1
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Mold JE, Weissman MH, Ratz M, Hagemann-Jensen M, Hård J, Eriksson CJ, Toosi H, Berghenstråhle J, Ziegenhain C, von Berlin L, Martin M, Blom K, Lagergren J, Lundeberg J, Sandberg R, Michaëlsson J, Frisén J. Clonally heritable gene expression imparts a layer of diversity within cell types. Cell Syst 2024; 15:149-165.e10. [PMID: 38340731 DOI: 10.1016/j.cels.2024.01.004] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 05/25/2023] [Accepted: 01/18/2024] [Indexed: 02/12/2024]
Abstract
Cell types can be classified according to shared patterns of transcription. Non-genetic variability among individual cells of the same type has been ascribed to stochastic transcriptional bursting and transient cell states. Using high-coverage single-cell RNA profiling, we asked whether long-term, heritable differences in gene expression can impart diversity within cells of the same type. Studying clonal human lymphocytes and mouse brain cells, we uncovered a vast diversity of heritable gene expression patterns among different clones of cells of the same type in vivo. We combined chromatin accessibility and RNA profiling on different lymphocyte clones to reveal thousands of regulatory regions exhibiting interclonal variation, which could be directly linked to interclonal variation in gene expression. Our findings identify a source of cellular diversity, which may have important implications for how cellular populations are shaped by selective processes in development, aging, and disease. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Jeff E Mold
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Martin H Weissman
- Mathematics Department, University of California, Santa Cruz, CA, USA.
| | - Michael Ratz
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden; SciLifeLab, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | | | - Joanna Hård
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Carl-Johan Eriksson
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Hosein Toosi
- SciLifeLab, Computational Science and Technology Department, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Joseph Berghenstråhle
- SciLifeLab, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Christoph Ziegenhain
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Leonie von Berlin
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Marcel Martin
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, SciLifeLab, Stockholm University, Stockholm, Sweden
| | - Kim Blom
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institute, Stockholm, Sweden
| | - Jens Lagergren
- SciLifeLab, Computational Science and Technology Department, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Joakim Lundeberg
- SciLifeLab, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Rickard Sandberg
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Jakob Michaëlsson
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institute, Stockholm, Sweden.
| | - Jonas Frisén
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
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2
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Moura PL, Mortera-Blanco T, Hofman IJ, Todisco G, Kretzschmar WW, Björklund AC, Creignou M, Hagemann-Jensen M, Ziegenhain C, Cabrerizo Granados D, Barbosa I, Walldin G, Jansson M, Ashley N, Mead AJ, Lundin V, Dimitriou M, Yoshizato T, Woll PS, Ogawa S, Sandberg R, Jacobsen SEW, Hellström-Lindberg E. Erythroid Differentiation Enhances RNA Mis-Splicing in SF3B1-Mutant Myelodysplastic Syndromes with Ring Sideroblasts. Cancer Res 2024; 84:211-225. [PMID: 37921711 PMCID: PMC10790130 DOI: 10.1158/0008-5472.can-23-3038] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 10/28/2023] [Accepted: 10/31/2023] [Indexed: 11/04/2023]
Abstract
Myelodysplastic syndromes with ring sideroblasts (MDS-RS) commonly develop from hematopoietic stem cells (HSC) bearing mutations in the splicing factor SF3B1 (SF3B1mt). Direct studies into MDS-RS pathobiology have been limited by a lack of model systems that fully recapitulate erythroid biology and RS development and the inability to isolate viable human RS. Here, we combined successful direct RS isolation from patient samples, high-throughput multiomics analysis of cells encompassing the SF3B1mt stem-erythroid continuum, and functional assays to investigate the impact of SF3B1mt on erythropoiesis and RS accumulation. The isolated RS differentiated, egressed into the blood, escaped traditional nonsense-mediated decay (NMD) mechanisms, and leveraged stress-survival pathways that hinder wild-type hematopoiesis through pathogenic GDF15 overexpression. Importantly, RS constituted a contaminant of magnetically enriched CD34+ cells, skewing bulk transcriptomic data. Mis-splicing in SF3B1mt cells was intensified by erythroid differentiation through accelerated RNA splicing and decreased NMD activity, and SF3B1mt led to truncations in several MDS-implicated genes. Finally, RNA mis-splicing induced an uncoupling of RNA and protein expression, leading to critical abnormalities in proapoptotic p53 pathway genes. Overall, this characterization of erythropoiesis in SF3B1mt RS provides a resource for studying MDS-RS and uncovers insights into the unexpectedly active biology of the "dead-end" RS. SIGNIFICANCE Ring sideroblast isolation combined with state-of-the-art multiomics identifies survival mechanisms underlying SF3B1-mutant erythropoiesis and establishes an active role for erythroid differentiation and ring sideroblasts themselves in SF3B1-mutant myelodysplastic syndrome pathogenesis.
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Affiliation(s)
- Pedro L. Moura
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Teresa Mortera-Blanco
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Isabel J. Hofman
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Gabriele Todisco
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Huddinge, Sweden
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Warren W. Kretzschmar
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Huddinge, Sweden
- Department of Cell and Molecular Biology (CMB), Karolinska Institutet, Stockholm, Sweden
| | - Ann-Charlotte Björklund
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Maria Creignou
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Huddinge, Sweden
- Department of Medicine, Division of Hematology, Karolinska University Hospital, Huddinge, Sweden
| | - Michael Hagemann-Jensen
- Department of Cell and Molecular Biology (CMB), Karolinska Institutet, Stockholm, Sweden
- Xpress Genomics AB, Stockholm, Sweden
| | - Christoph Ziegenhain
- Department of Cell and Molecular Biology (CMB), Karolinska Institutet, Stockholm, Sweden
- Xpress Genomics AB, Stockholm, Sweden
| | - David Cabrerizo Granados
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Indira Barbosa
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Gunilla Walldin
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Monika Jansson
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Neil Ashley
- Hematopoietic Stem Cell Laboratory, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Adam J. Mead
- Hematopoietic Stem Cell Laboratory, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Vanessa Lundin
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Marios Dimitriou
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Huddinge, Sweden
- Department of Cell and Molecular Biology (CMB), Karolinska Institutet, Stockholm, Sweden
| | - Tetsuichi Yoshizato
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Huddinge, Sweden
- Department of Cell and Molecular Biology (CMB), Karolinska Institutet, Stockholm, Sweden
| | - Petter S. Woll
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Huddinge, Sweden
- Department of Cell and Molecular Biology (CMB), Karolinska Institutet, Stockholm, Sweden
| | - Seishi Ogawa
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Huddinge, Sweden
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
| | - Rickard Sandberg
- Department of Cell and Molecular Biology (CMB), Karolinska Institutet, Stockholm, Sweden
- Xpress Genomics AB, Stockholm, Sweden
| | - Sten Eirik W. Jacobsen
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Huddinge, Sweden
- Department of Cell and Molecular Biology (CMB), Karolinska Institutet, Stockholm, Sweden
- Department of Medicine, Division of Hematology, Karolinska University Hospital, Huddinge, Sweden
- Hematopoietic Stem Cell Laboratory, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Eva Hellström-Lindberg
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Huddinge, Sweden
- Department of Medicine, Division of Hematology, Karolinska University Hospital, Huddinge, Sweden
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3
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Hunt G, Vaid R, Pirogov S, Pfab A, Ziegenhain C, Sandberg R, Reimegård J, Mannervik M. Tissue-specific RNA Polymerase II promoter-proximal pause release and burst kinetics in a Drosophila embryonic patterning network. Genome Biol 2024; 25:2. [PMID: 38166964 PMCID: PMC10763363 DOI: 10.1186/s13059-023-03135-0] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 11/30/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Formation of tissue-specific transcriptional programs underlies multicellular development, including dorsoventral (DV) patterning of the Drosophila embryo. This involves interactions between transcriptional enhancers and promoters in a chromatin context, but how the chromatin landscape influences transcription is not fully understood. RESULTS Here we comprehensively resolve differential transcriptional and chromatin states during Drosophila DV patterning. We find that RNA Polymerase II pausing is established at DV promoters prior to zygotic genome activation (ZGA), that pausing persists irrespective of cell fate, but that release into productive elongation is tightly regulated and accompanied by tissue-specific P-TEFb recruitment. DV enhancers acquire distinct tissue-specific chromatin states through CBP-mediated histone acetylation that predict the transcriptional output of target genes, whereas promoter states are more tissue-invariant. Transcriptome-wide inference of burst kinetics in different cell types revealed that while DV genes are generally characterized by a high burst size, either burst size or frequency can differ between tissues. CONCLUSIONS The data suggest that pausing is established by pioneer transcription factors prior to ZGA and that release from pausing is imparted by enhancer chromatin state to regulate bursting in a tissue-specific manner in the early embryo. Our results uncover how developmental patterning is orchestrated by tissue-specific bursts of transcription from Pol II primed promoters in response to enhancer regulatory cues.
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Affiliation(s)
- George Hunt
- Department Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Roshan Vaid
- Department Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Sergei Pirogov
- Department Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Alexander Pfab
- Department Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | | | - Rickard Sandberg
- Department Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Johan Reimegård
- Department Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Mattias Mannervik
- Department Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden.
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4
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Nikopoulou C, Kleinenkuhnen N, Parekh S, Sandoval T, Ziegenhain C, Schneider F, Giavalisco P, Donahue KF, Vesting AJ, Kirchner M, Bozukova M, Vossen C, Altmüller J, Wunderlich T, Sandberg R, Kondylis V, Tresch A, Tessarz P. Spatial and single-cell profiling of the metabolome, transcriptome and epigenome of the aging mouse liver. Nat Aging 2023; 3:1430-1445. [PMID: 37946043 PMCID: PMC10645594 DOI: 10.1038/s43587-023-00513-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: 05/08/2023] [Accepted: 09/27/2023] [Indexed: 11/12/2023]
Abstract
Tissues within an organism and even cell types within a tissue can age with different velocities. However, it is unclear whether cells of one type experience different aging trajectories within a tissue depending on their spatial location. Here, we used spatial transcriptomics in combination with single-cell ATAC-seq and RNA-seq, lipidomics and functional assays to address how cells in the male murine liver are affected by age-related changes in the microenvironment. Integration of the datasets revealed zonation-specific and age-related changes in metabolic states, the epigenome and transcriptome. The epigenome changed in a zonation-dependent manner and functionally, periportal hepatocytes were characterized by decreased mitochondrial fitness, whereas pericentral hepatocytes accumulated large lipid droplets. Together, we provide evidence that changing microenvironments within a tissue exert strong influences on their resident cells that can shape epigenetic, metabolic and phenotypic outputs.
