1
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Ozturk K, Panwala R, Sheen J, Ford K, Jayne N, Portell A, Zhang DE, Hutter S, Haferlach T, Ideker T, Mali P, Carter H. Interface-guided phenotyping of coding variants in the transcription factor RUNX1. Cell Rep 2024; 43:114436. [PMID: 38968069 DOI: 10.1016/j.celrep.2024.114436] [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: 12/08/2023] [Revised: 05/15/2024] [Accepted: 06/19/2024] [Indexed: 07/07/2024] Open
Abstract
Single-gene missense mutations remain challenging to interpret. Here, we deploy scalable functional screening by sequencing (SEUSS), a Perturb-seq method, to generate mutations at protein interfaces of RUNX1 and quantify their effect on activities of downstream cellular programs. We evaluate single-cell RNA profiles of 115 mutations in myelogenous leukemia cells and categorize them into three functionally distinct groups, wild-type (WT)-like, loss-of-function (LoF)-like, and hypomorphic, that we validate in orthogonal assays. LoF-like variants dominate the DNA-binding site and are recurrent in cancer; however, recurrence alone does not predict functional impact. Hypomorphic variants share characteristics with LoF-like but favor protein interactions, promoting gene expression indicative of nerve growth factor (NGF) response and cytokine recruitment of neutrophils. Accessible DNA near differentially expressed genes frequently contains RUNX1-binding motifs. Finally, we reclassify 16 variants of uncertain significance and train a classifier to predict 103 more. Our work demonstrates the potential of targeting protein interactions to better define the landscape of phenotypes reachable by missense mutations.
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Affiliation(s)
- Kivilcim Ozturk
- Division of Medical Genetics, Department of Medicine, University of California, San Diego, La Jolla, CA, USA; Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA
| | - Rebecca Panwala
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Jeanna Sheen
- School of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Kyle Ford
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Nathan Jayne
- School of Biological Sciences, University of California, San Diego, La Jolla, CA, USA; Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Andrew Portell
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Dong-Er Zhang
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Stephan Hutter
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377 Munich, Germany
| | - Torsten Haferlach
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377 Munich, Germany
| | - Trey Ideker
- Division of Medical Genetics, Department of Medicine, University of California, San Diego, La Jolla, CA, USA; Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA; Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Prashant Mali
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
| | - Hannah Carter
- Division of Medical Genetics, Department of Medicine, University of California, San Diego, La Jolla, CA, USA; Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA; Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA.
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2
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Yan B, Wang D, Ettwiller L. Simultaneous assessment of human genome and methylome data in a single experiment using limited deamination of methylated cytosine. Genome Res 2024; 34:904-913. [PMID: 38858087 PMCID: PMC11293541 DOI: 10.1101/gr.278294.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 06/04/2024] [Indexed: 06/12/2024]
Abstract
Multiomics require concerted recording of independent information, ideally from a single experiment. In this study, we introduce RIMS-seq2, a high-throughput technique to simultaneously sequence genomes and overlay methylation information while requiring only a small modification of the experimental protocol for high-throughput DNA sequencing to include a controlled deamination step. Importantly, the rate of deamination of 5-methylcytosine is negligible and thus does not interfere with standard DNA sequencing and data processing. Thus, RIMS-seq2 libraries from whole- or targeted-genome sequencing show the same germline variation calling accuracy and sensitivity compared with standard DNA-seq. Additionally, regional methylation levels provide an accurate map of the human methylome.
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Affiliation(s)
- Bo Yan
- New England Biolabs Incorporated, Ipswich, Massachusetts 01938, USA
| | - Duan Wang
- SLC Management, Wellesley Hills, Massachusetts 02481, USA
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3
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Chen BH, Zhou W. mLiftOver: harmonizing data across Infinium DNA methylation platforms. BIOINFORMATICS (OXFORD, ENGLAND) 2024; 40:btae423. [PMID: 38963309 PMCID: PMC11233119 DOI: 10.1093/bioinformatics/btae423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 06/07/2024] [Accepted: 07/03/2024] [Indexed: 07/05/2024]
Abstract
MOTIVATION Infinium DNA methylation BeadChips are widely used for genome-wide DNA methylation profiling at the population scale. Recent updates to probe content and naming conventions in the EPIC version 2 (EPICv2) arrays have complicated integrating new data with previous Infinium array platforms, such as the MethylationEPIC (EPIC) and the HumanMethylation450 (HM450) BeadChip. RESULTS We present mLiftOver, a user-friendly tool that harmonizes probe ID, methylation level, and signal intensity data across different Infinium platforms. It manages probe replicates, missing data imputation, and platform-specific bias for accurate data conversion. We validated the tool by applying HM450-based cancer classifiers to EPICv2 cancer data, achieving high accuracy. Additionally, we successfully integrated EPICv2 healthy tissue data with legacy HM450 data for tissue identity analysis and produced consistent copy number profiles in cancer cells. AVAILABILITY AND IMPLEMENTATION mLiftOver is implemented R and available in the Bioconductor package SeSAMe (version 1.21.13+): https://bioconductor.org/packages/release/bioc/html/sesame.html. Analysis of EPIC and EPICv2 platform-specific bias and high-confidence mapping is available at https://github.com/zhou-lab/InfiniumAnnotationV1/raw/main/Anno/EPICv2/EPICv2ToEPIC_conversion.tsv.gz. The source code is available at https://github.com/zwdzwd/sesame/blob/devel/R/mLiftOver.R under the MIT license.
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Affiliation(s)
- Brian H Chen
- California Pacific Medical Center Research Institute, Sutter Health, San Francisco, CA 94143, United States
| | - Wanding Zhou
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, United States
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
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4
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Wang X, Carvajal-Moreno J, Zhao X, Li J, Hernandez VA, Yalowich JC, Elton TS. Circumvention of Topoisomerase II α Intron 19 Intronic Polyadenylation in Acquired Etoposide-Resistant Human Leukemia K562 Cells. Mol Pharmacol 2024; 106:33-46. [PMID: 38719474 PMCID: PMC11187689 DOI: 10.1124/molpharm.124.000868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 04/12/2024] [Indexed: 06/20/2024] Open
Abstract
DNA topoisomerase IIα (TOP2α; 170 kDa, TOP2α/170) is an essential enzyme for proper chromosome dysjunction by producing transient DNA double-stranded breaks and is an important target for DNA damage-stabilizing anticancer agents, such as etoposide. Therapeutic effects of TOP2α poisons can be limited due to acquired drug resistance. We previously demonstrated decreased TOP2α/170 levels in an etoposide-resistant human leukemia K562 subline, designated K/VP.5, accompanied by increased expression of a C-terminal truncated TOP2α isoform (90 kDa; TOP2α/90), which heterodimerized with TOP2α/170 and was a determinant of resistance by exhibiting dominant-negative effects against etoposide activity. Based on 3'-rapid amplification of cDNA ends, we confirmed TOP2α/90 as the translation product of a TOP2α mRNA in which a cryptic polyadenylation site (PAS) harbored in intron 19 (I19) was used. In this report, we investigated whether the resultant intronic polyadenylation (IPA) would be attenuated by blocking or mutating the I19 PAS, thereby circumventing acquired drug resistance. An antisense morpholino oligonucleotide was used to hybridize/block the PAS in TOP2α pre-mRNA in K/VP.5 cells, resulting in decreased TOP2α/90 mRNA/protein levels in K/VP.5 cells and partially circumventing drug resistance. Subsequently, CRISPR/CRISPR-associated protein 9 with homology-directed repair was used to mutate the cryptic I19 PAS (AATAAA→ACCCAA) to prevent IPA. Gene-edited clones exhibited increased TOP2α/170 and decreased TOP2α/90 mRNA/protein and demonstrated restored sensitivity to etoposide and other TOP2α-targeted drugs. Together, results indicated that blocking/mutating a cryptic I19 PAS in K/VP.5 cells reduced IPA and restored sensitivity to TOP2α-targeting drugs. SIGNIFICANCE STATEMENT: The results presented in this study indicate that CRISPR/CRISPR-associated protein 9 gene editing of a cryptic polyadenylation site (PAS) within I19 of the TOP2α gene results in the reversal of acquired resistance to etoposide and other TOP2-targeted drugs. An antisense morpholino oligonucleotide targeting the PAS also partially circumvented resistance.
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Affiliation(s)
- Xinyi Wang
- Division of Pharmaceutics and Pharmacology, College of Pharmacy (X.W., J.C.-M., X.Z., V.A.H., J.C.Y., T.S.E.) and Division of Outcomes and Translational Science (J.L.), The Ohio State University, Columbus, Ohio
| | - Jessika Carvajal-Moreno
- Division of Pharmaceutics and Pharmacology, College of Pharmacy (X.W., J.C.-M., X.Z., V.A.H., J.C.Y., T.S.E.) and Division of Outcomes and Translational Science (J.L.), The Ohio State University, Columbus, Ohio
| | - Xinyu Zhao
- Division of Pharmaceutics and Pharmacology, College of Pharmacy (X.W., J.C.-M., X.Z., V.A.H., J.C.Y., T.S.E.) and Division of Outcomes and Translational Science (J.L.), The Ohio State University, Columbus, Ohio
| | - Junan Li
- Division of Pharmaceutics and Pharmacology, College of Pharmacy (X.W., J.C.-M., X.Z., V.A.H., J.C.Y., T.S.E.) and Division of Outcomes and Translational Science (J.L.), The Ohio State University, Columbus, Ohio
| | - Victor A Hernandez
- Division of Pharmaceutics and Pharmacology, College of Pharmacy (X.W., J.C.-M., X.Z., V.A.H., J.C.Y., T.S.E.) and Division of Outcomes and Translational Science (J.L.), The Ohio State University, Columbus, Ohio
| | - Jack C Yalowich
- Division of Pharmaceutics and Pharmacology, College of Pharmacy (X.W., J.C.-M., X.Z., V.A.H., J.C.Y., T.S.E.) and Division of Outcomes and Translational Science (J.L.), The Ohio State University, Columbus, Ohio
| | - Terry S Elton
- Division of Pharmaceutics and Pharmacology, College of Pharmacy (X.W., J.C.-M., X.Z., V.A.H., J.C.Y., T.S.E.) and Division of Outcomes and Translational Science (J.L.), The Ohio State University, Columbus, Ohio
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5
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Yin C, Hair SC, Byeon GW, Bromley P, Meuleman W, Seelig G. Iterative deep learning-design of human enhancers exploits condensed sequence grammar to achieve cell type-specificity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.14.599076. [PMID: 38915713 PMCID: PMC11195158 DOI: 10.1101/2024.06.14.599076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
An important and largely unsolved problem in synthetic biology is how to target gene expression to specific cell types. Here, we apply iterative deep learning to design synthetic enhancers with strong differential activity between two human cell lines. We initially train models on published datasets of enhancer activity and chromatin accessibility and use them to guide the design of synthetic enhancers that maximize predicted specificity. We experimentally validate these sequences, use the measurements to re-optimize the predictor, and design a second generation of enhancers with improved specificity. Our design methods embed relevant transcription factor binding site (TFBS) motifs with higher frequencies than comparable endogenous enhancers while using a more selective motif vocabulary, and we show that enhancer activity is correlated with transcription factor expression at the single cell level. Finally, we characterize causal features of top enhancers via perturbation experiments and show enhancers as short as 50bp can maintain specificity.
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Affiliation(s)
- Christopher Yin
- Department of Electrical & Computer Engineering, University of Washington, Seattle, WA
| | | | - Gun Woo Byeon
- Department of Electrical & Computer Engineering, University of Washington, Seattle, WA
| | - Peter Bromley
- Altius Institute for Biomedical Sciences, Seattle, WA
| | - Wouter Meuleman
- Altius Institute for Biomedical Sciences, Seattle, WA
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA
| | - Georg Seelig
- Department of Electrical & Computer Engineering, University of Washington, Seattle, WA
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA
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6
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Dorans E, Jagadeesh K, Dey K, Price AL. Linking regulatory variants to target genes by integrating single-cell multiome methods and genomic distance. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.24.24307813. [PMID: 38826240 PMCID: PMC11142273 DOI: 10.1101/2024.05.24.24307813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Methods that analyze single-cell paired RNA-seq and ATAC-seq multiome data have shown great promise in linking regulatory elements to genes. However, existing methods differ in their modeling assumptions and approaches to account for biological and technical noise-leading to low concordance in their linking scores-and do not capture the effects of genomic distance. We propose pgBoost, an integrative modeling framework that trains a non-linear combination of existing linking strategies (including genomic distance) on fine-mapped eQTL data to assign a probabilistic score to each candidate SNP-gene link. We applied pgBoost to single-cell multiome data from 85k cells representing 6 major immune/blood cell types. pgBoost attained higher enrichment for fine-mapped eSNP-eGene pairs (e.g. 21x at distance >10kb) than existing methods (1.2-10x; p-value for difference = 5e-13 vs. distance-based method and < 4e-35 for each other method), with larger improvements at larger distances (e.g. 35x vs. 0.89-6.6x at distance >100kb; p-value for difference < 0.002 vs. each other method). pgBoost also outperformed existing methods in enrichment for CRISPR-validated links (e.g. 4.8x vs. 1.6-4.1x at distance >10kb; p-value for difference = 0.25 vs. distance-based method and < 2e-5 for each other method), with larger improvements at larger distances (e.g. 15x vs. 1.6-2.5x at distance >100kb; p-value for difference < 0.009 for each other method). Similar improvements in enrichment were observed for links derived from Activity-By-Contact (ABC) scores and GWAS data. We further determined that restricting pgBoost to features from a focal cell type improved the identification of SNP-gene links relevant to that cell type. We highlight several examples where pgBoost linked fine-mapped GWAS variants to experimentally validated or biologically plausible target genes that were not implicated by other methods. In conclusion, a non-linear combination of linking strategies, including genomic distance, improves power to identify target genes underlying GWAS associations.
