<?xml version="1.0" ?><!DOCTYPE article PUBLIC "-//NLM//DTD JATS (Z39.96) Journal Archiving and Interchange DTD v1.3 20210610//EN"  "JATS-archivearticle1-mathml3.dtd"><article xmlns:ali="http://www.niso.org/schemas/ali/1.0/" xmlns:xlink="http://www.w3.org/1999/xlink" article-type="research-article" dtd-version="1.3" xml:lang="en">
<front>
<journal-meta>
<journal-id journal-id-type="nlm-ta">elife</journal-id>
<journal-id journal-id-type="publisher-id">eLife</journal-id>
<journal-title-group>
<journal-title>eLife</journal-title>
</journal-title-group>
<issn publication-format="electronic" pub-type="epub">2050-084X</issn>
<publisher>
<publisher-name>eLife Sciences Publications, Ltd</publisher-name>
</publisher>
</journal-meta>
<article-meta>
<article-id pub-id-type="publisher-id">87292</article-id>
<article-id pub-id-type="doi">10.7554/eLife.87292</article-id>
<article-id pub-id-type="doi" specific-use="version">10.7554/eLife.87292.1</article-id>
<article-version-alternatives>
<article-version article-version-type="publication-state">reviewed preprint</article-version>
<article-version article-version-type="preprint-version">1.1</article-version>
</article-version-alternatives>
<article-categories>
<subj-group subj-group-type="heading">
<subject>Cancer Biology</subject>
</subj-group>
</article-categories>
<title-group>
<article-title>DHODH inhibition enhances the efficacy of immune checkpoint blockade by increasing cancer cell antigen presentation</article-title>
</title-group>
<contrib-group>
<contrib contrib-type="author">
<contrib-id contrib-id-type="orcid">http://orcid.org/0000-0002-5045-0814</contrib-id>
<name>
<surname>Mullen</surname>
<given-names>Nicholas J.</given-names>
</name>
<xref ref-type="aff" rid="a1">1</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Shukla</surname>
<given-names>Surendra K.</given-names>
</name>
<xref ref-type="aff" rid="a2">2</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Thakur</surname>
<given-names>Ravi</given-names>
</name>
<xref ref-type="aff" rid="a2">2</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Kollala</surname>
<given-names>Sai Sundeep</given-names>
</name>
<xref ref-type="aff" rid="a1">1</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Wang</surname>
<given-names>Dezhen</given-names>
</name>
<xref ref-type="aff" rid="a1">1</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Chaika</surname>
<given-names>Nina</given-names>
</name>
<xref ref-type="aff" rid="a1">1</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>LaBreck</surname>
<given-names>Drew A.</given-names>
</name>
<xref ref-type="aff" rid="a2">2</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Mallareddy</surname>
<given-names>Jayapal Reddy</given-names>
</name>
<xref ref-type="aff" rid="a1">1</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Price</surname>
<given-names>David H.</given-names>
</name>
<xref ref-type="aff" rid="a3">3</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Natarajan</surname>
<given-names>Amarnath</given-names>
</name>
<xref ref-type="aff" rid="a1">1</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Mehla</surname>
<given-names>Kamiya</given-names>
</name>
<xref ref-type="aff" rid="a2">2</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Sykes</surname>
<given-names>David B.</given-names>
</name>
<xref ref-type="aff" rid="a4">4</xref>
<xref ref-type="aff" rid="a5">5</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Hollingsworth</surname>
<given-names>Michael A.</given-names>
</name>
<xref ref-type="aff" rid="a1">1</xref>
</contrib>
<contrib contrib-type="author" corresp="yes">
<contrib-id contrib-id-type="orcid">http://orcid.org/0000-0001-8903-0131</contrib-id>
<name>
<surname>Singh</surname>
<given-names>Pankaj K.</given-names>
</name>
<xref ref-type="aff" rid="a1">1</xref>
<xref ref-type="aff" rid="a2">2</xref>
<xref ref-type="aff" rid="a6">6</xref>
<xref ref-type="aff" rid="a7">7</xref>
<xref ref-type="corresp" rid="cor1">*</xref>
</contrib>
<aff id="a1"><label>1</label><institution>Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center</institution>, Omaha, NE 68198-5950, <country>USA</country></aff>
<aff id="a2"><label>2</label><institution>Department of Oncology Science, University of Oklahoma Health Sciences Center</institution>, Oklahoma City, OK, 73014, <country>USA</country></aff>
<aff id="a3"><label>3</label><institution>Department of Biochemistry and Molecular Biology, University of Iowa</institution>, Iowa City, Iowa, <country>USA</country></aff>
<aff id="a4"><label>4</label><institution>Center for Regenerative Medicine, Massachusetts General Hospital</institution>, Boston, MA, <country>USA</country></aff>
<aff id="a5"><label>5</label><institution>Harvard Stem Cell Institute</institution>, Cambridge, MA, <country>USA</country></aff>
<aff id="a6"><label>6</label><institution>Department of Pathology, University of Oklahoma Health Sciences Center</institution>, Oklahoma City, OK, 73104, <country>USA</country></aff>
<aff id="a7"><label>7</label><institution>OU Health Stephenson Cancer Center, University of Oklahoma Health Sciences Center</institution>, Oklahoma City, OK, 73104, <country>USA</country></aff>
</contrib-group>
<contrib-group content-type="section">
<contrib contrib-type="editor">
<name>
<surname>DeNicola</surname>
<given-names>Gina M</given-names>
</name>
<role>Reviewing Editor</role>
<aff>
<institution-wrap>
<institution>Moffitt Cancer Center</institution>
</institution-wrap>
<city>Tampa</city>
<country>United States of America</country>
</aff>
</contrib>
<contrib contrib-type="senior_editor">
<name>
<surname>Golemis</surname>
<given-names>Erica A</given-names>
</name>
<role>Senior Editor</role>
<aff>
<institution-wrap>
<institution>Fox Chase Cancer Center</institution>
</institution-wrap>
<city>Philadelphia</city>
<country>United States of America</country>
</aff>
</contrib>
</contrib-group>
<author-notes>
<corresp id="cor1"><label>*</label><bold>Correspondence:</bold> Pankaj K. Singh, 940 Stanton L. Young Blvd., BMSB 332A, Department of Oncology Science, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, Email: <email>pankaj-singh@ouhsc.edu</email> Phone: 405.271.8001 x52229</corresp>
</author-notes>
<pub-date date-type="original-publication" iso-8601-date="2023-05-23">
<day>23</day>
<month>05</month>
<year>2023</year>
</pub-date>
<volume>12</volume>
<elocation-id>RP87292</elocation-id>
<history>
<date date-type="sent-for-review" iso-8601-date="2023-04-03">
<day>03</day>
<month>04</month>
<year>2023</year>
</date>
</history>
<pub-history>
<event>
<event-desc>Preprint posted</event-desc>
<date date-type="preprint" iso-8601-date="2023-04-05">
<day>05</day>
<month>04</month>
<year>2023</year>
</date>
<self-uri content-type="preprint" xlink:href="https://doi.org/10.1101/2023.04.03.535399"/>
</event>
</pub-history>
<permissions>
<copyright-statement>© 2023, Mullen et al</copyright-statement>
<copyright-year>2023</copyright-year>
<copyright-holder>Mullen et al</copyright-holder>
<ali:free_to_read/>
<license xlink:href="https://creativecommons.org/licenses/by/4.0/">
<ali:license_ref>https://creativecommons.org/licenses/by/4.0/</ali:license_ref>
<license-p>This article is distributed under the terms of the <ext-link ext-link-type="uri" xlink:href="https://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution License</ext-link>, which permits unrestricted use and redistribution provided that the original author and source are credited.</license-p>
</license>
</permissions>
<self-uri content-type="pdf" xlink:href="elife-preprint-87292-v1.pdf"/>
<abstract>
<title>Abstract</title>
<p>Pyrimidine nucleotide biosynthesis is a druggable metabolic dependency of cancer cells, and chemotherapy agents targeting pyrimidine metabolism are the backbone of treatment for many cancers. Dihydroorotate dehydrogenase (DHODH) is an essential enzyme in the de novo pyrimidine biosynthesis pathway that can be targeted by clinically approved inhibitors. However, despite robust preclinical anticancer efficacy, DHODH inhibitors have shown limited single-agent efficacy in phase I clinical trials. Therefore, novel combination therapy strategies are necessary to realize the potential of these drugs. To search for therapeutic vulnerabilities induced by DHODH inhibition, we examined gene expression changes in cancer cells treated with the potent and selective DHODH inhibitor brequinar (BQ). This revealed that BQ treatment causes upregulation of antigen presentation pathway genes and cell surface MHC class I expression. Mechanistic studies showed that this effect is 1) strictly dependent on pyrimidine nucleotide depletion, 2) independent of canonical antigen presentation pathway transcriptional regulators, and 3) mediated by RNA polymerase II elongation control by positive transcription elongation factor B (P-TEFb). Furthermore, BQ showed impressive single-agent efficacy in the immunocompetent B16F10 melanoma model, and combination treatment with BQ and dual immune checkpoint blockade (anti-CTLA-4 plus anti-PD-1) significantly prolonged mouse survival compared to either therapy alone. Our results have important implications for the clinical development of DHODH inhibitors and provide a rationale for combination therapy with BQ and immune checkpoint blockade.</p>
