1
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Seo Y, Rhim J, Kim JH. RNA-binding proteins and exoribonucleases modulating miRNA in cancer: the enemy within. Exp Mol Med 2024; 56:1080-1106. [PMID: 38689093 PMCID: PMC11148060 DOI: 10.1038/s12276-024-01224-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 02/20/2024] [Accepted: 02/25/2024] [Indexed: 05/02/2024] Open
Abstract
Recent progress in the investigation of microRNA (miRNA) biogenesis and the miRNA processing machinery has revealed previously unknown roles of posttranscriptional regulation in gene expression. The molecular mechanistic interplay between miRNAs and their regulatory factors, RNA-binding proteins (RBPs) and exoribonucleases, has been revealed to play a critical role in tumorigenesis. Moreover, recent studies have shown that the proliferation of hepatocellular carcinoma (HCC)-causing hepatitis C virus (HCV) is also characterized by close crosstalk of a multitude of host RBPs and exoribonucleases with miR-122 and its RNA genome, suggesting the importance of the mechanistic interplay among these factors during the proliferation of HCV. This review primarily aims to comprehensively describe the well-established roles and discuss the recently discovered understanding of miRNA regulators, RBPs and exoribonucleases, in relation to various cancers and the proliferation of a representative cancer-causing RNA virus, HCV. These have also opened the door to the emerging potential for treating cancers as well as HCV infection by targeting miRNAs or their respective cellular modulators.
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Affiliation(s)
- Yoona Seo
- Cancer Molecular Biology Branch, Research Institute, National Cancer Center, Goyang, 10408, Korea
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, 10408, Korea
| | - Jiho Rhim
- Cancer Molecular Biology Branch, Research Institute, National Cancer Center, Goyang, 10408, Korea
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, 10408, Korea
| | - Jong Heon Kim
- Cancer Molecular Biology Branch, Research Institute, National Cancer Center, Goyang, 10408, Korea.
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, 10408, Korea.
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2
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Liu D, Yu H, Xue N, Bao H, Gao Q, Tian Y. Alternative splicing patterns of hnrnp genes in gill tissues of rainbow trout (Oncorhynchus mykiss) during salinity changes. Comp Biochem Physiol B Biochem Mol Biol 2024; 271:110948. [PMID: 38281704 DOI: 10.1016/j.cbpb.2024.110948] [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: 11/06/2023] [Revised: 01/25/2024] [Accepted: 01/25/2024] [Indexed: 01/30/2024]
Abstract
Alternative splicing (AS) plays an important role in various physiological processes in eukaryotes, such as the stress response. However, patterns of AS events remain largely unexplored during salinity acclimation in fishes. In this study, we conducted AS analysis using RNA-seq datasets to explore splicing patterns in the gill tissues of rainbow trout exposed to altered salinity environments, ranging from 0 ‰ (T0) to 30 ‰ (T30). The results revealed 1441, 351, 483, 1051 and 1049 differentially alternatively spliced (DAS) events in 5 pairwise comparisons, including T6 vs. T0, T12 vs. T0, T18 vs. T0, T24 vs. T0, and T30 vs. T0, respectively. These DAS events were derived from 1290, 328, 444, 963 and 948 genes. Enrichment analysis indicated that these DAS genes were related to RNA splicing and processing. Among these, 14 DAS genes were identified as members of the large heterogeneous nuclear RNP (hnRNP) gene family. Alternative 3' splice site (A3SS), exon skipping (SE) and intron retention (RI) events resulted in the fragmentation or even loss of the functional RNA recognition motif (RRM) domains in hnrnpa0, hnrnp1a, hnrnp1b and hnrnpc genes. The incomplete RRM domains would hinder the interactions between hnRNP genes and pre-mRNAs. It would in turn influence the splicing patterns and mRNA stability of downstream target genes in response to salinity changes. The study provides insights into salinity acclimation in gill tissues of rainbow trout and serves as a significant reference on the osmoregulation mechanisms at post-transcription regulation levels in fish.
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Affiliation(s)
- Dazhi Liu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, Shandong Province, China
| | - Han Yu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, Shandong Province, China
| | - Na Xue
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, Shandong Province, China
| | - Hancheng Bao
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, Shandong Province, China
| | - Qinfeng Gao
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, Shandong Province, China.
| | - Yuan Tian
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, Shandong Province, China.
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3
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Zhang TH, Jo S, Zhang M, Wang K, Gao SJ, Huang Y. Understanding YTHDF2-mediated mRNA degradation by m6A-BERT-Deg. Brief Bioinform 2024; 25:bbae170. [PMID: 38622358 PMCID: PMC11018547 DOI: 10.1093/bib/bbae170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 03/05/2024] [Accepted: 03/20/2024] [Indexed: 04/17/2024] Open
Abstract
N6-methyladenosine (m6A) is the most abundant mRNA modification within mammalian cells, holding pivotal significance in the regulation of mRNA stability, translation and splicing. Furthermore, it plays a critical role in the regulation of RNA degradation by primarily recruiting the YTHDF2 reader protein. However, the selective regulation of mRNA decay of the m6A-methylated mRNA through YTHDF2 binding is poorly understood. To improve our understanding, we developed m6A-BERT-Deg, a BERT model adapted for predicting YTHDF2-mediated degradation of m6A-methylated mRNAs. We meticulously assembled a high-quality training dataset by integrating multiple data sources for the HeLa cell line. To overcome the limitation of small training samples, we employed a pre-training-fine-tuning strategy by first performing a self-supervised pre-training of the model on 427 760 unlabeled m6A site sequences. The test results demonstrated the importance of this pre-training strategy in enabling m6A-BERT-Deg to outperform other benchmark models. We further conducted a comprehensive model interpretation and revealed a surprising finding that the presence of co-factors in proximity to m6A sites may disrupt YTHDF2-mediated mRNA degradation, subsequently enhancing mRNA stability. We also extended our analyses to the HEK293 cell line, shedding light on the context-dependent YTHDF2-mediated mRNA degradation.
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Affiliation(s)
- Ting-He Zhang
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA 15232, USA
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA,15261, USA
| | - Sumin Jo
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA 15232, USA
- Department of Electrical and Computer Engineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Michelle Zhang
- Department of Electrical and Computer Engineering, The University of Texas at San Antonio, San Antonio, TX, 78249, USA
| | - Kai Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Shou-Jiang Gao
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA 15232, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15219, USA
| | - Yufei Huang
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA 15232, USA
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA,15261, USA
- Department of Electrical and Computer Engineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Department of Pharmaceutical Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
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4
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Ascanelli C, Dahir R, Wilson CH. Manipulating Myc for reparative regeneration. Front Cell Dev Biol 2024; 12:1357589. [PMID: 38577503 PMCID: PMC10991803 DOI: 10.3389/fcell.2024.1357589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 02/15/2024] [Indexed: 04/06/2024] Open
Abstract
The Myc family of proto-oncogenes is a key node for the signal transduction of external pro-proliferative signals to the cellular processes required for development, tissue homoeostasis maintenance, and regeneration across evolution. The tight regulation of Myc synthesis and activity is essential for restricting its oncogenic potential. In this review, we highlight the central role that Myc plays in regeneration across the animal kingdom (from Cnidaria to echinoderms to Chordata) and how Myc could be employed to unlock the regenerative potential of non-regenerative tissues in humans for therapeutic purposes. Mastering the fine balance of harnessing the ability of Myc to promote transcription without triggering oncogenesis may open the door to many exciting opportunities for therapeutic development across a wide array of diseases.
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Affiliation(s)
| | | | - Catherine H. Wilson
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom
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5
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Tompkins VS, Xue Z, Peterson JM, Rouse WB, O’Leary CA, Moss WN. Identification of MYC intron 2 regions that modulate expression. PLoS One 2024; 19:e0296889. [PMID: 38236931 PMCID: PMC10795982 DOI: 10.1371/journal.pone.0296889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 12/19/2023] [Indexed: 01/22/2024] Open
Abstract
MYC pre-mRNA is spliced with high fidelity to produce the transcription factor known to regulate cellular differentiation, proliferation, apoptosis, and alternative splicing. The mechanisms underpinning the pre-mRNA splicing of MYC, however, remain mostly unexplored. In this study, we examined the interaction of heterogeneous nuclear ribonucleoprotein C (HNRNPC) with MYC intron 2. Building off published eCLIP studies, we confirmed this interaction with poly(U) regions in intron 2 of MYC and found that full binding is correlated with optimal protein production. The interaction appears to be compensatory, as mutational disruption of all three poly(U) regions was required to reduce both HNRNPC binding capacity and fidelity of either splicing or translation. Poly(U) sequences in MYC intron 2 were relatively conserved across sequences from several different species. Lastly, we identified a short sequence just upstream of an HNRNPC binding region that when removed enhances MYC translation.
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Affiliation(s)
- Van S. Tompkins
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa, United States of America
| | - Zheng Xue
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa, United States of America
| | - Jake M. Peterson
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa, United States of America
| | - Warren B. Rouse
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa, United States of America
| | - Collin A. O’Leary
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa, United States of America
| | - Walter N. Moss
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa, United States of America
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6
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Zhang TH, Jo S, Zhang M, Wang K, Gao SJ, Huang Y. Understanding YTHDF2-mediated mRNA Degradation By m 6A-BERT-Deg. ARXIV 2024:arXiv:2401.08004v1. [PMID: 38292306 PMCID: PMC10827231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
N6-methyladenosine (m6A) is the most abundant mRNA modification within mammalian cells, holding pivotal significance in the regulation of mRNA stability, translation, and splicing. Furthermore, it plays a critical role in the regulation of RNA degradation by primarily recruiting the YTHDF2 reader protein. However, the selective regulation of mRNA decay of the m6A-methylated mRNA through YTHDF2 binding is poorly understood. To improve our understanding, we developed m6A-BERT-Deg, a BERT model adapted for predicting YTHDF2-mediated degradation of m6A-methylated mRNAs. We meticulously assembled a high-quality training dataset by integrating multiple data sources for the HeLa cell line. To overcome the limitation of small training samples, we employed a pre-training-fine-tuning strategy by first performing a self-supervised pre-training of the model on 427,760 unlabeled m6A site sequences. The test results demonstrated the importance of this pre-training strategy in enabling m6A-BERT-Deg to outperform other benchmark models. We further conducted a comprehensive model interpretation and revealed a surprising finding that the presence of co-factors in proximity to m6A sites may disrupt YTHDF2-mediated mRNA degradation, subsequently enhancing mRNA stability. We also extended our analyses to the HEK293 cell line, shedding light on the context-dependent YTHDF2-mediated mRNA degradation.
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Affiliation(s)
- Ting-He Zhang
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Sumin Jo
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Electrical and Computer Engineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Michelle Zhang
- Department of Electrical and Computer Engineering, The University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Kai Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Shou-Jiang Gao
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Yufei Huang
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Electrical and Computer Engineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA, USA
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7
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Guo M, He M, Zhang Y, Liu W, Qi M, Liu Z, Yi G, Deng S, Li Y, Sun X, Zhao L, Chen T, Liu Y. Nucleo-cytoplasmic shuttling of 14-3-3 epsilon carrying hnRNP C promotes autophagy. Cancer Biol Ther 2023; 24:2246203. [PMID: 37599448 PMCID: PMC10443976 DOI: 10.1080/15384047.2023.2246203] [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: 10/04/2022] [Revised: 08/03/2023] [Accepted: 08/04/2023] [Indexed: 08/22/2023] Open
Abstract
Translocation of 14-3-3 protein epsilon (14-3-3ε) was found to be involved in Triptolide (Tp)-induced inhibition of colorectal cancer (CRC) cell proliferation. However, the form of cell death induced by 14-3-3ε translocation and mechanisms underlying this effect remain unclear. This study employed label-free LC-MS/MS to identify 14-3-3ε-associated proteins in CRC cells treated with or without Tp. Our results confirmed that heterogeneous nuclear ribonucleoproteins C1/C2 (hnRNP C) were exported out of the nucleus by 14-3-3ε and degraded by ubiquitination. The nucleo-cytoplasmic shuttling of 14-3-3ε carrying hnRNP C mediated Tp-induced proliferation inhibition, cell cycle arrest and autophagic processes. These findings have broad implications for our understanding of 14-3-3ε function, provide an explanation for the mechanism of nucleo-cytoplasmic shuttling of hnRNP C and provide new insights into the complex regulation of autophagy.
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Affiliation(s)
- Manlan Guo
- Department of Neurosurgery & Medical Research Center, Shunde Hospital, Southern Medical University (The First People’s Hospital of Shunde Foshan), Foshan, China
- Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, Guiyang, Guizhou, China
| | - Minyi He
- Center for Clinical Medical Education, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Yi Zhang
- Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, Guiyang, Guizhou, China
- Department of Oncology, Guizhou Cancer Hospital, Guiyang, Guizhou, China
| | - Weiwen Liu
- Department of Neurosurgery & Medical Research Center, Shunde Hospital, Southern Medical University (The First People’s Hospital of Shunde Foshan), Foshan, China
| | - Min Qi
- Department of Neurosurgery & Medical Research Center, Shunde Hospital, Southern Medical University (The First People’s Hospital of Shunde Foshan), Foshan, China
| | - Zhifeng Liu
- Guangdong Provincial Key Laboratory of Molecular Oncologic Pathology, Southern Medical University, Guangzhou, China
| | - Guozhong Yi
- Department of Neurosurgery & Medical Research Center, Shunde Hospital, Southern Medical University (The First People’s Hospital of Shunde Foshan), Foshan, China
| | - Shengze Deng
- Department of Neurosurgery & Medical Research Center, Shunde Hospital, Southern Medical University (The First People’s Hospital of Shunde Foshan), Foshan, China
| | - Yaomin Li
- Department of Neurosurgery & Medical Research Center, Shunde Hospital, Southern Medical University (The First People’s Hospital of Shunde Foshan), Foshan, China
| | - Xuegang Sun
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Liang Zhao
- Guangdong Provincial Key Laboratory of Molecular Oncologic Pathology, Southern Medical University, Guangzhou, China
| | - Tengxiang Chen
- Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, Guiyang, Guizhou, China
| | - Yawei Liu
- Department of Neurosurgery & Medical Research Center, Shunde Hospital, Southern Medical University (The First People’s Hospital of Shunde Foshan), Foshan, China
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8
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Jia R, Che X, Jia J, Guo J. FOXM1a Isoform of Oncogene FOXM1 Is a Tumor Suppressor Suppressed by hnRNP C in Oral Squamous Cell Carcinoma. Biomolecules 2023; 13:1331. [PMID: 37759731 PMCID: PMC10526205 DOI: 10.3390/biom13091331] [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: 07/18/2023] [Revised: 08/24/2023] [Accepted: 08/29/2023] [Indexed: 09/29/2023] Open
Abstract
FOXM1 is an oncogenic transcriptional factor and includes several isoforms generated by alternative splicing. Inclusion of alternative exon 9 produces FOXM1a, a transcriptionally inactive isoform. However, the role of FOXM1a in tumorigenesis remains unknown. In addition, the regulatory mechanisms of exon 9 splicing are also unclear. In the present study, we found that overexpression of FOXM1a significantly reduced cell proliferation and colony formation of oral squamous cell carcinoma (OSCC) cell proliferation in vitro. Importantly, OSCC cells with FOXM1a overexpression showed significantly slower tumor formation in nude mice. Moreover, we identified a U-rich exonic splicing suppressor (ESS) which is responsible for exon 9 skipping. Splicing factor heterogeneous nuclear ribonucleoprotein C (hnRNP C) can bind to the ESS and suppress exon 9 inclusion and FOXM1a expression. Silence of hnRNP C also significantly suppresses OSCC cell proliferation. HnRNP C is significantly co-expressed with FOXM1 in cancers. Our study uncovered a novel regulatory mechanism of oncogene FOXM1 expression in OSCC.