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7
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Hsiung CCS, Wilson CM, Sambold NA, Dai R, Chen Q, Teyssier N, Misiukiewicz S, Arab A, O'Loughlin T, Cofsky JC, Shi J, Gilbert LA. Engineered CRISPR-Cas12a for higher-order combinatorial chromatin perturbations. Nat Biotechnol 2024:10.1038/s41587-024-02224-0. [PMID: 38760567 DOI: 10.1038/s41587-024-02224-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 03/28/2024] [Indexed: 05/19/2024]
Abstract
Multiplexed genetic perturbations are critical for testing functional interactions among coding or non-coding genetic elements. Compared to double-stranded DNA cutting, repressive chromatin formation using CRISPR interference (CRISPRi) avoids genotoxicity and is more effective for perturbing non-coding regulatory elements in pooled assays. However, current CRISPRi pooled screening approaches are limited to targeting one to three genomic sites per cell. We engineer an Acidaminococcus Cas12a (AsCas12a) variant, multiplexed transcriptional interference AsCas12a (multiAsCas12a), that incorporates R1226A, a mutation that stabilizes the ribonucleoprotein-DNA complex via DNA nicking. The multiAsCas12a-KRAB fusion improves CRISPRi activity over DNase-dead AsCas12a-KRAB fusions, often rescuing the activities of lentivirally delivered CRISPR RNAs (crRNA) that are inactive when used with the latter. multiAsCas12a-KRAB supports CRISPRi using 6-plex crRNA arrays in high-throughput pooled screens. Using multiAsCas12a-KRAB, we discover enhancer elements and dissect the combinatorial function of cis-regulatory elements in human cells. These results instantiate a group testing framework for efficiently surveying numerous combinations of chromatin perturbations for biological discovery and engineering.
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Affiliation(s)
- C C-S Hsiung
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Urology, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Arc Institute, Palo Alto, CA, USA
| | - C M Wilson
- Department of Urology, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Arc Institute, Palo Alto, CA, USA
- Tetrad Graduate Program, University of California, San Francisco, CA, USA
| | | | - R Dai
- Department of Urology, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Arc Institute, Palo Alto, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Q Chen
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - N Teyssier
- Biological and Medical Informatics Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - S Misiukiewicz
- Department of Urology, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - A Arab
- Arc Institute, Palo Alto, CA, USA
| | - T O'Loughlin
- Department of Urology, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - J C Cofsky
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - J Shi
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - L A Gilbert
- Department of Urology, University of California, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
- Arc Institute, Palo Alto, CA, USA.
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8
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Chardon FM, McDiarmid TA, Page NF, Daza RM, Martin B, Domcke S, Regalado SG, Lalanne JB, Calderon D, Li X, Starita LM, Sanders SJ, Ahituv N, Shendure J. Multiplex, single-cell CRISPRa screening for cell type specific regulatory elements. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.03.28.534017. [PMID: 37034704 PMCID: PMC10081248 DOI: 10.1101/2023.03.28.534017] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
CRISPR-based gene activation (CRISPRa) is a promising therapeutic approach for gene therapy, upregulating gene expression by targeting promoters or enhancers in a tissue/cell-type specific manner. Here, we describe an experimental framework that combines highly multiplexed perturbations with single-cell RNA sequencing (sc-RNA-seq) to identify cell-type-specific, CRISPRa-responsive cis- regulatory elements and the gene(s) they regulate. Random combinations of many gRNAs are introduced to each of many cells, which are then profiled and partitioned into test and control groups to test for effect(s) of CRISPRa perturbations of both enhancers and promoters on the expression of neighboring genes. Applying this method to a library of 493 gRNAs targeting candidate cis- regulatory elements in both K562 cells and iPSC-derived excitatory neurons, we identify gRNAs capable of specifically upregulating intended target genes and no other neighboring genes within 1 Mb, including gRNAs yielding upregulation of six autism spectrum disorder (ASD) and neurodevelopmental disorder (NDD) risk genes in neurons. A consistent pattern is that the responsiveness of individual enhancers to CRISPRa is restricted by cell type, implying a dependency on either chromatin landscape and/or additional trans- acting factors for successful gene activation. The approach outlined here may facilitate large-scale screens for gRNAs that activate therapeutically relevant genes in a cell type-specific manner.
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9
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Kasai F, Mizukoshi K, Nakamura Y. Variable characteristics overlooked in human K-562 leukemia cell lines with a common signature. Sci Rep 2024; 14:9619. [PMID: 38671192 PMCID: PMC11053119 DOI: 10.1038/s41598-024-60271-8] [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: 01/30/2024] [Accepted: 04/21/2024] [Indexed: 04/28/2024] Open
Abstract
K-562 is a well-known in vitro cellular model that represents human leukemia cell lines. Although the K-562 cells have been extensively characterized, there are inconsistencies in the data across publications, showing the presence of multiple K-562 cell lines. This suggests that analyzing a single K-562 cell line is insufficient to provide reliable reference data. In this study, we compared three K-562 cell lines with different IDs (RCB0027, RCB1635, and RCB1897) to investigate the fundamental characteristics of K-562 cells. Amplifications of the BCR-ABL1 fusion gene and at 13q31 were detected in all three cell lines, whereas each genome exhibited distinctive features of sequence variants and loss of heterozygosity. This implies that each K-562 cell line can be characterized by common and unique features through a comparison of multiple K-562 cell lines. Variations in transcriptome profiles and hemoglobin synthesis were also observed among the three cell lines, indicating that they should be considered sublines that have diverged from the common ancestral K-562 despite no changes from the original cell name. This leads to unintentional differences in genotypes and/or phenotypes among cell lines that share the same name. These data show that characterizing a single K-562 cell line does not necessarily provide data that are applicable to other K-562 cells. In this context, it is essential to modify cell names in accordance with changes in characteristics during cell culture. Furthermore, our data could serve as a reference for evaluating other K-562 sublines, facilitating the discovery of new K-562 sublines with distinct characteristics. This approach results in the accumulation of K-562 sublines with diverged characteristics and expands the options available, which may help in selecting the most suitable K-562 subline for each experiment.
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Affiliation(s)
- Fumio Kasai
- RIKEN Cell Bank, Cell Engineering Division, RIKEN BioResource Research Center, Tsukuba, Japan.
| | - Kumiko Mizukoshi
- RIKEN Cell Bank, Cell Engineering Division, RIKEN BioResource Research Center, Tsukuba, Japan
| | - Yukio Nakamura
- RIKEN Cell Bank, Cell Engineering Division, RIKEN BioResource Research Center, Tsukuba, Japan
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10
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Carvajal-Moreno J, Wang X, Hernandez VA, Mondal M, Zhao X, Yalowich JC, Elton TS. Use of CRISPR/Cas9 with Homology-Directed Repair to Gene-Edit Topoisomerase II β in Human Leukemia K562 Cells: Generation of a Resistance Phenotype. J Pharmacol Exp Ther 2024; 389:186-196. [PMID: 38508753 PMCID: PMC11026151 DOI: 10.1124/jpet.123.002038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 02/27/2024] [Accepted: 02/27/2024] [Indexed: 03/22/2024] Open
Abstract
DNA topoisomerase IIβ (TOP2β/180; 180 kDa) is a nuclear enzyme that regulates DNA topology by generation of short-lived DNA double-strand breaks, primarily during transcription. TOP2β/180 can be a target for DNA damage-stabilizing anticancer drugs, whose efficacy is often limited by chemoresistance. Our laboratory previously demonstrated reduced levels of TOP2β/180 (and the paralog TOP2α/170) in an acquired etoposide-resistant human leukemia (K562) clonal cell line, K/VP.5, in part due to overexpression of microRNA-9-3p/5p impacting post-transcriptional events. To evaluate the effect on drug sensitivity upon reduction/elimination of TOP2β/180, a premature stop codon was generated at the TOP2β/180 gene exon 19/intron 19 boundary (AGAA//GTAA→ATAG//GTAA) in parental K562 cells (which contain four TOP2β/180 alleles) by CRISPR/Cas9 editing with homology-directed repair to disrupt production of full-length TOP2β/180. Gene-edited clones were identified and verified by quantitative polymerase chain reaction and Sanger sequencing, respectively. Characterization of TOP2β/180 gene-edited clones, with one or all four TOP2β/180 alleles mutated, revealed partial or complete loss of TOP2β mRNA/protein, respectively. The loss of TOP2β/180 protein correlated with decreased (2-{4-[(7-chloro-2-quinoxalinyl)oxy]phenoxy}propionic acid)-induced DNA damage and partial resistance in growth inhibition assays. Partial resistance to mitoxantrone was also noted in the gene-edited clone with all four TOP2β/180 alleles modified. No cross-resistance to etoposide or mAMSA was noted in the gene-edited clones. Results demonstrated the role of TOP2β/180 in drug sensitivity/resistance in K562 cells and revealed differential paralog activity of TOP2-targeted agents. SIGNIFICANCE STATEMENT: Data indicated that CRISPR/Cas9 editing of the exon 19/intron 19 boundary in the TOP2β/180 gene to introduce a premature stop codon resulted in partial to complete disruption of TOP2β/180 expression in human leukemia (K562) cells depending on the number of edited alleles. Edited clones were partially resistant to mitoxantrone and XK469, while lacking resistance to etoposide and mAMSA. Results demonstrated the import of TOP2β/180 in drug sensitivity/resistance in K562 cells and revealed differential paralog activity of TOP2-targeted agents.
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Affiliation(s)
- Jessika Carvajal-Moreno
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio
| | - Xinyi Wang
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio
| | - Victor A Hernandez
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio
| | - Milon Mondal
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio
| | - Xinyu Zhao
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio
| | - Jack C Yalowich
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio
| | - Terry S Elton
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio
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11
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Hsiung CC, Wilson CM, Sambold NA, Dai R, Chen Q, Misiukiewicz S, Arab A, Teyssier N, O'Loughlin T, Cofsky JC, Shi J, Gilbert LA. Higher-order combinatorial chromatin perturbations by engineered CRISPR-Cas12a for functional genomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.18.558350. [PMID: 37781594 PMCID: PMC10541102 DOI: 10.1101/2023.09.18.558350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Multiplexed genetic perturbations are critical for testing functional interactions among coding or non-coding genetic elements. Compared to double-stranded DNA cutting, repressive chromatin formation using CRISPR interference (CRISPRi) avoids genotoxicity and is more effective for perturbing non-coding regulatory elements in pooled assays. However, current CRISPRi pooled screening approaches are limited to targeting 1-3 genomic sites per cell. To develop a tool for higher-order ( > 3) combinatorial targeting of genomic sites with CRISPRi in functional genomics screens, we engineered an Acidaminococcus Cas12a variant -- referred to as mul tiplexed transcriptional interference AsCas12a (multiAsCas12a). multiAsCas12a incorporates a key mutation, R1226A, motivated by the hypothesis of nicking-induced stabilization of the ribonucleoprotein:DNA complex for improving CRISPRi activity. multiAsCas12a significantly outperforms prior state-of-the-art Cas12a variants in combinatorial CRISPRi targeting using high-order multiplexed arrays of lentivirally transduced CRISPR RNAs (crRNA), including in high-throughput pooled screens using 6-plex crRNA array libraries. Using multiAsCas12a CRISPRi, we discover new enhancer elements and dissect the combinatorial function of cis-regulatory elements. These results instantiate a group testing framework for efficiently surveying potentially numerous combinations of chromatin perturbations for biological discovery and engineering.
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Riepe C, Wąchalska M, Deol KK, Amaya AK, Porteus MH, Olzmann JA, Kopito RR. Small-molecule correctors divert CFTR-F508del from ERAD by stabilizing sequential folding states. Mol Biol Cell 2024; 35:ar15. [PMID: 38019608 PMCID: PMC10881158 DOI: 10.1091/mbc.e23-08-0336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 11/13/2023] [Accepted: 11/20/2023] [Indexed: 12/01/2023] Open
Abstract
Over 80% of people with cystic fibrosis (CF) carry the F508del mutation in the cystic fibrosis transmembrane conductance regulator (CFTR), a chloride ion channel at the apical plasma membrane (PM) of epithelial cells. F508del impairs CFTR folding causing it to be destroyed by endoplasmic reticulum associated degradation (ERAD). Small-molecule correctors, which act as pharmacological chaperones to divert CFTR-F508del from ERAD, are the primary strategy for treating CF, yet corrector development continues with only a rudimentary understanding of how ERAD targets CFTR-F508del. We conducted genome-wide CRISPR/Cas9 knockout screens to systematically identify the molecular machinery that underlies CFTR-F508del ERAD. Although the ER-resident ubiquitin ligase, RNF5 was the top E3 hit, knocking out RNF5 only modestly reduced CFTR-F508del degradation. Sublibrary screens in an RNF5 knockout background identified RNF185 as a redundant ligase and demonstrated that CFTR-F508del ERAD is robust. Gene-drug interaction experiments illustrated that correctors tezacaftor (VX-661) and elexacaftor (VX-445) stabilize sequential, RNF5-resistant folding states. We propose that binding of correctors to nascent CFTR-F508del alters its folding landscape by stabilizing folding states that are not substrates for RNF5-mediated ubiquitylation.
