EC signatures in MuSCs has been seen in several gene expression data sets (Figure 1—figure supplement 1A–1D, Supplementary file 1; Fukada et al., 2007; Charville et al., 2015; Ryall et al., 2015; van Velthoven et al., 2017). However, with the lack of EC control, we questioned whether these were true expression or artifact. To isolate EC and MuSC populations, we first crossed the Flk1^+/GFP mice to label the ECs of the vasculature (Ema et al., 2006) and the Pax7^+/CreERT2:ROSA26^{+/Loxp-stop-Loxp-tdTomato} (Pax7^+/CreERT2:R26R^+/tdT) mice to mark the MuSC lineage (Murphy et al., 2011; Verma et al., 2018). We performed bulk RNA sequencing (RNA-seq) on FACS sorted ECs and MuSCs as well as freshly isolated single muscle fibers (Figure 1A, Figure 1—figure supplement 1E–G). We found that single muscle fibers routinely have ECs fragments attached to the fiber (Figure 1—figure supplement 1G) and so we removed such fibers based on Flk1^GFP expression from the samples collected for sequencing. We surveyed for canonical genes for each cell type (Figure 1B) and found minimal but reliable expression of canonical ECs genes such as Pecam1, Cdh5, Kdr, and Flt1 in MuSCs.

It is possible that these EC signatures detected in MuSCs were due to small amounts of contaminating ECs with very high expression of the canonical EC genes skewing the average expression in MuSC RNA samples. To rule out this possibility, we performed single-cell RNA-seq (scRNA-seq) on MuSCs and ECs isolated from mouse hind limb muscle from both basal condition and 3 days post intramuscular cardiotoxin (CTX) injury to look at both quiescent and activated MuSCs from the reporter mice specified above (Figure 1A). We could reliably delineate injured and activated MuSCs via side and forward scatter (Figure 1—figure supplement 1H and I). We FACS isolated cells from both days separately and spiked in 20% of the ECs into the MuSCs from their respective time points, and performed scRNA-seq for each time point (Figure 1A). We performed sequencing with ~300 K read/cell compared with the commonly used sequencing with 60 K reads/cell, in order to maximize the possibility of detecting low-abundance transcripts (Zhang et al., 2020). In the aggregated dataset, the MuSCs showed low overlap between D0 and D3 owing to the different stages of the myogenic differentiation cycle, while the ECs clusters showed near perfect overlap (Figure 1C and D). While drastic morphological changes in ECs have been shown during muscle regeneration (Hardy et al., 2016), transcriptomic changes are much more tapered, especially compared with MuSCs (Latroche et al., 2017). We were able to deconvolve the quiescent MuSCs from the activated and differentiating MuSCs, ECs, and other cell types from gene signatures. (Figure 1—figure supplement 1J). Importantly, data from scRNA-seq were able to recapitulate the minimal expression of canonical EC genes in the MuSC clusters such as Cdh5 (Figure 1E) as seen in our Bulk RNA-seq results (Figure 1B). These included the Vegf receptors Flk1 (Kdr) and Flt1 (Figure 1E).

As a quality control measure, we introduced an artificial chromosome into our reference genome with sequences for the three transgene genes; eGFP from Flk1^+/GFP, tdTomato and CreERT2 from Pax7^+/CreERT2:R26R^+/tdT and used this genome to map our single cell RNA-seq data (Figure 1E, Figure 1—figure supplement 1K). Surprisingly, we also found eGFP in the MuSCs and tdTomato in EC fraction, while the CreERT2 expression remained mainly restricted to the MuSCs (Figure 1—figure supplement 1K). FACS analysis and FACS-sorted cells confirmed that GFP(+) and tdTomato(+) cells are exclusively restricted as ECs and MuSCs, respectively (Figure 1—figure supplement 1E and F). Therefore, we hypothesized that this was due to the ambient-free mRNA from the digested cells that is intrinsic to any droplet based single-cell sequencing platform. By using SoupX (Young and Behjati, 2020), we performed careful background subtraction using genes expressed exclusively in myofibers as our negative control and genes validated by in situ hybridization as a positive control (Kann and Krauss, 2019). We observed decreased but sustained eGFP expression in the MuSC fraction and tdTomato expression in the EC fraction after SoupX subtraction (Figure 1—figure supplement 1K). In addition, the EC signatures such as Cdh5 expression in the MuSC fraction was also sustained. These results conclude that MuSCs contain mRNAs from canonical ECs genes. We showed that the canonical EC genes, such as Cdh5, Flt1 and Flk1 were broadly expressed in the myogenic cells in our dataset (Figure 1E).