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Affiliation(s)
- Rong Jia
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan 430072, China; (R.J.); (X.C.)
| | - Xiaoxuan Che
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan 430072, China; (R.J.); (X.C.)
| | - Jun Jia
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan 430072, China; (R.J.); (X.C.)
- Department of Oral and Maxillofacial Surgery, School & Hospital of Stomatology, Wuhan University, Wuhan 430072, China
| | - Jihua Guo
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan 430072, China; (R.J.); (X.C.)
- Department of Endodontics, School & Hospital of Stomatology, Wuhan University, Wuhan 430072, China
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9
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Rapone R, Del Maestro L, Bouyioukos C, Albini S, Cruz-Tapias P, Joliot V, Cosson B, Ait-Si-Ali S. The cytoplasmic fraction of the histone lysine methyltransferase Setdb1 is essential for embryonic stem cells. iScience 2023; 26:107386. [PMID: 37559904 PMCID: PMC10407132 DOI: 10.1016/j.isci.2023.107386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 06/26/2023] [Accepted: 07/11/2023] [Indexed: 08/11/2023] Open
Abstract
The major lysine methyltransferase (KMT) Setdb1 is essential for self-renewal and viability of mouse embryonic stem cells (mESCs). Setdb1 was primarily known to methylate the lysine 9 of histone 3 (H3K9) in the nucleus, where it regulates chromatin functions. However, Setdb1 is also massively localized in the cytoplasm, including in mESCs, where its role remains elusive. Here, we show that the cytoplasmic Setdb1 (cSetdb1) is essential for the survival of mESCs. Yeast two-hybrid analysis revealed that cSetdb1 interacts with several regulators of mRNA stability and protein translation machinery, such as the ESCs-specific E3 ubiquitin ligase and mRNA silencer Trim71/Lin41. We found that cSetdb1 is required for the integrity of Trim71 complex(es) involved in mRNA metabolism and translation. cSetdb1 modulates the abundance of mRNAs and the rate of newly synthesized proteins. Altogether, our data uncovered the cytoplasmic post-transcriptional regulation of gene expression mediated by a key epigenetic regulator.
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Affiliation(s)
- Roberta Rapone
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, UMR7216, 75013 Paris, France
| | - Laurence Del Maestro
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, UMR7216, 75013 Paris, France
| | - Costas Bouyioukos
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, UMR7216, 75013 Paris, France
| | - Sonia Albini
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, UMR7216, 75013 Paris, France
| | - Paola Cruz-Tapias
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, UMR7216, 75013 Paris, France
| | - Véronique Joliot
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, UMR7216, 75013 Paris, France
| | - Bertrand Cosson
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, UMR7216, 75013 Paris, France
| | - Slimane Ait-Si-Ali
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, UMR7216, 75013 Paris, France
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10
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Niggl E, Bouman A, Briere LC, Hoogenboezem RM, Wallaard I, Park J, Admard J, Wilke M, Harris-Mostert EDRO, Elgersma M, Bain J, Balasubramanian M, Banka S, Benke PJ, Bertrand M, Blesson AE, Clayton-Smith J, Ellingford JM, Gillentine MA, Goodloe DH, Haack TB, Jain M, Krantz I, Luu SM, McPheron M, Muss CL, Raible SE, Robin NH, Spiller M, Starling S, Sweetser DA, Thiffault I, Vetrini F, Witt D, Woods E, Zhou D, Elgersma Y, van Esbroeck ACM. HNRNPC haploinsufficiency affects alternative splicing of intellectual disability-associated genes and causes a neurodevelopmental disorder. Am J Hum Genet 2023; 110:1414-1435. [PMID: 37541189 PMCID: PMC10432175 DOI: 10.1016/j.ajhg.2023.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 07/04/2023] [Accepted: 07/07/2023] [Indexed: 08/06/2023] Open
Abstract
Heterogeneous nuclear ribonucleoprotein C (HNRNPC) is an essential, ubiquitously abundant protein involved in mRNA processing. Genetic variants in other members of the HNRNP family have been associated with neurodevelopmental disorders. Here, we describe 13 individuals with global developmental delay, intellectual disability, behavioral abnormalities, and subtle facial dysmorphology with heterozygous HNRNPC germline variants. Five of them bear an identical in-frame deletion of nine amino acids in the extreme C terminus. To study the effect of this recurrent variant as well as HNRNPC haploinsufficiency, we used induced pluripotent stem cells (iPSCs) and fibroblasts obtained from affected individuals. While protein localization and oligomerization were unaffected by the recurrent C-terminal deletion variant, total HNRNPC levels were decreased. Previously, reduced HNRNPC levels have been associated with changes in alternative splicing. Therefore, we performed a meta-analysis on published RNA-seq datasets of three different cell lines to identify a ubiquitous HNRNPC-dependent signature of alternative spliced exons. The identified signature was not only confirmed in fibroblasts obtained from an affected individual but also showed a significant enrichment for genes associated with intellectual disability. Hence, we assessed the effect of decreased and increased levels of HNRNPC on neuronal arborization and neuronal migration and found that either condition affects neuronal function. Taken together, our data indicate that HNRNPC haploinsufficiency affects alternative splicing of multiple intellectual disability-associated genes and that the developing brain is sensitive to aberrant levels of HNRNPC. Hence, our data strongly support the inclusion of HNRNPC to the family of HNRNP-related neurodevelopmental disorders.
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Affiliation(s)
- Eva Niggl
- Department of Clinical Genetics, Erasmus MC, 3015 GD Rotterdam, the Netherlands; ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC, 3015 GD Rotterdam, the Netherlands
| | - Arjan Bouman
- Department of Clinical Genetics, Erasmus MC, 3015 GD Rotterdam, the Netherlands.
| | - Lauren C Briere
- Center for Genomic Medicine and Department of Pediatrics, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | - Ilse Wallaard
- Department of Clinical Genetics, Erasmus MC, 3015 GD Rotterdam, the Netherlands; ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC, 3015 GD Rotterdam, the Netherlands
| | - Joohyun Park
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
| | - Jakob Admard
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany; NGS Competence Center Tübingen, Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Martina Wilke
- Department of Clinical Genetics, Erasmus MC, 3015 GD Rotterdam, the Netherlands
| | - Emilio D R O Harris-Mostert
- Department of Clinical Genetics, Erasmus MC, 3015 GD Rotterdam, the Netherlands; ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC, 3015 GD Rotterdam, the Netherlands
| | - Minetta Elgersma
- Department of Clinical Genetics, Erasmus MC, 3015 GD Rotterdam, the Netherlands; ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC, 3015 GD Rotterdam, the Netherlands
| | - Jennifer Bain
- Department of Neurology Division of Child Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Meena Balasubramanian
- Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, S5 7AU Sheffield, UK; Department of Oncology & Metabolism, University of Sheffield, S5 7AU Sheffield, UK
| | - Siddharth Banka
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester M13 9WL, UK; Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, M13 9PL Manchester, UK
| | - Paul J Benke
- Division of Clinical Genetics, Joe DiMaggio Children's Hospital, Hollywood, FL 33021, USA
| | - Miriam Bertrand
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
| | - Alyssa E Blesson
- Department of Neurogenetics, Kennedy Krieger Institute, Baltimore, MD 21205, USA
| | - Jill Clayton-Smith
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester M13 9WL, UK; Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, M13 9PL Manchester, UK
| | - Jamie M Ellingford
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester M13 9WL, UK; Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, M13 9PL Manchester, UK
| | | | - Dana H Goodloe
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany; Center for Rare Diseases, University of Tübingen, 72076 Tübingen, Germany
| | - Mahim Jain
- Department of Neurogenetics, Kennedy Krieger Institute, Baltimore, MD 21205, USA
| | - Ian Krantz
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Sharon M Luu
- Waisman Center, University of Wisconsin Hospitals and Clinics, Madison, WI 53704, USA; Department of Medical and Molecular Genetics, Indiana University, Indianapolis, IN 46202, USA
| | - Molly McPheron
- Department of Medical and Molecular Genetics, Indiana University, Indianapolis, IN 46202, USA
| | - Candace L Muss
- Nemours / AI DuPont Hospital for Children, Wilmington, DE 19803, USA
| | - Sarah E Raible
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Nathaniel H Robin
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Michael Spiller
- Sheffield Diagnostic Genetics Service, Sheffield Children's NHS Foundation Trust, Sheffield, UK
| | - Susan Starling
- Division of Clinical Genetics, Children's Mercy, Kansas City, MO 64108, USA; School of Medicine, University of Missouri- Kansas City, Kansas City, MO 64108, USA
| | - David A Sweetser
- Center for Genomic Medicine and Department of Pediatrics, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Isabelle Thiffault
- Division of Clinical Genetics, Children's Mercy, Kansas City, MO 64108, USA; Genomic Medicine Center, Children's Mercy Research Institute, Kansas City, MO 64108, USA; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO 64108, USA
| | - Francesco Vetrini
- Department of Medical and Molecular Genetics, Indiana University, Indianapolis, IN 46202, USA; Undiagnosed Rare Disease Clinic (URDC), Indiana University, Indianapolis, IN 46202, USA
| | - Dennis Witt
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
| | - Emily Woods
- Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, S5 7AU Sheffield, UK
| | - Dihong Zhou
- Division of Clinical Genetics, Children's Mercy, Kansas City, MO 64108, USA; School of Medicine, University of Missouri- Kansas City, Kansas City, MO 64108, USA
| | - Ype Elgersma
- Department of Clinical Genetics, Erasmus MC, 3015 GD Rotterdam, the Netherlands; ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC, 3015 GD Rotterdam, the Netherlands.
| | - Annelot C M van Esbroeck
- Department of Clinical Genetics, Erasmus MC, 3015 GD Rotterdam, the Netherlands; ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC, 3015 GD Rotterdam, the Netherlands
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11
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Wang L, Ji Y, Chen Y, Bai J, Gao P, Feng P. A splicing silencer in SMN2 intron 6 is critical in spinal muscular atrophy. Hum Mol Genet 2023; 32:971-983. [PMID: 36255739 DOI: 10.1093/hmg/ddac260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 10/10/2022] [Accepted: 10/14/2022] [Indexed: 11/14/2022] Open
Abstract
Spinal muscular atrophy (SMA) is a fatal neuromuscular disease caused by homozygous deletions or mutations of the SMN1 gene. SMN2 is a paralogous gene of SMN1 and a modifying gene of SMA. A better understanding of how SMN2 exon 7 splicing is regulated helps discover new therapeutic targets for SMA therapy. Based on an antisense walk method to map exonic and intronic splicing silencers (ESSs and ISSs) in SMN2 exon 7 and the proximal regions of its flanking introns, we identified one ISS (ISS6-KH) at upstream of the branch point site in intron 6. By using mutagenesis-coupled RT-PCR with SMN1/2 minigenes, immunochromatography, overexpression and siRNA-knockdown, we found this ISS consists of a bipartite hnRNP A1 binding cis-element and a poly-U sequence located between the proximal hnRNP A1 binding site (UAGCUA) and the branch site. Both HuR and hnRNP C1 proteins promote exon 7 skipping through the poly-U stretch. Mutations or deletions of these motifs lead to efficient SMN2 exon 7 inclusion comparable to SMN1 gene. Furthermore, we identified an optimal antisense oligonucleotide that binds the intron six ISS and causes striking exon 7 inclusion in the SMN2 gene in patient fibroblasts and SMA mouse model. Our findings demonstrate that this novel ISS plays an important role in SMN2 exon 7 skipping and highlight a new therapeutic target for SMA therapy.
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Affiliation(s)
- Li Wang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Yinfeng Ji
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Yuqing Chen
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Jialin Bai
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Peng Gao
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Pengchao Feng
- Nanjing Antisense Biopharmaceutical Co., Ltd, Nanjing 210046, China
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12
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Xu C, Li B, Yu N, Yao B, Wang F, Mei Y. The c-Myc targeting hnRNPAB promotes lung adenocarcinoma cell proliferation via stabilization of CDK4 mRNA. Int J Biochem Cell Biol 2023; 156:106372. [PMID: 36657708 DOI: 10.1016/j.biocel.2023.106372] [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: 11/25/2022] [Revised: 01/12/2023] [Accepted: 01/16/2023] [Indexed: 01/19/2023]
Abstract
The c-Myc oncoprotein plays a pivotal role in tumorigenesis. The deregulated expression of c-Myc has been linked to a variety of human cancers including lung adenocarcinoma. The oncogenic function of c-Myc has been largely attributed to its intrinsic nature as a transcription factor. Here we reported the RNA binding protein hnRNPAB as a direct transcriptional target of c-Myc by performing quantitative real-time polymerase chain reaction (qRT-PCR), western blot, chromatin immunoprecipitation (ChIP), and luciferase reporter analyses. Flow cytometry, colony formation, and RNA immunoprecipitation (RIP) assays were used to investigate the role of hnRNPAB in lung adenocarcinoma cell proliferation, as well as the underlying mechanism. HnRNPAB was functionally shown to promote lung adenocarcinoma cell proliferation by accelerating G1/S cell cycle progression. Mechanistically, hnRNPAB interacted with and stabilized CDK4 mRNA, thereby increasing CDK4 expression. Moreover, hnRNPAB was able to promote G1/S cell cycle progression and cell proliferation via the regulation of CDK4. HnRNPAB was also revealed as a mediator of the promoting effect of c-Myc on cell proliferation. Together, these findings demonstrate that hnRNPAB is an important regulator of lung adenocarcinoma cell proliferation. They also add new insights into the mechanisms of how c-Myc promotes tumorigenesis.
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Affiliation(s)
- Chen Xu
- The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Bingyan Li
- The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Ning Yu
- The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Bo Yao
- The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Fang Wang
- The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.
| | - Yide Mei
- The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China; The CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.
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13
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Cai Y, Lyu T, Li H, Liu C, Xie K, Xu L, Li W, Liu H, Zhu J, Lyu Y, Feng X, Lan T, Yang J, Wu H. LncRNA CEBPA-DT promotes liver cancer metastasis through DDR2/β-catenin activation via interacting with hnRNPC. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2022; 41:335. [PMID: 36471363 PMCID: PMC9724427 DOI: 10.1186/s13046-022-02544-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 11/21/2022] [Indexed: 12/12/2022]
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is the world's third leading cause of cancer-related death; due to the fast growth and high prevalence of tumor recurrence, the prognosis of HCC patients remains dismal. Long non-coding RNA CEBPA-DT, a divergent transcript of the CCAAT Enhancer Binding Protein Alpha (CEBPA) gene, has been shown to participate in multiple tumor progression. However, no research has established its cancer-promoting mechanism in HCC yet. METHODS CEBPA-DT was identified in human HCC tissues through RNA sequencing. The expression level of CEBPA-DT was assessed by quantitative real-time PCR. The biological effects of CEBPA-DT were evaluated in vitro and in vivo through gain or loss of function experiments. RNA fluorescence in situ hybridization (FISH), RNA immunoprecipitation (RIP) and RNA pull-down assays were applied to investigate the downstream target of CEBPA-DT. Immunofluorescence, subcellular protein fractionation, western blot, and co-immunoprecipitation were performed to analyze the subcellular location of β-catenin and its interaction with Discoidin domain-containing receptor 2 (DDR2). RESULTS CEBPA-DT was upregulated in human HCC tissues with postoperative distant metastasis and intimately related to the worse prognosis of HCC patients. Silencing of CEBPA-DT inhibited the growth, migration and invasion of hepatoma cells in vitro and in vivo, while enhancement of CEBPA-DT played a contrasting role. Mechanistic investigations demonstrated that CEBPA-DT could bind to heterogeneous nuclear ribonucleoprotein C (hnRNPC), which facilitated cytoplasmic translocation of hnRNPC, enhanced the interaction between hnRNPC and DDR2 mRNA, subsequently promoted the expression of DDR2. Meanwhile, CEBPA-DT induced epithelial-mesenchymal transition (EMT) process through upregulation of Snail1 via facilitating nuclear translocation of β-catenin. Using DDR2 inhibitor, we revealed that the CEBPA-DT induced the interaction between DDR2 and β-catenin, thus promoting the nuclear translocation of β-catenin to activate transcription of Snail1, contributing to EMT and HCC metastasis. CONCLUSIONS Our results suggested that CEBPA-DT promoted HCC metastasis through DDR2/β-catenin mediated activation of Snail1 via interaction with hnRNPC, indicating that the CEBPA-DT-hnRNPC-DDR2/β-catenin axis may be used as a potential therapeutic target for HCC treatment.
