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<front>
<journal-meta>
<journal-id journal-id-type="publisher-id">Front. Pharmacol.</journal-id>
<journal-title>Frontiers in Pharmacology</journal-title>
<abbrev-journal-title abbrev-type="pubmed">Front. Pharmacol.</abbrev-journal-title>
<issn pub-type="epub">1663-9812</issn>
<publisher>
<publisher-name>Frontiers Media S.A.</publisher-name>
</publisher>
</journal-meta>
<article-meta>
<article-id pub-id-type="publisher-id">679511</article-id>
<article-id pub-id-type="doi">10.3389/fphar.2021.679511</article-id>
<article-categories>
<subj-group subj-group-type="heading">
<subject>Pharmacology</subject>
<subj-group>
<subject>Original Research</subject>
</subj-group>
</subj-group>
</article-categories>
<title-group>
<article-title>Gene Expression Pattern of Peyer&#x2019;s Patch Lymphocytes Exposed to Kagocel Suggests Pattern-Recognition Receptors Mediate Its Action</article-title>
<alt-title alt-title-type="left-running-head">Andreev-Andrievskiy et&#x20;al.</alt-title>
<alt-title alt-title-type="right-running-head">PPRs Mediate Kagocel&#x2019;s Effects on Lymphocytes</alt-title>
</title-group>
<contrib-group>
<contrib contrib-type="author">
<name>
<surname>Andreev-Andrievskiy</surname>
<given-names>Alexander A.</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<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/505226/overview"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Zinovkin</surname>
<given-names>Roman A.</given-names>
</name>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
<xref ref-type="aff" rid="aff4">
<sup>4</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/725292/overview"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Mashkin</surname>
<given-names>Mikhail A.</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/1264557/overview"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Frolova</surname>
<given-names>Olga Yu.</given-names>
</name>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/1413955/overview"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Kazaishvili</surname>
<given-names>Yuriy G.</given-names>
</name>
<xref ref-type="aff" rid="aff5">
<sup>5</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/1266355/overview"/>
</contrib>
<contrib contrib-type="author" corresp="yes">
<name>
<surname>Scherbakova</surname>
<given-names>Victoria S.</given-names>
</name>
<xref ref-type="aff" rid="aff5">
<sup>5</sup>
</xref>
<xref ref-type="corresp" rid="c001">&#x2a;</xref>
<uri xlink:href="https://loop.frontiersin.org/people/1278644/overview"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Rudoy</surname>
<given-names>Boris A.</given-names>
</name>
<xref ref-type="aff" rid="aff5">
<sup>5</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/1268394/overview"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Nesterenko</surname>
<given-names>Vladimir G.</given-names>
</name>
<xref ref-type="aff" rid="aff5">
<sup>5</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/1416033/overview"/>
</contrib>
</contrib-group>
<aff id="aff1">
<label>
<sup>1</sup>
</label>Biology Faculty, M.V. Lomonosov Moscow State University, <addr-line>Moscow</addr-line>, <country>Russia</country>
</aff>
<aff id="aff2">
<label>
<sup>2</sup>
</label>MSU Institute for Mitoengineering, <addr-line>Moscow</addr-line>, <country>Russia</country>
</aff>
<aff id="aff3">
<label>
<sup>3</sup>
</label>Institute of Biomedical Problems RAS, <addr-line>Moscow</addr-line>, <country>Russia</country>
</aff>
<aff id="aff4">
<label>
<sup>4</sup>
</label>A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, <addr-line>Moscow</addr-line>, <country>Russia</country>
</aff>
<aff id="aff5">
<label>
<sup>5</sup>
</label>N.F. Gamaleya Federal Research Centre of Epidemiology and Microbiology, <addr-line>Moscow</addr-line>, <country>Russia</country>
</aff>
<author-notes>
<fn fn-type="edited-by">
<p>
<bold>Edited by:</bold> <ext-link ext-link-type="uri" xlink:href="https://loop.frontiersin.org/people/11428/overview">Stefania Tacconelli</ext-link>, University of Studies G. d&#x27;Annunzio Chieti and Pescara, Italy</p>
</fn>
<fn fn-type="edited-by">
<p>
<bold>Reviewed by:</bold> <ext-link ext-link-type="uri" xlink:href="https://loop.frontiersin.org/people/380932/overview">Barbara Rossi</ext-link>, University of Verona, Italy</p>
<p>
<ext-link ext-link-type="uri" xlink:href="https://loop.frontiersin.org/people/591121/overview">Andrey Zamyatnin</ext-link>, I.M. Sechenov First Moscow State Medical University, Russia</p>
</fn>
<corresp id="c001">&#x2a;Correspondence: Victoria S. Scherbakova, <email>Viktoriya.Shcherbakova@nearmedic.ru</email>
</corresp>
<fn fn-type="other">
<p>This article was submitted to Inflammation Pharmacology, a section of the journal Frontiers in Pharmacology</p>
</fn>
</author-notes>
<pub-date pub-type="epub">
<day>03</day>
<month>08</month>
<year>2021</year>
</pub-date>
<pub-date pub-type="collection">
<year>2021</year>
</pub-date>
<volume>12</volume>
<elocation-id>679511</elocation-id>
<history>
<date date-type="received">
<day>12</day>
<month>03</month>
<year>2021</year>
</date>
<date date-type="accepted">
<day>16</day>
<month>07</month>
<year>2021</year>
</date>
</history>
<permissions>
<copyright-statement>Copyright &#xa9; 2021 Andreev-Andrievskiy, Zinovkin, Mashkin, Frolova, Kazaishvili, Scherbakova, Rudoy and Nesterenko.</copyright-statement>
<copyright-year>2021</copyright-year>
<copyright-holder>Andreev-Andrievskiy, Zinovkin, Mashkin, Frolova, Kazaishvili, Scherbakova, Rudoy and Nesterenko</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&#x20;terms.</p>
</license>
</permissions>
<abstract>