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Affiliation(s)
- Celeste Riepe
- Department of Biology, Stanford University, Stanford, CA 94305
| | - Magda Wąchalska
- Department of Biology, Stanford University, Stanford, CA 94305
| | - Kirandeep K. Deol
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA 94720
- Chan Zuckerberg Biohub Network, San Francisco, CA 94158
| | - Anais K. Amaya
- Department of Pediatrics, Stanford University, Stanford, CA 94305
| | | | - James A. Olzmann
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA 94720
- Chan Zuckerberg Biohub Network, San Francisco, CA 94158
| | - Ron R. Kopito
- Department of Biology, Stanford University, Stanford, CA 94305
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13
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Xu D, Tang L, Zhou J, Wang F, Cao H, Huang Y, Kapranov P. Evidence for widespread existence of functional novel and non-canonical human transcripts. BMC Biol 2023; 21:271. [PMID: 38001496 PMCID: PMC10675921 DOI: 10.1186/s12915-023-01753-5] [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: 01/24/2023] [Accepted: 10/31/2023] [Indexed: 11/26/2023] Open
Abstract
BACKGROUND Fraction of functional sequence in the human genome remains a key unresolved question in Biology and the subject of vigorous debate. While a plethora of studies have connected a significant fraction of human DNA to various biochemical processes, the classical definition of function requires evidence of effects on cellular or organismal fitness that such studies do not provide. Although multiple high-throughput reverse genetics screens have been developed to address this issue, they are limited to annotated genomic elements and suffer from non-specific effects, arguing for a strong need to develop additional functional genomics approaches. RESULTS In this work, we established a high-throughput lentivirus-based insertional mutagenesis strategy as a forward genetics screen tool in aneuploid cells. Application of this approach to human cell lines in multiple phenotypic screens suggested the presence of many yet uncharacterized functional elements in the human genome, represented at least in part by novel exons of known and novel genes. The novel transcripts containing these exons can be massively, up to thousands-fold, induced by specific stresses, and at least some can represent bi-cistronic protein-coding mRNAs. CONCLUSIONS Altogether, these results argue that many unannotated and non-canonical human transcripts, including those that appear as aberrant splice products, have biological relevance under specific biological conditions.
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Affiliation(s)
- Dongyang Xu
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Lu Tang
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Junjun Zhou
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Fang Wang
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Huifen Cao
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Yu Huang
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Philipp Kapranov
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China.
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, China.
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14
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Shen Y, Yu L, Qiu Y, Zhang T, Kingsford C. Improving Hi-C contact matrices using genome graphs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.08.566275. [PMID: 37986943 PMCID: PMC10659349 DOI: 10.1101/2023.11.08.566275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Three-dimensional chromosome structure plays an important role in fundamental genomic functions. Hi-C, a high-throughput, sequencing-based technique, has drastically expanded our comprehension of 3D chromosome structures. The first step of Hi-C analysis pipeline involves mapping sequencing reads from Hi-C to linear reference genomes. However, the linear reference genome does not incorporate genetic variation information, which can lead to incorrect read alignments, especially when analyzing samples with substantial genomic differences from the reference such as cancer samples. Using genome graphs as the reference facilitates more accurate mapping of reads, however, new algorithms are required for inferring linear genomes from Hi-C reads mapped on genome graphs and constructing corresponding Hi-C contact matrices, which is a prerequisite for the subsequent steps of the Hi-C analysis such as identifying topologically associated domains and calling chromatin loops. We introduce the problem of genome sequence inference from Hi-C data mediated by genome graphs. We formalize this problem, show the hardness of solving this problem, and introduce a novel heuristic algorithm specifically tailored to this problem. We provide a theoretical analysis to evaluate the efficacy of our algorithm. Finally, our empirical experiments indicate that the linear genomes inferred from our method lead to the creation of improved Hi-C contact matrices. These enhanced matrices show a reduction in erroneous patterns caused by structural variations and are more effective in accurately capturing the structures of topologically associated domains.
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Affiliation(s)
- Yihang Shen
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA
| | - Lingge Yu
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA
| | - Yutong Qiu
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA
| | - Tianyu Zhang
- Department of Statistics and Data Science, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA
| | - Carl Kingsford
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA
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15
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Erdmann-Pham DD, Batra SS, Turkalo TK, Durbin J, Blanchette M, Yeh I, Shain H, Bastian BC, Song YS, Rokhsar DS, Hockemeyer D. Tracing cancer evolution and heterogeneity using Hi-C. Nat Commun 2023; 14:7111. [PMID: 37932252 PMCID: PMC10628133 DOI: 10.1038/s41467-023-42651-2] [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: 10/29/2022] [Accepted: 10/09/2023] [Indexed: 11/08/2023] Open
Abstract
Chromosomal rearrangements can initiate and drive cancer progression, yet it has been challenging to evaluate their impact, especially in genetically heterogeneous solid cancers. To address this problem we developed HiDENSEC, a new computational framework for analyzing chromatin conformation capture in heterogeneous samples that can infer somatic copy number alterations, characterize large-scale chromosomal rearrangements, and estimate cancer cell fractions. After validating HiDENSEC with in silico and in vitro controls, we used it to characterize chromosome-scale evolution during melanoma progression in formalin-fixed tumor samples from three patients. The resulting comprehensive annotation of the genomic events includes copy number neutral translocations that disrupt tumor suppressor genes such as NF1, whole chromosome arm exchanges that result in loss of CDKN2A, and whole-arm copy-number neutral loss of homozygosity involving PTEN. These findings show that large-scale chromosomal rearrangements occur throughout cancer evolution and that characterizing these events yields insights into drivers of melanoma progression.
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Affiliation(s)
- Dan Daniel Erdmann-Pham
- Department of Mathematics, University of California, Berkeley, CA, 94720, USA
- Department of Statistics, Stanford University, Stanford, CA, 94305, USA
| | - Sanjit Singh Batra
- Computer Science Division, University of California, Berkeley, CA, 94720, USA
| | - Timothy K Turkalo
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA
| | - James Durbin
- Dovetail Genomics, Enterprise Way, Scotts Valley, CA, 95066, USA
| | - Marco Blanchette
- Dovetail Genomics, Enterprise Way, Scotts Valley, CA, 95066, USA
| | - Iwei Yeh
- Department of Dermatology and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, 94143, USA
- Department of Pathology, University of California, San Francisco, CA, 94143, USA
| | - Hunter Shain
- Department of Dermatology and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Boris C Bastian
- Department of Dermatology and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, 94143, USA
- Department of Pathology, University of California, San Francisco, CA, 94143, USA
| | - Yun S Song
- Computer Science Division, University of California, Berkeley, CA, 94720, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.
- Department of Statistics, University of California, Berkeley, CA, 94720, USA.
| | - Daniel S Rokhsar
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.
- Innovative Genomics Institute, University of California, Berkeley, CA, 94720, USA.
- Okinawa Institute for Science and Technology, Tancha, Okinawa, Japan.
| | - Dirk Hockemeyer
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.
- Innovative Genomics Institute, University of California, Berkeley, CA, 94720, USA.
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16
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Lin J, Xue X, Wang Y, Zhou Y, Wu J, Xie H, Liu M, Wen L, Tang F. scNanoCOOL-seq: a long-read single-cell sequencing method for multi-omics profiling within individual cells. Cell Res 2023; 33:879-882. [PMID: 37700167 PMCID: PMC10624858 DOI: 10.1038/s41422-023-00873-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 08/30/2023] [Indexed: 09/14/2023] Open
Affiliation(s)
- Jianli Lin
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
| | - Xiaohui Xue
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
- PKU-Tsinghua-NIBS Graduate Program, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Yan Wang
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
| | - Yuan Zhou
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China
| | - Jian Wu
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Science Key Lab, Beijing, China
| | - Haoling Xie
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
| | - Mengya Liu
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
| | - Lu Wen
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
| | - Fuchou Tang
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China.
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China.
- PKU-Tsinghua-NIBS Graduate Program, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
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17
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Bayona-Feliu A, Herrera-Moyano E, Badra-Fajardo N, Galván-Femenía I, Soler-Oliva ME, Aguilera A. The chromatin network helps prevent cancer-associated mutagenesis at transcription-replication conflicts. Nat Commun 2023; 14:6890. [PMID: 37898641 PMCID: PMC10613258 DOI: 10.1038/s41467-023-42653-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 10/09/2023] [Indexed: 10/30/2023] Open
Abstract
Genome instability is a feature of cancer cells, transcription being an important source of DNA damage. This is in large part associated with R-loops, which hamper replication, especially at head-on transcription-replication conflicts (TRCs). Here we show that TRCs trigger a DNA Damage Response (DDR) involving the chromatin network to prevent genome instability. Depletion of the key chromatin factors INO80, SMARCA5 and MTA2 results in TRCs, fork stalling and R-loop-mediated DNA damage which mostly accumulates at S/G2, while histone H3 Ser10 phosphorylation, a mark of chromatin compaction, is enriched at TRCs. Strikingly, TRC regions show increased mutagenesis in cancer cells with signatures of homologous recombination deficiency, transcription-coupled nucleotide excision repair (TC-NER) and of the AID/APOBEC cytidine deaminases, being predominant at head-on collisions. Thus, our results support that the chromatin network prevents R-loops and TRCs from genomic instability and mutagenic signatures frequently associated with cancer.
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Affiliation(s)
- Aleix Bayona-Feliu
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092, Seville, Spain.
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012, Seville, Spain.
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
| | - Emilia Herrera-Moyano
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092, Seville, Spain
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012, Seville, Spain
| | - Nibal Badra-Fajardo
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092, Seville, Spain
| | - Iván Galván-Femenía
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - María Eugenia Soler-Oliva
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092, Seville, Spain
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012, Seville, Spain
| | - Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092, Seville, Spain.
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012, Seville, Spain.
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18
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Li W, Lu J, Lu P, Gao Y, Bai Y, Chen K, Su X, Li M, Liu J, Chen Y, Wen L, Tang F. scNanoHi-C: a single-cell long-read concatemer sequencing method to reveal high-order chromatin structures within individual cells. Nat Methods 2023; 20:1493-1505. [PMID: 37640936 DOI: 10.1038/s41592-023-01978-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 07/19/2023] [Indexed: 08/31/2023]
Abstract
The high-order three-dimensional (3D) organization of regulatory genomic elements provides a topological basis for gene regulation, but it remains unclear how multiple regulatory elements across the mammalian genome interact within an individual cell. To address this, herein, we developed scNanoHi-C, which applies Nanopore long-read sequencing to explore genome-wide proximal high-order chromatin contacts within individual cells. We show that scNanoHi-C can reliably and effectively profile 3D chromatin structures and distinguish structure subtypes among individual cells. This method could also be used to detect genomic variations, including copy-number variations and structural variations, as well as to scaffold the de novo assembly of single-cell genomes. Notably, our results suggest that extensive high-order chromatin structures exist in active chromatin regions across the genome, and multiway interactions between enhancers and their target promoters were systematically identified within individual cells. Altogether, scNanoHi-C offers new opportunities to investigate high-order 3D genome structures at the single-cell level.
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Affiliation(s)
- Wen Li
- School of Life Sciences, Biomedical Pioneering Innovative Center, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
- Changping Laboratory, Beijing, China
| | - Jiansen Lu
- School of Life Sciences, Biomedical Pioneering Innovative Center, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
- Changping Laboratory, Beijing, China
| | - Ping Lu
- School of Life Sciences, Biomedical Pioneering Innovative Center, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
| | - Yun Gao
- School of Life Sciences, Biomedical Pioneering Innovative Center, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
| | - Yichen Bai
- School of Life Sciences, Biomedical Pioneering Innovative Center, Peking University, Beijing, China
| | - Kexuan Chen
- School of Life Sciences, Biomedical Pioneering Innovative Center, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
| | - Xinjie Su
- School of Life Sciences, Biomedical Pioneering Innovative Center, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Mengyao Li
- School of Life Sciences, Biomedical Pioneering Innovative Center, Peking University, Beijing, China
| | - Jun'e Liu
- School of Life Sciences, Biomedical Pioneering Innovative Center, Peking University, Beijing, China
| | - Yijun Chen
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
| | - Lu Wen
- School of Life Sciences, Biomedical Pioneering Innovative Center, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
| | - Fuchou Tang
- School of Life Sciences, Biomedical Pioneering Innovative Center, Peking University, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China.
- Changping Laboratory, Beijing, China.
