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Roesmann F, Sertznig H, Klaassen K, Wilhelm A, Heininger D, Heß S, Elsner C, Marschalek R, Santiago ML, Esser S, Sutter K, Dittmer U, Widera M. The interferon-regulated host factor hnRNPA0 modulates HIV-1 production by interference with LTR activity, mRNA trafficking, and programmed ribosomal frameshifting. J Virol 2024:e0053424. [PMID: 38899932 DOI: 10.1128/jvi.00534-24] [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: 03/23/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024] Open
Abstract
The interplay between host factors and viral components impacts viral replication efficiency profoundly. Members of the cellular heterogeneous nuclear ribonucleoprotein family (hnRNPs) have been extensively studied as HIV-1 host dependency factors, but whether they play a role in innate immunity is currently unknown. This study aimed to identify hnRNPA0 as a type I interferon (IFN)-repressed host factor in HIV-1-infected cells. Knockdown of hnRNPA0, a situation that mirrors conditions under IFN stimulation, increased LTR activity, export of unspliced HIV-1 mRNA, viral particle production, and thus, increased infectivity. Conversely, hnRNPA0 overexpression primarily reduced plasmid-driven and integrated HIV-1 long terminal repeat (LTR) activity, significantly decreasing total viral mRNA and protein levels. In addition, high levels of hnRNPA0 significantly reduced the HIV-1 programmed ribosomal frameshifting efficiency, resulting in a shift in the HIV-1 p55/p15 ratio. The HIV-1 alternative splice site usage remained largely unaffected by altered hnRNPA0 levels suggesting that the synergistic inhibition of the LTR activity and viral mRNA transcription, as well as impaired ribosomal frameshifting efficiency, are critical factors for efficient HIV-1 replication regulated by hnRNPA0. The pleiotropic dose-dependent effects under high or low hnRNPA0 levels were further confirmed in HIV-1-infected Jurkat cells. Finally, our study revealed that hnRNPA0 levels in PBMCs were lower in therapy-naive HIV-1-infected individuals compared to healthy controls. Our findings highlight a significant role for hnRNPA0 in HIV-1 replication and suggest that its IFN-I-regulated expression levels are critical for viral fitness allowing replication in an antiviral environment.IMPORTANCERNA-binding proteins, in particular, heterogeneous nuclear ribonucleoproteins (hnRNPs), have been extensively studied. Some act as host dependency factors for HIV-1 since they are involved in multiple cellular gene expression processes. Our study revealed hnRNPA0 as an IFN-regulated host factor, that is differently expressed after IFN-I treatment in HIV-1 target cells and lower expressed in therapy-naïve HIV-1-infected individuals. Our findings demonstrate the significant pleiotropic role of hnRNPA0 in viral replication: In high concentrations, hnRNPA0 limits viral replication by negatively regulating Tat-LTR transcription, retaining unspliced mRNA in the nucleus, and significantly impairing programmed ribosomal frameshifting. Low hnRNPA0 levels as observed in IFN-treated THP-1 cells, particularly facilitate HIV LTR activity and unspliced mRNA export, suggesting a role in innate immunity in favor of HIV replication. Understanding the mode of action between hnRNPA0 and HIV-1 gene expression might help to identify novel therapeutically strategies against HIV-1 and other viruses.
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Affiliation(s)
- Fabian Roesmann
- Goethe University Frankfurt, University Hospital, Institute for Medical Virology, Frankfurt, Germany
| | - Helene Sertznig
- Institute for Virology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Katleen Klaassen
- Goethe University Frankfurt, University Hospital, Institute for Medical Virology, Frankfurt, Germany
| | - Alexander Wilhelm
- Goethe University Frankfurt, University Hospital, Institute for Medical Virology, Frankfurt, Germany
| | - Delia Heininger
- Goethe University Frankfurt, University Hospital, Institute for Medical Virology, Frankfurt, Germany
| | - Stefanie Heß
- Goethe University Frankfurt, University Hospital, Institute for Medical Virology, Frankfurt, Germany
| | - Carina Elsner
- Institute for Virology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Rolf Marschalek
- Institute of Pharmaceutical Biology, Goethe-University, Frankfurt am Main, Hessen, Germany
| | - Mario L Santiago
- Department of Medicine, University of Colorado Denver, Aurora, Colorado, USA
| | - Stefan Esser
- Institute for the Research on HIV and AIDS-associated Diseases University Hospital Essen, University Duisburg-Essen, Essen, Germany
- Department of Dermatology, HPSTD Outpatient Clinic, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Kathrin Sutter
- Institute for Virology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
- Institute for the Research on HIV and AIDS-associated Diseases University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Ulf Dittmer
- Institute for Virology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
- Institute for the Research on HIV and AIDS-associated Diseases University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Marek Widera
- Goethe University Frankfurt, University Hospital, Institute for Medical Virology, Frankfurt, Germany
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2
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Jha RK, Kouzine F, Levens D. MYC function and regulation in physiological perspective. Front Cell Dev Biol 2023; 11:1268275. [PMID: 37941901 PMCID: PMC10627926 DOI: 10.3389/fcell.2023.1268275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 10/12/2023] [Indexed: 11/10/2023] Open
Abstract
MYC, a key member of the Myc-proto-oncogene family, is a universal transcription amplifier that regulates almost every physiological process in a cell including cell cycle, proliferation, metabolism, differentiation, and apoptosis. MYC interacts with several cofactors, chromatin modifiers, and regulators to direct gene expression. MYC levels are tightly regulated, and deregulation of MYC has been associated with numerous diseases including cancer. Understanding the comprehensive biology of MYC under physiological conditions is an utmost necessity to demark biological functions of MYC from its pathological functions. Here we review the recent advances in biological mechanisms, functions, and regulation of MYC. We also emphasize the role of MYC as a global transcription amplifier.
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Affiliation(s)
| | | | - David Levens
- Gene Regulation Section, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute (NCI), Bethesda, MD, United States
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3
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Lo R, Gonçalves-Carneiro D. Sensing nucleotide composition in virus RNA. Biosci Rep 2023; 43:BSR20230372. [PMID: 37606964 PMCID: PMC10500230 DOI: 10.1042/bsr20230372] [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: 06/13/2023] [Revised: 08/10/2023] [Accepted: 08/22/2023] [Indexed: 08/23/2023] Open
Abstract
Nucleotide composition plays a crucial role in the structure, function and recognition of RNA molecules. During infection, virus RNA is exposed to multiple endogenous proteins that detect local or global compositional biases and interfere with virus replication. Recent advancements in RNA:protein mapping technologies have enabled the identification of general RNA-binding preferences in the human proteome at basal level and in the context of virus infection. In this review, we explore how cellular proteins recognise nucleotide composition in virus RNA and the impact these interactions have on virus replication. Protein-binding G-rich and C-rich sequences are common examples of how host factors detect and limit infection, and, in contrast, viruses may have evolved to purge their genomes from such motifs. We also give examples of how human RNA-binding proteins inhibit virus replication, not only by destabilising virus RNA, but also by interfering with viral protein translation and genome encapsidation. Understanding the interplay between cellular proteins and virus RNA composition can provide insights into host-virus interactions and uncover potential targets for antiviral strategies.
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Affiliation(s)
- Raymon Lo
- Imperial College London, Department of Infectious Disease, Imperial College London, London, U.K
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Liu S, Duan Y, You R, Chen D, Tan J. HnRNP K regulates inflammatory gene expression by mediating splicing pattern of transcriptional factors. Exp Biol Med (Maywood) 2023; 248:1479-1491. [PMID: 35866661 PMCID: PMC10666726 DOI: 10.1177/15353702221110649] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 06/07/2022] [Indexed: 11/15/2022] Open
Abstract
HnRNP K is a heterogeneous nuclear ribonucleoprotein and has been identified as an oncogene in most solid tumors via regulating gene expression or alternative splicing of genes by binding both DNA and pre-mRNA. However, how hnRNP K affects tumorigenesis and regulates the gene expression in cervical cancer (CESC) remains to be elucidated. In these data, higher expression of hnRNP K was observed in CESC and was negatively correlated with the patient survival time. We then overexpressed hnRNP K (hnRNP K-OE) and found that its overexpression promoted cell proliferation in HeLa cells (P = 0.0052). Next, global transcriptome sequencing (RNA-seq) experiments were conducted to explore gene expression and alternative splicing profiles regulated by hnRNP K. It is shown that upregulated genes by hnRNP K-OE were associated with inflammatory response and an apoptotic process of neuron cells, which involves in cancer. In addition, the alternative splicing of those genes regulated by hnRNP K-OE was associated with transcriptional regulation. Analysis of the binding features of dysregulated transcription factors (TFs) in the promoter region of the inflammatory response genes regulated by hnRNP K revealed that hnRNP K may modulate the expression level of genes related to inflammatory response by influencing the alternative splicing of TFs. Among these hnRNP K-TFs-inflammatory gene regulatory networks, quantitative reverse transcription polymerase chain reaction (RT-qPCR) experiments and gene silencing were conducted to verify the hnRNP K-IRF1-CCL5 axis. In conclusion, the hnRNP K-TFs-inflammatory gene regulatory axis provides a novel molecular mechanism for hnRNP K in promoting CESC and offers a new therapeutic target.
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Affiliation(s)
- Siyi Liu
- Department of Orthopedics Trauma and Microsurgery, Zhongnan Hospital of Wuhan University, Wuchang District, Hubei 430071, China
| | - Yong Duan
- Department of Orthopedics Trauma and Microsurgery, Zhongnan Hospital of Wuhan University, Wuchang District, Hubei 430071, China
| | - Ran You
- Department of Orthopedics Trauma and Microsurgery, Zhongnan Hospital of Wuhan University, Wuchang District, Hubei 430071, China
| | - Dong Chen
- ABLife BioBigData Institute, Wuhan, Hubei 430075, China
| | - Jinhai Tan
- Department of Orthopedics Trauma and Microsurgery, Zhongnan Hospital of Wuhan University, Wuchang District, Hubei 430071, China
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Cho E, Che X, Ang MJ, Cheon S, Lee J, Kim KS, Lee CH, Lee SY, Yang HY, Moon C, Park C, Choi JY, Lee TH. Peroxiredoxin 5 regulates osteogenic differentiation through interaction with hnRNPK during bone regeneration. eLife 2023; 12:80122. [PMID: 36735291 PMCID: PMC9897727 DOI: 10.7554/elife.80122] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 01/18/2023] [Indexed: 02/04/2023] Open
Abstract
Peroxiredoxin 5 (Prdx5) is involved in pathophysiological regulation via the stress-induced cellular response. However, its function in the bone remains largely unknown. Here, we show that Prdx5 is involved in osteoclast and osteoblast differentiation, resulting in osteoporotic phenotypes in Prdx5 knockout (Prdx5Ko) male mice. To investigate the function of Prdx5 in the bone, osteoblasts were analyzed through immunoprecipitation (IP) and liquid chromatography combined with tandem mass spectrometry (LC-MS/MS) methods, while osteoclasts were analyzed through RNA-sequencing. Heterogeneous nuclear ribonucleoprotein K (hnRNPK) was identified as a potential binding partner of Prdx5 during osteoblast differentiation in vitro. Prdx5 acts as a negative regulator of hnRNPK-mediated osteocalcin (Bglap) expression. In addition, transcriptomic analysis revealed that in vitro differentiated osteoclasts from the bone marrow-derived macrophages of Prdx5Ko mice showed enhanced expression of several osteoclast-related genes. These findings indicate that Prdx5 might contribute to the maintenance of bone homeostasis by regulating osteoblast differentiation. This study proposes a new function of Prdx5 in bone remodeling that may be used in developing therapeutic strategies for bone diseases.
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Affiliation(s)
- Eunjin Cho
- Department of Oral Biochemistry, Korea Mouse Phenotype Center (KMPC), Dental Science Research Institute, School of Dentistry, Chonnam National UniversityGwangjuRepublic of Korea
| | - Xiangguo Che
- Department of Biochemistry and Cell Biology, BK21 Plus KNU Biomedical Convergence Program, Skeletal Diseases Analysis Center, Korea Mouse Phenotyping Center (KMPC), School of Medicine, Kyungpook National UniversityDaeguRepublic of Korea
| | - Mary Jasmin Ang
- Department of Basic Veterinary Sciences, College of Veterinary Medicine, University of the Philippines Los BañosLos BañosPhilippines
| | - Seongmin Cheon
- School of Biological Sciences and Technology, Chonnam National UniversityGwangjuRepublic of Korea,Proteomics Core Facility, Biomedical Research Institute, Seoul National University HospitalSeoulRepublic of Korea
| | - Jinkyung Lee
- Department of Oral Biochemistry, Korea Mouse Phenotype Center (KMPC), Dental Science Research Institute, School of Dentistry, Chonnam National UniversityGwangjuRepublic of Korea
| | - Kwang Soo Kim
- Department of Microbiology, Department of Molecular Medicine (BK21plus), Chonnam National University Medical SchoolGwangjuRepublic of Korea
| | - Chang Hoon Lee
- Therapeutic & Biotechnology Division, Drug Discovery Platform Research Center, Research Institute of Chemical Technology (KRICT)DaejeonRepublic of Korea
| | - Sang-Yeop Lee
- Research Center for Bioconvergence Analysis, Korea Basic Science InstituteOchangRepublic of Korea
| | - Hee-Young Yang
- Preclinical Research Center, Daegu-Gyeongbuk Medical Innovation FoundationDaeguRepublic of Korea
| | - Changjong Moon
- Department of Veterinary Anatomy and Animal Behavior, College of Veterinary Medicine and BK21 FOUR Program, Chonnam National UniversityGwangjuRepublic of Korea
| | - Chungoo Park
- School of Biological Sciences and Technology, Chonnam National UniversityGwangjuRepublic of Korea
| | - Je-Yong Choi
- Department of Biochemistry and Cell Biology, BK21 Plus KNU Biomedical Convergence Program, Skeletal Diseases Analysis Center, Korea Mouse Phenotyping Center (KMPC), School of Medicine, Kyungpook National UniversityDaeguRepublic of Korea
| | - Tae-Hoon Lee
- Department of Oral Biochemistry, Korea Mouse Phenotype Center (KMPC), Dental Science Research Institute, School of Dentistry, Chonnam National UniversityGwangjuRepublic of Korea
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Yokoi S, Ito T, Sahashi K, Nakatochi M, Nakamura R, Tohnai G, Fujioka Y, Ishigaki S, Udagawa T, Izumi Y, Morita M, Kano O, Oda M, Sone T, Okano H, Atsuta N, Katsuno M, Okada Y, Sobue G. The SYNGAP1 3'UTR Variant in ALS Patients Causes Aberrant SYNGAP1 Splicing and Dendritic Spine Loss by Recruiting HNRNPK. J Neurosci 2022; 42:8881-8896. [PMID: 36261283 PMCID: PMC9698725 DOI: 10.1523/jneurosci.0455-22.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 08/28/2022] [Accepted: 10/06/2022] [Indexed: 12/29/2022] Open
Abstract
Fused in sarcoma (FUS) is a pathogenic RNA-binding protein in amyotrophic lateral sclerosis (ALS). We previously reported that FUS stabilizes Synaptic Ras-GTPase activating protein 1 (Syngap1) mRNA at its 3' untranslated region (UTR) and maintains spine maturation. To elucidate the pathologic roles of this mechanism in ALS patients, we identified the SYNGAP1 3'UTR variant rs149438267 in seven (four males and three females) out of 807 ALS patients at the FUS binding site from a multicenter cohort in Japan. Human-induced pluripotent stem cell (hiPSC)-derived motor neurons with the SYNGAP1 variant showed aberrant splicing, increased isoform α1 levels, and decreased isoform γ levels, which caused dendritic spine loss. Moreover, the SYNGAP1 variant excessively recruited FUS and heterogeneous nuclear ribonucleoprotein K (HNRNPK), and antisense oligonucleotides (ASOs) blocking HNRNPK altered aberrant splicing and ameliorated dendritic spine loss. These data suggest that excessive recruitment of RNA-binding proteins, especially HNRNPK, as well as changes in SYNGAP1 isoforms, are crucial for spine formation in motor neurons.SIGNIFICANCE STATEMENT It is not yet known which RNAs cause the pathogenesis of amyotrophic lateral sclerosis (ALS). We previously reported that Fused in sarcoma (FUS), a pathogenic RNA-binding protein in ALS, stabilizes synaptic Ras-GTPase activating protein 1 (Syngap1) mRNA at its 3' untranslated region (UTR) and maintains dendritic spine maturation. To elucidate whether this mechanism is crucial for ALS, we identified the SYNGAP1 3'UTR variant rs149438267 at the FUS binding site. Human-induced pluripotent stem cell (hiPSC)-derived motor neurons with the SYNGAP1 variant showed aberrant splicing, which caused dendritic spine loss along with excessive recruitment of FUS and heterogeneous nuclear ribonucleoprotein K (HNRNPK). Our findings that dendritic spine loss is because of excess recruitment of RNA-binding proteins provide a basis for the future exploration of ALS-related RNA-binding proteins.
