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<front>
<journal-meta>
<journal-id journal-id-type="publisher-id">Front. Oncol.</journal-id>
<journal-title>Frontiers in Oncology</journal-title>
<abbrev-journal-title abbrev-type="pubmed">Front. Oncol.</abbrev-journal-title>
<issn pub-type="epub">2234-943X</issn>
<publisher>
<publisher-name>Frontiers Media S.A.</publisher-name>
</publisher>
</journal-meta>
<article-meta>
<article-id pub-id-type="doi">10.3389/fonc.2022.853979</article-id>
<article-categories>
<subj-group subj-group-type="heading">
<subject>Oncology</subject>
<subj-group>
<subject>Original Research</subject>
</subj-group>
</subj-group>
</article-categories>
<title-group>
<article-title>Identification of Cell Subpopulations and Interactive Signaling Pathways From a Single-Cell RNA Sequencing Dataset in Osteosarcoma: A Comprehensive Bioinformatics Analysis</article-title>
</title-group>
<contrib-group>
<contrib contrib-type="author">
<name>
<surname>Wu</surname>
<given-names>Rong</given-names>
</name>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Dou</surname>
<given-names>Xiaojie</given-names>
</name>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Li</surname>
<given-names>Haidong</given-names>
</name>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Sun</surname>
<given-names>Zhenguo</given-names>
</name>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Li</surname>
<given-names>Heng</given-names>
</name>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Shen</surname>
<given-names>Yuxin</given-names>
</name>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Weng</surname>
<given-names>Wei</given-names>
</name>
</contrib>
<contrib contrib-type="author" corresp="yes">
<name>
<surname>Min</surname>
<given-names>Jikang</given-names>
</name>
<xref ref-type="author-notes" rid="fn001">
<sup>*</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/1634535"/>
</contrib>
</contrib-group>
<aff id="aff1">
<institution>Department of Orthopaedics, The First People&#x2019;s Hospital of Huzhou, The First Affiliated Hospital of Huzhou University</institution>, <addr-line>Huzhou</addr-line>, <country>China</country>
</aff>
<author-notes>
<fn fn-type="edited-by">
<p>Edited by: Chang Zou, Jinan University, China</p>
</fn>
<fn fn-type="edited-by">
<p>Reviewed by: Fukuan Du, Southwest Medical University, China; Tao Tang, The Chinese University of Hong Kong, China</p>
</fn>
<fn fn-type="corresp" id="fn001">
<p>*Correspondence: Jikang Min, <email xlink:href="mailto:minjikang@163.com">minjikang@163.com</email> </p>
</fn>
<fn fn-type="other" id="fn002">
<p>This article was submitted to Pharmacology of Anti-Cancer Drugs, a section of the journal Frontiers in Oncology</p>
</fn>
</author-notes>
<pub-date pub-type="epub">
<day>20</day>
<month>04</month>
<year>2022</year>
</pub-date>
<pub-date pub-type="collection">
<year>2022</year>
</pub-date>
<volume>12</volume>
<elocation-id>853979</elocation-id>
<history>
<date date-type="received">
<day>13</day>
<month>01</month>
<year>2022</year>
</date>
<date date-type="accepted">
<day>03</day>
<month>03</month>
<year>2022</year>
</date>
</history>
<permissions>
<copyright-statement>Copyright &#xa9; 2022 Wu, Dou, Li, Sun, Li, Shen, Weng and Min</copyright-statement>
<copyright-year>2022</copyright-year>
<copyright-holder>Wu, Dou, Li, Sun, Li, Shen, Weng and Min</copyright-holder>
<license xlink:href="http://creativecommons.org/licenses/by/4.0/">
<p>This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.</p>
</license>
</permissions>
<abstract>
<p>Osteosarcoma is a type of highly aggressive bone tumor arising from primitive cells of mesenchymal origin in adults and is associated with a high rate of tumor relapse. However, there is an urgent need to clarify the molecular mechanisms underlying osteosarcoma development. The present study performed integrated bioinformatics analysis in a single-cell RNA sequencing dataset and explored the potential interactive signaling pathways associated with osteosarcoma development. Single-cell transcriptomic analysis of osteosarcoma tissues was performed by using the Seurat R package, the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of differentially expressed genes was performed by using the clusterProfiler R package, and the cell&#x2013;cell interaction analysis was performed by using the CellPhoneDB package. Our results showed that 11 clustered cell types were identified across 11 osteosarcoma tissues, with cell types including &#x201c;osteoblastic&#x201d;, &#x201c;myeloid&#x201d;, &#x201c;osteoblastic_proli&#x201d;, &#x201c;osteoclast&#x201d;, and &#x201c;tumor-infiltrating lymphocytes (TILs)&#x201d; as the main types. The DEGs between different cell types from primary, metastatic, and recurrent osteosarcomas were mainly enriched in the GO terms including &#x201c;negative regulation of hydrolase activity&#x201d;, &#x201c;regulation of peptidase activity&#x201d;, &#x201c;regulation of binding&#x201d;, &#x201c;negative regulation of proteolysis&#x201d;, and &#x201c;negative regulation of peptidase activity&#x201d; and in the KEGG pathways including &#x201c;transcriptional misregulation in cancer&#x201d;, &#x201c;cellular senescence&#x201d;, &#x201c;apoptosis&#x201d;, &#x201c;FoxO signaling pathway&#x201d;, &#x201c;cell cycle&#x201d;, &#x201c;NF-kappa B signaling pathway&#x201d;, &#x201c;p53 signaling pathway&#x201d;, &#x201c;pentose phosphate pathway&#x201d;, and &#x201c;protein export&#x201d;. For the cell&#x2013;cell communication network analysis, the different interaction profiles between cell types were detected among primary, metastatic, and recurrent osteosarcomas. Further exploration of the KEGG pathway revealed that these ligand/receptor interactions may be associated with the NF-&#x3ba;B signaling pathway and its interacted mediators. In conclusion, the present study for the first time explored the scRNA-seq dataset in osteosarcoma, and our results revealed the 11 clustered cell types and demonstrated the novel cell&#x2013;cell interactions among different cell types in primary, metastatic, and recurrent osteosarcomas. The NF-&#x3ba;B signaling pathway may play a key role in regulating the TME of osteosarcoma. The present study may provide new insights into understanding the molecular mechanisms of osteosarcoma pathophysiology.</p>
</abstract>
<kwd-group>
<kwd>osteosarcoma</kwd>
<kwd>scRNA sequencing</kwd>
<kwd>cell types</kwd>
<kwd>interaction</kwd>
<kwd>NF-&#x3ba;B</kwd>
</kwd-group>
<counts>
<fig-count count="5"/>
<table-count count="0"/>
<equation-count count="0"/>
<ref-count count="27"/>
<page-count count="9"/>
<word-count count="3335"/>
</counts>
</article-meta>
</front>
<body>
<sec id="s1" sec-type="intro">
<title>Introduction</title>
<p>Osteosarcoma is a type of highly aggressive bone tumor arising from primitive cells of mesenchymal origin in adults and is associated with a high rate of tumor relapse (<xref ref-type="bibr" rid="B1">1</xref>, <xref ref-type="bibr" rid="B2">2</xref>). The main treatments for this malignancy are surgical resection combined with multiagent chemotherapy. Unfortunately, the incidence of osteosarcoma is around 5/1,000,000, and patients with osteosarcoma had a 5-year overall survival rate of ~15% (<xref ref-type="bibr" rid="B3">3</xref>&#x2013;<xref ref-type="bibr" rid="B5">5</xref>). To our best knowledge, the pathophysiology of osteosarcoma remains unclear. The pathogenesis of osteosarcoma is complicated by the tumor microenvironment (TME) including immune cells, malignant mesenchymal tumor cells, vascular networks, and fibroblasts (<xref ref-type="bibr" rid="B6">6</xref>, <xref ref-type="bibr" rid="B7">7</xref>). Therefore, it is of great importance to examine the molecular mechanisms underlying the pathophysiology of osteosarcoma and develop novel therapies for the treatment of osteosarcoma.</p>
<p>The conventional transcriptomic profiling is performed on mixed cell populations, which has an insufficient resolution for detecting specific cellular types and fails to assess the complexity of intratumoral heterogeneity (<xref ref-type="bibr" rid="B8">8</xref>, <xref ref-type="bibr" rid="B9">9</xref>). Up to date, single-cell RNA sequencing (scRNA-seq) plays an important role in identifying the intratumor heterogeneity of different types of cancers and the cellular interaction within the TME. Davidson et&#xa0;al. performed scRNA-seq to examine the stromal compartment in murine melanoma and draining lymph nodes at points across tumor development and revealed a dynamic stromal niche that promoted tumor growth (<xref ref-type="bibr" rid="B10">10</xref>). Maynard et&#xa0;al. demonstrated that biological features revealed by scRNA-seq were biomarkers of clinical outcomes in human lung cancer, which highlighted how therapy-induced adaptation of the multicellular ecosystem of metastatic cancer shaped clinical outcomes (<xref ref-type="bibr" rid="B11">11</xref>). Chung et&#xa0;al. performed scRNA-seq and demonstrated that breast cancer transcriptome exhibited a wide range of intratumoral heterogeneity, which was shaped by the tumor cells and immune