<p>Kagocel is a synthetic carboxymethylcellulose derivative copolymerized with gossypol. Clinical data evidence its safety and efficiency for the treatment of flu and other viral infections via enhancement of interferon production. The gut-associated lymphoid tissue seems a likely site of kagocel action. The study was aimed to investigate the molecular mechanisms of its action using murine Peyer&#x2019;s patches lymphocytes as a test system and the cytokines production and gene expression patterns as the primary outcomes. The Peyer&#x2019;s patches lymphocytes isolated from BALB/c mice were stimulated with concanavalin A, or, to mimic viral infection, with a combination of concanavalin A and TLR3 ligand poly I:C. After 24&#xa0;h of stimulation the cells were treated with saline, 30, 100, or 300&#xa0;&#x3bc;g/ml of kagocel, or, as positive controls, 300&#xa0;&#x3bc;g/ml oats b-D-glucan or 300&#xa0;&#x3bc;g/ml lentinan. After 24 and 72&#xa0;h of incubation with these drugs cytokines production was analyzed with ELISA and gene expression pattern was investigated using nCounter Inflammation panel chips followed by bioinformatics analysis. Expression of genes involved in the inflammatory response, antiviral defense, lymphocytes survival and proliferation (C1qa, C2, C3, Ccl21a, Il11, Il1b, Il23a, Il5, Ltb4r2, Alox15, Pla2g4a, Ptger1, Mapkapk5, Hras, Ifna1, Tlr2, Mrc1, Mx2) was upregulated in kagocel-treated Peyer&#x2019;s patches lymphocytes. A list of plausible transcription factors (CEBPs, IRF, NF&#x3ba;B, RXR, Stat, Tead4, and ZSCAN) and master-regulators has been identified (cIAP, CIKS, dock9, MEKK1, FXR, IKK, IRAK, TRAF, dsRNA:TLR3:TRIF). The changes in gene expression pattern and the outcomes of bioinformatics analysis suggest that pattern recognition receptors, TLRs and dectin-1, are the key mediators of kagocel immunomodulatory action, with the possible involvement of interferon autocrine loop. The genes upregulated with kagocel include diverse components of the innate immune defense system.</p>
</abstract>
<kwd-group>
<kwd>kagocel</kwd>
<kwd>gene expression</kwd>
<kwd>cytokines</kwd>
<kwd>pattern recognition receptors</kwd>
<kwd>Peyer&#x2019;s patch lymphocytes</kwd>
</kwd-group>
</article-meta>
</front>
<body>
<sec id="s1">
<title>Introduction</title>
<p>The breakdown products of bacteria, fungi, and viruses trigger a rapid reaction of immune cells and some other cell types in the body as a part of an innate immune response (<xref ref-type="bibr" rid="B38">Kieser and Kagan, 2017</xref>). Among these breakdown products, (pathogen-associated molecular patterns, PAMPs) polysaccharides of the bacterial and fungal cell wall upon binding to toll-like receptors (<xref ref-type="bibr" rid="B34">Iwasaki and Medzhitov, 2004</xref>), dectin-1 receptors, and possibly other receptor types (<xref ref-type="bibr" rid="B7">Brown, 2005</xref>) induce inflammation, interferon production, promote immune cells survival and proliferation (<xref ref-type="bibr" rid="B34">Iwasaki and Medzhitov, 2004</xref>; <xref ref-type="bibr" rid="B7">Brown, 2005</xref>; <xref ref-type="bibr" rid="B38">Kieser and Kagan, 2017</xref>). Several polysaccharides of natural origin have been attributed immunomodulatory activity, among them lentinan (<xref ref-type="bibr" rid="B5">Borchers et&#x20;al., 1999</xref>) and plant &#x3b2;-D-glucans (<xref ref-type="bibr" rid="B19">Estrada et&#x20;al., 1997</xref>; <xref ref-type="bibr" rid="B66">Tada et&#x20;al., 2009</xref>) have drawn the most attention as possible therapeutical agents, while others, like zymosan (<xref ref-type="bibr" rid="B9">CARLO and FIORE, 1958</xref>) or carrageenan (<xref ref-type="bibr" rid="B50">Necas and Bartosikova, 2013</xref>) have proven to be useful research tools as immune response/inflammation inductors. Of note, the immunomodulatory effects of glucans have been reported in diverse species of mammals, birds, fish, and even invertebrates, indicating the involvement of an evolutionary conserved pathway/mechanism (<xref ref-type="bibr" rid="B72">Vos et&#x20;al., 2007</xref>).</p>
<p>The naturally occurring glucans stimulate macrophage activity, adaptive B- and T-cell mediated immune responses, and possess anti-cancer activity (<xref ref-type="bibr" rid="B8">Brown and Gordon, 2003</xref>). Some of the glucans are traditionally used as remedies for multiple diseases (<xref ref-type="bibr" rid="B4">Bisen et&#x20;al., 2010</xref>). Kagocel is a synthetic copolymer of modified carboxymethylcellulose and a natural polyphenol, gossypol, which was designed at the Gamaleya Research Institute of Epidemiology and Microbiology and further marketed as an oral interferon inductor in Russia and CIS countries by Nearmedic, LLC. Gossypol, no more than 3% by weight, is covalently bound to the carboxymethylcellulose backbone. The rationale for the inclusion of gossypol into the polymer was its immunomodulatory properties (<xref ref-type="bibr" rid="B18">Ershov et&#x20;al., 1988</xref>), while the covalent binding immobilized the polyphenol and thus reduced its toxicity (<xref ref-type="bibr" rid="B17">Eagle and Castillon, 1948</xref>) or possible male fertility effects (<xref ref-type="bibr" rid="B45">Lim et&#x20;al., 2019</xref>). Indeed, gossypol is not released from kagocel upon storage or incubation with gastric or intestinal juice (<xref ref-type="bibr" rid="B62">Sinitsin et&#x20;al., 2020</xref>). No adverse effects were identified in the chronic and reproduction toxicity studies with moderate doses of kagocel (<xref ref-type="bibr" rid="B6">Borovskaya, 2017</xref>).</p>
<p>Clinical data corroborate the efficacy of kagocel for influenza treatment (<xref ref-type="bibr" rid="B20">Fazylov et&#x20;al., 2016</xref>; <xref ref-type="bibr" rid="B63">Sologub and Tsvetkov, 2017</xref>) and for fighting other viral infections (<xref ref-type="bibr" rid="B23">Galegov et&#x20;al., 2002</xref>; <xref ref-type="bibr" rid="B46">Loginova et&#x20;al., 2020</xref>) as a monotherapy or a part of a combination treatment (<xref ref-type="bibr" rid="B57">Popov et&#x20;al., 2017b</xref>). Analysis of interferon concentrations in plasma of patients with influenza evidence increased cytokine levels upon kagocel administration (<xref ref-type="bibr" rid="B56">Popov et&#x20;al., 2017a</xref>). However, the molecular mechanisms of kagocel action are poorly understood. Aiming to provide cues to the possible mechanisms of kagocel action, we used murine Peyer&#x2019;s patches lymphocytes as a test system, deliberately avoiding further isolation of specific cell types to preserve cellular interactions. To preferentially stimulate T-lymphocytes, we used concanavalin A as a mitogen, or, to mimic viral infection, a combination of concanavalin A and TLR3 ligand poly I:C. The stimulated lymphocytes were incubated with different concentrations of kagocel or, as a positive control, with well-defined glucans, lentinan, and oats &#x3b2;-D-glucan, and analyzed for cytokine production and gene expression patterns at 24 and 72&#xa0;h after treatment.</p>
</sec>
<sec id="s2">
<title>Results</title>
<sec id="s2-1">
<title>Cytokines Production</title>