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Affiliation(s)
- Yunshi Cai
- grid.412901.f0000 0004 1770 1022Liver Transplantation Center, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041 China ,grid.412901.f0000 0004 1770 1022Laboratory of Liver Surgery, West China Hospital, Sichuan University, Chengdu, 610041 China
| | - Tao Lyu
- grid.412901.f0000 0004 1770 1022Liver Transplantation Center, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041 China ,grid.412901.f0000 0004 1770 1022Laboratory of Liver Surgery, West China Hospital, Sichuan University, Chengdu, 610041 China
| | - Hui Li
- grid.190737.b0000 0001 0154 0904Department of Hepatobiliary Pancreatic Tumor Center, Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing, 400030 China
| | - Chang Liu
- grid.412901.f0000 0004 1770 1022Liver Transplantation Center, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041 China ,grid.412901.f0000 0004 1770 1022Laboratory of Liver Surgery, West China Hospital, Sichuan University, Chengdu, 610041 China
| | - Kunlin Xie
- grid.412901.f0000 0004 1770 1022Liver Transplantation Center, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041 China ,grid.412901.f0000 0004 1770 1022Laboratory of Liver Surgery, West China Hospital, Sichuan University, Chengdu, 610041 China
| | - Lin Xu
- grid.412901.f0000 0004 1770 1022Laboratory of Liver Surgery, West China Hospital, Sichuan University, Chengdu, 610041 China
| | - Wei Li
- grid.412901.f0000 0004 1770 1022Department of Plastic and Burns Surgery, West China Hospital, Sichuan University, Chengdu, 610041 China
| | - Hu Liu
- grid.412901.f0000 0004 1770 1022Liver Transplantation Center, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041 China
| | - Jiang Zhu
- grid.412901.f0000 0004 1770 1022Liver Transplantation Center, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041 China
| | - Yinghao Lyu
- grid.412901.f0000 0004 1770 1022Liver Transplantation Center, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041 China
| | - Xuping Feng
- grid.412901.f0000 0004 1770 1022Laboratory of Liver Surgery, West China Hospital, Sichuan University, Chengdu, 610041 China
| | - Tian Lan
- grid.412901.f0000 0004 1770 1022Liver Transplantation Center, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041 China ,grid.412901.f0000 0004 1770 1022Laboratory of Liver Surgery, West China Hospital, Sichuan University, Chengdu, 610041 China
| | - Jiayin Yang
- grid.412901.f0000 0004 1770 1022Liver Transplantation Center, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041 China
| | - Hong Wu
- grid.412901.f0000 0004 1770 1022Liver Transplantation Center, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041 China
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14
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Dos Santos MGP, Gatti da Silva GH, Nagasse HY, Fuziwara CS, Edna Teruko K, Coltri PP. hnRNP A1 and hnRNP C associate with miR-17 and miR-18 in thyroid cancer cells. FEBS Open Bio 2022; 12:1253-1264. [PMID: 35417090 PMCID: PMC9157402 DOI: 10.1002/2211-5463.13409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 03/03/2022] [Accepted: 04/12/2022] [Indexed: 11/18/2022] Open
Abstract
Heterogeneous nuclear ribonucleoproteins (hnRNPs) are essential players in the regulation of gene expression. The majority of the twenty different hnRNP proteins act through the modulation of pre‐mRNA splicing. Most have been shown to regulate the expression of critical genes for the progression of tumorigenic processes and were also observed to be overexpressed in several types of cancer. Moreover, these proteins were described as essential components for the maturation of some microRNAs (miRNAs). In the human genome, over 70% of miRNAs are transcribed from introns; therefore, we hypothesized that regulatory proteins involved with splicing could be important for their maturation. Increased expression of the miR‐17‐92 cluster has already been shown to be related to the development of many cancers, such as thyroid, lung, and lymphoma. In this article, we show that overexpression of hnRNP A1 and hnRNP C in BCPAP thyroid cancer cells directly affects the expression of miR‐17‐92 miRNAs. Both proteins associate with the 5′‐end of this cluster, strongly precipitate miRNAs miR‐17 and miR‐18a and upregulate the expression of miR‐92a. Upon overexpression of these hnRNPs, BCPAP cells also show increased proliferation, migration, and invasion rates, suggesting upregulation of these proteins and miRNAs is related to an enhanced tumorigenic phenotype.
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Affiliation(s)
- Maria Gabriela Pereira Dos Santos
- Departamento de Biologia Celular e do Desenvolvimento, Instituto de Ciências Biomédicas, Universidade de São Paulo, 05508-000, São Paulo, Brazil.,National Center for Tumor Diseases (NCT) Dresden, Fetscherstraße 74, 01307, Dresden, Germany
| | - Guilherme Henrique Gatti da Silva
- Departamento de Biologia Celular e do Desenvolvimento, Instituto de Ciências Biomédicas, Universidade de São Paulo, 05508-000, São Paulo, Brazil
| | - Helder Yudi Nagasse
- Departamento de Biologia Celular e do Desenvolvimento, Instituto de Ciências Biomédicas, Universidade de São Paulo, 05508-000, São Paulo, Brazil
| | - Cesar Seigi Fuziwara
- Departamento de Biologia Celular e do Desenvolvimento, Instituto de Ciências Biomédicas, Universidade de São Paulo, 05508-000, São Paulo, Brazil
| | - Kimura Edna Teruko
- Departamento de Biologia Celular e do Desenvolvimento, Instituto de Ciências Biomédicas, Universidade de São Paulo, 05508-000, São Paulo, Brazil
| | - Patricia Pereira Coltri
- Departamento de Biologia Celular e do Desenvolvimento, Instituto de Ciências Biomédicas, Universidade de São Paulo, 05508-000, São Paulo, Brazil
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15
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Mo L, Meng L, Huang Z, Yi L, Yang N, Li G. An analysis of the role of HnRNP C dysregulation in cancers. Biomark Res 2022; 10:19. [PMID: 35395937 PMCID: PMC8994388 DOI: 10.1186/s40364-022-00366-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 03/20/2022] [Indexed: 12/21/2022] Open
Abstract
Heterogeneous nuclear ribonucleoproteins C (HnRNP C) is part of the hnRNP family of RNA-binding proteins. The relationship between hnRNP C and cancers has been extensively studied, and dysregulation of hnRNP C has been found in many cancers. According to existing public data, hnRNP C could promote the maturation of new heterogeneous nuclear RNAs (hnRNA s, also referred to as pre-mRNAs) into mRNAs and could stabilize mRNAs, controlling their translation. This paper reviews the regulation and dysregulation of hnRNP C in cancers. It interacts with some cancer genes and other biological molecules, such as microRNAs (miRNAs), long noncoding RNAs (lncRNAs), and double-stranded RNAs (dsRNAs). Even directly binds to them. The effects of hnRNP C on biological processes such as alternative cleavage and polyadenylation (APA) and N6-methyladenosine (m6A) modification differ among cancers. Its main function is regulating stability and level of translation of cancer genes, and the hnRNP C is regarded as a candidate biomarker and might be valuable for prognosis evaluation.
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Affiliation(s)
- Liyi Mo
- The Hengyang Key Laboratory of Cellular Stress Biology, Institute of Cytology and Genetics, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China
| | - Lijuan Meng
- Department of Ultrasonography, Second Affiliated Hospital, University of South China, Hengyang, 421001, Hunan, China
| | - Zhicheng Huang
- The Hengyang Key Laboratory of Cellular Stress Biology, Institute of Cytology and Genetics, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China
| | - Lan Yi
- The Hengyang Key Laboratory of Cellular Stress Biology, Institute of Cytology and Genetics, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China
| | - Nanyang Yang
- The Hengyang Key Laboratory of Cellular Stress Biology, Institute of Cytology and Genetics, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China.
| | - Guoqing Li
- The Hengyang Key Laboratory of Cellular Stress Biology, Institute of Cytology and Genetics, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China.
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16
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Pan C, Wu Q, Feng N. A systematic pan-cancer study demonstrates the oncogenic function of heterogeneous nuclear ribonucleoprotein C. Aging (Albany NY) 2022; 14:2880-2901. [PMID: 35344508 PMCID: PMC9004556 DOI: 10.18632/aging.203981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 03/14/2022] [Indexed: 12/24/2022]
Abstract
Although complex links between heterogeneous nuclear ribonucleoprotein C (HNRNPC) and numerous types of cancer have been shown in both cell and animal models, a comprehensive pan-cancer investigation on the features and activities of HNRNPC is still lacking. Based on the Cancer Genome Atlas and Gene Expression Omnibus datasets, we investigated the possible oncogenic effects of HNRNPC in thirty-three cancers. HNRNPC expression was detected in the majority of cancers, and its expression level was shown to be significantly linked with cancer patient prognosis. HNRNPC increased the phosphorylation of S220, which was detected in various cancers, including ovarian cancer and colon cancer. HNRNPC expression was also shown to be related to cancer-associated cell infiltration, most notably in uveal melanoma, testicular germ cell tumors, and thymoma. Additionally, the signaling pathway for vascular endothelial growth factors and RNA transport were implicated in HNRNPC's functioning processes. In short, HNRNPC may further influence cancer progression through gene mutation, protein phosphorylation, cancer associated fibroblasts infiltration and related molecular pathways. This work was intended to provide a relatively thorough knowledge of the oncogenic activities of HNRNPC across a variety of tumor types by performing a systematic pan-cancer investigation.
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Affiliation(s)
- Chenxi Pan
- Key Laboratory of Fermentation Engineering (Ministry of Education), National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei Key Laboratory of Industrial Microbiology, Hubei Research Center of Food Fermentation Engineering and Technology, Hubei University of Technology, Wuhan 430068, China.,The Second Affiliated Hospital of Dalian Medical University, Dalian 116027, China
| | - Qian Wu
- Key Laboratory of Fermentation Engineering (Ministry of Education), National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei Key Laboratory of Industrial Microbiology, Hubei Research Center of Food Fermentation Engineering and Technology, Hubei University of Technology, Wuhan 430068, China
| | - Nianjie Feng
- Key Laboratory of Fermentation Engineering (Ministry of Education), National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei Key Laboratory of Industrial Microbiology, Hubei Research Center of Food Fermentation Engineering and Technology, Hubei University of Technology, Wuhan 430068, China
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17
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Yang N, Liu L, Liu X, Chen Y, Lu J, Wang Z. hnRNPC Promotes Malignancy in Pancreatic Cancer through Stabilization of IQGAP3. BIOMED RESEARCH INTERNATIONAL 2022; 2022:6319685. [PMID: 35355828 PMCID: PMC8958073 DOI: 10.1155/2022/6319685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 02/25/2022] [Accepted: 03/02/2022] [Indexed: 12/24/2022]
Abstract
Due to challenges in early-stage detection, aggressive behavior, and poor response to systemic therapy, pancreatic cancer is one of the most fatal cancer types globally. The role of RNA-binding protein (RBP) transcription and translation of cancer cells has been well demonstrated, although their roles in pancreatic cancer is less well understood. In this study, we found that heterogeneous nuclear ribonucleoprotein C (hnRNPC), a RBP, is highly expressed in pancreatic ductal adenocarcinoma (PDAC) tissues and cells. In addition, we discovered that overexpression of hnRNPC in PDAC cells in vitro increased cell proliferation, migration, invasion, and metastasis. The presence of hnRNPC promoted tumorigenesis of pancreatic cells in metastatic in vivo models, which was also validated. In silico analyses revealed that hnRNPC is a strong positive regulator of IQ Motif Containing GTPase Activating Protein 3 (IQGAP3) activity. The experimental confirmation of this association revealed a direct interaction of IQGAP3 and hnRNPC to induce cell growth and invasion in PDAC cells by activating the epithelial-mesenchymal transition. In light of the findings that hnRNPC accelerates PDAC progression by interfering with IQGAP3, it appears that this technique for diagnosis and treatment of PDAC may have promise.
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Affiliation(s)
- Nannan Yang
- Department of Radiology, Ruijin Hospital Luwan Branch, Shanghai Jiao Tong University School of Medicine, Shanghai 200020, China
| | - Lin Liu
- Department of Radiology, Ruijin Hospital Luwan Branch, Shanghai Jiao Tong University School of Medicine, Shanghai 200020, China
| | - Xiaoyu Liu
- Department of Interventional Radiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yingjie Chen
- Department of Interventional Radiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jian Lu
- Department of Radiology, Ruijin Hospital Luwan Branch, Shanghai Jiao Tong University School of Medicine, Shanghai 200020, China
| | - Zhongmin Wang
- Department of Radiology, Ruijin Hospital Luwan Branch, Shanghai Jiao Tong University School of Medicine, Shanghai 200020, China
- Department of Interventional Radiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
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18
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Liu Y, Li R, Luo J, Zhang Z. Inferring RNA-binding protein target preferences using adversarial domain adaptation. PLoS Comput Biol 2022; 18:e1009863. [PMID: 35202389 PMCID: PMC8870515 DOI: 10.1371/journal.pcbi.1009863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 01/25/2022] [Indexed: 11/18/2022] Open
Abstract
Precise identification of target sites of RNA-binding proteins (RBP) is important to understand their biochemical and cellular functions. A large amount of experimental data is generated by in vivo and in vitro approaches. The binding preferences determined from these platforms share similar patterns but there are discernable differences between these datasets. Computational methods trained on one dataset do not always work well on another dataset. To address this problem which resembles the classic "domain shift" in deep learning, we adopted the adversarial domain adaptation (ADDA) technique and developed a framework (RBP-ADDA) that can extract RBP binding preferences from an integration of in vivo and vitro datasets. Compared with conventional methods, ADDA has the advantage of working with two input datasets, as it trains the initial neural network for each dataset individually, projects the two datasets onto a feature space, and uses an adversarial framework to derive an optimal network that achieves an optimal discriminative predictive power. In the first step, for each RBP, we include only the in vitro data to pre-train a source network and a task predictor. Next, for the same RBP, we initiate the target network by using the source network and use adversarial domain adaptation to update the target network using both in vitro and in vivo data. These two steps help leverage the in vitro data to improve the prediction on in vivo data, which is typically challenging with a lower signal-to-noise ratio. Finally, to further take the advantage of the fused source and target data, we fine-tune the task predictor using both data. We showed that RBP-ADDA achieved better performance in modeling in vivo RBP binding data than other existing methods as judged by Pearson correlations. It also improved predictive performance on in vitro datasets. We further applied augmentation operations on RBPs with less in vivo data to expand the input data and showed that it can improve prediction performances. Lastly, we explored the predictive interpretability of RBP-ADDA, where we quantified the contribution of the input features by Integrated Gradients and identified nucleotide positions that are important for RBP recognition.
