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<front>
<journal-meta>
<journal-id journal-id-type="publisher-id">Front. Immunol.</journal-id>
<journal-title-group>
<journal-title>Frontiers in Immunology</journal-title>
<abbrev-journal-title abbrev-type="pubmed">Front. Immunol.</abbrev-journal-title>
</journal-title-group>
<issn pub-type="epub">1664-3224</issn>
<publisher>
<publisher-name>Frontiers Media S.A.</publisher-name>
</publisher>
</journal-meta>
<article-meta>
<article-id pub-id-type="doi">10.3389/fimmu.2025.1644437</article-id>
<article-version article-version-type="Version of Record" vocab="NISO-RP-8-2008"/>
<article-categories>
<subj-group subj-group-type="heading">
<subject>Original Research</subject>
</subj-group>
</article-categories>
<title-group>
<article-title>In silico design of novel precision vaccine targeting sclerostin epitopes for osteoporosis prevention and treatment</article-title>
</title-group>
<contrib-group>
<contrib contrib-type="author">
<name><surname>Luo</surname><given-names>Jianzhou</given-names></name>
<xref ref-type="aff" rid="aff1"><sup>1</sup></xref>
<uri xlink:href="https://loop.frontiersin.org/people/1972982/overview"/>
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<contrib contrib-type="author">
<name><surname>Wu</surname><given-names>Tailin</given-names></name>
<xref ref-type="aff" rid="aff2"><sup>2</sup></xref>
<xref ref-type="aff" rid="aff3"><sup>3</sup></xref>
<uri xlink:href="https://loop.frontiersin.org/people/1864171/overview"/>
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<contrib contrib-type="author">
<name><surname>Guan</surname><given-names>Bin</given-names></name>
<xref ref-type="aff" rid="aff4"><sup>4</sup></xref>
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<contrib contrib-type="author">
<name><surname>Li</surname><given-names>Lin</given-names></name>
<xref ref-type="aff" rid="aff3"><sup>3</sup></xref>
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<contrib contrib-type="author">
<name><surname>Yang</surname><given-names>Zili</given-names></name>
<xref ref-type="aff" rid="aff1"><sup>1</sup></xref>
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<contrib contrib-type="author" corresp="yes">
<name><surname>Tao</surname><given-names>Huiren</given-names></name>
<xref ref-type="aff" rid="aff3"><sup>3</sup></xref>
<xref ref-type="corresp" rid="c001"><sup>*</sup></xref>
<uri xlink:href="https://loop.frontiersin.org/people/3095733/overview"/>
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<aff id="aff1"><label>1</label><institution>Department of Orthopedics, Shenzhen University General Hospital, Shenzhen University Health Science Center, Shenzhen University</institution>, <city>Shenzhen</city>, <state>Guangdong</state>,&#xa0;<country country="cn">China</country></aff>
<aff id="aff2"><label>2</label><institution>The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi&#x2019;an Jiaotong University</institution>, <city>Xi&#x2019;an</city>, <state>Shaanxi</state>,&#xa0;<country country="cn">China</country></aff>
<aff id="aff3"><label>3</label><institution>Orthopedic Centre, the University of Hong Kong Shenzhen Hospital, Shenzhen</institution>, <city>Guangdong</city>,&#xa0;<country country="cn">China</country></aff>
<aff id="aff4"><label>4</label><institution>Preventive Health Care Section, the Health Service Center of Weifang Community</institution>, <city>Shanghai</city>,&#xa0;<country country="cn">China</country></aff>
<author-notes>
<corresp id="c001"><label>*</label>Correspondence: Huiren Tao, <email xlink:href="mailto:1910244002@email.szu.edu.cn">1910244002@email.szu.edu.cn</email>; <email xlink:href="mailto:huiren_tao@163.com">huiren_tao@163.com</email></corresp>
</author-notes>
<pub-date publication-format="electronic" date-type="pub" iso-8601-date="2025-12-01">
<day>01</day>
<month>12</month>
<year>2025</year>
</pub-date>
<pub-date publication-format="electronic" date-type="collection">
<year>2025</year>
</pub-date>
<volume>16</volume>
<elocation-id>1644437</elocation-id>
<history>
<date date-type="received">
<day>10</day>
<month>06</month>
<year>2025</year>
</date>
<date date-type="accepted">
<day>10</day>
<month>11</month>
<year>2025</year>
</date>
<date date-type="rev-recd">
<day>26</day>
<month>10</month>
<year>2025</year>
</date>
</history>
<permissions>
<copyright-statement>Copyright &#xa9; 2025 Luo, Wu, Guan, Li, Yang and Tao.</copyright-statement>
<copyright-year>2025</copyright-year>
<copyright-holder>Luo, Wu, Guan, Li, Yang and Tao</copyright-holder>
<license>
<ali:license_ref start_date="2025-12-01">https://creativecommons.org/licenses/by/4.0/</ali:license_ref>
<license-p>This is an open-access article distributed under the terms of the <ext-link ext-link-type="uri" xlink:href="https://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution License (CC BY)</ext-link>. 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.</license-p>
</license>
</permissions>
<abstract>
<sec>
<title>Background</title>
<p>Osteoporosis has become an increasingly pressing global public health challenge. Monoclonal antibody romosozumab (ROMO), which targets sclerostin (SOST), a critical inhibitor of bone formation, demonstrates considerable therapeutic efficacy. However, its relatively high cost and potential cardiovascular risks may hinder broader clinical application. Current preventive measures remain inadequate.</p>
</sec>
<sec>
<title>Methods</title>
<p>This study presents a novel, cost-effective osteoporosis vaccine with dual preventive and therapeutic capabilities, derived from the high-affinity binding epitope of ROMO to SOST. ELISA screening determined that the SOST<sub>131&#x2013;163</sub> region within loop3 domain serves as the primary epitope for ROMO, suggesting a role in skeletal regulation with minimal impact on cardiovascular system. SOST<sub>131&#x2013;163</sub> was conjugated to the diphtheria toxin translocation domain (DTT) to create novel SOST-targeted vaccines.</p>
</sec>
<sec>
<title>Results</title>
<p>Immunogenicity assays demonstrated that both DDT-SOST<sub>(131-163)3</sub> (DS<sub>3</sub>) and DDT-SOST<sub>(131-163)5</sub> (DS<sub>5</sub>) elicited strong IgG2 antibody responses comparable to ROMO. Molecular docking studies indicated strong affinities of DS<sub>3</sub> and DS<sub>5</sub> for Toll-like receptor 2 (TLR2), enhancing TLR2-mediated humoral B-cell immunity and eliciting synergistic T-helper cell responses. Recombinant expression in Escherichia coli confirmed the successful production of DS<sub>3</sub> and DS<sub>5</sub>, with molecular weights of 31.8 kDa and 40.3 kDa, respectively. <italic>In vivo</italic> experiments showed that the vaccines effectively induced high-titer anti-SOST antibodies in mice, overcoming immune tolerance. Additionally, cell-based assays indicated that antiserum from vaccinated mice inhibited osteoclast differentiation and promoted osteoblast mineralization.</p>
</sec>
<sec>
<title>Conclusion</title>
<p>The SOST-targeted vaccination strategy offers a promising and cost-effective approach for the early prevention and sustained management of osteoporosis, demonstrating substantial potential for clinical translation.</p>
</sec>
</abstract>
<kwd-group>
<kwd>osteoporosis</kwd>
<kwd>sclerostin (SOST)</kwd>
<kwd>romosozumab (ROMO)</kwd>
<kwd>vaccine</kwd>
<kwd>translocation domain of diphtheria toxin (DTT)</kwd>
</kwd-group>
<funding-group>
<funding-statement>The author(s) declare financial support was received for the research and/or publication of this article. This study was funded by National Natural Science Foundation of China (81970761), Sanming Project of Medicine in Shenzhen (SZSM201911011), and Shenzhen Nanshan Technology Research Development and Creative Design Project (NS2023129).</funding-statement>
</funding-group>
<counts>
<fig-count count="11"/>
<table-count count="2"/>
<equation-count count="0"/>
<ref-count count="50"/>
<page-count count="21"/>
<word-count count="9298"/>
</counts>
<custom-meta-group>
<custom-meta>
<meta-name>section-at-acceptance</meta-name>
<meta-value>Vaccines and Molecular Therapeutics</meta-value>
</custom-meta>
</custom-meta-group>
</article-meta>
</front>
<body>
<sec id="s1" sec-type="intro">
<title>Introduction</title>
<p>Osteoporosis (OP) is a prevalent degenerative bone disease defined by diminished bone mass and an elevated risk of fractures, posing a significant global health challenge (<xref ref-type="bibr" rid="B1">1</xref>, <xref ref-type="bibr" rid="B2">2</xref>). It affects approximately one-third of women and one-fifth of men over the age of 50, with prevalence anticipated to rise population ages (<xref ref-type="bibr" rid="B2">2</xref>, <xref ref-type="bibr" rid="B3">3</xref>). The disorder results from an imbalance in bone remodeling, where bone resorption outpaces bone formation. Current therapies primarily focus on promoting bone formation, such as teriparatide, or inhibiting resorption with agents like alendronate and denosumab (<xref ref-type="bibr" rid="B4">4</xref>). Although romosozumab (ROMO), a dual-action monoclonal antibody, has demonstrated promising efficacy, its high cost and cardiovascular adverse events may limit broader application (<xref ref-type="bibr" rid="B1">1</xref>, <xref ref-type="bibr" rid="B5">5</xref>, <xref ref-type="bibr" rid="B6">6</xref>). Furthermore, existing preventative strategies do not effectively address early intervention, underscoring the pressing need for innovative therapies (<xref ref-type="bibr" rid="B1">1</xref>).</p>
<p>Sclerostin (SOST) is a critical negative regulator of osteoblast differentiation, primarily inhibiting the Wnt signaling pathway, thus decreasing bone formation and indirectly promoting osteoclastogenesis (<xref ref-type="bibr" rid="B7">7</xref>). An agent targeting SOST, such as ROMO, offers a dual mechanism for modulating bone dynamics (<xref ref-type="bibr" rid="B8">8</xref>); however, its antibody-based design poses challenges in both safety and affordability (<xref ref-type="bibr" rid="B5">5</xref>, <xref ref-type="bibr" rid="B9">9</xref>). Consequently, there is growing interest in vaccine-based strategies aimed at achieving safe, sustained preventive and therapeutic effects through the induction of long-lasting endogenous antibody production (<xref ref-type="bibr" rid="B10">10</xref>, <xref ref-type="bibr" rid="B11">11</xref>). Nonetheless, the development of SOST vaccines encounters two primary hurdles: identifying effective antigenic epitopes and overcoming immune tolerance to self-proteins (<xref ref-type="bibr" rid="B12">12</xref>).</p>
<p>Building upon our previous successes in addressing immune tolerance in osteoporosis vaccine development (<xref ref-type="bibr" rid="B10">10</xref>), we propose a novel vaccine strategy that integrates the SOST protein with a diphtheria toxin translocation domain (DTT) as an adjuvant scaffold. Our approach commenced with the identification of the high-affinity binding domain of SOST through ROMO, followed by its conjugation to DTT protein to create a subunit vaccine. We performed comprehensive physicochemical characterization, validated mass producibility via recombinant expression in E. coli, and evaluated immunogenicity along with <italic>in vivo</italic> efficacy in antibody induction. This strategy is designed to achieve three primary objectives: (1) Confirming antigen validity by identifying effective SOST epitopes for ROMO targeting; (2) Overcoming immune tolerance with DTT scaffold to enhance antibody induction; and (3) Developing a cost-effective and scalable osteoporosis vaccine to enable early intervention and sustained therapeutic benefits.</p>
