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Hochgerner H, Singh S, Tibi M, Lin Z, Skarbianskis N, Admati I, Ophir O, Reinhardt N, Netser S, Wagner S, Zeisel A. Author Correction: Neuronal types in the mouse amygdala and their transcriptional response to fear conditioning. Nat Neurosci 2024; 27:385. [PMID: 38243090 PMCID: PMC10849955 DOI: 10.1038/s41593-024-01578-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2024]
Affiliation(s)
- Hannah Hochgerner
- Faculty of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Shelly Singh
- Sagol Department of Neurobiology, University of Haifa, Haifa, Israel
| | - Muhammad Tibi
- Faculty of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Zhige Lin
- Faculty of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Niv Skarbianskis
- Faculty of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Inbal Admati
- Faculty of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Osnat Ophir
- Faculty of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Nuphar Reinhardt
- Faculty of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Shai Netser
- Sagol Department of Neurobiology, University of Haifa, Haifa, Israel
| | - Shlomo Wagner
- Sagol Department of Neurobiology, University of Haifa, Haifa, Israel
| | - Amit Zeisel
- Faculty of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel.
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Hochgerner H, Singh S, Tibi M, Lin Z, Skarbianskis N, Admati I, Ophir O, Reinhardt N, Netser S, Wagner S, Zeisel A. Neuronal types in the mouse amygdala and their transcriptional response to fear conditioning. Nat Neurosci 2023; 26:2237-2249. [PMID: 37884748 PMCID: PMC10689239 DOI: 10.1038/s41593-023-01469-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 09/20/2023] [Indexed: 10/28/2023]
Abstract
The amygdala is a brain region primarily associated with emotional response. The use of genetic markers and single-cell transcriptomics can provide insights into behavior-associated cell state changes. Here we present a detailed cell-type taxonomy of the adult mouse amygdala during fear learning and memory consolidation. We perform single-cell RNA sequencing on naïve and fear-conditioned mice, identify 130 neuronal cell types and validate their spatial distributions. A subset of all neuronal types is transcriptionally responsive to fear learning and memory retrieval. The activated engram cells upregulate activity-response genes and coordinate the expression of genes associated with neurite outgrowth, synaptic signaling, plasticity and development. We identify known and previously undescribed candidate genes responsive to fear learning. Our molecular atlas may be used to generate hypotheses to unveil the neuron types and neural circuits regulating the emotional component of learning and memory.
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Affiliation(s)
- Hannah Hochgerner
- Faculty of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Shelly Singh
- Sagol Department of Neurobiology, University of Haifa, Haifa, Israel
| | - Muhammad Tibi
- Faculty of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Zhige Lin
- Faculty of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Niv Skarbianskis
- Faculty of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Inbal Admati
- Faculty of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Osnat Ophir
- Faculty of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Nuphar Reinhardt
- Faculty of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Shai Netser
- Sagol Department of Neurobiology, University of Haifa, Haifa, Israel
| | - Shlomo Wagner
- Sagol Department of Neurobiology, University of Haifa, Haifa, Israel
| | - Amit Zeisel
- Faculty of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel.
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Munguba H, Nikouei K, Hochgerner H, Oberst P, Kouznetsova A, Ryge J, Muñoz-Manchado AB, Close J, Batista-Brito R, Linnarsson S, Hjerling-Leffler J. Transcriptional maintenance of cortical somatostatin interneuron subtype identity during migration. Neuron 2023; 111:3590-3603.e5. [PMID: 37625400 DOI: 10.1016/j.neuron.2023.07.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 06/08/2023] [Accepted: 07/27/2023] [Indexed: 08/27/2023]
Abstract
Although cardinal cortical interneuron identity is established upon cell-cycle exit, it remains unclear whether specific interneuron subtypes are pre-established, and if so, how their identity is maintained prior to circuit integration. We conditionally removed Sox6 (Sox6-cKO) in migrating somatostatin (Sst+) interneurons and assessed the effects on their mature identity. In adolescent mice, five of eight molecular Sst+ subtypes were nearly absent in the Sox6-cKO cortex without a reduction in cell number. Sox6-cKO cells displayed electrophysiological maturity and expressed genes enriched within the broad class of Sst+ interneurons. Furthermore, we could infer subtype identity prior to cortical integration (embryonic day 18.5), suggesting that the loss in subtype was due to disrupted subtype maintenance. Conversely, Sox6 removal at postnatal day 7 did not disrupt marker expression in the mature cortex. Therefore, Sox6 is necessary during migration for maintenance of Sst+ subtype identity, indicating that subtype maintenance requires active transcriptional programs.
