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Ji W, Guo X, Pan S, Long F, Ho TY, Schlichtmann U, Yao H. GNN-Based Concentration Prediction With Variable Input Flow Rates for Microfluidic Mixers. IEEE TRANSACTIONS ON BIOMEDICAL CIRCUITS AND SYSTEMS 2024; 18:622-635. [PMID: 38393851 DOI: 10.1109/tbcas.2024.3366691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
Recent years have witnessed significant advances brought by microfluidic biochips in automating biochemical protocols. Accurate preparation of fluid samples is an essential component of these protocols, where concentration prediction and generation are critical. Equipped with the advantages of convenient fabrication and control, microfluidic mixers demonstrate huge potential in sample preparation. Although finite element analysis (FEA) is the most commonly used simulation method for accurate concentration prediction of a given microfluidic mixer, it is time-consuming with poor scalability for large biochip sizes. Recently, machine learning models have been adopted in concentration prediction, with great potential in enhancing the efficiency over traditional FEA methods. However, the state-of-the-art machine learning-based method can only predict the concentration of mixers with fixed input flow rates and fixed sizes. In this paper, we propose a new concentration prediction method based on graph neural networks (GNNs), which can predict output concentrations for microfluidic mixters with variable input flow rates. Moreover, a transfer learning method is proposed to transfer the trained model to mixers of different sizes with reduced training data. Experimental results show that, for microfluidic mixers with fixed input flow rates, the proposed method obtains an average reduction of 88% in terms of prediction errors compared with the state-of-the-art method. For microfluidic mixers with variable input flow rates, the proposed method reduces the prediction error by 85% on average. Besides, the proposed transfer learning method reduces the training data by 84% for extending the pre-trained model for microfluidic mixers of different sizes with acceptable prediction error.
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Zhang W, Sun S, Wang Q, Li X, Xu M, Li Q, Zhao Y, Peng K, Yao C, Wang Y, Chang Y, Liu Y, Wu X, Gao Q, Shuai L. Haploid-genetic screening of trophectoderm specification identifies Dyrk1a as a repressor of totipotent-like status. SCIENCE ADVANCES 2023; 9:eadi5683. [PMID: 38117886 PMCID: PMC10732524 DOI: 10.1126/sciadv.adi5683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 11/17/2023] [Indexed: 12/22/2023]
Abstract
Trophectoderm (TE) and the inner cell mass are the first two lineages in murine embryogenesis and cannot naturally transit to each other. The barriers between them are unclear and fascinating. Embryonic stem cells (ESCs) and trophoblast stem cells (TSCs) retain the identities of inner cell mass and TE, respectively, and, thus, are ideal platforms to investigate these lineages in vitro. Here, we develop a loss-of-function genetic screening in haploid ESCs and reveal many mutations involved in the conversion of TSCs. The disruption of either Catip or Dyrk1a (candidates) in ESCs facilitates the conversion of TSCs. According to transcriptome analysis, we find that the repression of Dyrk1a activates totipotency, which is a possible reason for TE specification. Dyrk1a-null ESCs can contribute to embryonic and extraembryonic tissues in chimeras and can efficiently form blastocyst-like structures, indicating their totipotent developmental abilities. These findings provide insights into the mechanisms underlying cell fate alternation in embryogenesis.
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Affiliation(s)
- Wenhao Zhang
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy and Tianjin Central Hospital of Gynecology Obstetrics/Tianjin Key Laboratory of Human Development and Reproductive Regulation, Nankai University, Tianjin 300350, China
| | - Shengyi Sun
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy and Tianjin Central Hospital of Gynecology Obstetrics/Tianjin Key Laboratory of Human Development and Reproductive Regulation, Nankai University, Tianjin 300350, China
| | - Qing Wang
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy and Tianjin Central Hospital of Gynecology Obstetrics/Tianjin Key Laboratory of Human Development and Reproductive Regulation, Nankai University, Tianjin 300350, China
| | - Xu Li
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy and Tianjin Central Hospital of Gynecology Obstetrics/Tianjin Key Laboratory of Human Development and Reproductive Regulation, Nankai University, Tianjin 300350, China
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Mei Xu
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy and Tianjin Central Hospital of Gynecology Obstetrics/Tianjin Key Laboratory of Human Development and Reproductive Regulation, Nankai University, Tianjin 300350, China
| | - Qian Li
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Department of Cell Biology, Tianjin Medical University, Tianjin 300070, China
| | - Yiding Zhao
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy and Tianjin Central Hospital of Gynecology Obstetrics/Tianjin Key Laboratory of Human Development and Reproductive Regulation, Nankai University, Tianjin 300350, China
| | - Keli Peng
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy and Tianjin Central Hospital of Gynecology Obstetrics/Tianjin Key Laboratory of Human Development and Reproductive Regulation, Nankai University, Tianjin 300350, China
| | - Chunmeng Yao
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy and Tianjin Central Hospital of Gynecology Obstetrics/Tianjin Key Laboratory of Human Development and Reproductive Regulation, Nankai University, Tianjin 300350, China
| | - Yuna Wang
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy and Tianjin Central Hospital of Gynecology Obstetrics/Tianjin Key Laboratory of Human Development and Reproductive Regulation, Nankai University, Tianjin 300350, China
| | - Ying Chang
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy and Tianjin Central Hospital of Gynecology Obstetrics/Tianjin Key Laboratory of Human Development and Reproductive Regulation, Nankai University, Tianjin 300350, China
| | - Yan Liu
- Department of Obstetrics, Tianjin First Central Hospital, Nankai University, Tianjin 300192, China
| | - Xudong Wu
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Department of Cell Biology, Tianjin Medical University, Tianjin 300070, China
| | - Qian Gao
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy and Tianjin Central Hospital of Gynecology Obstetrics/Tianjin Key Laboratory of Human Development and Reproductive Regulation, Nankai University, Tianjin 300350, China
| | - Ling Shuai
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy and Tianjin Central Hospital of Gynecology Obstetrics/Tianjin Key Laboratory of Human Development and Reproductive Regulation, Nankai University, Tianjin 300350, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
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Komatsu V, Cooper B, Yim P, Chan K, Gong W, Wheatley L, Rohs R, Fraser SE, Trinh LA. Hand2 represses non-cardiac cell fates through chromatin remodeling at cis- regulatory elements. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.23.559156. [PMID: 37790542 PMCID: PMC10542161 DOI: 10.1101/2023.09.23.559156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Developmental studies have revealed the importance of the transcription factor Hand2 in cardiac development. Hand2 promotes cardiac progenitor differentiation and epithelial maturation, while repressing other tissue types. The mechanisms underlying the promotion of cardiac fates are far better understood than those underlying the repression of alternative fates. Here, we assess Hand2-dependent changes in gene expression and chromatin remodeling in cardiac progenitors of zebrafish embryos. Cell-type specific transcriptome analysis shows a dual function for Hand2 in activation of cardiac differentiation genes and repression of pronephric pathways. We identify functional cis- regulatory elements whose chromatin accessibility are increased in hand2 mutant cells. These regulatory elements associate with non-cardiac gene expression, and drive reporter gene expression in tissues associated with Hand2-repressed genes. We find that functional Hand2 is sufficient to reduce non-cardiac reporter expression in cardiac lineages. Taken together, our data support a model of Hand2-dependent coordination of transcriptional programs, not only through transcriptional activation of cardiac and epithelial maturation genes, but also through repressive chromatin remodeling at the DNA regulatory elements of non-cardiac genes.
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Wang HS, Ma XR, Niu WB, Shi H, Liu YD, Ma NZ, Zhang N, Jiang ZW, Sun YP. Generation of a human haploid neural stem cell line for genome-wide genetic screening. World J Stem Cells 2023; 15:734-750. [PMID: 37545755 PMCID: PMC10401418 DOI: 10.4252/wjsc.v15.i7.734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 06/01/2023] [Accepted: 06/21/2023] [Indexed: 07/25/2023] Open
Abstract
BACKGROUND Haploid embryonic stem cells (haESCs) have been established in many species. Differentiated haploid cell line types in mammals are lacking due to spontaneous diploidization during differentiation that compromises lineage-specific screens.
AIM To derive human haploid neural stem cells (haNSCs) to carry out lineage-specific screens.
METHODS Human haNSCs were differentiated from human extended haESCs with the help of Y27632 (ROCK signaling pathway inhibitor) and a series of cytokines to reduce diploidization. Neuronal differentiation of haNSCs was performed to examine their neural differentiation potency. Global gene expression analysis was con-ducted to compare haNSCs with diploid NSCs and haESCs. Fluorescence activated cell sorting was performed to assess the diploidization rate of extended haESCs and haNSCs. Genetic manipulation and screening were utilized to evaluate the significance of human haNSCs as genetic screening tools.
RESULTS Human haESCs in extended pluripotent culture medium showed more compact and smaller colonies, a higher efficiency in neural differentiation, a higher cell survival ratio and higher stability in haploidy maintenance. These characteristics effectively facilitated the derivation of human haNSCs. These human haNSCs can be generated by differentiation and maintain haploidy and multipotency to neurons and glia in the long term in vitro. After PiggyBac transfection, there were multiple insertion sites in the human haNSCs’ genome, and the insertion sites were evenly spread across all chromosomes. In addition, after the cells were treated with manganese, we were able to generate a list of manganese-induced toxicity genes, demonstrating their utility as genetic screening tools.
CONCLUSION This is the first report of a generated human haploid somatic cell line with a complete genome, proliferative ability and neural differentiation potential that provides cell resources for recessive inheritance and drug targeted screening.
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Affiliation(s)
- Hai-Song Wang
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450052, Henan Province, China
| | - Xin-Rui Ma
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450052, Henan Province, China
| | - Wen-Bin Niu
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450052, Henan Province, China
| | - Hao Shi
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450052, Henan Province, China
| | - Yi-Dong Liu
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450052, Henan Province, China
| | - Ning-Zhao Ma
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450052, Henan Province, China
| | - Nan Zhang
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450052, Henan Province, China
| | - Zi-Wei Jiang
- Basic Medical School, Zhengzhou University, Zhengzhou 450052, Henan Province, China
| | - Ying-Pu Sun
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450052, Henan Province, China
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Cao F, Jiang Y, Chang L, Du H, Chang D, Pan C, Huang X, Yu D, Zhang M, Fan Y, Bian X, Li K. High-throughput functional screen identifies YWHAZ as a key regulator of pancreatic cancer metastasis. Cell Death Dis 2023; 14:431. [PMID: 37452033 PMCID: PMC10349114 DOI: 10.1038/s41419-023-05951-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 06/27/2023] [Accepted: 07/05/2023] [Indexed: 07/18/2023]
Abstract
Pancreatic cancer is a leading cause of cancer death due to its early metastasis and limited response to the current therapies. Metastasis is a complicated multistep process, which is determined by complex genetic alterations. Despite the identification of many metastasis-related genes, distinguishing the drivers from numerous passengers and establishing the causality in cancer pathophysiology remains challenging. Here, we established a high-throughput and piggyBac transposon-based genetic screening platform, which enables either reduced or increased expression of chromosomal genes near the incorporation site of the gene search vector cassette that contains a doxycycline-regulated promoter. Using this strategy, we identified YWHAZ as a key regulator of pancreatic cancer metastasis. We demonstrated that functional activation of Ywhaz by the gene search vector led to enhanced metastatic capability in mouse pancreatic cancer cells. The metastasis-promoting role of YWHAZ was further validated in human pancreatic cancer cells. Overexpression of YWHAZ resulted in more aggressive metastatic phenotypes in vitro and a shorter survival rate in vivo by modulating epithelial-to-mesenchymal transition. Hence, our study established a high-throughput screening method to investigate the functional relevance of novel genes and validated YWHAZ as a key regulator of pancreatic cancer metastasis.
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Affiliation(s)
- Fang Cao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Pathology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Yunpeng Jiang
- Department of Biochemistry and Biophysics, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Lin Chang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Endoscopy Center, Peking University Cancer Hospital & Institute, Beijing, China
- Department of Pathology, Cell Resource Center, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & School of Basic Medicine, Peking Union Medical College (PUMC), Beijing, China
| | - Hongzhen Du
- Department of Pathology, Cell Resource Center, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & School of Basic Medicine, Peking Union Medical College (PUMC), Beijing, China
| | - De Chang
- Department of Pulmonary and Critical Care Medicine, 7th Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Chunxiao Pan
- Department of Pathology, Cell Resource Center, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & School of Basic Medicine, Peking Union Medical College (PUMC), Beijing, China
| | - Xiaozheng Huang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Pathology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Donglin Yu
- Department of Biochemistry and Biophysics, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Mi Zhang
- Department of Pulmonary and Critical Care Medicine, 7th Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Yongna Fan
- Department of Pathology, Cell Resource Center, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & School of Basic Medicine, Peking Union Medical College (PUMC), Beijing, China
| | - Xiaocui Bian
- Department of Pathology, Cell Resource Center, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & School of Basic Medicine, Peking Union Medical College (PUMC), Beijing, China.
| | - Kailong Li
- Department of Biochemistry and Biophysics, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.
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6
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Han HJ, Kim DH, Baik JY. A splinkerette PCR-based genome walking technique for the identification of transgene integration sites in CHO cells. J Biotechnol 2023:S0168-1656(23)00105-0. [PMID: 37257509 DOI: 10.1016/j.jbiotec.2023.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 05/02/2023] [Accepted: 05/28/2023] [Indexed: 06/02/2023]
Abstract
Identification of recombinant gene integrations sites in the Chinese hamster ovary (CHO) cell genome is increasingly important to assure monoclonality. While next-generation sequencing (NGS) is commonly used for the gene integration site analysis, it is a time-consuming and costly technique as it analyzes the entire genome. Hence, simple, easy, and inexpensive methods to analyze transgene insertion sites are necessary. To selectively capture the integration site of transgene in the CHO genome, we applied splinkerette-PCR (spPCR). SpPCR is an adaptor ligation-based method using splinkerette adaptors that have a stable hairpin loop. Restriction enzymes with high frequencies in the CHO genome were chosen using a Python script and used for the in vitro spPCR assay development. After testing on two CHO housekeeping genes with known loci, the spPCR-based genome walking technique was successfully applied to recombinant CHO cells to identify the transgene integration site. Finally, the comparison with NGS methods exhibited that the time and cost required for the analysis can be substantially reduced. Taken together, the established technique would aid the stable cell line development process by providing a rapid and cost-effective method for transgene integration site analysis.
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Affiliation(s)
- Hye-Jin Han
- Department of Biological Sciences and Bioengineering, Inha University, Incheon22212, Republic of Korea
| | - Dae Hoon Kim
- Department of Biological Sciences and Bioengineering, Inha University, Incheon22212, Republic of Korea
| | - Jong Youn Baik
- Department of Biological Sciences and Bioengineering, Inha University, Incheon22212, Republic of Korea.
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7
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Wang P, Kitano M, Keomanee-Dizon K, Truong TV, Fraser SE, Cutrale F. A single-shot hyperspectral phasor camera for fast, multi-color fluorescence microscopy. CELL REPORTS METHODS 2023; 3:100441. [PMID: 37159674 PMCID: PMC10162951 DOI: 10.1016/j.crmeth.2023.100441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 11/16/2022] [Accepted: 03/09/2023] [Indexed: 05/11/2023]
Abstract
Hyperspectral fluorescence imaging improves multiplexed observations of biological samples by utilizing multiple color channels across the spectral range to compensate for spectral overlap between labels. Typically, spectral resolution comes at a cost of decreased detection efficiency, which both hampers imaging speed and increases photo-toxicity to the samples. Here, we present a high-speed, high-efficiency snapshot spectral acquisition method, based on optical compression of the fluorescence spectra via Fourier transform, that overcomes the challenges of discrete spectral sampling: single-shot hyperspectral phasor camera (SHy-Cam). SHy-Cam captures fluorescence spatial and spectral information in a single exposure with a standard scientific CMOS camera, with photon efficiency of over 80%, easily and with acquisition rates exceeding 30 datasets per second, making it a powerful tool for multi-color in vivo imaging. Its simple design, using readily available optical components, and its easy integration provide a low-cost solution for multi-color fluorescence imaging with increased efficiency and speed.