</abstract>
<kwd-group kwd-group-type="author">
<title>Keywords</title>
<kwd>Pyrimidine biosynthesis</kwd>
<kwd>DHODH</kwd>
<kwd>brequinar</kwd>
<kwd>antigen presentation</kwd>
<kwd>immunotherapy</kwd>
<kwd>MHC class I</kwd>
<kwd>P-TEFb</kwd>
</kwd-group>

</article-meta>
<notes>
<notes notes-type="competing-interest-statement">
<title>Competing Interest Statement</title><p>DBS is a co-founder of and holds equity in Clear Creek Bio</p></notes>
</notes>
</front>
<body>
<sec id="s1">
<title>Introduction</title>
<p>Deranged cellular metabolism is a hallmark of malignant cells <sup><xref ref-type="bibr" rid="c1">1</xref>,<xref ref-type="bibr" rid="c2">2</xref></sup>. The de novo pyrimidine biosynthesis pathway, which generates pyrimidine nucleotides from aspartate and glutamine, is consistently hyperactive in cancer cells and druggable by clinically approved inhibitors <sup><xref ref-type="bibr" rid="c3">3</xref></sup>. Dihydroorotate dehydrogenase (DHODH) catalyzes the fourth step in this pathway and is essential for de novo pyrimidine synthesis. DHODH inhibitors have shown robust preclinical anticancer activity across diverse cancer types <sup><xref ref-type="bibr" rid="c4">4</xref>-<xref ref-type="bibr" rid="c13">13</xref></sup> and have recently entered clinical trials for multiple hematologic cancers (NCT04609826 and NCT02509052). Although there is a vast literature on DHODH inhibitors dating back to the early 1990s, and despite the “rediscovery” of DHODH in recent years as a critical cancer cell metabolic dependency, important questions about the cellular response to DHODH inhibition remain unanswered.</p>
<p>While combination chemotherapy is highly effective and potentially curative against certain cancers (e.g. Hodgkin lymphoma, testicular cancer, childhood leukemia, and others), many common malignancies are refractory to chemotherapy (e.g. lung cancer, pancreatic cancer, colorectal cancer, etc.) <sup><xref ref-type="bibr" rid="c14">14</xref></sup>. In some chemotherapy-refractory cancers, immunotherapeutic strategies have demonstrated strong efficacy and led to durable remissions in a subset of patients <sup><xref ref-type="bibr" rid="c15">15</xref></sup>. The efficacy of immunotherapy agents is dependent on multiple factors, including tumor antigen presentation, limited immune cells in the tumor milieu, and T-cell activation status <sup><xref ref-type="bibr" rid="c16">16</xref>,<xref ref-type="bibr" rid="c17">17</xref></sup>. Adoptive cell therapies and immune checkpoint blockade (ICB) can address the issues of limited immune cell recruitment into tumors and limited T-cell activation, respectively. However, optimal antigen presentation by tumor cells is still needed for immunotherapy efficacy.</p>
<p>The antigen presentation pathway (APP) mediates the presentation of endogenous peptide antigens to CD8 T-cells via MHC class I (MHC-I). This pathway entails the degradation of cellular proteins into small peptides by the proteasome, the import of these peptides into the endoplasmic reticulum by transporter associated with antigen presentation proteins (<italic>TAP1</italic> and <italic>TAP2</italic>), and the loading of these peptides into the MHC-I complex, which consists of a heavy chain (encoded by <italic>HLA-A, HLA-B</italic>, or <italic>HLA-C</italic>) and a light chain (encoded by <italic>B2M</italic>) <sup><xref ref-type="bibr" rid="c18">18</xref></sup>. APP genes are often downregulated in cancer cells, resulting in poor recognition of tumor antigens by immune cells <sup><xref ref-type="bibr" rid="c19">19</xref></sup>. Antigen presentation and T-cell recognition are crucial for T-cell-mediated killing of cancer cells <sup><xref ref-type="bibr" rid="c20">20</xref>-<xref ref-type="bibr" rid="c22">22</xref></sup>, and forced MHC-I expression enhances immunotherapy efficacy in preclinical models <sup><xref ref-type="bibr" rid="c23">23</xref>-<xref ref-type="bibr" rid="c26">26</xref></sup>. Furthermore, high tumoral expression of MHC-I, MHC-II, and other APP genes correlates with better overall survival in patients with melanoma treated with immune checkpoint blockade therapies <sup><xref ref-type="bibr" rid="c27">27</xref>-<xref ref-type="bibr" rid="c30">30</xref></sup>.</p>
<p>While previous reports have shown that pyrimidine nucleotide depletion triggers the expression of innate immunity-related genes and induces an interferon-like response <sup><xref ref-type="bibr" rid="c31">31</xref>-<xref ref-type="bibr" rid="c33">33</xref></sup>, the role of pyrimidine starvation in antigen presentation has not been reported. Herein, we report that DHODH inhibition induces the robust upregulation of APP genes and increases tumor cell antigen presentation. We further explored the mechanism and functional consequences of DHODH inhibitor-mediated APP induction in cancer.</p>
</sec>
<sec id="s2">
<title>Results</title>
<sec id="s2a">
<title>Brequinar induces upregulation of MHC-I and antigen presentation pathway genes</title>
<p>We examined gene expression changes following transient or prolonged DHODH inhibition by culturing human pancreatic ductal adenocarcinoma cell lines S2-013 and CFPAC-1 in the presence of BQ at two different doses for 16 hours and for a two-week duration (<xref rid="fig1" ref-type="fig">Fig 1A</xref>). Gene set enrichment analysis (GSEA) using Hallmark and KEGG gene sets from MSigDB <sup><xref ref-type="bibr" rid="c34">34</xref>,<xref ref-type="bibr" rid="c35">35</xref></sup> revealed 17 gene sets that were significantly upregulated (FDR q &lt; 0.25) across both cell lines following two-week BQ exposure (<xref rid="fig1" ref-type="fig">Fig 1B</xref>). Twelve of these gene sets (highlighted in purple) are ontologically related to antigen presentation and contain MHC class I, MHC class II, and/or APP genes such as <italic>TAP1</italic> in the leading edge. Certain gene sets, such as allograft rejection (KEGG), graft versus host disease (KEGG), and antigen processing and presentation (KEGG) are composed almost entirely of APP genes (<xref rid="fig1" ref-type="fig">Fig 1C</xref>).</p>
<fig id="fig1" position="float" fig-type="figure">
<label>Figure 1:</label>
<caption><title>Brequinar induces mRNA expression of antigen presentation pathway genes and upregulates cell surface MHC-I in diverse cancer cell lines.</title>
<p><bold>A)</bold> Schematic of RNA sequencing experiment for panels B-D, with de novo pyrimidine pathway shown to highlight the role of DHODH <bold>B)</bold> Normalized enrichment scores for gene sets commonly enriched (FDR q &lt; 0.25) in S2-013 (500nM) and CFPAC-1 (250nM) cells following two-week BQ treatment, as assessed by gene set enrichment analysis. <bold>C)</bold> GSEA plots for indicated gene sets following two-week BQ treatment of CFPAC-1 (left) or S2-013 (right) cells at the indicated doses <bold>D)</bold> Heatmap showing log2 fold change mRNA expression of APP genes in CFPAC-1 cells treated with BQ for indicated dose and duration. <bold>E)</bold> Heatmap showing log2 fold change mRNA expression for APP genes in A375 melanoma cells treated with the DHODH inhibitor teriflunomide (25µM) for indicated durations, data extracted from <sup><xref ref-type="bibr" rid="c37">37</xref></sup>. <bold>F)</bold> RT-qPCR quantification of <italic>HLA-A, HLA-B</italic>, and <italic>HLA-C</italic> mRNA levels in cancer cell lines after 24-hour BQ treatment. Numbers represent fold change relative to vehicle control for each cell line. Data are representative of at least 3 independent experiments. <italic>HLA-B</italic> was not detectable in MiaPaCa2 cells. <bold>G-H)</bold> Flow cytometry analysis of cell surface MHC-I in live CFPAC-1 (G) or B16F10 (H) cells following 10-day treatment with BQ (250nM for CFPAC-1 and 10µM for B16F10). <bold>I-J)</bold> LC-MS/MS metabolomics quantification of de novo pyrimidine pathway metabolites in CFPAC-1 (I) or B16F10 (J) cells following 8-hour BQ treatment at indicated doses. Data represent mean +/- SD of four (CFPAC-1) or six (B16F10) biological replicates. # indicates p &lt; 0.0001 by two-way ANOVA with Bonferonni’s post-comparison test.</p></caption>
