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Yao M, Pan Y, Ren T, Yang C, Lei Y, Xing X, Zhang L, Cui X, Zheng Y, Xing L, Wu C. Loss of Dip2b leads to abnormal neural differentiation from mESCs. Stem Cell Res Ther 2023; 14:248. [PMID: 37705068 PMCID: PMC10500737 DOI: 10.1186/s13287-023-03482-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 08/29/2023] [Indexed: 09/15/2023] Open
Abstract
BACKGROUND Disco-interacting protein 2 homolog B is a member of the Dip2 family encoded by the Dip2b gene. Dip2b is widely expressed in neuro-related tissues and is essential in axonal outgrowth during embryogenesis. METHODS Dip2b knockout mouse embryonic stem cell line was established by CRISPR/Cas9 gene-editing technology. The commercial kits were utilized to detect cell cycle and growth rate. Flow cytometry, qRT-PCR, immunofluorescence, and RNA-seq were employed for phenotype and molecular mechanism assessment. RESULTS Our results suggested that Dip2b is dispensable for the pluripotency maintenance of mESCs. Dip2b knockout could not alter the cell cycle and proliferation of mECSs, or the ability to differentiate into three germ layers in vitro. Furthermore, genes associated with axon guidance, channel activity, and synaptic membrane were significantly downregulated during neural differentiation upon Dip2b knockout. CONCLUSIONS Our results suggest that Dip2b plays an important role in neural differentiation, which will provide a valuable model for studying the exact mechanisms of Dip2b during neural differentiation.
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Affiliation(s)
- Mingze Yao
- Institutes of Biomedical Sciences, Shanxi Provincial Key Laboratory for Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, 030006, China.
| | - Yuanqing Pan
- Institutes of Biomedical Sciences, Shanxi Provincial Key Laboratory for Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, 030006, China
| | - Tinglin Ren
- Institutes of Biomedical Sciences, Shanxi Provincial Key Laboratory for Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, 030006, China
| | - Caiting Yang
- Institutes of Biomedical Sciences, Shanxi Provincial Key Laboratory for Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, 030006, China
| | - Yu Lei
- Institutes of Biomedical Sciences, Shanxi Provincial Key Laboratory for Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, 030006, China
| | - Xiaoyu Xing
- Institutes of Biomedical Sciences, Shanxi Provincial Key Laboratory for Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, 030006, China
| | - Lei Zhang
- Institutes of Biomedical Sciences, Shanxi Provincial Key Laboratory for Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, 030006, China
| | - Xiaogang Cui
- Institutes of Biomedical Sciences, Shanxi Provincial Key Laboratory for Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, 030006, China
| | - Yaowu Zheng
- Institutes of Biomedical Sciences, Shanxi Provincial Key Laboratory for Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, 030006, China
| | - Li Xing
- Institutes of Biomedical Sciences, Shanxi Provincial Key Laboratory for Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, 030006, China
| | - Changxin Wu
- Institutes of Biomedical Sciences, Shanxi Provincial Key Laboratory for Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, 030006, China
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Song C, Shang F, Tu W, Liu X. Integrated pancancer analysis reveals the oncogene characteristics and prognostic value of DIP2B in breast cancer. BMC Cancer 2023; 23:296. [PMID: 37004015 PMCID: PMC10064539 DOI: 10.1186/s12885-023-10751-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 03/20/2023] [Indexed: 04/03/2023] Open
Abstract
