Public RNA-seq data-based identification and functional analyses reveal that MXRA5 retains proliferative and migratory abilities of dental pulp stem cells

Dental pulp stem cells (DPSC) usually remain quiescent in the dental pulp tissue; however, once the dental pulp tissue is injured, DPSCs potently proliferate and migrate into the injury microenvironment and contribute to immuno-modulation and tissue repair. However, the key molecules that physiologically support the potent proliferation and migration of DPSCs have not been revealed. In this study, we searched publicly available transcriptome raw data sets, which contain comparable (i.e., equivalently cultured) DPSC and mesenchymal stem cell data. Three data sets were extracted from the Gene Expression Omnibus database and then processed and analyzed. MXRA5 was identified as the predominant DPSC-enriched gene associated with the extracellular matrix. MXRA5 is detected in human dental pulp tissues. Loss of MXRA5 drastically decreases the proliferation and migration of DSPCs, concomitantly with reduced expression of the genes associated with the cell cycle and microtubules. In addition to the known full-length isoform of MXRA5, a novel splice variant of MXRA5 was cloned in DPSCs. Recombinant MXRA5 coded by the novel splice variant potently induced the haptotaxis migration of DPSCs, which was inhibited by microtubule inhibitors. Collectively, MXRA5 is a key extracellular matrix protein in dental pulp tissue for maintaining the proliferation and migration of DPSCs.

Dental pulp stem cells (DPSC) are isolated from permanent teeth by general mesenchymal stem cell (MSC) markers such as CD44, CD73, CD90, and CD105 1 .Approximately 12% of isolated cells from human dental pulp tissue are identified as DPSCs by single-cell RNA-seq 2,3 .For dental regenerative therapies, DPSCs can differentiate into odontoblasts 4 , and several experimental animal models have shown the usefulness of DPSCs for dental pulp regeneration therapies, especially if combined with various types of growth factors and scaffolds 5 .The peripheral nerve system in the dental pulp tissue, particularly the area adjacent to the odontoblast layer, is well-developed and sensitive to stimuli such as bacteria, thermal changes, and the flow rate of liquid in dentinal tubules.Therefore, DPSCs possess a greater ability to differentiate into neuronal cells, and they have been experimentally applied to regenerate injured nerve tissue and support recovery from paralysis [6][7][8] .Furthermore, various animal models have been used to demonstrate the therapeutic potential of DPSCs for extraoral cell transplantation therapies in the treatment of skin wound injuries, liver fibrosis, myocardial infarction, and cerebral ischemia [9][10][11][12][13][14] .The main reason to use DPSCs in extraoral cell regeneration therapies is that teeth are often extracted for clinical purposes, such as non-occlusal third molars, supernumerary teeth, and orthodontic extraction, and the dental pulp tissue is easily accessed if the pulp chamber is opened by dental drilling.
In addition to the application of DPSCs for cell transplantation therapies, endogenous DPSCs may have pivotal roles in maintaining dental pulp tissue homeostasis, similar to MSCs in other tissues 15 .DPSCs usually MXRA5 is expressed in dental pulp tissue in vivo and selectively expressed in DPSCs.To examine the in vivo MXRA5 expression in human dental pulp tissue, whole pulp tissues were extracted from 3 premolars from different donors, and fixed pulp tissues were stained with MXRA5 and CD105, a marker of stem cells.MXRA5 and CD105 were detected in entire pulp tissue particularly in the perivascular tissue (arrow heads, Fig. 2A).Then, dental pulp tissues were newly extracted from premolars and organ-cultured for 24 h in the presence of TNF-α (10 ng/ml), and MXRA5 expression was significantly decreased (Fig. 2B).Increased IL-1β and IL-6 expression by TNF-α validated the inflammatory response of extracted dental pulp tissues against TNF-α.To validate the predominant expression pattern of MXRA5 in DPSCs compared with MSCs in the three GEO data sets, DPSCs and MSCs were equivalently cultured in our laboratory, and as expected, MXRA5 was 24-fold more highly expressed in our DPSCs than MSCs (Fig. 2C).Note that TGF-β1 strongly induced MXRA5 expression when DPSCs were cultured for 3-days in odontogenic induction medium.Then, DPSCs were cultured in the presence of LPS (10 and 100 ng/ml) or TNF-α (10 and 20 ng/ml), and the MXRA5 expression level was increased by LPS and decreased by TNF-α (Fig. 2D).Increased IL-1β and IL-6 expression by LPS and TNF-α validated the inflammatory response of DPSCs against LPS and TNF-α.These results suggest that MXRA5 was specifically expressed by DPSCs.

