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<front>
<journal-meta>
<journal-id journal-id-type="publisher-id">Front. Cell. Infect. Microbiol.</journal-id>
<journal-title>Frontiers in Cellular and Infection Microbiology</journal-title>
<abbrev-journal-title abbrev-type="pubmed">Front. Cell. Infect. Microbiol.</abbrev-journal-title>
<issn pub-type="epub">2235-2988</issn>
<publisher>
<publisher-name>Frontiers Media S.A.</publisher-name>
</publisher>
</journal-meta>
<article-meta>
<article-id pub-id-type="doi">10.3389/fcimb.2022.886901</article-id>
<article-categories>
<subj-group subj-group-type="heading">
<subject>Cellular and Infection Microbiology</subject>
<subj-group>
<subject>Original Research</subject>
</subj-group>
</subj-group>
</article-categories>
<title-group>
<article-title>Contribution of Puma to Inflammatory Resolution During Early Pneumococcal Pneumonia</article-title>
</title-group>
<contrib-group>
<contrib contrib-type="author">
<name>
<surname>Kennedy II</surname><given-names>Daniel E.</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>1</sup></xref>
<uri xlink:href="https://loop.frontiersin.org/people/1737323"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Mody</surname><given-names>Perceus</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>1</sup></xref>
<uri xlink:href="https://loop.frontiersin.org/people/1755802"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Gout</surname><given-names>Jean-Francois</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>1</sup></xref>
<uri xlink:href="https://loop.frontiersin.org/people/1315675"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Tan</surname><given-names>Wei</given-names>
</name>
<xref ref-type="aff" rid="aff2"><sup>2</sup></xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Seo</surname><given-names>Keun Seok</given-names>
</name>
<xref ref-type="aff" rid="aff2"><sup>2</sup></xref>
<uri xlink:href="https://loop.frontiersin.org/people/515625"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Olivier</surname><given-names>Alicia K.</given-names>
</name>
<xref ref-type="aff" rid="aff3"><sup>3</sup></xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Rosch</surname><given-names>Jason W.</given-names>
</name>
<xref ref-type="aff" rid="aff4"><sup>4</sup></xref>
</contrib>
<contrib contrib-type="author" corresp="yes">
<name>
<surname>Thornton</surname><given-names>Justin A.</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>1</sup></xref>
<xref ref-type="author-notes" rid="fn001"><sup>*</sup></xref>
<uri xlink:href="https://loop.frontiersin.org/people/358094"/>
</contrib>
</contrib-group>
<aff id="aff1"><sup>1</sup><institution>Department of Biological Sciences, Mississippi State University</institution>, <addr-line>Starkville, MS</addr-line>, <country>United States</country></aff>
<aff id="aff2"><sup>2</sup><institution>Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University</institution>, <addr-line>Starkville, MS</addr-line>, <country>United States</country></aff>
<aff id="aff3"><sup>3</sup><institution>Department of Population and Pathobiology, College of Veterinary Medicine, Mississippi State University</institution>, <addr-line>Starkville, MS</addr-line>, <country>United States</country></aff>
<aff id="aff4"><sup>4</sup><institution>Department of Infectious Diseases, St. Jude Children&#x2019;s Research Hospital</institution>, <addr-line>Memphis, TN</addr-line>, <country>United States</country></aff>
<author-notes>
<fn fn-type="edited-by">
<p>Edited by: Stephanie Rochelle Shames, Kansas State University, United States</p>
</fn>
<fn fn-type="edited-by">
<p>Reviewed by: Federico Iovino, Karolinska Institutet (KI), Sweden; Brandon Kim, University of Alabama, United States; Jeffrey Lee Bose, University of Kansas Medical Center, United States</p>
</fn>
<fn fn-type="corresp" id="fn001">
<p>*Correspondence: Justin A. Thornton, <email xlink:href="mailto:thornton@biology.msstate.edu">thornton@biology.msstate.edu</email></p>
</fn>
<fn fn-type="other" id="fn002">
<p>This article was submitted to Bacteria and Host, a section of the journal Frontiers in Cellular and Infection Microbiology</p>
</fn>
</author-notes>
<pub-date pub-type="epub">
<day>26</day>
<month>05</month>
<year>2022</year>
</pub-date>
<pub-date pub-type="collection">
<year>2022</year>
</pub-date>
<volume>12</volume>
<elocation-id>886901</elocation-id>
<history>
<date date-type="received">
<day>01</day>
<month>03</month>
<year>2022</year>
</date>
<date date-type="accepted">
<day>25</day>
<month>04</month>
<year>2022</year>
</date>
</history>
<permissions>
<copyright-statement>Copyright &#xa9; 2022 Kennedy II, Mody, Gout, Tan, Seo, Olivier, Rosch and Thornton</copyright-statement>
<copyright-year>2022</copyright-year>
<copyright-holder>Kennedy II, Mody, Gout, Tan, Seo, Olivier, Rosch and Thornton</copyright-holder>
<license xlink:href="http://creativecommons.org/licenses/by/4.0/">
<p>This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.</p>
</license>
</permissions>
<abstract>
<p>Apoptosis of cells at the site of infection is a requirement for shutdown of inflammatory signaling, avoiding tissue damage, and preventing progression of sepsis. <italic>Puma<sup>+/+</sup>
</italic> and <italic>Puma<sup>-/-</sup>
</italic> mice were challenged with TIGR4 strain pneumococcus and cytokines were quantitated from lungs and blood using a magnetic bead panel analysis. <italic>Puma<sup>-/-</sup>
</italic> mice exhibited higher lung and blood cytokine levels of several major inflammatory cytokines, including IL-6, G-CSF, RANTES, IL-12, IFN-&#x3d2;, and IP-10. <italic>Puma<sup>-/-</sup>
</italic> mice were more susceptible to bacterial dissemination and exhibited more weight loss than their wild-type counterparts. RNA sequencing analysis of whole pulmonary tissue revealed Puma-dependent regulation of <italic>Nrxn2</italic>, <italic>Adam19</italic>, and <italic>Eln</italic>. Enrichment of gene ontology groups differentially expressed in <italic>Puma<sup>-/-</sup>
</italic> tissues were strongly correlated to IFN-&#x3b2; and -&#x3d2; signaling. Here, we demonstrate for the first time the role of Puma in prohibition of the cytokine storm during bacterial pneumonia. These findings further suggest a role for targeting immunomodulation of IFN signaling during pulmonary inflammation. Additionally, our findings suggest previously undemonstrated roles for genes encoding regulatory and binding proteins during the early phase of the innate immune response of pneumococcal pneumonia.</p>
</abstract>
<kwd-group>
<kwd>PUMA (p53 upregulated modulator of apoptosis)</kwd>
<kwd>inflammation</kwd>
<kwd>streptococcus pneumoniae (pneumococcus)</kwd>
<kwd>apoptosis</kwd>
<kwd>innate immunity</kwd>
</kwd-group>
<counts>
<fig-count count="4"/>
<table-count count="3"/>
<equation-count count="0"/>
<ref-count count="89"/>
<page-count count="11"/>
<word-count count="5686"/>
</counts>
</article-meta>
</front>
<body>
<sec id="s1" sec-type="intro">
<title>Introduction</title>
<p>During pneumococcal infection, interaction of bacteria with the host epithelium initiates recruitment of neutrophils (<xref ref-type="bibr" rid="B85">Yamamoto et&#xa0;al., 2014</xref>). Following recruitment, activated neutrophils are capable of inducing programmed cell death in epithelial cells (<xref ref-type="bibr" rid="B42">Jia et&#xa0;al., 2014</xref>). Pneumococcus can induce both direct and indirect apoptosis in neutrophils (<xref ref-type="bibr" rid="B89">Zysk et&#xa0;al., 2000</xref>; <xref ref-type="bibr" rid="B22">Engelich et&#xa0;al., 2001</xref>), epithelial cells (<xref ref-type="bibr" rid="B70">Schmeck et&#xa0;al., 2004</xref>), and macrophages (<xref ref-type="bibr" rid="B56">Marriott et&#xa0;al., 2004</xref>), observations that have been mechanistically tied to PLY, cell wall components, and H<sub>2</sub>O<sub>2</sub> (<xref ref-type="bibr" rid="B57">Marriott and Dockrell, 2006</xref>; <xref ref-type="bibr" rid="B65">Rai et&#xa0;al., 2015</xref>). In murine pneumococcal pneumonia, macrophage apoptosis has been shown to be crucial for resolution of pulmonary inflammation (<xref ref-type="bibr" rid="B58">Marriott et&#xa0;al., 2006</xref>). Induction of apoptosis, depending on cell type, can have detrimental or beneficial results, but coordinated and organized cell death is essential during infection resolution. Apoptosis modulates innate immune signaling, cell fate of responding phagocytes, promotes resolution of inflammation, and limits tissue damage (<xref ref-type="bibr" rid="B37">Haslett, 1999</xref>; <xref ref-type="bibr" rid="B44">Kennedy and Deleo, 2009</xref>; <xref ref-type="bibr" rid="B23">Esmann et&#xa0;al., 2010</xref>; <xref ref-type="bibr" rid="B27">Fox et&#xa0;al., 2010</xref>; <xref ref-type="bibr" rid="B5">Bordon