<p>The cytokines content in the culture media was analyzed after 24 and 72&#xa0;h cultivation with different polysaccharides (<xref ref-type="fig" rid="F1">Figure&#x20;1</xref>). Analysis of variance, expectedly, revealed significant effects of time and mitogen stimulation applied on the concentration of all the cytokines studied, except for IL10, which was not affected by the type of mitogen (<xref ref-type="fig" rid="F1">Figure&#x20;1</xref>). Among the polysaccharides, &#x3b2;-D Glucan had significant effects on TNF&#x3b1; (F<sub>(1.000,</sub> <sub>10.00)</sub> &#x3d; 14.1, <italic>p</italic>&#x20;&#x3d; 0.004), IL2 (F<sub>(1.000,</sub> <sub>10.00)</sub> &#x3d; 5.26, <italic>p</italic>&#x20;&#x3d; 0.045), Il10 (F<sub>(1.000,</sub> <sub>10.00)</sub> &#x3d; 5.78, <italic>p</italic>&#x20;&#x3d; 0.037), and INF&#x3b3; levels (F<sub>(1.000,</sub> <sub>10.00)</sub> &#x3d; 5.46, <italic>p</italic>&#x20;&#x3d; 0.042). Lentinan increased the levels of TNF&#x3b1; (F<sub>(1.000,</sub> <sub>10.00)</sub> &#x3d; 5.81, <italic>p</italic>&#x20;&#x3d; 0.037) and IL6 (F<sub>(1.000,</sub> <sub>10.00)</sub> &#x3d; 8.68, <italic>p</italic>&#x20;&#x3d; 0.015), while INF&#x3b3; was decreased with this treatment (F<sub>(1.000, 10.00)</sub> &#x3d; 15.48, <italic>p</italic>&#x20;&#x3d; 0.003). Kagocel had no consistent effect on TNF&#x3b1;, IL2, IL6, and INF&#x3b3;, however, incubation of lymphocytes with kagocel elevated IL10 concentration (F<sub>(3.000,</sub> <sub>30.00)</sub> &#x3d; 6.27, <italic>p</italic>&#x20;&#x3d; 0.002) in a seemingly dose-dependent manner (<xref ref-type="fig" rid="F1">Figure&#x20;1D</xref>). The enhanced IL10 production by kagocel-treated cells might explain the lack of the drug&#x2019;s effects on pro-inflammatory cytokines production by stimulated lymphocytes.</p>
<fig id="F1" position="float">
<label>FIGURE 1</label>
<caption>
<p>TNF&#x3b1; <bold>(A)</bold>, IL6&#x20;<bold>(B)</bold>, IL2&#x20;<bold>(C)</bold>, IL10&#x20;<bold>(D)</bold> and INF&#x3b3; <bold>(E)</bold> concentration in the media after 24 (open bars) and 72&#xa0;h (hatched bars) of cultivation of Peyer&#x2019;s patch lymphocytes stimulated with concanavalin A (ConA, open bars) in absence or presence of TLR-3 ligand poly I:C. Cells were treated with saline (H<sub>2</sub>O), 300&#xa0;&#x3bc;g/ml oats &#x3b2;-D Glucan (&#x3b2;DGlu), 300&#xa0;&#x3bc;g/ml lentinan (Lent) or 30-300&#xa0;&#x3bc;g/ml kagocel. Results present mean&#x20;&#xb1; s.e.m from 6 independent runs of the experiment. For statistics on drug effects see&#x20;text.</p>
</caption>
<graphic xlink:href="fphar-12-679511-g001.tif"/>
</fig>
</sec>
<sec id="s2-2">
<title>Gene Expression</title>
<p>After obtaining the gene expression data expressed as normalized counts, first, we performed the cluster analysis. The derived clustering matched the design of the experiment, with the uppermost two factors in the output hierarchy being time and the mitogen applied (<xref ref-type="sec" rid="s10">Supplementary Table S1</xref>). Thus, we conclude our experimental design had effectively altered the expression patterns for inflammation-related genes in the murine Peyer&#x2019;s patches lymphocytes.</p>
<p>Next, for a bird&#x2019;s-eye view of the data, we&#x2019;ve counted the up- and down-regulated genes, as compared to the matching control cells, for each combination of the drug applied, mitogen stimulation, and time. As shown in <xref ref-type="fig" rid="F2">Figure&#x20;2</xref>, upon treatment with polysaccharides, downregulation prevailed in concanavalin A treated lymphocytes at 24&#xa0;h of incubation, except for lentinan, which upregulated the gene expression. At 72&#xa0;h of incubation, the number of upregulated genes exceeded the downregulated genes count. Unlike that, when concanavalin A stimulation was complemented with poly I:C as a TLR3 ligand, the number of upregulated genes was generally higher than the number of down-regulated inflammation-related genes. The number of down-regulated genes increased with the concentration of kagocel in the incubation media in concanavalin A stimulated cells. Of note, in presence of poly I:C, no downregulated genes have been identified in kagocel-treated lymphocytes poly I:C at some concentrations of the&#x20;drug.</p>
<fig id="F2" position="float">
<label>FIGURE 2</label>
<caption>
<p>The counts of up- (red) and downregulated (blue) inflammation-related genes in Peyer&#x2019;s patches lymphocytes stimulated with concanavalin A (ConA) in absence or presence of TLR-3 ligand poly I:C 24 and 72&#xa0;h after treatment with 300&#xa0;&#x3bc;g/ml oats &#x3b2;-D Glucan (&#x3b2;DGlu), 300&#xa0;&#x3bc;g/ml lentinan (Lent) or 30-300&#xa0;&#x3bc;g/ml kagocel as compared to control, saline-treated, lymphocytes. RNA was collected in 3 independent runs of the experiment.</p>
</caption>
<graphic xlink:href="fphar-12-679511-g002.tif"/>
</fig>
<p>The heat maps presented in <xref ref-type="fig" rid="F3">Figure&#x20;3</xref> give a more detailed view of the data (see <xref ref-type="sec" rid="s10">Supplementary Table S2</xref> for the complete list). For this presentation, we have grouped the responding genes by Gene Ontology biological process. Overall, the expression patterns had a similar profile for all the processes analyzed. Downregulation was prevalent in concanavalin A-stimulated cells, while upon a more robust stimulation with a combination of concanavalin A and poly I:C upregulation was more frequent. More pronounced changes of gene expression were observed at 72&#xa0;h of cultivation with the polysaccharides, while at 24&#xa0;h the gene expression responses were more temperate. Finally, while expression patterns upon cell treatment with &#x3b2;-D Glucan and lentinan were alike, the effects of kagocel were dissimilar to these two glucans. Kagocel was applied to the cells at three different concentrations; of note, the most pronounced effects on gene expression were observed, counterintuitively, with the lowest concentration of the&#x20;drug.</p>
<fig id="F3" position="float">
<label>FIGURE 3</label>
<caption>
<p>Heat map (log<sub>2</sub>-fold change of expression) of genes involved in innate immune response, GO:0045087&#x20;<bold>(A)</bold>, adaptive immune response, GO:0002250&#x20;<bold>(B)</bold>, defense response to bacteria, GO:0042742&#x20;<bold>(C)</bold>, defense response to virus, GO:0051607&#x20;<bold>(D)</bold>, and humoral immune response, GO:0019730&#x20;<bold>(E)</bold> in murine Peyer&#x2019;s patches lymphocytes stimulated with concanavalin A (ConA) in absence or presence of TLR-3 ligand poly I:C after 24 and 72&#xa0;h after treatment with 300&#xa0;&#x3bc;g/ml oats &#x3b2;-D Glucan, 300&#xa0;&#x3bc;g/ml lentinan or 30-300&#xa0;&#x3bc;g/ml kagocel (Kag) as compared to control, saline-treated, lymphocytes. RNA was collected in 3 independent runs of the experiment.</p>
</caption>
<graphic xlink:href="fphar-12-679511-g003.tif"/>
</fig>