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Affiliation(s)
- Ying Liu
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, Hunan, China
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Ruihui Li
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong, China
| | - Jiawei Luo
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, Hunan, China
| | - Zhaolei Zhang
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
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19
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Influence of N6-Methyladenosine Modification Gene HNRNPC on Cell Phenotype in Parkinson's Disease. PARKINSON'S DISEASE 2021; 2021:9919129. [PMID: 34966539 PMCID: PMC8712163 DOI: 10.1155/2021/9919129] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 12/03/2021] [Accepted: 12/07/2021] [Indexed: 12/20/2022]
Abstract
This study aimed to explore the N6-methyladenosine (m6A) modification genes involved in the pathogenesis of Parkinson's disease (PD) through data analysis of the two data sets GSE120306 and GSE22491 in the GEO database and further explore its influence on cell phenotype in PD. We analyzed the differentially expressed genes and function enrichment analysis of the two sets of data and found that the expression of the m6A-modification gene HNRNPC was significantly downregulated in the PD group, and it played an important role in DNA metabolism, RNA metabolism, and RNA processing and may be involved in PD. Then, we constructed the HNRNPC differential expression cell line to study the role of this gene in the pathogenesis of PD. The results showed that overexpression of HNRNPC can promote the proliferation of PC12 cells, inhibit their apoptosis, and inhibit the expression of inflammatory factors IFN-β, IL-6, and TNF-α, suggesting that HNRNPC may cause PD by inhibiting the proliferation of dopaminergic nerve cells, promoting their apoptosis, and causing immune inflammation. Our study also has certain limitations. For example, the data of the experimental group and the validation group come from different cell types, and the data of the experimental group involve individuals with G2019S LRRK2 mutations. In addition, due to the low expression of HNRNPC in PC12 cells, we used the method of overexpressing this gene to study its function. All these factors may cause our conclusions to be biased. Therefore, more research is still needed to corroborate it in the future.
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20
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Janecki DM, Swiatkowska A, Szpotkowska J, Urbanowicz A, Kabacińska M, Szpotkowski K, Ciesiołka J. Poly(C)-binding Protein 2 Regulates the p53 Expression via Interactions with the 5'-Terminal Region of p53 mRNA. Int J Mol Sci 2021; 22:ijms222413306. [PMID: 34948101 PMCID: PMC8708005 DOI: 10.3390/ijms222413306] [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: 11/10/2021] [Revised: 12/03/2021] [Accepted: 12/07/2021] [Indexed: 11/16/2022] Open
Abstract
The p53 protein is one of the major transcriptional factors which guards cell homeostasis. Here, we showed that poly(C)-binding protein 2 (PCBP2) can bind directly to the 5′ terminus of p53 mRNA by means of electrophoretic mobility shift assay. Binding sites of PCBP2 within this region of p53 mRNA were mapped using Pb2+-induced cleavage and SAXS methods. Strikingly, the downregulation of PCBP2 in HCT116 cells resulted in a lower level of p53 protein under normal and stress conditions. Quantitative analysis of p53 mRNA in PCBP2-downregulated cells revealed a lower level of p53 mRNA under normal conditions suggesting the involvement of PCBP2 in p53 mRNA stabilisation. However, no significant change in p53 mRNA level was observed upon PCBP2 depletion under genotoxic stress. Moreover, a higher level of p53 protein in the presence of rapamycin or doxorubicin and the combination of both antibiotics was noticed in PCBP2-overexpressed cells compared to control cells. These observations indicate the potential involvement of PCBP2 in cap-independent translation of p53 mRNA especially occurring under stress conditions. It has been postulated that the PCBP2 protein is engaged in the enhancement of p53 mRNA stability, probably via interacting with its 3′ end. Our data show that under stress conditions PCBP2 also modulates p53 translation through binding to the 5′ terminus of p53 mRNA. Thus PCBP2 emerges as a double-function factor in the p53 expression.
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21
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Dong R, Ye N, Zhao S, Wang G, Zhang Y, Wang T, Zou P, Wang J, Yao T, Chen M, Zhou C, Zhang T, Luo L. Studies on Novel Diagnostic and Predictive Biomarkers of Intrahepatic Cholestasis of Pregnancy Through Metabolomics and Proteomics. Front Immunol 2021; 12:733225. [PMID: 34721396 PMCID: PMC8552060 DOI: 10.3389/fimmu.2021.733225] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 09/27/2021] [Indexed: 11/25/2022] Open
Abstract
Background Intrahepatic cholestasis of pregnancy (ICP) usually occurs in the third trimester and is associated with increased risks in fetal complications. Currently, the exact mechanism of this disease is unknown. The purpose of this study was to develop potential biomarkers for the diagnosis and prediction of ICP. Methods We enrolled 40 pregnant women diagnosed with ICP and 40 healthy pregnant controls. The number of placental samples and serum samples between the two groups was 10 and 40 respectively. Ultra-performance liquid chromatography tandem high-resolution mass spectrometry was used to analyze placental metabolomics. Then, we verified the differentially expressed proteins and metabolites, both placental and blood serum, in the first, second, and third trimesters. Results Metabolomic analysis of placental tissue revealed that fatty acid metabolism and primary bile acid biosynthesis were enriched. In the integrated proteomic and metabolomic analysis of placental tissue, peroxisomal acyl-CoA oxidase 1 (ACOX1), L-palmitoylcarnitine, and glycocholic acid were found to be three potential biomarkers. In a follow–up analysis, expression levels of both placental and serum ACOX1, L-palmitoylcarnitine, and glycocholic acid in both placenta and serum were found to be significantly higher in third-trimester ICP patients; the areas under the ROC curves were 0.823, 0.896, and 0.985, respectively. Expression levels of serum ACOX1, L-palmitoylcarnitine, and glycocholic acid were also significantly higher in first- and second-trimester ICP patients; the areas under the ROC curves were 0.726, 0.657, and 0.686 in the first trimester and 0.718, 0.727, and 0.670 in the second trimester, respectively. Together, levels of the three aforementioned biomarkers increased the value for diagnosing and predicting ICP (AUC: 0.993 for the third, 0.891 for the second, and 0.932 for the first trimesters). Conclusions L-palmitoylcarnitine, ACOX1, and glycocholic acid levels taken together may serve as a new biomarker set for the diagnosis and prediction of ICP.
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Affiliation(s)
- Ruirui Dong
- The Affiliated Wuxi Matemity and Child Health Care Hospital of Nanjing Medical University, Wuxi, China
| | - Ningzhen Ye
- The Affiliated Wuxi Matemity and Child Health Care Hospital of Nanjing Medical University, Wuxi, China
| | - Shaojie Zhao
- The Affiliated Wuxi Matemity and Child Health Care Hospital of Nanjing Medical University, Wuxi, China
| | - Gaoying Wang
- The Affiliated Wuxi Matemity and Child Health Care Hospital of Nanjing Medical University, Wuxi, China
| | - Yan Zhang
- The Affiliated Wuxi Matemity and Child Health Care Hospital of Nanjing Medical University, Wuxi, China
| | - Tiejun Wang
- The Affiliated Wuxi Matemity and Child Health Care Hospital of Nanjing Medical University, Wuxi, China
| | - Ping Zou
- The Affiliated Wuxi Matemity and Child Health Care Hospital of Nanjing Medical University, Wuxi, China
| | - Jing Wang
- The Affiliated Wuxi Matemity and Child Health Care Hospital of Nanjing Medical University, Wuxi, China
| | - Tingting Yao
- The Affiliated Wuxi Matemity and Child Health Care Hospital of Nanjing Medical University, Wuxi, China
| | - Minjian Chen
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, School of Public Health, Nanjing Medical University, Nanjing, China.,Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Conghua Zhou
- School of Computer Science and Telecommunication Engineering, Jiangsu University, Zhenjiang, China
| | - Ting Zhang
- The Affiliated Wuxi Matemity and Child Health Care Hospital of Nanjing Medical University, Wuxi, China
| | - Liang Luo
- The Affiliated Wuxi No.2 People's Hospital of Nanjing Medical University, Wuxi, China
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22
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Huang XT, Li JH, Zhu XX, Huang CS, Gao ZX, Xu QC, Zhao W, Yin XY. HNRNPC impedes m 6A-dependent anti-metastatic alternative splicing events in pancreatic ductal adenocarcinoma. Cancer Lett 2021; 518:196-206. [PMID: 34271104 DOI: 10.1016/j.canlet.2021.07.016] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 07/07/2021] [Accepted: 07/10/2021] [Indexed: 10/20/2022]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a malignancy with poor prognosis due to early metastasis. The aberrant N6-methyladenosine (m6A) RNA modification has emerged as an important mechanism in cancer progression and metastasis, but its role in PDAC remained largely unknown. Here, we demonstrated that an m6A regulator, heterogeneous nuclear ribonucleoprotein C (HNRNPC), modulated alternative splicing events to promote PDAC metastasis. In clinical PDAC tissues, high expression of HNRNPC was correlated with metastasis, resulting in poor prognosis in PDAC patients. Knockdown of HNRNPC significantly reduced PDAC cell invasion in vitro and metastasis in vivo. In contrast, overexpression of HNRNPC provoked malignant phenotypes of PDAC cells. Mechanistically, HNRNPC antagonized the anti-metastatic isoform of TAF8 (TAF8L) but increased the pro-metastatic alternative splicing isoform of TAF8 (TAF8S). Mutation of the m6A-site of TAF8 attenuated the interaction between HNRNPC and TAF8 transcript, leading to the decrease of TAF8S. Furthermore, experimental manipulation of the anti-metastasis splicing isoform TAF8L revealed that splice isoform switching of TAF8 is crucial for PDAC metastasis. In conclusion, our findings demonstrate the essentiality of HNRNPC-mediated alternative splicing events that impinges on metastatic PDAC.
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Affiliation(s)
- Xi-Tai Huang
- Department of Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, Guangdong, China
| | - Jian-Hui Li
- Department of Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, Guangdong, China
| | - Xiao-Xu Zhu
- Department of Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, Guangdong, China
| | - Chen-Song Huang
- Department of Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, Guangdong, China
| | - Zhuo-Xing Gao
- Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China
| | - Qiong-Cong Xu
- Department of Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, Guangdong, China
| | - Wei Zhao
- Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China.
| | - Xiao-Yu Yin
- Department of Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, Guangdong, China.
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23
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Strand E, Hollås H, Sakya SA, Romanyuk S, Saraste MEV, Grindheim AK, Patil SS, Vedeler A. Annexin A2 binds the internal ribosomal entry site of c- myc mRNA and regulates its translation. RNA Biol 2021; 18:337-354. [PMID: 34346292 PMCID: PMC8677036 DOI: 10.1080/15476286.2021.1947648] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The expression and localization of the oncoprotein c-Myc is highly regulated at the level of transcription, mRNA transport, translation, as well as stability of the protein. We previously showed that Annexin A2 (AnxA2) binds to a specific localization element in the 3'untranslated region (UTR) of c-myc mRNA and is involved in its localization to the perinuclear region. In the present study, we demonstrate that AnxA2 binds in a Ca2+-dependent manner to the internal ribosomal entry site (IRES) containing two pseudo-knots in the 5´UTR of the c-myc mRNA. Here, we employ an in vitro rabbit reticulocyte lysate system with chimeric c-myc reporter mRNAs to demonstrate that binding of AnxA2 to the c-myc IRES modulates the expression of c-Myc. Notably, we show that low levels of AnxA2 appear to increase, while high levels of AnxA2 inhibits translation of the chimeric mRNA. However, when both the AnxA2-binding site and the ribosomal docking site in the c-myc IRES are deleted, AnxA2 has no effect on the translation of the reporter mRNA. Forskolin-treatment of PC12 cells results in upregulation of Ser25 phosphorylated AnxA2 expression while c-Myc expression is down-regulated. The effect of forskolin on c-Myc expression and the level of Ser25 phosphorylated AnxA2 was abolished in the presence of EGTA. These findings indicate that AnxA2 regulates both the transport and subsequent translation of the c-myc mRNA, possibly by silencing the mRNA during its transport. They also suggest that AnxA2 act as a switch to turn off the c-myc IRES activity in the presence of calcium.Abbreviations: AnxA2, Annexin A2; β2--µglob, β2-microglobulin; cpm, counts per minute; hnRNP, heterogenous nuclear ribonucleoprotein; IRES, internal ribosomal entry site; ITAF, IRES trans-acting factor; MM, multiple myeloma; PABP, poly(A)-binding protein; PCBP, poly(rC) binding protein; PSF, PTB-associated splicing factor; PTB, polypyrimidine tract binding protein; RRL, rabbit reticulocyte lysate; UTR, untranslated region; YB, Y-box binding protein.
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Affiliation(s)
- Elin Strand
- Department of Biomedicine, University of Bergen, Bergen, Norway.,Department of Immunology and Transfusion Medicine, Haukeland University Hospital, Bergen, Norway
| | - Hanne Hollås
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Siri Aastedatter Sakya
- Department of Biomedicine, University of Bergen, Bergen, Norway.,Department of Pharmacology, Institute of Clinical Medicine, University of Oslo, Norway
| | - Sofya Romanyuk
- Department of Biomedicine, University of Bergen, Bergen, Norway.,City Hospital №40, St. Petersburg, Russia
| | - Mikko E V Saraste
- Department of Biomedicine, University of Bergen, Bergen, Norway.,Quality Control Unit, Thermo Fisher Scientific - Life Technologies, Lillestrøm, Norway
| | | | | | - Anni Vedeler
- Department of Biomedicine, University of Bergen, Bergen, Norway
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24
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Wu S, Wagner G. Deep computational analysis details dysregulation of eukaryotic translation initiation complex eIF4F in human cancers. Cell Syst 2021; 12:907-923.e6. [PMID: 34358439 DOI: 10.1016/j.cels.2021.07.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 04/22/2021] [Accepted: 07/09/2021] [Indexed: 12/28/2022]
Abstract
eIF4F plays diverse roles in human cancers, which complicate the development of an overarching understanding of its functional and regulatory impacts across tumor types. Typically, eIF4F drives initiation from the mRNA 5' end (cap) and is composed of eIF4G1, eIF4A1, and cap-binding eIF4E. Cap-independent initiation is possible without eIF4E, from internal ribosomal entry sites (IRESs). By analyzing large public datasets, we found that cancers selectively overexpress EIF4G1 more than EIF4E. That expression imbalance supports EIF4G1 as a prognostic indicator in patients with cancer. It also attenuates "housekeeping" pathways that are usually regulated in a tissue-specific manner via cap-dependent initiation in healthy tissues and reinforce regulation of cancer-preferred pathways in cap-independent contexts. Cap-independent initiation is mechanistically attributable to eIF4G1 hyperphosphorylation that promotes binding to eIF4A1 and reduced eIF4E availability. Collectively, these findings reveal a novel model of dysregulated eIF4F function and highlight the clinical relevance of cap-(in)dependent initiation in cancer.