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Affiliation(s)
- Satoshi Yokoi
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Takuji Ito
- Department of Neurology, Aichi Medical University School of Medicine, Aichi 480-1195, Japan
- Department of Neural iPSC Research, Institute for Medical Science of Aging, Aichi Medical University, Aichi 480-1195, Japan
| | - Kentaro Sahashi
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Masahiro Nakatochi
- Public Health Informatics Unit, Department of Integrated Health Sciences, Nagoya University Graduate School of Medicine, Nagoya 461-8673, Japan
| | - Ryoichi Nakamura
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
- Department of Neurology, Aichi Medical University School of Medicine, Aichi 480-1195, Japan
| | - Genki Tohnai
- Division of ALS Research, Aichi Medical University, Aichi 480-1195, Japan
| | - Yusuke Fujioka
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Shinsuke Ishigaki
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
- Research Division of Dementia and Neurodegenerative Disease, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Tsuyoshi Udagawa
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya 467-8603, Japan
| | - Yuishin Izumi
- Department of Neurology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan
| | - Mitsuya Morita
- Division of Neurology, Department of Internal Medicine, Jichi Medical University, Shimotsuke 329-0498, Japan
| | - Osamu Kano
- Department of Neurology, Toho University Faculty of Medicine, Tokyo 143-8540, Japan
| | - Masaya Oda
- Department of Neurology, Vihara Hananosato Hospital, Miyoshi 728-0001, Japan
| | - Takefumi Sone
- Department of Physiology, Keio University School of Medicine, Tokyo 160-0016, Japan
| | - Hideyuki Okano
- Department of Physiology, Keio University School of Medicine, Tokyo 160-0016, Japan
| | - Naoki Atsuta
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
- Department of Neurology, Aichi Medical University School of Medicine, Aichi 480-1195, Japan
| | - Masahisa Katsuno
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Yohei Okada
- Department of Neurology, Aichi Medical University School of Medicine, Aichi 480-1195, Japan
- Department of Neural iPSC Research, Institute for Medical Science of Aging, Aichi Medical University, Aichi 480-1195, Japan
| | - Gen Sobue
- Research Division of Dementia and Neurodegenerative Disease, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
- Aichi Medical University, Aichi 480-1195, Japan
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Guo JT, Malik F. Single-Stranded DNA Binding Proteins and Their Identification Using Machine Learning-Based Approaches. Biomolecules 2022; 12:biom12091187. [PMID: 36139026 PMCID: PMC9496475 DOI: 10.3390/biom12091187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/11/2022] [Accepted: 08/24/2022] [Indexed: 11/25/2022] Open
Abstract
Single-stranded DNA (ssDNA) binding proteins (SSBs) are critical in maintaining genome stability by protecting the transient existence of ssDNA from damage during essential biological processes, such as DNA replication and gene transcription. The single-stranded region of telomeres also requires protection by ssDNA binding proteins from being attacked in case it is wrongly recognized as an anomaly. In addition to their critical roles in genome stability and integrity, it has been demonstrated that ssDNA and SSB-ssDNA interactions play critical roles in transcriptional regulation in all three domains of life and viruses. In this review, we present our current knowledge of the structure and function of SSBs and the structural features for SSB binding specificity. We then discuss the machine learning-based approaches that have been developed for the prediction of SSBs from double-stranded DNA (dsDNA) binding proteins (DSBs).
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Deletion of Hnrnpk Gene Causes Infertility in Male Mice by Disrupting Spermatogenesis. Cells 2022; 11:cells11081277. [PMID: 35455958 PMCID: PMC9028439 DOI: 10.3390/cells11081277] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/03/2022] [Accepted: 04/07/2022] [Indexed: 02/07/2023] Open
Abstract
HnRNPK is a heterogeneous nuclear ribonucleoprotein (hnRNP) that has been firmly implicated in transcriptional and post-transcriptional regulation. However, the molecular mechanisms by which hnRNPK orchestrates transcriptional or post-transcriptional regulation are not well understood due to early embryonic lethality in homozygous knockout mice, especially in a tissue-specific context. Strikingly, in this study, we demonstrated that hnRNPK is strongly expressed in the mouse testis and mainly localizes to the nucleus in spermatogonia, spermatocytes, and round spermatids, suggesting an important role for hnRNPK in spermatogenesis. Using a male germ cell-specific hnRNPK-depleted mouse model, we found that it is critical for testicular development and male fertility. The initiation of meiosis of following spermatogenesis was not affected in Hnrnpk cKO mice, while most germ cells were arrested at the pachytene stage of the meiosis and no mature sperm were detected in epididymides. The further RNA-seq analysis of Hnrnpk cKO mice testis revealed that the deletion of hnRNPK disturbed the expression of genes involved in male reproductive development, among which the meiosis genes were significantly affected, and Hnrnpk cKO spermatocytes failed to complete the meiotic prophase. Together, these results identify hnRNPK as an essential regulator of spermatogenesis and male fertility.
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Riccioni V, Trionfetti F, Montaldo C, Garbo S, Marocco F, Battistelli C, Marchetti A, Strippoli R, Amicone L, Cicchini C, Tripodi M. SYNCRIP Modulates the Epithelial-Mesenchymal Transition in Hepatocytes and HCC Cells. Int J Mol Sci 2022; 23:ijms23020913. [PMID: 35055098 PMCID: PMC8780347 DOI: 10.3390/ijms23020913] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/10/2022] [Accepted: 01/11/2022] [Indexed: 02/04/2023] Open
Abstract
Heterogeneous nuclear ribonucleoproteins (hnRNPs) control gene expression by acting at multiple levels and are often deregulated in epithelial tumors; however, their roles in the fine regulation of cellular reprogramming, specifically in epithelial–mesenchymal transition (EMT), remain largely unknown. Here, we focused on the hnRNP-Q (also known as SYNCRIP), showing by molecular analysis that in hepatocytes it acts as a “mesenchymal” gene, being induced by TGFβ and modulating the EMT. SYNCRIP silencing limits the induction of the mesenchymal program and maintains the epithelial phenotype. Notably, in HCC invasive cells, SYNCRIP knockdown induces a mesenchymal–epithelial transition (MET), negatively regulating their mesenchymal phenotype and significantly impairing their migratory capacity. In exploring possible molecular mechanisms underlying these observations, we identified a set of miRNAs (i.e., miR-181-a1-3p, miR-181-b1-3p, miR-122-5p, miR-200a-5p, and miR-let7g-5p), previously shown to exert pro- or anti-EMT activities, significantly impacted by SYNCRIP interference during EMT/MET dynamics and gathered insights, suggesting the possible involvement of this RNA binding protein in their transcriptional regulation.
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Affiliation(s)
- Veronica Riccioni
- Department of Molecular Medicine, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00161 Rome, Italy; (V.R.); (F.T.); (S.G.); (F.M.); (C.B.); (A.M.); (R.S.); (L.A.)
| | - Flavia Trionfetti
- Department of Molecular Medicine, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00161 Rome, Italy; (V.R.); (F.T.); (S.G.); (F.M.); (C.B.); (A.M.); (R.S.); (L.A.)
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, 00149 Rome, Italy;
| | - Claudia Montaldo
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, 00149 Rome, Italy;
| | - Sabrina Garbo
- Department of Molecular Medicine, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00161 Rome, Italy; (V.R.); (F.T.); (S.G.); (F.M.); (C.B.); (A.M.); (R.S.); (L.A.)
| | - Francesco Marocco
- Department of Molecular Medicine, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00161 Rome, Italy; (V.R.); (F.T.); (S.G.); (F.M.); (C.B.); (A.M.); (R.S.); (L.A.)
| | - Cecilia Battistelli
- Department of Molecular Medicine, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00161 Rome, Italy; (V.R.); (F.T.); (S.G.); (F.M.); (C.B.); (A.M.); (R.S.); (L.A.)
| | - Alessandra Marchetti
- Department of Molecular Medicine, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00161 Rome, Italy; (V.R.); (F.T.); (S.G.); (F.M.); (C.B.); (A.M.); (R.S.); (L.A.)
| | - Raffaele Strippoli
- Department of Molecular Medicine, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00161 Rome, Italy; (V.R.); (F.T.); (S.G.); (F.M.); (C.B.); (A.M.); (R.S.); (L.A.)
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, 00149 Rome, Italy;
| | - Laura Amicone
- Department of Molecular Medicine, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00161 Rome, Italy; (V.R.); (F.T.); (S.G.); (F.M.); (C.B.); (A.M.); (R.S.); (L.A.)
| | - Carla Cicchini
- Department of Molecular Medicine, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00161 Rome, Italy; (V.R.); (F.T.); (S.G.); (F.M.); (C.B.); (A.M.); (R.S.); (L.A.)
- Correspondence: (C.C.); (M.T.)
| | - Marco Tripodi
- Department of Molecular Medicine, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00161 Rome, Italy; (V.R.); (F.T.); (S.G.); (F.M.); (C.B.); (A.M.); (R.S.); (L.A.)
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, 00149 Rome, Italy;
- Correspondence: (C.C.); (M.T.)
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10
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Zhao H, Wei Z, Shen G, Chen Y, Hao X, Li S, Wang R. Poly(rC)-binding proteins as pleiotropic regulators in hematopoiesis and hematological malignancy. Front Oncol 2022; 12:1045797. [PMID: 36452487 PMCID: PMC9701828 DOI: 10.3389/fonc.2022.1045797] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 10/26/2022] [Indexed: 11/16/2022] Open
Abstract
Poly(rC)-binding proteins (PCBPs), a defined subfamily of RNA binding proteins, are characterized by their high affinity and sequence-specific interaction with poly-cytosine (poly-C). The PCBP family comprises five members, including hnRNP K and PCBP1-4. These proteins share a relatively similar structure motif, with triple hnRNP K homology (KH) domains responsible for recognizing and combining C-rich regions of mRNA and single- and double-stranded DNA. Numerous studies have indicated that PCBPs play a prominent role in hematopoietic cell growth, differentiation, and tumorigenesis at multiple levels of regulation. Herein, we summarized the currently available literature regarding the structural and functional divergence of various PCBP family members. Furthermore, we focused on their roles in normal hematopoiesis, particularly in erythropoiesis. More importantly, we also discussed and highlighted their involvement in carcinogenesis, including leukemia and lymphoma, aiming to clarify the pleiotropic roles and molecular mechanisms in the hematopoietic compartment.
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Affiliation(s)
- Huijuan Zhao
- Henan International Joint Laboratory of Thrombosis and Hemostasis, Henan University of Science and Technology, Luoyang, China.,Basic Medical College, Henan University of Science and Technology, Luoyang, China
| | - Ziqing Wei
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Guomin Shen
- Henan International Joint Laboratory of Thrombosis and Hemostasis, Henan University of Science and Technology, Luoyang, China.,Basic Medical College, Henan University of Science and Technology, Luoyang, China
| | - Yixiang Chen
- Henan International Joint Laboratory of Thrombosis and Hemostasis, Henan University of Science and Technology, Luoyang, China.,Basic Medical College, Henan University of Science and Technology, Luoyang, China
| | - Xueqin Hao
- Basic Medical College, Henan University of Science and Technology, Luoyang, China
| | - Sanqiang Li
- Basic Medical College, Henan University of Science and Technology, Luoyang, China
| | - Rong Wang
- Department of Clinical Laboratory, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, China
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11
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Puvvula PK, Buczkowski S, Moon AM. hnRNPK-derived cell-penetrating peptide inhibits cancer cell survival. Mol Ther Oncolytics 2021; 23:342-354. [PMID: 34820504 PMCID: PMC8586514 DOI: 10.1016/j.omto.2021.10.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 09/28/2021] [Accepted: 10/15/2021] [Indexed: 11/30/2022] Open
Abstract
hnRNPK is a multifunctional protein that plays an important role in cancer cell proliferation and metastasis via its RNA- and DNA-binding properties. Previously we showed that cell-penetrating peptides derived from the RGG RNA-binding domain of SAFA (hnRNPU) disrupt cancer cell proliferation and survival. Here we explore the efficacy of a peptide derived from the RGG domain of hnRNPK. This peptide acts in a dominant-negative manner on several hnRNPK functions to induce death of multiple types of cancer cells. The peptide phenocopies the effect of hnRNPK knockdown on its mRNA-stability targets such as KLF4 and EGR1 and alters the levels and locations of long non-coding RNAs (lncRNAs) and proteins required for nuclear and paraspeckle formation and function. The RGG-derived peptide also decreases euchromatin as evidenced by loss of active marks and polymerase II occupancy. Our findings reveal the potential therapeutic utility of the hnRNPK RGG-derived peptide in a range of cancers.
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Affiliation(s)
- Pavan Kumar Puvvula
- Department of Molecular and Functional Genomics, Weis Center for Research, Geisinger Clinic, Danville, PA, USA
- Corresponding author: Pavan Kumar Puvvula, PhD, Department of Molecular and Functional Genomics, Weis Center for Research, Geisinger Clinic, Danville, PA, USA.
| | - Stephanie Buczkowski
- Department of Molecular and Functional Genomics, Weis Center for Research, Geisinger Clinic, Danville, PA, USA
| | - Anne M. Moon
- Department of Molecular and Functional Genomics, Weis Center for Research, Geisinger Clinic, Danville, PA, USA
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
- The Mindich Child Health and Development Institute, Hess Center for Science and Medicine at Mount Sinai, New York, NY, USA
- Corresponding author: Anne M. Moon, MD, PhD, Department of Molecular and Functional Genomics, Weis Center for Research, Geisinger Clinic, Danville, PA, USA.
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12
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Cave JW, Willis DE. G-quadruplex regulation of neural gene expression. FEBS J 2021; 289:3284-3303. [PMID: 33905176 DOI: 10.1111/febs.15900] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 03/24/2021] [Accepted: 04/23/2021] [Indexed: 12/11/2022]
Abstract
G-quadruplexes are four-stranded helical nucleic acid structures characterized by stacked tetrads of guanosine bases. These structures are widespread throughout mammalian genomic DNA and RNA transcriptomes, and prevalent across all tissues. The role of G-quadruplexes in cancer is well-established, but there has been a growing exploration of these structures in the development and homeostasis of normal tissue. In this review, we focus on the roles of G-quadruplexes in directing gene expression in the nervous system, including the regulation of gene transcription, mRNA processing, and trafficking, as well as protein translation. The role of G-quadruplexes and their molecular interactions in the pathology of neurological diseases is also examined. Outside of cancer, there has been only limited exploration of G-quadruplexes as potential intervention targets to treat disease or injury. We discuss studies that have used small-molecule ligands to manipulate G-quadruplex stability in order to treat disease or direct neural stem/progenitor cell proliferation and differentiation into therapeutically relevant cell types. Understanding the many roles that G-quadruplexes have in the nervous system not only provides critical insight into fundamental molecular mechanisms that control neurological function, but also provides opportunities to identify novel therapeutic targets to treat injury and disease.