Since detection of rare subpopulation in single cell dataset is a factor of cell numbers, we re-analyzed previously published dataset with 2,232 myogenic cells across different states (Torre et al., 2018; De Micheli et al., 2020). We were able to classify cell as quiescent, proliferative vs. differentiating states based on the expression of Calcr, Cdk1, and Myog, respectively (Figure 1—figure supplement 1L). We noticed that EC prototypic markers such as Flt1 are broadly expressed with small amounts in MuSCs. Complementary data from different laboratories showed the clear expression of EC prototypic markers such as Cdh5, Flt1, and Kdr, using microarrays and Bulk-RNA-seq (Figure 1—figure supplement 1A and B; Fukada et al., 2007; Ryall et al., 2015). RNA-seq data from fixed quiescent, early activated and late activated MuSCs show that Flt1 may be transiently upregulated during the early activation process (Figure 1—figure supplement 1C; Yue et al., 2020). To confirm whether the EC gene mRNAs were transcribed from MuSCs, we utilized previously published MuSC nascent RNA transcriptome from TU-tagged samples (Gay et al., 2013; van Velthoven et al., 2017). As expected, Myh1 was represented in the whole muscle but was absent in the TU-tagged MuSCs (Figure 1F), indicating that the nascent MuSCs were devoid of cellular contamination from other cells in the muscle. Inversely, the nascent MuSC transcript was over-represented for MuSC related genes such as Calcr and Sdc4. Interestingly, we were able to detect EC genes such as Kdr and Pecam1 in the TU-tagged MuSC samples indicating that they were actively transcribed by MuSCs (Figure 1F, Figure 1—figure supplement 1D).

We also verified the expression of Vegfr genes (Kdr, Flt1, Nrp1, and Nrp2) in MuSCs using RT-qPCR (Figure 1G). In addition, we verified the expression of Flt1 by performing in situ hybridization using RNAScope on MuSC on whole muscle fiber, which we currently believe to be the gold standard for expression studies (Figure 1H). Finally, in MuSC-derived myoblasts, NRP1and NRP2 expression was detectable with comparable intensity compared with EC cell line, while FLT1 expression was detectable with lower intensity compared with EC cell line (Figure 1I). By contrast, PECAM1, VE-Cadherin and FLK1 expression, which was clearly detected in EC cell line, was undetectable level in myoblasts. Taken together, these data indicate that there are both transcripts of these EC canonical genes and EC canonical proteins in MuSCs.

Since VEGFRs were expressed in MuSCs in small amounts and their ligand, VEGFA, was highly expressed in MuSCs (Verma et al., 2018), we wanted to investigate whether there were any biological effects to induction by VEGFA. We found that treatment with VEGFA could increase proliferation of MuSC-derived myoblasts at low dose but inhibit proliferation at high dose of VEGFA, a phenomenon that has been previously described in ECs (Noren et al., 2016; Figure 2—figure supplement 1A). We saw no effect on differentiation by VEGFA as evaluated by myosin heavy chain (MyHC) staining, fusion index and RT-qPCR (Figure 2—figure supplement 1B–D). By contrast, crystal violet staining showed that VEGFA could significantly increase survival as judged by number of myoblasts following UV-mediated apoptotic cell death induction (Figure 2—figure supplement 1E and F). To investigate apoptosis in detail, we optimized Annexin V assay following thapsigargin-mediated endoplasmic reticulum (ER)-stress (Hirai et al., 2010) so that we could study deviation at ~ED50 while still performing experiments to remove the confounding variable to proliferation from the experimental setup (Figure 2—figure supplement 1G and H). We had previously shown that MuSCs are the predominant cells that secrete VEGFA in skeletal muscle (Verma et al., 2018) and while adding exogenous VEGFA did not improve cell survival, blocking VEGFA via a soluble form of FLT1-FC increased the number of apoptotic and necrotic myoblasts in vitro (Figure 2A and B).

To characterize the VEGF receptor responsible for the anti-apoptotic effect of VEGFA on MuSC-derived myoblasts, we used pharmacological inhibitors of the VEGF receptors (Figure 2C and D). We used blocking antibody for the VEGF receptors FLT1 (anti-FLT1 antibody), small molecule inhibitors for FLK1 (SU4502 and ZM306416) and the FLK1 co-receptor NRP1 (EG00229) following thapsigargin induction (Figure 2A and D). Surprisingly, inhibiting FLK1, the major signaling RTK for VEGFA, had no effect on myoblasts survival following thapsigargin induction (Figure 2D). By contrast, blocking FLT1 via blocking antibody greatly decreased the survival of myoblasts following thapsigargin induction (Figure 2D). To confirm this interesting result using genetic tools, we obtained myoblasts with Pax7-CreER-inducible deletion of Flt1 mice (Pax7^+/CreER:Flt1^Loxp/Loxp or MuSC-Flt1^Δ/Δ) and the control mice (Pax7^+/+:Flt1^Loxp/Loxp). In vitro 4-OHT-mediated genetic deletion of Flt1 (MuSC-Flt1^Δ/Δ) resulted in down-regulation of Flt1 RNA and FLT1 protein expression (Figure 2—figure supplement 1I and J), and increased spontaneous apoptotic cell death even without induction of apoptosis (Figure 2E). By contrast, Flt1 deletion did not affect cell proliferation assessed by EdU staining or myogenic differentiation assessed by MyHC staining (Figure 2—figure supplement 1K–M). When thapsigargin-induced apoptosis was induced, the MuSC-Flt1^Δ/Δ myoblasts had increased apoptosis that was not responsive to exogenous VEGFA (Figure 2F).

