151
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The Curious Case of the HepG2 Cell Line: 40 Years of Expertise. Int J Mol Sci 2021. [DOI: 10.3390/ijms222313135 union all select null,null,null,null-- aqie] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Liver cancer is the third leading cause of cancer death worldwide. Representing such a dramatic impact on our lives, liver cancer is a significant public health concern. Sustainable and reliable methods for preventing and treating liver cancer require fundamental research on its molecular mechanisms. Cell lines are treated as in vitro equivalents of tumor tissues, making them a must-have for basic research on the nature of cancer. According to recent discoveries, certified cell lines retain most genetic properties of the original tumor and mimic its microenvironment. On the other hand, modern technologies allowing the deepest level of detail in omics landscapes have shown significant differences even between samples of the same cell line due to cross- and mycoplasma infection. This and other observations suggest that, in some cases, cell cultures are not suitable as cancer models, with limited predictive value for the effectiveness of new treatments. HepG2 is a popular hepatic cell line. It is used in a wide range of studies, from the oncogenesis to the cytotoxicity of substances on the liver. In this regard, we set out to collect up-to-date information on the HepG2 cell line to assess whether the level of heterogeneity of the cell line allows in vitro biomedical studies as a model with guaranteed production and quality.
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152
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The Curious Case of the HepG2 Cell Line: 40 Years of Expertise. Int J Mol Sci 2021. [DOI: 10.3390/ijms222313135 union all select null,null,null,null,null,null-- bgcl] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Liver cancer is the third leading cause of cancer death worldwide. Representing such a dramatic impact on our lives, liver cancer is a significant public health concern. Sustainable and reliable methods for preventing and treating liver cancer require fundamental research on its molecular mechanisms. Cell lines are treated as in vitro equivalents of tumor tissues, making them a must-have for basic research on the nature of cancer. According to recent discoveries, certified cell lines retain most genetic properties of the original tumor and mimic its microenvironment. On the other hand, modern technologies allowing the deepest level of detail in omics landscapes have shown significant differences even between samples of the same cell line due to cross- and mycoplasma infection. This and other observations suggest that, in some cases, cell cultures are not suitable as cancer models, with limited predictive value for the effectiveness of new treatments. HepG2 is a popular hepatic cell line. It is used in a wide range of studies, from the oncogenesis to the cytotoxicity of substances on the liver. In this regard, we set out to collect up-to-date information on the HepG2 cell line to assess whether the level of heterogeneity of the cell line allows in vitro biomedical studies as a model with guaranteed production and quality.
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153
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The Curious Case of the HepG2 Cell Line: 40 Years of Expertise. Int J Mol Sci 2021. [DOI: 10.3390/ijms222313135 union all select null,null,null,null,null,null,null,null,null-- rtlm] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Liver cancer is the third leading cause of cancer death worldwide. Representing such a dramatic impact on our lives, liver cancer is a significant public health concern. Sustainable and reliable methods for preventing and treating liver cancer require fundamental research on its molecular mechanisms. Cell lines are treated as in vitro equivalents of tumor tissues, making them a must-have for basic research on the nature of cancer. According to recent discoveries, certified cell lines retain most genetic properties of the original tumor and mimic its microenvironment. On the other hand, modern technologies allowing the deepest level of detail in omics landscapes have shown significant differences even between samples of the same cell line due to cross- and mycoplasma infection. This and other observations suggest that, in some cases, cell cultures are not suitable as cancer models, with limited predictive value for the effectiveness of new treatments. HepG2 is a popular hepatic cell line. It is used in a wide range of studies, from the oncogenesis to the cytotoxicity of substances on the liver. In this regard, we set out to collect up-to-date information on the HepG2 cell line to assess whether the level of heterogeneity of the cell line allows in vitro biomedical studies as a model with guaranteed production and quality.
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154
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The Curious Case of the HepG2 Cell Line: 40 Years of Expertise. Int J Mol Sci 2021. [DOI: 10.3390/ijms222313135 union all select null,null,null,null,null,null,null,null,null,concat(0x716b6a7071,0x4e5a74626f536e4e454b6848696e426a4d5a45685441777574746c657376504b4e76416e724b6668,0x7178767871)#] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Liver cancer is the third leading cause of cancer death worldwide. Representing such a dramatic impact on our lives, liver cancer is a significant public health concern. Sustainable and reliable methods for preventing and treating liver cancer require fundamental research on its molecular mechanisms. Cell lines are treated as in vitro equivalents of tumor tissues, making them a must-have for basic research on the nature of cancer. According to recent discoveries, certified cell lines retain most genetic properties of the original tumor and mimic its microenvironment. On the other hand, modern technologies allowing the deepest level of detail in omics landscapes have shown significant differences even between samples of the same cell line due to cross- and mycoplasma infection. This and other observations suggest that, in some cases, cell cultures are not suitable as cancer models, with limited predictive value for the effectiveness of new treatments. HepG2 is a popular hepatic cell line. It is used in a wide range of studies, from the oncogenesis to the cytotoxicity of substances on the liver. In this regard, we set out to collect up-to-date information on the HepG2 cell line to assess whether the level of heterogeneity of the cell line allows in vitro biomedical studies as a model with guaranteed production and quality.
