1
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Frenz-Wiessner S, Fairley SD, Buser M, Goek I, Salewskij K, Jonsson G, Illig D, Zu Putlitz B, Petersheim D, Li Y, Chen PH, Kalauz M, Conca R, Sterr M, Geuder J, Mizoguchi Y, Megens RTA, Linder MI, Kotlarz D, Rudelius M, Penninger JM, Marr C, Klein C. Generation of complex bone marrow organoids from human induced pluripotent stem cells. Nat Methods 2024; 21:868-881. [PMID: 38374263 PMCID: PMC11093744 DOI: 10.1038/s41592-024-02172-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 01/09/2024] [Indexed: 02/21/2024]
Abstract
The human bone marrow (BM) niche sustains hematopoiesis throughout life. We present a method for generating complex BM-like organoids (BMOs) from human induced pluripotent stem cells (iPSCs). BMOs consist of key cell types that self-organize into spatially defined three-dimensional structures mimicking cellular, structural and molecular characteristics of the hematopoietic microenvironment. Functional properties of BMOs include the presence of an in vivo-like vascular network, the presence of multipotent mesenchymal stem/progenitor cells, the support of neutrophil differentiation and responsiveness to inflammatory stimuli. Single-cell RNA sequencing revealed a heterocellular composition including the presence of a hematopoietic stem/progenitor (HSPC) cluster expressing genes of fetal HSCs. BMO-derived HSPCs also exhibited lymphoid potential and a subset demonstrated transient engraftment potential upon xenotransplantation in mice. We show that the BMOs could enable the modeling of hematopoietic developmental aspects and inborn errors of hematopoiesis, as shown for human VPS45 deficiency. Thus, iPSC-derived BMOs serve as a physiologically relevant in vitro model of the human BM microenvironment to study hematopoietic development and BM diseases.
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Affiliation(s)
- Stephanie Frenz-Wiessner
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Savannah D Fairley
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
- Institute of Cardiovascular Prevention (IPEK), Ludwig-Maximilians-University Munich, Munich, Germany
| | - Maximilian Buser
- Institute of AI for Health, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Isabel Goek
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Kirill Salewskij
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Gustav Jonsson
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - David Illig
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Benedicta Zu Putlitz
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Daniel Petersheim
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Yue Li
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Pin-Hsuan Chen
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Martina Kalauz
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Raffaele Conca
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Michael Sterr
- Institute of Diabetes and Regeneration Research, Helmholtz Diabetes Center, Helmholtz Center Munich, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Technical University of Munich, Munich, Germany
| | - Johanna Geuder
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-University Munich, Martinsried, Germany
| | - Yoko Mizoguchi
- Department of Pediatrics, Graduate School of Biomedical Sciences, Hiroshima University, Hiroshima, Japan
| | - Remco T A Megens
- Institute of Cardiovascular Prevention (IPEK), Ludwig-Maximilians-University Munich, Munich, Germany
- Department of Biomedical Engineering (BME), Cardiovascular Research Institute Maastricht (CARIM), Maastricht University Medical Centre, Maastricht, The Netherlands
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Monika I Linder
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Daniel Kotlarz
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Martina Rudelius
- Institute of Pathology, Faculty of Medicine, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Josef M Penninger
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
- Helmholtz Centre for Infection Research, Braunschweig, Germany
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Carsten Marr
- Institute of AI for Health, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Christoph Klein
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany.
- Gene Center, Ludwig-Maximilians-University Munich, Munich, Germany.
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2
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Jocher J, Edenhofer FC, Müller S, Janssen P, Briem E, Geuder J, Enard W. Generation and characterization of two Vervet monkey induced pluripotent stem cell lines derived from fibroblasts. Stem Cell Res 2024; 75:103315. [PMID: 38277709 DOI: 10.1016/j.scr.2024.103315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/21/2023] [Accepted: 01/16/2024] [Indexed: 01/28/2024] Open
Abstract
Cross-species comparisons using pluripotent stem cells from primates are crucial to better understand human biology, disease, and evolution. The Vervet monkey (Chlorocebus aethiops sabaeus) serves as an important primate model for such studies, and therefore we reprogrammed skin fibroblasts derived from a male and a female individual, resulting in two induced pluripotent stem cell lines (iPSCs). These iPSCs display the characteristic ESC-like colony morphology, express key pluripotency markers, and possess the ability to differentiate into cells representing all three germ layers. Importantly, both generated cell lines can be maintained in feeder-free culture conditions using commercially available medium.
