PMID: 33477647 PMCID: PMC7831508 DOI: 10.3390/ijms22020922] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/15/2021] [Accepted: 01/16/2021] [Indexed: 12/20/2022] Open
Abstract
Nucleic acid-binding proteins are traditionally divided into two categories: With the ability to bind DNA or RNA. In the light of new knowledge, such categorizing should be overcome because a large proportion of proteins can bind both DNA and RNA. Another even more important features of nucleic acid-binding proteins are so-called sequence or structure specificities. Proteins able to bind nucleic acids in a sequence-specific manner usually contain one or more of the well-defined structural motifs (zinc-fingers, leucine zipper, helix-turn-helix, or helix-loop-helix). In contrast, many proteins do not recognize nucleic acid sequence but rather local DNA or RNA structures (G-quadruplexes, i-motifs, triplexes, cruciforms, left-handed DNA/RNA form, and others). Finally, there are also proteins recognizing both sequence and local structural properties of nucleic acids (e.g., famous tumor suppressor p53). In this mini-review, we aim to summarize current knowledge about the amino acid composition of various types of nucleic acid-binding proteins with a special focus on significant enrichment and/or depletion in each category.
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27
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Pluta A, Willems L, Douville RN, Kuźmak J. Effects of Naturally Occurring Mutations in Bovine Leukemia Virus 5'-LTR and Tax Gene on Viral Transcriptional Activity. Pathogens 2020; 9:pathogens9100836. [PMID: 33066207 PMCID: PMC7656303 DOI: 10.3390/pathogens9100836] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 10/05/2020] [Accepted: 10/09/2020] [Indexed: 01/28/2023] Open
Abstract
Bovine leukemia virus (BLV) is a deltaretrovirus infecting bovine B cells and causing enzootic bovine leucosis (EBL). The long terminal repeat (LTR) plays an indispensable role in viral gene expression. The BLV Tax protein acts as the main transactivator of LTR-driven transcription of BLV viral genes. The aim of this study was to analyze mutations in the BLV LTR region and tax gene to determine their association with transcriptional activity. LTRs were obtained from one hundred and six BLV isolates and analyzed for their genetic variability. Fifteen variants were selected and characterized based on mutations in LTR regulatory elements, and further used for in vitro transcription assays. Reporter vectors containing the luciferase gene under the control of each variant BLV promoter sequence, in addition to variant Tax expression vectors, were constructed. Both types of plasmids were used for cotransfection of HeLa cells and the level of luciferase activity was measured as a proxy of transcriptional activity. Marked differences in LTR promoter activity and Tax transactivation activity were observed amongst BLV variants. These results demonstrate that mutations in both the BLV LTR and tax gene can affect the promoter activity, which may have important consequences on proviral load, viral fitness, and transmissibility in BLV-infected cattle.
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Affiliation(s)
- Aneta Pluta
- Department of Biochemistry, National Veterinary Research Institute, 24-100 Puławy, Poland;
- Correspondence:
| | - Luc Willems
- Molecular and Cellular Epigenetics (Interdisciplinary Cluster for Applied Genoproteomics, GIGA) and Molecular Biology (TERRA), University of Liège (ULiège), 4000 Liege, Belgium;
| | - Renée N. Douville
- Department of Biology, The University of Winnipeg, Winnipeg, MB R3B 2E9, Canada;
- Department of Immunology, University of Manitoba, Winnipeg, MB R3E 0T5, Canada
| | - Jacek Kuźmak
- Department of Biochemistry, National Veterinary Research Institute, 24-100 Puławy, Poland;
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28
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Li S, Chen X, Wang J, Meydan C, Glass JL, Shih AH, Delwel R, Levine RL, Mason CE, Melnick AM. Somatic Mutations Drive Specific, but Reversible, Epigenetic Heterogeneity States in AML. Cancer Discov 2020; 10:1934-1949. [PMID: 32938585 DOI: 10.1158/2159-8290.cd-19-0897] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 07/09/2020] [Accepted: 09/11/2020] [Indexed: 11/16/2022]
Abstract
Epigenetic allele diversity is linked to inferior prognosis in acute myeloid leukemia (AML). However, the source of epiallele heterogeneity in AML is unknown. Herein we analyzed epiallele diversity in a genetically and clinically annotated AML cohort. Notably, AML driver mutations linked to transcription factors and favorable outcome are associated with epigenetic destabilization in a defined set of susceptible loci. In contrast, AML subtypes linked to inferior prognosis manifest greater abundance and highly stochastic epiallele patterning. We report an epiallele outcome classifier supporting the link between epigenetic diversity and treatment failure. Mouse models with TET2 or IDH2 mutations show that epiallele diversity is especially strongly induced by IDH mutations, precedes transformation to AML, and is enhanced by cooperation between somatic mutations. Furthermore, epiallele complexity was partially reversed by epigenetic therapies in AML driven by TET2/IDH2, suggesting that epigenetic therapy might function in part by reducing population complexity and fitness of AMLs. SIGNIFICANCE: We show for the first time that epigenetic clonality is directly linked to specific mutations and that epigenetic allele diversity precedes and potentially contributes to malignant transformation. Furthermore, epigenetic clonality is reversible with epigenetic therapy agents.This article is highlighted in the In This Issue feature, p. 1775.
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Affiliation(s)
- Sheng Li
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut.
- The Jackson Laboratory Cancer Center, Bar Harbor, Maine
- The Department of Genetics and Genomic Sciences, The University of Connecticut Health Center, Farmington, Connecticut
- Department of Computer Science and Engineering, University of Connecticut, Storrs, Connecticut
| | - Xiaowen Chen
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
| | - Jiahui Wang
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
| | - Cem Meydan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York
| | - Jacob L Glass
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Alan H Shih
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ruud Delwel
- Department of Hematology, Erasmus University Medical Center and Oncode Institute, Rotterdam, the Netherlands
| | - Ross L Levine
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York
| | - Ari M Melnick
- Division of Hematology/Oncology, Weill Cornell Medicine, New York, New York.
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29
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Punjani N, Lamb DJ. Male infertility and genitourinary birth defects: there is more than meets the eye. Fertil Steril 2020; 114:209-218. [PMID: 32741459 PMCID: PMC10590568 DOI: 10.1016/j.fertnstert.2020.06.042] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 06/24/2020] [Accepted: 06/24/2020] [Indexed: 12/17/2022]
Abstract
Male factor infertility is a significant problem present in up to 50% of infertile couples. The relationship between male infertility and systemic disease is of significant interest, and emerging evidence suggests a relationship between male infertility and male genitourinary (GU) birth defects (cryptorchidism, hypospadias, ambiguous genitalia, and congenital anomalies of the kidney and urinary tract). Many of these birth defects are treated in isolation by busy urologists without acknowledgment that these may be related to more global syndromic conditions. Conversely, geneticists and nonurologists who treat variable systemic phenotypes may overlook GU defects, which are indeed related conditions. Many of these defects are attributed to copy number variants dosage-sensitive genes due to chromosome microdeletions or microduplications. These variants are responsible for disease phenotypes seen in the general population. The copy number variants described in this review are syndromic in some cases and responsible for both GU birth defects as well as other systemic phenotypes. This review highlights the emerging evidence between these birth defects, male infertility, and other systemic conditions.
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Affiliation(s)
- Nahid Punjani
- James Buchanan Brady Foundation Institute of Urology, Weill Cornell Medical College, New York, New York
| | - Dolores J Lamb
- James Buchanan Brady Foundation Institute of Urology, Weill Cornell Medical College, New York, New York; Englander Institute for Precision Medicine, Weill Cornell Medical College, New York, New York; Center for Reproductive Genomics, Weill Cornell Medical College, New York, New York.