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Affiliation(s)
- Su Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
| | - Gerhard Wagner
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
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25
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Herzner AM, Khan Z, Van Nostrand EL, Chan S, Cuellar T, Chen R, Pechuan-Jorge X, Komuves L, Solon M, Modrusan Z, Haley B, Yeo GW, Behrens TW, Albert ML. ADAR and hnRNPC deficiency synergize in activating endogenous dsRNA-induced type I IFN responses. J Exp Med 2021; 218:212507. [PMID: 34297039 PMCID: PMC8313407 DOI: 10.1084/jem.20201833] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/11/2020] [Accepted: 06/24/2021] [Indexed: 01/26/2023] Open
Abstract
Cytosolic double-stranded RNA (dsRNA) initiates type I IFN responses. Endogenous retroelements, notably Alu elements, constitute a source of dsRNA. Adenosine-to-inosine (A-to-I) editing by ADAR induces mismatches in dsRNA and prevents recognition by MDA5 and autoinflammation. To identify additional endogenous dsRNA checkpoints, we conducted a candidate screen in THP-1 monocytes and found that hnRNPC and ADAR deficiency resulted in synergistic induction of MDA5-dependent IFN responses. RNA-seq analysis demonstrated dysregulation of Alu-containing introns in hnRNPC-deficient cells via utilization of unmasked cryptic splice sites, including introns containing ADAR-dependent A-to-I editing clusters. These putative MDA5 ligands showed reduced editing in the absence of ADAR, providing a plausible mechanism for the combined effects of hnRNPC and ADAR. This study contributes to our understanding of the control of repetitive element-induced autoinflammation and suggests that patients with hnRNPC-mutated tumors might maximally benefit from ADAR inhibition-based immunotherapy.
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Affiliation(s)
| | - Zia Khan
- Department of Human Genetics, Genentech, South San Francisco, CA
| | - Eric L Van Nostrand
- Department of Cellular and Molecular Medicine, Stem Cell Program and the Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA
| | - Sara Chan
- Department of Pathology, Genentech, South San Francisco, CA
| | - Trinna Cuellar
- Department of Molecular Biology, Genentech, South San Francisco, CA
| | - Ronald Chen
- Department of Human Genetics, Genentech, South San Francisco, CA
| | | | - Laszlo Komuves
- Department of Pathology, Genentech, South San Francisco, CA
| | - Margaret Solon
- Department of Pathology, Genentech, South San Francisco, CA
| | - Zora Modrusan
- Department of Microchemistry, Proteomics & Lipidomics and Next Generation Sequencing, Genentech, South San Francisco, CA
| | - Benjamin Haley
- Department of Molecular Biology, Genentech, South San Francisco, CA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, Stem Cell Program and the Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA
| | | | - Matthew L Albert
- Department of Cancer Immunology, Genentech, South San Francisco, CA
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26
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Sajidah ES, Lim K, Wong RW. How SARS-CoV-2 and Other Viruses Build an Invasion Route to Hijack the Host Nucleocytoplasmic Trafficking System. Cells 2021; 10:1424. [PMID: 34200500 PMCID: PMC8230057 DOI: 10.3390/cells10061424] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 05/31/2021] [Accepted: 06/03/2021] [Indexed: 12/14/2022] Open
Abstract
The host nucleocytoplasmic trafficking system is often hijacked by viruses to accomplish their replication and to suppress the host immune response. Viruses encode many factors that interact with the host nuclear transport receptors (NTRs) and the nucleoporins of the nuclear pore complex (NPC) to access the host nucleus. In this review, we discuss the viral factors and the host factors involved in the nuclear import and export of viral components. As nucleocytoplasmic shuttling is vital for the replication of many viruses, we also review several drugs that target the host nuclear transport machinery and discuss their feasibility for use in antiviral treatment.
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Affiliation(s)
- Elma Sakinatus Sajidah
- Division of Nano Life Science in the Graduate School of Frontier Science Initiative, Kanazawa University, Kanazawa 920-1192, Japan;
| | - Keesiang Lim
- WPI-Nano Life Science Institute, Kanazawa University, Kanazawa 920-1192, Japan
| | - Richard W. Wong
- Division of Nano Life Science in the Graduate School of Frontier Science Initiative, Kanazawa University, Kanazawa 920-1192, Japan;
- WPI-Nano Life Science Institute, Kanazawa University, Kanazawa 920-1192, Japan
- Cell-Bionomics Research Unit, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa 920-1192, Japan
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27
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Lee YQ, Rajadurai P, Abas F, Othman I, Naidu R. Proteomic Analysis on Anti-Proliferative and Apoptosis Effects of Curcumin Analog, 1,5-bis(4-Hydroxy-3-Methyoxyphenyl)-1,4-Pentadiene-3-One-Treated Human Glioblastoma and Neuroblastoma Cells. Front Mol Biosci 2021; 8:645856. [PMID: 33996900 PMCID: PMC8119891 DOI: 10.3389/fmolb.2021.645856] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 03/04/2021] [Indexed: 12/31/2022] Open
Abstract
Curcumin analogs with excellent biological properties have been synthesized to address and overcome the poor pharmacokinetic profiles of curcumin. This study aims to investigate the cytotoxicity, anti-proliferative, and apoptosis-inducing ability of curcumin analog, MS13 on human glioblastoma U-87 MG, and neuroblastoma SH-SY5Y cells, and to examine the global proteome changes in these cells following treatment. Our current findings showed that MS13 induced potent cytotoxicity and anti-proliferative effects on both cells. Increased caspase-3 activity and decreased bcl-2 concentration upon treatment indicate that MS13 induces apoptosis in these cells in a dose- and time-dependent manner. The label-free shotgun proteomic analysis has defined the protein profiles in both glioblastoma and neuroblastoma cells, whereby a total of nine common DEPs, inclusive of glyceraldehyde 3-phosphate dehydrogenase (GAPDH), alpha-enolase (ENO1), heat shock protein HSP 90-alpha (HSP90AA1), Heat shock protein HSP 90-beta (HSP90AB1), Eukaryotic translation initiation factor 5A-1 (EFI5A), heterogenous nuclear ribonucleoprotein K (HNRNPK), tubulin beta chain (TUBB), histone H2AX (H2AFX), and Protein SET were identified. Pathway analysis further elucidated that MS13 may induce its anti-tumor effects in both cells via the common enriched pathways, “Glycolysis” and “Post-translational protein modification.” Conclusively, MS13 demonstrates an anti-cancer effect that may indicate its potential use in the management of brain malignancies.
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Affiliation(s)
- Yee Qian Lee
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Subang Jaya, Malaysia
| | - Pathmanathan Rajadurai
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Subang Jaya, Malaysia
| | - Faridah Abas
- Laboratory of Natural Products, Faculty of Science, University Putra Malaysia, Seri Kembangan, Malaysia.,Department of Food Science, Faculty of Food Science and Technology, University Putra Malaysia, Seri Kembangan, Malaysia
| | - Iekhsan Othman
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Subang Jaya, Malaysia
| | - Rakesh Naidu
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Subang Jaya, Malaysia
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28
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Feng L, Yin YY, Liu CH, Xu KR, Li QR, Wu JR, Zeng R. Proteome-wide data analysis reveals tissue-specific network associated with SARS-CoV-2 infection. J Mol Cell Biol 2021; 12:946-957. [PMID: 32642770 PMCID: PMC7454804 DOI: 10.1093/jmcb/mjaa033] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 06/04/2020] [Accepted: 06/11/2020] [Indexed: 12/14/2022] Open
Abstract
For patients with COVID-19 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the damages to multiple organs have been clinically observed. Since most of current investigations for virus–host interaction are based on cell level, there is an urgent demand to probe tissue-specific features associated with SARS-CoV-2 infection. Based on collected proteomic datasets from human lung, colon, kidney, liver, and heart, we constructed a virus-receptor network, a virus-interaction network, and a virus-perturbation network. In the tissue-specific networks associated with virus–host crosstalk, both common and different key hubs are revealed in diverse tissues. Ubiquitous hubs in multiple tissues such as BRD4 and RIPK1 would be promising drug targets to rescue multi-organ injury and deal with inflammation. Certain tissue-unique hubs such as REEP5 might mediate specific olfactory dysfunction. The present analysis implies that SARS-CoV-2 could affect multi-targets in diverse host tissues, and the treatment of COVID-19 would be a complex task.
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Affiliation(s)
- Li Feng
- CAS Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Mollecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuan-Yuan Yin
- CAS Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Mollecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cong-Hui Liu
- CAS Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Mollecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ke-Ren Xu
- CAS Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Mollecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qing-Run Li
- CAS Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Mollecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jia-Rui Wu
- CAS Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Mollecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China.,CAS Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou 310024, China
| | - Rong Zeng
- CAS Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Mollecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China.,CAS Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou 310024, China
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Fan J, Li H, Xie R, Zhang X, Nie X, Shi X, Zhan J, Yin Z, Zhao Y, Dai B, Yuan S, Wen Z, Chen C, Wang DW. LncRNA ZNF593-AS Alleviates Contractile Dysfunction in Dilated Cardiomyopathy. Circ Res 2021; 128:1708-1723. [PMID: 33550812 DOI: 10.1161/circresaha.120.318437] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Jiahui Fan
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China (J.F., H.L., R.X., X.Z., X.N., J.Z., Z.Y., Y.Z., B.D., S.Y., Z.W., C.C., D.W.W.).,Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, China (J.F., H.L., R.X., X.Z., X.N., J.Z., Z.Y., Y.Z., B.D., S.Y., Z.W., C.C., D.W.W.)
| | - Huaping Li
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China (J.F., H.L., R.X., X.Z., X.N., J.Z., Z.Y., Y.Z., B.D., S.Y., Z.W., C.C., D.W.W.).,Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, China (J.F., H.L., R.X., X.Z., X.N., J.Z., Z.Y., Y.Z., B.D., S.Y., Z.W., C.C., D.W.W.)
| | - Rong Xie
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China (J.F., H.L., R.X., X.Z., X.N., J.Z., Z.Y., Y.Z., B.D., S.Y., Z.W., C.C., D.W.W.).,Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, China (J.F., H.L., R.X., X.Z., X.N., J.Z., Z.Y., Y.Z., B.D., S.Y., Z.W., C.C., D.W.W.)
| | - Xudong Zhang
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China (J.F., H.L., R.X., X.Z., X.N., J.Z., Z.Y., Y.Z., B.D., S.Y., Z.W., C.C., D.W.W.).,Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, China (J.F., H.L., R.X., X.Z., X.N., J.Z., Z.Y., Y.Z., B.D., S.Y., Z.W., C.C., D.W.W.)
| | - Xiang Nie
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China (J.F., H.L., R.X., X.Z., X.N., J.Z., Z.Y., Y.Z., B.D., S.Y., Z.W., C.C., D.W.W.).,Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, China (J.F., H.L., R.X., X.Z., X.N., J.Z., Z.Y., Y.Z., B.D., S.Y., Z.W., C.C., D.W.W.)
| | - Xiaolu Shi
- Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing, China (X.S.)
| | - Jiabing Zhan
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China (J.F., H.L., R.X., X.Z., X.N., J.Z., Z.Y., Y.Z., B.D., S.Y., Z.W., C.C., D.W.W.).,Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, China (J.F., H.L., R.X., X.Z., X.N., J.Z., Z.Y., Y.Z., B.D., S.Y., Z.W., C.C., D.W.W.)
| | - Zhongwei Yin
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China (J.F., H.L., R.X., X.Z., X.N., J.Z., Z.Y., Y.Z., B.D., S.Y., Z.W., C.C., D.W.W.).,Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, China (J.F., H.L., R.X., X.Z., X.N., J.Z., Z.Y., Y.Z., B.D., S.Y., Z.W., C.C., D.W.W.)
| | - Yanru Zhao
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China (J.F., H.L., R.X., X.Z., X.N., J.Z., Z.Y., Y.Z., B.D., S.Y., Z.W., C.C., D.W.W.).,Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, China (J.F., H.L., R.X., X.Z., X.N., J.Z., Z.Y., Y.Z., B.D., S.Y., Z.W., C.C., D.W.W.)
| | - Beibei Dai
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China (J.F., H.L., R.X., X.Z., X.N., J.Z., Z.Y., Y.Z., B.D., S.Y., Z.W., C.C., D.W.W.).,Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, China (J.F., H.L., R.X., X.Z., X.N., J.Z., Z.Y., Y.Z., B.D., S.Y., Z.W., C.C., D.W.W.)
| | - Shuai Yuan
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China (J.F., H.L., R.X., X.Z., X.N., J.Z., Z.Y., Y.Z., B.D., S.Y., Z.W., C.C., D.W.W.).,Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, China (J.F., H.L., R.X., X.Z., X.N., J.Z., Z.Y., Y.Z., B.D., S.Y., Z.W., C.C., D.W.W.)
| | - Zheng Wen
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China (J.F., H.L., R.X., X.Z., X.N., J.Z., Z.Y., Y.Z., B.D., S.Y., Z.W., C.C., D.W.W.).,Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, China (J.F., H.L., R.X., X.Z., X.N., J.Z., Z.Y., Y.Z., B.D., S.Y., Z.W., C.C., D.W.W.)
| | - Chen Chen
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China (J.F., H.L., R.X., X.Z., X.N., J.Z., Z.Y., Y.Z., B.D., S.Y., Z.W., C.C., D.W.W.).,Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, China (J.F., H.L., R.X., X.Z., X.N., J.Z., Z.Y., Y.Z., B.D., S.Y., Z.W., C.C., D.W.W.)
| | - Dao Wen Wang
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China (J.F., H.L., R.X., X.Z., X.N., J.Z., Z.Y., Y.Z., B.D., S.Y., Z.W., C.C., D.W.W.).,Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, China (J.F., H.L., R.X., X.Z., X.N., J.Z., Z.Y., Y.Z., B.D., S.Y., Z.W., C.C., D.W.W.)
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30
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Guo W, Huai Q, Zhang G, Guo L, Song P, Xue X, Tan F, Xue Q, Gao S, He J. Elevated Heterogeneous Nuclear Ribonucleoprotein C Expression Correlates With Poor Prognosis in Patients With Surgically Resected Lung Adenocarcinoma. Front Oncol 2021; 10:598437. [PMID: 33569346 PMCID: PMC7868529 DOI: 10.3389/fonc.2020.598437] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 12/07/2020] [Indexed: 12/13/2022] Open
Abstract
Background Lung adenocarcinoma (LUAD), as the most common histological subtype of lung cancer, is a high-grade malignancy and a leading cause of cancer-related death globally. Identification of biomarkers with prognostic value is of great significance for the diagnosis and treatment of LUAD. Heterogeneous nuclear ribonucleoprotein C (HNRNPC) is an RNA-binding protein “reader” of N6-methyladenosine (m6A) methylation, and is related to the progression of various cancers; however, its role in LUAD is unclear. The aims of this study aims were to study the expression and prognostic value of HNRNPC in LUAD. Methods The Oncomine database and gene expression profiling interactive analysis (GEPIA) were used for preliminary exploration of HNRNPC expression and prognostic value in LUAD. LUAD cases from The Cancer Genome Atlas (TCGA) (n = 416) and the Kaplan-Meier plotter database (n = 720) were extracted to study the differential expression and prognostic value of HNRNPC. HNRNPC expression in the National Cancer Center of China (NCC) cohort was analyzed by immunohistochemical staining, and the relationship between HNRNPC expression and survival rate evaluated using the Kaplan-Meier method and log-rank test. Univariate and multivariate Cox regression analyses were used to identify independent prognostic factors. Several pathways that were significantly enriched in the HNRNPC high expression group were identified by Gene Set Enrichment Analysis (GSEA). Results Five data sets from the Oncomine and GEPIA databases all supported that HNRNPC expression is significantly higher in LUAD than in normal lung tissue. In TCGA cohort, HNRNPC was highly expressed in LUAD tissues and significantly related to age, sex, smoking history, ethnicity, lymph node metastasis, and TNM staging (P < 0.001). High HNRNPC expression was significantly correlated with poor prognosis in the three cohorts (NCC, TCGA, and K-M plotter) (P < 0.05). Multivariate Cox regression analysis showed that HNRNPC expression was an independent prognostic factor in both TCGA and NCC cohorts (P < 0.05). Further, 10 significantly enriched pathways were identified from TCGA data and 118 lung cancer cell lines in CCLE, respectively. Conclusions High HNRNPC expression is significantly related to poor overall survival in patients with LUAD, suggesting that HNRNPC may be a cancer-promoting factor and a potential prognostic biomarker in LUAD.
