Design of sgRNAs
To target the regions R153C and R182C of the human NOTCH3 gene, sgRNAs were designed. The Benchling web tool (https://www.benchling.com/) was used to select the optimal target sites for the CRISPR-Cas9 base editing system. Five sgRNAs were used in subsequent experiments. The sgRNAs were ligated to a backbone plasmid containing the U6 promoter, which was derived from the pSpCas9(BB)-2A-GFP plasmid (Addgene plasmid #48138). The U6-sgRNA construct was amplified by PCR for further use.
Construction of a base-editing vector
The base editor was created by assembling components from multiple plasmids. First, the AncBE4max gene was isolated from the pCMV-AncBE4max-P2A-GFP vector (Addgene plasmid #112100), and the nSpCas9-NG gene was obtained from the pSI-Target-AID-NG plasmid (Addgene plasmid #119861). The AncBE4max gene was fused to the 5'-end of the nSpCas9-NG gene using the In-Fusion® HD cloning kit (TaKaRa). To generate the final construct, the EF1α-AncBE4max-P2A-GFP construct was fused to the U6-sgRNA construct.
Base-editor efficiency test
HEK293 cells were maintain in DMEM containing 5% fetal bovine serum (FBS) medium at 37°C with 5% CO2. Cells were seeded onto 12-well plates at a density of 5 × 105 per well and allowed to attach and grow for 16–24 hours prior to transfection.
For transfection, the following conditions were employed: Lipofectamine 3000 (Thermo Fisher Scientific) was used at 3 µL, and the base editor plasmid containing the sgRNA sequence was added at 1.2 µg. The transfection mixture was prepared by combining and diluting these components with Opti-MEM to a total of 106 µL, following the manufacturer's protocol. After 2–3 days, GFP-expressing cells were sorted using flow cytometry to isolate single cells. Each individual colony derived from the sorted cells was subjected to genomic DNA isolation. The DNA samples were subsequently sequenced at the target location to analyze the genetic alterations.
Off-target analysis
Base editing can generate nonspecific and unintended genetic modifications due to mismatch tolerance. To characterize potential off-target effects in the hiPSCs, we selected top-ranking off-target exonic sites in the human genome using the benching web tool (Extended Data Table 1). We performed targeted sequencing of the top 13 potential off-target sites from control, R153C monoallelic, and R153C biallelic hiPSCs (Extended Data Fig. 1). None of the off-target sequences had mutations, indicating that off-target cleavage was unlikely to have contributed to CADASIL-like pathology.
Targeted NGS/sample processing for deep sequencing
The primers used for PCR are listed in Supplementary Table 3. Genomic DNA of GFP + hiPSCs was amplified by two-step PCR. For the first PCR (adapter PCR), specific staggered primers were used to amplify the integrated fragment. For the second PCR (index PCR), Illumina barcoded sequences were added to distinguish the samples.
Maintenance of feeder-independent hiPSCs
Cell culture plates were coated with a Matrigel matrix (Corning, 354234) dissolved in KO-DMEM (Gibco, 10829018) to a final concentration of 0.3 mg/mL. Mouse embryonic fibroblast (MEF)-free hiPSCs were cultured in E8 medium on the matrix-coated plates. Passaging of hiPSCs was performed using ReLeSR (Stemcell Technology, ST05872) every 4–5 days.