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30
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Schlag K, Steinhilber D, Karas M, Sorg BL. Analysis of proximal ALOX5 promoter binding proteins by quantitative proteomics. FEBS J 2020; 287:4481-4499. [PMID: 32096311 DOI: 10.1111/febs.15259] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 10/15/2019] [Accepted: 02/23/2020] [Indexed: 01/01/2023]
Abstract
5-Lipoxygenase (5-LO) is the initial enzyme in the biosynthesis of leukotrienes, which are mediators involved in pathophysiological conditions such as asthma and certain cancer types. Knowledge of proteins involved in 5-LO pathway regulation, including gene regulatory proteins, is needed to evaluate all options for therapeutic intervention in these diseases. Here, we present a mass spectrometric screening of ALOX5 promoter-interacting proteins, obtained by DNA pulldown and label-free quantitative mass spectrometry. Protein preparations from myeloid and B-lymphocytic cell lines were screened for promoter DNA interactors. Through statistical analysis, 66 proteins were identified as specific ALOX5 promotor binding proteins. Among those, the 15 most likely candidates for a prominent role in ALOX5 gene regulation are the known ALOX5 interactors Sp1 and Sp3, the related factor Sp2, two Krüppel-like factors (KLF13 and KLF16) and six other zinc finger proteins (MAZ, PRDM10, VEZF1, ZBTB7A, ZNF281 and ZNF579). Intriguingly, we also identified two helicases (BLM and DHX36) and the proteins hnRNPD and hnRNPK, which are, together with the protein MAZ, known to interact with DNA G-quadruplex structures. As G-quadruplexes are implicated in gene regulation, spectroscopic and antibody-based methods were used to confirm their presence within the GC-rich sequence of the ALOX5 promoter. In summary, we have systematically characterized the interactome of the ALOX5 promoter, identifying several zinc finger proteins as novel potential ALOX5 gene regulators. Further, we have shown that the ALOX5 promoter can form DNA G-quadruplex structures, which may play a functional role in ALOX5 gene regulation.
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Affiliation(s)
- Katharina Schlag
- Institute of Pharmaceutical Chemistry/ZAFES, Goethe-University, Frankfurt am Main, Germany
| | - Dieter Steinhilber
- Institute of Pharmaceutical Chemistry/ZAFES, Goethe-University, Frankfurt am Main, Germany
| | - Michael Karas
- Institute of Pharmaceutical Chemistry/ZAFES, Goethe-University, Frankfurt am Main, Germany
| | - Bernd L Sorg
- Institute of Pharmaceutical Chemistry/ZAFES, Goethe-University, Frankfurt am Main, Germany
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31
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Capasso M, Lasorsa VA, Cimmino F, Avitabile M, Cantalupo S, Montella A, De Angelis B, Morini M, de Torres C, Castellano A, Locatelli F, Iolascon A. Transcription Factors Involved in Tumorigenesis Are Over-Represented in Mutated Active DNA-Binding Sites in Neuroblastoma. Cancer Res 2019; 80:382-393. [PMID: 31784426 DOI: 10.1158/0008-5472.can-19-2883] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 10/24/2019] [Accepted: 11/22/2019] [Indexed: 11/16/2022]
Abstract
The contribution of coding mutations to oncogenesis has been largely clarified, whereas little is known about somatic mutations in noncoding DNA and their role in driving tumors remains controversial. Here, we used an alternative approach to interpret the functional significance of noncoding somatic mutations in promoting tumorigenesis. Noncoding somatic mutations of 151 neuroblastomas were integrated with ENCODE data to locate somatic mutations in regulatory elements specifically active in neuroblastoma cells, nonspecifically active in neuroblastoma cells, and nonactive. Within these types of elements, transcription factors (TF) were identified whose binding sites were enriched or depleted in mutations. For these TFs, a gene expression signature was built to assess their implication in neuroblastoma. DNA- and RNA-sequencing data were integrated to assess the effects of those mutations on mRNA levels. The pathogenicity of mutations was significantly higher in transcription factor binding site (TFBS) of regulatory elements specifically active in neuroblastoma cells, as compared with the others. Within these elements, there were 18 over-represented TFs involved mainly in cell-cycle phase transitions and 15 under-represented TFs primarily regulating cell differentiation. A gene expression signature based on over-represented TFs correlated with poor survival and unfavorable prognostic markers. Moreover, recurrent mutations in TFBS of over-represented TFs such as EZH2 affected MCF2L and ADP-ribosylhydrolase like 1 expression, among the others. We propose a novel approach to study the involvement of regulatory variants in neuroblastoma that could be extended to other cancers and provide further evidence that alterations of gene expression may have relevant effects in neuroblastoma development. SIGNIFICANCE: These findings propose a novel approach to study regulatory variants in neuroblastoma and suggest that noncoding somatic mutations have relevant implications in neuroblastoma development.
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Affiliation(s)
- Mario Capasso
- Department of Molecular Medicine and Medical Biotechnology, Università degli Studi di Napoli Federico II, Napoli, Italy. .,CEINGE Biotecnologie Avanzate, Napoli, Italy.,IRCCS SDN, Napoli, Italy
| | - Vito Alessandro Lasorsa
- Department of Molecular Medicine and Medical Biotechnology, Università degli Studi di Napoli Federico II, Napoli, Italy.,CEINGE Biotecnologie Avanzate, Napoli, Italy
| | - Flora Cimmino
- Department of Molecular Medicine and Medical Biotechnology, Università degli Studi di Napoli Federico II, Napoli, Italy.,CEINGE Biotecnologie Avanzate, Napoli, Italy
| | - Marianna Avitabile
- Department of Molecular Medicine and Medical Biotechnology, Università degli Studi di Napoli Federico II, Napoli, Italy.,CEINGE Biotecnologie Avanzate, Napoli, Italy
| | | | - Annalaura Montella
- Department of Molecular Medicine and Medical Biotechnology, Università degli Studi di Napoli Federico II, Napoli, Italy.,CEINGE Biotecnologie Avanzate, Napoli, Italy
| | - Biagio De Angelis
- Department of Pediatric Haematology and Oncology, IRCCS Ospedale Pediatrico Bambino Gesù, Roma, Italy
| | - Martina Morini
- Laboratory of Molecular Biology, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Carmen de Torres
- Developmental Tumor Biology Laboratory, Department of Oncology, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Aurora Castellano
- Department of Pediatric Haematology and Oncology, IRCCS Ospedale Pediatrico Bambino Gesù, Roma, Italy
| | - Franco Locatelli
- Department of Pediatric Haematology and Oncology, IRCCS Ospedale Pediatrico Bambino Gesù, Roma, Italy.,Department of Paediatrics, Sapienza University of Rome, Roma, Italy
| | - Achille Iolascon
- Department of Molecular Medicine and Medical Biotechnology, Università degli Studi di Napoli Federico II, Napoli, Italy. .,CEINGE Biotecnologie Avanzate, Napoli, Italy
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32
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Yang Q, Lang C, Wu Z, Dai Y, He S, Guo W, Huang S, Du H, Ren D, Peng X. MAZ promotes prostate cancer bone metastasis through transcriptionally activating the KRas-dependent RalGEFs pathway. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2019; 38:391. [PMID: 31488180 PMCID: PMC6729064 DOI: 10.1186/s13046-019-1374-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 08/09/2019] [Indexed: 01/22/2023]
Abstract
Background Clinically, prostate cancer (PCa) exhibits a high avidity to metastasize to bone. Myc-associated zinc-finger protein (MAZ) is a well-documented oncogene involved in the progression and metastasis of multiple cancer types, even in PCa. However, the clinical significance and biological roles of MAZ in bone metastasis of PCa remain unclear. Methods MAZ expression was examined in PCa tissues with bone metastasis, PCa tissues without bone metastasis and metastatic bone tissues by real-time PCR and immunohistochemistry (IHC), respectively. Statistical analysis was performed to evaluate the clinical correlation between MAZ expression and clinicopathological features and bone metastasis-free survival in PCa patients. Biological roles of MAZ in bone metastasis of PCa were investigated both in vitro by transwell assay, and in vivo by a mouse model of left cardiac ventricle inoculation. The bioinformatics analysis, western blot, pull-down assays, chromatin immunoprecipitation (ChIP) and luciferase reporter assays were applied to demonstrate and examine the relationship between MAZ and its potential downstream signalling pathway. TaqMan copy number assay was performed to identify the underlying mechanism responsible for MAZ overexpression in PCa tissues. Results MAZ expression is elevated in PCa tissues with bone metastasis compared with that in PCa tissues without bone metastasis, and is further increased in metastatic bone tissues. High expression of MAZ positively correlates with poor overall and bone metastasis-free survival in PCa patients. Upregulating MAZ elevates, while silencing MAZ represses the invasion and migration abilities of PCa cells in vitro and bone metastasis ability in vivo. Our results further reveal that MAZ promotes bone metastasis of PCa dependent on KRas signalling, although MAZ transcriptionally upregulates KRas and HRas expression, where the Ral guanine nucleotide exchange factor (RalGEF) signaling is responsible for the different roles of KRas and HRas in mediating the pro-bone metastasis of MAZ in PCa. Finally, our results indicate that recurrent gains contribute to MAZ overexpression in a small portion of PCa tissues. Conclusion These results indicate that the MAZ/Kras/ RalGEF signalling axis plays a crucial role in promoting PCa cell bone metastasis, suggesting a potential therapeutic utility of MAZ in bone metastasis of PCa. Electronic supplementary material The online version of this article (10.1186/s13046-019-1374-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Qing Yang
- Department of Orthopaedic Surgery, The First Affiliated Hospital, Sun Yat-sen University, 58# Zhongshan 2rd Road, Guangzhou, 510080, Guangdong Province, China.,Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, Guangzhou, 510080, Guangdong Province, China
| | - Chuandong Lang
- Department of Orthopaedic Surgery, The First Affiliated Hospital, Sun Yat-sen University, 58# Zhongshan 2rd Road, Guangzhou, 510080, Guangdong Province, China.,Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, Guangzhou, 510080, Guangdong Province, China
| | - Zhengquan Wu
- Department of Orthopaedic Surgery, The First Affiliated Hospital, Sun Yat-sen University, 58# Zhongshan 2rd Road, Guangzhou, 510080, Guangdong Province, China.,Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, Guangzhou, 510080, Guangdong Province, China
| | - Yuhu Dai
- Department of Orthopaedic Surgery, The First Affiliated Hospital, Sun Yat-sen University, 58# Zhongshan 2rd Road, Guangzhou, 510080, Guangdong Province, China.,Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, Guangzhou, 510080, Guangdong Province, China
| | - Shaofu He
- Department of Radiology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, Guangdong Province, China
| | - Wei Guo
- Department of Orthopaedic Surgery, The First Affiliated Hospital, Sun Yat-sen University, 58# Zhongshan 2rd Road, Guangzhou, 510080, Guangdong Province, China.,Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, Guangzhou, 510080, Guangdong Province, China
| | - Shuai Huang
- Department of Orthopaedic Surgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
| | - Hong Du
- Department of Pathology, The First People's Hospital of Guangzhou City, Guangzhou, 510180, Guangdong, China
| | - Dong Ren
- Department of Orthopaedic Surgery, The First Affiliated Hospital, Sun Yat-sen University, 58# Zhongshan 2rd Road, Guangzhou, 510080, Guangdong Province, China. .,Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, Guangzhou, 510080, Guangdong Province, China.