<p>The responder genes in kagocel-treated lymphocytes were involved in the regulation of macromolecule synthesis (GO:0031326, GO:0010556, GO:2000112), regulation of transcription (GO:0006355, GO:2001141, GO:1903506), and apoptosis (GO:0006915, GO:0012501, GO:0008219). Specifically, the genes upregulated in Peyer&#x2019;s patch lymphocytes were those encoding for the components of the complement system (C1qa, C2, C3), cytokine, chemokine, and lipid signaling (Ccl21a, Il11, Il1b, Il23a, Il5, Ltb4r2, Alox15, Pla2g4a, Ptger1), intracellular signal transduction (Mapkapk5, Hras) and, importantly, innate sensing and response to pathogens (Defa-rs1, Ifna1, Tlr2, Mrc1,&#x20;Mx2).</p>
</sec>
<sec id="s2-3">
<title>Transcription Factors Associated With Gene Response</title>
<p>Aiming to elucidate the possible mechanism of kagocel action, we used the responder genes as an input for the enrichment analysis of the transcription factor binding sites. By cross-tabulating the results of this analysis for different experimental conditions we have identified several transcription factors that could potentially govern the kagocel-induced changes of expression in the Peyer&#x2019;s patch lymphocytes. Among these factors, the CEBPs, homeobox, interferon regulatory factors, NF&#x3ba;B, retinoid X receptor alpha, Stat, Tead4, and Zinc finger and SCAN domain-containing proteins had the greatest fold enrichment. Of note, virtually identical transcription factors were highlighted for the two control glucans, oats &#x3b2;-D glucan and lentinan. The complete list of identified transcriptional factors is presented in <xref ref-type="sec" rid="s10">Supplementary Table&#x20;S3</xref>.</p>
</sec>
<sec id="s2-4">
<title>Master Regulators</title>
<p>We extended our search for the mechanisms of kagocel action further and performed the analysis of potential master regulators and pathways. Typically for this type of analysis, the output brought a wide range of possible regulators, rather than a single candidate. To exclude the unmeaningful results, we cross-tabulated the data for the same drug at different experimental conditions (mitogen and time point), while in the case of kagocel we could also include the data for the three doses into this analysis. The regulators and pathways with single or unsystematic entries were disregarded. Thus, we were able to identify cIAP, CIKS, dock9, MEKK1, FXR, IKK, IRAK, TRAF, dsRNA:TLR3:TRIF pathway, and several pathways involving TLR signaling as the potential regulators underlying kagocel action on the lymphocyte&#x2019;s gene expression. The complete list of identified master regulators is presented in <xref ref-type="sec" rid="s10">Supplementary Table&#x20;S4</xref>.</p>
</sec>
</sec>
<sec sec-type="discussion" id="s3">
<title>Discussion</title>
<p>Here we report the results of gene expression analysis in murine Peyer&#x2019;s patch lymphocytes upon treatment with a carboxymethylcellulose and gossypol copolymer, kagocel, or naturally occurring glucans, lentinan, and oats &#x3b2;-D glucan, as positive controls. The polysaccharides induced pronounced changes of inflammation and immune genes expression that highlight pattern-recognition receptors as the plausible targets of kagocel action.</p>
<p>We used the primary culture of murine Peyer&#x2019;s patch lymphocytes as a test system to investigate the effects of kagocel. There are several reasons for this choice. Firstly, it is well documented that the glucans are effective upon oral administration, and the same is true for the synthetic glucan, kagocel, which is taken orally as an immunostimulant. However, due to the high molecular weight of these polymers ( &#x3e;10<sup>5</sup>), they are poorly absorbed from the intestine (<xref ref-type="bibr" rid="B72">Vos et&#x20;al., 2007</xref>). The pharmacokinetic data for polysaccharides of a similar molecular mass evidence that their bioavailability upon oral exposure is in the range of hundredths to tenths of percent (<xref ref-type="bibr" rid="B48">Mehvar and Shepard, 1992</xref>). In line with that, only about 10% of the kagocel dose is absorbed from the gastrointestinal tract of rats upon oral administration, presumably, the lower-molecular weight fraction of the polymer (<xref ref-type="bibr" rid="B2">Andreev-Andrievskiy et&#x20;al., 2019</xref>). The discrepancy between the apparent effects of the glucans upon the immune system and their poor absorbance can be resolved by observations of specific accumulation of the polysaccharides in the Peyer&#x2019;s patches after oral exposure. Thus, after ingestion of carrageenan, it has been identified in the Peyer&#x2019;s patches (<xref ref-type="bibr" rid="B52">Nicklin et&#x20;al., 1988</xref>). Glucans can be internalized by M-cells upon binding to dectin-1 receptor (<xref ref-type="bibr" rid="B13">Smet et&#x20;al., 2013</xref>), and intestinal epitheliocytes might contribute to the uptake of particulate antigens above the Peyer&#x2019;s patches (<xref ref-type="bibr" rid="B31">Howe et&#x20;al., 2014</xref>). Although kagocel distribution in different tissues of the intestinal wall has not been studied, we speculate that kagocel may penetrate the Peyer&#x2019;s patches upon oral exposure, which would make them a potential site of its action upon immunity.</p>
<p>The Peyer&#x2019;s patches lymphocytes are a mixed population, consisting of 60% B-cells, 25% of T-cells, 10% of dendritic cells (CD11c&#x2b;), and less than 5% of macrophages or polymorphonuclear neutrophils (<xref ref-type="bibr" rid="B43">Lefran&#xe7;ois and Lycke, 1996</xref>; <xref ref-type="bibr" rid="B35">Jung et&#x20;al., 2010</xref>). While this is true for the freshly isolated cells, we utilized the stimulation protocol specifically favoring T-cell proliferation (<xref ref-type="bibr" rid="B16">Dwyer and Johnson, 1981</xref>). Thus, considering the relatively long period of cultivation with the mitogens before application of the drugs, diverse subsets of T-cells, presumably, comprised the majority of the culture studied.</p>