et&#xa0;al., 2013</xref>; <xref ref-type="bibr" rid="B35">Greenlee-Wacker, 2016</xref>). The resultant effects of pneumococcal injury and apoptosis within the tissues strongly correlates with wound healing and repair (<xref ref-type="bibr" rid="B59">Matute-bello and Martin, 2003</xref>; <xref ref-type="bibr" rid="B31">Geiser et&#xa0;al., 2004</xref>; <xref ref-type="bibr" rid="B83">Wu and Chen, 2014</xref>; <xref ref-type="bibr" rid="B17">Domon et&#xa0;al., 2016</xref>; <xref ref-type="bibr" rid="B40">Holzmann et&#xa0;al., 2016</xref>). Numerous experimental <italic>in vitro</italic>, <italic>in vivo</italic>, and clinical studies have reported several pro-inflammatory cytokines up-regulated during the early phase of pneumococcal pneumonia, including IL-6, G-CSF, TNF-&#x3b1;, IL-1&#x3b2;, IL-12, IFN-&#x3d2;, and IP-10 (<xref ref-type="bibr" rid="B77">Van Der Poll et&#xa0;al., 1997</xref>; <xref ref-type="bibr" rid="B24">Ethuin et&#xa0;al., 2004</xref>; <xref ref-type="bibr" rid="B86">Yamamoto et&#xa0;al., 2004</xref>; <xref ref-type="bibr" rid="B62">Palaniappan et&#xa0;al., 2006</xref>; <xref ref-type="bibr" rid="B75">Sun et&#xa0;al., 2007</xref>; <xref ref-type="bibr" rid="B21">Endeman et&#xa0;al., 2011</xref>; <xref ref-type="bibr" rid="B84">Yamada et&#xa0;al., 2011</xref>; <xref ref-type="bibr" rid="B32">Gomez et&#xa0;al., 2015</xref>; <xref ref-type="bibr" rid="B73">Skovbjerg et&#xa0;al., 2017</xref>; <xref ref-type="bibr" rid="B53">Loughran et&#xa0;al., 2018</xref>). However, in the last two decades, over-expression of IL-12, IFN-&#x3d2;, and IP-10 has emerged as a highly potent pro-inflammatory, neutrophil-mediated signaling axis in murine models of pneumococcal pneumonia (<xref ref-type="bibr" rid="B86">Yamamoto et&#xa0;al., 2004</xref>; <xref ref-type="bibr" rid="B75">Sun et&#xa0;al., 2007</xref>; <xref ref-type="bibr" rid="B71">Seyoum and Yano, 2011</xref>; <xref ref-type="bibr" rid="B84">Yamada et&#xa0;al., 2011</xref>; <xref ref-type="bibr" rid="B32">Gomez et&#xa0;al., 2015</xref>).</p>
<p>Neutrophils are the primary effector cells of the host innate response to pneumococcal pneumonia (<xref ref-type="bibr" rid="B12">Craig et&#xa0;al., 2009</xref>). In pneumococcal pneumonia patients, the activation of neutrophils after extravasation into the lungs delays the rate of spontaneous apoptosis (<xref ref-type="bibr" rid="B20">Droemann et&#xa0;al., 2000</xref>). However, apoptosis of neutrophils is an essential feature of pneumococcal infection, as apoptotic neutrophils must be cleared from the site upon performing their effector functions (<xref ref-type="bibr" rid="B47">Koedel et&#xa0;al., 2009</xref>). Pneumococcus can induce apoptosis in neutrophils in an H<sub>2</sub>O<sub>2</sub>-dependent fashion and accelerate apoptosis by PLY membrane perforation at relatively lower multiplicities of infection (MOI) (<xref ref-type="bibr" rid="B89">Zysk et&#xa0;al., 2000</xref>).</p>
<p>PUMA (p53-up-regulated modulator of apoptosis), a pro-apoptotic member of the BH3-only family of the BCL-2 superfamily of eukaryotic proteins, is one of the primary effector proteins that promotes apoptosis (<xref ref-type="bibr" rid="B60">Nakano and Vousden, 2001</xref>; <xref ref-type="bibr" rid="B78">Vousden, 2005</xref>). In a murine model of pneumococcal infection, neutrophil-mediated protection against lethal dissemination of pneumococci was shown to be Puma-dependent apoptosis (<xref ref-type="bibr" rid="B29">Garrison et&#xa0;al., 2010</xref>). However, it is unclear which steps of apoptosis signaling pathways are involved in the early phase interactions between neutrophils and pneumococcus. Subsequently, the effects of Puma-dependent apoptosis on global gene expression and innate immune signaling in the lung during the early phase of pneumococcal pneumonia have not yet been investigated.</p>
<p>In this study, we attempted to characterize Puma-dependent responses in the lung during the early phase of pneumococcal pneumonia. Given the clinical relevance of targeting the cytokine response during the early phase of the innate immune response during acute community acquired pneumonia (<xref ref-type="bibr" rid="B82">Woods and Jos&#xe9;, 2017</xref>), we sought to quantitate differences in inflammatory cytokines in the lungs of <italic>Puma<sup>+/+</sup>
</italic> and <italic>Puma<sup>-/-</sup>
</italic> mice. Finally, to further understand what Puma-dependent transcriptional responses may be induced during early pneumococcal infection, we attempted to characterize changes in the lung transcriptome.</p>
</sec>
<sec id="s2" sec-type="materials|methods">
<title>Materials and Methods</title>
<sec id="s2_1">
<title>Bacterial Culture</title>
<p><italic>S. pneumoniae</italic> strain TIGR4 (<xref ref-type="bibr" rid="B76">Tettelin et&#xa0;al., 2001</xref>) was cultured overnight on tryptic soy agar (TSA) plates supplemented with 5% sheep&#x2019;s blood (EMD Millipore) and subsequently inoculated into 10 mL pre-warmed C+Y medium (<xref ref-type="bibr" rid="B50">Lacks and Hotchkiss, 1960</xref>). TIGR4 was cultured to mid-log, centrifuged for 10 minutes at 15,871 x g and 4&#xb0;C, and resuspended in 1 mL of C+Y with 20% glycerol (Thermo Fisher Scientific). Resuspended TIGR4 was aliquoted by volumes of 100 &#x3bc;L and stored at -80&#xb0;C until used in animal challenges. Before challenging animals, one aliquot TIGR4 was thawed on ice, serially diluted in 1X PBS (Thermo Fisher Scientific), cultured on blood agar overnight, and quantitated.</p>
</sec>
<sec id="s2_2">
<title>Statement of Ethics, Animal Handling, and Challenges</title>
<p>All experiments involving animals were planned and conducted in accordance with guidelines of the MSU Institutional Animal Care and Use Committee (Protocol number 19-537). The committee-approved procedures performed in the study presented here. Puma heterozygote mice were crossed and resulting C57BL/6 or <italic>Puma<sup>-/-</sup>
</italic> (The Jackson Laboratory, C57BL/6-Bbc3<sup>tm1Ast</sup>/J, RRID: IMSR_JAX: 011067) mice from generations F5 and F6 were used in challenges. Animals were maintained at Biosafety Level 1 and 2 facilities in the Mississippi State University Animal Facility at Harned Hall. Animals were housed among litter mates until isolated overnight for challenge. On the days of challenges, TIGR4 aliquots were removed from -80&#xb0;C, thawed on ice, and resuspended in 900 &#x3bc;L 1X PBS, then further diluted to a working dilution of 2 x 10<sup>6</sup> CFU/mL. Fifty microliters of working dilution TIGR4 or 1X PBS were administered intranasally. Twenty-four hours post-infection (p.i.), signs of disease and body weight were recorded immediately before euthanasia. To determine CFU within tissues, nasopharyngeal tissues were aseptically flushed with filter-sterilized 1X PBS and collected in-tube, pulmonary tissues mechanically homogenized in 1 mL 1X PBS using an electric tissue homogenizer, and blood was drawn retroorbitally. Crude samples (bood or homogenized respiratory tissues) were appropriately diluted to determine CFU titres onto TSA supplemented with 5% sheep&#x2019;s blood and incubated overnight at 37&#xb0;C under CO<sub>2</sub>. Tracheae were surgically transversely severed and whole pulmonary tissues were prepared as follows: transferred to 1X PBS to be homogenized for cytokine analysis; perfused with and homogenized in Trizol (Thermo Fisher Scientific) reagent for RNA extraction and library preparation; perfused with and transferred to 10% neutral buffered formalin (Thermo Fisher Scientific) for paraffin embedding.</p>
</sec>
<sec id="s2_3">
<title>Histopathological Analysis</title>
<p>Tissues were collected, fixed in 10% neutral buffered formalin, routinely processed, embedded in paraffin, sectioned at 5 &#x3bc;m and stained with hematoxylin and eosin (<xref ref-type="bibr" rid="B9">Cardiff et&#xa0;al., 2014</xref>). Lung sections were scored for inflammation based on the following parameters: patchy interstitial hypercellularity due to increased mononuclear cells (0-absent; 1-present), perivascular suppurative inflammation with edema (0-absent; 1-present but focal (3 or fewer vessels affected); 2-present &#x2013; extensive (more than 3 vessels affected), vasculitis (0-absent; 1-present) and increased alveolar macrophages (0-absent; 1-present). All scoring was done blinded to genotype (<xref ref-type="supplementary-material" rid="ST1"><bold>Supplementary Table S1</bold></xref>).</p>
</sec>
<sec id="s2_4">
<title>Cytokine Analysis</title>