</sec>
<sec id="s2" sec-type="materials|methods">
<label>2</label>
<title>Materials and methods</title>
<sec id="s2_1">
<label>2.1</label>
<title>SOST peptide fragments</title>
<p>Peptides were synthesized based on the human SOST (GenBank: AAK16158.1) fragment encompassing amino acids 24 to 211, excluding the signal peptide, yielding approximately 30-amino-acid segments. An indirect enzyme-linked immunosorbent assay (ELISA) was performed to identify a high-affinity SOST peptide fragment for ROMO. The polypeptides were synthesized by Sangon Biotech (Shanghai, China).</p>
</sec>
<sec id="s2_2">
<label>2.2</label>
<title>Enzyme-linked immunosorbent assay (ELISA) for peptide screening</title>
<p>96-well plates (Abcam, Cambridge, MA, USA) were coated with 100 &#xb5;L of 1 &#xb5;g/mL human SOST-synthesized polypeptides in the provided coating buffer overnight at 4 &#xb0;C. Following coating, the plates were washed with 1&#xd7; washing buffer and subsequently blocked using 1&#xd7; blocking buffer. Diluted ROMO (AntibodySystem, Schiltigheim, France) was then added to the wells and incubated for 2 hour at 37 &#xb0;C. After additional washing, 100 &#xb5;L of 1:10,000 diluted horseradish peroxidase (HRP)-labeled goat anti-human antibodies (Bioss, Beijing, China) was introduced to the wells, followed by another 2-hour incubation at 37 &#xb0;C. Finally, 100 &#xb5;L of TMB was dispensed into each well, and after a 20-minute incubation at 37 &#xb0;C, the absorbance was measured at 450 nm.</p>
<p>The high-affinity SOST peptide fragment for ROMO was then identified using ELISA. The binding affinity of the high-affinity SOST fragment to the heavy and light chains of ROMO was assessed using the HawkDock server (<xref ref-type="bibr" rid="B13">13</xref>), while interactions between the SOST fragment and ROMO were analyzed with PDBsum (<xref ref-type="bibr" rid="B14">14</xref>).</p>
</sec>
<sec id="s2_3">
<label>2.3</label>
<title>Prediction of T cell and B cell epitope</title>
<p>Prediction of major histocompatibility complex (MHC) class I-restricted cytotoxic T lymphocyte (CTL) epitopes for the high-affinity SOST fragment was performed using NetMHCpan 4.1 EL tool (<xref ref-type="bibr" rid="B15">15</xref>). A comprehensive analysis of 9-mer epitopes was conducted across the A1, A2, A3, A24, and B7 supertypes. Epitopes with a percentage rank (&lt; 0.5%) were categorized as strong binders (SB), whereas those with a percentage rank (&lt; 2%) were classified as weak binders (WB). In parallel, the identification of helper T lymphocyte (HTL) epitopes, comprising 15-mer peptides that bind to MHC class II, was accomplished using the NetMHCIIpan 4.1 EL server (<xref ref-type="bibr" rid="B16">16</xref>), with strong binders defined as having a percentage rank (&lt; 1%) and weak binders defined as having a percentage rank (&lt; 5%).</p>
<p>To predict linear B cell epitopes within the high-affinity SOST fragment, we employed BepiPred2.0 tool (<xref ref-type="bibr" rid="B17">17</xref>), applying a default filtering threshold of 0.5. Additionally, conformational B cell epitopes for both the screening peptide and the designed vaccines were predicted using the ElliPro application (<xref ref-type="bibr" rid="B18">18</xref>), with a minimum score threshold set at 0.5 and a maximum distance of 6 Angstroms.</p>
</sec>
<sec id="s2_4">
<label>2.4</label>
<title>Construction and prediction of candidate vaccines</title>
<p>The high-affinity SOST fragment was selected as the target antigen for the development of a recombinant subunit vaccine. Based on our previous experimental experience (<xref ref-type="bibr" rid="B10">10</xref>), the DTT fragment (amino acids 203&#x2013;378; WP_371890660.1) was chosen as immune scaffold to facilitate conjugation with SOST fragment, thereby enhancing immune recognition and promoting antibody production. The DTT scaffold was conjugated with varying copy numbers of SOST peptide, ranging from 0 to 5, to generate a series of chimeric molecules. These conjugations were connected via a (GGGGS)<sub>2</sub> flexible linker to ensure optimal conformational flexibility. The resulting vaccine candidates were designated as DDT-SOST<sub>(131-163)0</sub> (DS<sub>0</sub>) to DDT-SOST<sub>(131-163)5</sub> (DS<sub>5</sub>), with the numerical suffix denoting specific number of SOST peptide fragments fused to DTT scaffold.</p>
<p>Tertiary structure of candidate vaccines was predicted using AlphaFold2 server (<xref ref-type="bibr" rid="B19">19</xref>), based on their amino acid sequences. Five structural models were generated, demonstrating close alignment with experimental accuracy. Top-ranked model was selected for further analysis. The quality of vaccine structure was assessed using the predicted Local Distance Difference Test (pLDDT).</p>
</sec>
<sec id="s2_5">
<label>2.5</label>
<title>Immune response simulation</title>
<p>To evaluate the immunogenic potential of candidate vaccines, we employed the C-ImmSim server (<xref ref-type="bibr" rid="B20">20</xref>), a platform capable of simulating immune responses. This computational tool mimics the activation of B and T lymphocytes following hypothetical vaccine administration, allowing for the exploration of immune response dynamics. The simulation parameters were configured as follows: Random Seed = 12,345, Simulation Volume = 10, Simulation Steps = 240, and HLA selections: A0101, B0702, and DRB1_0101. The simulation framework was designed to include three administrations of 400 antigens, each spaced by a two-week interval. Each time step was delineated to represent an elapsed duration of 8 hours in real-world time, leading to time periods set at 1, 42, and 84. The simulation predicted the cellular immune responses provoked by candidate vaccines, encompassing antibody production, B cell and T cell activation, and cytokine release. The vaccine demonstrating the highest titer of IgG2 antibody were subsequently selected for further analysis, given that the IgG2 subtype is known to mediate the function against SOST in ROMO (<xref ref-type="bibr" rid="B21">21</xref>).</p>
</sec>
<sec id="s2_6">
<label>2.6</label>
<title>Prediction of immunological and physicochemical properties</title>
<p>Immunological properties of the selected vaccines were systematically evaluated. Allergenicity assessments were performed using AllerTOP v.2.1 server (<xref ref-type="bibr" rid="B22">22</xref>), while antigenic potential was analyzed with VaxiJen v2.0 server (<xref ref-type="bibr" rid="B23">23</xref>). To assess solubility of the vaccines, SOLpro server (<xref ref-type="bibr" rid="B24">24</xref>) was employed. Additionally, the physicochemical properties&#x2014;including chemical formula, total atom count, molecular weight, theoretical isoelectric point (pI), half-life, instability index, aliphatic index, and the grand average of hydropathicity (GRAVY)&#x2014;were predicted using ExPASy ProtParam tool (<xref ref-type="bibr" rid="B25">25</xref>).</p>
</sec>
<sec id="s2_7">
<label>2.7</label>
<title>Prediction and analysis of secondary structure</title>
<p>Secondary structure elements of the selected vaccines, including &#x3b1;-helices, extended strands, &#x3b2;-turns, and random coils, were predicted using SOPMA server (<xref ref-type="bibr" rid="B26">26</xref>) and PSIPRED web server (<xref ref-type="bibr" rid="B27">27</xref>). For these predictions, all parameters were maintained at their default settings. Additionally, the solubility characteristics of the selected vaccines were assessed using Protein-Sol server (<xref ref-type="bibr" rid="B28">28</xref>).</p>
</sec>
<sec id="s2_8">
<label>2.8</label>
<title>Refinement and validation of tertiary structure</title>
<p>Top-ranked model of tertiary structure for the selected vaccines, generated by AlphaFold2, was refined using GalaxyRefine web server (<xref ref-type="bibr" rid="B29">29</xref>). This refinement yielded reliable core structures based on multiple templates, while less reliable loops and terminal regions were constructed through optimization-based modeling. The structural quality of the refined vaccine model was further assessed using ProSA-web (<xref ref-type="bibr" rid="B30">30</xref>), ERRAT (<xref ref-type="bibr" rid="B31">31</xref>) and PROCHECK (<xref ref-type="bibr" rid="B32">32</xref>).</p>
</sec>
<sec id="s2_9">
<label>2.9</label>
<title>Molecular docking and molecular dynamic simulations</title>
<p>Molecular docking analyses were conducted using HawkDock server (<xref ref-type="bibr" rid="B13">13</xref>) to evaluate the interactions between vaccine candidates and Toll-Like Receptor 2 (TLR2) immune receptor (PDB ID: 6NIG). This platform organizes docking models based on surface complementarity and clustering characteristics. The highest-ranking model derived from the docking evaluations was selected for further analysis and visualized with PyMOL software. Binding energy and interaction surfaces within the docking complex were assessed using Prodigy (<xref ref-type="bibr" rid="B33">33</xref>), PDBePISA (<xref ref-type="bibr" rid="B34">34</xref>), and PDBsum (<xref ref-type="bibr" rid="B14">14</xref>).</p>
<p>Molecular dynamics simulations of the vaccine-TLR2 docking complex were performed utilizing the internal coordinate normal mode analysis server (iMODS) (<xref ref-type="bibr" rid="B35">35</xref>). This platform employs Normal Mode Analysis (NMA) in internal coordinates to identify collective motions that are critical for the functional dynamics of macromolecules. iMODS provides interactive tools for visualizing these modes, including vibration analysis, motion animations, and morphing trajectories.</p>
</sec>
<sec id="s2_10">
<label>2.10</label>
<title>Vaccines cloning, expression and immunization</title>
<p>Codon-optimized cDNA sequences for the selected vaccine candidates were generated in silico using the Java Codon Adaptation Tool (JCAT) (<xref ref-type="bibr" rid="B36">36</xref>). Optimized sequences were then cloned into pSmartI plasmids. Following cloning, the recombinant plasmids were transformed into Escherichia coli BL21 (DE3) for protein expression. The resulting recombinant proteins were purified through a two-step chromatography process, which involved ion exchange chromatography followed by gel filtration chromatography. Purity and quality of protein products were assessed using 10% sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) (Sangon Biotech, Shanghai, China).</p>
<p>For immunization studies, C57BL/6J mice (purchased from Guangdong Medical Laboratory Animal Center, China) received two subcutaneous injections of 200 &#xb5;g of each vaccine candidate, administered two weeks apart(n=3). Freund&#x2019;s Complete Adjuvant was used for the initial dose, while Freund&#x2019;s Incomplete Adjuvant (Sigma, USA) was employed for the booster injection. Blood samples were collected five weeks after the final immunization, and anti-SOST antibody titers were measured using ELISA.</p>
</sec>
<sec id="s2_11">
<label>2.11</label>
<title>Detection of anti-SOST antibodies in vaccinated mice</title>
<p>The antiserum from vaccine-immunized mice was obtained. The titers of specific anti-SOST antibodies were assessed using an indirect ELISA. In brief, 1 &#xb5;g/mL of human SOST protein (MedChemExpress Inc.) was coated onto the wells of MaxiSorp microtiter plates (Thermo Fisher Scientific Inc.) and incubated overnight at 4&#xb0;C. Mouse serum samples were diluted 1:200 in sample dilution buffer and added to the pre-coated plates, followed by incubation at room temperature for 2 hours. After washing the plates with washing buffer, bound IgG was detected using a horseradish peroxidase-conjugated goat anti-mouse IgG antibody (1:10,000, Abcam). The absorbance was measured at 450 nm using a Multiskan FC microplate reader (Thermo Fisher Scientific, San Jose, USA).</p>
