1
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Huang J, Li H, Shu F, Zhou W, Wu Y, Wang Y, Lv X, Gao M, Song Z, Zhao S. Low-Temperature and High-Efficiency Solid-Phase Amplification Based on Formamide. MICROMACHINES 2024; 15:565. [PMID: 38793138 PMCID: PMC11123353 DOI: 10.3390/mi15050565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 04/19/2024] [Accepted: 04/23/2024] [Indexed: 05/26/2024]
Abstract
The thermal stability of DNA immobilized on a solid surface is one of the factors that affects the efficiency of solid-phase amplification (SP-PCR). Although variable temperature amplification ensures high specificity of the reaction by precisely controlling temperature changes, excessively high temperatures during denaturation can negatively affect DNA stability. Formamide (FA) enables DNA denaturation at lower temperatures, showing potential for SP-PCR. Research on FA's impacts on DNA microarrays is still limited, necessitating further optimization in exploring the characteristics of FA in SP-PCR according to particular application needs. We immobilized DNA on a chip using a crosslinker and generated DNA microarrays through bridge amplification based on FA denaturation on our automated reaction device. We optimized the denaturation and hybridization parameters of FA, achieving a maximum cluster density of 2.83 × 104 colonies/mm2. Compared to high-temperature denaturation, FA denaturation required a lower template concentration and milder reaction conditions and produced higher cluster density, demonstrating that FA effectively improves hybridization rates on surfaces. Regarding the immobilized DNA stability, the FA group exhibited a 45% loss of DNA, resulting in a 15% higher DNA retention rate compared to the high-temperature group, indicating that FA can better maintain DNA stability. Our study suggests that using FA improves the immobilized DNA stability and amplification efficiency in SP-PCR.
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Affiliation(s)
- Jialing Huang
- School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou 325035, China
| | - Huan Li
- Changchun Institute of Optics, Fine Mechanics and Physics (CIOMP), Chinese Academy of Sciences, Changchun 130033, China
| | - Fengfeng Shu
- Changchun Institute of Optics, Fine Mechanics and Physics (CIOMP), Chinese Academy of Sciences, Changchun 130033, China
| | - Wenchao Zhou
- Changchun Institute of Optics, Fine Mechanics and Physics (CIOMP), Chinese Academy of Sciences, Changchun 130033, China
| | - Yihui Wu
- School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou 325035, China
- Changchun Institute of Optics, Fine Mechanics and Physics (CIOMP), Chinese Academy of Sciences, Changchun 130033, China
| | - Yue Wang
- Changchun Institute of Optics, Fine Mechanics and Physics (CIOMP), Chinese Academy of Sciences, Changchun 130033, China
| | - Xiao Lv
- Changchun Institute of Optics, Fine Mechanics and Physics (CIOMP), Chinese Academy of Sciences, Changchun 130033, China
| | - Ming Gao
- Changchun Institute of Optics, Fine Mechanics and Physics (CIOMP), Chinese Academy of Sciences, Changchun 130033, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zihan Song
- Changchun Institute of Optics, Fine Mechanics and Physics (CIOMP), Chinese Academy of Sciences, Changchun 130033, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shixun Zhao
- Changchun Institute of Optics, Fine Mechanics and Physics (CIOMP), Chinese Academy of Sciences, Changchun 130033, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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2
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Kagan Ben Tikva S, Gurwitz N, Sivan E, Hirsch D, Hezroni-Barvyi H, Biram A, Moss L, Wigoda N, Egozi A, Monziani A, Golani O, Gross M, Tenenbaum A, Shulman Z. T cell help induces Myc transcriptional bursts in germinal center B cells during positive selection. Sci Immunol 2024; 9:eadj7124. [PMID: 38552029 DOI: 10.1126/sciimmunol.adj7124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 02/09/2024] [Indexed: 04/02/2024]
Abstract
Antibody affinity maturation occurs in secondary lymphoid organs within germinal centers (GCs). At these sites, B cells mutate their antibody-encoding genes in the dark zone, followed by preferential selection of the high-affinity variants in the light zone by T cells. The strength of the T cell-derived selection signals is proportional to the B cell receptor affinity and to the magnitude of subsequent Myc expression. However, because the lifetime of Myc mRNA and its corresponding protein is very short, it remains unclear how T cells induce sustained Myc levels in positively selected B cells. Here, by direct visualization of mRNA and active transcription sites in situ, we found that an increase in transcriptional bursts promotes Myc expression during B cell positive selection in GCs. Elevated T cell help signals predominantly enhance the percentage of cells expressing Myc in GCs as opposed to augmenting the quantity of Myc transcripts per individual cell. Visualization of transcription start sites in situ revealed that T cell help promotes an increase in the frequency of transcriptional bursts at the Myc locus in GC B cells located primarily in the LZ apical rim. Thus, the rise in Myc, which governs positive selection of B cells in GCs, reflects an integration of transcriptional activity over time rather than an accumulation of transcripts at a specific time point.