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19
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Riepe C, Wąchalska M, Deol KK, Amaya AK, Porteus MH, Olzmann JA, Kopito RR. Small molecule correctors divert CFTR-F508del from ERAD by stabilizing sequential folding states. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.15.556420. [PMID: 37745470 PMCID: PMC10515913 DOI: 10.1101/2023.09.15.556420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Over 80% of people with cystic fibrosis (CF) carry the F508del mutation in the cystic fibrosis transmembrane conductance regulator (CFTR), a chloride ion channel at the apical plasma membrane (PM) of epithelial cells. F508del impairs CFTR folding causing it to be destroyed by endoplasmic reticulum associated degradation (ERAD). Small molecule correctors, which act as pharmacological chaperones to divert CFTR-F508del from ERAD, are the primary strategy for treating CF, yet corrector development continues with only a rudimentary understanding of how ERAD targets CFTR-F508del. We conducted genome-wide CRISPR/Cas9 knockout screens to systematically identify the molecular machinery that underlies CFTR-F508del ERAD. Although the ER-resident ubiquitin ligase, RNF5 was the top E3 hit, knocking out RNF5 only modestly reduced CFTR-F508del degradation. Sublibrary screens in an RNF5 knockout background identified RNF185 as a redundant ligase, demonstrating that CFTR-F508del ERAD is highly buffered. Gene-drug interaction experiments demonstrated that correctors tezacaftor (VX-661) and elexacaftor (VX-445) stabilize sequential, RNF5-resistant folding states. We propose that binding of correctors to nascent CFTR-F508del alters its folding landscape by stabilizing folding states that are not substrates for RNF5-mediated ubiquitylation.
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Affiliation(s)
- Celeste Riepe
- Department of Biology, Stanford University, Stanford, CA, USA 94305
| | - Magda Wąchalska
- Department of Biology, Stanford University, Stanford, CA, USA 94305
| | - Kirandeep K. Deol
- Department of Molecular and Cell Biology, University of California, Berkeley, CA USA 94720
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA USA 94720
- Chan Zuckerberg Biohub, San Francisco, CA, USA 94158
| | - Anais K. Amaya
- Department of Pediatrics, Stanford University, Stanford, CA, USA 94305
| | | | - James A. Olzmann
- Department of Molecular and Cell Biology, University of California, Berkeley, CA USA 94720
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA USA 94720
- Chan Zuckerberg Biohub, San Francisco, CA, USA 94158
| | - Ron R. Kopito
- Department of Biology, Stanford University, Stanford, CA, USA 94305
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20
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Ozturk K, Panwala R, Sheen J, Ford K, Payne N, Zhang DE, Hutter S, Haferlach T, Ideker T, Mali P, Carter H. Interface-guided phenotyping of coding variants in the transcription factor RUNX1 with SEUSS. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.03.551876. [PMID: 37577681 PMCID: PMC10418284 DOI: 10.1101/2023.08.03.551876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Understanding the consequences of single amino acid substitutions in cancer driver genes remains an unmet need. Perturb-seq provides a tool to investigate the effects of individual mutations on cellular programs. Here we deploy SEUSS, a Perturb-seq like approach, to generate and assay mutations at physical interfaces of the RUNX1 Runt domain. We measured the impact of 115 mutations on RNA profiles in single myelogenous leukemia cells and used the profiles to categorize mutations into three functionally distinct groups: wild-type (WT)-like, loss-of-function (LOF)-like and hypomorphic. Notably, the largest concentration of functional mutations (non-WT-like) clustered at the DNA binding site and contained many of the more frequently observed mutations in human cancers. Hypomorphic variants shared characteristics with loss of function variants but had gene expression profiles indicative of response to neural growth factor and cytokine recruitment of neutrophils. Additionally, DNA accessibility changes upon perturbations were enriched for RUNX1 binding motifs, particularly near differentially expressed genes. Overall, our work demonstrates the potential of targeting protein interaction interfaces to better define the landscape of prospective phenotypes reachable by amino acid substitutions.
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21
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McKinley S, Taylor A, Peeples C, Jacob M, Khaparde G, Walter Y, Ekpenyong A. Simulated Microgravity-Induced Changes to Drug Response in Cancer Cells Quantified Using Fluorescence Morphometry. Life (Basel) 2023; 13:1683. [PMID: 37629540 PMCID: PMC10455503 DOI: 10.3390/life13081683] [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: 06/20/2023] [Revised: 07/31/2023] [Accepted: 08/02/2023] [Indexed: 08/27/2023] Open
Abstract
Unlike plants that have special gravity-sensing cells, such special cells in animals are yet to be discovered. However, microgravity, the condition of apparent weightlessness, causes bone, muscular and immune system dysfunctions in astronauts following spaceflights. Decades of investigations show correlations between these organ and system-level dysfunctions with changes induced at the cellular level both by simulated microgravity as well as microgravity conditions in outer space. Changes in single bone, muscle and immune cells include morphological abnormalities, altered gene expression, protein expression, metabolic pathways and signaling pathways. These suggest that human cells mount some response to microgravity. However, the implications of such adjustments on many cellular functions and responses are not clear. Here, we addressed the question whether microgravity induces alterations to drug response in cancer cells. We used both adherent cancer cells (T98G) and cancer cells in suspension (K562) to confirm the known effects of simulated microgravity and then treated the K562 cells with common cancer drugs (hydroxyurea and paclitaxel) following 48 h of exposure to simulated microgravity via a NASA-developed rotary cell culture system. Through fluorescence-guided morphometry, we found that microgravity abolished a significant reduction (p < 0.01) in the nuclear-to-cytoplasm ratio of cancer cells treated with hydroxyurea. Our results call for more studies on the impact of microgravity on cellular drug response, in light of the growing need for space medicine, as space exploration grows.
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Affiliation(s)
- Spencer McKinley
- Biology Department, Creighton University, Omaha, NE 68178, USA; (S.M.); (A.T.); (M.J.); (G.K.)
| | - Adam Taylor
- Biology Department, Creighton University, Omaha, NE 68178, USA; (S.M.); (A.T.); (M.J.); (G.K.)
| | - Conner Peeples
- Physics Department, Creighton University, Omaha, NE 68178, USA; (C.P.); (Y.W.)
| | - Megha Jacob
- Biology Department, Creighton University, Omaha, NE 68178, USA; (S.M.); (A.T.); (M.J.); (G.K.)
| | - Gargee Khaparde
- Biology Department, Creighton University, Omaha, NE 68178, USA; (S.M.); (A.T.); (M.J.); (G.K.)
| | - Yohan Walter
- Physics Department, Creighton University, Omaha, NE 68178, USA; (C.P.); (Y.W.)
| | - Andrew Ekpenyong
- Physics Department, Creighton University, Omaha, NE 68178, USA; (C.P.); (Y.W.)
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22
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Barshad G, Lewis JJ, Chivu AG, Abuhashem A, Krietenstein N, Rice EJ, Ma Y, Wang Z, Rando OJ, Hadjantonakis AK, Danko CG. RNA polymerase II dynamics shape enhancer-promoter interactions. Nat Genet 2023; 55:1370-1380. [PMID: 37430091 DOI: 10.1038/s41588-023-01442-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 06/09/2023] [Indexed: 07/12/2023]
Abstract
How enhancers control target gene expression over long genomic distances remains an important unsolved problem. Here we investigated enhancer-promoter communication by integrating data from nucleosome-resolution genomic contact maps, nascent transcription and perturbations affecting either RNA polymerase II (Pol II) dynamics or the activity of thousands of candidate enhancers. Integration of new Micro-C experiments with published CRISPRi data demonstrated that enhancers spend more time in close proximity to their target promoters in functional enhancer-promoter pairs compared to nonfunctional pairs, which can be attributed in part to factors unrelated to genomic position. Manipulation of the transcription cycle demonstrated a key role for Pol II in enhancer-promoter interactions. Notably, promoter-proximal paused Pol II itself partially stabilized interactions. We propose an updated model in which elements of transcriptional dynamics shape the duration or frequency of interactions to facilitate enhancer-promoter communication.
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Affiliation(s)
- Gilad Barshad
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - James J Lewis
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA
| | - Alexandra G Chivu
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Abderhman Abuhashem
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York City, NY, USA
- Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York City, NY, USA
- Biochemistry Cell and Molecular Biology Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York City, NY, USA
| | - Nils Krietenstein
- The Novo Nordisk Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Edward J Rice
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Yitian Ma
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Dalian, China
| | - Zhong Wang
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Dalian, China
| | - Oliver J Rando
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Anna-Katerina Hadjantonakis
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York City, NY, USA
- Biochemistry Cell and Molecular Biology Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York City, NY, USA
| | - Charles G Danko
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA.
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA.
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23
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Zwaig M, Johnston MJ, Lee JJ, Farooq H, Gallo M, Jabado N, Taylor MD, Ragoussis J. Linked-read based analysis of the medulloblastoma genome. Front Oncol 2023; 13:1221611. [PMID: 37576901 PMCID: PMC10419201 DOI: 10.3389/fonc.2023.1221611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 07/06/2023] [Indexed: 08/15/2023] Open
Abstract
Introduction Medulloblastoma is the most common type of malignant pediatric brain tumor with group 4 medulloblastomas (G4 MBs) accounting for 40% of cases. However, the molecular mechanisms that underlie this subgroup are still poorly understood. Point mutations are detected in a large number of genes at low incidence per gene while the detection of complex structural variants in recurrently affected genes typically requires the application of long-read technologies. Methods Here, we applied linked-read sequencing, which combines the long-range genome information of long-read sequencing with the high base pair accuracy of short read sequencing and very low sample input requirements. Results We demonstrate the detection of complex structural variants and point mutations in these tumors, and, for the first time, the detection of extrachromosomal DNA (ecDNA) with linked-reads. We provide further evidence for the high heterogeneity of somatic mutations in G4 MBs and add new complex events associated with it. Discussion We detected several enhancer-hijacking events, an ecDNA containing the MYCN gene, and rare structural rearrangements, such a chromothripsis in a G4 medulloblastoma, chromoplexy involving 8 different chromosomes, a TERT gene rearrangement, and a PRDM6 duplication.
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Affiliation(s)
- Melissa Zwaig
- Victor Phillip Dahdaleh Institute of Genomic Medicine and Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Michael J. Johnston
- Alberta Children’s Hospital Research Institute, Arnie Charbonneau Cancer Institute, and Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - John J.Y. Lee
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
- Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA, United States
| | | | - Marco Gallo
- Alberta Children’s Hospital Research Institute, Arnie Charbonneau Cancer Institute, and Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Nada Jabado
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- The Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Department of Pediatrics, McGill University, Montreal, QC, Canada
| | - Michael D. Taylor
- Division of Neurosurgery, The Arthur and Sonia Labatt Brain Tumour Research Centre and the Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Texas Children’s Cancer Center , Hematology-Oncology Section and Department of Pediatrics – Hematology/Oncology and Neurosurgery, Baylor College of Medicine, Houston, TX, United States
| | - Jiannis Ragoussis
- Victor Phillip Dahdaleh Institute of Genomic Medicine and Department of Human Genetics, McGill University, Montreal, QC, Canada
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24
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Lin J, Jia P, Wang S, Kosters W, Ye K. Comparison and benchmark of structural variants detected from long read and long-read assembly. Brief Bioinform 2023:7169138. [PMID: 37200087 DOI: 10.1093/bib/bbad188] [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: 01/16/2023] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 05/20/2023] Open
Abstract
Structural variant (SV) detection is essential for genomic studies, and long-read sequencing technologies have advanced our capacity to detect SVs directly from read or de novo assembly, also known as read-based and assembly-based strategy. However, to date, no independent studies have compared and benchmarked the two strategies. Here, on the basis of SVs detected by 20 read-based and eight assembly-based detection pipelines from six datasets of HG002 genome, we investigated the factors that influence the two strategies and assessed their performance with well-curated SVs. We found that up to 80% of the SVs could be detected by both strategies among different long-read datasets, whereas variant type, size, and breakpoint detected by read-based strategy were greatly affected by aligners. For the high-confident insertions and deletions at non-tandem repeat regions, a remarkable subset of them (82% in assembly-based calls and 93% in read-based calls), accounting for around 4000 SVs, could be captured by both reads and assemblies. However, discordance between two strategies was largely caused by complex SVs and inversions, which resulted from inconsistent alignment of reads and assemblies at these loci. Finally, benchmarking with SVs at medically relevant genes, the recall of read-based strategy reached 77% on 5X coverage data, whereas assembly-based strategy required 20X coverage data to achieve similar performance. Therefore, integrating SVs from read and assembly is suggested for general-purpose detection because of inconsistently detected complex SVs and inversions, whereas assembly-based strategy is optional for applications with limited resources.
