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McLean ZL, Gao D, Correia K, Roy JCL, Shibata S, Farnum IN, Valdepenas-Mellor Z, Kovalenko M, Rapuru M, Morini E, Ruliera J, Gillis T, Lucente D, Kleinstiver BP, Lee JM, MacDonald ME, Wheeler VC, Mouro Pinto R, Gusella JF. Splice modulators target PMS1 to reduce somatic expansion of the Huntington's disease-associated CAG repeat. Nat Commun 2024; 15:3182. [PMID: 38609352 PMCID: PMC11015039 DOI: 10.1038/s41467-024-47485-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 03/30/2024] [Indexed: 04/14/2024] Open
Abstract
Huntington's disease (HD) is a dominant neurological disorder caused by an expanded HTT exon 1 CAG repeat that lengthens huntingtin's polyglutamine tract. Lowering mutant huntingtin has been proposed for treating HD, but genetic modifiers implicate somatic CAG repeat expansion as the driver of onset. We find that branaplam and risdiplam, small molecule splice modulators that lower huntingtin by promoting HTT pseudoexon inclusion, also decrease expansion of an unstable HTT exon 1 CAG repeat in an engineered cell model. Targeted CRISPR-Cas9 editing shows this effect is not due to huntingtin lowering, pointing instead to pseudoexon inclusion in PMS1. Homozygous but not heterozygous inactivation of PMS1 also reduces CAG repeat expansion, supporting PMS1 as a genetic modifier of HD and a potential target for therapeutic intervention. Although splice modulation provides one strategy, genome-wide transcriptomics also emphasize consideration of cell-type specific effects and polymorphic variation at both target and off-target sites.
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Affiliation(s)
- Zachariah L McLean
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Neurology, Harvard Medical School, Boston, MA, 02115, USA
- Medical and Population Genetics Program, the Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA
| | - Dadi Gao
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Neurology, Harvard Medical School, Boston, MA, 02115, USA
- Medical and Population Genetics Program, the Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA
| | - Kevin Correia
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Jennie C L Roy
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Neurology, Harvard Medical School, Boston, MA, 02115, USA
| | - Shota Shibata
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Neurology, Harvard Medical School, Boston, MA, 02115, USA
- Medical and Population Genetics Program, the Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA
| | - Iris N Farnum
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Zoe Valdepenas-Mellor
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Marina Kovalenko
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Manasa Rapuru
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Elisabetta Morini
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Neurology, Harvard Medical School, Boston, MA, 02115, USA
| | - Jayla Ruliera
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Tammy Gillis
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Diane Lucente
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Benjamin P Kleinstiver
- Center for Genomic Medicine and Department of Pathology, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Pathology, Harvard Medical School, Boston, MA, 02115, USA
| | - Jong-Min Lee
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Neurology, Harvard Medical School, Boston, MA, 02115, USA
- Medical and Population Genetics Program, the Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA
| | - Marcy E MacDonald
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Neurology, Harvard Medical School, Boston, MA, 02115, USA
- Medical and Population Genetics Program, the Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA
| | - Vanessa C Wheeler
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Neurology, Harvard Medical School, Boston, MA, 02115, USA
- Medical and Population Genetics Program, the Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA
| | - Ricardo Mouro Pinto
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Neurology, Harvard Medical School, Boston, MA, 02115, USA
- Medical and Population Genetics Program, the Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA
| | - James F Gusella
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA.
- Medical and Population Genetics Program, the Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA.
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA.
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McLean ZL, Gao D, Correia K, Roy JCL, Shibata S, Farnum IN, Valdepenas-Mellor Z, Rapuru M, Morini E, Ruliera J, Gillis T, Lucente D, Kleinstiver BP, Lee JM, MacDonald ME, Wheeler VC, Pinto RM, Gusella JF. PMS1 as a target for splice modulation to prevent somatic CAG repeat expansion in Huntington's disease. bioRxiv 2023:2023.07.25.550489. [PMID: 37547003 PMCID: PMC10402039 DOI: 10.1101/2023.07.25.550489] [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: 08/08/2023]
Abstract
Huntington's disease (HD) is a dominantly inherited neurodegenerative disorder whose motor, cognitive, and behavioral manifestations are caused by an expanded, somatically unstable CAG repeat in the first exon of HTT that lengthens a polyglutamine tract in huntingtin. Genome-wide association studies (GWAS) have revealed DNA repair genes that influence the age-at-onset of HD and implicate somatic CAG repeat expansion as the primary driver of disease timing. To prevent the consequent neuronal damage, small molecule splice modulators (e.g., branaplam) that target HTT to reduce the levels of huntingtin are being investigated as potential HD therapeutics. We found that the effectiveness of the splice modulators can be influenced by genetic variants, both at HTT and other genes where they promote pseudoexon inclusion. Surprisingly, in a novel hTERT-immortalized retinal pigment epithelial cell (RPE1) model for assessing CAG repeat instability, these drugs also reduced the rate of HTT CAG expansion. We determined that the splice modulators also affect the expression of the mismatch repair gene PMS1, a known modifier of HD age-at-onset. Genome editing at specific HTT and PMS1 sequences using CRISPR-Cas9 nuclease confirmed that branaplam suppresses CAG expansion by promoting the inclusion of a pseudoexon in PMS1, making splice modulation of PMS1 a potential strategy for delaying HD onset. Comparison with another splice modulator, risdiplam, suggests that other genes affected by these splice modulators also influence CAG instability and might provide additional therapeutic targets.
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Affiliation(s)
- Zachariah L. McLean
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
- Medical and Population Genetics Program, the Broad Institute of M.I.T. and Harvard, Cambridge, MA 02142, USA
| | - Dadi Gao
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
- Medical and Population Genetics Program, the Broad Institute of M.I.T. and Harvard, Cambridge, MA 02142, USA
| | - Kevin Correia
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jennie C. L. Roy
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
| | - Shota Shibata
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
- Medical and Population Genetics Program, the Broad Institute of M.I.T. and Harvard, Cambridge, MA 02142, USA
| | - Iris N. Farnum
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Zoe Valdepenas-Mellor
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Manasa Rapuru
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Elisabetta Morini
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
| | - Jayla Ruliera
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Tammy Gillis
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Diane Lucente
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Benjamin P. Kleinstiver
- Center for Genomic Medicine and Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Jong-Min Lee
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
- Medical and Population Genetics Program, the Broad Institute of M.I.T. and Harvard, Cambridge, MA 02142, USA
| | - Marcy E. MacDonald
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
- Medical and Population Genetics Program, the Broad Institute of M.I.T. and Harvard, Cambridge, MA 02142, USA
| | - Vanessa C. Wheeler
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
| | - Ricardo Mouro Pinto
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
- Medical and Population Genetics Program, the Broad Institute of M.I.T. and Harvard, Cambridge, MA 02142, USA
| | - James F. Gusella
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Medical and Population Genetics Program, the Broad Institute of M.I.T. and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
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