| | - Xinsheng Peng
- Department of Orthopaedic Surgery, The First Affiliated Hospital, Sun Yat-sen University, 58# Zhongshan 2rd Road, Guangzhou, 510080, Guangdong Province, China. .,Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, Guangzhou, 510080, Guangdong Province, China.
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Ray A, Ray BK. Suppression of vascular endothelial growth factor expression in breast cancer cells by microRNA-125b-mediated attenuation of serum amyloid A activating factor-1 level. Oncoscience 2019; 6:337-348. [PMID: 31360737 PMCID: PMC6650169 DOI: 10.18632/oncoscience.483] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 04/05/2019] [Indexed: 12/27/2022] Open
Abstract
Increased level of an inflammation-responsive transcription factor called serum amyloid A-activating factor (SAF-1) has been linked to the pathogenesis in human breast cancer. SAF-1 is found to promote vascular endothelial growth factor (VEGF) expression in breast carcinoma cells and boost angiogenesis. In an effort to develop a cellular mechanism to control VEGF expression, we sought to limit SAF-1 activity in breast cancer cells. We report here several targets within the SAF-1 mRNA for binding of microRNA-125b (miR-125b) and we show that VEGF expression is reduced in breast cancer cells when SAF-1 level is reduced with the microRNA action. Within the 3' un-translated region (UTR) of SAF-1 transcript, we have identified four highly conserved miR-125b responsive elements. We show that these miR-125b binding sites mediate repression of SAF-1 by miR-125b. Ectopic expression of miR-125b in nonmetastatic and metastatic breast cancer cells repressed SAF-1-mediated activity on VEGF promoter function and inhibited cancer cell migration and invasion potentials in vitro. Together, these results suggest that termination of SAF-1 function by miR-125b could be developed as a potential anti-VEGF and anti-angiogenic agent, which has high clinical relevance.
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Affiliation(s)
- Alpana Ray
- Department of Veterinary Pathobiology, University of Missouri, Columbia, Missouri
| | - Bimal K Ray
- Department of Veterinary Pathobiology, University of Missouri, Columbia, Missouri
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Association of SHMT1, MAZ, ERG, and L3MBTL3 Gene Polymorphisms with Susceptibility to Multiple Sclerosis. Biochem Genet 2018; 57:355-370. [PMID: 30456721 DOI: 10.1007/s10528-018-9894-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 11/07/2018] [Indexed: 01/08/2023]
Abstract
Multiple sclerosis (MS) is the most common inflammatory and chronic disease of the central nervous system (CNS). A complex interaction between genetic, environmental, and epigenetic factors is involved in the pathogenesis of MS. With the advancement of GWAS, various variants associated with MS have been identified. This study aimed to evaluate the association of single-nucleotide polymorphisms (SNPs) rs4925166 and rs1979277 in the SHMT1, MAZ rs34286592, ERG rs2836425, and L3MBTL3 rs4364506 with MS. In this case-control study, the association of five SNPs in SHMT1, MAZ, ERG, and L3MBTL3 genes with relapsing-remitting MS (RR-MS) was investigated in 190 patients and 200 healthy individuals. Four SNPs including SHMT1 rs4925166, SHMT1 rs1979277, MAZ rs34286592, and L3MBTL3 rs4364506 were genotyped using PCR-RFLP and genotyping of ERG rs2836425 was performed by tetra-primer ARMS PCR. Our findings showed a significant difference in the allelic frequencies for the four SNPs of SHMT1 rs4925166, SHMT1 rs1979277, MAZ rs34286592, and ERG rs2836425, while there were no differences in the allele and genotype frequencies for L3MBTL3 rs4364506. These significant associations were observed for the following genotypes: TT and GG genotypes of SHMT1 rs4925166 (OR 0.47 and 1.90, respectively) genotype GG of SHMT1 rs1979277 (OR 0.63), genotype GG of MAZ rs34286592 (OR 0.61), TC and CC genotypes of ERG rs2836425 (OR 1.89 and 0.50, respectively). Our study highlighted that people who are carrying genotypes including GG (SHMT1 rs4925166) and TC (ERG rs2836425) have the highest susceptibility chance for MS, respectively. However, genotypes TT (SHMT1 rs4925166), CC (ERG rs2836425), GG (MAZ rs34286592), and GG (SHMT1 rs1979277) had the highest negative association (protective effect) with MS, respectively. L3MBTL3 rs4364506 was found neither as a predisposing nor a protective variant.
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Myc-Associated Zinc Finger Protein Regulates the Proinflammatory Response in Colitis and Colon Cancer via STAT3 Signaling. Mol Cell Biol 2018; 38:MCB.00386-18. [PMID: 30181395 DOI: 10.1128/mcb.00386-18] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 08/27/2018] [Indexed: 12/11/2022] Open
Abstract
Myc-associated zinc finger (MAZ) is a transcription factor highly upregulated in chronic inflammatory disease and several human cancers. In the present study, we found that MAZ protein is highly expressed in human ulcerative colitis and colon cancer. However, the precise role for MAZ in the progression of colitis and colon cancer is not well defined. To determine the function of MAZ, a novel mouse model of intestinal epithelial cell-specific MAZ overexpression was generated. Expression of MAZ in intestinal epithelial cells was sufficient to enhance inflammatory injury in two complementary models of colitis. Moreover, MAZ expression increased tumorigenesis in an in vivo model of inflammation-induced colon cancer and was important for growth of human colon cancer cell lines in vitro and in vivo Mechanistically, MAZ is critical in the regulation of oncogenic STAT3 signaling. MAZ-expressing mice have enhanced STAT3 activation in the acute response to colitis. Moreover, MAZ was essential for cytokine- and bacterium-induced STAT3 signaling in colon cancer cells. Furthermore, we show that STAT3 is essential for MAZ-induced colon tumorigenesis using a chemical inhibitor. These data indicate an important functional role for MAZ in the inflammatory progression of colon cancer through regulation of STAT3 signaling and suggest that MAZ is a potential therapeutic target to dampen STAT3 signaling in colon cancer.
