Data Repository: LRRK2 G2019S mutation affects human iPSC-derived endothelial cells (line H1)

Description

Abstract

The blood-brain barrier (BBB) serves as an interface between the periphery and central nervous system. It limits the movement of molecules and immune cells, regulates the entry of nutrients, and removes waste products from the brain. The dysfunction of the BBB has been identified in Parkinson´s disease (PD) but the role of the BBB and endothelial cells (ECs) has not been well studied. LRRK2 G2019S mutation is the most common PD causing mutation with similar pathophysiology than in sporadic cases. How the mutation affects EC function has not been investigated previously in patient’s cells. In the study, we used iPSC-derived ECs from PD patients with the LRRK2 mutation as well as cells from healthy individuals. We report that PD ECs have higher levels of α-synuclein, altered mitochondrial respiration and response to inflammatory exposure, especially to TNFα. In addition, transcriptomic analysis showed upregulation of fatty acid synthesis related pathways in PD ECs and downregulation of lncRNA MEG3, both of which have been associated with PD. Altogether, PD ECs manifest some of the PD related hallmarks and are likely to contribute to the pathogenesis of PD.

Technical info

RNA sequencing of human induced pluripotent stem cell (hiPSC) derived endothelial cells (ECs).

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

line 1: (TS1_R1_001.fastq.gz, TS1_R2_001.fastq.gz, TS1_R1_001.fastq.gz.md5, TS1_R2_001.fastq.gz.md5, TS1.counts.txt)

line 1 TNFalpha+IL-1beta (TS7_R1_001.fastq.gz, TS7_R2_001.fastq.gz, TS7_R1_001.fastq.gz.md5, TS7_R2_001.fastq.gz.md5, TS7.counts.txt)

line 1 TNFalpha (TS13_R1_001.fastq.gz, TS13_R2_001.fastq.gz, TS13_R1_001.fastq.gz.md5, TS13_R2_001.fastq.gz.md5, TS13.counts.txt)

Methods

Line information

• Genotype: normal
• Reference: TakaraBio

Cell culturing: hiPSCs were cultured in matrigel (Corning) coated dishes in E8 (Gibco) media. EC were differentiated according to previously published protocol (Harding et al. 2017).

Treatments

• Nonexposed (TS1)
• 4 h TNFalpha+IL-1beta exposed (TS7)
• 4 h TNFalpha exposed (TS13)

RNA sequencing: Cells were lysed on ice (Buffer RLT + β-mercaptoethanol 10 µl/ml), and RNA was extracted directly after lysis with the Qiagen RNeasy Mini Kit (Qiagen) with DNase I digestion (Qiagen). 1-4 µg of RNA were sent for library preparation and sequencing (performed by Azenta). Quality was evaluated with FastQC, and sequencing was done with Illumina NovaSeq, PE 2x150. Sequence reads were trimmed by using Trimmomatic v.0.36 to remove possible adaptor sequences and nucleotides of poor quality. Trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.