cells in the surrounding microenvironment (<xref ref-type="bibr" rid="B12">12</xref>). To our best knowledge, various studies have performed scRNA-seq in osteosarcoma under different experimental settings. For example, Liu et&#xa0;al. showed that single-cell transcriptomics elucidated the complexity of the tumor microenvironment of treatment-naive osteosarcoma (<xref ref-type="bibr" rid="B13">13</xref>). Zhou et&#xa0;al. identified 11 major cell clusters based on unbiased clustering of gene expression profiles and canonical markers <italic>via</italic> RN sequencing of 100,987 individual cells from 7 primary, 2 recurrent, and 2 lung metastatic osteosarcoma lesions (<xref ref-type="bibr" rid="B14">14</xref>). These studies highlighted the important applications of scRNA-seq in deciphering the molecular mechanisms underlying osteosarcoma pathophysiology.</p>
<p>Recently, reanalysis of high-throughput datasets including the scRNA-seq data in cancer studies has revealed many important findings. In the present study, we further explored the scRNA-seq data from the GEO database (GSE152048) and investigated the novel signaling pathways that may contribute to osteosarcoma metastasis.</p>
</sec>
<sec id="s2" sec-type="materials|methods">
<title>Materials and Methods</title>
<sec id="s2_1">
<title>Data Source Collection</title>
<p>The scRNA-seq files were accessed from GSE152048 <italic>via</italic> the GEO database. The dataset was based on the 10X Genomics platform. The dataset includes 11 tumor samples from 11 osteosarcoma patients. Among them, eight lesions were osteoblastic osteosarcoma, consisting of six primary, one recurrent, and one lung metastatic lesions, and three were chondroblastic osteosarcoma, each being derived from primary, recurrent, and lung metastasis sites.</p>
</sec>
<sec id="s2_2">
<title>Analysis of scRNA-seq Data</title>
<p>The scRNA-seq data were processed by using the Seurat R package according to standard protocols (<xref ref-type="bibr" rid="B15">15</xref>). We excluded cells with less than 200 detected genes and also genes that were detected in less than 3 cells and limited the mitochondria proportion to less than 20%. The data normalization was performed by using the LogNormalize method. T-distributed stochastic neighbor embedding (t-SNE), a non-linear dimensionality reduction method, was applied after principal component analysis (PCA) for unsupervised clustering and unbiased visualizing of cell populations on a two-dimensional map. The marker genes of each cluster were detected using the &#x201c;FindAllMarkers&#x201d; function, and the criteria for identifying marker genes were set as follows: absolute log2 fold change (FC) &#x2265;1 and the minimum cell population fraction in either of the two populations was 0.25. The expression pattern of each marker gene among clusters was visualized by applying the &#x201c;DotPlot&#x201d; function in Seurat. Marker-based cell-type annotation was performed by using the SingleR package.</p>
</sec>
<sec id="s2_3">
<title>Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes Analyses</title>
<p>The clusterProfiler R package was used to perform the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway functional enrichment analysis. The marker genes were assigned to various biological processes (BPs), cellular components (CCs), molecular functions (MFs), and pathways. Significant enrichment was set as <italic>P &lt;</italic>0.05.</p>
</sec>
<sec id="s2_4">
<title>Cell&#x2013;Cell Interaction Prediction in Single-Cell Transcriptomics Data</title>
<p>Cell&#x2013;cell interactions among all cell types were predicted based on the single-cell RNA sequencing data with the CellPhoneDB package (version 2.0.0) (<xref ref-type="bibr" rid="B16">16</xref>). The mean of the individual partner average expression values in the corresponding interacting pairs between different cell types was compared, and only the ligand&#x2013;receptor interaction with <italic>P</italic>-value &lt;0.05 was used to predict cell&#x2013;cell interaction in the cell types. All the R codes for plotting the figures are presented in the <xref ref-type="supplementary-material" rid="SM1">
<bold>Supplemental Materials</bold>
</xref>.</p>
</sec>
</sec>
<sec id="s3" sec-type="results">
<title>Results</title>
<sec id="s3_1">
<title>Single-Cell Transcriptomic Analysis of Osteosarcoma Tissues</title>
<p>Based on the analysis of GSE152048, unbiased clustering of the cells identified 11 main clusters in parallel. The t-SNE plot of the different cell types based on the gene profiles and canonical markers in osteosarcoma tissues is shown in <xref ref-type="fig" rid="f1">