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Affiliation(s)
- Hermany Munguba
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Kasra Nikouei
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Hannah Hochgerner
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Polina Oberst
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Alexandra Kouznetsova
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Jesper Ryge
- Brain Mind Institute, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Ana Belén Muñoz-Manchado
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden; Departamento de Anatomía Patológica, Biología Celular, Histología, Historia de la Ciencia, Medicina Legal y Forense y Toxicología, Instituto de Investigación e Innovación Biomédica de Cádiz (INiBICA), Universidad de Cádiz, Cádiz, Spain
| | - Jennie Close
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Renata Batista-Brito
- Einstein College of Medicine, Dominick Purpura Department of Neuroscience, 1300 Morris Park Ave, The Bronx, NY 10461, USA; Einstein College of Medicine, Department of Psychiatry and Behavioral Sciences, 1300 Morris Park Ave, The Bronx, NY 10461, USA; Einstein College of Medicine, Department of Genetics, 1300 Morris Park Ave, The Bronx, NY 10461, USA
| | - Sten Linnarsson
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Jens Hjerling-Leffler
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
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Tibi M, Biton Hayun S, Hochgerner H, Lin Z, Givon S, Ophir O, Shay T, Mueller T, Segev R, Zeisel A. A telencephalon cell type atlas for goldfish reveals diversity in the evolution of spatial structure and cell types. Sci Adv 2023; 9:eadh7693. [PMID: 37910612 PMCID: PMC10619943 DOI: 10.1126/sciadv.adh7693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 09/29/2023] [Indexed: 11/03/2023]
Abstract
Teleost fish form the largest group of vertebrates and show a tremendous variety of adaptive behaviors, making them critically important for the study of brain evolution and cognition. The neural basis mediating these behaviors remains elusive. We performed a systematic comparative survey of the goldfish telencephalon. We mapped cell types using single-cell RNA sequencing and spatial transcriptomics, resulting in de novo molecular neuroanatomy parcellation. Glial cells were highly conserved across 450 million years of evolution separating mouse and goldfish, while neurons showed diversity and modularity in gene expression. Specifically, somatostatin interneurons, famously interspersed in the mammalian isocortex for local inhibitory input, were curiously aggregated in a single goldfish telencephalon nucleus but molecularly conserved. Cerebral nuclei including the striatum, a hub for motivated behavior in amniotes, had molecularly conserved goldfish homologs. We suggest elements of a hippocampal formation across the goldfish pallium. Last, aiding study of the teleostan everted telencephalon, we describe substantial molecular similarities between goldfish and zebrafish neuronal taxonomies.
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Affiliation(s)
- Muhammad Tibi
- Faculty of Biotechnology and Food Engineering, Technion–Israel Institute of Technology, 3200003 Haifa, Israel
| | - Stav Biton Hayun
- Department of Biomedical Engineering, Ben-Gurion University of the Negev, 8410501 Beer Sheva, Israel
| | - Hannah Hochgerner
- Faculty of Biotechnology and Food Engineering, Technion–Israel Institute of Technology, 3200003 Haifa, Israel
| | - Zhige Lin
- Faculty of Biotechnology and Food Engineering, Technion–Israel Institute of Technology, 3200003 Haifa, Israel
| | - Shachar Givon
- Department of Life Sciences, Ben-Gurion University of the Negev, 8410501 Beer Sheva, Israel
| | - Osnat Ophir
- Faculty of Biotechnology and Food Engineering, Technion–Israel Institute of Technology, 3200003 Haifa, Israel
| | - Tal Shay
- Department of Life Sciences, Ben-Gurion University of the Negev, 8410501 Beer Sheva, Israel
| | - Thomas Mueller
- Department of Biology, Montclair State University, 1 Normal Avenue, Montclair, NJ 07043, USA
| | - Ronen Segev
- Department of Biomedical Engineering, Ben-Gurion University of the Negev, 8410501 Beer Sheva, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, 8410501 Beer Sheva, Israel
- The School of Brain Sciences and Cognition, Ben-Gurion University of the Negev, 8410501 Beer Sheva, Israel
| | - Amit Zeisel
- Faculty of Biotechnology and Food Engineering, Technion–Israel Institute of Technology, 3200003 Haifa, Israel
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Admati I, Skarbianskis N, Hochgerner H, Ophir O, Weiner Z, Yagel S, Solt I, Zeisel A. Two distinct molecular faces of preeclampsia revealed by single-cell transcriptomics. Med 2023; 4:687-709.e7. [PMID: 37572658 DOI: 10.1016/j.medj.2023.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 06/04/2023] [Accepted: 07/14/2023] [Indexed: 08/14/2023]