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Affiliation(s)
- John W Cave
- InVitro Cell Research LLC, Englewood, NJ, USA
| | - Dianna E Willis
- Burke Neurological Institute, White Plains, NY, USA.,Feil Family Brain & Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
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13
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Malaney P, Velasco-Estevez M, Aguilar-Garrido P, Aitken MJL, Chan LE, Zhang X, Post SM, Gallardo M. The Eµ-hnRNP K Murine Model of Lymphoma: Novel Insights into the Role of hnRNP K in B-Cell Malignancies. Front Immunol 2021; 12:634584. [PMID: 33912162 PMCID: PMC8072109 DOI: 10.3389/fimmu.2021.634584] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 03/23/2021] [Indexed: 01/18/2023] Open
Abstract
B-cell lymphomas are one of the most biologically and molecularly heterogeneous group of malignancies. The inherent complexity of this cancer subtype necessitates the development of appropriate animal model systems to characterize the disease with the ultimate objective of identifying effective therapies. In this article, we discuss a new driver of B-cell lymphomas - hnRNP K (heterogenous nuclear ribonucleoprotein K)-an RNA-binding protein. We introduce the Eµ-Hnrnpk mouse model, a murine model characterized by hnRNP K overexpression in B cells, which develops B-cell lymphomas with high penetrance. Molecular analysis of the disease developed in this model reveals an upregulation of the c-Myc oncogene via post-transcriptional and translational mechanisms underscoring the impact of non-genomic MYC activation in B-cell lymphomas. Finally, the transplantability of the disease developed in Eµ-Hnrnpk mice makes it a valuable pre-clinical platform for the assessment of novel therapeutics.
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MESH Headings
- Animals
- Animals, Genetically Modified
- B-Lymphocytes/immunology
- B-Lymphocytes/metabolism
- B-Lymphocytes/pathology
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/immunology
- Cell Transformation, Neoplastic/metabolism
- Cell Transformation, Neoplastic/pathology
- Disease Models, Animal
- Gene Expression Regulation, Neoplastic
- Genetic Predisposition to Disease
- Heterogeneous-Nuclear Ribonucleoprotein K/genetics
- Heterogeneous-Nuclear Ribonucleoprotein K/metabolism
- Lymphoma, B-Cell/genetics
- Lymphoma, B-Cell/immunology
- Lymphoma, B-Cell/metabolism
- Lymphoma, B-Cell/pathology
- Phenotype
- Proto-Oncogene Proteins c-myc/genetics
- Proto-Oncogene Proteins c-myc/metabolism
- Up-Regulation
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Affiliation(s)
- Prerna Malaney
- Department of Leukemia, MD Anderson Cancer Center, Houston, TX, United States
| | | | | | - Marisa J. L. Aitken
- Department of Leukemia, MD Anderson Cancer Center, Houston, TX, United States
| | - Lauren E. Chan
- Department of Leukemia, MD Anderson Cancer Center, Houston, TX, United States
| | - Xiaorui Zhang
- Department of Leukemia, MD Anderson Cancer Center, Houston, TX, United States
| | - Sean M. Post
- Department of Leukemia, MD Anderson Cancer Center, Houston, TX, United States
| | - Miguel Gallardo
- H12O–CNIO Haematological Malignancies Clinical Research Unit, CNIO, Madrid, Spain
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14
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Mahendra CK, Abidin SAZ, Htar TT, Chuah LH, Khan SU, Ming LC, Tang SY, Pusparajah P, Goh BH. Counteracting the Ramifications of UVB Irradiation and Photoaging with Swietenia macrophylla King Seed. Molecules 2021; 26:molecules26072000. [PMID: 33916053 PMCID: PMC8037697 DOI: 10.3390/molecules26072000] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/24/2021] [Accepted: 03/26/2021] [Indexed: 11/16/2022] Open
Abstract
In this day and age, the expectation of cosmetic products to effectively slow down skin photoaging is constantly increasing. However, the detrimental effects of UVB on the skin are not easy to tackle as UVB dysregulates a wide range of molecular changes on the cellular level. In our research, irradiated keratinocyte cells not only experienced a compromise in their redox system, but processes from RNA translation to protein synthesis and folding were also affected. Aside from this, proteins involved in various other processes like DNA repair and maintenance, glycolysis, cell growth, proliferation, and migration were affected while the cells approached imminent cell death. Additionally, the collagen degradation pathway was also activated by UVB irradiation through the upregulation of inflammatory and collagen degrading markers. Nevertheless, with the treatment of Swietenia macrophylla (S. macrophylla) seed extract and fractions, the dysregulation of many genes and proteins by UVB was reversed. The reversal effects were particularly promising with the S. macrophylla hexane fraction (SMHF) and S. macrophylla ethyl acetate fraction (SMEAF). SMHF was able to oppose the detrimental effects of UVB in several different processes such as the redox system, DNA repair and maintenance, RNA transcription to translation, protein maintenance and synthesis, cell growth, migration and proliferation, and cell glycolysis, while SMEAF successfully suppressed markers related to skin inflammation, collagen degradation, and cell apoptosis. Thus, in summary, our research not only provided a deeper insight into the molecular changes within irradiated keratinocytes, but also serves as a model platform for future cosmetic research to build upon. Subsequently, both SMHF and SMEAF also displayed potential photoprotective properties that warrant further fractionation and in vivo clinical trials to investigate and obtain potential novel bioactive compounds against photoaging.
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Affiliation(s)
- Camille Keisha Mahendra
- Biofunctional Molecule Exploratory Research Group, School of Pharmacy, Monash University Malaysia, Bandar Sunway 47500, Malaysia; (C.K.M.); (T.T.H.); (L.-H.C.); (S.U.K.)
| | - Syafiq Asnawi Zainal Abidin
- Liquid Chromatography Mass Spectrometry (LCMS) Platform, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway 47500, Malaysia;
| | - Thet Thet Htar
- Biofunctional Molecule Exploratory Research Group, School of Pharmacy, Monash University Malaysia, Bandar Sunway 47500, Malaysia; (C.K.M.); (T.T.H.); (L.-H.C.); (S.U.K.)
| | - Lay-Hong Chuah
- Biofunctional Molecule Exploratory Research Group, School of Pharmacy, Monash University Malaysia, Bandar Sunway 47500, Malaysia; (C.K.M.); (T.T.H.); (L.-H.C.); (S.U.K.)
| | - Shafi Ullah Khan
- Biofunctional Molecule Exploratory Research Group, School of Pharmacy, Monash University Malaysia, Bandar Sunway 47500, Malaysia; (C.K.M.); (T.T.H.); (L.-H.C.); (S.U.K.)
- Department of Pharmacy, Abasyn University, Peshawar 25000, Pakistan
| | - Long Chiau Ming
- PAP Rashidah Sa’adatul Bolkiah Institute of Health Sciences, Universiti Brunei Darussalam, Gadong BE1410, Brunei;
| | - Siah Ying Tang
- Chemical Engineering Discipline, School of Engineering, Monash University Malaysia, Bandar Sunway 47500, Malaysia;
- Advanced Engineering Platform, School of Engineering, Monash University Malaysia, Bandar Sunway 47500, Malaysia
- Tropical Medicine and Biology Platform, School of Science, Monash University Malaysia, Bandar Sunway 47500, Malaysia
| | - Priyia Pusparajah
- Medical Health and Translational Research Group, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway 47500, Malaysia
- Correspondence: (P.P.); (B.H.G.)
| | - Bey Hing Goh
- Biofunctional Molecule Exploratory Research Group, School of Pharmacy, Monash University Malaysia, Bandar Sunway 47500, Malaysia; (C.K.M.); (T.T.H.); (L.-H.C.); (S.U.K.)
- College of Pharmaceutical Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
- Health and Well-Being Cluster, Global Asia in the 21st Century (GA21) Platform, Monash University Malaysia, Bandar Sunway 47500, Malaysia
- Correspondence: (P.P.); (B.H.G.)
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15
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Kwon PK, Kim HM, Kang B, Kim SW, Hwang SM, Im SH, Roh TY, Kim KT. hnRNP K supports the maintenance of RORγ circadian rhythm through ERK signaling. FASEB J 2021; 35:e21507. [PMID: 33724572 DOI: 10.1096/fj.202002076r] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 02/11/2021] [Accepted: 02/22/2021] [Indexed: 11/11/2022]
Abstract
Retinoic acid-related orphan receptor γ (RORγ) maintains the circadian rhythms of its downstream genes. However, the mechanism behind the transcriptional activation of RORγ itself remains unclear. Here, we demonstrate that transcription of RORγ is activated by heterogeneous nuclear ribonucleoprotein K (hnRNP K) via the poly(C) motif within its proximal promoter. Interestingly, we confirmed the binding of endogenous hnRNP K within RORγ1 and RORγ2 promoter along with the recruitment of RNA polymerase 2 through chromatin immunoprecipitation (ChIP). Furthermore, an assay for transposase accessible chromatin (ATAC)-qPCR showed that hnRNP K induced higher chromatin accessibility within the RORγ1 and RORγ2 promoter. Then we found that the knockdown of hnRNP K lowers RORγ mRNA oscillation amplitude in both RORγ and RORγ-dependent metabolic genes. Moreover, we demonstrated that time-dependent extracellular signal-regulated kinase (ERK) activation controls mRNA oscillation of RORγ and RORγ-dependent metabolic genes through hnRNP K. Taken together, our results provide new insight into the regulation of RORγ by hnRNP K as a transcriptional activator, along with its physiological significance in metabolism.
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Affiliation(s)
- Paul Kwangho Kwon
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Hyo-Min Kim
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Byunghee Kang
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Sung Wook Kim
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Sung-Min Hwang
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Sin-Hyeog Im
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea.,Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Tae-Young Roh
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea.,Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Kyong-Tai Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea.,Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Republic of Korea
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16
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Wang S, Han C, Liu T, Ma Z, Qiu M, Wang J, You Q, Zheng X, Xu W, Xia W, Xu Y, Hu J, Xu L, Yin R. FAM83H-AS1 is a noncoding oncogenic driver and therapeutic target of lung adenocarcinoma. Clin Transl Med 2021; 11:e316. [PMID: 33634993 PMCID: PMC7882096 DOI: 10.1002/ctm2.316] [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: 08/22/2020] [Revised: 01/20/2021] [Accepted: 01/25/2021] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Little is known about noncoding oncogenes of lung adenocarcinoma (LUAD), and these potential drivers might provide novel therapeutic targets. METHODS Since abnormally overexpression of oncogenic drivers is induced by genomic variation, we here utilized genomic, transcriptomic, and clinical prognosis data of The Cancer Genome Atlas (TCGA) LUAD datasets to discover novel drivers from long noncoding RNAs. We further used zebrafish models to validate the biological function of candidates in vivo. The full length of FAM83H-AS1 was obtained by rapid amplification of the cDNA ends assay. RNA pull-down, RNA immunoprecipitation, quantitative mass spectrometry, and RNA sequencing assays were conducted to explore the potential mechanisms. Additionally, we used CRISPR interference (CRISPRi) method and patient-derived tumor xenograft (PDTX) model to evaluate the therapeutic potential of targeting FAM83H-AS1. RESULTS The results suggest that FAM83H-AS1 is a potential oncogenic driver due to chromosome 8q24 amplification. Upregulation of FAM83H-AS1 results in poor prognosis of LUAD patients in both Jiangsu Cancer Hospital (JSCH) and TCGA cohorts. Functional assays revealed that FAM83H-AS1 promotes malignant progression and inhibits apoptosis. Mechanistically, FAM83H-AS1 binds HNRNPK to enhance the translation of antiapoptotic oncogenes RAB8B and RAB14. Experiments using CRISPRi-mediated xenografts and PDTX models indicated that targeting FAM83H-AS1 inhibited LUAD progression in vivo. CONCLUSIONS Our work demonstrates that FAM83H-AS1 is a noncoding oncogenic driver that inhibits LUAD apoptosis via the FAM83H-AS1-HNRNPK-RAB8B/RAB14 axis, which highlights the importance and potential roles that FAM83H-AS1 may serve as a novel therapeutic target for LUAD.
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Affiliation(s)
- Siwei Wang
- Department of Thoracic Surgery, Jiangsu Key Laboratory of Molecular and Translational Cancer ResearchNanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer ResearchNanjingChina
| | - Chencheng Han
- Department of Thoracic Surgery, Jiangsu Key Laboratory of Molecular and Translational Cancer ResearchNanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer ResearchNanjingChina
| | - Tongyan Liu
- Department of Thoracic Surgery, Jiangsu Key Laboratory of Molecular and Translational Cancer ResearchNanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer ResearchNanjingChina
- Department of Science and technologyNanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer ResearchNanjingChina
| | - Zhifei Ma
- Department of Thoracic Surgery, Jiangsu Key Laboratory of Molecular and Translational Cancer ResearchNanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer ResearchNanjingChina
| | - Mantang Qiu
- Department of Thoracic SurgeryPeking University People's HospitalBeijingChina
| | - Jie Wang
- Department of Thoracic Surgery, Jiangsu Key Laboratory of Molecular and Translational Cancer ResearchNanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer ResearchNanjingChina
- Department of Science and technologyNanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer ResearchNanjingChina
- Biobank of Lung CancerJiangsu Biobank of Clinical ResourcesNanjingChina
| | - Qingjun You
- Department of Thoracic SurgeryThe Affiliated Hospital of Jiangnan UniversityWuxiChina
| | - Xiufen Zheng
- Department of Thoracic Surgery, Jiangsu Key Laboratory of Molecular and Translational Cancer ResearchNanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer ResearchNanjingChina
| | - Weizhang Xu
- Department of Thoracic Surgery, Jiangsu Key Laboratory of Molecular and Translational Cancer ResearchNanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer ResearchNanjingChina
| | - Wenjia Xia
- Department of Thoracic Surgery, Jiangsu Key Laboratory of Molecular and Translational Cancer ResearchNanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer ResearchNanjingChina
| | - Youtao Xu
- Department of Thoracic Surgery, Jiangsu Key Laboratory of Molecular and Translational Cancer ResearchNanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer ResearchNanjingChina
| | - Jingwen Hu
- Department of Thoracic Surgery, Jiangsu Key Laboratory of Molecular and Translational Cancer ResearchNanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer ResearchNanjingChina
| | - Lin Xu
- Department of Thoracic Surgery, Jiangsu Key Laboratory of Molecular and Translational Cancer ResearchNanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer ResearchNanjingChina
- Collaborative Innovation Center for Cancer Personalized MedicineNanjing Medical UniversityNanjingChina
| | - Rong Yin
- Department of Thoracic Surgery, Jiangsu Key Laboratory of Molecular and Translational Cancer ResearchNanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer ResearchNanjingChina
- Department of Science and technologyNanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer ResearchNanjingChina
- Biobank of Lung CancerJiangsu Biobank of Clinical ResourcesNanjingChina
- Collaborative Innovation Center for Cancer Personalized MedicineNanjing Medical UniversityNanjingChina
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17
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Brown SL, Kendrick S. The i-Motif as a Molecular Target: More Than a Complementary DNA Secondary Structure. Pharmaceuticals (Basel) 2021; 14:ph14020096. [PMID: 33513764 PMCID: PMC7911047 DOI: 10.3390/ph14020096] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/20/2021] [Accepted: 01/22/2021] [Indexed: 12/25/2022] Open
Abstract
Stretches of cytosine-rich DNA are capable of adopting a dynamic secondary structure, the i-motif. When within promoter regions, the i-motif has the potential to act as a molecular switch for controlling gene expression. However, i-motif structures in genomic areas of repetitive nucleotide sequences may play a role in facilitating or hindering expansion of these DNA elements. Despite research on the i-motif trailing behind the complementary G-quadruplex structure, recent discoveries including the identification of a specific i-motif antibody are pushing this field forward. This perspective reviews initial and current work characterizing the i-motif and providing insight into the biological function of this DNA structure, with a focus on how the i-motif can serve as a molecular target for developing new therapeutic approaches to modulate gene expression and extension of repetitive DNA.