<graphic xlink:href="535399v1_fig1.tif" mimetype="image" mime-subtype="tiff"/>
</fig>
<p>Heatmap analysis showed that APP genes were robustly upregulated in a dose- and duration-dependent manner in CFPAC-1 (<xref rid="fig1" ref-type="fig">Fig 1D</xref>) and S2-013 (<xref rid="figS1" ref-type="fig">Fig S1A</xref>) cells. The effect size was generally smaller for S2-013 cells, likely because they are resistant to DHODH inhibition due to efficient nucleoside salvage, as we previously reported <sup><xref ref-type="bibr" rid="c36">36</xref></sup>. Publicly available RNA-seq data from human A375 melanoma cells treated with the clinically approved DHODH inhibitor teriflunomide <sup><xref ref-type="bibr" rid="c37">37</xref></sup> corroborated our findings, as teriflunomide caused a rapid (within 12 hours) and time-dependent increase in MHC-I/II and APP transcript levels (<xref rid="fig1" ref-type="fig">Fig 1E</xref>).</p>
<p>We validated these gene expression changes in CFPAC-1 cells by RT-qPCR (<xref rid="figS1" ref-type="fig">Fig S1B</xref>) and then performed RT-qPCR to assess the mRNA levels of genes coding for MHC-I across a panel of human cancer cell lines treated with BQ for 24 hours (<xref rid="fig1" ref-type="fig">Fig 1F</xref>). This confirmed that MHC-I heavy chain transcripts (<italic>HLA-A, HLA-B</italic>, and <italic>HLA-C</italic>) are consistently upregulated in response to BQ across diverse cancer types (<xref rid="fig1" ref-type="fig">Fig 1F</xref>). To optimize conditions for <italic>in vivo</italic> studies, we tested the long-term response and observed that two-week BQ treatment of B16F10 murine melanoma cells also caused dramatic APP gene upregulation (<xref rid="figS1" ref-type="fig">Fig S1C</xref>). Flow cytometry confirmed a marked increase in cell surface MHC-I levels in nonpermeabilized live CFPAC-1 (<xref rid="fig1" ref-type="fig">Fig 1G</xref>) and B16F10 (<xref rid="fig1" ref-type="fig">Fig 1H</xref>) cells following a two-week BQ treatment, confirming that transcriptional upregulation of APP genes results in greater cell surface antigen presentation.</p>
<p>In parallel, we confirmed pyrimidine nucleotide depletion upon treatment with BQ at different doses by performing metabolomics analysis of CFPAC-1 and B16F10 cells following BQ treatment. The results demonstrated a rapid (8-hour treatment) and dose-dependent accumulation of dihydroorotate and N-carbamoyl-aspartate (upstream of DHODH) as well as depletion of pyrimidine nucleotides UTP and CTP (<xref rid="fig1" ref-type="fig">Fig 1I-J</xref>) and other pyrimidine species (<xref rid="figS1" ref-type="fig">Fig S1D-E</xref>). These results confirm on-target DHODH inhibition and resultant pyrimidine nucleotide depletion followed by transcriptional induction of APP genes and enhanced antigen presentation via MHC-I.</p>
</sec>
<sec id="s2b">
<title>BQ-mediated APP induction depends on pyrimidine nucleotide depletion</title>
<p>To confirm that BQ- or teriflunomide-mediated APP induction was specifically related to DHODH inhibition (i.e., on-target effect), we asked whether the effect could be reversed by restoring pyrimidine nucleotides. As we previously observed <sup><xref ref-type="bibr" rid="c36">36</xref></sup>, media supplementation with uridine rescued cell viability (<xref rid="fig2" ref-type="fig">Fig 2A</xref>) and pyrimidine levels (<xref rid="fig2" ref-type="fig">Fig 2B</xref>) following BQ treatment and partially rescued viability following teriflunomide treatment (<xref rid="figS2" ref-type="fig">Fig S2A</xref>). Uridine supplementation likewise blocked mRNA induction of <italic>Nlrc5</italic> (a major MHC-I transcriptional coactivator) and <italic>Tap1</italic> (required for peptide import into the ER, a key step in MHC-I antigen presentation) by BQ or teriflunomide (<xref rid="fig2" ref-type="fig">Fig 2C</xref>), while uridine alone had no effect (<xref rid="figS2" ref-type="fig">Fig S2B</xref>). Concordantly, cell surface MHC-I upregulation by BQ or teriflunomide (24-hour treatment) was abrogated by uridine supplementation (<xref rid="fig2" ref-type="fig">Fig 2D</xref>), while uridine alone again had no effect (<xref rid="figS2" ref-type="fig">Fig S2C</xref>). These results demonstrate that DHODH inhibitor-mediated APP induction is due to pyrimidine nucleotide depletion.</p>
<fig id="fig2" position="float" fig-type="figure">
<label>Figure 2:</label>
<caption><title>BQ-mediated APP induction requires pyrimidine nucleotide depletion.</title>
<p><bold>A)</bold> Dose-response cell viability experiment in B16F10 cells treated with BQ +/- uridine (100µM) for 72 hours. Data represent mean +/- SEM of three biological replicates. One representative result of three independent experiments is shown. <bold>B)</bold> Quantification of pyrimidine metabolites following 24-hour treatment of B16F10 cells with vehicle, BQ (10µM), or BQ + uridine (100µM). Data represent mean +/- SEM of six biological replicates. # indicates p &lt; 0.0001 by two-way ANOVA with Bonferonni post-comparison test. <bold>C)</bold> RT-qPCR of indicated genes in B16F10 cells following 24-hour treatment with BQ or teriflunomide (100µM) +/- uridine (100µM) as in (B). Data represent mean +/- SEM of four technical replicates. One representative result of three independent experiments is shown. <bold>D)</bold> Left: flow cytometry analysis of cell surface MHC-I (H2-Db) on live B16F10 cells following 24-hour treatment with indicated agents (BQ 10µM, teriflunomide 100µM, uridine 1mM). Right: quantification of H2-Db mean fluorescence intensity normalized to vehicle control. Data represent mean +/- SEM of three independent experiments. # indicates p &lt; 0.0001 with two-way ANOVA with Bonferroni post-comparison test. <bold>E)</bold> RT-qPCR analysis of indicated genes in S2-013 cells with DHODH knockout (sgDHODH) or non-targeting control vector (sgNT) treated with indicated agents for 72 hours. Data represent mean +/- SD of four determinations. One representative result of three independent experiments is shown. <bold>F)</bold> RT-qPCR analysis of indicated genes in CFPAC-1 cells following 72-hour treatment with indicated agents. Numbers in the heatmap represent mean fold change versus vehicle control with four determinations.</p></caption>
<graphic xlink:href="535399v1_fig2.tif" mimetype="image" mime-subtype="tiff"/>
</fig>
<p>To further validate this finding, we assessed MHC-I heavy chain mRNA levels in S2-013 cells with DHODH deletion (sgDHODH). We have previously demonstrated that these cells require exogenous uridine for viability and experience profound pyrimidine depletion (&gt;95% depletion of UTP and CTP) after 8-hour incubation in nucleoside-free media <sup><xref ref-type="bibr" rid="c36">36</xref></sup>. After growing these cells with supplemented uridine (1 mM), we withdrew exogenous nucleosides by changing to new media containing 10% dialyzed FBS. After 72-hour exposure to nucleoside-free media, sgDHODH cells upregulated <italic>HLA-A, HLA-B</italic>, and <italic>HLA-C</italic>, and this was reversed by adding back uridine (<xref rid="fig2" ref-type="fig">Fig 2E</xref>).</p>
<p>Importantly, treatment with BQ did not further increase MHC-I mRNA expression (<xref rid="fig2" ref-type="fig">Fig 2E</xref>, compare blue and red bars). Together with our other data, these results indicate that BQ-mediated APP induction is an on-target phenomenon with respect to DHODH inhibition.</p>
<p>Since uridine addback rescued BQ- and teriflunomide-mediated loss of viability (<xref rid="fig2" ref-type="fig">Fig 2A</xref>, <xref ref-type="fig" rid="figS2">S2A</xref>), we queried whether BQ-mediated APP induction was caused by pyrimidine depletion <italic>per se</italic>, or if it was the result of some nonspecific downstream consequence of pyrimidine starvation, such as DNA damage or loss of cell viability. To address this, we screened a panel of genotoxic chemotherapy agents and small molecule inhibitors for their ability to induce APP genes following 72-hour exposure at previously determined cytotoxic doses in CFPAC-1 cells (<xref rid="fig2" ref-type="fig">Fig 2F</xref>). Besides interferon gamma (a positive control), BQ, teriflunomide, and GSK983 (another DHODH inhibitor), the only agent that induced APP gene transcription in this assay was mycophenolate, a clinically approved inhibitor of the <italic>de novo</italic> GTP synthesis enzymes inosine monophosphate dehydrogenase 1 and 2 (IMPDH1/2). The effect of mycophenolate on APP gene expression was subsequently validated in B16F10 cells (<xref rid="figS2" ref-type="fig">Fig S2D</xref>), demonstrating that either purine or pyrimidine nucleotide depletion can induce cancer cell APP mRNA expression <italic>in vitro</italic>.</p>