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155
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Bu F, Cheng Q, Zhang Y, Zhang X, Yan K, Liu F, Li Z, Lu X, Ren Y, Liu S. Discovery of Missing Proteins from an Aneuploidy Cell Line Using a Proteogenomic Approach. J Proteome Res 2021; 20:5329-5339. [PMID: 34748338 DOI: 10.1021/acs.jproteome.1c00772] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
With the steadfast development of proteomic technology, the number of missing proteins (MPs) has been continuously shrinking, with approximately 1470 MPs that have not been explored yet. Due to this phenomenon, the discovery of MPs has been increasingly more difficult and elusive. In order to face this challenge, we have hypothesized that a stable aneuploid cell line with increased chromosomes serves as a useful material for assisting MP exploration. Ker-CT cell line with trisomy at chromosome 5 and 20 was selected for this purpose. With a combination strategy of RNA-Seq and LC-MS/MS, a total of 22 178 transcripts and 8846 proteins were identified in Ker-CT. Although the transcripts corresponding to 15 and 15 MP genes located at chromosome 5 and 20 were detected, none of the MPs were found in Ker-CT. Surprisingly, 3 MPs containing at least two unique non-nest peptides of length ≥9 amino acids were identified in Ker-CT, whose genes are located on chromosome 3 and 10, respectively. Furthermore, the 3 MPs were verified using the method of parallel reaction monitoring (PRM). These results suggest that the abnormal status of chromosomes may not only impact the expression of the corresponding genes in trisomy chromosomes, but also influence that of other chromosomes, which benefits MP discovery. The data obtained in this study are available via ProteomeXchange (PXD028647) and PeptideAtlas (PASS01700), respectively.
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Affiliation(s)
- Fanyu Bu
- BGI-Shenzhen, Beishan Industrial Zone 11th Building, Yantian District, Shenzhen, Guangdong 518083, China.,Department of BGI Education, School of Life Sciences, University of Chinese Academy of Sciences, Shenzhen, Guangdong 518083, China
| | - Qingqiu Cheng
- Clinical Laboratory Center of Dongguan Eighth People's Hospital, Dongguan 523325, China
| | - Yuxing Zhang
- BGI-Shenzhen, Beishan Industrial Zone 11th Building, Yantian District, Shenzhen, Guangdong 518083, China.,Department of BGI Education, School of Life Sciences, University of Chinese Academy of Sciences, Shenzhen, Guangdong 518083, China
| | - Xia Zhang
- BGI-Shenzhen, Beishan Industrial Zone 11th Building, Yantian District, Shenzhen, Guangdong 518083, China.,Department of BGI Education, School of Life Sciences, University of Chinese Academy of Sciences, Shenzhen, Guangdong 518083, China
| | - Keqiang Yan
- BGI-Shenzhen, Beishan Industrial Zone 11th Building, Yantian District, Shenzhen, Guangdong 518083, China.,Department of BGI Education, School of Life Sciences, University of Chinese Academy of Sciences, Shenzhen, Guangdong 518083, China
| | - Frank Liu
- BGI-Shenzhen, Beishan Industrial Zone 11th Building, Yantian District, Shenzhen, Guangdong 518083, China
| | - Zelong Li
- Biological Resource Center of Plants, Animals and Microorganisms, China National Gene Bank, BGI-Shenzhen, Guangdong 518120, China
| | - Xiaomei Lu
- Clinical Laboratory Center of Dongguan Eighth People's Hospital, Dongguan 523325, China
| | - Yan Ren
- BGI-Shenzhen, Beishan Industrial Zone 11th Building, Yantian District, Shenzhen, Guangdong 518083, China
| | - Siqi Liu
- BGI-Shenzhen, Beishan Industrial Zone 11th Building, Yantian District, Shenzhen, Guangdong 518083, China.,Department of BGI Education, School of Life Sciences, University of Chinese Academy of Sciences, Shenzhen, Guangdong 518083, China
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156
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Antisense-Mediated Down-Regulation of Factor V-Short Splicing in a Liver Cell Line Model. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11209621] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Coagulation factor V (FV) is a liver-derived protein encoded by the F5 gene. Alternative splicing of F5 exon 13 produces a low-abundance splicing isoform, known as FV-short, which binds the anticoagulant protein tissue factor pathway inhibitor (TFPIα) with high affinity, stabilising it in the circulation and potently enhancing its anticoagulant activity. Accordingly, rare F5 gene mutations that up-regulate FV-short splicing are associated with bleeding. In this study we have explored the possibility of decreasing FV-short splicing by antisense-based splicing modulation. To this end, we have designed morpholino antisense oligonucleotides (MAOs) targeting the FV-short-specific donor and acceptor splice sites and tested their efficacy in a liver cell line (HepG2) that naturally expresses full-length FV and FV-short. Cells were treated with 0–20 µM MAO, and full-length FV and FV-short mRNA expression was analysed by RT-(q)PCR. Both MAOs, alone or in combination, decreased the FV-short/full-length FV mRNA ratio down to ~50% of its original value in a specific and dose-dependent manner. This pilot study provides proof-of-principle for the possibility to decrease FV-short expression by antisense-mediated splicing modulation. In turn, this may form the basis for novel therapeutic approaches to bleeding disorders caused by FV-short over-expression and/or elevated TFPIα (activity) levels.
