RNA isolation
The total RNA was isolated using the TRIzol reagent (Thermo Fisher Scientific Inc., Waltham, MA, USA). RNA quality was assessed using the RNA 6000 Nano Chip (Agilent Technologies, Amstelveen, The Netherlands) and an Agilent 2100 bioanalyzer, while RNA quantification was performed using an ND-2000 spectrophotometer (Thermo Fisher Scientific Inc.).
Library preparation and Whole mRNA-sequencing
For control and test RNAs, library construction was performed using the QuantSeq 3′ mRNA-Seq Library Prep Kit (Lexogen, Inc., Vienna, Austria) according to the manufacturer’s instructions. In brief, 500 ng of total RNA was prepared and an oligo-dT primer containing an Illumina-compatible sequence at its 5′ end was hybridized to the RNA to initiate reverse transcription. After degradation of the RNA template, second strand synthesis was initiated using a random primer containing an Illumina-compatible linker sequence at its 5′ end. The double-stranded library was purified using magnetic beads. Subsequently, the library was amplified to allow the addition of complete adapter sequences required for cluster generation, followed by purification. High-throughput (single-end 75) sequencing was performed using NextSeq 500 (Illumina, Inc., San Diego, CA, USA).
Data analysis
QuantSeq 3′ mRNA-Seq reads were aligned using Bowtie2 (Langmead and Salzberg, 2012). Bowtie2 indices were either generated from the genome assembly sequence or the representative transcript sequences for aligning to the genome and transcriptome, respectively. The alignment file was used for assembling transcripts, estimating their abundances, and detecting the differential expression of genes. Differentially expressed genes were determined based on counts from unique and multiple alignments using coverage in Bedtools (Quinlan AR, 2010). Read count (RT) data were processed based on the global normalization method using the Genowiz ™ version 4.0.5.6 (Ocimum Biosolutions, Telangana, India). Gene classification was based on searches performed using DAVID (http://david.abcc.ncifcrf.gov/) and Medline databases (http://www.ncbi.nlm.nih.gov/).
Human iPS cell (hiPSC) line
We constructed a hiPSC line by reprogramming newborn foreskin fibroblast cells (NuFF, GSC-3006G; AMS Biotechnology (GlobalStem), Abingdon, UK) through transduction with the four Yamanaka factors. The prepared hiPSC line was cultured on a STO feeder cell (SIM, ATCC® number: CRL-1503™, Manassas, VA, USA).
Real-time PCR
RNA was isolated and purified from cells harvested at the representative time points using the RNeasy® mini kit (74104, Qiagen, Hilden, Germany) and QIAshredder. A qPCR RT master mix (FSQ-201, TOYOBO, Osaka, Japan) was used to synthesize cDNA from RNA. Primer sequences are shown in Supplementary Material Online Table S1.
Western blotting
Western blotting was performed to confirm the protein expression patterns of MESP1 and SOX17 during hiPSC-derived cardiac differentiation: anti-MESP1 (sc-130461, Santa Cruz Biotechnology, TX, USA), anti-SOX17 (AF1924, R&D systems, Minneapolis, MN, USA), and anti-GAPDH (sc-47724, Santa Cruz Biotechnology, TX, USA). 30µg of protein was transferred onto the nitrocellulose membrane (IB23001, Thermo Fisher Scientific Inc.) using iBlot 2 Gel Transfer Device (IB21001, Thermo Fisher Scientific Inc.). HRP-donkey anti-mouse IgG (H + L) (715-035-151, Jackson ImmunoResearch, Philadelphia, PA, USA) and HRP-donkey anti-goat IgG (H + L) (705-035-147, Jackson ImmunoResearch) were used as secondary antibodies.
Fluorescence-Activated Cell Sorting (FACS)
We harvested BM cells from BM, tibias, as well as femurs and passed them through a 40 µm cell strainer (352340, Corning, New York, USA) to obtain single cells. We also dissected hearts into the smallest size possible using dissection scissors, incubated them with heart digestion enzymes at 37°C for 1 h, and passed them through a 70 µm cell strainer (352350, Corning, New York, USA) to obtain single cells. Isolated single cells from the BM and heart were incubated on ice for 30 minutes with the following antibodies for flow cytometry analysis: LPAR4 (PA549727, Thermo Fisher Scientific Inc.), GFP (ab13970, Abcam, Cambridge, UK), CD45 (sc-53665, Santa Cruz Biotechnology), and Nkx2.5 (ab91196, Abcam).
Immunofluorescence (IF)
Mouse heart and liver tissues were harvested at representative time points relative to the MI after BMT, and enclosed in paraffin blocks. Following sectioning (4 µm), IF was performed. Sectioned tissues were incubated with the following antibodies: GFP (ab13970, Abcam), αSA (A2172, Sigma-Aldrich, St. Louis, MO, USA), LPAR4 (PA549727, Thermo Fisher Scientific Inc.), SOX17 (AF1924, R&D systems), Sca1 (13-5981-28, Thermo Fisher Scientific Inc.), and Nkx2.5 (ab91196, Abcam).