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Geltinger C, Hörtnagel K, Polack A. TATA box and Sp1 sites mediate the activation of c-myc promoter P1 by immunoglobulin kappa enhancers. Gene Expr 2018; 6:113-27. [PMID: 8979089 PMCID: PMC6148303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
In Burkitt's lymphoma (BL) cells the proto-oncogene c-myc is transcriptionally activated by chromosomal translocation to the immunoglobulin (Ig) gene loci. This activation is characterized by preferential transcription from the c-myc promoter P1 and accomplished by juxtaposed Ig enhancer elements. To identify promoter elements required for enhancer-activated P1 transcription, we studied the activation of c-myc reporter gene constructs by the Ig kappa intron and 3' enhancers. Deletion analysis defined the core promoter with a TATA box and two adjacent GC/GT boxes upstream sufficient for basal and enhancer-activated transcription. Gel retardation assays revealed Sp1's binding affinity to the GC/GT box proximal to the TATA box to be higher than to the distal one. This difference correlated well with the resulting levels of transcription mediated by Sp1 in contransfection experiments in BL and Sp1-deficient SL2 cells. Sp3 also bound to the core promoter in vitro, but failed to transactivate in vivo. Mutation of the distal Sp1 site moderately affected basal transcription concomitant with a modest decrease in enhancer stimulation. Mutation of the proximal Sp1 site almost entirely abolished basal as well as enhanced transcription. A considerable level of basal transcription was maintained upon mutation of the TATA box, whereas enhancer-activated transcription largely was abolished. Stable transfection of the BL cell line Raji with constructs containing core promoter mutations confirmed that the proximal Sp1 site and the TATA box are essential for the activation of promoter P1 by the Ig kappa enhancers.
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Affiliation(s)
- C Geltinger
- GSF-National Research Center for Environment and Health, Institute of Clinical Molecular Biology and Tumour Genetics, München, Germany
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Maity G, Haque I, Ghosh A, Dhar G, Gupta V, Sarkar S, Azeem I, McGregor D, Choudhary A, Campbell DR, Kambhampati S, Banerjee SK, Banerjee S. The MAZ transcription factor is a downstream target of the oncoprotein Cyr61/CCN1 and promotes pancreatic cancer cell invasion via CRAF-ERK signaling. J Biol Chem 2018; 293:4334-4349. [PMID: 29414775 PMCID: PMC5868262 DOI: 10.1074/jbc.ra117.000333] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 02/01/2018] [Indexed: 01/18/2023] Open
Abstract
Myc-associated zinc-finger protein (MAZ) is a transcription factor with dual roles in transcription initiation and termination. Deregulation of MAZ expression is associated with the progression of pancreatic ductal adenocarcinoma (PDAC). However, the mechanism of action of MAZ in PDAC progression is largely unknown. Here, we present evidence that MAZ mRNA expression and protein levels are increased in human PDAC cell lines, tissue samples, a subcutaneous tumor xenograft in a nude mouse model, and spontaneous cancer in the genetically engineered PDAC mouse model. We also found that MAZ is predominantly expressed in pancreatic cancer stem cells. Functional analysis indicated that MAZ depletion in PDAC cells inhibits invasive phenotypes such as the epithelial-to-mesenchymal transition, migration, invasion, and the sphere-forming ability of PDAC cells. Mechanistically, we detected no direct effects of MAZ on the expression of K-Ras mutants, but MAZ increased the activity of CRAF-ERK signaling, a downstream signaling target of K-Ras. The MAZ-induced activation of CRAF-ERK signaling was mediated via p21-activated protein kinase (PAK) and protein kinase B (AKT/PKB) signaling cascades and promoted PDAC cell invasiveness. Moreover, we found that the matricellular oncoprotein cysteine-rich angiogenic inducer 61 (Cyr61/CCN1) regulates MAZ expression via Notch-1-sonic hedgehog signaling in PDAC cells. We propose that Cyr61/CCN1-induced expression of MAZ promotes invasive phenotypes of PDAC cells not through direct K-Ras activation but instead through the activation of CRAF-ERK signaling. Collectively, these results highlight key molecular players in PDAC invasiveness and may help inform therapeutic strategies to improve clinical management and outcomes of PDAC.
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Affiliation(s)
- Gargi Maity
- From the Cancer Research Unit, Veterans Affairs Medical Center
- the Department of Pathology and Laboratory Medicine, and
| | - Inamul Haque
- From the Cancer Research Unit, Veterans Affairs Medical Center
- the Department of Pathology and Laboratory Medicine, and
| | - Arnab Ghosh
- From the Cancer Research Unit, Veterans Affairs Medical Center
- the Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, Kansas
| | - Gopal Dhar
- From the Cancer Research Unit, Veterans Affairs Medical Center
| | | | - Sandipto Sarkar
- From the Cancer Research Unit, Veterans Affairs Medical Center
- the Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, Kansas
| | - Imaan Azeem
- From the Cancer Research Unit, Veterans Affairs Medical Center
| | - Douglas McGregor
- From the Cancer Research Unit, Veterans Affairs Medical Center
- the Department of Pathology and Laboratory Medicine, and
- the Pathology Department, Veterans Affairs Medical Center, Kansas City, Missouri 64128
| | - Abhishek Choudhary
- the Gastroenterology Department, Veterans Affairs Medical Center, Kansas City, Missouri 64128
| | - Donald R Campbell
- From the Cancer Research Unit, Veterans Affairs Medical Center
- the University of Missouri Kansas City and Saint Luke's Hospital of Kansas City, Kansas City, Missouri, and
| | - Suman Kambhampati
- From the Cancer Research Unit, Veterans Affairs Medical Center
- the Sarah Cannon Cancer Center at HCA Midwest Health, Kansas City, Missouri 64131
| | - Sushanta K Banerjee
- From the Cancer Research Unit, Veterans Affairs Medical Center,
- the Department of Pathology and Laboratory Medicine, and
- the Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, Kansas
| | - Snigdha Banerjee
- From the Cancer Research Unit, Veterans Affairs Medical Center,
- the Department of Pathology and Laboratory Medicine, and
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38
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16p11.2 transcription factor MAZ is a dosage-sensitive regulator of genitourinary development. Proc Natl Acad Sci U S A 2018; 115:E1849-E1858. [PMID: 29432158 DOI: 10.1073/pnas.1716092115] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Genitourinary (GU) birth defects are among the most common yet least studied congenital malformations. Congenital anomalies of the kidney and urinary tract (CAKUTs) have high morbidity and mortality rates and account for ∼30% of structural birth defects. Copy number variation (CNV) mapping revealed that 16p11.2 is a hotspot for GU development. The only gene covered collectively by all of the mapped GU-patient CNVs was MYC-associated zinc finger transcription factor (MAZ), and MAZ CNV frequency is enriched in nonsyndromic GU-abnormal patients. Knockdown of MAZ in HEK293 cells results in differential expression of several WNT morphogens required for normal GU development, including Wnt11 and Wnt4. MAZ knockdown also prevents efficient transition into S phase, affects transcription of cell-cycle regulators, and abrogates growth of human embryonic kidney cells. Murine Maz is ubiquitously expressed, and a CRISPR-Cas9 mouse model of Maz deletion results in perinatal lethality with survival rates dependent on Maz copy number. Homozygous loss of Maz results in high penetrance of CAKUTs, and Maz is haploinsufficient for normal bladder development. MAZ, once thought to be a simple housekeeping gene, encodes a dosage-sensitive transcription factor that regulates urogenital development and contributes to both nonsyndromic congenital malformations of the GU tract as well as the 16p11.2 phenotype.
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Álvaro-Blanco J, Urso K, Chiodo Y, Martín-Cortázar C, Kourani O, Arco PGD, Rodríguez-Martínez M, Calonge E, Alcamí J, Redondo JM, Iglesias T, Campanero MR. MAZ induces MYB expression during the exit from quiescence via the E2F site in the MYB promoter. Nucleic Acids Res 2017; 45:9960-9975. [PMID: 28973440 PMCID: PMC5622404 DOI: 10.1093/nar/gkx641] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 07/13/2017] [Indexed: 12/27/2022] Open
Abstract
Most E2F-binding sites repress transcription through the recruitment of Retinoblastoma (RB) family members until the end of the G1 cell-cycle phase. Although the MYB promoter contains an E2F-binding site, its transcription is activated shortly after the exit from quiescence, before RB family members inactivation, by unknown mechanisms. We had previously uncovered a nuclear factor distinct from E2F, Myb-sp, whose DNA-binding site overlapped the E2F element and had hypothesized that this factor might overcome the transcriptional repression of MYB by E2F-RB family members. We have purified Myb-sp and discovered that Myc-associated zinc finger proteins (MAZ) are major components. We show that various MAZ isoforms are present in Myb-sp and activate transcription via the MYB-E2F element. Moreover, while forced RB or p130 expression repressed the activity of a luciferase reporter driven by the MYB-E2F element, co-expression of MAZ proteins not only reverted repression, but also activated transcription. Finally, we show that MAZ binds the MYB promoter in vivo, that its binding site is critical for MYB transactivation, and that MAZ knockdown inhibits MYB expression during the exit from quiescence. Together, these data indicate that MAZ is essential to bypass MYB promoter repression by RB family members and to induce MYB expression.
