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Turan G, Olgun ÇE, Ayten H, Toker P, Ashyralyyev A, Savaş B, Karaca E, Muyan M. Dynamic proximity interaction profiling suggests that YPEL2 is involved in cellular stress surveillance. Protein Sci 2024; 33:e4859. [PMID: 38145972 PMCID: PMC10804680 DOI: 10.1002/pro.4859] [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: 08/17/2023] [Revised: 11/30/2023] [Accepted: 12/03/2023] [Indexed: 12/27/2023]
Abstract
YPEL2 is a member of the evolutionarily conserved YPEL family involved in cellular proliferation, mobility, differentiation, senescence, and death. However, the mechanism by which YPEL2, or YPEL proteins, mediates its effects is largely unknown. Proteins perform their functions in a network of proteins whose identities, amounts, and compositions change spatiotemporally in a lineage-specific manner in response to internal and external stimuli. Here, we explored interaction partners of YPEL2 by using dynamic TurboID-coupled mass spectrometry analyses to infer a function for the protein. Our results using inducible transgene expressions in COS7 cells indicate that proximity interaction partners of YPEL2 are mainly involved in RNA and mRNA metabolic processes, ribonucleoprotein complex biogenesis, regulation of gene silencing by miRNA, and cellular responses to stress. We showed that YPEL2 interacts with the RNA-binding protein ELAVL1 and the selective autophagy receptor SQSTM1. We also found that YPEL2 localizes stress granules in response to sodium arsenite, an oxidative stress inducer, which suggests that YPEL2 participates in stress granule-related processes. Establishing a point of departure in the delineation of structural/functional features of YPEL2, our results suggest that YPEL2 may be involved in stress surveillance mechanisms.
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Affiliation(s)
- Gizem Turan
- Department of Biological SciencesMiddle East Technical UniversityAnkaraTürkiye
| | - Çağla Ece Olgun
- Department of Biological SciencesMiddle East Technical UniversityAnkaraTürkiye
| | - Hazal Ayten
- Department of Biological SciencesMiddle East Technical UniversityAnkaraTürkiye
| | - Pelin Toker
- Department of Biological SciencesMiddle East Technical UniversityAnkaraTürkiye
| | | | - Büşra Savaş
- İzmir Biomedicine and Genome CenterİzmirTürkiye
- Izmir International Biomedicine and Genome InstituteDokuz Eylül UniversityIzmirTürkiye
| | - Ezgi Karaca
- İzmir Biomedicine and Genome CenterİzmirTürkiye
- Izmir International Biomedicine and Genome InstituteDokuz Eylül UniversityIzmirTürkiye
| | - Mesut Muyan
- Department of Biological SciencesMiddle East Technical UniversityAnkaraTürkiye
- CanSyl LaboratoriesMiddle East Technical UniversityAnkaraTürkiye
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2
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Federico A, Pavel A, Möbus L, McKean D, del Giudice G, Fortino V, Niehues H, Rastrick J, Eyerich K, Eyerich S, van den Bogaard E, Smith C, Weidinger S, de Rinaldis E, Greco D. The integration of large-scale public data and network analysis uncovers molecular characteristics of psoriasis. Hum Genomics 2022; 16:62. [PMID: 36437479 PMCID: PMC9703794 DOI: 10.1186/s40246-022-00431-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 11/07/2022] [Indexed: 11/29/2022] Open
Abstract
In recent years, a growing interest in the characterization of the molecular basis of psoriasis has been observed. However, despite the availability of a large amount of molecular data, many pathogenic mechanisms of psoriasis are still poorly understood. In this study, we performed an integrated analysis of 23 public transcriptomic datasets encompassing both lesional and uninvolved skin samples from psoriasis patients. We defined comprehensive gene co-expression network models of psoriatic lesions and uninvolved skin. Moreover, we curated and exploited a wide range of functional information from multiple public sources in order to systematically annotate the inferred networks. The integrated analysis of transcriptomics data and co-expression networks highlighted genes that are frequently dysregulated and show aberrant patterns of connectivity in the psoriatic lesion compared with the unaffected skin. Our approach allowed us to also identify plausible, previously unknown, actors in the expression of the psoriasis phenotype. Finally, we characterized communities of co-expressed genes associated with relevant molecular functions and expression signatures of specific immune cell types associated with the psoriasis lesion. Overall, integrating experimental driven results with curated functional information from public repositories represents an efficient approach to empower knowledge generation about psoriasis and may be applicable to other complex diseases.