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157
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Integrative analysis of liver-specific non-coding regulatory SNPs associated with the risk of coronary artery disease. Am J Hum Genet 2021; 108:411-430. [PMID: 33626337 DOI: 10.1016/j.ajhg.2021.02.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 02/04/2021] [Indexed: 02/08/2023] Open
Abstract
Genetic factors underlying coronary artery disease (CAD) have been widely studied using genome-wide association studies (GWASs). However, the functional understanding of the CAD loci has been limited by the fact that a majority of GWAS variants are located within non-coding regions with no functional role. High cholesterol and dysregulation of the liver metabolism such as non-alcoholic fatty liver disease confer an increased risk of CAD. Here, we studied the function of non-coding single-nucleotide polymorphisms in CAD GWAS loci located within liver-specific enhancer elements by identifying their potential target genes using liver cis-eQTL analysis and promoter Capture Hi-C in HepG2 cells. Altogether, 734 target genes were identified of which 121 exhibited correlations to liver-related traits. To identify potentially causal regulatory SNPs, the allele-specific enhancer activity was analyzed by (1) sequence-based computational predictions, (2) quantification of allele-specific transcription factor binding, and (3) STARR-seq massively parallel reporter assay. Altogether, our analysis identified 1,277 unique SNPs that display allele-specific regulatory activity. Among these, susceptibility enhancers near important cholesterol homeostasis genes (APOB, APOC1, APOE, and LIPA) were identified, suggesting that altered gene regulatory activity could represent another way by which genetic variation regulates serum lipoprotein levels. Using CRISPR-based perturbation, we demonstrate how the deletion/activation of a single enhancer leads to changes in the expression of many target genes located in a shared chromatin interaction domain. Our integrative genomics approach represents a comprehensive effort in identifying putative causal regulatory regions and target genes that could predispose to clinical manifestation of CAD by affecting liver function.
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158
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van Belzen IAEM, Schönhuth A, Kemmeren P, Hehir-Kwa JY. Structural variant detection in cancer genomes: computational challenges and perspectives for precision oncology. NPJ Precis Oncol 2021; 5:15. [PMID: 33654267 PMCID: PMC7925608 DOI: 10.1038/s41698-021-00155-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 01/12/2021] [Indexed: 01/31/2023] Open
Abstract
Cancer is generally characterized by acquired genomic aberrations in a broad spectrum of types and sizes, ranging from single nucleotide variants to structural variants (SVs). At least 30% of cancers have a known pathogenic SV used in diagnosis or treatment stratification. However, research into the role of SVs in cancer has been limited due to difficulties in detection. Biological and computational challenges confound SV detection in cancer samples, including intratumor heterogeneity, polyploidy, and distinguishing tumor-specific SVs from germline and somatic variants present in healthy cells. Classification of tumor-specific SVs is challenging due to inconsistencies in detected breakpoints, derived variant types and biological complexity of some rearrangements. Full-spectrum SV detection with high recall and precision requires integration of multiple algorithms and sequencing technologies to rescue variants that are difficult to resolve through individual methods. Here, we explore current strategies for integrating SV callsets and to enable the use of tumor-specific SVs in precision oncology.
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Affiliation(s)
| | - Alexander Schönhuth
- Genome Data Science, Faculty of Technology, Bielefeld University, Bielefeld, Germany
| | - Patrick Kemmeren
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Jayne Y Hehir-Kwa
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.
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159
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Marchetti AL, Guo H. New Insights on Molecular Mechanism of Hepatitis B Virus Covalently Closed Circular DNA Formation. Cells 2020; 9:cells9112430. [PMID: 33172220 PMCID: PMC7694973 DOI: 10.3390/cells9112430] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/03/2020] [Accepted: 11/04/2020] [Indexed: 12/15/2022] Open
Abstract
The chronic factor of the Hepatitis B Virus (HBV), specifically the covalently closed circular DNA (cccDNA), is a highly stable and active viral episomal genome established in the livers of chronic hepatitis B patients as a constant source of disease. Being able to target and eliminate cccDNA is the end goal for a genuine cure for HBV. Yet how HBV cccDNA is formed from the viral genomic relaxed circular DNA (rcDNA) and by what host factors had been long-standing research questions. It is generally acknowledged that HBV hijacks cellular functions to turn the open circular DNA conformation of rcDNA into cccDNA through DNA repair mechanisms. With great efforts from the HBV research community, there have been several recent leaps in our understanding of cccDNA formation. It is our goal in this review to analyze the recent reports showing evidence of cellular factor's involvement in the molecular pathway of cccDNA biosynthesis.
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Affiliation(s)
- Alexander L. Marchetti
- Department of Microbiology and Immunology, School of Medicine, Indiana University, Indianapolis, IN 46202, USA;
- Cancer Virology Program, Hillman Cancer Center, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Haitao Guo
- Cancer Virology Program, Hillman Cancer Center, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Correspondence:
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160
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Zhou Q, Wang Z, Li J, Sung WK, Li G. MethHaplo: combining allele-specific DNA methylation and SNPs for haplotype region identification. BMC Bioinformatics 2020; 21:451. [PMID: 33045983 PMCID: PMC7552496 DOI: 10.1186/s12859-020-03798-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 10/02/2020] [Indexed: 12/26/2022] Open
Abstract
Background DNA methylation is an important epigenetic modification that plays a critical role in most eukaryotic organisms. Parental alleles in haploid genomes may exhibit different methylation patterns, which can lead to different phenotypes and even different therapeutic and drug responses to diseases. However, to our knowledge, no software is available for the identification of DNA methylation haplotype regions with combined allele-specific DNA methylation, single nucleotide polymorphisms (SNPs) and high-throughput chromosome conformation capture (Hi-C) data. Results In this paper, we developed a new method, MethHaplo, that identify DNA methylation haplotype regions with allele-specific DNA methylation and SNPs from whole-genome bisulfite sequencing (WGBS) data. Our results showed that methylation haplotype regions were ten times longer than haplotypes with SNPs only. When we integrate WGBS and Hi-C data, MethHaplo could call even longer haplotypes. Conclusions This study illustrates the usefulness of methylation haplotypes. By constructing methylation haplotypes for various cell lines, we provide a clearer picture of the effect of DNA methylation on gene expression, histone modification and three-dimensional chromosome structure at the haplotype level. Our method could benefit the study of parental inheritance-related disease and hybrid vigor in agriculture.