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Affiliation(s)
- Pu Wang
- Translational Imaging Center, University of Southern California, 1002 West Childs Way, Los Angeles, CA 90089, USA
- Biomedical Engineering, University of Southern California, 1002 West Childs Way, Los Angeles, CA 90089, USA
| | - Masahiro Kitano
- Translational Imaging Center, University of Southern California, 1002 West Childs Way, Los Angeles, CA 90089, USA
- Molecular and Computational Biology, University of Southern California, 1002 West Childs Way, Los Angeles, CA 90089, USA
| | - Kevin Keomanee-Dizon
- Translational Imaging Center, University of Southern California, 1002 West Childs Way, Los Angeles, CA 90089, USA
- Joseph Henry Laboratories of Physics, Princeton University, Princeton, NJ 08544, USA
| | - Thai V. Truong
- Translational Imaging Center, University of Southern California, 1002 West Childs Way, Los Angeles, CA 90089, USA
- Molecular and Computational Biology, University of Southern California, 1002 West Childs Way, Los Angeles, CA 90089, USA
| | - Scott E. Fraser
- Translational Imaging Center, University of Southern California, 1002 West Childs Way, Los Angeles, CA 90089, USA
- Biomedical Engineering, University of Southern California, 1002 West Childs Way, Los Angeles, CA 90089, USA
- Molecular and Computational Biology, University of Southern California, 1002 West Childs Way, Los Angeles, CA 90089, USA
| | - Francesco Cutrale
- Translational Imaging Center, University of Southern California, 1002 West Childs Way, Los Angeles, CA 90089, USA
- Biomedical Engineering, University of Southern California, 1002 West Childs Way, Los Angeles, CA 90089, USA
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8
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Vaishnavi A, Juan J, Jacob M, Stehn C, Gardner EE, Scherzer MT, Schuman S, Van Veen JE, Murphy B, Hackett CS, Dupuy AJ, Chmura SA, van der Weyden L, Newberg JY, Liu A, Mann K, Rust AG, Weiss WA, Kinsey CG, Adams DJ, Grossmann A, Mann MB, McMahon M. Transposon Mutagenesis Reveals RBMS3 Silencing as a Promoter of Malignant Progression of BRAFV600E-Driven Lung Tumorigenesis. Cancer Res 2022; 82:4261-4273. [PMID: 36112789 PMCID: PMC9664136 DOI: 10.1158/0008-5472.can-21-3214] [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: 09/22/2021] [Revised: 06/29/2022] [Accepted: 09/13/2022] [Indexed: 01/09/2023]
Abstract
Mutationally activated BRAF is detected in approximately 7% of human lung adenocarcinomas, with BRAFT1799A serving as a predictive biomarker for treatment of patients with FDA-approved inhibitors of BRAFV600E oncoprotein signaling. In genetically engineered mouse (GEM) models, expression of BRAFV600E in the lung epithelium initiates growth of benign lung tumors that, without additional genetic alterations, rarely progress to malignant lung adenocarcinoma. To identify genes that cooperate with BRAFV600E for malignant progression, we used Sleeping Beauty-mediated transposon mutagenesis, which dramatically accelerated the emergence of lethal lung cancers. Among the genes identified was Rbms3, which encodes an RNA-binding protein previously implicated as a putative tumor suppressor. Silencing of RBMS3 via CRISPR/Cas9 gene editing promoted growth of BRAFV600E lung organoids and promoted development of malignant lung cancers with a distinct micropapillary architecture in BRAFV600E and EGFRL858R GEM models. BRAFV600E/RBMS3Null lung tumors displayed elevated expression of Ctnnb1, Ccnd1, Axin2, Lgr5, and c-Myc mRNAs, suggesting that RBMS3 silencing elevates signaling through the WNT/β-catenin signaling axis. Although RBMS3 silencing rendered BRAFV600E-driven lung tumors resistant to the effects of dabrafenib plus trametinib, the tumors were sensitive to inhibition of porcupine, an acyltransferase of WNT ligands necessary for their secretion. Analysis of The Cancer Genome Atlas patient samples revealed that chromosome 3p24, which encompasses RBMS3, is frequently lost in non-small cell lung cancer and correlates with poor prognosis. Collectively, these data reveal the role of RBMS3 as a lung cancer suppressor and suggest that RBMS3 silencing may contribute to malignant NSCLC progression. SIGNIFICANCE Loss of RBMS3 cooperates with BRAFV600E to induce lung tumorigenesis, providing a deeper understanding of the molecular mechanisms underlying mutant BRAF-driven lung cancer and potential strategies to more effectively target this disease.
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Affiliation(s)
- Aria Vaishnavi
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Joseph Juan
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Maebh Jacob
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | | | - Eric E. Gardner
- Meyer Cancer Center, Weill Cornell Medicine, New York City, New York
- Palo Alto Wellness, Menlo Park, California
| | - Michael T. Scherzer
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
- Department of Oncological Sciences, University of Utah, Salt Lake City, Utah
| | - Sophia Schuman
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - J. Edward Van Veen
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Brandon Murphy
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Christopher S. Hackett
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Adam J. Dupuy
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, Iowa
| | - Steven A. Chmura
- Meyer Cancer Center, Weill Cornell Medicine, New York City, New York
- Palo Alto Wellness, Menlo Park, California
| | - Louise van der Weyden
- Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Justin Y. Newberg
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, Florida
| | - Annie Liu
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Karen Mann
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, Florida
| | - Alistair G. Rust
- Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - William A. Weiss
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
- Department of Neurology, University of California, San Francisco, California
- Department of Dermatology, University of Utah, Salt Lake City, Utah
- Department of Pediatrics, University of California, San Francisco, California
- Department of Neurological Surgery, University of California, San Francisco, California
| | - Conan G. Kinsey
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
- Department of Internal Medicine, University of Utah, Salt Lake City, Utah
| | - David J. Adams
- Department of Dermatology, University of Utah, Salt Lake City, Utah
- Department of Pediatrics, University of California, San Francisco, California
| | - Allie Grossmann
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
- Department of Pathology, University of Utah, Salt Lake City, Utah
| | - Michael B. Mann
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, Florida
| | - Martin McMahon
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
- Department of Oncological Sciences, University of Utah, Salt Lake City, Utah
- Department of Dermatology, University of Utah, Salt Lake City, Utah
- Department of Pediatrics, University of California, San Francisco, California
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California
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9
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Proviral ALV-LTR Sequence Is Essential for Continued Proliferation of the ALV-Transformed B Cell Line. Int J Mol Sci 2022; 23:ijms231911263. [PMID: 36232572 PMCID: PMC9569804 DOI: 10.3390/ijms231911263] [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: 05/23/2022] [Revised: 08/30/2022] [Accepted: 09/14/2022] [Indexed: 11/25/2022] Open
Abstract
Avian leukosis virus (ALV) induces B-cell lymphomas and other malignancies in chickens through insertional activation of oncogenes, and c-myc activation has been commonly identified in ALV-induced tumors. Using ALV-transformed B-lymphoma-derived HP45 cell line, we applied in situ CRISPR-Cas9 editing of integrated proviral long terminal repeat (LTR) to examine the effects on gene expression and cell proliferation. Targeted deletion of LTR resulted in significant reduction in expression of a number of LTR-regulated genes including c-myc. LTR deletion also induced apoptosis of HP45 cells, affecting their proliferation, demonstrating the significance of LTR-mediated regulation of critical genes. Compared to the global effects on expression and functions of multiple genes in LTR-deleted cells, deletion of c-myc had a major effect on the HP45 cells proliferation with the phenotype similar to the LTR deletion, demonstrating the significance of c-myc expression in ALV-induced lymphomagenesis. Overall, our studies have not only shown the potential of targeted editing of the LTR for the global inhibition of retrovirus-induced transformation, but also have provided insights into the roles of LTR-regulated genes in ALV-induced neoplastic transformation.
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10
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Nonlinear control of transcription through enhancer-promoter interactions. Nature 2022; 604:571-577. [PMID: 35418676 PMCID: PMC9021019 DOI: 10.1038/s41586-022-04570-y] [Citation(s) in RCA: 153] [Impact Index Per Article: 76.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 02/21/2022] [Indexed: 12/19/2022]
Abstract
Chromosome structure in mammals is thought to regulate transcription by modulating three-dimensional interactions between enhancers and promoters, notably through CTCF-mediated loops and topologically associating domains (TADs)1–4. However, how chromosome interactions are actually translated into transcriptional outputs remains unclear. Here, to address this question, we use an assay to position an enhancer at large numbers of densely spaced chromosomal locations relative to a fixed promoter, and measure promoter output and interactions within a genomic region with minimal regulatory and structural complexity. A quantitative analysis of hundreds of cell lines reveals that the transcriptional effect of an enhancer depends on its contact probabilities with the promoter through a nonlinear relationship. Mathematical modelling suggests that nonlinearity might arise from transient enhancer–promoter interactions being translated into slower promoter bursting dynamics in individual cells, therefore uncoupling the temporal dynamics of interactions from those of transcription. This uncovers a potential mechanism of how distal enhancers act from large genomic distances, and of how topologically associating domain boundaries block distal enhancers. Finally, we show that enhancer strength also determines absolute transcription levels as well as the sensitivity of a promoter to CTCF-mediated transcriptional insulation. Our measurements establish general principles for the context-dependent role of chromosome structure in long-range transcriptional regulation. The transcriptional effect of an enhancer depends on its contact probabilities with the promoter through a nonlinear relationship, and enhancer strength determines absolute transcription levels as well as the sensitivity of a promoter to CTCF-mediated transcriptional insulation.
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11
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Genome-wide screening in the haploid system reveals Slc25a43 as a target gene of oxidative toxicity. Cell Death Dis 2022; 13:284. [PMID: 35354792 PMCID: PMC8967898 DOI: 10.1038/s41419-022-04738-4] [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: 10/23/2021] [Revised: 03/02/2022] [Accepted: 03/15/2022] [Indexed: 11/23/2022]
Abstract
Reactive oxygen species (ROS) are extensively assessed in physiological and pathological studies; however, the genes and mechanisms involved in antioxidant reactions are elusive. To address this knowledge gap, we used a forward genetic approach with mouse haploid embryonic stem cells (haESCs) to generate high-throughput mutant libraries, from which numerous oxidative stress-targeting genes were screened out. We performed proof-of-concept experiments to validate the potential inserted genes. Slc25a43 (one of the candidates) knockout (KO) ESCs presented reduced damage caused by ROS and higher cell viability when exposed to H2O2. Subsequently, ROS production and mitochondrial function analysis also confirmed that Slc25a43 was a main target gene of oxidative toxicity. In addition, we identified that KO of Slc25a43 activated mitochondria-related genes including Nlrx1 to protect ESCs from oxidative damage. Overall, our findings facilitated revealing target genes of oxidative stress and shed lights on the mechanism underlying oxidative death.
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12
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Reavey CE, Walker AS, Joyce SP, Broom L, Willse A, Ercit K, Poletto M, Barnes ZH, Marubbi T, Troczka BJ, Treanor D, Beadle K, Granville B, de Mello V, Teal J, Sulston E, Ashton A, Akilan L, Naish N, Stevens O, Humphreys-Jones N, Warner SAJ, Spinner SAM, Rose NR, Head G, Morrison NI, Matzen KJ. Self-limiting fall armyworm: a new approach in development for sustainable crop protection and resistance management. BMC Biotechnol 2022; 22:5. [PMID: 35086540 PMCID: PMC8793274 DOI: 10.1186/s12896-022-00735-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 01/11/2022] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND The fall armyworm, Spodoptera frugiperda, is a significant and widespread pest of maize, sorghum, rice, and other economically important crops. Successful management of this caterpillar pest has historically relied upon application of synthetic insecticides and through cultivation of genetically engineered crops expressing insecticidal proteins (Bt crops). Fall armyworm has, however, developed resistance to both synthetic insecticides and Bt crops, which risks undermining the benefits delivered by these important crop protection tools. Previous modelling and empirical studies have demonstrated that releases of insecticide- or Bt-susceptible insects genetically modified to express conditional female mortality can both dilute insecticide resistance and suppress pest populations. RESULTS Here, we describe the first germline transformation of the fall armyworm and the development of a genetically engineered male-selecting self-limiting strain, OX5382G, which exhibits complete female mortality in the absence of an additive in the larval diet. Laboratory experiments showed that males of this strain are competitive against wild-type males for copulations with wild-type females, and that the OX5382G self-limiting transgene declines rapidly to extinction in closed populations following the cessation of OX5382G male releases. Population models simulating the release of OX5382G males in tandem with Bt crops and non-Bt 'refuge' crops show that OX5382G releases can suppress fall armyworm populations and delay the spread of resistance to insecticidal proteins. CONCLUSIONS This article describes the development of self-limiting fall armyworm designed to control this pest by suppressing pest populations, and population models that demonstrate its potential as a highly effective method of managing resistance to Bt crops in pest fall armyworm populations. Our results provide early promise for a potentially valuable future addition to integrated pest management strategies for fall armyworm and other pests for which resistance to existing crop protection measures results in damage to crops and impedes sustainable agriculture.
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Affiliation(s)
| | - Adam S Walker
- Oxitec Ltd, 71 Innovation Drive, Milton Park, Abingdon, OX14 4RQ, UK
| | - Stephen P Joyce
- Oxitec Ltd, 71 Innovation Drive, Milton Park, Abingdon, OX14 4RQ, UK
| | - Lucy Broom
- Oxitec Ltd, 71 Innovation Drive, Milton Park, Abingdon, OX14 4RQ, UK
- Centre for Medicines Discovery, University of Oxford, Old Road Campus Research Build, Roosevelt Dr, Headington, Oxford, OX3 7DQ, UK
| | - Alan Willse
- Bayer Crop Science, Chesterfield, MO, 63017, USA
| | - Kyla Ercit
- Oxitec Ltd, 71 Innovation Drive, Milton Park, Abingdon, OX14 4RQ, UK
| | - Mattia Poletto
- Oxitec Ltd, 71 Innovation Drive, Milton Park, Abingdon, OX14 4RQ, UK
| | - Zoe H Barnes
- Oxitec Ltd, 71 Innovation Drive, Milton Park, Abingdon, OX14 4RQ, UK
| | - Thea Marubbi
- Oxitec Ltd, 71 Innovation Drive, Milton Park, Abingdon, OX14 4RQ, UK
| | | | - David Treanor
- Oxitec Ltd, 71 Innovation Drive, Milton Park, Abingdon, OX14 4RQ, UK
| | - Katherine Beadle
- Oxitec Ltd, 71 Innovation Drive, Milton Park, Abingdon, OX14 4RQ, UK
| | - Ben Granville
- Oxitec Ltd, 71 Innovation Drive, Milton Park, Abingdon, OX14 4RQ, UK
| | - Vanessa de Mello
- Oxitec Ltd, 71 Innovation Drive, Milton Park, Abingdon, OX14 4RQ, UK
| | - Joss Teal
- Oxitec Ltd, 71 Innovation Drive, Milton Park, Abingdon, OX14 4RQ, UK
| | - Edward Sulston
- Oxitec Ltd, 71 Innovation Drive, Milton Park, Abingdon, OX14 4RQ, UK
| | - Anna Ashton
- Oxitec Ltd, 71 Innovation Drive, Milton Park, Abingdon, OX14 4RQ, UK
| | - Luxziyah Akilan
- Oxitec Ltd, 71 Innovation Drive, Milton Park, Abingdon, OX14 4RQ, UK
| | - Neil Naish
- Oxitec Ltd, 71 Innovation Drive, Milton Park, Abingdon, OX14 4RQ, UK
| | - Oliver Stevens
- Oxitec Ltd, 71 Innovation Drive, Milton Park, Abingdon, OX14 4RQ, UK
| | | | - Simon A J Warner
- Oxitec Ltd, 71 Innovation Drive, Milton Park, Abingdon, OX14 4RQ, UK
- Oxford University Innovation, Buxton Court, 3 West Way, Oxford, OX2 0JB, UK
| | - Sian A M Spinner
- Oxitec Ltd, 71 Innovation Drive, Milton Park, Abingdon, OX14 4RQ, UK
| | - Nathan R Rose
- Oxitec Ltd, 71 Innovation Drive, Milton Park, Abingdon, OX14 4RQ, UK.
| | - Graham Head
- Bayer Crop Science, Chesterfield, MO, 63017, USA
| | - Neil I Morrison
- Oxitec Ltd, 71 Innovation Drive, Milton Park, Abingdon, OX14 4RQ, UK
| | - Kelly J Matzen
- Oxitec Ltd, 71 Innovation Drive, Milton Park, Abingdon, OX14 4RQ, UK.
