1
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Spratt J, Dias JM, Kolonelou C, Kiriako G, Engström E, Petrova E, Karampelias C, Cervenka I, Papanicolaou N, Lentini A, Reinius B, Andersson O, Ambrosetti E, Ruas JL, Teixeira AI. Multivalent insulin receptor activation using insulin-DNA origami nanostructures. Nat Nanotechnol 2024; 19:237-245. [PMID: 37813939 PMCID: PMC10873203 DOI: 10.1038/s41565-023-01507-y] [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] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 08/15/2023] [Indexed: 10/11/2023]
Abstract
Insulin binds the insulin receptor (IR) and regulates anabolic processes in target tissues. Impaired IR signalling is associated with multiple diseases, including diabetes, cancer and neurodegenerative disorders. IRs have been reported to form nanoclusters at the cell membrane in several cell types, even in the absence of insulin binding. Here we exploit the nanoscale spatial organization of the IR to achieve controlled multivalent receptor activation. To control insulin nanoscale spatial organization and valency, we developed rod-like insulin-DNA origami nanostructures carrying different numbers of insulin molecules with defined spacings. Increasing the insulin valency per nanostructure markedly extended the residence time of insulin-DNA origami nanostructures at the receptors. Both insulin valency and spacing affected the levels of IR activation in adipocytes. Moreover, the multivalent insulin design associated with the highest levels of IR activation also induced insulin-mediated transcriptional responses more effectively than the corresponding monovalent insulin nanostructures. In an in vivo zebrafish model of diabetes, treatment with multivalent-but not monovalent-insulin nanostructures elicited a reduction in glucose levels. Our results show that the control of insulin multivalency and spatial organization with nanoscale precision modulates the IR responses, independent of the insulin concentration. Therefore, we propose insulin nanoscale organization as a design parameter in developing new insulin therapies.
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Affiliation(s)
- Joel Spratt
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - José M Dias
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Christina Kolonelou
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Georges Kiriako
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Enya Engström
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Ekaterina Petrova
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Christos Karampelias
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Igor Cervenka
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Natali Papanicolaou
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Antonio Lentini
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Björn Reinius
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Olov Andersson
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Elena Ambrosetti
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Center for Life Nano- and Neuro-Science, Istituto Italiano di Tecnologia, Rome, Italy
| | - Jorge L Ruas
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Ana I Teixeira
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden.
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2
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Smyrlaki I, Fördős F, Rocamonde-Lago I, Wang Y, Shen B, Lentini A, Luca VC, Reinius B, Teixeira AI, Högberg B. Soluble and multivalent Jag1 DNA origami nanopatterns activate Notch without pulling force. Nat Commun 2024; 15:465. [PMID: 38238313 PMCID: PMC10796381 DOI: 10.1038/s41467-023-44059-4] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 11/28/2023] [Indexed: 01/22/2024] Open
Abstract
The Notch signaling pathway has fundamental roles in embryonic development and in the nervous system. The current model of receptor activation involves initiation via a force-induced conformational change. Here, we define conditions that reveal pulling force-independent Notch activation using soluble multivalent constructs. We treat neuroepithelial stem-like cells with molecularly precise ligand nanopatterns displayed from solution using DNA origami. Notch signaling follows with clusters of Jag1, and with chimeric structures where most Jag1 proteins are replaced by other binders not targeting Notch. Our data rule out several confounding factors and suggest a model where Jag1 activates Notch upon prolonged binding without appearing to need a pulling force. These findings reveal a distinct mode of activation of Notch and lay the foundation for the development of soluble agonists.
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Affiliation(s)
- Ioanna Smyrlaki
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Ferenc Fördős
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Iris Rocamonde-Lago
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Yang Wang
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Boxuan Shen
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, Alto, Finland
| | - Antonio Lentini
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Vincent C Luca
- Department of Immunology, Moffitt Cancer Center, Tampa, FL, USA
| | - Björn Reinius
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Ana I Teixeira
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Björn Högberg
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
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3
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Tayyab M, Barrett D, van Riel G, Liu S, Reinius B, Scharfe C, Griffin P, Steinmetz LM, Javanmard M, Pelechano V. Digital assay for rapid electronic quantification of clinical pathogens using DNA nanoballs. Sci Adv 2023; 9:eadi4997. [PMID: 37672583 PMCID: PMC10482329 DOI: 10.1126/sciadv.adi4997] [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: 04/29/2023] [Accepted: 08/04/2023] [Indexed: 09/08/2023]
Abstract
Fast and accurate detection of nucleic acids is key for pathogen identification. Methods for DNA detection generally rely on fluorescent or colorimetric readout. The development of label-free assays decreases costs and test complexity. We present a novel method combining a one-pot isothermal generation of DNA nanoballs with their detection by electrical impedance. We modified loop-mediated isothermal amplification by using compaction oligonucleotides that self-assemble the amplified target into nanoballs. Next, we use capillary-driven flow to passively pass these nanoballs through a microfluidic impedance cytometer, thus enabling a fully compact system with no moving parts. The movement of individual nanoballs is detected by a change in impedance providing a quantized readout. This approach is flexible for the detection of DNA/RNA of numerous targets (severe acute respiratory syndrome coronavirus 2, HIV, β-lactamase gene, etc.), and we anticipate that its integration into a standalone device would provide an inexpensive (<$5), sensitive (10 target copies), and rapid test (<1 hour).
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Affiliation(s)
- Muhammad Tayyab
- Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Donal Barrett
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Gijs van Riel
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Shujing Liu
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
- International Institute of Tea Industry Innovation for the Belt and Road, Nanjing Agricultural University, Nanjing 210095, China
| | - Björn Reinius
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden
| | | | - Peter Griffin
- Stanford Genome Technology Center, Stanford, CA, USA
| | - Lars M. Steinmetz
- Stanford Genome Technology Center, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Mehdi Javanmard
- Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Vicent Pelechano
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
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4
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Csillag V, Bizzozzero MH, Noble JC, Reinius B, Fuzik J. Voltage-Seq: all-optical postsynaptic connectome-guided single-cell transcriptomics. Nat Methods 2023; 20:1409-1416. [PMID: 37474808 PMCID: PMC10482676 DOI: 10.1038/s41592-023-01965-1] [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: 12/14/2022] [Accepted: 06/21/2023] [Indexed: 07/22/2023]
Abstract
Understanding the routing of neuronal information requires the functional characterization of connections. Neuronal projections recruit large postsynaptic ensembles with distinct postsynaptic response types (PRTs). PRT is typically probed by low-throughput whole-cell electrophysiology and is not a selection criterion for single-cell RNA-sequencing (scRNA-seq). To overcome these limitations and target neurons based on specific PRTs for soma harvesting and subsequent scRNA-seq, we created Voltage-Seq. We established all-optical voltage imaging and recorded the PRT of 8,347 neurons in the mouse periaqueductal gray (PAG) evoked by the optogenetic activation of ventromedial hypothalamic (VMH) terminals. PRTs were classified and spatially resolved in the entire VMH-PAG connectome. We built an onsite analysis tool named VoltView to navigate soma harvesting towards target PRTs guided by a classifier that used the VMH-PAG connectome database as a reference. We demonstrated Voltage-seq by locating VMH-driven γ-aminobutyric acid-ergic neurons in the PAG, guided solely by the onsite classification in VoltView.
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Affiliation(s)
- Veronika Csillag
- Department of Neuroscience, Karolinska Institute, Stockholm, Sweden
| | | | - J C Noble
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Björn Reinius
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - János Fuzik
- Department of Neuroscience, Karolinska Institute, Stockholm, Sweden.
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5
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Calvigioni D, Fuzik J, Le Merre P, Slashcheva M, Jung F, Ortiz C, Lentini A, Csillag V, Graziano M, Nikolakopoulou I, Weglage M, Lazaridis I, Kim H, Lenzi I, Park H, Reinius B, Carlén M, Meletis K. Esr1 + hypothalamic-habenula neurons shape aversive states. Nat Neurosci 2023:10.1038/s41593-023-01367-8. [PMID: 37349481 DOI: 10.1038/s41593-023-01367-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 05/18/2023] [Indexed: 06/24/2023]
Abstract
Excitatory projections from the lateral hypothalamic area (LHA) to the lateral habenula (LHb) drive aversive responses. We used patch-sequencing (Patch-seq) guided multimodal classification to define the structural and functional heterogeneity of the LHA-LHb pathway. Our classification identified six glutamatergic neuron types with unique electrophysiological properties, molecular profiles and projection patterns. We found that genetically defined LHA-LHb neurons signal distinct aspects of emotional or naturalistic behaviors, such as estrogen receptor 1-expressing (Esr1+) LHA-LHb neurons induce aversion, whereas neuropeptide Y-expressing (Npy+) LHA-LHb neurons control rearing behavior. Repeated optogenetic drive of Esr1+ LHA-LHb neurons induces a behaviorally persistent aversive state, and large-scale recordings showed a region-specific neural representation of the aversive signals in the prelimbic region of the prefrontal cortex. We further found that exposure to unpredictable mild shocks induced a sex-specific sensitivity to develop a stress state in female mice, which was associated with a specific shift in the intrinsic properties of bursting-type Esr1+ LHA-LHb neurons. In summary, we describe the diversity of LHA-LHb neuron types and provide evidence for the role of Esr1+ neurons in aversion and sexually dimorphic stress sensitivity.