<p>The other drugs screened included nucleotide synthesis inhibitors (5-fluorouracil, methotrexate, gemcitabine, and hydroxyurea), DNA damage inducers (oxaliplatin, irinotecan, and cytarabine), a microtubule targeting drug (paclitaxel), a DNA methylation inhibitor (azacytidine), and other small molecule inhibitors (<xref rid="fig2" ref-type="fig">Fig 2F</xref>). While we cannot rule out the possibility that these agents induce APP transcription in other cell lines or under other dose/duration conditions, the inertness of these compounds (with respect to APP gene expression) in our screen suggests that BQ-mediated APP induction in CFPAC-1 cells is not a general phenomenon that occurs downstream of DNA damage or some other response to therapy-induced stress.</p>
</sec>
<sec id="s2c">
<title>BQ-mediated APP induction does not depend on canonical APP transcriptional regulators</title>
<p>To elucidate the molecular pathway leading to APP induction downstream of pyrimidine depletion, we extended our findings to HEK-293T cells, which also display rapid (within 4 hours) transcriptional induction of MHC-I upon BQ treatment (<xref rid="figS3" ref-type="fig">Fig S3A</xref>). Reasoning that the mechanism of this phenomenon in HEK-293T cells is less likely to involve idiosyncratic genetic aberrations than in cancer cell lines, we chose to conduct our initial mechanistic studies in this system and then extend our findings to cancer cell lines if possible.</p>
<p>We used a candidate-based chemical biology screening approach to ask if drugs targeting suspected pathways might block BQ-mediated APP induction in HEK-293T cells. We first interrogated pathways that are known to control MHC/APP expression, including IFN-JAK-STAT <sup><xref ref-type="bibr" rid="c38">38</xref></sup>, NF-κB <sup><xref ref-type="bibr" rid="c26">26</xref>,<xref ref-type="bibr" rid="c39">39</xref></sup>, and cGAS-STING-TBK1 <sup><xref ref-type="bibr" rid="c40">40</xref></sup>. Neither ruxolitinib (a JAK1/2 inhibitor with activity against STAT3) nor GSK8612 (a TBK1 inhibitor) <sup><xref ref-type="bibr" rid="c41">41</xref></sup>, nor TPCA-1 (an IKK2 inhibitor) <sup><xref ref-type="bibr" rid="c42">42</xref></sup> abrogated BQ-mediated APP induction (<xref rid="fig3" ref-type="fig">Fig 3A</xref>), despite blocking APP induction downstream of poly(dA:dT) and interferon gamma (<xref rid="figS3" ref-type="fig">Fig S3B</xref>) as expected. This indicates that these canonical regulators of MHC/APP expression are dispensable for APP induction downstream of DHODH inhibition.</p>
<fig id="fig3" position="float" fig-type="figure">
<label>Figure 3:</label>
<caption><title>IKK2 inhibitor BMS-345541 abrogates BQ-mediated APP induction in an IKK2-independent manner.</title>
<p><bold>A-B)</bold> HEK-293T cells were treated with indicated agents for 24 hours and then subjected to RT-qPCR analysis for indicated genes. Numbers in the heatmap represent mean of four determinations. <bold>C-E, G)</bold> B16F10 (C), CFPAC-1 (D), HCT116 (E) or MiaPaCa2-IKK2-KO (G) cells were treated with indicated agents for 24 hours and subjected to RT-qPCR analysis of indicated genes. Data in D,E, and G represent mean +/- SD of three independent experiments. * indicates p &lt; 0.05, ** p &lt; 0.01, *** p &lt; 0.001, and # p &lt; 0.0001 with two-way ANOVA with Bonferroni post-comparison test. For C, numbers in the heatmap represent mean fold change versus vehicle with three determinations. Representative result of three independent experiments is shown. <bold>F)</bold> Flow cytometry analysis of cell surface MHC-I in HCT116 cells treated with indicated agents for 24 hours.</p></caption>
<graphic xlink:href="535399v1_fig3.tif" mimetype="image" mime-subtype="tiff"/>
</fig>
<p>Interestingly, the IKK2 inhibitor BMS-345541 <sup><xref ref-type="bibr" rid="c43">43</xref></sup> mostly abrogated BQ-mediated APP induction (<xref rid="fig3" ref-type="fig">Fig 3A</xref>). BMS-345541 effectively blocked BQ- and Ter-mediated APP induction at concentrations of 10 µM and 40 µM, but not 2.5 µM (<xref rid="fig3" ref-type="fig">Fig 3B</xref>). The effect of BMS-345541 was confirmed in B16F10 (<xref rid="fig3" ref-type="fig">Fig 3C</xref>), CFPAC-1 (<xref rid="fig3" ref-type="fig">Fig 3D</xref>), and HCT116 (<xref rid="fig3" ref-type="fig">Fig 3E</xref>) cells. Furthermore, BQ treatment (24 hours) of HCT116 cells caused increased cell surface expression of MHC-I, which could be reversed by either uridine supplementation or by treatment with BMS-345541; neither uridine nor BMS-345541 alone affected cell surface MHC-I expression (<xref rid="fig3" ref-type="fig">Fig 3F</xref>).</p>
<p>Given that TPCA-1 (an established IKK2 inhibitor <sup><xref ref-type="bibr" rid="c42">42</xref></sup>) did not block BQ-mediated APP induction (<xref rid="fig3" ref-type="fig">Fig 3A</xref>, <xref ref-type="fig" rid="fig3">3C</xref>), we suspected that this effect of BMS-345541 was independent of IKK2. To test this, we used previously reported MiaPaCa2 cells with CRISPR-Cas9 deletion of <italic>IKK2</italic> (MiaPaCa2-<italic>IKK2</italic>-KO) <sup><xref ref-type="bibr" rid="c44">44</xref></sup>. Increased APP mRNA expression was observed upon BQ, teriflunomide, or GSK983 treatment (all DHODH inhibitors) of either wild-type or <italic>IKK2</italic>-KO MiaPaCa2 cells (<xref rid="figS3" ref-type="fig">Fig S3C</xref>). However, while TNF-alpha stimulation induced APP and <italic>CCL5</italic> (a canonical NF-κB target gene downstream of TNF-alpha <sup><xref ref-type="bibr" rid="c45">45</xref></sup>) expression in wild-type cells, this was not observed in <italic>IKK2</italic>-KO cells, as expected (<xref rid="figS3" ref-type="fig">Fig S3C</xref>, far right). Finally, BQ-mediated APP induction in <italic>IKK2</italic>-KO cells was significantly reversed with concurrent BMS-345541 treatment (<xref rid="fig3" ref-type="fig">Fig 3G</xref>). Together, these results demonstrate that IKK2 is dispensable for BQ-mediated APP induction and that the observed reversal effect of BMS-345541 is independent of IKK2.</p>
</sec>
<sec id="s2d">
<title>Nucleotide starvation induces APP transcription in a P-TEFb-dependent manner</title>
<p>To further investigate the mechanism by which BMS-345541 blocks APP induction downstream of pyrimidine starvation, we leveraged publicly available data on the target profile of BMS-345541 and other agents tested in the cell-free KINOMEscan assay <sup><xref ref-type="bibr" rid="c46">46</xref></sup>. BMS-345541 reproducibly bound more than 20 kinases, with dissociation constants (Kd) ranging from 130-8100 nM (<xref rid="fig4" ref-type="fig">Fig 4A</xref>). We prioritized potential targets with a Kd in the low micromolar range, given that 2.5 µM BMS-345541 did not block BQ-mediated APP induction in our previous experiments, and the effect seemed to be maximal at 10 µM, with no significant increase in the magnitude of the effect between 10 µM and 40 µM (<xref rid="fig3" ref-type="fig">Fig 3B</xref>). Additionally, we prioritized targets that were &gt;50% inhibited with 10 µM BMS-345541 treatment. These two conditions correspond to the upper left quadrant of <xref rid="fig4" ref-type="fig">Fig 4A</xref>.</p>
<fig id="fig4" position="float" fig-type="figure">
<label>Figure 4:</label>
<caption><title>P-TEFb inhibitor flavopiridol abrogates APP induction downstream of nucleotide depletion.</title>
<p><bold>A)</bold> Plot of percent inhibition (10µM treatment) vs -log(dissociation constant) for kinases bound by BMS-345541 in KINOMEscan assays <sup><xref ref-type="bibr" rid="c46">46</xref></sup>. Each data point represents an individual kinase. <bold>B-</bold>RT-qPCR analysis for indicated genes in HEK-293T cells treated with indicated agents for 24 hours. Data represent mean +/- SD of three independent experiments. # indicates p &lt; 0.0001 by two-way ANOVA with Bonferonni’s post-comparison test <bold>D)</bold> Western blot analysis for CDK9 performed on HEK-293T cells treated with CDK9-targeted PROTAC (PROTAC2) and/or pomalidomide (POM) for 24 hours. Beta actin was used as a loading control. <bold>E)</bold> Visualization of Pol II occupancy after 48-hour treatment with teriflunomide (red) or vehicle control (blue) in A375 melanoma cells reported by Tan et al <sup><xref ref-type="bibr" rid="c37">37</xref></sup>.</p></caption>
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</fig>