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Affiliation(s)
- Sharon Kagan Ben Tikva
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Neta Gurwitz
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ehud Sivan
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Dana Hirsch
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Hadas Hezroni-Barvyi
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Adi Biram
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Lihee Moss
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Noa Wigoda
- Bioinformatics unit, Life Science Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Adi Egozi
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Alan Monziani
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ofra Golani
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Menachem Gross
- Department of Otolaryngology-Head and Neck Surgery, Hadassah Medical Center, Jerusalem 9112102, Israel
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Ariel Tenenbaum
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 9112102, Israel
- Department of Pediatrics, Hadassah Medical Organization and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Ziv Shulman
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
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3
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Burdziak C, Alonso-Curbelo D, Walle T, Reyes J, Barriga FM, Haviv D, Xie Y, Zhao Z, Zhao CJ, Chen HA, Chaudhary O, Masilionis I, Choo ZN, Gao V, Luan W, Wuest A, Ho YJ, Wei Y, Quail DF, Koche R, Mazutis L, Chaligné R, Nawy T, Lowe SW, Pe’er D. Epigenetic plasticity cooperates with cell-cell interactions to direct pancreatic tumorigenesis. Science 2023; 380:eadd5327. [PMID: 37167403 PMCID: PMC10316746 DOI: 10.1126/science.add5327] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 03/31/2023] [Indexed: 05/13/2023]
Abstract
The response to tumor-initiating inflammatory and genetic insults can vary among morphologically indistinguishable cells, suggesting as yet uncharacterized roles for epigenetic plasticity during early neoplasia. To investigate the origins and impact of such plasticity, we performed single-cell analyses on normal, inflamed, premalignant, and malignant tissues in autochthonous models of pancreatic cancer. We reproducibly identified heterogeneous cell states that are primed for diverse, late-emerging neoplastic fates and linked these to chromatin remodeling at cell-cell communication loci. Using an inference approach, we revealed signaling gene modules and tissue-level cross-talk, including a neoplasia-driving feedback loop between discrete epithelial and immune cell populations that was functionally validated in mice. Our results uncover a neoplasia-specific tissue-remodeling program that may be exploited for pancreatic cancer interception.
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Affiliation(s)
- Cassandra Burdziak
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
- Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Medicine; New York, NY 10065, USA
| | - Direna Alonso-Curbelo
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology; Barcelona 08028, Spain
| | - Thomas Walle
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
- Clinical Cooperation Unit Virotherapy, German Cancer Research Center (DKFZ); Heidelberg 69120, Germany
- Department of Medical Oncology, National Center for Tumor Diseases; Heidelberg University Hospital, Heidelberg 69120, Germany
- German Cancer Consortium (DKTK); Heidelberg 69120, Germany
| | - José Reyes
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
| | - Francisco M. Barriga
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
| | - Doron Haviv
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
- Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Medicine; New York, NY 10065, USA
| | - Yubin Xie
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
- Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Medicine; New York, NY 10065, USA
| | - Zhen Zhao