<p>To characterize the pneumococcal-induced cytokine profile 24 hours p.i., pulmonary tissues were harvested as described above and blood was retroorbitally drawn. Crude pulmonary tissue homogenates prepared as described above were centrifuged for 10 minutes at 9,400 x g and 4&#xb0;C. Supernatants were transferred to clean tubes and stored at -80&#xb0;C for analysis. Tissue homogenate pellets were washed once with 1X PBS and centrifuged for 10 minutes at 21,130 x g and 4&#xb0;C. Whole tissue lysates were centrifuged for 4 minutes at 690 x g. Whole tissue lysates were transferred to clean tubes and stored at -80&#xb0;C for analysis. Blood samples were centrifuged for 3 minutes at 1,550 x g. Sera were transferred to clean tubes and store at -80&#xb0;C for analysis. Concentrations of granulocyte-colony stimulating factor (G-CSF), granulocyte macrophage-colony stimulating factor (GM-CSF), interleukin-1 alpha (IL-1&#x3b1;), IL-1&#x3b2;, IL-2, IL-4, IL-5, IL-6, IL-9, IL-10, IL-12p40, IL-12p70, IL-13, IL-15, IL-17, interferon-inducible protein-10 (IP-10), keratinocyte-derived chemokine (KC), monocyte chemotactic protein-1 alpha (MCP-1&#x3b1;), macrophage inflammatory protein-1alpha (MIP-1&#x3b1;), MIP-1&#x3b2;, MIP-2, regulated on activation normal T cells expressed and secreted (RANTES), tumor necrosis factor-alpha (TNF-&#x3b1;), and interferon-gamma (IFN-&#x3d2;) were determined using the MILLIPLEX MAP Mouse Cytokine/Chemokine Magnetic Bead Panel (EMD Millipore # MCYTOMAG-70K) according to the manufacturer&#x2019;s instructions.</p>
</sec>
<sec id="s2_5">
<title>RNA Isolation and Library Preparation</title>
<p>To characterize the post-pharyngeal pulmonary transcriptome 24 hour p.i., tissues were mechanically homogenized using an electrical tissue homogenizer in 5 mL Trizol reagent. From crude pulmonary homogenates, 1mL was transferred to a clean tube and incubated at room temperature for 5 minutes. The remaining crude Trizol homogenate was stored at -80&#xb0;C for curation and further analysis. Two-hundred microliters chloroform (Thermo Fisher Scientific) were added, shaken, and incubated at room temperature for 2 minutes. Samples were centrifuged 20 minutes at 15,900 x g and 4&#xb0;C. RNA was purified using the RNeasy kit (Qiagen) according to the vendor&#x2019;s instructions. RNA purity was determined using a Qubit 2.0 fluorometer and Qubit RNA BR and dsDNA HS assay kits (Thermo Fisher Scientific). Ten micrograms total RNA served as starting material with the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs), and cDNA libraries were generated using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs). Samples of cDNA from all mice were normalized for concentration, pooled, and sequenced on their own lane of a NOVASeq 6000 sequencer at 100 base-pair paired-end reads and yielded at least 10 million reads.</p>
</sec>
<sec id="s2_6">
<title>Demultiplexing, Alignment, Normalization, &amp; Bioinformatics Analysis</title>
<p>RNAseq reads were trimmed with BBDuk (part of BBMap version 38.5) for both quality (minimum quality set to 20 with: &#x201c;qtrim=rl trimq=20&#x201d;) and adapters trimming. Transcript abundances for each sample were computed with Kallisto version 0.45.0 using default parameters (kallisto quant &#x2013;bias) for pseudoalignment against the <italic>Mus musculus</italic> annotated transcripts from the Ensembl database (GRCm39, release 103) (<xref ref-type="bibr" rid="B7">Bray et&#xa0;al., 2016</xref>; <xref ref-type="bibr" rid="B87">Yates et&#xa0;al., 2020</xref>). Differentially expressed genes were detected using the DESeq2 package (<xref ref-type="bibr" rid="B54">Love et&#xa0;al., 2014</xref>). Clustering of samples based on gene expression patterns was performed with the vsn and pheatmap packages and revealed that 3 samples of infected mice clustered with mock-infected mice. Blood CFU data confirmed that the infection status of these three mice was questionable, and they were removed from the analysis (<xref ref-type="table" rid="T1"><bold>Table&#xa0;1</bold></xref>). Gene Ontology enrichment was performed using the topGO package in R, using the ks/classic statistic/algorithm combination.</p>
<table-wrap id="T1" position="float">
<label>Table&#xa0;1</label>
<caption>
<p>CFU counts per individual mice used in RNAseq pneumococcal challenges.</p>
</caption>
<table frame="hsides">
<thead>
<tr>
<th valign="top" align="left">Mouse_id</th>
<th valign="top" align="center">Stimulus</th>
<th valign="top" align="center">i7_primer</th>
<th valign="top" align="center">i7_index</th>
<th valign="top" align="center">i5_primer</th>
<th valign="top" align="center">i5_index</th>
<th valign="top" align="center">CFU_blood</th>
</tr>
</thead>
<tbody>
<tr>
<td valign="top" align="left"><italic>854WTM</italic>
</td>
<td valign="top" align="left">Spn</td>
<td valign="top" align="center">i701</td>
<td valign="top" align="left">ATTACTCG</td>
<td valign="top" align="center">i501</td>
<td valign="top" align="left">TATAGCCT</td>
<td valign="top" align="center">8.00E+03</td>
</tr>
<tr>
<td valign="top" align="left"><italic>859WTF</italic>
</td>
<td valign="top" align="left">Spn</td>
<td valign="top" align="center">i703</td>
<td valign="top" align="left">CGCTCATT</td>
<td valign="top" align="center">i501</td>
<td valign="top" align="left">TATAGCCT</td>
<td valign="top" align="center">5.10E+04</td>
</tr>
<tr>
<td valign="top" align="left"><italic>860WTM</italic>
</td>
<td valign="top" align="left">Spn</td>
<td valign="top" align="center">i702</td>
<td valign="top" align="left">TCCGGAGA</td>
<td valign="top" align="center">i501</td>
<td valign="top" align="left">TATAGCCT</td>
<td valign="top" align="center">2.34E+05</td>
</tr>
<tr>
<td valign="top" align="left"><italic>864WTF</italic>
</td>
<td valign="top" align="left">Spn</td>
<td valign="top" align="center">i704</td>
<td valign="top" align="left">GAGATTCC</td>
<td valign="top" align="center">i501</td>
<td valign="top" align="left">TATAGCCT</td>
<td valign="top" align="center">0.00E+00</td>
</tr>
<tr>
<td valign="top" align="left"><italic>868WTF</italic>
</td>
<td valign="top" align="left">Spn</td>
<td valign="top" align="center">i705</td>
<td valign="top" align="left">ATTCAGAA</td>
<td valign="top" align="center">i501</td>
<td valign="top" align="left">TATAGCCT</td>
<td valign="top" align="center">6.00E+03</td>
</tr>
<tr>
<td valign="top" align="left"><italic>406KOM</italic>
</td>
<td valign="top" align="left">Spn</td>
<td valign="top" align="center">i703</td>
<td valign="top" align="left">CGCTCATT</td>
<td valign="top" align="center">i501</td>
<td valign="top" align="left">TATAGCCT</td>
<td valign="top" align="center">2.46E+05</td>
</tr>
<tr>
<td valign="top" align="left"><italic>413KOF</italic>
</td>
<td valign="top" align="left">Spn</td>
<td valign="top" align="center">i704</td>
<td valign="top" align="left">GAGATTCC</td>
<td valign="top" align="center">i501</td>
<td valign="top" align="left">TATAGCCT</td>
<td valign="top" align="center">0.00E+00</td>
</tr>
<tr>
<td valign="top" align="left"><italic>867KOF</italic>
</td>
<td valign="top" align="left">Spn</td>
<td valign="top" align="center">i701</td>
<td valign="top" align="left">ATTACTCG</td>
<td valign="top" align="center">i503</td>
<td valign="top" align="left">CCTATCCT</td>
<td valign="top" align="center">1.24E+05</td>
</tr>
<tr>
<td valign="top" align="left"><italic>870KOF</italic>
</td>
<td valign="top" align="left">Spn</td>
<td valign="top" align="center">i705</td>
<td valign="top" align="left">ATTCAGAA</td>
<td valign="top" align="center">i501</td>
<td valign="top" align="left">TATAGCCT</td>
<td valign="top" align="center">0.00E+00</td>
</tr>
<tr>
<td valign="top" align="left"><italic>872KOM</italic>
</td>
<td valign="top" align="left">Spn</td>
<td valign="top" align="center">i702</td>
<td valign="top" align="left">TCCGGAGA</td>
<td valign="top" align="center">i501</td>
<td valign="top" align="left">TATAGCCT</td>
<td valign="top" align="center">1.65E+05</td>
</tr>
<tr>
<td valign="top" align="left"><italic>408WTM</italic>
</td>
<td valign="top" align="left">PBS</td>
<td valign="top" align="center">i703</td>
<td valign="top" align="left">CGCTCATT</td>
<td valign="top" align="center">i505</td>
<td valign="top" align="left">AGGCGAAG</td>
<td valign="top" align="center">NA</td>
</tr>
<tr>
<td valign="top" align="left"><italic>415WTF</italic>
</td>
<td valign="top" align="left">PBS</td>
<td valign="top" align="center">i709</td>
<td valign="top" align="left">CGGCTATG</td>
<td valign="top" align="center">i502</td>
<td valign="top" align="left">ATAGAGGC</td>
<td valign="top" align="center">NA</td>
</tr>
<tr>
<td valign="top" align="left"><italic>889WTF</italic>
</td>
<td valign="top" align="left">PBS</td>
<td valign="top" align="center">i708</td>
<td valign="top" align="left">TAATGCGC</td>
<td valign="top" align="center">i502</td>
<td valign="top" align="left">ATAGAGGC</td>
<td valign="top" align="center">NA</td>
</tr>
<tr>
<td valign="top" align="left"><italic>890WTM</italic>
</td>
<td valign="top" align="left">PBS</td>
<td valign="top" align="center">i702</td>