MXRA5 suppression decreases the expression of genes associated with the cell cycle.
To delineate the roles of MXRA5 in DPSCs, two independent specific siRNAs for MXRA5 were generated.si-MXRA5-1 and si-MXRA5-2 targeted exon 7 and the 3′UTR region, respectively (Table 1).
To investigate the effects of MXRA5 knockdown in DPSCs for the activation of mitogen-activated protein kinase (MAPK), the phosphorylation degree and total amount of ERK, p38, and JNK were evaluated by SDS-PAGE analyses (Fig. 4D).Phosphorylation of ERK and JNK, but not p38, was significantly decreased in DPSCsi-MXRA5-1 and DPSC-si-MXRA5-2 compared with DPSC-si-con (Fig. 4D).Additionally, the total amount of JNK, but not ERK or p-38, was significantly decreased in DPSC-MXRA5-1 and DPSC-si-MXRA5-2.These results indicate that the ERK signal activity was modulated by phosphorylation status, and the JNK signal activity was modulated by the decrease of JNK expression and concomitant phosphorylation status when MXRA5 expression was suppressed.Neither phosphorylation nor expression of p-38 was altered by MXRA5 knockdown.Next, the roles of MXRA5 in chemotaxis cell migration from the serum-free upper chamber to the serum-containing lower chamber were evaluated by Boyden chamber assay.DPSC-si-MXRA5-1 and DPSC-si-MXRA5-2 exhibited significantly decreased numbers of migrated cells compared with DPSC-si-con (Fig. 4E).LDH and terminal deoxynucleotidyl transferase (TdT)-mediated dUTP-biotin nick end labeling (TUNEL) assays of DPSCs transfected with siRNAs indicated that transfection of si-MXRA5-1 and si-MXRA5-2 did not differentially induce cell death or cell apoptosis compared with transfection of si-con.DPSCs were treated with 1% of Triton X-100 for the LDH assays and 10 μM of Actinomycin D for TUNEL assays, used as positive control experiments.These results verified that the decrease in cell migration was specifically attributed to the down-regulation of MXRA5 and not due to cell apoptosis or cell death.As shown in Supplemental Fig. 1, which lists the original top-ranked terms of www.nature.com/scientificreports/ the common si-MXRA5-down-regulated genes (Fig. 3D), in addition to cell cycle-related terms (colored blue), 3 microtubule-related pathways (colored red) were ranked.The expression changes in NEK2, CENPA, CDC20, and NUF2, which were classified into microtubule-related terms by the GO analyses and are known to support microtubule-related cell migration, were comparatively analyzed, and all these genes were down-regulated in DPSC-si-MXRA5-1 and DPSC-si-MXRA5-2 compared with DPSC-si-con (Fig. 4F).Fig. 2).Sequence reads of amplified products revealed two isoforms of MXRA5 that were expressed by DPSCs.The larger one is the known full-length MXRA5 and the smaller one is the novel MXRA5 isoform lacking exons 3, 4, 5, and 6 (Fig. 5A).From the schematic views shown in Fig. 5A, the amino acid sequence indicated that the novel splicing isoform, namely the pulp variant of MXRA5 (PV-MXRA5), lacked the leucine-rich repeat N-terminal (LRRNT) cap, leucine-rich repeat (LRR), and the leucine-rich repeat C-terminal (LRRCT) cap, but retained most of the immunoglobulin-like (Ig-like) domains.Entire amino acid sequences of full-length MXRA5 and PV-MXRA5 are shown in Supplemental Fig. 2. To examine the effects of full-length MXRA5 and PV-MXRA5 overexpression for the proliferation of DPSCs, DPSCs stably expressing either full-length MXRA5 or PV-MXRA5 tagged with FLAG were generated.However, because of the large size of full-length MXRA5 (2828 amino acids), we were unable to establish DPSCs stably expressing substantial levels of exogenous fulllength MXRA5.Consequently, only DPSCs overexpressing PV-MXRA5 (DPSC-PV-MXRA5) were used for the gain of function assays.Expression of transgenes tagged with FLAG was identified using anti-MXRA5 and anti-FLAG antibodies (Fig. 5B).Next, DPSC-PV-MXRA5 and DPSCs stably expressing empty expression plasmids (DPSC-empty) were cultured for 6 days, and the numbers of cells in 96-well plates were counted by WST assay (Fig. 5C).DPSC-PV-MXRA5 showed a significantly higher number of cells on day 4 compared with DPSCempty.Treatment with MAPK inhibitors showed that SP600125, a JNK inhibitor, significantly decreased the cell numbers of DPSC-PV-MXRA5 toward that of DPSC-empty at day 6 and day 9, and SB203580, a p38 inhibitor, significantly decreased the cell numbers of DPSC-PV-MXRA5 toward that of DPSC-empty at day 9. FR180204, an ERK1/2 inhibitor, did not decrease the cell numbers of DPSC-PV-MXRA5 (Fig. 5D).