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18
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Congrains A, Niemann FS, Duarte ADSS, Ferro KPV, Olalla-Saad ST. Novel Non-Coding Transcript in NR4A3 Locus, LncNR4A3, Regulates RNA Processing Machinery Proteins and NR4A3 Expression. Front Oncol 2020; 10:569668. [PMID: 33330042 PMCID: PMC7719789 DOI: 10.3389/fonc.2020.569668] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 10/19/2020] [Indexed: 11/30/2022] Open
Abstract
NR4A3 is a key tumor suppressor in myeloid malignancy, mice lacking both NR4A1 and family member NR4A3 rapidly develop lethal acute myeloid leukemia (AML). We identified a long non-coding transcript in the NR4A3 locus and pursued the characterization of this anonymous transcript and the study of its role in leukemogenesis. We characterized this novel long non-coding transcript as a sense polyadenylated transcript. Bone marrow cells from AML patients expressed significantly reduced levels of lncNR4A3 compared to healthy controls (controls = 15, MDS= 20, p=0.05., AML= 21, p<0.01). Expression of NR4A3, as previously reported, was also significantly reduced in AML. Interestingly, the expression of both coding and non-coding transcripts was highly correlated (Pearson R = 0.3771, P<0.01). Transient over-expression of LncNR4A3 by nucleofection led to an increase in the RNA and protein level of NR4A3, reduction of proliferation in myeloid cell lines K-562 and KG1 (n=3 and 2 respectively, p<0.05) and reduced colony formation capacity in primary leukemic cells. A mass spectrometry-based quantitative proteomics approach was used to identify proteins dysregulated after lncNR4A3 over-expression in K-562. Enrichment analysis showed that the altered proteins are biologically connected (n=4, p<0.001) and functionally associated to RNA binding, transcription elongation, and splicing. Remarkably, we were able to validate the most significant results by WB. We showed that this novel transcript, lncNR4A3 regulates NR4A3 and we hypothesize this regulatory mechanism is mediated by the modulation of the RNA processing machinery.
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Affiliation(s)
- Ada Congrains
- Hematology and Transfusion Medicine Center, University of Campinas, Campinas, Brazil
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19
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Low YH, Asi Y, Foti SC, Lashley T. Heterogeneous Nuclear Ribonucleoproteins: Implications in Neurological Diseases. Mol Neurobiol 2020; 58:631-646. [PMID: 33000450 PMCID: PMC7843550 DOI: 10.1007/s12035-020-02137-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 09/17/2020] [Indexed: 12/13/2022]
Abstract
Heterogenous nuclear ribonucleoproteins (hnRNPs) are a complex and functionally diverse family of RNA binding proteins with multifarious roles. They are involved, directly or indirectly, in alternative splicing, transcriptional and translational regulation, stress granule formation, cell cycle regulation, and axonal transport. It is unsurprising, given their heavy involvement in maintaining functional integrity of the cell, that their dysfunction has neurological implications. However, compared to their more established roles in cancer, the evidence of hnRNP implication in neurological diseases is still in its infancy. This review aims to consolidate the evidences for hnRNP involvement in neurological diseases, with a focus on spinal muscular atrophy (SMA), Alzheimer’s disease (AD), amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), multiple sclerosis (MS), congenital myasthenic syndrome (CMS), and fragile X-associated tremor/ataxia syndrome (FXTAS). Understanding more about hnRNP involvement in neurological diseases can further elucidate the pathomechanisms involved in these diseases and perhaps guide future therapeutic advances.
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Affiliation(s)
- Yi-Hua Low
- The Queen Square Brain Bank for Neurological Disorders, Department of Clinical and Movement Disorders, UCL Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK.,Duke-NUS Medical School, Singapore, Singapore
| | - Yasmine Asi
- The Queen Square Brain Bank for Neurological Disorders, Department of Clinical and Movement Disorders, UCL Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Sandrine C Foti
- The Queen Square Brain Bank for Neurological Disorders, Department of Clinical and Movement Disorders, UCL Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK.,Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Tammaryn Lashley
- The Queen Square Brain Bank for Neurological Disorders, Department of Clinical and Movement Disorders, UCL Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK. .,Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, UK.
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20
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Liu W, Yang D, Sun C, Wang H, Zhao B, Zhou G, Yu L. hnRNP K Is a Novel Internal Ribosomal Entry Site-Transacting Factor That Negatively Regulates Foot-and-Mouth Disease Virus Translation and Replication and Is Antagonized by Viral 3C Protease. J Virol 2020; 94:e00803-20. [PMID: 32581104 PMCID: PMC7431795 DOI: 10.1128/jvi.00803-20] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 06/16/2020] [Indexed: 12/26/2022] Open
Abstract
Cap-independent translation initiation on picornavirus mRNAs is mediated by an internal ribosomal entry site (IRES) in the 5' untranslated region. The regulation of internal initiation requires the interaction of IRES-transacting factors (ITAFs) with the IRES. In this study, we identified a novel ITAF, heterogeneous nuclear ribonucleoprotein K (hnRNP K), which negatively regulates foot-and-mouth disease virus (FMDV) translation and viral replication. Further investigation revealed that the KH2 and KH3 domains of hnRNP K directly bind to domains II, III, and IV of the FMDV IRES, resulting in the inhibition of IRES-mediated translation by interfering with the recognition of another positive ITAF, polypyrimidine tract-binding protein (PTB). Conversely, hnRNP K-mediated inhibition was antagonized by the viral 3C protease through the cleavage of hnRNP K at the Glu-364 residue during FMDV infection. Interestingly, the N-terminal cleavage product, hnRNP K1-364, retained partial inhibitory effects on IRES activity, whereas the C-terminal cleavage product, hnRNP K364-465, became a positive regulator of FMDV replication. Our findings expand the current understanding of virus-host interactions concerning viral recruitment and the modulation of ITAFs, providing new insights into translational control during viral infection.IMPORTANCE The translation of picornaviral genome RNA mediated by the internal ribosomal entry site (IRES) is a crucial step for virus infections. Virus-host interactions play a critical role in the regulation of IRES-dependent translation, but the regulatory mechanism remains largely unknown. In this study, we identified an ITAF, hnRNP K, that negatively regulates FMDV replication by inhibiting viral IRES-mediated translation. In addition, we describe a novel translational regulation mechanism involving the proteolytic cleavage of hnRNP K by FMDV protease 3C. The cleavage of hnRNP K yields two cleavage products with opposite functions: the cleavage product hnRNP K1-364 retains a partial inhibitory effect on IRES activity, and the cleavage product hnRNP K364-465 becomes a positive regulator of FMDV replication. Our findings shed light on the effect of a novel ITAF on the translational regulation of picornavirus and provide new insights into translational control during viral infection.
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Affiliation(s)
- Wenming Liu
- Division of Livestock Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
| | - Decheng Yang
- Division of Livestock Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
| | - Chao Sun
- Division of Livestock Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
| | - Haiwei Wang
- Division of Livestock Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
| | - Bo Zhao
- Division of Livestock Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
| | - Guohui Zhou
- Division of Livestock Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
| | - Li Yu
- Division of Livestock Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
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21
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Swiatkowska A, Dutkiewicz M, Machtel P, Janecki DM, Kabacinska M, Żydowicz-Machtel P, Ciesiołka J. Regulation of the p53 expression profile by hnRNP K under stress conditions. RNA Biol 2020; 17:1402-1415. [PMID: 32449427 DOI: 10.1080/15476286.2020.1771944] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The p53 protein is one of the transcription factors responsible for cell cycle regulation and prevention of cancer development. Its expression is regulated at the transcriptional, translational and post-translational levels. Recent years of research have shown that the 5' terminus of p53 mRNA plays an important role in this regulation. This region seems to be a docking platform for proteins involved in p53 expression, particularly under stress conditions. Here, we applied RNA-centric affinity chromatography to search for proteins that bind to the 5' terminus of p53 mRNA and thus may be able to regulate the p53 expression profile. We found heterogeneous nuclear ribonucleoprotein K, hnRNP K, to be one of the top candidates. Binding of hnRNP K to the 5'-terminal region of p53 mRNA was confirmed in vitro. We demonstrated that changes in the hnRNP K level in the cell strongly affected the p53 expression profile under various stress conditions. Downregulation or overexpression of hnRNP K caused a decrease or an increase in the p53 mRNA amount, respectively, pointing to the transcriptional mode of expression regulation. However, when hnRNP K was overexpressed under endoplasmic reticulum stress and the p53 amount has elevated no changes in the p53 mRNA level were detected suggesting translational regulation of p53 expression. Our findings have shown that hnRNP K is not only a mutual partner of p53 in the transcriptional activation of target genes under stress conditions but it also acts as a regulator of p53 expression at the transcriptional and potentially translational levels.
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Affiliation(s)
- Agata Swiatkowska
- Polish Academy of Sciences, Institute of Bioorganic Chemistry , Poznan, Poland
| | - Mariola Dutkiewicz
- Polish Academy of Sciences, Institute of Bioorganic Chemistry , Poznan, Poland
| | - Piotr Machtel
- Polish Academy of Sciences, Institute of Bioorganic Chemistry , Poznan, Poland
| | - Damian M Janecki
- Polish Academy of Sciences, Institute of Bioorganic Chemistry , Poznan, Poland
| | - Martyna Kabacinska
- Polish Academy of Sciences, Institute of Bioorganic Chemistry , Poznan, Poland
| | | | - Jerzy Ciesiołka
- Polish Academy of Sciences, Institute of Bioorganic Chemistry , Poznan, Poland
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22
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RNA-Binding Proteins in Acute Leukemias. Int J Mol Sci 2020; 21:ijms21103409. [PMID: 32408494 PMCID: PMC7279408 DOI: 10.3390/ijms21103409] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/07/2020] [Accepted: 05/10/2020] [Indexed: 12/12/2022] Open
Abstract
Acute leukemias are genetic diseases caused by translocations or mutations, which dysregulate hematopoiesis towards malignant transformation. However, the molecular mode of action is highly versatile and ranges from direct transcriptional to post-transcriptional control, which includes RNA-binding proteins (RBPs) as crucial regulators of cell fate. RBPs coordinate RNA dynamics, including subcellular localization, translational efficiency and metabolism, by binding to their target messenger RNAs (mRNAs), thereby controlling the expression of the encoded proteins. In view of the growing interest in these regulators, this review summarizes recent research regarding the most influential RBPs relevant in acute leukemias in particular. The reported RBPs, either dysregulated or as components of fusion proteins, are described with respect to their functional domains, the pathways they affect, and clinical aspects associated with their dysregulation or altered functions.
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23
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Cai Z, Cao C, Ji L, Ye R, Wang D, Xia C, Wang S, Du Z, Hu N, Yu X, Chen J, Wang L, Yang X, He S, Xue Y. RIC-seq for global in situ profiling of RNA-RNA spatial interactions. Nature 2020; 582:432-437. [PMID: 32499643 DOI: 10.1038/s41586-020-2249-1] [Citation(s) in RCA: 148] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 03/02/2020] [Indexed: 01/23/2023]
Abstract
Highly structured RNA molecules usually interact with each other, and associate with various RNA-binding proteins, to regulate critical biological processes. However, RNA structures and interactions in intact cells remain largely unknown. Here, by coupling proximity ligation mediated by RNA-binding proteins with deep sequencing, we report an RNA in situ conformation sequencing (RIC-seq) technology for the global profiling of intra- and intermolecular RNA-RNA interactions. This technique not only recapitulates known RNA secondary structures and tertiary interactions, but also facilitates the generation of three-dimensional (3D) interaction maps of RNA in human cells. Using these maps, we identify noncoding RNA targets globally, and discern RNA topological domains and trans-interacting hubs. We reveal that the functional connectivity of enhancers and promoters can be assigned using their pairwise-interacting RNAs. Furthermore, we show that CCAT1-5L-a super-enhancer hub RNA-interacts with the RNA-binding protein hnRNPK, as well as RNA derived from the MYC promoter and enhancer, to boost MYC transcription by modulating chromatin looping. Our study demonstrates the power and applicability of RIC-seq in discovering the 3D structures, interactions and regulatory roles of RNA.
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Affiliation(s)
- Zhaokui Cai
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Changchang Cao
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Lei Ji
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Rong Ye
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Di Wang
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Cong Xia
- School of Life Sciences, Henan Normal University, Xinxiang, China
| | - Sui Wang
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Zongchang Du
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Naijing Hu
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiaohua Yu
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Juan Chen
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Lei Wang
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Xianguang Yang
- School of Life Sciences, Henan Normal University, Xinxiang, China
| | - Shunmin He
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yuanchao Xue
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China. .,University of Chinese Academy of Sciences, Beijing, China.
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24
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hnRNP K Supports High-Amplitude D Site-Binding Protein mRNA ( Dbp mRNA) Oscillation To Sustain Circadian Rhythms. Mol Cell Biol 2020; 40:MCB.00537-19. [PMID: 31907279 DOI: 10.1128/mcb.00537-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 12/20/2019] [Indexed: 01/24/2023] Open
Abstract
Circadian gene expression is defined by the gene-specific phase and amplitude of daily oscillations in mRNA and protein levels. D site-binding protein mRNA (Dbp mRNA) shows high-amplitude oscillation; however, the underlying mechanism remains elusive. Here, we demonstrate that heterogeneous nuclear ribonucleoprotein K (hnRNP K) is a key regulator that activates Dbp transcription via the poly(C) motif within its proximal promoter. Biochemical analyses identified hnRNP K as a specific protein that directly associates with the poly(C) motif in vitro Interestingly, we further confirmed the rhythmic binding of endogenous hnRNP K within the Dbp promoter through chromatin immunoprecipitation as well as the cycling expression of hnRNP K. Finally, knockdown of hnRNP K decreased mRNA oscillation in both Dbp and Dbp-dependent clock genes. Taken together, our results show rhythmic protein expression of hnRNP K and provide new insights into its function as a transcriptional amplifier of Dbp.
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25
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Wu Z, Fang X, Zhu D, Dean C. Autonomous Pathway: FLOWERING LOCUS C Repression through an Antisense-Mediated Chromatin-Silencing Mechanism. PLANT PHYSIOLOGY 2020; 182:27-37. [PMID: 31740502 PMCID: PMC6945862 DOI: 10.1104/pp.19.01009] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 10/28/2019] [Indexed: 05/19/2023]
Abstract
The timing of flowering is vital for plant reproductive success and is therefore tightly regulated by endogenous and exogenous cues. In summer annual Arabidopsis (Arabidopsis thaliana) accessions, like Columbia-0, rapid flowering is promoted by repression of the floral repressor FLOWERING LOCUS C (FLC). This is through the activity of the autonomous pathway, a group of proteins with diverse functions including RNA 3'-end processing factors, spliceosome components, a transcription elongation factor, and chromatin modifiers. These factors function at the FLC locus linking alternative processing of an antisense long noncoding RNA, called COOLAIR, with delivery of a repressive chromatin environment that affects the transcriptional output. The transcriptional output feeds back to influence the chromatin environment, reinforcing and stabilizing that state. This review summarizes our current knowledge of the autonomous pathway and compares it with similar cotranscriptional mechanisms in other organisms.
