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Marcuccio F, Chau CC, Tanner G, Elpidorou M, Finetti MA, Ajaib S, Taylor M, Lascelles C, Carr I, Macaulay I, Stead LF, Actis P. Single-cell nanobiopsy enables multigenerational longitudinal transcriptomics of cancer cells. SCIENCE ADVANCES 2024; 10:eadl0515. [PMID: 38446884 PMCID: PMC10917339 DOI: 10.1126/sciadv.adl0515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 01/31/2024] [Indexed: 03/08/2024]
Abstract
Single-cell RNA sequencing has revolutionized our understanding of cellular heterogeneity, but routine methods require cell lysis and fail to probe the dynamic trajectories responsible for cellular state transitions, which can only be inferred. Here, we present a nanobiopsy platform that enables the injection of exogenous molecules and multigenerational longitudinal cytoplasmic sampling from a single cell and its progeny. The technique is based on scanning ion conductance microscopy (SICM) and, as a proof of concept, was applied to longitudinally profile the transcriptome of single glioblastoma (GBM) brain tumor cells in vitro over 72 hours. The GBM cells were biopsied before and after exposure to chemotherapy and radiotherapy, and our results suggest that treatment either induces or selects for more transcriptionally stable cells. We envision the nanobiopsy will contribute to transforming standard single-cell transcriptomics from a static analysis into a dynamic assay.
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Affiliation(s)
- Fabio Marcuccio
- Faculty of Medicine, Imperial College London, London, UK
- Bragg Centre for Materials Research, University of Leeds, Leeds, UK
- School of Electronic and Electrical Engineering, University of Leeds, Leeds, UK
- Leeds Institute of Medical Research at St James’s, University of Leeds, Leeds, UK
| | - Chalmers C. Chau
- Bragg Centre for Materials Research, University of Leeds, Leeds, UK
- School of Electronic and Electrical Engineering, University of Leeds, Leeds, UK
- Leeds Institute of Medical Research at St James’s, University of Leeds, Leeds, UK
| | - Georgette Tanner
- Leeds Institute of Medical Research at St James’s, University of Leeds, Leeds, UK
| | - Marilena Elpidorou
- School of Electronic and Electrical Engineering, University of Leeds, Leeds, UK
- Leeds Institute of Medical Research at St James’s, University of Leeds, Leeds, UK
| | - Martina A. Finetti
- Leeds Institute of Medical Research at St James’s, University of Leeds, Leeds, UK
| | - Shoaib Ajaib
- Leeds Institute of Medical Research at St James’s, University of Leeds, Leeds, UK
| | - Morag Taylor
- Leeds Institute of Medical Research at St James’s, University of Leeds, Leeds, UK
| | - Carolina Lascelles
- Leeds Institute of Medical Research at St James’s, University of Leeds, Leeds, UK
| | - Ian Carr
- Leeds Institute of Medical Research at St James’s, University of Leeds, Leeds, UK
| | - Iain Macaulay
- Earlham Institute, Norwich Research Park, Norwich, UK
| | - Lucy F. Stead
- Leeds Institute of Medical Research at St James’s, University of Leeds, Leeds, UK
| | - Paolo Actis
- Bragg Centre for Materials Research, University of Leeds, Leeds, UK
- School of Electronic and Electrical Engineering, University of Leeds, Leeds, UK
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2
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Eck E, Moretti B, Schlomann BH, Bragantini J, Lange M, Zhao X, VijayKumar S, Valentin G, Loureiro C, Soroldoni D, Royer LA, Oates AC, Garcia HG. Single-cell transcriptional dynamics in a living vertebrate. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.03.574108. [PMID: 38260569 PMCID: PMC10802376 DOI: 10.1101/2024.01.03.574108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The ability to quantify transcriptional dynamics in individual cells via live imaging has revolutionized our understanding of gene regulation. However, such measurements are lacking in the context of vertebrate embryos. We addressed this deficit by applying MS2-MCP mRNA labeling to the quantification of transcription in zebrafish, a model vertebrate. We developed a platform of transgenic organisms, light sheet fluorescence microscopy, and optimized image analysis that enables visualization and quantification of MS2 reporters. We used these tools to obtain the first single-cell, real-time measurements of transcriptional dynamics of the segmentation clock. Our measurements challenge the traditional view of smooth clock oscillations and instead suggest a model of discrete transcriptional bursts that are organized in space and time. Together, these results highlight how measuring single-cell transcriptional activity can reveal unexpected features of gene regulation and how this data can fuel the dialogue between theory and experiment.