<td valign="top" align="left">TCCGGAGA</td>
<td valign="top" align="center">i504</td>
<td valign="top" align="left">GGCTCTGA</td>
<td valign="top" align="center">NA</td>
</tr>
<tr>
<td valign="top" align="left"><italic>894WTM</italic>
</td>
<td valign="top" align="left">PBS</td>
<td valign="top" align="center">i707</td>
<td valign="top" align="left">CTGAAGCT</td>
<td valign="top" align="center">i502</td>
<td valign="top" align="left">ATAGAGGC</td>
<td valign="top" align="center">NA</td>
</tr>
<tr>
<td valign="top" align="left"><italic>402KOF</italic>
</td>
<td valign="top" align="left">PBS</td>
<td valign="top" align="center">i706</td>
<td valign="top" align="left">GAATTCGT</td>
<td valign="top" align="center">i502</td>
<td valign="top" align="left">ATAGAGGC</td>
<td valign="top" align="center">NA</td>
</tr>
<tr>
<td valign="top" align="left"><italic>409KOF</italic>
</td>
<td valign="top" align="left">PBS</td>
<td valign="top" align="center">i709</td>
<td valign="top" align="left">CGGCTATG</td>
<td valign="top" align="center">i502</td>
<td valign="top" align="left">ATAGAGGC</td>
<td valign="top" align="center">NA</td>
</tr>
<tr>
<td valign="top" align="left"><italic>411KOM</italic>
</td>
<td valign="top" align="left">PBS</td>
<td valign="top" align="center">i710</td>
<td valign="top" align="left">TCCGCGAA</td>
<td valign="top" align="center">i502</td>
<td valign="top" align="left">ATAGAGGC</td>
<td valign="top" align="center">NA</td>
</tr>
<tr>
<td valign="top" align="left"><italic>893KOM</italic>
</td>
<td valign="top" align="left">PBS</td>
<td valign="top" align="center">i708</td>
<td valign="top" align="left">TAATGCGC</td>
<td valign="top" align="center">i502</td>
<td valign="top" align="left">ATAGAGGC</td>
<td valign="top" align="center">NA</td>
</tr>
<tr>
<td valign="top" align="left"><italic>900KOF</italic>
</td>
<td valign="top" align="left">PBS</td>
<td valign="top" align="center">i707</td>
<td valign="top" align="left">CTGAAGCT</td>
<td valign="top" align="center">i502</td>
<td valign="top" align="left">ATAGAGGC</td>
<td valign="top" align="center">NA</td>
</tr>
</tbody>
</table>
<table-wrap-foot>
<fn>
<p>WT and KO mice were challenged with 2 x 10<sup>5</sup> total CFU TIGR4 or mock-infected with equivalent volumes of PBS. Lungs were harvested as described in methods 24&#xa0;h p.i. CFU were quantitated from blood. Outliers are shown in red. For each group, WT (n = 5), KO (n = 5).</p>
</fn>
<fn>
<p>NA, Not applicable.</p>
</fn>
</table-wrap-foot>
</table-wrap>
</sec>
</sec>
<sec id="s3" sec-type="results">
<title>Results</title>
<sec id="s3_1">
<title>PUMA Limits Pneumococcal Inflammation &amp; Sepsis</title>
<p>To investigate the role of Puma during early pneumococcal infection, <italic>Puma<sup>+/+</sup>
</italic> (WT) and <italic>Puma<sup>-/-</sup>
</italic> (KO) mice were intranasally infected with 2 x 10<sup>5</sup> total CFU TIGR4. At 24 hours p.i., TIGR4 CFU were quantitated from nasal lavage fluid (NLF), pulmonary homogenates, and blood. While numbers of TIGR4 recovered from NLF were similar among all mice, <italic>Puma<sup>-/-</sup>
</italic> mice demonstrated significantly higher bacterial counts in the lungs and bloodstream at 24 hours p.i. compared to <italic>Puma<sup>+/+</sup>
</italic> mice (<xref ref-type="fig" rid="f1"><bold>Figure&#xa0;1A</bold></xref>). In the same timeframe, only 30% of <italic>Puma<sup>+/+</sup>
</italic> mice exhibited TIGR4 disseminated to blood, compared to 100% of <italic>Puma<sup>-/-</sup>
</italic> mice. <italic>Puma<sup>-/-</sup>
</italic> mice lost significantly more weight (mean of 1.42&#xa0;g) than <italic>Puma<sup>+/+</sup>
</italic> mice (mean of 0.2&#xa0;g) over the 24-hour course of infection (<xref ref-type="fig" rid="f1"><bold>Figure&#xa0;1B</bold></xref>) indicating excessive disease burden. These data suggest that pneumococcus is more invasive in <italic>Puma<sup>-/-</sup>
</italic> mice.</p>
<fig id="f1" position="float">
<label>Figure&#xa0;1</label>
<caption>
<p>Puma attenuates sepsis and morbidity. <bold>(A)</bold> Mice were intranasally challenged with 2 x 10<sup>5</sup> total CFU. Pneumonia was allowed to develop for 24&#xa0;h, at which time mice were euthanized and tissues were sampled. For each group, WT (<italic>n</italic> = 10), KO (<italic>n</italic> = 7). Horizontal lines represent means. A Mann-Whitney U test was performed, &#x3b1; = 0.05. <bold>(B)</bold> Mice were weighed immediately before challenge and before sacrifice. A two-tailed, unpaired T-test was performed, &#x3b1; = 0.05. *p = 0.0003.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fcimb-12-886901-g001.tif"/>
</fig>
<p>Histological analysis showed that peribronchiolar and perivascular inflammation was noted in both <italic>Puma<sup>+/+</sup>
</italic> and <italic>Puma<sup>-/-</sup>
</italic> lungs (<xref ref-type="fig" rid="f2"><bold>Figure&#xa0;2</bold></xref>). In the <italic>Puma<sup>+/+</sup>
</italic> group, one of five mice had no histologic changes (<xref ref-type="fig" rid="f2"><bold>Figure&#xa0;2A</bold></xref>), while four of five had patchy areas of increased cellularity of the interstitium with three of five classified as mild (<xref ref-type="fig" rid="f2"><bold>Figure&#xa0;2B</bold></xref>). No evidence of vasculitis was detected in <italic>Puma<sup>+/+</sup>
</italic> lungs. In the <italic>Puma<sup>-/-</sup>
</italic> group, one of five mice had increased alveolar macrophages as the only histologic change (<xref ref-type="fig" rid="f2"><bold>Figure&#xa0;2D</bold></xref>), while four of five had patchy areas of increased cellularity of the interstitium with two of five lungs scored moderate (<xref ref-type="fig" rid="f2"><bold>Figure&#xa0;2C</bold></xref>). One <italic>Puma<sup>-/-</sup>
</italic> mouse exhibited evidence of vasculitis (<xref ref-type="fig" rid="f2"><bold>Figure&#xa0;2E</bold></xref>).</p>
<fig id="f2" position="float">
<label>Figure&#xa0;2</label>
<caption>
<p>Puma protects against tissue inflammation. <bold>(A, B)</bold> <italic>Puma<sup>+/+</sup>
</italic> mice exhibited mild peribronchioloar inflammation with edema and neutrophils and macrophages. <bold>(C&#x2013;E)</bold> <italic>Puma<sup>-/-</sup>
</italic> mice exhibited moderate peribronchiolar/perivascular inflammation, abundant neutrophils, macrophages, vasculitis (eosinophilic material, vascular thickening). Scale bars: <bold>A&#x2013;C</bold>, <bold>E</bold>, 50 &#x3bc;m; <bold>D</bold>, 20 &#x3bc;m. Images shown are representative of the pathology described in the results from 3 sections each from 5 mice.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fcimb-12-886901-g002.tif"/>
</fig>
</sec>
<sec id="s3_2">
<title>Puma Dampens Cytokine Signaling and Prevents Onset of the Cytokine Storm</title>
<p>To characterize the effect of Puma on the cytokine response elicited by pneumococcus, lung and blood cytokine levels from <italic>Puma<sup>+/+</sup>
</italic> and <italic>Puma<sup>-/-</sup>
</italic> mice were quantitated 24 hours p.i. (<xref ref-type="table" rid="T2"><bold>Table&#xa0;2</bold></xref>). The cytokines IL-1&#x3b2;, -6, -12, -13, IP-10, MCP-1, MIP-1&#x3b1;, -1&#x3b2;, TNF-&#x3b1;, and IFN-&#x3d2; were significantly over-expressed in <italic>Puma<sup>-/-</sup>
</italic> lungs and blood compared to those of <italic>Puma<sup>+/+</sup>
</italic>. Similarly, in <italic>Puma<sup>-/-</sup>
</italic>, differences in G-CSF, GM-CSF, IL-1&#x3b1;, -17, KC, MIP-2, and RANTES were significant only in lung, while IL-9, -10, and -12(p40) were only significantly different in blood. Differences in IL-2, -4, -5, and -15 were observed in <italic>Puma<sup>+/+</sup>
</italic> and <italic>Puma<sup>-/-</sup>
</italic> mouse lungs and blood, all concentrations being higher in <italic>Puma<sup>-/-</sup>
</italic> tissues, but none were statistically significant (<xref ref-type="fig" rid="f3"><bold>Figure&#xa0;3</bold></xref>).</p>
<table-wrap id="T2" position="float">
<label>Table&#xa0;2</label>
<caption>
<p>Pro-inflammatory cytokine profile of <italic>Puma<sup>-/-</sup>
</italic> mice during early innate immune response.</p>
</caption>
<table frame="hsides">
<thead>
<tr>
<th valign="top" rowspan="2" align="left">Cytokine</th>
<th valign="top" colspan="2" align="center">Higher in <italic>Puma<sup>-/-</sup>
</italic> (*)</th>
<th valign="top" rowspan="2" align="center">Known or suspected role in innate response during pneumococcal pneumonia</th>
</tr>
<tr>
<th valign="top" align="center"><italic>Blood</italic>
</th>
<th valign="top" align="center"><italic>Lungs</italic>
</th>
</tr>
</thead>
<tbody>
<tr>
<td valign="top" align="left">G-CSF</td>
<td valign="top" align="center"/>
<td valign="top" align="center">*</td>
<td valign="top" align="left">Activates PMN and reduces pro-inflammatory cytokines IL-1&#x3b2;, TNF-&#x3b1;, KC (<xref ref-type="bibr" rid="B45">Knapp et&#xa0;al., 2004</xref>)</td>