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Affiliation(s)
- Jessica Jocher
- Anthropology & Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhaderner Straße 2, 82152 Martinsried, Germany
| | - Fiona C Edenhofer
- Anthropology & Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhaderner Straße 2, 82152 Martinsried, Germany
| | - Stefan Müller
- Institute of Human Genetics, Munich University Hospital, Ludwig-Maximilians-Universität München, 80336 Munich, Germany
| | - Philipp Janssen
- Anthropology & Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhaderner Straße 2, 82152 Martinsried, Germany
| | - Eva Briem
- Anthropology & Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhaderner Straße 2, 82152 Martinsried, Germany
| | - Johanna Geuder
- Anthropology & Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhaderner Straße 2, 82152 Martinsried, Germany
| | - Wolfgang Enard
- Anthropology & Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhaderner Straße 2, 82152 Martinsried, Germany.
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3
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Jocher J, Edenhofer FC, Müller S, Janssen P, Briem E, Geuder J, Enard W. Generation and characterization of two fibroblast-derived Baboon induced pluripotent stem cell lines. Stem Cell Res 2024; 75:103316. [PMID: 38246118 DOI: 10.1016/j.scr.2024.103316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/21/2023] [Accepted: 01/16/2024] [Indexed: 01/23/2024] Open
Abstract
Cross-species comparisons studying primate pluripotent stem cells and their derivatives are crucial to better understand the molecular and cellular mechanisms behind human disease and development. Within this context, Baboons (Papio anubis) have emerged as a prominent primate model for such investigations. Herein, we reprogrammed skin fibroblasts of one male individual and generated two induced pluripotent stem cell (iPSC) lines, which exhibit the characteristic ESC-like morphology, demonstrated robust expression of key pluripotency factors and displayed multilineage differentiation potential. Notably, both iPSC lines can be cultured under feeder-free conditions in commercially available medium, enhancing their value for cross-species comparisons.
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Affiliation(s)
- Jessica Jocher
- Anthropology & Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhaderner Straße 2, 82152 Martinsried, Germany
| | - Fiona C Edenhofer
- Anthropology & Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhaderner Straße 2, 82152 Martinsried, Germany
| | - Stefan Müller
- Institute of Human Genetics, Munich University Hospital, Ludwig-Maximilians-Universität München, 80336 Munich, Germany
| | - Philipp Janssen
- Anthropology & Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhaderner Straße 2, 82152 Martinsried, Germany
| | - Eva Briem
- Anthropology & Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhaderner Straße 2, 82152 Martinsried, Germany
| | - Johanna Geuder
- Anthropology & Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhaderner Straße 2, 82152 Martinsried, Germany
| | - Wolfgang Enard
- Anthropology & Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhaderner Straße 2, 82152 Martinsried, Germany.
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4
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Jocher J, Edenhofer FC, Janssen P, Müller S, Lopez-Parra DC, Geuder J, Enard W. Generation and characterization of three fibroblast-derived Rhesus Macaque induced pluripotent stem cell lines. Stem Cell Res 2024; 74:103277. [PMID: 38103336 DOI: 10.1016/j.scr.2023.103277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/30/2023] [Accepted: 12/06/2023] [Indexed: 12/19/2023] Open
Abstract
Cross-species comparisons using pluripotent stem cells from primates are crucial to better understand human biology, disease, and evolution. An important primate model is the Rhesus macaque (Macaca mulatta), and we reprogrammed skin fibroblasts from a male individual to generate three induced pluripotent stem cell (iPSC) lines. These cells exhibit the typical ESC-like colony morphology, express common pluripotency markers, and can differentiate into cells of the three germ layers. All generated iPSC lines can be cultured under feeder-free conditions in commercially available medium and are therefore valuable resources for cross-species comparisons.