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Affiliation(s)
- Antonio Federico
- grid.502801.e0000 0001 2314 6254Faculty of Medicine and Health Technology, Tampere University, Kauppi Campus, Arvo Ylpön Katu 34, 33520 Tampere, Finland ,grid.502801.e0000 0001 2314 6254BioMeditech Institute, Tampere University, Tampere, Finland ,grid.502801.e0000 0001 2314 6254Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere University, Tampere, Finland ,grid.502801.e0000 0001 2314 6254Tampere Institute for Advanced Studies, Tampere University, Tampere, Finland
| | - Alisa Pavel
- grid.502801.e0000 0001 2314 6254Faculty of Medicine and Health Technology, Tampere University, Kauppi Campus, Arvo Ylpön Katu 34, 33520 Tampere, Finland ,grid.502801.e0000 0001 2314 6254BioMeditech Institute, Tampere University, Tampere, Finland ,grid.502801.e0000 0001 2314 6254Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere University, Tampere, Finland
| | - Lena Möbus
- grid.502801.e0000 0001 2314 6254Faculty of Medicine and Health Technology, Tampere University, Kauppi Campus, Arvo Ylpön Katu 34, 33520 Tampere, Finland ,grid.502801.e0000 0001 2314 6254BioMeditech Institute, Tampere University, Tampere, Finland ,grid.502801.e0000 0001 2314 6254Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere University, Tampere, Finland
| | - David McKean
- Sanofi Immunology and Inflammation Research Therapeutic Area, Precision Immunology Cluster, Cambridge, Massachusetts USA
| | - Giusy del Giudice
- grid.502801.e0000 0001 2314 6254Faculty of Medicine and Health Technology, Tampere University, Kauppi Campus, Arvo Ylpön Katu 34, 33520 Tampere, Finland ,grid.502801.e0000 0001 2314 6254BioMeditech Institute, Tampere University, Tampere, Finland ,grid.502801.e0000 0001 2314 6254Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere University, Tampere, Finland
| | - Vittorio Fortino
- grid.9668.10000 0001 0726 2490Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Hanna Niehues
- grid.461760.20000 0004 0580 1253Department of Dermatology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Joe Rastrick
- grid.418727.f0000 0004 5903 3819Immunology Therapeutic Area, UCB Pharma, Slough, UK
| | - Kilian Eyerich
- grid.6936.a0000000123222966Department of Dermatology and Allergy, Technical University of Munich, Munich, Germany ,grid.24381.3c0000 0000 9241 5705Unit of Dermatology and Venerology, Department of Medicine, Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden
| | - Stefanie Eyerich
- grid.6936.a0000000123222966ZAUM-Center of Allergy and Environment, Technical University and Helmholtz Center Munich, Munich, Germany
| | - Ellen van den Bogaard
- grid.461760.20000 0004 0580 1253Department of Dermatology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Catherine Smith
- grid.13097.3c0000 0001 2322 6764St. John’s Institute of Dermatology, King’s College London, London, UK
| | - Stephan Weidinger
- grid.9764.c0000 0001 2153 9986Department of Dermatology, Kiel University, 24105 Kiel, Germany
| | - Emanuele de Rinaldis
- Sanofi Immunology and Inflammation Research Therapeutic Area, Precision Immunology Cluster, Cambridge, Massachusetts USA
| | - Dario Greco
- grid.502801.e0000 0001 2314 6254Faculty of Medicine and Health Technology, Tampere University, Kauppi Campus, Arvo Ylpön Katu 34, 33520 Tampere, Finland ,grid.502801.e0000 0001 2314 6254BioMeditech Institute, Tampere University, Tampere, Finland ,grid.502801.e0000 0001 2314 6254Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere University, Tampere, Finland ,grid.7737.40000 0004 0410 2071Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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Comprehensive analysis of the expression and prognosis of YPEL family members in clear cell renal cell cancer. Oncol Rep 2022; 48:134. [PMID: 35674183 PMCID: PMC9204605 DOI: 10.3892/or.2022.8345] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 05/03/2022] [Indexed: 12/31/2022] Open
Abstract