</tr>
<tr>
<td valign="top" align="left">GM-CSF</td>
<td valign="top" align="center"/>
<td valign="top" align="center">*</td>
<td valign="top" align="left">Enhances PMN recruitment, decreases Spn burden, protects pulmonary macs and PMN from Spn-induced apoptosis (<xref ref-type="bibr" rid="B74">Steinwede et&#xa0;al., 2011</xref>)</td>
</tr>
<tr>
<td valign="top" align="left">IL-1&#x3b1;</td>
<td valign="top" align="center"/>
<td valign="top" align="center">*</td>
<td valign="top" align="left">Induced by PLY, enhances clearance of colonization by activating IL-1 signaling (<xref ref-type="bibr" rid="B49">Kuipers et&#xa0;al., 2018</xref>)</td>
</tr>
<tr>
<td valign="top" align="left">IL-1&#x3b2;</td>
<td valign="top" align="center">*</td>
<td valign="top" align="center">*</td>
<td valign="top" align="left">Enhances clearance of colonization and Th17-induced recruitment of macs (<xref ref-type="bibr" rid="B51">Lemon et&#xa0;al., 2015</xref>)</td>
</tr>
<tr>
<td valign="top" align="left">IL-2</td>
<td valign="top" align="center"/>
<td valign="top" align="center"/>
<td valign="top" align="left">Unknown</td>
</tr>
<tr>
<td valign="top" align="left">IL-4</td>
<td valign="top" align="center"/>
<td valign="top" align="center"/>
<td valign="top" align="left">Unknown</td>
</tr>
<tr>
<td valign="top" align="left">IL-5</td>
<td valign="top" align="center"/>
<td valign="top" align="center"/>
<td valign="top" align="left">Unknown</td>
</tr>
<tr>
<td valign="top" align="left">IL-6</td>
<td valign="top" align="center">*</td>
<td valign="top" align="center">*</td>
<td valign="top" align="left">Promotes inflammation during early infection (<xref ref-type="bibr" rid="B64">Wang et&#xa0;al., 2005</xref>)</td>
</tr>
<tr>
<td valign="top" align="left">IL-9</td>
<td valign="top" align="center">*</td>
<td valign="top" align="center"/>
<td valign="top" align="left">Unknown</td>
</tr>
<tr>
<td valign="top" align="left">IL-10</td>
<td valign="top" align="center">*</td>
<td valign="top" align="center"/>
<td valign="top" align="left">Reduces infiltration of activated PMN and production of pro-inflammatory cytokines (<xref ref-type="bibr" rid="B63">Penoloza et&#xa0;al., 2015</xref>; <xref ref-type="bibr" rid="B64">Penoloza et&#xa0;al., 2018</xref>)</td>
</tr>
<tr>
<td valign="top" align="left">IL-12 (p40)</td>
<td valign="top" align="center">*</td>
<td valign="top" align="center"/>
<td valign="top" align="left">Essential for functional IL-12 (p70) PMN-dependent recruitment (<xref ref-type="bibr" rid="B86">Yamamoto et&#xa0;al., 2004</xref>)</td>
</tr>
<tr>
<td valign="top" align="left">IL-12 (p70)</td>
<td valign="top" align="center">*</td>
<td valign="top" align="center">*</td>
<td valign="top" align="left">Enhances PMN recruitment and stimulates IFN-&#x3d2; production (<xref ref-type="bibr" rid="B75">Sun et&#xa0;al., 2007</xref>; <xref ref-type="bibr" rid="B53">Loughran et&#xa0;al., 2018</xref>)</td>
</tr>
<tr>
<td valign="top" align="left">IL-13</td>
<td valign="top" align="center">*</td>
<td valign="top" align="center">*</td>
<td valign="top" align="left">Unknown</td>
</tr>
<tr>
<td valign="top" align="left">IL-15</td>
<td valign="top" align="center"/>
<td valign="top" align="center"/>
<td valign="top" align="left">Inhibits Spn-induced apoptosis in lung epithelial cells (<xref ref-type="bibr" rid="B39">Hocke et&#xa0;al., 2008</xref>)</td>
</tr>
<tr>
<td valign="top" align="left">IL-17</td>
<td valign="top" align="center"/>
<td valign="top" align="center">*</td>
<td valign="top" align="left">Induced by PLY (<xref ref-type="bibr" rid="B16">Dockrell et&#xa0;al., 2012</xref>); Augments neutrophil recruitment (<xref ref-type="bibr" rid="B67">Ritchie et&#xa0;al., 2018</xref>)</td>
</tr>
<tr>
<td valign="top" align="left">IP-10</td>
<td valign="top" align="center">*</td>
<td valign="top" align="center">*</td>
<td valign="top" align="left">Spn strain-dependent bactericidal activity (<xref ref-type="bibr" rid="B8">Bruce et&#xa0;al., 2018</xref>); Induced in PMN (<xref ref-type="bibr" rid="B33">Gomez et&#xa0;al., 2017</xref>)</td>
</tr>
<tr>
<td valign="top" align="left">KC</td>
<td valign="top" align="center"/>
<td valign="top" align="center">*</td>
<td valign="top" align="left">Induced by Spn H<sub>2</sub>O<sub>2</sub> in epithelial cells (<xref ref-type="bibr" rid="B52">Loose et&#xa0;al., 2014</xref>)</td>
</tr>
<tr>
<td valign="top" align="left">MCP-1</td>
<td valign="top" align="center">*</td>
<td valign="top" align="center">*</td>
<td valign="top" align="left">Recruits MDM to alveoli, reduces Spn burden, and improves survival (<xref ref-type="bibr" rid="B81">Winter et&#xa0;al., 2007</xref>)</td>
</tr>
<tr>
<td valign="top" align="left">MIP-1&#x3b1;</td>
<td valign="top" align="center">*</td>
<td valign="top" align="center">*</td>
<td valign="top" align="left">Increases MDM,PMN recruitment (<xref ref-type="bibr" rid="B80">Williams et&#xa0;al., 2015</xref>)</td>
</tr>
<tr>
<td valign="top" align="left">MIP-1&#x3b2;</td>
<td valign="top" align="center">*</td>
<td valign="top" align="center">*</td>
<td valign="top" align="left">Increases MDM,PMN recruitment (<xref ref-type="bibr" rid="B80">Williams et&#xa0;al., 2015</xref>)</td>
</tr>
<tr>
<td valign="top" align="left">MIP-2</td>
<td valign="top" align="center"/>
<td valign="top" align="center">*</td>
<td valign="top" align="left">Increases PMN recruitment (<xref ref-type="bibr" rid="B13">Dallaire et&#xa0;al., 2001</xref>)</td>
</tr>
<tr>
<td valign="top" align="left">RANTES</td>
<td valign="top" align="center"/>
<td valign="top" align="center">*</td>
<td valign="top" align="left">Augments colonization clearance (<xref ref-type="bibr" rid="B61">Pallaniappan et&#xa0;al., 2006</xref>); Recruits PMN (<xref ref-type="bibr" rid="B48">Koppe et&#xa0;al., 2012</xref>)</td>
</tr>
<tr>
<td valign="top" align="left">TNF-&#x3b1;</td>
<td valign="top" align="center">*</td>
<td valign="top" align="center">*</td>
<td valign="top" align="left">Reduces Spn burden and enhances PMN recruitment (<xref ref-type="bibr" rid="B41">Jeong et&#xa0;al., 2015</xref>)</td>
</tr>
<tr>
<td valign="top" align="left">IFN-&#x3d2;</td>
<td valign="top" align="center">*</td>
<td valign="top" align="center">*</td>
<td valign="top" align="left">Augments PMN-mediated clearance (Yamada et&#xa0;al., 2010)</td>
</tr>
</tbody>
</table>
<table-wrap-foot>
<fn>
<p>Lungs and blood were harvested from mice challenged with TIGR4 pneumococcus 24 p.i. More than 80% of cytokines probed were significantly higher in Puma<sup>-/-</sup> tissues. &#x3b1; = 0.05.</p>
</fn>
</table-wrap-foot>
</table-wrap>
<fig id="f3" position="float">
<label>Figure&#xa0;3</label>
<caption>
<p>Puma-dependent host responses during early pneumococcal pneumonia suppress production of cytokines in the lung. Cytokines expressed more than 3-fold in <italic>Puma<sup>-/-</sup>
</italic> mouse lungs <bold>(A)</bold> and sera <bold>(B)</bold> are shown here. Cytokines were detected <italic>via</italic> magnetic bead panel using flow cytometry analysis. Values are reported as pg/mL. Mann-Whitney U tests were performed to determine significance, &#x3b1; = 0.05.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fcimb-12-886901-g003.tif"/>
</fig>
</sec>
<sec id="s3_3">
<title>Loss of Puma Induces Changes in the Pulmonary Transcriptome</title>
<p>To further investigate Puma-dependent transcriptional responses during the early phase of pneumonia, total RNA was extracted from lungs of five mice per challenge group 24 hours p.i., purified, and pooled for RNA-seq analysis. Using DEseq2, 21 differentially expressed genes, 15 of which had annotations, were detected with an adjusted p-value &lt; 0.05 (<xref ref-type="table" rid="T3"><bold>Table&#xa0;3</bold></xref>). Of note, the genes <italic>Nrxn2</italic>, <italic>Adam19</italic>, and <italic>Eln</italic> were each up-regulated in <italic>Puma<sup>+/+</sup>
</italic> lungs and down-regulated in those of <italic>Puma<sup>-/-</sup>
</italic> mice. We performed a gene ontology (GO) analysis on all three sub-ontologies: Biological Process (BP), Molecular Function (MF), and Cellular Component (CC). We found 28, 4, and 7 GO categories significantly enriched for genes differentially regulated in <italic>Puma<sup>-/-</sup>