Abstract
INTRODUCTION Preeclampsia is a multisystemic, pregnancy-specific disorder united by new-onset hypertension but with considerable variation in clinical manifestation, onset, and severity. For symptoms to regress, delivery of the placenta is required. For symptoms to regress, delivery of the placenta is required, making the placenta central to preeclampsia pathophysiology. To dissect which placental functions were impacted in two forms of preeclampsia, we studied molecular changes across the cell types of the placenta. METHODS We performed a transcriptomic survey of single-cells and single-nuclei on cases of early- and late-onset preeclampsia with gestation-matched controls. FINDINGS Our data revealed massive dysregulation of gene expression in all cell classes that was almost exclusive to early preeclampsia. For example, an important known receptor/ligand imbalance hallmarking angiogenic disfunction, sFLT1/placental growth factor (PGF), was reflected in striking, cell-autonomous dysregulation of FLT1 and PGF transcription in the syncytium in early preeclampsia only. Stromal cells and vasculature echoed an inflamed, stressed, anti-angiogenic environment. Finally, the placental immune niche set the tone for inflammation in early but not late preeclampsia. Here, fetal-origin Hofbauer and maternal-origin TREM2 macrophages were revealed as surprising main actors, while local cells of the adaptive immune system were largely unaffected. Late preeclampsia showed minimal cellular impact on the placenta. CONCLUSIONS Our survey provides systematic molecular evidence for two distinct diseases. We resolved systematic molecular dysregulation to individual cell types with strong implications for definition, early detection, diagnosis, and treatment. FUNDING Funded by the Preeclampsia Foundation through the Peter Joseph Pappas Research Grant.
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Affiliation(s)
- Inbal Admati
- Faculty of Biotechnology and Food Engineering, Technion Israel Institute of Technology, Haifa, Israel
| | - Niv Skarbianskis
- Faculty of Biotechnology and Food Engineering, Technion Israel Institute of Technology, Haifa, Israel
| | - Hannah Hochgerner
- Faculty of Biotechnology and Food Engineering, Technion Israel Institute of Technology, Haifa, Israel
| | - Osnat Ophir
- Faculty of Biotechnology and Food Engineering, Technion Israel Institute of Technology, Haifa, Israel
| | - Zeev Weiner
- Department of Obstetrics and Gynecology, Rappaport Faculty of Medicine, Technion Israel Institute of Technology, Haifa, Israel
| | - Simcha Yagel
- Division of Obstetrics and Gynecology Hadassah, Hebrew University Medical Centers, Jerusalem, Israel
| | - Ido Solt
- Department of Obstetrics and Gynecology, Rappaport Faculty of Medicine, Technion Israel Institute of Technology, Haifa, Israel.
| | - Amit Zeisel
- Faculty of Biotechnology and Food Engineering, Technion Israel Institute of Technology, Haifa, Israel.
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Aloni E, Tibi M, Hochgerner H, Zeisel A. Sexual dimorphism in synaptic inputs to the mouse amygdala and orbital cortex. Front Neurosci 2023; 17:1258284. [PMID: 37901417 PMCID: PMC10601666 DOI: 10.3389/fnins.2023.1258284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 09/21/2023] [Indexed: 10/31/2023] Open
Abstract
The medial amygdala (MeA) is a sexually dimorphic brain region that regulates fear responses, emotional memories, and social behaviors. It is known to be larger and contains more cells in males. The MeA integrates information through input connections from olfactory regions, bed nucleus of the stria terminalis, ventral hippocampus, and thalamic and hypothalamic structures. We hypothesize that in addition to the size differences, there are differences in regional connectivity between the sexes. In this study, we utilized G-deleted rabies monosynaptic retrograde tracing to compare amygdala presynaptic cells in male and female whole mouse brains. We report differences in connection patterns to the amygdala, with higher overall connectivity (presynaptic per starter) in males and a larger fraction of inputs originating from the bed nucleus of the stria terminalis, lateral septum, and medial preoptic area. Furthermore, we examined input connections to the orbital cortex (ORB), a brain region shown to be larger in volume in females, and found the opposite trend, where females had more total inputs. Together, our findings extend the evidence for sexual dimorphism in the brain to the neuronal wiring pattern, with likely impacts on behavior and disease susceptibility.