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Affiliation(s)
- Chrysa Nikopoulou
- Max Planck Research Group 'Chromatin and Ageing', Max Planck Institute for Biology of Ageing, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-associated Diseases (CECAD), Cologne, Germany
| | - Niklas Kleinenkuhnen
- Max Planck Research Group 'Chromatin and Ageing', Max Planck Institute for Biology of Ageing, Cologne, Germany
- Institute of Medical Statistics and Computational Biology, Faculty of Medicine, University of Cologne, Cologne, Germany
| | - Swati Parekh
- Max Planck Research Group 'Chromatin and Ageing', Max Planck Institute for Biology of Ageing, Cologne, Germany
- Global Computational Biology and Digital Sciences, Boehringer Ingelheim Pharma, Biberach, Germany
| | - Tonantzi Sandoval
- Max Planck Research Group 'Chromatin and Ageing', Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Christoph Ziegenhain
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Farina Schneider
- Institute for Pathology, University Hospital Cologne, Cologne, Germany
| | - Patrick Giavalisco
- Metabolic Core Facility, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Kat-Folz Donahue
- FACS and Imaging Core Facility, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | | | - Marcel Kirchner
- FACS and Imaging Core Facility, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Mihaela Bozukova
- Max Planck Research Group 'Chromatin and Ageing', Max Planck Institute for Biology of Ageing, Cologne, Germany
| | | | - Janine Altmüller
- Cologne Center for Genomics, University of Cologne, Cologne, Germany; Berlin Institute of Health at Charité, Core Facility Genomics, Berlin, Germany; Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Thomas Wunderlich
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-associated Diseases (CECAD), Cologne, Germany
- Max Planck Institute for Metabolism Research, Cologne, Germany
| | - Rickard Sandberg
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Vangelis Kondylis
- Institute for Pathology, University Hospital Cologne, Cologne, Germany
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Medical Faculty at Heinrich-Heine-University, Duesseldorf, Germany
| | - Achim Tresch
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-associated Diseases (CECAD), Cologne, Germany.
- Institute of Medical Statistics and Computational Biology, Faculty of Medicine, University of Cologne, Cologne, Germany.
| | - Peter Tessarz
- Max Planck Research Group 'Chromatin and Ageing', Max Planck Institute for Biology of Ageing, Cologne, Germany.
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-associated Diseases (CECAD), Cologne, Germany.
- Department of Human Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands.
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5
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Belander Strålin K, Carrelha J, Winroth A, Ziegenhain C, Hagemann-Jensen M, Kettyle LM, Hillen A, Högstrand K, Markljung E, Grasso F, Seki M, Mazzi S, Meng Y, Wu B, Chari E, Lehander M, Sandberg R, Woll PS, Jacobsen SEW. Platelet and myeloid lineage biases of transplanted single perinatal mouse hematopoietic stem cells. Cell Res 2023; 33:883-886. [PMID: 37674010 PMCID: PMC10624660 DOI: 10.1038/s41422-023-00866-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 08/02/2023] [Indexed: 09/08/2023] Open
Affiliation(s)
- Karin Belander Strålin
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Pediatric Oncology, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Joana Carrelha
- Haematopoietic Stem Cell Biology Laboratory, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Axel Winroth
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Christoph Ziegenhain
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | | | - Laura M Kettyle
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Amy Hillen
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Kari Högstrand
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Ellen Markljung
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Francesca Grasso
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Masafumi Seki
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Stefania Mazzi
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Yiran Meng
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Bishan Wu
- Haematopoietic Stem Cell Biology Laboratory, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Edwin Chari
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Madeleine Lehander
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Rickard Sandberg
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Petter S Woll
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Sten Eirik W Jacobsen
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden.
- Haematopoietic Stem Cell Biology Laboratory, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
- Karolinska University Hospital Huddinge, Stockholm, Sweden.
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6
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Lause J, Ziegenhain C, Hartmanis L, Berens P, Kobak D. Compound models and Pearson residuals for normalization of single-cell RNA-seq data without UMIs. bioRxiv 2023:2023.08.02.551637. [PMID: 37577688 PMCID: PMC10418209 DOI: 10.1101/2023.08.02.551637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Before downstream analysis can reveal biological signals in single-cell RNA sequencing data, normalization and variance stabilization are required to remove technical noise. Recently, Pearson residuals based on negative binomial models have been suggested as an efficient normalization approach. These methods were developed for UMI-based sequencing protocols, where unique molecular identifiers (UMIs) help to remove PCR amplification noise by keeping track of the original molecules. In contrast, full-length protocols such as Smart-seq2 lack UMIs and retain amplification noise, making negative binomial models inapplicable. Here, we extend Pearson residuals to such read count data by modeling them as a compound process: we assume that the captured RNA molecules follow the negative binomial distribution, but are replicated according to an amplification distribution. Based on this model, we introduce compound Pearson residuals and show that they can be analytically obtained without explicit knowledge of the amplification distribution. Further, we demonstrate that compound Pearson residuals lead to a biologically meaningful gene selection and low-dimensional embeddings of complex Smart-seq2 datasets. Finally, we empirically study amplification distributions across several sequencing protocols, and suggest that they can be described by a broken power law. We show that the resulting compound distribution captures overdispersion and zero-inflation patterns characteristic of read count data. In summary, compound Pearson residuals provide an efficient and effective way to normalize read count data based on simple mechanistic assumptions.
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Affiliation(s)
- Jan Lause
- Hertie Institute for AI in Brain Health, University of Tübingen, Germany
- Tübingen AI Center, Tübingen, Germany
| | | | - Leonard Hartmanis
- Department of Cell & Molecular Biology, Karolinska Institutet, Sweden
| | - Philipp Berens
- Hertie Institute for AI in Brain Health, University of Tübingen, Germany
- Tübingen AI Center, Tübingen, Germany
| | - Dmitry Kobak
- Hertie Institute for AI in Brain Health, University of Tübingen, Germany
- Tübingen AI Center, Tübingen, Germany
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7
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Mentz M, Keay W, Strobl CD, Antoniolli M, Adolph L, Heide M, Lechner A, Haebe S, Osterode E, Kridel R, Ziegenhain C, Wange LE, Hildebrand JA, Shree T, Silkenstedt E, Staiger AM, Ott G, Horn H, Szczepanowski M, Richter J, Levy R, Rosenwald A, Enard W, Zimber-Strobl U, von Bergwelt-Baildon M, Hiddemann W, Klapper W, Schmidt-Supprian M, Rudelius M, Bararia D, Passerini V, Weigert O. PARP14 is a novel target in STAT6 mutant follicular lymphoma. Leukemia 2022; 36:2281-2292. [PMID: 35851155 PMCID: PMC9417990 DOI: 10.1038/s41375-022-01641-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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: 02/13/2022] [Revised: 06/21/2022] [Accepted: 06/29/2022] [Indexed: 12/02/2022]
Abstract
The variable clinical course of follicular lymphoma (FL) is determined by the molecular heterogeneity of tumor cells and complex interactions within the tumor microenvironment (TME). IL-4 producing follicular helper T cells (TFH) are critical components of the FL TME. Binding of IL-4 to IL-4R on FL cells activates JAK/STAT signaling. We identified STAT6 mutations (STAT6MUT) in 13% of FL (N = 33/258), all clustered within the DNA binding domain. Gene expression data and immunohistochemistry showed upregulation of IL-4/STAT6 target genes in STAT6MUT FL, including CCL17, CCL22, and FCER2 (CD23). Functionally, STAT6MUT was gain-of-function by serial replating phenotype in pre-B CFU assays. Expression of STAT6MUT enhanced IL-4 induced FCER2/CD23, CCL17 and CCL22 expression and was associated with nuclear accumulation of pSTAT6. RNA sequencing identified PARP14 -a transcriptional switch and co-activator of STAT6- among the top differentially upregulated genes in IL-4 stimulated STAT6MUT lymphoma cells and in STAT6MUT primary FL cells. Quantitative chromatin immunoprecipitation (qChIP) demonstrated binding of STAT6MUT but not STAT6WT to the PARP14 promotor. Reporter assays showed increased IL-4 induced transactivation activity of STAT6MUT at the PARP14 promotor, suggesting a self-reinforcing regulatory circuit. Knock-down of PARP14 or PARP-inhibition abrogated the STAT6MUT gain-of-function phenotype. Thus, our results identify PARP14 as a novel therapeutic target in STAT6MUT FL.
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Affiliation(s)
- Michael Mentz
- Department of Medicine III, Laboratory for Experimental Leukemia and Lymphoma Research (ELLF), Ludwig-Maximilians-University (LMU) Hospital, Munich, Germany
- Research Unit Gene Vectors, Helmholtz- Center Munich, German Research Center for Environmental Health, Munich, Germany
| | - William Keay
- Department of Medicine III, Laboratory for Experimental Leukemia and Lymphoma Research (ELLF), Ludwig-Maximilians-University (LMU) Hospital, Munich, Germany
| | - Carolin Dorothea Strobl
- Department of Medicine III, Laboratory for Experimental Leukemia and Lymphoma Research (ELLF), Ludwig-Maximilians-University (LMU) Hospital, Munich, Germany
| | - Martina Antoniolli
- Department of Medicine III, Laboratory for Experimental Leukemia and Lymphoma Research (ELLF), Ludwig-Maximilians-University (LMU) Hospital, Munich, Germany
| | - Louisa Adolph
- Department of Medicine III, Laboratory for Experimental Leukemia and Lymphoma Research (ELLF), Ludwig-Maximilians-University (LMU) Hospital, Munich, Germany
| | - Michael Heide
- Department of Medicine III, Laboratory for Experimental Leukemia and Lymphoma Research (ELLF), Ludwig-Maximilians-University (LMU) Hospital, Munich, Germany
| | - Axel Lechner
- Department of Otolaryngology, Ludwig-Maximilians-University (LMU) Hospital, Munich, Germany
| | - Sarah Haebe
- Department of Medicine III, Laboratory for Experimental Leukemia and Lymphoma Research (ELLF), Ludwig-Maximilians-University (LMU) Hospital, Munich, Germany
- Division of Oncology, Department of Medicine, School of Medicine, Stanford, CA, USA
| | - Elisa Osterode
- Department of Medicine III, Laboratory for Experimental Leukemia and Lymphoma Research (ELLF), Ludwig-Maximilians-University (LMU) Hospital, Munich, Germany
| | - Robert Kridel
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Christoph Ziegenhain
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-University, Munich, Germany
| | - Lucas Esteban Wange
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-University, Munich, Germany
| | - Johannes Adrian Hildebrand
- Department of Medicine III, Laboratory for Experimental Leukemia and Lymphoma Research (ELLF), Ludwig-Maximilians-University (LMU) Hospital, Munich, Germany
| | - Tanaya Shree
- Division of Oncology, Department of Medicine, School of Medicine, Stanford, CA, USA
| | - Elisabeth Silkenstedt
- Department of Medicine III, Laboratory for Experimental Leukemia and Lymphoma Research (ELLF), Ludwig-Maximilians-University (LMU) Hospital, Munich, Germany
| | - Annette M Staiger
- Department of Clinical Pathology, Robert Bosch Hospital, Stuttgart, Germany
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart and University of Tübingen, Tübingen, Germany
| | - German Ott
- Department of Clinical Pathology, Robert Bosch Hospital, Stuttgart, Germany
| | - Heike Horn
- Department of Clinical Pathology, Robert Bosch Hospital, Stuttgart, Germany
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart and University of Tübingen, Tübingen, Germany
| | - Monika Szczepanowski
- Institute of Pathology, Hematopathology Section, University of Schleswig-Holstein, Kiel, Germany
| | - Julia Richter
- Institute of Pathology, Hematopathology Section, University of Schleswig-Holstein, Kiel, Germany
| | - Ronald Levy
- Division of Oncology, Department of Medicine, School of Medicine, Stanford, CA, USA
| | - Andreas Rosenwald
- Institute of Pathology, University of Würzburg and Comprehensive Cancer Centre Mainfranken, Würzburg, Germany
| | - Wolfgang Enard
- Division of Oncology, Department of Medicine, School of Medicine, Stanford, CA, USA
| | - Ursula Zimber-Strobl
- Research Unit Gene Vectors, Helmholtz- Center Munich, German Research Center for Environmental Health, Munich, Germany
| | - Michael von Bergwelt-Baildon
- Department of Medicine III, Laboratory for Experimental Leukemia and Lymphoma Research (ELLF), Ludwig-Maximilians-University (LMU) Hospital, Munich, Germany
- German Cancer Consortium (DKTK), Munich, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Wolfgang Hiddemann
- Department of Medicine III, Laboratory for Experimental Leukemia and Lymphoma Research (ELLF), Ludwig-Maximilians-University (LMU) Hospital, Munich, Germany
- German Cancer Consortium (DKTK), Munich, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Wolfram Klapper
- Institute of Pathology, Hematopathology Section, University of Schleswig-Holstein, Kiel, Germany
| | - Marc Schmidt-Supprian
- German Cancer Consortium (DKTK), Munich, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Experimental Hematology, School of Medicine, Center for Translational Cancer Research (TranslaTUM), Technical University of Munich, Munich, Germany
| | - Martina Rudelius
- Institute of Pathology, Faculty of Medicine, Ludwig-Maximilians-University, Munich, Germany
| | - Deepak Bararia
- Department of Medicine III, Laboratory for Experimental Leukemia and Lymphoma Research (ELLF), Ludwig-Maximilians-University (LMU) Hospital, Munich, Germany
| | - Verena Passerini
- Department of Medicine III, Laboratory for Experimental Leukemia and Lymphoma Research (ELLF), Ludwig-Maximilians-University (LMU) Hospital, Munich, Germany
| | - Oliver Weigert
- Department of Medicine III, Laboratory for Experimental Leukemia and Lymphoma Research (ELLF), Ludwig-Maximilians-University (LMU) Hospital, Munich, Germany.