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Affiliation(s)
| | - Janos Fuzik
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Pierre Le Merre
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Marina Slashcheva
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Felix Jung
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Cantin Ortiz
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Antonio Lentini
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Veronika Csillag
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Marta Graziano
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | | | - Moritz Weglage
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Iakovos Lazaridis
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Hoseok Kim
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Irene Lenzi
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Hyunsoo Park
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Björn Reinius
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Marie Carlén
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden.
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Lentini A, Reinius B. Limitations of X:autosome ratio as a measurement of X-chromosome upregulation. Curr Biol 2023; 33:R395-R396. [PMID: 37220727 DOI: 10.1016/j.cub.2023.03.059] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/22/2023] [Indexed: 05/25/2023]
Abstract
Lentini and Reinius address issues in interpreting non-allelic gene expression measurements of dosage compensation during murine embryonic development.
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Affiliation(s)
- Antonio Lentini
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
| | - Björn Reinius
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
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7
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Vaid R, Mendez A, Thombare K, Burgos Panadero R, Robinot R, Fonseca BF, Gandasi NR, Ringlander J, Hassan Baig M, Dong JJ, Cho JY, Reinius B, Chakrabarti LA, Nystrom K, Mondal T. Global loss of cellular m6A RNA methylation following infection with different SARS-CoV-2 variants. Genome Res 2023:gr.276407.121. [PMID: 36859333 PMCID: PMC10078285 DOI: 10.1101/gr.276407.121] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 02/17/2023] [Indexed: 03/03/2023]
Abstract
Host-viral interactions during SARS-CoV-2 infection are needed to understand COVID-19 pathogenesis and may help to guide the design of novel antiviral therapeutics. N6-methyladenosine modification (m6A), one of the most abundant cellular RNA modifications, regulates key processes in RNA metabolism during a stress response. Gene expression profiles observed post-infection with different SARS-CoV-2 variants show changes in the expression of genes related to RNA catabolism, including m6A readers and erasers. We found that infection with SARS-CoV-2 variants caused a loss of m6A in cellular RNAs, whereas m6A was detected abundantly in viral RNA. METTL3, the m6A methyltransferase, showed an unusual cytoplasmic localization post-infection. The B.1.351 variant had a less pronounced effect on METTL3 localization and loss of m6A than the B.1 and B.1.1.7 variants. We also observed a loss of m6A upon SARS-CoV-2 infection in air/liquid interface cultures of human airway epithelia, confirming that m6A loss is characteristic of SARS-CoV-2 infected cells. Further, transcripts with m6A modification were preferentially down-regulated post-infection. Inhibition of the export protein XPO1 resulted in the restoration of METTL3 localization, recovery of m6A on cellular RNA, and increased mRNA expression. Stress granule formation, which was compromised by SARS-CoV-2 infection, was restored by XPO1 inhibition and accompanied by a reduced viral infection in vitro. Together, our study elucidates how SARS-CoV-2 inhibits the stress response and perturbs cellular gene expression in an m6A-dependent manner.
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Affiliation(s)
- Roshan Vaid
- Institute of Biomedicine, University of Gothenburg
| | - Akram Mendez
- Institute of Biomedicine, University of Gothenburg
| | | | | | - Rémy Robinot
- Institut Pasteur, Université Paris Cité, CNRS UMR
| | | | | | | | | | - Jae-June Dong
- Gangnam Severance Hospital, Yonsei University College of Medicine
| | - Jae Yong Cho
- Gangnam Severance Hospital, Yonsei University College of Medicine
| | | | | | | | - Tanmoy Mondal
- Institute of Biomedicine, University of Gothenburg, Sahlgrenska University Hospital
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Rufino de Sousa N, Steponaviciute L, Margerie L, Nissen K, Kjellin M, Reinius B, Salaneck E, Udekwu KI, Rothfuchs AG. Plaque-forming units from air samples: Letter to Editor. Re: Jefferson et al., Indoor Air, 2022. Indoor Air 2022; 32:e13169. [PMID: 36437649 DOI: 10.1111/ina.13169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 10/26/2022] [Accepted: 10/27/2022] [Indexed: 06/16/2023]
Affiliation(s)
- Nuno Rufino de Sousa
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
| | - Laura Steponaviciute
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
| | - Lucille Margerie
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
| | - Karolina Nissen
- Department of Medical Sciences, Infectious Diseases, Uppsala University, University Hospital Uppsala, Uppsala, Sweden
| | - Midori Kjellin
- Department of Medical Sciences, Infectious Diseases, Uppsala University, University Hospital Uppsala, Uppsala, Sweden
| | - Björn Reinius
- Department of Medical Biochemistry and Biophysics (MBB), Karolinska Institutet, Stockholm, Sweden
| | - Erik Salaneck
- Department of Medical Sciences, Infectious Diseases, Uppsala University, University Hospital Uppsala, Uppsala, Sweden
| | - Klas I Udekwu
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
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9
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Lentini A, Pereira A, Winqvist O, Reinius B. Monitoring of the SARS-CoV-2 Omicron BA.1/BA.2 lineage transition in the Swedish population reveals increased viral RNA levels in BA.2 cases. Med (N Y) 2022; 3:636-643.e4. [PMID: 35981541 PMCID: PMC9359497 DOI: 10.1016/j.medj.2022.07.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/31/2022] [Accepted: 07/21/2022] [Indexed: 11/17/2022]
Abstract
Background Throughout the SARS-CoV-2 pandemic, multiple waves of variants of concern have swept across populations, leading to a chain of new and yet more contagious variants dominating COVID-19 cases. Here, we tracked the remarkably rapid shift from Omicron BA.1 to BA.2 sublineage dominance in the Swedish population in early 2022 at a day-by-day basis. Methods Using a custom SARS-CoV-2 Omicron BA.1 lineage-typing RT-PCR assay, we analyzed 174,933 clinical upper airway samples collected during January to March 2022. Findings Our study demonstrates the feasibility and reliability of parallel lineage assignment of select variants at population scale, tracking the dominant sublineage transition from BA.1 to BA.2 at day-to-day resolution and uncovering nearly 2-fold higher levels of viral RNA in cases infected with Omicron BA.2 relative to BA.1. Conclusions Our data provide unique insights into the Omicron BA.1 to BA.2 transition that occurred in Sweden during early 2022, and later, across the world. This may help to understand the increased transmissibility of the BA.2 variant. Early population tracking is critical for informed decision-making and handling of the SARS-CoV-2 pandemic during outbreaks of variant strains of concern. Omicron variant infections emerged during late 2021, but at the time, lineage assignment relied on sequencing or separate genotyping assays in addition to the clinical SARS-CoV-2 RT-PCR, burdening laboratories and restricting the scope of lineage monitoring. Here, researchers at the Karolinska Institute and ABC Labs developed a single RT-PCR assay to simultaneously classify COVID-19 and Omicron BA.1 lineage status and demonstrated the feasibility of parallel lineage assignment of select variants at population scale. The authors show, at day-to-day resolution, the rapid transition from Omicron BA.1 to BA.2 sublineage dominance in the Swedish population, exposing factors that could influence this transition.
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Affiliation(s)
- Antonio Lentini
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Solna, Sweden
| | | | | | - Björn Reinius
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Solna, Sweden.
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10
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Rufino de Sousa N, Steponaviciute L, Margerie L, Nissen K, Kjellin M, Reinius B, Salaneck E, Udekwu KI, Rothfuchs AG. Corrigendum. Re: de Sousa, N.R., et al., 2022. Detection and isolation of airborne SARS-CoV-2 in a hospital setting. Indoor air, 32(3), e13023. Indoor Air 2022; 32:e13085. [PMID: 36040276 PMCID: PMC10117284 DOI: 10.1111/ina.13085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 07/19/2022] [Indexed: 06/15/2023]
Affiliation(s)
- Nuno Rufino de Sousa
- Department of Microbiology, Tumor
and Cell Biology (MTC)Karolinska InstitutetStockholmSweden
| | - Laura Steponaviciute
- Department of Microbiology, Tumor
and Cell Biology (MTC)Karolinska InstitutetStockholmSweden
| | - Lucille Margerie
- Department of Microbiology, Tumor
and Cell Biology (MTC)Karolinska InstitutetStockholmSweden
| | - Karolina Nissen
- Department of Medical Sciences,
Infectious DiseasesUppsala University, University Hospital UppsalaSweden
| | - Midori Kjellin
- Department of Medical Sciences,
Infectious DiseasesUppsala University, University Hospital UppsalaSweden
| | - Björn Reinius
- Department of Medical Biochemistry
and Biophysics (MBB)Karolinska InstitutetStockholmSweden
| | - Erik Salaneck
- Department of Medical Sciences,
Infectious DiseasesUppsala University, University Hospital UppsalaSweden
| | - Klas I. Udekwu
- Department of Aquatic Sciences and
AssessmentSwedish University of Agricultural SciencesUppsalaSweden
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11
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Lentini A, Cheng H, Noble JC, Papanicolaou N, Coucoravas C, Andrews N, Deng Q, Enge M, Reinius B. Elastic dosage compensation by X-chromosome upregulation. Nat Commun 2022; 13:1854. [PMID: 35388014 PMCID: PMC8987076 DOI: 10.1038/s41467-022-29414-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 03/14/2022] [Indexed: 12/24/2022] Open
Abstract
X-chromosome inactivation and X-upregulation are the fundamental modes of chromosome-wide gene regulation that collectively achieve dosage compensation in mammals, but the regulatory link between the two remains elusive and the X-upregulation dynamics are unknown. Here, we use allele-resolved single-cell RNA-seq combined with chromatin accessibility profiling and finely dissect their separate effects on RNA levels during mouse development. Surprisingly, we uncover that X-upregulation elastically tunes expression dosage in a sex- and lineage-specific manner, and moreover along varying degrees of X-inactivation progression. Male blastomeres achieve X-upregulation upon zygotic genome activation while females experience two distinct waves of upregulation, upon imprinted and random X-inactivation; and ablation of Xist impedes female X-upregulation. Female cells carrying two active X chromosomes lack upregulation, yet their collective RNA output exceeds that of a single hyperactive allele. Importantly, this conflicts the conventional dosage compensation model in which naïve female cells are initially subject to biallelic X-upregulation followed by X-inactivation of one allele to correct the X dosage. Together, our study provides key insights to the chain of events of dosage compensation, explaining how transcript copy numbers can remain remarkably stable across developmental windows wherein severe dose imbalance would otherwise be experienced by the cell.
