PXD025602

PXD025602 is an original dataset announced via ProteomeXchange.

Title	In vitro genome editing rescue parkinsonism phenotypes in induced pluripotent stem cell-derived dopaminergic neurons carrying LRRK2 p.G2019S mutation
Description	The gain-of-function mutation of c.G6055A (p.G2019S) in Leucine-rich repeat kinase 2 (LRRK2) gene is the most prevalent genetic cause of Parkinson’s disease (PD). Although clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9-based genome editing has been used to generate isogenic control lines, there are risks of creating indels and genomic instability together with a lower efficiency in non-dividing cells. The recent advance of adenine base editors (ABEs) could convert targeted A•T base pairs to G•C base pairs without double-strand DNA breaks or donor DNA templates and function in post-mitotic cells. Here, we demonstrate a complete correction of an induced pluripotent stem cell (iPSC) line derived from a PD patient having LRRK2 p.G2019S mutation using variable genome editing methods, including CRISPR/Cas9-based homology-directed repair (HDR) and ABEs. The corrected isogenic iPSCs derived dopaminergic neurons showed a down-regulated LRRK2 kinase activity, decreased phospho-a-synuclein accumulations, reduced apoptosis and restored neurite shrinkage phenotypes. The mutation correction efficacy, off-target and indels rates between CRISPR/Cas9-HDR and ABE were compared. Among the 47 clones generated by HDR, 3 clones (6.4%) were on-targeted corrected, while ABE showed a much higher correction rate (13 of 53 clones, 24.5%). Whole genome sequencing analysis revealed that there are 27 clones of HDR (57.4%) having deletions but none in clones of ABE, albeit ABE created 14 clones (26.4%) having off-target missense mutations. RNA sequencing and proteomic analysis of the mutant line identified 2220 differentially expressed genes compared with its isogenic control. Enrichment analysis demonstrated an over-representation of PD relevant pathways, including calcium ion dependent exocytosis, synaptic transports well as potential novel targets relevant to PD pathophysiology. These results envision that ABE could directly correct the pathogenic PD mutation in iPSCs for exploring the earliest events in PD pathophysiology and providing dopaminergic neurons for future cell therapies.
HostingRepository	jPOST
AnnounceDate	2022-04-24
AnnouncementXML	Submission_2022-09-18_03:57:40.202.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Miao-Hsia Lin
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	S-carboxamidomethyl-L-cysteine; alpha-amino acetylated residue; L-methionine sulfoxide
Instrument	instrument

Revision	Datetime	Status	ChangeLog Entry
0	2021-04-24 07:10:52	ID requested
1	2022-04-23 08:00:05	announced
⏵ 2	2022-09-18 03:57:40	announced	2022-09-18: Updated FTP location.

Dataset with its publication pending

submitter keyword: LRRK2, Parkinson's disease, label-free quantification

Miao-Hsia Lin
lab head
Miao-Hsia Lin
contact affiliation	Institute of Chemistry, Academia Sinica
dataset submitter

jPOST dataset URI

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.jpostdb.org/JPST001139/