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Affiliation(s)
- Jessica Jocher
- Anthropology & Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhaderner Straße 2, 82152 Martinsried, Germany
| | - Fiona C Edenhofer
- Anthropology & Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhaderner Straße 2, 82152 Martinsried, Germany
| | - Philipp Janssen
- Anthropology & Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhaderner Straße 2, 82152 Martinsried, Germany
| | - Stefan Müller
- Institute of Human Genomics, Munich University Hospital, Ludwig-Maximilians-Universität München, 80336 Munich, Germany
| | - Dana C Lopez-Parra
- Anthropology & Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhaderner Straße 2, 82152 Martinsried, Germany
| | - Johanna Geuder
- Anthropology & Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhaderner Straße 2, 82152 Martinsried, Germany
| | - Wolfgang Enard
- Anthropology & Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhaderner Straße 2, 82152 Martinsried, Germany
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5
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Buschhorn L, Odoni DI, Geuder J, Odinius TO, Wagner CV, Jilg S, Höckendorf U, Wahida A, Schlesner M, Reiter A, Jawhar M, Jost PJ. Transcriptomic profiling does not refine mastocytosis diagnosis. Haematologica 2023; 108:3125-3130. [PMID: 37165843 PMCID: PMC10620558 DOI: 10.3324/haematol.2022.282617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 05/04/2023] [Indexed: 05/12/2023] Open
Affiliation(s)
- Lars Buschhorn
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany; Division of Gynecological Oncology, National Center for Tumor Diseases (NCT), Heidelberg, Germany; Department of Internal Medicine III, School of Medicine, Technical University of Munich, Munich
| | - Dorett I Odoni
- Bioinformatics and Omics Data Analytics, German Cancer Research Center, Heidelberg, Germany; Biomedical Informatics, Data Mining and Data Analytics, Augsburg University, Augsburg
| | - Johanna Geuder
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians University, Martinsried
| | - Timo O Odinius
- Department of Internal Medicine III, School of Medicine, Technical University of Munich, Munich
| | - Celina V Wagner
- Department of Internal Medicine III, School of Medicine, Technical University of Munich, Munich
| | - Stefanie Jilg
- Department of Internal Medicine III, School of Medicine, Technical University of Munich, Munich, Germany; Onkologie Erding, Erding
| | - Ulrike Höckendorf
- Department of Internal Medicine III, School of Medicine, Technical University of Munich, Munich
| | - Adam Wahida
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany; Division of Gynecological Oncology, National Center for Tumor Diseases (NCT), Heidelberg, Germany; Department of Internal Medicine III, School of Medicine, Technical University of Munich, Munich
| | - Matthias Schlesner
- Bioinformatics and Omics Data Analytics, German Cancer Research Center, Heidelberg, Germany; Biomedical Informatics, Data Mining and Data Analytics, Augsburg University, Augsburg
| | - Andreas Reiter
- Medical Department III for Hematology and Oncology, University Clinic Mannheim, Mannheim
| | - Mohamad Jawhar
- Medical Department III for Hematology and Oncology, University Clinic Mannheim, Mannheim
| | - Philipp J Jost
- Department of Internal Medicine III, School of Medicine, Technical University of Munich, Munich, Germany; Division of Clinical Oncology, Department of Internal Medicine, Medical University of Graz, Graz.
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6
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Radmer J, Geuder J, Edenhofer FC, Enard W, Ohnuki M. Generation and Maintenance of Primate Induced Pluripotent Stem Cells Derived from Urine. J Vis Exp 2023. [PMID: 37590551 DOI: 10.3791/64922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2023] Open
Abstract
Cross-species approaches studying primate pluripotent stem cells and their derivatives are crucial to better understand the molecular and cellular mechanisms of disease, development, and evolution. To make primate induced pluripotent stem cells (iPSCs) more accessible, this paper presents a non-invasive method to generate human and non-human primate iPSCs from urine-derived cells, and their maintenance using a feeder-free culturing method. The urine can be sampled from a non-sterile environment (e.g., the cage of the animal) and treated with a broad-spectrum antibiotic cocktail during primary cell culture to reduce contamination efficiently. After propagation of the urine-derived cells, iPSCs are generated by a modified transduction method of a commercially available Sendai virus vector system. First iPSC colonies may already be visible after 5 days, and can be picked after 10 days at the earliest. Routine clump passaging with enzyme-free dissociation buffer supports pluripotency of the generated iPSCs for more than 50 passages.