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Affiliation(s)
- Antonio Lentini
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Huaitao Cheng
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
| | - J C Noble
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Natali Papanicolaou
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Christos Coucoravas
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Nathanael Andrews
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Qiaolin Deng
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Martin Enge
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Björn Reinius
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
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12
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Johnsson P, Ziegenhain C, Hartmanis L, Hendriks GJ, Hagemann-Jensen M, Reinius B, Sandberg R. Transcriptional kinetics and molecular functions of long noncoding RNAs. Nat Genet 2022; 54:306-317. [PMID: 35241826 PMCID: PMC8920890 DOI: 10.1038/s41588-022-01014-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 01/05/2022] [Indexed: 12/21/2022]
Abstract
An increasing number of long noncoding RNAs (lncRNAs) have experimentally confirmed functions, yet little is known about their transcriptional dynamics and it is challenging to determine their regulatory effects. Here, we used allele-sensitive single-cell RNA sequencing to demonstrate that, compared to messenger RNAs, lncRNAs have twice as long duration between two transcriptional bursts. Additionally, we observed increased cell-to-cell variability in lncRNA expression due to lower frequency bursting producing larger numbers of RNA molecules. Exploiting heterogeneity in asynchronously growing cells, we identified and experimentally validated lncRNAs with cell state-specific functions involved in cell cycle progression and apoptosis. Finally, we identified cis-functioning lncRNAs and showed that knockdown of these lncRNAs modulated the nearby protein-coding gene’s transcriptional burst frequency or size. In summary, we identified distinct transcriptional regulation of lncRNAs and demonstrated a role for lncRNAs in the regulation of mRNA transcriptional bursting. Allele-sensitive single-cell RNA sequencing analysis of long noncoding RNA (lncRNA) transcriptional kinetics shows that their lower expression compared to mRNA is due to lower burst frequencies and highlights cell-state-specific functions for several lncRNAs.
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Affiliation(s)
- Per Johnsson
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Christoph Ziegenhain
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Leonard Hartmanis
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Gert-Jan Hendriks
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | | | - Björn Reinius
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Rickard Sandberg
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
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13
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Rufino de Sousa N, Steponaviciute L, Margerie L, Nissen K, Kjellin M, Reinius B, Salaneck E, Udekwu KI, Rothfuchs AG. Detection and isolation of airborne SARS-CoV-2 in a hospital setting. Indoor Air 2022; 32:e13023. [PMID: 35347788 PMCID: PMC9111425 DOI: 10.1111/ina.13023] [Citation(s) in RCA: 4] [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] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 02/21/2022] [Accepted: 03/10/2022] [Indexed: 05/15/2023]
Abstract
Transmission mechanisms for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are incompletely understood. In particular, aerosol transmission remains unclear, with viral detection in air and demonstration of its infection potential being actively investigated. To this end, we employed a novel electrostatic collector to sample air from rooms occupied by COVID-19 patients in a major Swedish hospital. Electrostatic air sampling in conjunction with extraction-free, reverse-transcriptase polymerase chain reaction (hid-RT-PCR) enabled detection of SARS-CoV-2 in air from patient rooms (9/22; 41%) and adjoining anterooms (10/22; 45%). Detection with hid-RT-PCR was concomitant with viral RNA presence on the surface of exhaust ventilation channels in patients and anterooms more than 2 m from the COVID-19 patient. Importantly, it was possible to detect active SARS-CoV-2 particles from room air, with a total of 496 plaque-forming units (PFUs) being isolated, establishing the presence of infectious, airborne SARS-CoV-2 in rooms occupied by COVID-19 patients. Our results support circulation of SARS-CoV-2 via aerosols and urge the revision of existing infection control frameworks to include airborne transmission.
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Affiliation(s)
- Nuno Rufino de Sousa
- Department of Microbiology, Tumor and Cell Biology (MTC)Karolinska InstitutetStockholmSweden
| | - Laura Steponaviciute
- Department of Microbiology, Tumor and Cell Biology (MTC)Karolinska InstitutetStockholmSweden
| | - Lucille Margerie
- Department of Microbiology, Tumor and Cell Biology (MTC)Karolinska InstitutetStockholmSweden
| | - Karolina Nissen
- Department of Medical SciencesInfectious DiseasesUppsala UniversityUniversity Hospital UppsalaUppsalaSweden
| | - Midori Kjellin
- Department of Medical SciencesInfectious DiseasesUppsala UniversityUniversity Hospital UppsalaUppsalaSweden
| | - Björn Reinius
- Department of Medical Biochemistry and Biophysics (MBB)Karolinska InstitutetStockholmSweden
| | - Erik Salaneck
- Department of Medical SciencesInfectious DiseasesUppsala UniversityUniversity Hospital UppsalaUppsalaSweden
| | - Klas I. Udekwu
- Department of Aquatic Sciences and AssessmentSwedish University of Agricultural SciencesUppsalaSweden
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14
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Mold JE, Modolo L, Hård J, Zamboni M, Larsson AJM, Stenudd M, Eriksson CJ, Durif G, Ståhl PL, Borgström E, Picelli S, Reinius B, Sandberg R, Réu P, Talavera-Lopez C, Andersson B, Blom K, Sandberg JK, Picard F, Michaëlsson J, Frisén J. Divergent clonal differentiation trajectories establish CD8 + memory T cell heterogeneity during acute viral infections in humans. Cell Rep 2021; 35:109174. [PMID: 34038736 DOI: 10.1016/j.celrep.2021.109174] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 04/28/2020] [Revised: 02/15/2021] [Accepted: 05/04/2021] [Indexed: 02/08/2023] Open
Abstract
The CD8+ T cell response to an antigen is composed of many T cell clones with unique T cell receptors, together forming a heterogeneous repertoire of effector and memory cells. How individual T cell clones contribute to this heterogeneity throughout immune responses remains largely unknown. In this study, we longitudinally track human CD8+ T cell clones expanding in response to yellow fever virus (YFV) vaccination at the single-cell level. We observed a drop in clonal diversity in blood from the acute to memory phase, suggesting that clonal selection shapes the circulating memory repertoire. Clones in the memory phase display biased differentiation trajectories along a gradient from stem cell to terminally differentiated effector memory fates. In secondary responses, YFV- and influenza-specific CD8+ T cell clones are poised to recapitulate skewed differentiation trajectories. Collectively, we show that the sum of distinct clonal phenotypes results in the multifaceted human T cell response to acute viral infections.
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Affiliation(s)
- Jeff E Mold
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Laurent Modolo
- LBBE, UMR CNRS 5558, Université Lyon 1, Villeurbanne, France LBMC UMR 5239 CNRS/ENS Lyon, Lyon, France
| | - Joanna Hård
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Margherita Zamboni
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Anton J M Larsson
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Moa Stenudd
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Carl-Johan Eriksson
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Ghislain Durif
- LBBE, UMR CNRS 5558, Université Lyon 1, Villeurbanne, France LBMC UMR 5239 CNRS/ENS Lyon, Lyon, France
| | - Patrik L Ståhl
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden; Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, 106 91 Stockholm, Sweden
| | - Erik Borgström
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, 106 91 Stockholm, Sweden
| | - Simone Picelli
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Björn Reinius
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden; Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Rickard Sandberg
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Pedro Réu
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Carlos Talavera-Lopez
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Björn Andersson
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Kim Blom
- Center for Infectious Medicine, Department of Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, 141 86 Stockholm, Sweden
| | - Johan K Sandberg
- Center for Infectious Medicine, Department of Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, 141 86 Stockholm, Sweden
| | - Franck Picard
- LBBE, UMR CNRS 5558, Université Lyon 1, Villeurbanne, France LBMC UMR 5239 CNRS/ENS Lyon, Lyon, France
| | - Jakob Michaëlsson
- Center for Infectious Medicine, Department of Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, 141 86 Stockholm, Sweden.
| | - Jonas Frisén
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden.