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Affiliation(s)
- Josué Álvaro-Blanco
- Department of Cancer Biology, Instituto de Investigaciones Biomédicas Alberto Sols, CSIC-UAM, Madrid 28029, Spain
| | - Katia Urso
- Gene regulation in cardiovascular remodeling and inflammation group, Centro Nacional de Investigaciones Cardiovasculares, Madrid 28029, Spain
| | - Yuri Chiodo
- Department of Cancer Biology, Instituto de Investigaciones Biomédicas Alberto Sols, CSIC-UAM, Madrid 28029, Spain
| | - Carla Martín-Cortázar
- Department of Cancer Biology, Instituto de Investigaciones Biomédicas Alberto Sols, CSIC-UAM, Madrid 28029, Spain
| | - Omar Kourani
- Department of Cancer Biology, Instituto de Investigaciones Biomédicas Alberto Sols, CSIC-UAM, Madrid 28029, Spain
| | - Pablo Gómez-Del Arco
- Gene regulation in cardiovascular remodeling and inflammation group, Centro Nacional de Investigaciones Cardiovasculares, Madrid 28029, Spain.,Department of Molecular Biology, Universidad Autónoma de Madrid, Centro de Biología Molecular, Cantoblanco, Madrid 28049, Spain.,CIBERCV, Spain
| | - María Rodríguez-Martínez
- Department of Cancer Biology, Instituto de Investigaciones Biomédicas Alberto Sols, CSIC-UAM, Madrid 28029, Spain
| | - Esther Calonge
- Unidad de Inmunopatología del SIDA, Centro Nacional de Microbiología, Majadahonda 28220, Spain
| | - José Alcamí
- Unidad de Inmunopatología del SIDA, Centro Nacional de Microbiología, Majadahonda 28220, Spain
| | - Juan Miguel Redondo
- Gene regulation in cardiovascular remodeling and inflammation group, Centro Nacional de Investigaciones Cardiovasculares, Madrid 28029, Spain.,CIBERCV, Spain
| | - Teresa Iglesias
- Department of Endocrine and Nervous Systems Pathophysiology, Instituto de Investigaciones Biomédicas Alberto Sols, CSIC-UAM, Madrid 28029, Spain.,CIBERNED, Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas, Spain
| | - Miguel R Campanero
- Department of Cancer Biology, Instituto de Investigaciones Biomédicas Alberto Sols, CSIC-UAM, Madrid 28029, Spain.,CIBERCV, Spain
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40
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Liu Q, Wang J, Zhao Y, Li CI, Stengel KR, Acharya P, Johnston G, Hiebert SW, Shyr Y. Identification of active miRNA promoters from nuclear run-on RNA sequencing. Nucleic Acids Res 2017; 45:e121. [PMID: 28460090 PMCID: PMC5737662 DOI: 10.1093/nar/gkx318] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 04/13/2017] [Indexed: 12/27/2022] Open
Abstract
The genome-wide identification of microRNA transcription start sites (miRNA TSSs) is essential for understanding how miRNAs are regulated in development and disease. In this study, we developed mirSTP (mirna transcription Start sites Tracking Program), a probabilistic model for identifying active miRNA TSSs from nascent transcriptomes generated by global run-on sequencing (GRO-seq) and precision run-on sequencing (PRO-seq). MirSTP takes advantage of characteristic bidirectional transcription signatures at active TSSs in GRO/PRO-seq data, and provides accurate TSS prediction for human intergenic miRNAs at a high resolution. MirSTP performed better than existing generalized and experiment specific methods, in terms of the enrichment of various promoter-associated marks. MirSTP analysis of 27 human cell lines in 183 GRO-seq and 28 PRO-seq experiments identified TSSs for 480 intergenic miRNAs, indicating a wide usage of alternative TSSs. By integrating predicted miRNA TSSs with matched ENCODE transcription factor (TF) ChIP-seq data, we connected miRNAs into the transcriptional circuitry, which provides a valuable source for understanding the complex interplay between TF and miRNA. With mirSTP, we not only predicted TSSs for 72 miRNAs, but also identified 12 primary miRNAs with significant RNA polymerase pausing alterations after JQ1 treatment; each miRNA was further validated through BRD4 binding to its predicted promoter. MirSTP is available at http://bioinfo.vanderbilt.edu/mirSTP/.
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Affiliation(s)
- Qi Liu
- Center for Quantitative Sciences, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.,Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
| | - Jing Wang
- Center for Quantitative Sciences, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.,Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Yue Zhao
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Chung-I Li
- Department of Statistics, National Cheng Kung University, Tainan 70101, Taiwan
| | - Kristy R Stengel
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Pankaj Acharya
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Gretchen Johnston
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Scott W Hiebert
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.,Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Yu Shyr
- Center for Quantitative Sciences, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.,Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.,Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.,Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
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Myc target gene, long intergenic noncoding RNA, Linc00176 in hepatocellular carcinoma regulates cell cycle and cell survival by titrating tumor suppressor microRNAs. Oncogene 2017; 37:75-85. [DOI: 10.1038/onc.2017.312] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 07/25/2017] [Accepted: 07/28/2017] [Indexed: 12/12/2022]
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42
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Goldie BJ, Fitzsimmons C, Weidenhofer J, Atkins JR, Wang DO, Cairns MJ. miRNA Enriched in Human Neuroblast Nuclei Bind the MAZ Transcription Factor and Their Precursors Contain the MAZ Consensus Motif. Front Mol Neurosci 2017; 10:259. [PMID: 28878619 PMCID: PMC5573442 DOI: 10.3389/fnmol.2017.00259] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 07/31/2017] [Indexed: 12/31/2022] Open
Abstract
While the cytoplasmic function of microRNA (miRNA) as post-transcriptional regulators of mRNA has been the subject of significant research effort, their activity in the nucleus is less well characterized. Here we use a human neuronal cell model to show that some mature miRNA are preferentially enriched in the nucleus. These molecules were predominantly primate-specific and contained a sequence motif with homology to the consensus MAZ transcription factor binding element. Precursor miRNA containing this motif were shown to have affinity for MAZ protein in nuclear extract. We then used Ago1/2 RIP-Seq to explore nuclear miRNA-associated mRNA targets. Interestingly, the genes for Ago2-associated transcripts were also significantly enriched with MAZ binding sites and neural function, whereas Ago1-transcripts were associated with general metabolic processes and localized with SC35 spliceosomes. These findings suggest the MAZ transcription factor is associated with miRNA in the nucleus and may influence the regulation of neuronal development through Ago2-associated miRNA induced silencing complexes. The MAZ transcription factor may therefore be important for organizing higher order integration of transcriptional and post-transcriptional processes in primate neurons.