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Affiliation(s)
- Zhe Wu
- SUSTech-PKU Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Xiaofeng Fang
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Danling Zhu
- SUSTech-PKU Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Caroline Dean
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
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26
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Gallardo M, Malaney P, Aitken MJL, Zhang X, Link TM, Shah V, Alybayev S, Wu MH, Pageon LR, Ma H, Jacamo R, Yu L, Xu-Monette ZY, Steinman H, Lee HJ, Sarbassov D, Rapado I, Barton MC, Martinez-Lopez J, Bueso-Ramos C, Young KH, Post SM. Uncovering the Role of RNA-Binding Protein hnRNP K in B-Cell Lymphomas. J Natl Cancer Inst 2020; 112:95-106. [PMID: 31077320 PMCID: PMC7489062 DOI: 10.1093/jnci/djz078] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 03/22/2019] [Accepted: 04/29/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Heterogeneous nuclear ribonucleoprotein K (hnRNP K) is an RNA-binding protein that is aberrantly expressed in cancers. We and others have previously shown that reduced hnRNP K expression downmodulates tumor-suppressive programs. However, overexpression of hnRNP K is the more commonly observed clinical phenomenon, yet its functional consequences and clinical significance remain unknown. METHODS Clinical implications of hnRNP K overexpression were examined through immunohistochemistry on samples from patients with diffuse large B-cell lymphoma who did not harbor MYC alterations (n = 75). A novel transgenic mouse model that overexpresses hnRNP K specifically in B cells was generated to directly examine the role of hnRNP K overexpression in mice (three transgenic lines). Molecular consequences of hnRNP K overexpression were determined through proteomics, formaldehyde-RNA-immunoprecipitation sequencing, and biochemical assays. Therapeutic response to BET-bromodomain inhibition in the context of hnRNP K overexpression was evaluated in vitro and in vivo (n = 3 per group). All statistical tests were two-sided. RESULTS hnRNP K is overexpressed in diffuse large B-cell lymphoma patients without MYC genomic alterations. This overexpression is associated with dismal overall survival and progression-free survival (P < .001). Overexpression of hnRNP K in transgenic mice resulted in the development of lymphomas and reduced survival (P < .001 for all transgenic lines; Line 171[n = 30]: hazard ratio [HR] = 64.23, 95% confidence interval [CI] = 26.1 to 158.0; Line 173 [n = 31]: HR = 25.27, 95% CI = 10.3 to 62.1; Line 177 [n = 25]: HR = 119.5, 95% CI = 42.7 to 334.2, compared with wild-type mice). Clinical samples, mouse models, global screening assays, and biochemical studies revealed that hnRNP K's oncogenic potential stems from its ability to posttranscriptionally and translationally regulate MYC. Consequently, Hnrnpk overexpression renders cells sensitive to BET-bromodomain-inhibition in both in vitro and transplantation models, which represents a strategy for mitigating hnRNP K-mediated c-Myc activation in patients. CONCLUSION Our findings indicate that hnRNP K is a bona fide oncogene when overexpressed and represents a novel mechanism for c-Myc activation in the absence of MYC lesions.
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Affiliation(s)
- Miguel Gallardo
- Department of Leukemia
- H12O-CNIO Haematological Malignancies Clinical Research Unit, Clinical Research Programme, CNIO, Madrid, Spain
| | | | - Marisa J L Aitken
- Department of Leukemia
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences
| | | | | | - Vrutant Shah
- Department of Epigenetics and Molecular Carcinogenesis
| | | | | | | | | | | | - Li Yu
- Department of Hematopathology
| | | | | | - Hun Ju Lee
- Department of Lymphoma and Myeloma The University of Texas, MD Anderson Cancer Center, Houston, TX
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27
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Jiang H, Hou P, He H, Wang H. Cell apoptosis regulated by interaction between viral gene alpha 3 and host heterogeneous nuclear ribonucleoprotein K facilitates bovine ephemeral fever virus replication. Vet Microbiol 2020; 240:108510. [DOI: 10.1016/j.vetmic.2019.108510] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 11/13/2019] [Accepted: 11/14/2019] [Indexed: 02/06/2023]
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28
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Euteneuer AM, Seeger‐Nukpezah T, Nolte H, Henjakovic M. Estrogen receptor α (ERα) indirectly induces transcription of human renal organic anion transporter 1 (OAT1). Physiol Rep 2019; 7:e14229. [PMID: 31724834 PMCID: PMC6854606 DOI: 10.14814/phy2.14229] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 08/20/2019] [Indexed: 01/05/2023] Open
Abstract
Organic anion transporter 1 (OAT1) is a polyspecific transport protein located in the basolateral membrane of renal proximal tubule cells. OAT1 plays a pivotal role in drug clearance. Adverse drug reactions (ADR) are observed more frequently in women than in men, especially ADR are higher in women for drugs which are known interactors of OAT1. Sex-dependent expression of Oat1 has been observed in rodents with a tendency to male-dominant expression. This study aims at elucidating the transcriptional regulation of human OAT1 and tests the effect of estrogen receptor α (ERα). Promoter activation of OAT1 was assessed by luciferase assays carried out by Opossum kidney (OK) cells, transiently transfected with promoter constructs of human OAT1 and expression vectors for ERα and exposed to 100 nmol/L 17β-estradiol. Furthermore, a transcription factor array and proteomic analysis was performed to identify estrogen-induced transcription factors. Human OAT1 was significantly activated by ligand activated ERα. However, activation occurred without a direct interaction of ERα with the OAT1 promoter. Our data rather show an activation of the transcription factors CCAAT-box-binding transcription factor (CBF) and heterogeneous nuclear ribonucleoprotein K (HNRNPK) by ERα, which in turn bind and initiate OAT1 promoter activity. Herewith, we provide novel evidence of estrogen-dependent, transcriptional regulation of polyspecific drug transporters including the estrogen-induced transcription factors CBF and HNRNPK.
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Affiliation(s)
- Anna M. Euteneuer
- Department I of Internal Medicine and Center for Integrated OncologyUniversity of CologneCologneGermany
| | - Tamina Seeger‐Nukpezah
- Department I of Internal Medicine and Center for Integrated OncologyUniversity of CologneCologneGermany
| | - Hendrik Nolte
- Institute of Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging‐Associated Diseases (CECAD)University of CologneCologneGermany
| | - Maja Henjakovic
- Department I of Internal Medicine and Center for Integrated OncologyUniversity of CologneCologneGermany
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29
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Wang Z, Qiu H, He J, Liu L, Xue W, Fox A, Tickner J, Xu J. The emerging roles of hnRNPK. J Cell Physiol 2019; 235:1995-2008. [PMID: 31538344 DOI: 10.1002/jcp.29186] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Accepted: 08/23/2019] [Indexed: 12/15/2022]
Abstract
Heterogeneous nuclear ribonucleoprotein K (hnRNPK) is an DNA/RNA-binding protein and regulates a wide range of biological processes and disease pathogenesis. It contains 3 K-homologous (KH) domains, which are conserved in other RNA-binding proteins, mediate nucleic acid binding activity, and function as an enhancer or repressor of gene transcription. Phosphorylation of the protein alters its regulatory function, which also enables the protein to serve as a docking platform for the signal transduction proteins. In terms of the function of hnRNPK, it is central to many cellular events, including long noncoding RNA (lncRNA) regulation, cancer development and bone homoeostasis. Many studies have identified hnRNPK as an oncogene, where it is overexpressed in cancer tissues compared with the nonneoplastic tissues and its expression level is related to the prognosis of different types of host malignancies. However, hnRNPK has also been identified as a tumour suppressor, as it is important for the activation of the p53/p21 pathway. Recently, the protein is also found to be exclusively related to the regulation of paraspeckles and lncRNAs such as Neat1, Lncenc1 and Xist. Interestingly, hnRNPK has been found to associate with the Kabuki-like syndrome and Au-Kline syndrome with prominent skeletal abnormalities. In vitro study revealed that the hnRNPK protein is essential for the formation of osteoclast, in line with its importance in the skeletal system.
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Affiliation(s)
- Ziyi Wang
- School of Biomedical Sciences, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Heng Qiu
- School of Biomedical Sciences, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Jianbo He
- School of Biomedical Sciences, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia.,Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Langxia Liu
- Key laboratory of functional protein research of Guangdong higher education institutes, Institute of life and health engineering, Jinan University, Guangzhou, China
| | - Wei Xue
- Department of Biomedical Engineering, Jinan University, Guangzhou, China
| | - Archa Fox
- School of Human Sciences and Molecular Sciences, The University of Western Australia and Harry Perkins Institute of Medical Research, Centre for Medical Research, The University of Western Australia, Perth, Western Australia, Australia
| | - Jennifer Tickner
- School of Biomedical Sciences, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Jiake Xu
- School of Biomedical Sciences, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia
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30
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Abstract
Mammalian genomes are extensively transcribed, which produces a large number of both coding and non-coding transcripts. Various RNAs are physically associated with chromatin, through being either retained in cis at their site of transcription or recruited in trans to other genomic regions. Driven by recent technological innovations for detecting chromatin-associated RNAs, diverse roles are being revealed for these RNAs and associated RNA-binding proteins (RBPs) in gene regulation and genome function. Such functions include locus-specific roles in gene activation and silencing, as well as emerging roles in higher-order genome organization, such as involvement in long-range enhancer-promoter interactions, transcription hubs, heterochromatin, nuclear bodies and phase transitions.
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Affiliation(s)
- Xiao Li
- Department of Cellular and Molecular Medicine and Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Xiang-Dong Fu
- Department of Cellular and Molecular Medicine and Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA.
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31
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Xiao R, Chen JY, Liang Z, Luo D, Chen G, Lu ZJ, Chen Y, Zhou B, Li H, Du X, Yang Y, San M, Wei X, Liu W, Lécuyer E, Graveley BR, Yeo GW, Burge CB, Zhang MQ, Zhou Y, Fu XD. Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-Based Regulation of Transcription. Cell 2019; 178:107-121.e18. [PMID: 31251911 PMCID: PMC6760001 DOI: 10.1016/j.cell.2019.06.001] [Citation(s) in RCA: 197] [Impact Index Per Article: 39.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 03/21/2019] [Accepted: 05/31/2019] [Indexed: 01/03/2023]
Abstract
Increasing evidence suggests that transcriptional control and chromatin activities at large involve regulatory RNAs, which likely enlist specific RNA-binding proteins (RBPs). Although multiple RBPs have been implicated in transcription control, it has remained unclear how extensively RBPs directly act on chromatin. We embarked on a large-scale RBP ChIP-seq analysis, revealing widespread RBP presence in active chromatin regions in the human genome. Like transcription factors (TFs), RBPs also show strong preference for hotspots in the genome, particularly gene promoters, where their association is frequently linked to transcriptional output. Unsupervised clustering reveals extensive co-association between TFs and RBPs, as exemplified by YY1, a known RNA-dependent TF, and RBM25, an RBP involved in splicing regulation. Remarkably, RBM25 depletion attenuates all YY1-dependent activities, including chromatin binding, DNA looping, and transcription. We propose that various RBPs may enhance network interaction through harnessing regulatory RNAs to control transcription.
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Affiliation(s)
- Rui Xiao
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Medical Research Institute, Wuhan University, Wuhan, Hubei 430071, China.
| | - Jia-Yu Chen
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Zhengyu Liang
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA; MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing 100084, China
| | - Daji Luo
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA; School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei 430071, China
| | - Geng Chen
- College of Life Sciences and Institute for Advanced Studies, Wuhan University, Wuhan, Hubei 430072, China
| | - Zhi John Lu
- MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing 100084, China
| | - Yang Chen
- MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing 100084, China
| | - Bing Zhou
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Hairi Li
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Xian Du
- College of Life Sciences and Institute for Advanced Studies, Wuhan University, Wuhan, Hubei 430072, China
| | - Yang Yang
- College of Life Sciences and Institute for Advanced Studies, Wuhan University, Wuhan, Hubei 430072, China
| | - Mingkui San
- Medical Research Institute, Wuhan University, Wuhan, Hubei 430071, China
| | - Xintao Wei
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health Science Center, Farmington, CT 06030, USA
| | - Wen Liu
- School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Eric Lécuyer
- Institut de Recherches Cliniques de Montréal, Département de Biochimie and Médecine Moléculaire, Université de Montréal, Montréal, QC H2W 1R7, Canada
| | - Brenton R Graveley
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health Science Center, Farmington, CT 06030, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Christopher B Burge
- Program in Computational and Systems Biology, Department of Biology, MIT, Cambridge, MA 02139, USA
| | - Michael Q Zhang
- MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing 100084, China; Department of Biological Sciences, Center for Systems Biology, University of Texas, Dallas, TX 75080, USA
| | - Yu Zhou
- College of Life Sciences and Institute for Advanced Studies, Wuhan University, Wuhan, Hubei 430072, China
| | - Xiang-Dong Fu
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
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Bakhmet EI, Nazarov IB, Gazizova AR, Vorobyeva NE, Kuzmin AA, Gordeev MN, Sinenko SA, Aksenov ND, Artamonova TO, Khodorkovskii MA, Alenina N, Onichtchouk D, Wu G, Schöler HR, Tomilin AN. hnRNP-K Targets Open Chromatin in Mouse Embryonic Stem Cells in Concert with Multiple Regulators. Stem Cells 2019; 37:1018-1029. [PMID: 31021473 DOI: 10.1002/stem.3025] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 04/12/2019] [Accepted: 04/13/2019] [Indexed: 01/02/2023]
Abstract
The transcription factor Oct4 plays a key regulatory role in the induction and maintenance of cellular pluripotency. In this article, we show that ubiquitous and multifunctional poly(C) DNA/RNA-binding protein hnRNP-K occupies Oct4 (Pou5f1) enhancers in embryonic stem cells (ESCs) but is dispensable for the initiation, maintenance, and downregulation of Oct4 gene expression. Nevertheless, hnRNP-K has an essential cell-autonomous function in ESCs to maintain their proliferation and viability. To better understand mechanisms of hnRNP-K action in ESCs, we have performed ChIP-seq analysis of genome-wide binding of hnRNP-K and identified several thousands of hnRNP-K target sites that are frequently co-occupied by pluripotency-related and common factors (Oct4, TATA-box binding protein, Sox2, Nanog, Otx2, etc.), as well as active histone marks. Furthermore, hnRNP-K localizes exclusively within open chromatin, implying its role in the onset and/or maintenance of this chromatin state. Stem Cells 2019;37:1018-1029.