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Affiliation(s)
- Wei Guo
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qilin Huai
- Department of Graduate School, Zunyi Medical University, Zunyi, China
| | - Guochao Zhang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lei Guo
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Peng Song
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xuemin Xue
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Fengwei Tan
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qi Xue
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shugeng Gao
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jie He
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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31
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Ying P, Li Y, Yang N, Wang X, Wang H, He H, Li B, Peng X, Zou D, Zhu Y, Zhong R, Miao X, Tian J, Chang J. Identification of genetic variants in m 6A modification genes associated with pancreatic cancer risk in the Chinese population. Arch Toxicol 2021; 95:1117-1128. [PMID: 33474615 DOI: 10.1007/s00204-021-02978-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 01/04/2021] [Indexed: 12/24/2022]
Abstract
N6-Methyladenosine (m6A) is the most prevalent modification of RNA in eukaryotes, and is associated with many cellular processes and even the development of cancers. We hypothesized that single-nucleotide polymorphisms (SNPs) in m6A modification genes, including its "writers", "erasers" and "readers", might affect the m6A functions and associate with the susceptibility to pancreatic ductal adenocarcinoma (PDAC). We first conducted a two-stage case-control study in Chinese population to interrogate all SNPs in 22 m6A modification genes. In the discovery stage, a total of 2735 SNPs were genotyped in 980 patients and 1991 controls. Then, the promising SNP was replicated in another independent population consisting of 858 cases and 2084 controls. As a result, we found the rs7495 in 3'UTR of hnRNPC was significantly associated with increased risk of PDAC in both stages (combined odds ratio = 1.22, 95% confidence interval = 1.12-1.32, P = 2.39 × 10-6). To further reveal the biological function of rs7495 and hnRNPC, we performed a series of biochemical experiments. Luciferase reporter assays indicated that rs7495G allele promoted hnRNPC expression through disrupting a putative binding site for has-miR-183-3p. Cell viability assay demonstrated that knockdown of hnRNPC suppressed the proliferation of PDAC cells. RNA-seq analysis suggested that as an m6A "reader", hnRNPC played an important role in RNA biological processes. In conclusion, our findings elucidated that rs7495G could confer higher risk of PDAC via promoting the expression of hnRNPC through a miRNA-mediated manner. These results provided a novel insight into the critical role of m6A modification in tumorigenesis.
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Affiliation(s)
- Pingting Ying
- Department of Epidemiology and Biostatistics, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yao Li
- Department of Epidemiology and Biostatistics, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Nan Yang
- Department of Epidemiology and Biostatistics, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Xiaoyang Wang
- Department of Epidemiology and Biostatistics, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Haoxue Wang
- Department of Epidemiology and Biostatistics, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Heng He
- Department of Epidemiology and Biostatistics, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Bin Li
- Department of Epidemiology and Biostatistics, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Xiating Peng
- Department of Epidemiology and Biostatistics, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Danyi Zou
- Department of Epidemiology and Biostatistics, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Ying Zhu
- Department of Epidemiology and Biostatistics, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Rong Zhong
- Department of Epidemiology and Biostatistics, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Xiaoping Miao
- Department of Epidemiology and Biostatistics, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Jianbo Tian
- Department of Epidemiology and Biostatistics, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Jiang Chang
- Department of Epidemiology and Biostatistics, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
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Lambrianidou A, Sereti E, Soupsana K, Komini C, Dimas K, Trangas T. mTORC2 deploys the mRNA binding protein IGF2BP1 to regulate c-MYC expression and promote cell survival. Cell Signal 2021; 80:109912. [PMID: 33388443 DOI: 10.1016/j.cellsig.2020.109912] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 12/23/2020] [Accepted: 12/29/2020] [Indexed: 11/15/2022]
Abstract
mTORC2 promotes cell survival by phosphorylating AKT and enhancing its activity. Inactivation of mTORC2 reduces viability through down-regulation of E2F1 caused by up-regulation of c-MYC. An additional target of mTORC2 is IGF2BP1, an oncofetal RNA binding protein expressed de novo in a wide array of malignancies. IGF2BP1 enhances c-MYC expression by protecting the coding region instability sequence (CRD) of its mRNA from endonucleolytic cleavage. Here we show that repression of mTORC2 signalling and prevention of Ser181 phosphorylation of IGF2BP1 enhanced translation and destabilization of the endogenous c-myc mRNA as well as the mRNA of reporter transcripts carrying the CRD sequence in frame. The consequent increase in c-MYC protein was accompanied by the emergence of an apoptotic c-MYC overexpressing population. On the other hand, preventing phosphorylation of IGF2BP1 on Tyr396 by Src kinase caused the accumulation of translationally silent transcripts through sequestration by IGF2BP1 into cytoplasmic granules. The apoptotic effect of mTORC2 signalling deprivation was augmented when preceded by inhibition of IGF2BP1 phosphorylation by the Src kinase in concert with further increase of c-MYC levels because of enhanced translation of the previously stored mRNA only in the presence of IGF2BP1. Furthermore, the combined administration of mTORC2 and Src inhibitors exhibited synergism in delaying xenograft growth in female NOD.CB17-Prkdcscid/J mice. The above in vitro and in vivo findings may be applied for the induction of targeted apoptosis of cells expressing de novo the oncofetal protein IGF2BP1, a feature of aggressive malignancies resulting in a more focused anticancer therapeutic approach.
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Affiliation(s)
- Andromachi Lambrianidou
- Biochemistry Laboratory, Department of Biological Applications and Technology, University of Ioannina, Ioannina, Greece
| | - Evangelia Sereti
- Department of Pharmacology, Faculty of Medicine, University of Thessaly, Larissa, Greece
| | - Katerina Soupsana
- Laboratory of Biological Chemistry, University of Ioannina, Faculty of Medicine, Ioannina, Greece
| | - Chrysoula Komini
- Biochemistry Laboratory, Department of Biological Applications and Technology, University of Ioannina, Ioannina, Greece
| | - Konstantinos Dimas
- Department of Pharmacology, Faculty of Medicine, University of Thessaly, Larissa, Greece
| | - Theoni Trangas
- Biochemistry Laboratory, Department of Biological Applications and Technology, University of Ioannina, Ioannina, Greece.
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Li L, Peng G, Liu X, Zhang Y, Han H, Liu ZR. Pyruvate Kinase M2 Coordinates Metabolism Switch between Glycolysis and Glutaminolysis in Cancer Cells. iScience 2020; 23:101684. [PMID: 33196019 PMCID: PMC7644948 DOI: 10.1016/j.isci.2020.101684] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 08/03/2020] [Accepted: 10/12/2020] [Indexed: 12/21/2022] Open
Abstract
Cancer cells alter their nutrition metabolism to cope the stressful environment. One important metabolism adjustment is that cancer cells activate glutaminolysis in response to the reduced carbon from glucose entering into the TCA cycle due to inactivation of several enzymes in glycolysis. An important question is how the cancer cells coordinate the changes of glycolysis and glutaminolysis. In this report, we demonstrate that the pyruvate kinase inactive dimer PKM2 facilitates activation of glutaminolysis. Our experiments show that growth stimulations promote PKM2 dimer. The dimer PKM2 plays a role in regulation of glutaminolysis by upregulation of mitochondrial glutaminase I (GLS-1). PKM2 dimer regulates the GLS-1 expression by controlling internal ribosome entry site (IRES)-dependent c-myc translation. Growth stimulations promote PKM2 interacting with c-myc IRES-RNA, thus facilitating c-myc IRES-dependent translation. Our study reveals an important linker that coordinates the metabolism adjustment in cancer cells.
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Affiliation(s)
- Liangwei Li
- Department of Biology, Georgia State University, 145 Piedmont Ave SE, Atlanta, GA 30303, USA
| | - Guangda Peng
- Department of Biology, Georgia State University, 145 Piedmont Ave SE, Atlanta, GA 30303, USA
| | - Xiaowei Liu
- Department of Biology, Georgia State University, 145 Piedmont Ave SE, Atlanta, GA 30303, USA
| | - Yinwei Zhang
- Department of Biology, Georgia State University, 145 Piedmont Ave SE, Atlanta, GA 30303, USA
| | - Hongwei Han
- Department of Biology, Georgia State University, 145 Piedmont Ave SE, Atlanta, GA 30303, USA
| | - Zhi-Ren Liu
- Department of Biology, Georgia State University, 145 Piedmont Ave SE, Atlanta, GA 30303, USA
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Wang H, Zhu Y, Hu L, Li Y, Liu G, Xia T, Xiong D, Luo Y, Liu B, An Y, Li M, Huang Y, Zhong Q, Zeng M. Internal Ribosome Entry Sites Mediate Cap-Independent Translation of Bmi1 in Nasopharyngeal Carcinoma. Front Oncol 2020; 10:1678. [PMID: 33014838 PMCID: PMC7506037 DOI: 10.3389/fonc.2020.01678] [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: 10/30/2019] [Accepted: 07/29/2020] [Indexed: 01/03/2023] Open
Abstract
Bmi1 is overexpressed in multiple human cancers. We previously reported the oncogenic function and the transcription regulation mechanisms of Bmi1 in nasopharyngeal carcinoma (NPC). In this study, we observed that the mRNA and the protein levels of Bmi1 were strictly inconsistent in NPC cell lines and cancer tissues. The inhibitors of proteasome and lysosome could not enhance the protein level of Bmi1, indicating that Bmi1 may be post-transcriptionally regulated. The IRESite analysis showed that there were two potential internal ribosome entry sites (IRESs) in the 5'-untranslated region (5'-UTR) of Bmi1. The luciferase assay demonstrated that the 5'-UTR of Bmi1 has IRES activity, which may mediate cap-independent translation. The IRES activity of the Bmi1 5'-UTR was significantly reduced after the mutation of the two IRES elements. Taken together, these results suggested that the IRES elements mediating translation is a novel post-transcriptional regulation mechanism of Bmi1.
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Affiliation(s)
- Hongbo Wang
- Guangdong Provincial Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.,State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yunjia Zhu
- Guangdong Provincial Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Lijuan Hu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.,Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Peking University People's Hospital, Peking University Institute of Hematology, Beijing, China
| | - Yangyang Li
- Department of Pathology, Sun Yat-sen Memorial Hospital, Guangzhou, China
| | - Guihong Liu
- Tungwah Hospital of Sun Yat-sen University, Dongguan, China
| | - Tianliang Xia
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Dan Xiong
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.,Department of Laboratory Medicine, Luohu District People's Hospital, Shenzhen, China
| | - Yiling Luo
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Binliu Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yu An
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Manzhi Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yuehua Huang
- Guangdong Provincial Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Qian Zhong
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Musheng Zeng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
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35
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Spiniello M, Steinbrink MI, Cesnik AJ, Miller RM, Scalf M, Shortreed MR, Smith LM. Comprehensive in vivo identification of the c-Myc mRNA protein interactome using HyPR-MS. RNA (NEW YORK, N.Y.) 2019; 25:1337-1352. [PMID: 31296583 PMCID: PMC6800478 DOI: 10.1261/rna.072157.119] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Accepted: 06/27/2019] [Indexed: 05/10/2023]
Abstract
Proteins bind mRNA through their entire life cycle from transcription to degradation. We analyzed c-Myc mRNA protein interactors in vivo using the HyPR-MS method to capture the crosslinked mRNA by hybridization and then analyzed the bound proteins using mass spectrometry proteomics. Using HyPR-MS, 229 c-Myc mRNA-binding proteins were identified, confirming previously proposed interactors, suggesting new interactors, and providing information related to the roles and pathways known to involve c-Myc. We performed structural and functional analysis of these proteins and validated our findings with a combination of RIP-qPCR experiments, in vitro results released in past studies, publicly available RIP- and eCLIP-seq data, and results from software tools for predicting RNA-protein interactions.
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Affiliation(s)
- Michele Spiniello
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Department of Medicine of Precision, University of Studi della Campania Luigi Vanvitelli, Naples 80138, Italy
- Division of Immuno-Hematology and Transfusion Medicine, Cardarelli Hospital, Naples 80131, Italy
| | - Maisie I Steinbrink
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Anthony J Cesnik
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Rachel M Miller
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Mark Scalf
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Michael R Shortreed
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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Balaguer N, Moreno I, Herrero M, González M, Simón C, Vilella F. Heterogeneous nuclear ribonucleoprotein C1 may control miR-30d levels in endometrial exosomes affecting early embryo implantation. Mol Hum Reprod 2019; 24:411-425. [PMID: 29846695 DOI: 10.1093/molehr/gay026] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 05/28/2018] [Indexed: 12/19/2022] Open
Abstract
STUDY QUESTION Is there a specific mechanism to load the microRNA (miRNA), hsa-miR-30d, into exosomes to facilitate maternal communication with preimplantation embryos? SUMMARY ANSWER The heterogeneous nuclear ribonucleoprotein C1 (hnRNPC1) is involved in the internalization of endometrial miR-30d into exosomes to prepare for its subsequent incorporation into trophectoderm cells. WHAT IS KNOWN ALREADY Our group previously described a novel cell-to-cell communication mechanism involving the delivery of endometrial miRNAs from the maternal endometrium to the trophectoderm cells of preimplantation embryos. Specifically, human endometrial miR-30d is taken up by murine blastocysts causing the overexpression of certain genes involved in embryonic adhesion (Itb3, Itga7 and Cdh5) increasing embryo adhesion rates. STUDY DESIGN, SIZE, DURATION Transfer of maternal miR-30d to preimplantation embryos was confirmed by co-culture of wild-type (WT) and miR-30d knockout (KO) murine embryos with primary cultures of human endometrial epithelial cells (hEECs) in which mir-30d was labeled with specific Molecular Beacon (MB) or SmartFlare probes. Potential molecules responsible for the miR-30d loading into exosomes were purified by pull-down analysis with a biotinylated form of miR-30d on protein lysates from human endometrial exosomes, identified using mass spectrometry and assessed by flow cytometry, western blotting and co-localization studies. The role of hnRNPC1 in the miR-30d loading and transportation was interrogated by quantification of this miRNA in exosomes isolated from endometrial cells in which hnRNPC1 was transiently silenced using small interference RNA. Finally, the transfer of miR-30d to WT and KO embryos was assessed upon co-culture with sihnRNPC1 transfected cells. PARTICIPANTS/MATERIALS, SETTING, METHODS Murine embryos from miR-30d WT and KO mice, (strain MirC26tm1Mtm/Mmjax), were obtained by oviduct flushing of superovulated females. Endometrial Exosomes were purified by ultracentrifugation of supernatants from primary cultures of hEECs or Ishikawa cells. MB and Smartflare miR-30d probes were detected by confocal and/or transmission electron microscopy (TEM). hEECs and exosomes derived from them were subjected to pull-down with a biotinylated form of miR-30d. Captured proteins were identified by mass spectrometry (MS/MS). Western blotting was performed to detect hnRNPC1 and CYR61 in whole lysates, subcellular fractions and secreted vesicles from hEECs. Co-localization studies of the selected proteins with the exosomal marker CD63 were performed. FACS analysis was carried out to determine the presence of hnRNPC1 inside exosomes. Silencing of hnRNPC1 was conducted in the Ishikawa Cell Line with the Smart Pool Accell HNRNPC siRNA at a final concentration of 50 nM. RT-qPCRs were done to determine the messenger levels of miR-30d in cells and exosomes. Co-cultures of WT and KO embryos were established with Ishikawa cells double-transfected with sihnRPNC1 and MB probes. MAIN RESULTS AND THE ROLE OF CHANCE MS/MS analysis allowed us to identify hnRNPC1 as a possible protein to influence miR-30d loading into exosomes. Co-localization studies of hnRNPC1 with CD63 and FACS analyses suggested the presence of hnRNPC1 inside exosomes. Silencing of hnRNPC1 in Ishikawa cells resulted in a sharp decrease of the levels of miR-30d in both epithelial-like cells (P = 0.0001) and exosomes (P = 0.0152), suggesting its potential role in miR-30d biogenesis and transfer. Co-culture assays of miR-30d KO embryos with sihnRNPC1 hEECs revealed a decrease in embryo-miR-30d acquisition during the adhesion and invasion stages. In turn, transient silencing of hnRNPC1 results in a significant decrease of blastocyst adhesion compared to mock transfection conditions using Block-it, in both WT [Mean ± SD; 67 ± 10.0% vs. 38 ± 8.5%(P = 0.0006)] and miR-30d KO embryos [Mean ± SD; 50 ± 11.5% vs. 26 ± 8.8% (P = 0.0029) (n = 2); 14 embryos transferred per condition tested]. LARGE-SCALE DATA MS/MS data are available via ProteomeXchange with identifier PXD008773. LIMITATIONS, REASONS FOR CAUTION The Ishikawa Cell Line was used as a model of hEECs in silencing experiments due to the low survival rates of primary hEECs after transfection. WIDER IMPLICATIONS OF THE FINDINGS The data show that hnRNPC1 may be involved in the internalization of miR-30d inside exosomes. The decreased rates of embryo adhesion in endometrial epithelial-like cells transiently silenced with sihnRNPC1evidence that hnRNPC1 could be an important player in the maternal-embryo communication established in the early stages of implantation. STUDY FUNDING AND COMPETING INTEREST(S) This work was supported by the Miguel Servet Program Type I of Instituto de Salud Carlos III [CP13/00038]; FIS project [PI14/00545] to F.V.; the 'Atracció de Talent' Program from VLC-CAMPUS [UV-INV-PREDOC14-178329 to NB]; a Torres-Quevedo grant (PTQ-13-06133) by the Spanish Ministry of Economy and Competitiveness to IM and MINECO/FEDER Grant [SAF2015-67154-R] to C.S. The authors declare there is no conflict of interest.