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15
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Larsson AJM, Ziegenhain C, Hagemann-Jensen M, Reinius B, Jacob T, Dalessandri T, Hendriks GJ, Kasper M, Sandberg R. Transcriptional bursts explain autosomal random monoallelic expression and affect allelic imbalance. PLoS Comput Biol 2021; 17:e1008772. [PMID: 33690599 PMCID: PMC7978379 DOI: 10.1371/journal.pcbi.1008772] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 03/19/2021] [Accepted: 02/03/2021] [Indexed: 12/02/2022] Open
Abstract
Transcriptional bursts render substantial biological noise in cellular transcriptomes. Here, we investigated the theoretical extent of allelic expression resulting from transcriptional bursting and how it compared to the amount biallelic, monoallelic and allele-biased expression observed in single-cell RNA-sequencing (scRNA-seq) data. We found that transcriptional bursting can explain the allelic expression patterns observed in single cells, including the frequent observations of autosomal monoallelic gene expression. Importantly, we identified that the burst frequency largely determined the fraction of cells with monoallelic expression, whereas the burst size had little effect on monoallelic observations. The high consistency between the bursting model predictions and scRNA-seq observations made it possible to assess the heterogeneity of a group of cells as their deviation in allelic observations from the expected. Finally, both burst frequency and size contributed to allelic imbalance observations and reinforced that studies of allelic imbalance can be confounded from the inherent noise in transcriptional bursting. Altogether, we demonstrate that allele-level transcriptional bursting renders widespread, although predictable, amounts of monoallelic and biallelic expression in single cells and cell populations. Genes are transcribed into RNA and further translated into proteins. The maternal and paternal copy of each gene are typically transcribed independently, and transcription itself occur in discrete stochastic bursts (transcriptional bursts). Pioneering single-cell analysis of RNA across cells revealed abundant fluctuations in the amounts of maternal and paternal RNA in cells, with frequent observations of RNA from only the maternal or paternal gene copy (monoallelic expression). In this study, we investigated to which extent the observed monoallelic expression across single cells can be explained by transcriptional bursting. We demonstrate that the process of transcriptional bursting is sufficient to explain the amount of monoallelic expression, and we further demonstrate that the frequency of bursts mainly determines the frequency of monoallelic observations. Furthermore, we show that transcriptional bursts may lead to false positive observations of monoallelic expression across cell populations. Therefore, stochastic transcription renders large fluctuations in allelic origin of RNA in cells over time, including frequent monoallelic observations when profiling single cells.
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Affiliation(s)
- Anton J. M. Larsson
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Christoph Ziegenhain
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | | | - Björn Reinius
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Tina Jacob
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Tim Dalessandri
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Gert-Jan Hendriks
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Maria Kasper
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Rickard Sandberg
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
- * E-mail:
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16
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Strunz B, Bister J, Jönsson H, Filipovic I, Crona-Guterstam Y, Kvedaraite E, Sleiers N, Dumitrescu B, Brännström M, Lentini A, Reinius B, Cornillet M, Willinger T, Gidlöf S, Hamilton RS, Ivarsson MA, Björkström NK. Continuous human uterine NK cell differentiation in response to endometrial regeneration and pregnancy. Sci Immunol 2021; 6:6/56/eabb7800. [PMID: 33617461 DOI: 10.1126/sciimmunol.abb7800] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 01/21/2021] [Indexed: 02/06/2023]
Abstract
Immune cell differentiation is critical for adequate tissue-specific immune responses to occur. Here, we studied differentiation of human uterine natural killer cells (uNK cells). These cells reside in a tissue undergoing constant regeneration and represent the major leukocyte population at the maternal-fetal interface. However, their physiological response during the menstrual cycle and in pregnancy remains elusive. By surface proteome and transcriptome analysis as well as using humanized mice, we identify a differentiation pathway of uNK cells in vitro and in vivo with sequential acquisition of killer cell immunoglobulin-like receptors and CD39. uNK cell differentiation occurred continuously in response to the endometrial regeneration and was driven by interleukin-15. Differentiated uNK cells displayed reduced proliferative capacity and immunomodulatory function including enhanced angiogenic capacity. By studying human uterus transplantation and monozygotic twins, we found that the uNK cell niche could be replenished from circulation and that it was under genetic control. Together, our study uncovers a continuous differentiation pathway of human NK cells in the uterus that is coupled to profound functional changes in response to local tissue regeneration and pregnancy.
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Affiliation(s)
- Benedikt Strunz
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden.
| | - Jonna Bister
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Hanna Jönsson
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Iva Filipovic
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Ylva Crona-Guterstam
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden.,Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden.,Department of Gynecology and Reproductive Medicine, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Egle Kvedaraite
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden.,Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Natalie Sleiers
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Bogdan Dumitrescu
- Department of Obstetrics and Gynecology, Mälarsjukhuset, Eskilstuna, Sweden
| | - Mats Brännström
- Department of Obstetrics and Gynecology, University of Gothenburg, Gothenburg, Sweden
| | - Antonio Lentini
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Björn Reinius
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Martin Cornillet
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Tim Willinger
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Sebastian Gidlöf
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden.,Department of Gynecology and Reproductive Medicine, Karolinska University Hospital Huddinge, Stockholm, Sweden.,Department of Obstetrics and Gynecology, Stockholm South General Hospital, Stockholm, Sweden
| | - Russell S Hamilton
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK.,Department of Genetics, University of Cambridge, Cambridge, UK
| | - Martin A Ivarsson
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Niklas K Björkström
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden.
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17
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Alekseenko A, Barrett D, Pareja-Sanchez Y, Howard RJ, Strandback E, Ampah-Korsah H, Rovšnik U, Zuniga-Veliz S, Klenov A, Malloo J, Ye S, Liu X, Reinius B, Elsässer SJ, Nyman T, Sandh G, Yin X, Pelechano V. Direct detection of SARS-CoV-2 using non-commercial RT-LAMP reagents on heat-inactivated samples. Sci Rep 2021; 11:1820. [PMID: 33469065 PMCID: PMC7815738 DOI: 10.1038/s41598-020-80352-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [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: 09/28/2020] [Accepted: 12/20/2020] [Indexed: 12/13/2022] Open
Abstract
RT-LAMP detection of SARS-CoV-2 has been shown to be a valuable approach to scale up COVID-19 diagnostics and thus contribute to limiting the spread of the disease. Here we present the optimization of highly cost-effective in-house produced enzymes, and we benchmark their performance against commercial alternatives. We explore the compatibility between multiple DNA polymerases with high strand-displacement activity and thermostable reverse transcriptases required for RT-LAMP. We optimize reaction conditions and demonstrate their applicability using both synthetic RNA and clinical patient samples. Finally, we validate the optimized RT-LAMP assay for the detection of SARS-CoV-2 in unextracted heat-inactivated nasopharyngeal samples from 184 patients. We anticipate that optimized and affordable reagents for RT-LAMP will facilitate the expansion of SARS-CoV-2 testing globally, especially in sites and settings where the need for large scale testing cannot be met by commercial alternatives.
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Affiliation(s)
- Alisa Alekseenko
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Tomtebodavägen 23A, 17165, Solna, Sweden
| | - Donal Barrett
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Tomtebodavägen 23A, 17165, Solna, Sweden
| | - Yerma Pareja-Sanchez
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Tomtebodavägen 23A, 17165, Solna, Sweden
| | - Rebecca J Howard
- SciLifeLab, Department of Biochemistry and Biophysics, Stockholm University, 17121, Solna, Sweden
| | - Emilia Strandback
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden
| | - Henry Ampah-Korsah
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden
| | - Urška Rovšnik
- SciLifeLab, Department of Biochemistry and Biophysics, Stockholm University, 17121, Solna, Sweden
| | - Silvia Zuniga-Veliz
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Alexander Klenov
- Hudak Lab, Department of Biology, York University, 4700 Keele St, Toronto, ON, M3J 1P3, Canada
| | - Jayshna Malloo
- Hudak Lab, Department of Biology, York University, 4700 Keele St, Toronto, ON, M3J 1P3, Canada
| | - Shenglong Ye
- Biotech and Biomedicine Science (Shenyang) Co. Ltd, Shenyang, 110000, China
| | - Xiyang Liu
- Biotech and Biomedicine Science (Shenyang) Co. Ltd, Shenyang, 110000, China
| | - Björn Reinius
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden
| | - Simon J Elsässer
- SciLifeLab, Department of Medical Biochemistry and Biophysics, Division of Genome Biology, Karolinska Institutet, Solna, Sweden
| | - Tomas Nyman
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden
| | - Gustaf Sandh
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Xiushan Yin
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Tomtebodavägen 23A, 17165, Solna, Sweden
- Biotech and Biomedicine Science (Shenyang) Co. Ltd, Shenyang, 110000, China
- Applied Biology Laboratory, Shenyang University of Chemical Technology, Shenyang, 110142, China
| | - Vicent Pelechano
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Tomtebodavägen 23A, 17165, Solna, Sweden.