The Yippee‑like (YPEL) gene family is composed of five members encoding a protein containing a zinc finger‑like metal‑binding domain. Due to its structure and location in cells, this domain is considered to be involved in cell multiplication and numerous types of cancer. However, the relationship between the protein and the prognosis of clear cell renal cell carcinoma (ccRCC) remains unknown. In the present study, using pan‑cancer data from the updated public database, the expression and correlation of YPEL genes in 33 types of cancer was systematically and comprehensively analyzed. The prognostic value of YPEL genes was evaluated by survival and Cox regression analysis. Considering the relationship between the tumor microenvironment and stem cell indices, the function of superoxide dismutase was evaluated. Tumor Immune Assessment Resources (TIMER) and CIBERSORT algorithm analysis were used to evaluate the correlation between YPEL genes and tumor immune infiltrating cells (TIICs). Furthermore, knockdown experiments of YPEL genes were developed to explore their effects on ccRCC cell proliferation, migration and invasion in ccRCC cell lines. Members of the YPEL family were differentially expressed in ccRCC. Increased expression levels of YPEL1, YPEL2, and YPEL5 were associated with improved overall survival and disease‑specific survival. TIMER and CIBERSORT analyses showed remarkable correlation between YPEL family members and TIICs. More importantly, the results of Cell Counting Kit‑8, EdU and Transwell assays revealed that the multiplication, migration and invasion abilities of ccRCC cell lines could be promoted by knocking out YPEL1, YPEL2 and YPEL5. In conclusion, the present study provided new insight into the different roles of YPEL1, YPEL2 and YPEL5 in ccRCC, and the relationship between YPEL1 and immune infiltration may offer new options for future clinical treatment.
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Li W, Huang W, Wu K, Long Y. Yippee Like 1 Suppresses Glioma Progression and Serves as a Novel Prognostic Factor. TOHOKU J EXP MED 2022; 256:141-150. [DOI: 10.1620/tjem.256.141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Weimin Li
- Department of Neurosurgery, Suining Central Hospital
| | - Wei Huang
- Department of Neurosurgery, Suining Central Hospital
| | - Ke Wu
- Department of Neurosurgery, Xichang People’s Hospital
| | - Yong Long
- Department of Neurosurgery, Suining Central Hospital
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Yippee like 4 (Ypel4) is essential for normal mouse red blood cell membrane integrity. Sci Rep 2021; 11:15898. [PMID: 34354145 PMCID: PMC8342551 DOI: 10.1038/s41598-021-95291-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 07/22/2021] [Indexed: 11/08/2022] Open
Abstract
The YPEL family genes are highly conserved across a diverse range of eukaryotic organisms and thus potentially involved in essential cellular processes. Ypel4, one of five YPEL family gene orthologs in mouse and human, is highly and specifically expressed in late terminal erythroid differentiation (TED). In this study, we investigated the role of Ypel4 in murine erythropoiesis, providing for the first time an in-depth description of a Ypel4-null phenotype in vivo. We demonstrated that the Ypel4-null mice displayed a secondary polycythemia with macro- and reticulocytosis. While lack of Ypel4 did not affect steady-state TED in the bone marrow or spleen, the anemia-recovering capacity of Ypel4-null cells was diminished. Furthermore, Ypel4-null red blood cells (RBC) were cleared from the circulation at an increased rate, demonstrating an intrinsic defect of RBCs. Scanning electron micrographs revealed an ovalocytic morphology of Ypel4-null RBCs and functional testing confirmed reduced deformability. Even though Band 3 protein levels were shown to be reduced in Ypel4-null RBC membranes, we could not find support for a physical interaction between YPEL4 and the Band 3 protein. In conclusion, our findings provide crucial insights into the role of Ypel4 in preserving normal red cell membrane integrity.