</italic> mice in BP, MF, and CC, respectively (<xref ref-type="supplementary-material" rid="ST2"><bold>Supplementary  Table S2</bold></xref>). To focus on the categories most likely to have a biologically significant contribution to the infection response, we added a fold-enrichment (FE) criteria and retained only GO sub-categories with FE &gt; 2.5. This resulted in 16, 4, and 3 categories being retained, respectively, in the BP, MF, and CC sub-ontologies. In accordance with detection of IL-12 cytokine, the GO group &#x2018;positive regulation of IL-12 production&#x2019; (GO:0032735) was enriched 3.6 fold (<xref ref-type="fig" rid="f4"><bold>Figure&#xa0;4</bold></xref>). Notably, GO groups &#x2018;cellular response to IFN-&#x3b2;&#x2019; (GO:0035458) and &#x2018;cellular response to IFN-&#x3d2;&#x2019; (GO:0071346) were enriched 5.46 and 3.45, respectively. Individual lists of gene expression from each of these GO groups are shown in <xref ref-type="supplementary-material" rid="ST3"><bold>Supplementary Table S3</bold></xref>.</p>
<table-wrap id="T3" position="float">
<label>Table&#xa0;3</label>
<caption>
<p>Differentially expressed genes in <italic>Puma<sup>-/-</sup>
</italic> lungs.</p>
</caption>
<table frame="hsides">
<thead>
<tr>
<th valign="top" align="left">Gene</th>
<th valign="top" align="center">baseMean</th>
<th valign="top" align="center">log2FoldChange</th>
<th valign="top" align="center">lfcSE</th>
<th valign="top" align="center">stat</th>
<th valign="top" align="center">pvalue</th>
<th valign="top" align="center">padj</th>
</tr>
</thead>
<tbody>
<tr>
<td valign="top" align="left"><bold><italic>Nrxn2 *</italic>
</bold>
</td>
<td valign="top" align="center">278.41809</td>
<td valign="top" align="center">-1.6401589</td>
<td valign="top" align="center">0.2631083</td>
<td valign="top" align="center">-6.233778</td>
<td valign="top" align="center">0.00E+00</td>
<td valign="top" align="center">0.0000078</td>
</tr>
<tr>
<td valign="top" align="left"><bold><italic>Prrt2</italic>
</bold>
</td>
<td valign="top" align="center">60.30429</td>
<td valign="top" align="center">-2.4003748</td>
<td valign="top" align="center">0.4447364</td>
<td valign="top" align="center">-5.397298</td>
<td valign="top" align="center">1.00E-07</td>
<td valign="top" align="center">0.0005823</td>
</tr>
<tr>
<td valign="top" align="left"><bold><italic>Adam19 *</italic>
</bold>
</td>
<td valign="top" align="center">1378.17251</td>
<td valign="top" align="center">-0.6234511</td>
<td valign="top" align="center">0.1175516</td>
<td valign="top" align="center">-5.303639</td>
<td valign="top" align="center">1.00E-07</td>
<td valign="top" align="center">0.0006413</td>
</tr>
<tr>
<td valign="top" align="left"><bold><italic>Eln *</italic>
</bold>
</td>
<td valign="top" align="center">3187.73317</td>
<td valign="top" align="center">-1.6045925</td>
<td valign="top" align="center">0.3054167</td>
<td valign="top" align="center">-5.253781</td>
<td valign="top" align="center">1.00E-07</td>
<td valign="top" align="center">0.0006413</td>
</tr>
<tr>
<td valign="top" align="left"><bold><italic>Grk4 *</italic>
</bold>
</td>
<td valign="top" align="center">142.06737</td>
<td valign="top" align="center">-1.6525749</td>
<td valign="top" align="center">0.3551424</td>
<td valign="top" align="center">-4.653274</td>
<td valign="top" align="center">3.30E-06</td>
<td valign="top" align="center">0.0070303</td>
</tr>
<tr>
<td valign="top" align="left"><bold><italic>Olfr2</italic>
</bold>
</td>
<td valign="top" align="center">23.35589</td>
<td valign="top" align="center">2.4365302</td>
<td valign="top" align="center">0.5408849</td>
<td valign="top" align="center">4.504711</td>
<td valign="top" align="center">6.60E-06</td>
<td valign="top" align="center">0.0115342</td>
</tr>
<tr>
<td valign="top" align="left"><bold><italic>Mturn</italic>
</bold>
</td>
<td valign="top" align="center">981.39638</td>
<td valign="top" align="center">-0.8387504</td>
<td valign="top" align="center">0.1914976</td>
<td valign="top" align="center">-4.379953</td>
<td valign="top" align="center">1.19E-05</td>
<td valign="top" align="center">0.0185773</td>
</tr>
<tr>
<td valign="top" align="left"><bold><italic>Cracr2b</italic>
</bold>
</td>
<td valign="top" align="center">1193.88323</td>
<td valign="top" align="center">-0.9459835</td>
<td valign="top" align="center">0.220296</td>
<td valign="top" align="center">-4.294147</td>
<td valign="top" align="center">1.75E-05</td>
<td valign="top" align="center">0.0232225</td>
</tr>
<tr>
<td valign="top" align="left"><bold><italic>Tmem204</italic>
</bold>
</td>
<td valign="top" align="center">2313.99531</td>
<td valign="top" align="center">-1.1646703</td>
<td valign="top" align="center">0.2736711</td>
<td valign="top" align="center">-4.25573</td>
<td valign="top" align="center">2.08E-05</td>
<td valign="top" align="center">0.0256219</td>
</tr>
<tr>
<td valign="top" align="left"><bold><italic>Aoah</italic>
</bold>
</td>
<td valign="top" align="center">155.09042</td>
<td valign="top" align="center">1.8136874</td>
<td valign="top" align="center">0.4283164</td>
<td valign="top" align="center">4.234457</td>
<td valign="top" align="center">2.29E-05</td>
<td valign="top" align="center">0.0262935</td>
</tr>
<tr>
<td valign="top" align="left"><bold><italic>Rab8b</italic>
</bold>
</td>
<td valign="top" align="center">1760.31877</td>
<td valign="top" align="center">0.8942729</td>
<td valign="top" align="center">0.2158181</td>
<td valign="top" align="center">4.143641</td>
<td valign="top" align="center">3.42E-05</td>
<td valign="top" align="center">0.0338506</td>
</tr>
<tr>
<td valign="top" align="left"><bold><italic>Nckap5l</italic>
</bold>
</td>
<td valign="top" align="center">225.00742</td>
<td valign="top" align="center">-1.4002127</td>
<td valign="top" align="center">0.336441</td>
<td valign="top" align="center">-4.161837</td>
<td valign="top" align="center">3.16E-05</td>
<td valign="top" align="center">0.0338506</td>
</tr>
<tr>
<td valign="top" align="left"><bold><italic>Triobp</italic>
</bold>
</td>
<td valign="top" align="center">865.65297</td>
<td valign="top" align="center">0.926385</td>
<td valign="top" align="center">0.2250176</td>
<td valign="top" align="center">4.116945</td>
<td valign="top" align="center">3.84E-05</td>
<td valign="top" align="center">0.0347858</td>
</tr>
<tr>
<td valign="top" align="left"><bold><italic>Tbc1d1</italic>
</bold>
</td>
<td valign="top" align="center">896.23624</td>
<td valign="top" align="center">0.9062004</td>
<td valign="top" align="center">0.2232808</td>
<td valign="top" align="center">4.058569</td>
<td valign="top" align="center">4.94E-05</td>
<td valign="top" align="center">0.0424989</td>
</tr>
<tr>
<td valign="top" align="left"><bold><italic>Crybg1</italic>
</bold>
</td>
<td valign="top" align="center">829.49315</td>
<td valign="top" align="center">1.0914384</td>
<td valign="top" align="center">0.2717405</td>
<td valign="top" align="center">4.016472</td>
<td valign="top" align="center">5.91E-05</td>
<td valign="top" align="center">0.0484281</td>
</tr>
</tbody>
</table>
<table-wrap-foot>
<fn>
<p>Lungs and blood were harvested from mice challenged with TIGR4 pneumococcus 24 p.i. Gene symbols with asterisks indicate transcripts up-regulated in Puma<sup>+/+</sup> and down-regulated in Puma<sup>-/-</sup>. &#x3b1; = 0.05.</p>
</fn>
</table-wrap-foot>
</table-wrap>
<fig id="f4" position="float">
<label>Figure&#xa0;4</label>
<caption>
<p>Gene ontology analysis reveals Puma limits IL-12 and Type I and II IFN signaling. Genes significantly expressed (red dots) in their respective GO groups are plotted against all other genes (blue dots). Significance was determined using the Kolmogorov-Smirnov test and p-values were adjusted for multiple-testing. The area above the black line indicates higher expression in <italic>Puma<sup>-/-</sup>
</italic> mice, while the area under the black line indicates higher expression in <italic>Puma<sup>+/+</sup>
</italic> mice.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fcimb-12-886901-g004.tif"/>
</fig>
</sec>
</sec>
<sec id="s4" sec-type="discussion">
<title>Discussion/Conclusion</title>
<p>Apoptosis is integral in the host defense response against pneumococcal infection. Neutrophils are the primary cell type responsible for direct clearance of pneumococcus from the lung (<xref ref-type="bibr" rid="B29">Garrison et&#xa0;al., 2010</xref>). Phagocytosis of pneumococcus induces apoptosis in neutrophils <italic>via</italic> phagocytosis-induced cell death (PICD) (<xref ref-type="bibr" rid="B46">Kobayashi et&#xa0;al., 2017</xref>). As neutrophils become apoptotic, they are rapidly cleared by macrophages to avoid the detrimental effects of secondary necrosis and prolonged inflammation within the lung (<xref ref-type="bibr" rid="B69">Savill, 1997</xref>; <xref ref-type="bibr" rid="B38">Henson and Bratton, 2013</xref>). Neutrophil apoptosis directly and indirectly signals surrounding cells to aid in resolution (<xref ref-type="bibr" rid="B38">Henson and Bratton, 2013</xref>; <xref ref-type="bibr" rid="B42">Jia et&#xa0;al., 2014</xref>). Apoptosis of other cell types also contributes to pneumococcal infection resolution, including macrophages (<xref ref-type="bibr" rid="B56">Marriott et&#xa0;al., 2004</xref>; <xref ref-type="bibr" rid="B65">Rai et&#xa0;al., 2015</xref>), epithelial cells (<xref ref-type="bibr" rid="B70">Schmeck et&#xa0;al., 2004</xref>; <xref ref-type="bibr" rid="B57">Marriott and Dockrell, 2006</xref>), and T-cells (<xref ref-type="bibr" rid="B43">Kemp et&#xa0;al., 2002</xref>). During the early innate immune response in the lung, all of these cell types may contribute to apoptosis-induced signaling. Multiple cell types have been documented undergoing PUMA-induced apoptosis, including epithelial cells (<xref ref-type="bibr" rid="B14">Dang et&#xa0;al., 2020</xref>), neutrophils (<xref ref-type="bibr" rid="B29">Garrison et&#xa0;al., 2010</xref>), and T-cells (<xref ref-type="bibr" rid="B26">Fischer et&#xa0;al., 2008</xref>).</p>