- German Cancer Consortium (DKTK), Munich, Germany.
- German Cancer Research Center (DKFZ), Heidelberg, Germany.
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8
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Janjic A, Wange LE, Bagnoli JW, Geuder J, Nguyen P, Richter D, Vieth B, Vick B, Jeremias I, Ziegenhain C, Hellmann I, Enard W. Prime-seq, efficient and powerful bulk RNA sequencing. Genome Biol 2022; 23:88. [PMID: 35361256 PMCID: PMC8969310 DOI: 10.1186/s13059-022-02660-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [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: 09/27/2021] [Accepted: 03/23/2022] [Indexed: 12/21/2022] Open
Abstract
Cost-efficient library generation by early barcoding has been central in propelling single-cell RNA sequencing. Here, we optimize and validate prime-seq, an early barcoding bulk RNA-seq method. We show that it performs equivalently to TruSeq, a standard bulk RNA-seq method, but is fourfold more cost-efficient due to almost 50-fold cheaper library costs. We also validate a direct RNA isolation step, show that intronic reads are derived from RNA, and compare cost-efficiencies of available protocols. We conclude that prime-seq is currently one of the best options to set up an early barcoding bulk RNA-seq protocol from which many labs would profit.
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Affiliation(s)
- Aleksandar Janjic
- Anthropology & Human Genomics, Faculty of Biology, Ludwig-Maximilians University, Großhaderner Str. 2, 82152, Martinsried, Germany.,Graduate School of Systemic Neurosciences, Faculty of Biology, Ludwig-Maximilians University, Martinsried, Germany
| | - Lucas E Wange
- Anthropology & Human Genomics, Faculty of Biology, Ludwig-Maximilians University, Großhaderner Str. 2, 82152, Martinsried, Germany
| | - Johannes W Bagnoli
- Anthropology & Human Genomics, Faculty of Biology, Ludwig-Maximilians University, Großhaderner Str. 2, 82152, Martinsried, Germany
| | - Johanna Geuder
- Anthropology & Human Genomics, Faculty of Biology, Ludwig-Maximilians University, Großhaderner Str. 2, 82152, Martinsried, Germany
| | - Phong Nguyen
- Anthropology & Human Genomics, Faculty of Biology, Ludwig-Maximilians University, Großhaderner Str. 2, 82152, Martinsried, Germany
| | - Daniel Richter
- Anthropology & Human Genomics, Faculty of Biology, Ludwig-Maximilians University, Großhaderner Str. 2, 82152, Martinsried, Germany
| | - Beate Vieth
- Anthropology & Human Genomics, Faculty of Biology, Ludwig-Maximilians University, Großhaderner Str. 2, 82152, Martinsried, Germany
| | - Binje Vick
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Zentrum München, German Research Center for Environmental Health (HMGU), Munich, Germany.,German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
| | - Irmela Jeremias
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Zentrum München, German Research Center for Environmental Health (HMGU), Munich, Germany.,German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany.,Department of Pediatrics, Dr. von Hauner Children's Hospital, Ludwig-Maximilians University, Munich, Germany
| | - Christoph Ziegenhain
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Ines Hellmann
- Anthropology & Human Genomics, Faculty of Biology, Ludwig-Maximilians University, Großhaderner Str. 2, 82152, Martinsried, Germany
| | - Wolfgang Enard
- Anthropology & Human Genomics, Faculty of Biology, Ludwig-Maximilians University, Großhaderner Str. 2, 82152, Martinsried, Germany.
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9
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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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10
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Abstract
The risks associated with re-identification of human genetic data are severely limiting open data sharing in life sciences, even in studies where donor-related genetic variant information is not of primary interest. Here, we developed BAMboozle, a versatile tool to eliminate critical types of sensitive genetic information in human sequence data by reverting aligned reads to the genome reference sequence. Applying BAMboozle to functional genomics data, such as single-cell RNA-seq (scRNA-seq) and scATAC-seq datasets, confirmed the removal of donor-related single nucleotide polymorphisms (SNPs) and indels in a manner that did not disclose the altered positions. Importantly, BAMboozle only removes the genetic sequence variants of the sample (i.e., donor) while preserving other important aspects of the raw sequence data. For example, BAMboozled scRNA-seq data contained accurate cell-type associated gene expression signatures, splice kinetic information, and can be used for methods benchmarking. Altogether, BAMboozle efficiently removes genetic variation in aligned sequence data, which represents a step forward towards open data sharing in many areas of genomics where the genetic variant information is not of primary interest.
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Affiliation(s)
- Christoph Ziegenhain
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Rickard Sandberg
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden.
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11
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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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12
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Kober-Hasslacher M, Oh-Strauß H, Kumar D, Soberon V, Diehl C, Lech M, Engleitner T, Katab E, Fernández-Sáiz V, Piontek G, Li H, Menze B, Ziegenhain C, Enard W, Rad R, Böttcher JP, Anders HJ, Rudelius M, Schmidt-Supprian M. c-Rel gain in B cells drives germinal center reactions and autoantibody production. J Clin Invest 2021; 130:3270-3286. [PMID: 32191641 DOI: 10.1172/jci124382] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 08/23/2018] [Accepted: 03/11/2020] [Indexed: 12/11/2022] Open
Abstract
Single-nucleotide polymorphisms and locus amplification link the NF-κB transcription factor c-Rel to human autoimmune diseases and B cell lymphomas, respectively. However, the functional consequences of enhanced c-Rel levels remain enigmatic. Here, we overexpressed c-Rel specifically in mouse B cells from BAC-transgenic gene loci and demonstrate that c-Rel protein levels linearly dictated expansion of germinal center B (GCB) cells and isotype-switched plasma cells. c-Rel expression in B cells of otherwise c-Rel-deficient mice fully rescued terminal B cell differentiation, underscoring its critical B cell-intrinsic roles. Unexpectedly, in GCB cells transcription-independent regulation produced the highest c-Rel protein levels among B cell subsets. In c-Rel-overexpressing GCB cells this caused enhanced nuclear translocation, a profoundly altered transcriptional program, and increased proliferation. Finally, we provide a link between c-Rel gain and autoimmunity by showing that c-Rel overexpression in B cells caused autoantibody production and renal immune complex deposition.
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Affiliation(s)
- Maike Kober-Hasslacher
- Institute of Experimental Hematology, School of Medicine, Technical University of Munich, Munich, Germany.,Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Hyunju Oh-Strauß
- Institute of Experimental Hematology, School of Medicine, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Dilip Kumar
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Valeria Soberon
- Institute of Experimental Hematology, School of Medicine, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Carina Diehl
- Institute of Experimental Hematology, School of Medicine, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Maciej Lech
- Renal Division, Medizinische Klinik und Poliklinik IV, Klinikum der Ludwig-Maximilians-Universität, Munich, Germany
| | - Thomas Engleitner
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Institute of Molecular Oncology and Functional Genomics and
| | - Eslam Katab
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany.,Department of Medicine III, School of Medicine, Technical University of Munich, Munich, Germany
| | - Vanesa Fernández-Sáiz
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany.,Department of Medicine III, School of Medicine, Technical University of Munich, Munich, Germany
| | - Guido Piontek
- Institute of Pathology, Klinikum der Ludwig-Maximilians-Universität, Munich, Germany
| | - Hongwei Li
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany.,Department of Informatics, Technical University of Munich, Munich, Germany
| | - Björn Menze
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany.,Department of Informatics, Technical University of Munich, Munich, Germany
| | - Christoph Ziegenhain
- Anthropology and Human Genomics, Department of Biology II, Ludwig-Maximilians-Universität, Martinsried, Germany
| | - Wolfgang Enard
- Anthropology and Human Genomics, Department of Biology II, Ludwig-Maximilians-Universität, Martinsried, Germany
| | - Roland Rad
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Institute of Molecular Oncology and Functional Genomics and
| | - Jan P Böttcher
- Institute of Molecular Immunology and Experimental Oncology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Hans-Joachim Anders
- Renal Division, Medizinische Klinik und Poliklinik IV, Klinikum der Ludwig-Maximilians-Universität, Munich, Germany
| | - Martina Rudelius
- Institute of Pathology, Klinikum der Ludwig-Maximilians-Universität, Munich, Germany
| | - Marc Schmidt-Supprian
- Institute of Experimental Hematology, School of Medicine, Technical University of Munich, Munich, Germany.,Max Planck Institute of Biochemistry, Martinsried, Germany.,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
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13
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Mulholland CB, Nishiyama A, Ryan J, Nakamura R, Yiğit M, Glück IM, Trummer C, Qin W, Bartoschek MD, Traube FR, Parsa E, Ugur E, Modic M, Acharya A, Stolz P, Ziegenhain C, Wierer M, Enard W, Carell T, Lamb DC, Takeda H, Nakanishi M, Bultmann S, Leonhardt H. Recent evolution of a TET-controlled and DPPA3/STELLA-driven pathway of passive DNA demethylation in mammals. Nat Commun 2020; 11:5972. [PMID: 33235224 PMCID: PMC7686362 DOI: 10.1038/s41467-020-19603-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [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: 03/24/2020] [Accepted: 10/22/2020] [Indexed: 12/12/2022] Open
Abstract
Genome-wide DNA demethylation is a unique feature of mammalian development and naïve pluripotent stem cells. Here, we describe a recently evolved pathway in which global hypomethylation is achieved by the coupling of active and passive demethylation. TET activity is required, albeit indirectly, for global demethylation, which mostly occurs at sites devoid of TET binding. Instead, TET-mediated active demethylation is locus-specific and necessary for activating a subset of genes, including the naïve pluripotency and germline marker Dppa3 (Stella, Pgc7). DPPA3 in turn drives large-scale passive demethylation by directly binding and displacing UHRF1 from chromatin, thereby inhibiting maintenance DNA methylation. Although unique to mammals, we show that DPPA3 alone is capable of inducing global DNA demethylation in non-mammalian species (Xenopus and medaka) despite their evolutionary divergence from mammals more than 300 million years ago. Our findings suggest that the evolution of Dppa3 facilitated the emergence of global DNA demethylation in mammals.
