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Fujiwara Y, Takahashi RU, Saito M, Umakoshi M, Shimada Y, Koyama K, Yatabe Y, Watanabe SI, Koyota S, Minamiya Y, Tahara H, Kono K, Shiraishi K, Kohno T, Goto A, Tsuchiya N. Oncofetal IGF2BP3-mediated control of microRNA structural diversity in the malignancy of early-stage lung adenocarcinoma. Proc Natl Acad Sci U S A 2024; 121:e2407016121. [PMID: 39196622 PMCID: PMC11388381 DOI: 10.1073/pnas.2407016121] [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: 04/08/2024] [Accepted: 08/02/2024] [Indexed: 08/29/2024] Open
Abstract
The nature of microRNA (miRNA) dysfunction in carcinogenesis remains controversial because of the complex connection between miRNA structural diversity and biological processes. Here, we found that oncofetal IGF2BP3 regulates the selective production of a subset of 3'-isoforms (3'-isomiRs), including miR-21-5p and Let-7 family, which induces significant changes in their cellular seed occupancy and structural components, establishing a cancer-specific gene expression profile. The D-score, reflecting dominant production of a representative miR-21-5p+C (a 3'-isomiR), discriminated between clinical early-stage lung adenocarcinoma (LUAD) cases with low and high recurrence risks, and was associated with molecular features of cell cycle progression, epithelial-mesenchymal transition pressure, and immune evasion. We found that IGF2BP3 controls the production of miR-21-5p+C by directing the nuclear Drosha complex to select the cleavage site. IGF2BP3 was also involved in the production of 3'-isomiRs of miR-425-5p and miR-454-3p. IGF2BP3-regulated these three miRNAs are suggested to be associated with the regulation of p53, TGF-β, and TNF pathways in LUAD. Knockdown of IGF2BP3 also induced a selective upregulation of Let-7 3'-isomiRs, leading to increased cellular Let-7 seed occupancy and broad repression of its target genes encoding cell cycle regulators. The D-score is an index that reflects this cellular situation. Our results suggest that the aberrant regulation of miRNA structural diversity is a critical component for controlling cellular networks, thus supporting the establishment of a malignant gene expression profile in early stage LUAD.
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Affiliation(s)
- Yuko Fujiwara
- Laboratory of Molecular Carcinogenesis, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Ryou-U Takahashi
- Department of Cellular and Molecular Biology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8553, Japan
| | - Motonobu Saito
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima 960-1295, Japan
| | - Michinobu Umakoshi
- Department of Cellular and Organ Pathology, Graduate School of Medicine, Akita University, Akita 010-8543, Japan
| | - Yoko Shimada
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Kei Koyama
- Department of Cellular and Organ Pathology, Graduate School of Medicine, Akita University, Akita 010-8543, Japan
| | - Yasushi Yatabe
- Department of Diagnostic Pathology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Shun-Ichi Watanabe
- Department of Thoracic Surgery, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Souichi Koyota
- Molecular Medicine Laboratory, Bioscience Education and Research Support Center, Akita University, Akita 010-8543, Japan
| | - Yoshihiro Minamiya
- Department of Thoracic Surgery, Akita University Hospital, Akita 010-8543, Japan
| | - Hidetoshi Tahara
- Department of Cellular and Molecular Biology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8553, Japan
| | - Koji Kono
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima 960-1295, Japan
| | - Kouya Shiraishi
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo 104-0045, Japan
- Department of Clinical Genomics, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Takashi Kohno
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Akiteru Goto
- Department of Cellular and Organ Pathology, Graduate School of Medicine, Akita University, Akita 010-8543, Japan
| | - Naoto Tsuchiya
- Laboratory of Molecular Carcinogenesis, National Cancer Center Research Institute, Tokyo 104-0045, Japan
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Wang B, Liu X, Xu S, Liu Z, Zhu Y, Zhang X, Xu R. Sporadic Parkinson's Disease Potential Risk Loci Identified in Han Ancestry of Chinese Mainland. Front Aging Neurosci 2021; 12:603793. [PMID: 33510632 PMCID: PMC7835639 DOI: 10.3389/fnagi.2020.603793] [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: 09/07/2020] [Accepted: 11/30/2020] [Indexed: 11/13/2022] Open
Abstract
Recent investigations demonstrated that genetic factors might play an important role in sporadic Parkinson's disease (sPD). To clarify the specific loci susceptibility to sPD, we analyze the relationship between 30 candidate single nucleotide polymorphisms (SNPs) and sPD in the population of Han ancestry from Chinese mainland (HACM) by using genome-wide association study, sequenom massARRAY, DNA sequence, and biological information analysis. Results showed that the subjects carrying the T allele of rs863108 and rs28499371 exhibited a decreased risk for sPD. The subjects carrying the T allele of rs80315856 exhibited an increased risk for sPD. The A/T genotype of rs863108 and the C/T genotype of rs28499371 were a potential increased risk for sPD, and the G/T genotype of rs80315856 and T/T genotype of rs2270568 were a potential decreased risk for sPD. The minor allele frequency (MAF) of rs80315856 and rs2270568 was higher in sPD. The T allele of rs80315856 and rs2270568 might be a risk locus for sPD. Our data suggested that the alteration of these SNPs might play some roles through changing/affecting LINC01524/LOC105372666, DMRT2/SMARCA2, PLEKHN1, and FLJ23172/FNDC3B genes in the pathogenesis of sPD.