</sec>
<sec id="s2_12">
<label>2.12</label>
<title>Assessment of T cell immune responses post-vaccine stimulation</title>
<p>Splenocytes were isolated immediately post-euthanasia via mechanical dissociation of the spleen tissue. Mononuclear cells were then separated using density gradient centrifugation with a murine spleen mononuclear cell isolation kit (Solarbio, Beijing, China). Isolated cells were resuspended at a concentration of 1&#xd7;10^6 cells/mL in RPMI 1640 medium supplemented with 10% fetal bovine serum. Cells were subsequently stimulated <italic>in vitro</italic> with recombinant SOST protein (100 ng/mL), vaccine protein (100 ng/mL), or PBS as a control, and incubated for 48 hours at 37 &#xb0;C in a humidified atmosphere containing 5% CO<sub>2</sub>. Post-incubation, culture supernatants were collected and analyzed for cytokine concentrations (IL-4, IL-10, and IFN-&#x3b3;) using ELISA kits (Meimian Industrial Co., Ltd., China), following the manufacturer&#x2019;s instructions.</p>
</sec>
<sec id="s2_13">
<label>2.13</label>
<title><italic>In vitro</italic> validation of anti-SOST antiserum function</title>
<p>Functional activity of anti-SOST antiserum from vaccine-immunized mice was evaluated using primary osteoclasts and osteoblasts. Mice were euthanized via CO<sub>2</sub> inhalation, starting with a flow rate of 10% of chamber volume per minute to gradually increase CO<sub>2</sub> concentration to 30%, inducing unconsciousness. Once righting reflex was lost, the flow rate was increased to 30% per minute to maintain a CO<sub>2</sub> concentration of &#x2265;70% for 5 minutes, ensuring humane euthanasia. All procedures complied with animal welfare guidelines. Primary osteoclasts were isolated from tibiae and femora of 8-week-old C57BL/6J mice. Bone marrow mononuclear cells were extracted using an isolation kit, filtered, and cultured in &#x3b1;-MEM supplemented with 50 ng/mL M-CSF and 80 ng/mL sRANKL (PeproTech) for 4&#x2013;6 days to induce differentiation. During the second medium change, anti-SOST antiserum and 100 ng/mL recombinant SOST protein (Novoprotein) were added. Osteoclast differentiation was confirmed by TRAP staining (Servicebio). Primary osteoblasts were obtained from bone marrow stromal cells, and the MC3T3-E1 subclone 14 osteoblast cell line (purchased from Pricella Biotechnology Co., Ltd.) was cultured in osteogenic medium. Co-cultures of osteoblasts with anti-SOST antiserum and 200 ng/mL SOST were established, and mineralization was evaluated on day 21 via Alizarin Red S staining (Solarbio). The culture medium was refreshed every 2&#x2013;3 days throughout the experiment.</p>
</sec>
<sec id="s2_14">
<label>2.14</label>
<title>Statistical analysis</title>
<p>Data are presented as means &#xb1; standard deviation (SD). Differences between two independent groups were analyzed using one-way ANOVA followed by Tukey&#x2019;s multiple comparisons test. Data visualization was conducted utilizing GraphPad Prism software version 10 (GraphPad Software, San Diego, CA, USA). A p-value of less than 0.05 was considered statistically significant.</p>
</sec>
</sec>
<sec id="s3" sec-type="results">
<label>3</label>
<title>Results</title>
<sec id="s3_1">
<label>3.1</label>
<title>Screening of high-affinity SOST epitope for ROMO binding</title>
<p>To identify potential interaction sites of SOST with ROMO for development of recombinant subunit vaccines, we initially fragmented SOST protein into six peptides, each comprising approximately 30 amino acids. Screening through ELISA pinpointed two peptides, SOST<sub>114&#x2013;143</sub> and SOST<sub>144-173</sub>, that exhibited high-affinity binding to ROMO (<xref ref-type="fig" rid="f1"><bold>Figure&#xa0;1A</bold></xref>). We further dissected the identified region (amino acids 114-173) into four peptides based on their biological properties (<xref ref-type="fig" rid="f1"><bold>Figure&#xa0;1B</bold></xref>). A subsequent ELISA revealed that SOST<sub>131&#x2013;163</sub> peptide served as a specific epitope with substantial affinity for ROMO (<xref ref-type="fig" rid="f1"><bold>Figure&#xa0;1C</bold></xref>), located within loop3 domain of SOST (<xref ref-type="fig" rid="f1"><bold>Figure&#xa0;1D-a</bold></xref>).</p>
<fig id="f1" position="float">
<label>Figure&#xa0;1</label>
<caption>
<p>Screening and analysis of high-affinity epitopes on SOST. <bold>(A)</bold> ELISA experiments were conducted to identify SOST fragments with strong binding affinity for ROMO, revealing that SOST<sub>114&#x2013;143</sub> and SOST<sub>143&#x2013;173</sub> exhibit significantly higher affinity (<italic>P</italic>&lt;0.01). <bold>(B)</bold> A schematic diagram delineating the binding functional regions associated with the high-affinity fragments of SOST. <bold>(C)</bold> ELISA results indicate that SOST<sub>131&#x2013;163</sub> displays the highest affinity for ROMO (<italic>P</italic>&lt;0.01), thereby identifying it as a potent functional epitope of SOST. <bold>(D-a)</bold> SOST<sub>131&#x2013;163</sub> fragment (highlighted in yellow) is located within the loop3 domain of SOST protein. <bold>(D-b)</bold> Docking studies indicate that SOST<sub>131&#x2013;163</sub> fragment interacts with ROMO light chain, yielding a binding free energy of -25.8 kcal/mol and an interface area of 712.9 &#xc5;&#xb2;. <bold>(D-c)</bold> Additionally, SOST<sub>131&#x2013;163</sub> fragment can bind to the ROMO heavy chain, resulting in a binding free energy of -33.19 kcal/mol and an interface area of 451.6 &#xc5;&#xb2;. <bold>(E)</bold> CTL epitopes within SOST<sub>131&#x2013;163</sub> sequence include two strong binder epitopes and four weak binder epitopes. <bold>(F)</bold> HTL epitopes in SOST<sub>131&#x2013;163</sub> sequence comprise one strong binder epitope and four weak binder epitopes. Predictions of B cell epitopes for SOST<sub>131&#x2013;163</sub> sequence are illustrated, including predicted linear B cell epitopes <bold>(G)</bold> and predicted discontinuous B cell epitopes <bold>(H)</bold>.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fimmu-16-1644437-g001.tif">
<alt-text content-type="machine-generated">Bar graphs, diagrams, and illustrations related to SOST peptides and epitopes.   A: Bar graph showing optical density at 450 nm for various SOST peptides with significance indicators.  B: Diagram showing the amino acid sequence range for SOST peptides.  C: Bar graph displaying optical density at 450 nm for SOST fragments with significance indicators.  D: Illustrations of SOST protein structure and interface areas with ROMO chains.  E, F: Bar graphs of CTL and HTL peptides ranked by HLA percentage for strong and weak binding.  G, H: Predicted linear and discontinuous epitopes with scores and molecular structures in yellow.</alt-text>
</graphic></fig>
<p>Molecular docking studies indicated that SOST<sub>131&#x2013;163</sub> fragment interacts with the light chain of ROMO&#x2019;s variable domain, establishing 4 hydrogen bonds and 105 non-bonded contacts, resulting in a binding free energy of -25.8 kcal/mol and an interface area of 712.9 &#xc5;&#xb2; (<xref ref-type="fig" rid="f1"><bold>Figure&#xa0;1D-b</bold></xref>, <xref ref-type="supplementary-material" rid="SF1"><bold>Supplementary Figure S1A</bold></xref>). Furthermore, SOST<sub>131&#x2013;163</sub> demonstrated affinity for the heavy chain&#x2019;s variable domain, forming 2 salt bridges and 90 non-bonded contacts, with a binding free energy of -33.19 kcal/mol and an interface area of 451.6 &#xc5;&#xb2; (<xref ref-type="fig" rid="f1"><bold>Figure&#xa0;1D-c</bold></xref>, <xref ref-type="supplementary-material" rid="SF1"><bold>Supplementary Figure S1B</bold></xref>). These docking results corroborate that SOST<sub>131&#x2013;163</sub> is a critical and distinctive peptide for ROMO, aligning with our ELISA observations.</p>
<p>Identification of immunodominant epitopes is pivotal for effective vaccine design. In this study, NetMHCpan 4.1 EL tool was utilized to predict six cytotoxic T lymphocyte (CTL) epitopes in SOST<sub>131&#x2013;163</sub> fragment, consisting of four weak binders and two strong binders (<xref ref-type="fig" rid="f1"><bold>Figure&#xa0;1E</bold></xref>). Additionally, NetMHCIIpan 4.1 EL server was employed to forecast five helper T lymphocyte (HTL) epitopes, comprising four weak binders and one strong binder (<xref ref-type="fig" rid="f1"><bold>Figure&#xa0;1F</bold></xref>). For the prediction of B cell epitopes, linear epitopes were analyzed using BepiPred 2.0 tool, resulting in the identification of two distinct epitopes within SOST<sub>131&#x2013;163</sub> fragment (<xref ref-type="fig" rid="f1"><bold>Figure&#xa0;1G</bold></xref>). Furthermore, conformational B cell epitopes were evaluated using ElliPro tool, which yielded two additional epitopes (<xref ref-type="fig" rid="f1"><bold>Figure&#xa0;1H</bold></xref>).</p>
</sec>
<sec id="s3_2">
<label>3.2</label>
<title>Construction and immunogenicity prediction of candidate vaccines</title>
<p>To enhance vaccine efficacy in inducing antibodies, we conjugated DTT scaffold, which contains substantial T-helper epitopes capable of disrupting immune tolerance to autoantigens, with varying quantities of repetitive SOST<sub>131&#x2013;163</sub> epitopes via a (GGGGS)<sub>2</sub> linker. Six recombinant vaccines were constructed using this method, labeled DS<sub>0</sub> to DS<sub>5</sub>, corresponding to the incorporation of 0 to 5 copies of SOST<sub>131&#x2013;163</sub> epitopes into DTT scaffold (<xref ref-type="fig" rid="f2"><bold>Figure&#xa0;2A</bold></xref>). Tertiary structures of these candidate vaccines were predicted using AlphaFold2 server, which generated five structural models for each vaccine. The top-ranked model for each vaccine was selected based on the highest predicted Local Distance Difference Test (pLDDT) score, and the resulting structures are presented (<xref ref-type="fig" rid="f2"><bold>Figure&#xa0;2B</bold></xref>).</p>
<fig id="f2" position="float">
<label>Figure&#xa0;2</label>
<caption>
<p>Construction plan and immune stimulation simulation of SOST candidate vaccines. <bold>(A)</bold> Schematic representation for the construction of SOST candidate vaccines. <bold>(B)</bold> Predicted three-dimensional structure of SOST candidate vaccines, modeled using AlphaFold2 server based on amino acid sequence. The cyan region denotes DTT protein scaffold, while the yellow regions represent the various repeated SOST<sub>131&#x2013;163</sub> peptides. <bold>(C)</bold> Immune stimulation simulation conducted using C-IMMSIM online server demonstrates that DS<sub>3</sub> and DS<sub>5</sub> vaccines simultaneously stimulate the production of IgM, IgG1, and IgG2 (Romosozumab is classified as an IgG2 antibody), whereas other candidate vaccines primarily induced IgM and IgG1 antibodies. Consequently, DS<sub>3</sub> and DS<sub>5</sub> vaccines were selected for further analysis.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fimmu-16-1644437-g002.tif">
<alt-text content-type="machine-generated">Panel A shows a schematic diagram of DTT linked to SOST using (GGGGS)&#x2082; linkers, displayed from DS&#x2080; to DS&#x2085; with varying linker lengths. Panel B features molecular structures of DS&#x2080; through DS&#x2085;, illustrating protein folding differences, with cyan and yellow highlighting. Panel C presents graphs of antigen and antibody counts over time for DS&#x2080; to DS&#x2085;, indicating variable immune responses.</alt-text>
