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Yu H, Jiang L, Li CI, Ness S, Piccirillo SGM, Guo Y. Somatic mutation effects diffused over microRNA dysregulation. Bioinformatics 2023; 39:btad520. [PMID: 37624931 PMCID: PMC10474951 DOI: 10.1093/bioinformatics/btad520] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/14/2023] [Accepted: 08/23/2023] [Indexed: 08/27/2023] Open
Abstract
MOTIVATION As an important player in transcriptome regulation, microRNAs may effectively diffuse somatic mutation impacts to broad cellular processes and ultimately manifest disease and dictate prognosis. Previous studies that tried to correlate mutation with gene expression dysregulation neglected to adjust for the disparate multitudes of false positives associated with unequal sample sizes and uneven class balancing scenarios. RESULTS To properly address this issue, we developed a statistical framework to rigorously assess the extent of mutation impact on microRNAs in relation to a permutation-based null distribution of a matching sample structure. Carrying out the framework in a pan-cancer study, we ascertained 9008 protein-coding genes with statistically significant mutation impacts on miRNAs. Of these, the collective miRNA expression for 83 genes showed significant prognostic power in nine cancer types. For example, in lower-grade glioma, 10 genes' mutations broadly impacted miRNAs, all of which showed prognostic value with the corresponding miRNA expression. Our framework was further validated with functional analysis and augmented with rich features including the ability to analyze miRNA isoforms; aggregative prognostic analysis; advanced annotations such as mutation type, regulator alteration, somatic motif, and disease association; and instructive visualization such as mutation OncoPrint, Ideogram, and interactive mRNA-miRNA network. AVAILABILITY AND IMPLEMENTATION The data underlying this article are available in MutMix, at http://innovebioinfo.com/Database/TmiEx/MutMix.php.
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Affiliation(s)
- Hui Yu
- Department of Public Health, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33136, U.S.A
| | - Limin Jiang
- Department of Public Health, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33136, U.S.A
| | - Chung-I Li
- Department of Statistics, National Cheng Kung University, Tainan 701401, Taiwan
| | - Scott Ness
- Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87109, United States
| | - Sara G M Piccirillo
- Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87109, United States
| | - Yan Guo
- Department of Public Health, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33136, U.S.A
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Brayer KJ, Kang H, El-Naggar AK, Andreasen S, Homøe P, Kiss K, Mikkelsen L, Heegaard S, Pelaez D, Moeyersoms A, Tse DT, Guo Y, Lee DY, Ness SA. Dominant Gene Expression Profiles Define Adenoid Cystic Carcinoma (ACC) from Different Tissues: Validation of a Gene Signature Classifier for Poor Survival in Salivary Gland ACC. Cancers (Basel) 2023; 15:1390. [PMID: 36900183 PMCID: PMC10000625 DOI: 10.3390/cancers15051390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 02/11/2023] [Accepted: 02/17/2023] [Indexed: 02/25/2023] Open
Abstract
Adenoid cystic carcinoma (ACC) is an aggressive malignancy that most often arises in salivary or lacrimal glands but can also occur in other tissues. We used optimized RNA-sequencing to analyze the transcriptomes of 113 ACC tumor samples from salivary gland, lacrimal gland, breast or skin. ACC tumors from different organs displayed remarkedly similar transcription profiles, and most harbored translocations in the MYB or MYBL1 genes, which encode oncogenic transcription factors that may induce dramatic genetic and epigenetic changes leading to a dominant 'ACC phenotype'. Further analysis of the 56 salivary gland ACC tumors led to the identification of three distinct groups of patients, based on gene expression profiles, including one group with worse survival. We tested whether this new cohort could be used to validate a biomarker developed previously with a different set of 68 ACC tumor samples. Indeed, a 49-gene classifier developed with the earlier cohort correctly identified 98% of the poor survival patients from the new set, and a 14-gene classifier was almost as accurate. These validated biomarkers form a platform to identify and stratify high-risk ACC patients into clinical trials of targeted therapies for sustained clinical response.