Novel splicing isoforms of
Next, DPSC-empty and DPSC-PV-MXRA5 were seeded onto the upper chamber of the Boyden chamber, and chemotaxis cell migration was evaluated (Fig. 5E).DPSC-PVMXRA5 showed a significantly higher number of migrated cells.The addition of microtubule inhibitor-1 (paclitaxel) and microtubule inhibitor-2 (combretastatin A4) drastically inhibited cell migration (Fig. 5E).
Next, to evaluate the effect of PV-MXRA5 protein on DPSC migration, recombinant PV-MXRA5 (rePV-MXRA5) was generated using a mammalian expression system, and haptotaxis migration toward rePV-MXRA5 was investigated.The lower surface of the Boyden chamber was coated with various concentrations of either recombinant PV MXRA5 or vitronectin (0, 0.01, 0.1, 0.2, 0.5, and 1.0 μM), and an equal number of DPSCs was seeded onto the upper chamber.Vitronectin was comparatively evaluated because it is a well-known adhesion and migration substrate for many types of cells.The number of migrated cells was significantly increased if rePV-MXRA5 was seeded at 0.2, 0.5, and 1.0 μM (Fig. 5F).However, the number of migrated cells toward vitronectin was not significantly altered compared with DPBS-coated (equivalent to non-coated).Finally, the effects of microtubule inhibitors on haptotaxis cell migration of DPSCs toward rePV-MXRA5 (0.2 μM) were investigated (Fig. 5G).The number of DPSCs that migrated toward rePV-MXRA5 was drastically inhibited in the presence of microtubule inhibitors (5 and 10 μM).