</graphic></fig>
<p>To evaluate immune-stimulating potential of the top-ranked model for each candidate vaccine, we employed C-IMMSIM online server. The results demonstrated that all vaccine candidates elicited relatively high antibody titers following three immunization injections. Notably, the DS<sub>3</sub> and DS<sub>5</sub> vaccines stimulated the production of multiple antibody isotypes, including IgM, IgG1 and IgG2, while other candidate predominantly induced IgM and IgG1 responses (<xref ref-type="fig" rid="f2"><bold>Figure&#xa0;2C</bold></xref>). Importantly, the production of the IgG2 subtype is particularly significant as it is the functional antibody associated with ROMO. Since the candidate vaccines are designed to elicit an IgG2 antibody response that closely resembles that of ROMO (<xref ref-type="bibr" rid="B21">21</xref>), we selected the DS<sub>3</sub> and DS<sub>5</sub> vaccines for further analysis and investigation.</p>
</sec>
<sec id="s3_3">
<label>3.3</label>
<title>Immunological and physicochemical properties of DS<sub>3</sub> and DS<sub>5</sub> vaccines</title>
<p>Safety and efficacy are critical criteria for evaluating vaccines. Analysis using AllerTOP v.2.1 revealed that both DS<sub>3</sub> and DS<sub>5</sub> vaccines are non-allergenic. Antigenicity of these vaccines was assessed through VaxiJen v2.0, yielding scores of 0.7434 for DS<sub>3</sub> and 0.7948 for DS<sub>5</sub>, both surpassing the threshold value of 0.5. These results indicate that DS<sub>3</sub> and DS<sub>5</sub> vaccines are not only safe but also exhibit high immunogenicity. Solubility assessments conducted via SolPro server produced favorable scores of 0.713 for DS<sub>3</sub> and 0.925 for DS<sub>5</sub>. Additional physicochemical parameters were predicted using ExPASy ProtParam server. Both vaccines are classified as recombinant proteins, with molecular weights of 31.8 kDa for DS<sub>3</sub> and 40.3 kDa for DS<sub>5</sub>, and isoelectric points of 9.14 and 9.61, respectively. The total atom counts were recorded as 4463 for DS<sub>3</sub> and 5657 for DS<sub>5</sub>. Estimated half-lives for both vaccines are approximately 30 hours in mammalian reticulocytes, over 20 hours in yeast, and exceeding 10 hours in Escherichia coli. The instability indices were calculated to be 42.19 for DS<sub>3</sub> and 39.93 for DS<sub>5</sub>, while aliphatic indices measured 82.72 and 79.38, respectively. The grand average of hydropathicity (GRAVY) values were -0.257 for DS<sub>3</sub> and -0.294 for DS<sub>5</sub> (<xref ref-type="table" rid="T1"><bold>Table&#xa0;1</bold></xref>).</p>
<table-wrap id="T1" position="float">
<label>Table&#xa0;1</label>
<caption>
<p>Prediction of immunological and physicochemical properties for DS<sub>3</sub> and DS<sub>5</sub> vaccines.</p>
</caption>
<table frame="hsides">
<thead>
<tr>
<th valign="middle" align="left">Property</th>
<th valign="middle" align="left">DS<sub>3</sub></th>
<th valign="middle" align="left">DS<sub>5</sub></th>
</tr>
</thead>
<tbody>
<tr>
<td valign="middle" align="left">Allergenicity(AllerTOP v2.1)</td>
<td valign="middle" align="left">NON-ALLERGEN</td>
<td valign="middle" align="left">NON-ALLERGEN</td>
</tr>
<tr>
<td valign="middle" align="left">Antigenicity (VaxiJen v2.0)</td>
<td valign="middle" align="left">0.7434</td>
<td valign="middle" align="left">0.7948</td>
</tr>
<tr>
<td valign="middle" align="left">Solubility (SOLpro)</td>
<td valign="middle" align="left">0.713771</td>
<td valign="middle" align="left">0.925892</td>
</tr>
<tr>
<td valign="middle" align="left">Number of amino acids</td>
<td valign="middle" align="left">302</td>
<td valign="middle" align="left">386</td>
</tr>
<tr>
<td valign="middle" align="left">Molecular weight</td>
<td valign="middle" align="left">31804.32</td>
<td valign="middle" align="left">40334.16</td>
</tr>
<tr>
<td valign="middle" align="left">Theoretical Isoelectric point (pI)</td>
<td valign="middle" align="left">9.14</td>
<td valign="middle" align="left">9.61</td>
</tr>
<tr>
<td valign="middle" align="left">Formula</td>
<td valign="middle" align="left">C<sub>1362</sub>H<sub>2240</sub>N<sub>424</sub>O<sub>421</sub>S<sub>16</sub></td>
<td valign="middle" align="left">C<sub>1716</sub>H<sub>2840</sub>N<sub>556</sub>O<sub>523</sub>S<sub>22</sub></td>
</tr>
<tr>
<td valign="middle" align="left">Total number of atoms</td>
<td valign="middle" align="left">4463</td>
<td valign="middle" align="left">5657</td>
</tr>
<tr>
<td valign="middle" align="left">Estimated half-life</td>
<td valign="middle" align="left">30 hours (mammalian reticulocytes, <italic>in vitro</italic>).<break/>&gt;20 hours (yeast, <italic>in vivo</italic>).<break/>&gt;10 hours (Escherichia coli, <italic>in vivo</italic>).</td>
<td valign="middle" align="left">30 hours (mammalian reticulocytes, <italic>in vitro</italic>).<break/>&gt;20 hours (yeast, <italic>in vivo</italic>).<break/>&gt;10 hours (Escherichia coli, <italic>in vivo</italic>)</td>
</tr>
<tr>
<td valign="middle" align="left">Instability index</td>
<td valign="middle" align="left">42.19(unstable)</td>
<td valign="middle" align="left">39.93(stable)</td>
</tr>
<tr>
<td valign="middle" align="left">Aliphatic index</td>
<td valign="middle" align="left">82.72</td>
<td valign="middle" align="left">79.38</td>
</tr>
<tr>
<td valign="middle" align="left">Grand average of hydropathicity (GRAVY)</td>
<td valign="middle" align="left">-0.257</td>
<td valign="middle" align="left">-0.294</td>
</tr>
</tbody>
</table>
</table-wrap>
</sec>
<sec id="s3_4">
<label>3.4</label>
<title>Assessment of secondary structure of DS<sub>3</sub> and DS<sub>5</sub> vaccines</title>
<p>Secondary structure compositions of DS<sub>3</sub> and DS<sub>5</sub> vaccine were analyzed using SOPMA server. DS<sub>3</sub> candidate exhibited a secondary structure composed of 50.33% &#x3b1;-helices (152/302), 37.09% random coils (112/302), and 12.58% extended strands (38/302) (<xref ref-type="fig" rid="f3"><bold>Figure&#xa0;3A</bold></xref>). Additionally, DS<sub>3</sub> demonstrated enhanced solubility, with a Protein-Sol score of 0.574, surpassing the baseline threshold of 0.45 (<xref ref-type="fig" rid="f3"><bold>Figure&#xa0;3B</bold></xref>). Confidence in the secondary structure predictions for DS<sub>3</sub> was further assessed using the PESIPRED web server, which provided favorable results (<xref ref-type="fig" rid="f3"><bold>Figure&#xa0;3C</bold></xref>). In contrast, DS<sub>5</sub> candidate displayed a distinct secondary structure profile, characterized by 11.66% &#x3b1;-helices (45/386), 72.28% random coils (279/386), and 16.06% extended strands (62/386) (<xref ref-type="fig" rid="f3"><bold>Figure&#xa0;3D</bold></xref>). Similarly, DS<sub>5</sub> exhibited enhanced solubility, with a Protein-Sol score of 0.647, exceeding the baseline value of 0.45 (<xref ref-type="fig" rid="f3"><bold>Figure&#xa0;3E</bold></xref>). Confidence of the secondary structure predictions for DS<sub>5</sub> was also assessed using PESIPRED web server, yielding favorable results (<xref ref-type="fig" rid="f3"><bold>Figure&#xa0;3F</bold></xref>).</p>
<fig id="f3" position="float">
<label>Figure&#xa0;3</label>
<caption>
<p>Analysis of the secondary structure and solubility characteristics of DS<sub>3</sub> and DS<sub>5</sub> vaccine. Secondary structure of DS<sub>3</sub><bold>(A)</bold> and DS<sub>5</sub><bold>(D)</bold> was assessed using SOPMA server. Solubility characteristics of DS<sub>3</sub><bold>(B)</bold> and DS<sub>5</sub><bold>(E)</bold> vaccines were evaluated using Protein-Sol server, resulting in solubility scores of 0.574 and 0.647, respectively, both exceeding the baseline value of 0.45, indicating enhanced solubility. Secondary structure analysis of DS<sub>3</sub><bold>(C)</bold> and DS<sub>5</sub><bold>(F)</bold> was performed using PESIPRED web server, the blue bars show the confidence of prediction.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fimmu-16-1644437-g003.tif">
<alt-text content-type="machine-generated">Comparison of protein properties and sequences in two panels.Panel A displays predicted features and secondary structure, with a solubility chartshowing values of 0.450 and 0.574 in panel B. Panel C shows a detailed sequencealignment with structural predictions. Panel D presents similar features for a differentprotein, with solubility values of 0.450 and 0.647 in panel E. Panel F offers alignedsequences and structure predictions, indicating strand, helix, and coil regions. Bothpanels emphasize confidence in predictions and sequence specifics.</alt-text>
</graphic></fig>
</sec>
<sec id="s3_5">
<label>3.5</label>
<title>Analysis and refinement of tertiary structures of DS<sub>3</sub> and DS<sub>5</sub> vaccine</title>
<p>Top-ranked models for DS<sub>3</sub> and DS<sub>5</sub> vaccines, predicted using AlphaFold2, exhibited pLDDT scores of 37.1 and 45.1, respectively. The pLDDT scores, which range from 0 to 100, serve as an indicator of model confidence, where values above 80 reflect high confidence in the accuracy of residue structure, and scores below 50 suggest the presence of disordered regions. Both DS<sub>3</sub> and DS<sub>5</sub> displayed pLDDT scores below the confidence threshold of 50, warranting further refinement.</p>
<p>Refinement was conducted using GalaxyRefine server, resulting in the generation of five refined models for each vaccine candidate. Optimal model quality is characterized by higher Global Distance Test High Accuracy (GDT-HA) and Ramachandran values, and lower root-mean-square deviation (RMSD), MolProbity scores, clash scores, and counts of poor rotamers. For DS3, Model 1 demonstrated the most favorable refinement metrics, achieving GDT-HA of 0.9007, RMSD of 0.580 &#xc5;, MolProbity score of 1.459, clash score of 3.7, poor rotamer count of 0.4, and Ramachandran favored percentage of 95.7% (<xref ref-type="fig" rid="f4"><bold>Figure&#xa0;4A</bold></xref>, <xref ref-type="supplementary-material" rid="SM2"><bold>Supplementary Table S1</bold></xref>). Similarly, Model 1 of DS5 exhibited optimal refinement results, with GDT-HA of 0.9424, RMSD of 0.480 &#xc5;, MolProbity score of 1.772, clash score of 10.2, poor rotamer count of 0.0, and Ramachandran favored of 96.4% (<xref ref-type="fig" rid="f4"><bold>Figure&#xa0;4E</bold></xref>, <xref ref-type="supplementary-material" rid="SM3"><bold>Supplementary Table S2</bold></xref>).</p>
<fig id="f4" position="float">
<label>Figure&#xa0;4</label>
<caption>
<p>Refinement and validation of tertiary structures for DS<sub>3</sub> and DS<sub>5</sub> vaccines. Tertiary structures of DS<sub>3</sub><bold>(A)</bold> and DS<sub>5</sub><bold>(E)</bold> were refined using GalaxyRefine web server, with initial structures depicted in gray and refined structures shown in rainbow colors. Ramachandran plots for refined structures, generated via PROCHECK, indicate that 94.3% of DS<sub>3</sub> residues <bold>(B)</bold> are located in the most favored regions, 5.7% in additional allowed regions, 0.0% in generously allowed regions, and 0.0% in disallowed regions. For DS<sub>5</sub><bold>(F)</bold>, 93.7% of residues are in the most favored regions, 6.3% in additional allowed regions, and 0.0% in both generously allowed and disallowed. Z-scores obtained from ProSA-web for DS<sub>3</sub><bold>(C)</bold> and DS<sub>5</sub><bold>(G)</bold> models are -5.69 and -7.33, respectively (black dots), both within the conformational score range for experimentally validated protein structures. Panels <bold>(D)</bold> and <bold>(H)</bold> display energy plots of the amino acid compositions for DS<sub>3</sub> and DS<sub>5</sub>, respectively.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fimmu-16-1644437-g004.tif">