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Affiliation(s)
- Belinda J Goldie
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, CallaghanNSW, Australia.,Centre for Brain and Mental Health Research, Hunter Medical Research Institute, The University of Newcastle, CallaghanNSW, Australia.,World Premier International Research Center - Institute for Integrated Cell-Material Sciences, Kyoto UniversityKyoto, Japan
| | - Chantel Fitzsimmons
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, CallaghanNSW, Australia.,Centre for Brain and Mental Health Research, Hunter Medical Research Institute, The University of Newcastle, CallaghanNSW, Australia
| | - Judith Weidenhofer
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, CallaghanNSW, Australia
| | - Joshua R Atkins
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, CallaghanNSW, Australia.,Centre for Brain and Mental Health Research, Hunter Medical Research Institute, The University of Newcastle, CallaghanNSW, Australia
| | - Dan O Wang
- World Premier International Research Center - Institute for Integrated Cell-Material Sciences, Kyoto UniversityKyoto, Japan.,The Keihanshin Consortium for Fostering the Next Generation of Global Leaders in ResearchKyoto, Japan
| | - Murray J Cairns
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, CallaghanNSW, Australia.,Centre for Brain and Mental Health Research, Hunter Medical Research Institute, The University of Newcastle, CallaghanNSW, Australia
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Yu ZH, Lun SM, He R, Tian HP, Huang HJ, Wang QS, Li XQ, Feng YM. Dual function of MAZ mediated by FOXF2 in basal-like breast cancer: Promotion of proliferation and suppression of progression. Cancer Lett 2017; 402:142-152. [DOI: 10.1016/j.canlet.2017.05.020] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 05/03/2017] [Accepted: 05/24/2017] [Indexed: 11/16/2022]
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Zhao M, Zhang WQ, Liu JL. A study on regional differences in decidualization of the mouse uterus. Reproduction 2017; 153:645-653. [PMID: 28250238 DOI: 10.1530/rep-16-0486] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Revised: 02/06/2017] [Accepted: 02/28/2017] [Indexed: 01/01/2023]
Abstract
Although regional differences in mouse decidualization have been recognized for decades, the molecular mechanisms remain understudied. In the present study, by using RNA-seq, we compared transcriptomic differences between the anti-mesometrial (AM) region and the mesometrial (M) region of mouse uterus on day 8 of pregnancy. A total of 1423 differentially expressed genes were identified, of which 811 genes were upregulated and 612 genes were downregulated in the AM region compared to those in the M region. Gene ontology analysis showed that upregulated genes were generally involved in cell metabolism and differentiation, whereas downregulated genes were associated with lymphocyte themes and immune response. Through network analysis, we identified a total of 6 hub genes. These hub genes are likely more important than other genes due to their key positions in the network. We also examined the promoter regions of differentially expressed genes for the enrichment of transcription factor-binding sites. In the end, we demonstrated that a similar regional gene expression pattern can be observed in the artificial decidualization model. Our study contributes to an increase in the knowledge on the molecular mechanisms underlying regional decidualization in mice.
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Affiliation(s)
- Miao Zhao
- College of Veterinary MedicineSouth China Agricultural University, Guangzhou, China
| | - Wen-Qian Zhang
- College of Veterinary MedicineSouth China Agricultural University, Guangzhou, China
| | - Ji-Long Liu
- College of Veterinary MedicineSouth China Agricultural University, Guangzhou, China
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45
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Andlauer TFM, Buck D, Antony G, Bayas A, Bechmann L, Berthele A, Chan A, Gasperi C, Gold R, Graetz C, Haas J, Hecker M, Infante-Duarte C, Knop M, Kümpfel T, Limmroth V, Linker RA, Loleit V, Luessi F, Meuth SG, Mühlau M, Nischwitz S, Paul F, Pütz M, Ruck T, Salmen A, Stangel M, Stellmann JP, Stürner KH, Tackenberg B, Then Bergh F, Tumani H, Warnke C, Weber F, Wiendl H, Wildemann B, Zettl UK, Ziemann U, Zipp F, Arloth J, Weber P, Radivojkov-Blagojevic M, Scheinhardt MO, Dankowski T, Bettecken T, Lichtner P, Czamara D, Carrillo-Roa T, Binder EB, Berger K, Bertram L, Franke A, Gieger C, Herms S, Homuth G, Ising M, Jöckel KH, Kacprowski T, Kloiber S, Laudes M, Lieb W, Lill CM, Lucae S, Meitinger T, Moebus S, Müller-Nurasyid M, Nöthen MM, Petersmann A, Rawal R, Schminke U, Strauch K, Völzke H, Waldenberger M, Wellmann J, Porcu E, Mulas A, Pitzalis M, Sidore C, Zara I, Cucca F, Zoledziewska M, Ziegler A, Hemmer B, Müller-Myhsok B. Novel multiple sclerosis susceptibility loci implicated in epigenetic regulation. SCIENCE ADVANCES 2016; 2:e1501678. [PMID: 27386562 PMCID: PMC4928990 DOI: 10.1126/sciadv.1501678] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 04/27/2016] [Indexed: 05/11/2023]
Abstract
We conducted a genome-wide association study (GWAS) on multiple sclerosis (MS) susceptibility in German cohorts with 4888 cases and 10,395 controls. In addition to associations within the major histocompatibility complex (MHC) region, 15 non-MHC loci reached genome-wide significance. Four of these loci are novel MS susceptibility loci. They map to the genes L3MBTL3, MAZ, ERG, and SHMT1. The lead variant at SHMT1 was replicated in an independent Sardinian cohort. Products of the genes L3MBTL3, MAZ, and ERG play important roles in immune cell regulation. SHMT1 encodes a serine hydroxymethyltransferase catalyzing the transfer of a carbon unit to the folate cycle. This reaction is required for regulation of methylation homeostasis, which is important for establishment and maintenance of epigenetic signatures. Our GWAS approach in a defined population with limited genetic substructure detected associations not found in larger, more heterogeneous cohorts, thus providing new clues regarding MS pathogenesis.
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Affiliation(s)
- Till F. M. Andlauer
- Max Planck Institute of Psychiatry, 80804 Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), 81377 Munich, Germany
| | - Dorothea Buck
- Department of Neurology, Klinikum rechts der Isar, Technical University of Munich, 81675 Munich, Germany
| | - Gisela Antony
- Central Information Office KKNMS, Philipps University Marburg, 35043 Marburg, Germany
| | - Antonios Bayas
- Department of Neurology, Klinikum Augsburg, 86156 Augsburg, Germany
| | - Lukas Bechmann
- Department of Neurology, University of Leipzig, 04103 Leipzig, Germany
- Institute of Medical Microbiology, Otto-von-Guericke University, 39120 Magdeburg, Germany
| | - Achim Berthele
- Department of Neurology, Klinikum rechts der Isar, Technical University of Munich, 81675 Munich, Germany
| | - Andrew Chan
- Department of Neurology, St. Josef Hospital, Ruhr-University Bochum, 44791 Bochum, Germany
- Department of Neurology, University Hospital Bern and University of Bern, 3010 Bern, Switzerland
| | - Christiane Gasperi
- Department of Neurology, Klinikum rechts der Isar, Technical University of Munich, 81675 Munich, Germany
| | - Ralf Gold
- Department of Neurology, St. Josef Hospital, Ruhr-University Bochum, 44791 Bochum, Germany
| | - Christiane Graetz
- Department of Neurology, Focus Program Translational Neurosciences (FTN) and Research Center for Immunotherapy (FZI), Rhine-Main Neuroscience Network (rmn), University Medical Center of the Johannes Gutenberg University Mainz, 55131 Mainz, Germany
| | - Jürgen Haas
- Department of Neurology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Michael Hecker
- Department of Neurology, University of Rostock, 18147 Rostock, Germany
| | - Carmen Infante-Duarte
- NeuroCure Clinical Research Center, Department of Neurology, and Experimental and Clinical Research Center, Max Delbrück Center for Molecular Medicine, and Charité University Medicine Berlin, 10117 Berlin, Germany
| | - Matthias Knop
- Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Tania Kümpfel
- Institute of Clinical Neuroimmunology, Ludwigs-Maximilians-Universität, 81377 Munich, Germany
| | - Volker Limmroth
- Department of Neurology, Hospital Köln-Merheim, 51109 Köln, Germany
| | - Ralf A. Linker
- Department of Neurology, University Hospital Erlangen, 91054 Erlangen, Germany
| | - Verena Loleit
- Department of Neurology, Klinikum rechts der Isar, Technical University of Munich, 81675 Munich, Germany
| | - Felix Luessi
- Department of Neurology, Focus Program Translational Neurosciences (FTN) and Research Center for Immunotherapy (FZI), Rhine-Main Neuroscience Network (rmn), University Medical Center of the Johannes Gutenberg University Mainz, 55131 Mainz, Germany
| | - Sven G. Meuth