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13
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Zhang Q, Zhao S, Tian X, Qiu JG, Zhang CY. Development of a CRISPR-Cas-Based Biosensor for Rapid and Sensitive Detection of 8-Oxoguanine DNA Glycosylase. Anal Chem 2022; 94:2119-2125. [PMID: 35050578 DOI: 10.1021/acs.analchem.1c04453] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
8-Oxoguanine DNA glycosylase is essential for maintaining genomic integrity and stability, while its abnormal activity may lead to the disturbance in the normal DNA damage repair and the occurrence of carcinogenicity and teratogenicity. Herein, we construct a CRISPR-Cas-based biosensor for rapid and sensitive measurement of 8-oxoguanine DNA glycosylases. This biosensor involves a hairpin probe and integrates quadratic strand displacement amplification (SDA) with a CRISPR/Cas12a effector with the characteristics of rapidity (within 40 min) and isothermal assay. The presence of 8-oxoguanine DNA glycosylase can initiate the quadratic SDA to produce large amounts of activators with the assistance of polynucleotide kinase (PNK). Subsequently, the activators can bind with crRNA to activate Cas12a, cleaving signal probes and recovering Cy5 fluorescence, which can be accurately quantified by single-molecule imaging. Notably, the designed hairpin probes can effectively block the hybridization of the generated activators with free hairpin probes, endowing this biosensor with high sensitivity. In addition, the utilization of PNK instead of apurinic/apyrimidinic endonuclease (APE1) greatly simplifies the experimental procedure to only a one-step reaction. The introduction of a single-molecule detection further reduces the sample consumption and improves the sensitivity. This biosensor displays a detection limit of 4.24 × 10-9 U μL-1, and it can accurately quantify cellular human 8-oxoguanine DNA glycosylase at a single-cell level. Furthermore, this biosensor can be applied for the screening of inhibitors, the analysis of kinetic parameters, and the discrimination of cancer cells from normal cells, with potential applications in molecular diagnostic and point-of-care testing.
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Affiliation(s)
- Qian Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Shuangnan Zhao
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Xiaorui Tian
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Jian-Ge Qiu
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450000, Henan, China
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
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14
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Lyu M, Liu H, Waititu JK, Sun Y, Wang H, Fu J, Chen Y, Liu J, Ku L, Cheng X. TEAseq-based identification of 35,696 Dissociation insertional mutations facilitates functional genomic studies in maize. J Genet Genomics 2021; 48:961-971. [PMID: 34654681 DOI: 10.1016/j.jgg.2021.07.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 07/11/2021] [Accepted: 07/17/2021] [Indexed: 11/26/2022]
Abstract
In plants, transposable element (TE)-triggered mutants are important resources for functional genomic studies. However, conventional approaches for genome-wide identification of TE insertion sites are costly and laborious. This study developed a novel, rapid, and high-throughput TE insertion site identification workflow based on next-generation sequencing and named it Transposable Element Amplicon Sequencing (TEAseq). Using TEAseq, we systemically profiled the Dissociation (Ds) insertion sites in 1606 independent Ds insertional mutants in advanced backcross generation using K17 as background. The Ac-containing individuals were excluded for getting rid of the potential somatic insertions. We characterized 35,696 germinal Ds insertions tagging 10,323 genes, representing approximately 23.3% of the total genes in the maize genome. The insertion sites were presented in chromosomal hotspots around the ancestral Ds loci, and insertions occurred preferentially in gene body regions. Furthermore, we mapped a loss-of-function AGL2 gene using bulked segregant RNA-sequencing assay and proved that AGL2 is essential for seed development. We additionally established an open-access database named MEILAM for easy access to Ds insertional mutations. Overall, our results have provided an efficient workflow for TE insertion identification and rich sequence-indexed mutant resources for maize functional genomic studies.
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Affiliation(s)
- Mingjie Lyu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Huafeng Liu
- College of Agronomy, Collaborative Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Joram Kiriga Waititu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ying Sun
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Huan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Junjie Fu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yanhui Chen
- College of Agronomy, Collaborative Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Jun Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Lixia Ku
- College of Agronomy, Collaborative Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, Henan 450002, China.
| | - Xiliu Cheng
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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15
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Langsdorf E, Yu L, Kanevskaia L, Felkner R, Sturner S, McVey D, Khetan A. Retrospective assessment of clonal origin of cell lines. Biotechnol Prog 2021; 37:e3157. [PMID: 33896120 DOI: 10.1002/btpr.3157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 04/11/2021] [Accepted: 04/19/2021] [Indexed: 11/08/2022]
Abstract
Cell lines used for the manufacture of recombinant proteins are expected to arise from a single cell as a control strategy to limit variability and ensure consistent protein production. Health authorities require a minimum of two rounds of limiting dilution cloning or its equivalent to meet the requirement of single cell origin. However, many legacy cell lines may not have been generated with process meeting this criteria potentially impeding the path to commercialization. A general monoclonality assessment strategy was developed based on using the site of plasmid integration for a cell's identity. By comparing the identities of subclones from a master cell bank (MCB) to each other and that of the MCB, a probability of monoclonality was established. Two technologies were used for cell identity, Southern blot and a PCR assay based on plasmid-genome junction sequences identified by splinkerette PCR. Southern blot analysis revealed that subclones may have banding patterns that differ from each other and yet indicate monoclonal origin. Splinkerette PCR identifies cellular sequence flanking the point(s) of plasmid integration. The two assays together provide complimentary data for cell identity that enables proper monoclonality assessment and establishes that the three legacy cell lines investigated are all of clonal origin.
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Affiliation(s)
- Erik Langsdorf
- Biologics Development, Global Product Development and Supply, Bristol-Myers Squibb, New Brunswick, New Jersey, USA
| | - Le Yu
- Biologics Development, Global Product Development and Supply, Bristol-Myers Squibb, New Brunswick, New Jersey, USA
| | - Lioudmila Kanevskaia
- Biologics Development, Global Product Development and Supply, Bristol-Myers Squibb, New Brunswick, New Jersey, USA
| | - Roland Felkner
- Biologics Development, Global Product Development and Supply, Bristol-Myers Squibb, New Brunswick, New Jersey, USA
| | - Stephen Sturner
- Biologics Development, Global Product Development and Supply, Bristol-Myers Squibb, New Brunswick, New Jersey, USA
| | - Duncan McVey
- Biologics Development, Global Product Development and Supply, Bristol-Myers Squibb, New Brunswick, New Jersey, USA
| | - Anurag Khetan
- Biologics Development, Global Product Development and Supply, Bristol-Myers Squibb, New Brunswick, New Jersey, USA
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16
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Grassi L, Harris C, Zhu J, Hardman C, Hatton D. DetectIS: a pipeline to rapidly detect exogenous DNA integration sites using DNA or RNA paired-end sequencing data. Bioinformatics 2021; 37:4230-4232. [PMID: 33978747 PMCID: PMC9502153 DOI: 10.1093/bioinformatics/btab366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 05/07/2021] [Accepted: 05/11/2021] [Indexed: 11/13/2022] Open
Abstract
Motivation Recombinant DNA technology is widely used for different applications in biology, medicine and bio-technology. Viral transduction and plasmid transfection are among the most frequently used techniques to generate recombinant cell lines. Many of these methods result in the random integration of the plasmid into the host genome. Rapid identification of the integration sites is highly desirable in order to characterize these engineered cell lines. Results We developed detectIS: a pipeline specifically designed to identify genomic integration sites of exogenous DNA, either a plasmid containing one or more transgenes or a virus. The pipeline is based on a Nextflow workflow combined with a Singularity image containing all the necessary software, ensuring high reproducibility and scalability of the analysis. We tested it on simulated datasets and RNA-seq data from a human sample infected with Hepatitis B virus. Comparisons with other state of the art tools show that our method can identify the integration site in different recombinant cell lines, with accurate results, lower computational demand and shorter execution times. Availability and implementation The Nextflow workflow, the Singularity image and a test dataset are available at https://github.com/AstraZeneca/detectIS. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Luigi Grassi
- Biopharmaceutical Development, BioPharmaceuticals R&D, AstraZenec, Cambridge, UK a
| | - Claire Harris
- Biopharmaceutical Development, BioPharmaceuticals R&D, AstraZenec, Cambridge, UK a
| | - Jie Zhu
- Biopharmaceutical Development, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, USA
| | - Colin Hardman
- Data Science & Artificial Intelligence, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Diane Hatton
- Biopharmaceutical Development, BioPharmaceuticals R&D, AstraZenec, Cambridge, UK a
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17
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Alquezar‐Planas DE, Löber U, Cui P, Quedenau C, Chen W, Greenwood AD. DNA sonication inverse PCR for genome scale analysis of uncharacterized flanking sequences. Methods Ecol Evol 2020. [DOI: 10.1111/2041-210x.13497] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- David E. Alquezar‐Planas
- Department of Wildlife Diseases Leibniz Institute for Zoo and Wildlife Research Berlin Germany
- Australian Museum Research InstituteAustralian Museum Sydney NSW Australia
| | - Ulrike Löber
- Department of Wildlife Diseases Leibniz Institute for Zoo and Wildlife Research Berlin Germany
- The Berlin Center for Genomics in Biodiversity Research Berlin Germany
- Experimental and Clinical Research Center A Cooperation of Charité – Universitätsmedizin Berlin and Max Delbruck Center for Molecular Medicine Berlin Germany
| | - Pin Cui
- Department of Wildlife Diseases Leibniz Institute for Zoo and Wildlife Research Berlin Germany
| | - Claudia Quedenau
- Genomics Max Delbrück Center for Molecular Medicine Berlin Germany
| | - Wei Chen
- Berlin Institute for Medical Systems BiologyMax‐Delbrück Center for Molecular Medicine Berlin Germany
| | - Alex D. Greenwood
- Department of Wildlife Diseases Leibniz Institute for Zoo and Wildlife Research Berlin Germany
- Department of Veterinary Medicine Freie Universität Berlin Berlin Germany
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18
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Senigl F, Maman Y, Dinesh RK, Alinikula J, Seth RB, Pecnova L, Omer AD, Rao SSP, Weisz D, Buerstedde JM, Aiden EL, Casellas R, Hejnar J, Schatz DG. Topologically Associated Domains Delineate Susceptibility to Somatic Hypermutation. Cell Rep 2020; 29:3902-3915.e8. [PMID: 31851922 PMCID: PMC6980758 DOI: 10.1016/j.celrep.2019.11.039] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 06/26/2019] [Accepted: 11/08/2019] [Indexed: 12/26/2022] Open
Abstract
Somatic hypermutation (SHM) introduces point mutations into immunoglobulin (Ig) genes but also causes mutations in other parts of the genome. We have used lentiviral SHM reporter vectors to identify regions of the genome that are susceptible (“hot”) and resistant (“cold”) to SHM, revealing that SHM susceptibility and resistance are often properties of entire topologically associated domains (TADs). Comparison of hot and cold TADs reveals that while levels of transcription are equivalent, hot TADs are enriched for the cohesin loader NIPBL, super-enhancers, markers of paused/stalled RNA polymerase 2, and multiple important B cell transcription factors. We demonstrate that at least some hot TADs contain enhancers that possess SHM targeting activity and that insertion of a strong Ig SHM-targeting element into a cold TAD renders it hot. Our findings lead to a model for SHM susceptibility involving the cooperative action of cis-acting SHM targeting elements and the dynamic and architectural properties of TADs. Senigl et al. show that genome susceptibility to somatic hypermutation (SHM) is confined within topologically associated domains (TADs) and is linked to markers of strong enhancers and stalled transcription and high levels of the cohesin loader NIPBL. Insertion of an ectopic SHM targeting element renders an entire TAD susceptible to SHM.
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Affiliation(s)
- Filip Senigl
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 14220 Prague 4, Czech Republic.
| | - Yaakov Maman
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Ravi K Dinesh
- Department of Immunobiology, Yale School of Medicine, 300 Cedar Street, Box 208011, New Haven, CT 06520-8011, USA
| | - Jukka Alinikula
- Institute of Biomedicine, University of Turku, Kiinamyllynkatu 10, 20520 Turku, Finland
| | - Rashu B Seth
- Department of Immunobiology, Yale School of Medicine, 300 Cedar Street, Box 208011, New Haven, CT 06520-8011, USA
| | - Lubomira Pecnova
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 14220 Prague 4, Czech Republic
| | - Arina D Omer
- Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | - Suhas S P Rao
- Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | - David Weisz
- Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Erez Lieberman Aiden
- Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
| | - Rafael Casellas
- Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA; Center of Cancer Research, NCI, NIH, Bethesda, MD 20892, USA
| | - Jiri Hejnar
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 14220 Prague 4, Czech Republic
| | - David G Schatz
- Department of Immunobiology, Yale School of Medicine, 300 Cedar Street, Box 208011, New Haven, CT 06520-8011, USA.
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19
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Wandler AM, Huang BJ, Craig JW, Hayes K, Yan H, Meyer LK, Scacchetti A, Monsalve G, Dail M, Li Q, Wong JC, Weinberg O, Hasserjian RP, Kogan SC, Jonsson P, Yamamoto K, Sampath D, Nakitandwe J, Downing JR, Zhang J, Aster JC, Taylor BS, Shannon K. Loss of glucocorticoid receptor expression mediates in vivo dexamethasone resistance in T-cell acute lymphoblastic leukemia. Leukemia 2020; 34:2025-2037. [PMID: 32066867 PMCID: PMC7440098 DOI: 10.1038/s41375-020-0748-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 01/31/2020] [Accepted: 02/06/2020] [Indexed: 02/08/2023]
Abstract
Despite decades of clinical use, mechanisms of glucocorticoid resistance are poorly understood. We treated primary murine T lineage acute lymphoblastic leukemias (T-ALLs) with the glucocorticoid dexamethasone (DEX) alone and in combination with the pan-PI3 kinase inhibitor GDC-0941 and observed a robust response to DEX that was modestly enhanced by GDC-0941. Continuous in vivo treatment invariably resulted in outgrowth of drug-resistant clones, ~30% of which showed markedly reduced glucocorticoid receptor (GR) protein expression. A similar proportion of relapsed human T-ALLs also exhibited low GR protein levels. De novo or preexisting mutations in the gene encoding GR (Nr3c1) occurred in relapsed clones derived from multiple independent parental leukemias. CRISPR/Cas9 gene editing confirmed that loss of GR expression confers DEX resistance. Exposing drug-sensitive T-ALLs to DEX in vivo altered transcript levels of multiple genes, and this response was attenuated in relapsed T-ALLs. These data implicate reduced GR protein expression as a frequent cause of glucocorticoid resistance in T-ALL.
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Affiliation(s)
- Anica M Wandler
- Department of Pediatrics, University of California, San Francisco, CA, USA
| | - Benjamin J Huang
- Department of Pediatrics, University of California, San Francisco, CA, USA
| | - Jeffrey W Craig
- Department of Pathology, Brigham & Women's Hospital, Boston, MA, USA
| | - Kathryn Hayes
- Department of Pediatrics, University of California, San Francisco, CA, USA
| | - Hannah Yan
- Department of Pediatrics, University of California, San Francisco, CA, USA
| | - Lauren K Meyer
- Department of Pediatrics, University of California, San Francisco, CA, USA
| | - Alessandro Scacchetti
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
| | - Gabriela Monsalve
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
| | - Monique Dail
- Department of Translational Oncology, Genentech Inc., South San Francisco, CA, USA
| | - Qing Li
- Department of Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Jasmine C Wong
- Department of Pediatrics, University of California, San Francisco, CA, USA
| | - Olga Weinberg
- Department of Pathology, Boston Children's Hospital, Boston, MA, USA
| | | | - Scott C Kogan
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Philip Jonsson
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Keith Yamamoto
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
| | - Deepak Sampath
- Department of Translational Oncology, Genentech Inc., South San Francisco, CA, USA
| | - Joy Nakitandwe
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - James R Downing
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jon C Aster
- Department of Pathology, Brigham & Women's Hospital, Boston, MA, USA
| | - Barry S Taylor
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kevin Shannon
- Department of Pediatrics, University of California, San Francisco, CA, USA.