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Affiliation(s)
| | | | | | - Amit Zeisel
- Faculty of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa, Israel
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Elkind D, Hochgerner H, Aloni E, Shental N, Zeisel A. Sex-, strain and lateral differences in brain cytoarchitecture across a large mouse population. eLife 2023; 12:82376. [PMID: 37144870 DOI: 10.7554/elife.82376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 05/04/2023] [Indexed: 05/06/2023] Open
Abstract
The mouse brain is by far the most intensively studied among mammalian brains, yet basic measures of its cytoarchitecture remain obscure. For example, quantifying cell numbers, and the interplay of sex-, strain-, and individual variability in cell density and volume is out of reach for many regions. The Allen Mouse Brain Connectivity project produces high-resolution full brain images of hundreds of brains. Although these were created for a different purpose, they reveal details of neuroanatomy and cytoarchitecture. Here, we used this population to systematically characterize cell density and volume for each anatomical unit in the mouse brain. We developed a deep neural network-based segmentation pipeline that uses the auto-fluorescence intensities of images to segment cell nuclei even within the densest regions, such as the dentate gyrus. We applied our pipeline to 507 brains of males and females from C57BL/6J and FVB.CD1 strains. Globally, we found that increased overall brain volume does not result in uniform expansion across all regions. Moreover, region-specific density changes are often negatively correlated with the volume of the region, therefore cell count does not scale linearly with volume. Many regions, including layer 2/3 across several cortical areas, showed distinct lateral bias. We identified strain-specific or sex-specific differences. For example, males tended to have more cells in extended amygdala and hypothalamic regions (MEA, BST, BLA, BMA, and LPO, AHN) while females had more cells in the orbital cortex (ORB). Yet, inter-individual variability was always greater than the effect size of a single qualifier. We provide the results of this analysis as an accessible resource for the community.
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Affiliation(s)
- David Elkind
- Department of Computer Science, Open University of Israel, Raanana, Israel
| | - Hannah Hochgerner
- Faculty of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa, Israel
| | - Etay Aloni
- Faculty of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa, Israel
| | - Noam Shental
- Department of Computer Science, Open University of Israel, Raanana, Israel
| | - Amit Zeisel
- Faculty of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa, Israel
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Zeisel A, Hochgerner H, Lönnerberg P, Johnsson A, Memic F, van der Zwan J, Häring M, Braun E, Borm LE, La Manno G, Codeluppi S, Furlan A, Lee K, Skene N, Harris KD, Hjerling-Leffler J, Arenas E, Ernfors P, Marklund U, Linnarsson S. Molecular Architecture of the Mouse Nervous System. Cell 2018; 174:999-1014.e22. [PMID: 30096314 PMCID: PMC6086934 DOI: 10.1016/j.cell.2018.06.021] [Citation(s) in RCA: 1438] [Impact Index Per Article: 239.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Revised: 06/04/2018] [Accepted: 06/08/2018] [Indexed: 12/14/2022]
Abstract
The mammalian nervous system executes complex behaviors controlled by specialized, precisely positioned, and interacting cell types. Here, we used RNA sequencing of half a million single cells to create a detailed census of cell types in the mouse nervous system. We mapped cell types spatially and derived a hierarchical, data-driven taxonomy. Neurons were the most diverse and were grouped by developmental anatomical units and by the expression of neurotransmitters and neuropeptides. Neuronal diversity was driven by genes encoding cell identity, synaptic connectivity, neurotransmission, and membrane conductance. We discovered seven distinct, regionally restricted astrocyte types that obeyed developmental boundaries and correlated with the spatial distribution of key glutamate and glycine neurotransmitters. In contrast, oligodendrocytes showed a loss of regional identity followed by a secondary diversification. The resource presented here lays a solid foundation for understanding the molecular architecture of the mammalian nervous system and enables genetic manipulation of specific cell types.