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Affiliation(s)
- Christopher B Mulholland
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Atsuya Nishiyama
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Joel Ryan
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Ryohei Nakamura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Merve Yiğit
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Ivo M Glück
- Physical Chemistry, Department of Chemistry, Center for Nanoscience, Nanosystems Initiative Munich and Center for Integrated Protein Science Munich, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Carina Trummer
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Weihua Qin
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Michael D Bartoschek
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Franziska R Traube
- Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Edris Parsa
- Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Enes Ugur
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Miha Modic
- The Francis Crick Institute and UCL Queen Square Institute of Neurology, London, UK
| | - Aishwarya Acharya
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Paul Stolz
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Christoph Ziegenhain
- Department of Biology II, Anthropology and Human Genomics, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Michael Wierer
- Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Wolfgang Enard
- Department of Biology II, Anthropology and Human Genomics, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Thomas Carell
- Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Don C Lamb
- Physical Chemistry, Department of Chemistry, Center for Nanoscience, Nanosystems Initiative Munich and Center for Integrated Protein Science Munich, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Hiroyuki Takeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Makoto Nakanishi
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Sebastian Bultmann
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany.
| | - Heinrich Leonhardt
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany.
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14
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Abstract
The recent rapid spread of single cell RNA sequencing (scRNA-seq) methods has created a large variety of experimental and computational pipelines for which best practices have not yet been established. Here, we use simulations based on five scRNA-seq library protocols in combination with nine realistic differential expression (DE) setups to systematically evaluate three mapping, four imputation, seven normalisation and four differential expression testing approaches resulting in ~3000 pipelines, allowing us to also assess interactions among pipeline steps. We find that choices of normalisation and library preparation protocols have the biggest impact on scRNA-seq analyses. Specifically, we find that library preparation determines the ability to detect symmetric expression differences, while normalisation dominates pipeline performance in asymmetric DE-setups. Finally, we illustrate the importance of informed choices by showing that a good scRNA-seq pipeline can have the same impact on detecting a biological signal as quadrupling the sample size.
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Affiliation(s)
- Beate Vieth
- Anthropology and Human Genomics, Department of Biology II, Ludwig-Maximilians University, Munich, Germany
| | - Swati Parekh
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Christoph Ziegenhain
- Department of Cell and Molecular Biology, Karolinska Institutet, SE-171 65, Stockholm, Sweden
| | - Wolfgang Enard
- Anthropology and Human Genomics, Department of Biology II, Ludwig-Maximilians University, Munich, Germany
| | - Ines Hellmann
- Anthropology and Human Genomics, Department of Biology II, Ludwig-Maximilians University, Munich, Germany.
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15
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Wang S, Gegenfurtner FA, Crevenna AH, Ziegenhain C, Kliesmete Z, Enard W, Müller R, Vollmar AM, Schneider S, Zahler S. Chivosazole A Modulates Protein-Protein Interactions of Actin. J Nat Prod 2019; 82:1961-1970. [PMID: 31260301 DOI: 10.1021/acs.jnatprod.9b00335] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Actin is a protein of central importance for many cellular key processes. It is regulated by local interactions with a large number of actin binding proteins (ABPs). Various compounds are known to either increase or decrease the polymerization dynamics of actin. However, no actin binding compound has been developed for clinical applications yet because of selectivity issues. We provide a crystal structure of the natural product chivosazole A (ChivoA) bound to actin and show that-in addition to inhibiting nucleation, polymerization, and severing of F-actin filaments-it selectively modulates binding of ABPs to G-actin: Although unphysiological actin dimers are induced by ChivoA, interaction with gelsolin, profilin, cofilin, and thymosin-β4 is inhibited. Moreover, ChivoA causes transcriptional effects differing from latrunculin B, an actin binder with a different binding site. Our data show that ChivoA and related compounds could serve as scaffolds for the development of actin binding molecules selectively targeting specific actin functions.
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Affiliation(s)
- Shuaijun Wang
- Department of Pharmacy , Ludwig-Maximilians-University , 81377 Munich , Germany
| | | | - Alvaro H Crevenna
- Biomolecular Self-Organization Laboratory , ITQB-Universidade Nova de Lisboa , 2780-157 Oeiras , Portugal
| | - Christoph Ziegenhain
- Department of Biology II , Ludwig-Maximilians-University , 82152 Planegg-Martinsried , Germany
| | - Zane Kliesmete
- Department of Biology II , Ludwig-Maximilians-University , 82152 Planegg-Martinsried , Germany
| | - Wolfgang Enard
- Department of Biology II , Ludwig-Maximilians-University , 82152 Planegg-Martinsried , Germany
| | - Rolf Müller
- Department of Pharmacy , Saarland University , 66125 Saarbrücken , Germany
- Department of Microbial Natural Products , Helmholtz Institute for Pharmaceutical Research Saarland and Helmholtz Centre for Infection Research , 66123 Saarbrücken , Germany
| | - Angelika M Vollmar
- Department of Pharmacy , Ludwig-Maximilians-University , 81377 Munich , Germany
| | - Sabine Schneider
- Department of Chemistry , Technical University Munich , 85748 Garching , Germany
| | - Stefan Zahler
- Department of Pharmacy , Ludwig-Maximilians-University , 81377 Munich , Germany
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16
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Medvedeva VP, Rieger MA, Vieth B, Mombereau C, Ziegenhain C, Ghosh T, Cressant A, Enard W, Granon S, Dougherty JD, Groszer M. Altered social behavior in mice carrying a cortical Foxp2 deletion. Hum Mol Genet 2019; 28:701-717. [PMID: 30357341 PMCID: PMC6381386 DOI: 10.1093/hmg/ddy372] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Revised: 09/30/2018] [Accepted: 10/16/2018] [Indexed: 11/14/2022] Open
Abstract
Genetic disruptions of the forkhead box transcription factor FOXP2 in humans cause an autosomal-dominant speech and language disorder. While FOXP2 expression pattern are highly conserved, its role in specific brain areas for mammalian social behaviors remains largely unknown. Here we studied mice carrying a homozygous cortical Foxp2 deletion. The postnatal development and gross morphological architecture of mutant mice was indistinguishable from wildtype (WT) littermates. Unbiased behavioral profiling of adult mice revealed abnormalities in approach behavior towards conspecifics as well as in the reciprocal responses of WT interaction partners. Furthermore mutant mice showed alterations in acoustical parameters of ultrasonic vocalizations, which also differed in function of the social context. Cell type-specific gene expression profiling of cortical pyramidal neurons revealed aberrant regulation of genes involved in social behavior. In particular Foxp2 mutants showed the downregulation of Mint2 (Apba2), a gene involved in approach behavior in mice and autism spectrum disorder in humans. Taken together these data demonstrate that cortical Foxp2 is required for normal social behaviors in mice.
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Affiliation(s)
- Vera P Medvedeva
- Inserm, Institut du Fer à Moulin, Sorbonne Université, Paris, France
| | - Michael A Rieger
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA; Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Beate Vieth
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians-University, Planegg-Martinsried, Germany
| | - Cédric Mombereau
- Inserm, Institut du Fer à Moulin, Sorbonne Université, Paris, France
| | - Christoph Ziegenhain
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians-University, Planegg-Martinsried, Germany
| | - Tanay Ghosh
- Inserm, Institut du Fer à Moulin, Sorbonne Université, Paris, France
| | - Arnaud Cressant
- Institut des Neurosciences Paris-Saclay, Centre National de la Recherche Scientifique UMR, Orsay, France
| | - Wolfgang Enard
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians-University, Planegg-Martinsried, Germany
| | - Sylvie Granon
- Institut des Neurosciences Paris-Saclay, Centre National de la Recherche Scientifique UMR, Orsay, France
| | - Joseph D Dougherty
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA; Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Matthias Groszer
- Inserm, Institut du Fer à Moulin, Sorbonne Université, Paris, France
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17
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Granato ET, Ziegenhain C, Marvig RL, Kümmerli R. Low spatial structure and selection against secreted virulence factors attenuates pathogenicity in Pseudomonas aeruginosa. ISME J 2018; 12:2907-2918. [PMID: 30065310 DOI: 10.1038/s41396-018-0231-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 06/14/2018] [Accepted: 06/19/2018] [Indexed: 02/01/2023]
Abstract
Bacterial opportunistic pathogens are feared for their difficult-to-treat nosocomial infections and for causing morbidity in immunocompromised patients. Here, we study how such a versatile opportunist, Pseudomonas aeruginosa, adapts to conditions inside and outside its model host Caenorhabditis elegans, and use phenotypic and genotypic screens to identify the mechanistic basis of virulence evolution. We found that virulence significantly dropped in unstructured environments both in the presence and absence of the host, but remained unchanged in spatially structured environments. Reduction of virulence was either driven by a substantial decline in the production of siderophores (in treatments without hosts) or toxins and proteases (in treatments with hosts). Whole-genome sequencing of evolved clones revealed positive selection and parallel evolution across replicates, and showed an accumulation of mutations in regulator genes controlling virulence factor expression. Our study identifies the spatial structure of the non-host environment as a key driver of virulence evolution in an opportunistic pathogen.
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Affiliation(s)
- Elisa T Granato
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland. .,Department of Zoology, University of Oxford, Oxford, United Kingdom.
| | - Christoph Ziegenhain
- Department Biology II, Ludwig-Maximilians-University, Munich, Germany.,Department of Cell and Molecular Biology, Karolinska Institutet, Solna, Sweden
| | - Rasmus L Marvig
- Center for Genomic Medicine, Rigshospitalet, Copenhagen, Denmark
| | - Rolf Kümmerli
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
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18
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Bagnoli JW, Ziegenhain C, Janjic A, Wange LE, Vieth B, Parekh S, Geuder J, Hellmann I, Enard W. Sensitive and powerful single-cell RNA sequencing using mcSCRB-seq. Nat Commun 2018; 9:2937. [PMID: 30050112 PMCID: PMC6062574 DOI: 10.1038/s41467-018-05347-6] [Citation(s) in RCA: 122] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 06/26/2018] [Indexed: 01/09/2023] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) has emerged as a central genome-wide method to characterize cellular identities and processes. Consequently, improving its sensitivity, flexibility, and cost-efficiency can advance many research questions. Among the flexible plate-based methods, single-cell RNA barcoding and sequencing (SCRB-seq) is highly sensitive and efficient. Here, we systematically evaluate experimental conditions of this protocol and find that adding polyethylene glycol considerably increases sensitivity by enhancing cDNA synthesis. Furthermore, using Terra polymerase increases efficiency due to a more even cDNA amplification that requires less sequencing of libraries. We combined these and other improvements to develop a scRNA-seq library protocol we call molecular crowding SCRB-seq (mcSCRB-seq), which we show to be one of the most sensitive, efficient, and flexible scRNA-seq methods to date.