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20
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Nandety RS, Serrani‐Yarce JC, Gill US, Oh S, Lee H, Zhang X, Dai X, Zhang W, Krom N, Wen J, Zhao PX, Mysore KS. Insertional mutagenesis of Brachypodium distachyon using the Tnt1 retrotransposable element. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:1924-1936. [PMID: 32410353 PMCID: PMC7496502 DOI: 10.1111/tpj.14813] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 04/29/2020] [Accepted: 05/05/2020] [Indexed: 06/11/2023]
Abstract
Brachypodium distachyon is an annual C3 grass used as a monocot model system in functional genomics research. Insertional mutagenesis is a powerful tool for both forward and reverse genetics studies. In this study, we explored the possibility of using the tobacco retrotransposon Tnt1 to create a transposon-based insertion mutant population in B. distachyon. We developed transgenic B. distachyon plants expressing Tnt1 (R0) and in the subsequent regenerants (R1) we observed that Tnt1 actively transposed during somatic embryogenesis, generating an average of 6.37 insertions per line in a population of 19 independent R1 regenerant plants analyzed. In seed-derived progeny of R1 plants, Tnt1 segregated in a Mendelian ratio of 3:1 and no new Tnt1 transposition was observed. A total of 126 flanking sequence tags (FSTs) were recovered from the analyzed R0 and R1 lines. Analysis of the FSTs showed a uniform pattern of insertion in all the chromosomes (1-5) without any preference for a particular chromosome region. Considering the average length of a gene transcript to be 3.37 kb, we estimated that 29 613 lines are required to achieve a 90% possibility of tagging a given gene in the B. distachyon genome using the Tnt1-based mutagenesis approach. Our results show the possibility of using Tnt1 to achieve near-saturation mutagenesis in B. distachyon, which will aid in functional genomics studies of other C3 grasses.
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Affiliation(s)
| | - Juan C. Serrani‐Yarce
- Noble Research InstituteLLC.2510 Sam Noble ParkwayArdmoreOK73401USA
- Present address:
Department of Biological SciencesUniversity of North TexasDentonTX76203USA
| | - Upinder S. Gill
- Noble Research InstituteLLC.2510 Sam Noble ParkwayArdmoreOK73401USA
- Present address:
Department of Plant PathologyNorth Dakota State UniversityFargoND58102USA
| | - Sunhee Oh
- Noble Research InstituteLLC.2510 Sam Noble ParkwayArdmoreOK73401USA
| | - Hee‐Kyung Lee
- Noble Research InstituteLLC.2510 Sam Noble ParkwayArdmoreOK73401USA
| | - Xinji Zhang
- Noble Research InstituteLLC.2510 Sam Noble ParkwayArdmoreOK73401USA
| | - Xinbin Dai
- Noble Research InstituteLLC.2510 Sam Noble ParkwayArdmoreOK73401USA
| | - Wenchao Zhang
- Noble Research InstituteLLC.2510 Sam Noble ParkwayArdmoreOK73401USA
| | - Nick Krom
- Noble Research InstituteLLC.2510 Sam Noble ParkwayArdmoreOK73401USA
| | - Jiangqi Wen
- Noble Research InstituteLLC.2510 Sam Noble ParkwayArdmoreOK73401USA
| | - Patrick X. Zhao
- Noble Research InstituteLLC.2510 Sam Noble ParkwayArdmoreOK73401USA
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21
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Sonnabend MS, Klein K, Beier S, Angelov A, Kluj R, Mayer C, Groß C, Hofmeister K, Beuttner A, Willmann M, Peter S, Oberhettinger P, Schmidt A, Autenrieth IB, Schütz M, Bohn E. Identification of Drug Resistance Determinants in a Clinical Isolate of Pseudomonas aeruginosa by High-Density Transposon Mutagenesis. Antimicrob Agents Chemother 2020; 64:e01771-19. [PMID: 31818817 PMCID: PMC7038268 DOI: 10.1128/aac.01771-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 11/25/2019] [Indexed: 01/02/2023] Open
Abstract
With the aim to identify potential new targets to restore antimicrobial susceptibility of multidrug-resistant (MDR) Pseudomonas aeruginosa isolates, we generated a high-density transposon (Tn) insertion mutant library in an MDR P. aeruginosa bloodstream isolate (isolate ID40). The depletion of Tn insertion mutants upon exposure to cefepime or meropenem was measured in order to determine the common resistome for these clinically important antipseudomonal β-lactam antibiotics. The approach was validated by clean deletions of genes involved in peptidoglycan synthesis/recycling, such as the genes for the lytic transglycosylase MltG, the murein (Mur) endopeptidase MepM1, the MurNAc/GlcNAc kinase AmgK, and the uncharacterized protein YgfB, all of which were identified in our screen as playing a decisive role in survival after treatment with cefepime or meropenem. We found that the antibiotic resistance of P. aeruginosa can be overcome by targeting usually nonessential genes that turn essential in the presence of therapeutic concentrations of antibiotics. For all validated genes, we demonstrated that their deletion leads to the reduction of ampC expression, resulting in a significant decrease in β-lactamase activity, and consequently, these mutants partly or completely lost resistance against cephalosporins, carbapenems, and acylaminopenicillins. In summary, the determined resistome may comprise promising targets for the development of drugs that may be used to restore sensitivity to existing antibiotics, specifically in MDR strains of P. aeruginosa.
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Affiliation(s)
- Michael S Sonnabend
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin Tübingen (IMIT), Institut für Medizinische Mikrobiologie und Hygiene, Universitätsklinikum Tübingen, Tübingen, Germany
- NGS Competence Center Tübingen (NCCT), Institut für Medizinische Mikrobiologie und Hygiene, Universitätsklinikum Tübingen, Tübingen, Germany
| | - Kristina Klein
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin Tübingen (IMIT), Institut für Medizinische Mikrobiologie und Hygiene, Universitätsklinikum Tübingen, Tübingen, Germany
| | - Sina Beier
- Center for Bioinformatics (ZBIT), Universität Tübingen, Tübingen, Germany
| | - Angel Angelov
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin Tübingen (IMIT), Institut für Medizinische Mikrobiologie und Hygiene, Universitätsklinikum Tübingen, Tübingen, Germany
- NGS Competence Center Tübingen (NCCT), Institut für Medizinische Mikrobiologie und Hygiene, Universitätsklinikum Tübingen, Tübingen, Germany
| | - Robert Kluj
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin Tübingen (IMIT), Department of Biology, Microbiology & Biotechnology, Universität Tübingen, Tübingen, Germany
| | - Christoph Mayer
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin Tübingen (IMIT), Department of Biology, Microbiology & Biotechnology, Universität Tübingen, Tübingen, Germany
| | - Caspar Groß
- Institut für Medizinische Genetik und Angewandte Genomik, Universitätsklinikum Tübingen, Tübingen, Germany
| | - Kathrin Hofmeister
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin Tübingen (IMIT), Institut für Medizinische Mikrobiologie und Hygiene, Universitätsklinikum Tübingen, Tübingen, Germany
| | - Antonia Beuttner
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin Tübingen (IMIT), Institut für Medizinische Mikrobiologie und Hygiene, Universitätsklinikum Tübingen, Tübingen, Germany
| | - Matthias Willmann
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin Tübingen (IMIT), Institut für Medizinische Mikrobiologie und Hygiene, Universitätsklinikum Tübingen, Tübingen, Germany
- NGS Competence Center Tübingen (NCCT), Institut für Medizinische Mikrobiologie und Hygiene, Universitätsklinikum Tübingen, Tübingen, Germany
| | - Silke Peter
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin Tübingen (IMIT), Institut für Medizinische Mikrobiologie und Hygiene, Universitätsklinikum Tübingen, Tübingen, Germany
- NGS Competence Center Tübingen (NCCT), Institut für Medizinische Mikrobiologie und Hygiene, Universitätsklinikum Tübingen, Tübingen, Germany
| | - Philipp Oberhettinger
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin Tübingen (IMIT), Institut für Medizinische Mikrobiologie und Hygiene, Universitätsklinikum Tübingen, Tübingen, Germany
| | - Annika Schmidt
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin Tübingen (IMIT), Institut für Medizinische Mikrobiologie und Hygiene, Universitätsklinikum Tübingen, Tübingen, Germany
| | - Ingo B Autenrieth
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin Tübingen (IMIT), Institut für Medizinische Mikrobiologie und Hygiene, Universitätsklinikum Tübingen, Tübingen, Germany
- NGS Competence Center Tübingen (NCCT), Institut für Medizinische Mikrobiologie und Hygiene, Universitätsklinikum Tübingen, Tübingen, Germany
| | - Monika Schütz
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin Tübingen (IMIT), Institut für Medizinische Mikrobiologie und Hygiene, Universitätsklinikum Tübingen, Tübingen, Germany
| | - Erwin Bohn
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin Tübingen (IMIT), Institut für Medizinische Mikrobiologie und Hygiene, Universitätsklinikum Tübingen, Tübingen, Germany
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22
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Dawes JC, Webster P, Iadarola B, Garcia-Diaz C, Dore M, Bolt BJ, Dewchand H, Dharmalingam G, McLatchie AP, Kaczor J, Caceres JJ, Paccanaro A, Game L, Parrinello S, Uren AG. LUMI-PCR: an Illumina platform ligation-mediated PCR protocol for integration site cloning, provides molecular quantitation of integration sites. Mob DNA 2020; 11:7. [PMID: 32042315 PMCID: PMC7001329 DOI: 10.1186/s13100-020-0201-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 01/08/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Ligation-mediated PCR protocols have diverse uses including the identification of integration sites of insertional mutagens, integrating vectors and naturally occurring mobile genetic elements. For approaches that employ NGS sequencing, the relative abundance of integrations within a complex mixture is typically determined through the use of read counts or unique fragment lengths from a ligation of sheared DNA; however, these estimates may be skewed by PCR amplification biases and saturation of sequencing coverage. RESULTS Here we describe a modification of our previous splinkerette based ligation-mediated PCR using a novel Illumina-compatible adapter design that prevents amplification of non-target DNA and incorporates unique molecular identifiers. This design reduces the number of PCR cycles required and improves relative quantitation of integration abundance for saturating sequencing coverage. By inverting the forked adapter strands from a standard orientation, the integration-genome junction can be sequenced without affecting the sequence diversity required for cluster generation on the flow cell. Replicate libraries of murine leukemia virus-infected spleen samples yielded highly reproducible quantitation of clonal integrations as well as a deep coverage of subclonal integrations. A dilution series of DNAs bearing integrations of MuLV or piggyBac transposon shows linearity of the quantitation over a range of concentrations. CONCLUSIONS Merging ligation and library generation steps can reduce total PCR amplification cycles without sacrificing coverage or fidelity. The protocol is robust enough for use in a 96 well format using an automated liquid handler and we include programs for use of a Beckman Biomek liquid handling workstation. We also include an informatics pipeline that maps reads, builds integration contigs and quantitates integration abundance using both fragment lengths and unique molecular identifiers. Suggestions for optimizing the protocol to other target DNA sequences are included. The reproducible distinction of clonal and subclonal integration sites from each other allows for analysis of populations of cells undergoing selection, such as those found in insertional mutagenesis screens.
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Affiliation(s)
- Joanna C. Dawes
- MRC London Institute of Medical Sciences (LMS), Du Cane Road, London, W12 0NN UK
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London, UK
| | - Philip Webster
- MRC London Institute of Medical Sciences (LMS), Du Cane Road, London, W12 0NN UK
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London, UK
- Imperial College Healthcare NHS Trust, London, UK
| | - Barbara Iadarola
- MRC London Institute of Medical Sciences (LMS), Du Cane Road, London, W12 0NN UK
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London, UK
| | - Claudia Garcia-Diaz
- Samantha Dickson Brain Cancer Unit, UCL Cancer Institute, WC1E 6DD, London, UK
| | - Marian Dore
- MRC London Institute of Medical Sciences (LMS), Du Cane Road, London, W12 0NN UK
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London, UK
| | - Bruce J. Bolt
- MRC London Institute of Medical Sciences (LMS), Du Cane Road, London, W12 0NN UK
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London, UK
| | - Hamlata Dewchand
- MRC London Institute of Medical Sciences (LMS), Du Cane Road, London, W12 0NN UK
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London, UK
| | - Gopuraja Dharmalingam
- MRC London Institute of Medical Sciences (LMS), Du Cane Road, London, W12 0NN UK
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London, UK
| | | | - Jakub Kaczor
- MRC London Institute of Medical Sciences (LMS), Du Cane Road, London, W12 0NN UK
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London, UK
| | - Juan J. Caceres
- Centre for Systems and Synthetic Biology, Department of Computer Science, Royal Holloway, University of London, London, UK
| | - Alberto Paccanaro
- Centre for Systems and Synthetic Biology, Department of Computer Science, Royal Holloway, University of London, London, UK
| | - Laurence Game
- MRC London Institute of Medical Sciences (LMS), Du Cane Road, London, W12 0NN UK
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London, UK
| | - Simona Parrinello
- Samantha Dickson Brain Cancer Unit, UCL Cancer Institute, WC1E 6DD, London, UK
| | - Anthony G. Uren
- MRC London Institute of Medical Sciences (LMS), Du Cane Road, London, W12 0NN UK
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London, UK
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23
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Ye L, Park JJ, Dong MB, Yang Q, Chow RD, Peng L, Du Y, Guo J, Dai X, Wang G, Errami Y, Chen S. In vivo CRISPR screening in CD8 T cells with AAV-Sleeping Beauty hybrid vectors identifies membrane targets for improving immunotherapy for glioblastoma. Nat Biotechnol 2019; 37:1302-1313. [PMID: 31548728 PMCID: PMC6834896 DOI: 10.1038/s41587-019-0246-4] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 08/01/2019] [Indexed: 12/14/2022]
Abstract
Targeting membrane proteins could improve the efficacy of T cell-based immunotherapies. To facilitate the identification of T cell targets, we developed a hybrid genetic screening system where the Sleeping Beauty (SB) transposon and single guide RNA cassette are nested in an adeno-associated virus (AAV). SB-mediated genomic integration of the single guide RNA cassette enables efficient gene editing in primary murine T cells as well as a screen readout. We performed in vivo AAV-SB-CRISPR screens for membrane protein targets in CD8+ T cells in mouse models of glioblastoma (GBM). We validated screen hits by demonstrating that adoptive transfer of CD8+ T cells with Pdia3, Mgat5, Emp1 or Lag3 gene editing enhances the survival of GBM-bearing mice in both syngeneic and T-cell receptor transgenic models. Transcriptome profiling, single cell sequencing, cytokine assays and T cell signaling analysis showed that Pdia3 editing in T cells enhances effector functions. Engineered PDIA3 mutant EGFRvIII chimeric antigen T cells are more potent in antigen-specific killing of human GBM cells.
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Affiliation(s)
- Lupeng Ye
- System Biology Institute, Integrated Science & Technology Center, West Haven, CT, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Center for Cancer Systems Biology, Integrated Science & Technology Center, West Haven, CT, USA
| | - Jonathan J Park
- System Biology Institute, Integrated Science & Technology Center, West Haven, CT, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Center for Cancer Systems Biology, Integrated Science & Technology Center, West Haven, CT, USA
- Yale M.D.-Ph.D. Program, Yale University School of Medicine, New Haven, CT, USA
| | - Matthew B Dong
- System Biology Institute, Integrated Science & Technology Center, West Haven, CT, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Center for Cancer Systems Biology, Integrated Science & Technology Center, West Haven, CT, USA
- Yale M.D.-Ph.D. Program, Yale University School of Medicine, New Haven, CT, USA
- Immunobiology Program, Yale University School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Quanjun Yang
- System Biology Institute, Integrated Science & Technology Center, West Haven, CT, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Center for Cancer Systems Biology, Integrated Science & Technology Center, West Haven, CT, USA
| | - Ryan D Chow
- System Biology Institute, Integrated Science & Technology Center, West Haven, CT, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Center for Cancer Systems Biology, Integrated Science & Technology Center, West Haven, CT, USA
- Yale M.D.-Ph.D. Program, Yale University School of Medicine, New Haven, CT, USA
| | - Lei Peng
- System Biology Institute, Integrated Science & Technology Center, West Haven, CT, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Center for Cancer Systems Biology, Integrated Science & Technology Center, West Haven, CT, USA
| | - Yaying Du
- System Biology Institute, Integrated Science & Technology Center, West Haven, CT, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Center for Cancer Systems Biology, Integrated Science & Technology Center, West Haven, CT, USA
| | - Jianjian Guo
- System Biology Institute, Integrated Science & Technology Center, West Haven, CT, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Center for Cancer Systems Biology, Integrated Science & Technology Center, West Haven, CT, USA
| | - Xiaoyun Dai
- System Biology Institute, Integrated Science & Technology Center, West Haven, CT, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Center for Cancer Systems Biology, Integrated Science & Technology Center, West Haven, CT, USA
| | - Guangchuan Wang
- System Biology Institute, Integrated Science & Technology Center, West Haven, CT, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Center for Cancer Systems Biology, Integrated Science & Technology Center, West Haven, CT, USA
| | - Youssef Errami
- System Biology Institute, Integrated Science & Technology Center, West Haven, CT, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Center for Cancer Systems Biology, Integrated Science & Technology Center, West Haven, CT, USA
| | - Sidi Chen
- System Biology Institute, Integrated Science & Technology Center, West Haven, CT, USA.