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Affiliation(s)
- Bo Wang
- Department of Neurology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xin Liu
- Department of Neurology, Jiangxi Provincial People's Hospital, The Affiliated People's Hospital of Nanchang University, Nanchang, China
| | - Shengyuan Xu
- Department of Neurology, Jiangxi Provincial People's Hospital, The Affiliated People's Hospital of Nanchang University, Nanchang, China
| | - Zheng Liu
- Department of Neurology, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Yu Zhu
- Department of Neurology, Jiangxi Provincial People's Hospital, The Affiliated People's Hospital of Nanchang University, Nanchang, China
| | - Xiong Zhang
- Department of Neurology, Maoming People's Hospital, Maoming, China
| | - Renshi Xu
- Department of Neurology, The First Affiliated Hospital of Nanchang University, Nanchang, China.,Department of Neurology, Jiangxi Provincial People's Hospital, The Affiliated People's Hospital of Nanchang University, Nanchang, China
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Yuan M, Song ZH, Ying MD, Zhu H, He QJ, Yang B, Cao J. N-myristoylation: from cell biology to translational medicine. Acta Pharmacol Sin 2020; 41:1005-1015. [PMID: 32203082 PMCID: PMC7468318 DOI: 10.1038/s41401-020-0388-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Accepted: 02/20/2020] [Indexed: 02/07/2023] Open
Abstract
Various lipids and lipid metabolites are bound to and modify the proteins in eukaryotic cells, which are known as ‘protein lipidation’. There are four major types of the protein lipidation, i.e. myristoylation, palmitoylation, prenylation, and glycosylphosphatidylinositol anchor. N-myristoylation refers to the attachment of 14-carbon fatty acid myristates to the N-terminal glycine of proteins by N-myristoyltransferases (NMT) and affects their physiology such as plasma targeting, subcellular tracking and localization, thereby influencing the function of proteins. With more novel pathogenic N-myristoylated proteins are identified, the N-myristoylation will attract great attentions in various human diseases including infectious diseases, parasitic diseases, and cancers. In this review, we summarize the current understanding of N-myristoylation in physiological processes and discuss the hitherto implication of crosstalk between N-myristoylation and other protein modification. Furthermore, we mention several well-studied NMT inhibitors mainly in infectious diseases and cancers and generalize the relation of NMT and cancer progression by browsing the clinic database. This review also aims to highlight the further investigation into the dynamic crosstalk of N-myristoylation in physiological processes as well as the potential application of protein N-myristoylation in translational medicine.
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Cernikova L, Faso C, Hehl AB. Phosphoinositide-binding proteins mark, shape and functionally modulate highly-diverged endocytic compartments in the parasitic protist Giardia lamblia. PLoS Pathog 2020; 16:e1008317. [PMID: 32092130 PMCID: PMC7058353 DOI: 10.1371/journal.ppat.1008317] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 03/05/2020] [Accepted: 01/14/2020] [Indexed: 12/18/2022] Open
Abstract
Phosphorylated derivatives of phosphatidylinositol (PIPs) are key membrane lipid residues involved in clathrin-mediated endocytosis (CME). CME relies on PIP species PI(4,5)P2 to mark endocytic sites at the plasma membrane (PM) associated to clathrin-coated vesicle (CCV) formation. The highly diverged parasitic protist Giardia lamblia presents disordered and static clathrin assemblies at PM invaginations, contacting specialized endocytic organelles called peripheral vacuoles (PVs). The role for clathrin assemblies in fluid phase uptake and their link to internal membranes via PIP-binding adaptors is unknown. Here we provide evidence for a robust link between clathrin assemblies and fluid-phase uptake in G. lamblia mediated by proteins carrying predicted PX, FYVE and NECAP1 PIP-binding modules. We show that chemical and genetic perturbation of PIP-residue binding and turnover elicits novel uptake and organelle-morphology phenotypes. A combination of co-immunoprecipitation and in silico analysis techniques expands the initial PIP-binding network with addition of new members. Our data indicate that, despite the partial conservation of lipid markers and protein cohorts known to play important roles in dynamic endocytic events in well-characterized model systems, the Giardia lineage presents a strikingly divergent clathrin-centered network. This includes several PIP-binding modules, often associated to domains of currently unknown function that shape and modulate fluid-phase uptake at PVs. In well-characterized model eukaryotes, clathrin-mediated endocytosis is a key process for uptake of extracellular material and is regulated by more than 50 known proteins. A large number of these carry phosphoinositide (PIP)-binding domains and play a central role in the regulation of endocytosis. Here, we report on the detailed functional characterization of PIP-binding proteins in the intestinal parasitic protist Giardia lamblia. We show evidence that proteins carrying specific PIP-binding domains are directly involved in fluid-phase uptake. Furthermore, using co-immunoprecipitation assays, we confirm these proteins’ association to G. lamblia’s clathrin assemblies. In addition, using state-of-the-art imaging strategies, we demonstrate a previously unappreciated level of complexity involving PIPs and their partner proteins in marking and shaping G. lamblia’s unique endocytic compartments. Our data contribute substantially to an updated working model for G. lamblia’s host-parasite interface, demonstrating how uptake in this parasite is directly regulated by a variety of PIP residues and PIP-binding modules, which have been re-routed from conserved pathways, likely as a result of host-parasite co-evolution.
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Affiliation(s)
- Lenka Cernikova
- Institute of Parasitology, University of Zurich, Zurich, Switzerland
| | - Carmen Faso
- Institute of Parasitology, University of Zurich, Zurich, Switzerland
- Institute of Cell Biology, University of Bern, Bern, Switzerland
- * E-mail: (CF); (AH)
| | - Adrian B. Hehl
- Institute of Parasitology, University of Zurich, Zurich, Switzerland
- * E-mail: (CF); (AH)
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