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Affiliation(s)
- Johannes W Bagnoli
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians-University, Großhaderner Straße 2, 82152, Martinsried, Germany
| | - Christoph Ziegenhain
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians-University, Großhaderner Straße 2, 82152, Martinsried, Germany
- Department of Cell & Molecular Biology, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Aleksandar Janjic
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians-University, Großhaderner Straße 2, 82152, Martinsried, Germany
| | - Lucas E Wange
- 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
- Max Planck Institute for Biology of Ageing, 50931, Cologne, Germany
| | - Johanna Geuder
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians-University, Großhaderner Straße 2, 82152, Martinsried, Germany
| | - 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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19
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Vieth B, Ziegenhain C, Parekh S, Enard W, Hellmann I. powsimR: power analysis for bulk and single cell RNA-seq experiments. Bioinformatics 2018; 33:3486-3488. [PMID: 29036287 DOI: 10.1093/bioinformatics/btx435] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 07/04/2017] [Indexed: 11/14/2022] Open
Abstract
Summary Power analysis is essential to optimize the design of RNA-seq experiments and to assess and compare the power to detect differentially expressed genes in RNA-seq data. PowsimR is a flexible tool to simulate and evaluate differential expression from bulk and especially single-cell RNA-seq data making it suitable for a priori and posterior power analyses. Availability and implementation The R package and associated tutorial are freely available at https://github.com/bvieth/powsimR. Contact vieth@bio.lmu.de or hellmann@bio.lmu.de. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Beate Vieth
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians University, 82152 Munich, Germany
| | - Christoph Ziegenhain
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians University, 82152 Munich, Germany
| | - Swati Parekh
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians University, 82152 Munich, Germany
| | - Wolfgang Enard
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians University, 82152 Munich, Germany
| | - Ines Hellmann
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians University, 82152 Munich, Germany
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20
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Mueller S, Engleitner T, Maresch R, Zukowska M, Lange S, Kaltenbacher T, Konukiewitz B, Öllinger R, Zwiebel M, Strong A, Yen HY, Banerjee R, Louzada S, Fu B, Seidler B, Götzfried J, Schuck K, Hassan Z, Schönhuber N, Klein S, Veltkamp C, Friedrich M, Rad L, Barenboim M, Ziegenhain C, Hess J, Dovey OM, Eser S, Parekh S, Constantino-Casas F, Rosa JDL, Sierra MI, Fraga M, Mayerle J, Klöppel G, Schmid RM, Cadiñanos J, Liu P, Vassiliou G, Weichert W, Steiger K, Enard W, Yang F, Unger K, Schneider G, Varela I, Bradley A, Saur D, Rad R. Abstract 391: Evolutionary trajectories and KRAS gene dosage define pancreatic cancer phenotypes. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-391] [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] [Indexed: 11/16/2022]
Abstract
Abstract
Pancreatic ductal adenocarcinoma (PDAC) has frequent alterations in few genes (KRAS, CDKN2A/TP53/SMAD4) and extensive heterogeneity of cancer drivers beyond. The expectation that mutational landscapes of rare drivers could explain phenotypic diversity has -with few exceptions- not come true. Likewise, PDAC metastasis is not understood, and comparisons of primary/metastasis pairs did not find recurrently mutated “metastasis genes”. Here we show that key aspects of PDAC biology are defined by gene-dosage variation of PDAC signature genes, evolving along distinct evolutionary routes. We found increased gene dosage of the initiating KRAS mutation (KRASMUT-iGD) in human PDAC precursors. Mouse models revealed the importance of KrasMUT-iGD for both, early progression and metastasis, rationalizing the high frequency of PDAC dissemination at diagnosis. To overcome limitations posed to gene dosage studies by PDAC´s stroma-richness, we developed murine cell culture resources comprising 135 primaries/metastases. Integrative analyses of their genomes, transcriptomes and tumor phenotypes, combined with human studies and functional analyses revealed a series of additional KrasMUT-dosage effects: different KrasMUT-levels define distinct cellular morphologies, histopathologies and clinical outcomes, with highest KrasMUT-expression underlying the most aggressive undifferentiated phenotypes. We also observed KrasMUT-dosage-associated cellular plasticity, including epithelial-to-mesenchymal transition. Mechanistically, oncogenic dosage-variation is linked to distinct evolutionary routes, characterized by defined types/states of tumor-suppressor alterations: Phylogenetic tracking studies revealed convergent evolution of KrasMUT-iGD-gains, with dependence on prior homozygous Cdkn2a- or Trp53-loss. By contrast, in Cdkn2aHET cancers, amplifications of known and novel oncogenes (Myc, Yap1, Nfkb2) collaborate with KrasMUT-HET to drive progression, yet with lower metastatic potential. These results also reveal oncogene-selective/context-dependent Cdkn2a-haploinsufficiency, for which Tgfβ pathway alterations provide permissiveness. Our study uncovers universal principles underlying PDAC biology and phenotypic diversification. It describes evolutionary trajectories, identifies their genetic hallmarks and shows how oncogenic dosage-variation is differentially licensed along individual routes to control critical disease characteristics, including early progression, histopathology, metastasis, cellular plasticity and clinical aggressiveness.
Citation Format: Sebastian Mueller, Thomas Engleitner, Roman Maresch, Magdalena Zukowska, Sebastian Lange, Thorsten Kaltenbacher, Björn Konukiewitz, Rupert Öllinger, Maximilian Zwiebel, Alex Strong, Hsi-Yu Yen, Ruby Banerjee, Sandra Louzada, Beiyuan Fu, Barbara Seidler, Juliana Götzfried, Kathleen Schuck, Zonera Hassan, Nina Schönhuber, Sabine Klein, Christian Veltkamp, Mathias Friedrich, Lena Rad, Maxim Barenboim, Christoph Ziegenhain, Julia Hess, Oliver M. Dovey, Stefan Eser, Swati Parekh, Fernando Constantino-Casas, Jorge de la Rosa, Marta I. Sierra, Mario Fraga, Julia Mayerle, Günter Klöppel, Roland M. Schmid, Juan Cadiñanos, Pentao Liu, George Vassiliou, Wilko Weichert, Katja Steiger, Wolfgang Enard, Fengtang Yang, Kristian Unger, Günter Schneider, Ignacio Varela, Allan Bradley, Dieter Saur, Roland Rad. Evolutionary trajectories and KRAS gene dosage define pancreatic cancer phenotypes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 391.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Alex Strong
- 3The Wellcome Trust Sanger Institute, Genome Campus, United Kingdom
| | - Hsi-Yu Yen
- 4German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Munich, Germany
| | - Ruby Banerjee
- 3The Wellcome Trust Sanger Institute, Genome Campus, United Kingdom
| | - Sandra Louzada
- 3The Wellcome Trust Sanger Institute, Genome Campus, United Kingdom
| | - Beiyuan Fu
- 3The Wellcome Trust Sanger Institute, Genome Campus, United Kingdom
| | | | | | | | | | | | | | | | | | - Lena Rad
- 1University Hospital TU Munich, Munich, Germany
| | | | - Christoph Ziegenhain
- 5Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians Universität, Munich, Germany
| | - Julia Hess
- 6Helmholtz Zentrum München, Research Unit Radiation Cytogenetics, Germany
| | - Oliver M. Dovey
- 3The Wellcome Trust Sanger Institute, Genome Campus, United Kingdom
| | - Stefan Eser
- 1University Hospital TU Munich, Munich, Germany
| | - Swati Parekh
- 5Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians Universität, Munich, Germany
| | | | - Jorge de la Rosa
- 3The Wellcome Trust Sanger Institute, Genome Campus, United Kingdom
| | - Marta I. Sierra
- 8Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo, Spain
| | - Mario Fraga
- 8Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo, Spain
| | - Julia Mayerle
- 9Medizinische Klinik und Poliklinik II, Klinikum der LMU München-Grosshadern, Germany
| | - Günter Klöppel
- 2Institute of Pathology, Technische Universität München, Germany
| | | | - Juan Cadiñanos
- 3The Wellcome Trust Sanger Institute, Genome Campus, United Kingdom
| | - Pentao Liu
- 3The Wellcome Trust Sanger Institute, Genome Campus, United Kingdom
| | - George Vassiliou
- 3The Wellcome Trust Sanger Institute, Genome Campus, United Kingdom
| | - Wilko Weichert
- 2Institute of Pathology, Technische Universität München, Germany
| | - Katja Steiger
- 2Institute of Pathology, Technische Universität München, Germany
| | - Wolfgang Enard
- 5Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians Universität, Munich, Germany
| | - Fengtang Yang
- 3The Wellcome Trust Sanger Institute, Genome Campus, United Kingdom
| | - Kristian Unger
- 6Helmholtz Zentrum München, Research Unit Radiation Cytogenetics, Germany
| | | | - Ignacio Varela
- 10Instituto de Biomedicina y Biotecnología de Cantabria (UC-CSIC), Munich, Spain
| | - Allan Bradley
- 3The Wellcome Trust Sanger Institute, Genome Campus, United Kingdom
| | - Dieter Saur
- 1University Hospital TU Munich, Munich, Germany
| | - Roland Rad
- 1University Hospital TU Munich, Munich, Germany
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21
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Abstract
Single-cell RNA sequencing (scRNA-seq) is currently transforming our understanding of biology, as it is a powerful tool to resolve cellular heterogeneity and molecular networks. Over 50 protocols have been developed in recent years and also data processing and analyzes tools are evolving fast. Here, we review the basic principles underlying the different experimental protocols and how to benchmark them. We also review and compare the essential methods to process scRNA-seq data from mapping, filtering, normalization and batch corrections to basic differential expression analysis. We hope that this helps to choose appropriate experimental and computational methods for the research question at hand.
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Affiliation(s)
- Christoph Ziegenhain
- Anthropology and Human Genomics, Department of Biology II, Ludwig-Maximilians University, Großhaderner Str. 2, Martinsried, Germany
| | - Beate Vieth
- Anthropology and Human Genomics, Department of Biology II, Ludwig-Maximilians University, Großhaderner Str. 2, Martinsried, Germany
| | - Swati Parekh
- Anthropology and Human Genomics, Department of Biology II, Ludwig-Maximilians University, Großhaderner Str. 2, Martinsried, Germany
| | - Ines Hellmann
- Anthropology and Human Genomics, Department of Biology II, Ludwig-Maximilians University, Großhaderner Str. 2, Martinsried, Germany
| | - Wolfgang Enard
- Anthropology and Human Genomics, Department of Biology II, Ludwig-Maximilians University, Großhaderner Str. 2, Martinsried, Germany
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22
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Parekh S, Ziegenhain C, Vieth B, Enard W, Hellmann I. zUMIs - A fast and flexible pipeline to process RNA sequencing data with UMIs. Gigascience 2018; 7:5005022. [PMID: 29846586 PMCID: PMC6007394 DOI: 10.1093/gigascience/giy059] [Citation(s) in RCA: 179] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 03/16/2018] [Accepted: 05/15/2018] [Indexed: 11/21/2022] Open
Abstract
Background Single-cell RNA-sequencing (scRNA-seq) experiments typically analyze hundreds or thousands of cells after amplification of the cDNA. The high throughput is made possible by the early introduction of sample-specific bar codes (BCs), and the amplification bias is alleviated by unique molecular identifiers (UMIs). Thus, the ideal analysis pipeline for scRNA-seq data needs to efficiently tabulate reads according to both BC and UMI. Findings zUMIs is a pipeline that can handle both known and random BCs and also efficiently collapse UMIs, either just for exon mapping reads or for both exon and intron mapping reads. If BC annotation is missing, zUMIs can accurately detect intact cells from the distribution of sequencing reads. Another unique feature of zUMIs is the adaptive downsampling function that facilitates dealing with hugely varying library sizes but also allows the user to evaluate whether the library has been sequenced to saturation. To illustrate the utility of zUMIs, we analyzed a single-nucleus RNA-seq dataset and show that more than 35% of all reads map to introns. Also, we show that these intronic reads are informative about expression levels, significantly increasing the number of detected genes and improving the cluster resolution. Conclusions zUMIs flexibility makes if possible to accommodate data generated with any of the major scRNA-seq protocols that use BCs and UMIs and is the most feature-rich, fast, and user-friendly pipeline to process such scRNA-seq data.