BACKGROUND Disco-interaction protein 2 homologue B (DIP2B) plays an important role in DNA methylation. There have been many reports on DIP2B in various diseases, but neither the diagnostic value nor the prognostic value of DIP2B across cancer types has been deeply explored. METHODS The expression levels of DIP2B in 33 cancer types were analysed based on data sets from The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression (GTEx) database. The relationships of DIP2B expression with immune cell infiltration and immune-related gene expression were studied via the CIBERSORT, ESTIMATE and TISIDB tools. Gene set variation analysis (GSVA) was performed to identify pathways related to DIP2B. DIP2B knockdown by siRNA was performed in breast cancer cell lines to investigate the effect on proliferation, apoptosis and migration. The relationships of DIP2B expression with clinicopathological features and prognosis were analysed based on immunohistochemistry. RESULTS DIP2B was highly expressed in 26 of 33 cancer types and was significantly associated with poor overall survival (OS) in breast invasive carcinoma (BRCA), mesothelioma and chromophobe renal cell carcinoma (each P < 0.05). DIP2B showed a negative correlation with the immune score, the infiltration levels of key immune killer cells (CD8 + T cells, activated NK cells and plasma cells), and the expression of major histocompatibility complex-related genes and chemokine-related genes in BRCA. Subtype analysis showed that DIP2B expression was associated with poor OS in Her-2 + BRCA patients (P < 0.05). DIP2B showed a negative correlation with immune killer cell infiltration and immune regulatory genes in BRCA subtypes. In BRCA, the GSVA results revealed that genes correlating positively with DIP2B were enriched in cancer-related pathways (PI3K-AKT) and cell-cycle-related pathways (MITOTIC_SPINDLE, G2M_CHECKPOINT and E2F_TARGETS), while genes correlating negatively with DIP2B were enriched in DNA_REPAIR. Knockdown of the DIP2B gene induced a reduction in proliferation and migration and an increase in apoptosis in breast cancer cell lines. DIP2B expression was associated with lymph node metastasis and poor histological grade in BRCA according to immunohistochemistry (each P < 0.05). DIP2B expression predicted reduced disease-free survival and OS in BRCA patients (each P < 0.05), especially those with the Her-2 + subtype (P = 0.023 and P = 0.069). CONCLUSIONS DIP2B may be a prognostic biomarker for BRCA, especially for the Her-2 + subtype. DIP2B is associated with a "cold" tumour immune microenvironment in BRCA and might serve as a future target for immunotherapy.
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Affiliation(s)
- Chengyang Song
- Department of Thoracic and Cardiovascular Surgery, the Fourth Affiliated Hospital of China Medical University, Shenyang, China
| | - Fangjian Shang
- Department of General Surgery, the Fourth Affiliated Hospital of China Medical University, Shenyang, China
| | - Wei Tu
- Department of General Surgery, the Fourth Affiliated Hospital of China Medical University, Shenyang, China
| | - Xiaodan Liu
- Department of General Surgery, the Fourth Affiliated Hospital of China Medical University, Shenyang, China.
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Frerker N, Karlsen TA, Stensland M, Nyman TA, Rayner S, Brinchmann JE. Comparison between articular chondrocytes and mesenchymal stromal cells for the production of articular cartilage implants. Front Bioeng Biotechnol 2023; 11:1116513. [PMID: 36896010 PMCID: PMC9989206 DOI: 10.3389/fbioe.2023.1116513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 01/31/2023] [Indexed: 02/23/2023] Open
Abstract
Focal lesions of articular cartilage give rise to pain and reduced joint function and may, if left untreated, lead to osteoarthritis. Implantation of in vitro generated, scaffold-free autologous cartilage discs may represent the best treatment option. Here we compare articular chondrocytes (ACs) and bone marrow-derived mesenchymal stromal cells (MSCs) for their ability to make scaffold-free cartilage discs. Articular chondrocytes produced more extracellular matrix per seeded cell than mesenchymal stromal cells. Quantitative proteomics analysis showed that articular chondrocyte discs contained more articular cartilage proteins, while mesenchymal stromal cell discs had more proteins associated with cartilage hypertrophy and bone formation. Sequencing analysis revealed more microRNAs associated with normal cartilage in articular chondrocyte discs, and large-scale target predictions, performed for the first time for in vitro chondrogenesis, suggested that differential expression of microRNAs in the two disc types were important mechanisms behind differential synthesis of proteins. We conclude that articular chondrocytes should be preferred over mesenchymal stromal cells for tissue engineering of articular cartilage.