<alt-text content-type="machine-generated">(A) and (E) are protein structure models labeled DS3 and DS5, with color gradients indicating structure. (B) and (F) are Ramachandran plots showing torsion angles, with clusters in red and yellow. (C) and (G) depict Z-score scatter plots for number of residues with noted scores of -5.69 and -7.33. (D) and (H) show line graphs of knowledge-based energy versus sequence position, with different window sizes in light and dark green.</alt-text>
</graphic></fig>
<p>Ramachandran plots generated via PROCHECK indicated that 94.3% of DS<sub>3</sub> residues reside in the most favored regions, with 5.7% in additional allowed regions, while no residues were found in generously allowed or disallowed regions (<xref ref-type="fig" rid="f4"><bold>Figure&#xa0;4B</bold></xref>). Conversely, for DS<sub>5</sub>, 93.7% of residues were in the most favored regions, 6.3% in additional allowed regions, with none in generously allowed or disallowed regions (<xref ref-type="fig" rid="f4"><bold>Figure&#xa0;4F</bold></xref>). The Z-scores calculated from ProSA-web were -5.69 for DS<sub>3</sub> model and -7.33 for DS<sub>5</sub> model (<xref ref-type="fig" rid="f4"><bold>Figures&#xa0;4C, G</bold></xref>), both of which fall within the acceptable range for conformational scores typical of experimentally validated protein structures. DS<sub>3</sub> vaccine exhibited a quality factor of 90.8451 according to ERRAT, while DS<sub>5</sub> vaccine received a quality factor of 63.2867. Furthermore, energy plots corresponding to the amino acid compositions for both DS<sub>3</sub> (<xref ref-type="fig" rid="f4"><bold>Figure&#xa0;4D</bold></xref>) and DS<sub>5</sub> (<xref ref-type="fig" rid="f4"><bold>Figure&#xa0;4H</bold></xref>) were analyzed, providing additional evidence for structural integrity of the refined models.</p>
</sec>
<sec id="s3_6">
<label>3.6</label>
<title>T-cell and B-cell epitopes of DS<sub>3</sub> and DS<sub>5</sub> vaccine</title>
<p>Analysis using IEDB reveals that DS<sub>3</sub> vaccine exhibits a high density of T-cell
epitopes, comprising 13 strong and 34 weak CTL binders, as well as 3 strong and 47 weak HTL binders
(<xref ref-type="supplementary-material" rid="SM3"><bold>Supplementary Table S3</bold></xref>). Additionally, the ElliPro tool identifies 14 conformational B-cell epitopes associated with DS<sub>3</sub> vaccine (<xref ref-type="fig" rid="f5"><bold>Figure&#xa0;5A</bold></xref>, <xref ref-type="table" rid="T2"><bold>Table&#xa0;2</bold></xref>). In contrast, DS<sub>5</sub> vaccine also demonstrates a rich repertoire of T-cell
epitopes, featuring 17 strong and 42 weak CTL binders, along with 5 strong and 55 weak HTL binders
(<xref ref-type="supplementary-material" rid="SM3"><bold>Supplementary Table S3</bold></xref>). Moreover, a total of 10 conformational B-cell epitopes are predicted for DS<sub>5</sub> vaccine, as indicated by ElliPro (<xref ref-type="fig" rid="f5"><bold>Figure&#xa0;5B</bold></xref>, <xref ref-type="table" rid="T2"><bold>Table&#xa0;2</bold></xref>).</p>
<fig id="f5" position="float">
<label>Figure&#xa0;5</label>
<caption>
<p>Three-dimensional representation of discontinuous B-cell epitopes predicted for the refined DS<sub>3</sub> and DS<sub>5</sub> vaccines. <bold>(A)</bold> Fourteen discontinuous B-cell epitopes of the refined DS<sub>3</sub> vaccine are displayed, while <bold>(B)</bold> ten discontinuous B-cell epitopes of the refined DS<sub>5</sub> vaccine are shown. The discontinuous B-cell epitopes are represented as yellow spheres, with the remaining vaccine residues illustrated as gray sticks.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fimmu-16-1644437-g005.tif">
<alt-text content-type="machine-generated">Diagram showing two sets of molecular structures labeled A and B. Each set contains multiple images of molecular models with highlighted yellow clusters. The images are scored from 0.512 to 0.844, indicating varying configurations of yellow clusters within the molecular structures.</alt-text>
</graphic></fig>
<table-wrap id="T2" position="float">
<label>Table&#xa0;2</label>
<caption>
<p>Predicted discontinuous B-cell epitopes of the refined DS<sub>3</sub> and DS<sub>5</sub> vaccines.</p>
</caption>
<table frame="hsides">
<thead>
<tr>
<th valign="middle" align="left">Vaccine</th>
<th valign="middle" align="center">No.</th>
<th valign="middle" align="center">Residues</th>
<th valign="middle" align="center">No. of residues</th>
<th valign="middle" align="center">Score</th>
</tr>
</thead>
<tbody>
<tr>
<td valign="middle" rowspan="14" align="center">DS<sub>3</sub></td>
<td valign="middle" align="center">1</td>
<td valign="middle" align="left">A:R277, A:A278, A:Q279, A:R280, A:V281, A:Q282, A:L283, A:L284, A:C285, A:P286, A:G287, A:G288, A:E289, A:A290, A:P291, A:R292, A:A293, A:R294, A:K295, A:V296</td>
<td valign="middle" align="center">20</td>
<td valign="middle" align="center">0.809</td>
</tr>
<tr>
<td valign="middle" align="center">2</td>
<td valign="middle" align="left">A:C271, A:I272, A:P273, A:D274, A:R275</td>
<td valign="middle" align="center">5</td>
<td valign="middle" align="center">0.761</td>
</tr>
<tr>
<td valign="middle" align="center">3</td>
<td valign="middle" align="left">A:V197, A:Q198, A:L199, A:L200, A:C201, A:P202, A:G203, A:G204, A:E205, A:A206, A:P207, A:A209</td>
<td valign="middle" align="center">12</td>
<td valign="middle" align="center">0.745</td>
</tr>
<tr>
<td valign="middle" align="center">4</td>
<td valign="middle" align="left">A:I167, A:P168, A:L169, A:V170, A:G171, A:E172, A:L173, A:V174, A:D175, A:I176, A:G177, A:G178, A:G179, A:G180, A:S181, A:G182, A:G183, A:G184</td>
<td valign="middle" align="center">18</td>
<td valign="middle" align="center">0.739</td>
</tr>
<tr>
<td valign="middle" align="center">5</td>
<td valign="middle" align="left">A:G220, A:G221, A:G222, A:S223, A:G224, A:G225, A:G226, A:G227, A:R228, A:C229, A:I230, A:P231, A:D232, A:A258, A:S259, A:C260, A:G261, A:G262, A:G263, A:G264, A:S265, A:G266, A:G267, A:G268, A:G269, A:R270</td>
<td valign="middle" align="center">26</td>
<td valign="middle" align="center">0.731</td>
</tr>
<tr>
<td valign="middle" align="center">6</td>
<td valign="middle" align="left">A:S56, A:P57, A:N58, A:K59, A:T60, A:V61, A:S62, A:E63, A:E64, A:K65, A:A66, A:K67, A:Q68, A:Y69, A:D113, A:S114, A:E115, A:T116, A:A117, A:D118, A:N119</td>
<td valign="middle" align="center">21</td>
<td valign="middle" align="center">0.705</td>
</tr>
<tr>
<td valign="middle" align="center">7</td>
<td valign="middle" align="left">A:T38, A:E41, A:S42, A:K44, A:E45, A:H46</td>
<td valign="middle" align="center">6</td>
<td valign="middle" align="center">0.703</td>
</tr>
<tr>
<td valign="middle" align="center">8</td>
<td valign="middle" align="left">A:R238, A:L241, A:L242, A:C243, A:P244, A:G245, A:G246, A:E247, A:A248, A:P249, A:A251, A:R252</td>
<td valign="middle" align="center">12</td>
<td valign="middle" align="center">0.698</td>
</tr>
<tr>
<td valign="middle" align="center">9</td>
<td valign="middle" align="left">A:G47, A:P48, A:K50, A:N51, A:K52, A:M53, A:S54, A:E55, A:Q75, A:T76, A:E79</td>
<td valign="middle" align="center">11</td>
<td valign="middle" align="center">0.669</td>
</tr>
<tr>
<td valign="middle" align="center">10</td>
<td valign="middle" align="left">A:V14, A:R15, A:R16</td>
<td valign="middle" align="center">3</td>
<td valign="middle" align="center">0.623</td>
</tr>
<tr>
<td valign="middle" align="center">11</td>
<td valign="middle" align="left">A:S17, A:V18, A:G19, A:S20, A:S21, A:L22, A:S23, A:C24, A:I25, A:N26, A:L27</td>
<td valign="middle" align="center">11</td>
<td valign="middle" align="center">0.62</td>
</tr>
<tr>
<td valign="middle" align="center">12</td>
<td valign="middle" align="left">A:R297, A:L298, A:V299, A:A300, A:S301, A:C302</td>
<td valign="middle" align="center">6</td>
<td valign="middle" align="center">0.566</td>
</tr>
<tr>
<td valign="middle" align="center">13</td>
<td valign="middle" align="left">A:D28, A:D30, A:V31, A:D34, A:K35</td>
<td valign="middle" align="center">5</td>
<td valign="middle" align="center">0.56</td>
</tr>
<tr>
<td valign="middle" align="center">14</td>
<td valign="middle" align="left">A:H80, A:P81, A:E82, A:L83</td>
<td valign="middle" align="center">4</td>
<td valign="middle" align="center">0.512</td>
</tr>
<tr>
<td valign="middle" rowspan="10" align="center">DS<sub>5</sub></td>
<td valign="middle" align="center">1</td>
<td valign="middle" align="left">A:V14, A:R15, A:R16</td>
<td valign="middle" align="center">3</td>
<td valign="middle" align="center">0.844</td>
</tr>
<tr>
<td valign="middle" align="center">2</td>
<td valign="middle" align="left">A:I40, A:E41, A:S42, A:L43, A:K44, A:E45, A:H46, A:G47, A:P48, A:I49, A:K50, A:N51, A:K52, A:M53, A:S54, A:E55, A:Q75, A:T76, A:E79</td>
<td valign="middle" align="center">19</td>
<td valign="middle" align="center">0.792</td>
</tr>
<tr>
<td valign="middle" align="center">3</td>
<td valign="middle" align="left">A:S56, A:P57, A:N58, A:K59, A:T60, A:V61, A:S62, A:E63, A:E64, A:K65, A:A66, A:Q68, A:Y69, A:E72, A:I112, A:D113, A:S114, A:E115, A:T116, A:A117, A:D118, A:N119, A:L120, A:K122</td>
<td valign="middle" align="center">24</td>
<td valign="middle" align="center">0.773</td>
</tr>
<tr>
<td valign="middle" align="center">4</td>
<td valign="middle" align="left">A:L200, A:C201, A:P202, A:G203, A:G204, A:E205, A:A206, A:P207, A:R208, A:L242, A:C243, A:P244, A:G245, A:G246, A:E247, A:A248, A:P249, A:R250, A:L284, A:C285, A:P286, A:G287, A:G288, A:E289, A:A290, A:P291, A:R292, A:L326, A:C327, A:P328, A:G329, A:G330, A:E331, A:A332, A:P333, A:R334, A:Q366, A:L367, A:L368, A:C369, A:P370, A:G371, A:G372, A:E373, A:A374, A:P375, A:R376</td>
<td valign="middle" align="center">47</td>
<td valign="middle" align="center">0.761</td>
</tr>
<tr>
<td valign="middle" align="center">5</td>
<td valign="middle" align="left">A:A6, A:C9, A:A10, A:G11, A:N12, A:S17, A:V18, A:G19, A:S20, A:S21, A:L22, A:S23, A:C24, A:I25, A:N26, A:L27, A:D28, A:D30, A:V31, A:I32, A:D34, A:K35, A:K37, A:T38, A:K39, A:H80, A:P81, A:E82, A:L83, A:S84, A:K87</td>
<td valign="middle" align="center">31</td>
<td valign="middle" align="center">0.744</td>
</tr>
<tr>
<td valign="middle" align="center">6</td>
<td valign="middle" align="left">A:G180, A:S181, A:G182, A:G183, A:G184, A:G185, A:R186, A:C187, A:I188, A:P189, A:D190, A:R191</td>
<td valign="middle" align="center">12</td>
<td valign="middle" align="center">0.691</td>
</tr>
<tr>
<td valign="middle" align="center">7</td>
<td valign="middle" align="left">A:I314, A:P315, A:D316, A:C355, A:I356, A:P357, A:D358, A:R359, A:C386</td>
<td valign="middle" align="center">9</td>
<td valign="middle" align="center">0.667</td>
</tr>
<tr>
<td valign="middle" align="center">8</td>
<td valign="middle" align="left">A:R336, A:A377, A:R378</td>
<td valign="middle" align="center">3</td>
<td valign="middle" align="center">0.646</td>
</tr>
<tr>
<td valign="middle" align="center">9</td>
<td valign="middle" align="left">A:A140, A:D141, A:G142, A:A143, A:V144, A:H145, A:H146, A:N147, A:T148</td>
<td valign="middle" align="center">9</td>
<td valign="middle" align="center">0.632</td>
</tr>
<tr>
<td valign="middle" align="center">10</td>
<td valign="middle" align="left">A:G222, A:S223, A:G224, A:G225, A:G226, A:G227, A:R228, A:I230, A:P231, A:D232, A:G264, A:S265, A:G266, A:G267, A:G268, A:G269, A:R270, A:P273, A:D274, A:R275, A:R277, A:G306, A:S307, A:G308, A:G309, A:G310, A:G311, A:R312, A:R317, A:R319, A:G347, A:G348, A:S349, A:G350, A:G351, A:G352, A:G353, A:R354</td>
<td valign="middle" align="center">38</td>