Discussion
By analyzing public data sets containing DPSC and MSC transcriptome raw data, the present study demonstrated that MXRA5 is predominantly expressed by DPSCs, and MXRA5 is required for maintaining the strong proliferative and migratory properties of DPSCs by inducing cell cycle-and microtubule-related gene expression.Furthermore, recombinant proteins of the novel MXRA5 variant can potently induce haptotaxis migration of DPSCs.
Since three terms were associated with the extracellular matrix among the top 8 GO terms for common DPSC-enriched genes in all GEO data sets (Fig. 1A), the potent extracellular matrix secretion of DPSCs may be based on the potent regeneration ability of DPSCs.For example, the combination of polylactic acid with a decellularized extracellular matrix scaffold obtained from a DPSC culture enhanced the bone regeneration of experimental calvarial bone defects compared with polylactic acid alone 23 .The experimental details of the cell culture procedures used in GSE123973, GSE105145, and GSE113297, such as seeding density, passage number, serum concentration, and serum source, were different.However, it should be noted that MXRA5 was often highly ranked as a DPSC-up-regulated gene (Fig. 1B), showed a higher DPSC/MSC fold change (Fig. 1B, C),   and possessed the highest fold change among the MXRA family of genes (Fig. 1E).TNF-α stimulation, which suppresses DPSC proliferation and migration 24 , down-regulated MXRA5 in DPSCs (Fig. 2) in vitro and in vivo.To examine the effects of TNF-α for MXRA5 expression in dental pulp tissues, we conducted organ culturing, which retained the cell-to-cell and ECM-to-cell communications.IHC indicated that not only DPSCs, which is around 12% of human dental pulp tissue 2,3 , but also other dental pulp tissue residential cells may express a certain amount of MXRA5.Notably, the reduced expression of MXRA5 shown in Fig. 2C was caused by dental pulp residential cells, rather than DPSCs alone.Notably, cell cycle-related terms, such as "mitotic cell cycle, " "cell cycle, " "mitotic cell cycle process, " and "cell cycle process, " were predominantly enriched in GSE123973, in which the highest ranking of MXRA5 was observed compared with GSE105145 and GSE113297 (Fig. 1D).These trends indicate the positive role of MXRA5 in cell proliferation.As expected, it was revealed that cell cycle-related terms were selectively enriched in suppressed pathway terms by MXRA5 knockdown (Fig. 3) and drastically decreased in cell proliferation by MXRA5 knockdown (Fig. 4).
Proteins belonging to the Polo-like kinase (Plk) family, such as PLK1, PLK2, and PLK4, are serine/threonine kinases that regulate the cell cycle, particularly the control of sister chromatid separation 25 .Therefore, the loss of PLK1 or pharmacological inhibition of PLK activity resulted in slower cell proliferation concomitantly with spindle checkpoint blockade and G2/M phase arrest in tumor cells 26,27 .Consistently, a drastic decrease of PLK1 and PLK4 induced cell cycle arrest at the G2/M phase in DPSCs (Fig. 4B).MXRA5 suppression in WPMY-1 cells, the SV40 large T antigen immortalized stromal cell line, also inhibited cell proliferation, but in contrast to DPSCs, cell cycle arrest was identified in the G0/1 phase with down-regulation of CDK4, CDK2, Cyclin D1, and Cyclin A1/2 28 .This result indicated that different cell cycle-related target genes are relied on by different cell types.The mechanism by which MXRA5 suppression results in the down-regulation of cell cycle-related genes remains unknown in all cell types.However, in the promoter region of PLK1, there are transcriptional factor consensus DNA sequences for E2A, AP-1, AP2, SP1, and NFκB.Moreover, Forkhead transcription factors were reported to bind to the PLK1 promoter and induce PLK1 expression 29,30 .Among the Forkhead transcription factors, FoxM1, which is expressed in a cell cycle-dependent manner, regulated PLK1 expression.As FoxM1 functions were directly connected with Raf-MEK mediated MAPK activation 31 , MXRA5-induced MAPK activation possibly activates PLK expression by promoting transcriptional activities of Forkhead transcription factors in PLK gene loci.MAPKs, including ERK1/2, p38, and JNK pathways, have been identified as key intracellular signaling pathways triggered by MXRA5 28,32,33 .MXRA5 overexpression induced trophoblast cell invasion, and both the p38 and ERK1/2 inhibitors suppressed the MXRA5-induced invasive ability 32,33 .MXRA5 suppression resulted in the decreased phosphorylation of ERK1/2 and p38 without alteration of the total amount of ERK1/2 and p38 in the above trophoblast cells.Thus, similar to trophoblast cells and immortalized stromal cells, the genetic gain and loss of function assays revealed that MXRA5 positively regulated DPSC proliferation and migration (Figs. 4 and 5).However, the downstream pathway of MAPKs stimulated with MXRA5 appears to be different.As shown in Fig. 4, the MXRA5-dependent cell proliferation property of DPSCs relied on the ERK1/2 and JNK signal pathways but not the p38 pathway.Moreover, PV-MXRA5 enhanced cell proliferation depending on p38 and JNK (Fig. 5G).Even though the receptors of MXRA5 remain unknown, the different types, combinations, and interactions of MAPK upstream molecules, such as MAP4Ks and MAP3Ks 34 , are assumed to be involved in the activation of different MAPK downstream pathways among different cell types.
Target sequences of si-MXRA5-1 and si-MXRA5-2 are common for full-length MXRA5 and PV-MXRA5.However, endogenous PV-MXRA5 expression was undetectable owing to lower expression levels (Figs.3B and  5B).The estimated core protein size of PV-MXRA5 is 76.41 kDa, as shown in Supplemental Fig. 2.There were two slight bands in the vicinity of exogenous PV-MXRA5 (α-MXRA5 long exposure, Fig. 5B).However, these bands were non-specific because the band intensity was not reduced by the transfection of si-MXRA5-1 and si-MXRA5-2 (blue arrows, Fig. 3B).Therefore, phenotypic changes obtained by si-MXRA5-1 and si-MXRA5-2 were consequences of knockdown in both isoforms but mainly relied on full-length MXRA5.Full-length MXRA5 consists of 2828 amino acids, and the estimated core protein size is 312.15 kDa, as shown in Supplemental Fig. 2. Thus, it has been difficult to prepare DPSCs overexpressing full-length MXRA5 and full-length recombinant MXRA5 protein because of the lower transfection efficiency of the expression vector into DPSCs and recombinant protein-expressing cells, the low amount of recombinant protein secretion from the recombinant proteinexpressing cells, and insufficient enrichment of recombinant protein during the purification process.Instead, PV-MXRA5 was prepared, and its inducible roles for cell migration were disclosed (Fig. 5).Because vitronectin induced the haptotaxis migration of osteosarcoma MG63 cells and dental pulp fibroblastic cells 35,36 , DPSCs were also seeded onto the vitronectin-coated Boyden chamber.Considering that PV-MXRA5, but not vitronectin, induced haptotaxis migration of DPSCs, vitronectin might not be suitable for inducing DPSC migration, and PV-MXRA5 might be useful for specifically inducing DPSCs if applied as pulp direct capping materials and for accelerating dentin/pulp tissue wound healing.Ig-like domains of MXRA5, which are mostly conserved in PV-MXRA5, might be key for enhancing the migration of DSPCs.Ig-like domains are one of the frequentlyidentified protein domains recognized in various types of protein families and contribute to various molecular pathways such as ligand recognition by T cell antigen receptors, cell adhesion, and protein-protein binding 37,38 .Thus, Ig-like domains in MXRA5 may act as ligands of unknown receptors or extracellular competitors of ligand binding to receptors containing Ig-like domains for ligand recognition, and consequently, induce the expression of microtubule-related genes.Microtubules are major components in the cytoskeleton of eukaryotic cells and contribute to cell organization, especially for relatively larger cells such as MSCs 39,40 .However, microtubules dynamically polymerize and de-polymerize to modulate their length, and this dynamism is required for cell migration.Thus, up-regulation of microtubule-related genes by MXRA5 may be key for MXRA5-induced DPSC migration, although further studies are necessary to identify the functional amino acid part of MXRA5, MXRA5 receptors, and the intracellular molecular mechanisms linked with the induction of microtubule-related gene expression.