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Affiliation(s)
- Nadine Frerker
- Department of Immunology, Oslo University Hospital, Oslo, Norway
| | - Tommy A Karlsen
- Department of Immunology, Oslo University Hospital, Oslo, Norway
| | - Maria Stensland
- Department of Immunology, Oslo University Hospital, Oslo, Norway
| | - Tuula A Nyman
- Department of Immunology, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Simon Rayner
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.,Department of Medical Genetics, Oslo University Hospital, Oslo, Norway.,Hybrid Technology Hub-Centre of Excellence, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Jan E Brinchmann
- Department of Immunology, Oslo University Hospital, Oslo, Norway.,Department of Molecular Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
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Adlat S, Hayel F, Chen Y, Sah RK, Mar Oo Z, Al-Azab M, Zun Zaw Myint M, Bahadar N, Binta Bah F, Mi N, Safi M, Feng X, Zhu P, Zheng Y. Heterozygous loss of Dip2B enhances tumor growth and metastasis by altering immune microenvironment. Int Immunopharmacol 2022; 105:108559. [DOI: 10.1016/j.intimp.2022.108559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/12/2022] [Accepted: 01/18/2022] [Indexed: 11/26/2022]
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Bahadar N, Ullah H, Adlat S, Kumar Sah R, Zun Zaw Myint M, Mar Oo Z, Binta Bah F, Hayel Nagi F, Htoo H, Ud Din A, Feng X, Zheng Y. Analyzing differentially expressed genes and pathways of Bex2-deficient mouse lung via RNA-Seq. Turk J Biol 2021; 45:588-598. [PMID: 34803456 PMCID: PMC8574191 DOI: 10.3906/biy-2104-4] [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: 04/01/2021] [Accepted: 06/28/2021] [Indexed: 11/17/2022] Open
Abstract
Bex2 is well known for its role in the nervous system, and is associated with neurological disorders, but its role in the lung’s physiology is still not reported. To elucidate the functional role of Bex2 in the lung, we generated a Bex2 knock-out (KO) mouse model using the CRISPR-Cas9 technology and performed transcriptomic analysis. A total of 652 genes were identified as differentially expressed between Bex2-/- and Bex2+/+ mice, out of which 500 were downregulated, while 152 were upregulated genes. Among these DEGs, Ucp1, Myh6, Coxa7a1, Myl3, Ryr2, RNaset2b, Npy, Enob1, Krt5, Myl2, Hba-a2, and Nrob2 are the most prominent genes. Myl2, was the most downregulated gene, followed by Npy, Hba-a2, Rnaset2b, nr0b2, Klra8, and Ucp1. Tcte3, Eno1b, Zfp990, and Pcdha9 were the most upregulated DEGs. According to gene enrichment analysis, PPAR pathway, cardiac muscle contraction, and cytokine-cytokine receptor interaction were the most enriched pathways. Besides, the nuclear factor-κB signaling pathway and hematopoietic cell linage pathways were also enriched. Chronic obstructive pulmonary disease (COPD) is enriched among KEGG disease pathways. RT-qPCR assays confirmed the RNA-Seq results. This study opens a new window toward the biological functions of Bex2 in different systems.