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Affiliation(s)
- Qiangwei Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.,Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ze Wang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jing Li
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wing-Kin Sung
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China.,Department of Computer Science, National University of Singapore, Singapore, 117417, Singapore.,Department of Computational and Systems Biology, Genome Institute of Singapore, Singapore, 138672, Singapore
| | - Guoliang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China. .,Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China.
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161
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Zhuang X, Ye R, So MT, Lam WY, Karim A, Yu M, Ngo ND, Cherny SS, Tam PKH, Garcia-Barcelo MM, Tang CSM, Sham PC. A random forest-based framework for genotyping and accuracy assessment of copy number variations. NAR Genom Bioinform 2020; 2:lqaa071. [PMID: 33575619 PMCID: PMC7671382 DOI: 10.1093/nargab/lqaa071] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 08/18/2020] [Accepted: 08/26/2020] [Indexed: 12/24/2022] Open
Abstract
Detection of copy number variations (CNVs) is essential for uncovering genetic factors underlying human diseases. However, CNV detection by current methods is prone to error, and precisely identifying CNVs from paired-end whole genome sequencing (WGS) data is still challenging. Here, we present a framework, CNV-JACG, for Judging the Accuracy of CNVs and Genotyping using paired-end WGS data. CNV-JACG is based on a random forest model trained on 21 distinctive features characterizing the CNV region and its breakpoints. Using the data from the 1000 Genomes Project, Genome in a Bottle Consortium, the Human Genome Structural Variation Consortium and in-house technical replicates, we show that CNV-JACG has superior sensitivity over the latest genotyping method, SV2, particularly for the small CNVs (≤1 kb). We also demonstrate that CNV-JACG outperforms SV2 in terms of Mendelian inconsistency in trios and concordance between technical replicates. Our study suggests that CNV-JACG would be a useful tool in assessing the accuracy of CNVs to meet the ever-growing needs for uncovering the missing heritability linked to CNVs.
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Affiliation(s)
- Xuehan Zhuang
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Rui Ye
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Man-Ting So
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Wai-Yee Lam
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Anwarul Karim
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Michelle Yu
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Ngoc Diem Ngo
- National Hospital of Pediatrics, Ha Noi 100000, Vietnam
| | - Stacey S Cherny
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Paul Kwong-Hang Tam
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | | | - Clara Sze-Man Tang
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Pak Chung Sham
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
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162
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Soifer L, Fong NL, Yi N, Ireland AT, Lam I, Sooknah M, Paw JS, Peluso P, Concepcion GT, Rank D, Hastie AR, Jojic V, Ruby JG, Botstein D, Roy MA. Fully Phased Sequence of a Diploid Human Genome Determined de Novo from the DNA of a Single Individual. G3 (BETHESDA, MD.) 2020; 10:2911-2925. [PMID: 32631951 PMCID: PMC7466960 DOI: 10.1534/g3.119.400995] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 06/26/2020] [Indexed: 12/17/2022]
Abstract
In recent years, improved sequencing technology and computational tools have made de novo genome assembly more accessible. Many approaches, however, generate either an unphased or only partially resolved representation of a diploid genome, in which polymorphisms are detected but not assigned to one or the other of the homologous chromosomes. Yet chromosomal phase information is invaluable for the understanding of phenotypic trait inheritance in the cases of compound heterozygosity, allele-specific expression or cis-acting variants. Here we use a combination of tools and sequencing technologies to generate a de novo diploid assembly of the human primary cell line WI-38. First, data from PacBio single molecule sequencing and Bionano Genomics optical mapping were combined to generate an unphased assembly. Next, 10x Genomics linked reads were combined with the hybrid assembly to generate a partially phased assembly. Lastly, we developed and optimized methods to use short-read (Illumina) sequencing of flow cytometry-sorted metaphase chromosomes to provide phase information. The final genome assembly was almost fully (94%) phased with the addition of approximately 2.5-fold coverage of Illumina data from the sequenced metaphase chromosomes. The diploid nature of the final de novo genome assembly improved the resolution of structural variants between the WI-38 genome and the human reference genome. The phased WI-38 sequence data are available for browsing and download at wi38.research.calicolabs.com. Our work shows that assembling a completely phased diploid genome de novo from the DNA of a single individual is now readily achievable.