<bold>Figure&#xa0;1A</bold>
</xref>. As shown in <xref ref-type="fig" rid="f1">
<bold>Figure&#xa0;1B</bold>
</xref>, the relative proportion of each cell type in all osteosarcoma tissues was shown, and the osteoblastic cells were the largest population among all the cell types. Furthermore, the t-SNE plot of different cell types colored according to the individual osteosarcoma sample was shown (<xref ref-type="fig" rid="f1">
<bold>Figure&#xa0;1C</bold>
</xref>). The relative proportion of each cell cluster according to different types of osteosarcoma is shown in <xref ref-type="fig" rid="f1">
<bold>Figure&#xa0;1D</bold>
</xref>, and all the cell types except chondroblastic cells were found in primary osteosarcoma, while a large proportion of chondroblastic cells was detected in recurrent osteosarcoma.</p>
<fig id="f1" position="float">
<label>Figure&#xa0;1</label>
<caption>
<p>Single-cell transcriptomic analysis of osteosarcoma tissues. <bold>(A)</bold> The t-SNE plot of different cell types in osteosarcoma tissues. <bold>(B)</bold> The relative proportion of each cell cluster in all osteosarcoma tissues was shown. <bold>(C)</bold> Similar t-SNE plot of different cell types colored according to the individual osteosarcoma sample. <bold>(D)</bold> The relative proportion of each cell cluster according to different types of osteosarcoma was shown.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fonc-12-853979-g001.tif"/>
</fig>
</sec>
<sec id="s3_2">
<title>Functional Enrichment Analysis of Differentially Expressed Genes</title>
<p>Differentially expressed genes (DEGs) compared between different groups are shown in <xref ref-type="fig" rid="f2">
<bold>Figure&#xa0;2A</bold>
</xref>, and the overlapped genes between different groups are illustrated in the Venn diagram (<xref ref-type="fig" rid="f2">
<bold>Figure&#xa0;2A</bold>
</xref>). A total of 16, 1, 3, 1, and 1 DEGs were, respectively, detected between the chondroblastic.MP and the chondroblastic.RP groups, the chondroblastic.MP and the osteoblastic.MP groups, the chondroblastic.RP and the osteoblastic.MP groups, the chondroblastic.RP and the osteoblastic.RP groups, and the osteoblastic.MP and the osteoblastic.RP groups. The 22 overlapped DEGs were subjected to GO and KEGG pathway enrichment analysis. The DEGs were mainly enriched in the GO terms including &#x201c;negative regulation of hydrolase activity&#x201d;, &#x201c;regulation of peptidase activity&#x201d;, &#x201c;regulation of binding&#x201d;, &#x201c;negative regulation of proteolysis&#x201d;, &#x201c;negative regulation of peptidase activity&#x201d;, and so on (<xref ref-type="fig" rid="f2">
<bold>Figure&#xa0;2B</bold>
</xref>). The DEGs were mainly enriched in the KEGG pathways including &#x201c;transcriptional misregulation in cancer&#x201d;, &#x201c;cellular senescence&#x201d;, &#x201c;apoptosis&#x201d;, &#x201c;FoxO signaling pathway&#x201d;, &#x201c;cell cycle&#x201d;, &#x201c;NF-kappa B signaling pathway&#x201d;, &#x201c;p53 signaling pathway&#x201d;, &#x201c;pentose phosphate pathway&#x201d;, and &#x201c;protein export&#x201d; (<xref ref-type="fig" rid="f2">
<bold>Figure&#xa0;2C</bold>
</xref>).</p>
<fig id="f2" position="float">
<label>Figure&#xa0;2</label>
<caption>
<p>Functional enrichment analysis of differentially expressed genes (DEGs). <bold>(A)</bold> The Venn diagram showed the overlapped DEGs according to different cell types. Chondroblastic. MP = the DEGs in chondroblastic cells from metastatic osteosarcoma as compared with those from primary osteosarcoma. Chondroblastic. RP = the DEGs in chondroblastic cells from recurrent osteosarcoma as compared with those from primary osteosarcoma. Osteoblastic. MP = the DEGs in osteoblastic cells from metastatic osteosarcoma as compared with those from primary osteosarcoma. Osteoblastic. RP = the DEGs in osteoblastic cells from recurrent osteosarcoma as compared with those from primary osteosarcoma. <bold>(B)</bold> The GO enrichment analysis of overlapped DEGs between each of two groups. <bold>(C)</bold> The KEGG pathway enrichment analysis of overlapped DEGs between each of two groups.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fonc-12-853979-g002.tif"/>
</fig>
</sec>
<sec id="s3_3">
<title>Cell&#x2013;Cell Communication Network Among Different Cell Types in Primary, Metastatic, and Recurrent Osteosarcomas</title>
<p>The cell&#x2013;cell communication network among different cell types in primary osteosarcoma is shown in <xref ref-type="fig" rid="f3">