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Affiliation(s)
- Jiadong Lin
- MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China
- Genome Institute, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061 China
- Leiden Institute of Advanced Computer Science, Faculty of Science, Leiden University, Leiden 2311 EZ, The Netherlands
| | - Peng Jia
- MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China
| | - Songbo Wang
- MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China
| | - Walter Kosters
- Leiden Institute of Advanced Computer Science, Faculty of Science, Leiden University, Leiden 2311 EZ, The Netherlands
| | - Kai Ye
- MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China
- Genome Institute, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061 China
- The School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China
- Faculty of Science, Leiden University, Leiden 2311 , The Netherlands
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25
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Li J, Gao L, Ye Y. HiSV: A control-free method for structural variation detection from Hi-C data. PLoS Comput Biol 2023; 19:e1010760. [PMID: 36608109 DOI: 10.1371/journal.pcbi.1010760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 11/24/2022] [Indexed: 01/07/2023] Open
Abstract
Structural variations (SVs) play an essential role in the evolution of human genomes and are associated with cancer genetics and rare disease. High-throughput chromosome capture (Hi-C) technology probed all genome-wide crosslinked chromatin to study the spatial architecture of chromosomes. Hi-C read pairs can span megabases, making the technology useful for detecting large-scale SVs. So far, the identification of SVs from Hi-C data is still in the early stages with only a few methods available. Especially, no algorithm has been developed that can detect SVs without control samples. Therefore, we developed HiSV (Hi-C for Structural Variation), a control-free method for identifying large-scale SVs from a Hi-C sample. Inspired by the single image saliency detection model, HiSV constructed a saliency map of interaction frequencies and extracted saliency segments as large-scale SVs. By evaluating both simulated and real data, HiSV not only detected all variant types, but also achieved a higher level of accuracy and sensitivity than existing methods. Moreover, our results on cancer cell lines showed that HiSV effectively detected eight complex SV events and identified two novel SVs of key factors associated with cancer development. Finally, we found that integrating the result of HiSV helped the WGS method to identify a total number of 94 novel SVs in two cancer cell lines.
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Affiliation(s)
- Junping Li
- Department of Computer Science, School of Computer Science and Technology, Xidian University, Xi'an, Shaanxi, China
| | - Lin Gao
- Department of Computer Science, School of Computer Science and Technology, Xidian University, Xi'an, Shaanxi, China
| | - Yusen Ye
- Department of Computer Science, School of Computer Science and Technology, Xidian University, Xi'an, Shaanxi, China
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26
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Han S, Dias GB, Basting PJ, Viswanatha R, Perrimon N, Bergman C. Local assembly of long reads enables phylogenomics of transposable elements in a polyploid cell line. Nucleic Acids Res 2022; 50:e124. [PMID: 36156149 PMCID: PMC9757076 DOI: 10.1093/nar/gkac794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 07/21/2022] [Accepted: 09/16/2022] [Indexed: 12/24/2022] Open
Abstract
Animal cell lines often undergo extreme genome restructuring events, including polyploidy and segmental aneuploidy that can impede de novo whole-genome assembly (WGA). In some species like Drosophila, cell lines also exhibit massive proliferation of transposable elements (TEs). To better understand the role of transposition during animal cell culture, we sequenced the genome of the tetraploid Drosophila S2R+ cell line using long-read and linked-read technologies. WGAs for S2R+ were highly fragmented and generated variable estimates of TE content across sequencing and assembly technologies. We therefore developed a novel WGA-independent bioinformatics method called TELR that identifies, locally assembles, and estimates allele frequency of TEs from long-read sequence data (https://github.com/bergmanlab/telr). Application of TELR to a ∼130x PacBio dataset for S2R+ revealed many haplotype-specific TE insertions that arose by transposition after initial cell line establishment and subsequent tetraploidization. Local assemblies from TELR also allowed phylogenetic analysis of paralogous TEs, which revealed that proliferation of TE families in vitro can be driven by single or multiple source lineages. Our work provides a model for the analysis of TEs in complex heterozygous or polyploid genomes that are recalcitrant to WGA and yields new insights into the mechanisms of genome evolution in animal cell culture.
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Affiliation(s)
| | | | - Preston J Basting
- Institute of Bioinformatics, University of Georgia, 120 E. Green St., Athens, GA, USA
| | - Raghuvir Viswanatha
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, USA
| | - Norbert Perrimon
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, USA,Howard Hughes Medical Institute, Boston, MA, USA
| | - Casey M Bergman
- To whom correspondence should be addressed. Tel: +1 706 542 1764; Fax: +1 706 542 3910;
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27
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Liu Y, Fu Y, Yang Y, Yi G, Lian J, Xie B, Yao Y, Chen M, Niu Y, Liu L, Wang L, Zhang Y, Fan X, Tang Y, Yuan P, Zhu M, Li Q, Zhang S, Chen Y, Wang B, He J, Lu D, Liachko I, Sullivan ST, Pang B, Chen Y, He X, Li K, Tang Z. Integration of multi-omics data reveals cis-regulatory variants that are associated with phenotypic differentiation of eastern from western pigs. GENETICS SELECTION EVOLUTION 2022; 54:62. [PMID: 36104777 PMCID: PMC9476355 DOI: 10.1186/s12711-022-00754-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 09/02/2022] [Indexed: 11/10/2022]
Abstract
Abstract
Background
The genetic mechanisms that underlie phenotypic differentiation in breeding animals have important implications in evolutionary biology and agriculture. However, the contribution of cis-regulatory variants to pig phenotypes is poorly understood. Therefore, our aim was to elucidate the molecular mechanisms by which non-coding variants cause phenotypic differences in pigs by combining evolutionary biology analyses and functional genomics.
Results
We obtained a high-resolution phased chromosome-scale reference genome with a contig N50 of 18.03 Mb for the Luchuan pig breed (a representative eastern breed) and profiled potential selective sweeps in eastern and western pigs by resequencing the genomes of 234 pigs. Multi-tissue transcriptome and chromatin accessibility analyses of these regions suggest that tissue-specific selection pressure is mediated by promoters and distal cis-regulatory elements. Promoter variants that are associated with increased expression of the lysozyme (LYZ) gene in the small intestine might enhance the immunity of the gastrointestinal tract and roughage tolerance in pigs. In skeletal muscle, an enhancer-modulating single-nucleotide polymorphism that is associated with up-regulation of the expression of the troponin C1, slow skeletal and cardiac type (TNNC1) gene might increase the proportion of slow muscle fibers and affect meat quality.
Conclusions
Our work sheds light on the molecular mechanisms by which non-coding variants shape phenotypic differences in pigs and provides valuable resources and novel perspectives to dissect the role of gene regulatory evolution in animal domestication and breeding.
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28
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Megquier K, Turner-Maier J, Morrill K, Li X, Johnson J, Karlsson EK, London CA, Gardner HL. The genomic landscape of canine osteosarcoma cell lines reveals conserved structural complexity and pathway alterations. PLoS One 2022; 17:e0274383. [PMID: 36099278 PMCID: PMC9469990 DOI: 10.1371/journal.pone.0274383] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 08/25/2022] [Indexed: 01/09/2023] Open
Abstract
The characterization of immortalized canine osteosarcoma (OS) cell lines used for research has historically been based on phenotypic features such as cellular morphology and expression of bone specific markers. With the increasing use of these cell lines to investigate novel therapeutic approaches prior to in vivo translation, a much more detailed understanding regarding the genomic landscape of these lines is required to ensure accurate interpretation of findings. Here we report the first whole genome characterization of eight canine OS cell lines, including single nucleotide variants, copy number variants and other structural variants. Many alterations previously characterized in primary canine OS tissue were observed in these cell lines, including TP53 mutations, MYC copy number gains, loss of CDKN2A, PTEN, DLG2, MAGI2, and RB1 and structural variants involving SETD2, DLG2 and DMD. These data provide a new framework for understanding how best to incorporate in vitro findings generated using these cell lines into the design of future clinical studies involving dogs with spontaneous OS.
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Affiliation(s)
- Kate Megquier
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Jason Turner-Maier
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Kathleen Morrill
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- University of Massachusetts Chan Medical School, Worcester, Massachusetts, United States of America
| | - Xue Li
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- University of Massachusetts Chan Medical School, Worcester, Massachusetts, United States of America
| | - Jeremy Johnson
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Elinor K Karlsson
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- University of Massachusetts Chan Medical School, Worcester, Massachusetts, United States of America
| | - Cheryl A London
- Cummings School of Veterinary Medicine at Tufts University, North Grafton, Massachusetts, United States of America
| | - Heather L Gardner
- Cummings School of Veterinary Medicine at Tufts University, North Grafton, Massachusetts, United States of America
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29
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Elton TS, Hernandez VA, Carvajal-Moreno J, Wang X, Ipinmoroti D, Yalowich JC. Intronic Polyadenylation in Acquired Cancer Drug Resistance Circumvented by Utilizing CRISPR/Cas9 with Homology-Directed Repair: The Tale of Human DNA Topoisomerase IIα. Cancers (Basel) 2022; 14:cancers14133148. [PMID: 35804920 PMCID: PMC9265003 DOI: 10.3390/cancers14133148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/23/2022] [Accepted: 06/24/2022] [Indexed: 12/02/2022] Open
Abstract
Simple Summary DNA topoisomerase IIα (170 kDa, TOP2α/170) resolves nucleic acid topological entanglements by generating transient double-strand DNA breaks. TOP2α inhibitors/poisons stabilize TOP2α-DNA covalent complexes resulting in persistent DNA damage and are frequently utilized to treat a variety of cancers. Acquired resistance to these chemotherapeutic agents is often associated with decreased TOP2α/170 expression levels. Studies have demonstrated that a reduction in TOP2α/170 results from a type of alternative polyadenylation designated intronic polyadenylation (IPA). As a consequence of IPA, variant TOP2α mRNA transcripts have been characterized that have resulted in the translation of C-terminal truncated TOP2α isoforms with altered biological activities. In this paper, an example is discussed where circumvention of acquired TOP2α-mediated drug resistance was achieved by utilizing CRISPR/Cas9 specific gene editing of an exon/intron boundary through homology directed repair (HDR) to reduce TOP2α IPA. These results illustrate the therapeutic potential of CRISPR/Cas9/HDR to impact drug resistance associated with aberrant IPA. Abstract Intronic polyadenylation (IPA) plays a critical role in malignant transformation, development, progression, and cancer chemoresistance by contributing to transcriptome/proteome alterations. DNA topoisomerase IIα (170 kDa, TOP2α/170) is an established clinical target for anticancer agents whose efficacy is compromised by drug resistance often associated with a reduction of nuclear TOP2α/170 levels. In leukemia cell lines with acquired resistance to TOP2α-targeted drugs and reduced TOP2α/170 expression, variant TOP2α mRNA transcripts have been reported due to IPA that resulted in the translation of C-terminal truncated isoforms with altered nuclear-cytoplasmic distribution or heterodimerization with wild-type TOP2α/170. This review provides an overview of the various mechanisms regulating pre-mRNA processing and alternative polyadenylation, as well as the utilization of CRISPR/Cas9 specific gene editing through homology directed repair (HDR) to decrease IPA when splice sites are intrinsically weak or potentially mutated. The specific case of TOP2α exon 19/intron 19 splice site editing is discussed in etoposide-resistant human leukemia K562 cells as a tractable strategy to circumvent acquired TOP2α-mediated drug resistance. This example supports the importance of aberrant IPA in acquired drug resistance to TOP2α-targeted drugs. In addition, these results demonstrate the therapeutic potential of CRISPR/Cas9/HDR to impact drug resistance associated with aberrant splicing/polyadenylation.
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30
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Rinzema NJ, Sofiadis K, Tjalsma SJD, Verstegen MJAM, Oz Y, Valdes-Quezada C, Felder AK, Filipovska T, van der Elst S, de Andrade Dos Ramos Z, Han R, Krijger PHL, de Laat W. Building regulatory landscapes reveals that an enhancer can recruit cohesin to create contact domains, engage CTCF sites and activate distant genes. Nat Struct Mol Biol 2022; 29:563-574. [PMID: 35710842 PMCID: PMC9205769 DOI: 10.1038/s41594-022-00787-7] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 04/25/2022] [Indexed: 12/14/2022]
Abstract
Developmental gene expression is often controlled by distal regulatory DNA elements called enhancers. Distant enhancer action is restricted to structural chromosomal domains that are flanked by CTCF-associated boundaries and formed through cohesin chromatin loop extrusion. To better understand how enhancers, genes and CTCF boundaries together form structural domains and control expression, we used a bottom-up approach, building series of active regulatory landscapes in inactive chromatin. We demonstrate here that gene transcription levels and activity over time reduce with increased enhancer distance. The enhancer recruits cohesin to stimulate domain formation and engage flanking CTCF sites in loop formation. It requires cohesin exclusively for the activation of distant genes, not of proximal genes, with nearby CTCF boundaries supporting efficient long-range enhancer action. Our work supports a dual activity model for enhancers: its classic role of stimulating transcription initiation and elongation from target gene promoters and a role of recruiting cohesin for the creation of chromosomal domains, the engagement of CTCF sites in chromatin looping and the activation of distal target genes.
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Affiliation(s)
- Niels J Rinzema
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Konstantinos Sofiadis
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Sjoerd J D Tjalsma
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Marjon J A M Verstegen
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Yuva Oz
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Christian Valdes-Quezada
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Anna-Karina Felder
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Teodora Filipovska
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Stefan van der Elst
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Zaria de Andrade Dos Ramos
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Ruiqi Han
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Peter H L Krijger
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Wouter de Laat
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands.