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Affiliation(s)
- Amit Zeisel
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, S-17177 Stockholm, Sweden
| | - Hannah Hochgerner
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, S-17177 Stockholm, Sweden
| | - Peter Lönnerberg
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, S-17177 Stockholm, Sweden
| | - Anna Johnsson
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, S-17177 Stockholm, Sweden
| | - Fatima Memic
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, S-17177 Stockholm, Sweden
| | - Job van der Zwan
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, S-17177 Stockholm, Sweden
| | - Martin Häring
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, S-17177 Stockholm, Sweden
| | - Emelie Braun
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, S-17177 Stockholm, Sweden
| | - Lars E Borm
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, S-17177 Stockholm, Sweden
| | - Gioele La Manno
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, S-17177 Stockholm, Sweden
| | - Simone Codeluppi
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, S-17177 Stockholm, Sweden
| | - Alessandro Furlan
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, S-17177 Stockholm, Sweden
| | - Kawai Lee
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, S-17177 Stockholm, Sweden
| | - Nathan Skene
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, S-17177 Stockholm, Sweden
| | | | - Jens Hjerling-Leffler
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, S-17177 Stockholm, Sweden
| | - Ernest Arenas
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, S-17177 Stockholm, Sweden
| | - Patrik Ernfors
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, S-17177 Stockholm, Sweden
| | - Ulrika Marklund
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, S-17177 Stockholm, Sweden
| | - Sten Linnarsson
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, S-17177 Stockholm, Sweden.
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La Manno G, Soldatov R, Zeisel A, Braun E, Hochgerner H, Petukhov V, Lidschreiber K, Kastriti ME, Lönnerberg P, Furlan A, Fan J, Borm LE, Liu Z, van Bruggen D, Guo J, He X, Barker R, Sundström E, Castelo-Branco G, Cramer P, Adameyko I, Linnarsson S, Kharchenko PV. RNA velocity of single cells. Nature 2018; 560:494-498. [PMID: 30089906 PMCID: PMC6130801 DOI: 10.1038/s41586-018-0414-6] [Citation(s) in RCA: 1871] [Impact Index Per Article: 311.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 07/03/2018] [Indexed: 11/09/2022]
Abstract
RNA abundance is a powerful indicator of the state of individual cells. Single-cell RNA sequencing can reveal RNA abundance with high quantitative accuracy, sensitivity and throughput1. However, this approach captures only a static snapshot at a point in time, posing a challenge for the analysis of time-resolved phenomena such as embryogenesis or tissue regeneration. Here we show that RNA velocity-the time derivative of the gene expression state-can be directly estimated by distinguishing between unspliced and spliced mRNAs in common single-cell RNA sequencing protocols. RNA velocity is a high-dimensional vector that predicts the future state of individual cells on a timescale of hours. We validate its accuracy in the neural crest lineage, demonstrate its use on multiple published datasets and technical platforms, reveal the branching lineage tree of the developing mouse hippocampus, and examine the kinetics of transcription in human embryonic brain. We expect RNA velocity to greatly aid the analysis of developmental lineages and cellular dynamics, particularly in humans.
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Affiliation(s)
- Gioele La Manno
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Solna, Sweden
| | - Ruslan Soldatov
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Amit Zeisel
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Solna, Sweden
| | - Emelie Braun
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Solna, Sweden
| | - Hannah Hochgerner
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Solna, Sweden
| | - Viktor Petukhov
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Department of Applied Mathematics, Peter The Great St. Petersburg Polytechnic University, St, Petersburg, Russia
| | - Katja Lidschreiber
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Maria E Kastriti
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Peter Lönnerberg
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Solna, Sweden
| | - Alessandro Furlan
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Jean Fan
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Lars E Borm
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Solna, Sweden
| | - Zehua Liu
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - David van Bruggen
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Jimin Guo
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Xiaoling He
- John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Roger Barker
- John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Erik Sundström
- Division of Neurodegeneration, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
| | - Gonçalo Castelo-Branco
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Patrick Cramer
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Göttingen, Germany
| | - Igor Adameyko
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Sten Linnarsson
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
- Science for Life Laboratory, Solna, Sweden.
| | - Peter V Kharchenko
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Harvard Stem Cell Institute, Cambridge, MA, USA.