B A
regulatory system of MXRA5 expression by the NF-κB pathway must exist in DPSCs.NF-κB is known to inhibit Smad guiding to Smad-responsive elements and subsequent Smad transcriptional activity 47 .Therefore, the balance among TGF-β1 secreted from dentin, LPS from pathogenic bacteria, and TNF-α from immunological cells and pulp residential cells is key for MXRA5 expression in DPSCs during dentin/pulp healing processes and reparative dentin formation.
The present results demonstrated for the first time that MXRA5 is one of the key extracellular proteins that differentiate DPSCs from MSCs, and MXRA5 contributes to the proliferative and migratory properties of DPSCs through the induction of Pol family proteins, which are required for cell proliferation, and microtubule-related molecules, which are required for cell migration.Therefore, as a potential therapeutic for clinical use, MXRA5 may have genetic and extracellular applications in producing large-scale cultures of high-quality DPSCs and improving the outcomes of dental pulp wound healing therapies, such as pulp capping, by enhancing DPSC infiltration to the injury site.

Methods
Ethics.Dental pulp tissues were collected in compliance with the Hiroshima University ethical guidelines for epidemiological research.All experimental procedures were approved by the Committee of Research Ethics at Hiroshima University (Permit Number: E2021-2741).Informed consent was obtained from all participants of the study.

Bioinformatics analyses.
The GEO database was searched using "DPSC" or "dental pulp stem cells" and "MSC, " and as a result, two RNA-seq data sets (GSE123973 20 and GSE105145 21 ) and a microarray data set (GSE113297 22 ) were identified.The raw RNA expression data obtained from MSCs and DPSCs in GSE123973, GSE105145, and GSE113297 were downloaded and extracted.For processing of the RNA-seq data sets (GSE123973, GSE105145), adapter trimming was conducted using Trim Galore version 0.6.6 (http:// www.bioin forma tics.babra ham.ac.uk/ proje cts/ trim_ galore/) with default settings and then aligned to a reference genome (hg38) using HISAT2 version 2.2.1 48 .Tag directories were generated using "makeTagDirectory" in HOMER 49 , and gene expression at the exons was quantified using the "analyzeRepeast.pl"command in HOMER with "-strand both" and "-count exons" to identify differentially expressed genes using 3 raw data points of independent DPSC lines as targets and three raw data points of independent MSC lines as backgrounds in both the GSE123973 and GSE105145 data sets.For analyzing the microarray data set (GSE113297), expression profiles of all genes (GSE113297.top.table.tsv)were downloaded.Collectively, in the three GSE data sets (GSE123973, GSE105145, and GSE113297), the expression ratio of all transcripts was calculated by dividing the expression level in DPSCs by that in MSCs (DPSC/MSC), and the transcripts with DPSC/MSC ratios of more than 2 were extracted.
For analyzing whole-genomic gene expression changes in DPSCs after MXRA5 suppression, total RNA was purified from DPSCs transfected with si-MXRA5-1, si-MXRA5-2, or si-control.Purified RNA was DNase-treated and used in RNA-seq analyses as described previously 50 .Raw data sets were processed as described above, and tag directories were generated using "makeTagDirectory" in HOMER 49 .To identify the differentially expressed genes by the treatment with si-MXRA5-1, gene expression at the exons was quantified using the "analyzeRepeast.pl" command in HOMER with "-strand both" and "-count exons" for DPSCs treated with si-control as the target and DPSCs treated with si-MXRA5-1 as the background.The expression ratio was calculated for all obtained transcripts by dividing the expression level in DPSCs treated with si-control by that in DPSCs treated with si-MXRA5-1 (si-control/si-MXRA5-1), and the transcripts with si-control/si-MXRA5-1 ratios of more than 2 were extracted as suppressed genes by MXRA5 suppression and those with ratios of less than 0.5 were extracted as induced genes by MXRA5 suppression.Similarly, the differentially suppressed genes by the treatment with si-MXRA5-2 were identified, and si-control/si-MXRA5-2 was calculated.Regarding visualization in the UCSC (F) Undersides of the transwell membranes were pre-coated with the indicated concentrations of rePV-MXRA5 and vitronectin, seeded with DPSC in serum-free medium, and incubated for 16 h.(G) Undersides of the transwell membranes were pre-coated with 0.2 M rePV-MXRA5.DPSCs were seeded with microtubule inhibitors at the indicated concentrations and incubated for 16 h.After washing non-adherent cells, the attached cells were stained with 0.2% crystal violet and dissolved in 1% SDS solution.Absorbance was measured at 570 nm.Each column represents the mean ± SD, where n = 5 for each group in (C, D) and n = 4 for each group in (E, F, G). *p < 0.05; **p < 0.01; ***p < 0.001 significantly higher than DPSC-empty (C) and higher than DMSOtreated DPSC-empty at each time point (D), higher than DMSO-treated DPSC-empty (E), higher than DPSC seeded onto DPBS-coated chamber (F), and lower than DMSO-treated DPSC (G).n.s.means not significantly higher than DMSO-treated DPSC-empty, which indicates that a higher number of cells obtained by PV-MXRA5 was eliminated by the addition of MAPK inhibitors.Cell culture and stable cell generation.Human DPSCs and MSCs were purchased from Lonza Inc.
Quantitative PCR (qPCR) analysis.Total RNA from DPSCs and MSCs was purified, and cDNA was prepared as described previously 50,53 .Human HPRT was used as an internal reference control.PCR primer sequences for target genes are shown in Table 2.
Tissue extraction and immunohistochemistry. Healthy teeth were extracted for orthodontic purposes with informed consent, as described previously 54 .Briefly, the pulp chamber was opened by minimum drilling and pulp tissue was removed from the chamber using a barbed broach.For TNF-α stimulation, extracted pulp tissue was stimulated with and without 10 ng/ml of TNF-α (210-TA, R&D Systems, Minneapolis, MN) in DMEM with 10% serum for 24 h, and then, total RNA was extracted.For immunostaining, extracted pulp tissue was fixed using 4% paraformaldehyde in DPBS at 4 °C for 24 h.They were then dehydrated by passing through a graded ethanol series, placed in xylene, and embedded in paraffin.Immunostaining was performed on 5 µm-thick paraffin sections as described previously 52,55 .The primary antibodies used for immunostaining are described in Table 3.
Transient transfection of siRNA.RNA sequences for targeting MXRA5 by siRNA were selected using Enhanced siDirect, a web-based target-specific siRNA design software.Control siRNA was previously described 53,56,57 .siRNAs were generated by Sigma-Aldrich.The siRNA sequences of two types of siR-NAs for MXRA5 (si-MXRA5), and that of control siRNA (si-control), are shown in Table 1.siRNAs were