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Affiliation(s)
- Elizabeth Eck
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, USA
| | - Bruno Moretti
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Chan Zuckerberg Biohub – San Francisco, San Francisco, CA, USA
| | - Brandon H. Schlomann
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | | | - Merlin Lange
- Chan Zuckerberg Biohub – San Francisco, San Francisco, CA, USA
| | - Xiang Zhao
- Chan Zuckerberg Biohub – San Francisco, San Francisco, CA, USA
| | | | | | | | | | - Loïc A. Royer
- Chan Zuckerberg Biohub – San Francisco, San Francisco, CA, USA
| | - Andrew C. Oates
- Institute of Bioengineering, EPFL; Lausanne, CH
- Department of Cell and Developmental Biology, UCL; London, UK
- The Francis Crick Institute; London, UK
| | - Hernan G. Garcia
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Department of Physics, University of California, Berkeley, CA, USA
- Institute for Quantitative Biosciences-QB3, University of California, Berkeley, CA, USA
- Chan Zuckerberg Biohub – San Francisco, San Francisco, CA, USA
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3
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Harden TT, Vincent BJ, DePace AH. Transcriptional activators in the early Drosophila embryo perform different kinetic roles. Cell Syst 2023; 14:258-272.e4. [PMID: 37080162 PMCID: PMC10473017 DOI: 10.1016/j.cels.2023.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 06/26/2022] [Accepted: 03/21/2023] [Indexed: 04/22/2023]
Abstract
Combinatorial regulation of gene expression by transcription factors (TFs) may in part arise from kinetic synergy-wherein TFs regulate different steps in the transcription cycle. Kinetic synergy requires that TFs play distinguishable kinetic roles. Here, we used live imaging to determine the kinetic roles of three TFs that activate transcription in the Drosophila embryo-Zelda, Bicoid, and Stat92E-by introducing their binding sites into the even-skipped stripe 2 enhancer. These TFs influence different sets of kinetic parameters, and their influence can change over time. All three TFs increased the fraction of transcriptionally active nuclei; Zelda also shortened the first-passage time into transcription and regulated the interval between transcription events. Stat92E also increased the lifetimes of active transcription. Different TFs can therefore play distinct kinetic roles in activating the transcription. This has consequences for understanding the composition and flexibility of regulatory DNA sequences and the biochemical function of TFs. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Timothy T Harden
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Ben J Vincent
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Angela H DePace
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
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4
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Unveiling dynamic enhancer–promoter interactions in Drosophila melanogaster. Biochem Soc Trans 2022; 50:1633-1642. [DOI: 10.1042/bst20220325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/18/2022] [Accepted: 10/20/2022] [Indexed: 11/11/2022]
Abstract
Proper enhancer–promoter interactions are essential to maintaining specific transcriptional patterns and preventing ectopic gene expression. Drosophila is an ideal model organism to study transcriptional regulation due to extensively characterized regulatory regions and the ease of implementing new genetic and molecular techniques for quantitative analysis. The mechanisms of enhancer–promoter interactions have been investigated over a range of length scales. At a DNA level, compositions of both enhancer and promoter sequences affect transcriptional dynamics, including duration, amplitude, and frequency of transcriptional bursting. 3D chromatin topology is also important for proper enhancer–promoter contacts. By working competitively or cooperatively with one another, multiple, simultaneous enhancer–enhancer, enhancer–promoter, and promoter–promoter interactions often occur to maintain appropriate levels of mRNAs. For some long-range enhancer–promoter interactions, extra regulatory elements like insulators and tethering elements are required to promote proper interactions while blocking aberrant ones. This review provides an overview of our current understanding of the mechanism of enhancer–promoter interactions and how perturbations of such interactions affect transcription and subsequent physiological outcomes.