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.
- Center for Cancer Systems Biology, Integrated Science & Technology Center, West Haven, CT, USA.
- Yale M.D.-Ph.D. Program, Yale University School of Medicine, New Haven, CT, USA.
- Immunobiology Program, Yale University School of Medicine, New Haven, CT, USA.
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA.
- Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA.
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA.
- Yale Liver Center, Yale University School of Medicine, New Haven, CT, USA.
- Yale Center for Biomedical Data Science, Yale University School of Medicine, New Haven, CT, USA.
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24
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Hockman D, Chong-Morrison V, Green SA, Gavriouchkina D, Candido-Ferreira I, Ling ITC, Williams RM, Amemiya CT, Smith JJ, Bronner ME, Sauka-Spengler T. A genome-wide assessment of the ancestral neural crest gene regulatory network. Nat Commun 2019; 10:4689. [PMID: 31619682 PMCID: PMC6795873 DOI: 10.1038/s41467-019-12687-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 09/23/2019] [Indexed: 12/17/2022] Open
Abstract
The neural crest (NC) is an embryonic cell population that contributes to key vertebrate-specific features including the craniofacial skeleton and peripheral nervous system. Here we examine the transcriptional and epigenomic profiles of NC cells in the sea lamprey, in order to gain insight into the ancestral state of the NC gene regulatory network (GRN). Transcriptome analyses identify clusters of co-regulated genes during NC specification and migration that show high conservation across vertebrates but also identify transcription factors (TFs) and cell-adhesion molecules not previously implicated in NC migration. ATAC-seq analysis uncovers an ensemble of cis-regulatory elements, including enhancers of Tfap2B, SoxE1 and Hox-α2 validated in the embryo. Cross-species deployment of lamprey elements identifies the deep conservation of lamprey SoxE1 enhancer activity, mediating homologous expression in jawed vertebrates. Our data provide insight into the core GRN elements conserved to the base of the vertebrates and expose others that are unique to lampreys.
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Affiliation(s)
- Dorit Hockman
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Division of Cell Biology, Department of Human Biology, Neuroscience Institute, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Vanessa Chong-Morrison
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Division of Biosciences, Faculty of Life Sciences, University College London, London, UK
| | - Stephen A Green
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Daria Gavriouchkina
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Okinawa Institute of Science and Technology, Molecular Genetics Unit, Onna, Japan
| | - Ivan Candido-Ferreira
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Irving T C Ling
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Ruth M Williams
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Chris T Amemiya
- Molecular Cell Biology, School of Natural Sciences, University of California, Merced, CA, USA
| | - Jeramiah J Smith
- Department of Biology, University of Kentucky, Lexington, KY, USA
| | - Marianne E Bronner
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Tatjana Sauka-Spengler
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
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25
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Spiegel A, Bachmann M, Jurado Jiménez G, Sarov M. CRISPR/Cas9-based knockout pipeline for reverse genetics in mammalian cell culture. Methods 2019; 164-165:49-58. [PMID: 31051255 DOI: 10.1016/j.ymeth.2019.04.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 03/04/2019] [Accepted: 04/24/2019] [Indexed: 12/14/2022] Open
Abstract
We present a straightforward protocol for reverse genetics in cultured mammalian cells, using CRISPR/Cas9-mediated homology-dependent repair (HDR) based insertion of a protein trap cassette, resulting in a termination of the endogenous gene expression. Complete loss of function can be achieved with monoallelic trap cassette insertion, as the second allele is frequently disrupted by an error-prone non-homologous end joining (NHEJ) mechanism. The method should be applicable to any expressed gene in most cell lines, including those with low HDR efficiency, as the knockout alleles can be directly selected for.
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Affiliation(s)
- Aleksandra Spiegel
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Mandy Bachmann
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Gabriel Jurado Jiménez
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Mihail Sarov
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany.
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26
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Generation of Inducible Gene-Switched GAL4 Expressed in the Drosophila Female Germline Stem Cell Niche. G3-GENES GENOMES GENETICS 2019; 9:2007-2016. [PMID: 31018943 PMCID: PMC6553524 DOI: 10.1534/g3.119.400246] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The stem cell niche, a regulatory microenvironment, houses and regulates stem cells for maintenance of tissues throughout an organism's lifespan. While it is known that stem cell function declines with age, the role of niche cells in this decline is not completely understood. Drosophila exhibits a short lifespan with well-characterized ovarian germline stem cells (GSCs) and niche compartments, providing a good model with which to study stem cell biology. However, no inducible tools for temporal and spatial control of gene expression in the GSC-niche unit have been previously developed for aging studies. The current UAS-GAL4 systems are not ideal for aging studies because fly physiological aging may be affected by the temperature shifts used to manipulate GAL4 activity. Additionally, the actual needs of the aged niche may be masked by continuously driven gene expression. Since GeneSwitch GAL4 is conveniently activated by the steroid RU486 (mifepristone), we conducted an enhancer-trap screen to isolate GeneSwitch GAL4 lines with expression in the GSC-niche unit. We identified six lines with expression in germarial somatic cells, and two lines (#2305 and #2261) with expression in niche cap cells, the major constituent of the GSC niche. The use of lines #2305 or #2261 to overexpress Drosophila insulin-like peptide 2, which maintains GSC lifespan, in aged niche cap cells significantly delayed age-dependent GSC loss. These results support the notion that insulin signaling is beneficial for maintaining aged stem cells and also validate the utility of our GeneSwitch GAL4 lines for studying stem cell aging.
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27
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Spontaneous mutations in maize pollen are frequent in some lines and arise mainly from retrotranspositions and deletions. Proc Natl Acad Sci U S A 2019; 116:10734-10743. [PMID: 30992374 DOI: 10.1073/pnas.1903809116] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
While studying spontaneous mutations at the maize bronze (bz) locus, we made the unexpected discovery that specific low-copy number retrotransposons are mobile in the pollen of some maize lines, but not of others. We conducted large-scale genetic experiments to isolate new bz mutations from several Bz stocks and recovered spontaneous stable mutations only in the pollen parent in reciprocal crosses. Most of the new stable bz mutations resulted from either insertions of low-copy number long terminal repeat (LTR) retrotransposons or deletions, the same two classes of mutations that predominated in a collection of spontaneous wx mutations [Wessler S (1997) The Mutants of Maize, pp 385-386]. Similar mutations were recovered at the closely linked sh locus. These events occurred with a frequency of 2-4 × 10-5 in two lines derived from W22 and in 4Co63, but not at all in B73 or Mo17, two inbreds widely represented in Corn Belt hybrids. Surprisingly, the mutagenic LTR retrotransposons differed in the active lines, suggesting differences in the autonomous element make-up of the lines studied. Some active retrotransposons, like Hopscotch, Magellan, and Bs2, a Bs1 variant, were described previously; others, like Foto and Focou in 4Co63, were not. By high-throughput sequencing of retrotransposon junctions, we established that retrotranposition of Hopscotch, Magellan, and Bs2 occurs genome-wide in the pollen of active lines, but not in the female germline or in somatic tissues. We discuss here the implications of these results, which shed light on the source, frequency, and nature of spontaneous mutations in maize.
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Phillips NE, Mandic A, Omidi S, Naef F, Suter DM. Memory and relatedness of transcriptional activity in mammalian cell lineages. Nat Commun 2019; 10:1208. [PMID: 30872573 PMCID: PMC6418128 DOI: 10.1038/s41467-019-09189-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 02/21/2019] [Indexed: 12/03/2022] Open
Abstract
Phenotypically identical mammalian cells often display considerable variability in transcript levels of individual genes. How transcriptional activity propagates in cell lineages, and how this varies across genes is poorly understood. Here we combine live-cell imaging of short-lived transcriptional reporters in mouse embryonic stem cells with mathematical modelling to quantify the propagation of transcriptional activity over time and across cell generations in phenotypically homogenous cells. In sister cells we find mean transcriptional activity to be strongly correlated and transcriptional dynamics tend to be synchronous; both features control how quickly transcriptional levels in sister cells diverge in a gene-specific manner. Moreover, mean transcriptional activity is transmitted from mother to daughter cells, leading to multi-generational transcriptional memory and causing inter-family heterogeneity in gene expression.
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Affiliation(s)
- Nicholas E Phillips
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
| | - Aleksandra Mandic
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
| | - Saeed Omidi
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
| | - Felix Naef
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland.
| | - David M Suter
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland.
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29
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Cypser JR, Chick WS, Fahy GM, Schumacher GJ, Johnson TE. Genetic suppression of cryoprotectant toxicity. Cryobiology 2019; 86:95-102. [PMID: 30458175 PMCID: PMC7001869 DOI: 10.1016/j.cryobiol.2018.11.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 11/15/2018] [Accepted: 11/16/2018] [Indexed: 12/25/2022]
Abstract
We report here a new, unbiased forward genetic method that uses transposon-mediated mutagenesis to enable the identification of mutations that confer cryoprotectant toxicity resistance (CTR). Our method is to select for resistance to the toxic effects of M22, a much-studied whole-organ vitrification solution. We report finding and characterizing six mutants that are resistant to M22. These mutants fall into six independent biochemical pathways not previously linked to cryoprotectant toxicity (CT). The genes associated with the mutations were Gm14005, Myh9, Nrg2, Pura, Fgd2, Pim1, Opa1, Hes1, Hsbp1, and Ywhag. The mechanisms of action of the mutations remain unknown, but two of the mutants involve MYC signaling, which was previously implicated in CT. Several of the mutants may up-regulate cellular stress defense pathways. Several of the M22-resistant mutants were also resistant to dimethyl sulfoxide (Me2SO), and many of the mutants showed significantly improved survival after freezing and thawing in 10% (v/v) Me2SO. This new approach to overcoming CT has many advantages over alternative methods such as transcriptomic profiling. Our method directly identifies specific genetic loci that unequivocally affect CT. More generally, our results provide the first direct evidence that CT can be reduced in mammalian cells by specific molecular interventions. Thus, this approach introduces remarkable new opportunities for pharmacological blockade of CT.
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Affiliation(s)
- James R Cypser
- Institute for Behavioral Genetics, University of Colorado Boulder, USA
| | - Wallace S Chick
- Department of Cell and Developmental Biology, University of Colorado Denver, Aurora, CO, USA; Charles C. Gates Center for Regenerative Medicine, University of Colorado Denver, Aurora, CO, USA
| | | | | | - Thomas E Johnson
- Institute for Behavioral Genetics, University of Colorado Boulder, USA; Department of Integrative Physiology, University of Colorado Boulder, USA.
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30
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Weissbein U, Peretz M, Plotnik O, Yanuka O, Sagi I, Golan-Lev T, Benvenisty N. Genome-wide Screen for Culture Adaptation and Tumorigenicity-Related Genes in Human Pluripotent Stem Cells. iScience 2019; 11:398-408. [PMID: 30660107 PMCID: PMC6348297 DOI: 10.1016/j.isci.2018.12.031] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 11/19/2018] [Accepted: 12/27/2018] [Indexed: 01/08/2023] Open
Abstract
Human pluripotent stem cells (hPSCs) acquire genetic changes during their propagation in culture that can affect their use in research and future therapies. To identify the key genes involved in selective advantage during culture adaptation and tumorigenicity of hPSCs, we generated a genome-wide screening system for genes and pathways that provide a growth advantage either in vitro or in vivo. We found that hyperactivation of the RAS pathway confers resistance to selection with the hPSC-specific drug PluriSIn-1. We also identified that inactivation of the RHO-ROCK pathway gives growth advantage during culture adaptation. Last, we demonstrated the importance of the PI3K-AKT and HIPPO pathways for the teratoma formation process. Our screen revealed key genes and pathways relevant to the tumorigenicity and survival of hPSCs and should thus assist in understanding and confronting their tumorigenic potential. Large-scale analysis of genes and pathways involved in growth and survival of hPSCs Activation of the RAS pathways confers enhanced resistance to PluriSIn-1 treatment Inactivation of the RHO-ROCK pathway gives selective growth advantage to hPSCs The PI3K-AKT and HIPPO pathways are involved in the process of teratoma formation
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Affiliation(s)
- Uri Weissbein
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel
| | - Mordecai Peretz
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel
| | - Omer Plotnik
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel
| | - Ofra Yanuka
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel
| | - Ido Sagi
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel
| | - Tamar Golan-Lev
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel
| | - Nissim Benvenisty
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel.
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31
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Wang Y, Lei T, Dai Q, Ding P, Qiu T, Fang Y. Identification of Potential Molecular Determinants of Murine Embryonic Stem Cell Differentiation by a Transposon-Based Approach. Mol Biotechnol 2018; 60:791-798. [PMID: 30171517 DOI: 10.1007/s12033-018-0110-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Embryonic stem cells (ESCs) are self-renewing pluripotent cells, capable of differentiating into all somatic cell types. The molecular control of self-renewal is relatively well-characterized, whereas how ESCs exit pluripotent state to differentiate is poorly understood. Here we identify two genes are required for differentiation and dozens of intergenic regions that potentially regulate ESC differentiation. We used PiggyBac (PB) transposon-based approach to randomly mutate the genome of ESCs, and generated hundreds of clones that resisted differentiation signals. Each clone was sequenced to determine genomic regions mutated by PB insertion. Intriguingly, many mutations were localized among intergenic regions and we identified two genes are required for differentiation. This study should facilitate further exploration of novel molecular determinants of embryonic stem cell differentiation.
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Affiliation(s)
- Yan Wang
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Tingjun Lei
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.,Center of Growth, Metabolism, and Aging, College of Life Sciences, Sichuan University, Chengdu, 610041, Sichuan, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Qian Dai
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Ping Ding
- Sichuan Cunde Therapeutics, Chengdu, 610093, China
| | - Tong Qiu
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, 610041, Sichuan, China. .,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, Sichuan, China.
| | - Yin Fang
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, 610041, Sichuan, China. .,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, Sichuan, China.
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32
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Webster P, Dawes JC, Dewchand H, Takacs K, Iadarola B, Bolt BJ, Caceres JJ, Kaczor J, Dharmalingam G, Dore M, Game L, Adejumo T, Elliott J, Naresh K, Karimi M, Rekopoulou K, Tan G, Paccanaro A, Uren AG. Subclonal mutation selection in mouse lymphomagenesis identifies known cancer loci and suggests novel candidates. Nat Commun 2018; 9:2649. [PMID: 29985390 PMCID: PMC6037733 DOI: 10.1038/s41467-018-05069-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 05/30/2018] [Indexed: 12/23/2022] Open
Abstract
Determining whether recurrent but rare cancer mutations are bona fide driver mutations remains a bottleneck in cancer research. Here we present the most comprehensive analysis of murine leukemia virus-driven lymphomagenesis produced to date, sequencing 700,000 mutations from >500 malignancies collected at time points throughout tumor development. This scale of data allows novel statistical approaches for identifying selected mutations and yields a high-resolution, genome-wide map of the selective forces surrounding cancer gene loci. We also demonstrate negative selection of mutations that may be deleterious to tumor development indicating novel avenues for therapy. Screening of two BCL2 transgenic models confirmed known drivers of human non-Hodgkin lymphoma, and implicates novel candidates including modifiers of immunosurveillance and MHC loci. Correlating mutations with genotypic and phenotypic features independently of local variance in mutation density also provides support for weakly evidenced cancer genes. An online resource http://mulvdb.org allows customized queries of the entire dataset. Evidence implicating cancer drivers can be sparse when limited to clonal events. Here, the authors present a retrovirus driven in vivo lymphomagenesis time course including hundreds of thousands of subclonal mutations and demonstrate the utility of these in mapping the selective forces affecting cancer gene loci, including negatively selected mutations.