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Affiliation(s)
- N Balaguer
- Department of Pediatrics, Obstetrics and Gynecology, School of Medicine, University of Valencia, Valencia, Spain
| | - I Moreno
- Department of Basic Research, Igenomix, S.L. Parque Tecnológico de Paterna, Valencia, Spain.,Department of Obstetrics and Gynecology, School of Medicine, Stanford University, CA, USA
| | - M Herrero
- Department of Basic Research, Igenomix, S.L. Parque Tecnológico de Paterna, Valencia, Spain
| | - M González
- Department of Basic Research, Igenomix, S.L. Parque Tecnológico de Paterna, Valencia, Spain
| | - C Simón
- Department of Pediatrics, Obstetrics and Gynecology, School of Medicine, University of Valencia, Valencia, Spain.,Department of Basic Research, Igenomix, S.L. Parque Tecnológico de Paterna, Valencia, Spain.,Department of Obstetrics and Gynecology, School of Medicine, Stanford University, CA, USA.,Department of Reproductive Medicine, Igenomix Foundation, Instituto de Investigación Sanitaria Hospital Clínico (INCLIVA), Valencia, Spain
| | - F Vilella
- Department of Obstetrics and Gynecology, School of Medicine, Stanford University, CA, USA.,Department of Reproductive Medicine, Igenomix Foundation, Instituto de Investigación Sanitaria Hospital Clínico (INCLIVA), Valencia, Spain
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Rodríguez-Ulloa A, Ramos Y, Sánchez-Puente A, Perera Y, Musacchio-Lasa A, Fernández-de-Cossio J, Padrón G, López LJ, Besada V, Perea SE. The Combination of the CIGB-300 Anticancer Peptide and Cisplatin Modulates Proteins Related to Cell Survival, DNA Repair and Metastasis in a Lung Cancer Cell Line Model. CURR PROTEOMICS 2019. [DOI: 10.2174/1570164616666190126104325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
CIGB-300 is a pro-apoptotic peptide that abrogates CK2-mediated phosphorylation,
and can elicit synergistic interaction in vitro and in vivo when combined with certain anticancer
drugs.
Objective:
The combination of CIGB-300 with cisplatin is studied through data mining and expressionbased
proteomics to reveal the molecular basis of this interaction. Cisplatin resistance-associated proteins,
which have also been reported as CK2 substrates, were first identified by bioinformatic analyses.
Methods:
Data from these analyses suggested that the cisplatin resistance phenotype could be directly
improved by inhibiting CK2 phosphorylation on specific substrates. Furthermore, 157 proteins were
differentially modulated on the NCI-H125 lung cancer cell line in response to CIGB-300, cisplatin or
both drugs as determined by LC-MS/MS.
Results:
The expression of 28 cisplatin resistance-associated proteins was changed when cisplatin was
combined with CIGB-300. Overall, the proteins identified are also related to cell survival, cell proliferation
and metastasis. Furthermore, the CIGB-300 regulated proteome revealed proteins that were initially
involved in the mechanism of action of CIGB-300 and cisplatin as single agents.
Conclusion:
This is the first report describing the protein array modulated by combining CIGB-300
and cisplatin that will support the rationale for future clinical settings based on a multi-target cancer
therapy.
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Affiliation(s)
| | - Yassel Ramos
- Department of Proteomics, Center for Genetic Engineering and Biotechnology, Havana, Cuba
| | - Aniel Sánchez-Puente
- Department of Proteomics, Center for Genetic Engineering and Biotechnology, Havana, Cuba
| | - Yasser Perera
- Laboratory of Molecular Oncology, Center for Genetic Engineering and Biotechnology, Havana, Cuba
| | - Alexis Musacchio-Lasa
- Department of Bioinformatics, Center for Genetic Engineering and Biotechnology, Havana, Cuba
| | | | - Gabriel Padrón
- Department of Proteomics, Center for Genetic Engineering and Biotechnology, Havana, Cuba
| | - Luis J.G. López
- Department of Proteomics, Center for Genetic Engineering and Biotechnology, Havana, Cuba
| | - Vladimir Besada
- Department of Proteomics, Center for Genetic Engineering and Biotechnology, Havana, Cuba
| | - Silvio E. Perea
- Laboratory of Molecular Oncology, Center for Genetic Engineering and Biotechnology, Havana, Cuba
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Godet AC, David F, Hantelys F, Tatin F, Lacazette E, Garmy-Susini B, Prats AC. IRES Trans-Acting Factors, Key Actors of the Stress Response. Int J Mol Sci 2019; 20:ijms20040924. [PMID: 30791615 PMCID: PMC6412753 DOI: 10.3390/ijms20040924] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 02/12/2019] [Accepted: 02/14/2019] [Indexed: 12/16/2022] Open
Abstract
The cellular stress response corresponds to the molecular changes that a cell undergoes in response to various environmental stimuli. It induces drastic changes in the regulation of gene expression at transcriptional and posttranscriptional levels. Actually, translation is strongly affected with a blockade of the classical cap-dependent mechanism, whereas alternative mechanisms are activated to support the translation of specific mRNAs. A major mechanism involved in stress-activated translation is the internal ribosome entry site (IRES)-driven initiation. IRESs, first discovered in viral mRNAs, are present in cellular mRNAs coding for master regulators of cell responses, whose expression must be tightly controlled. IRESs allow the translation of these mRNAs in response to different stresses, including DNA damage, amino-acid starvation, hypoxia or endoplasmic reticulum stress, as well as to physiological stimuli such as cell differentiation or synapse network formation. Most IRESs are regulated by IRES trans-acting factor (ITAFs), exerting their action by at least nine different mechanisms. This review presents the history of viral and cellular IRES discovery as well as an update of the reported ITAFs regulating cellular mRNA translation and of their different mechanisms of action. The impact of ITAFs on the coordinated expression of mRNA families and consequences in cell physiology and diseases are also highlighted.
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Affiliation(s)
- Anne-Claire Godet
- UMR 1048-I2MC, Inserm, Université de Toulouse, UT3, 31432 Toulouse cedex 4, France.
| | - Florian David
- UMR 1048-I2MC, Inserm, Université de Toulouse, UT3, 31432 Toulouse cedex 4, France.
| | - Fransky Hantelys
- UMR 1048-I2MC, Inserm, Université de Toulouse, UT3, 31432 Toulouse cedex 4, France.
| | - Florence Tatin
- UMR 1048-I2MC, Inserm, Université de Toulouse, UT3, 31432 Toulouse cedex 4, France.
| | - Eric Lacazette
- UMR 1048-I2MC, Inserm, Université de Toulouse, UT3, 31432 Toulouse cedex 4, France.
| | - Barbara Garmy-Susini
- UMR 1048-I2MC, Inserm, Université de Toulouse, UT3, 31432 Toulouse cedex 4, France.
| | - Anne-Catherine Prats
- UMR 1048-I2MC, Inserm, Université de Toulouse, UT3, 31432 Toulouse cedex 4, France.
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40
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Wu Y, Zhao W, Liu Y, Tan X, Li X, Zou Q, Xiao Z, Xu H, Wang Y, Yang X. Function of HNRNPC in breast cancer cells by controlling the dsRNA-induced interferon response. EMBO J 2018; 37:embj.201899017. [PMID: 30158112 PMCID: PMC6276880 DOI: 10.15252/embj.201899017] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 08/02/2018] [Accepted: 08/07/2018] [Indexed: 01/03/2023] Open
Abstract
Elevated expression of RNA binding protein HNRNPC has been reported in cancer cells, while the essentialness and functions of HNRNPC in tumors were not clear. We showed that repression of HNRNPC in the breast cancer cells MCF7 and T47D inhibited cell proliferation and tumor growth. Our computational inference of the key pathways and extensive experimental investigations revealed that the cascade of interferon responses mediated by RIG‐I was responsible for such tumor‐inhibitory effect. Interestingly, repression of HNRNPC resulted in accumulation of endogenous double‐stranded RNA (dsRNA), the binding ligand of RIG‐I. These up‐regulated dsRNA species were highly enriched by Alu sequences and mostly originated from pre‐mRNA introns that harbor the known HNRNPC binding sites. Such source of dsRNA is different than the recently well‐characterized endogenous retroviruses that encode dsRNA. In summary, essentialness of HNRNPC in the breast cancer cells was attributed to its function in controlling the endogenous dsRNA and the down‐stream interferon response. This is a novel extension from the previous understandings about HNRNPC in binding with introns and regulating RNA splicing.
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Affiliation(s)
- Yusheng Wu
- Tsinghua-Peking Joint Center for Life Sciences, Beijing, China.,MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China
| | - Wenwei Zhao
- MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China
| | - Yang Liu
- MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China.,Joint Graduate Program of Peking-Tsinghua-National Institute of Biological Science, Tsinghua University, Beijing, China
| | - Xiangtian Tan
- MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China
| | - Xin Li
- MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China
| | - Qin Zou
- MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China.,Joint Graduate Program of Peking-Tsinghua-National Institute of Biological Science, Tsinghua University, Beijing, China
| | - Zhengtao Xiao
- Tsinghua-Peking Joint Center for Life Sciences, Beijing, China.,MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China
| | - Hui Xu
- Tsinghua-Peking Joint Center for Life Sciences, Beijing, China.,MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China
| | - Yuting Wang
- MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China.,Joint Graduate Program of Peking-Tsinghua-National Institute of Biological Science, Tsinghua University, Beijing, China
| | - Xuerui Yang
- Tsinghua-Peking Joint Center for Life Sciences, Beijing, China .,MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China
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41
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Kim JK, Kim I, Choi K, Choi JH, Kim E, Lee HY, Park J, Kim Yoon S. Poly(rC) binding protein 2 acts as a negative regulator of IRES-mediated translation of Hr mRNA. Exp Mol Med 2018; 50:e441. [PMID: 29422543 PMCID: PMC5903819 DOI: 10.1038/emm.2017.262] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 08/16/2017] [Accepted: 08/26/2017] [Indexed: 12/21/2022] Open
Abstract
During the hair follicle (HF) cycle, HR protein expression is not concordant with the presence of the Hr mRNA transcript, suggesting an elaborate regulation of Hr gene expression. Here we present evidence that the 5' untranslated region (UTR) of the Hr gene has internal ribosome entry site (IRES) activity and this activity is regulated by the binding of poly (rC) binding protein 2 (PCBP2) to Hr mRNA. Overexpression and knockdown of PCBP2 resulted in a decrease in Hr 5' UTR IRES activity and an increase in HR protein expression without changing mRNA levels. We also found that this regulation was disrupted in a mutant Hr 5' UTR that has a mutation responsible for Marie Unna hereditary hypotrichosis (MUHH) in both mice and humans. These findings suggest that Hr mRNA expression is regulated at the post-transcriptional level via IRES-mediated translation control through interaction with PCPB2, but not in MUHH.
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Affiliation(s)
- Jeong-Ki Kim
- Department of Medical Lifesciences, The Catholic University of Korea, Seoul, Korea
| | - Injung Kim
- Department of Medical Lifesciences, The Catholic University of Korea, Seoul, Korea
| | - Keonwoo Choi
- Department of Medical Lifesciences, The Catholic University of Korea, Seoul, Korea
| | - Jee-Hyun Choi
- Department of Medical Lifesciences, The Catholic University of Korea, Seoul, Korea
| | - Eunmin Kim
- Department of Medical Lifesciences, The Catholic University of Korea, Seoul, Korea
| | - Hwa-Young Lee
- Department of Medical Lifesciences, The Catholic University of Korea, Seoul, Korea
| | - Jongkeun Park
- Department of Medical Lifesciences, The Catholic University of Korea, Seoul, Korea
| | - Sungjoo Kim Yoon
- Department of Medical Lifesciences, The Catholic University of Korea, Seoul, Korea
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Aviner R, Hofmann S, Elman T, Shenoy A, Geiger T, Elkon R, Ehrlich M, Elroy-Stein O. Proteomic analysis of polyribosomes identifies splicing factors as potential regulators of translation during mitosis. Nucleic Acids Res 2017; 45:5945-5957. [PMID: 28460002 PMCID: PMC5449605 DOI: 10.1093/nar/gkx326] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 04/16/2017] [Indexed: 12/16/2022] Open
Abstract
Precise regulation of mRNA translation is critical for proper cell division, but little is known about the factors that mediate it. To identify mRNA-binding proteins that regulate translation during mitosis, we analyzed the composition of polysomes from interphase and mitotic cells using unbiased quantitative mass-spectrometry (LC–MS/MS). We found that mitotic polysomes are enriched with a subset of proteins involved in RNA processing, including alternative splicing and RNA export. To demonstrate that these may indeed be regulators of translation, we focused on heterogeneous nuclear ribonucleoprotein C (hnRNP C) as a test case and confirmed that it is recruited to elongating ribosomes during mitosis. Then, using a combination of pulsed SILAC, metabolic labeling and ribosome profiling, we showed that knockdown of hnRNP C affects both global and transcript-specific translation rates and found that hnRNP C is specifically important for translation of mRNAs that encode ribosomal proteins and translation factors. Taken together, our results demonstrate how proteomic analysis of polysomes can provide insight into translation regulation under various cellular conditions of interest and suggest that hnRNP C facilitates production of translation machinery components during mitosis to provide daughter cells with the ability to efficiently synthesize proteins as they enter G1 phase.