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Sheng G, Thompson E, Newgreen D, Denker HW. Twenty Years on for The Epithelial-Mesenchymal Transition International Association (TEMTIA): An Interview with Co-Founders Erik Thompson and Donald Newgreen. Cells Tissues Organs 2021; 211:252-260. [PMID: 34530422 DOI: 10.1159/000518250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 11/19/2022] Open
Affiliation(s)
- Guojun Sheng
- International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Erik Thompson
- School of Biomedical Sciences and Translational Research Institute, Queensland University of Technology, Woolloongabba, Queensland, Australia
| | - Donald Newgreen
- Murdoch Children's Research Institute, Parkville, Victoria, Australia
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Yu J, Xiong C, Zhuo B, Wen Z, Shen J, Liu C, Chang L, Wang K, Wang M, Wu C, Wu X, Xu X, Ruan H, Li G. Analysis of Local Chromatin States Reveals Gene Transcription Potential during Mouse Neural Progenitor Cell Differentiation. Cell Rep 2021; 32:107953. [PMID: 32726618 DOI: 10.1016/j.celrep.2020.107953] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 05/25/2020] [Accepted: 07/02/2020] [Indexed: 01/23/2023] Open
Abstract
Chromatin dynamics play a critical role in cell fate determination and maintenance by regulating the expression of genes essential for development and differentiation. In mouse embryonic stem cells (mESCs), maintenance of pluripotency coincides with a poised chromatin state containing active and repressive histone modifications. However, the structural features of poised chromatin are largely uncharacterized. By adopting mild time-course MNase-seq with computational analysis, the low-compact chromatin in mESCs is featured in two groups: one in more open regions, corresponding to an active state, and the other enriched with bivalent histone modifications, considered the poised state. A parameter called the chromatin opening potential index (COPI) is also devised to quantify the transcription potential based on the dynamic changes of MNase-seq signals at promoter regions. Use of COPI provides effective prediction of gene activation potential and, more importantly, reveals a few developmental factors essential for mouse neural progenitor cell (NPC) differentiation.
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Affiliation(s)
- Juan Yu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Chaoyang Xiong
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Baowen Zhuo
- Baoan Maternal and Child Health Hospital, Jinan University, Shenzhen 518102, China
| | - Zengqi Wen
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jie Shen
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Cuifang Liu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Luyuan Chang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Kehui Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Min Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Chenyi Wu
- Molecular Biophysics Laboratories, School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK
| | - Xudong Wu
- Department of Cell Biology, Tianjin Medical University, Qixiangtai Road 22, Tianjin 300070, China
| | - Xueqing Xu
- Baoan Maternal and Child Health Hospital, Jinan University, Shenzhen 518102, China.
| | - Haihe Ruan
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Guohong Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of the Chinese Academy of Sciences, Beijing 100049, China.
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Zamariolli M, Colovati M, Moysés-Oliveira M, Nunes N, Caires Dos Santos L, Alvarez Perez AB, Bragagnolo S, Melaragno MI. Rare single-nucleotide variants in oculo-auriculo-vertebral spectrum (OAVS). Mol Genet Genomic Med 2019; 7:e00959. [PMID: 31469246 PMCID: PMC6785430 DOI: 10.1002/mgg3.959] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 08/07/2019] [Indexed: 01/13/2023] Open
Abstract
Background Oculo‐auriculo‐vertebral spectrum (OAVS) is a craniofacial developmental disorder that affects structures derived from the first and second pharyngeal arches. The clinically heterogeneous phenotype involves mandibular, oral, and ear development anomalies. Etiology is complex and poorly understood. Genetic factors have been associated, evidenced by chromosomal abnormalities affecting different genomic regions and genes. However, known pathogenic single‐nucleotide variants (SNVs) have only been identified in MYT1 in a restricted number of patients. Therefore, investigations of SNVs on candidate genes may reveal other pathogenic mechanisms. Methods In a cohort of 73 patients, coding and untranslated regions (UTR) of 10 candidate genes (CRKL, YPEL1, MAPK1, NKX3‐2, HMX1, MYT1, OTX2, GSC, PUF60, HOXA2) were sequenced. Rare SNVs were selected and in silico predictions were performed to ascertain pathogenicity. Likely pathogenic variants were validated by Sanger sequencing and heritability was assessed when possible. Results Four likely pathogenic variants in heterozygous state were identified in different patients. Two SNVs were located in the 5’UTR of YPEL1; one in the 3’UTR of CRKL and one in the 3’UTR of OTX2. Conclusion Our work described variants in candidate genes for OAVS and supported the genetic heterogeneity of the spectrum.
