1
|
Xu J, Hörner M, Nagel M, Korneck M, Noß M, Hauser S, Schöls L, Admard J, Casadei N, Schüle R. Unraveling Axonal Transcriptional Landscapes: Insights from iPSC-Derived Cortical Neurons and Implications for Motor Neuron Degeneration. bioRxiv 2024:2024.03.26.586780. [PMID: 38585749 PMCID: PMC10996649 DOI: 10.1101/2024.03.26.586780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Neuronal function and pathology are deeply influenced by the distinct molecular profiles of the axon and soma. Traditional studies have often overlooked these differences due to the technical challenges of compartment specific analysis. In this study, we employ a robust RNA-sequencing (RNA-seq) approach, using microfluidic devices, to generate high-quality axonal transcriptomes from iPSC-derived cortical neurons (CNs). We achieve high specificity of axonal fractions, ensuring sample purity without contamination. Comparative analysis revealed a unique and specific transcriptional landscape in axonal compartments, characterized by diverse transcript types, including protein-coding mRNAs, ribosomal proteins (RPs), mitochondrial-encoded RNAs, and long non-coding RNAs (lncRNAs). Previous works have reported the existence of transcription factors (TFs) in the axon. Here, we detect a subset of previously unreported TFs specific to the axon and indicative of their active participation in transcriptional regulation. To investigate transcripts and pathways essential for central motor neuron (MN) degeneration and maintenance we analyzed KIF1C-knockout (KO) CNs, modeling hereditary spastic paraplegia (HSP), a disorder associated with prominent length-dependent degeneration of central MN axons. We found that several key factors crucial for survival and health were absent in KIF1C-KO axons, highlighting a possible role of these also in other neurodegenerative diseases. Taken together, this study underscores the utility of microfluidic devices in studying compartment-specific transcriptomics in human neuronal models and reveals complex molecular dynamics of axonal biology. The impact of KIF1C on the axonal transcriptome not only deepens our understanding of MN diseases but also presents a promising avenue for exploration of compartment specific disease mechanisms.
Collapse
|
2
|
Schmitz AS, Korneck M, Raju J, Lamsfus-Calle A, Daniel-Moreno A, Antony JS, Mezger M, Schöls L, Hauser S, Hayer SN. Generation of a heterozygous and a homozygous CSF1R knockout line from iPSC using CRISPR/Cas9. Stem Cell Res 2023; 69:103066. [PMID: 36947995 DOI: 10.1016/j.scr.2023.103066] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 03/05/2023] [Accepted: 03/08/2023] [Indexed: 03/13/2023] Open
Abstract
Mutations in Colony-stimulating factor 1 receptor (CSF1R) lead to CSF1R-related leukoencephalopathy, also known as Adult-onset leukoencephalopathy with axonal spheroids and pigmented glia (ALSP), a rapidly progressing neurodegenerative disease with severe cognitive and motor impairment. In this study, a homozygous and a heterozygous CSF1R knockout induced pluripotent stem cell (iPSC) line were generated by CRISPR/Cas9-based gene editing. These in vitro models will provide a helpful tool for investigating the still largely unknown pathophysiology of CSF1R-related leukoencephalopathy.
Collapse
Affiliation(s)
- Anne S Schmitz
- Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany; German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Milena Korneck
- Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany; German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany; Department of Neurology, University Hospital Tübingen, Tübingen, Germany
| | - Janani Raju
- Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany; German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Andrés Lamsfus-Calle
- University Children's Hospital, Department of Pediatrics I, Hematology and Oncology, University of Tübingen, Germany
| | - Alberto Daniel-Moreno
- University Children's Hospital, Department of Pediatrics I, Hematology and Oncology, University of Tübingen, Germany
| | - Justin S Antony
- University Children's Hospital, Department of Pediatrics I, Hematology and Oncology, University of Tübingen, Germany
| | - Markus Mezger
- University Children's Hospital, Department of Pediatrics I, Hematology and Oncology, University of Tübingen, Germany
| | - Ludger Schöls
- Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany; German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany; Department of Neurology, University Hospital Tübingen, Tübingen, Germany
| | - Stefan Hauser
- Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany; German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Stefanie N Hayer
- Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany; German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany; Department of Neurology, University Hospital Tübingen, Tübingen, Germany.