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai; New York, NY 10029, USA
| | - Chujun Julia Zhao
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
- Department of Biomedical Engineering, Columbia University; New York, NY 10027, USA
| | - Hsuan-An Chen
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
| | - Ojasvi Chaudhary
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
- Alan and Sandra Gerry Metastasis and Tumor Ecosystems Center; Memorial Sloan Kettering Cancer Center, New York 10065, NY, USA
| | - Ignas Masilionis
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
- Alan and Sandra Gerry Metastasis and Tumor Ecosystems Center; Memorial Sloan Kettering Cancer Center, New York 10065, NY, USA
| | - Zi-Ning Choo
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
| | - Vianne Gao
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
- Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Medicine; New York, NY 10065, USA
| | - Wei Luan
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
| | - Alexandra Wuest
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
| | - Yu-Jui Ho
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
| | - Yuhong Wei
- Rosalind and Morris Goodman Cancer Institute, McGill University; Montreal, QC H3A 1A3, Canada
| | - Daniela F Quail
- Rosalind and Morris Goodman Cancer Institute, McGill University; Montreal, QC H3A 1A3, Canada
| | - Richard Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
| | - Linas Mazutis
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
- Department of Biomedical Engineering, Columbia University; New York, NY 10027, USA
- Institute of Biotechnology, Life Sciences Centre; Vilnius University, Vilnius LT 02158, Lithuania
| | - Ronan Chaligné
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
- Alan and Sandra Gerry Metastasis and Tumor Ecosystems Center; Memorial Sloan Kettering Cancer Center, New York 10065, NY, USA
| | - Tal Nawy
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
| | - Scott W. Lowe
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
- Howard Hughes Medical Institute; Chevy Chase, MD 20815, USA
| | - Dana Pe’er
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
- Howard Hughes Medical Institute; Chevy Chase, MD 20815, USA
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4
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Paramasivam P, Stöter M, Corradi E, Dalla Costa I, Höijer A, Bartesaghi S, Sabirsh A, Lindfors L, Yanez Arteta M, Nordberg P, Andersson S, Baudet ML, Bickle M, Zerial M. Quantitative intracellular retention of delivered RNAs through optimized cell fixation and immunostaining. RNA (NEW YORK, N.Y.) 2022; 28:433-446. [PMID: 34949721 PMCID: PMC8848937 DOI: 10.1261/rna.078895.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 12/12/2021] [Indexed: 06/14/2023]
Abstract
Detection of nucleic acids within subcellular compartments is key to understanding their function. Determining the intracellular distribution of nucleic acids requires quantitative retention and estimation of their association with different organelles by immunofluorescence microscopy. This is particularly important for the delivery of nucleic acid therapeutics, which depends on endocytic uptake and endosomal escape. However, the current protocols fail to preserve the majority of exogenously delivered nucleic acids in the cytoplasm. To solve this problem, by monitoring Cy5-labeled mRNA delivered to primary human adipocytes via lipid nanoparticles (LNP), we optimized cell fixation, permeabilization, and immunostaining of a number of organelle markers, achieving quantitative retention of mRNA and allowing visualization of levels that escape detection using conventional procedures. The optimized protocol proved effective on exogenously delivered siRNA, miRNA, as well as endogenous miRNA. Our protocol is compatible with RNA probes of single molecule fluorescence in situ hybridization (smFISH) and molecular beacon, thus demonstrating that it is broadly applicable to study a variety of nucleic acids in cultured cells.