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Affiliation(s)
- Malú Zamariolli
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Mileny Colovati
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Mariana Moysés-Oliveira
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Natália Nunes
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Leonardo Caires Dos Santos
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Ana B Alvarez Perez
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Silvia Bragagnolo
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Maria Isabel Melaragno
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
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Distinct roles of the YPEL gene family in development and pathogenicity in the ascomycete fungus Magnaporthe oryzae. Sci Rep 2018; 8:14461. [PMID: 30262874 PMCID: PMC6160453 DOI: 10.1038/s41598-018-32633-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 09/12/2018] [Indexed: 11/13/2022] Open
Abstract
Members of the Yippee-like (YPEL) gene family are highly conserved in eukaryotes and are homologous to the Drosophila yippee gene. In this study, we functionally characterized two YPEL-homologous genes, MoYPEL1 and MoYPEL2, in the rice blast pathogen Magnaporthe oryzae using the deletion mutants ΔMoypel1, ΔMoypel2, and ΔΔMoypel1,2. The MoYPEL1 deletion mutant was significantly defective in conidiation and unable to undergo appressorium development; however, deletion of MoYPEL2 resulted in a significant increase in conidiation and the abnormal development of two appressoria per conidium. These data demonstrate the opposite roles of each member of the YPEL gene family during the development of M. oryzae. The double mutant was phenotypically similar to the ΔMoypel1 mutant in conidiation, but similar to the ΔMoypel2 mutant in appressorium development. Subcellular localization of the MoYPEL1 protein was dynamic during appressorium development, while the MoYPEL2 protein consistently localized within the nuclei during developmental stages. Our studies indicate that the two YPEL gene family members play distinct roles in the developmental stages of M. oryzae, furthering our understanding of disease dissemination and development in fungi.
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Distal deletion at 22q11.2 as differential diagnosis in Craniofacial Microsomia: Case report and literature review. Eur J Med Genet 2017; 61:262-268. [PMID: 29288792 DOI: 10.1016/j.ejmg.2017.12.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 12/17/2017] [Accepted: 12/23/2017] [Indexed: 01/23/2023]
Abstract
Craniofacial Microsomia (CFM) also known as Oculo-auriculo-vertebral Spectrum (OAVS) or Goldenhar Syndrome, presents wide phenotypic and etiological heterogeneity. It affects mainly the structures originated from the first and second pharyngeal arches. In addition, other major anomalies may also be found, including congenital heart diseases. In this study, we report a patient with distal deletion in the 22q11.2 region and a phenotype which resembles CFM. The proband is a girl, who presented bilateral preauricular tags, left auditory canal stenosis, malar hypoplasia, cleft lip and palate, mild asymmetry of soft tissue in face, congenital heart disease, intestinal atresia, annular pancreas and hydronephrosis. The genomic imbalances investigation by Multiplex Ligation-dependent Probe Amplification (MLPA) and Chromosomal Microarray Analysis (CMA) revealed a distal deletion of 1,048 kb at 22q11.2 encompassing the region from Low Copy Repeats (LCRs) D to E. We did review of the literature and genotype-phenotype correlation. This is the sixth case of distal 22q11.2 deletion resembling CFM and the second encompassing the region between LCRs D to E. All cases share some phenotypic signs, such as preauricular tags, facial asymmetry, cleft lip and palate, and congenital heart diseases. Candidate genes in this region have been studied by having an important role in pharyngeal arches developmental and in congenital heart diseases, such as HIC2, YPEL1and MAPK1/ERK2. This case corroborates the phenotypic similarity between 22q11.2 distal deletion and CFM/OAVS. It also contributes to genotype-phenotype correlation and reinforces that candidate genes for CFM, in the 22q11.2 region, might be located between LCRs D and E.
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11
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Wu X. Up-regulation of YPEL1 and YPEL5 and down-regulation of ITGA2 in erlotinib-treated EGFR-mutant non-small cell lung cancer: A bioinformatic analysis. Gene 2017; 643:74-82. [PMID: 29221754 DOI: 10.1016/j.gene.2017.12.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 11/17/2017] [Accepted: 12/04/2017] [Indexed: 10/18/2022]
Abstract
PURPOSE This study aimed to identify genes with significant alteration following treatment of epidermal growth factor receptor (EGFR)-mutant non-small cell lung cancer (NSCLC) with tyrosine kinase inhibitors (TKIs). METHODS We downloaded microarray data of GSE67051 from the Gene Expression Omnibus (GEO) database. Genes with differential expression were identified in two groups: erlotinib-treated versus DMSO-treated PC9 cells and erlotinib-treated versus DMSO-treated HCC827 cells. Functional enrichment analysis and protein-protein interaction (PPI) network were performed on the overlapping differentially expressed genes (DEGs). Additionally, miRNAs that can regulate the DEGs were predicted. Small-molecule drugs, with possible synergistic or antagonistic actions with respect to erlotinib, were screened; data validation using another dataset was conducted. RESULTS In total, 1466 and 839 DEGs were identified in the aforementioned comparison groups, respectively, among which 267 overlapping up-regulated and 73 down-regulated were observed. The overlapping up- and down-regulated genes were significantly associated with different functions and pathways. ITGA2 had higher centrality scores in the PPI network. Seventy small-molecule drugs, with either possible synergistic or antagonistic roles with erlotinib, were identified. Moreover, up-regulated YPEL1, YPEL2, and YPEL5 were enriched in the miRNA-target regulatory network. Implementing data validation, we found YPEL1, YPEL5, and ITGA2 displayed similar expression profiles in the two datasets. CONCLUSION YPEL1 and YPEL5 may be related to the action of erlotinib, and down-regulation of ITGA2 may be associated with the development of acquired resistance to erlotinib in EGFR-mutant NSCLCs. Furthermore, several small-molecule drugs that may have synergistic and antagonistic roles with erlotinib were identified.