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31
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Hernandez VA, Carvajal-Moreno J, Wang X, Pietrzak M, Yalowich JC, Elton TS. Use of CRISPR/Cas9 with homology-directed repair to silence the human topoisomerase IIα intron-19 5’ splice site: Generation of etoposide resistance in human leukemia K562 cells. PLoS One 2022; 17:e0265794. [PMID: 35617303 PMCID: PMC9135202 DOI: 10.1371/journal.pone.0265794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 05/06/2022] [Indexed: 11/19/2022] Open
Abstract
DNA Topoisomerase IIα (TOP2α/170) is an enzyme essential for proliferating cells. For rapidly multiplying malignancies, this has made TOP2α/170 an important target for etoposide and other clinically active anticancer drugs. Efficacy of these agents is often limited by chemoresistance related to alterations in TOP2α/170 expression levels. Our laboratory recently demonstrated reduced levels of TOP2α/170 and overexpression of a C-terminal truncated 90-kDa isoform, TOP2α/90, due to intronic polyadenylation (IPA; within intron 19) in an acquired etoposide-resistant K562 clonal cell line, K/VP.5. We previously reported that this isoform heterodimerized with TOP2α/170 and was a determinant of acquired resistance to etoposide. Optimization of the weak TOP2α exon 19/intron 19 5′ splice site in drug-resistant K/VP.5 cells by gene-editing restored TOP2α/170 levels, diminished TOP2α/90 expression, and circumvented drug resistance. Conversely, in the present study, silencing of the exon 19/intron 19 5′ splice site in parental K562 cells by CRISPR/Cas9 with homology-directed repair (HDR), and thereby forcing intron 19 retention, was used to induce resistance by disrupting normal RNA processing (i.e., gene knockout), and to further evaluate the role of TOP2α/170 and TOP2α/90 isoforms as resistance determinants. Gene-edited clones were identified by quantitative polymerase chain reaction (qPCR) and verified by Sanger sequencing. TOP2α/170 mRNA/protein expression levels were attenuated in the TOP2α gene-edited clones which resulted in resistance to etoposide as assessed by reduced etoposide-induced DNA damage (γH2AX, Comet assays) and growth inhibition. RNA-seq and qPCR studies suggested that intron 19 retention leads to decreased TOP2α/170 expression by degradation of the TOP2α edited mRNA transcripts. Forced expression of TOP2α/90 in the gene-edited K562 cells further decreased etoposide-induced DNA damage in support of a dominant negative role for this truncated isoform. Together results support the important role of both TOP2α/170 and TOP2α/90 as determinants of sensitivity/resistance to TOP2α-targeting agents.
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Affiliation(s)
- Victor A. Hernandez
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio, United States of America
| | - Jessika Carvajal-Moreno
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio, United States of America
| | - Xinyi Wang
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio, United States of America
| | - Maciej Pietrzak
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - Jack C. Yalowich
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio, United States of America
- * E-mail: (JCY); (TSE)
| | - Terry S. Elton
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio, United States of America
- * E-mail: (JCY); (TSE)
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32
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Weighill D, Ben Guebila M, Glass K, Quackenbush J, Platig J. Predicting genotype-specific gene regulatory networks. Genome Res 2022; 32:524-533. [PMID: 35193937 PMCID: PMC8896459 DOI: 10.1101/gr.275107.120] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 01/11/2022] [Indexed: 11/25/2022]
Abstract
Understanding how each person's unique genotype influences their individual patterns of gene regulation has the potential to improve our understanding of human health and development, and to refine genotype-specific disease risk assessments and treatments. However, the effects of genetic variants are not typically considered when constructing gene regulatory networks, despite the fact that many disease-associated genetic variants are thought to have regulatory effects, including the disruption of transcription factor (TF) binding. We developed EGRET (Estimating the Genetic Regulatory Effect on TFs), which infers a genotype-specific gene regulatory network for each individual in a study population. EGRET begins by constructing a genotype-informed TF-gene prior network derived using TF motif predictions, expression quantitative trait locus (eQTL) data, individual genotypes, and the predicted effects of genetic variants on TF binding. It then uses a technique known as message passing to integrate this prior network with gene expression and TF protein–protein interaction data to produce a refined, genotype-specific regulatory network. We used EGRET to infer gene regulatory networks for two blood-derived cell lines and identified genotype-associated, cell line–specific regulatory differences that we subsequently validated using allele-specific expression, chromatin accessibility QTLs, and differential ChIP-seq TF binding. We also inferred EGRET networks for three cell types from each of 119 individuals and identified cell type–specific regulatory differences associated with diseases related to those cell types. EGRET is, to our knowledge, the first method that infers networks reflective of individual genetic variation in a way that provides insight into the genetic regulatory associations driving complex phenotypes.
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Affiliation(s)
- Deborah Weighill
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
| | | | - Kimberly Glass
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA.,Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA.,Harvard Medical School, Boston, Massachusetts 02115, USA
| | - John Quackenbush
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA.,Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - John Platig
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA.,Harvard Medical School, Boston, Massachusetts 02115, USA
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33
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Schep R, Leemans C, Brinkman EK, van Schaik T, van Steensel B. Protocol: A Multiplexed Reporter Assay to Study Effects of Chromatin Context on DNA Double-Strand Break Repair. Front Genet 2022; 12:785947. [PMID: 35173762 PMCID: PMC8842231 DOI: 10.3389/fgene.2021.785947] [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: 09/29/2021] [Accepted: 11/16/2021] [Indexed: 11/13/2022] Open
Abstract
DNA double-strand breaks (DSBs) can be repaired through various pathways. Understanding how these pathways are regulated is of great interest for cancer research and optimization of gene editing. The local chromatin environment can affect the balance between repair pathways, but this is still poorly understood. Here we provide a detailed protocol for DSB-TRIP, a technique that utilizes the specific DNA scars left by DSB repair pathways to study pathway usage throughout the genome. DSB-TRIP randomly integrates a repair reporter into many genomic locations, followed by the induction of DSBs in the reporter. Multiplexed sequencing of the resulting scars at all integration sites then reveals the balance between several repair pathways, which can be linked to the local chromatin state of the integration sites. Here we present a step-by-step protocol to perform DSB-TRIP in K562 cells and to analyse the data by a dedicated computational pipeline. We discuss strengths and limitations of the technique, as well as potential additional applications to study DNA repair.
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Affiliation(s)
- Ruben Schep
- Oncode Institute and Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Christ Leemans
- Oncode Institute and Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Eva K Brinkman
- Oncode Institute and Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Tom van Schaik
- Oncode Institute and Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Bas van Steensel
- Oncode Institute and Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, Netherlands.,Department of Cell Biology, Erasmus University Medical Centre, Rotterdam, Netherlands
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34
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Ribeiro-Dos-Santos AM, Hogan MS, Luther RD, Brosh R, Maurano MT. Genomic context sensitivity of insulator function. Genome Res 2022; 32:425-436. [PMID: 35082140 PMCID: PMC8896466 DOI: 10.1101/gr.276449.121] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 01/25/2022] [Indexed: 11/24/2022]
Abstract
The specificity of interactions between genomic regulatory elements and potential target genes is influenced by the binding of insulator proteins such as CTCF, which can act as potent enhancer blockers when interposed between an enhancer and a promoter in a reporter assay. But not all CTCF sites genome-wide function as insulator elements, depending on cellular and genomic context. To dissect the influence of genomic context on enhancer blocker activity, we integrated reporter constructs with promoter-only, promoter and enhancer, and enhancer blocker configurations at hundreds of thousands of genomic sites using the Sleeping Beauty transposase. Deconvolution of reporter activity by genomic position reveals distinct expression patterns subject to genomic context, including a compartment of enhancer blocker reporter integrations with robust expression. The high density of integration sites permits quantitative delineation of characteristic genomic context sensitivity profiles and their decomposition into sensitivity to both local and distant DNase I hypersensitive sites. Furthermore, using a single-cell expression approach to test the effect of integrated reporters for differential expression of nearby endogenous genes reveals that CTCF insulator elements do not completely abrogate reporter effects on endogenous gene expression. Collectively, our results lend new insight into genomic regulatory compartmentalization and its influence on the determinants of promoter–enhancer specificity.
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Affiliation(s)
| | - Megan S Hogan
- Institute for Systems Genetics, NYU Grossman School of Medicine
| | - Raven D Luther
- Institute for Systems Genetics, NYU Grossman School of Medicine
| | - Ran Brosh
- Institute for Systems Genetics, NYU Grossman School of Medicine
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35
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van Hees M, Slott S, Hansen AH, Kim HS, Ji HP, Astakhova K. New approaches to moderate CRISPR-Cas9 activity: Addressing issues of cellular uptake and endosomal escape. Mol Ther 2022; 30:32-46. [PMID: 34091053 PMCID: PMC8753288 DOI: 10.1016/j.ymthe.2021.06.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 03/15/2021] [Accepted: 05/27/2021] [Indexed: 02/09/2023] Open
Abstract
CRISPR-Cas9 is rapidly entering molecular biology and biomedicine as a promising gene-editing tool. A unique feature of CRISPR-Cas9 is a single-guide RNA directing a Cas9 nuclease toward its genomic target. Herein, we highlight new approaches for improving cellular uptake and endosomal escape of CRISPR-Cas9. As opposed to other recently published works, this review is focused on non-viral carriers as a means to facilitate the cellular uptake of CRISPR-Cas9 through endocytosis. The majority of non-viral carriers, such as gold nanoparticles, polymer nanoparticles, lipid nanoparticles, and nanoscale zeolitic imidazole frameworks, is developed with a focus toward optimizing the endosomal escape of CRISPR-Cas9 by taking advantage of the acidic environment in the late endosomes. Among the most broadly used methods for in vitro and ex vivo ribonucleotide protein transfection are electroporation and microinjection. Thus, other delivery formats are warranted for in vivo delivery of CRISPR-Cas9. Herein, we specifically revise the use of peptide and nanoparticle-based systems as platforms for CRISPR-Cas9 delivery in vivo. Finally, we highlight future perspectives of the CRISPR-Cas9 gene-editing tool and the prospects of using non-viral vectors to improve its bioavailability and therapeutic potential.
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Affiliation(s)
- Maja van Hees
- Department of Chemistry, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Sofie Slott
- Department of Chemistry, Technical University of Denmark, 2800 Lyngby, Denmark
| | | | - Heon Seok Kim
- School of Medicine, Stanford University, Stanford, CA 94350, USA
| | - Hanlee P. Ji
- School of Medicine, Stanford University, Stanford, CA 94350, USA
| | - Kira Astakhova
- Department of Chemistry, Technical University of Denmark, 2800 Lyngby, Denmark,Corresponding author: Kira Astakhova, Department of Chemistry, Technical University of Denmark, 2800 Lyngby, Denmark.
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36
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The FORCE Panel: An All-in-One SNP Marker Set for Confirming Investigative Genetic Genealogy Leads and for General Forensic Applications. Genes (Basel) 2021; 12:genes12121968. [PMID: 34946917 PMCID: PMC8702142 DOI: 10.3390/genes12121968] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/07/2021] [Accepted: 12/08/2021] [Indexed: 12/03/2022] Open
Abstract
The FORensic Capture Enrichment (FORCE) panel is an all-in-one SNP panel for forensic applications. This panel of 5422 markers encompasses common, forensically relevant SNPs (identity, ancestry, phenotype, X- and Y-chromosomal SNPs), a novel set of 3931 autosomal SNPs for extended kinship analysis, and no clinically relevant/disease markers. The FORCE panel was developed as a custom hybridization capture assay utilizing ~20,000 baits to target the selected SNPs. Five non-probative, previously identified World War II (WWII) cases were used to assess the kinship panel. Each case included one bone sample and associated family reference DNA samples. Additionally, seven reference quality samples, two 200-year-old bone samples, and four control DNAs were processed for kit performance and concordance assessments. SNP recovery after capture resulted in a mean of ~99% SNPs exceeding 10X coverage for reference and control samples, and 44.4% SNPs for bone samples. The WWII case results showed that the FORCE panel could predict first to fifth degree relationships with strong statistical support (likelihood ratios over 10,000 and posterior probabilities over 99.99%). To conclude, SNPs will be important for further advances in forensic DNA analysis. The FORCE panel shows promising results and demonstrates the utility of a 5000 SNP panel for forensic applications.
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37
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Autio MI, Bin Amin T, Perrin A, Wong JY, Foo RSY, Prabhakar S. Transposable elements that have recently been mobile in the human genome. BMC Genomics 2021; 22:789. [PMID: 34732136 PMCID: PMC8567694 DOI: 10.1186/s12864-021-08085-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 10/14/2021] [Indexed: 11/29/2022] Open
Abstract
Background Transposable elements (TE) comprise nearly half of the human genome and their insertions have profound effects to human genetic diversification and as well as disease. Despite their abovementioned significance, there is no consensus on the TE subfamilies that remain active in the human genome. In this study, we therefore developed a novel statistical test for recently mobile subfamilies (RMSs), based on patterns of overlap with > 100,000 polymorphic indels. Results Our analysis produced a catalogue of 20 high-confidence RMSs, which excludes many false positives in public databases. Intriguingly though, it includes HERV-K, an LTR subfamily previously thought to be extinct. The RMS catalogue is strongly enriched for contributions to germline genetic disorders (P = 1.1e-10), and thus constitutes a valuable resource for diagnosing disorders of unknown aetiology using targeted TE-insertion screens. Remarkably, RMSs are also highly enriched for somatic insertions in diverse cancers (P = 2.8e-17), thus indicating strong correlations between germline and somatic TE mobility. Using CRISPR/Cas9 deletion, we show that an RMS-derived polymorphic TE insertion increased the expression of RPL17, a gene associated with lower survival in liver cancer. More broadly, polymorphic TE insertions from RMSs were enriched near genes with allele-specific expression, suggesting widespread effects on gene regulation. Conclusions By using a novel statistical test we have defined a catalogue of 20 recently mobile transposable element subfamilies. We illustrate the gene regulatory potential of RMS-derived polymorphic TE insertions, using CRISPR/Cas9 deletion in vitro on a specific candidate, as well as by genome wide analysis of allele-specific expression. Our study presents novel insights into TE mobility and regulatory potential and provides a key resource for human disease genetics and population history studies. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08085-0.