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5
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Fu Y, Liu Y, Wen T, Fang J, Chen Y, Zhou Z, Gu X, Wu H, Sheng J, Xu Z, Zou W, Chen B. Real-time imaging of RNA polymerase I activity in living human cells. J Biophys Biochem Cytol 2022; 222:213608. [PMID: 36282216 PMCID: PMC9606689 DOI: 10.1083/jcb.202202110] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 08/19/2022] [Accepted: 09/27/2022] [Indexed: 11/22/2022] Open
Abstract
RNA polymerase I (Pol I) synthesizes about 60% of cellular RNA by transcribing multiple copies of the ribosomal RNA gene (rDNA). The transcriptional activity of Pol I controls the level of ribosome biogenesis and cell growth. However, there is currently a lack of methods for monitoring Pol I activity in real time. Here, we develop LiveArt (live imaging-based analysis of rDNA transcription) to visualize and quantify the spatiotemporal dynamics of endogenous ribosomal RNA (rRNA) synthesis. LiveArt reveals mitotic silencing and reactivation of rDNA transcription, as well as the transcriptional kinetics of interphase rDNA. Using LiveArt, we identify SRFBP1 as a potential regulator of rRNA synthesis. We show that rDNA transcription occurs in bursts and can be altered by modulating burst duration and amplitude. Importantly, LiveArt is highly effective in the screening application for anticancer drugs targeting Pol I transcription. These approaches pave the way for a deeper understanding of the mechanisms underlying nucleolar functions.
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Affiliation(s)
- Yujuan Fu
- Department of Cell Biology and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China,Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
| | - Yaxin Liu
- Institute of Environmental Medicine, and Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Tanye Wen
- Department of Cell Biology and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jie Fang
- Department of Cell Biology and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China,Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
| | - Yalong Chen
- Department of Cell Biology and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ziying Zhou
- Department of Cell Biology and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xinyi Gu
- Department of Cell Biology and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hao Wu
- Department of Cell Biology and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jinghao Sheng
- Institute of Environmental Medicine, and Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhengping Xu
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China,Institute of Environmental Medicine, and Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Wei Zou
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, China,Insititute of Translational Medicine, Zhejiang University, Hangzhou, China,Wei Zou:
| | - Baohui Chen
- Department of Cell Biology and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China,Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China,Institute of Hematology, Zhejiang University and Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China,Zhejiang Provincial Key Laboratory of Genetic & Developmental Disorders, Hangzhou, China,Correspondence to Baohui Chen:
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Gibbons MD, Fang Y, Spicola AP, Linzer N, Jones SM, Johnson BR, Li L, Xie M, Bungert J. Enhancer-Mediated Formation of Nuclear Transcription Initiation Domains. Int J Mol Sci 2022; 23:ijms23169290. [PMID: 36012554 PMCID: PMC9409229 DOI: 10.3390/ijms23169290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/14/2022] [Accepted: 08/16/2022] [Indexed: 11/16/2022] Open
Abstract
Enhancers in higher eukaryotes and upstream activating sequences (UASs) in yeast have been shown to recruit components of the RNA polymerase II (Pol II) transcription machinery. At least a fraction of Pol II recruited to enhancers in higher eukaryotes initiates transcription and generates enhancer RNA (eRNA). In contrast, UASs in yeast do not recruit transcription factor TFIIH, which is required for transcription initiation. For both yeast and mammalian systems, it was shown that Pol II is transferred from enhancers/UASs to promoters. We propose that there are two modes of Pol II recruitment to enhancers in higher eukaryotes. Pol II complexes that generate eRNAs are recruited via TFIID, similar to mechanisms operating at promoters. This may involve the binding of TFIID to acetylated nucleosomes flanking the enhancer. The resulting eRNA, together with enhancer-bound transcription factors and co-regulators, contributes to the second mode of Pol II recruitment through the formation of a transcription initiation domain. Transient contacts with target genes, governed by proteins and RNA, lead to the transfer of Pol II from enhancers to TFIID-bound promoters.