<p>One potential target that met the selection criteria was CDK9, which together with cyclin T1 or T2 forms positive transcription elongation factor B (P-TEFb). P-TEFb is required for the release of promoter-proximal paused RNA polymerase II (Pol II) into productive elongation and therefore is essential for Pol II transcription from paused promoters <sup><xref ref-type="bibr" rid="c47">47</xref>,<xref ref-type="bibr" rid="c48">48</xref></sup>. The potent P-TEFb inhibitor flavopiridol <sup><xref ref-type="bibr" rid="c49">49</xref></sup> phenocopied BMS-345541 in our assays, as it blocked APP induction downstream of DHODH, IMPDH1/2 (by mycophenolate), or CTP synthase (by 3-deazauridine <sup><xref ref-type="bibr" rid="c50">50</xref></sup>) inhibition (<xref rid="figS4" ref-type="fig">Fig S4A</xref>). This suggests that APP induction downstream of nucleotide starvation requires P-TEFb-mediated paused Pol II release. It also suggests that the BMS-345541 effect of reversing BQ-induced APP upregulation is due to P-TEFb inhibition.</p>
<p>Within the list of kinases bound by BMS-345541 (<xref rid="fig4" ref-type="fig">Fig 4A</xref>) we eliminated those that were a) not expressed by CFPAC-1 cells in our RNA-seq data, b) not bound by flavopiridol in KINOMEscan data, or c) bound by ruxolitinib in KINOMEscan data with Kd &lt; 500 nM (as 2.5 µM ruxolitinib failed to reverse BQ-mediated APP induction (<xref rid="fig3" ref-type="fig">Fig 3A</xref>)). Five candidates (besides CDK9) remained that were bound by both BMS-345541 and flavopiridol in KINOMEscan assays. Of these, three are CDKs known to play a role in transcription (CDK7, CDK13, and CDK16). Inhibition of any of these CDKs could theoretically account for the observed effects of flavopiridol and BMS-345541. However, previous studies suggest that flavopiridol inhibition of these CDKs in vivo is much less efficient than in cell-free assays because it is competitive with ATP (and thus less efficient in living cells where the ATP concentration is in the 1-10 mM range, which is much higher than in cell-free assay conditions), while its inhibition of P-TEFb is not affected by ATP concentration <sup><xref ref-type="bibr" rid="c49">49</xref></sup>. Furthermore, flavopiridol and the CDK7 inhibitor THZ1 have very different (and mutually exclusive) effects on transcriptional processes <sup><xref ref-type="bibr" rid="c51">51</xref></sup>, arguing against CDK7 inhibition as the mechanism of flavopiridol’s effect.</p>
<p>To further probe whether the observed effect of flavopiridol was due to CDK9 inhibition, we tested two other CDK9 inhibitors (AT7519 and dinaciclib). Both CDK9 inhibitors phenocopied flavopiridol in our assays (<xref rid="fig4" ref-type="fig">Fig 4B</xref>). Furthermore, a previously characterized CDK9-targeted proteolysis targeting chimera (PROTAC), termed PROTAC2 <sup><xref ref-type="bibr" rid="c52">52</xref></sup>, had the same effect (<xref rid="fig4" ref-type="fig">Fig 4B</xref>). PROTAC2 consists of a CDK9-binding aminopyrazole warhead conjugated to pomalidomide, which recruits the E3 ubiquitin ligase Cereblon (<italic>CRBN</italic>). Cereblon in turn ubiquitinates CDK9, resulting in its proteasomal degradation. Co-treatment of HEK-293 cells with PROTAC2 and pomalidomide prevents PROTAC2-mediated CDK9 degradation, as free pomalidomide competes with PROTAC2 for Cereblon binding <sup><xref ref-type="bibr" rid="c52">52</xref></sup>. We observed that PROTAC2 (1 µM) blocked BQ-mediated APP induction, and this effect was reversed by co-treatment with 10-fold excess pomalidomide (10 µM); however, when we increased the concentration of PROTAC2 to 10 µM (so that PROTAC2 and pomalidomide concentrations were equal), pomalidomide no longer had this effect (<xref rid="fig4" ref-type="fig">Fig 4C</xref>). Consistently, immunoblot analysis showed that 10 µM pomalidomide prevents CDK9 degradation upon 1 µM but not 10 µM PROTAC2 treatment (<xref rid="fig4" ref-type="fig">Fig 4D</xref>). Taken together, these results demonstrate that CDK9 degradation is necessary for the reversal effect of PROTAC2 and that CDK9 is required for BQ-mediated APP induction.</p>
<p>The dependence of BQ-mediated APP induction on CDK9 strongly suggests that nucleotide starvation enforces nascent transcription of APP genes, as opposed to increased mRNA stability. This is further supported by the rapid buildup of APP transcripts following DHODH inhibitor treatment (within 4 hours, <xref rid="figS3" ref-type="fig">Fig S3A</xref>). Additionally, ChIP-seq analysis of global Pol II occupancy following 48-hour teriflunomide treatment in A375 cells <sup><xref ref-type="bibr" rid="c37">37</xref></sup> shows increased Pol II engagement in the promoter-proximal pause region and gene body of many APP genes, including <italic>HLA-B</italic> (<xref rid="fig4" ref-type="fig">Fig 4E</xref>). Overall, these results show that nucleotide starvation induces an antigen presentation gene expression program that is independent of canonical APP regulators but depends on CDK9/P-TEFb.</p>
</sec>
<sec id="s2e">
<title>BQ suppresses tumor growth, induces MHC-I expression, and increases immunotherapy efficacy in a syngeneic melanoma model</title>
<p>Enforced MHC-I upregulation by various interventions can facilitate anticancer immunity and enhance the efficacy of immune checkpoint blockade (ICB) by antibodies directed at PD-(L)1 and/or CTLA-4 <sup><xref ref-type="bibr" rid="c23">23</xref>-<xref ref-type="bibr" rid="c26">26</xref></sup>. Moreover, high MHC-I expression has been proposed as a predictor of ICB response <sup><xref ref-type="bibr" rid="c27">27</xref>-<xref ref-type="bibr" rid="c30">30</xref></sup>, and high expression of MHC-I and other APP genes, including <italic>NLRC5</italic> and <italic>TAP1</italic>, correlates with better survival in patients with melanoma (<xref rid="figS5" ref-type="fig">Fig S5A</xref>), for whom ICB is a first-line therapy. Therefore, we asked if BQ could improve anticancer immunity in the B16F10 melanoma immunocompetent mouse model, which is typically refractory to dual ICB (i.e., anti-PD-1 plus anti-CTLA-4) <sup><xref ref-type="bibr" rid="c53">53</xref></sup>. BQ (10 mg/kg daily IP injection) markedly suppresses tumor growth and leads to reduced tumor burden (<xref rid="fig5" ref-type="fig">Fig 5A-B</xref>). Historically, the lead tool compound that was ultimately modified to BQ (called NSC 339768) was prioritized in part based on its activity against B16 melanoma <sup><xref ref-type="bibr" rid="c54">54</xref></sup>; to our knowledge, this is the first direct demonstration of BQ activity in this model system. Consistent with our <italic>in vitro</italic> metabolomics data (<xref rid="fig1" ref-type="fig">Fig 1I-J</xref>, <xref ref-type="fig" rid="figS1">S1B</xref>), BQ treatment caused marked buildup of metabolites upstream of DHODH and depletion of downstream pyrimidine nucleotide species in B16F10 tumors (<xref rid="fig5" ref-type="fig">Fig 5C</xref>), confirming target engagement <italic>in vivo</italic>. Metabolomics analysis of BQ- and vehicle-treated tumors separated in principal component analysis (<xref rid="figS5" ref-type="fig">Fig S5B</xref>) and unsupervised hierarchical clustering (<xref rid="figS5" ref-type="fig">Fig S5C</xref>), confirming the perturbation of tumor metabolism following DHODH inhibition.</p>
<fig id="fig5" position="float" fig-type="figure">
<label>Figure 5:</label>
<caption><title>BQ inhibits tumor growth, increases tumor MHC-I, and enhances immune checkpoint blockade efficacy in B16F10 murine melanoma model.</title>
<p><bold>A-D)</bold> B16F10 cells were injected subcutaneously into syngeneic hosts and mice were treated with brequinar (BQ; 10mg/kg IP daily) or vehicle control starting at day 7 post implantation. <bold>A)</bold> Longitudinal measurement of B16F10 subcutaneous tumors with BQ (10mg/kg IP daily) or vehicle treatment. <bold>B)</bold> Weight (left) and volume (right) of tumors at necropsy. <bold>C)</bold> Quantification of metabolites from B16F10 tumors harvested at necropsy. <bold>D)</bold> RT-qPCR analysis of APP genes from tumors harvested at necropsy. For (A-D), data represent mean +/- SD of n = 5 mice per group (n = 4 for BQ group in C). * indicates p &lt; 0.05, ** p &lt; 0.01, *** p &lt; 0.001, and **** p &lt; 0.0001 by unpaired t-test. <bold>E)</bold> Kaplan-Meier survival analysis for mice implanted with B16F10 tumors as in (A-D) and treated with indicated regimens; see <xref ref-type="fig" rid="figS5">Fig S5D</xref> for treatment timeline. * indicates p &lt; 0.05, # p &lt; 0.0001 by Mantel-Cox logrank test. For vehicle, immune checkpoint blockade (ICB; Anti-CTLA-4 and anti-PD-1; 100µg/mouse each, IP twice per week), and BQ (10mg/kg IP daily) + concurrent ICB, n = 15. For BQ, n = 7. For BQ + delayed ICB, n = 8.</p></caption>
<graphic xlink:href="535399v1_fig5.tif" mimetype="image" mime-subtype="tiff"/>