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Affiliation(s)
- Kathryn J. Brayer
- Department of Internal Medicine, Division of Molecular Medicine, University of New Mexico School of Medicine, Albuquerque, NM 87131, USA
- University of New Mexico Comprehensive Cancer Center, Albuquerque, NM 87131, USA
| | - Huining Kang
- University of New Mexico Comprehensive Cancer Center, Albuquerque, NM 87131, USA
- Department of Internal Medicine, Division of Epidemiology, University of New Mexico School of Medicine, Albuquerque, NM 87131, USA
| | - Adel K. El-Naggar
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Simon Andreasen
- Department of Otorhinolaryngology and Maxillofacial Surgery, Zealand University Hospital, 4600 Køge, Denmark
| | - Preben Homøe
- Department of Otorhinolaryngology and Maxillofacial Surgery, Zealand University Hospital, 4600 Køge, Denmark
| | - Katalin Kiss
- Department of Pathology, Rigshospitalet, University of Copenhagen, 1165 Copenhagen, Denmark
| | - Lauge Mikkelsen
- Department of Pathology, Rigshospitalet, University of Copenhagen, 1165 Copenhagen, Denmark
- Department of Ophthalmology, Rigshospitalet-Glostrup, University of Copenhagen, 1165 Copenhagen, Denmark
| | - Steffen Heegaard
- Department of Ophthalmology, Rigshospitalet-Glostrup, University of Copenhagen, 1165 Copenhagen, Denmark
| | - Daniel Pelaez
- Dr. Nasser Al-Rashid Orbital Vision Research Center, Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Acadia Moeyersoms
- Dr. Nasser Al-Rashid Orbital Vision Research Center, Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- The Sheila and David Fuente Graduate Program in Cancer Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - David T. Tse
- Dr. Nasser Al-Rashid Orbital Vision Research Center, Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Yan Guo
- Department of Internal Medicine, Division of Molecular Medicine, University of New Mexico School of Medicine, Albuquerque, NM 87131, USA
- University of New Mexico Comprehensive Cancer Center, Albuquerque, NM 87131, USA
| | - David Y. Lee
- University of New Mexico Comprehensive Cancer Center, Albuquerque, NM 87131, USA
- Department of Internal Medicine, Division of Hematology/Oncology, Section of Radiation Oncology, University of New Mexico School of Medicine, Albuquerque, NM 87131, USA
| | - Scott A. Ness
- Department of Internal Medicine, Division of Molecular Medicine, University of New Mexico School of Medicine, Albuquerque, NM 87131, USA
- University of New Mexico Comprehensive Cancer Center, Albuquerque, NM 87131, USA
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Guo Y, van der Heijden YF, Maruri F, Jiang L, Morrison R, Sterling TR. RNA editing in Mycobacterium tuberculosis. Microbiol Res 2022; 264:127174. [PMID: 36067705 PMCID: PMC11332325 DOI: 10.1016/j.micres.2022.127174] [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: 07/28/2022] [Revised: 08/17/2022] [Accepted: 08/19/2022] [Indexed: 11/28/2022]
Abstract
RNA editing, while studied thoroughly in humans, has been sporadically described in bacteria, and to our knowledge, has not been reported in Mycobacterium tuberculosis (Mtb). After thorough quality control and validation by repeated sequencing, by comparing sequences from RNA and DNA from high-throughput sequencing data, we report the first finding of three RNA editing events in two Mtb isolates.
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Affiliation(s)
- Yan Guo
- Department of Internal Medicine, University of New Mexico, Albuquerque, NM, USA
| | - Yuri F van der Heijden
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA; Vanderbilt Tuberculosis Center, Vanderbilt University School of Medicine, Nashville, TN, USA; The Aurum Institute, Johannesburg, South Africa
| | - Fernanda Maruri
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA; Vanderbilt Tuberculosis Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Limin Jiang
- Department of Internal Medicine, University of New Mexico, Albuquerque, NM, USA
| | | | - Timothy R Sterling
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA; Vanderbilt Tuberculosis Center, Vanderbilt University School of Medicine, Nashville, TN, USA.
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Song M, Yu J, Li B, Dong J, Gao J, Shang L, Zhou X, Bai Y. Identification of functionally important miRNA targeted genes associated with child obesity trait in genome-wide association studies. BMC Genomics 2022; 23:360. [PMID: 35546387 PMCID: PMC9092671 DOI: 10.1186/s12864-022-08576-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 04/21/2022] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Genome-wide association studies (GWAS) have uncovered thousands of genetic variants that are associated with complex human traits and diseases. miRNAs are single-stranded non-coding RNAs. In particular, genetic variants located in the 3'UTR region of mRNAs may play an important role in gene regulation through their interaction with miRNAs. Existing studies have not been thoroughly conducted to elucidate 3'UTR variants discovered through GWAS. The goal of this study is to analyze patterns of GWAS functional variants located in 3'UTRs about their relevance in the network between hosting genes and targeting miRNAs, and elucidate the association between the genes harboring these variants and genetic traits. METHODS We employed MIGWAS, ANNOVAR, MEME, and DAVID software packages to annotate the variants obtained from GWAS for 31 traits and elucidate the association between their harboring genes and their related traits. We identified variants that occurred in the motif regions that may be functionally important in affecting miRNA binding. We also conducted pathway analysis and functional annotation on miRNA targeted genes harboring 3'UTR variants for a trait with the highest percentage of 3'UTR variants occurring. RESULTS The Child Obesity trait has the highest percentage of 3'UTR variants (75%). Of the 16 genes related to the Child Obesity trait, 5 genes (ETV7, GMEB1, NFIX, ZNF566, ZBTB40) had a significant association with the term DNA-Binding (p < 0.05). EQTL analysis revealed 2 relevant tissues and 10 targeted genes associated with the Child Obesity trait. In addition, Red Blood Cells (RBC), Hemoglobin (HB), and Package Cell Volume (PCV) have overlapping variants. In particular, the PIM1 variant occurred inside the HB Motif region 37,174,641-37,174,660, and LUC7L3 variant occurred inside RBC Motif region 50,753,918-50,753,937. CONCLUSION Variants located in 3'UTR can alter the binding affinity of miRNA and impact gene regulation, thus warranting further annotation and analysis. We have developed a bioinformatics bash pipeline to automatically annotate variants, determine the number of variants in different categories for each given trait, and check common variants across different traits. This is a valuable tool to annotate a large number of GWAS result files.