Generation of spin embryoid bodies
MEF-independent hiPSCs were washed twice with DPBS to remove debris and remaining medium. The hiPSCs were dissociated by adding 1 mL of Accutase (Stemcell Technologies, 07922) to each well and incubating for 3–5 minutes at 37°C. The detached hiPSCs were filtered using a 70 µm strainer and resuspended in 9 mL of KO-DMEM and transferred to a 15 mL tube. The tube was centrifuged at 1,200 rpm for 2 minutes, and the medium was aspirated. The hiPSCs were resuspended in 1 mL of E8 medium containing 5 µM Y-27632 (MCE, HY-10583). For manual cell counting, 10 µL of cell suspension were mixed with 10 µL of 0.1% Trypan blue solution in an extra-flat 96-well plate. A hemocytometer (Merck, Z359629) was used to enumerate live cells under a microscope. The desired number of cells (2000 or 4000) was transferred to each well of an ultra-low attachment 96-well plate, and the volume was adjusted accordingly. To each well, 50 µL of E8 medium with 5 µM Y-27632 were added after transferring hiPSCs. The plate was centrifuged at 1500 rpm for 5 minutes and incubated overnight at 37°C.
Generation of human blood vessel organoids
To differentiate the spin embryoid bodies (2000 hiPSCs) into hBVOs, the spin embryoid bodies incubated in vascular organoid differentiation medium. The medium consisted of a 1:1 mixture of DMEM-F12 (Gibco, 11320033) and neurobasal medium supplemented with B27 supplement (Gibco, 12587010), N2 supplement (Gibco, 17502048), 1 mM GlutaMax (Gibco, 35050061), 1% penicillin-streptomycin, and 55 nM 2-mercaptoethanol. The spin embryoid bodies were treated with 12 µM CHIR99021 (Tocris, 4423) and 30 ng/mL BMP4 (Peprotech, 120-05) from days 0 to 2. On days 3 to 5, the medium was switched to a medium containing 100 ng/mL VEGF-A (Peprotech, 100 − 20) and 30 ng/mL forskolin (Stemgent, 04–0025).
On day 5, the organoids were embedded in a 1:2 mixture of phenol-free Matrigel (Corning, 356231) and collagen I (Advanced BioMatrix, 5005) solution. The embedded organoids were then treated with StemPro34 medium (Gibco, 10639011) containing inactivated FBS (0%, 5%, 10%, or 15%), 100 ng/mL VEGF-A, and 100 ng/mL FGF-2 (R&D Systems, 233-FB/CF). The medium was changed every 2 days throughout the culture period.
On day 7 or 8, ECs sprouted from the aggregates, and vascular networks were established. On day 10, individual BVOs were isolated from the gel and transferred to 96-well ultra-low attachment plates for further maintenance until sampling.
Whole-mount immunostaining of organoids
The organoids were subjected to immunofluorescence staining. First, they were rinsed twice with phosphate-buffered saline (PBS) and treated with cell recovery solution (Corning, 354253) at 4°C for 1 hour to eliminate non-specific signals caused by Matrigel. After the PBS rinses, the organoids were fixed in 4% paraformaldehyde at room temperature (RT) for 1 hour and washed with PBS for a minimum of 30 minutes.
The organoids were cleared using the CytoVista™ 3D Culture Clearing Kit (Invitrogen, MAN0017942), following the manufacturer’s instructions. All procedures were carried out on a shaker. The organoids were subjected to a gradient series of methanol (50%, 80%, and 100%) at 4°C to achieve permeabilization. Subsequently, they were washed at RT using a series of methanol (80%, 50%, PBST, and PBS). The samples were next immersed in antibody penetration buffer at RT for 1 hour and blocked with blocking buffer at 37°C. Primary antibodies were diluted in antibody dilution buffer, and the samples were incubated overnight at 37°C in the antibody solution.
Next, the organoids were washed five times for 10 minutes each in a washing buffer and incubated overnight at 37°C with a diluted solution of secondary antibody and DAPI. Subsequently, the samples were washed 10 times for 10 minutes in washing buffer. Samples were dehydrated using increasing concentrations of methanol (50%, 80%, and 100%) and incubated in CytoVista tissue clearing reagent overnight at 4°C. Z-stack imaging was performed using a confocal microscope.
