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Impact of 100 LRRK2 variants linked to Parkinson's disease on kinase activity and microtubule binding
Open accessPublished version of a preprint
Abstract
Mutations enhancing the kinase activity of leucine-rich repeat kinase-2 (LRRK2) cause Parkinson's disease (PD) and therapies that reduce LRRK2 kinase activity are being tested in clinical trials. Numerous rare variants of unknown clinical significance have been reported, but how the vast majority impact on LRRK2 function is unknown. Here, we investigate 100 LRRK2 variants linked to PD, including previously described pathogenic mutations. We identify 23 LRRK2 variants that robustly stimulate kinase activity, including variants within the N-terminal non-catalytic regions (ARM (E334K, A419V), ANK (R767H), LRR (R1067Q, R1325Q)), as well as variants predicted to destabilize the ROC:CORB interface (ROC (A1442P, V1447M), CORA (R1628P) CORB (S1761R, L1795F)) and COR:COR dimer interface (CORB (R1728H/L)). Most activating variants decrease LRRK2 biomarker site phosphorylation (pSer935/pSer955/pSer973), consistent with the notion that the active kinase conformation blocks their phosphorylation. We conclude that the impact of variants on kinase activity is best evaluated by deploying a cellular assay of LRRK2-dependent Rab10 substrate phosphorylation, compared with a biochemical kinase assay, as only a minority of activating variants (CORB (Y1699C, R1728H/L, S1761R) and kinase (G2019S, I2020T, T2031S)), enhance in vitro kinase activity of immunoprecipitated LRRK2. Twelve variants including several that activate LRRK2 and have been linked to PD, suppress microtubule association in the presence of a Type I kinase inhibitor (ARM (M712V), LRR (R1320S), ROC (A1442P, K1468E, S1508R), CORA (A1589S), CORB (Y1699C, R1728H/L) and WD40 (R2143M, S2350I, G2385R)). Our findings will stimulate work to better understand the mechanisms by which variants impact biology and provide rationale for variant carrier inclusion or exclusion in ongoing and future LRRK2 inhibitor clinical trials.
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![Figure 7. Structural analysis of identified activating LRRK2 variants. (A) Schematic domain overview of LRRK2 with domain boundaries. (B) Cartoon representation of LRRK2 [558–2527] with domains colored as in (A). Domain interfaces harboring activating mutations and kinase domain are indicated by black arrows. (C) Schematic representation of LRRK2 domains as viewed in (B). (D–L) Detailed views of LRRK2 variants in kinase active site (D), domain interfaces (E–L), coloring as in (A) and variants highlighted in magenta. Second LRRK2 molecule of dimer shown in gray (G,L). (G) R1728 side chain modeled in PyMOL shown as semi-transparent stick model. Distance measurements in Å are indicated by dark gray dashed lines. (M) Alphafold model of LRRK2 ARM domain colored by local confidence score (pLDDT) with variant residues shown as stick models. LRRK2 structures used are PDB 7LI4 (B,D,E,H–K), PDB 7LHT (F,G), PDB 6DLO (L), AFDB AF-Q5S007-F1_v1 (M).](/paper-figures/14f19802dba34a4597beff2b0aad367e/impact-of-100-lrrk2-variants-linked-to-parkinson-s-disease-on-kinase-activity-figure-7.jpg)
![Figure 8. Structure-guided mutations in the N-terminus of LRRK2 stimulate LRRK2-mediated Rab10 phosphorylation. (A,B) Cartoon representation of LRRK2 [558–2527] with detailed views of ANK (blue):CT α-helix (magenta) (A) and LRR (green):CORA (yellow) (B) interactions. Distance measurements in Å are indicated by dark gray dashed lines. (Right panel) HEK293 cells were transfected with wildtype, kinase dead (KD = D2017A), and the indicated LRRK2 variants. Each lane represents a different dish of cells. Cells were harvested 24 h post-transfection and subjected to quantitative immunoblot analysis with the indicated antibodies. Each lane represents a different dish of cells. The ratios of phospho-Rab10 Thr73/total Rab10 and phospho-LRRK2 Ser935/total LRRK2 were normalized to wildtype LRRK2 values. Quantified data are presented as mean ± SD and are representative of two independent experiments.](/paper-figures/3b526a5324bb43b6bd3bee57b9c1d34d/impact-of-100-lrrk2-variants-linked-to-parkinson-s-disease-on-kinase-activity-figure-8.jpg)