</fig>
<p>BQ-treated B16F10 tumors showed increased mRNA expression of MHC-I (<italic>H2-Db</italic> and <italic>H2-Kb</italic>) and <italic>Nlrc5</italic> (<xref rid="fig5" ref-type="fig">Fig 5D</xref>). We thus addressed whether BQ could augment the efficacy of dual ICB (anti-CTLA-4 plus anti-PD-1) with the knowledge that enforced MHC-I antigen presentation has also been shown to boost the effect of ICB <sup><xref ref-type="bibr" rid="c23">23</xref>,<xref ref-type="bibr" rid="c25">25</xref>,<xref ref-type="bibr" rid="c26">26</xref></sup>. While BQ is not an approved medication, two FDA-approved low potency DHODH inhibitors (leflunomide, teriflunomide) are effective in treating autoimmune conditions such as rheumatoid arthritis and multiple sclerosis and act to decrease the activity of auto-reactive T-lymphocytes <sup><xref ref-type="bibr" rid="c55">55</xref>-<xref ref-type="bibr" rid="c57">57</xref></sup>. It was possible that BQ treatment may actually impair the effectiveness of ICB by inhibiting T-lymphocytes despite augmented cancer cell antigen presentation. We, therefore, tested both concurrent, upfront administration of BQ plus dual ICB and sequential administration of BQ followed by dual ICB (<xref rid="figS5" ref-type="fig">Fig S5D</xref>).</p>
<p>Similar to its impressive activity in our first experiment (<xref rid="fig5" ref-type="fig">Fig 5A-B</xref>), BQ monotherapy conferred marked survival benefit. This was significantly enhanced by subsequent dual ICB, while dual ICB alone conferred only marginally prolonged survival, and concurrent BQ plus dual ICB did not significantly improve survival versus BQ monotherapy (<xref rid="fig5" ref-type="fig">Fig 5E</xref>). This suggests that sequential (rather than concurrent) administration of DHODH inhibitor and ICB may be superior. Hypotheses that may explain these findings include: a) Concurrent BQ dampens the initial anticancer immune response generated by dual ICB, or b) cancer cell MHC-I and related genes are not maximally upregulated at the time of ICB administration with concurrent treatment. Taken together, these results show that BQ causes pyrimidine nucleotide depletion, MHC-I and APP gene transcriptional upregulation, and additive survival benefit with dual ICB in a highly aggressive and ICB-refractory mouse melanoma model.</p>
</sec>
</sec>
<sec id="s3">
<title>Discussion</title>
<p>Our results demonstrate that pyrimidine nucleotide depletion by DHODH inhibition causes increased expression of APP genes and increased cell surface abundance of MHC-I across a diverse panel of cancer cell lines. This effect is strictly dependent on pyrimidine nucleotide depletion, as it was abrogated by restoration of pyrimidine levels with exogenous uridine. Our inhibitor reversal studies determined that BQ-mediated APP induction is independent of several canonical APP regulatory pathways, including IFN-JAK-STAT, cGAS-STING-TBK1, and NF-κB. We showed that this effect relies on P-TEFb-mediated release of Pol II from promoter-proximal paused state to productive elongation.</p>
<p>These findings were extended to inhibition of IMPDH (which depletes cellular GTP) and CTPS (which depletes cellular CTP), as these effects were also reversible with P-TEFb inhibition (<xref rid="figS4" ref-type="fig">Fig S4A</xref>). This suggests that pharmacologic depletion of these nucleotides also triggers APP upregulation in a P-TEFb-dependent manner. Since T cell recognition of antigens via MHC-I is required for T cell-mediated elimination of cancer cells or virus-infected cells, these results have important implications for the development of nucleotide synthesis inhibitors as anticancer/antiviral therapies. We provide proof of concept evidence that pretreatment with DHODH inhibitors can improve the efficacy of immune checkpoint blockade in a highly aggressive and ICB-refractory mouse melanoma model.</p>
<p>Immune checkpoint blockade has revolutionized cancer immunotherapy and has led to long-term, durable remission for a subset of patients with metastatic melanoma and other malignancies.</p>
<p>However, only a subset of patients treated with ICB respond. Emerging evidence suggests that cancer cell MHC-I expression predicts favorable response to ICB, and several recent studies have shown that enforced cancer cell MHC-I expression enhances anticancer immunity and ICB efficacy in various mouse models. Accordingly, functional genomic screens for regulators of cancer cell MHC-I expression have recently been undertaken, and these efforts have revealed novel molecular targets to induce cancer cell APP activity <sup><xref ref-type="bibr" rid="c26">26</xref>,<xref ref-type="bibr" rid="c58">58</xref></sup>. Agents shown to increase cancer cell antigen presentation include hydroxychloroquine (by autophagy inhibition) <sup><xref ref-type="bibr" rid="c23">23</xref></sup>, poly(I:C) (by NF-κB activation downstream of dsRNA sensing) <sup><xref ref-type="bibr" rid="c25">25</xref></sup>, SMAC mimetics (by NF-κB activation) <sup><xref ref-type="bibr" rid="c26">26</xref></sup>, CDK4/6 inhibitors (by activation of endogenous genomic retroviral elements) <sup><xref ref-type="bibr" rid="c24">24</xref></sup>, and others. It is very likely that many other anticancer drugs perturb cancer cell antigen presentation and/or have other immunomodulatory properties in addition to their cell-intrinsic antiproliferative activity <sup><xref ref-type="bibr" rid="c59">59</xref></sup>, and this area requires further scrutiny. In this study, we identified DHODH inhibition as a powerful inducer of antigen presentation and MHC-I expression in diverse cancer cell lines and in HEK-293T cells.</p>
<p>Previous studies have linked pyrimidine depletion with upregulation of innate immunity and interferon-stimulated genes <sup><xref ref-type="bibr" rid="c32">32</xref>,<xref ref-type="bibr" rid="c33">33</xref></sup>, and this was confirmed by our transcriptomic profiling experiments (<xref rid="fig1" ref-type="fig">Fig 1B-C</xref>). However, the mechanistic explanation for these observations varies. Lucas-Hourani et al. proposed that interferon-stimulated gene expression requires the DNA damage checkpoint kinase ATM <sup><xref ref-type="bibr" rid="c32">32</xref></sup>, while Sprenger et al. conclude that pyrimidine depletion causes accumulation of mitochondrial DNA in the cytosol, which is sensed by the cGAS-STING-TBK1 pathway to promote innate immunity <sup><xref ref-type="bibr" rid="c33">33</xref></sup>. In our models, neither ATM/ATR nor TBK1 inhibition blocked BQ-mediated APP induction (<xref rid="fig4" ref-type="fig">Fig 4A</xref>), It is possible that pyrimidine nucleotide shortage leads to APP induction by multiple redundant mechanisms, any of which may predominate based on the cellular context. We speculate that cells may have evolved multiple means of sensing acute pyrimidine shortage as a way to detect viral infection or malignant transformation (as both viral replication and uncontrolled cell proliferation avidly consume nucleotides).</p>
<p>Our focused chemical screen for MHC-I inducers (<xref rid="fig2" ref-type="fig">Fig 2F</xref>) identified the approved IMPDH1/2 inhibitor mycophenolate, which was subsequently validated in multiple other cell types (<xref rid="figS2" ref-type="fig">Fig S2D</xref>, <xref ref-type="fig" rid="figS4">S4A</xref>). This is consistent with a recent study in which IMPDH inhibition was shown to enhance ICB efficacy by favorably altering the MHC-I peptide repertoire and increasing immunoproteasome expression <sup><xref ref-type="bibr" rid="c60">60</xref></sup>.</p>
<p>However, in this study, the cancer cells were pretreated with IMPDH inhibitor before implantation into syngeneic hosts, and so possible countervailing immunosuppression by systemic IMPDH inhibitor treatment was not addressed <sup><xref ref-type="bibr" rid="c60">60</xref></sup>. Our <italic>in vivo</italic> results (<xref rid="fig5" ref-type="fig">Fig 5F</xref>) highlight the importance of timing/sequence when administering immunotherapy in combination with nucleotide synthesis inhibitors and suggest that upfront BQ followed by ICB may be superior to concurrent administration.</p>
<p>Thymidylate synthase inhibition was recently shown to induce MHC-I in a model of diffuse large B cell lymphoma <sup><xref ref-type="bibr" rid="c58">58</xref></sup>. The failure of thymidylate synthase inhibitors 5-fluorouracil and methotrexate to induce MHC-I in our screen (<xref rid="fig2" ref-type="fig">Fig 2F</xref>) may be attributable to cell line differences (PDAC vs DLBCL), dose/duration considerations, or the use of different thymidylate synthase inhibitors than in their study (which used pemetrexed and raltitrexed). Thus, it appears that nucleotide abundance exerts context-dependent influence on MHC and APP gene expression, and key details of this relationship remain to be elucidated.</p>