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Affiliation(s)
- Xiaoli Wu
- Department of pharmacy, Huai'an First People's Hospital, Nanjing Medical University, No. 1 West Huanghe Road, Huaiyin District, Huai'an, Jiangsu 223300, China.
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12
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Tan TY, Gordon CT, Miller KA, Amor DJ, Farlie PG. YPEL1
overexpression in early avian craniofacial mesenchyme causes mandibular dysmorphogenesis by up‐regulating apoptosis. Dev Dyn 2015; 244:1022-30. [DOI: 10.1002/dvdy.24299] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Revised: 05/24/2015] [Accepted: 05/26/2015] [Indexed: 11/10/2022] Open
Affiliation(s)
- Tiong Yang Tan
- Victorian Clinical Genetics Services, Royal Children's HospitalMelbourne Australia
- Murdoch Children's Research InstituteMelbourne Australia
- Department of PaediatricsUniversity of MelbourneMelbourne Australia
| | | | - Kerry A Miller
- Murdoch Children's Research InstituteMelbourne Australia
| | - David J. Amor
- Victorian Clinical Genetics Services, Royal Children's HospitalMelbourne Australia
- Murdoch Children's Research InstituteMelbourne Australia
- Department of PaediatricsUniversity of MelbourneMelbourne Australia
| | - Peter G. Farlie
- Murdoch Children's Research InstituteMelbourne Australia
- Department of PaediatricsUniversity of MelbourneMelbourne Australia
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13
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Atypical copy number abnormalities in 22q11.2 region: Report of three cases. Eur J Med Genet 2013; 56:515-20. [DOI: 10.1016/j.ejmg.2013.07.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 07/05/2013] [Indexed: 11/23/2022]
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Tan TY, Collins A, James PA, McGillivray G, Stark Z, Gordon CT, Leventer RJ, Pope K, Forbes R, Crolla JA, Ganesamoorthy D, Burgess T, Bruno DL, Slater HR, Farlie PG, Amor DJ. Phenotypic variability of distal 22q11.2 copy number abnormalities. Am J Med Genet A 2011; 155A:1623-33. [PMID: 21671380 DOI: 10.1002/ajmg.a.34051] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2010] [Accepted: 03/17/2011] [Indexed: 01/09/2023]
Abstract
The availability of microarray technology has led to the recent recognition of copy number abnormalities of distal chromosome 22q11.2 that are distinct from the better-characterized deletions and duplications of the proximal region. This report describes five unrelated individuals with copy number abnormalities affecting distal chromosome 22q11.2. We report on novel phenotypic features including diaphragmatic hernia and uterine didelphys associated with the distal microdeletion syndrome; and frontomedial polymicrogyria and callosal agenesis associated with the distal microduplication syndrome. We describe the third distal chromosome 22q11.2 microdeletion patient with Goldenhar syndrome. Patients with distal chromosome 22q11.2 copy number abnormalities exhibit inter- and intra-familial phenotypic variability, and challenge our ability to draw meaningful genotype-phenotype correlations.