<p>Substantial evidence accumulated over the recent years suggests that the link between the respiratory tract and the intestinal immune systems is critically important for host antiviral defense. On the one hand, respiratory viruses may induce intestinal injury as seen for influenza (<xref ref-type="bibr" rid="B73">Wang et&#x20;al., 2014</xref>), or, more recently for SARS-CoV-2 (<xref ref-type="bibr" rid="B60">Scaldaferri et&#x20;al., 2020</xref>). The infected epithelial cells can present viral antigens to promote cell-mediated immunity (<xref ref-type="bibr" rid="B51">Nguyen et&#x20;al., 1998</xref>). At the same time, the intestinal immune system, primarily the Peyer&#x2019;s patch, is an important site of the lymphocytes emigration (<xref ref-type="bibr" rid="B58">Rothk&#xf6;tter et&#x20;al., 1999</xref>; <xref ref-type="bibr" rid="B30">Heidegger et&#x20;al., 2013</xref>). Of note, dendritic cells constitute up to 4% of the immigrating cells (<xref ref-type="bibr" rid="B58">Rothk&#xf6;tter et&#x20;al., 1999</xref>). Basing on the existing links between the microbiota, the intestinal immune system, and overall hosts&#x2019; resistivity to infection (<xref ref-type="bibr" rid="B32">Ichinohe et&#x20;al., 2011</xref>; <xref ref-type="bibr" rid="B11">Clemente et&#x20;al., 2012</xref>), several strategies have been suggested employing the modification of a diet or direct introduction of some strains of commensal bacteria (<xref ref-type="bibr" rid="B70">Villena et&#x20;al., 2012</xref>; <xref ref-type="bibr" rid="B25">Goto et&#x20;al., 2013</xref>; <xref ref-type="bibr" rid="B33">Illiano et&#x20;al., 2020</xref>). Interestingly, the outcomes of anti-influenza vaccination rely on commensal microbiota sensing via TLRs (<xref ref-type="bibr" rid="B54">Oh et&#x20;al., 2014</xref>), thus the oral influenza vaccines that are being developed directly utilize TLR ligands as adjuvants (<xref ref-type="bibr" rid="B47">Lycke, 2012</xref>). Moreover, some polysaccharides have been suggested as adjuvants for oral vaccines (<xref ref-type="bibr" rid="B13">Smet et&#x20;al., 2013</xref>).</p>
<p>The genes upregulated in the intestinal lymphocytes after incubation with kagocel include several important players of the innate immune response, components of the complement system, antiviral defense systems and chemokines. While the significance of the plasma complement system for immunity is apparent, the importance of the recently reported expression of the complement system components in T-cells is not completely clear, but might be related to cell survival and differentiation (<xref ref-type="bibr" rid="B28">Hansen et&#x20;al., 2018</xref>). The interaction of signaling from TLRs and the receptors to complement anaphylatoxins significantly alters the immune response (<xref ref-type="bibr" rid="B65">Song, 2012</xref>). Less is known about the relevance of kininogen expression in the lymphocytes. Hras1, a. k.a. p21, is a negative regulator of the cell cycle (<xref ref-type="bibr" rid="B37">Khanna et&#x20;al., 2005</xref>), capable of inducing cell-cycle arrest following TLR4/TRIF activation as a part of the antiviral response (<xref ref-type="bibr" rid="B49">Mlcochova et&#x20;al., 2020</xref>). Importantly, H-Ras is capable of enhancing interferon signaling (<xref ref-type="bibr" rid="B10">Chen et&#x20;al., 2017</xref>). Heat shock protein 27&#xa0;kDa, has a variety of functions, of note, after release to extracellular space HSP27 is capable of activating NF-&#x3ba;B in a TLR4 dependent manner (<xref ref-type="bibr" rid="B61">Shi et&#x20;al., 2019</xref>).</p>
<p>Several genes, important for the lymphocytes migration or chemotaxis, were among the responder genes in kagocel-treated lymphocytes. Thus, CCL21, a ligand of CCR7, was upregulated in PP lymphocytes co-stimulated with concanavalin A and Poly I:C, but not upon stimulation with concanavalin A only. Of relevance, disruption of CCL21/CCR7 signaling weakens the immune response to a variety of viruses, by interfering with the cells&#x2019; migration and proper interactions during antigen presentation (<xref ref-type="bibr" rid="B12">Comerford et&#x20;al., 2013</xref>). Leukotriene B4 receptor 2 is another up-regulated mediator of cellular migration. Interestingly, the chemotactic effects of TLR ligands are mediated by this receptor (<xref ref-type="bibr" rid="B42">Lefebvre et&#x20;al., 2010</xref>). Upon treatment with kagocel, the PP lymphocytes expressed more RNA for TLR2, a sensor of bacterial lipoproteins, and lipoteichoic acids. One of the diverse ligands of this receptor is zymosan, a fungal &#x3b2;-glucan (<xref ref-type="bibr" rid="B59">Sato et&#x20;al., 2003</xref>). However, TLR2 is known to bind a wide variety of ligands, and to form functional heterodimers with other types of TLR and non-TLR molecules (<xref ref-type="bibr" rid="B55">Oliveira-Nascimento et&#x20;al., 2012</xref>). One of the TLR2 dimerization partners is TLR6, which was also upregulated in kagocel treated cells, along with 7 and 9, however to a lesser extent as compared to&#x20;TLR2.</p>
<p>IL23 is a pro-inflammatory cytokine with a multi-faceted effect on T-cell differentiation and INF&#x3b3; production (<xref ref-type="bibr" rid="B26">Guo et&#x20;al., 2019</xref>). As reviewed in (<xref ref-type="bibr" rid="B53">Novelli and Casanova, 2004</xref>), IL23 deficiency results in a substantial decrease of resistivity to diverse DNA and RNA viruses, thus induction of IL23 expression is one of the apparent positive effects of kagocel for antiviral defense in the lymphocytes. IFIT3 is an interferon-induced protein, also up-regulated with virus infection and double-stranded RNA, capable of inhibiting viral replication and translational initiation, along with cellular migration and proliferation (<xref ref-type="bibr" rid="B21">Fensterl and Sen, 2011</xref>). Overexpression of IFIT3 alone was sufficient to suppress viral replication in a porcine model (<xref ref-type="bibr" rid="B44">Li et&#x20;al., 2015</xref>). Another gene up-regulated in kagocel treated PP lymphocytes is defensin-related sequence 1, a cysteine-rich protein specific to the rodent intestine and not found in the human (<xref ref-type="bibr" rid="B1">Andersson et&#x20;al., 2012</xref>).</p>
<p>Myxovirus resistance proteins 1 and 2 were both up-regulated with kagocel treatment, providing another mechanistic explanation for the efficacy of the drug. These GTPases inhibit different viruses by blocking the early steps of viral replication (<xref ref-type="bibr" rid="B27">Haller et&#x20;al., 2015</xref>). Recombinant Mx-1, modified to facilitate cell penetration, was capable of effectively suppressing influenza infection <italic>in&#x20;vitro</italic> and <italic>in vivo</italic> (<xref ref-type="bibr" rid="B36">Jung et&#x20;al., 2019</xref>). Interestingly, the MX protein can be induced by both type I and III interferons (<xref ref-type="bibr" rid="B27">Haller et&#x20;al., 2015</xref>). Due to the limitations of the gene expression analysis system, we have no experimental data on type III interferon expression. Considering that both types I and III interferons are concurrently induced by TLR (<xref ref-type="bibr" rid="B3">Ank et&#x20;al., 2008</xref>) and dectin-1 activation (<xref ref-type="bibr" rid="B15">Dutta et&#x20;al., 2020</xref>), it is tempting to speculate that type III interferon was upregulated in kagocel-treated cells in our study and mediated some of the effects of the drug. Yet another component of the cellular anti-viral defense systems responsive to kagocel application was 2&#x2013;5&#x2032; Oligoadenylate synthetase 2, an enzyme capable of interrupting viral replication via activation of rnase L and in an oligoadenylate-independent manner (<xref ref-type="bibr" rid="B40">Kristiansen et&#x20;al., 2010</xref>).</p>