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18
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Smyrlaki I, Ekman M, Lentini A, Rufino de Sousa N, Papanicolaou N, Vondracek M, Aarum J, Safari H, Muradrasoli S, Rothfuchs AG, Albert J, Högberg B, Reinius B. Massive and rapid COVID-19 testing is feasible by extraction-free SARS-CoV-2 RT-PCR. Nat Commun 2020; 11:4812. [PMID: 32968075 PMCID: PMC7511968 DOI: 10.1038/s41467-020-18611-5] [Citation(s) in RCA: 294] [Impact Index Per Article: 73.5] [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: 05/12/2020] [Accepted: 09/02/2020] [Indexed: 11/24/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is commonly diagnosed by reverse transcription polymerase chain reaction (RT-PCR) to detect viral RNA in patient samples, but RNA extraction constitutes a major bottleneck in current testing. Methodological simplification could increase diagnostic availability and efficiency, benefitting patient care and infection control. Here, we describe methods circumventing RNA extraction in COVID-19 testing by performing RT-PCR directly on heat-inactivated or lysed samples. Our data, including benchmarking using 597 clinical patient samples and a standardised diagnostic system, demonstrate that direct RT-PCR is viable option to extraction-based tests. Using controlled amounts of active SARS-CoV-2, we confirm effectiveness of heat inactivation by plaque assay and evaluate various generic buffers as transport medium for direct RT-PCR. Significant savings in time and cost are achieved through RNA-extraction-free protocols that are directly compatible with established PCR-based testing pipelines. This could aid expansion of COVID-19 testing.
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Affiliation(s)
- Ioanna Smyrlaki
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Martin Ekman
- Department of Clinical Microbiology, Karolinska University Hospital, 171 76, Stockholm, Sweden
| | - Antonio Lentini
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Nuno Rufino de Sousa
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Natali Papanicolaou
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Martin Vondracek
- Department of Clinical Microbiology, Karolinska University Hospital, 171 76, Stockholm, Sweden
| | - Johan Aarum
- Department of Clinical Microbiology, Karolinska University Hospital, 171 76, Stockholm, Sweden
| | - Hamzah Safari
- Department of Clinical Microbiology, Karolinska University Hospital, 171 76, Stockholm, Sweden
| | | | | | - Jan Albert
- Department of Clinical Microbiology, Karolinska University Hospital, 171 76, Stockholm, Sweden
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Björn Högberg
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Björn Reinius
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77, Stockholm, Sweden.
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19
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Maucourant C, Filipovic I, Ponzetta A, Aleman S, Cornillet M, Hertwig L, Strunz B, Lentini A, Reinius B, Brownlie D, Cuapio A, Ask EH, Hull RM, Haroun-Izquierdo A, Schaffer M, Klingström J, Folkesson E, Buggert M, Sandberg JK, Eriksson LI, Rooyackers O, Ljunggren HG, Malmberg KJ, Michaëlsson J, Marquardt N, Hammer Q, Strålin K, Björkström NK. Natural killer cell immunotypes related to COVID-19 disease severity. Sci Immunol 2020; 5:eabd6832. [PMID: 32826343 PMCID: PMC7665314 DOI: 10.1126/sciimmunol.abd6832] [Citation(s) in RCA: 288] [Impact Index Per Article: 72.0] [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: 07/06/2020] [Accepted: 08/19/2020] [Indexed: 01/08/2023]
Abstract
Understanding innate immune responses in COVID-19 is important to decipher mechanisms of host responses and interpret disease pathogenesis. Natural killer (NK) cells are innate effector lymphocytes that respond to acute viral infections but might also contribute to immunopathology. Using 28-color flow cytometry, we here reveal strong NK cell activation across distinct subsets in peripheral blood of COVID-19 patients. This pattern was mirrored in scRNA-seq signatures of NK cells in bronchoalveolar lavage from COVID-19 patients. Unsupervised high-dimensional analysis of peripheral blood NK cells furthermore identified distinct NK cell immunotypes that were linked to disease severity. Hallmarks of these immunotypes were high expression of perforin, NKG2C, and Ksp37, reflecting increased presence of adaptive NK cells in circulation of patients with severe disease. Finally, arming of CD56bright NK cells was observed across COVID-19 disease states, driven by a defined protein-protein interaction network of inflammatory soluble factors. This study provides a detailed map of the NK cell activation landscape in COVID-19 disease.
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Affiliation(s)
- Christopher Maucourant
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Iva Filipovic
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Andrea Ponzetta
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Soo Aleman
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- Division of Infectious Diseases and Dermatology, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Martin Cornillet
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Laura Hertwig
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Benedikt Strunz
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Antonio Lentini
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Björn Reinius
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Demi Brownlie
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Angelica Cuapio
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Eivind Heggernes Ask
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- The KG Jebsen Center for Cancer Immunotherapy, Institute of Clinical Medicine, University of .Oslo, Oslo, Norway
| | - Ryan M Hull
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Alvaro Haroun-Izquierdo
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Marie Schaffer
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Jonas Klingström
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Elin Folkesson
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- Division of Infectious Diseases, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Marcus Buggert
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Johan K Sandberg
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Lars I Eriksson
- Department of Physiology and Pharmacology, Section for Anesthesiology and Intensive Care, Karolinska Institutet, Stockholm, Sweden
- Function Perioperative Medicine and Intensive Care, Karolinska University Hospital, Stockholm, Sweden
| | - Olav Rooyackers
- Function Perioperative Medicine and Intensive Care, Karolinska University Hospital, Stockholm, Sweden
- Department Clinical Interventions and Technology CLINTEC, Division for Anesthesiology and Intensive Care, Karolinska Institutet, Stockholm, Sweden
| | - Hans-Gustaf Ljunggren
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Karl-Johan Malmberg
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- The KG Jebsen Center for Cancer Immunotherapy, Institute of Clinical Medicine, University of .Oslo, Oslo, Norway
| | - Jakob Michaëlsson
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Nicole Marquardt
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Quirin Hammer
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Kristoffer Strålin
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- Division of Infectious Diseases and Dermatology, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Niklas K Björkström
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden.
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20
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Maucourant C, Filipovic I, Ponzetta A, Aleman S, Cornillet M, Hertwig L, Strunz B, Lentini A, Reinius B, Brownlie D, Cuapio A, Ask EH, Hull RM, Haroun-Izquierdo A, Schaffer M, Klingström J, Folkesson E, Buggert M, Sandberg JK, Eriksson LI, Rooyackers O, Ljunggren HG, Malmberg KJ, Michaëlsson J, Marquardt N, Hammer Q, Strålin K, Björkström NK. Natural killer cell immunotypes related to COVID-19 disease severity. Sci Immunol 2020. [PMID: 32826343 DOI: 10.1126/sciimmunol.abd68] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
Understanding innate immune responses in COVID-19 is important to decipher mechanisms of host responses and interpret disease pathogenesis. Natural killer (NK) cells are innate effector lymphocytes that respond to acute viral infections but might also contribute to immunopathology. Using 28-color flow cytometry, we here reveal strong NK cell activation across distinct subsets in peripheral blood of COVID-19 patients. This pattern was mirrored in scRNA-seq signatures of NK cells in bronchoalveolar lavage from COVID-19 patients. Unsupervised high-dimensional analysis of peripheral blood NK cells furthermore identified distinct NK cell immunotypes that were linked to disease severity. Hallmarks of these immunotypes were high expression of perforin, NKG2C, and Ksp37, reflecting increased presence of adaptive NK cells in circulation of patients with severe disease. Finally, arming of CD56bright NK cells was observed across COVID-19 disease states, driven by a defined protein-protein interaction network of inflammatory soluble factors. This study provides a detailed map of the NK cell activation landscape in COVID-19 disease.
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Affiliation(s)
- Christopher Maucourant
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Iva Filipovic
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Andrea Ponzetta
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Soo Aleman
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- Division of Infectious Diseases and Dermatology, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Martin Cornillet
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Laura Hertwig
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Benedikt Strunz
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Antonio Lentini
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Björn Reinius
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Demi Brownlie
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Angelica Cuapio
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Eivind Heggernes Ask
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- The KG Jebsen Center for Cancer Immunotherapy, Institute of Clinical Medicine, University of .Oslo, Oslo, Norway
| | - Ryan M Hull
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Alvaro Haroun-Izquierdo
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Marie Schaffer
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Jonas Klingström
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Elin Folkesson
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- Division of Infectious Diseases, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Marcus Buggert
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Johan K Sandberg
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Lars I Eriksson
- Department of Physiology and Pharmacology, Section for Anesthesiology and Intensive Care, Karolinska Institutet, Stockholm, Sweden
- Function Perioperative Medicine and Intensive Care, Karolinska University Hospital, Stockholm, Sweden
| | - Olav Rooyackers
- Function Perioperative Medicine and Intensive Care, Karolinska University Hospital, Stockholm, Sweden
- Department Clinical Interventions and Technology CLINTEC, Division for Anesthesiology and Intensive Care, Karolinska Institutet, Stockholm, Sweden
| | - Hans-Gustaf Ljunggren
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Karl-Johan Malmberg
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- The KG Jebsen Center for Cancer Immunotherapy, Institute of Clinical Medicine, University of .Oslo, Oslo, Norway
| | - Jakob Michaëlsson
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Nicole Marquardt
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Quirin Hammer
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Kristoffer Strålin
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- Division of Infectious Diseases and Dermatology, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Niklas K Björkström
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden.