<p>Overall, our study establishes P-TEFb and Pol II elongation control as a mechanistic link between nucleotide depletion and APP induction. We provide proof of concept evidence for combinatorial benefit of DHODH inhibition and immune checkpoint blockade in an aggressive and poorly immunogenic mouse model of melanoma. A deeper understanding of metabolic control of antigen presentation will enable rational therapy development for cancer and viral infection.</p>
</sec>
<sec id="s4">
<title>Materials and Methods</title>
<sec id="s4a">
<title>Cell culture and cell lines</title>
<p>The S2-013 cell line is a clonal derivative of the Suit2 cell line and was a kind gift from the Tony Hollingsworth laboratory at the University of Nebraska Medical Center. The MiaPaCa2 <italic>IKK2</italic>-KO and parental wild-type MiaPaCa2 cell lines were a kind gift from the Amar Natarajan laboratory at the University of Nebraska Medical Center. All other cell lines in this study were obtained from American Type Culture Collection (Manassas, VA, USA). All human cell lines were authenticated by STR profiling by the Genetics Core at the University of Arizona. Cells were routinely (at the time of initial revival from liquid nitrogen storage and at least every 6 months) determined to be free of mycoplasma contamination by PCR-based methods. Cells were cultured in Dulbecco’s modified Eagle medium (Sigma-Aldrich, St Louis, MO, USA) supplemented with 50 IU/mL penicillin, 50 μg/mL streptomycin, and incubated at 37 °C in a humidified incubator with 5% CO<sub>2</sub>. Cells were maintained at 10% fetal bovine serum (FBS). Upon reaching 70–80% confluency, cells were passaged by washing with phosphate-buffered saline (PBS) before adding 0.25% trypsin (Caisson Labs, Smithfield, UT, USA) and plating at 25% confluency.</p>
</sec>
<sec id="s4b">
<title>Drug treatment of cultured cells for RT-qPCR and flow cytometry experiments</title>
<p>Drug treatment dose and duration are indicated for each experiment. A table of manufacturer and catalog number for each agent described can be found in Supplementary Table 1. For stimulation with poly(dA:dT), 2µg of poly(dA:dT) and 2µl of Lipofectamine2000 (Invitrogen #11668027) were incubated in 400µl Opti-MEM (Gibco #11058021) for 30 minutes at room temperature and then added to cells in 2ml final volume of complete media.</p>
</sec>
<sec id="s4c">
<title>Cell viability assays</title>
<p>Cells were seeded in 96 well plates (1000 cells per well in 90µl media) and allowed to equilibrate overnight. Cells were then treated with indicated compounds (final volume 100µl) for 72 hours, and viability was assessed by CellTiter-Glo assay (Promega, Madison, WI). Luminescence values for each condition were normalized to the average luminescence of the vehicle-treated control replicates.</p>
<p>Experiments were performed at least three times using biological triplicates for each condition. Dose-response curves were fit to nonlinear regression models using Prism9 software.</p>
</sec>
<sec id="s4d">
<title>Liquid chromatography – tandem mass spectrometry-based metabolomics analysis</title>
<p>For in vitro metabolomics experiments, 5 × 10<sup>5</sup> cells were seeded in 6-well plates and allowed to equilibrate overnight. At the start of each assay, the cell culture media was changed, and fresh media with desired conditions was added (to eliminate metabolite depletion from overnight equilibration as a confounding variable). Following 8-hour treatment of cancer cell lines with BQ (or in the case of <xref rid="fig2" ref-type="fig">Fig 2B</xref>, 24-hour treatment with BQ +/- 100µM uridine), polar metabolites were extracted and quantified as previously described <sup><xref ref-type="bibr" rid="c61">61</xref></sup>. For B16F10 tumor metabolomics, subcutaneous tumors were harvested at necropsy and immediately snap frozen in liquid nitrogen and stored at -80 °C. Tumors were subsequently ground into fine powder in liquid nitrogen using a mortar and pestle, and metabolites were extracted using the same method as for cultured cells. Peak areas were normalized to the mass of tumor tissue that was input.</p>
<p>Datasets were processed using Skyline (MacCoss Lab Software), and Metaboanalyst5.0 web tool was used to generate principal component analysis and heatmap visualizations of resulting datasets. Raw LC-MS/MS data and R-command history for Metaboanalyst analysis are available upon request. Relative metabolite abundances were normalized to the average peak area of the experimental control group and were compared using two-way ANOVA with Bonferonni’s post-test correction for multiple comparisons. P &lt; 0.05 was considered significant.</p>
</sec>
<sec id="s4e">
<title>Mice studies</title>
<p>For animal studies, 10<sup>4</sup> B16F10 cells in a 1:1 vol/vol ratio (100µl final volume) with Matrigel were injected subcutaneously into the right flank of 10-week-old female C57BL/6J mice (Jackson labs). Tumors of live mice were serially measured in two dimensions using digital calipers, and tumor volume for <xref rid="fig5" ref-type="fig">Fig 5A</xref> was calculated as (0.5L x W<sup><xref ref-type="bibr" rid="c2">2</xref></sup>), where L is the long dimension and W is the short dimension. For <xref rid="fig5" ref-type="fig">Fig 5B-C</xref>, tumors were harvested at necropsy, weighed on an analytical balance (for <xref rid="fig5" ref-type="fig">Fig 5B</xref>), and measured in three perpendicular dimensions by calipers to generate volume measurements for <xref rid="fig5" ref-type="fig">Fig 5C</xref>, which were calculated as (dimension 1 x dimension 2 x dimension 3).</p>
<p>For survival experiments (<xref rid="fig5" ref-type="fig">Fig 5F</xref>), mice were monitored daily for signs of euthanasia criteria or actual demise. When tumor volume reached 2000cm<sup>3</sup> as determined by the above formula for live mice (0.5L x W<sup><xref ref-type="bibr" rid="c2">2</xref></sup>), mice were sacrificed according to protocol euthanasia criteria.</p>
<p>Brequinar was obtained from Clear Creek Bio and dissolved in 0.9% NaCl. For both endpoint and survival studies, BQ (10mg/kg) or vehicle solvent (0.9% NaCl) was injected intraperitoneally daily. Anti-CTLA-4 and anti-PD-1 antibodies, as well as their respective isotype controls, were obtained from BioXCell. Antibodies were dosed at 100µg/mouse IP twice per week. All procedures were approved by the Institutional Animal Care and Use Committee (IACUC) at the University of Nebraska Medical Center.</p>
</sec>
<sec id="s4f">
<title>Real time quantitative PCR analysis for mRNA expression</title>
<p>For in vitro RT-qPCR experiments, RNA was harvested using Trizol reagent (Thermo Fisher Scientific, Waltham, MA, USA) according to manufacturer’s instructions. For tumor RT-qPCR, tumors were crushed with mortar and pestle in liquid nitrogen, and Trizol was used to extract RNA from the resulting powder, just as for cultured cells. cDNA synthesis was performed (1µg RNA input) using BioRad (Hercules, CA, USA) iScript cDNA synthesis kit (catalog number 1708891) according to manufacturer’s instructions. For RT-qPCR reactions, 3µl of diluted cDNA, 2µl of primer mix (diluted to a final concentration of 200 nM for forward and reverse primers), and 5µl SYBR green master mix (cat #) were mixed (10µl final volume), and reactions were analyzed using Applied Biosystems QuantStudio5 instrument with previously reported thermocycling parameters <sup><xref ref-type="bibr" rid="c62">62</xref></sup>.</p>
<p>18S rRNA was used as a loading control to generate delta Ct values, and each sample was normalized to the experimental control delta Ct values to generate delta delta Ct values which were converted to fold change by (2^-ddCt). For all experiments, <italic>ACTB</italic> (beta-actin) mRNA expression was quantified and used as an additional loading control, and results were concordant regardless of whether 18S or <italic>ACTB</italic> was used for normalization. For <xref rid="fig5" ref-type="fig">Fig 5E</xref>, each data point represents the average expression value of 4 technical replicates for an individual tumor.</p>
<p>For pairwise comparisons, an unpaired student’s t-test was used. For comparisons of 3 or more conditions, a two-way ANOVA with Bonferonni’s post-test correction for multiple comparisons was used. P &lt; 0.05 was considered significant. Primer sequences for RT-qPCR reactions are provided in Supplementary Table 2.</p>
</sec>
<sec id="s4g">
<title>Flow cytometry measurement of cell surface MHC-I</title>