VEGFA signaling is mediated through Extracellular signal-Regulated Kinase (ERK), p38 Mitogen-Activated Protein Kinase (MAPK), and Protein kinase B (AKT1). In ECs, VEGFA is known to protect cells from apoptosis via AKT1 (Domigan et al., 2015; Lee et al., 2007). However, it is not known whether VEGFA can similarly activate AKT1 in MuSC-derived myoblasts. While the role of AKT1 has been explored in proliferation and differentiation in myoblasts, its role in apoptosis has not been well characterized (Loiben et al., 2017). We assessed for AKT1 activation via phosphorylated AKT1 (pAKT1) in MuSC-derived myoblasts. We found that exogenous VEGFA could induce AKT1 phosphorylation (pAKT1) (Figure 2G and H, Figure 2—figure supplement 1N and O). This response was blunted in MuSC-Flt1^Δ/Δ myoblasts and was no longer responsive to VEGFA (Figure 2G and H, Figure 2—figure supplement 1N and O). Lastly, we wanted to confirm that AKT1 activation could improve myoblast survival. We infected lentiviral E4ORF1 or MyrAKT1 vectors in myoblasts, both of which gene products have been shown to specifically activate AKT1 without activating ERK or p38 (Kobayashi et al., 2010). We found that overexpression of either of these genes improved cell survival compared with the control in vitro following induction of apoptosis via thapsigargin (Figure 2I). These data establish FLT1-AKT1 as the cascade linking VEGFA to apoptosis in MuSC-derived myoblasts during muscle regeneration (Figure 2J).

Endogenous and exogenous VEGFA have been shown to regulate cell survival and protect ECs from apoptosis (Gerber et al., 1998; Lee et al., 2007). To assess whether additional VEGFA had an effect on MuSC behaviors in vivo, we used mice carrying the Vegfa^+/Hyper allele for injury-mediated TA muscle regeneration following BaCl₂ injection (Figure 3A and B; Miquerol et al., 1999). MuSC-derived myoblasts from Pax7^+/tdT:Vegfa^+/Hyper mice showed around 2.8-fold increased expression of Vegfa but not the Vegfr genes compared with myoblasts from wild-type mice (Figure 3—figure supplement 1A). Interestingly, while treatment with VEGFA alone had no effect on apoptosis in vitro, the MuSCs from Pax7^+/tdT:Vegfa^+/Hyper mice showed decreased cell death in regenerating muscle by 1 day following BaCl₂ injection (Figure 3C). Consequently, single muscle fibers from Pax7^+/tdT:Vegfa^+/Hyper mice showed increased number of MuSCs, compared with those from Pax7^+/tdT:Vegfa^+/+ mice by 28 days following BaCl₂ injection (Figure 3D). In addition, muscle regeneration was promoted in Vegfa^+/Hyper mice in the early (14 days) and late (28 days) muscle repair processes as judged by fiber diameter and increase in eMHC(+) regenerating muscle fibers (Figure 3E and F, Figure 3—figure supplement 1B–F).

We then performed the reciprocal experiment to investigate the consequence of Vegfa loss in MuSCs in vivo, and utilized MuSC-specific Vegfa knockout mice (Pax7^+/CreER:Vegfa^Loxp/Loxp). We have previously shown that vasculature in the MuSC-Vegfa^Δ/Δ mouse muscle is perturbed and the proximity between the MuSC and EC is increased (Verma et al., 2018). However, the functional consequences of this remained unknown. We confirmed that clear downregulation of VEGFA protein in MuSC-derived myoblasts isolated from MuSC-Vegfa^Δ/Δ mice (Figure 3—figure supplement 2A). We noticed that deletion of Vegfa in MuSCs in the MuSC-Vegfa^Δ/Δ mouse muscle led to an increase in the proportion of dead MuSCs following BaCl₂ injection (Figure 3G). Consequently, the number of MuSCs in the MuSC-Vegfa^Δ/Δ muscle were significantly reduced following recovery after injury without difference in the MuSC numbers in MuSC-Vegfa^Δ/Δ muscle at homeostasis (Figure 3H). In addition, the muscle had a regenerative defect as indicated by the shift in fiber size distribution, decrease in the size of regenerating eMHC(+) fiber and increased adipose following muscle injury (Figure 3B, I and J, Figure 3—figure supplement 2B–E, Figure 3—figure supplement 1E and F). While a limitation of this experiment is that the MuSC fusion into the fiber also deletes Vegfa from the fiber themselves, muscle-fiber-specific deletion of Vegfa has not shown an effect on fiber size (Delavar et al., 2014). These data indicate that cell intrinsic VEGFA improves cell survival of MuSCs and that loss of MuSC-derived VEGFA results in reduced muscle regeneration.