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Affiliation(s)
- Swati Parekh
- Anthropology and Human Genomics, Department of Biology II, Ludwig-Maximilians University, Grosshaderner Str. 2, 82152 Martinsried, Germany
| | - Christoph Ziegenhain
- Anthropology and Human Genomics, Department of Biology II, Ludwig-Maximilians University, Grosshaderner Str. 2, 82152 Martinsried, Germany
| | - Beate Vieth
- Anthropology and Human Genomics, Department of Biology II, Ludwig-Maximilians University, Grosshaderner Str. 2, 82152 Martinsried, Germany
| | - Wolfgang Enard
- Anthropology and Human Genomics, Department of Biology II, Ludwig-Maximilians University, Grosshaderner Str. 2, 82152 Martinsried, Germany
| | - Ines Hellmann
- Anthropology and Human Genomics, Department of Biology II, Ludwig-Maximilians University, Grosshaderner Str. 2, 82152 Martinsried, Germany
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23
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Gegenfurtner FA, Jahn B, Wagner H, Ziegenhain C, Enard W, Geistlinger L, Rädler JO, Vollmar AM, Zahler S. Micropatterning as a tool to identify regulatory triggers and kinetics of actin-mediated endothelial mechanosensing. J Cell Sci 2018; 131:jcs.212886. [PMID: 29724912 DOI: 10.1242/jcs.212886] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [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: 11/03/2017] [Accepted: 04/25/2018] [Indexed: 12/11/2022] Open
Abstract
Developmental processes, such as angiogenesis, are associated with a constant remodeling of the actin cytoskeleton in response to different mechanical stimuli. The mechanosensitive transcription factors MRTF-A (MKL1) and YAP (also known as YAP1) are important mediators of this challenging adaptation process. However, it is as yet unknown whether both pathways respond in an identical or in a divergent manner to a given microenvironmental guidance cue. Here, we use a micropatterning approach to dissect single aspects of cellular behavior in a spatiotemporally controllable setting. Using the exemplary process of angiogenesis, we show that cell-cell contacts and adhesive surface area are shared regulatory parameters of MRTF and YAP on rigid 2D surfaces. By analyzing MRTF and YAP under laminar flow conditions and during cell migration on dumbbell-shaped microstructures, we demonstrate that they exhibit different translocation kinetics. In conclusion, our work promotes the application of micropatterning techniques as a cell biological tool to study mechanosensitive signaling in the context of angiogenesis.
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Affiliation(s)
- Florian A Gegenfurtner
- Ludwig-Maximilians-University Munich, Department of Pharmacy, Center for Drug Research, 81377 Munich, Germany
| | - Berenice Jahn
- Ludwig-Maximilians-University Munich, Department of Pharmacy, Center for Drug Research, 81377 Munich, Germany
| | - Helga Wagner
- ibidi GmbH, Am Klopferspitz 19, 82152 Martinsried, Germany
| | - Christoph Ziegenhain
- Ludwig-Maximilians-University Munich, Department of Biology II, Anthropology and Human Genomics, 82152 Martinsried, Germany
| | - Wolfgang Enard
- Ludwig-Maximilians-University Munich, Department of Biology II, Anthropology and Human Genomics, 82152 Martinsried, Germany
| | - Ludwig Geistlinger
- Ludwig-Maximilians-University Munich, Institute for Informatics, Teaching and Research Unit Bioinformatics, 80333 Munich, Germany
| | - Joachim O Rädler
- Ludwig-Maximilians-University Munich, Faculty of Physics, Soft Condensed Matter Group, 80539 Munich, Germany
| | - Angelika M Vollmar
- Ludwig-Maximilians-University Munich, Department of Pharmacy, Center for Drug Research, 81377 Munich, Germany
| | - Stefan Zahler
- Ludwig-Maximilians-University Munich, Department of Pharmacy, Center for Drug Research, 81377 Munich, Germany
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24
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Mueller S, Engleitner T, Maresch R, Zukowska M, Lange S, Kaltenbacher T, Konukiewitz B, Öllinger R, Zwiebel M, Strong A, Yen HY, Banerjee R, Louzada S, Fu B, Seidler B, Götzfried J, Schuck K, Hassan Z, Arbeiter A, Schönhuber N, Klein S, Veltkamp C, Friedrich M, Rad L, Barenboim M, Ziegenhain C, Hess J, Dovey OM, Eser S, Parekh S, Constantino-Casas F, de la Rosa J, Sierra MI, Fraga M, Mayerle J, Klöppel G, Cadiñanos J, Liu P, Vassiliou G, Weichert W, Steiger K, Enard W, Schmid RM, Yang F, Unger K, Schneider G, Varela I, Bradley A, Saur D, Rad R. Evolutionary routes and KRAS dosage define pancreatic cancer phenotypes. Nature 2018; 554:62-68. [PMID: 29364867 PMCID: PMC6097607 DOI: 10.1038/nature25459] [Citation(s) in RCA: 262] [Impact Index Per Article: 43.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 12/20/2017] [Indexed: 12/11/2022]
Abstract
The poor correlation of mutational landscapes with phenotypes limits our understanding of the pathogenesis and metastasis of pancreatic ductal adenocarcinoma (PDAC). Here we show that oncogenic dosage-variation has a critical role in PDAC biology and phenotypic diversification. We find an increase in gene dosage of mutant KRAS in human PDAC precursors, which drives both early tumorigenesis and metastasis and thus rationalizes early PDAC dissemination. To overcome the limitations posed to gene dosage studies by the stromal richness of PDAC, we have developed large cell culture resources of metastatic mouse PDAC. Integration of cell culture genomes, transcriptomes and tumour phenotypes with functional studies and human data reveals additional widespread effects of oncogenic dosage variation on cell morphology and plasticity, histopathology and clinical outcome, with the highest KrasMUT levels underlying aggressive undifferentiated phenotypes. We also identify alternative oncogenic gains (Myc, Yap1 or Nfkb2), which collaborate with heterozygous KrasMUT in driving tumorigenesis, but have lower metastatic potential. Mechanistically, different oncogenic gains and dosages evolve along distinct evolutionary routes, licensed by defined allelic states and/or combinations of hallmark tumour suppressor alterations (Cdkn2a, Trp53, Tgfβ-pathway). Thus, evolutionary constraints and contingencies direct oncogenic dosage gain and variation along defined routes to drive the early progression of PDAC and shape its downstream biology. Our study uncovers universal principles of Ras-driven oncogenesis that have potential relevance beyond pancreatic cancer.
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Affiliation(s)
- Sebastian Mueller
- Center for Translational Cancer Research (TranslaTUM), Technische Universität München, Munich, Germany
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Thomas Engleitner
- Center for Translational Cancer Research (TranslaTUM), Technische Universität München, Munich, Germany
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Roman Maresch
- Center for Translational Cancer Research (TranslaTUM), Technische Universität München, Munich, Germany
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Magdalena Zukowska
- Center for Translational Cancer Research (TranslaTUM), Technische Universität München, Munich, Germany
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Sebastian Lange
- Center for Translational Cancer Research (TranslaTUM), Technische Universität München, Munich, Germany
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Thorsten Kaltenbacher
- Center for Translational Cancer Research (TranslaTUM), Technische Universität München, Munich, Germany
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Björn Konukiewitz
- Institute of Pathology, Technische Universität München, Munich, Germany
| | - Rupert Öllinger
- Center for Translational Cancer Research (TranslaTUM), Technische Universität München, Munich, Germany
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Maximilian Zwiebel
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Alex Strong
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton/Cambridge, UK
| | - Hsi-Yu Yen
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Comparative Experimental Pathology, Technische Universität München, Munich, Germany
| | - Ruby Banerjee
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton/Cambridge, UK
| | - Sandra Louzada
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton/Cambridge, UK
| | - Beiyuan Fu
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton/Cambridge, UK
| | - Barbara Seidler
- Center for Translational Cancer Research (TranslaTUM), Technische Universität München, Munich, Germany
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Juliana Götzfried
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Kathleen Schuck
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Zonera Hassan
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Andreas Arbeiter
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Nina Schönhuber
- Center for Translational Cancer Research (TranslaTUM), Technische Universität München, Munich, Germany
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Sabine Klein
- Center for Translational Cancer Research (TranslaTUM), Technische Universität München, Munich, Germany
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Christian Veltkamp
- Center for Translational Cancer Research (TranslaTUM), Technische Universität München, Munich, Germany
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Mathias Friedrich
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton/Cambridge, UK
| | - Lena Rad
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Maxim Barenboim
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christoph Ziegenhain
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians Universität, Martinsried, Germany
| | - Julia Hess
- Helmholtz Zentrum München, Research Unit Radiation Cytogenetics, Neuherberg, Germany
| | - Oliver M. Dovey
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton/Cambridge, UK
| | - Stefan Eser
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Swati Parekh
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians Universität, Martinsried, Germany
| | | | - Jorge de la Rosa
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton/Cambridge, UK
- Instituto de Medicina Oncológicay Molecular de Asturias (IMOMA), Oviedo, Spain
- Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, Oviedo, Spain
| | - Marta I. Sierra
- Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo, Oviedo, Spain
| | - Mario Fraga
- Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo, Oviedo, Spain
- Nanomaterials and Nanotechnology Research Center (CINN-CSIC), Universidad de Oviedo, El Entrego, Spain
| | - Julia Mayerle
- Medizinische Klinik und Poliklinik II, Klinikum der LMU München-Grosshadern, Munich, Germany
| | - Günter Klöppel
- Institute of Pathology, Technische Universität München, Munich, Germany
| | - Juan Cadiñanos
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton/Cambridge, UK
- Instituto de Medicina Oncológicay Molecular de Asturias (IMOMA), Oviedo, Spain
| | - Pentao Liu
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton/Cambridge, UK
| | - George Vassiliou
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton/Cambridge, UK
| | - Wilko Weichert
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Pathology, Technische Universität München, Munich, Germany
| | - Katja Steiger
- Institute of Pathology, Technische Universität München, Munich, Germany
- Comparative Experimental Pathology, Technische Universität München, Munich, Germany
| | - Wolfgang Enard
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians Universität, Martinsried, Germany
| | - Roland M. Schmid
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Fengtang Yang
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton/Cambridge, UK
| | - Kristian Unger
- Helmholtz Zentrum München, Research Unit Radiation Cytogenetics, Neuherberg, Germany
| | - Günter Schneider
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ignacio Varela
- Instituto de Biomedicina y Biotecnología de Cantabria (UC-CSIC), Santander, Spain
| | - Allan Bradley
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton/Cambridge, UK
| | - Dieter Saur
- Center for Translational Cancer Research (TranslaTUM), Technische Universität München, Munich, Germany
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Roland Rad
- Center for Translational Cancer Research (TranslaTUM), Technische Universität München, Munich, Germany
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
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25
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Garz AK, Wolf S, Grath S, Gaidzik V, Habringer S, Vick B, Rudelius M, Ziegenhain C, Herold S, Weickert MT, Smets M, Peschel C, Oostendorp RAJ, Bultmann S, Jeremias I, Thiede C, Döhner K, Keller U, Götze KS. Azacitidine combined with the selective FLT3 kinase inhibitor crenolanib disrupts stromal protection and inhibits expansion of residual leukemia-initiating cells in FLT3-ITD AML with concurrent epigenetic mutations. Oncotarget 2017; 8:108738-108759. [PMID: 29312564 PMCID: PMC5752477 DOI: 10.18632/oncotarget.21877] [Citation(s) in RCA: 13] [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: 05/18/2017] [Accepted: 09/20/2017] [Indexed: 12/18/2022] Open
Abstract
Effectively targeting leukemia-initiating cells (LIC) in FLT3-ITD-mutated acute myeloid leukemia (AML) is crucial for cure. Tyrosine kinase inhibitors (TKI) have limited impact as single agents, failing to eradicate LIC in the bone marrow. Using primary AML samples and a patient-derived xenograft model, we investigated whether combining the FLT3-selective TKI crenolanib with the hypomethylating agent azacitidine (AZA) eliminates FLT3-ITD LIC and whether efficacy of this combination depends on co-existing mutations. Using multiparameter flow cytometry, we show FLT3-ITD occurs within the most primitive Lin-/CD33(+)/CD45dim/CD34+CD38- LIC compartment. Crenolanib alone could not target FLT3-ITD LIC in contact with niche cells while addition of AZA overcame stromal protection resulting in dramatically reduced clonogenic capacity of LIC in vitro and severely impaired engraftment in NSG mice. Strikingly, FLT3-mutated samples harboring TET2 mutations were completely resistant to crenolanib whereas neither NPM1 nor DNMT3A mutations influenced response. Conversely, primary AML LIC harboring either TET2, DNMT3A or NPM1 mutations did not show increased sensitivity to AZA. In summary, resistance of FLT3-ITD LIC to TKI depends on co-existing epigenetic mutations. However, AZA + crenolanib effectively abrogates stromal protection and inhibits survival of FLT3-ITD LIC irrespective of mutations, providing evidence for this combination as a means to suppress residual LIC.