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Affiliation(s)
- Philip Webster
- MRC London Institute of Medical Sciences (LMS), Du Cane Road, London, W12 0NN, UK.,Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK.,Imperial College Healthcare NHS Trust, London, W12 0HS, UK
| | - Joanna C Dawes
- MRC London Institute of Medical Sciences (LMS), Du Cane Road, London, W12 0NN, UK.,Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Hamlata Dewchand
- MRC London Institute of Medical Sciences (LMS), Du Cane Road, London, W12 0NN, UK.,Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Katalin Takacs
- MRC London Institute of Medical Sciences (LMS), Du Cane Road, London, W12 0NN, UK.,Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Barbara Iadarola
- MRC London Institute of Medical Sciences (LMS), Du Cane Road, London, W12 0NN, UK.,Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Bruce J Bolt
- MRC London Institute of Medical Sciences (LMS), Du Cane Road, London, W12 0NN, UK.,Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Juan J Caceres
- Centre for Systems and Synthetic Biology, Department of Computer Science, Royal Holloway, University of London, Egham, TW20 0EX, UK
| | - Jakub Kaczor
- MRC London Institute of Medical Sciences (LMS), Du Cane Road, London, W12 0NN, UK.,Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Gopuraja Dharmalingam
- MRC London Institute of Medical Sciences (LMS), Du Cane Road, London, W12 0NN, UK.,Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Marian Dore
- MRC London Institute of Medical Sciences (LMS), Du Cane Road, London, W12 0NN, UK.,Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Laurence Game
- MRC London Institute of Medical Sciences (LMS), Du Cane Road, London, W12 0NN, UK.,Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Thomas Adejumo
- MRC London Institute of Medical Sciences (LMS), Du Cane Road, London, W12 0NN, UK.,Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - James Elliott
- MRC London Institute of Medical Sciences (LMS), Du Cane Road, London, W12 0NN, UK.,Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Kikkeri Naresh
- Imperial College Healthcare NHS Trust, London, W12 0HS, UK
| | - Mohammad Karimi
- MRC London Institute of Medical Sciences (LMS), Du Cane Road, London, W12 0NN, UK.,Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Katerina Rekopoulou
- MRC London Institute of Medical Sciences (LMS), Du Cane Road, London, W12 0NN, UK.,Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Ge Tan
- MRC London Institute of Medical Sciences (LMS), Du Cane Road, London, W12 0NN, UK.,Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Alberto Paccanaro
- Centre for Systems and Synthetic Biology, Department of Computer Science, Royal Holloway, University of London, Egham, TW20 0EX, UK
| | - Anthony G Uren
- MRC London Institute of Medical Sciences (LMS), Du Cane Road, London, W12 0NN, UK. .,Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK.
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Lu IL, Chen C, Tung CY, Chen HH, Pan JP, Chang CH, Cheng JS, Chen YA, Wang CH, Huang CW, Kang YN, Chang HY, Li LL, Chang KP, Shih YH, Lin CH, Kwan SY, Tsai JW. Identification of genes associated with cortical malformation using a transposon-mediated somatic mutagenesis screen in mice. Nat Commun 2018; 9:2498. [PMID: 29950674 PMCID: PMC6021418 DOI: 10.1038/s41467-018-04880-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 05/23/2018] [Indexed: 12/12/2022] Open
Abstract
Mutations in genes involved in the production, migration, or differentiation of cortical neurons often lead to malformations of cortical development (MCDs). However, many genetic mutations involved in MCD pathogenesis remain unidentified. Here we developed a genetic screening paradigm based on transposon-mediated somatic mutagenesis by in utero electroporation and the inability of mutant neuronal precursors to migrate to the cortex and identified 33 candidate MCD genes. Consistent with the screen, several genes have already been implicated in neural development and disorders. Functional disruption of the candidate genes by RNAi or CRISPR/Cas9 causes altered neuronal distributions that resemble human cortical dysplasia. To verify potential clinical relevance of these candidate genes, we analyzed somatic mutations in brain tissue from patients with focal cortical dysplasia and found that mutations are enriched in these candidate genes. These results demonstrate that this approach is able to identify potential mouse genes involved in cortical development and MCD pathogenesis. Cortical malformations have a variety of causes. Here the authors use transposon mutagenesis to insert mutations into neural stem cells in the developing mouse cortex to screen for new candidate genes for cortical malformation, and validate some targets in human brain tissue.
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Affiliation(s)
- I-Ling Lu
- Institute of Brain Science, National Yang-Ming University, Taipei, 112, Taiwan
| | - Chien Chen
- Department of Neurology, Neurological Institute, Taipei Veterans General Hospital, Taipei, 112, Taiwan.,National Yang-Ming University School of Medicine, Taipei, 112, Taiwan
| | - Chien-Yi Tung
- VYM Genome Research Center of National Yang-Ming University, Taipei, 112, Taiwan.,Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, 112, Taiwan
| | - Hsin-Hung Chen
- National Yang-Ming University School of Medicine, Taipei, 112, Taiwan.,Department of Neurosurgery, Neurological Institute, Taipei Veterans General Hospital, Taipei, 112, Taiwan
| | - Jia-Ping Pan
- VYM Genome Research Center of National Yang-Ming University, Taipei, 112, Taiwan
| | - Chia-Hsiang Chang
- Institute of Brain Science, National Yang-Ming University, Taipei, 112, Taiwan.,Taiwan International Graduate Program (TIGP) in Molecular Medicine, National Yang-Ming University and Academia Sinica, Taipei, 112, Taiwan
| | - Jia-Shing Cheng
- Institute of Brain Science, National Yang-Ming University, Taipei, 112, Taiwan
| | - Yi-An Chen
- Institute of Brain Science, National Yang-Ming University, Taipei, 112, Taiwan
| | - Chun-Hung Wang
- Institute of Brain Science, National Yang-Ming University, Taipei, 112, Taiwan
| | - Chia-Wei Huang
- Institute of Brain Science, National Yang-Ming University, Taipei, 112, Taiwan
| | - Yi-Ning Kang
- Institute of Brain Science, National Yang-Ming University, Taipei, 112, Taiwan
| | - Hsin-Yun Chang
- Institute of Brain Science, National Yang-Ming University, Taipei, 112, Taiwan
| | - Lei-Li Li
- Institute of Brain Science, National Yang-Ming University, Taipei, 112, Taiwan
| | - Kai-Ping Chang
- National Yang-Ming University School of Medicine, Taipei, 112, Taiwan.,Department of Pediatrics, Taipei Veterans General Hospital, Taipei, 112, Taiwan
| | - Yang-Hsin Shih
- National Yang-Ming University School of Medicine, Taipei, 112, Taiwan.,Department of Neurosurgery, Neurological Institute, Taipei Veterans General Hospital, Taipei, 112, Taiwan
| | - Chi-Hung Lin
- VYM Genome Research Center of National Yang-Ming University, Taipei, 112, Taiwan.,Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, 112, Taiwan.,Institute of Biophotonics, National Yang-Ming University, Taipei, 112, Taiwan
| | - Shang-Yeong Kwan
- Department of Neurology, Neurological Institute, Taipei Veterans General Hospital, Taipei, 112, Taiwan.,National Yang-Ming University School of Medicine, Taipei, 112, Taiwan
| | - Jin-Wu Tsai
- Institute of Brain Science, National Yang-Ming University, Taipei, 112, Taiwan. .,Brain Research Center, National Yang-Ming University, Taipei, 112, Taiwan. .,Biophotonics and Molecular Imaging Research Center, National Yang-Ming University, Taipei, 112, Taiwan.
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Proviruses with Long-Term Stable Expression Accumulate in Transcriptionally Active Chromatin Close to the Gene Regulatory Elements: Comparison of ASLV-, HIV- and MLV-Derived Vectors. Viruses 2018. [PMID: 29517993 PMCID: PMC5869509 DOI: 10.3390/v10030116] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Individual groups of retroviruses and retroviral vectors differ in their integration site preference and interaction with the host genome. Hence, immediately after infection genome-wide distribution of integrated proviruses is non-random. During long-term in vitro or persistent in vivo infection, the genomic position and chromatin environment of the provirus affects its transcriptional activity. Thus, a selection of long-term stably expressed proviruses and elimination of proviruses, which have been gradually silenced by epigenetic mechanisms, helps in the identification of genomic compartments permissive for proviral transcription. We compare here the extent and time course of provirus silencing in single cell clones of the K562 human myeloid lymphoblastoma cell line that have been infected with retroviral reporter vectors derived from avian sarcoma/leukosis virus (ASLV), human immunodeficiency virus type 1 (HIV) and murine leukaemia virus (MLV). While MLV proviruses remain transcriptionally active, ASLV proviruses are prone to rapid silencing. The HIV provirus displays gradual silencing only after an extended time period in culture. The analysis of integration sites of long-term stably expressed proviruses shows a strong bias for some genomic features-especially integration close to the transcription start sites of active transcription units. Furthermore, complex analysis of histone modifications enriched at the site of integration points to the accumulation of proviruses of all three groups in gene regulatory segments, particularly close to the enhancer loci. We conclude that the proximity to active regulatory chromatin segments correlates with stable provirus expression in various retroviral species.
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35
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Šenigl F, Miklík D, Auxt M, Hejnar J. Accumulation of long-term transcriptionally active integrated retroviral vectors in active promoters and enhancers. Nucleic Acids Res 2018; 45:12752-12765. [PMID: 29244184 PMCID: PMC5727404 DOI: 10.1093/nar/gkx889] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 09/26/2017] [Indexed: 01/13/2023] Open
Abstract
Most retroviruses preferentially integrate into certain genomic locations and, as a result, their genome-wide integration patterns are non-random. We investigate the epigenetic landscape of integrated retroviral vectors and correlate it with the long-term stability of proviral transcription. Retroviral vectors derived from the avian sarcoma/leukosis virus expressing the GFP reporter were used to transduce the human myeloid lymphoblastoma cell line K562. Because of efficient silencing of avian retrovirus in mammalian cells, only ∼3% of established clones displayed stable proviral expression. We analyzed the vector integration sites in non-selected cells and in clones selected for the GFP expression. This selection led to overrepresentation of proviruses integrated in active transcription units, with particular accumulation in promoter-proximal areas. In parallel, we investigated the integration of vectors equipped with an anti-silencing CpG island core sequence. Such modification increased the frequency of stably expressing proviruses by one order. The modified vectors are also overrepresented in active transcription units, but stably expressed in distal parts of transcriptional units further away from promoters with marked accumulation in enhancers. These results suggest that integrated retroviruses subject to gradual epigenetic silencing during long-term cultivation. Among most genomic compartments, however, active promoters and enhancers protect the adjacent retroviruses from transcriptional silencing.
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Affiliation(s)
- Filip Šenigl
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, CZ-14220 Prague 4, Czech Republic
| | - Dalibor Miklík
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, CZ-14220 Prague 4, Czech Republic
| | - Miroslav Auxt
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, CZ-14220 Prague 4, Czech Republic
| | - Jirí Hejnar
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, CZ-14220 Prague 4, Czech Republic
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36
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Kundu S, Ali MA, Handin N, Padhan N, Larsson J, Karoutsou M, Ban K, Wiśniewski JR, Artursson P, He L, Hellström M, Sjöblom T. Linking FOXO3, NCOA3, and TCF7L2 to Ras pathway phenotypes through a genome-wide forward genetic screen in human colorectal cancer cells. Genome Med 2018; 10:2. [PMID: 29301589 PMCID: PMC5755028 DOI: 10.1186/s13073-017-0511-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 12/13/2017] [Indexed: 12/20/2022] Open
Abstract
Background The Ras pathway genes KRAS, BRAF, or ERBBs have somatic mutations in ~ 60% of human colorectal carcinomas. At present, it is unknown whether the remaining cases lack mutations activating the Ras pathway or whether they have acquired mutations in genes hitherto unknown to belong to the pathway. Methods To address the second possibility and extend the compendium of Ras pathway genes, we used genome-wide transposon mutagenesis of two human colorectal cancer cell systems deprived of their activating KRAS or BRAF allele to identify genes enabling growth in low glucose, a Ras pathway phenotype, when targeted. Results Of the 163 recurrently targeted genes in the two different genetic backgrounds, one-third were known cancer genes and one-fifth had links to the EGFR/Ras/MAPK pathway. When compared to cancer genome sequencing datasets, nine genes also mutated in human colorectal cancers were identified. Among these, stable knockdown of FOXO3, NCOA3, and TCF7L2 restored growth in low glucose but reduced MEK/MAPK phosphorylation, reduced anchorage-independent growth, and modulated expressions of GLUT1 and Ras pathway related proteins. Knockdown of NCOA3 and FOXO3 significantly decreased the sensitivity to cetuximab of KRAS mutant but not wild-type cells. Conclusions This work establishes a proof-of-concept that human cell-based genome-wide forward genetic screens can assign genes to pathways with clinical importance in human colorectal cancer. Electronic supplementary material The online version of this article (doi:10.1186/s13073-017-0511-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Snehangshu Kundu
- Department of Immunology, Science For Life Laboratory, Genetics and Pathology, Rudbeck Laboratory, Dag Hammarskjölds väg 21, Uppsala, 751 85, Sweden
| | - Muhammad Akhtar Ali
- Department of Immunology, Science For Life Laboratory, Genetics and Pathology, Rudbeck Laboratory, Dag Hammarskjölds väg 21, Uppsala, 751 85, Sweden
| | - Niklas Handin
- Department of Pharmacy, Uppsala University, Uppsala, 751 23, Sweden
| | - Narendra Padhan
- Department of Immunology, Science For Life Laboratory, Genetics and Pathology, Rudbeck Laboratory, Dag Hammarskjölds väg 21, Uppsala, 751 85, Sweden
| | - Jimmy Larsson
- Department of Immunology, Science For Life Laboratory, Genetics and Pathology, Rudbeck Laboratory, Dag Hammarskjölds väg 21, Uppsala, 751 85, Sweden
| | - Maria Karoutsou
- Department of Immunology, Science For Life Laboratory, Genetics and Pathology, Rudbeck Laboratory, Dag Hammarskjölds väg 21, Uppsala, 751 85, Sweden
| | - Kenneth Ban
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, #02-06, Singapore, 117597, Republic of Singapore.,Institute of Molecular and Cell Biology, A*STAR, Singapore, 138673, Republic of Singapore
| | - Jacek R Wiśniewski
- Department of Proteomics and Signal Transduction, Biochemical Proteomics Group, Max-Planck Institute of Biochemistry, Martinsried, 82152, Germany
| | - Per Artursson
- Department of Pharmacy, Uppsala University, Uppsala, 751 23, Sweden
| | - Liqun He
- Department of Immunology, Science For Life Laboratory, Genetics and Pathology, Rudbeck Laboratory, Dag Hammarskjölds väg 21, Uppsala, 751 85, Sweden.,Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin Neurological Institute, Key Laboratory of Post-Neuroinjury Neuro-Repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin, 300052, China
| | - Mats Hellström
- Department of Immunology, Science For Life Laboratory, Genetics and Pathology, Rudbeck Laboratory, Dag Hammarskjölds väg 21, Uppsala, 751 85, Sweden
| | - Tobias Sjöblom
- Department of Immunology, Science For Life Laboratory, Genetics and Pathology, Rudbeck Laboratory, Dag Hammarskjölds väg 21, Uppsala, 751 85, Sweden.
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Li X, Song G, Zhao Y, Zhao F, Liu C, Liu D, Li Q, Cui Z. Claudin7b is required for the formation and function of inner ear in zebrafish. J Cell Physiol 2017; 233:3195-3206. [DOI: 10.1002/jcp.26162] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Accepted: 08/21/2017] [Indexed: 11/07/2022]
Affiliation(s)
- Xiaohui Li
- State Key Laboratory of Freshwater Ecology and Biotechnology; Institute of Hydrobiology; Chinese Academy of Sciences; Wuhan China
- University of Chinese Academy of Sciences; Beijing China
| | - Guili Song
- State Key Laboratory of Freshwater Ecology and Biotechnology; Institute of Hydrobiology; Chinese Academy of Sciences; Wuhan China
| | - Yasong Zhao
- State Key Laboratory of Freshwater Ecology and Biotechnology; Institute of Hydrobiology; Chinese Academy of Sciences; Wuhan China
- University of Chinese Academy of Sciences; Beijing China
| | - Feng Zhao
- Department of Biology; Southern University of Science and Technology; Shenzhen China
| | - Chunyan Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology; Institute of Hydrobiology; Chinese Academy of Sciences; Wuhan China
| | - Dong Liu
- Department of Biology; Southern University of Science and Technology; Shenzhen China
| | - Qing Li
- State Key Laboratory of Freshwater Ecology and Biotechnology; Institute of Hydrobiology; Chinese Academy of Sciences; Wuhan China
| | - Zongbin Cui
- State Key Laboratory of Freshwater Ecology and Biotechnology; Institute of Hydrobiology; Chinese Academy of Sciences; Wuhan China
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38
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Cain-Hom C, Splinter E, van Min M, Simonis M, van de Heijning M, Martinez M, Asghari V, Cox JC, Warming S. Efficient mapping of transgene integration sites and local structural changes in Cre transgenic mice using targeted locus amplification. Nucleic Acids Res 2017; 45:e62. [PMID: 28053125 PMCID: PMC5416772 DOI: 10.1093/nar/gkw1329] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 12/20/2016] [Indexed: 12/23/2022] Open
Abstract
Cre/LoxP technology is widely used in the field of mouse genetics for spatial and/or temporal regulation of gene function. For Cre lines generated via pronuclear microinjection of a Cre transgene construct, the integration site is random and in most cases not known. Integration of a transgene can disrupt an endogenous gene, potentially interfering with interpretation of the phenotype. In addition, knowledge of where the transgene is integrated is important for planning of crosses between animals carrying a conditional allele and a given Cre allele in case the alleles are on the same chromosome. We have used targeted locus amplification (TLA) to efficiently map the transgene location in seven previously published Cre and CreERT2 transgenic lines. In all lines, transgene insertion was associated with structural changes of variable complexity, illustrating the importance of testing for rearrangements around the integration site. In all seven lines the exact integration site and breakpoint sequences were identified. Our methods, data and genotyping assays can be used as a resource for the mouse community and our results illustrate the power of the TLA method to not only efficiently map the integration site of any transgene, but also provide additional information regarding the transgene integration events.