Since FLT1 but not FLK1 was detected in MuSCs and MuSC-derived myoblasts, we asked whether the Flt1 had an effect on MuSC survival in vivo, we evaluated cell death in MuSCs from MuSC-Flt1^Δ/Δ mouse muscle. We induced muscle regeneration using BaCl₂ for 1 day and assessed for cell death in MuSCs. As seen in vitro, we found that loss of Flt1 in MuSCs (Figure 2—figure supplement 1I and J) resulted in increased cell death during early regeneration (Figure 3K). Consequently, single muscle fibers from MuSC-Flt1^Δ/Δ mice showed a decreased number of MuSCs, compared with those from MuSC-Flt1^+/+ mice by 28 days following BaCl₂ injection (Figure 3L). We also examined the long-term in vivo consequence of deleting Flt1 from MuSC. There was no significant muscle phenotype in MuSC-Flt1^Δ/Δ muscle at homeostasis (Figure 3B, M and N). However, following injury, the MuSC-Flt1^Δ/Δ muscle had a modest regenerative defect as indicated by the shift in fiber size distribution following muscle injury and decrease in size of eMHC(+) regenerating fibers (Figure 3B, M and N, Figure 3—figure supplement 2F–J, Figure 3—figure supplement 1E and F).

While angiogenic defects have been reported in the mdx mice as well as in golden retrieval muscular dystrophy (GRMD; canine model of DMD) (Verma et al., 2010; Latroche et al., 2015; Verma et al., 2019; Kodippili et al., 2021; Podkalicka et al., 2021), it is not clear whether VEGF family and its receptors are implicated in human dystrophinopathies. We probed the VEGF ligands and receptors in microarrays (Supplementary file 1) from skeletal muscles and MuSCs from mdx mice (Tseng et al., 2002; Pallafacchina et al., 2010) and skeletal muscles from the GRMD (Vieira et al., 2015). Vegfa was downregulated in both models (Figure 4—figure supplement 1A). Flt1 was also downregulated in GRMD but not mdx muscles. To examine whether VEGF signaling is altered in DMD patients, we performed gene expression analysis on previously available data from microarrays from patients with DMD (Chen et al., 2000). We also aggregated and probed microarray data from muscle biopsies of patients with various neuromuscular diseases or of healthy individuals after exercise (Bakay et al., 2006). In the microarray data, Vegfa expression was increased after an acute bout of exercise, and Vegfa expression was reduced in ALS muscle, BMD muscle, as well as both early and late phases of DMD muscle (Figure 4—figure supplement 1A). These data indicate that Vegfa expression is decreased in dystrophinopathy, and thus increasing VEGFA may be a therapeutic target for DMD.

Therefore, we crossed the MuSC-Flt1^Δ/Δ mice with the chronically regenerating DMD model mice (mdx) to generate mdx:MuSC-Flt1^Δ/Δ mice, and analyzed long-term effects of Flt1 deletion (Figure 4A, Figure 4—figure supplement 1B and C). Importantly, we found a significant decrease in fiber diameter, increased fibrosis and CD31(+) capillary density (Figure 4B–D, Figure 4—figure supplement 1C and D) in TA muscle. This was accompanied by a physiological decrease in muscle perfusion as shown by laser Doppler flow at 12 months (Figure 4E) as well as a functional decline in muscle strength as judged by grip strength both acutely and chronically (Figure 4F).

By contrast, when we crossed the Vegfa^+/Hyper mice with mdx mice (Figure 4A), we noticed a significant increase in fiber diameter, increase in capillary density and decreased fibrosis (Figure 4G–I, Figure 4—figure supplement 1D–F) in both TA and diaphragm muscle of mdx:Vegfa^+/Hyper mice. This was accompanied by a physiological increase in muscle perfusion as shown by laser Doppler flow at 12 months age (Figure 4J) as well as a functional increase in muscle strength as judged by grip strength (Figure 4K) without a change in body mass (Figure 4—figure supplement 1E). Lastly, when the muscle was injured acutely, with BaCl₂, the Vegfa^+/Hyper mouse had lower number of apoptotic MuSC (Figure 4—figure supplement 2A–C). These data indicate that VEGFA-FLT1 axis is a therapeutic target for the pathology seen in the DMD model mdx mice.