| |
Collapse
|
3
|
Hauser S, Helm J, Kraft M, Korneck M, Hübener-Schmid J, Schöls L. Allele-specific targeting of mutant ataxin-3 by antisense oligonucleotides in SCA3-iPSC-derived neurons. Mol Ther Nucleic Acids 2022; 27:99-108. [PMID: 34938609 PMCID: PMC8649108 DOI: 10.1016/j.omtn.2021.11.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 11/16/2021] [Indexed: 12/01/2022]
Abstract
Spinocerebellar ataxia type 3 (SCA3) is caused by an expanded polyglutamine stretch in ataxin-3. While wild-type ataxin-3 has important functions, e.g., as a deubiquitinase, downregulation of mutant ataxin-3 is likely to slow down the course of this fatal disease. We established a screening platform with human neurons of patients and controls derived from induced pluripotent stem cells to test antisense oligonucleotides (ASOs) for their effects on ataxin-3 expression. We identified an ASO that suppressed mutant and wild-type ataxin-3 levels by >90% after a singular treatment. Next, we screened pairs of ASOs designed to selectively target the mutant or the wild-type allele by taking advantage of a SNP (c.987G > C) in ATXN3 that is present in most SCA3 patients. We found ASOmut4 to reduce levels of mutant ataxin-3 by 80% after 10 days while leaving expression of wild-type ataxin-3 largely unaffected. In a long-term study we proved this effect to last for about 4 weeks after a single treatment without signs of neurotoxicity. This study provides proof of principle that allele-specific lowering of poly(Q)-expanded ataxin-3 by selective ASOs is feasible and long lasting, with sparing of wild-type ataxin-3 expression in a human cell culture model that is genetically identical to SCA3 patients.
Collapse
Affiliation(s)
- Stefan Hauser
- German Center for Neurodegenerative Diseases (DZNE), 72076 Tübingen, Germany.,Hertie Institute for Clinical Brain Research, University of Tübingen, 72076 Tübingen, Germany
| | - Jacob Helm
- German Center for Neurodegenerative Diseases (DZNE), 72076 Tübingen, Germany.,Hertie Institute for Clinical Brain Research, University of Tübingen, 72076 Tübingen, Germany.,Graduate School of Cellular and Molecular Neuroscience, University of Tübingen, 72076 Tübingen, Germany
| | - Melanie Kraft
- German Center for Neurodegenerative Diseases (DZNE), 72076 Tübingen, Germany.,Hertie Institute for Clinical Brain Research, University of Tübingen, 72076 Tübingen, Germany
| | - Milena Korneck
- German Center for Neurodegenerative Diseases (DZNE), 72076 Tübingen, Germany.,Hertie Institute for Clinical Brain Research, University of Tübingen, 72076 Tübingen, Germany.,Graduate School of Cellular and Molecular Neuroscience, University of Tübingen, 72076 Tübingen, Germany
| | - Jeannette Hübener-Schmid
- Institute of Medical Genetics and Applied Genomics and Center of Rare Diseases, University of Tübingen, 72076 Tübingen, Germany
| | - Ludger Schöls
- German Center for Neurodegenerative Diseases (DZNE), 72076 Tübingen, Germany.,Hertie Institute for Clinical Brain Research, University of Tübingen, 72076 Tübingen, Germany
| |
Collapse
|
4
|
Klatt A, Salzmann E, Schneider LJ, Reifschneider A, Korneck M, Hermle P, Bürkle A, Stoll D, Kadereit S. Toxicity of ionizing radiation (IR) in a human induced pluripotent stem cell (hiPSC)-derived 3D early neurodevelopmental model. Arch Toxicol 2019; 93:2879-2893. [DOI: 10.1007/s00204-019-02553-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 08/22/2019] [Indexed: 01/04/2023]
|