ChIP assay
To identify the MESP1 and SOX17 binding sites, the consensus sequences of MESP1 and SOX17 were compared with the sequence located 3017 bp upstream from the LPAR4 transcription start site. For cell crosslinking, 1% formaldehyde (F8775, Sigma-Aldrich) was added to a cell culture dish, fixed at 25°C for 10 min, and collected in a tube. ChIP RIPA buffer (50 mM Tris-Cl, 1 mM EDTA, 0.5% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate (SDC), 140 mM NaCl, 1× protease inhibitor cocktail (PIC)) was added to the cell pellet. For DNA shearing, both fractions were sonicated 15 times using a Bioruptor (30 s on/30 s off per cycle). Sonicated DNA was treated with 2 µg each of MESP1 (sc-130461, Santa Cruz Biotechnology, TX, USA) and SOX17 (AF1924, R&D systems) antibodies overnight. Protein A/G sepharose (ab193262, Abcam) was added to pull down the antibody-bound DNA, which was then washed thrice with a wash buffer. DNA was incubated at 65°C for at least 2 h for decrosslinking. Finally, DNA was recovered using a PCR purification kit (28104, Qiagen) and analyzed using semi-quantitative PCR.
Luciferase assay
HiPSC-derived cells on day 4 of cardiac differentiation were simultaneously transfected with the firefly pGL3-control luciferase reporter vector (E1751, Promega, Madison, WI, USA) and the Renilla luciferase reporter plasmid pRL-TK (E2241, Promega) using the FuGENE® HD transfection reagent (E2311, Promega).
The Dual-Glo® Luciferase Assay system (E2920, Promega) was used to detect LPAR4 promoter-driven luciferase activity according to the manufacturer’s protocol.
Animals
For animal experiments, 60 C57BL/6 wild-type mice were purchased from Orient Bio (Seongnam-si, Seoul, Korea) and used for generating the murine MI model. Mice were allowed to adapt to the animal facility for 7 days before the experiments. All mice were free of murine viruses, pathogenic bacteria, and endo- as well as ectoparasites. All animal experiments were approved by the Institutional Animal Care and Use Committee (IACUC, IACUC no.: SNU-201028-3-1) of the Seoul National University Hospital.
Lineage tracing mouse model and TG DNA sample preparation
The DNA prep for the microinjection of the LPAR4_CreERT2_IRES_EGFP TG vector was as follows:
The LPAR4_CreERT2_IRES_EGFP plasmid DNA for the microinjection comprised a fragment (~ 6.6 kb) containing the LPAR4 promoter. AfeI and FspI restriction enzymes, each located at the start and outside part of the promoter were used to secure the fragment. Consecutively, the ~ 1.9 kb backbone fragment was excised through gel-extraction, whereas the ~ 6.6 kb fragment was introduced.
Generation of TG Mice
LPAR4_CreERT2_IRES_EGFP_TG mice were generated by Macrogen Inc. (Seoul, Korea) as well as inbred and maintained under pathogen-free. All manipulations were conducted with the approval of the Macrogen Institutional Animal Care and Use Committee (IACUC no.: 2018-01). Briefly C57BL/6N female mice were treated with PMSG and hCG for superovulation. More specifically, PMSG (7.5 IU) and hCG were intraperitoneally (i.p.) injected at 48 h intervals (5 IU) into 5- to 8-week-old female mice. After the hCG injection, female mice were mated with C57BL/6N stud male mice. The next day, following an impregnation check using a vaginal plug, female mice were sacrificed (as a method of euthanasia, 5–6 mg of phenobarbital sodium was i.p. injected) and the fertilized embryos were harvested. LPAR4_CreERT2_IRES_EGFP DNA was co-microinjected into single-cell embryos. Standard microinjection procedures were used for the production of transgenic mice (Macrogen Inc.). Briefly, 4 ng/µL DNA was directly injected into the male pronucleus of the zygote using a micromanipulator, and microinjected embryos were incubated at 37°C for 1–2 h. In total, 14 to 16 injected single-cell staged embryos were transplanted by surgical methods into the oviducts of pseudopregnant recipient mice. After F0 was born, genotyping was performed using tail cut samples and the presence of the transgene was confirmed using PCR analyses of their genomic DNA (forward: 5′-CTGCAAAGACAGGCAGACAAG-3′, reverse: 5′-CATTGCTGTCACTTGGTCGTG-3′).
Bone Marrow Transplantation
C57BL/6 wild-type mice were sub-lethally irradiated (7.5 Gray) using a Cesium-137 Irradiator (IBL437C, CIS Bio Inc., Codolet, France). Donor mice (LPAR4_CreERT2_IRES_EGFP_TG mice) were euthanized and GFP+ BM cells were collected from the tibia and femur. Next, 5 × 107 GFP+ BM cells were systemically transplanted via the jugular vein into the sub-lethally irradiated recipient mice (C57BL/6 wild-type mice). We used a mouse model and performed a ligation of the left anterior descending artery after BMT. After four weeks of BMT, FACS analysis was performed against GFP+CD45+ cells for measuring the donor engraftment rate.
Statistical analysis
All data are expressed as the mean ± SEM. One-way analysis of variance (ANOVA) using Newman-Keuls multiple comparison tests was used to each compare groups. GraphPad Prism v8 software was used (GraphPad Software Inc, San Diego, CA, USA). A P value < 0.01 was considered statistically significant.