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Affiliation(s)
- Prasath Paramasivam
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Martin Stöter
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Eloina Corradi
- Department CIBIO, University of Trento, Trento 38123, Italy
| | | | - Andreas Höijer
- Advanced Drug Delivery, Pharmaceutical Science R&D, AstraZeneca, 43150 Gothenburg, Sweden
| | - Stefano Bartesaghi
- Bioscience Metabolism, Research and Early Development Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, 43150 Gothenburg, Sweden
| | - Alan Sabirsh
- Advanced Drug Delivery, Pharmaceutical Science R&D, AstraZeneca, 43150 Gothenburg, Sweden
| | - Lennart Lindfors
- Advanced Drug Delivery, Pharmaceutical Science R&D, AstraZeneca, 43150 Gothenburg, Sweden
| | - Marianna Yanez Arteta
- Advanced Drug Delivery, Pharmaceutical Science R&D, AstraZeneca, 43150 Gothenburg, Sweden
| | - Peter Nordberg
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, 43150 Gothenburg, Sweden
| | - Shalini Andersson
- Oligonucleotide Discovery, Discovery Sciences R&D, AstraZeneca, 43150 Gothenburg, Sweden
| | | | - Marc Bickle
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Marino Zerial
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
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5
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Yanowski E, Yacovzada NS, David E, Giladi A, Jaitin D, Farack L, Egozi A, Ben-Zvi D, Itzkovitz S, Amit I, Hornstein E. Physically interacting beta-delta pairs in the regenerating pancreas revealed by single-cell sequencing. Mol Metab 2022; 60:101467. [PMID: 35240340 PMCID: PMC8983436 DOI: 10.1016/j.molmet.2022.101467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 02/05/2022] [Accepted: 02/25/2022] [Indexed: 11/12/2022] Open
Abstract
Objectives Until recently, communication between neighboring cells in islets of Langerhans was overlooked by genomic technologies, which require rigorous tissue dissociation into single cells. Methods We utilize sorting of physically interacting cells (PICs) with single-cell RNA-sequencing to systematically map cellular interactions in the endocrine pancreas after pancreatectomy. Results The pancreas cellular landscape features pancreatectomy associated heterogeneity of beta-cells, including an interaction-specific program between paired beta and delta-cells. Conclusions Our analysis suggests that the particular cluster of beta-cells that pairs with delta-cells benefits from stress protection, implying that the interaction between beta- and delta-cells might safeguard against pancreatectomy associated challenges. The work encourages testing the potential relevance of physically-interacting beta-delta-cells also in diabetes mellitus. Single-cell RNA-sequencing systematically maps physically interacting endocrine cells in the pancreas. The landscape of pancreatectomy associated beta-cell heterogeneity is mapped in a single cell resolution. Interaction-specific beta - delta cellular program safeguards beta cells against pancreatectomy-associated stress. Physically interacting beta delta pairs were discovered in an injury model and may also be relevant in diabetes.
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Affiliation(s)
- Eran Yanowski
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel; Department of Molecular neuroscience, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Nancy-Sarah Yacovzada
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel; Department of Molecular neuroscience, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Eyal David
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Amir Giladi
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Diego Jaitin
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Lydia Farack
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Adi Egozi
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Danny Ben-Zvi
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, 9112102, Israel
| | - Shalev Itzkovitz
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ido Amit
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Eran Hornstein
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel; Department of Molecular neuroscience, Weizmann Institute of Science, Rehovot 7610001, Israel.
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6
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Liu M, Yang B, Hu M, Radda JS, Chen Y, Jin S, Cheng Y, Wang S. Chromatin tracing and multiplexed imaging of nucleome architectures (MINA) and RNAs in single mammalian cells and tissue. Nat Protoc 2021; 16:2667-2697. [PMID: 33903756 PMCID: PMC9007104 DOI: 10.1038/s41596-021-00518-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 02/05/2021] [Indexed: 02/02/2023]
Abstract
The genome is hierarchically organized into several 3D architectures, including chromatin loops, domains, compartments and regions associated with nuclear lamina and nucleoli. Changes in these architectures have been associated with normal development, aging and a wide range of diseases. Despite its critical importance, understanding how the genome is spatially organized in single cells, how organization varies in different cell types in mammalian tissue and how organization affects gene expression remains a major challenge. Previous approaches have been limited by a lack of capacity to directly trace chromatin folding in 3D and to simultaneously measure genomic organization in relation to other nuclear components and gene expression in the same single cells. We have developed an image-based 3D genomics technique termed 'chromatin tracing', which enables direct 3D tracing of chromatin folding along individual chromosomes in single cells. More recently, we also developed multiplexed imaging of nucleome architectures (MINA), which enables simultaneous measurements of multiscale chromatin folding, associations of genomic regions with nuclear lamina and nucleoli and copy numbers of numerous RNA species in the same single cells in mammalian tissue. Here, we provide detailed protocols for chromatin tracing in cell lines and MINA in mammalian tissue, which take 3-4 d for experimental work and 2-3 d for data analysis. We expect these developments to be broadly applicable and to affect many lines of research on 3D genomics by depicting multiscale genomic architectures associated with gene expression, in different types of cells and tissue undergoing different biological processes.