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15
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Liang P, Wan Y, Yan Y, Wang Y, Luo N, Deng Y, Fan X, Zhou J, Li Y, Wang Z, Yuan W, Tang M, Mo X, Wu X. MVP interacts with YPEL4 and inhibits YPEL4-mediated activities of the ERK signal pathway. Biochem Cell Biol 2010; 88:445-50. [PMID: 20555386 DOI: 10.1139/o09-166] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Human YPEL4 is a member of YPEL family. It contains a Yippee domain, which is a putative zinc-finger-like, metal-binding domain. The human YPEL4 gene maps to chromosome 11q12.1, is ubiquitously expressed in adult tissues, and encodes a nuclear protein of 127 amino acids, the function of which remains unknown. To gain insights into the cellular function of this protein, we searched for YPEL4-interacting proteins using a yeast two-hybrid screen. The major vault protein (MVP), a lung resistance associated protein, was identified as a binding partner of YPEL4. The interaction between YPEL4 and MVP in mammalian cells was further demonstrated by a series of biochemical assays including the mammalian two-hybrid assay, GST pull-down assay, co-immunoprecipitation assay, and immunocytochemistry. Using a reporter system, we found that MVP can inhibit YPEL4's ability to activate Elk-1 in the MAPK signaling pathway. This study provides new clues for understanding the molecular mechanism of YPEL4 in cell division and signal transduction pathways and should be helpful for understanding molecular functions of the YPEL family.
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Affiliation(s)
- Pei Liang
- The Center for Heart Development, Key Laboratory of MOE for Developmental Biology and Protein Chemistry, College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, People's Republic of China
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16
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Hosono K, Noda S, Shimizu A, Nakanishi N, Ohtsubo M, Shimizu N, Minoshima S. YPEL5 protein of the YPEL gene family is involved in the cell cycle progression by interacting with two distinct proteins RanBPM and RanBP10. Genomics 2010; 96:102-11. [PMID: 20580816 DOI: 10.1016/j.ygeno.2010.05.003] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2009] [Revised: 05/07/2010] [Accepted: 05/16/2010] [Indexed: 10/19/2022]
Abstract
YPEL5 is a member of the YPEL gene family that is highly conserved in the eukaryotic species and apparently involved in a certain cell division-related function. In this study, we examined the functional and phylogenetic aspects of YPEL5 protein in more detail. During cell cycle, YPEL5 protein was detected at different subcellular localizations; at interphase, it was located in the nucleus and centrosome, then it changed location sequentially to spindle poles, mitotic spindle, and spindle midzone during mitosis, and finally transferred to midbody at cytokinesis. Knockdown of YPEL5 function by siRNA or anti-sense morpholino oligonucleotide inhibited the growth of cultured COS-7 cells and early development of medaka fish embryos, indicating its involvement in cell cycle progression. Interestingly, RanBPM (Ran Binding Protein in the Microtubule organizing center, encoded by RANBP9) was identified as a YPEL5-binding protein by yeast two-hybrid method. A paralog of RanBPM, namely RanBP10 (encoded by RANBP10), was found to be another YPEL5-binding protein, and these two protein genes are highly conserved each other. Comparative genomic analysis allowed us to define a new gene family consisting of RanBPM and RanBP10, named Scorpin, providing a basis to better understand how they interact with YPEL5.
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Affiliation(s)
- Katsuhiro Hosono
- Department of Medical Photobiology, Photon Medical Research Center, Hamamatsu University School of Medicine, Higashi-ku, Japan.
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17
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Tan TY, Gordon CT, Amor DJ, Farlie PG. Developmental perspectives on copy number abnormalities of the 22q11.2 region. Clin Genet 2010; 78:201-18. [DOI: 10.1111/j.1399-0004.2010.01456.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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18
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Abstract
Craniofacial disorders are associated with one-third of human birth defects but the underlying molecular and cellular causes remain poorly understood. Proteomics seems well-placed to benefit this medically important area but the scarcity of embryonic tissues poses a major challenge. In this study, we applied a microsample proteomics strategy to investigate the first branchial arch, an embryonic structure crucial for facial development, and found that proteome analysis is both practicable and informative despite the scarcity of tissue. Exploiting the embryonic chick as a tractable source of accurately staged tissue, we developed a sequential extraction procedure to interface with one-dimensional polyacrylamide gel electrophoresis (1-D PAGE) and 2-D PAGE. In 2-D gels, about 8% of the visible proteome changed between embryonic days 3 and 5, and the identities determined for 21 proteins accorded with the rapid growth during this period. These results led to the first molecular identification of chicken alpha-fetoprotein, and an unusual localisation of vimentin to endoderm. With over 470 protein spots accessible, this comparative proteomics approach has good prospects for providing new markers, functional hypotheses and genes to target in functional tests. A broader value of extending these approaches to facial development in other species and to other areas in embryology can be anticipated.