Flt1^LoxP/LoxP were obtained from Gua-Hua Fong (Ho et al., 2012). B6.Cg-Pax7^{tm1(cre/ERT2)Gaka/J} (Pax7^+/CreERT2; JAX stock# 017763; Murphy et al., 2011), B6.Cg-Gt(ROSA)^{26Sortm9(CAG-tdTomato)Hze/J} (Ai9; JAX stock # 007909; Madisen et al., 2010), Vegfa^+/Hyper (Vegfatm1.1Nagy/J; JAX stock# 027314; Miquerol et al., 1999) and B6Ros.Cg-Dmd^mdx-5cv/J (mdx^5cv; JAX stock #002379; Chapman et al., 1989) were obtained from Jackson Laboratory. Kdr^tm2.1Jrt/J (Flk1^+/GFP) were obtained from Masatsugu Ema (Ema et al., 2006). B6.Cg-Pax7^{tm1(cre/ERT2)Gaka/J} (Pax7^+/CreERT2) mice were crossed with the B6.Cg-Gt(ROSA)^{26Sortm9(CAG-tdTomato)Hze/J} (Ai9) to yield the Pax7^+/CreERT2:R26R^tdT(Pax7^tdT) mice. Pax7^tdT mice were bred with the Vegfa^+/Hyper and Flk1^+/GFP to obtain Pax7^+/tdT:Vegfa^+/Hyper and Pax7^+/tdT:Flk1^+/GFP mice. Vegfa^LoxP/LoxP mice obtained from Napoleone Ferrara (Gerber et al., 1999) were crossed with Pax7^+/CreERT2 to yield the Pax7^+/CreERT: Vegfa^LoxP/LoxP mice. Flt1^LoxP/LoxP mice obtained from Guo-Hua Fong (Gerber et al., 1999) were crossed with Pax7^+/CreERT2 to yield the Pax7^+/CreERT:Flt1^LoxP/LoxP mice. Colonies for all the mice were established in the laboratory. Cre recombination was induced using tamoxifen (T5648, MilliporeSigma) dosed as 75 mg/kg body weight x 3 times over 1 week at 3–6 weeks of age. Mice carrying the wild-type CreERT2 allele were used for control experiments. TA muscle regeneration was induced by intramuscular injection of 20 µl of 1% BaCl₂ (342920, MilliporeSigma) or 20 µl of 10 µM Cardiotoxin (CTX) (V9125, MilliporeSigma). Mice used for this study is summarized in Key Resources Table.

Genotyping to detect the transgenic and mutant alleles was performed by PCR using the primers described on the web site of Jackson Laboratory shown in Key Resources Table. All primers were synthesized as custom DNA oligos from Integrated DNA technologies (IDT). Genotyping to detect the mutated allele of mdx^5cv was performed by PCR using the primers (0981 and 0982) shown in Key Resources Table. The PCR product DNA was digested with DraIII restriction enzyme (R3510S, New England Biolabs). Wild-type allele generated 180 bp and mutant allele generated 50 and 130 bp bands.

The animals were housed in an SPF environment and were monitored by the Research Animal Resources (RAR) of the University of Minnesota. All protocols (2204–39969A) were approved by the Institutional Animal Care and Usage Committee (IACUC) of the University of Minnesota and complied with the NIH guidelines for the use of animals in research.

Pax7^tdT:Flk1^GFP mice were utilized for FACS-mediated MuSC and EC isolation as previously described (Asakura et al., 2002; Verma et al., 2018). We performed extensive validation of the fluorescent reporter mice as previously described (Figure 1—figure supplement 1A–C; Verma et al., 2018). Briefly, quiescent MuSCs and ECs were isolated from the hind limb skeletal muscle of 1- to 2-month-old Pax7^tdT:Flk1^GFP mice after digestion with collagenase type II. FACS was performed on an FACS sorter (BD FACSAria) and data were analyzed using FlowJo (BD Biosciences). Sorting gates, tdTomato(+) for MuSCs and GFP(+) for ECs, were strictly defined based on control cells isolated from wild-type mice and the forward scatter and side scatter gating. Sorted cells were immediately characterized by immunostaining on slide glasses, utilized for RNA preparation or cultured on collagen-coated plates in the myoblast growth medium as below to obtain MuSC-derived myoblasts and ECs. FACS analysis was performed as previously described (Turaç et al., 2013). Cells were either trypsinized (cultured cells) or a single cell suspension was obtained following enzymatic digestion as whole muscle-derived cells (Asakura et al., 2001; Asakura et al., 2002). Cells were then washed with FACS buffer (2% BSA and 1 mM EDTA in PBS) followed by live/dead staining using ZombieNIR (423105, Biolegends). Cells were washed, then immunostained for cell surface markers. Blocking cells was performed with 1% BSA/PBS, and cells were incubated in fluorescently-conjugated antibody. FACS was performed on a Fortessa X-20 (BD Biosciences) with a 355 nm, 405 nm, 488 nm, 561 nm, and 640 nm lasers.