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Affiliation(s)
- Melinda Song
- University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Jiaqi Yu
- College Preparatory School, 6100 Broadway, Oakland, CA 94618 USA
| | - Binze Li
- Bellaire High School, 5100 Maple St, Bellaire, TX 77401 USA
- Department of Statistics, University of California, Los Angeles, Los Angeles, CA 90095 USA
| | - Julian Dong
- Northville High School, 45700 Six Mile Road, Northville, MI 48168 USA
- College of Engineering, University of Michigan, Ann Arbor, MI 48109 USA
| | - Jeslyn Gao
- Simsbury High School, 34 Farms Village Rd, Simsbury, CT 06070 USA
| | - Lulu Shang
- Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109 USA
| | - Xiang Zhou
- Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109 USA
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109 USA
| | - Yongsheng Bai
- Department of Biology, Eastern Michigan University, Ypsilanti, MI 48197 USA
- Next-Gen Intelligent Science Training, Ann Arbor, MI 48105 USA
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Jiang L, Yu H, Ness S, Mao P, Guo F, Tang J, Guo Y. Comprehensive Analysis of Co-Mutations Identifies Cooperating Mechanisms of Tumorigenesis. Cancers (Basel) 2022; 14:415. [PMID: 35053577 PMCID: PMC8774165 DOI: 10.3390/cancers14020415] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/07/2022] [Accepted: 01/11/2022] [Indexed: 12/16/2022] Open
Abstract
Somatic mutations are one of the most important factors in tumorigenesis and are the focus of most cancer-sequencing efforts. The co-occurrence of multiple mutations in one tumor has gained increasing attention as a means of identifying cooperating mutations or pathways that contribute to cancer. Using multi-omics, phenotypical, and clinical data from 29,559 cancer subjects and 1747 cancer cell lines covering 78 distinct cancer types, we show that co-mutations are associated with prognosis, drug sensitivity, and disparities in sex, age, and race. Some co-mutation combinations displayed stronger effects than their corresponding single mutations. For example, co-mutation TP53:KRAS in pancreatic adenocarcinoma is significantly associated with disease specific survival (hazard ratio = 2.87, adjusted p-value = 0.0003) and its prognostic predictive power is greater than either TP53 or KRAS as individually mutated genes. Functional analyses revealed that co-mutations with higher prognostic values have higher potential impact and cause greater dysregulation of gene expression. Furthermore, many of the prognostically significant co-mutations caused gains or losses of binding sequences of RNA binding proteins or micro RNAs with known cancer associations. Thus, detailed analyses of co-mutations can identify mechanisms that cooperate in tumorigenesis.
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Affiliation(s)
- Limin Jiang
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China;
- School of Computer Science and Technology, College of Intelligence and Computing, Tianjin University, Tianjin 300350, China
| | - Hui Yu
- Department of Internal Medicine, Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131, USA; (H.Y.); (S.N.); (P.M.)
| | - Scott Ness
- Department of Internal Medicine, Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131, USA; (H.Y.); (S.N.); (P.M.)
| | - Peng Mao
- Department of Internal Medicine, Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131, USA; (H.Y.); (S.N.); (P.M.)
| | - Fei Guo
- School of Computer Science and Engineering, Central South University, Changsha 410083, China;
| | - Jijun Tang
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China;
| | - Yan Guo
- Department of Internal Medicine, Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131, USA; (H.Y.); (S.N.); (P.M.)