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21
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Larsson AJM, Coucoravas C, Sandberg R, Reinius B. X-chromosome upregulation is driven by increased burst frequency. Nat Struct Mol Biol 2019; 26:963-969. [PMID: 31582851 DOI: 10.1038/s41594-019-0306-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 08/20/2019] [Indexed: 12/14/2022]
Abstract
Ohno's hypothesis postulates that upregulation of X-linked genes rectifies their dosage imbalance relative to autosomal genes, which are present in two active copies per cell. Here we have dissected X-chromosome upregulation into the kinetics of transcription, inferred from allele-specific single-cell RNA sequencing data from somatic and embryonic mouse cells. We confirmed increased X-chromosome expression levels in female and male cells and found that the X chromosome achieved upregulation by elevated burst frequencies. By monitoring transcriptional kinetics in differentiating female mouse embryonic stem cells, we found that increased burst frequency was established on the active X chromosome when X inactivation took place on the other allele. Thus, our study provides mechanistic insights into X-chromosome upregulation.
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Affiliation(s)
- Anton J M Larsson
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Christos Coucoravas
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Rickard Sandberg
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Björn Reinius
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
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22
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Affiliation(s)
- Björn Reinius
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.,Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Rickard Sandberg
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
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23
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Cheng S, Pei Y, He L, Peng G, Reinius B, Tam PP, Jing N, Deng Q. Single-Cell RNA-Seq Reveals Cellular Heterogeneity of Pluripotency Transition and X Chromosome Dynamics during Early Mouse Development. Cell Rep 2019; 26:2593-2607.e3. [DOI: 10.1016/j.celrep.2019.02.031] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 10/29/2018] [Accepted: 02/08/2019] [Indexed: 01/13/2023] Open
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24
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Ziegenhain C, Vieth B, Parekh S, Reinius B, Guillaumet-Adkins A, Smets M, Leonhardt H, Heyn H, Hellmann I, Enard W. Comparative Analysis of Single-Cell RNA Sequencing Methods. Mol Cell 2017; 65:631-643.e4. [PMID: 28212749 DOI: 10.1016/j.molcel.2017.01.023] [Citation(s) in RCA: 817] [Impact Index Per Article: 116.7] [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: 08/08/2016] [Revised: 12/01/2016] [Accepted: 01/17/2017] [Indexed: 02/06/2023]
Abstract
Single-cell RNA sequencing (scRNA-seq) offers new possibilities to address biological and medical questions. However, systematic comparisons of the performance of diverse scRNA-seq protocols are lacking. We generated data from 583 mouse embryonic stem cells to evaluate six prominent scRNA-seq methods: CEL-seq2, Drop-seq, MARS-seq, SCRB-seq, Smart-seq, and Smart-seq2. While Smart-seq2 detected the most genes per cell and across cells, CEL-seq2, Drop-seq, MARS-seq, and SCRB-seq quantified mRNA levels with less amplification noise due to the use of unique molecular identifiers (UMIs). Power simulations at different sequencing depths showed that Drop-seq is more cost-efficient for transcriptome quantification of large numbers of cells, while MARS-seq, SCRB-seq, and Smart-seq2 are more efficient when analyzing fewer cells. Our quantitative comparison offers the basis for an informed choice among six prominent scRNA-seq methods, and it provides a framework for benchmarking further improvements of scRNA-seq protocols.
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Affiliation(s)
- Christoph Ziegenhain
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians University, Großhaderner Straße 2, 82152 Martinsried, Germany
| | - Beate Vieth
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians University, Großhaderner Straße 2, 82152 Martinsried, Germany
| | - Swati Parekh
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians University, Großhaderner Straße 2, 82152 Martinsried, Germany
| | - Björn Reinius
- Ludwig Institute for Cancer Research, Box 240, 171 77 Stockholm, Sweden; Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Amy Guillaumet-Adkins
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
| | - Martha Smets
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians University, Großhaderner Straße 2, 82152 Martinsried, Germany
| | - Heinrich Leonhardt
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians University, Großhaderner Straße 2, 82152 Martinsried, Germany
| | - Holger Heyn
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
| | - Ines Hellmann
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians University, Großhaderner Straße 2, 82152 Martinsried, Germany
| | - Wolfgang Enard
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians University, Großhaderner Straße 2, 82152 Martinsried, Germany.
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25
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Reinius B, Mold JE, Ramsköld D, Deng Q, Johnsson P, Michaëlsson J, Frisén J, Sandberg R. Analysis of allelic expression patterns in clonal somatic cells by single-cell RNA-seq. Nat Genet 2016; 48:1430-1435. [PMID: 27668657 PMCID: PMC5117254 DOI: 10.1038/ng.3678] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 08/29/2016] [Indexed: 12/16/2022]
Abstract
Cellular heterogeneity can emerge from the expression of only one parental allele. However, it has remained controversial whether, or to what degree, random monoallelic expression of autosomal genes (aRME) is mitotically inherited (clonal) or stochastic (dynamic) in somatic cells, particularly in vivo. Here we used allele-sensitive single-cell RNA-seq on clonal primary mouse fibroblasts and freshly isolated human CD8+ T cells to dissect clonal and dynamic monoallelic expression patterns. Dynamic aRME affected a considerable portion of the cells' transcriptomes, with levels dependent on the cells' transcriptional activity. Notably, clonal aRME was detected, but it was surprisingly scarce (<1% of genes) and mainly affected the most weakly expressed genes. Consequently, the overwhelming majority of aRME occurs transiently within individual cells, and patterns of aRME are thus primarily scattered throughout somatic cell populations rather than, as previously hypothesized, confined to patches of clonally related cells.
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Affiliation(s)
- Björn Reinius
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden.,Ludwig Institute for Cancer Research, 171 77 Stockholm, Sweden
| | - Jeff E Mold
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Daniel Ramsköld
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden.,Ludwig Institute for Cancer Research, 171 77 Stockholm, Sweden
| | - Qiaolin Deng
- Ludwig Institute for Cancer Research, 171 77 Stockholm, Sweden
| | - Per Johnsson
- Ludwig Institute for Cancer Research, 171 77 Stockholm, Sweden
| | - Jakob Michaëlsson
- Center for Infectious Medicine, Department of Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, 141 86 Stockholm, Sweden
| | - Jonas Frisén
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Rickard Sandberg
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden.,Ludwig Institute for Cancer Research, 171 77 Stockholm, Sweden
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26
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Petropoulos S, Edsgärd D, Reinius B, Deng Q, Panula SP, Codeluppi S, Reyes AP, Linnarsson S, Sandberg R, Lanner F. Single-Cell RNA-Seq Reveals Lineage and X Chromosome Dynamics in Human Preimplantation Embryos. Cell 2016; 167:285. [PMID: 27662094 PMCID: PMC5628172 DOI: 10.1016/j.cell.2016.08.009] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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27
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Abstract
Summary: Determination of haplotypes is important for modelling the phenotypic consequences of genetic variation in diploid organisms, including cis-regulatory control and compound heterozygosity. We realized that single-cell RNA-seq (scRNA-seq) data are well suited for phasing genetic variants, since both transcriptional bursts and technical bottlenecks cause pronounced allelic fluctuations in individual single cells. Here we present scphaser, an R package that phases alleles at heterozygous variants to reconstruct haplotypes within transcribed regions of the genome using scRNA-seq data. The devised method efficiently and accurately reconstructed the known haplotype for ≥93% of phasable genes in both human and mouse. It also enables phasing of rare and de novo variants and variants far apart within genes, which is hard to attain with population-based computational inference. Availability and Implementation: scphaser is implemented as an R package. Tutorial and code are available at https://github.com/edsgard/scphaser Contact:rickard.sandberg@ki.se Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Daniel Edsgärd
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Björn Reinius
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Rickard Sandberg
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden Ludwig Institute for Cancer Research, Box 240, 171 77 Stockholm, Sweden
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28
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Chen G, Schell JP, Benitez JA, Petropoulos S, Yilmaz M, Reinius B, Alekseenko Z, Shi L, Hedlund E, Lanner F, Sandberg R, Deng Q. Single-cell analyses of X Chromosome inactivation dynamics and pluripotency during differentiation. Genome Res 2016; 26:1342-1354. [PMID: 27486082 PMCID: PMC5052059 DOI: 10.1101/gr.201954.115] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 07/29/2016] [Indexed: 12/18/2022]
Abstract
Pluripotency, differentiation, and X Chromosome inactivation (XCI) are key aspects of embryonic development. However, the underlying relationship and mechanisms among these processes remain unclear. Here, we systematically dissected these features along developmental progression using mouse embryonic stem cells (mESCs) and single-cell RNA sequencing with allelic resolution. We found that mESCs grown in a ground state 2i condition displayed transcriptomic profiles diffused from preimplantation mouse embryonic cells, whereas EpiStem cells closely resembled the post-implantation epiblast. Sex-related gene expression varied greatly across distinct developmental states. We also identified novel markers that were highly enriched in each developmental state. Moreover, we revealed that several novel pathways, including PluriNetWork and Focal Adhesion, were responsible for the delayed progression of female EpiStem cells. Importantly, we "digitalized" XCI progression using allelic expression of active and inactive X Chromosomes and surprisingly found that XCI states exhibited profound variability in each developmental state, including the 2i condition. XCI progression was not tightly synchronized with loss of pluripotency and increase of differentiation at the single-cell level, although these processes were globally correlated. In addition, highly expressed genes, including core pluripotency factors, were in general biallelically expressed. Taken together, our study sheds light on the dynamics of XCI progression and the asynchronicity between pluripotency, differentiation, and XCI.