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10
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Harris KD, Hochgerner H, Skene NG, Magno L, Katona L, Bengtsson Gonzales C, Somogyi P, Kessaris N, Linnarsson S, Hjerling-Leffler J. Classes and continua of hippocampal CA1 inhibitory neurons revealed by single-cell transcriptomics. PLoS Biol 2018; 16:e2006387. [PMID: 29912866 PMCID: PMC6029811 DOI: 10.1371/journal.pbio.2006387] [Citation(s) in RCA: 160] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 07/03/2018] [Accepted: 05/22/2018] [Indexed: 01/19/2023] Open
Abstract
Understanding any brain circuit will require a categorization of its constituent neurons. In hippocampal area CA1, at least 23 classes of GABAergic neuron have been proposed to date. However, this list may be incomplete; additionally, it is unclear whether discrete classes are sufficient to describe the diversity of cortical inhibitory neurons or whether continuous modes of variability are also required. We studied the transcriptomes of 3,663 CA1 inhibitory cells, revealing 10 major GABAergic groups that divided into 49 fine-scale clusters. All previously described and several novel cell classes were identified, with three previously described classes unexpectedly found to be identical. A division into discrete classes, however, was not sufficient to describe the diversity of these cells, as continuous variation also occurred between and within classes. Latent factor analysis revealed that a single continuous variable could predict the expression levels of several genes, which correlated similarly with it across multiple cell types. Analysis of the genes correlating with this variable suggested it reflects a range from metabolically highly active faster-spiking cells that proximally target pyramidal cells to slower-spiking cells targeting distal dendrites or interneurons. These results elucidate the complexity of inhibitory neurons in one of the simplest cortical structures and show that characterizing these cells requires continuous modes of variation as well as discrete cell classes.
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Affiliation(s)
- Kenneth D. Harris
- University College London Institute of Neurology, London, United Kingdom
- University College London Department of Neuroscience, Physiology and Pharmacology, London, United Kingdom
| | - Hannah Hochgerner
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Nathan G. Skene
- University College London Institute of Neurology, London, United Kingdom
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Lorenza Magno
- University College London Wolfson Institute for Biomedical Research, London, United Kingdom
| | - Linda Katona
- Department of Pharmacology, University of Oxford, Oxford, United Kingdom
| | - Carolina Bengtsson Gonzales
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Peter Somogyi
- Department of Pharmacology, University of Oxford, Oxford, United Kingdom
| | - Nicoletta Kessaris
- University College London Wolfson Institute for Biomedical Research, London, United Kingdom
| | - Sten Linnarsson
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Jens Hjerling-Leffler
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
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11
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Hochgerner H, Zeisel A, Lönnerberg P, Linnarsson S. Conserved properties of dentate gyrus neurogenesis across postnatal development revealed by single-cell RNA sequencing. Nat Neurosci 2018; 21:290-299. [PMID: 29335606 DOI: 10.1038/s41593-017-0056-2] [Citation(s) in RCA: 236] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 11/22/2017] [Indexed: 12/12/2022]
Abstract
The dentate gyrus of the hippocampus is a brain region in which neurogenesis persists into adulthood; however, the relationship between developmental and adult dentate gyrus neurogenesis has not been examined in detail. Here we used single-cell RNA sequencing to reveal the molecular dynamics and diversity of dentate gyrus cell types in perinatal, juvenile, and adult mice. We found distinct quiescent and proliferating progenitor cell types, linked by transient intermediate states to neuroblast stages and fully mature granule cells. We observed shifts in the molecular identity of quiescent and proliferating radial glia and granule cells during the postnatal period that were then maintained through adult stages. In contrast, intermediate progenitor cells, neuroblasts, and immature granule cells were nearly indistinguishable at all ages. These findings demonstrate the fundamental similarity of postnatal and adult neurogenesis in the hippocampus and pinpoint the early postnatal transformation of radial glia from embryonic progenitors to adult quiescent stem cells.
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Affiliation(s)
- Hannah Hochgerner
- Division of Molecular Neurobiology, Dept. of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.,Science for Life Laboratory, Solna, Sweden
| | - Amit Zeisel
- Division of Molecular Neurobiology, Dept. of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.,Science for Life Laboratory, Solna, Sweden
| | - Peter Lönnerberg
- Division of Molecular Neurobiology, Dept. of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.,Science for Life Laboratory, Solna, Sweden
| | - Sten Linnarsson
- Division of Molecular Neurobiology, Dept. of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden. .,Science for Life Laboratory, Solna, Sweden.