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Affiliation(s)
- Anne-Kathrin Garz
- Department of Medicine III, Klinikum rechts der Isar, Technische Universität München (TUM), Munich, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Saskia Wolf
- Department of Medicine III, Klinikum rechts der Isar, Technische Universität München (TUM), Munich, Germany
| | - Sonja Grath
- Department of Biology II, Ludwig-Maximilians-University (LMU), Munich, Germany
| | - Verena Gaidzik
- Department of Internal Medicine III, University of Ulm, Ulm, Germany
| | - Stefan Habringer
- Department of Medicine III, Klinikum rechts der Isar, Technische Universität München (TUM), Munich, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Binje Vick
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
| | - Martina Rudelius
- Department of Pathology, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | | | - Sylvia Herold
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Internal Medicine I, Gustav Carus University Dresden, Dresden, Germany
| | - Marie-Theresa Weickert
- Department of Medicine III, Klinikum rechts der Isar, Technische Universität München (TUM), Munich, Germany
| | - Martha Smets
- Department of Biology II, Ludwig-Maximilians-University (LMU), Munich, Germany
| | - Christian Peschel
- Department of Medicine III, Klinikum rechts der Isar, Technische Universität München (TUM), Munich, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Robert A J Oostendorp
- Department of Medicine III, Klinikum rechts der Isar, Technische Universität München (TUM), Munich, Germany
| | - Sebastian Bultmann
- Department of Biology II, Ludwig-Maximilians-University (LMU), Munich, Germany
| | - Irmela Jeremias
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
| | - Christian Thiede
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Internal Medicine I, Gustav Carus University Dresden, Dresden, Germany
| | - Konstanze Döhner
- Department of Internal Medicine III, University of Ulm, Ulm, Germany
| | - Ulrich Keller
- Department of Medicine III, Klinikum rechts der Isar, Technische Universität München (TUM), Munich, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Katharina S Götze
- Department of Medicine III, Klinikum rechts der Isar, Technische Universität München (TUM), Munich, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
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26
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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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27
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Witzel M, Petersheim D, Fan Y, Bahrami E, Racek T, Rohlfs M, Puchałka J, Mertes C, Gagneur J, Ziegenhain C, Enard W, Stray-Pedersen A, Arkwright PD, Abboud MR, Pazhakh V, Lieschke GJ, Krawitz PM, Dahlhoff M, Schneider MR, Wolf E, Horny HP, Schmidt H, Schäffer AA, Klein C. Chromatin-remodeling factor SMARCD2 regulates transcriptional networks controlling differentiation of neutrophil granulocytes. Nat Genet 2017; 49:742-752. [PMID: 28369036 DOI: 10.1038/ng.3833] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 03/10/2017] [Indexed: 02/06/2023]
Abstract
We identify SMARCD2 (SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily D, member 2), also known as BAF60b (BRG1/Brahma-associated factor 60b), as a critical regulator of myeloid differentiation in humans, mice, and zebrafish. Studying patients from three unrelated pedigrees characterized by neutropenia, specific granule deficiency, myelodysplasia with excess of blast cells, and various developmental aberrations, we identified three homozygous loss-of-function mutations in SMARCD2. Using mice and zebrafish as model systems, we showed that SMARCD2 controls early steps in the differentiation of myeloid-erythroid progenitor cells. In vitro, SMARCD2 interacts with the transcription factor CEBPɛ and controls expression of neutrophil proteins stored in specific granules. Defective expression of SMARCD2 leads to transcriptional and chromatin changes in acute myeloid leukemia (AML) human promyelocytic cells. In summary, SMARCD2 is a key factor controlling myelopoiesis and is a potential tumor suppressor in leukemia.
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Affiliation(s)
- Maximilian Witzel
- Department of Pediatrics, Dr. von Hauner Children's Hospital, Ludwig-Maximilians-Universität München, Munich, Germany.,Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Daniel Petersheim
- Department of Pediatrics, Dr. von Hauner Children's Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Yanxin Fan
- Department of Pediatrics, Dr. von Hauner Children's Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Ehsan Bahrami
- Department of Pediatrics, Dr. von Hauner Children's Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Tomas Racek
- Department of Pediatrics, Dr. von Hauner Children's Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Meino Rohlfs
- Department of Pediatrics, Dr. von Hauner Children's Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Jacek Puchałka
- Department of Pediatrics, Dr. von Hauner Children's Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Christian Mertes
- Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Julien Gagneur
- Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany.,Department of Informatics, Technical University of Munich, Munich, Germany
| | - Christoph Ziegenhain
- Anthropology and Human Genomics, Department of Biology II, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Wolfgang Enard
- Anthropology and Human Genomics, Department of Biology II, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | | | - Peter D Arkwright
- Department of Paediatric Allergy and Immunology, University of Manchester, Royal Manchester Children's Hospital, Manchester, UK
| | - Miguel R Abboud
- Department of Pediatrics and Adolescent Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Vahid Pazhakh
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Graham J Lieschke
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Peter M Krawitz
- Medical Genetics and Human Genetic, Charite University Hospital, Berlin, Germany
| | - Maik Dahlhoff
- Molecular Animal Breeding and Biotechnology, Gene Center Ludwig-Maximilians-Universität München, Munich, Germany
| | - Marlon R Schneider
- Molecular Animal Breeding and Biotechnology, Gene Center Ludwig-Maximilians-Universität München, Munich, Germany
| | - Eckhard Wolf
- Molecular Animal Breeding and Biotechnology, Gene Center Ludwig-Maximilians-Universität München, Munich, Germany
| | - Hans-Peter Horny
- Pathology Institute, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Heinrich Schmidt
- Department of Pediatrics, Dr. von Hauner Children's Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Alejandro A Schäffer
- National Center for Biotechnology Information, US National Institutes of Health, US Department of Health and Human Services, Bethesda, Maryland, USA
| | - Christoph Klein
- Department of Pediatrics, Dr. von Hauner Children's Hospital, Ludwig-Maximilians-Universität München, Munich, Germany.,Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
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28
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Schreck C, Istvánffy R, Ziegenhain C, Sippenauer T, Ruf F, Henkel L, Gärtner F, Vieth B, Florian MC, Mende N, Taubenberger A, Prendergast Á, Wagner A, Pagel C, Grziwok S, Götze KS, Guck J, Dean DC, Massberg S, Essers M, Waskow C, Geiger H, Schiemann M, Peschel C, Enard W, Oostendorp RAJ. Niche WNT5A regulates the actin cytoskeleton during regeneration of hematopoietic stem cells. J Exp Med 2016; 214:165-181. [PMID: 27998927 PMCID: PMC5206491 DOI: 10.1084/jem.20151414] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [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: 08/31/2015] [Revised: 08/25/2016] [Accepted: 11/17/2016] [Indexed: 01/04/2023] Open
Abstract
Schreck et al. show that environmental Wnt5a regulates the transcriptome of HSCs during regeneration, particularly the expression of actin-regulatory mediators. In this manner, the niche affects engraftment through regulation of adhesion, migration, and homing of both normal and malignant cells. Here, we show that the Wnt5a-haploinsufficient niche regenerates dysfunctional HSCs, which do not successfully engraft in secondary recipients. RNA sequencing of the regenerated donor Lin− SCA-1+ KIT+ (LSK) cells shows dysregulated expression of ZEB1-associated genes involved in the small GTPase-dependent actin polymerization pathway. Misexpression of DOCK2, WAVE2, and activation of CDC42 results in apolar F-actin localization, leading to defects in adhesion, migration and homing of HSCs regenerated in a Wnt5a-haploinsufficient microenvironment. Moreover, these cells show increased differentiation in vitro, with rapid loss of HSC-enriched LSK cells. Our study further shows that the Wnt5a-haploinsufficient environment similarly affects BCR-ABLp185 leukemia-initiating cells, which fail to generate leukemia in 42% of the studied recipients, or to transfer leukemia to secondary hosts. Thus, we show that WNT5A in the bone marrow niche is required to regenerate HSCs and leukemic cells with functional ability to rearrange the actin cytoskeleton and engraft successfully.