Mouse bEnd.3 EC cells (CRL-229), C166 EC cells (CRL-2581), and C2C12 myoblast cells (CRL-1772) were obtained from American Type Culture Collection (ATCC). Human 293 FT cells (R70007) were obtained from ThermoFisher Scientific. All cell lines were cultured in DMEM medium with 10% FBS, 100 units/ml of penicillin, and 100 μg of streptomycin at 37 °C in 5% O₂ and 5% CO₂. All cell lines were STR profiled to confirm their identity and tested negative for mycoplasma. MuSC-derived myoblast isolation from adult mice was performed as previously described (Motohashi et al., 2014). Briefly, after collagenase type II (CLS-2, Worthington) treatment, dissociated cells from mouse hindlimb muscle were incubated with anti-CD31-PE (12-0311-82, eBiosciences), anti-CD45-PE (12-0451-81, eBiosciences), anti-Sca1-PE (A18486, eBiosciences) and anti-Integrin α7 (ABIN487462, MBL International), followed by anti-PE microbeads (130-048-801, Miltenyi Biotec), and then performed LD column (130-042-901, Miltenyi Biotec) separation. Negative cell populations will be incubated with anti-Mouse IgG beads (130-048-402, Miltenyi Biotec), and then MS column (130-042-201, Miltenyi Biotec) separation was performed to isolate Integrin α7(+) MuSCs. MuSC-derived myoblasts were maintained in culture on collagen coated plates in myoblast medium containing 20% FBS, 20 ng/ml bFGF (PHG0263, Invitrogen), 100 units/ml of penicillin and 100 μg of streptomycin in HAM’s-F10 medium. Cell cultures were maintained in a humidified incubator at 37 °C with 5% CO₂ and 5% O₂. 4-Hydroxy tamoxifen (4-OHT, H6278, MilliporeSigma) treatment (1 µM in EtOH) was used to induce Flt1 deletion in myoblasts isolated from Flt1^LoxP/LoxP:Pax7^CreERT2 mice. For cell survival assay, 1 x 10⁵ cells were allowed to adhere for 1 day and starved overnight in 0.1% FBS in HAM’s F10 medium. Then, cells were exposed to 1 µM EdU along with or without 2–100 ng/ml recombinant VEGFA (493 MV, R&D Systems) for 8 hr before being fixed and stained by the Click-iT EdU Alexa Fluor 488 Imaging Kit (C10337, Thermo Fisher Scientific). For induction of apoptosis in myoblasts, (1–2 x 10⁵) cells were allowed to adhere to the plates for 16 hr. Thapsigargin-mediated apoptosis was induced by 1 µM of thapsigargin (T9033, MilliporeSigma) dissolved in EtOH with or without VEGFA, 100 ng/ml recombinant FLT1-FC (7756-FL, R&D Systems), 1 µg/ml anti-FLT1 monoclonal antibody (Angio-Proteomie, MAB7072), inhibitors of FLK1, 3 µM ZM306416 (2499/1, R&D Systems) and 10 µM of SU5402 (3300/1, R&D Systems) and an inhibitor of NRP1, 30 µM of EG00229 (6986/10, R&D Systems) for 24 hours. UV light-mediated apoptosis was induced by exposing the cells to UV light in cell culture hood for 45 s without medium. After UV exposure, cell survival was assessed 24 hr following culture in 0.1% FBS in HAM’s F10 medium with or without VEGFA using the Crystal violet Assay Kit (ab232855, Abcam) and quantified the Crystal violet dye after solubilization by absorbance at 570 nm. To induce differentiation of myoblasts, the myoblast medium was replaced with differentiation medium that contained DMEM supplemented with 5% horse serum with or without VEGFA or bFGF for 1 or 3 days followed by anti-sarcomeric myosin heavy chain antibody (MF-20, Developmental Study Hybridoma Bank).

The lentiviral pCCL-E4ORF1 and pCCL-myrAkt1 constructs were a kind gift from Dr. Jason Butler (Kobayashi et al., 2010). A total of 293 FT cells (R70007, Thermo Fisher Scientific) were seeded in DMEM with 10% FBS and transfected with the lentivirus vectors along with pCMV-VSV-G (8454, Addgene), pRSV-Rev (12253, Addgene), and pMDLg/pRRE (12251, Addgene) using PolyJet transfection reagent (SL100688, Signagen Laboratories). The culture supernatant of the transfected 293 FT cells was added to MuSC-derived myoblast culture with 0.8 μg/ml polybrene (MilliporeSigma, H9268). pAKT1(+) cells were stained with anti-pAKT1 antibody (4060, Cell Signaling).

Protein extracts of MuSC-derived myoblast culture obtained with an NE-PER Nuclear and Cytoplasmic Extraction reagents (78833, Thermo Fisher Scientific) was used for western blotting. Protein concentration was determined by the Micro BCA Protein Assay Reagent kit (Thermo Fisher Scientific). Following electrophoresis, the proteins were transferred to an Immobilon P membrane (IPVH00010, EMD Millipore) overnight. pAKT1 was detected by Western blotting with anti-pAKT1 antibody (4060, Cell Signaling) followed by anti–rabbit IgG HRP (31460, Cell Signaling Technology). To verify equal loading proteins, the same blots were stripped and reprobed with anti-GAPDH HRP conjugated (3683, Cell Signaling) as a cytosolic marker. The reaction was developed using SuperSignal West Femto chemiluminescent substrate (PI37074, Fisher Scientific) in accordance with the manufacturer’s instructions. Protein signals were detected and quantitated by iBright FL1500 (A44241, ThermoFisher Scientific).