<p>Ifna1 was one of the genes with the highest fold-change ( &#x3e;5) in kagocel-treated cells as compared to control PP lymphocytes. A similar increase in interferon production induced by kagocel has been reported previously using human cell lines (<xref ref-type="bibr" rid="B69">Vershinina et&#x20;al., 2002</xref>). The antiviral properties of interferon are subject to years of scrutiny and a PubMed search &#x201c;interferon alpha AND virus&#x201d; yields more than 23 thousand references. Yet more information is available on the use of interferons for the treatment of diverse viral infectious diseases. Importantly, the potentiating effect of kagocel on Ifna expression was evident in presence of TLR-3 ligand poly I:C, evidencing the involvement of additional mechanisms of interferon induction. Both dectin-1 (<xref ref-type="bibr" rid="B14">Dragicevic et&#x20;al., 2012</xref>) and TLR2 receptors (<xref ref-type="bibr" rid="B68">Vanhoutte et&#x20;al., 2008</xref>) have been reported to interact with TLR-3 signaling to significantly modify lymphocyte functions.</p>
<p>Noteworthy, the majority of kagocel-responder genes involved in anti-viral defense were up-regulated only in concanavalin A and poly I:C co-stimulated lymphocytes, while in absence of dsRNA these genes were down-regulated in kagocel-treated cells as compared to control lymphocytes. Among them, Oasl, Il17, Ifit1, and Ccr1 should be listed. On the contrary, Il5 was up-regulated by kagocel in concanavalin A stimulated PP lymphocytes, but no effect upon this cytokine expression was found in Con A and poly I:C co-stimulated cells. Another intriguing possibility is the involvement of type I interferon autocrine loop in the effects of kagocel. Upon activation of TLR receptors, INF&#x3b1; can stimulate the cell in an autocrine manner via INFAR1 (<xref ref-type="bibr" rid="B64">Song et&#x20;al., 2015</xref>), and, importantly, this mechanism has been reported to be involved in the effects of &#x3b2;-D-glucans (<xref ref-type="bibr" rid="B29">Hassanzadeh-Kiabi et&#x20;al., 2017</xref>). Furthermore, type I interferon is capable to increase IL10 production by diverse types of immune cells stimulated with TLR ligands (<xref ref-type="bibr" rid="B22">Gabry&#x161;ov&#xe1; et&#x20;al., 2014</xref>). Thus, increased IL10 production upon treatment of Peyer&#x2019;s patch lymphocytes with kagocel (<xref ref-type="fig" rid="F1">Figure&#x20;1D</xref>) supports involvement of INF&#x3b1; in the realization of kagocel effects.</p>
<p>Prior to commencing the study, we hypothesized that either Toll-like receptors or the dectin-1 receptor could mediate the immunomodulatory effects of kagocel. In this study, we have performed the search of master molecules mediating the changes in gene expression patterns. Among the candidates for mediating the kagocel action, the key components of TLR-signaling pathways TRAF, Tab, TAK, IKK&#x3b1; and IKK&#x3b2;, RIP, and IRFs have been identified with high scores and low FDRs, and IRF3 and IFF7 expression was moderately up-regulated with kagocel (<xref ref-type="fig" rid="F3">Figure&#x20;3</xref>). Identification of IFN&#x3b1;, IFN&#x3b2;/IFNAR/Tyk2/Jak pathway, and its separate components among the candidates, supports the hypothesis of interferon autocrine loop involvement in kagocel action upon the PP lymphocytes. Next, our findings support the possibility of dectin-1 receptor involvement in the realization of kagocel effects. Despite dectin-1 signaling is less fully elucidated as compared to other PRRs (<xref ref-type="bibr" rid="B67">Tang et&#x20;al., 2018</xref>), it is apparent that dectin and TLR2 signaling closely interact to mediate glucan-activated anti-fungal immunity (<xref ref-type="bibr" rid="B7">Brown, 2005</xref>). In support of the possibility of dectin-1 activation by kagocel, SYK and ZAP-70 have been identified among the master-molecule candidates. Moreover, the signaling from both possible kagocel receptors is convergent in orchestrating the inflammatory response (<xref ref-type="bibr" rid="B24">Gantner et&#x20;al., 2003</xref>). Finally, co-stimulation of TLR and Dectin-1 receptors enhances IL-10 production (<xref ref-type="bibr" rid="B22">Gabry&#x161;ov&#xe1; et&#x20;al., 2014</xref>), providing one of the possible explanations for enhanced IL10 production observed in kagocel-treated lymphocytes in this study (<xref ref-type="fig" rid="F1">Figure&#x20;1D</xref>).</p>
<p>The findings of our study are summarized in <xref ref-type="fig" rid="F4">Figure&#x20;4</xref>. We conclude that the Peyer&#x2019;s patches lymphocytes, as important players in the antiviral defense, might be accessible for kagocel upon oral administration, which makes gut-associated lymphoid tissue the likely site of kagocel action. When the mixed population of PP lymphocytes is exposed to kagocel, the drug presumably binds to TLR2 and/or dectin-1 receptors to induce downstream signaling and activation of the innate antiviral response with possible involvement of interferon autocrine loop. These genes up-regulated by kagocel treatment are involved in different stages of antiviral and antibacterial immunity, ranging from sensing the pathogen and the immune response modulation to the effector proteins. Further research is needed to verify the involvement of these mechanisms in the immunomodulatory action of kagocel.</p>
<fig id="F4" position="float">
<label>FIGURE 4</label>
<caption>
<p>The possible mechanism of kagocel action, as summarized from the study findings. The elements of the network highlighted with bold colors are either genes up-regulated in Peyer&#x2019;s patch lymphocytes, or the transcription factors/master regulators identified using bioinformatics&#x20;tools.</p>
</caption>
<graphic xlink:href="fphar-12-679511-g004.tif"/>
</fig>
<sec id="s3-1">
<title>Materials and Methods</title>
<sec id="s3-1-1">
<title>Isolation of Peyer&#x2019;s Patches Lymphocytes</title>