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Affiliation(s)
- Evgeny I Bakhmet
- Laboratory of the Molecular Biology of Stem Cells, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
| | - Igor B Nazarov
- Laboratory of the Molecular Biology of Stem Cells, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
| | - Adel R Gazizova
- Laboratory of the Molecular Biology of Stem Cells, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
| | - Nadezhda E Vorobyeva
- Group of transcriptional complexes dynamics, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Andrey A Kuzmin
- Laboratory of the Molecular Biology of Stem Cells, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
| | - Mikhail N Gordeev
- Laboratory of the Molecular Biology of Stem Cells, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
| | - Sergey A Sinenko
- Laboratory of the Molecular Biology of Stem Cells, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
| | - Nikolai D Aksenov
- Laboratory of the Molecular Biology of Stem Cells, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
| | - Tatyana O Artamonova
- Institute of Nanobiotechnologies, Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
| | - Mikhail A Khodorkovskii
- Institute of Nanobiotechnologies, Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
| | - Natalia Alenina
- Molecular Biology of Peptide Hormones, Max-Delbrück Center for Molecular Medicine, Berlin-Buch, Germany
| | - Daria Onichtchouk
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Guangming Wu
- Department of Cell and Developmental Biology, Max-Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Hans R Schöler
- Department of Cell and Developmental Biology, Max-Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Alexey N Tomilin
- Laboratory of the Molecular Biology of Stem Cells, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia.,Laboratory of Cellular and Molecular Biology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
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33
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Debnath M, Fatma K, Dash J. Chemical Regulation of DNA i‐Motifs for Nanobiotechnology and Therapeutics. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201813288] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Manish Debnath
- School of Chemical SciencesIndian Association for the Cultivation of Science Jadavpur Kolkata- 700032 India
| | - Khushnood Fatma
- School of Chemical SciencesIndian Association for the Cultivation of Science Jadavpur Kolkata- 700032 India
| | - Jyotirmayee Dash
- School of Chemical SciencesIndian Association for the Cultivation of Science Jadavpur Kolkata- 700032 India
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34
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Debnath M, Fatma K, Dash J. Chemical Regulation of DNA i-Motifs for Nanobiotechnology and Therapeutics. Angew Chem Int Ed Engl 2019; 58:2942-2957. [PMID: 30600876 DOI: 10.1002/anie.201813288] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 12/27/2018] [Indexed: 12/20/2022]
Abstract
DNA sequences rich in cytosine have the propensity, under acidic pH, to fold into four-stranded intercalated DNA structures called i-motifs. Recent studies have provided significant breakthroughs that demonstrate how chemists can manipulate these structures for nanobiotechnology and therapeutics. The first section of this Minireview discusses the development of advanced functional nanostructures by synthetic conjugation of i-motifs with organic scaffolds and metal nanoparticles and their role in therapeutics. The second section highlights the therapeutic targeting of i-motifs with chemical scaffolds and their significance in biology. For this, first we shed light on the long-lasting debate regarding the stability of i-motifs under physiological conditions. Next, we present a comparative analysis of recently reported small molecules for specifically targeting i-motifs over other abundant DNA structures and modulating their function in cellular systems. These advances provide new insights into i-motif-targeted regulation of gene expression, telomere maintenance, and therapeutic applications.
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Affiliation(s)
- Manish Debnath
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-, 700032, India
| | - Khushnood Fatma
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-, 700032, India
| | - Jyotirmayee Dash
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-, 700032, India
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35
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Debaize L, Troadec MB. The master regulator FUBP1: its emerging role in normal cell function and malignant development. Cell Mol Life Sci 2019; 76:259-281. [PMID: 30343319 PMCID: PMC11105487 DOI: 10.1007/s00018-018-2933-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 09/06/2018] [Accepted: 10/01/2018] [Indexed: 12/20/2022]
Abstract
The human Far Upstream Element (FUSE) Binding Protein 1 (FUBP1) is a multifunctional DNA- and RNA-binding protein involved in diverse cellular processes. FUBP1 is a master regulator of transcription, translation, and RNA splicing. FUBP1 has been identified as a potent pro-proliferative and anti-apoptotic factor by modulation of complex networks. FUBP1 is also described either as an oncoprotein or a tumor suppressor. Especially, FUBP1 overexpression is observed in a growing number of cancer and leads to a deregulation of targets that includes the fine-tuned MYC oncogene. Moreover, recent loss-of-function analyses of FUBP1 establish its essential functions in hematopoietic stem cell maintenance and survival. Therefore, FUBP1 appears as an emerging suspect in hematologic disorders in addition to solid tumors. The scope of the present review is to describe the advances in our understanding of the molecular basis of FUBP1 functions in normal cells and carcinogenesis. We also delineate the recent progresses in the understanding of the master role of FUBP1 in normal and pathological hematopoiesis. We conclude that FUBP1 is not only worth studying biologically but is also of clinical relevance through its pivotal role in regulating multiple cellular processes and its involvement in oncogenesis.
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Affiliation(s)
- Lydie Debaize
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes)-UMR 6290, F-35000, Rennes, France
| | - Marie-Bérengère Troadec
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes)-UMR 6290, F-35000, Rennes, France.
- Univ Brest, INSERM, EFS, UMR 1078, GGB, F-29200, Brest, France.
- CHRU de Brest, laboratoire de cytogénétique, F-29200, Brest, France.
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36
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Shu B, Zeng P, Kang S, Li PH, Hu D, Kuang G, Cao J, Li X, Zhang M, An LK, Huang ZS, Li D. Syntheses and evaluation of new Quinoline derivatives for inhibition of hnRNP K in regulating oncogene c-myc transcription. Bioorg Chem 2018; 85:1-17. [PMID: 30599408 DOI: 10.1016/j.bioorg.2018.12.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 12/13/2018] [Accepted: 12/14/2018] [Indexed: 12/22/2022]
Abstract
Aberrant overexpression of heterogeneous nuclear ribonucleoprotein K (hnRNP K) is a key feature in oncogenesis and progression of many human cancers. hnRNP K has been found to be a transcriptional activator to up-regulate c-myc gene transcription, a critical proto-oncogene for regulation of cell growth and differentiation. Therefore, down-regulation of c-myc transcription by inhibiting hnRNP K through disrupting its binding to c-myc gene promoter is a potential approach for cancer therapy. In the present study, we synthesized and screened a series of Quinoline derivatives and evaluated their binding affinity for hnRNP K. Among these derivatives, (E)-1-(4-methoxyphenyl)-3-(4-morpholino-6-nitroquinolin-2-yl)prop-2-en-1-one (compound 25) was determined to be the first-reported hnRNP K binding ligand with its KD values of 4.6 and 2.6 μM measured with SPR and MST, respectively. Subsequent evaluation showed that the binding of compound 25 to hnRNP K could disrupt its unfolding of c-myc promoter i-motif, resulting in down-regulation of c-myc transcription. Compound 25 showed a selective anti-proliferative effect on human cancer cell lines with IC50 values ranged from 1.36 to 3.59 μM. Compound 25 exhibited good tumor growth inhibition in a Hela xenograft tumor model, which might be related to its binding with hnRNP K. These findings illustrated that inhibition of DNA-binding protein hnRNP K by compound 25 could be a new and selective strategy of regulating oncogene transcription instead of targeting promoter DNA secondary structures such as G-quadruplexes or i-motifs.
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Affiliation(s)
- Bing Shu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou University City, 132 Waihuan East Road, Guangzhou 510006, PR China; School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, PR China
| | - Ping Zeng
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou University City, 132 Waihuan East Road, Guangzhou 510006, PR China
| | - Shuangshuang Kang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou University City, 132 Waihuan East Road, Guangzhou 510006, PR China
| | - Peng-Hui Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou University City, 132 Waihuan East Road, Guangzhou 510006, PR China
| | - Dexuan Hu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou University City, 132 Waihuan East Road, Guangzhou 510006, PR China
| | - Guotao Kuang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou University City, 132 Waihuan East Road, Guangzhou 510006, PR China
| | - Jiaojiao Cao
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou University City, 132 Waihuan East Road, Guangzhou 510006, PR China
| | - Xiaoya Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou University City, 132 Waihuan East Road, Guangzhou 510006, PR China
| | - Meiling Zhang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou University City, 132 Waihuan East Road, Guangzhou 510006, PR China
| | - Lin-Kun An
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou University City, 132 Waihuan East Road, Guangzhou 510006, PR China
| | - Zhi-Shu Huang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou University City, 132 Waihuan East Road, Guangzhou 510006, PR China
| | - Ding Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou University City, 132 Waihuan East Road, Guangzhou 510006, PR China.
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37
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Characterization of acute myeloid leukemia with del(9q) - Impact of the genes in the minimally deleted region. Leuk Res 2018; 76:15-23. [PMID: 30476680 DOI: 10.1016/j.leukres.2018.11.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 11/13/2018] [Accepted: 11/15/2018] [Indexed: 02/06/2023]
Abstract
Acute myeloid leukemia is an aggressive disease that arises from clonal expansion of malignant hematopoietic precursor cells of the bone marrow. Deletions on the long arm of chromosome 9 (del(9q)) are observed in 2% of acute myeloid leukemia patients. Our deletion analysis in a cohort of 31 del(9q) acute myeloid leukemia patients further supports the importance of a minimally deleted region composed of seven genes potentially involved in leukemogenesis: GKAP1, KIF27, C9ORF64, HNRNPK, RMI1, SLC28A3 and NTRK2. Importantly, among them HNRNPK, encoding heterogeneous nuclear ribonucleoprotein K is proposed to function in leukemogenesis. We show that expression of HNRNPK and the other genes of the minimally deleted region is significantly reduced in patients with del(9q) compared with normal karyotype acute myeloid leukemia. Also, two mRNAs interacting with heterogeneous nuclear ribonucleoprotein K, namely CDKN1A and CEBPA are significantly downregulated. While the deletion size is not correlated with outcome, associated genetic aberrations are important. Patients with an additional t(8;21) show a good prognosis. RUNX1-RUNX1T1, which emerges from the t(8;21) leads to transcriptional down-regulation of CEBPA. Acute myeloid leukemia patients with mutations in CEBPA have a good prognosis as well. Interestingly, in del(9q) patients with CEBPA mutation mRNA levels of HNRNPK and the other genes located in the minimally deleted region is restored to normal karyotype level. Our data indicate that a link between CEBPA and the genes of the minimally deleted region, among them HNRNPK contributes to leukemogenesis in acute myeloid leukemia with del(9q).
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38
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Zaytseva O, Quinn LM. DNA Conformation Regulates Gene Expression: The MYC Promoter and Beyond. Bioessays 2018; 40:e1700235. [PMID: 29504137 DOI: 10.1002/bies.201700235] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 01/29/2018] [Indexed: 01/07/2023]
Abstract
Emerging evidence suggests that DNA topology plays an instructive role in cell fate control through regulation of gene expression. Transcription produces torsional stress, and the resultant supercoiling of the DNA molecule generates an array of secondary structures. In turn, local DNA architecture is harnessed by the cell, acting within sensory feedback mechanisms to mediate transcriptional output. MYC is a potent oncogene, which is upregulated in the majority of cancers; thus numerous studies have focused on detailed understanding of its regulation. Dissection of regulatory regions within the MYC promoter provided the first hint that intimate feedback between DNA topology and associated DNA remodeling proteins is critical for moderating transcription. As evidence of such regulation is also found in the context of many other genes, here we expand on the prototypical example of the MYC promoter, and also explore DNA architecture in a genome-wide context as a global mechanism of transcriptional control.
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Affiliation(s)
- Olga Zaytseva
- ACRF Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, The Australian National University, ACT 2600, Canberra City, Australia.,School of Biomedical Sciences, University of Melbourne, 3010, Parkville, Australia
| | - Leonie M Quinn
- ACRF Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, The Australian National University, ACT 2600, Canberra City, Australia.,School of Biomedical Sciences, University of Melbourne, 3010, Parkville, Australia
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39
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Zhu Y, Gong Y, Li A, Chen M, Kang D, Liu J, Yuan Y. Differential Proteomic Analysis Reveals Protein Networks and Pathways that May Contribute to Helicobacter pylori FKBP-Type PPIase-Associated Gastric Diseases. Proteomics Clin Appl 2017; 12:e1700127. [PMID: 29148176 DOI: 10.1002/prca.201700127] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Revised: 10/21/2017] [Indexed: 12/18/2022]
Abstract
PURPOSE Though Helicobacter pylori (H. pylori) has been classified as class I carcinogen, key virulence factor generated by H. pylori that causes gastric cancer remains to be fully determined. Recently, we identified a gastric cancer-associated H. pylori gene, peptidylprolyl isomerase-FK506 binding protein (PPIase-FKBP), and showed that PPIase-FKBP was capable of inducing oncogenic transformation of gastric epithelial cells. But its mechanism was unclear. EXPERIMENTAL DESIGN We carried out a comparative proteomic analysis of human gastric epithelial cells that either express PPIase-FKBP or green fluorescent protein using 2-DE and then MALDI-TOF-MS/MS. RESULTS Our results identified 28 differentially expressed proteins induced by PPIase-FKBP. These proteins participate in some cellular biological processes, such as cell proliferation, cell apoptosis and DNA replication, mRNA splicing, and protein biosynthesis. Ingenuity Pathway Analysis categorized the 28 proteins into two molecular interaction networks, involved primarily in cancer and gastrointestinal diseases. CONCLUSIONS AND CLINICAL RELEVANCE Our results provided insight on the protein interaction networks and signaling pathways that may contribute to PPIase-FKBP-associated gastric diseases and may lead to a better understanding of the mechanisms indicating the oncogenic effects of H. pylori PPIase-FKBP.
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Affiliation(s)
- Yanmei Zhu
- Department of Pathology, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang, China.,Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Affiliated Hospital of China Medical University, Key Laboratory of Cancer Etiology and Prevention, Liaoning Provincial Education Department, China Medical University, Shenyang, China.,West Virginia University Cancer Institute, West Virginia University, Morgantown, WV, USA
| | - Yuehua Gong
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Affiliated Hospital of China Medical University, Key Laboratory of Cancer Etiology and Prevention, Liaoning Provincial Education Department, China Medical University, Shenyang, China
| | - Aodi Li
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Affiliated Hospital of China Medical University, Key Laboratory of Cancer Etiology and Prevention, Liaoning Provincial Education Department, China Medical University, Shenyang, China
| | - Moye Chen
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Affiliated Hospital of China Medical University, Key Laboratory of Cancer Etiology and Prevention, Liaoning Provincial Education Department, China Medical University, Shenyang, China
| | - Dan Kang
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Affiliated Hospital of China Medical University, Key Laboratory of Cancer Etiology and Prevention, Liaoning Provincial Education Department, China Medical University, Shenyang, China
| | - Jun Liu
- West Virginia University Cancer Institute, West Virginia University, Morgantown, WV, USA
| | - Yuan Yuan
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Affiliated Hospital of China Medical University, Key Laboratory of Cancer Etiology and Prevention, Liaoning Provincial Education Department, China Medical University, Shenyang, China
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40
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Shin CH, Lee H, Kim HR, Choi KH, Joung JG, Kim HH. Regulation of PLK1 through competition between hnRNPK, miR-149-3p and miR-193b-5p. Cell Death Differ 2017; 24:1861-1871. [PMID: 28708135 PMCID: PMC5635212 DOI: 10.1038/cdd.2017.106] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Revised: 04/19/2017] [Accepted: 05/29/2017] [Indexed: 11/09/2022] Open
Abstract
Polo-like kinase 1 (PLK1) is a critical regulator of cell cycle progression and apoptosis. However, its regulation remains poorly understood. In the present study, we investigated the molecular mechanism underlying the post-transcriptional regulation of PLK1. We observed that heterogeneous nuclear ribonucleoprotein K (hnRNPK) and PLK1 were positively associated in several different cancers and high expression levels of them correlated with poor prognosis in patients with cancer. Knockdown of hnRNPK resulted in reduced expression of PLK1, whereas conversely, PLK1 expression was increased in hnRNPK-overexpressing cells. We found that hnRNPK regulated PLK1 expression through KH1- and KH2-dependent interactions with the 3'UTR of PLK1 mRNA. In addition, microRNA-149-3p (miR-149-3p) and miR-193b-5p suppressed PLK1 expression by targeting the 3'UTR of PLK1 mRNA. MicroRNA-elicited enrichment of PLK1 mRNA in Ago2 immunoprecipitation was altered by the presence or absence of hnRNPK. Furthermore, the deletion of the cytosine (C)-rich sequences of the 3'UTR of PLK1 mRNA abolished the decreased PLK1 expression observed via hnRNPK silencing and administration of miRNAs, a finding that suggests that hnRNPK shares this C-rich motif with miR-149-3p and miR-193b-5p. We also found that downregulation of PLK1 by either silencing hnRNPK or overexpression of miR-149-3p and miR-193b-5p decreased clonogenicity and induced apoptosis. Our findings from this study demonstrate that hnRNPK regulates PLK1 expression by competing with the PLK1-targeting miRNAs, miR-149-3p and miR-193b-5p.
