DOI: 10.5281/zenodo.13735938
title: Data Repository: Human iPSC-derived pericyte-like cells carrying LRRK2 mutation induce a reactive phenotype and alters migration (PD lines differentiated with TGFb3)

description: Data Repository for publication: Human iPSC-derived pericyte-like cells carrying LRRK2 mutation induce a reactive phenotype and alters migration (PD lines differentiated with TGFb3)
description: BACKGROUND: Pericytes play a crucial role in controlling inflammation and vascular functions in the central nervous system, which are disrupted in Parkinson’s disease (PD). Still, there is a lack of studies on the impact of pericytes on neurodegenerative diseases, and their involvement in the pathology of PD is unclear. 

OBJECTIVE: Our objective was to investigate the molecular and functional differences between healthy pericytes and pericytes with the LRRK2 G2019S mutation, which is one of the most common mutations associated with PD. 

METHODS: Our study employed pericyte-like cells obtained from induced pluripotent stem cells produced from PD patients with the LRRK2 G2019S mutation as well as from healthy individuals. We examined the gene expression profiles of the cells and analyzed how the alterations reflect on their functionality. 

RESULTS: We have shown differences in the expression of genes related to inflammation and angiogenesis. Furthermore, we observe modified migration speed in PD pericyte-like cells as well as enhanced secretion of inflammatory mediators, such as soluble VCAM-1 and MCP-1, in these pericyte-like cells following exposure to proinflammatory stimuli. 

CONCLUSIONS: In summary, our findings support the notion that pericytes play a role in the inflammatory and vascular changes observed in PD. Further investigation of pericytes could provide valuable insight into understanding the pathogenesis of PD. 
description: RNA sequencing of human induced pluripotent stem cell (hiPSC) derived pericyte-like cells.

raw data files (.fastq.gz), processed data files (.txt), MD5 files for raw data (.md5)

PD line 1:  (SP12_R1_001.fastq.gz, SP12_R2_001.fastq.gz, SP12_R1_001.fastq.gz.md5, SP12_R2_001.fastq.gz.md5, SP12.counts.txt)

PD line 2:  (SP11_R1_001.fastq.gz, SP11_R2_001.fastq.gz, SP11_R1_001.fastq.gz.md5, SP11_R2_001.fastq.gz.md5, SP11.counts.txt)

PD line 3:  (SP10_R1_001.fastq.gz, SP10_R2_001.fastq.gz, SP10_R1_001.fastq.gz.md5, SP10_R2_001.fastq.gz.md5, SP10.counts.txt)
description: Line information:

Parkinson's disease lines with LRRK2 G2019S mutation

PD 1: Reference: Holmqvist et al. 2016

PD 2: EBiSC, STBCi007-A

PD 3: EBiSC, STBCi004-A

Cell culturing:

hiPSCs were cultured in matrigel (Corning) coated dishes in E8 (Gibco) media. The protocol used in differentiation of pericyte-like cells is based on the protocol from Faal et al. (2019) 

RNA sequencing:

For RNA sequencing, the RNA was collected directly after cultures. The cells were lysed on ice (Buffer RLT with β-mercaptoethanol 10 µl/ml) and the RNA was extracted using RNeasy Mini Kit (Qiagen) with DNase I digestion using RNase-Free DNase Set (Qiagen). The RNA concentration was measured with DS-11 FX Spectrophotometer/Fluorometer (DeNovix), and 2 µg of the RNA-samples were sent to Azenta Life Sciences for RNA sequencing. Library preparation included the following steps: ribosomal RNA depletion, RNA fragmentation and random priming, cDNA synthesis, end repair, 5’ phosphorylation and dA tailing, and finally adaptor ligation and PCR enrichment.  The sequencing was made with an Illumina NovaSeq 6000 instrument, PE 2x150. The reads were trimmed with trimmomatic v.0.36 to remove possible adapter sequences and poor-quality reads and trimmed reads were mapped to the Homo sapiens GRCh38 reference genome using STAR aligner v.2.5.2b. Unique gene hit counts were calculated with featureCounts from the Subread package v.1.5.2.