<td valign="middle" align="center">0.618</td>
</tr>
</tbody>
</table>
</table-wrap>
</sec>
<sec id="s3_7">
<label>3.7</label>
<title>Molecular docking and molecular dynamics simulation</title>
<p>Molecular docking and molecular dynamics simulations were performed to elucidate the interactions between the DS<sub>3</sub> and DS<sub>5</sub> vaccines and Toll-like receptor 2 (TLR2). For molecular docking analysis, HawkDock was conducted to generate ten docking models for each vaccine. The optimized docking models revealed binding scores of -6618.72 kcal/mol for DS<sub>3</sub> and -8177.20 kcal/mol for DS<sub>5</sub>, suggesting a stronger interaction between DS<sub>5</sub> and TLR2. Further structural analysis of DS<sub>3</sub>-TLR2 and DS<sub>5</sub>-TLR2 complexes indicated distinct binding energies and interface areas. Specifically, DS<sub>3</sub>-TLR2 complex demonstrated a binding energy of -46.21 kcal/mol with an interface area of 1285.9 &#xc5;&#xb2; (<xref ref-type="fig" rid="f6"><bold>Figure&#xa0;6A</bold></xref>), whereas DS<sub>5</sub>-TLR2 complex exhibited a higher binding energy of -79.05 kcal/mol and a surface area of 1245.0 &#xc5;&#xb2; (<xref ref-type="fig" rid="f7"><bold>Figure&#xa0;7A</bold></xref>). DS<sub>3</sub>-TLR2 complex was characterized by the presence of 1 salt bridge, 6 hydrogen bonds, and 137 non-bonded contacts (<xref ref-type="fig" rid="f6"><bold>Figure&#xa0;6B</bold></xref>), while DS<sub>5</sub>-TLR2 complex featured 6 salt bridges, 7 hydrogen bonds, and 142 non-bonded contacts (<xref ref-type="fig" rid="f7"><bold>Figure&#xa0;7B</bold></xref>).</p>
<fig id="f6" position="float">
<label>Figure&#xa0;6</label>
<caption>
<p>Molecular docking and normal mode analysis of DS<sub>3</sub> with TLR2. <bold>(A)</bold> 3D model of the DS<sub>3</sub> &#x2013;TLR2 docking complex illustrating their interactions; DS<sub>3</sub> is colored cyan-yellow and TLR2 is shown in white. Overall structures are represented as cartoons, with key interface residues emphasized. Potential interactions are depicted as sticks and surface. The measured binding free energy is -46.21 kcal/mol, with an interface area of 1285.9 &#xc5;&#xb2;. <bold>(B)</bold> Detailed interactions between DS<sub>3</sub> and TLR2, including 1 salt bridges (red), 6 hydrogen bonds (blue), and 137 non-bonded contacts (yellow-orange). <bold>(C)</bold> B-factor representation of the docking complex. <bold>(D)</bold> Deformability plot of the complex. <bold>(E)</bold> Eigenvalues associated with the docked complex. <bold>(F)</bold> Variance analysis of the docked complex. <bold>(G)</bold> Covariance map of atomic pairs of amino acid residues; correlated interactions are shown in red, uncorrelated in white, and anti-correlated in blue. <bold>(H)</bold> Elastic network model of the docking complex, with darker gray indicating stiffer springs.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fimmu-16-1644437-g006.tif">
<alt-text content-type="machine-generated">A collection of scientific visuals depicting protein interactions andstructural analysis. A) Illustrates the interface between DS3 and TLR2 proteins, highlightinginteraction areas. B) Shows a diagram of amino acid interactions including salt bridgesand hydrogen bonds. C) and D) Present graphs of B-factor and deformability versus atomindex. E) and F) Display eigenvalue and variance graphs as functions of mode index. G)Offers a residue index correlation map, color-coded from red to blue. H) Contains agrayscale atom index scatter plot indicating data distribution.</alt-text>
</graphic></fig>
<fig id="f7" position="float">
<label>Figure&#xa0;7</label>
<caption>
<p>Molecular docking and normal mode analysis of DS<sub>5</sub> with TLR2. <bold>(A)</bold> 3D model of the DS<sub>5</sub> &#x2013;TLR2 docking complex illustrating their interactions; DS<sub>3</sub> is colored cyan-yellow and TLR2 is shown in white. Overall structures are represented as cartoons, with key interface residues emphasized. Potential interactions are depicted as sticks and surface. The measured binding free energy is -79.05 kcal/mol, with an interface area of 1245.0 &#xc5;&#xb2;. <bold>(B)</bold> Detailed interactions between DS<sub>5</sub> and TLR2, including 6 salt bridges (red), 7 hydrogen bonds (blue), and 142 non-bonded contacts (yellow-orange). <bold>(C)</bold> B-factor representation of the docking complex. <bold>(D)</bold> Deformability plot of the complex. <bold>(E)</bold> Eigenvalues associated with the docked complex. <bold>(F)</bold> Variance analysis of the docked complex. <bold>(G)</bold> Covariance map of atomic pairs of amino acid residues; correlated interactions are shown in red, uncorrelated in white, and anti-correlated in blue. <bold>(H)</bold> Elastic network model of the docking complex, with darker gray indicating stiffer springs.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fimmu-16-1644437-g007.tif">
<alt-text content-type="machine-generated">Panel A shows a molecular structure visualization with highlightedinterface areas. Panel B provides a color-coded diagram of interactions between DS5 andTLR2. Panel C presents a graph comparing NMA and PDB B-factors across atom indices.Panel D displays a deformability graph over atom indices. Panel E contains a graph ofeigenvalue mode indices. Panel F shows percentage variance across mode indices. PanelG visualizes a correlation matrix with a color gradient. Panel H depicts a grayscale atomindex scatter plot.</alt-text>
</graphic></fig>
<p>Both complexes demonstrated stability, as evidenced by their B-factors (<xref ref-type="fig" rid="f6"><bold>Figures&#xa0;6C</bold></xref>, <xref ref-type="fig" rid="f7"><bold>7C</bold></xref>), deformability profiles (<xref ref-type="fig" rid="f6"><bold>Figures&#xa0;6D</bold></xref>, <xref ref-type="fig" rid="f7"><bold>7D</bold></xref>), and low eigenvalues (8.476709e-06 for DS<sub>5</sub>-TLR2 and 1.077629e-05 for DS<sub>3</sub>-TLR2) (<xref ref-type="fig" rid="f6"><bold>Figures&#xa0;6E</bold></xref>, <xref ref-type="fig" rid="f7"><bold>7E</bold></xref>), as well as variance analyses (<xref ref-type="fig" rid="f6"><bold>Figures&#xa0;6F</bold></xref>, <xref ref-type="fig" rid="f7"><bold>7F</bold></xref>). Covariance matrix evaluations highlighted correlations, as well as uncorrelated and anti-correlated motions among the residues within the complexes (<xref ref-type="fig" rid="f6"><bold>Figures&#xa0;6G</bold></xref>, <xref ref-type="fig" rid="f7"><bold>7G</bold></xref>). Elastic network analysis illustrated spring-like interactions between atoms, with darker gray depicting stiffer springs (<xref ref-type="fig" rid="f6"><bold>Figures&#xa0;6H</bold></xref>, <xref ref-type="fig" rid="f7"><bold>7H</bold></xref>). Collectively, these findings suggest that both DS<sub>3</sub> and DS<sub>5</sub> vaccines effectively engage TLR2, potentially eliciting robust immune responses.</p>
</sec>
<sec id="s3_8">
<label>3.8</label>
<title>Immune response simulation induced by vaccines</title>
<p>To assess the adaptive immune responses elicited by DS<sub>3</sub> and DS<sub>5</sub> vaccines, we employed C-IMMSIM server to simulate <italic>in vivo</italic> immune reactions. Our analysis revealed an increase in the total B cell population, including B-memory cells and IgM isotypes, which contributed to a significant rise in activated B cells in the host (<xref ref-type="fig" rid="f8"><bold>Figures&#xa0;8</bold></xref>, <xref ref-type="fig" rid="f9"><bold>9A, B</bold></xref>). Following the second immunization, the total count of T helper (TH) cells exhibited a rapid increase, peaking after the third immunization (<xref ref-type="fig" rid="f8"><bold>Figures&#xa0;8</bold></xref>, <xref ref-type="fig" rid="f9"><bold>9C</bold></xref>). Both activated and resting TH cell populations surged after each injection, primarily comprising TH1 cells (<xref ref-type="fig" rid="f8"><bold>Figures&#xa0;8</bold></xref>, <xref ref-type="fig" rid="f9"><bold>9D, E</bold></xref>), suggesting effective antibody maturation processes. Notably, the population of anergic (y2) T cells remained stable throughout the duration of the study (<xref ref-type="fig" rid="f8"><bold>Figures&#xa0;8</bold></xref>, <xref ref-type="fig" rid="f9"><bold>9F</bold></xref>). In contrast, the count of activated T cytotoxic (TC) cells showed a transient increase followed by a decline, while resting TC cells exhibited the opposite trend (<xref ref-type="fig" rid="f8"><bold>Figures&#xa0;8</bold></xref>, <xref ref-type="fig" rid="f9"><bold>9G</bold></xref>).</p>
<fig id="f8" position="float">
<label>Figure&#xa0;8</label>
<caption>
<p>Predicted immune response induced by three administrations of DS<sub>3</sub> vaccine via C-IMMSIM online server. Vaccinations were conducted on Day 1, Day 14, and Day 28. <bold>(A)</bold> Changes in B cell populations after vaccination, with specific subclasses color-coded. <bold>(B)</bold> Levels of B cell production post-immunization; active B cells (depicted in purple) show the highest secretion among subtypes. <bold>(C)</bold> Production of CD4+ T-helper (TH) cells in response to antigen exposure. <bold>(D)</bold> Distribution of TH cell states, including active, duplicating, resting, and anergic cells. <bold>(E)</bold> Quantification and proportion of different TH cell subtypes. <bold>(F)</bold> Levels of cytotoxic T (TC) cell production. <bold>(G)</bold> Overview of the TC cell population, categorized into resting and active states over time after DS<sub>3</sub> vaccination. <bold>(H)</bold> Distribution of natural killer (NK) cells. <bold>(I)</bold> States of macrophages (MA). <bold>(J)</bold> Status of dendritic <bold>(DC)</bold> cells. <bold>(K)</bold> Production levels of epithelial cells. <bold>(L)</bold> Cytokine levels following DS<sub>3</sub> vaccination. The main plot depicts overall cytokine concentrations, while the inset illustrates the levels of danger signals alongside the leukocyte growth factor IL-2.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fimmu-16-1644437-g008.tif">
<alt-text content-type="machine-generated">Charts depict the populations and states of various immune cells over time. Graphs A through L show trends for B cells, T helper cells, T cytotoxic cells, NK cells, macrophages, dendritic cells, and epithelial cells. Each chart includes lines for specific cell populations and states, such as memory, active, and anergic, over time in days. Data labels identify cell types and states, with some charts combining multiple axes to represent different measures. The data visualizes immune response dynamics.</alt-text>
</graphic></fig>
<fig id="f9" position="float">
<label>Figure&#xa0;9</label>
<caption>
<p>Predicted immune response induced by three administrations of DS<sub>5</sub> vaccine via C-IMMSIM online server. Vaccinations were conducted on Day 1, Day 14, and Day 28. <bold>(A)</bold> Changes in B cell populations after vaccination, with specific subclasses color-coded. <bold>(B)</bold> Levels of B cell production post-immunization; active B cells (depicted in purple) show the highest secretion among subtypes. <bold>(C)</bold> Production of CD4+ T-helper (TH) cells in response to antigen exposure. <bold>(D)</bold> Distribution of TH cell states, including active, duplicating, resting, and anergic cells. <bold>(E)</bold> Quantification and proportion of different TH cell subtypes. <bold>(F)</bold> Levels of cytotoxic T (TC) cell production. <bold>(G)</bold> Overview of the TC cell population, categorized into resting and active states over time after DS<sub>5</sub> vaccination. <bold>(H)</bold> Distribution of natural killer (NK) cells. <bold>(I)</bold> States of macrophages (MA). <bold>(J)</bold> Status of dendritic <bold>(DC)</bold> cells. <bold>(K)</bold> Production levels of epithelial cells. <bold>(L)</bold> Cytokine levels following DS<sub>5</sub> vaccination. The main plot depicts overall cytokine concentrations, while the inset plot shows danger signal together with leukocyte growth factor IL-2.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fimmu-16-1644437-g009.tif">