- Department of Neurology, Klinik für Allgemeine Neurologie, University of Münster, 48149 Münster, Germany
| | - Mark Mühlau
- Munich Cluster for Systems Neurology (SyNergy), 81377 Munich, Germany
- Department of Neurology, Klinikum rechts der Isar, Technical University of Munich, 81675 Munich, Germany
| | | | - Friedemann Paul
- NeuroCure Clinical Research Center, Department of Neurology, and Experimental and Clinical Research Center, Max Delbrück Center for Molecular Medicine, and Charité University Medicine Berlin, 10117 Berlin, Germany
| | - Michael Pütz
- Clinical Neuroimmunology Group, Department of Neurology, Philipps-University of Marburg, 35043 Marburg, Germany
| | - Tobias Ruck
- Department of Neurology, Klinik für Allgemeine Neurologie, University of Münster, 48149 Münster, Germany
| | - Anke Salmen
- Department of Neurology, St. Josef Hospital, Ruhr-University Bochum, 44791 Bochum, Germany
- Department of Neurology, University Hospital Bern and University of Bern, 3010 Bern, Switzerland
| | - Martin Stangel
- Department of Neurology, Hannover Medical School, 30625 Hannover, Germany
| | - Jan-Patrick Stellmann
- Institute of Neuroimmunology and Multiple Sclerosis and Department of Neurology, University Medical Centre Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Klarissa H. Stürner
- Institute of Neuroimmunology and Multiple Sclerosis and Department of Neurology, University Medical Centre Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Björn Tackenberg
- Clinical Neuroimmunology Group, Department of Neurology, Philipps-University of Marburg, 35043 Marburg, Germany
| | - Florian Then Bergh
- Department of Neurology and Translational Center for Regenerative Medicine, University of Leipzig, 04103 Leipzig, Germany
| | - Hayrettin Tumani
- Department of Neurology, University of Ulm, 89081 Ulm, Germany
- Neurological Clinic Dietenbronn, 88477 Schwendi, Germany
| | - Clemens Warnke
- Department of Neurology, Medical Faculty, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Frank Weber
- Max Planck Institute of Psychiatry, 80804 Munich, Germany
- Neurological Clinic, Medical Park, 65520 Bad Camberg, Germany
| | - Heinz Wiendl
- Department of Neurology, Klinik für Allgemeine Neurologie, University of Münster, 48149 Münster, Germany
| | - Brigitte Wildemann
- Department of Neurology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Uwe K. Zettl
- Department of Neurology, University of Rostock, 18147 Rostock, Germany
| | - Ulf Ziemann
- Department of Neurology and Stroke, and Hertie Institute for Clinical Brain Research, Eberhard-Karls-Universität Tübingen, 72076 Tübingen, Germany
| | - Frauke Zipp
- Department of Neurology, Focus Program Translational Neurosciences (FTN) and Research Center for Immunotherapy (FZI), Rhine-Main Neuroscience Network (rmn), University Medical Center of the Johannes Gutenberg University Mainz, 55131 Mainz, Germany
| | - Janine Arloth
- Max Planck Institute of Psychiatry, 80804 Munich, Germany
- Institute of Computational Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Peter Weber
- Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | | | - Markus O. Scheinhardt
- Institut für Medizinische Biometrie und Statistik, Universität zu Lübeck, Universitätsklinikum Schleswig-Holstein, Campus Lübeck, 23562 Lübeck, Germany
| | - Theresa Dankowski
- Institut für Medizinische Biometrie und Statistik, Universität zu Lübeck, Universitätsklinikum Schleswig-Holstein, Campus Lübeck, 23562 Lübeck, Germany
| | | | - Peter Lichtner
- Institute of Human Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
- Institute of Human Genetics, Technische Universität München, 81675 Munich, Germany
| | - Darina Czamara
- Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | | | - Elisabeth B. Binder
- Max Planck Institute of Psychiatry, 80804 Munich, Germany
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA 30329, USA
| | - Klaus Berger
- Institut für Epidemiologie und Sozialmedizin der Universität Münster, 48149 Münster, Germany
| | - Lars Bertram
- Lübeck Interdisciplinary Platform for Genome Analytics, Institutes of Neurogenetics and Integrative and Experimental Genomics, University of Lübeck, 23562 Lübeck, Germany
- School of Public Health, Faculty of Medicine, Imperial College London, SW7 2AZ London, UK
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, 24105 Kiel, Germany
| | - Christian Gieger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Stefan Herms
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany
- Department of Biomedicine, Division of Medical Genetics, University of Basel, 4031 Basel, Switzerland
| | - Georg Homuth
- Interfaculty Institute for Genetics and Functional Genomics, Ernst Moritz Arndt University and University Medicine Greifswald, 17475 Greifswald, Germany
| | - Marcus Ising
- Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Karl-Heinz Jöckel
- Institute of Medical Informatics, Biometry, and Epidemiology, University Hospital Essen, University Duisburg-Essen, 45122 Essen, Germany
| | - Tim Kacprowski
- Interfaculty Institute for Genetics and Functional Genomics, Ernst Moritz Arndt University and University Medicine Greifswald, 17475 Greifswald, Germany
| | - Stefan Kloiber
- Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Matthias Laudes
- Department I of Internal Medicine, Kiel University, 24105 Kiel, Germany
| | - Wolfgang Lieb
- Institute of Epidemiology and Biobank popgen, Kiel University, 24105 Kiel, Germany
| | - Christina M. Lill
- Department of Neurology, Focus Program Translational Neurosciences (FTN) and Research Center for Immunotherapy (FZI), Rhine-Main Neuroscience Network (rmn), University Medical Center of the Johannes Gutenberg University Mainz, 55131 Mainz, Germany
- Lübeck Interdisciplinary Platform for Genome Analytics, Institutes of Neurogenetics and Integrative and Experimental Genomics, University of Lübeck, 23562 Lübeck, Germany
| | - Susanne Lucae
- Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
- Institute of Human Genetics, Technische Universität München, 81675 Munich, Germany
| | - Susanne Moebus
- Institute of Medical Informatics, Biometry, and Epidemiology, University Hospital Essen, University Duisburg-Essen, 45122 Essen, Germany
| | - Martina Müller-Nurasyid
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
- Department of Medicine I, Ludwig-Maximilians-Universität, 81377 Munich, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, 80802 Munich, Germany
| | - Markus M. Nöthen
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany
| | - Astrid Petersmann
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Rajesh Rawal
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Ulf Schminke
- Department of Neurology, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
- Institute of Medical Informatics, Biometry, and Epidemiology, Chair of Genetic Epidemiology, Ludwig-Maximilians-Universität, 81377 Munich, Germany
| | - Henry Völzke
- Institute for Community Medicine, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Jürgen Wellmann
- Institut für Epidemiologie und Sozialmedizin der Universität Münster, 48149 Münster, Germany
| | - Eleonora Porcu
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Monserrato, 09042 Cagliari, Italy
| | - Antonella Mulas
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Monserrato, 09042 Cagliari, Italy
- Dipartimento di Scienze Biomediche, Università degli Studi di Sassari, 07100 Sassari, Italy
| | - Maristella Pitzalis
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Monserrato, 09042 Cagliari, Italy
| | - Carlo Sidore
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Monserrato, 09042 Cagliari, Italy
| | - Ilenia Zara
- Center for Advanced Studies, Research and Development in Sardinia (CRS4), Pula, 09010 Cagliari, Italy
| | - Francesco Cucca
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Monserrato, 09042 Cagliari, Italy
- Dipartimento di Scienze Biomediche, Università degli Studi di Sassari, 07100 Sassari, Italy
| | - Magdalena Zoledziewska
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Monserrato, 09042 Cagliari, Italy
- Dipartimento di Scienze Biomediche, Università degli Studi di Sassari, 07100 Sassari, Italy
| | - Andreas Ziegler
- Institut für Medizinische Biometrie und Statistik, Universität zu Lübeck, Universitätsklinikum Schleswig-Holstein, Campus Lübeck, 23562 Lübeck, Germany
- Zentrum für Klinische Studien, Universität zu Lübeck, 23562 Lübeck, Germany
- School of Mathematics, Statistics, and Computer Science, University of KwaZulu-Natal, Pietermaritzburg, Scottsville 3209, South Africa
| | - Bernhard Hemmer
- Munich Cluster for Systems Neurology (SyNergy), 81377 Munich, Germany
- Department of Neurology, Klinikum rechts der Isar, Technical University of Munich, 81675 Munich, Germany
- Corresponding author. (B.H.); (B.M.-M.)
| | - Bertram Müller-Myhsok
- Max Planck Institute of Psychiatry, 80804 Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), 81377 Munich, Germany
- Institute of Translational Medicine, University of Liverpool, Liverpool L69 3BX, UK
- Corresponding author. (B.H.); (B.M.-M.)