<bold>Figure&#xa0;3A</bold>
</xref>. The detailed analysis revealed that chondroblastic cells mainly interacted with cell types including &#x201c;fibroblast&#x201d;, &#x201c;osteoblastic&#x201d;, &#x201c;osteoblastic_proli&#x201d;, &#x201c;osteoclast&#x201d;, &#x201c;MSC&#x201d;, and so on (<xref ref-type="fig" rid="f3">
<bold>Figure&#xa0;3B</bold>
</xref>); osteoblastic cells mainly interacted with cell types including &#x201c;osteoblastic_proli&#x201d;, &#x201c;fibroblast&#x201d;, &#x201c;endothelial&#x201d;, &#x201c;MSC&#x201d;, &#x201c;pericyte&#x201d;, &#x201c;osteoclast&#x201d;, and so on (<xref ref-type="fig" rid="f3">
<bold>Figure&#xa0;3C</bold>
</xref>). The cell&#x2013;cell communication network for different types of cells in metastatic osteosarcoma is illustrated in <xref ref-type="fig" rid="f3">
<bold>Figure&#xa0;3D</bold>
</xref>. Further detailed analysis showed that chondroblastic cells mainly interacted with cell types including &#x201c;osteoblastic_proli&#x201d;, &#x201c;endothelial&#x201d;, &#x201c;MSC&#x201d;, &#x201c;pericyte&#x201d;, &#x201c;myoblast&#x201d;, &#x201c;myeloid&#x201d;, and so on (<xref ref-type="fig" rid="f3">
<bold>Figure&#xa0;3E</bold>
</xref>); osteoblastic cells mainly interacted with cell types including &#x201c;osteoblastic_proli&#x201d;, &#x201c;MSC&#x201d;, &#x201c;endothelial&#x201d;, &#x201c;pericyte&#x201d;, and so on (<xref ref-type="fig" rid="f3">
<bold>Figure&#xa0;3F</bold>
</xref>). The cell&#x2013;cell communication network for different types of cells in recurrent osteosarcoma is shown in <xref ref-type="fig" rid="f3">
<bold>Figure&#xa0;3G</bold>
</xref>. The detailed analysis showed that chondroblastic cells mainly interacted with cell types including &#x201c;pericyte&#x201d;, &#x201c;MSC&#x201d;, &#x201c;osteoblastic_proli&#x201d;, &#x201c;osteoblastic&#x201d;, &#x201c;endothelial&#x201d;, and so on (<xref ref-type="fig" rid="f3">
<bold>Figure&#xa0;3H</bold>
</xref>); osteoblastic cells mainly interacted with cell types including &#x201c;osteoblastic_proli&#x201d;, &#x201c;pericyte&#x201d;, &#x201c;MSC&#x201d;, &#x201c;endothelial&#x201d;, &#x201c;chondroblastic&#x201d;, and so on (<xref ref-type="fig" rid="f3">
<bold>Figure&#xa0;3I</bold>
</xref>).</p>
<fig id="f3" position="float">
<label>Figure&#xa0;3</label>
<caption>
<p>Cell&#x2013;cell communication network among different cell types in primary, metastatic, and recurrent osteosarcomas. <bold>(A)</bold> The cell&#x2013;cell communication network among different cell types in primary osteosarcoma. <bold>(B)</bold> The communication network between chondroblastic cells and other types of cells in primary osteosarcoma. <bold>(C)</bold> The communication network between osteoblastic cells and other types of cells in primary osteosarcoma. <bold>(D)</bold> The cell&#x2013;cell communication network among different cell types in metastatic osteosarcoma. <bold>(E)</bold> The communication network between chondroblastic cells and other types of cells in metastatic osteosarcoma. <bold>(F)</bold> The communication network between osteoblastic cells and other types of cells in metastatic osteosarcoma. The thickness of the line or the number on the line is proportional to the number of ligand&#x2013;receptor pairs connecting the two cell types. <bold>(G)</bold> The cell&#x2013;cell communication network among different cell types in recurrent osteosarcoma. <bold>(H)</bold> The communication network between chondroblastic cells and other types of cells in recurrent osteosarcoma. <bold>(I)</bold> The communication network between osteoblastic cells and other types of cells in recurrent osteosarcoma.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fonc-12-853979-g003.tif"/>
</fig>
</sec>
<sec id="s3_4">
<title>Ligand&#x2013;Receptor Interactions Between Various Types of Cells From Primary, Metastatic, and Recurrent Osteosarcomas</title>
<p>The common ligands/receptors in all types of cells among primary, metastatic, and recurrent osteosarcomas are shown in <xref ref-type="fig" rid="f4">
<bold>Figure&#xa0;4A</bold>
</xref>, and a total of 1,075 common ligands/receptors were detected among primary, metastatic, and recurrent osteosarcomas. In addition, the expression of ligands/receptors in different types of cells in primary, metastatic, and recurrent osteosarcomas was illustrated as a heatmap plot (<xref ref-type="fig" rid="f4">
<bold>Figures&#xa0;4B&#x2013;D</bold>
</xref>).</p>
<fig id="f4" position="float">
<label>Figure&#xa0;4</label>
<caption>