Quantitative reverse-transcription PCR (qRT-PCR)
Samples were washed with PBS and immediately flash-frozen in liquid nitrogen. Total RNA was extracted using the RNeasy Mini Kit (Qiagen), and cDNA was synthesized from the RNA using random primers and reverse transcriptase (Toyobo). qRT-PCR was performed on a real-time PCR system (Thermo Fisher Scientific), and relative mRNA quantification was determined using the 2∆∆CT method.
Mural cell differentiation
Mural cell differentiation was carried out using a neuroectodermal intermediate protocol as described in a previous study (Kelleher, Dickinson et al. 2019). hiPSCs were dissociated using ReleSR and plated onto Matrigel-coated six-well plates at a density of approximately 30,000 cells per well in E8 medium supplemented with 10 µM Y-27632. After 24 hours, the culture medium was switched to Y-27632-free E8 medium. The following day, the cells were cultured in E6 medium containing 10 µM SB-431542 and 20 ng/mL FGF2. The medium was refreshed daily until day 6 of differentiation when the supplements were replaced with 2 ng/mL TGF-β and 5 ng/mL PDGF-BB. Daily medium changes were performed until day 18 of differentiation.
Flow cytometry
To assess the proportions of cell types in hBVOs, flow cytometry was performed. hBVOs were dissociated using collagenase B for 30–40 minutes. The dissociated cells were pipetted and washed in PBS supplemented with 5% FBS. Subsequently, single cells were stained with fluorescence-conjugated antibodies for 30 minutes at 4°C. For intracellular antigen staining, cells were fixed using 4% paraformaldehyde and permeabilized with 0.1% saponin. Antibodies (CD31 and CD140b), diluted in PBS containing 5% FBS, were used to stain the cells. Flow cytometry data were acquired using the BD FACS Aria flow cytometer and analyzed using FlowJo software.
Preparation of samples for TEM
To visualize GOM in Notch3 mutant hBVOs, we followed a previous protocol [17] for sample preparation and imaging using TEM. hBVO samples were fixed in a solution of 2% glutaraldehyde and 2% paraformaldehyde in 0.1 M phosphate buffer. Subsequently, the samples were postfixed in buffered osmium tetroxide. Dehydration of the samples was performed using a series of graded alcohols. Finally, the samples were embedded in an Epon-Araldite mixture. Semi-thin sections (2 µm) were obtained from the embedded samples using a microtome and stained with toluidine blue for examination. Thin sections were cut from the blocks using an ultramicrotome and stained with lead citrate for TEM imaging. The stained samples were carefully examined using TEM to visualize the presence of GOM. This process enabled capture of high-resolution images of GOM in Notch3 mutant hBVOs.
PI staining
After differentiation, mural cells were fixed overnight at -20°C in 70% ethanol. Following two washes with PBS, the cells were incubated with propidium iodide (PI) in the dark at room temperature for 15 minutes. Subsequently, the cells were analyzed using flow cytometry to determine the cell cycle distribution.
Inhibitor study
The following inhibitors or activators were used: SB203580 for p38 inhibition (10 µM; Millipore, 559389), SP600125 for JNK inhibition (10 µM; Calbiochem, 420119), U0126 for ERK inhibition (10 µM; Millipore, 662005), LY294002 for PI3K/Akt inhibition (1 µM; Millipore, 440202), PD98059 for MEK1/2 inhibition (10 µM; Millipore, 513000), rapamycin for mTOR inhibition (100 nM; Sigma, R0395), CHIR99021 for GSK3β inhibition (10 µM; Tocris, 4423), Y27632 for ROCK inhibition (10 µM; MCE, HY-10583), DAPT for γ-secretase inhibition (25 µM; Sigma, D5942), purmorphamine for SHH activation (2 µM; Sigma, SML0868), and LDN93189 for TGFβ inhibition (100 nM, Cayman, 11802). hBVOs were treated with these compounds at days 13 to 15 of differentiation.
Statistical analysis
Quantitative analysis of the datasets was conducted using GraphPad Prism software. The results are presented as means ± standard error of the mean (SEM).