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12
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Hochgerner H, Lönnerberg P, Hodge R, Mikes J, Heskol A, Hubschle H, Lin P, Picelli S, La Manno G, Ratz M, Dunne J, Husain S, Lein E, Srinivasan M, Zeisel A, Linnarsson S. STRT-seq-2i: dual-index 5' single cell and nucleus RNA-seq on an addressable microwell array. Sci Rep 2017; 7:16327. [PMID: 29180631 PMCID: PMC5703850 DOI: 10.1038/s41598-017-16546-4] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 11/06/2017] [Indexed: 11/09/2022] Open
Abstract
Single-cell RNA-seq has become routine for discovering cell types and revealing cellular diversity, but archived human brain samples still pose a challenge to current high-throughput platforms. We present STRT-seq-2i, an addressable 9600-microwell array platform, combining sampling by limiting dilution or FACS, with imaging and high throughput at competitive cost. We applied the platform to fresh single mouse cortical cells and to frozen post-mortem human cortical nuclei, matching the performance of a previous lower-throughput platform while retaining a high degree of flexibility, potentially also for other high-throughput applications.
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Affiliation(s)
- Hannah Hochgerner
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Solna, Sweden
| | - Peter Lönnerberg
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Solna, Sweden
| | - Rebecca Hodge
- Allen Institute for Brain Science, Seattle, Washington, USA
| | | | - Abeer Heskol
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | | | - Philip Lin
- WaferGen Biosystems Inc., Fremont, California, USA
| | - Simone Picelli
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Solna, Sweden
| | - Gioele La Manno
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Solna, Sweden
| | - Michael Ratz
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Jude Dunne
- WaferGen Biosystems Inc., Fremont, California, USA
| | - Syed Husain
- WaferGen Biosystems Inc., Fremont, California, USA
| | - Ed Lein
- Allen Institute for Brain Science, Seattle, Washington, USA
| | | | - Amit Zeisel
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
- Science for Life Laboratory, Solna, Sweden.
| | - Sten Linnarsson
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
- Science for Life Laboratory, Solna, Sweden.
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13
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Morarach K, Memic F, Zeisel A, Hochgerner H, Marklund U, Linnarsson S. Single-cell molecular interrogation of enteric nervous system development. Mech Dev 2017. [DOI: 10.1016/j.mod.2017.04.151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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14
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Furlan A, La Manno G, Lübke M, Häring M, Abdo H, Hochgerner H, Kupari J, Usoskin D, Airaksinen MS, Oliver G, Linnarsson S, Ernfors P. Visceral motor neuron diversity delineates a cellular basis for nipple- and pilo-erection muscle control. Nat Neurosci 2016; 19:1331-40. [PMID: 27571008 DOI: 10.1038/nn.4376] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 08/04/2016] [Indexed: 01/19/2023]
Abstract
Despite the variety of physiological and target-related functions, little is known regarding the cellular complexity in the sympathetic ganglion. We explored the heterogeneity of mouse stellate and thoracic ganglia and found an unexpected variety of cell types. We identified specialized populations of nipple- and pilo-erector muscle neurons. These neurons extended axonal projections and were born among other neurons during embryogenesis, but remained unspecialized until target organogenesis occurred postnatally. Target innervation and cell-type specification was coordinated by an intricate acquisition of unique combinations of growth factor receptors and the initiation of expression of concomitant ligands by the nascent erector muscles. Overall, our results provide compelling evidence for a highly sophisticated organization of the sympathetic nervous system into discrete outflow channels that project to well-defined target tissues and offer mechanistic insight into how diversity and connectivity are established during development.