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7
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Keenan SE, Avdeeva M, Yang L, Alber DS, Wieschaus EF, Shvartsman SY. Dynamics of Drosophila endoderm specification. Proc Natl Acad Sci U S A 2022; 119:e2112892119. [PMID: 35412853 PMCID: PMC9169638 DOI: 10.1073/pnas.2112892119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 02/06/2022] [Indexed: 11/18/2022] Open
Abstract
During early Drosophila embryogenesis, a network of gene regulatory interactions orchestrates terminal patterning, playing a critical role in the subsequent formation of the gut. We utilized CRISPR gene editing at endogenous loci to create live reporters of transcription and light-sheet microscopy to monitor the individual components of the posterior gut patterning network across 90 min prior to gastrulation. We developed a computational approach for fusing imaging datasets of the individual components into a common multivariable trajectory. Data fusion revealed low intrinsic dimensionality of posterior patterning and cell fate specification in wild-type embryos. The simple structure that we uncovered allowed us to construct a model of interactions within the posterior patterning regulatory network and make testable predictions about its dynamics at the protein level. The presented data fusion strategy is a step toward establishing a unified framework that would explore how stochastic spatiotemporal signals give rise to highly reproducible morphogenetic outcomes.
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Affiliation(s)
- Shannon E. Keenan
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08540
- The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540
| | - Maria Avdeeva
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY 10010
| | - Liu Yang
- The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540
| | - Daniel S. Alber
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08540
- The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540
| | - Eric F. Wieschaus
- The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540
| | - Stanislav Y. Shvartsman
- The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY 10010
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540
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8
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Epigenome editing and epigenetic gene regulation in disease phenotypes. KOREAN J CHEM ENG 2022; 39:1361-1367. [DOI: 10.1007/s11814-022-1076-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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9
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Degree of Freedom of Gene Expression in Saccharomyces cerevisiae. Microbiol Spectr 2022; 10:e0083821. [PMID: 35230153 PMCID: PMC9045123 DOI: 10.1128/spectrum.00838-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The complexity of genome-wide gene expression has not yet been adequately addressed due to a lack of comprehensive statistical analyses. In the present study, we introduce degree of freedom (DOF) as a summary statistic for evaluating gene expression complexity. Because DOF can be interpreted by a state-space representation, application of the DOF is highly useful for understanding gene activities. We used over 11,000 gene expression data sets to reveal that the DOF of gene expression in Saccharomyces cerevisiae is not greater than 450. We further demonstrated that various degrees of freedom of gene expression can be interpreted by different sequence motifs within promoter regions and Gene Ontology (GO) terms. The well-known TATA box is the most significant one among the identified motifs, while the GO term "ribosome genesis" is an associated biological process. On the basis of transcriptional freedom, our findings suggest that the regulation of gene expression can be modeled using only a few state variables. IMPORTANCE Yeast works like a well-organized factory. Each of its components works in its own way, while affecting the activities of others. The order of all activities is largely governed by the regulation of gene expression. In recent decades, biologists have recognized many regulations for yeast genes. However, it is not known how closely the regulation links each gene together to make all components of the cell work as a whole. In other words, biologists are very interested in how many independent control factors are needed to operate an artificial "cell" that works the same as a real one. In this work, we suggested that only 450 control factors were sufficient to represent the regulation of all 5800 yeast genes.
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10
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Nojima T, Proudfoot NJ. Mechanisms of lncRNA biogenesis as revealed by nascent transcriptomics. Nat Rev Mol Cell Biol 2022; 23:389-406. [DOI: 10.1038/s41580-021-00447-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2021] [Indexed: 12/14/2022]
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11
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Zhou J, Cheng T, Li X, Hu J, Li E, Ding M, Shen R, Pineda JP, Li C, Lu S, Yu H, Sun J, Huang W, Wang X, Si H, Shi P, Liu J, Chang M, Dou M, Shi M, Chen X, Yung RC, Wang Q, Zhou N, Bai C. Epigenetic imprinting alterations as effective diagnostic biomarkers for early-stage lung cancer and small pulmonary nodules. Clin Epigenetics 2021; 13:220. [PMID: 34906185 PMCID: PMC8672623 DOI: 10.1186/s13148-021-01203-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 11/28/2021] [Indexed: 01/18/2023] Open
Abstract
Background Early lung cancer detection remains a clinical challenge for standard diagnostic biopsies due to insufficient tumor morphological evidence. As epigenetic alterations precede morphological changes, expression alterations of certain imprinted genes could serve as actionable diagnostic biomarkers for malignant lung lesions. Results Using the previously established quantitative chromogenic imprinted gene in situ hybridization (QCIGISH) method, elevated aberrant allelic expression of imprinted genes GNAS, GRB10, SNRPN and HM13 was observed in lung cancers over benign lesions and normal controls, which were pathologically confirmed among histologically stained normal, paracancerous and malignant tissue sections. Based on the differential imprinting signatures, a diagnostic grading model was built on 246 formalin-fixed and paraffin-embedded (FFPE) surgically resected lung tissue specimens, tested against 30 lung cytology and small biopsy specimens, and blindly validated in an independent cohort of 155 patients. The QCIGISH diagnostic model demonstrated 99.1% sensitivity (95% CI 97.5–100.0%) and 92.1% specificity (95% CI 83.5–100.0%) in the blinded validation set. Of particular importance, QCIGISH achieved 97.1% sensitivity (95% CI 91.6–100.0%) for carcinoma in situ to stage IB cancers with 100% sensitivity and 91.7% specificity (95% CI 76.0–100.0%) noted for pulmonary nodules with diameters ≤ 2 cm. Conclusions Our findings demonstrated the diagnostic value of epigenetic imprinting alterations as highly accurate translational biomarkers for a more definitive diagnosis of suspicious lung lesions. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01203-5.