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Jiang L, Guo F, Tang J, Yu H, Ness S, Duan M, Mao P, Zhao YY, Guo Y. SBSA: an online service for somatic binding sequence annotation. Nucleic Acids Res 2021; 50:e4. [PMID: 34606615 PMCID: PMC8500130 DOI: 10.1093/nar/gkab877] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 09/10/2021] [Accepted: 09/17/2021] [Indexed: 12/11/2022] Open
Abstract
Efficient annotation of alterations in binding sequences of molecular regulators can help identify novel candidates for mechanisms study and offer original therapeutic hypotheses. In this work, we developed Somatic Binding Sequence Annotator (SBSA) as a full-capacity online tool to annotate altered binding motifs/sequences, addressing diverse types of genomic variants and molecular regulators. The genomic variants can be somatic mutation, single nucleotide polymorphism, RNA editing, etc. The binding motifs/sequences involve transcription factors (TFs), RNA-binding proteins, miRNA seeds, miRNA-mRNA 3′-UTR binding target, or can be any custom motifs/sequences. Compared to similar tools, SBSA is the first to support miRNA seeds and miRNA-mRNA 3′-UTR binding target, and it unprecedentedly implements a personalized genome approach that accommodates joint adjacent variants. SBSA is empowered to support an indefinite species, including preloaded reference genomes for SARS-Cov-2 and 25 other common organisms. We demonstrated SBSA by annotating multi-omics data from over 30,890 human subjects. Of the millions of somatic binding sequences identified, many are with known severe biological repercussions, such as the somatic mutation in TERT promoter region which causes a gained binding sequence for E26 transformation-specific factor (ETS1). We further validated the function of this TERT mutation using experimental data in cancer cells. Availability:http://innovebioinfo.com/Annotation/SBSA/SBSA.php.
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Affiliation(s)
- Limin Jiang
- Faculty of Life Science & Medicine, Northwest University, No. 229 Taibai North Road, Xi'an 710069, China.,School of Computer Science and Technology, College of Intelligence and Computing, Tianjin University, Tianjin 300350, China.,Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Fei Guo
- School of Computer Science and Technology, College of Intelligence and Computing, Tianjin University, Tianjin 300350, China
| | - Jijun Tang
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Hui Yu
- Comprehensive cancer center, Department of Internal Medicine, University of New Mexico, Albuquerque, NM 87109, USA
| | - Scott Ness
- Comprehensive cancer center, Department of Internal Medicine, University of New Mexico, Albuquerque, NM 87109, USA
| | - Mingrui Duan
- Comprehensive cancer center, Department of Internal Medicine, University of New Mexico, Albuquerque, NM 87109, USA
| | - Peng Mao
- Comprehensive cancer center, Department of Internal Medicine, University of New Mexico, Albuquerque, NM 87109, USA
| | - Ying-Yong Zhao
- Faculty of Life Science & Medicine, Northwest University, No. 229 Taibai North Road, Xi'an 710069, China
| | - Yan Guo
- Comprehensive cancer center, Department of Internal Medicine, University of New Mexico, Albuquerque, NM 87109, USA
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Wu Y, Guo Y, Yu H, Guo T. RNA editing affects cis-regulatory elements and predicts adverse cancer survival. Cancer Med 2021; 10:6114-6127. [PMID: 34319007 PMCID: PMC8419749 DOI: 10.1002/cam4.4146] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 06/10/2021] [Accepted: 06/11/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND RNA editing exerts critical impacts on numerous biological processes and thus are implicated in crucial human phenotypes, including tumorigenesis and prognosis. While previous studies have analyzed aggregate RNA editing activity at the sample level and associated it with overall cancer survival, there is not yet a large-scale disease-specific survival study to examine genome-wide RNA editing sites' prognostic value taking into account the host gene expression and clinical variables. METHODS In this study, we solved comprehensive Cox proportional models of disease-specific survival on individual RNA-editing sites plus host gene expression and critical demographic covariates. This allowed us to interrogate the prognostic value of a large number of RNA-editing sites at single-nucleotide resolution. RESULTS As a result, we identified 402 gene-proximal RNA-editing sites that generally predict adverse cancer survival. For example, an RNA-editing site residing in ZNF264 indicates poor survival of uterine corpus endometrial carcinoma, with a hazard ratio of 2.13 and an adjusted p-value of 4.07 × 10-7 . Some of these prognostic RNA-editing sites mediate the binding of RNA binding proteins and microRNAs, thus propagating their impacts to extensive regulatory targets. CONCLUSIONS In conclusion, RNA editing affects cis-regulatory elements and predicts adverse cancer survival.
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Affiliation(s)
- Yuan‐Ming Wu
- School of Basic Medical SciencesGuizhou Medical UniversityGuiyangChina
- Stem Cell and Tissue Engineering Research CenterGuizhou Medical UniversityGuizhouChina
| | - Yan Guo
- Comprehensive Cancer CenterUniversity of New MexicoAlbuquerqueNMUSA
| | - Hui Yu
- Comprehensive Cancer CenterUniversity of New MexicoAlbuquerqueNMUSA
| | - Tao Guo
- Guizhou Provincial People’s HospitalGuiyangChina
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