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Affiliation(s)
- Carol Cain-Hom
- Department of Transgenic Technology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Erik Splinter
- Cergentis BV, Yalelaan 62, 3584 CM Utrecht, the Netherlands
| | - Max van Min
- Cergentis BV, Yalelaan 62, 3584 CM Utrecht, the Netherlands
| | | | | | - Maria Martinez
- Department of Transgenic Technology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Vida Asghari
- Department of Transgenic Technology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - J Colin Cox
- Department of Transgenic Technology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Søren Warming
- Department of Molecular Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
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39
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Fate mapping of human glioblastoma reveals an invariant stem cell hierarchy. Nature 2017; 549:227-232. [PMID: 28854171 PMCID: PMC5608080 DOI: 10.1038/nature23666] [Citation(s) in RCA: 255] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 07/24/2017] [Indexed: 12/30/2022]
Abstract
Human glioblastomas harbour a subpopulation of glioblastoma stem cells that drive tumorigenesis. However, the origin of intratumoural functional heterogeneity between glioblastoma cells remains poorly understood. Here we study the clonal evolution of barcoded glioblastoma cells in an unbiased way following serial xenotransplantation to define their individual fate behaviours. Independent of an evolving mutational signature, we show that the growth of glioblastoma clones in vivo is consistent with a remarkably neutral process involving a conserved proliferative hierarchy rooted in glioblastoma stem cells. In this model, slow-cycling stem-like cells give rise to a more rapidly cycling progenitor population with extensive self-maintenance capacity, which in turn generates non-proliferative cells. We also identify rare 'outlier' clones that deviate from these dynamics, and further show that chemotherapy facilitates the expansion of pre-existing drug-resistant glioblastoma stem cells. Finally, we show that functionally distinct glioblastoma stem cells can be separately targeted using epigenetic compounds, suggesting new avenues for glioblastoma-targeted therapy.
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40
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Polymorphic Nature of Human T-Cell Leukemia Virus Type 1 Particle Cores as Revealed through Characterization of a Chronically Infected Cell Line. J Virol 2017; 91:JVI.00369-17. [PMID: 28615198 DOI: 10.1128/jvi.00369-17] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Accepted: 05/05/2017] [Indexed: 12/18/2022] Open
Abstract
Human T-cell leukemia virus type 1 (HTLV-1) is the etiological agent of adult T-cell leukemia (ATL) and HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP). HTLV-1 cell-to-cell transmission is dependent on the release of infectious virus particles into the virological synapse. The HTLV-1 particle structure is still poorly understood, and previous studies analyzed viruses produced by transformed lymphocytic cell lines chronically infected with HTLV-1, particularly the MT-2 cell line, which harbors truncated proviruses and expresses aberrant forms of the Gag protein. In this study, we demonstrate that the chronically infected SP cell line harbors a relatively low number of proviruses, making it a more promising experimental system for the study of the HTLV-1 particle structure. We first identified the genomic sites of integration and characterized the genetic structure of the gag region in each provirus. We also determined that despite encoding a truncated Gag protein, only the full-length Gag protein was incorporated into virus particles. Cryo-transmission electron microscopy analyses of the purified virus particles revealed three classes of particles based upon capsid core morphology: complete cores, incomplete cores, and particles without distinct electron densities that would correlate with the capsid region of a core structure. Observed cores were generally polygonal, and virus particles were on average 115 nm in diameter. These data corroborate particle morphologies previously observed for MT-2 cells and provide evidence that the known poor infectivity of HTLV-1 particles may correlate with HTLV-1 particle populations containing few virus particles possessing a complete capsid core structure.IMPORTANCE Studies of retroviral particle core morphology have demonstrated a correlation between capsid core stability and the relative infectivity of the virus. In this study, we used cryo-transmission electron microscopy to demonstrate that HTLV-1 particles produced from a distinct chronically infected cell line are polymorphic in nature, with many particles lacking organized electron densities that would correlate with a complete core structure. These findings have important implications for infectious HTLV-1 spread, particularly in the context of cell-to-cell transmission, a critical step in HTLV-1 transmission and pathogenesis.
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41
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Genome-Wide Screening Uncovers the Significance of N-Sulfation of Heparan Sulfate as a Host Cell Factor for Chikungunya Virus Infection. J Virol 2017; 91:JVI.00432-17. [PMID: 28404855 DOI: 10.1128/jvi.00432-17] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 04/03/2017] [Indexed: 02/07/2023] Open
Abstract
The molecular mechanisms underlying chikungunya virus (CHIKV) infection are poorly characterized. In this study, we analyzed the host factors involved in CHIKV infection using genome-wide screening. Human haploid HAP1 cells, into which an exon-trapping vector was introduced, were challenged with a vesicular stomatitis virus pseudotype bearing the CHIKV E3 to E1 envelope proteins. Analysis of genes enriched in the cells resistant to the pseudotyped virus infection unveiled a critical role of N-sulfation of heparan sulfate (HS) for the infectivity of the clinically isolated CHIKV Thai#16856 strain to HAP1 cells. Knockout of NDST1 that catalyzes N-sulfation of HS greatly decreased the binding and infectivity of CHIKV Thai#16856 strain but not infectivity of Japanese encephalitis virus (JEV) and yellow fever virus (YFV). While glycosaminoglycans were commonly required for the efficient infectivity of CHIKV, JEV, and YFV, as shown by using B3GAT3 knockout cells, the tropism for N-sulfate was specific to CHIKV. Expression of chondroitin sulfate (CS) in NDST1-knockout HAP1 cells did not restore the binding of CHIKV Thai#16856 strain and the infectivity of its pseudotype but restored the infectivity of authentic CHIKV Thai#16856, suggesting that CS functions at later steps after CHIKV binding. Among the genes enriched in this screening, we found that TM9SF2 is critical for N-sulfation of HS and therefore for CHIKV infection because it is involved in the proper localization and stability of NDST1. Determination of the significance of and the relevant proteins to N-sulfation of HS may contribute to understanding mechanisms of CHIKV propagation, cell tropism, and pathogenesis.IMPORTANCE Recent outbreaks of chikungunya fever have increased its clinical importance. Chikungunya virus (CHIKV) utilizes host glycosaminoglycans to bind efficiently to its target cells. However, the substructure in glycosaminoglycans required for CHIKV infection have not been characterized. Here, we unveil that N-sulfate in heparan sulfate is essential for the efficient infection of a clinical CHIKV strain to HAP1 cells and that chondroitin sulfate does not help the CHIKV binding but does play roles at the later steps in HAP1 cells. We show, by comparing previous reports using Chinese hamster ovary cells, along with another observation that enhanced infectivity of CHIKV bearing Arg82 in envelope E2 does not depend on glycosaminoglycans in HAP1 cells, that the infection manner of CHIKV varies among host cells. We also show that TM9SF2 is required for CHIKV infection to HAP1 cells because it is involved in the N-sulfation of heparan sulfate through ensuring NDST1 activity.
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42
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Transposon insertional mutagenesis in mice identifies human breast cancer susceptibility genes and signatures for stratification. Proc Natl Acad Sci U S A 2017; 114:E2215-E2224. [PMID: 28251929 PMCID: PMC5358385 DOI: 10.1073/pnas.1701512114] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Despite concerted efforts to identify causal genes that drive breast cancer (BC) initiation and progression, we have yet to establish robust signatures to stratify patient risk. Here we used in vivo transposon-based forward genetic screening to identify potentially relevant BC driver genes. Integrating this approach with survival prediction analysis, we identified six gene pairs that could prognose human BC subtypes into high-, intermediate-, and low-risk groups with high confidence and reproducibility. Furthermore, we identified susceptibility gene sets for basal and claudin-low subtypes (21 and 16 genes, respectively) that stratify patients into three relative risk subgroups. These signatures offer valuable prognostic insight into the genetic basis of BC and allow further exploration of the interconnectedness of BC driver genes during disease progression. Robust prognostic gene signatures and therapeutic targets are difficult to derive from expression profiling because of the significant heterogeneity within breast cancer (BC) subtypes. Here, we performed forward genetic screening in mice using Sleeping Beauty transposon mutagenesis to identify candidate BC driver genes in an unbiased manner, using a stabilized N-terminal truncated β-catenin gene as a sensitizer. We identified 134 mouse susceptibility genes from 129 common insertion sites within 34 mammary tumors. Of these, 126 genes were orthologous to protein-coding genes in the human genome (hereafter, human BC susceptibility genes, hBCSGs), 70% of which are previously reported cancer-associated genes, and ∼16% are known BC suppressor genes. Network analysis revealed a gene hub consisting of E1A binding protein P300 (EP300), CD44 molecule (CD44), neurofibromin (NF1) and phosphatase and tensin homolog (PTEN), which are linked to a significant number of mutated hBCSGs. From our survival prediction analysis of the expression of human BC genes in 2,333 BC cases, we isolated a six-gene-pair classifier that stratifies BC patients with high confidence into prognostically distinct low-, moderate-, and high-risk subgroups. Furthermore, we proposed prognostic classifiers identifying three basal and three claudin-low tumor subgroups. Intriguingly, our hBCSGs are mostly unrelated to cell cycle/mitosis genes and are distinct from the prognostic signatures currently used for stratifying BC patients. Our findings illustrate the strength and validity of integrating functional mutagenesis screens in mice with human cancer transcriptomic data to identify highly prognostic BC subtyping biomarkers.
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43
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Zhou Y, Zhang H, Wei W. Simultaneous generation of multi-gene knockouts in human cells. FEBS Lett 2016; 590:4343-4353. [PMID: 27800615 PMCID: PMC5396285 DOI: 10.1002/1873-3468.12469] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 10/16/2016] [Accepted: 10/18/2016] [Indexed: 11/10/2022]
Abstract
Genome‐editing techniques enable the generation of gene knockouts in various mammalian cell lines. However, it remains technically challenging to completely disrupt a targeted gene using a canonical method in a timely manner. To improve the efficiency of producing reliable genomic modifications, we designed a method using a linear donor fragment containing a reporter system. Combined with a homologous recombination‐independent knock‐in strategy, we successfully enriched those cell clones that specifically carry the target gene mutations. We observed a much improved success rate when generating single‐ and multiple‐gene knockouts in a one‐step procedure using this special protocol coupled with the CRISPR/Cas9 system. This new approach further empowers the molecular biological study of genes and their functions.
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Affiliation(s)
- Yuexin Zhou
- Biodynamic Optical Imaging Center (BIOPIC), Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Hongmin Zhang
- Biodynamic Optical Imaging Center (BIOPIC), Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.,Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Wensheng Wei
- Biodynamic Optical Imaging Center (BIOPIC), Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
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44
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Jung CJ, Ménoret S, Brusselle L, Tesson L, Usal C, Chenouard V, Remy S, Ouisse LH, Poirier N, Vanhove B, de Jong PJ, Anegon I. Comparative Analysis of piggyBac, CRISPR/Cas9 and TALEN Mediated BAC Transgenesis in the Zygote for the Generation of Humanized SIRPA Rats. Sci Rep 2016; 6:31455. [PMID: 27530248 PMCID: PMC4987655 DOI: 10.1038/srep31455] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 07/14/2016] [Indexed: 01/12/2023] Open
Abstract
BAC transgenic mammalian systems offer an important platform for recapitulating human gene expression and disease modeling. While the larger body mass, and greater genetic and physiologic similarity to humans render rats well suited for reproducing human immune diseases and evaluating therapeutic strategies, difficulties of generating BAC transgenic rats have hindered progress. Thus, an efficient method for BAC transgenesis in rats would be valuable. Immunodeficient mice carrying a human SIRPA transgene have previously been shown to support improved human cell hematopoiesis. Here, we have generated for the first time, human SIRPA BAC transgenic rats, for which the gene is faithfully expressed, functionally active, and germline transmissible. To do this, human SIRPA BAC was modified with elements to work in coordination with genome engineering technologies-piggyBac, CRISPR/Cas9 or TALEN. Our findings show that piggyBac transposition is a more efficient approach than the classical BAC transgenesis, resulting in complete BAC integration with predictable end sequences, thereby permitting precise assessment of the integration site. Neither CRISPR/Cas9 nor TALEN increased BAC transgenesis. Therefore, an efficient generation of human SIRPA transgenic rats using piggyBac opens opportunities for expansion of humanized transgenic rat models in the future to advance biomedical research and therapeutic applications.
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Affiliation(s)
- Chris J Jung
- Center for Genetics, Children's Hospital Oakland Research Institute, CA 94609, Oakland, USA
| | - Séverine Ménoret
- Platform Rat Transgenesis Immunophenomic, SFR Francois Bonamy, CNRS UMS3556 Nantes, F44093, France.,INSERM UMR 1064-ITUN; CHU de Nantes, Nantes F44093, France
| | - Lucas Brusselle
- Platform Rat Transgenesis Immunophenomic, SFR Francois Bonamy, CNRS UMS3556 Nantes, F44093, France.,INSERM UMR 1064-ITUN; CHU de Nantes, Nantes F44093, France
| | - Laurent Tesson
- Platform Rat Transgenesis Immunophenomic, SFR Francois Bonamy, CNRS UMS3556 Nantes, F44093, France.,INSERM UMR 1064-ITUN; CHU de Nantes, Nantes F44093, France
| | - Claire Usal
- Platform Rat Transgenesis Immunophenomic, SFR Francois Bonamy, CNRS UMS3556 Nantes, F44093, France.,INSERM UMR 1064-ITUN; CHU de Nantes, Nantes F44093, France
| | - Vanessa Chenouard
- Platform Rat Transgenesis Immunophenomic, SFR Francois Bonamy, CNRS UMS3556 Nantes, F44093, France.,INSERM UMR 1064-ITUN; CHU de Nantes, Nantes F44093, France
| | - Séverine Remy
- Platform Rat Transgenesis Immunophenomic, SFR Francois Bonamy, CNRS UMS3556 Nantes, F44093, France.,INSERM UMR 1064-ITUN; CHU de Nantes, Nantes F44093, France
| | - Laure-Hélène Ouisse
- Platform Rat Transgenesis Immunophenomic, SFR Francois Bonamy, CNRS UMS3556 Nantes, F44093, France.,INSERM UMR 1064-ITUN; CHU de Nantes, Nantes F44093, France
| | - Nicolas Poirier
- INSERM UMR 1064-ITUN; CHU de Nantes, Nantes F44093, France.,OSE Immunotherapeutics, 44000 Nantes, France
| | - Bernard Vanhove
- INSERM UMR 1064-ITUN; CHU de Nantes, Nantes F44093, France.,OSE Immunotherapeutics, 44000 Nantes, France
| | - Pieter J de Jong
- Center for Genetics, Children's Hospital Oakland Research Institute, CA 94609, Oakland, USA
| | - Ignacio Anegon
- Platform Rat Transgenesis Immunophenomic, SFR Francois Bonamy, CNRS UMS3556 Nantes, F44093, France.,INSERM UMR 1064-ITUN; CHU de Nantes, Nantes F44093, France
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45
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Wojtowicz EE, Lechman ER, Hermans KG, Schoof EM, Wienholds E, Isserlin R, van Veelen PA, Broekhuis MJC, Janssen GMC, Trotman-Grant A, Dobson SM, Krivdova G, Elzinga J, Kennedy J, Gan OI, Sinha A, Ignatchenko V, Kislinger T, Dethmers-Ausema B, Weersing E, Alemdehy MF, de Looper HWJ, Bader GD, Ritsema M, Erkeland SJ, Bystrykh LV, Dick JE, de Haan G. Ectopic miR-125a Expression Induces Long-Term Repopulating Stem Cell Capacity in Mouse and Human Hematopoietic Progenitors. Cell Stem Cell 2016; 19:383-96. [PMID: 27424784 DOI: 10.1016/j.stem.2016.06.008] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 04/01/2016] [Accepted: 06/15/2016] [Indexed: 12/25/2022]
Abstract
Umbilical cord blood (CB) is a convenient and broadly used source of hematopoietic stem cells (HSCs) for allogeneic stem cell transplantation. However, limiting numbers of HSCs remain a major constraint for its clinical application. Although one feasible option would be to expand HSCs to improve therapeutic outcome, available protocols and the molecular mechanisms governing the self-renewal of HSCs are unclear. Here, we show that ectopic expression of a single microRNA (miRNA), miR-125a, in purified murine and human multipotent progenitors (MPPs) resulted in increased self-renewal and robust long-term multi-lineage repopulation in transplanted recipient mice. Using quantitative proteomics and western blot analysis, we identified a restricted set of miR-125a targets involved in conferring long-term repopulating capacity to MPPs in humans and mice. Our findings offer the innovative potential to use MPPs with enhanced self-renewal activity to augment limited sources of HSCs to improve clinical protocols.
