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 : THE PREPRINT SERVER FOR BIOLOGY 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] [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
|
Delle Vedove A, Natarajan J, Zanni G, Eckenweiler M, Muiños-Bühl A, Storbeck M, Guillén Boixet J, Barresi S, Pizzi S, Hölker I, Körber F, Franzmann TM, Bertini ES, Kirschner J, Alberti S, Tartaglia M, Wirth B. CAPRIN1 P512L causes aberrant protein aggregation and associates with early-onset ataxia. Cell Mol Life Sci 2022; 79:526. [PMID: 36136249 PMCID: PMC9499908 DOI: 10.1007/s00018-022-04544-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/15/2022] [Accepted: 08/31/2022] [Indexed: 12/26/2022]
Abstract
CAPRIN1 is a ubiquitously expressed protein, abundant in the brain, where it regulates the transport and translation of mRNAs of genes involved in synaptic plasticity. Here we describe two unrelated children, who developed early-onset ataxia, dysarthria, cognitive decline and muscle weakness. Trio exome sequencing unraveled the identical de novo c.1535C > T (p.Pro512Leu) missense variant in CAPRIN1, affecting a highly conserved residue. In silico analyses predict an increased aggregation propensity of the mutated protein. Indeed, overexpressed CAPRIN1P512L forms insoluble ubiquitinated aggregates, sequestrating proteins associated with neurodegenerative disorders (ATXN2, GEMIN5, SNRNP200 and SNCA). Moreover, the CAPRIN1P512L mutation in isogenic iPSC-derived cortical neurons causes reduced neuronal activity and altered stress granule dynamics. Furthermore, nano-differential scanning fluorimetry reveals that CAPRIN1P512L aggregation is strongly enhanced by RNA in vitro. These findings associate the gain-of-function Pro512Leu mutation to early-onset ataxia and neurodegeneration, unveiling a critical residue of CAPRIN1 and a key role of RNA–protein interactions.
Collapse
Affiliation(s)
- Andrea Delle Vedove
- Institute of Human Genetics, University Hospital of Cologne, University Cologne, 50931, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, 50931, Cologne, Germany.,Institute for Genetics, University of Cologne, 50674, Cologne, Germany
| | - Janani Natarajan
- Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, 01307, Dresden, Germany
| | - Ginevra Zanni
- Genetics and Rare Diseases Research Division and Unit of Muscular and Neurodegenerative Disorders - the Department of Neurosciences of the Bambino Gesù Childrens' Hospital, IRCCS, Rome, Italy
| | - Matthias Eckenweiler
- Department of Neuropediatrics and Muscle Disorders, Faculty of Medicine, Medical Center-University of Freiburg, University of Freiburg, 79106, Freiburg, Germany
| | - Anixa Muiños-Bühl
- Institute of Human Genetics, University Hospital of Cologne, University Cologne, 50931, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, 50931, Cologne, Germany.,Institute for Genetics, University of Cologne, 50674, Cologne, Germany
| | - Markus Storbeck
- Institute of Human Genetics, University Hospital of Cologne, University Cologne, 50931, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, 50931, Cologne, Germany.,Institute for Genetics, University of Cologne, 50674, Cologne, Germany
| | - Jordina Guillén Boixet
- Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, 01307, Dresden, Germany
| | - Sabina Barresi
- Genetics and Rare Diseases Research Division and Unit of Muscular and Neurodegenerative Disorders - the Department of Neurosciences of the Bambino Gesù Childrens' Hospital, IRCCS, Rome, Italy
| | - Simone Pizzi
- Genetics and Rare Diseases Research Division and Unit of Muscular and Neurodegenerative Disorders - the Department of Neurosciences of the Bambino Gesù Childrens' Hospital, IRCCS, Rome, Italy
| | - Irmgard Hölker
- Institute of Human Genetics, University Hospital of Cologne, University Cologne, 50931, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, 50931, Cologne, Germany.,Institute for Genetics, University of Cologne, 50674, Cologne, Germany
| | - Friederike Körber
- Institute of Diagnostic and Interventional Radiology, 50937, Cologne, Germany
| | - Titus M Franzmann
- Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, 01307, Dresden, Germany
| | - Enrico S Bertini
- Genetics and Rare Diseases Research Division and Unit of Muscular and Neurodegenerative Disorders - the Department of Neurosciences of the Bambino Gesù Childrens' Hospital, IRCCS, Rome, Italy
| | - Janbernd Kirschner
- Department of Neuropediatrics and Muscle Disorders, Faculty of Medicine, Medical Center-University of Freiburg, University of Freiburg, 79106, Freiburg, Germany
| | - Simon Alberti
- Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, 01307, Dresden, Germany
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division and Unit of Muscular and Neurodegenerative Disorders - the Department of Neurosciences of the Bambino Gesù Childrens' Hospital, IRCCS, Rome, Italy
| | - Brunhilde Wirth
- Institute of Human Genetics, University Hospital of Cologne, University Cologne, 50931, Cologne, Germany. .,Center for Molecular Medicine Cologne, University of Cologne, 50931, Cologne, Germany. .,Institute for Genetics, University of Cologne, 50674, Cologne, Germany. .,Center for Rare Diseases, University Hospital of Cologne, 50931, Cologne, 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. MOLECULAR THERAPY. 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] [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
|
Patient-Specific iPSCs-Based Models of Neurodegenerative Diseases: Focus on Aberrant Calcium Signaling. Int J Mol Sci 2022; 23:ijms23020624. [PMID: 35054808 PMCID: PMC8776084 DOI: 10.3390/ijms23020624] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 12/30/2021] [Accepted: 12/31/2021] [Indexed: 02/04/2023] Open
Abstract
The development of cell reprogramming technologies became a breakthrough in the creation of new models of human diseases, including neurodegenerative pathologies. The iPSCs-based models allow for the studying of both hereditary and sporadic cases of pathologies and produce deep insight into the molecular mechanisms underlying neurodegeneration. The use of the cells most vulnerable to a particular pathology makes it possible to identify specific pathological mechanisms and greatly facilitates the task of selecting the most effective drugs. To date, a large number of studies on patient-specific models of neurodegenerative diseases has been accumulated. In this review, we focused on the alterations of such a ubiquitous and important intracellular regulatory pathway as calcium signaling. Here, we reviewed and analyzed the data obtained from iPSCs-based models of different neurodegenerative disorders that demonstrated aberrant calcium signaling.
Collapse
|
5
|
Dias C, Nita E, Faktor J, Tynan AC, Hernychova L, Vojtesek B, Nylandsted J, Hupp TR, Kunath T, Ball KL. CHIP-dependent regulation of the actin cytoskeleton is linked to neuronal cell membrane integrity. iScience 2021; 24:102878. [PMID: 34401662 PMCID: PMC8350547 DOI: 10.1016/j.isci.2021.102878] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 04/13/2021] [Accepted: 07/15/2021] [Indexed: 12/12/2022] Open
Abstract
CHIP is an E3-ubiquitin ligase that contributes to healthy aging and has been characterized as neuroprotective. To elucidate dominant CHIP-dependent changes in protein steady-state levels in a patient-derived human neuronal model, CHIP function was ablated using gene-editing and an unbiased proteomic analysis conducted to compare knock-out and wild-type isogenic induced pluripotent stem cell (iPSC)-derived cortical neurons. Rather than a broad effect on protein homeostasis, loss of CHIP function impacted on a focused cohort of proteins from actin cytoskeleton signaling and membrane integrity networks. In support of the proteomics, CHIP knockout cells had enhanced sensitivity to induced membrane damage. We conclude that the major readout of CHIP function in cortical neurons derived from iPSC of a patient with elevate α-synuclein, Parkinson's disease and dementia, is the modulation of substrates involved in maintaining cellular "health". Thus, regulation of the actin cytoskeletal and membrane integrity likely contributes to the neuroprotective function(s) of CHIP.