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Affiliation(s)
- Jian Zhou
- Department of Pulmonary Medicine, Shanghai Respiratory Research Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.,Shanghai Engineering Research Center of Internet of Things for Respiratory Medicine, Shanghai, 200032, China
| | - Tong Cheng
- Epigenetics Lab, Chinese Alliance Against Lung Cancer, 6th Floor, Building 5, No.66, Jinghuidongdao Road, Wuxi, 214135, Jiangsu, China
| | - Xing Li
- Epigenetics Lab, Chinese Alliance Against Lung Cancer, 6th Floor, Building 5, No.66, Jinghuidongdao Road, Wuxi, 214135, Jiangsu, China
| | - Jie Hu
- Department of Pulmonary Medicine, Shanghai Respiratory Research Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Encheng Li
- Department of Respiratory Medicine, The Second Hospital Affiliated to Dalian Medical University, Dalian, 116044, Liaoning, China
| | - Ming Ding
- Department of Respiratory Medicine, The Affiliated Zhongda Hospital of Southeast University, Nanjing, 210009, Jiangsu, China
| | - Rulong Shen
- Department of Pathology, Ohio State University Wexner Medical Center, Columbus, OH, 43210, USA
| | - John P Pineda
- Epigenetics Lab, Chinese Alliance Against Lung Cancer, 6th Floor, Building 5, No.66, Jinghuidongdao Road, Wuxi, 214135, Jiangsu, China
| | - Chun Li
- Department of Pulmonary Medicine, Shanghai Respiratory Research Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Shaohua Lu
- Department of Pulmonary Medicine, Shanghai Respiratory Research Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Hongyu Yu
- Department of Pathology, Changzheng Hospital, Navy Medical University, Shanghai, 200003, China
| | - Jiayuan Sun
- Department of Respiratory Endoscopy and Respiratory and Critical Care Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Wenbin Huang
- Department of Pathology, Nanjing First Hospital, Nanjing, 210006, Jiangsu, China
| | - Xiaonan Wang
- Epigenetics Lab, Chinese Alliance Against Lung Cancer, 6th Floor, Building 5, No.66, Jinghuidongdao Road, Wuxi, 214135, Jiangsu, China
| | - Han Si
- Epigenetics Lab, Chinese Alliance Against Lung Cancer, 6th Floor, Building 5, No.66, Jinghuidongdao Road, Wuxi, 214135, Jiangsu, China
| | - Panying Shi
- Epigenetics Lab, Chinese Alliance Against Lung Cancer, 6th Floor, Building 5, No.66, Jinghuidongdao Road, Wuxi, 214135, Jiangsu, China
| | - Jing Liu
- Department of Pathology, The Affiliated Yantai Yuhuangding Hospital, Qingdao University, Yantai, 264000, Shandong, China
| | - Meijia Chang
- Department of Pulmonary Medicine, Shanghai Respiratory Research Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Maosen Dou
- Department of Pulmonary Medicine, Shanghai Respiratory Research Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Meng Shi
- Department of Cardiothoracic Surgery, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Xiaofeng Chen
- Department of Cardiothoracic Surgery, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Rex C Yung
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21207, USA
| | - Qi Wang
- Department of Respiratory Medicine, The Second Hospital Affiliated to Dalian Medical University, Dalian, 116044, Liaoning, China
| | - Ning Zhou
- Epigenetics Lab, Chinese Alliance Against Lung Cancer, 6th Floor, Building 5, No.66, Jinghuidongdao Road, Wuxi, 214135, Jiangsu, China.