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Affiliation(s)
- Miao Liu
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Bing Yang
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Mengwei Hu
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Jonathan S.D. Radda
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Yanbo Chen
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Shengyan Jin
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Yubao Cheng
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Siyuan Wang
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA,Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA,Yale Combined Program in the Biological and Biomedical Sciences, Yale University, New Haven, CT, USA,Molecular Cell Biology, Genetics and Development Program, Yale University, New Haven, CT, USA,Biochemistry, Quantitative Biology, Biophysics and Structural Biology Program, Yale University, New Haven, CT, USA,M.D.-Ph.D. Program, Yale University, New Haven, CT, USA,Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT, USA,Yale Liver Center, Yale University School of Medicine, New Haven, CT, USA,Correspondence:
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7
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Raj B, Farrell JA, Liu J, El Kholtei J, Carte AN, Navajas Acedo J, Du LY, McKenna A, Relić Đ, Leslie JM, Schier AF. Emergence of Neuronal Diversity during Vertebrate Brain Development. Neuron 2020; 108:1058-1074.e6. [PMID: 33068532 PMCID: PMC8286448 DOI: 10.1016/j.neuron.2020.09.023] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 08/05/2020] [Accepted: 09/17/2020] [Indexed: 01/03/2023]
Abstract
Neurogenesis comprises many highly regulated processes including proliferation, differentiation, and maturation. However, the transcriptional landscapes underlying brain development are poorly characterized. We describe a developmental single-cell catalog of ∼220,000 zebrafish brain cells encompassing 12 stages from embryo to larva. We characterize known and novel gene markers for ∼800 clusters and provide an overview of the diversification of neurons and progenitors across these time points. We also introduce an optimized GESTALT lineage recorder that enables higher expression and recovery of Cas9-edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post-embryonic stages. Reconstruction of cell specification trajectories reveals that late-stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis.
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Affiliation(s)
- Bushra Raj
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA.
| | - Jeffrey A Farrell
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Unit on Cell Specification and Differentiation, National Institute of Child Health and Human Development, NIH, Bethesda, MD 20814, USA
| | - Jialin Liu
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA; Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Jakob El Kholtei
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA; Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Adam N Carte
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Biozentrum, University of Basel, 4056 Basel, Switzerland; Systems, Synthetic, and Quantitative Biology Program, Harvard University, Cambridge, MA 02138, USA
| | - Joaquin Navajas Acedo
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA; Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Lucia Y Du
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA; Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Aaron McKenna
- Department of Molecular and Systems Biology, Dartmouth Geisel School of Medicine, Lebanon, NH 03756, USA
| | - Đorđe Relić
- Biozentrum, University of Basel, 4056 Basel, Switzerland; Swiss Institute of Bioinformatics (SIB), 4056 Basel, Switzerland
| | - Jessica M Leslie
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Alexander F Schier
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA; Biozentrum, University of Basel, 4056 Basel, Switzerland; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA; Center for Brain Science, Harvard University, Cambridge, MA 02138, USA.
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8
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Egozi A, Bahar Halpern K, Farack L, Rotem H, Itzkovitz S. Zonation of Pancreatic Acinar Cells in Diabetic Mice. Cell Rep 2020; 32:108043. [PMID: 32814046 PMCID: PMC7443616 DOI: 10.1016/j.celrep.2020.108043] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 04/02/2020] [Accepted: 07/24/2020] [Indexed: 12/25/2022] Open
Abstract
The islets of Langerhans are dynamic structures that can change in size, number of cells, and molecular function in response to physiological and pathological stress. Molecular cues originating from the surrounding "peri-islet" acinar cells that could facilitate this plasticity have not been explored. Here, we combine single-molecule transcript imaging in the intact pancreas and transcriptomics to identify spatial heterogeneity of acinar cell gene expression. We find that peri-islet acinar cells exhibit a distinct molecular signature in db/db diabetic mice that includes upregulation of trypsin family genes and elevated mTOR activity. This zonated expression program seems to be induced by CCK that is secreted from islet cells. Elevated peri-islet trypsin secretion could facilitate the islet expansion observed in this model via modulation of the islet capsule matrix components. Our study highlights a molecular axis of communication between the pancreatic exocrine and endocrine compartments that may be relevant to islet expansion.
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Affiliation(s)
- Adi Egozi
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Keren Bahar Halpern
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Lydia Farack
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Hagar Rotem
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Shalev Itzkovitz
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel.
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