<p>Peyer&#x2019;s patches lymphocytes were isolated from male BALB/c mice as described previously (<xref ref-type="bibr" rid="B43">Lefran&#xe7;ois and Lycke, 1996</xref>). Briefly, mice were humanely killed, the small intestines were excised and placed on ice. The intestinal lumen was flushed with 20&#xa0;ml ice-cold PBS and the Peyer&#x2019;s patches were microdissected under the microscope and rinsed thrice with ice-cold PBS supplemented with gentamicin (100&#xa0;&#x3bc;g/ml). Patches from 6-8 mice were pooled.</p>
<p>To facilitate tissue dissociation, the patches were incubated in CMF (85% HBSS without Mg<sup>2&#x2b;</sup>, Ca<sup>2&#x2b;</sup>, and NaHCO<sub>3</sub>; 1xHEPES-bicarbonate buffer and 5% FBS) on a rotation shaker for 30&#xa0;min at 37&#xb0;&#x421;. After that the tissue was forced through a 70&#xa0;&#x3bc;m&#xa0;cell strainer, the suspension was pelleted (5&#xa0;min at 500 rcf) and washed thrice with CMF. Lymphocytes were separated by centrifugation in 44% Percoll layered over 80% Percoll for 20&#xa0;min at 600 rcf, washed four times in HBSS, and resuspended to 1&#xd7;10<sup>6</sup>/&#xa0;ml in RPMI 1640 supplemented with <sc>l</sc>-glutamine, 10% FBS, and 100&#xa0;&#x3bc;g/ml gentamicin. To verify the number of viable lymphocytes, cells were differentially stained with propidium iodide (10&#xa0;&#xb5;M) and SYBR Green (1&#xa0;&#xb5;M), and the number of living cells counted from the microphotographs. In six separate experiments, on average 90&#x20;&#xb1; 3% of the cells were viable.</p>
</sec>
<sec id="s3-1-2">
<title>Lymphocyte Culture</title>
<p>The isolated lymphocytes were split into two aliquots and stimulated with 10&#xa0;&#x3bc;g/ml concanavalin A or a combination of 10&#xa0;&#x3bc;g/ml concanavalin A and 10&#xa0;&#x3bc;g/ml of TLR-3 agonist poly I:C. To ensure proper annealing, poly I:C was heated for 5&#xa0;min at 55&#xb0;&#x421; and cooled to room temperature for 1&#xa0;h. The stimulated lymphocytes were seeded into 24-well plates (SPL life sciences, South Korea), 1.5 &#xd7; 10<sup>6</sup>&#xa0;cells per well, and incubated at 37&#xb0;&#x421; in 5% CO<sub>2</sub> atmosphere (MCO-5AC incubator, Sanyo, Japan).</p>
<p>After 24&#xa0;h of cultivation with the mitogens, water (H<sub>2</sub>O) or 30, 100, or 300&#xa0;&#x3bc;g/ml kagocel (Kag) were added to the cells in a volume of 15&#xa0;&#xb5;L (1:100 v:v). Positive control lymphocytes were treated with 300&#xa0;&#x3bc;g/ml lentinan (Lent) or 300&#xa0;&#x3bc;g/ml oats &#x3b2;-D-glucan (&#x3b2;DGlu).</p>
<p>Samples were collected after 24 and 72&#xa0;h of incubation with the drugs, one well per treatment, at each of the two time points. The cells were pelleted by centrifugation at 500 rcf for 5&#xa0;min. The culture media was collected and frozen at 80&#xb0;&#x421; for subsequent analysis of cytokines content, while the cells were immediately lysed with 500&#xa0;&#xb5;L TRI Reagent for 20&#xa0;min on a rotation shaker at room temperature.</p>
<p>Thus, expression patterns and the cytokines production for each of the drugs were studied at two time points for each of the two mitogen stimulation protocols. A total of six independent replications of this design were performed. Cytokine concentration was measured in all the runs, while the gene expression pattern was investigated in the three last runs&#x20;only.</p>
</sec>
<sec id="s3-1-3">
<title>ELISA</title>
<p>The culture media were analyzed for INF&#x3b1;, INF&#x3b3;, IL2, IL10, and TNF&#x3b1; content using RnD kits according to the manufacturer&#x2019;s instructions.</p>
<p>The statistical analysis of the cytokine concentrations was performed separately for each of the tested drugs using three-way ANOVA (factors &#x201c;Time,&#x201d; &#x201c;Mitogen&#x201d; and &#x201c;Drug&#x201d;) with Prism (v. 8.0, GraphPad, United&#x20;States). Only the main effects and interactions were analyzed and considered significant at <italic>p</italic>&#x20;&#x3c;&#x20;0.05.</p>
</sec>
<sec id="s3-1-4">
<title>RNA Isolation</title>
<p>To achieve phase separation, the TRI Reagent lysates were treated with 1 bromo-3-chloropropane (1:10 v:v), thoroughly mixed, and centrifuged at 12,000 rcf and 4&#xb0;C for 15&#xa0;min. The aqueous phase was collected and further purified using RNeasy micro kits (Qiagen, United&#x20;States) according to the manufacturer&#x2019;s instructions. The average yield was &#x2248;800&#xa0;ng per sample, as measured with Qubit 4 Fluorometer (Invitrogen, United&#x20;States). RNA preparation purity was analyzed with NanoDrop (Thermo Scientific, United&#x20;States) and preparations with suboptimal quality (A<sub>260</sub>/A<sub>280</sub> &#x3c; 1.8, A<sub>260</sub>/A<sub>230</sub> &#x3c; 1.8) were excluded from further analysis. The replicate samples from three independent runs were mixed at equal quantities and stored at &#x2212;80&#xb0;&#x421; until subsequent analysis.</p>
</sec>
<sec id="s3-1-5">
<title>Gene Expression Analysis</title>
<p>Analysis of gene expression was performed using murine nCounter Inflammation panel chips and analyzed using nCounter software (NanoStiring Technologies, United&#x20;States) according to the manufacturer&#x2019;s instructions (<xref ref-type="bibr" rid="B41">Kulkarni, 2011</xref>). Briefly, the raw counts were thresholded using the mean plus 2 standard deviations of the in-built negative controls counts, individually for each chip. Next, the counts were normalized to the coefficient derived from the in-built positive controls counts. Finally, the second normalization to the geometric mean of the housekeeping genes expression for individual samples was applied.</p>
</sec>
<sec id="s3-1-6">
<title>Prediction of Transcription Factors</title>