<alt-text content-type="machine-generated">Graphs A to L illustrate various cell populations and states over time, presented in different charts. Each graph represents a distinct type of cell, such as B cells, Th cells, TC cells, NK cells, MA cells, DC cells, and EP cells, with metrics like active, duplicating, resting, and anergic states. Time is on the x-axis, and cell count or percentage is on the y-axis. These visualizations provide insights into cell behavior and immune responses over days, with specific patterns and trends depicted in each chart.</alt-text>
</graphic></fig>
<p>Additionally, we evaluated the effects of DS<sub>3</sub> and DS<sub>5</sub> vaccines on innate immune cell populations. Natural killer (NK) cells, dendritic cells (DCs), and active epithelial cell populations demonstrated a relatively stable response upon immunization (<xref ref-type="fig" rid="f8"><bold>Figures&#xa0;8</bold></xref>, <xref ref-type="fig" rid="f9"><bold>9H, J, K</bold></xref>). Upon initial immunization, there was a marked increase in both active and resting macrophage populations in a short time, which subsequently reached a peak and stabilized (<xref ref-type="fig" rid="f8"><bold>Figures&#xa0;8</bold></xref>, <xref ref-type="fig" rid="f9"><bold>9I</bold></xref>). Approximately four weeks after the third immunization, we observed a decline in the number of active macrophages, coinciding with a rapid increase in resting macrophages (<xref ref-type="fig" rid="f8"><bold>Figures&#xa0;8</bold></xref>, <xref ref-type="fig" rid="f9"><bold>9I</bold></xref>). Following the administration of DS<sub>3</sub> and DS<sub>5</sub> vaccines, there was an activation of downstream inflammatory mediators, with significant elevations in levels of IFN-&#x3b3; and IL-2 (<xref ref-type="fig" rid="f8"><bold>Figures&#xa0;8</bold></xref>, <xref ref-type="fig" rid="f9"><bold>9L</bold></xref>). Collectively, these findings indicated that the DS<sub>3</sub> and DS<sub>5</sub> vaccines effectively stimulate both innate and adaptive immune responses, highlighting their potential as effective vaccine candidates.</p>
</sec>
<sec id="s3_9">
<label>3.9</label>
<title>Cloning, expression and immunogenicity of vaccines</title>
<p>Codons for the optimized DS<sub>3</sub> and DS<sub>5</sub> sequences were successfully cloned into pSmartI plasmids at XhoI restriction sites (<xref ref-type="fig" rid="f10"><bold>Figures&#xa0;10A, D</bold></xref>). The recombinant plasmids were confirmed through PCR amplification, as shown by agarose gel electrophoresis (<xref ref-type="fig" rid="f10"><bold>Figures&#xa0;10B, E</bold></xref>). Subsequently, the recombinant plasmids were transformed into Escherichia coli BL21(DE3), leading to the successful expression and purification of DS<sub>3</sub> and DS<sub>5</sub> vaccine proteins, which exhibited molecular weights of 31.8 kDa and 40.3 kDa, respectively (<xref ref-type="fig" rid="f10"><bold>Figures&#xa0;10C, F</bold></xref>).</p>
<fig id="f10" position="float">
<label>Figure&#xa0;10</label>
<caption>
<p>Cloning, expression, and immunogenicity assessment of DS<sub>3</sub> and DS<sub>5</sub> vaccines. <bold>(A)</bold> DS<sub>3</sub> vaccine sequence (red) was inserted into the pSmartI expression vector (black) via seamless cloning using XhoI. <bold>(B)</bold> Agarose gel electrophoresis showing: Lane 1, recombinant plasmid; Lane 2, target fragment (1268 bp) along with vector sequence; Lane M, 1 kb DNA ladder. <bold>(C)</bold> Expression and purification of DS<sub>3</sub> vaccine. <bold>(D)</bold> DS<sub>5</sub> vaccine sequence (red) was cloned into the pSmartI expression vector (black) via seamless cloning using XhoI. <bold>(E)</bold> Agarose gel electrophoresis illustrating: Lane 1, recombinant plasmid; Lane 2, target fragment (1520 bp) along with vector sequence; Lane M, 1 kb DNA ladder. <bold>(F)</bold> Expression and purification of DS<sub>5</sub>. <bold>(G)</bold> Schematic overview of the mouse immunization protocol; each group comprised three mice (n=3), serving as independent biological replicates. <bold>(H)</bold> ELISA measurements indicating significantly elevated serum titers of anti-SOST antibodies in mice immunized with DS<sub>3</sub> and DS<sub>5</sub> compared to PBS controls (serum dilution 1:200). Antibody assays were performed in technical duplicates per mouse. <bold>(I&#x2013;K)</bold> Cytokine levels of IL-4, IL-10, and IFN-&#x3b3; in supernatants from splenocyte stimulation assays. Data are expressed as mean &#xb1; SD. Statistical significance was determined by one-way ANOVA followed by Tukey&#x2019;s multiple comparisons test. (<sup>*</sup>p &lt; 0.05, <sup>**</sup>P &lt; 0.01, <sup>***</sup>P &lt; 0.001, <sup>****</sup>P &lt; 0.0001, ns = no significance).</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fimmu-16-1644437-g010.tif">
<alt-text content-type="machine-generated">Panel A shows a circular plasmid map of DS3 with restrictionsites. Panel B displays a gel electrophoresis result with lanes labeled plasmid and DNAmarker. Panel C is a protein gel with labeled bands, indicating DS3 at 31.8 kDa. Panel Dfeatures a plasmid map of DS5. Panel E shows gel electrophoresis for DS5 with labeledbands. Panel F depicts a protein gel with DS5 at 40.3 kDa. Panel G illustrates a vaccinationtimeline in mice. Panels H-J present bar graphs of antiserum titers and cytokineconcentrations (IL-4, IL-10, IFN-g) with statistical significance markers.</alt-text>
</graphic></fig>
<p>To evaluate immunogenic potential of DS<sub>3</sub> and DS<sub>5</sub> vaccines, mice were immunized with DS<sub>3</sub> and DS<sub>5</sub> proteins at a dose of 200 &#xb5;g per mouse, with a two-week interval between doses (n=3). Serum was collected at the seventh week to assess antibody production against SOST (<xref ref-type="fig" rid="f10"><bold>Figure&#xa0;10G</bold></xref>). Our results demonstrated that both DS<sub>3</sub> and DS<sub>5</sub> effectively elicited a significant immune response, resulting in the production of high titers of anti-SOST antibodies in the immunized mice. The antibody titers induced by both vaccines were&#xa0;significantly higher than those observed in PBS control group (<xref ref-type="fig" rid="f10"><bold>Figures&#xa0;10H</bold></xref>).</p>
<p>To assess T cell responses to vaccine stimulation, cytokine production associated with Th1 and Th2 responses was quantified using DS<sub>5</sub> as a representative antigen. Specifically, levels of IL-4 and IL-10 (Th2 markers) and IFN-&#x3b3; (Th1 marker) were measured in splenocyte cultures stimulated with PBS, SOST, or DS<sub>5</sub> (<xref ref-type="fig" rid="f10"><bold>Figures&#xa0;10I&#x2013;K</bold></xref>). IFN-&#x3b3; levels did not differ significantly among the PBS and DS<sub>5</sub> groups, indicating that DS<sub>5</sub> does not elicit a robust Th1-mediated cytotoxic response (<xref ref-type="fig" rid="f10"><bold>Figure&#xa0;10K</bold></xref>). In contrast, IL-4 and IL-10 secretion were reduced following stimulation with both SOST and DS<sub>5</sub> (<xref ref-type="fig" rid="f10"><bold>Figures&#xa0;10I, J</bold></xref>). Notably, cytokine levels in DS<sub>5</sub>-treated splenocytes remained higher than in SOST-treated cells, suggesting that the DS<sub>5</sub> vaccine induces a moderated Th2 response that may support B cell-mediated anti-SOST antibody production.</p>
</sec>
<sec id="s3_10">
<label>3.10</label>
<title>Validation of anti-SOST antiserum function <italic>in vitro</italic></title>
<p>The antiserum obtained from vaccinated mice, which exhibited the highest antibody titer, was selected for <italic>in vitro</italic> functional assays using primary osteoclasts and osteoblasts. To model the <italic>in vivo</italic> role of SOST, which promotes osteoclast differentiation and inhibits osteoblast maturation, recombinant SOST was co-cultured with the respective cell types. Results showed that SOST supplementation had no sinificantly effect on osteoclast differentiation and maturation, however, the addition of the antiserum significantly attenuated osteoclast differentiation and maturation, leading to a marked reduction in osteoclastogenesis (<xref ref-type="fig" rid="f11"><bold>Figures&#xa0;11 A, B</bold></xref>). In primary osteoblasts (<xref ref-type="fig" rid="f11"><bold>Figures&#xa0;11C, D</bold></xref>) and the MC3T3-E1 subclone 14 cell line (<xref ref-type="fig" rid="f11"><bold>Figures&#xa0;11E, F</bold></xref>), SOST partially suppressed differentiation and mineralization; however, the presence of antiserum mitigated these inhibitory effects, thereby restoring osteoblast mineralization capacity (<xref ref-type="fig" rid="f11"><bold>Figures&#xa0;11C&#x2013;F</bold></xref>). These findings demonstrate that the vaccine-induced antiserum effectively inhibits osteoclast activity and enhances osteoblast function, confirming its functional efficacy. Moreover, these results provide preliminary evidence supporting the vaccine&#x2019;s potential as a therapeutic strategy for osteoporosis.</p>
<fig id="f11" position="float">
<label>Figure&#xa0;11</label>
<caption>
<p>Effects of anti-SOST antiserum derived from vaccine-immunized mice on osteoclast and osteoblast differentiation. <bold>(A)</bold> TRAP staining of bone marrow-derived macrophages treated with SOST and anti-SOST antiserum at a 1:500 dilution, demonstrating inhibition of osteoclast differentiation (n=4). <bold>(B)</bold> Quantification of TRAP-positive osteoclasts in <bold>(A)</bold>. <bold>(C)</bold> Alizarin Red S staining of bone marrow mesenchymal stem cell-derived osteoblasts cultured with osteogenic medium and treated with SOST and anti-SOST antiserum at a 1:100 dilution, indicating enhanced osteoblast differentiation and mineralization upon vaccine antiserum treatment (n=4). <bold>(D)</bold> Quantitative analysis of mineralization in <bold>(C)</bold>. <bold>(E)</bold> Alizarin Red S staining of MC3T3-E1 subclone 14 cells cultured with osteogenic medium and treated with SOST and vaccine antiserum at a 1:100 dilution, showing rescue of SOST-mediated inhibition of osteoblast differentiation and mineralization (n=6). <bold>(F)</bold> Quantitative analysis of mineralization in <bold>(E)</bold>. Scale bars, 250 &#x3bc;m and 500 &#x3bc;m. Data are expressed as mean &#xb1; SD; <sup>*</sup>p &lt; 0.05, <sup>**</sup>p &lt; 0.01, <sup>***</sup>p &lt; 0.001; ns, not significant. Statistical significance was determined by one-way ANOVA followed by Tukey&#x2019;s multiple comparisons test.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fimmu-16-1644437-g011.tif">
<alt-text content-type="machine-generated">Three panels display microscopy images and bar graphs related to osteoclast and mineralized nodule formation under different treatments. Panel A shows osteoclast cell images and a bar graph comparing cell counts. Panel C displays mineralized nodules and a bar graph for relative nodule levels. Panel E also depicts mineralized nodules with another bar graph. Treatments include M-CSF+RANKL, SOST+PBS, SOST+WT antiserum, and SOST+Vaccine antiserum, with statistical significance marked in the graphs.</alt-text>
</graphic></fig>
</sec>
</sec>
<sec id="s4" sec-type="discussion">
<label>4</label>
<title>Discussion</title>