Cell proliferation assay.
DPSCs were seeded at a density of 1.5 × 10 3 cells/well onto a 96-well plate and then cultured.The next day of the seeding was set as day 0, and the medium was replaced every 3 days.The number of DPSCs was quantified using the Cell Counting Kit-8 (Dojindo, Kumamoto, Japan).

Cell cycle determination.
Cells were trypsinized and collected, and the cell cycle phase was determined using the cell cycle phase determination kit (Cayman Chemical, ANN Arbor, MI).After the staining procedure, flow cytometry was conducted using a 488 nm excitation laser.
Immunoblotting.For detecting secreted MXRA5, the supernatant of DPSC transfectants was precipitated and 40-fold concentrated with trichloroacetic acid, and precipitants were washed twice with acetone before reducing them.For detecting intracellular proteins, DPSCs were seeded onto a 24-well plate, and the next day, cells were transfected with siRNAs for 24 h.Then, the medium was replaced with DMEM supplemented with 10% serum for 3 days.Next, DPSCs transfected with control siRNA were directly lysed with 100 μl of LDS sample buffer (Thermo Fisher Scientific) and DTT (Thermo Fisher Scientific) before reducing.Similarly, DPSCs transfected with either si-MXRA5-1 or si-MXRA5-2 were directly lysed with 50 μl of LDS sample buffer and DTT before reducing.Because the number of cells decreased by MXRA5 knockdown, half of the LDS sample buffer with DTT for DPSCs transfected with control siRNA was used for DPSCs transfected with either si-MXRA5-1 or si-MXRA5-2.Then, reduced samples were loaded onto NuPAGE Bis-Tris (Thermo Fisher Scientific) gels in MOPS buffer for immunodetection with the primary and secondary antibodies described in Table 3.
LDH release assay.LDF assay was conducted as described previously 55 .DPSC cells were transfected with siRNAs for 24 h as described above, and then the supernatants were collected.To conduct a positive control experiment for the LDH release assay, DPSCs were treated with 1% Triton X-100 for 24 h, and then the supernatants were collected.The LDH release assay was performed using the LDH Cytotoxicity Detection Kit (Takara Bio Inc.).The supernatants were mixed with an equal amount of the detection buffer containing diaphorase, NAD+, and tetrazolium.The mixtures were incubated for 20 min at room temperature and quantified by measuring absorbance at 490 and 600 nm as reference wavelengths using a microtiter plate reader (Multiskan, Life Technologies).TUNEL assay.DPSC cells were transfected with siRNAs for 24 h as described above.As a positive control of apoptotic induction, DPSC cells were treated with 10 μM of Actinomycin D (FUJIFILM Wako Pure Chemical Corporation, Japan) for 48 h.Then, apoptotic DPSC cells were detected by TUNEL assay using Apoptosis Detection Kit (Takara bio, Japan).For quantification, DAPI-positive nuclei associated with siRNAs transfection or Actinomycin D treatment were considered and the fraction of TUNEL-positive nuclei was determined.At least 14,000 siRNA-transfected cells and 5700 Actinomycin D-treated cells were examined.