<p>As a next step, separately for each of the substances tested, fold-change was calculated for each of the target genes against expression level in the control (saline-treated) sample at the corresponding time point and expressed as log<sub>2</sub>. Genes with a twofold change of expression as compared to the time-matched control (saline-treated) were referred to as responder genes (RG) and included into further analysis. The transcription factors that could potentially govern the expression of the RGs were identified using the position weight matrix method. To this end, the transcription factor binding sites in the promoter region (&#x2212;1,500 to &#x2b;500&#x20;bp relative to the transcriptional start site) of the RGs were found. For this, the coordinates of the transcription start site of each investigated gene were identified by &#x27;biomaRt&#x27; package in the R environment using the coordinates of the 5&#x2032;UTR of the most abundant mRNA isoform evaluated by Cufflinks (v. 2.2.1, NIH) basing on the RNA sequencing data of Peyer&#x2019;s patch CD<sup>4&#x2b;</sup> T-lymphocytes (<xref ref-type="bibr" rid="B71">Visekruna et&#x20;al., 2019</xref>). The search of the potential transcription factors binding sites and binding site enrichment analysis in the promoter regions was performed for the up- and downregulated genes separately relative to a set of random 5,000&#x20;protein-encoding genes promoters using the GeneExplain platform (&#x201c;Search enriched TBFS in tracks&#x201d; function) and TRANSFAC v. 2020.2 database of transcription factors binding sites (TBFS) (<xref ref-type="bibr" rid="B39">Koschmann et&#x20;al., 2015</xref>). Briefly, the algorithm searches for the TBFSs in the promoter region of the investigated and the reference genes. Then the number of promoter regions containing specific TBFS is calculated for the investigated and the reference genes, followed by statistical analysis with the exact Fisher&#x2019;s test. During the TFBS search, the positional weight matrix (PWM) cut-off is optimized to maximize the adjusted fold enrichment (odds ratio with a 99% confidence interval). The transcription factors binding sites with the adjusted fold enrichment (odds ratio with a 99% confidence interval) of 1.1 and FDR &#x3c;0.1 (Fisher&#x2019;s test) were considered to be meaningful.</p>
</sec>
<sec id="s3-1-7">
<title>Gene Ontology Analysis</title>
<p>The functional enrichment of the responder genes was examined relative to the entire set of analyzed genes (248 genes) by the PANTHER Overrepresentation Test (Released 2020-07-28) tool using the GO biological process complete and PANTHER Pathways databases. Gene Ontology terms with <italic>p</italic>&#x20;&#x3c; 0.05 (Bonferroni corrected binomial test) were considered significantly enriched.</p>
</sec>
<sec id="s3-1-8">
<title>Prediction of Upstream Signaling Pathways and Master-Regulators</title>
<p>The transcription factor sets obtained for up- and downregulated genes for a given combination of the tested substance and time point were used as an input for analysis of upstream signaling pathways and master-regulators (GeneExplain platform with Transpath v. 2020.2 database and workflow &#x201c;Find master regulators in networks&#x201d;) as described in (<xref ref-type="bibr" rid="B39">Koschmann et&#x20;al., 2015</xref>). The search was done with a maximum radius of 10 steps upstream of an input gene set, and potential master regulators filtered with cutoffs: score &#x3e;0.2, FDR &#x3c;0.05, and Z score &#x3e;1.0 (where score reflects the degree of a regulator molecule connectivity with other molecules in the database and with the input list; Z-score reflects the specificity of each master molecule for the input list; FDR represents the probability of the molecule to occupy the observed or a higher rank by random chance; FDR and Z-score is calculated on 1,000 random results).</p>
</sec>
<sec id="s3-1-9">
<title>Materials and Reagents</title>
<p>Gentamicin, Concanavalin A, <sc>l</sc>-glutamine supplemented RPMI-1640, HBSS, 10&#x20;&#xd7; PBS, and 1&#xa0;M HEPES sodium salt solution were purchased from PanEco (Russia). Percoll<sup>&#xae;</sup>, Propidium iodide, &#x3b2;-D-Glucan, and Polyinosinic&#x2013;polycytidylic acid potassium salt (Poly I:C) were purchased from Sigma-Aldrich (Russia). SYBRGreen was purchased from Lumiprobe (Russia). TRI REAGENT<sup>&#xae;</sup> was purchased from Molecular Research Center, Inc. (United&#x20;States). Fetal Bovine Serum was purchased from BioSera (France). Lentinan was purchased from Toronto Research Chemicals (Canada). RNeasy Micro Kit was purchased from Qiagen (United&#x20;States). Kagocel was provided by NearMedic Plus (Russia).</p>
</sec>
</sec>
</sec>
</body>
<back>
<sec id="s4">
<title>Data Availability Statement</title>
<p>The original contributions presented in the study are included in the article/<xref ref-type="sec" rid="s10">Supplementary Material</xref>, further inquiries can be directed to the corresponding author.</p>
</sec>
<sec id="s5">
<title>Ethics Statement</title>
<p>The animal study was reviewed and approved by Bioethics commission of MSU institute for Mitoengineering, LLC (Protocol No 143 of March 11, 2019).</p>
</sec>
<sec id="s6">
<title>Author Contributions</title>
<p>All authors listed have made a substantial, direct, and intellectual contribution to the work and approved it for publication.</p>
</sec>
<sec id="s7">
<title>Funding</title>
<p>The study was performed by MSU Institute for mitoengineering by contract with Nearmedic, LLC. In part, funding was provided by the Interdisciplinary Scientific and Educational School of Moscow University &#xab;Molecular Technologies of the Living Systems and Synthetic Biology&#xbb;.</p>
</sec>
<sec sec-type="COI-statement" id="s8">
<title>Conflict of Interest</title>
<p>The reviewer AZ declared a past co-authorship with one of the authors RZ to the handling editor.</p>
<p>The study was performed by MSU Institute for mitoengineering by contract with Nearmedic, LLC. The funder, acting as a study sponsor, had approved the study design, but had no role in data collection, analysis and interpretation or the decision to publish.</p>
</sec>
<sec id="s9" 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>
<ack>
<p>The authors thank Irina Savchenko, Anfisa Popova, Evgeniya Lagereva, Olga Fadeeva, and Ekaterina Telyatnikova for technical assistance with data collection. The bioinformatic analysis of the data was performed by Daniil Popov and Pavel Makhnovskiy of IMBP RAS by contract to MSU Institute of Mitoengineering. <xref ref-type="fig" rid="F4">Figure&#x20;4</xref> was created using Biorender. The authors are indebted to Dr. Rupert Holms for proofreading and editing the manuscript.</p>
</ack>
<sec id="s10">
<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/fphar.2021.679511/full#supplementary-material">https://www.frontiersin.org/articles/10.3389/fphar.2021.679511/full&#x23;supplementary-material</ext-link>
</p>
<supplementary-material xlink:href="Table1.DOCX" id="SM1" mimetype="application/DOCX" xmlns:xlink="http://www.w3.org/1999/xlink"/>
<supplementary-material xlink:href="Image1.JPEG" id="SM2" mimetype="application/JPEG" xmlns:xlink="http://www.w3.org/1999/xlink"/>
<supplementary-material xlink:href="Table2.DOCX" id="SM3" mimetype="application/DOCX" xmlns:xlink="http://www.w3.org/1999/xlink"/>
<supplementary-material xlink:href="Table3.DOCX" id="SM4" mimetype="application/DOCX" xmlns:xlink="http://www.w3.org/1999/xlink"/>
</sec>
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