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Affiliation(s)
- Edyta E Wojtowicz
- Laboratory of Ageing Biology and Stem Cells, European Research Institute for the Biology of Ageing, University Medical Centre Groningen, University of Groningen, Antonius Deusinglaan 1, 9700 AV Groningen, the Netherlands
| | - Eric R Lechman
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Karin G Hermans
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Erwin M Schoof
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Erno Wienholds
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Ruth Isserlin
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Peter A van Veelen
- Departments of Immunohematology and Blood Transfusion, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Mathilde J C Broekhuis
- Laboratory of Ageing Biology and Stem Cells, European Research Institute for the Biology of Ageing, University Medical Centre Groningen, University of Groningen, Antonius Deusinglaan 1, 9700 AV Groningen, the Netherlands
| | - George M C Janssen
- Departments of Immunohematology and Blood Transfusion, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Aaron Trotman-Grant
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Stephanie M Dobson
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Gabriela Krivdova
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Jantje Elzinga
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - James Kennedy
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Olga I Gan
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Ankit Sinha
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Vladimir Ignatchenko
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Thomas Kislinger
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Bertien Dethmers-Ausema
- Laboratory of Ageing Biology and Stem Cells, European Research Institute for the Biology of Ageing, University Medical Centre Groningen, University of Groningen, Antonius Deusinglaan 1, 9700 AV Groningen, the Netherlands
| | - Ellen Weersing
- Laboratory of Ageing Biology and Stem Cells, European Research Institute for the Biology of Ageing, University Medical Centre Groningen, University of Groningen, Antonius Deusinglaan 1, 9700 AV Groningen, the Netherlands
| | - Mir Farshid Alemdehy
- Department of Hematology, Erasmus University Medical Center Cancer Institute, Wytemaweg 80, 3015 CN Rotterdam, the Netherlands
| | - Hans W J de Looper
- Department of Hematology, Erasmus University Medical Center Cancer Institute, Wytemaweg 80, 3015 CN Rotterdam, the Netherlands
| | - Gary D Bader
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Martha Ritsema
- Laboratory of Ageing Biology and Stem Cells, European Research Institute for the Biology of Ageing, University Medical Centre Groningen, University of Groningen, Antonius Deusinglaan 1, 9700 AV Groningen, the Netherlands
| | - Stefan J Erkeland
- Department of Immunology, Erasmus University Medical Center, Wytemaweg 80, 3015CN Rotterdam, the Netherlands
| | - Leonid V Bystrykh
- Laboratory of Ageing Biology and Stem Cells, European Research Institute for the Biology of Ageing, University Medical Centre Groningen, University of Groningen, Antonius Deusinglaan 1, 9700 AV Groningen, the Netherlands
| | - John E Dick
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
| | - Gerald de Haan
- Laboratory of Ageing Biology and Stem Cells, European Research Institute for the Biology of Ageing, University Medical Centre Groningen, University of Groningen, Antonius Deusinglaan 1, 9700 AV Groningen, the Netherlands.
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46
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Palangat M, Larson DR. Single-gene dual-color reporter cell line to analyze RNA synthesis in vivo. Methods 2016; 103:77-85. [PMID: 27068658 PMCID: PMC7781226 DOI: 10.1016/j.ymeth.2016.04.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 04/07/2016] [Indexed: 10/22/2022] Open
Abstract
RNA synthesis occurs through the multi-step process of transcription which consists of initiation, elongation, termination, and cleavage of the nascent RNA. In recent years, post-initiation events have attracted considerable attention as regulatory steps in gene expression. In particular, changes in elongation rate have been proposed to alter RNA fate either through changes in RNA secondary structure or recruitment of trans-acting factors, but systematic approaches for perturbing and measuring elongation rate are currently lacking. Here, we describe a system for precisely measuring elongation dynamics for single nascent transcripts at a single gene locus in human cell lines. The system is based on observing the production of fluorescently labeled RNA stem loops which flank a region of interest. The region of interest can be altered using flp recombinases, thus allowing one to study the effects of cis-acting sequences on transcription rate. The dual-color RNAs which are made during this process are exported and translated, thus enabling visualization of each step in gene expression.
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Affiliation(s)
- Murali Palangat
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Daniel R Larson
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States.
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Sokol M, Jessen KM, Pedersen FS. Utility of next-generation RNA-sequencing in identifying chimeric transcription involving human endogenous retroviruses. APMIS 2016; 124:127-39. [PMID: 26818267 DOI: 10.1111/apm.12477] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 10/12/2015] [Indexed: 12/13/2022]
Abstract
Several studies have shown that human endogenous retroviruses and endogenous retrovirus-like repeats (here collectively HERVs) impose direct regulation on human genes through enhancer and promoter motifs present in their long terminal repeats (LTRs). Although chimeric transcription in which novel gene isoforms containing retroviral and human sequence are transcribed from viral promoters are commonly associated with disease, regulation by HERVs is beneficial in other settings; for example, in human testis chimeric isoforms of TP63 induced by an ERV9 LTR protect the male germ line upon DNA damage by inducing apoptosis, whereas in the human globin locus the γ- and β-globin switch during normal hematopoiesis is mediated by complex interactions of an ERV9 LTR and surrounding human sequence. The advent of deep sequencing or next-generation sequencing (NGS) has revolutionized the way researchers solve important scientific questions and develop novel hypotheses in relation to human genome regulation. We recently applied next-generation paired-end RNA-sequencing (RNA-seq) together with chromatin immunoprecipitation with sequencing (ChIP-seq) to examine ERV9 chimeric transcription in human reference cell lines from Encyclopedia of DNA Elements (ENCODE). This led to the discovery of advanced regulation mechanisms by ERV9s and other HERVs across numerous human loci including transcription of large gene-unannotated genomic regions, as well as cooperative regulation by multiple HERVs and non-LTR repeats such as Alu elements. In this article, well-established examples of human gene regulation by HERVs are reviewed followed by a description of paired-end RNA-seq, and its application in identifying chimeric transcription genome-widely. Based on integrative analyses of RNA-seq and ChIP-seq, data we then present novel examples of regulation by ERV9s of tumor suppressor genes CADM2 and SEMA3A, as well as transcription of an unannotated region. Taken together, this article highlights the high suitability of contemporary sequencing methods in future analyses of human biology in relation to evolutionary acquired retroviruses in the human genome.
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Affiliation(s)
- Martin Sokol
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | | | - Finn Skou Pedersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
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Bronner IF, Otto TD, Zhang M, Udenze K, Wang C, Quail MA, Jiang RHY, Adams JH, Rayner JC. Quantitative insertion-site sequencing (QIseq) for high throughput phenotyping of transposon mutants. Genome Res 2016; 26:980-9. [PMID: 27197223 PMCID: PMC4937560 DOI: 10.1101/gr.200279.115] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 05/04/2016] [Indexed: 01/06/2023]
Abstract
Genetic screening using random transposon insertions has been a powerful tool for uncovering biology in prokaryotes, where whole-genome saturating screens have been performed in multiple organisms. In eukaryotes, such screens have proven more problematic, in part because of the lack of a sensitive and robust system for identifying transposon insertion sites. We here describe quantitative insertion-site sequencing, or QIseq, which uses custom library preparation and Illumina sequencing technology and is able to identify insertion sites from both the 5′ and 3′ ends of the transposon, providing an inbuilt level of validation. The approach was developed using piggyBac mutants in the human malaria parasite Plasmodium falciparum but should be applicable to many other eukaryotic genomes. QIseq proved accurate, confirming known sites in >100 mutants, and sensitive, identifying and monitoring sites over a >10,000-fold dynamic range of sequence counts. Applying QIseq to uncloned parasites shortly after transfections revealed multiple insertions in mixed populations and suggests that >4000 independent mutants could be generated from relatively modest scales of transfection, providing a clear pathway to genome-scale screens in P. falciparum. QIseq was also used to monitor the growth of pools of previously cloned mutants and reproducibly differentiated between deleterious and neutral mutations in competitive growth. Among the mutants with fitness defects was a mutant with a piggyBac insertion immediately upstream of the kelch protein K13 gene associated with artemisinin resistance, implying mutants in this gene may have competitive fitness costs. QIseq has the potential to enable the scale-up of piggyBac-mediated genetics across multiple eukaryotic systems.
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Affiliation(s)
- Iraad F Bronner
- Malaria Programme, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Thomas D Otto
- Malaria Programme, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Min Zhang
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, Tampa, Florida 33612, USA
| | - Kenneth Udenze
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, Tampa, Florida 33612, USA
| | - Chengqi Wang
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, Tampa, Florida 33612, USA
| | - Michael A Quail
- Malaria Programme, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Rays H Y Jiang
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, Tampa, Florida 33612, USA
| | - John H Adams
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, Tampa, Florida 33612, USA
| | - Julian C Rayner
- Malaria Programme, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
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Pandzic T, Larsson J, He L, Kundu S, Ban K, Akhtar-Ali M, Hellström AR, Schuh A, Clifford R, Blakemore SJ, Strefford JC, Baumann T, Lopez-Guillermo A, Campo E, Ljungström V, Mansouri L, Rosenquist R, Sjöblom T, Hellström M. Transposon Mutagenesis Reveals Fludarabine Resistance Mechanisms in Chronic Lymphocytic Leukemia. Clin Cancer Res 2016; 22:6217-6227. [PMID: 26957556 DOI: 10.1158/1078-0432.ccr-15-2903] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 02/16/2016] [Accepted: 02/17/2016] [Indexed: 11/16/2022]
Abstract
PURPOSE To identify resistance mechanisms for the chemotherapeutic drug fludarabine in chronic lymphocytic leukemia (CLL), as innate and acquired resistance to fludarabine-based chemotherapy represents a major challenge for long-term disease control. EXPERIMENTAL DESIGN We used piggyBac transposon-mediated mutagenesis, combined with next-generation sequencing, to identify genes that confer resistance to fludarabine in a human CLL cell line. RESULTS In total, this screen identified 782 genes with transposon integrations in fludarabine-resistant pools of cells. One of the identified genes is a known resistance mediator DCK (deoxycytidine kinase), which encodes an enzyme that is essential for the phosphorylation of the prodrug to the active metabolite. BMP2K, a gene not previously linked to CLL, was also identified as a modulator of response to fludarabine. In addition, 10 of 782 transposon-targeted genes had previously been implicated in treatment resistance based on somatic mutations seen in patients refractory to fludarabine-based therapy. Functional characterization of these genes supported a significant role for ARID5B and BRAF in fludarabine sensitivity. Finally, pathway analysis of transposon-targeted genes and RNA-seq profiling of fludarabine-resistant cells suggested deregulated MAPK signaling as involved in mediating drug resistance in CLL. CONCLUSIONS To our knowledge, this is the first forward genetic screen for chemotherapy resistance in CLL. The screen pinpointed novel genes and pathways involved in fludarabine resistance along with previously known resistance mechanisms. Transposon screens can therefore aid interpretation of cancer genome sequencing data in the identification of genes modifying sensitivity to chemotherapy. Clin Cancer Res; 22(24); 6217-27. ©2016 AACR.
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Affiliation(s)
- Tatjana Pandzic
- Department of Immunology, Genetics and Pathology, Science for Life laboratory, Uppsala University, Uppsala, Sweden
| | - Jimmy Larsson
- Department of Immunology, Genetics and Pathology, Science for Life laboratory, Uppsala University, Uppsala, Sweden
| | - Liqun He
- Department of Immunology, Genetics and Pathology, Science for Life laboratory, Uppsala University, Uppsala, Sweden
| | - Snehangshu Kundu
- Department of Immunology, Genetics and Pathology, Science for Life laboratory, Uppsala University, Uppsala, Sweden
| | - Kenneth Ban
- Department of Immunology, Genetics and Pathology, Science for Life laboratory, Uppsala University, Uppsala, Sweden.,Department of Biochemistry, Yong Loo Lin School of Medicine, NUS, Institute of Molecular and Cell Biology, A*STAR, Singapore
| | - Muhammad Akhtar-Ali
- Department of Immunology, Genetics and Pathology, Science for Life laboratory, Uppsala University, Uppsala, Sweden
| | - Anders R Hellström
- Department of Immunology, Genetics and Pathology, Science for Life laboratory, Uppsala University, Uppsala, Sweden
| | - Anna Schuh
- Radcliffe Department of Medicine, Oxford University, Oxford, United Kingdom
| | - Ruth Clifford
- Radcliffe Department of Medicine, Oxford University, Oxford, United Kingdom
| | - Stuart J Blakemore
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Jonathan C Strefford
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Tycho Baumann
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | | | - Elias Campo
- Unitat de Hematología, Hospital Clíınic, IDIBAPS, Universitat de Barcelona, Barcelona, Spain
| | - Viktor Ljungström
- Department of Immunology, Genetics and Pathology, Science for Life laboratory, Uppsala University, Uppsala, Sweden
| | - Larry Mansouri
- Department of Immunology, Genetics and Pathology, Science for Life laboratory, Uppsala University, Uppsala, Sweden
| | - Richard Rosenquist
- Department of Immunology, Genetics and Pathology, Science for Life laboratory, Uppsala University, Uppsala, Sweden
| | - Tobias Sjöblom
- Department of Immunology, Genetics and Pathology, Science for Life laboratory, Uppsala University, Uppsala, Sweden
| | - Mats Hellström
- Department of Immunology, Genetics and Pathology, Science for Life laboratory, Uppsala University, Uppsala, Sweden.
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Ichise H, Hori A, Shiozawa S, Kondo S, Kanegae Y, Saito I, Ichise T, Yoshida N. Establishment of a tamoxifen-inducible Cre-driver mouse strain for widespread and temporal genetic modification in adult mice. Exp Anim 2016; 65:231-44. [PMID: 26923756 PMCID: PMC4976237 DOI: 10.1538/expanim.15-0126] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Temporal genetic modification of mice using the ligand-inducible Cre/loxP system is an
important technique that allows the bypass of embryonic lethal phenotypes and access to
adult phenotypes. In this study, we generated a tamoxifen-inducible Cre-driver mouse
strain for the purpose of widespread and temporal Cre recombination. The new line, named
CM32, expresses the GFPneo-fusion gene in a wide variety of tissues before FLP
recombination and tamoxifen-inducible Cre after FLP recombination. Using FLP-recombined
CM32 mice (CM32Δ mice) and Cre reporter mouse lines, we evaluated the efficiency of Cre
recombination with and without tamoxifen administration to adult mice, and found
tamoxifen-dependent induction of Cre recombination in a variety of adult tissues. In
addition, we demonstrated that conditional activation of an oncogene could be achieved in
adults using CM32Δ mice. CM32Δ;T26 mice, which harbored a Cre recombination-driven, SV40
large T antigen-expressing transgene, were viable and fertile. No overt phenotype was
found in the mice up to 3 months after birth. Although they displayed pineoblastomas
(pinealoblastomas) and/or thymic enlargement due to background Cre recombination by 6
months after birth, they developed epidermal hyperplasia when administered tamoxifen.
Collectively, our results suggest that the CM32Δ transgenic mouse line can be applied to
the assessment of adult phenotypes in mice with loxP-flanked transgenes.
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Affiliation(s)
- Hirotake Ichise
- Laboratory of Developmental Genetics, Center for Experimental Medicine and Systems Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
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