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Affiliation(s)
- Chang Hoon Shin
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, Korea
| | - Hong Lee
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, Korea
| | - Hye Ree Kim
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, Korea
| | - Kyung Hee Choi
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, Korea
| | - Je-Gun Joung
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea
| | - Hyeon Ho Kim
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, Korea
- Research Institute for Future Medicine, Samsung Medical Center, Seoul, Korea
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41
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He D, Huang C, Zhou Q, Liu D, Xiong L, Xiang H, Ma G, Zhang Z. HnRNPK/miR-223/FBXW7 feedback cascade promotes pancreatic cancer cell growth and invasion. Oncotarget 2017; 8:20165-20178. [PMID: 28423622 PMCID: PMC5386752 DOI: 10.18632/oncotarget.15529] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 01/23/2017] [Indexed: 12/16/2022] Open
Abstract
Several studies have identified miR-223 critically involved in various types of cancer, including pancreatic ductal adenocarcinoma (PDAC). However, its action and regulatory mechanisms in PDAC remains largely unclear. In this study, we found that the expression levels of miR-223 were increased in clinical samples with PDAC (81.6%). The upregulation of miR-223 increases the proliferation, migration, and invasive abilities of PDAC cells in vitro and in vivo. Mechanistically, miR-223 directly targeted FBXW7 and overexpression of FBXW7 reverted miR-223- induced drastic proliferation in PDAC cells. Interestingly, miR-223 promoter was found to form a coprecipitable complex with hnRNPK, and siRNA knockdown of hnRNPK in PDAC cells reduced the levels of miR-223. These results show that hnRNPK is a cellular protein that binds and affects the accumulation of miR-223 in PDAC. Furthermore, FBXW7 interacts with hnRNPK and promotes its degradation, which requires phosphorylation of hnRNPK at threonine 1695 by GSK3. Consistently, we observed an inverse expression pattern between FBXW7 and miR-223, whereas a positive expression pattern between miR-223 and hnRNPK was found in human PDAC tissues. These data unveiled an important new miR-223/FBXW7/HnRNPK feedback cascade in human PDAC.
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Affiliation(s)
- D He
- Department of General Surgery, The Affiliated Baoan Hospital of Southern Medical University, Shenzhen, Guangdong, 518101, China
| | - Cheng Huang
- Department of General Surgery, The Affiliated Baoan Hospital of Southern Medical University, Shenzhen, Guangdong, 518101, China.,Guangdong Medical University Graduate School, Zhanjiang, Guangdong, 524001, China
| | - Qingxin Zhou
- Department of Gastrointestinal Oncology, Cancer Hospital of Harbin Medical University, Harbin, Heilongjiang, 150086, China
| | - Dawei Liu
- Department of General Surgery, The Affiliated Baoan Hospital of Southern Medical University, Shenzhen, Guangdong, 518101, China.,Guangdong Medical University Graduate School, Zhanjiang, Guangdong, 524001, China
| | - Longhui Xiong
- Department of General Surgery, The Affiliated Baoan Hospital of Southern Medical University, Shenzhen, Guangdong, 518101, China
| | - Hongxia Xiang
- Department of General Surgery, The Affiliated Baoan Hospital of Southern Medical University, Shenzhen, Guangdong, 518101, China
| | - Guangnian Ma
- Department of General Surgery, The Affiliated Baoan Hospital of Southern Medical University, Shenzhen, Guangdong, 518101, China
| | - Zhiyong Zhang
- Department of Surgery, Robert-Wood-Johnson Medical School University Hospital, Rutgers University, New Brunswick, NJ 08901, USA
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42
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Cornella N, Tebaldi T, Gasperini L, Singh J, Padgett RA, Rossi A, Macchi P. The hnRNP RALY regulates transcription and cell proliferation by modulating the expression of specific factors including the proliferation marker E2F1. J Biol Chem 2017; 292:19674-19692. [PMID: 28972179 DOI: 10.1074/jbc.m117.795591] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 09/18/2017] [Indexed: 12/31/2022] Open
Abstract
The heterogeneous nuclear ribonucleoproteins (hnRNP) form a large family of RNA-binding proteins that exert numerous functions in RNA metabolism. RALY is a member of the hnRNP family that binds poly-U-rich elements within several RNAs and regulates the expression of specific transcripts. RALY is up-regulated in different types of cancer, and its down-regulation impairs cell cycle progression. However, the RALY's role in regulating RNA levels remains elusive. Here, we show that numerous genes coding for factors involved in transcription and cell cycle regulation exhibit an altered expression in RALY-down-regulated HeLa cells, consequently causing impairments in transcription, cell proliferation, and cell cycle progression. Interestingly, by comparing the list of RALY targets with the list of genes affected by RALY down-regulation, we found an enrichment of RALY mRNA targets in the down-regulated genes upon RALY silencing. The affected genes include the E2F transcription factor family. Given its role as proliferation-promoting transcription factor, we focused on E2F1. We demonstrate that E2F1 mRNA stability and E2F1 protein levels are reduced in cells lacking RALY expression. Finally, we also show that RALY interacts with transcriptionally active chromatin in both an RNA-dependent and -independent manner and that this association is abolished in the absence of active transcription. Taken together, our results highlight the importance of RALY as an indirect regulator of transcription and cell cycle progression through the regulation of specific mRNA targets, thus strengthening the possibility of a direct gene expression regulation exerted by RALY.
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Affiliation(s)
- Nicola Cornella
- From the Laboratory of Molecular and Cellular Neurobiology, Centre for Integrative Biology, University of Trento, via Sommarive 9, 38123 Trento, Italy
| | - Toma Tebaldi
- the Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, via Sommarive 9, 38123 Trento, Italy
| | - Lisa Gasperini
- From the Laboratory of Molecular and Cellular Neurobiology, Centre for Integrative Biology, University of Trento, via Sommarive 9, 38123 Trento, Italy
| | | | | | - Annalisa Rossi
- From the Laboratory of Molecular and Cellular Neurobiology, Centre for Integrative Biology, University of Trento, via Sommarive 9, 38123 Trento, Italy,
| | - Paolo Macchi
- From the Laboratory of Molecular and Cellular Neurobiology, Centre for Integrative Biology, University of Trento, via Sommarive 9, 38123 Trento, Italy,
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43
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Kshirsagar R, Khan K, Joshi MV, Hosur RV, Muniyappa K. Probing the Potential Role of Non-B DNA Structures at Yeast Meiosis-Specific DNA Double-Strand Breaks. Biophys J 2017; 112:2056-2074. [PMID: 28538144 DOI: 10.1016/j.bpj.2017.04.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 04/13/2017] [Accepted: 04/19/2017] [Indexed: 12/29/2022] Open
Abstract
A plethora of evidence suggests that different types of DNA quadruplexes are widely present in the genome of all organisms. The existence of a growing number of proteins that selectively bind and/or process these structures underscores their biological relevance. Moreover, G-quadruplex DNA has been implicated in the alignment of four sister chromatids by forming parallel guanine quadruplexes during meiosis; however, the underlying mechanism is not well defined. Here we show that a G/C-rich motif associated with a meiosis-specific DNA double-strand break (DSB) in Saccharomyces cerevisiae folds into G-quadruplex, and the C-rich sequence complementary to the G-rich sequence forms an i-motif. The presence of G-quadruplex or i-motif structures upstream of the green fluorescent protein-coding sequence markedly reduces the levels of gfp mRNA expression in S. cerevisiae cells, with a concomitant decrease in green fluorescent protein abundance, and blocks primer extension by DNA polymerase, thereby demonstrating the functional significance of these structures. Surprisingly, although S. cerevisiae Hop1, a component of synaptonemal complex axial/lateral elements, exhibits strong affinity to G-quadruplex DNA, it displays a much weaker affinity for the i-motif structure. However, the Hop1 C-terminal but not the N-terminal domain possesses strong i-motif binding activity, implying that the C-terminal domain has a distinct substrate specificity. Additionally, we found that Hop1 promotes intermolecular pairing between G/C-rich DNA segments associated with a meiosis-specific DSB site. Our results support the idea that the G/C-rich motifs associated with meiosis-specific DSBs fold into intramolecular G-quadruplex and i-motif structures, both in vitro and in vivo, thus revealing an important link between non-B form DNA structures and Hop1 in meiotic chromosome synapsis and recombination.
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Affiliation(s)
- Rucha Kshirsagar
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Krishnendu Khan
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Mamata V Joshi
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Ramakrishna V Hosur
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - K Muniyappa
- Department of Biochemistry, Indian Institute of Science, Bangalore, India.
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Kaiser CE, Van Ert NA, Agrawal P, Chawla R, Yang D, Hurley LH. Insight into the Complexity of the i-Motif and G-Quadruplex DNA Structures Formed in the KRAS Promoter and Subsequent Drug-Induced Gene Repression. J Am Chem Soc 2017; 139:8522-8536. [PMID: 28570076 PMCID: PMC5978000 DOI: 10.1021/jacs.7b02046] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Activating KRAS mutations frequently occur in pancreatic, colorectal, and lung adenocarcinomas. While many attempts have been made to target oncogenic KRAS, no clinically useful therapies currently exist. Most efforts to target KRAS have focused on inhibiting the mutant protein; a less explored approach involves targeting KRAS at the transcriptional level. The promoter element of the KRAS gene contains a GC-rich nuclease hypersensitive site with three potential DNA secondary structure-forming regions. These are referred to as the Near-, Mid-, and Far-regions, on the basis of their proximity to the transcription start site. As a result of transcription-induced negative superhelicity, these regions can open up to form unique DNA secondary structures: G-quadruplexes on the G-rich strand and i-motifs on the C-rich strand. While the G-quadruplexes have been well characterized, the i-motifs have not been investigated as thoroughly. Here we show that the i-motif that forms in the C-rich Mid-region is the most stable and exists in a dynamic equilibrium with a hybrid i-motif/hairpin species and an unfolded hairpin species. The transcription factor heterogeneous nuclear ribonucleoprotein K (hnRNP K) was found to bind selectively to the i-motif species and to positively modulate KRAS transcription. Additionally, we identified a benzophenanthridine alkaloid that dissipates the hairpin species and destabilizes the interaction of hnRNP K with the Mid-region i-motif. This same compound stabilizes the three existing KRAS G-quadruplexes. The combined effect of the compound on the Mid-region i-motif and the G-quadruplexes leads to downregulation of KRAS gene expression. This dual i-motif/G-quadruplex-interactive compound presents a new mechanism to modulate gene expression.
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Affiliation(s)
- Christine E. Kaiser
- College of Pharmacy, University of Arizona, Tucson, Arizona 85721, United States
| | - Natalie A. Van Ert
- College of Pharmacy, University of Arizona, Tucson, Arizona 85721, United States
| | - Prashansa Agrawal
- College of Pharmacy, University of Arizona, Tucson, Arizona 85721, United States
| | - Reena Chawla
- BIO5 Institute, University of Arizona, Tucson, Arizona 85721, United States
| | - Danzhou Yang
- College of Pharmacy, University of Arizona, Tucson, Arizona 85721, United States
- University of Arizona Cancer Center, University of Arizona, Tucson, Arizona 85724, United States
- BIO5 Institute, University of Arizona, Tucson, Arizona 85721, United States
| | - Laurence H. Hurley
- College of Pharmacy, University of Arizona, Tucson, Arizona 85721, United States
- University of Arizona Cancer Center, University of Arizona, Tucson, Arizona 85724, United States
- BIO5 Institute, University of Arizona, Tucson, Arizona 85721, United States
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45
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Liu HY, Chen AC, Yin QK, Li Z, Huang SM, Du G, He JH, Zan LP, Wang SK, Xu YH, Tan JH, Ou TM, Li D, Gu LQ, Huang ZS. New Disubstituted Quindoline Derivatives Inhibiting Burkitt's Lymphoma Cell Proliferation by Impeding c-MYC Transcription. J Med Chem 2017; 60:5438-5454. [PMID: 28603988 DOI: 10.1021/acs.jmedchem.7b00099] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The c-MYC oncogene is overactivated during Burkitt's lymphoma pathogenesis. Targeting c-MYC to inhibit its transcriptional activity has emerged as an effective anticancer strategy. We synthesized four series of disubstituted quindoline derivatives by introducing the second cationic amino side chain and 5-N-methyl group based on a previous study of SYUIQ-5 (1) as c-MYC promoter G-quadruplex ligands. The in vitro evaluations showed that all new compounds exhibited higher stabilities and binding affinities, and most of them had better selectivity (over duplex DNA) for the c-MYC G-quadruplex compared to 1. Moreover, the new ligands prevented NM23-H2, a transcription factor, from effectively binding to the c-MYC G-quadruplex. Further studies showed that the selected ligand, 7a4, down-regulated c-MYC transcription by targeting promoter G-quadruplex and disrupting the NM23-H2/c-MYC interaction in RAJI cells. 7a4 could inhibit Burkitt's lymphoma cell proliferation through cell cycle arrest and apoptosis and suppress tumor growth in a human Burkitt's lymphoma xenograft.
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Affiliation(s)
- Hui-Yun Liu
- Institute of Medicinal Chemistry, School of Pharmaceutical Sciences, Sun Yat-sen University , Guangzhou 510006, People's Republic of China
| | - Ai-Chun Chen
- Institute of Medicinal Chemistry, School of Pharmaceutical Sciences, Sun Yat-sen University , Guangzhou 510006, People's Republic of China
| | - Qi-Kun Yin
- Institute of Medicinal Chemistry, School of Pharmaceutical Sciences, Sun Yat-sen University , Guangzhou 510006, People's Republic of China
| | - Zeng Li
- Institute of Medicinal Chemistry, School of Pharmaceutical Sciences, Sun Yat-sen University , Guangzhou 510006, People's Republic of China
| | - Su-Mei Huang
- Institute of Medicinal Chemistry, School of Pharmaceutical Sciences, Sun Yat-sen University , Guangzhou 510006, People's Republic of China
| | - Gang Du
- Institute of Medicinal Chemistry, School of Pharmaceutical Sciences, Sun Yat-sen University , Guangzhou 510006, People's Republic of China
| | - Jin-Hui He
- Institute of Medicinal Chemistry, School of Pharmaceutical Sciences, Sun Yat-sen University , Guangzhou 510006, People's Republic of China
| | - Li-Peng Zan
- Institute of Medicinal Chemistry, School of Pharmaceutical Sciences, Sun Yat-sen University , Guangzhou 510006, People's Republic of China
| | - Shi-Ke Wang
- Institute of Medicinal Chemistry, School of Pharmaceutical Sciences, Sun Yat-sen University , Guangzhou 510006, People's Republic of China
| | - Yao-Hao Xu
- Institute of Medicinal Chemistry, School of Pharmaceutical Sciences, Sun Yat-sen University , Guangzhou 510006, People's Republic of China
| | - Jia-Heng Tan
- Institute of Medicinal Chemistry, School of Pharmaceutical Sciences, Sun Yat-sen University , Guangzhou 510006, People's Republic of China
| | - Tian-Miao Ou
- Institute of Medicinal Chemistry, School of Pharmaceutical Sciences, Sun Yat-sen University , Guangzhou 510006, People's Republic of China
| | - Ding Li
- Institute of Medicinal Chemistry, School of Pharmaceutical Sciences, Sun Yat-sen University , Guangzhou 510006, People's Republic of China
| | - Lian-Quan Gu
- Institute of Medicinal Chemistry, School of Pharmaceutical Sciences, Sun Yat-sen University , Guangzhou 510006, People's Republic of China
| | - Zhi-Shu Huang
- Institute of Medicinal Chemistry, School of Pharmaceutical Sciences, Sun Yat-sen University , Guangzhou 510006, People's Republic of China
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46
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Gallardo M, Hornbaker MJ, Zhang X, Hu P, Bueso-Ramos C, Post SM. Aberrant hnRNP K expression: All roads lead to cancer. Cell Cycle 2017; 15:1552-7. [PMID: 27049467 DOI: 10.1080/15384101.2016.1164372] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The classification of a gene as an oncogene or a tumor suppressor has been a staple of cancer biology for decades. However, as we delve deeper into the biology of these genes, this simple classification has become increasingly difficult for some. In the case of heterogeneous nuclear ribonuclear protein K (hnRNP K), its role as a tumor suppressor has recently been described in acute myeloid leukemia and demonstrated in a haploinsufficient mouse model. In contrast, data from other clinical correlation studies suggest that hnRNP K may be more fittingly described as an oncogene, due to its increased levels in a variety of malignancies. hnRNP K is a multifunctional protein that can regulate both oncogenic and tumor suppressive pathways through a bevy of chromatin-, DNA-, RNA-, and protein-mediated activates, suggesting its aberrant expression may have broad-reaching cellular impacts. In this review, we highlight our current understanding of hnRNP K, with particular emphasis on its apparently dichotomous roles in tumorigenesis.