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Affiliation(s)
- Matias I Autio
- Laboratory of Epigenomics and Chromatin Organization, Genome Institute of Singapore, A*STAR, Singapore, 138672, Singapore.,Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore
| | - Talal Bin Amin
- Spatial and Single Cell Systems, Genome Institute of Singapore, A*STAR, 60 Biopolis St, Genome #02-01, Singapore, 138672, Singapore
| | - Arnaud Perrin
- Laboratory of Epigenomics and Chromatin Organization, Genome Institute of Singapore, A*STAR, Singapore, 138672, Singapore.,Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore
| | - Jen Yi Wong
- Spatial and Single Cell Systems, Genome Institute of Singapore, A*STAR, 60 Biopolis St, Genome #02-01, Singapore, 138672, Singapore
| | - Roger S-Y Foo
- Laboratory of Epigenomics and Chromatin Organization, Genome Institute of Singapore, A*STAR, Singapore, 138672, Singapore.,Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore
| | - Shyam Prabhakar
- Spatial and Single Cell Systems, Genome Institute of Singapore, A*STAR, 60 Biopolis St, Genome #02-01, Singapore, 138672, Singapore.
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38
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Wang K, Xiao Z, Yan Y, Ye R, Hu M, Bai S, Sei E, Qiao Y, Chen H, Lim B, Lin SH, Navin NE. Simple oligonucleotide-based multiplexing of single-cell chromatin accessibility. Mol Cell 2021; 81:4319-4332.e10. [PMID: 34686316 PMCID: PMC8611914 DOI: 10.1016/j.molcel.2021.09.026] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 07/02/2021] [Accepted: 09/22/2021] [Indexed: 11/22/2022]
Abstract
Microdroplet single-cell ATAC-seq is widely used to measure chromatin accessibility, however, highly scalable and simple sample multiplexing procedures are not available. Here, we present a transposome-assisted single nucleus barcoding approach for ATAC-seq (SNuBar-ATAC) that utilizes a single oligonucleotide adaptor for multiplexing samples during the existing tagmentation step and does not require a pre-labeling procedure. The accuracy and scalability of SNuBar-ATAC was evaluated using cell line mixture experiments. We applied SNuBar-ATAC to investigate treatment-induced chromatin accessibility dynamics by multiplexing 28 mice with lung tumors that received different combinations of chemo, radiation, and targeted immunotherapy. We also applied SNuBar-ATAC to study spatial epigenetic heterogeneity by multiplexing 32 regions from a human breast tissue. Additionally, we show that SNuBar can multiplex single cell ATAC and RNA multiomic assays in cell lines and human breast tissue samples. Our data show that SNuBar is a highly accurate, easy-to-use, and scalable system for multiplexing scATAC-seq and scATAC and RNA co-assay experiments.
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Affiliation(s)
- Kaile Wang
- Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Zhenna Xiao
- Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yun Yan
- Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Graduate School of Biological Sciences, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Rui Ye
- Graduate School of Biological Sciences, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Radiation Oncology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Min Hu
- Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Shanshan Bai
- Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Emi Sei
- Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yawei Qiao
- Department of Radiation Oncology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hui Chen
- Department of Pathology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Bora Lim
- Department of Breast Medical Oncology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Steven H Lin
- Graduate School of Biological Sciences, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Radiation Oncology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Nicholas E Navin
- Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Graduate School of Biological Sciences, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Bioinformatics and Computational Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA.
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39
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The SWI/SNF chromatin remodeling complex helps resolve R-loop-mediated transcription-replication conflicts. Nat Genet 2021; 53:1050-1063. [PMID: 33986538 DOI: 10.1038/s41588-021-00867-2] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 04/06/2021] [Indexed: 02/03/2023]
Abstract
ATP-dependent chromatin remodelers are commonly mutated in human cancer. Mammalian SWI/SNF complexes comprise three conserved multisubunit chromatin remodelers (cBAF, ncBAF and PBAF) that share the BRG1 (also known as SMARCA4) subunit responsible for the main ATPase activity. BRG1 is the most frequently mutated Snf2-like ATPase in cancer. In the present study, we have investigated the role of SWI/SNF in genome instability, a hallmark of cancer cells, given its role in transcription, DNA replication and DNA-damage repair. We show that depletion of BRG1 increases R-loops and R-loop-dependent DNA breaks, as well as transcription-replication (T-R) conflicts. BRG1 colocalizes with R-loops and replication fork blocks, as determined by FANCD2 foci, with BRG1 depletion being epistatic to FANCD2 silencing. Our study, extended to other components of SWI/SNF, uncovers a key role of the SWI/SNF complex, in particular cBAF, in helping resolve R-loop-mediated T-R conflicts, thus, unveiling a new mechanism by which chromatin remodeling protects genome integrity.
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40
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Fan X, Yang C, Li W, Bai X, Zhou X, Xie H, Wen L, Tang F. SMOOTH-seq: single-cell genome sequencing of human cells on a third-generation sequencing platform. Genome Biol 2021; 22:195. [PMID: 34193237 PMCID: PMC8247186 DOI: 10.1186/s13059-021-02406-y] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 06/08/2021] [Indexed: 04/27/2023] Open
Abstract
There is no effective way to detect structure variations (SVs) and extra-chromosomal circular DNAs (ecDNAs) at single-cell whole-genome level. Here, we develop a novel third-generation sequencing platform-based single-cell whole-genome sequencing (scWGS) method named SMOOTH-seq (single-molecule real-time sequencing of long fragments amplified through transposon insertion). We evaluate the method for detecting CNVs, SVs, and SNVs in human cancer cell lines and a colorectal cancer sample and show that SMOOTH-seq reliably and effectively detects SVs and ecDNAs in individual cells, but shows relatively limited accuracy in detection of CNVs and SNVs. SMOOTH-seq opens a new chapter in scWGS as it generates high fidelity reads of kilobases long.
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Affiliation(s)
- Xiaoying Fan
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, 510005, China
| | - Cheng Yang
- Beijing Advanced Innovation Center for Genomics (ICG), School of Life Sciences, Department of General Surgery, Third Hospital, Peking University, Beijing, 100871, China
| | - Wen Li
- Beijing Advanced Innovation Center for Genomics (ICG), School of Life Sciences, Department of General Surgery, Third Hospital, Peking University, Beijing, 100871, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Xiuzhen Bai
- Beijing Advanced Innovation Center for Genomics (ICG), School of Life Sciences, Department of General Surgery, Third Hospital, Peking University, Beijing, 100871, China
| | - Xin Zhou
- Beijing Advanced Innovation Center for Genomics (ICG), School of Life Sciences, Department of General Surgery, Third Hospital, Peking University, Beijing, 100871, China
| | - Haoling Xie
- Beijing Advanced Innovation Center for Genomics (ICG), School of Life Sciences, Department of General Surgery, Third Hospital, Peking University, Beijing, 100871, China
| | - Lu Wen
- Beijing Advanced Innovation Center for Genomics (ICG), School of Life Sciences, Department of General Surgery, Third Hospital, Peking University, Beijing, 100871, China
| | - Fuchou Tang
- Beijing Advanced Innovation Center for Genomics (ICG), School of Life Sciences, Department of General Surgery, Third Hospital, Peking University, Beijing, 100871, China.
- Biomedical Pioneering Innovation Center, Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, 100871, China.
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China.
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41
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Raeisi Dehkordi S, Luebeck J, Bafna V. FaNDOM: Fast nested distance-based seeding of optical maps. PATTERNS (NEW YORK, N.Y.) 2021; 2:100248. [PMID: 34027500 PMCID: PMC8134938 DOI: 10.1016/j.patter.2021.100248] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 03/08/2021] [Accepted: 04/01/2021] [Indexed: 12/25/2022]
Abstract
Optical mapping (OM) provides single-molecule readouts of fluorescently labeled sequence motifs on long fragments of DNA, resolved to nucleotide-level coordinates. With the advent of microfluidic technologies for analysis of DNA molecules, it is possible to inexpensively generate long OM data ( > 150 kbp) at high coverage. In addition to scaffolding for de novo assembly, OM data can be aligned to a reference genome for identification of genomic structural variants. We introduce FaNDOM (Fast Nested Distance Seeding of Optical Maps)-an optical map alignment tool that greatly reduces the search space of the alignment process. On four benchmark human datasets, FaNDOM was significantly (4-14×) faster than competing tools while maintaining comparable sensitivity and specificity. We used FaNDOM to map variants in three cancer cell lines and identified many biologically interesting structural variants, including deletions, duplications, gene fusions and gene-disrupting rearrangements. FaNDOM is publicly available at https://github.com/jluebeck/FaNDOM.
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Affiliation(s)
- Siavash Raeisi Dehkordi
- Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jens Luebeck
- Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA 92093, USA
- Bioinformatics & Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Vineet Bafna
- Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA 92093, USA
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42
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Kim K, Kim M, Kim Y, Lee D, Jung I. Hi-C as a molecular rangefinder to examine genomic rearrangements. Semin Cell Dev Biol 2021; 121:161-170. [PMID: 33992531 DOI: 10.1016/j.semcdb.2021.04.024] [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] [Received: 01/15/2021] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 11/16/2022]
Abstract
The mammalian genome is highly packed into the nucleus. Over the past decade, the development of Hi-C has contributed significantly to our understanding of the three-dimensional (3D) chromatin structure, uncovering the principles and functions of higher-order chromatin organizations. Recent studies have repositioned its property in spatial proximity measurement to address challenging problems in genome analyses including genome assembly, haplotype phasing, and the detection of genomic rearrangements. In particular, the power of Hi-C in detecting large-scale structural variations (SVs) in the cancer genome has been demonstrated, which is challenging to be addressed solely with short-read-based whole-genome sequencing analyses. In this review, we first provide a comprehensive view of Hi-C as an intuitive and effective SV detection tool. Then, we introduce recently developed bioinformatics tools utilizing Hi-C to investigate genomic rearrangements. Finally, we discuss the potential application of single-cell Hi-C to address the heterogeneity of genomic rearrangements and sub-population identification in the cancer genome.
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Affiliation(s)
- Kyukwang Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Mooyoung Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Yubin Kim
- Department of Life Science, University of Seoul, Seoul 02504, Republic of Korea
| | - Dongsung Lee
- Department of Life Science, University of Seoul, Seoul 02504, Republic of Korea.
| | - Inkyung Jung
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea.
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43
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Determination of complete chromosomal haplotypes by bulk DNA sequencing. Genome Biol 2021; 22:139. [PMID: 33957932 PMCID: PMC8101039 DOI: 10.1186/s13059-021-02330-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 03/25/2021] [Indexed: 01/02/2023] Open
Abstract
Haplotype phase represents the collective genetic variation between homologous chromosomes and is an essential feature of non-haploid genomes. Here we describe a computational strategy to reliably determine complete whole-chromosome haplotypes using a combination of bulk long-range sequencing and Hi-C sequencing. We demonstrate that this strategy can resolve the haplotypes of parental chromosomes in diploid human genomes with high precision (>99%) and completeness (>98%) and assemble the syntenic structure of rearranged chromosomes in aneuploid cancer genomes at base pair level resolution. Our work enables direct interrogation of chromosome-specific alterations and chromatin reorganization using bulk DNA sequencing.
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Pan W, Gong D, Sun D, Luo H. HICANCER: accurate and complete cancer genome phasing with Hi-C reads. Sci Rep 2021; 11:6609. [PMID: 33758310 PMCID: PMC7987978 DOI: 10.1038/s41598-021-86104-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/09/2021] [Indexed: 11/10/2022] Open
Abstract
Due to the high complexity of cancer genome, it is too difficult to generate complete cancer genome map which contains the sequence of every DNA molecule until now. Nevertheless, phasing each chromosome in cancer genome into two haplotypes according to germline mutations provides a suboptimal solution to understand cancer genome. However, phasing cancer genome is also a challenging problem, due to the limit in experimental and computational technologies. Hi-C data is widely used in phasing in recent years due to its long-range linkage information and provides an opportunity for solving the problem of phasing cancer genome. The existing Hi-C based phasing methods can not be applied to cancer genome directly, because the somatic mutations in cancer genome such as somatic SNPs, copy number variations and structural variations greatly reduce the correctness and completeness. Here, we propose a new Hi-C based pipeline for phasing cancer genome called HiCancer. HiCancer solves different kinds of somatic mutations and variations, and take advantage of allelic copy number imbalance and linkage disequilibrium to improve the correctness and completeness of phasing. According to our experiments in K562 and KBM-7 cell lines, HiCancer is able to generate very high-quality chromosome-level haplotypes for cancer genome with only Hi-C data.