<p>Osteoporosis represents a significant global public health challenge, with osteoporotic fractures incurring substantial economic costs and imposing considerable demands on individual healthcare resources and societal medical systems (<xref ref-type="bibr" rid="B1">1</xref>, <xref ref-type="bibr" rid="B2">2</xref>). Among the available anti-osteoporotic treatments, ROMO is noteworthy for its significant ability to increase bone mass (<xref ref-type="bibr" rid="B37">37</xref>). Nevertheless, its high cost and strict eligibility criteria, which restrict its use to patients with diagnosed osteoporosis, hinder its broader applicability for early prevention strategies (<xref ref-type="bibr" rid="B5">5</xref>, <xref ref-type="bibr" rid="B38">38</xref>). The potential risk of cardiovascular adverse events associated with ROMO raises important safety concerns that warrant careful consideration (<xref ref-type="bibr" rid="B38">38</xref>).</p>
<p>Recent advancements in vaccine immunology have effectively demonstrated the potential of active immunization strategies to stimulate endogenous antibody production across various chronic conditions, including ankylosing spondylitis (<xref ref-type="bibr" rid="B39">39</xref>), hypertension (<xref ref-type="bibr" rid="B40">40</xref>), diabetes (<xref ref-type="bibr" rid="B41">41</xref>), Alzheimer&#x2019;s disease (<xref ref-type="bibr" rid="B42">42</xref>), and so on. Building on these innovations, our team has focused on developing a vaccine-based immunotherapy for osteoporosis (<xref ref-type="bibr" rid="B10">10</xref>, <xref ref-type="bibr" rid="B11">11</xref>). This approach aims to achieve sustained regulation of bone formation and resorption through proactive immunization, offering a cost-effective solution that could enhance both early prevention and adjunctive long-term treatment of advanced osteoporosis.</p>
<p>In this study, we present an innovative osteoporosis vaccine targeting the SOST epitope (SOST<sub>131-163</sub>), which was identified through ROMO screening. The SOST<sub>131&#x2013;163</sub> epitope, situated within the loop3 region (amino acids 134&#x2013;163 in SOST (<xref ref-type="bibr" rid="B43">43</xref>), including a 23-amino acid signal peptide), partially overlaps with previously identified antibody-binding sites in both loop2 and loop3 (<xref ref-type="bibr" rid="B43">43</xref>&#x2013;<xref ref-type="bibr" rid="B45">45</xref>). However, we did not detect specific binding sites in loop2, likely due to challenges in preserving the native three-dimensional structure during separate synthesis. While ROMO effectively inhibits SOST by targeting both loops and demonstrates substantial anti-osteoporosis benefits, this broad inhibition may elevate the risk of cardiovascular side effects (<xref ref-type="bibr" rid="B5">5</xref>, <xref ref-type="bibr" rid="B6">6</xref>). In contrast, our targeted vaccine approach focuses solely on loop3, which promotes bone formation while preserving cardiovascular health (<xref ref-type="bibr" rid="B45">45</xref>&#x2013;<xref ref-type="bibr" rid="B47">47</xref>). Thus, our vaccine strategically aims to enhance bone mass while ensuring cardiovascular safety, offering a promising option for osteoporosis management.</p>
<p>In vaccine design, antigenicity and immunogenicity are crucial for eliciting robust and specific immune responses. Our study reveals that the SOST<sub>131&#x2013;163</sub> epitope contains six CTL epitopes, five HTL epitopes, two linear B-cell epitopes, and two conformational B-cell epitopes, highlighting its considerable immunogenic potential to activate both T-cell-mediated immunity and B-cell antibody production. To overcome immune tolerance associated with autologous protein vaccines, we utilized DTT protein as a carrier to enhance immunogenicity, which effectively expanded specific helper T-cell populations and promoted the differentiation and proliferation of polysaccharide-specific B cells. The candidate vaccines, DS<sub>1</sub>-DS<sub>5</sub>, successfully disrupted immune tolerance and elicited robust antibody responses in immune simulations. Notably, the DS<sub>3</sub> and DS<sub>5</sub> vaccines produced unique profiles by generating IgM, IgG1, and IgG2 antibodies, while the other candidates primarily generated IgM and IgG1, lacking IgG2. Given the clinical efficacy of ROMO as an IgG2 monoclonal antibody (<xref ref-type="bibr" rid="B21">21</xref>), our primary goal was to stimulate endogenous IgG2 antibody production, similar to ROMO. Consequently, we selected DS<sub>3</sub> and DS<sub>5</sub> for further exploration of their immunological mechanisms and potential applications. In selecting the immunological scaffold, we directly employed DTT to facilitate the overcoming of immune tolerance, informed by our prior findings (<xref ref-type="bibr" rid="B10">10</xref>). Nonetheless, the considerable potential of alternative scaffolds warrants further investigation to enhance vaccine efficacy and optimize antibody titers.</p>
<p>Structural analysis revealed that 94.3% of residues in the DS<sub>3</sub> vaccine and 93.7% in the DS<sub>5</sub> vaccine occupied favorable regions, indicating high modeling quality. Bioinformatics assessments further demonstrated these vaccines&#x2019; strong antigenicity, favorable physicochemical properties, and non-allergenic nature, establishing them as promising vaccine candidates. Molecular docking studies showed that both DS<sub>3</sub> and DS<sub>5</sub> vaccines effectively bind to Toll-like receptor 2 (TLR2), thereby activating this receptor and facilitating the induction of both humoral and cellular immune responses. TLR2, expressed in dendritic cells and involved in bone metabolism through the mechanism of osteoimmunology (<xref ref-type="bibr" rid="B48">48</xref>), is critical for osteoporosis management, as its activation inhibits inflammatory osteoclast differentiation and mitigates bone loss (<xref ref-type="bibr" rid="B49">49</xref>, <xref ref-type="bibr" rid="B50">50</xref>). Experimental validation confirmed the successful construction of DS<sub>3</sub> and DS<sub>5</sub> vaccines using recombinant plasmids, with efficient expression in E. coli. The purified DS<sub>3</sub> and DS<sub>5</sub> vaccines elicited a significant production of anti-SOST antibodies in immunized mice, demonstrating their efficacy in overcoming immune tolerance. Further cellular assays confirmed that sera from vaccinated mice contain anti-SOST antibodies capable of inhibiting osteoclast activity and promoting osteoblast function, thereby restoring the balance between bone resorption and formation disrupted in osteoporosis. These findings highlight the potential of these vaccines as promising immunotherapeutic strategies for the prevention and treatment of osteoporosis.</p>
</sec>
<sec id="s5" sec-type="conclusions">
<label>5</label>
<title>Conclusions</title>
<p>This study introduces a SOST-targeted vaccine specifically designed for osteoporosis, demonstrating several advantages: (1) high specificity for the loop 3 domain of SOST, which may confer protective effects against osteoporosis while minimizing cardiovascular side effects; and (2) robust immunogenicity coupled with favorable physicochemical properties, effectively inducing endogenous ROMO-like antibodies. Preliminary <italic>in vivo</italic> experiments confirm the vaccine&#x2019;s ability to overcome immune tolerance and elicit SOST-specific antibodies in murine models. Additionally, <italic>in vitro</italic> analyses reveal that the generated antiserum can inhibit osteoclast differentiation and enhance osteoblast activity, underscoring its therapeutic potential for osteoporosis. This innovative strategy offers a promising approach for early prevention and sustained management of the disease. Future investigations will aim to validate vaccine&#x2019;s efficacy and safety <italic>in vivo</italic>, facilitating its progression toward clinical application.</p>
</sec>
</body>
<back>
<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="ethics-statement">
<title>Ethics statement</title>
<p>The animal study was approved by Institutional Animal Care and Use Committee (IACUC) of Shenzhen University Medical School. The study was conducted in accordance with the local legislation and institutional requirements.</p></sec>
<sec id="s8" sec-type="author-contributions">
<title>Author contributions</title>
<p>JL: Formal Analysis, Writing &#x2013; original draft, Methodology, Visualization, Data curation, Validation, Resources, Investigation, Writing &#x2013; review &amp; editing, Conceptualization. TW: Funding acquisition, Validation, Writing &#x2013; review &amp; editing, Conceptualization, Supervision, Software. BG: Resources, Writing &#x2013; review &amp; editing, Methodology, Software. LL: Writing &#x2013; review &amp; editing, Software, Resources, Data curation, Methodology. ZY: Data curation, Visualization, Writing &#x2013; review &amp; editing, Resources. HT: Conceptualization, Resources, Writing &#x2013; review &amp; editing, Funding acquisition.</p></sec>
<sec id="s10" 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="s11" sec-type="ai-statement">
<title>Generative AI statement</title>
<p>The author(s) declare that no Generative AI was used in the creation of this manuscript.</p>
<p>Any alternative text (alt text) provided alongside figures in this article has been generated by Frontiers with the support of artificial intelligence and reasonable efforts have been made to ensure accuracy, including review by the authors wherever possible. If you identify any issues, please contact us.</p></sec>
<sec id="s12" 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>
<sec id="s13" 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/fimmu.2025.1644437/full#supplementary-material">https://www.frontiersin.org/articles/10.3389/fimmu.2025.1644437/full#supplementary-material</ext-link></p>
<supplementary-material xlink:href="Table1.docx" id="SF1" mimetype="application/vnd.openxmlformats-officedocument.wordprocessingml.document"><label>Supplementary Figure&#xa0;1</label>
<caption>
<p>Interaction of SOST<sub>131&#x2013;163</sub> fragment with ROMO light and heavy chains. <bold>(A)</bold> SOST<sub>131&#x2013;163</sub> fragment docked with ROMO light chain, forming four hydrogen bonds and 105 non-bonded contacts. <bold>(B)</bold> SOST<sub>131&#x2013;163</sub> fragment docked with ROMO heavy chain, establishing two salt bridges and 90 non-bonded contacts.</p>
</caption></supplementary-material>
<supplementary-material xlink:href="Table1.docx" id="SM1" mimetype="application/vnd.openxmlformats-officedocument.wordprocessingml.document"><label>Supplementary Table&#xa0;1</label>
<caption>
<p>Structure information of DS<sub>3</sub> after refinement using Galaxyrefine.</p>
</caption></supplementary-material>
<supplementary-material xlink:href="Table2.docx" id="SM2" mimetype="application/vnd.openxmlformats-officedocument.wordprocessingml.document"><label>Supplementary Table&#xa0;2</label>
<caption>
<p>Structure information of DS<sub>5</sub> after refinement using Galaxyrefine.</p>
</caption></supplementary-material>
<supplementary-material xlink:href="DataSheet1.xlsx" id="SM3" mimetype="application/vnd.openxmlformats-officedocument.spreadsheetml.sheet"><label>Supplementary Table&#xa0;3</label>
<caption>
<p>Prediction of cytotoxic T lymphocyte and helper T lymphocyte epitopes for DS<sub>3</sub> and DS<sub>5</sub> vaccine.</p>
</caption></supplementary-material>
<supplementary-material xlink:href="Image1.jpeg" id="SM4" mimetype="image/jpeg"/></sec>
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