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Affiliation(s)
- Jonathan E Mangum
- School of Dental Science, University of Melbourne, Melbourne, Australia
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19
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Wakeham DE, Abi-Rached L, Towler MC, Wilbur JD, Parham P, Brodsky FM. Clathrin heavy and light chain isoforms originated by independent mechanisms of gene duplication during chordate evolution. Proc Natl Acad Sci U S A 2005; 102:7209-14. [PMID: 15883369 PMCID: PMC1091751 DOI: 10.1073/pnas.0502058102] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In humans, there are two isoforms each of clathrin heavy chain (CHC17 and CHC22) and light chain (LCa and LCb) subunits, all encoded by separate genes. CHC17 forms the ubiquitous clathrin-coated vesicles that mediate membrane traffic. CHC22 is implicated in specialized membrane organization in skeletal muscle. CHC17 is bound and regulated by LCa and LCb, whereas CHC22 does not functionally interact with either light chain. The imbalanced interactions between clathrin subunit isoforms suggest a distinct evolutionary history for each isoform pair. Phylogenetic and sequence analysis placed both heavy and light chain gene duplications during chordate evolution, 510-600 million years ago. Genes encoding CHC22 orthologues were found in several vertebrate species, with only a pseudogene present in mice. Multiple paralogons surrounding the CHC genes (CLTC and CLTD) were identified, evidence that genomic or large-scale gene duplication produced the two CHC isoforms. In contrast, clathrin light chain genes (CLTA and CLTB) apparently arose by localized duplication, within 1-11 million years of CHC gene duplication. Analysis of sequence divergence patterns suggested that structural features of the CHCs were maintained after gene duplication, but new interactions with regulatory proteins evolved for the CHC22 isoform. Thus, independent mechanisms of gene duplication expanded clathrin functions, concomitant with development of neuromuscular sophistication in chordates.
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Affiliation(s)
- Diane E Wakeham
- The G. W. Hooper Foundation and Department of Biopharmaceutical Sciences, University of California, San Francisco, CA 94143-0552, USA
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Hosono K, Sasaki T, Minoshima S, Shimizu N. Identification and characterization of a novel gene family YPEL in a wide spectrum of eukaryotic species. Gene 2004; 340:31-43. [PMID: 15556292 DOI: 10.1016/j.gene.2004.06.014] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2004] [Revised: 05/21/2004] [Accepted: 06/03/2004] [Indexed: 11/19/2022]
Abstract
During comprehensive sequence analysis of human chromosome 22, we identified a novel gene family consisting of five members (YPEL1 through YPEL5) which has high homology with Drosophila yippee gene. We cloned and sequenced cDNAs for all five genes and determined their exon/intron organization. These YPEL genes showed high homology (43.8-96.6%) at amino acid sequence level among them. Mouse counterparts (Ypel1 through Ypel5) were also identified in the syntenic region of mouse chromosomes and their cDNAs were cloned and sequenced. Each of five pairs of human/mouse orthologs revealed extremely high homology. Thus, we named these genes as members of YPEL gene family. We searched YPEL family genes from the public databases, and found 100 genes from 68 species including animals, plants and fungi. Amino acid sequences of these 100 YPEL proteins were extremely similar and a consensus sequence of C-X(2)-C-X(19)-G-X(3)-L-X(5)-N-X(13)-G-X(8)-C-X(2)-C-X(4)-GWXY-X(10)-K-X(6)-E was established for all the YPEL family proteins without exception. Interestingly, the indirect immunofluorescent staining indicated that YPEL1-4 proteins are localized to the centrosome and nucleolus during interphase and at several dot-like structures around the mitotic apparatus during mitotic phase of COS-7 cells. YPEL5 protein is localized to the centrosome and nucleus during interphase and at the mitotic spindle during mitosis of the same cell line. Thus, the YPEL family proteins were found in essentially all the eukaryotes and hence they must play important roles in the maintenance of life. The subcellular localization of YPEL proteins in association with centrosome or mitotic spindle suggests a novel function involved in the cell division.
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Affiliation(s)
- Katsuhiro Hosono
- Department of Molecular Biology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo 160-8582, Japan
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