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Affiliation(s)
- Geng Chen
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden; School of Pharmacy, Fudan University, 201203 Shanghai, China
| | - John Paul Schell
- Department of Clinical Science, Intervention and Technology and Division of Obstetrics and Gynecology, Karolinska Universitetssjukhuset, 14186 Stockholm, Sweden
| | - Julio Aguila Benitez
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden; Department of Neuroscience, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Sophie Petropoulos
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden; Department of Clinical Science, Intervention and Technology and Division of Obstetrics and Gynecology, Karolinska Universitetssjukhuset, 14186 Stockholm, Sweden
| | - Marlene Yilmaz
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Björn Reinius
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Zhanna Alekseenko
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Leming Shi
- School of Pharmacy, Fudan University, 201203 Shanghai, China
| | - Eva Hedlund
- Department of Neuroscience, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Fredrik Lanner
- Department of Clinical Science, Intervention and Technology and Division of Obstetrics and Gynecology, Karolinska Universitetssjukhuset, 14186 Stockholm, Sweden
| | - Rickard Sandberg
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden; Ludwig Institute for Cancer Research, 171 77 Stockholm, Sweden
| | - Qiaolin Deng
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
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29
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Abstract
Random monoallelic expression (RME) of genes represents a striking example of how stochastic molecular processes can result in cellular heterogeneity. Recent transcriptome-wide studies have revealed both mitotically stable and cell-to-cell dynamic forms of autosomal RME, with the latter presumably resulting from burst-like stochastic transcription. Here, we discuss the distinguishing features of these two forms of RME and revisit literature on their nature, pervasiveness and regulation. Finally, we explore how RME may contribute to phenotypic variation, including the incomplete penetrance and variable expressivity often seen in genetic disease.
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Affiliation(s)
- Björn Reinius
- Ludwig Institute for Cancer Research, Box 240, and the Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Rickard Sandberg
- Ludwig Institute for Cancer Research, Box 240, and the Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
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30
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Reinius B, Blunder M, Brett FM, Eriksson A, Patra K, Jonsson J, Jazin E, Kullander K. Conditional targeting of medium spiny neurons in the striatal matrix. Front Behav Neurosci 2015; 9:71. [PMID: 25870547 PMCID: PMC4375991 DOI: 10.3389/fnbeh.2015.00071] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 03/05/2015] [Indexed: 01/15/2023] Open
Abstract
The striatum serves as the main input to the basal ganglia, and is key for the regulation of motor behaviors, compulsion, addiction, and various cognitive and emotional states. Its deterioration is associated with degenerative disorders such as Huntington's disease. Despite its apparent anatomical uniformity, it consists of intermingled cell populations, which have precluded straightforward anatomical sub-classifications adhering to functional dissections. Approximately 95% of the striatal neurons are inhibitory projection neurons termed medium spiny neurons (MSNs). They are commonly classified according to their expression of either dopamine receptor D1 or D2, which also determines their axonal projection patterns constituting the direct and indirect pathway in the basal ganglia. Immunohistochemical patterns have further indicated compartmentalization of the striatum to the striosomes and the surrounding matrix, which integrate MSNs of both the D1 and D2 type. Here, we present a transgenic mouse line, Gpr101-Cre, with Cre recombinase activity localized to matrix D1 and D2 MSNs. Using two Gpr101-Cre founder lines with different degrees of expression in the striatum, we conditionally deleted the vesicular inhibitory amino acid transporter (VIAAT), responsible for storage of GABA and glycine in synaptic vesicles. Partial ablation of VIAAT (in ~36% of MSNs) resulted in elevated locomotor activity compared to control mice, when provoked with the monoamine reuptake inhibitor cocaine. Near complete targeting of matrix MSNs led to profoundly changed motor behaviors, which increased in severity as the mice aged. Moreover, these mice had exaggerated muscle rigidity, retarded growth, increased rate of spontaneous deaths, and defective memory. Therefore, our data provide a link between dysfunctional GABA signaling of matrix MSNs to specific behavioral alterations, which are similar to the symptoms of Huntington's disease.
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Affiliation(s)
- Björn Reinius
- Unit of Developmental Genetics, Department of Neuroscience, BMC, Uppsala University Uppsala, Sweden ; Department of Organismal Biology, EBC, Uppsala University Uppsala, Sweden
| | - Martina Blunder
- Unit of Developmental Genetics, Department of Neuroscience, BMC, Uppsala University Uppsala, Sweden
| | - Frances M Brett
- Unit of Developmental Genetics, Department of Neuroscience, BMC, Uppsala University Uppsala, Sweden
| | - Anders Eriksson
- Unit of Developmental Genetics, Department of Neuroscience, BMC, Uppsala University Uppsala, Sweden
| | - Kalicharan Patra
- Unit of Developmental Genetics, Department of Neuroscience, BMC, Uppsala University Uppsala, Sweden
| | - Jörgen Jonsson
- Unit of Developmental Genetics, Department of Neuroscience, BMC, Uppsala University Uppsala, Sweden
| | - Elena Jazin
- Department of Organismal Biology, EBC, Uppsala University Uppsala, Sweden
| | - Klas Kullander
- Unit of Developmental Genetics, Department of Neuroscience, BMC, Uppsala University Uppsala, Sweden
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Picelli S, Björklund AK, Reinius B, Sagasser S, Winberg G, Sandberg R. Tn5 transposase and tagmentation procedures for massively scaled sequencing projects. Genome Res 2014; 24:2033-40. [PMID: 25079858 PMCID: PMC4248319 DOI: 10.1101/gr.177881.114] [Citation(s) in RCA: 473] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Massively parallel DNA sequencing of thousands of samples in a single machine-run is now possible, but the preparation of the individual sequencing libraries is expensive and time-consuming. Tagmentation-based library construction, using the Tn5 transposase, is efficient for generating sequencing libraries but currently relies on undisclosed reagents, which severely limits development of novel applications and the execution of large-scale projects. Here, we present simple and robust procedures for Tn5 transposase production and optimized reaction conditions for tagmentation-based sequencing library construction. We further show how molecular crowding agents both modulate library lengths and enable efficient tagmentation from subpicogram amounts of cDNA. The comparison of single-cell RNA-sequencing libraries generated using produced and commercial Tn5 demonstrated equal performances in terms of gene detection and library characteristics. Finally, because naked Tn5 can be annealed to any oligonucleotide of choice, for example, molecular barcodes in single-cell assays or methylated oligonucleotides for bisulfite sequencing, custom Tn5 production and tagmentation enable innovation in sequencing-based applications.
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Affiliation(s)
- Simone Picelli
- Ludwig Institute for Cancer Research, 171 77 Stockholm, Sweden
| | - Asa K Björklund
- Ludwig Institute for Cancer Research, 171 77 Stockholm, Sweden; Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Björn Reinius
- Ludwig Institute for Cancer Research, 171 77 Stockholm, Sweden; Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Sven Sagasser
- Ludwig Institute for Cancer Research, 171 77 Stockholm, Sweden; Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Gösta Winberg
- Ludwig Institute for Cancer Research, 171 77 Stockholm, Sweden; Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Rickard Sandberg
- Ludwig Institute for Cancer Research, 171 77 Stockholm, Sweden; Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
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Abstract
Expression from both alleles is generally observed in analyses of diploid cell populations, but studies addressing allelic expression patterns genome-wide in single cells are lacking. Here, we present global analyses of allelic expression across individual cells of mouse preimplantation embryos of mixed background (CAST/EiJ × C57BL/6J). We discovered abundant (12 to 24%) monoallelic expression of autosomal genes and that expression of the two alleles occurs independently. The monoallelic expression appeared random and dynamic because there was considerable variation among closely related embryonic cells. Similar patterns of monoallelic expression were observed in mature cells. Our allelic expression analysis also demonstrates the de novo inactivation of the paternal X chromosome. We conclude that independent and stochastic allelic transcription generates abundant random monoallelic expression in the mammalian cell.