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Affiliation(s)
- Christina Schreck
- Third Department of Internal Medicine, Klinikum rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Rouzanna Istvánffy
- Third Department of Internal Medicine, Klinikum rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Christoph Ziegenhain
- Anthropology and Human Genomics, Department of Biology II, Ludwig-Maximilian-Universität, 81377 Munich, Germany
| | - Theresa Sippenauer
- Third Department of Internal Medicine, Klinikum rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Franziska Ruf
- Third Department of Internal Medicine, Klinikum rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Lynette Henkel
- Department of Medical Microbiology, Immunology, and Hygiene, Technische Universität München, 81675 Munich, Germany
| | - Florian Gärtner
- Department of Internal Medicine I, Ludwig-Maximilian-Universität, 81377 Munich, Germany
| | - Beate Vieth
- Anthropology and Human Genomics, Department of Biology II, Ludwig-Maximilian-Universität, 81377 Munich, Germany
| | | | - Nicole Mende
- Regeneration in Hematopoiesis and Animal Models in Hematopoiesis, Institute for Immunology, TU Dresden, 01309 Dresden, Germany
| | | | - Áine Prendergast
- German Cancer Research Center (DKFZ) and Heidelberg Institute for Stem Cell Technology and Experimental Medicine, 69120 Heidelberg, Germany
| | - Alina Wagner
- Third Department of Internal Medicine, Klinikum rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Charlotta Pagel
- Third Department of Internal Medicine, Klinikum rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Sandra Grziwok
- Third Department of Internal Medicine, Klinikum rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Katharina S Götze
- Third Department of Internal Medicine, Klinikum rechts der Isar, Technische Universität München, 81675 Munich, Germany.,German Cancer Consortium, DKFZ, 69120 Heidelberg, Germany
| | - Jochen Guck
- Biotechnology Center TU Dresden, 01307 Dresden, Germany
| | - Douglas C Dean
- Molecular Targets Program, James Brown Cancer Center, University of Louisville Health Sciences Center, Louisville, KY 40202
| | - Steffen Massberg
- Department of Internal Medicine I, Ludwig-Maximilian-Universität, 81377 Munich, Germany
| | - Marieke Essers
- German Cancer Research Center (DKFZ) and Heidelberg Institute for Stem Cell Technology and Experimental Medicine, 69120 Heidelberg, Germany
| | - Claudia Waskow
- Regeneration in Hematopoiesis and Animal Models in Hematopoiesis, Institute for Immunology, TU Dresden, 01309 Dresden, Germany
| | - Hartmut Geiger
- Institute of Molecular Medicine, University of Ulm, 89081 Ulm, Germany
| | - Mathias Schiemann
- Department of Medical Microbiology, Immunology, and Hygiene, Technische Universität München, 81675 Munich, Germany
| | - Christian Peschel
- Third Department of Internal Medicine, Klinikum rechts der Isar, Technische Universität München, 81675 Munich, Germany.,German Cancer Consortium, DKFZ, 69120 Heidelberg, Germany
| | - Wolfgang Enard
- Anthropology and Human Genomics, Department of Biology II, Ludwig-Maximilian-Universität, 81377 Munich, Germany
| | - Robert A J Oostendorp
- Third Department of Internal Medicine, Klinikum rechts der Isar, Technische Universität München, 81675 Munich, Germany
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29
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Ebinger S, Özdemir EZ, Ziegenhain C, Tiedt S, Castro Alves C, Grunert M, Dworzak M, Lutz C, Turati VA, Enver T, Horny HP, Sotlar K, Parekh S, Spiekermann K, Hiddemann W, Schepers A, Polzer B, Kirsch S, Hoffmann M, Knapp B, Hasenauer J, Pfeifer H, Panzer-Grümayer R, Enard W, Gires O, Jeremias I. Characterization of Rare, Dormant, and Therapy-Resistant Cells in Acute Lymphoblastic Leukemia. Cancer Cell 2016; 30:849-862. [PMID: 27916615 PMCID: PMC5156313 DOI: 10.1016/j.ccell.2016.11.002] [Citation(s) in RCA: 164] [Impact Index Per Article: 20.5] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Revised: 06/11/2016] [Accepted: 10/31/2016] [Indexed: 01/06/2023]
Abstract
Tumor relapse is associated with dismal prognosis, but responsible biological principles remain incompletely understood. To isolate and characterize relapse-inducing cells, we used genetic engineering and proliferation-sensitive dyes in patient-derived xenografts of acute lymphoblastic leukemia (ALL). We identified a rare subpopulation that resembled relapse-inducing cells with combined properties of long-term dormancy, treatment resistance, and stemness. Single-cell and bulk expression profiling revealed their similarity to primary ALL cells isolated from pediatric and adult patients at minimal residual disease (MRD). Therapeutically adverse characteristics were reversible, as resistant, dormant cells became sensitive to treatment and started proliferating when dissociated from the in vivo environment. Our data suggest that ALL patients might profit from therapeutic strategies that release MRD cells from the niche.
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Affiliation(s)
- Sarah Ebinger
- Department of Gene Vectors, Helmholtz Zentrum München, German Center for Environmental Health (HMGU), 81377 Munich, Germany
| | - Erbey Ziya Özdemir
- Department of Gene Vectors, Helmholtz Zentrum München, German Center for Environmental Health (HMGU), 81377 Munich, Germany
| | - Christoph Ziegenhain
- Anthropology and Human Genomics, Department Biology II, Faculty of Biology, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany
| | - Sebastian Tiedt
- Department of Gene Vectors, Helmholtz Zentrum München, German Center for Environmental Health (HMGU), 81377 Munich, Germany
| | - Catarina Castro Alves
- Department of Gene Vectors, Helmholtz Zentrum München, German Center for Environmental Health (HMGU), 81377 Munich, Germany
| | - Michaela Grunert
- Department of Gene Vectors, Helmholtz Zentrum München, German Center for Environmental Health (HMGU), 81377 Munich, Germany
| | - Michael Dworzak
- Children's Cancer Research Institute and St. Anna Kinderspital, Department of Pediatrics, Medical University of Vienna, 1090 Vienna, Austria
| | - Christoph Lutz
- Department of Medicine V, University of Heidelberg, 69120 Heidelberg, Germany
| | | | - Tariq Enver
- University College London Cancer Institute, London WC1E, UK
| | - Hans-Peter Horny
- Institute of Pathology, Ludwig-Maximilians-Universität München, 80337 Munich, Germany
| | - Karl Sotlar
- Institute of Pathology, Ludwig-Maximilians-Universität München, 80337 Munich, Germany
| | - Swati Parekh
- Anthropology and Human Genomics, Department Biology II, Faculty of Biology, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany
| | - Karsten Spiekermann
- Department of Internal Medicine III, University Hospital Grosshadern, Ludwig-Maximilians-Universität München, 81377 Munich, Germany; German Consortium for Translational Cancer Research (DKTK), Partnering Site, Munich, 81377 Munich, Germany
| | - Wolfgang Hiddemann
- Department of Internal Medicine III, University Hospital Grosshadern, Ludwig-Maximilians-Universität München, 81377 Munich, Germany; German Consortium for Translational Cancer Research (DKTK), Partnering Site, Munich, 81377 Munich, Germany
| | - Aloys Schepers
- Department of Gene Vectors, Helmholtz Zentrum München, German Center for Environmental Health (HMGU), 81377 Munich, Germany
| | - Bernhard Polzer
- Project Group Personalized Tumor Therapy, Fraunhofer Institute for Toxicology and Experimental Medicine ITEM, 93053 Regensburg, Germany
| | - Stefan Kirsch
- Project Group Personalized Tumor Therapy, Fraunhofer Institute for Toxicology and Experimental Medicine ITEM, 93053 Regensburg, Germany
| | - Martin Hoffmann
- Project Group Personalized Tumor Therapy, Fraunhofer Institute for Toxicology and Experimental Medicine ITEM, 93053 Regensburg, Germany
| | - Bettina Knapp
- Institute of Computational Biology, Helmholtz Zentrum München, German Center for Environmental Health (HMGU), 85764 Neuherberg, Germany
| | - Jan Hasenauer
- Institute of Computational Biology, Helmholtz Zentrum München, German Center for Environmental Health (HMGU), 85764 Neuherberg, Germany; Department of Mathematics, Technische Universität München (TUM), 85748 Munich, Germany
| | - Heike Pfeifer
- Department of Medicine, Hematology and Oncology, Goethe University, 60590 Frankfurt, Germany
| | - Renate Panzer-Grümayer
- Children's Cancer Research Institute and St. Anna Kinderspital, Department of Pediatrics, Medical University of Vienna, 1090 Vienna, Austria
| | - Wolfgang Enard
- Anthropology and Human Genomics, Department Biology II, Faculty of Biology, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany
| | - Olivier Gires
- Department of Otorhinolaryngology, Head and Neck Surgery, Grosshadern Medical Center, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Irmela Jeremias
- Department of Gene Vectors, Helmholtz Zentrum München, German Center for Environmental Health (HMGU), 81377 Munich, Germany; German Consortium for Translational Cancer Research (DKTK), Partnering Site, Munich, 81377 Munich, Germany; Department of Pediatrics, Dr. von Hauner Children's Hospital, Ludwig Maximilians University München, 80337 Munich, Germany.
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30
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Ebinger S, Ozdemir E, Tiedt S, Ziegenhain C, Castro-Alves C, Enard W, Jeremias I. Characterization of a novel dormant, drug resistant, stem cell subpopulation in acute lymphoblastic leukemia. Eur J Cancer 2016. [DOI: 10.1016/s0959-8049(16)61729-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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31
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Parekh S, Ziegenhain C, Vieth B, Enard W, Hellmann I. The impact of amplification on differential expression analyses by RNA-seq. Sci Rep 2016; 6:25533. [PMID: 27156886 PMCID: PMC4860583 DOI: 10.1038/srep25533] [Citation(s) in RCA: 152] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 04/20/2016] [Indexed: 01/20/2023] Open
Abstract
Currently, quantitative RNA-seq methods are pushed to work with increasingly small starting amounts of RNA that require amplification. However, it is unclear how much noise or bias amplification introduces and how this affects precision and accuracy of RNA quantification. To assess the effects of amplification, reads that originated from the same RNA molecule (PCR-duplicates) need to be identified. Computationally, read duplicates are defined by their mapping position, which does not distinguish PCR- from natural duplicates and hence it is unclear how to treat duplicated reads. Here, we generate and analyse RNA-seq data sets prepared using three different protocols (Smart-Seq, TruSeq and UMI-seq). We find that a large fraction of computationally identified read duplicates are not PCR duplicates and can be explained by sampling and fragmentation bias. Consequently, the computational removal of duplicates does improve neither accuracy nor precision and can actually worsen the power and the False Discovery Rate (FDR) for differential gene expression. Even when duplicates are experimentally identified by unique molecular identifiers (UMIs), power and FDR are only mildly improved. However, the pooling of samples as made possible by the early barcoding of the UMI-protocol leads to an appreciable increase in the power to detect differentially expressed genes.
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Affiliation(s)
- Swati Parekh
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians University, Großhaderner Str. 2, 82152 Martinsried, Germany
| | - Christoph Ziegenhain
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians University, Großhaderner Str. 2, 82152 Martinsried, Germany
| | - Beate Vieth
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians University, Großhaderner Str. 2, 82152 Martinsried, Germany
| | - Wolfgang Enard
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians University, Großhaderner Str. 2, 82152 Martinsried, Germany
| | - Ines Hellmann
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians University, Großhaderner Str. 2, 82152 Martinsried, Germany
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