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Affiliation(s)
- Alessandro Furlan
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Gioele La Manno
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Moritz Lübke
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Martin Häring
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Hind Abdo
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Hannah Hochgerner
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Jussi Kupari
- Department of Anatomy, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Dmitry Usoskin
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Matti S Airaksinen
- Department of Anatomy, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Guillermo Oliver
- Center for Vascular and Developmental Biology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Sten Linnarsson
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Patrik Ernfors
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
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15
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Marques S, Zeisel A, Codeluppi S, van Bruggen D, Mendanha Falcão A, Xiao L, Li H, Häring M, Hochgerner H, Romanov RA, Gyllborg D, Muñoz Manchado A, La Manno G, Lönnerberg P, Floriddia EM, Rezayee F, Ernfors P, Arenas E, Hjerling-Leffler J, Harkany T, Richardson WD, Linnarsson S, Castelo-Branco G. Oligodendrocyte heterogeneity in the mouse juvenile and adult central nervous system. Science 2016; 352:1326-1329. [PMID: 27284195 DOI: 10.1126/science.aaf6463] [Citation(s) in RCA: 627] [Impact Index Per Article: 78.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 05/10/2016] [Indexed: 12/15/2022]
Abstract
Oligodendrocytes have been considered as a functionally homogeneous population in the central nervous system (CNS). We performed single-cell RNA sequencing on 5072 cells of the oligodendrocyte lineage from 10 regions of the mouse juvenile and adult CNS. Thirteen distinct populations were identified, 12 of which represent a continuum from Pdgfra(+) oligodendrocyte precursor cells (OPCs) to distinct mature oligodendrocytes. Initial stages of differentiation were similar across the juvenile CNS, whereas subsets of mature oligodendrocytes were enriched in specific regions in the adult brain. Newly formed oligodendrocytes were detected in the adult CNS and were responsive to complex motor learning. A second Pdgfra(+) population, distinct from OPCs, was found along vessels. Our study reveals the dynamics of oligodendrocyte differentiation and maturation, uncoupling them at a transcriptional level and highlighting oligodendrocyte heterogeneity in the CNS.
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Affiliation(s)
- Sueli Marques
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Amit Zeisel
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Simone Codeluppi
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden.,Department of Physiology and Pharmacology, Karolinska Institutet SE-17177 Stockholm, Sweden
| | - David van Bruggen
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Ana Mendanha Falcão
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Lin Xiao
- Wolfson Institute for Biomedical Research, University College London, Gower Street, London WC1E 6BT, United Kingdom.,Institute of Neuroscience, Second Military Medical University, 800 Xiangyin Road, Shanghai 200433, China
| | - Huiliang Li
- Wolfson Institute for Biomedical Research, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Martin Häring
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Hannah Hochgerner
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Roman A Romanov
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden.,Department of Molecular Neurosciences, Center for Brain Research, Medical University of Vienna, Austria
| | - Daniel Gyllborg
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Ana Muñoz Manchado
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Gioele La Manno
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Peter Lönnerberg
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Elisa M Floriddia
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Fatemah Rezayee
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Patrik Ernfors
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Ernest Arenas
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Jens Hjerling-Leffler
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Tibor Harkany
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden.,Department of Molecular Neurosciences, Center for Brain Research, Medical University of Vienna, Austria
| | - William D Richardson
- Wolfson Institute for Biomedical Research, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Sten Linnarsson
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Gonçalo Castelo-Branco
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden
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16
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Zajac P, Islam S, Hochgerner H, Lönnerberg P, Linnarsson S. Base preferences in non-templated nucleotide incorporation by MMLV-derived reverse transcriptases. PLoS One 2013; 8:e85270. [PMID: 24392002 PMCID: PMC3877366 DOI: 10.1371/journal.pone.0085270] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Accepted: 11/26/2013] [Indexed: 11/21/2022] Open
Abstract
Reverse transcriptases derived from Moloney Murine Leukemia Virus (MMLV) have an intrinsic terminal transferase activity, which causes the addition of a few non-templated nucleotides at the 3´ end of cDNA, with a preference for cytosine. This mechanism can be exploited to make the reverse transcriptase switch template from the RNA molecule to a secondary oligonucleotide during first-strand cDNA synthesis, and thereby to introduce arbitrary barcode or adaptor sequences in the cDNA. Because the mechanism is relatively efficient and occurs in a single reaction, it has recently found use in several protocols for single-cell RNA sequencing. However, the base preference of the terminal transferase activity is not known in detail, which may lead to inefficiencies in template switching when starting from tiny amounts of mRNA. Here, we used fully degenerate oligos to determine the exact base preference at the template switching site up to a distance of ten nucleotides. We found a strong preference for guanosine at the first non-templated nucleotide, with a greatly reduced bias at progressively more distant positions. Based on this result, and a number of careful optimizations, we report conditions for efficient template switching for cDNA amplification from single cells.
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Affiliation(s)
- Pawel Zajac
- Laboratory for Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Saiful Islam
- Laboratory for Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Hannah Hochgerner
- Laboratory for Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Peter Lönnerberg
- Laboratory for Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Sten Linnarsson
- Laboratory for Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
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