Apoptosis was measured using measured using Annexin V-Biotin Apoptosis Detection Kit (BMS500BT-100, eBioscience) as per the manufacture’s instruction. Streptavidin-conjugated Alexa-Fluro-488 was used for detection. Propidium Iodide (PI) was used in all assays except when Pax7tdT(+) cells were utilized or when ZombieNIR (423105, Biolegends) was used. FACS was performed on a Fortessa X-20 (BD Biosciences) equipped with a 355 nm, 405 nm, 488 nm, 561 nm, and 640 nm lasers. For detection of apoptotic cells in TA muscle sections 3 days following BaCl₂ injection, TMX was injected into mdx:Vegfa^+/+:Pax7^tdT and mdx:Vegfa^+/Hyper:Pax7^tdT mice before BaCl₂ injection to label MuSCs during muscle regeneration. To detect apoptotic cells, the TA muscle sections were incubated with anti–activated caspase-3 antibody (ab214430, Abcam) followed by anti–rabbit Alexa-488 antibodies (A11008, ThermoFisher Scientific) for double immunostaining. DAPI (10236276001, MilliporeSigma) was used for counterstaining of nuclei. Microscopic images were captured by a DP-1 digital camera attached to BX51 fluorescence microscope with 10×, 20×or 40×UPlanFLN objectives with cellSens Entry 1.11 (all from Olympus).

Immunostaining for PECAM1, VE-Cadherin, VEGFA, VEGFRs was performed on collagen coated coverslips. Other immunostaining was performed on 35 mm tissue culture plates. Cells were fixed with 2% PFA for 5 min and immunostained as previously described (Verma et al., 2010). For membrane receptor staining, cells were permeabilized with 0.01% saponin (ICN10285525, ThermoFisher Scientific) which was kept in the staining solution until the primary antibodies were washed off. At which time, 0.01% Triton-X was added to all the buffers. The antibodies used for this study are listed in Key Resources Table.

Extensor digitorum longus (EDL) muscle was dissected and digested with 0.2% collagenase type I (C0130, MilliporeSigma) for single muscle fiber isolation as previously described (Verma et al., 2010). Single muscle fibers were fixed with 2% PFA/PBS, permeabilized with 0.2% Triton-X100 and counterstained with DAPI. Anti-Pax7 antibody(+) or tdTomato(+) MuSCs per single muscle fiber were counted manually.

RNAscope for Flt1 transcripts was performed as previously described (Kann and Krauss, 2019) on single muscle fibers from Pax7^tdT mice using the RNAscope Probe - Mm-Flt1 (C1) (415541, ACDBio). Briefly, isolated EDL fibers are fixed in 4% PFA, washed with PBS, and dehydrated in 100% methanol. Subsequently, fibers are rehydrated in a stepwise gradient of decreasing methanol concentrations in PBS/0.1% Tween-20. Fibers are treated with a proteinase for 10 min, followed by hybridization, amplification, and fluorophore conjugation steps.

The mouse tibialis anterior (TA) muscle was used for all histological analysis. Tissues were frozen fresh using LiN₂ chilled isopentane and stored at –80 °C. Eight μm thick transverse cryosections were used for all histological analysis. Hematoxylin & Eosin (HE) staining were performed as previously described (Verma et al., 2010). Sirius red (Direct Red 80, 365548, MilliporeSigma) staining was performed for muscle sections for fibrosis as previously described (Shimizu-Motohashi et al., 2015). Muscle sections were stained in Oil Red O solution (O1391-250ML, MilliporeSigma) as previously described (Wang et al., 2017). Anti-eMHC (F1.652, Developmental Study Hybridoma Bank) and anti-Laminin (L0663, MilliporeSigma) antibodies followed by anti-mouse Alexa-488 (A11001, ThermoFisher Scientific) and anti-rat Alexa-568 antibodies (A11077, ThermoFisher Scientific) were used for detection of regenerating muscle fibers. For capillary density measurement, anti-CD31 antibody (550274, BD Biosciences) was used for TA muscle sections followed by anti-rat Alexa-488 (A11006, ThermoFisher Scientific). Microscopic images were captured by a DP-1 digital camera attached to BX51 fluorescence microscope with 10×, 20×or 40×UPlanFLN objectives with cellSens Entry 1.11 (all from Olympus). Photoshop (Adobe) and Fiji (NIH) were used for image processing and manually enumerating the fiber feret’s diameter (Schindelin et al., 2012).

Forelimb grip strength test was performed following a previously published procedure (Aartsma-Rus and van Putten, 2014). Briefly, mice were gently pulled by the tail after fore limb-grasping a metal bar attached to a force transducer (Grip Strength Meter, 1027CSM-D52, Columbus Instruments). Grip strength tests were performed by the same blinded examiner. Five consecutive grip strength tests were recorded, and then mice were returned to the cage for a resting period of 20 min. Then, three series of pulls were performed each followed by 20 min resting period. The average of the three highest values out of the 15 values collected was normalized to the body weight for comparison.