<p>Ligand&#x2013;receptor interactions between various types of cells from primary, metastatic, and recurrent osteosarcomas. <bold>(A)</bold> The common ligands/receptors in primary, metastatic, and recurrent osteosarcomas were illustrated as a Venn diagram. <bold>(B)</bold> The expression levels of ligands/receptors in all types of cells from primary osteosarcoma were shown as a heatmap plot. <bold>(C)</bold> The expression levels of ligands/receptors in all types of cells from metastatic osteosarcoma were shown as a heatmap plot. <bold>(D)</bold> The expression levels of ligands/receptors in all types of cells from recurrent osteosarcoma were shown as a heatmap plot.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fonc-12-853979-g004.tif"/>
</fig>
</sec>
<sec id="s3_5">
<title>Functional Enrichment Analysis and Interaction Between Nuclear Factor-&#x3ba;B Signaling Pathway and Ligands/Receptors</title>
<p>As shown in <xref ref-type="fig" rid="f5">
<bold>Figure&#xa0;5A</bold>
</xref>, the common ligands/receptors were significantly enriched in the GO terms including &#x201c;leukocyte migration&#x201d;, &#x201c;cell chemotaxis&#x201d;, &#x201c;peptidyl-tyrosine modification&#x201d;, &#x201c;peptidyl-tyrosine phosphorylation&#x201d;, &#x201c;regulation of cell&#x2013;cell adhesion&#x201d;, &#x201c;positive regulation of cell adhesion&#x201d;, and so on. For the KEGG pathway, the common ligands/receptors were significantly enriched in &#x201c;cytokine&#x2013;cytokine receptor interaction&#x201d;, &#x201c;neuroactive ligand&#x2013;receptor interaction&#x201d;, &#x201c;PI3K&#x2013;Akt signaling pathway&#x201d;, &#x201c;MAPK signaling pathway&#x201d;, &#x201c;NF-&#x3ba;B signaling pathway&#x201d;, and so on (<xref ref-type="fig" rid="f5">
<bold>Figure&#xa0;5B</bold>
</xref>).</p>
<fig id="f5" position="float">
<label>Figure&#xa0;5</label>
<caption>
<p>Functional enrichment analysis and interaction between the NF-&#x3ba;B signaling pathway and ligands/receptors. <bold>(A)</bold> GO enrichment analysis of common ligands/receptors among primary, metastatic, and recurrent osteosarcomas; <bold>(B)</bold> KEGG enrichment analysis of common ligands/receptors among primary, metastatic, and recurrent osteosarcomas. <bold>(C)</bold> The interaction between the NF-&#x3ba;B signaling pathway and common ligands/receptors in osteoblastic cells. <bold>(D)</bold> The interaction between the NF-&#x3ba;B signaling pathway and common ligands/receptors in chondroblastic cells.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fonc-12-853979-g005.tif"/>
</fig>
<p>For the interaction between nuclear factor-&#x3ba;B (NF-&#x3ba;B) signaling pathway and common ligands/receptors in osteoblastic cells, the NF-&#x3ba;B signaling pathway showed a strong correlation with CCL4, TNFRSF1A, CXCL3, CXCL2, LTBR, CCL4L2, CXCL8, and CXCL12 (<xref ref-type="fig" rid="f5">
<bold>Figure&#xa0;5C</bold>
</xref>). For the interaction between NF-&#x3ba;B signaling pathway and common ligands/receptors in chondroblastic cells, the NF-&#x3ba;B signaling pathway showed a strong correlation with CXCL8, CCL4L2, CXCL2, CXCL3, and CCL4 (<xref ref-type="fig" rid="f5">
<bold>Figure&#xa0;5D</bold>
</xref>).</p>
</sec>
</sec>
<sec id="s4" sec-type="discussion">
<title>Discussion</title>
<p>Accumulating evidence has implied that the biological behaviors of tumor cells are heavily affected by the tumor microenvironment. Network interactions among various types of tumor cells and the TME have been shown to promote tumor progression at multiple levels (<xref ref-type="bibr" rid="B1">1</xref>, <xref ref-type="bibr" rid="B7">7</xref>, <xref ref-type="bibr" rid="B17">17</xref>). Therefore, further understanding the underlying interactions should give rise to a novel therapeutic approach. Our results showed that 11 clustered cell types were identified across 11 osteosarcoma tissues, with cell types including &#x201c;osteoblastic&#x201d;, &#x201c;myeloid&#x201d;, &#x201c;osteoblastic_proli&#x201d;, &#x201c;osteoclast&#x201d;, and &#x201c;tumor-infiltrating lymphocytes (TILs)&#x201d; being the main types. The DEGs between different cell types from primary, metastatic, and recurrent osteosarcomas were mainly enriched in the GO terms including &#x201c;negative regulation of hydrolase activity&#x201d;, &#x201c;regulation of peptidase activity&#x201d;, &#x201c;regulation of binding&#x201d;, &#x201c;negative regulation of proteolysis&#x201d;, and &#x201c;negative regulation of peptidase activity&#x201d; and in the KEGG pathways including &#x201c;transcriptional misregulation in