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Affiliation(s)
- Llya Soifer
- Calico Life Sciences LLC, South San Francisco, CA 94080
| | - Nicole L Fong
- Calico Life Sciences LLC, South San Francisco, CA 94080
| | - Nelda Yi
- Calico Life Sciences LLC, South San Francisco, CA 94080
| | | | - Irene Lam
- Calico Life Sciences LLC, South San Francisco, CA 94080
| | | | | | | | | | - David Rank
- Pacific Biosciences, Menlo Park, CA 94025
| | | | | | - J Graham Ruby
- Calico Life Sciences LLC, South San Francisco, CA 94080
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163
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Greer SU, Ji HP. Structural variant analysis for linked-read sequencing data with gemtools. Bioinformatics 2020; 35:4397-4399. [PMID: 30938757 DOI: 10.1093/bioinformatics/btz239] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 03/24/2019] [Accepted: 03/31/2019] [Indexed: 11/14/2022] Open
Abstract
SUMMARY Linked-read sequencing generates synthetic long reads which are useful for the detection and analysis of structural variants (SVs). The software associated with 10× Genomics linked-read sequencing, Long Ranger, generates the essential output files (BAM, VCF, SV BEDPE) necessary for downstream analyses. However, to perform downstream analyses requires the user to customize their own tools to handle the unique features of linked-read sequencing data. Here, we describe gemtools, a collection of tools for the downstream and in-depth analysis of SVs from linked-read data. Gemtools uses the barcoded aligned reads and the Megabase-scale phase blocks to determine haplotypes of SV breakpoints and delineate complex breakpoint configurations at the resolution of single DNA molecules. The gemtools package is a suite of tools that provides the user with the flexibility to perform basic functions on their linked-read sequencing output in order to address even more questions. AVAILABILITY AND IMPLEMENTATION The gemtools package is freely available for download at: https://github.com/sgreer77/gemtools. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- S U Greer
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - H P Ji
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.,Stanford Genome Technology Center, Department of Biochemistry, Stanford University, Palo Alto, CA, USA
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164
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Do C, Dumont ELP, Salas M, Castano A, Mujahed H, Maldonado L, Singh A, DaSilva-Arnold SC, Bhagat G, Lehman S, Christiano AM, Madhavan S, Nagy PL, Green PHR, Feinman R, Trimble C, Illsley NP, Marder K, Honig L, Monk C, Goy A, Chow K, Goldlust S, Kaptain G, Siegel D, Tycko B. Allele-specific DNA methylation is increased in cancers and its dense mapping in normal plus neoplastic cells increases the yield of disease-associated regulatory SNPs. Genome Biol 2020; 21:153. [PMID: 32594908 PMCID: PMC7322865 DOI: 10.1186/s13059-020-02059-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 05/27/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Mapping of allele-specific DNA methylation (ASM) can be a post-GWAS strategy for localizing regulatory sequence polymorphisms (rSNPs). The advantages of this approach, and the mechanisms underlying ASM in normal and neoplastic cells, remain to be clarified. RESULTS We perform whole genome methyl-seq on diverse normal cells and tissues and three cancer types. After excluding imprinting, the data pinpoint 15,112 high-confidence ASM differentially methylated regions, of which 1838 contain SNPs in strong linkage disequilibrium or coinciding with GWAS peaks. ASM frequencies are increased in cancers versus matched normal tissues, due to widespread allele-specific hypomethylation and focal allele-specific hypermethylation in poised chromatin. Cancer cells show increased allele switching at ASM loci, but disruptive SNPs in specific classes of CTCF and transcription factor binding motifs are similarly correlated with ASM in cancer and non-cancer. Rare somatic mutations affecting these same motif classes track with de novo ASM. Allele-specific transcription factor binding from ChIP-seq is enriched among ASM loci, but most ASM differentially methylated regions lack such annotations, and some are found in otherwise uninformative "chromatin deserts." CONCLUSIONS ASM is increased in cancers but occurs by a shared mechanism involving disruptive SNPs in CTCF and transcription factor binding sites in both normal and neoplastic cells. Dense ASM mapping in normal plus cancer samples reveals candidate rSNPs that are difficult to find by other approaches. Together with GWAS data, these rSNPs can nominate specific transcriptional pathways in susceptibility to autoimmune, cardiometabolic, neuropsychiatric, and neoplastic diseases.
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Affiliation(s)
- Catherine Do
- Hackensack-Meridian Health Center for Discovery and Innovation, Nutley, NJ, 07110, USA.
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ, 07601, USA.
| | - Emmanuel L P Dumont
- Hackensack-Meridian Health Center for Discovery and Innovation, Nutley, NJ, 07110, USA
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ, 07601, USA
| | - Martha Salas
- Hackensack-Meridian Health Center for Discovery and Innovation, Nutley, NJ, 07110, USA
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ, 07601, USA
| | - Angelica Castano
- Hackensack-Meridian Health Center for Discovery and Innovation, Nutley, NJ, 07110, USA
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ, 07601, USA
| | - Huthayfa Mujahed
- Department of Medicine, Huddinge, Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Leonel Maldonado
- Department of Gynecology and Obstetrics, Johns Hopkins Medical Institutions, Baltimore, MD, 21287, USA
| | - Arunjot Singh
- Division of Gastroenterology, Hepatology and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Sonia C DaSilva-Arnold
- Department of Obstetrics and Gynecology, Hackensack University Medical Center, Hackensack, NJ, 07601, USA
| | - Govind Bhagat
- Department of Pathology & Cell Biology, Columbia University Medical Center, New York, NY, 10032, USA
- Division of Gastroenterology and Celiac Center, Department of Medicine, Columbia University Medical Center, New York, NY, 10032, USA
| | - Soren Lehman
- Department of Medicine, Huddinge, Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Angela M Christiano
- Departments of Dermatology and Genetics and Development, Columbia University Medical Center, New York, NY, 10032, USA
| | - Subha Madhavan
- Lombardi Comprehensive Cancer Center of Georgetown University, Washington, DC, 20057, USA
| | | | - Peter H R Green
- Division of Gastroenterology and Celiac Center, Department of Medicine, Columbia University Medical Center, New York, NY, 10032, USA
| | - Rena Feinman
- Hackensack-Meridian Health Center for Discovery and Innovation, Nutley, NJ, 07110, USA
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ, 07601, USA
- Lombardi Comprehensive Cancer Center of Georgetown University, Washington, DC, 20057, USA
| | - Cornelia Trimble
- Department of Gynecology and Obstetrics, Johns Hopkins Medical Institutions, Baltimore, MD, 21287, USA
| | - Nicholas P Illsley