Collapse
Affiliation(s)
- Catarina Dias
- Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
- Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, The University of Edinburgh, Edinburgh EH16 4UU, UK
| | - Erisa Nita
- Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Jakub Faktor
- Research Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic
- University of Gdansk, International Centre for Cancer Vaccine Science, 80-822 Gdansk, Poland
| | - Ailish C. Tynan
- Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Lenka Hernychova
- Research Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic
| | - Borivoj Vojtesek
- Research Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic
| | - Jesper Nylandsted
- Membrane Integrity Group, Danish Cancer Society Research Center, Strandboulevarden 49, 2100, Copenhagen, Denmark
| | - Ted R. Hupp
- Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
- University of Gdansk, International Centre for Cancer Vaccine Science, 80-822 Gdansk, Poland
| | - Tilo Kunath
- Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, The University of Edinburgh, Edinburgh EH16 4UU, UK
| | - Kathryn L. Ball
- Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| |
Collapse
|
6
|
Mengel D, Traschütz A, Reich S, Leyva-Gutiérrez A, Bender F, Hauser S, Haack TB, Synofzik M. A de novo STUB1 variant associated with an early adult-onset multisystemic ataxia phenotype. J Neurol 2021; 268:3845-3851. [PMID: 33811518 PMCID: PMC8463406 DOI: 10.1007/s00415-021-10524-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 03/03/2021] [Accepted: 03/15/2021] [Indexed: 11/28/2022]
Abstract
Background Biallelic STUB1 variants are a well-established cause of autosomal-recessive early-onset multisystemic ataxia (SCAR16). Evidence for STUB1 variants causing autosomal-dominant ataxia (SCA48) so far largely relies on segregation data in larger families. Presenting the first de novo occurrence of a heterozygous STUB1 variant, we here present additional qualitative evidence for STUB1-disease as an autosomal-dominant disorder. Methods Whole exome sequencing on an index patient with sporadic early-onset ataxia, followed by Sanger sequencing in all family members, was used to identify causative variants as well as to rule out alternative genetic hits and intronic STUB1 variants. STUB1 mRNA and protein levels in PBMCs in all family members were analysed using qRT-PCR and Western Blot. Results A previously unreported start-lost loss-of-function variant c.3G>A in the start codon of STUB1 was identified in the index case, occurring de novo and without evidence for a second (potentially missed) variant (e.g., intronic or copy number) in STUB1. The patient showed an early adult-onset multisystemic ataxia complicated by spastic gait disorder, distal myoclonus and cognitive dysfunction, thus closely mirroring the systems affected in autosomal-recessive STUB1-associated disease. In line with the predicted start-lost effect of the variant, functional investigations demonstrated markedly reduced STUB1 protein expression in PBMCs, whereas mRNA levels were intact. Conclusion De novo occurrence of the loss-of-function STUB1 variant in our case with multisystemic ataxia provides a qualitatively additional line of evidence for STUB1-disease as an autosomal-dominant disorder, in which the same neurological systems are affected as in its autosomal-recessive counterpart. Moreover, this finding adds support for loss-of-function as a mechanism underlying autosomal-dominant STUB1-disease, thus mirroring its autosomal-recessive counterpart also in terms of the underlying mutational mechanism.
Collapse
Affiliation(s)
- David Mengel
- Department of Neurodegenerative Diseases, Center for Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.,German Centre for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Andreas Traschütz
- Department of Neurodegenerative Diseases, Center for Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.,German Centre for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Selina Reich
- Department of Neurodegenerative Diseases, Center for Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.,German Centre for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Alejandra Leyva-Gutiérrez
- Department of Neurodegenerative Diseases, Center for Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.,German Centre for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Friedemann Bender
- Department of Neurodegenerative Diseases, Center for Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.,German Centre for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Stefan Hauser
- Department of Neurodegenerative Diseases, Center for Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.,German Centre for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.,Centre for Rare Diseases, University of Tübingen, Tübingen, Germany
| | - Matthis Synofzik
- Department of Neurodegenerative Diseases, Center for Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany. .,German Centre for Neurodegenerative Diseases (DZNE), Tübingen, Germany.
| |
Collapse
|