cancer&#x201d;, &#x201c;cellular senescence&#x201d;, &#x201c;apoptosis&#x201d;, &#x201c;FoxO signaling pathway&#x201d;, &#x201c;cell cycle&#x201d;, &#x201c;NF-kappa B signaling pathway&#x201d;, &#x201c;p53 signaling pathway&#x201d;, &#x201c;pentose phosphate pathway&#x201d;, and &#x201c;protein export&#x201d;. For the cell&#x2013;cell communication network analysis, the different interaction profiles between cell types were detected among primary, metastatic, and recurrent osteosarcomas. Further exploration of the KEGG pathway revealed that these ligand/receptor interactions may be associated with the NF-&#x3ba;B signaling pathway and its interacted mediators. In conclusion, the present study for the first time explored the scRNA-seq dataset in osteosarcoma, and our results revealed the 11 clustered cell types and demonstrated the novel cell&#x2013;cell interactions among different cell types in primary, metastatic, and recurrent osteosarcomas. The present study may provide new insights into understanding the molecular mechanisms of osteosarcoma pathophysiology.</p>
<p>Based on the study of Zhou et&#xa0;al., the researchers characterized the transcriptomic properties, regulators, and dynamics of osteosarcoma malignant cells together with their TME, particularly stromal and immune cells (<xref ref-type="bibr" rid="B14">14</xref>). In addition, the study revealed that the proinflammatory fatty acid-binding protein 4+ macrophage infiltration was identified in lung metastatic osteosarcoma lesions. Lower osteoclast infiltration was detected in chondroblastic, recurrent, and lung metastatic osteosarcoma lesions compared with primary osteoblastic osteosarcoma lesions. They found that TIGIT blockade enhanced the cytotoxicity effects of primary CD3+ T cells with a high proportion of TIGIT+ cells against osteosarcoma (<xref ref-type="bibr" rid="B14">14</xref>). In our analysis, the main cell types include &#x201c;osteoblastic&#x201d;, &#x201c;myeloid&#x201d;, &#x201c;osteoblastic_proli&#x201d;, and &#x201c;osteoclast&#x201d;. In metastatic osteosarcoma, there is a large proportion of TIL, MSC, and osteoblastic and mesenchymal stem cells (MSCs); in recurrent osteosarcoma, there is a large proportion of chondroblastic cells.</p>
<p>Several studies have proposed the importance of TIL in osteosarcoma. TILs were recruited to the tumor site; however, tumor cells had the capability of escaping the immune response (<xref ref-type="bibr" rid="B18">18</xref>). Studies found that the neutrophil&#x2013;lymphocyte ratio was strongly correlated with the overall survival and progression-free survival of patients with osteosarcoma (<xref ref-type="bibr" rid="B18">18</xref>). Recent studies showed that higher infiltration of immune cells was correlated with better clinical outcomes in osteosarcoma (<xref ref-type="bibr" rid="B18">18</xref>). Sundara et&#xa0;al. showed that PD-L1 and T-cell infiltration were increased in the presence of HLA class I expression in metastatic high-grade osteosarcoma (<xref ref-type="bibr" rid="B19">19</xref>). The role of MSCs has also been reported in metastatic osteosarcoma. Tsukamoto et&#xa0;al. showed that mesenchymal stem cells promoted tumor engraftment and metastatic colonization in a rat osteosarcoma model (<xref ref-type="bibr" rid="B20">20</xref>); mechanistic studies showed that MSCs under stress increased osteosarcoma migration and apoptosis resistance <italic>via</italic> extracellular vesicle-mediated communication (<xref ref-type="bibr" rid="B21">21</xref>). Cortini et&#xa0;al. found that tumor-activated MSCs promoted osteosarcoma stemness and migratory potential <italic>via</italic> interleukin-6 secretion (<xref ref-type="bibr" rid="B22">22</xref>). Chondroblastic osteosarcoma ranks as the second commonly diagnosed osteosarcoma in young adults. The cellular origin of chondroblastic osteosarcoma is still unclear. In recurrent and metastatic osteosarcomas, the strong interaction between chondroblastic and osteoblastic cells was detected in our study, suggesting the transdifferentiation of malignant osteoblastic cells from malignant chondroblastic cells.</p>