Preparation and purification of recombinant MXRA5-pulp variant protein.
For detecting fulllength and pulp variant MXRA5 in DPSCs, PCR was prepared with forward primers (GAC AAG ATG CCC AAG CGC GCG CAC TGG GGG GCC CTC T) binding to exon 2, which includes nucleotides coding the start codon, and reverse primers (TCA GAA GAC GTG GAT GTA AGT TGT TTT GGA GTC ACT G) binding to exon 7, which includes nucleotides coding the stop codon, and the 2 amplified products were sequenced.PV-MXRA5 cDNA used for generating pLVSIN-CMV-PV-MXRA5 was cloned into the pCEP4-Mul-PURD expression vector 35,[58][59][60] such that the amino-terminus of recombinant proteins was 6 × His-tagged.The PV-MXRA5 vector was transfected into 293EBNA cells using X-tremeGENE (Roche, Indianapolis, IN) and incubated for 24 h.The transfection medium was replaced with a growth medium containing puromycin (5 μg/ml), and transfected cells were then cultured for 3 days.Surviving cells were routinely cultured with puromycin (0.5 μg/ml) and used in the expression of the His-tagged recombinant PV-MXRA5 (rPV-MXRA5) protein, and rPV-MXRA5 was purified from the supernatants as described previously 35,[58][59][60] .

Figure 1 .
Figure 1.MXRA5 is selectively expressed by extracellular matrix-coding genes in DPSCs.(A) Venn diagram of genes selectively expressed in DPSCs compared with MSCs reveals 131 overlapping genes from the three GEO data sets (GSE123973, GSE105145, GSE113297), and the top 8 pathways of DPSC-up-regulated genes from the 131 genes are indicated.(B) The type of each GEO data set and the status of MXRA5 in each data set.(C) UCSC Genomic Browser tracks of MXRA5 gene locus in GEO data sets (GSE123973, GSE105145).Each data set contains three DPSC and three MSC RNA-seq data points.(D) Top 7 pathways of DPSC-up-regulated genes in GSE123973 (1841 genes), GSE105145 (1843 genes), and GSE113297 (832 genes).(E) Comparative FPKM ratio of MXRA family genes (MXRA1 to MXRA8) obtained by dividing the FPKM value of DPSCs by those of MSCs.ND = Not detected.

3 Figure 2 .
Figure 2. MXRA5 detection in vivo for dental pulp tissue and physiologically strong expression of MXRA5 in DPSCs.(A) Expression of MXRA5 and CD105, a marker of stem cells, in normal dental pulp tissues extracted from orthodontic extracted teeth.Fixed dental pulp tissues were stained with α-MXRA5 and α-CD105.Perivascular tissue was enlarged.(B) Extracted dental pulp tissues were divided in half and each half was either stimulated with or without TNF-α for 24 h, and then the total RNA was extracted to analyze MXRA5, IL-1β, and IL-6 expression.(C) DPSCs and MSCs were simultaneously cultured in the presence or absence of TGF-β1 under odontogenic induction by supplementation with ascorbic acid (50 μg/ml) and β-glycerophosphate (10 mM) for 3 days, and the total RNA was collected to analyze MXRA5.(D) DPSCs were stimulated with LPS (0, 10, and 100 ng/ml) or TNF-α (0, 10, and 20 ng/ml) for 24 h, and the total RNA was collected to analyze MXRA5, IL-1β, and IL-6 expression.Each column represents the mean ± SD, where n = 4 for each group in (B, D) and n = 3 for each group in (C).Scale bars correspond to 50 μm.*p < 0.05; ***p < 0.001 significantly different from the non-treated cells (B, D).
MXRA5 promote DPSC proliferation and migration.By conducting PCR using the primer pairs associated with the 2nd and last exons, two bands were visualized (Supplemental