- Department of Obstetrics and Gynecology, Hackensack University Medical Center, Hackensack, NJ, 07601, USA
| | - Karen Marder
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, 10032, USA
- Department of Neurology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Lawrence Honig
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, 10032, USA
- Department of Neurology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Catherine Monk
- Departments of Psychiatry and Behavioral Medicine and Obstetrics and Gynecology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Andre Goy
- Hackensack-Meridian Health Center for Discovery and Innovation, Nutley, NJ, 07110, USA
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ, 07601, USA
- Lombardi Comprehensive Cancer Center of Georgetown University, Washington, DC, 20057, USA
| | - Kar Chow
- Hackensack-Meridian Health Center for Discovery and Innovation, Nutley, NJ, 07110, USA
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ, 07601, USA
- Lombardi Comprehensive Cancer Center of Georgetown University, Washington, DC, 20057, USA
| | - Samuel Goldlust
- Hackensack-Meridian Health Center for Discovery and Innovation, Nutley, NJ, 07110, USA
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ, 07601, USA
| | - George Kaptain
- Hackensack-Meridian Health Center for Discovery and Innovation, Nutley, NJ, 07110, USA
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ, 07601, USA
| | - David Siegel
- Hackensack-Meridian Health Center for Discovery and Innovation, Nutley, NJ, 07110, USA
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ, 07601, USA
- Lombardi Comprehensive Cancer Center of Georgetown University, Washington, DC, 20057, USA
| | - Benjamin Tycko
- Hackensack-Meridian Health Center for Discovery and Innovation, Nutley, NJ, 07110, USA.
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ, 07601, USA.
- Lombardi Comprehensive Cancer Center of Georgetown University, Washington, DC, 20057, USA.
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165
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Concentration-dependent toxicogenomic changes of silver nanoparticles in hepatocyte-like cells derived from human induced pluripotent stem cells. Cell Biol Toxicol 2020; 37:245-259. [PMID: 32447489 DOI: 10.1007/s10565-020-09529-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 04/28/2020] [Indexed: 02/06/2023]
Abstract
The application of silver nanoparticles (AgNPs) in consumer products has been increasing rapidly over the past decades. Therefore, in vitro models capable of accurately predicting the toxicity of AgNPs are much needed. Hepatocyte-like cells (HLCs) derived from human induced pluripotent stem cells (iPSCs) represent an attractive alternative in vitro hepatotoxicity model. Yet, the use of iPSC-derived HLCs (iPSC-HLCs) for the study of nanoparticle toxicity has not been reported so far. In the present study, transcriptomic changes induced by varying concentrations (5-25 μg/ml) of AgNPs were characterized in iPSC-HLCs after 24-h exposure. AgNPs caused concentration-dependent gene expression changes in iPSC-HLCs. At all the concentrations, members of the metallothionein (MT) and the heat shock protein (HSP) families were the dominating upregulated genes, suggesting that exposure to AgNPs induced oxidative stresses in iPSC-HLCs and as a result elicited cellular protective responses in the cells. Functional analysis showed that the differentially expressed genes (DEGs) were majorly involved in the biological processes of metabolism, response to stress, and cell organization and biogenesis. Ingenuity Pathway Analysis revealed that cancer was at the top of diseases and disorders associated with the DEGs at all concentrations. These results were in accordance with those reported previously on hepatoma cell lines and primary hepatocytes. Considering the advantages iPSC-HLCs have over other liver cell models in terms of unlimited supply, consistency in quality, sustainability of function in long-term culture, and, more importantly, affordability of donor specificity, the results of the current study suggest that iPSC-HLCs may serve as a better in vitro model for liver nanotoxicology.
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166
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Abstract
Identifying structural variation (SV) is essential for genome interpretation but has been historically difficult due to limitations inherent to available genome technologies. Detection methods that use ensemble algorithms and emerging sequencing technologies have enabled the discovery of thousands of SVs, uncovering information about their ubiquity, relationship to disease and possible effects on biological mechanisms. Given the variability in SV type and size, along with unique detection biases of emerging genomic platforms, multiplatform discovery is necessary to resolve the full spectrum of variation. Here, we review modern approaches for investigating SVs and proffer that, moving forwards, studies integrating biological information with detection will be necessary to comprehensively understand the impact of SV in the human genome.
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Affiliation(s)
- Steve S Ho
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Alexander E Urban
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Ryan E Mills
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA.
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
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167
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Refined detection and phasing of structural aberrations in pediatric acute lymphoblastic leukemia by linked-read whole-genome sequencing. Sci Rep 2020; 10:2512. [PMID: 32054878 PMCID: PMC7018692 DOI: 10.1038/s41598-020-59214-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 01/23/2020] [Indexed: 12/15/2022] Open
Abstract
Structural chromosomal rearrangements that can lead to in-frame gene-fusions are a leading source of information for diagnosis, risk stratification, and prognosis in pediatric acute lymphoblastic leukemia (ALL). Traditional methods such as karyotyping and FISH struggle to accurately identify and phase such large-scale chromosomal aberrations in ALL genomes. We therefore evaluated linked-read WGS for detecting chromosomal rearrangements in primary samples of from 12 patients diagnosed with ALL. We assessed the effect of input DNA quality on phased haplotype block size and the detectability of copy number aberrations and structural variants in the ALL genomes. We found that biobanked DNA isolated by standard column-based extraction methods was sufficient to detect chromosomal rearrangements even at low 10x sequencing coverage. Linked-read WGS enabled precise, allele-specific, digital karyotyping at a base-pair resolution for a wide range of structural variants including complex rearrangements and aneuploidy assessment. With use of haplotype information from the linked-reads, we also identified previously unknown structural variants, such as a compound heterozygous deletion of ERG in a patient with the DUX4-IGH fusion gene. We conclude that linked-read WGS allows detection of important pathogenic variants in ALL genomes at a resolution beyond that of traditional karyotyping and FISH.