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Affiliation(s)
- Qiaolin Deng
- Ludwig Institute for Cancer Research, Box 240, 171 77 Stockholm, Sweden
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Abstract
The catalogue of genes expressed at different levels in the two sexes is growing, and the mechanisms underlying sex differences in regulation of the mammalian transcriptomes are being explored. Here we report that the expression of the imprinted non-protein-coding maternally expressed gene H19 was female-biased specifically in the female mouse eye (1.9-fold, p = 3.0E−6) while not being sex-biased in other somatic tissues. The female-to-male expression fold-change of H19 fell in the range expected from an effect of biallelic versus monoallelic expression. Recently, the possibility of sex-specific parent-of-origin allelic expression has been debated. This led us to hypothesize that H19 might express biallelically in the female mouse eye, thus escape its silencing imprint on the paternal allele specifically in this tissue. We therefore performed a sex-specific imprinting assay of H19 in female and male eye derived from a cross between Mus musculus and Mus spretus. However, this analysis demonstrated that H19 was exclusively expressed from the maternal gene copy, disproving the escape hypothesis. Instead, this supports that the female-biased expression of H19 is the result of upregulation of the single maternal. Furthermore, if H19 would have been expressed from both gene copies in the female eye, an associated downregulation of Insulin-like growth factor 2 (Igf2) was expected, since H19 and Igf2 compete for a common enhancer element located in the H19/Igf2 imprinted domain. On the contrary we found that also Igf2 was significantly upregulated in its expression in the female eye (1.2-fold, p = 6.1E−3), in further agreement with the conclusion that H19 is monoallelically elevated in females. The female-biased expression of H19 and Igf2 specifically in the eye may contribute to our understanding of sex differences in normal as well as abnormal eye physiology and processes.
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Affiliation(s)
- Björn Reinius
- Institute of Biomedicine, Department of Medical and Clinical Genetics, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
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Radomska KJ, Halvardson J, Reinius B, Lindholm Carlström E, Emilsson L, Feuk L, Jazin E. RNA-binding protein QKI regulates Glial fibrillary acidic protein expression in human astrocytes. Hum Mol Genet 2013; 22:1373-82. [PMID: 23321059 DOI: 10.1093/hmg/dds553] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Linkage, association and expression studies previously pointed to the human QKI, KH domain containing, RNA-binding (QKI) as a candidate gene for schizophrenia. Functional studies of the mouse orthologue Qk focused mainly on its role in oligodendrocyte development and myelination, while its function in astroglia remained unexplored. Here, we show that QKI is highly expressed in human primary astrocytes and that its splice forms encode proteins targeting different subcellular localizations. Uncovering the role of QKI in astrocytes is of interest in light of growing evidence implicating astrocyte dysfunction in the pathogenesis of several disorders of the central nervous system. We selectively silenced QKI splice variants in human primary astrocytes and used RNA sequencing to identify differential expression and splice variant composition at the genome-wide level. We found that an mRNA expression of Glial fibrillary acidic protein (GFAP), encoding a major component of astrocyte intermediate filaments, was down-regulated after QKI7 splice variant silencing. Moreover, we identified a potential QKI-binding site within the 3' untranslated region of human GFAP. This sequence was not conserved between mice and humans, raising the possibility that GFAP is a target for QKI in humans but not rodents. Haloperidol treatment of primary astrocytes resulted in coordinated increases in QKI7 and GFAP expression. Taken together, our results provide the first link between QKI and GFAP, two genes with alterations previously observed independently in schizophrenic patients. Our findings for QKI, together with its well-known role in myelination, suggest that QKI is a hub regulator of glia function in humans.
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Affiliation(s)
- Katarzyna J Radomska
- Department of Evolution and Development, Evolutionary Biology Centre, Uppsala University, Uppsala,Sweden
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Reinius B, Shi C, Hengshuo L, Sandhu KS, Radomska KJ, Rosen GD, Lu L, Kullander K, Williams RW, Jazin E. Female-biased expression of long non-coding RNAs in domains that escape X-inactivation in mouse. BMC Genomics 2010; 11:614. [PMID: 21047393 PMCID: PMC3091755 DOI: 10.1186/1471-2164-11-614] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2010] [Accepted: 11/03/2010] [Indexed: 02/01/2023] Open
Abstract
Background Sexual dimorphism in brain gene expression has been recognized in several animal species. However, the relevant regulatory mechanisms remain poorly understood. To investigate whether sex-biased gene expression in mammalian brain is globally regulated or locally regulated in diverse brain structures, and to study the genomic organisation of brain-expressed sex-biased genes, we performed a large scale gene expression analysis of distinct brain regions in adult male and female mice. Results This study revealed spatial specificity in sex-biased transcription in the mouse brain, and identified 173 sex-biased genes in the striatum; 19 in the neocortex; 12 in the hippocampus and 31 in the eye. Genes located on sex chromosomes were consistently over-represented in all brain regions. Analysis on a subset of genes with sex-bias in more than one tissue revealed Y-encoded male-biased transcripts and X-encoded female-biased transcripts known to escape X-inactivation. In addition, we identified novel coding and non-coding X-linked genes with female-biased expression in multiple tissues. Interestingly, the chromosomal positions of all of the female-biased non-coding genes are in close proximity to protein-coding genes that escape X-inactivation. This defines X-chromosome domains each of which contains a coding and a non-coding female-biased gene. Lack of repressive chromatin marks in non-coding transcribed loci supports the possibility that they escape X-inactivation. Moreover, RNA-DNA combined FISH experiments confirmed the biallelic expression of one such novel domain. Conclusion This study demonstrated that the amount of genes with sex-biased expression varies between individual brain regions in mouse. The sex-biased genes identified are localized on many chromosomes. At the same time, sexually dimorphic gene expression that is common to several parts of the brain is mostly restricted to the sex chromosomes. Moreover, the study uncovered multiple female-biased non-coding genes that are non-randomly co-localized on the X-chromosome with protein-coding genes that escape X-inactivation. This raises the possibility that expression of long non-coding RNAs may play a role in modulating gene expression in domains that escape X-inactivation in mouse.
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Affiliation(s)
- Björn Reinius
- Department of Evolution and Development, EBC, Uppsala University, Sweden.
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Reinius B, Saetre P, Leonard JA, Blekhman R, Merino-Martinez R, Gilad Y, Jazin E. An evolutionarily conserved sexual signature in the primate brain. PLoS Genet 2008; 4:e1000100. [PMID: 18566661 PMCID: PMC2413013 DOI: 10.1371/journal.pgen.1000100] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.8] [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: 11/19/2007] [Accepted: 05/16/2008] [Indexed: 11/19/2022] Open
Abstract
The question of a potential biological sexual signature in the human brain is a heavily disputed subject. In order to provide further insight into this issue, we used an evolutionary approach to identify genes with sex differences in brain expression level among primates. We reasoned that expression patterns important to uphold key male and female characteristics may be conserved during evolution. We selected cortex for our studies because this specific brain region is responsible for many higher behavioral functions. We compared gene expression profiles in the occipital cortex of male and female humans (Homo sapiens, a great ape) and cynomolgus macaques (Macaca fascicularis, an old world monkey), two catarrhine species that show abundant morphological sexual dimorphism, as well as in common marmosets (Callithrix Jacchus, a new world monkey) which are relatively sexually monomorphic. We identified hundreds of genes with sex-biased expression patterns in humans and macaques, while fewer than ten were differentially expressed between the sexes in marmosets. In primates, a general rule is that many of the morphological and behavioral sexual dimorphisms seen in polygamous species, such as macaques, are typically less pronounced in monogamous species such as the marmosets. Our observations suggest that this correlation may also be reflected in the extent of sex-biased gene expression in the brain. We identified 85 genes with common sex-biased expression, in both human and macaque and 2 genes, X inactivation-specific transcript (XIST) and Heat shock factor binding protein 1 (HSBP1), that were consistently sex-biased in the female direction in human, macaque, and marmoset. These observations imply a conserved signature of sexual gene expression dimorphism in cortex of primates. Further, we found that the coding region of female-biased genes is more evolutionarily constrained compared to the coding region of both male-biased and non sex-biased brain expressed genes. We found genes with conserved sexual gene expression dimorphism in the occipital cortex of humans, cynomolgus macaques, and common marmosets. Genes within sexual expression profiles may underlie important functional differences between the sexes, with possible importance during primate evolution. The contribution of genetics versus environment to behavioral differences between the sexes is a fundamental question in neuroscience. We hypothesized that some differences between the sexes might be partially explained by sexually dependent gene expression differences in the brain. We further speculated that if differences in gene expression between males and females are functionally important, they may be conserved in the evolution of primates. To test these hypotheses, we measured gene expression in the brains of male and female primates from three species: humans (Homo sapiens), macaques (Macaca fascicularis), and marmosets (Callithrix jacchus). Our results point to a conserved signature of sexual gene expression dimorphism in the brains of primates. Interestingly, we found that genes with conserved sexual gene expression dimorphism in the brain also evolve under more evolutionary constraint, compared with other genes, suggesting that they may have important roles during evolution of sex in primates. Moreover, we found higher evolutionary constrains in the coding regions of female-biased genes as compared to both male-biased and non sex-biased brain expressed genes. The study of sex dimorphic genes may in the future shed light on the basis of psychiatric diseases with differences in prevalence between the sexes.
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Affiliation(s)
- Björn Reinius
- Department of Development and Genetics, Uppsala University, Uppsala, Sweden
| | - Peter Saetre
- Department of Development and Genetics, Uppsala University, Uppsala, Sweden
- Department of Clinical Neuroscience, HUBIN Project, Karolinska Institutet and Hospital, Stockholm, Sweden
| | | | - Ran Blekhman
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Roxana Merino-Martinez
- Department of Molecular Medicine and Surgery, Karolinska Institutet and Hospital, Stockholm, Sweden
| | - Yoav Gilad
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Elena Jazin
- Department of Development and Genetics, Uppsala University, Uppsala, Sweden
- * E-mail:
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