<p>PUMA distinctly contributes to protective infectious disease responses during acute viral infection by herpes simplex virus (HSV-1) in T-cells (<xref ref-type="bibr" rid="B26">Fischer et&#xa0;al., 2008</xref>), and degradation of PUMA induced by <italic>Chlamydia trachomatis</italic> contributes to persistent infection (<xref ref-type="bibr" rid="B18">Dong et&#xa0;al., 2005</xref>). However, PUMA-induced apoptosis contributes to <italic>Helicobacter pylori</italic> pathogenesis during gastritis (<xref ref-type="bibr" rid="B14">Dang et&#xa0;al., 2020</xref>). These opposing roles of PUMA during infection may lie in the pathophysiology of the respective pathogen and the cell types involved. Puma-deficient mice have been intensively studied for their resistance to cancer-causing stimuli (<xref ref-type="bibr" rid="B29">Garrison et&#xa0;al., 2010</xref>). HSV-1 can induce oral cancer in mice and is a suspected causative cancer agent in humans (<xref ref-type="bibr" rid="B26">Fischer et&#xa0;al., 2008</xref>), and <italic>H. pylori</italic> is now recognized as a causative agent of gastric cancer. <italic>C. trachomatis</italic> is an obligate intracellular pathogen and epidemiologically correlated with cancers of the female urogenital epithelium, and almost exclusively infects epithelial cells (<xref ref-type="bibr" rid="B88">Zhu et&#xa0;al., 2016</xref>). HSV-1 can invade most cell types but primarily infects epithelial cells and resides in neurons as long-term reservoirs within the host. <italic>H. pylori</italic> and pneumococcus are both generally acknowledged as extracellular pathogens and each induces strong neutrophil recruitment, which exacerbates local tissue damage. The up- and down-stream inducers of <italic>puma</italic> in the context of the immune response to infection are currently poorly understood. The contradictory observations on the <italic>Puma<sup>-/-</sup>
</italic> mouse model in cancer studies versus our pneumococcal pneumonia model continue to make the Puma phenotype and its up- and down-stream regulators molecules of interest. Our findings support the notion that Puma&#x2019;s role in infectious disease immunobiology is multifactorial and further demonstrates that loss of Puma may enhance risk of negative health outcomes during infection. The precise pathways involved in the protective phenotype of Puma remain to be thoroughly investigated in the context of infection.</p>
<p>While many cytokines have been associated with inflammation modulation during pneumococcal infection, the pro-inflammatory IL-12/IFN-&#x3d2;/IP-10 signaling axis has emerged as a potent arm of the innate immune response. Infection-induced IL-12 secretion was first identified from dendritic cells and neutrophils and can be induced by pneumococcus <italic>via</italic> TLR3 activation (<xref ref-type="bibr" rid="B66">Rijneveld et&#xa0;al., 2002</xref>; <xref ref-type="bibr" rid="B36">Groom and Luster, 2011</xref>). The effects of increased IL-12 during pneumococcal pneumonia also include stimulating IFN-&#x3d2;-dependent neutrophil recruitment through increased abundance of MIP-2 and TNF-&#x3b1; (<xref ref-type="bibr" rid="B24">Ethuin et&#xa0;al., 2004</xref>; <xref ref-type="bibr" rid="B75">Sun et&#xa0;al., 2007</xref>). At 24 hours p.i. <italic>Puma<sup>+/+</sup>
</italic> mice expressed less IL-12 in their lungs than <italic>Puma<sup>-/-</sup>
</italic>. This could be due to the anti-inflammatory effects of apoptotic neutrophils, as pro-inflammatory signaling is dampened once apoptosis is initiated in neutrophils (<xref ref-type="bibr" rid="B37">Haslett, 1999</xref>). In accordance with this notion, we previously demonstrated that <italic>Puma<sup>-/-</sup>
</italic> lungs contained more neutrophils than their <italic>Puma<sup>+/+</sup>
</italic> counterparts (<xref ref-type="bibr" rid="B29">Garrison et&#xa0;al., 2010</xref>). However, pro-inflammatory efferocytosis of neutrophils also induces an IL-12<sup>low</sup> phenotype in macrophages (<xref ref-type="bibr" rid="B25">Filardy et&#xa0;al., 2010</xref>). This likely contributes to the low levels of IL-12 in <italic>Puma<sup>+/+</sup>
</italic> lungs following infection, but the precise mechanisms of temporal IL-12 production and its effect on cell death in specific cellular subsets within the lung during early pneumococcal pneumonia need to be further investigated.</p>
<p>The importance of IFN-&#x3d2; signaling is well demonstrated during the early host response to pneumococcal infection. A previous study showed that pneumococcal infection induced significant increases of IFN-&#x3d2; from greater than 98% of neutrophil in the lungs at 24 hours p.i (<xref ref-type="bibr" rid="B84">Yamada et&#xa0;al., 2011</xref>). Neutrophilic production of IFN-&#x3d2; during early pneumococcal pneumonia is likely mediated through NADPH oxidase activity, suggesting IFN-&#x3d2; production in neutrophils may be ROS-dependent, the generation of which is also a result of induction of apoptosis (<xref ref-type="bibr" rid="B32">Gomez et&#xa0;al., 2015</xref>). Production of IFN-&#x3d2; in pneumococcal pneumonia models has been linked to strain-dependent effects, and suppresses pneumococcal outgrowth during the early phase by recruiting neutrophils (<xref ref-type="bibr" rid="B68">Rubins and Pomeroy, 1997</xref>; <xref ref-type="bibr" rid="B36">Groom and Luster, 2011</xref>). As a ligand for the CXCR3 receptor, IP-10 can recruit and activate effector CD4<sup>+</sup> Th1, CD8<sup>+</sup> CTL, natural killer (NK), and the hybrid NK-T cells (<xref ref-type="bibr" rid="B11">Christaki et&#xa0;al., 2015</xref>). In human neutrophils, the combination of IFN-&#x3d2; and TNF-&#x3b1; is the most potent inducer of IP-10 secretion (<xref ref-type="bibr" rid="B10">Cassatella et&#xa0;al., 1997</xref>; <xref ref-type="bibr" rid="B30">Gasperini et&#xa0;al., 2019</xref>). In accordance with this observation, IFN-&#x3d2; and TNF-&#x3b1; were significantly higher in <italic>Puma<sup>-/-</sup>
</italic> mice. IP-10 expression is also strain-dependent and associated with acute lung injury during early pneumococcal pneumonia (<xref ref-type="bibr" rid="B71">Seyoum and Yano, 2011</xref>). Interestingly, secretion of IL-12 and IP-10 are increased by human peripheral blood monocytes upon exposure to intact pneumococci, but inhibited when exposed to autolyzed pneumococci (<xref ref-type="bibr" rid="B73">Skovbjerg et&#xa0;al., 2017</xref>). In pneumococcal pneumonia, IFN-&#x3d2; signaling is thought to exert beneficial effects by activating NK-T cells but detrimental effects upon activating NK cells (<xref ref-type="bibr" rid="B11">Christaki et&#xa0;al., 2015</xref>). However, a role for Puma in these cell types has not yet been characterized. It should be noted, though, that in an experimental pneumonia murine model at 24 hours p.i., T cells, NK cells, and macrophages did not produce IFN-&#x3d2; (<xref ref-type="bibr" rid="B32">Gomez et&#xa0;al., 2015</xref>). The increase of IFN-&#x3d2; and subsequent IP-10 production in <italic>Puma<sup>-/-</sup>
</italic> mice 24 hours p.i. underscores the importance of apoptosis in resolving inflammation. While both groups displayed increased interstitial inflammation, overall, <italic>Puma<sup>-/-</sup>
</italic> mice exhibited a greater degree of&#xa0;inflammation with multiple foci and vasculitis. The excessive inflammation observed in the <italic>Puma<sup>-/-</sup>