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Affiliation(s)
- Noor Bahadar
- Key Laboratory of Molecular Epigenetics, Institute of Genetics and Cytology, Northeast Normal University, Changchun, Jilin China
| | - Hanif Ullah
- School of medicine, Tsinghua University, Beijing China
| | - Salah Adlat
- Key Laboratory of Molecular Epigenetics, Institute of Genetics and Cytology, Northeast Normal University, Changchun, Jilin China
| | - Rajiv Kumar Sah
- Key Laboratory of Molecular Epigenetics, Institute of Genetics and Cytology, Northeast Normal University, Changchun, Jilin China
| | - May Zun Zaw Myint
- Key Laboratory of Molecular Epigenetics, Institute of Genetics and Cytology, Northeast Normal University, Changchun, Jilin China
| | - Zin Mar Oo
- Key Laboratory of Molecular Epigenetics, Institute of Genetics and Cytology, Northeast Normal University, Changchun, Jilin China
| | - Fatoumata Binta Bah
- Key Laboratory of Molecular Epigenetics, Institute of Genetics and Cytology, Northeast Normal University, Changchun, Jilin China
| | - Farooq Hayel Nagi
- Key Laboratory of Molecular Epigenetics, Institute of Genetics and Cytology, Northeast Normal University, Changchun, Jilin China
| | - Hsu Htoo
- Key Laboratory of Molecular Epigenetics, Institute of Genetics and Cytology, Northeast Normal University, Changchun, Jilin China
| | - Ahmad Ud Din
- Drug Discovery Research Center, Southwest Medical University, Luzhou China
| | - Xuechao Feng
- Key Laboratory of Molecular Epigenetics, Institute of Genetics and Cytology, Northeast Normal University, Changchun, Jilin China
| | - Yaowu Zheng
- Key Laboratory of Molecular Epigenetics, Institute of Genetics and Cytology, Northeast Normal University, Changchun, Jilin China
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Yang L, Zhao S, Ma N, Liu L, Li D, Li X, Wang Z, Song X, Wang Y, Wang D. Novel DIP2C gene splicing variant in an individual with focal infantile epilepsy. Am J Med Genet A 2021; 188:210-215. [PMID: 34617658 DOI: 10.1002/ajmg.a.62524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 08/15/2021] [Accepted: 09/07/2021] [Indexed: 11/06/2022]
Abstract
Disco-interacting protein 2 C (DIP2C) encodes a disco-interacting protein and is highly expressed in the nervous system. Most variants of DIP2C are microdeletions on chromosome 10p15.3. This study reports a 17-month-old infant with focal infantile epilepsy who has a single-nucleotide variation in DIP2C that results in alternative splicing. The de novo variation (NM_014974.3: c.1057+2T>G) in DIP2C was uncovered through whole-exome sequencing. Minigene assays were performed and verified the alternative splicing caused by the variation. Finally, an 80-bp nucleotide deletion in the 3' end of Exon 8 was detected. Our study identified a de novo splicing variant that affects the coding length of DIP2C. This finding provides a new candidate gene for focal infantile epilepsy. Importantly, our finding is the first to associate a single nucleotide variant in DIP2C with focal infantile epilepsy.
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Affiliation(s)
- Le Yang
- Department of Pediatric neurology, Xi'an Children's Hospital, Xi'an, China
| | - Siyu Zhao
- Department of Pediatric neurology, Xi'an Children's Hospital, Xi'an, China
| | - Nan Ma
- Department of Pediatric neurology, Xi'an Children's Hospital, Xi'an, China
| | - Liang Liu
- Department of Pediatric neurology, Xi'an Children's Hospital, Xi'an, China
| | - Dongjing Li
- Department of Pediatric neurology, Xi'an Children's Hospital, Xi'an, China
| | - Xia Li
- Department of Pediatric neurology, Xi'an Children's Hospital, Xi'an, China
| | - Zhijing Wang
- Department of Pediatric neurology, Xi'an Children's Hospital, Xi'an, China
| | - Xixiao Song
- Department of Pediatric neurology, Xi'an Children's Hospital, Xi'an, China
| | - Yan Wang
- Department of Pediatric neurology, Xi'an Children's Hospital, Xi'an, China
| | - Dong Wang
- Department of Pediatric neurology, Xi'an Children's Hospital, Xi'an, China