| | - Chunxue Bai
- Department of Pulmonary Medicine, Shanghai Respiratory Research Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China. .,Shanghai Engineering Research Center of Internet of Things for Respiratory Medicine, Shanghai, 200032, China.
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12
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Xu H, Wang J, Liang Y, Fu Y, Li S, Huang J, Xu H, Zou W, Chen B. TriTag: an integrative tool to correlate chromatin dynamics and gene expression in living cells. Nucleic Acids Res 2021; 48:e127. [PMID: 33104788 PMCID: PMC7736787 DOI: 10.1093/nar/gkaa906] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 08/29/2020] [Accepted: 10/21/2020] [Indexed: 02/07/2023] Open
Abstract
A wealth of single-cell imaging studies have contributed novel insights into chromatin organization and gene regulation. However, a comprehensive understanding of spatiotemporal gene regulation requires developing tools to combine multiple monitoring systems in a single study. Here, we report a versatile tag, termed TriTag, which integrates the functional capabilities of CRISPR-Tag (DNA labeling), MS2 aptamer (RNA imaging) and fluorescent protein (protein tracking). Using this tag, we correlate changes in chromatin dynamics with the progression of endogenous gene expression, by recording both transcriptional bursting and protein production. This strategy allows precise measurements of gene expression at single-allele resolution across the cell cycle or in response to stress. TriTag enables capturing an integrated picture of gene expression, thus providing a powerful tool to study transcriptional heterogeneity and regulation.
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Affiliation(s)
- Haiyue Xu
- Department of Cell Biology, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Junyan Wang
- Department of Cell Biology, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Ying Liang
- Department of Cell Biology, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Yujuan Fu
- Department of Cell Biology, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Sihui Li
- Department of Cell Biology, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Jinghan Huang
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Heng Xu
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China.,Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wei Zou
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu 322000, China.,Insititute of Translational Medicine, Zhejiang University, Hangzhou 310003, China
| | - Baohui Chen
- Department of Cell Biology, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China.,Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou 310058, China.,Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou 311121, China.,Zhejiang Provincial Key Laboratory of Genetic & Developmental Disorders, Hangzhou 310058, China
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Wissink EM, Vihervaara A, Tippens ND, Lis JT. Nascent RNA analyses: tracking transcription and its regulation. Nat Rev Genet 2019; 20:705-723. [PMID: 31399713 PMCID: PMC6858503 DOI: 10.1038/s41576-019-0159-6] [Citation(s) in RCA: 135] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/04/2019] [Indexed: 12/19/2022]
Abstract
The programmes that direct an organism's development and maintenance are encoded in its genome. Decoding of this information begins with regulated transcription of genomic DNA into RNA. Although transcription and its control can be tracked indirectly by measuring stable RNAs, it is only by directly measuring nascent RNAs that the immediate regulatory changes in response to developmental, environmental, disease and metabolic signals are revealed. Multiple complementary methods have been developed to quantitatively track nascent transcription genome-wide at nucleotide resolution, all of which have contributed novel insights into the mechanisms of gene regulation and transcription-coupled RNA processing. Here we critically evaluate the array of strategies used for investigating nascent transcription and discuss the recent conceptual advances they have provided.
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Affiliation(s)
- Erin M Wissink
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Anniina Vihervaara
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Nathaniel D Tippens
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
- Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY, USA
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.