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Affiliation(s)
- Jessica Radmer
- Faculty of Biology, Ludwig Maximilian University of Munich
| | - Johanna Geuder
- Faculty of Biology, Ludwig Maximilian University of Munich
| | | | - Wolfgang Enard
- Faculty of Biology, Ludwig Maximilian University of Munich
| | - Mari Ohnuki
- Faculty of Biology, Ludwig Maximilian University of Munich; Institute for the Advanced Study of Human Biology, Kyoto University; Hakubi Center, Kyoto University;
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7
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Kliesmete Z, Wange LE, Vieth B, Esgleas M, Radmer J, Hülsmann M, Geuder J, Richter D, Ohnuki M, Götz M, Hellmann I, Enard W. Regulatory and coding sequences of TRNP1 co-evolve with brain size and cortical folding in mammals. eLife 2023; 12:83593. [PMID: 36947129 PMCID: PMC10032658 DOI: 10.7554/elife.83593] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 03/01/2023] [Indexed: 03/23/2023] Open
Abstract
Brain size and cortical folding have increased and decreased recurrently during mammalian evolution. Identifying genetic elements whose sequence or functional properties co-evolve with these traits can provide unique information on evolutionary and developmental mechanisms. A good candidate for such a comparative approach is TRNP1, as it controls proliferation of neural progenitors in mice and ferrets. Here, we investigate the contribution of both regulatory and coding sequences of TRNP1 to brain size and cortical folding in over 30 mammals. We find that the rate of TRNP1 protein evolution (ω) significantly correlates with brain size, slightly less with cortical folding and much less with body size. This brain correlation is stronger than for >95% of random control proteins. This co-evolution is likely affecting TRNP1 activity, as we find that TRNP1 from species with larger brains and more cortical folding induce higher proliferation rates in neural stem cells. Furthermore, we compare the activity of putative cis-regulatory elements (CREs) of TRNP1 in a massively parallel reporter assay and identify one CRE that likely co-evolves with cortical folding in Old World monkeys and apes. Our analyses indicate that coding and regulatory changes that increased TRNP1 activity were positively selected either as a cause or a consequence of increases in brain size and cortical folding. They also provide an example how phylogenetic approaches can inform biological mechanisms, especially when combined with molecular phenotypes across several species.
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Affiliation(s)
- Zane Kliesmete
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität, Munich, Germany
| | - Lucas Esteban Wange
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität, Munich, Germany
| | - Beate Vieth
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität, Munich, Germany
| | - Miriam Esgleas
- Physiological Genomics, BioMedical Center - BMC, Ludwig-Maximilians-Universität, Munich, Germany
- Institute for Stem Cell Research, Helmholtz Zentrum München, Germany Research Center for Environmental Health, Munich, Germany
| | - Jessica Radmer
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität, Munich, Germany
| | - Matthias Hülsmann
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität, Munich, Germany
- Department of Environmental Microbiology, Eawag, Dübendorf, Switzerland
- Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
| | - Johanna Geuder
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität, Munich, Germany
| | - Daniel Richter
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität, Munich, Germany
| | - Mari Ohnuki
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität, Munich, Germany
| | - Magdelena Götz
- Physiological Genomics, BioMedical Center - BMC, Ludwig-Maximilians-Universität, Munich, Germany
- Institute for Stem Cell Research, Helmholtz Zentrum München, Germany Research Center for Environmental Health, Munich, Germany
- SYNERGY, Excellence Cluster of Systems Neurology, BioMedical Center (BMC), Ludwig-Maximilians-Universität München, Munich, Germany
| | - Ines Hellmann
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität, Munich, Germany
| | - Wolfgang Enard
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität, Munich, 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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Oostendorp R, Enard W, Götze K, Geiger H, Geuder J, Hecker J, Hettler F, Landspersky T, Marquez SR, Sacma M, Schreck C, verbeek M. 3156 – BONE MARROW TRANSPLANTATION COMPROMISES THE REGENERATIVE CAPACITY OF THE NICHE. Exp Hematol 2022. [DOI: 10.1016/j.exphem.2022.07.212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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10
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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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Felig DM, Geuder J. Gastric outlet obstruction due to a large duodenal tubulovillous adenoma. Gastrointest Endosc 2001; 53:340-1. [PMID: 11231397 DOI: 10.1067/mge.2001.112044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Affiliation(s)
- D M Felig
- Hackensack University Medical Center, Hackensack, New Jersey, USA
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Abstract
Carotidynia is a syndrome of pain in the neck and face accompanied by local tenderness of the carotid artery. The symptoms are often misdiagnosed due to similarities with more common syndromes involving the cervical region. Spontaneous remission is common; more severe cases generally respond to anti-inflammatory medication or prophylactic drugs used for migraine. A case of severe carotidynia, unassociated with migraine is reported. Failure to respond to medical therapy led to surgical denervation of the carotid bulb. The immediate relief of symptoms following surgery confirms earlier observations regarding the mechanism of the symptoms. In severe cases of carotidynia, surgical denervation of the carotid artery may be indicated if medical therapy has failed.
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Geuder J, Rush BF, Theodore G. Functional aspects of ileal reservoirs. Curr Surg 1984; 41:467-9. [PMID: 6518814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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