RBC flux was evaluated using the moorLabTM laser Doppler flow meter as previously described (Verma et al., 2010) with the MP7a probe that allows for collecting light from a deeper tissue level than standard probes according to the manufacturer’s instructions (Moor Instruments). The fur from the right hind leg was removed using a chemical depilatory. Readings were taken using the probe from at least 10 different spots on the TA muscle. The AU was determined as the average AU value during a plateau phase of each measurement.

Cultured cells were washed with ice cold PBS and lysed on the place with Trizol. RNA was isolated using the DirectZol RNA Microprep Kit (R2062, Zymo Research) with on-column DNase digestion followed by cDNA synthesis using the Transcriptor First Strand cDNA synthesis kit (04379012001, Roche Molecular Diagnostics) using random primers. Genomic DNA for genotyping was isolated from mouse tail snips with lysis buffer containing Proteinase K (P2308, MilliporeSigma). qPCR was performed using GoTaq qPCR Master Mix (A6002, Promega). The input RNA amount was normalized across all samples and 18 S rRNA or HtatsF1 was used for normalization of qPCR across samples. Primer sequences are listed in Key Resources Table. All primers were synthesized as custom DNA oligos from Integrated DNA technologies (IDT).

Cells for single-cell RNA-seq (scRNA-seq) were obtained from hind limb muscles of 2–3 month-old Pax7^tdT:Flk1^GFP mice following enzymatic digestion as previously described (Liu et al., 2015). Dead cells were excluded from the analysis using ZombieNIR (423105, Biolegends). TdTomato(+) and GFP(+) cells were sorted individually and then 20% of GFP(+) cells were spiked into 80% tdTomato(+). We loaded ~5000 cells into 1 channel of the Chromium system for each of these samples and prepared libraries according to the manufacturer’s protocol using version 2.0 chemistry (10 x Genomics). Following capture and lysis, we synthesized cDNA and amplified for 12 cycles as per the manufacturer’s protocol (10 X Genomics). The amplified cDNA was used to construct Illumina sequencing libraries that were each sequenced with ~300 K read/cell on one lane of an Illumina HiSeq 2500 machine. We used Cell Ranger 3.1 (10X Genomics) to process raw sequencing data. For A custom genome was constructed to include eGFP-SV40, tdTomato-WPRE-BGHPolyA and Pax7-IRES-CreERT2 transgenes. Detailed step-by-step instructions can be found at https://github.com/verma014/10XCustomRef, (copy archived at Verma, 2020). We carried out analyses of the filtered data using Seurat suite version 3.0 Stuart et al., 2019 in RStudio Team, 2020. For cell imputation, we utilized ALRA through the Seurat wrapper with default settings (Linderman et al., 2022). Additional scRNA-seq datasets were obtained from GEO and analyzed using the same method as listed above. A myogenic score was calculated based on the expression of Myog, Pax7, Myod1, and Myf5. Step-by-step instructions for the analysis can be found on https://github.com/verma014/10XCustomRef, (copy archived at Verma, 2020).

10 x Genomics scRNA-seq platform uses many more droplets than cells and so following a run, there are many droplets that do not have cells. These droplets still get sequenced with some of the RNA that is in the solution. This floating RNA can be used to estimate the ‘background’ in each droplet. A better description of this can be found by the developers of 'SoupX' (Young and Behjati, 2020). Since Cdh5 expression has previously been verified in MuSCs using RNAscope, we were able to use it as a positive control to remove the background or ‘soup’ from our data. If Cdh5 is absent from MuSC, we know that the background subtraction was too aggressive and that subtracting the Soup is not reliable in our case. In addition, we know certain genes that are considered to be specific for MuSCs, muscle ECs or muscle fibers based on the bulk RNA-seq (Verma et al., 2018). The top 5 genes that are specific to these population (and also detected by 10 x) were selected and used to show the background in our data set was 14.40% and 13.89% for the D0 and D3 dataset, respectively. The step-by-step instructions can be found on https://github.com/verma014/10XCustomRef, (copy archived at Verma, 2020).

FASTQ files were downloaded from SRA using SRA-toolkit. Sequences were trimmed using trimmomatic to remove adapter contamination and low-quality reads. Trimmed sequences were mapped to mouse mm10 using Hisat2 (Pertea et al., 2016). Transcript assembly was performed using StringTie (Pertea et al., 2016). Cell type specificity was determined as previously described (Verma et al., 2018). Microarray analysis was performed using the Affymetrix Transcriptome Analysis Console (TAC). Samples in each experiment were RNA normalized and the expression was acquired using the Affeymetrix Expression analysis console with gene level expression. Heatmaps were generated in Prism 9 (Graphpad, La Jolla, CA).

Statistical analysis was performed using Prism 9 (Graphpad, La Jolla, CA) or RStudio (RStudio Team, 2020). For comparison between two groups, an unpaired T-test was used. For comparison between multiple groups, a one-way ANOVA was used with multiple comparisons to the control. Distributions were compared using a chi-squared test. Graphing of the data was performed using Prism 9. Vector diagrams were modified using Graphic (Autodesk). All values are means ± SD unless noted otherwise. * indicates p<0.05, ** indicates p<0.01, *** indicates p<0.001.