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168
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Structural variation and its potential impact on genome instability: Novel discoveries in the EGFR landscape by long-read sequencing. PLoS One 2020; 15:e0226340. [PMID: 31940362 PMCID: PMC6961855 DOI: 10.1371/journal.pone.0226340] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 11/25/2019] [Indexed: 12/29/2022] Open
Abstract
Structural variation (SV) is typically defined as variation within the human genome that exceeds 50 base pairs (bp). SV may be copy number neutral or it may involve duplications, deletions, and complex rearrangements. Recent studies have shown SV to be associated with many human diseases. However, studies of SV have been challenging due to technological constraints. With the advent of third generation (long-read) sequencing technology, exploration of longer stretches of DNA not easily examined previously has been made possible. In the present study, we utilized third generation (long-read) sequencing techniques to examine SV in the EGFR landscape of four haplotypes derived from two human samples. We analyzed the EGFR gene and its landscape (+/- 500,000 base pairs) using this approach and were able to identify a region of non-coding DNA with over 90% similarity to the most common activating EGFR mutation in non-small cell lung cancer. Based on previously published Alu-element genome instability algorithms, we propose a molecular mechanism to explain how this non-coding region of DNA may be interacting with and impacting the stability of the EGFR gene and potentially generating this cancer-driver gene. By these techniques, we were also able to identify previously hidden structural variation in the four haplotypes and in the human reference genome (hg38). We applied previously published algorithms to compare the relative stabilities of these five different EGFR gene landscape haplotypes to estimate their relative potentials to generate the EGFR exon 19, 15 bp canonical deletion. To our knowledge, the present study is the first to use the differences in genomic architecture between targeted cancer-linked phased haplotypes to estimate their relative potentials to form a common cancer-linked driver mutation.
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169
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Pan G, Cavalli M, Carlsson B, Skrtic S, Kumar C, Wadelius C. rs953413 Regulates Polyunsaturated Fatty Acid Metabolism by Modulating ELOVL2 Expression. iScience 2020; 23:100808. [PMID: 31928966 PMCID: PMC7033636 DOI: 10.1016/j.isci.2019.100808] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 11/26/2019] [Accepted: 12/23/2019] [Indexed: 12/11/2022] Open
Abstract
Long-chain polyunsaturated fatty acids (LC-PUFAs) influence human health in several areas, including cardiovascular disease, diabetes, fatty liver disease, and cancer. ELOVL2 encodes one of the key enzymes in the in vivo synthesis of LC-PUFAs from their precursors. Variants near ELOVL2 have repeatedly been associated with levels of LC-PUFA-derived metabolites in genome-wide association studies (GWAS), but the mechanisms behind these observations remain poorly defined. In this study, we found that rs953413, located in the first intron of ELOVL2, lies within a functional FOXA and HNF4α cooperative binding site. The G allele of rs953413 increases binding of FOXA1/FOXA2 and HNF4α to an evolutionarily conserved enhancer element, conferring allele-specific upregulation of the rs953413-associated gene ELOVL2. The expression of ELOVL2 was significantly downregulated by both FOXA1 and HNF4α knockdown and CRISPR/Cas9-mediated direct mutation to the enhancer element. Our results suggest that rs953413 regulates LC-PUFAs metabolism by altering ELOVL2 expression through FOXA1/FOXA2 and HNF4α cooperation. rs953413 resides in an evolutionarily conserved enhancer region rs953413 mediates the cooperative binding of FOXA and HNF4α to the enhancer region The rs953413 locus plays a key role in regulating ELOVL2 expression rs953413 is implicated in PUFA metabolism by regulating ELOVL2 expression
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Affiliation(s)
- Gang Pan
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Marco Cavalli
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Björn Carlsson
- Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Stanko Skrtic
- Pharmaceutical Technology & Development, AstraZeneca AB, Gothenburg, Sweden; Department of Medicine, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Chanchal Kumar
- Translational Science & Experimental Medicine, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden; Karolinska Institutet/AstraZeneca Integrated CardioMetabolic Center (KI/AZ ICMC), Department of Medicine, Novum, Huddinge, Sweden
| | - Claes Wadelius
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
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170
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Viswanathan R, Cheruba E, Cheow LF. DNA Analysis by Restriction Enzyme (DARE) enables concurrent genomic and epigenomic characterization of single cells. Nucleic Acids Res 2019; 47:e122. [PMID: 31418018 PMCID: PMC6821369 DOI: 10.1093/nar/gkz717] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 06/21/2019] [Accepted: 08/13/2019] [Indexed: 12/11/2022] Open
Abstract
Genome-wide profiling of copy number alterations and DNA methylation in single cells could enable detailed investigation into the genomic and epigenomic heterogeneity of complex cell populations. However, current methods to do this require complex sample processing and cleanup steps, lack consistency, or are biased in their genomic representation. Here, we describe a novel single-tube enzymatic method, DNA Analysis by Restriction Enzyme (DARE), to perform deterministic whole genome amplification while preserving DNA methylation information. This method was evaluated on low amounts of DNA and single cells, and provides accurate copy number aberration calling and representative DNA methylation measurement across the whole genome. Single-cell DARE is an attractive and scalable approach for concurrent genomic and epigenomic characterization of cells in a heterogeneous population.