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Shorey-Kendrick LE, McEvoy CT, O'Sullivan SM, Milner K, Vuylsteke B, Tepper RS, Haas DM, Park B, Gao L, Vu A, Morris CD, Spindel ER. Impact of vitamin C supplementation on placental DNA methylation changes related to maternal smoking: association with gene expression and respiratory outcomes. Clin Epigenetics 2021; 13:177. [PMID: 34538263 PMCID: PMC8451157 DOI: 10.1186/s13148-021-01161-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 08/28/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Maternal smoking during pregnancy (MSDP) affects development of multiple organ systems including the placenta, lung, brain, and vasculature. In particular, children exposed to MSDP show lifelong deficits in pulmonary function and increased risk of asthma and wheeze. Our laboratory has previously shown that vitamin C supplementation during pregnancy prevents some of the adverse effects of MSDP on offspring respiratory outcomes. Epigenetic modifications, including DNA methylation (DNAm), are a likely link between in utero exposures and adverse health outcomes, and MSDP has previously been associated with DNAm changes in blood, placenta, and buccal epithelium. Analysis of placental DNAm may reveal critical targets of MSDP and vitamin C relevant to respiratory health outcomes. RESULTS DNAm was measured in placentas obtained from 72 smokers enrolled in the VCSIP RCT: NCT03203603 (37 supplemented with vitamin C, 35 with placebo) and 24 never-smokers for reference. Methylation at one CpG, cg20790161, reached Bonferroni significance and was hypomethylated in vitamin C supplemented smokers versus placebo. Analysis of spatially related CpGs identified 93 candidate differentially methylated regions (DMRs) between treatment groups, including loci known to be associated with lung function, oxidative stress, fetal development and growth, and angiogenesis. Overlap of nominally significant differentially methylated CpGs (DMCs) in never-smokers versus placebo with nominally significant DMCs in vitamin C versus placebo identified 9059 candidate "restored CpGs" for association with placental transcript expression and respiratory outcomes. Methylation at 274 restored candidate CpG sites was associated with expression of 259 genes (FDR < 0.05). We further identified candidate CpGs associated with infant lung function (34 CpGs) and composite wheeze (1 CpG) at 12 months of age (FDR < 0.05). Increased methylation in the DIP2C, APOH/PRKCA, and additional candidate gene regions was associated with improved lung function and decreased wheeze in offspring of vitamin C-treated smokers. CONCLUSIONS Vitamin C supplementation to pregnant smokers ameliorates changes associated with maternal smoking in placental DNA methylation and gene expression in pathways potentially linked to improved placental function and offspring respiratory health. Further work is necessary to validate candidate loci and elucidate the causal pathway between placental methylation changes and outcomes of offspring exposed to MSDP. Clinical trial registration ClinicalTrials.gov, NCT01723696. Registered November 6, 2012. https://clinicaltrials.gov/ct2/show/record/NCT01723696 .
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Affiliation(s)
- Lyndsey E Shorey-Kendrick
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health and Science University, 505 NW 185th Ave, Beaverton, OR, 97006, USA.
| | - Cindy T McEvoy
- Department of Pediatrics, Oregon Health and Science University, Portland, OR, USA
| | - Shannon M O'Sullivan
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health and Science University, 505 NW 185th Ave, Beaverton, OR, 97006, USA
| | - Kristin Milner
- Department of Pediatrics, Oregon Health and Science University, Portland, OR, USA
| | - Brittany Vuylsteke
- Department of Pediatrics, Oregon Health and Science University, Portland, OR, USA
| | - Robert S Tepper
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - David M Haas
- Department of Obstetrics and Gynecology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Byung Park
- Biostatistics Shared Resources, Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
- Bioinformatics and Biostatistics Core, Oregon National Primate Research Center, Oregon Health and Science University, Portland, OR, USA
- School of Public Health, Oregon Health and Science University-Portland State University, Portland, OR, USA
| | - Lina Gao
- Biostatistics Shared Resources, Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
- Bioinformatics and Biostatistics Core, Oregon National Primate Research Center, Oregon Health and Science University, Portland, OR, USA
| | - Annette Vu
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR, USA
| | - Cynthia D Morris
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR, USA
- Oregon Clinical and Translational Research Institute, Oregon Health and Science, Portland, OR, USA
| | - Eliot R Spindel
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health and Science University, 505 NW 185th Ave, Beaverton, OR, 97006, USA
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