Figure 3 .
Figure 3. Suppression of MXRA5 expression inhibits cell cycle-related gene expression in DPSCs.(A, B) DPSCs were transfected with si-control, si-MXRA5-1, or si-MXRA5-2.MXRA5 mRNA expression (A) and MXRA5 secretion (B) were analyzed using HPRT for normalization and extracellular HSP90β for loading amount validation.The black arrow indicates the MXRA5-specific band.Blue and green arrows indicate nonspecific bands.Original blots are presented in Supplementary Fig.3.(C) Total RNAs were collected from DPSCs transfected with si-control, si-MXRA5-1, or si-MXRA5-2, and whole-genomic transcriptional changes were assessed by RNA-seq.The scatter plot shows a comparison of the FPKM ratio obtained by dividing the FPKM value of si-con-DPSCs by that of si-MXRA5-1-DPSCs (x-axis) and by dividing the FPKM value of si-con-DPSCs by that of si-MXRA5-2-DPSCs (y-axis).(D) The upper Venn diagram of genes down-regulated by si-MXRA5-1 transfection (579 genes) and genes down-regulated by si-MXRA5-2 transfection (1057 genes) reveals 281 overlapping genes.The lower Venn diagram of genes up-regulated by si-MXRA5-1 transfection (472 genes) and genes up-regulated by si-MXRA5-2 transfection (619 genes) reveals 115 overlapping genes.The top 5 pathways of commonly down-regulated and up-regulated genes from the 281 and 115 overlapping genes are indicated, respectively.(E) UCSC Genomic Browser tracks of MXRA5, PLK1, PLK4, and CDK1 genes show exon-specific tag accumulation in si-con-DPSC duplicates and a drastic decrease in tag accumulation in si-MXRA5-1-DPSC and si-MXRA5-2-DPSC duplicates.(F) Suppressed expression of PLK1, PLK4, and CDK1 confirmed by qPCR.Each column represents the mean ± SD, and n = 3 for each group in (A, F). ***p < 0.001 significantly lower than si-con-DPSC.

Figure 4 .
Figure 4. Suppression of MXRA5 expression inhibits cell proliferation and migration in DPSCs.(A-F) DPSCs were transfected with si-control, si-MXRA5-1, or si-MXRA5-2.Knockdown of MXRA5 inhibited cell proliferation (A), increased cell population in G2/M phases (B), inhibited PLK1, PLK4, and CDK1 expression (C), inhibited phosphorylation of ERK and JNK, and total JNK expression (D), inhibited migration toward 10% serum (E), and suppressed microtubule-related genes (F).The LDH release and TUNEL-positive fraction of siRNA-transfected cells were examined, and the treatment with 1% Triton X-100 and Actinomycin D (Act D) was conducted as an experimental positive control (E).Original blots are presented in Supplementary Figs. 4, 5, 6, and 7.Each column represents the mean ± SD, where n = 5 for each group in (A), n = 4 for each group in (E), and n = 3 for each group in (B, C, D, F). *p < 0.05; **p < 0.01; ***p < 0.001 significantly lower than DPSCs transfected with si-control at each time point (A), higher than DPSCs transfected with si-control (B), lower than DPSCs transfected with si-control (C, D, E, F).

Figure 5 .
Figure 5. Novel splicing variant of MXRA5 enhances cell proliferation and migration in DPSCs.(A) Schematic exon views and protein functional motifs of two isoforms of MXRA5.(B) Stable transfection of pulp variant MXRA5 (PV-MXRA5) into DPSC to generate DPSC-PV-MXRA5 was validated by SDS-PAGE analyses.The red arrow indicates exogenous PV-MXRA5.The green arrow indicates full-length MXRA5.The blue arrow indicates a non-specific band.(C) DPSC-PV-MXRA5 showed aggressive proliferation compared with DPSC transfected with the control plasmid (DPSC-empty).Original blots are presented in Supplementary Fig. 8. (D) MAPK inhibitors differentially decreased accelerated proliferative properties of DPSC-PV-MXRA5.(E) Transwell plates were seeded with DPSC-empty or DPSC-PV-MXRA5 in the upper chamber in the presence or absence of microtubules inhibitors, paclitaxel and combretastatin A4, and cell migration toward 10% serum was evaluated.(F)Undersides of the transwell membranes were pre-coated with the indicated concentrations of rePV-MXRA5 and vitronectin, seeded with DPSC in serum-free medium, and incubated for 16 h.(G) Undersides of the transwell membranes were pre-coated with 0.2 M rePV-MXRA5.DPSCs were seeded with microtubule inhibitors at the indicated concentrations and incubated for 16 h.After washing non-adherent cells, the attached cells were stained with 0.2% crystal violet and dissolved in 1% SDS solution.Absorbance was measured at 570 nm.Each column represents the mean ± SD, where n = 5 for each group in (C, D) and n = 4 for each group in (E, F, G). *p < 0.05; **p < 0.01; ***p < 0.001 significantly higher than DPSC-empty (C) and higher than DMSOtreated DPSC-empty at each time point (D), higher than DMSO-treated DPSC-empty (E), higher than DPSC seeded onto DPBS-coated chamber (F), and lower than DMSO-treated DPSC (G).n.s.means not significantly higher than DMSO-treated DPSC-empty, which indicates that a higher number of cells obtained by PV-MXRA5 was eliminated by the addition of MAPK inhibitors.

Table 1 .
Target sequences for siRNA duplex.