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Akt phosphorylates myc-associated zinc finger protein (MAZ), releases P-MAZ from the p53 promoter, and activates p53 transcription. Cancer Lett 2016; 375:9-19. [DOI: 10.1016/j.canlet.2016.02.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 02/12/2016] [Accepted: 02/12/2016] [Indexed: 11/21/2022]
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47
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Franz H, Greschik H, Willmann D, Ozretić L, Jilg CA, Wardelmann E, Jung M, Buettner R, Schüle R. The histone code reader SPIN1 controls RET signaling in liposarcoma. Oncotarget 2016; 6:4773-89. [PMID: 25749382 PMCID: PMC4467114 DOI: 10.18632/oncotarget.3000] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 12/21/2014] [Indexed: 12/20/2022] Open
Abstract
The histone code reader Spindlin1 (SPIN1) has been implicated in tumorigenesis and tumor growth, but the underlying molecular mechanisms remain poorly understood. Here, we show that reducing SPIN1 levels strongly impairs proliferation and increases apoptosis of liposarcoma cells in vitro and in xenograft mouse models. Combining signaling pathway, genome-wide chromatin binding, and transcriptome analyses, we found that SPIN1 directly enhances expression of GDNF, an activator of the RET signaling pathway, in cooperation with the transcription factor MAZ. Accordingly, knockdown of SPIN1 or MAZ results in reduced levels of GDNF and activated RET explaining diminished liposarcoma cell proliferation and survival. In line with these observations, levels of SPIN1, GDNF, activated RET, and MAZ are increased in human liposarcoma compared to normal adipose tissue or lipoma. Importantly, a mutation of SPIN1 within the reader domain interfering with chromatin binding reduces liposarcoma cell proliferation and survival. Together, our data describe a molecular mechanism for SPIN1 function in liposarcoma and suggest that targeting SPIN1 chromatin association with small molecule inhibitors may represent a novel therapeutic strategy.
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Affiliation(s)
- Henriette Franz
- Urologische Klinik und Zentrale Klinische Forschung, Klinikum der Universität Freiburg, Freiburg, Germany
| | - Holger Greschik
- Urologische Klinik und Zentrale Klinische Forschung, Klinikum der Universität Freiburg, Freiburg, Germany
| | - Dominica Willmann
- Urologische Klinik und Zentrale Klinische Forschung, Klinikum der Universität Freiburg, Freiburg, Germany
| | - Luka Ozretić
- Universitätsklinikum Köln, Institut für Pathologie, Köln, Germany
| | - Cordula Annette Jilg
- Urologische Klinik und Zentrale Klinische Forschung, Klinikum der Universität Freiburg, Freiburg, Germany
| | - Eva Wardelmann
- Universitätsklinikum Münster, Gerhard-Domagk-Insitut für Pathologie, Münster, Germany
| | - Manfred Jung
- Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany.,Deutsches Konsortium für Translationale Krebsforschung (DKTK), Standort Freiburg, Germany
| | | | - Roland Schüle
- Urologische Klinik und Zentrale Klinische Forschung, Klinikum der Universität Freiburg, Freiburg, Germany.,BIOSS Centre of Biological Signaling Studies, Albert-Ludwigs-University, Freiburg, Germany.,Deutsches Konsortium für Translationale Krebsforschung (DKTK), Standort Freiburg, Germany
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48
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Podbevšek P, Plavec J. KRAS promoter oligonucleotide with decoy activity dimerizes into a unique topology consisting of two G-quadruplex units. Nucleic Acids Res 2015; 44:917-25. [PMID: 26656490 PMCID: PMC4737153 DOI: 10.1093/nar/gkv1359] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 11/23/2015] [Indexed: 12/31/2022] Open
Abstract
Mutations of the KRAS proto-oncogene are associated with several tumor types, which is why it is being considered as a target for anti-cancer drug development. The human KRAS promoter contains a nuclease hypersensitive element (NHE), which can bind to nuclear proteins and is believed to form G-quadruplex structures. Previous studies showed that a 32-nt oligonucleotide (32R-3n) mimicking the KRAS NHE can reduce gene transcription by sequestering MAZ, a crucial transcription factor. Here we show that 32R-3n has to dimerize in order to fold into a G-quadruplex structure. Individual 5′- and 3′-end G-quadruplex units are formed and both feature a symmetric head-to-head topology with edge-type loops. The MAZ binding sequence is located within the 3′-end unit. Nuclear magnetic resonance data complemented by CD and UV spectra show that nucleotides of the MAZ binding G-rich motif are dynamic and could be available for sequence or structure based recognition. Both stable G-quadruplex structures could protect 5′- and 3′-ends of 32R-3n and enhance its anti-cancer activity. Single stranded genomic KRAS NHE including nucleotides flanking the 32R-3n sequence could favor a different monomeric fold, which remains unknown.
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Affiliation(s)
- Peter Podbevšek
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia EN-FIST Centre of Excellence, Trg OF 13, SI-1000 Ljubljana, Slovenia
| | - Janez Plavec
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia EN-FIST Centre of Excellence, Trg OF 13, SI-1000 Ljubljana, Slovenia Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
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49
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A Transcriptomic Study of Maternal Thyroid Adaptation to Pregnancy in Rats. Int J Mol Sci 2015; 16:27339-49. [PMID: 26580608 PMCID: PMC4661888 DOI: 10.3390/ijms161126030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Revised: 11/03/2015] [Accepted: 11/10/2015] [Indexed: 01/22/2023] Open
Abstract
Thyroid disorders are relatively frequently observed in pregnant women. However, the impact of pregnancy on maternal thyroid has not been systematically evaluated. In the present study, using the rat as an animal model, we observed that the weight of maternal thyroid increased by about 18% in late pregnancy. To gain an insight into the molecular mechanisms, we took advantage of RNA-seq approaches to investigate global gene expression changes in the maternal thyroid. We identified a total of 615 differentially expressed genes, most of which (558 genes or 90.7%) were up-regulated in late pregnancy compared to the non-pregnant control. Gene ontology analysis showed that genes involved in cell cycle and metabolism were significantly enriched among up-regulated genes. Unexpectedly, pathway analysis revealed that expression levels for key components of the thyroid hormone synthesis pathway were not significantly altered. In addition, by examining of the promoter regions of up-regulated genes, we identified MAZ (MYC-associated zinc finger protein) and TFCP2 (transcription factor CP2) as two causal transcription factors. Our study contributes to an increase in the knowledge on the maternal thyroid adaptation to pregnancy.
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50
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Oh-Hashi K, Sone A, Hikiji T, Hirata Y, Vitiello M, Fedele M, Ishigaki S, Sobue G, Kiuchi K. Transcriptional and post-transcriptional regulation of transmembrane protein 132A. Mol Cell Biochem 2015; 405:291-9. [PMID: 25926156 DOI: 10.1007/s11010-015-2419-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 04/18/2015] [Indexed: 01/03/2023]
Abstract
Transmembrane protein 132A (TMEM132A) was first isolated from rat brain using PCR-selected cDNA subtraction, and it was found to be predominantly expressed in the brain. However, the transcriptional regulation of the TMEM132A gene has not been fully characterized. In this study, we characterized the promoter activity of the 880-bp region upstream of the mouse TMEM132A, identifying several putative sites recognized by transcription factors, which are highly conserved between the mouse and human TMEM132A genes. Using four different mouse cell lines (Neuro2a, NSC-34, NIH3T3, and Raw264.7), we first evaluated the intrinsic levels of TMEM132A mRNA and protein expression. Interestingly, TMEM132A mRNA was expressed in all four cell lines, whereas the protein was negligible in Raw264.7 cells even by transfection of TMEM132A gene. Then, we analyzed the TMEM132A promoter activity using serial deleted constructs, finding it was nearly same pattern in all four cell lines. A mutational analysis of the TMEM132A promoter identified a critical region for its activation just upstream of the transcriptional start site. Finally, we investigated the levels of TMEM132A mRNA and protein after exposure to five different neurotoxic stimuli, including thapsigargin, tunicamycin, serum starvation, homocysteine, and hydrogen peroxide. Treatment with thapsigargin, a calcium modulating agent, markedly attenuated the levels of TMEM132A mRNA and protein in NSC-34 cells. These results give new insight into the mechanisms involved in regulating TMEM132A expression, and suggest that several transcriptional and post-transcriptional pathways regulate TMEM132A expression under developmental and pathophysiological conditions.
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Affiliation(s)
- Kentaro Oh-Hashi
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan,
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