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Affiliation(s)
- Weihua Pan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.
| | - Desheng Gong
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Da Sun
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Haohui Luo
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
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45
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Hernandez VA, Carvajal-Moreno J, Papa JL, Shkolnikov N, Li J, Ozer HG, Yalowich JC, Elton TS. CRISPR/Cas9 Genome Editing of the Human Topoisomerase II α Intron 19 5' Splice Site Circumvents Etoposide Resistance in Human Leukemia K562 Cells. Mol Pharmacol 2021; 99:226-241. [PMID: 33446509 DOI: 10.1124/molpharm.120.000173] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 12/28/2020] [Indexed: 01/17/2023] Open
Abstract
An essential function of DNA topoisomerase IIα (TOP2α; 170 kDa, TOP2α/170) is to resolve DNA topologic entanglements during chromosome disjunction by introducing transient DNA double-stranded breaks. TOP2α/170 is an important target for DNA damage-stabilizing anticancer drugs, whose clinical efficacy is compromised by drug resistance often associated with decreased TOP2α/170 expression. We recently demonstrated that an etoposide-resistant K562 clonal subline, K/VP.5, with reduced levels of TOP2α/170, expresses high levels of a novel C-terminal truncated TOP2α isoform (90 kDa, TOP2α/90). TOP2α/90, the translation product of a TOP2α mRNA that retains a processed intron 19 (I19), heterodimerizes with TOP2α/170 and is a resistance determinant through a dominant-negative effect on drug activity. We hypothesized that genome editing to enhance I19 removal would provide a tractable strategy to circumvent acquired TOP2α-mediated drug resistance. To enhance I19 removal in K/VP.5 cells, CRISPR/Cas9 was used to make changes (GAG//GTAA AC →GAG//GTAA GT ) in the TOP2α gene's suboptimal exon 19/intron 19 5' splice site (E19/I19 5' SS). Gene-edited clones were identified by quantitative polymerase chain reaction and verified by sequencing. Characterization of a clone with all TOP2α alleles edited revealed improved I19 removal, decreased TOP2α/90 mRNA/protein, and increased TOP2α/170 mRNA/protein. Sensitivity to etoposide-induced DNA damage (γH2AX, Comet assays) and growth inhibition was restored to levels comparable to those in parental K562 cells. Together, the results indicate that our gene-editing strategy for optimizing the TOP2α E19/I19 5' SS in K/VP.5 cells circumvents resistance to etoposide and other TOP2α-targeted drugs. SIGNIFICANCE STATEMENT: Results presented here indicate that CRISPR/Cas9 gene editing of a suboptimal exon 19/intron 19 5' splice site in the DNA topoisomerase IIα (TOP2α) gene results in circumvention of acquired drug resistance to etoposide and other TOP2α-targeted drugs in a clonal K562 cell line by enhancing removal of intron 19 and thereby decreasing formation of a truncated TOP2α 90 kDa isoform and increasing expression of full-length TOP2α 170 kDa in these resistant cells. Results demonstrate the importance of RNA processing in acquired drug resistance to TOP2α-targeted drugs.
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Affiliation(s)
- Victor A Hernandez
- Division of Pharmaceutics and Pharmacology, College of Pharmacy (V.A.H., J.C.-M., J.L.P., J.L., J.C.Y., T.S.E., N.S.) and Department of Biomedical Informatics, College of Medicine (H.G.O), The Ohio State University, Columbus, Ohio
| | - Jessika Carvajal-Moreno
- Division of Pharmaceutics and Pharmacology, College of Pharmacy (V.A.H., J.C.-M., J.L.P., J.L., J.C.Y., T.S.E., N.S.) and Department of Biomedical Informatics, College of Medicine (H.G.O), The Ohio State University, Columbus, Ohio
| | - Jonathan L Papa
- Division of Pharmaceutics and Pharmacology, College of Pharmacy (V.A.H., J.C.-M., J.L.P., J.L., J.C.Y., T.S.E., N.S.) and Department of Biomedical Informatics, College of Medicine (H.G.O), The Ohio State University, Columbus, Ohio
| | - Nicholas Shkolnikov
- Division of Pharmaceutics and Pharmacology, College of Pharmacy (V.A.H., J.C.-M., J.L.P., J.L., J.C.Y., T.S.E., N.S.) and Department of Biomedical Informatics, College of Medicine (H.G.O), The Ohio State University, Columbus, Ohio
| | - Junan Li
- Division of Pharmaceutics and Pharmacology, College of Pharmacy (V.A.H., J.C.-M., J.L.P., J.L., J.C.Y., T.S.E., N.S.) and Department of Biomedical Informatics, College of Medicine (H.G.O), The Ohio State University, Columbus, Ohio
| | - Hatice Gulcin Ozer
- Division of Pharmaceutics and Pharmacology, College of Pharmacy (V.A.H., J.C.-M., J.L.P., J.L., J.C.Y., T.S.E., N.S.) and Department of Biomedical Informatics, College of Medicine (H.G.O), The Ohio State University, Columbus, Ohio
| | - Jack C Yalowich
- Division of Pharmaceutics and Pharmacology, College of Pharmacy (V.A.H., J.C.-M., J.L.P., J.L., J.C.Y., T.S.E., N.S.) and Department of Biomedical Informatics, College of Medicine (H.G.O), The Ohio State University, Columbus, Ohio
| | - Terry S Elton
- Division of Pharmaceutics and Pharmacology, College of Pharmacy (V.A.H., J.C.-M., J.L.P., J.L., J.C.Y., T.S.E., N.S.) and Department of Biomedical Informatics, College of Medicine (H.G.O), The Ohio State University, Columbus, Ohio
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46
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Danner E, Lebedin M, de la Rosa K, Kühn R. A homology independent sequence replacement strategy in human cells using a CRISPR nuclease. Open Biol 2021; 11:200283. [PMID: 33499763 PMCID: PMC7881171 DOI: 10.1098/rsob.200283] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 11/30/2020] [Indexed: 01/01/2023] Open
Abstract
Precision genomic alterations largely rely on homology directed repair (HDR), but targeting without homology using the non-homologous end-joining (NHEJ) pathway has gained attention as a promising alternative. Previous studies demonstrated precise insertions formed by the ligation of donor DNA into a targeted genomic double-strand break in both dividing and non-dividing cells. Here, we demonstrate the use of NHEJ repair to replace genomic segments with donor sequences; we name this method 'Replace' editing (Rational end-joining protocol delivering a targeted sequence exchange). Using CRISPR/Cas9, we create two genomic breaks and ligate a donor sequence in-between. This exchange of a genomic for a donor sequence uses neither microhomology nor homology arms. We target four loci in cell lines and show successful exchange of exons in 16-54% of human cells. Using linear amplification methods and deep sequencing, we quantify the diversity of outcomes following Replace editing and profile the ligated interfaces. The ability to replace exons or other genomic sequences in cells not efficiently modified by HDR holds promise for both basic research and medicine.
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Affiliation(s)
- Eric Danner
- Max Delbrück Center for Molecular Medicine of the Helmholtz Association, Berlin, Germany
| | | | | | - Ralf Kühn
- Max Delbrück Center for Molecular Medicine of the Helmholtz Association, Berlin, Germany
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47
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Reduced thermal tolerance in a coral carrying CRISPR-induced mutations in the gene for a heat-shock transcription factor. Proc Natl Acad Sci U S A 2020; 117:28899-28905. [PMID: 33168726 DOI: 10.1073/pnas.1920779117] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Reef-building corals are keystone species that are threatened by anthropogenic stresses including climate change. To investigate corals' responses to stress and other aspects of their biology, numerous genomic and transcriptomic studies have been performed, generating many hypotheses about the roles of particular genes and molecular pathways. However, it has not generally been possible to test these hypotheses rigorously because of the lack of genetic tools for corals or closely related cnidarians. CRISPR technology seems likely to alleviate this problem. Indeed, we show here that microinjection of single-guide RNA/Cas9 ribonucleoprotein complexes into fertilized eggs of the coral Acropora millepora can produce a sufficiently high frequency of mutations to detect a clear phenotype in the injected generation. Based in part on experiments in a sea-anemone model system, we targeted the gene encoding Heat Shock Transcription Factor 1 (HSF1) and obtained larvae in which >90% of the gene copies were mutant. The mutant larvae survived well at 27 °C but died rapidly at 34 °C, a temperature that did not produce detectable mortality over the duration of the experiment in wild-type (WT) larvae or larvae injected with Cas9 alone. We conclude that HSF1 function (presumably its induction of genes in response to heat stress) plays an important protective role in corals. More broadly, we conclude that CRISPR mutagenesis in corals should allow wide-ranging and rigorous tests of gene function in both larval and adult corals.
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48
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Wu Y, Yang Y, Gu H, Tao B, Zhang E, Wei J, Wang Z, Liu A, Sun R, Chen M, Fan Y, Mao R. Multi-omics analysis reveals the functional transcription and potential translation of enhancers. Int J Cancer 2020; 147:2210-2224. [PMID: 32573785 DOI: 10.1002/ijc.33132] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 04/22/2020] [Accepted: 05/19/2020] [Indexed: 12/23/2022]
Abstract
Enhancer can transcribe RNAs, however, most of them were neglected in traditional RNA-seq analysis workflow. Here, we developed a Pipeline for Enhancer Transcription (PET, http://fun-science.club/PET) for quantifying enhancer RNAs (eRNAs) from RNA-seq. By applying this pipeline on lung cancer samples and cell lines, we showed that the transcribed enhancers are enriched with histone marks and transcription factor motifs (JUNB, Hand1-Tcf3 and GATA4). By training a machine learning model, we demonstrate that enhancers can predict prognosis better than their nearby genes. Integrating the Hi-C, ChIP-seq and RNA-seq data, we observe that transcribed enhancers associate with cancer hallmarks or oncogenes, among which LcsMYC-1 (Lung cancer-specific MYC eRNA-1) potentially supports MYC expression. Surprisingly, a significant proportion of transcribed enhancers contain small protein-coding open reading frames (sORFs) and can be translated into microproteins. Our study provides a computational method for eRNA quantification and deepens our understandings of the DNA, RNA and protein nature of enhancers.
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Affiliation(s)
- Yingcheng Wu
- Laboratory of Medical Science, School of Medicine, Nantong University, Nantong, Jiangsu, China.,Department of Pathophysiology, School of Medicine, Nantong University, Nantong, Jiangsu, China
| | - Yang Yang
- Department of Thoracic Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Hongyan Gu
- Department of Respiratory Medicine, Nantong Sixth People's Hospital, Nantong, Jiangsu, China
| | - Baorui Tao
- Laboratory of Medical Science, School of Medicine, Nantong University, Nantong, Jiangsu, China
| | - Erhao Zhang
- Laboratory of Medical Science, School of Medicine, Nantong University, Nantong, Jiangsu, China
| | - Jinhuan Wei
- Laboratory of Medical Science, School of Medicine, Nantong University, Nantong, Jiangsu, China
| | - Zhou Wang
- School of Life Sciences, Nantong University, Nantong, Jiangsu, China
| | - Aifen Liu
- Laboratory of Medical Science, School of Medicine, Nantong University, Nantong, Jiangsu, China
| | - Rong Sun
- Laboratory of Medical Science, School of Medicine, Nantong University, Nantong, Jiangsu, China
| | - Miaomiao Chen
- Laboratory of Medical Science, School of Medicine, Nantong University, Nantong, Jiangsu, China
| | - Yihui Fan
- Laboratory of Medical Science, School of Medicine, Nantong University, Nantong, Jiangsu, China.,Department of Pathogenic Biology, School of Medicine, Nantong University, Nantong, Jiangsu, China
| | - Renfang Mao
- Laboratory of Medical Science, School of Medicine, Nantong University, Nantong, Jiangsu, China.,Department of Pathophysiology, School of Medicine, Nantong University, Nantong, Jiangsu, China
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49
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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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50
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Berger E, Yorukoglu D, Zhang L, Nyquist SK, Shalek AK, Kellis M, Numanagić I, Berger B. Improved haplotype inference by exploiting long-range linking and allelic imbalance in RNA-seq datasets. Nat Commun 2020; 11:4662. [PMID: 32938926 PMCID: PMC7494856 DOI: 10.1038/s41467-020-18320-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 08/07/2020] [Indexed: 01/04/2023] Open
Abstract
Haplotype reconstruction of distant genetic variants remains an unsolved problem due to the short-read length of common sequencing data. Here, we introduce HapTree-X, a probabilistic framework that utilizes latent long-range information to reconstruct unspecified haplotypes in diploid and polyploid organisms. It introduces the observation that differential allele-specific expression can link genetic variants from the same physical chromosome, thus even enabling using reads that cover only individual variants. We demonstrate HapTree-X's feasibility on in-house sequenced Genome in a Bottle RNA-seq and various whole exome, genome, and 10X Genomics datasets. HapTree-X produces more complete phases (up to 25%), even in clinically important genes, and phases more variants than other methods while maintaining similar or higher accuracy and being up to 10× faster than other tools. The advantage of HapTree-X's ability to use multiple lines of evidence, as well as to phase polyploid genomes in a single integrative framework, substantially grows as the amount of diverse data increases.
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Affiliation(s)
- Emily Berger
- Computer Science & Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Mathematics, UC Berkeley, Berkeley, CA, 94720, USA
| | - Deniz Yorukoglu
- Computer Science & Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Lillian Zhang
- Computer Science & Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Sarah K Nyquist
- Computer Science & Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Alex K Shalek
- Computer Science & Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Manolis Kellis
- Computer Science & Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Ibrahim Numanagić
- Computer Science & Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Department of Computer Science, University of Victoria, Victoria, BC, V8P 5C2, Canada.
| | - Bonnie Berger
- Computer Science & Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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