![Figure 9. Correlation between activating LRRK2 mutations and high REVEL pathogenicity prediction or high evolutionary amino acid conservation scores. (A) Schematic summarizing biochemical data of 100 LRRK2 variants and categorization of variants based on Rab10 phosphorylation, LRRK2 Ser1292 phosphorylation, and biomarker phosphorylation. Variants that enhance in vitro LRRK2 kinase activity or block MLi-2 induced microtubule binding are marked with a superscript highlighted in red. (B) REVEL scores for LRRK2 variants were acquired from Bryant et al. [41] or through the online pathogenicity prediction tool http://database.liulab.science/dbNSFP. REVEL scores were plotted against phospho-Rab10/total Rab10 ratios acquired for each LRRK2 variant that were normalized to wildtype. High activity variants (pRab10Thr73 > 1.5-fold relative to wildtype) are marked in green, low activity variants (similar to kinase-inactive LRRK2) are marked in red, protective variants are marked in yellow, and variants that block MLi-2 induced microtubule binding are represented with an open circle. The REVEL pathogenicity threshold is marked with a dashed line (0.6). Above this line are variants predicted to be ‘likely pathogenic or damaging,' and variants below this line are predicted to be ‘likely benign.' (C) LRRK2 orthologue sequences were acquired from OrthoDB. Orthologue sequences were aligned using MAFFT. The multiple sequence alignment of LRRK2 orthologues was submitted to the ConSurf server to determine evolutionary conservation scores for LRRK2 amino acids (1 is low conservation and 9 is high conservation). Conservation scores were plotted against pRab10Thr73/total Rab10 ratios acquired for each LRRK2 variant that were normalized to wildtype. Activating variants (pRab10Thr73 > 1.5-fold relative to wildtype) are marked in green, low activity variants (similar to kinase-inactive LRRK2) are marked in red, protective variants are marked in yellow, and variants that block MLi-2 induced microtubule binding are represented with an open circle.](/paper-figures/0681168c8f2143d6ab582ca02d6a58b1/impact-of-100-lrrk2-variants-linked-to-parkinson-s-disease-on-kinase-activity-figure-9.jpg)
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Metadata
- Authors
- Kalogeropulou, A. F., Purlyte, E., Tonelli, F., Lange, S. M., Wightman, M., Prescott, A. R., Padmanabhan, S., Sammler, E., & Alessi, D. R.
- Affiliations
- University of Dundee (GB)
- Michael J. Fox Foundation (US)
- Corresponding author
- Alessi, Dario R.
- ORCID
- Venue
- Biochemical Journal
- Publisher
- Portland Press Ltd.
- Published
- 2022-09-06
- Volume
- 479
- Issue
- 17
- Pages
- 1759-1783
- ISSN
- 0264-6021 (ISSN-L)
- 1470-8728
- PMC
- PMC9472821
- OpenAlex
- W4290803974
- Cited by
- 129
- References
- 71
- Citations by year
- 2026: 32 · 2025: 33 · 2024: 35 · 2023: 25 · 2022: 4
- FWCI
- 12.89
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Biochemical Journal (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Discovery Research Portal (University of Dundee) (acceptedVersion, cc-by)
- Funders
- Michael J. Fox Foundation for Parkinson's Research (ASAP‐000463)
- GlaxoSmithKline
- Merck KGaA
- Parkinson's UK (H-1701)
- Medical Research Council (MC_UU_00018/1)
- Topics
- Health Sciences › Medicine › Clinical Neurology › Parkinson's Disease Mechanisms and Treatments
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Kinase Regulation and GTPase Signaling
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Nuclear Receptors and Signaling
- Keywords
- LRRK2, Parkinson's disease, kinase activity, microtubule binding, variants of uncertain significance, kinase activation, Rab10 phosphorylation, LRRK2 inhibitors, protein stability, rare variants
- MeSH terms
- Leucine-Rich Repeat Serine-Threonine Protein Kinase-2, Humans, Microtubules, Mutation, Parkinson Disease, Phosphorylation, Protein Binding
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