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Neubacher S, Hennig S. RNA Structure and Cellular Applications of Fluorescent Light-Up Aptamers. Angew Chem Int Ed Engl 2019; 58:1266-1279. [PMID: 30102012 PMCID: PMC6391945 DOI: 10.1002/anie.201806482] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Indexed: 12/16/2022]
Abstract
The cellular functions of RNA are not limited to their role as blueprints for protein synthesis. In particular, noncoding RNA, such as, snRNAs, lncRNAs, miRNAs, play important roles. With increasing numbers of RNAs being identified, it is well known that the transcriptome outnumbers the proteome by far. This emphasizes the great importance of functional RNA characterization and the need to further develop tools for these investigations, many of which are still in their infancy. Fluorescent light-up aptamers (FLAPs) are RNA sequences that can bind nontoxic, cell-permeable small-molecule fluorogens and enhance their fluorescence over many orders of magnitude upon binding. FLAPs can be encoded on the DNA level using standard molecular biology tools and are subsequently transcribed into RNA by the cellular machinery, so that they can be used as fluorescent RNA tags (FLAP-tags). In this Minireview, we give a brief overview of the fluorogens that have been developed and their binding RNA aptamers, with a special focus on published crystal structures. A summary of current and future cellular FLAP applications with an emphasis on the study of RNA-RNA and RNA-protein interactions using split-FLAP and Förster resonance energy transfer (FRET) systems is given.
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Affiliation(s)
- Saskia Neubacher
- Department of Chemistry & Pharmaceutical SciencesVU University AmsterdamDe Boelelaan 11081081HZAmsterdamThe Netherlands
| | - Sven Hennig
- Department of Chemistry & Pharmaceutical SciencesVU University AmsterdamDe Boelelaan 11081081HZAmsterdamThe Netherlands
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Gurumurthy A, Shen Y, Gunn E, Bungert J. Phase Separation and Transcription Regulation: Are Super-Enhancers and Locus Control Regions Primary Sites of Transcription Complex Assembly? Bioessays 2019; 41:e1800164. [PMID: 30500078 PMCID: PMC6484441 DOI: 10.1002/bies.201800164] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 10/31/2018] [Indexed: 01/10/2023]
Abstract
It is proposed that the multiple enhancer elements associated with locus control regions and super-enhancers recruit RNA polymerase II and efficiently assemble elongation competent transcription complexes that are transferred to target genes by transcription termination and transient looping mechanisms. It is well established that transcription complexes are recruited not only to promoters but also to enhancers, where they generate enhancer RNAs. Transcription at enhancers is unstable and frequently aborted. Furthermore, the Integrator and WD-domain containing protein 82 mediate transcription termination at enhancers. Abortion and termination of transcription at the multiple enhancers of locus control regions and super-enhancers provide a large pool of elongation competent transcription complexes. These are efficiently captured by strong basal promoter elements at target genes during transient looping interactions.
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Affiliation(s)
- Aishwarya Gurumurthy
- Department of Biochemistry and Molecular Biology, College of Medicine,
UF Health Cancer Center, Genetics Institute, Powell Gene Therapy Center,
University of Florida, Gainesville, Florida, 32610, U.S.A., Phone: 352-273-8098,
Fax: 352-3f92-2953
| | - Yong Shen
- Department of Biochemistry and Molecular Biology, College of Medicine,
UF Health Cancer Center, Genetics Institute, Powell Gene Therapy Center,
University of Florida, Gainesville, Florida, 32610, U.S.A., Phone: 352-273-8098,
Fax: 352-3f92-2953
| | - Eliot Gunn
- Department of Biochemistry and Molecular Biology, College of Medicine,
UF Health Cancer Center, Genetics Institute, Powell Gene Therapy Center,
University of Florida, Gainesville, Florida, 32610, U.S.A., Phone: 352-273-8098,
Fax: 352-3f92-2953
| | - Jörg Bungert
- Department of Biochemistry and Molecular Biology, College of Medicine,
UF Health Cancer Center, Genetics Institute, Powell Gene Therapy Center,
University of Florida, Gainesville, Florida, 32610, U.S.A., Phone: 352-273-8098,
Fax: 352-3f92-2953
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Neubacher S, Hennig S. RNA Structure and Cellular Applications of Fluorescent Light-Up Aptamers. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201806482] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Saskia Neubacher
- Department of Chemistry & Pharmaceutical Sciences; VU University Amsterdam; De Boelelaan 1108 1081 HZ Amsterdam The Netherlands
| | - Sven Hennig
- Department of Chemistry & Pharmaceutical Sciences; VU University Amsterdam; De Boelelaan 1108 1081 HZ Amsterdam The Netherlands
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