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Affiliation(s)
- Miguel Gallardo
- a Department of Leukemia , The University of Texas, MD Anderson Cancer Center , Houston , TX , USA
| | - Marisa J Hornbaker
- a Department of Leukemia , The University of Texas, MD Anderson Cancer Center , Houston , TX , USA.,b The University of Texas Graduate School of Biomedical Sciences at Houston , Houston , TX , USA
| | - Xiaorui Zhang
- a Department of Leukemia , The University of Texas, MD Anderson Cancer Center , Houston , TX , USA
| | - Peter Hu
- c School of Health Professions, The University of Texas, MD Anderson Cancer Center , Houston , TX , USA
| | - Carlos Bueso-Ramos
- d Department of Hematopathology , The University of Texas, MD Anderson Cancer Center , Houston , TX , USA
| | - Sean M Post
- a Department of Leukemia , The University of Texas, MD Anderson Cancer Center , Houston , TX , USA
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47
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Odorant Sensory Input Modulates DNA Secondary Structure Formation and Heterogeneous Ribonucleoprotein Recruitment on the Tyrosine Hydroxylase and Glutamic Acid Decarboxylase 1 Promoters in the Olfactory Bulb. J Neurosci 2017; 37:4778-4789. [PMID: 28411275 DOI: 10.1523/jneurosci.1363-16.2017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 03/15/2017] [Accepted: 03/16/2017] [Indexed: 12/25/2022] Open
Abstract
Adaptation of neural circuits to changes in sensory input can modify several cellular processes within neurons, including neurotransmitter biosynthesis levels. For a subset of olfactory bulb interneurons, activity-dependent changes in GABA are reflected by corresponding changes in Glutamate decarboxylase 1 (Gad1) expression levels. Mechanisms regulating Gad1 promoter activity are poorly understood, but here we show that a conserved G:C-rich region in the mouse Gad1 proximal promoter region both recruits heterogeneous nuclear ribonucleoproteins (hnRNPs) that facilitate transcription and forms single-stranded DNA secondary structures associated with transcriptional repression. This promoter architecture and function is shared with Tyrosine hydroxylase (Th), which is also modulated by odorant-dependent activity in the olfactory bulb. This study shows that the balance between DNA secondary structure formation and hnRNP binding on the mouse Th and Gad1 promoters in the olfactory bulb is responsive to changes in odorant-dependent sensory input. These findings reveal that Th and Gad1 share a novel transcription regulatory mechanism that facilitates sensory input-dependent regulation of dopamine and GABA expression.SIGNIFICANCE STATEMENT Adaptation of neural circuits to changes in sensory input can modify several cellular processes within neurons, including neurotransmitter biosynthesis levels. This study shows that transcription of genes encoding rate-limiting enzymes for GABA and dopamine biosynthesis (Gad1 and Th, respectively) in the mammalian olfactory bulb is regulated by G:C-rich regions that both recruit heterogeneous nuclear ribonucleoproteins (hnRNPs) to facilitate transcription and form single-stranded DNA secondary structures associated with repression. hnRNP binding and formation of DNA secondary structure on the Th and Gad1 promoters are mutually exclusive, and odorant sensory input levels regulate the balance between these regulatory features. These findings reveal that Th and Gad1 share a transcription regulatory mechanism that facilitates odorant-dependent regulation of dopamine and GABA expression levels.
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48
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Zhang Y, Zhang Q, Zhang M, Yuan M, Wang Z, Zhang J, Zhou X, Zhang Y, Lin F, Na H, Ren S, Zuo Y. DC - SIGNR by influencing the lncRNA HNRNPKP2 upregulates the expression of CXCR4 in gastric cancer liver metastasis. Mol Cancer 2017; 16:78. [PMID: 28403883 PMCID: PMC5390362 DOI: 10.1186/s12943-017-0639-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 03/16/2017] [Indexed: 12/25/2022] Open
Abstract
Background Profiling evidences of selectin demonstrate that they play an crucial role in cancer progression and metastasis. However, DC-SIGNR as a family member of selectin participates in gastric cancer liver metastasis remains unknown. Methods The serum level of DC-SIGNR was evaluated in gastric cancer patients by ELISA. Manipulation DC-SIGNR expression in BGC823 and SGC7901 cell lines was mediated by lentivirus. Investigation the biological effects of DC-SIGNR were verified by MTT, wounding and transwell in vitro and experiments on animals to confirm gastric cancer liver metastasis by IVIS. Insights of the mechanism were employed microarray and bioinformatic analysis. Further to confirm the results were conducted by qRT-PCR, western blot and by flow cytometry. Results DC-SIGNR serum level was significantly increased in gastric cancer patients compared with healthy group. Additionally, DC-SIGNR level was associated with an advanced pathological stage in gastric cancer patients. DC-SIGNR knockdown inhibited the proliferation, migration and invasion of gastric cancer cells in vitro and suppressed the liver metastasis in vivo. While, DC-SIGNR overexpression promoted cell proliferation, migration and invasion. In mechanism, HNRNPKP2 as a lncRNA was upregulated after DC-SIGNR knockdown. Importantly, STAT5A promoted HNRNPKP2 expression after knockdown DC-SIGNR. Furthermore after HNRNPKP2 depletion, the downstream target gene CXCR4 was downregulated. Conclusions DC-SIGNR promoted gastric cancer liver metastasis mediated with HNRNPKP2 which expression was regulated by STAT5A. And HNRNPKP2 decreased the expression of downstream target gene CXCR4. These findings indicated potential therapeutic candidates for gastric cancer liver metastasis. Electronic supplementary material The online version of this article (doi:10.1186/s12943-017-0639-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yu Zhang
- Department of Clinical Biochemistry, College of Laboratory Diagnostic Medicine, Dalian Medical University, lvshun South Road West 9, Dalian, 116044, China
| | - Qianshi Zhang
- Department of General Surgery, The Second Affiliated Hospital of Dalian Medical University, Dalian, Shahekou District Zhongshan Road no. 467, 116023, Dalian, China
| | - Mengyang Zhang
- Department of General Surgery, The Second Affiliated Hospital of Dalian Medical University, Dalian, Shahekou District Zhongshan Road no. 467, 116023, Dalian, China
| | - Menglang Yuan
- Department of General Surgery, The Second Affiliated Hospital of Dalian Medical University, Dalian, Shahekou District Zhongshan Road no. 467, 116023, Dalian, China
| | - Zhaohui Wang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Dalian Medical University, Dalian, 116023, China
| | - Jingbo Zhang
- Department of Clinical Biochemistry, College of Laboratory Diagnostic Medicine, Dalian Medical University, lvshun South Road West 9, Dalian, 116044, China
| | - Xu Zhou
- Department of Clinical Biochemistry, College of Laboratory Diagnostic Medicine, Dalian Medical University, lvshun South Road West 9, Dalian, 116044, China
| | - Yinan Zhang
- Department of Clinical Biochemistry, College of Laboratory Diagnostic Medicine, Dalian Medical University, lvshun South Road West 9, Dalian, 116044, China
| | - Fang Lin
- Department of Clinical Biochemistry, College of Laboratory Diagnostic Medicine, Dalian Medical University, lvshun South Road West 9, Dalian, 116044, China
| | - Heya Na
- Department of Clinical Biochemistry, College of Laboratory Diagnostic Medicine, Dalian Medical University, lvshun South Road West 9, Dalian, 116044, China
| | - Shuangyi Ren
- Department of General Surgery, The Second Affiliated Hospital of Dalian Medical University, Dalian, Shahekou District Zhongshan Road no. 467, 116023, Dalian, China.
| | - Yunfei Zuo
- Department of Clinical Biochemistry, College of Laboratory Diagnostic Medicine, Dalian Medical University, lvshun South Road West 9, Dalian, 116044, China.
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49
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Suk FM, Lin SY, Lin RJ, Hsine YH, Liao YJ, Fang SU, Liang YC. Bortezomib inhibits Burkitt's lymphoma cell proliferation by downregulating sumoylated hnRNP K and c-Myc expression. Oncotarget 2016; 6:25988-6001. [PMID: 26317903 PMCID: PMC4694880 DOI: 10.18632/oncotarget.4620] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 07/06/2015] [Indexed: 11/26/2022] Open
Abstract
Bortezomib (Velcal) was the first proteasome inhibitor to be approved by the US Food and Drug Administration to treat patients with relapsed/refractory multiple myelomas. Previous studies have demonstrated that bortezomib inhibits tumor cell proliferation and induces apoptosis by blocking the nuclear factor (NF)-κB pathway. However, the exact mechanism by which bortezomib induces cancer cell apoptosis is still not well understood. In this study, we found that bortezomib significantly inhibited cell proliferation in both human Burkitt's lymphoma CA46 and Daudi cells. Through proteomic analysis, we found that bortezomib treatment changed the expression of various proteins in distinct functional categories including unfolding protein response (UPS), RNA processing, protein targeting and biosynthesis, apoptosis, and signal transduction. Among the proteins with altered expression, hnRNP K, hnRNP H, Hsp90α, Grp78, and Hsp7C were common to both Daudi and CA46 cells. Interestingly, bortezomib treatment downregulated the expression of high-molecular-weight (HMw) hnRNP K and c-Myc but upregulated the expression of low-molecular-weight (LMw) hnRNP K. Moreover, cell proliferation was significantly correlated with high expression of HMw hnRNP K and c-Myc. HMw and LMw hnRNP K were identified as sumoylated and desumoylated hnRNP K, respectively. Using transient transfection, we found that sumoylated hnRNP K increased c-Myc expression at the translational level and contributed to cell proliferation, and that Lys422 of hnRNP K is the candidate sumoylated residue. Our results suggest that besides inhibiting the ubiquitin-proteasome pathway, bortezomib may inhibit cell proliferation by downregulating sumoylated hnRNP K and c-Myc expression in Burkitt's lymphoma cells.
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Affiliation(s)
- Fat-Moon Suk
- Division of Gastroenterology, Department of Internal Medicine, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan.,Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Shyr-Yi Lin
- Department of Primary Care Medicine, Taipei Medical University Hospital, Taipei, Taiwan.,Department of General Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Ren-Jye Lin
- Department of Primary Care Medicine, Taipei Medical University Hospital, Taipei, Taiwan.,Department of General Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Yung-Hsin Hsine
- School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Yen-Ju Liao
- School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Sheng-Uei Fang
- Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.,Division of Gastroenterology and Hepatology, Department of Internal Medicine, Taipei Medical University Hospital, Taipei, Taiwan
| | - Yu-Chih Liang
- School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan.,Traditional Herbal Medicine Research Center, Taipei Medical University Hospital, Taipei, Taiwan
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50
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Zhang L, Feng J, Kong S, Wu M, Xi Z, Zhang B, Fu W, Lao Y, Tan H, Xu H. Nujiangexathone A, a novel compound from Garcinia nujiangensis, suppresses cervical cancer growth by targeting hnRNPK. Cancer Lett 2016; 380:447-456. [PMID: 27424288 DOI: 10.1016/j.canlet.2016.07.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 05/24/2016] [Accepted: 07/06/2016] [Indexed: 12/18/2022]
Abstract
Cervical cancer is among the most frequently diagnosed cancers in females worldwide. Nujiangexathone A (NJXA), a novel compound from Garcinia nujiangensis, has been shown to have anti-cancer potential. In this study, the anti-tumor effects and the underlying mechanisms of NJXA action were investigated. Our results suggested that NJXA induced G0/G1 cell cycle arrest in HeLa and SiHa cells by down-regulating cyclins B1, E1, and A and cyclin-dependent kinases 2, 4 and 6, while selectively restoring p27. Using two-dimensional gel electrophoresis, we showed that NJXA reduced the expression of heterogeneous nuclear ribonucleoprotein K (hnRNPK) by accelerating ubiquitin-proteasome-dependent hnRNPK degradation, which then induced cell cycle arrest through the c-Myc-cyclin/Cdk-Rb-E2F1 pathway. The loss-of-function study showed NJXA induced cell cycle arrest was mediated by down regulation of hnRNPK protein. In vivo results further confirmed the tumor inhibitory effect of NJXA via the down-regulation of hnRNPK, and NJXA induced no apparent toxicity. Our study suggests that NJXA may be a novel anti-cancer drug candidate, especially for treating cancers with abnormally high hnRNPK expression.
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Affiliation(s)
- Li Zhang
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; Institute of Arthritis Research, Shanghai Academy of Chinese Medical Sciences, Guanghua Integrative Medicine Hospital, Shanghai University of T.C.M, Shanghai 201203, China; Engineering Research Center of Shanghai Colleges for TCM New Drug Discovery, Shanghai 201203, China
| | - Jiling Feng
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; Engineering Research Center of Shanghai Colleges for TCM New Drug Discovery, Shanghai 201203, China
| | - Siyuan Kong
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; Engineering Research Center of Shanghai Colleges for TCM New Drug Discovery, Shanghai 201203, China
| | - Man Wu
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; Engineering Research Center of Shanghai Colleges for TCM New Drug Discovery, Shanghai 201203, China
| | - Zhichao Xi
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; Engineering Research Center of Shanghai Colleges for TCM New Drug Discovery, Shanghai 201203, China
| | - Baojun Zhang
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; Engineering Research Center of Shanghai Colleges for TCM New Drug Discovery, Shanghai 201203, China
| | - Wenwei Fu
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; Engineering Research Center of Shanghai Colleges for TCM New Drug Discovery, Shanghai 201203, China
| | - Yuanzhi Lao
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; Engineering Research Center of Shanghai Colleges for TCM New Drug Discovery, Shanghai 201203, China
| | - Hongsheng Tan
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; Engineering Research Center of Shanghai Colleges for TCM New Drug Discovery, Shanghai 201203, China.
| | - Hongxi Xu
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; Institute of Arthritis Research, Shanghai Academy of Chinese Medical Sciences, Guanghua Integrative Medicine Hospital, Shanghai University of T.C.M, Shanghai 201203, China; Engineering Research Center of Shanghai Colleges for TCM New Drug Discovery, Shanghai 201203, China.
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