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Affiliation(s)
- Ranen Aviner
- Department of Cell Research & Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Sarah Hofmann
- Department of Cell Research & Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Tamar Elman
- Department of Cell Research & Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Anjana Shenoy
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Tamar Geiger
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ran Elkon
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Marcelo Ehrlich
- Department of Cell Research & Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Orna Elroy-Stein
- Department of Cell Research & Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
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43
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Esnault S, Shen ZJ, Malter JS. Protein Translation and Signaling in Human Eosinophils. Front Med (Lausanne) 2017; 4:150. [PMID: 28971096 PMCID: PMC5609579 DOI: 10.3389/fmed.2017.00150] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 09/01/2017] [Indexed: 01/01/2023] Open
Abstract
We have recently reported that, unlike IL-5 and GM-CSF, IL-3 induces increased translation of a subset of mRNAs. In addition, we have demonstrated that Pin1 controls the activity of mRNA binding proteins, leading to enhanced mRNA stability, GM-CSF protein production and prolonged eosinophil (EOS) survival. In this review, discussion will include an overview of cap-dependent protein translation and its regulation by intracellular signaling pathways. We will address the more general process of mRNA post-transcriptional regulation, especially regarding mRNA binding proteins, which are critical effectors of protein translation. Furthermore, we will focus on (1) the roles of IL-3-driven sustained signaling on enhanced protein translation in EOS, (2) the mechanisms regulating mRNA binding proteins activity in EOS, and (3) the potential targeting of IL-3 signaling and the signaling leading to mRNA binding activity changes to identify therapeutic targets to treat EOS-associated diseases.
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Affiliation(s)
- Stephane Esnault
- Department of Medicine, Allergy, Pulmonary, and Critical Care Medicine Division, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, United States
| | - Zhong-Jian Shen
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - James S Malter
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, United States
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44
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Role of Eukaryotic Initiation Factors during Cellular Stress and Cancer Progression. J Nucleic Acids 2016; 2016:8235121. [PMID: 28083147 PMCID: PMC5204094 DOI: 10.1155/2016/8235121] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Accepted: 11/14/2016] [Indexed: 12/12/2022] Open
Abstract
Protein synthesis can be segmented into distinct phases comprising mRNA translation initiation, elongation, and termination. Translation initiation is a highly regulated and rate-limiting step of protein synthesis that requires more than 12 eukaryotic initiation factors (eIFs). Extensive evidence shows that the transcriptome and corresponding proteome do not invariably correlate with each other in a variety of contexts. In particular, translation of mRNAs specific to angiogenesis, tumor development, and apoptosis is altered during physiological and pathophysiological stress conditions. In cancer cells, the expression and functions of eIFs are hampered, resulting in the inhibition of global translation and enhancement of translation of subsets of mRNAs by alternative mechanisms. A precise understanding of mechanisms involving eukaryotic initiation factors leading to differential protein expression can help us to design better strategies to diagnose and treat cancer. The high spatial and temporal resolution of translation control can have an immediate effect on the microenvironment of the cell in comparison with changes in transcription. The dysregulation of mRNA translation mechanisms is increasingly being exploited as a target to treat cancer. In this review, we will focus on this context by describing both canonical and noncanonical roles of eIFs, which alter mRNA translation.
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45
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Lim I, Jung Y, Kim DY, Kim KT. HnRNP Q Has a Suppressive Role in the Translation of Mouse Cryptochrome1. PLoS One 2016; 11:e0159018. [PMID: 27392095 PMCID: PMC4938544 DOI: 10.1371/journal.pone.0159018] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 06/24/2016] [Indexed: 11/19/2022] Open
Abstract
Precise regulation of gene expression is especially important for circadian timekeeping which is maintained by the proper oscillation of the mRNA and protein of clock genes and clock-controlled genes. As a main component of the core negative arm feedback loops in the circadian clock, the Cry1 gene contributes to the maintenance of behavioral and molecular rhythmicity. Despite the central role of Cry1, the molecular mechanisms regulating expression levels of Cry1 mRNA and protein are not well defined. In particular, the post-transcriptional regulation of Cry1 mRNA fate decisions is unclear. Here, we demonstrate that hnRNP Q binds to mCry1 mRNA via the 5'UTR. Furthermore, hnRNP Q inhibits the translation of mCry1 mRNA, leading to altered rhythmicity in the mCRY1 protein profile.
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Affiliation(s)
- Ilgye Lim
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, Republic of Korea
- School of Medicine, CHA University, Seongnam, Republic of Korea
| | - Youngseob Jung
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, Republic of Korea
| | - Do-Yeon Kim
- Department of Pharmacology, School of Dentistry, Brain Science and Engineering Institute, Kyungpook National University, Daegu, Republic of Korea
- * E-mail: (KTK); (DYK)
| | - Kyong-Tai Kim
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, Republic of Korea
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, Republic of Korea
- * E-mail: (KTK); (DYK)
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Welch JD, Hu Y, Prins JF. Robust detection of alternative splicing in a population of single cells. Nucleic Acids Res 2016; 44:e73. [PMID: 26740580 PMCID: PMC4856971 DOI: 10.1093/nar/gkv1525] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 12/18/2015] [Indexed: 12/30/2022] Open
Abstract
Single cell RNA-seq experiments provide valuable insight into cellular heterogeneity but suffer from low coverage, 3' bias and technical noise. These unique properties of single cell RNA-seq data make study of alternative splicing difficult, and thus most single cell studies have restricted analysis of transcriptome variation to the gene level. To address these limitations, we developed SingleSplice, which uses a statistical model to detect genes whose isoform usage shows biological variation significantly exceeding technical noise in a population of single cells. Importantly, SingleSplice is tailored to the unique demands of single cell analysis, detecting isoform usage differences without attempting to infer expression levels for full-length transcripts. Using data from spike-in transcripts, we found that our approach detects variation in isoform usage among single cells with high sensitivity and specificity. We also applied SingleSplice to data from mouse embryonic stem cells and discovered a set of genes that show significant biological variation in isoform usage across the set of cells. A subset of these isoform differences are linked to cell cycle stage, suggesting a novel connection between alternative splicing and the cell cycle.
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Affiliation(s)
- Joshua D. Welch
- Department of Computer Science, University of North Carolina, Chapel Hill, NC 27599-3175, USA,Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC 27599-7264, USA
| | - Yin Hu
- Computational Oncology, Sage Bionetworks, 1100 Fairview Ave. N., Seattle, WA 98109, USA
| | - Jan F. Prins
- Department of Computer Science, University of North Carolina, Chapel Hill, NC 27599-3175, USA,Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC 27599-7264, USA,To whom correspondence should be addressed. Tel: +919 590 6213; Fax: +919 590 6111;
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47
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Systematic analysis of the contribution of c-myc mRNA constituents upon cap and IRES mediated translation. Biol Chem 2015; 396:1301-13. [DOI: 10.1515/hsz-2015-0190] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 07/16/2015] [Indexed: 11/15/2022]
Abstract
Abstract
Fine tuning of c-MYC expression is critical for its action and is achieved by several regulatory mechanisms. The contribution of c-myc mRNA regulatory sequences on its translational control has been investigated individually. However, putative interactions have not been addressed so far. The effect of these interactions upon the translatability of monocistronic and bicistronic chimaeric mRNAs, carrying combinations of the c-myc mRNA 5′-untranlated region (UTR), 3′-UTR, and coding region instability element (CRD) was investigated on this study. The presence of the 5′-UTR induced an increase in translatability of 50%. The presence of the CRD element, when in frame, reduced translatability by approximately 50%, regardless of the expression levels of the wild type CRD- binding protein (CRD-BP/IMP1). Conversely, overexpression of a mutated CRD-BP/IMP1 (Y396F) further impeded translation of the chimaeric mRNAs carrying its cognate sequences. The presence of the c-myc 3′-UTR increased translatability by approximately 300% affecting both cap and c-myc internal ribosome entry site (IRES) mediated translation. In addition, 3′-UTR rescued the cap mediated translation in the presence of the polyadenylation inhibitor cordycepin. Furthermore, the 3′-UTR rescued cap mediated translation under metabolic stress conditions and this was enhanced in the absence of a long poly (A) tail.
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48
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Cieniková Z, Jayne S, Damberger FF, Allain FHT, Maris C. Evidence for cooperative tandem binding of hnRNP C RRMs in mRNA processing. RNA (NEW YORK, N.Y.) 2015; 21:1931-42. [PMID: 26370582 PMCID: PMC4604433 DOI: 10.1261/rna.052373.115] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 07/21/2015] [Indexed: 05/20/2023]
Abstract
The human hnRNP C is a ubiquitous cellular protein involved in mRNA maturation. Recently, we have shown that this protein specifically recognizes uridine (U) pentamers through its single RNA recognition motif (RRM). However, a large fraction of natural RNA targets of hnRNP C consists of much longer contiguous uridine stretches. To understand how these extended sites are recognized, we studied the binding of the RRM to U-tracts of 8-11 bases. In vivo investigation of internal translation activation of unr (upstream of N-ras) mRNA indicates that the conservation of the entire hnRNP C binding site, UC(U)8, is required for hnRNP C-dependent IRES activation. The assays further suggest a synergistic interplay between hnRNP C monomers, dependent on the protein's ability to oligomerize. In vitro spectroscopic and thermodynamic analyses show that isolated RRMs bind to (U)11 oligomers as dimers. Structural modeling of a ternary double-RRM/RNA complex indicates additionally that two RRM copies can be accommodated on the canonical sequence UC(U)8. The proposed tandem RRM binding is in very good agreement with the transcriptome-wide recognition of extended U-tracts by full-length hnRNP C, which displays a cross-linking pattern consistent with a positively cooperative RRM dimer binding model.
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Affiliation(s)
- Zuzana Cieniková
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
| | - Sandrine Jayne
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
| | - Fred Franz Damberger
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
| | - Frédéric Hai-Trieu Allain
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
| | - Christophe Maris
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
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49
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Lupberger J, Casanova C, Fischer B, Weiss A, Fofana I, Fontaine N, Fujiwara T, Renaud M, Kopp A, Schuster C, Brino L, Baumert TF, Thoma C. PI4K-beta and MKNK1 are regulators of hepatitis C virus IRES-dependent translation. Sci Rep 2015; 5:13344. [PMID: 26323588 PMCID: PMC4555030 DOI: 10.1038/srep13344] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 07/22/2015] [Indexed: 12/12/2022] Open
Abstract
Cellular translation is down-regulated by host antiviral responses. Picornaviridae and Flaviviridae including hepatitis C virus (HCV) evade this process using internal ribosomal entry sequences (IRESs). Although HCV IRES translation is a prerequisite for HCV replication, only few host factors critical for IRES activity are known and the global regulator network remains largely unknown. Since signal transduction is an import regulator of viral infections and the host antiviral response we combined a functional RNAi screen targeting the human signaling network with a HCV IRES-specific reporter mRNA assay. We demonstrate that the HCV host cell cofactors PI4K and MKNK1 are positive regulators of HCV IRES translation representing a novel pathway with a functional relevance for the HCV life cycle and IRES-mediated translation of viral RNA.
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Affiliation(s)
- Joachim Lupberger
- Inserm U1110, Institut de Recherche sur les Maladies Virales et Hépatiques Strasbourg, France.,Université de Strasbourg, France
| | - Claudia Casanova
- Department of Medicine II, University of Freiburg, Freiburg, Germany
| | - Benoit Fischer
- High Throughput Screening platform, IGBMC, UMR7104 CNRS UdS, Inserm, U964, Illkirch, France
| | - Amelie Weiss
- High Throughput Screening platform, IGBMC, UMR7104 CNRS UdS, Inserm, U964, Illkirch, France
| | - Isabel Fofana
- Inserm U1110, Institut de Recherche sur les Maladies Virales et Hépatiques Strasbourg, France.,Université de Strasbourg, France
| | - Nelly Fontaine
- Inserm U1110, Institut de Recherche sur les Maladies Virales et Hépatiques Strasbourg, France.,Université de Strasbourg, France
| | - Toshinobu Fujiwara
- Laboratory of Hygienic Chemistry, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan
| | - Mickael Renaud
- High Throughput Screening platform, IGBMC, UMR7104 CNRS UdS, Inserm, U964, Illkirch, France
| | - Arnaud Kopp
- High Throughput Screening platform, IGBMC, UMR7104 CNRS UdS, Inserm, U964, Illkirch, France
| | - Catherine Schuster
- Inserm U1110, Institut de Recherche sur les Maladies Virales et Hépatiques Strasbourg, France.,Université de Strasbourg, France
| | - Laurent Brino
- High Throughput Screening platform, IGBMC, UMR7104 CNRS UdS, Inserm, U964, Illkirch, France
| | - Thomas F Baumert
- Inserm U1110, Institut de Recherche sur les Maladies Virales et Hépatiques Strasbourg, France.,Université de Strasbourg, France.,Institut Hospitalo-Universitaire, Pôle Hépato-digestif, Nouvel Hôpital Civil, Strasbourg, France
| | - Christian Thoma
- Department of Medicine II, University of Freiburg, Freiburg, Germany
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50
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Chen J, Li L, Su J, Li B, Zhang X, Chen T. Proteomic Analysis of G2/M Arrest Triggered by Natural Borneol/Curcumin in HepG2 Cells, the Importance of the Reactive Oxygen Species-p53 Pathway. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:6440-6449. [PMID: 26051007 DOI: 10.1021/acs.jafc.5b01773] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Curcumin (Cur), an active ingredient from the rhizome of the plant Curcuma longa, has wide anticancer activities. However, due to its poor solubility and hence poor absorption, Cur has limited clinical applications. It is therefore important to develop an effective method to improve its absorption. Natural borneol (NB), a terpene and bicyclic organic compound, has been extensively used as a food additive, and our previous studies show that it can improve the uptake of Cur in cancer cells. However, the anticancer mechanism of NB/Cur remains unclear. In this study, the effects of NB/Cur on HepG2 cells were investigated by proteomic analysis. The results showed that 32 differentially expressed proteins identified by matrix assisted laser desorption ionization time-of-flight mass spectrometry were significantly changed after NB/Cur treated HepG2 cells for 24 h. Moreover, 17 proteins increased and 12 proteins decreased significantly. Biological progress categorization demonstrated that the identified proteins were mainly associated with cell cycle and apoptosis (28.1%). Subcellular location categorization exhibited that the identified proteins were mainly located in nucleus (28.1%) and mitochondrion (21.9%). Among of all proteins, we selected three differential proteins (hnRNPC1/C2, NPM, and PSMA5), which were associated with the p53 pathway. Down-regulation of hnRNPC1/C2 and NPM contributed to the enhancement of phosphorylated p53. Activated p53 and down-regulation of PSMA5 resulted in an increase in p21 protein. Further studies showed that NB/Cur induced reactive oxygen species (ROS) generation, indicating that ROS might be upstream of the G2/M arrest signaling pathway. In summary, the results exhibited the whole proteomic response of HepG2 cells to NB/Cur, which might lead to a better understanding of its underlying anticancer mechanisms.
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Affiliation(s)
- Jianping Chen
- †College of Light Industry and Food Sciences, South China University of Technology, Guangzhou 510640, China
- §College of Food Science and Technology, Guangdong Ocean University, Zhanjiang 524088, China
| | - Lin Li
- †College of Light Industry and Food Sciences, South China University of Technology, Guangzhou 510640, China
| | - Jianyu Su
- †College of Light Industry and Food Sciences, South China University of Technology, Guangzhou 510640, China
- #Guangdong Hua Qing Yuan Biological Technology Co., Ltd., Meizhou, 514600, China
| | - Bing Li
- †College of Light Industry and Food Sciences, South China University of Technology, Guangzhou 510640, China
| | - Xia Zhang
- †College of Light Industry and Food Sciences, South China University of Technology, Guangzhou 510640, China
| | - Tianfeng Chen
- ‡Department of Chemistry, Jinan University, Guangzhou, 510632, China
- #Guangdong Hua Qing Yuan Biological Technology Co., Ltd., Meizhou, 514600, China
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