</italic> mice is likely a result of accumulation of neutrophils that remain active and continue to propagate the IL-12/IFN-&#x3d2;/IP-10 axis. Previous works of others using murine models and data presented here strongly suggest that PUMA-dependent neutrophil apoptosis suppresses the IL-12/IFN-&#x3d2;/IP-10 signaling axis, thereby limiting inflammation and consequent pneumococcal dissemination. However, it is currently unknown if the reported IL-12/IFN-&#x3d2;/IP-10 signaling in mice recapitulates the acute-phase cytokine signaling in humans. Previously, IFN-&#x3d2; had been ruled out as an acute-phase cytokine in humans (<xref ref-type="bibr" rid="B21">Endeman et&#xa0;al., 2011</xref>). Although, another clinical study found significant differences in bronchoalveolar lavage fluid IFN-&#x3d2; between healthy control subjects and those with CAP and in serum between severe and non-severe CAP patients upon admission (<xref ref-type="bibr" rid="B61">Paats et&#xa0;al., 2013</xref>). Beyond the intrinsic differences in murine and human physiology, a likely explanation for these differences may be the temporal differences in surveillance and detection of infection in humans, with testing only occurring within about 72 hours of the first onset of symptoms (<xref ref-type="bibr" rid="B55">Mandell et&#xa0;al., 2007</xref>). Consequently, the mechanistic details of apoptotic suppression of the IL-12/IFN-&#x3d2;/IP-10 pro-inflammatory axis, temporospatial regulation of the intercellular signaling, and whether the cascade results in feedback in humans during development of bacterial pneumonia remain unknown.</p>
<p>Puma-dependent responses also regulate the pulmonary transcriptome. In the lung, ADAM19 is expressed in a variety of cell and tissue types. ADAM19 is expressed higher in bronchiolar than alveolar epithelial cells but expressed higher in smooth muscle cells than in bronchiolar epithelial cells (<xref ref-type="bibr" rid="B15">Dijkstra et&#xa0;al., 2009</xref>). However, ADAM19 is only weakly expressed in vascular endothelial cells. The detection of ADAM19 on the apical surfaces of airway epithelial cells may suggest a role in the positive regulation in the early innate immune response to infection since ADAM19 can induce inflammation <italic>via</italic> shedding of TNF-&#x3b1; (<xref ref-type="bibr" rid="B2">Becherer et&#xa0;al., 2003</xref>). ADAM19 also contributes to angiogenesis, neurogenesis, synaptogenesis, and adhesion of and invasion by leukocytes (<xref ref-type="bibr" rid="B72">Shirakabe et&#xa0;al., 2001</xref>; <xref ref-type="bibr" rid="B19">Dreymueller et&#xa0;al., 2012</xref>; <xref ref-type="bibr" rid="B28">Fukazawa et&#xa0;al., 2013</xref>). Several of the other ADAM family members have reportedly been observed modulating the immune response to multiple infectious agents, including pneumococcus (<xref ref-type="bibr" rid="B1">Aljohmani and Yildiz, 2020</xref>). Down-regulation of <italic>Adam19</italic> in <italic>Puma<sup>-/-</sup>
</italic> lungs suggests an immunomodulatory role in the early innate immune response that is short-lived due to yet unidentified Puma-dependent responses to pneumococcal infection. <italic>Nrxn2</italic>, a member of the neurexin gene family, encodes a transmembrane protein on pre-synaptic neurons that forms a Ca<sup>2+</sup>-dependent complex with the protein neuroligin on post-synaptic neurons (<xref ref-type="bibr" rid="B6">Bottos et&#xa0;al., 2009</xref>). In addition to regulation of synaptic transmission in the nervous system, neurexin-neuroligin complexation has been observed in vascular tissue. Each neurexin gene encodes a long (&#x3b1;) and short (&#x3b2;) isoform. While the sequence mapping could not discern <italic>Nrxn2</italic> &#x3b1; or &#x3b2; transcripts in the analysis reported here, &#x3b2; isoforms have been detected in complexes with neuroligin in the vascular system while positively modulating angiogenesis in conjunction with vascular endothelial growth factor and increasing vascular tone (<xref ref-type="bibr" rid="B4">Berk et&#xa0;al., 2005</xref>; <xref ref-type="bibr" rid="B34">Graziano et&#xa0;al., 2013</xref>). <italic>Eln</italic>, the gene encoding elastin, was also up-regulated in a Puma-dependent manner. One explanation for this observation could be that the accumulation of neutrophils in the lung and the hypoxic nature of pneumonia suppress elastin fiber deposition and repair (<xref ref-type="bibr" rid="B4">Berk et&#xa0;al., 2005</xref>; <xref ref-type="bibr" rid="B3">Benjamin et&#xa0;al., 2021</xref>). Together, these data suggest a Puma-dependent integrated systems physiologic host response to pneumococcal pneumonia. However, the details of these intermolecular and intercellular interactions within the lung have not been thoroughly interrogated during infection.</p>
<p>For the first time, we have demonstrated the immunomodulatory effects of Puma during pneumococcal pneumonia. Puma-dependent responses suppressed pro-inflammatory cytokine signaling, including the highly inflammatory, neutrophil-mediated IL-12/IFN-&#x3d2;/IP-10 signaling axis. Dissemination of pneumococcus and erosion of the pulmonary vasculature was attenuated by Puma-dependent responses. The precise, temporal expression and regulation of IFN-inducible genes remains to be elucidated in the context of Puma-dependent resolution of inflammation. Finally, the activity of ADAM19 during pneumococcal and other bacterial infections also requires further, more intensive study, as well as to what degree, if any, NRXN2 is playing in pulmonary blood pressure regulation during the early phase of acute pneumonia.</p>
</sec>
<sec id="s5" sec-type="data-availability">
<title>Data Availability Statement</title>
<p>The sequencing raw reads have been deposited in the NCBI Short Read Archive under Bioproject accession number: PRJNA748408.</p>
</sec>
<sec id="s6" sec-type="ethics-statement">
<title>Ethics Statement</title>
<p>The animal study was reviewed and approved by Mississippi State University Institutional Animal Care and Use Committee.</p>
</sec>
<sec id="s7" sec-type="author-contributions">
<title>Author Contributions</title>
<p>DK, PM, WT, and JR obtained the data. DK, J-FG, AO, JR, KS, and JT, performed the data analysis. DK, JT, and KS wrote the manuscript. JT was responsible for study concept and design. JT was a supervisor of laboratory analysis of this study. JT is the guarantor of this study and, as such, had full access to all the data in the study and takes responsibility for the integrity of the data and the accuracy of the data analysis. All authors participated in data interpretation and review of the manuscript and approved the final manuscript.</p>
</sec>
<sec id="s8" sec-type="funding-information">
<title>Funding</title>
<p>Research reported in this publication was supported by the Center for Biomedical Research Excellence (COBRE) in Pathogen&#x2013;Host Interactions, National Institute of General Medical Sciences, National Institutes of Health (P20 472 GM103646-06). The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.</p>
</sec>
<sec id="s9" sec-type="COI-statement">
<title>Conflict of Interest</title>
<p>The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.</p>
</sec>
<sec id="s10" sec-type="disclaimer">
<title>Publisher&#x2019;s Note</title>
<p>All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.</p>
</sec>
</body>
<back>
<sec id="s11" sec-type="supplementary-material">
<title>Supplementary Material</title>
<p>The Supplementary Material for this article can be found online at: <ext-link ext-link-type="uri" xlink:href="https://www.frontiersin.org/articles/10.3389/fcimb.2022.886901/full#supplementary-material">https://www.frontiersin.org/articles/10.3389/fcimb.2022.886901/full#supplementary-material</ext-link>
</p>
<supplementary-material xlink:href="Table_1.xlsx" id="ST1" mimetype="application/vnd.openxmlformats-officedocument.spreadsheetml.sheet">
<label>Supplementary Table&#xa0;1</label>
<caption>
<p>Histopathology report from lung sections of WT and KO mice challenged with <italic>S. pneumoniae.</italic> Lung sections were prepared as described in the main text and scored for inflammation. Histology scores from inflamed WT and KO lungs are plotted with mean (horizontal line) and standard deviation (error bars).</p>
</caption>
</supplementary-material>
<supplementary-material xlink:href="Table_2.xlsx" id="ST2" mimetype="application/vnd.openxmlformats-officedocument.spreadsheetml.sheet">
<label>Supplementary Table&#xa0;2</label>
<caption>
<p>GO enrichment analysis in KO pulmonary tissues. BP, MF, and CC GO categories and their respective significant differentially expressed genes are listed. Adjusted p-values and fold-enrichment scores are shown.</p>
</caption>
</supplementary-material>
<supplementary-material xlink:href="Table_3.xlsx" id="ST3" mimetype="application/vnd.openxmlformats-officedocument.spreadsheetml.sheet">
<label>Supplementary Table&#xa0;3</label>
<caption>
<p>From <xref ref-type="fig" rid="f4"><bold>Figure&#xa0;4</bold></xref> in the main text, individual gene identities represented by red dots plotted for each of the three significantly different GO groups between WT and KO mice are provided. Gene expression differences are shown as log-fold change relative to PBS mock-infected WT or KO cohorts.</p>
</caption>
</supplementary-material>
</sec>
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