<p>Based on the analysis of signaling pathways, we noticed that the NF-&#x3ba;B signaling pathway is key in the pathophysiology of osteosarcoma. NF-&#x3ba;B is involved in the early stress response to cellular DNA damage, and tumor necrosis factor &#x3b1; (TNF&#x3b1;) is an activator of the classical NF-&#x3ba;B pathway (<xref ref-type="bibr" rid="B23">23</xref>). After TNF&#x3b1; stimulation, I&#x3ba;B kinases (IKKs), such as IKK&#x3b1; and IKK&#x3b2;, are first activated in cells. IKKs degrade intracellular I&#x3ba;B, thus releasing NF-&#x3ba;B molecules such as RelA, which are phosphorylated at S536, and this allows RelA to enter the nucleus (<xref ref-type="bibr" rid="B23">23</xref>), bind to genes at corresponding binding sites, and initiate the transcription of downstream genes, such as CCND1 and Bcl-2, to regulate cell cycle progression, proliferation, and survival (<xref ref-type="bibr" rid="B23">23</xref>). Nishimura et&#xa0;al. showed that transfection of NF-&#x3ba;B decoy oligodeoxynucleotide suppressed pulmonary metastasis by murine osteosarcoma (<xref ref-type="bibr" rid="B24">24</xref>). Londhe et&#xa0;al. showed that classical NF-&#x3ba;B metabolically reprogramed sarcoma cells through regulation of hexokinase 2 (<xref ref-type="bibr" rid="B25">25</xref>). Activation of the NF-&#x3ba;B axis could enhance CRL4B DCAF11 E3 ligase activity and regulate cell cycle progression in human osteosarcoma cells (<xref ref-type="bibr" rid="B26">26</xref>). Inhibition of NF-&#x3ba;B signaling could attenuate osteosarcoma progression (<xref ref-type="bibr" rid="B26">26</xref>, <xref ref-type="bibr" rid="B27">27</xref>). In the present study, the costimulatory analysis revealed that ligands and receptors were correlated with NF-&#x3ba;B signaling. In future studies, we may perform functional studies to examine if disturbance of the ligands/receptors could lead to modulation of the NF-&#x3ba;B signaling pathway, which may eventually regulate the osteosarcoma progression.</p>
<p>The present was only focused on the bioinformatics analysis, which may limit the significance of the current findings. Thus, further studies especially validating the potential mediators detected in this study by using experimental assays should be considered. Due to the limited source of the scRNA-seq dataset for osteosarcoma, the present study only analyzed one dataset, and future studies should consider exploring other available scRNA-seq datasets to confirm the present findings. Moreover, our analysis only focused on the NF-&#x3ba;B signaling pathway and its interacted mediators in osteosarcoma, and other signaling pathways may be considered for exploration in our future studies.</p>
</sec>
<sec id="s5" sec-type="conclusions">
<title>Conclusions</title>
<p>In conclusion, the present study for the first time explored the scRNA-seq dataset in osteosarcoma, and our results revealed the 11 clustered cell types and demonstrated the novel cell&#x2013;cell interactions among different cell types in primary, metastatic, and recurrent osteosarcomas. The NF-&#x3ba;B signaling pathway may play a key role in regulating the TME of osteosarcoma. The present study may provide new insights into understanding the molecular mechanisms of osteosarcoma pathophysiology.</p>
</sec>
<sec id="s6" sec-type="data-availability">
<title>Data Availability Statement</title>
<p>The original contributions presented in the study are included in the article/<xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Material</bold>
</xref>. Further inquiries can be directed to the corresponding author.</p>
</sec>
<sec id="s7" sec-type="author-contributions">
<title>Author Contributions</title>
<p>JM and RW designed and supervised the whole project. RW, XD, HaL, ZS, and HeL processed the datasets and analyzed the data. JM wrote the manuscript. YS and WW revised the drafted manuscript. All authors contributed to the article and approved the submitted version.</p>
</sec>
<sec id="s8" sec-type="funding-information">
<title>Funding</title>
<p>This study was supported by the Basic Public Welfare Research Program of Zhejiang (LGF19H060002).</p>
</sec>
<sec id="s9" sec-type="COI-statement">
<title>Conflict of Interest</title>
<p>The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.</p>
</sec>
<sec id="s10" sec-type="disclaimer">
<title>Publisher&#x2019;s Note</title>
<p>All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.</p>
</sec>
</body>
<back>
<sec id="s11" sec-type="supplementary-material">
<title>Supplementary Material</title>
<p>The Supplementary Material for this article can be found online at: <ext-link ext-link-type="uri" xlink:href="https://www.frontiersin.org/articles/10.3389/fonc.2022.853979/full#supplementary-material">https://www.frontiersin.org/articles/10.3389/fonc.2022.853979/full#supplementary-material</ext-link>
</p>
<supplementary-material xlink:href="DataSheet_1.pdf" id="SM1" mimetype="application/pdf"/>
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