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Affiliation(s)
- Ramya Viswanathan
- Department of Biomedical Engineering, National University of Singapore, Singapore 117583, Singapore.,Institute for Health Innovation and Technology (iHealthtech), National University of Singapore, Singapore 117583, Singapore
| | - Elsie Cheruba
- Department of Biomedical Engineering, National University of Singapore, Singapore 117583, Singapore.,Institute for Health Innovation and Technology (iHealthtech), National University of Singapore, Singapore 117583, Singapore
| | - Lih Feng Cheow
- Department of Biomedical Engineering, National University of Singapore, Singapore 117583, Singapore.,Institute for Health Innovation and Technology (iHealthtech), National University of Singapore, Singapore 117583, Singapore
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171
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Abubakar SD. Characterization of Chromosomal Abnormalities in Cancer by Spectral Karyotyping. MEDICAL LABORATORY JOURNAL 2019. [DOI: 10.29252/mlj.13.6.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
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172
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Yang EW, Bahn JH, Hsiao EYH, Tan BX, Sun Y, Fu T, Zhou B, Van Nostrand EL, Pratt GA, Freese P, Wei X, Quinones-Valdez G, Urban AE, Graveley BR, Burge CB, Yeo GW, Xiao X. Allele-specific binding of RNA-binding proteins reveals functional genetic variants in the RNA. Nat Commun 2019; 10:1338. [PMID: 30902979 PMCID: PMC6430814 DOI: 10.1038/s41467-019-09292-w] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 03/05/2019] [Indexed: 12/31/2022] Open
Abstract
Allele-specific protein-RNA binding is an essential aspect that may reveal functional genetic variants (GVs) mediating post-transcriptional regulation. Recently, genome-wide detection of in vivo binding of RNA-binding proteins is greatly facilitated by the enhanced crosslinking and immunoprecipitation (eCLIP) method. We developed a new computational approach, called BEAPR, to identify allele-specific binding (ASB) events in eCLIP-Seq data. BEAPR takes into account crosslinking-induced sequence propensity and variations between replicated experiments. Using simulated and actual data, we show that BEAPR largely outperforms often-used count analysis methods. Importantly, BEAPR overcomes the inherent overdispersion problem of these methods. Complemented by experimental validations, we demonstrate that the application of BEAPR to ENCODE eCLIP-Seq data of 154 proteins helps to predict functional GVs that alter splicing or mRNA abundance. Moreover, many GVs with ASB patterns have known disease relevance. Overall, BEAPR is an effective method that helps to address the outstanding challenge of functional interpretation of GVs.
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Affiliation(s)
- Ei-Wen Yang
- Department of Integrative Biology and Physiology, UCLA, Los Angeles, CA, 90095, USA
| | - Jae Hoon Bahn
- Department of Integrative Biology and Physiology, UCLA, Los Angeles, CA, 90095, USA
| | - Esther Yun-Hua Hsiao
- Department of Integrative Biology and Physiology, UCLA, Los Angeles, CA, 90095, USA
- Department of Bioengineering, UCLA, Los Angeles, CA, 90095, USA
| | - Boon Xin Tan
- Department of Integrative Biology and Physiology, UCLA, Los Angeles, CA, 90095, USA
| | - Yiwei Sun
- Department of Integrative Biology and Physiology, UCLA, Los Angeles, CA, 90095, USA
| | - Ting Fu
- Department of Integrative Biology and Physiology, UCLA, Los Angeles, CA, 90095, USA
- Molecular, Cellular and Integrative Physiology Interdepartmental Program, UCLA, Los Angeles, CA, 90095, USA
| | - Bo Zhou
- Department of Psychiatry and Behavioral Sciences, Department of Genetics, Stanford University School of Medicine, Palo Alto, CA, 94305, USA
| | - Eric L Van Nostrand
- Department of Cellular and Molecular Medicine, UCSD, La Jolla, CA, 92093, USA
- Institute for Genomic Medicine, UCSD, La Jolla, CA, 92093, USA
| | - Gabriel A Pratt
- Department of Cellular and Molecular Medicine, UCSD, La Jolla, CA, 92093, USA
- Institute for Genomic Medicine, UCSD, La Jolla, CA, 92093, USA
| | - Peter Freese
- Department of Biology, MIT, Cambridge, MA, 02139, USA
| | - Xintao Wei
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT, 06030, USA
| | | | - Alexander E Urban
- Department of Psychiatry and Behavioral Sciences, Department of Genetics, Stanford University School of Medicine, Palo Alto, CA, 94305, USA
| | - Brenton R Graveley
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT, 06030, USA
| | | | - Gene W Yeo
- Department of Cellular and Molecular Medicine, UCSD, La Jolla, CA, 92093, USA
- Institute for Genomic Medicine, UCSD, La Jolla, CA, 92093, USA
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117593, Singapore
- Molecular Engineering Laboratory, A*STAR, Singapore, 138673, Singapore
| | - Xinshu Xiao
- Department of Integrative Biology and Physiology, UCLA, Los Angeles, CA, 90095, USA.
- Department of Bioengineering, UCLA, Los Angeles, CA, 90095, USA.
- Molecular, Cellular and Integrative Physiology Interdepartmental Program, UCLA, Los Angeles, CA, 90095, USA.
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA.
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