<p>Cells were treated as described and then detached with Accutase (Sigma Aldrich #A6964), washed twice with PBS, stained with fluorescent dye-conjugated antibodies against H2-Db (BioLegend #111508) or HLA-A/B/C (BioLegend #311418, BioLegend #311406) for 30 minutes at 4 °C in PBS, washed once more with PBS, and then resuspended in FACS buffer and subjected to flow cytometry analysis for fluorescence intensity. Aqua live/dead dye (Invitrogen #L34957) or propidium iodide was used to exclude dead cells from the analysis.</p>
</sec>
<sec id="s4h">
<title>Western blot</title>
<p>Protein isolation from cultured cells and western blotting procedure were described previously <sup><xref ref-type="bibr" rid="c61">61</xref></sup>. CDK9 antibody was obtained from Cell Signaling Technology (catalog number 2316, clone C12F7), and beta-actin antibody was obtained from Santa Cruz Biotechnology (catalog number sc-4778, clone C4). Blots were incubated with primary antibody overnight at 4°C, washed, incubated with secondary antibody conjugated with horseradish peroxidase for 45 min at room temperature, washed, developed with ECL reagent and visualized by autoradiography.</p>
</sec>
</sec>
</body>
<back>
<ack>
<title>Acknowledgments</title>
<p>This work was supported in part by funding from the National Institutes of Health, including R01CA163649 and U54CA274329 to PKS, F30CA265277 to NJM, R21CA251151 to AN, and R35GM126908 to DHP.</p>
</ack>
<sec id="s5">
<title>Conflict of Interest Statement</title>
<p>DBS is a co-founder and holds equity in Clear Creek Bio. The other authors declare no competing interests.</p>
</sec>
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<sec id="s6">
<title>Figure legends</title>
<fig id="figS1" position="float" fig-type="figure">
<label>Figure S1:</label>
<caption><title>BQ treatment upregulates APP genes and depletes pyrimidine nucleotides.</title>
<p><bold>A)</bold> Heatmap showing log2 fold change mRNA expression of APP genes in S2-013 cells treated with BQ for indicated dose and duration. <bold>B-C)</bold> RT-qPCR quantification of APP genes after two-week BQ treatment of CFPAC-1 (250nM) (B) or B16F10 (10µM) (C) cells. <bold>D-E)</bold> Quantification of pyrimidine metabolites in CFPAC-1 (C) or B16F10 (D) cells treated with BQ for 8 hours at indicated doses. Data represent mean +/- SEM of four (CFPAC-1) or six (B16F10) biological replicates. * indicates p &lt; 0.05, ** p &lt; 0.01, *** p &lt; 0.001, and # p &lt; 0.0001 by unpaired t-test (B, C) or two-way ANOVA with Bonferonni’s post-comparison test (D, E).</p></caption>
<graphic xlink:href="535399v1_figS1.tif" mimetype="image" mime-subtype="tiff"/>
</fig>
<fig id="figS2" position="float" fig-type="figure">
<label>Figure S2:</label>
<caption><title>Uridine rescues B16F10 cells from teriflunomide toxicity but does not alter APP expression by itself.</title>
<p><bold>A)</bold> Dose-response cell viability experiment as in <xref rid="fig2" ref-type="fig">Fig 2A</xref> but with teriflunomide (Ter) instead of BQ. <bold>B)</bold> RT-qPCR analysis of indicated genes +/- single agent uridine treatment for 24 hours. Data represent mean +/- SEM of 4 determinations. One representative result of three independent experiments is shown. <bold>C)</bold> Flow cytometry analysis of cell surface MHC-I (H2-Db) following 24-hour uridine (1mM) treatment. Data represent mean +/- SEM of three independent experiments. <bold>D)</bold> RT-qPCR analysis of indicated genes in B16F10 cells following 24-hour treatment with MPA (5µM). Data represent mean +/- SEM of four determinations. One representative result of three independent experiments is shown.</p></caption>
<graphic xlink:href="535399v1_figS2.tif" mimetype="image" mime-subtype="tiff"/>
</fig>
<fig id="figS3" position="float" fig-type="figure">
<label>Figure S3:</label>
<caption><p><bold>A)</bold> RT-qPCR time course analysis for MHC-I genes in HEK-293T cells treated for indicated times with BQ (10µM). Data represent mean +/- SD of four determinations. <bold>B)</bold> RT-qPCR analysis for <italic>Nlrc5</italic> (left) or <italic>Tap1</italic> (right) in B16F10 cells treated for 24 hours with indicated agents. Data represent mean +/- SD of four determinations. # indicates p &lt; 0.0001 with two-way ANOVA with Bonferroni post-comparison test. Representative results for one of three independent experiments are shown. <bold>C)</bold> Heatmap indicating RT-qPCR analysis for indicated genes in wild-type or <italic>IKK2</italic>-KO MiaPaCa2 cells treated with indicated agents for 24 hours. Numbers in the heatmap represent mean of four determinations.</p></caption>
<graphic xlink:href="535399v1_figS3.tif" mimetype="image" mime-subtype="tiff"/>
</fig>
<fig id="figS4" position="float" fig-type="figure">
<label>Figure S4:</label>
<caption><p><bold>A)</bold> RT-qPCR analysis for indicated genes in HCT116 cells treated with indicated agents in the presence or absence of flavopiridol (1µM). Numbers in the heatmap represent mean of three determinations.</p></caption>
<graphic xlink:href="535399v1_figS4.tif" mimetype="image" mime-subtype="tiff"/>
</fig>
<fig id="figS5" position="float" fig-type="figure">
<label>Figure S5:</label>
<caption><p><bold>A)</bold> Overall survival in melanoma patients (SKCM) from the Cancer Genome Atlas (TCGA) with above (indicated in red) and below median (indicated in blue) mRNA expression of indicated genes. <bold>B-C)</bold> Principal component analysis (PCA) plot (B) and unsupervised hierarchical clustering (C) from metabolomics analysis of B16F10 tumors at necropsy (<xref rid="fig5" ref-type="fig">Fig 5C</xref>). Treatment regimen of mice from <xref rid="fig5" ref-type="fig">Fig 5E</xref>.</p></caption>
<graphic xlink:href="535399v1_figS5.tif" mimetype="image" mime-subtype="tiff"/>
</fig>
</sec>
</back>
<sub-article id="sa0" article-type="editor-report">
<front-stub>
<article-id pub-id-type="doi">10.7554/eLife.87292.1.sa3</article-id>
<title-group>
<article-title>eLife Assessment</article-title>
</title-group>
<contrib-group>
<contrib contrib-type="author">
<name>
<surname>DeNicola</surname>
<given-names>Gina M</given-names>
</name>
<role specific-use="editor">Reviewing Editor</role>
<aff>
<institution-wrap>
<institution>Moffitt Cancer Center</institution>
</institution-wrap>
<city>Tampa</city>
<country>United States of America</country>
</aff>
</contrib>
</contrib-group>
<kwd-group kwd-group-type="evidence-strength">
<kwd>Compelling</kwd>
<kwd>Incomplete</kwd>
<kwd>Solid</kwd>
</kwd-group>
<kwd-group kwd-group-type="claim-importance">
<kwd>Important</kwd>
</kwd-group>
</front-stub>
<body>
<p>This <bold>important</bold> study reports a novel mechanism linking DHODH inhibition-mediated pyrimidine nucleotide depletion to antigen presentation. Alternative means of inducing antigen presentation provide therapeutic opportunities to augment immune checkpoint blockade for cancer treatment. While the <bold>solid</bold> mechanistic data in vitro are <bold>compelling</bold>, in vivo assessments of the functional relevance of this mechanism are still <bold>incomplete</bold>.</p>
</body>
</sub-article>
<sub-article id="sa1" article-type="referee-report">
<front-stub>
<article-id pub-id-type="doi">10.7554/eLife.87292.1.sa2</article-id>
<title-group>
<article-title>Reviewer #1 (Public Review):</article-title>
</title-group>
<contrib-group>
<contrib contrib-type="author">
<anonymous/>
<role specific-use="referee">Reviewer</role>
</contrib>
</contrib-group>
</front-stub>
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<p>The manuscript by Mullen et al. investigated the gene expression changes in cancer cells treated with the DHODH inhibitor brequinar (BQ), to explore the therapeutic vulnerabilities induced by DHODH inhibition. The study found that BQ treatment causes upregulation of antigen presentation pathway (APP) genes and cell surface MHC class I expression, mechanistically which is mediated by the CDK9/PTEFb pathway triggered by pyrimidine nucleotide depletion. The combination of BQ and immune checkpoint therapy demonstrated a synergistic (or additive) anti-cancer effect against xenografted melanoma, suggesting the potential use of BQ and immune checkpoint blockade as a combination therapy in clinical therapeutics.</p>
<p>The interesting findings in the present study include demonstrating a novel cellular response in cancer cells induced by DHODH inhibition. However, whether the increased antigen presentation by DHODH inhibition actually contributed to the potentiation of the efficacy of immune-check blockade (ICB) is not directly examined is the limitation of the study. Moreover, the mechanism of the increased antigen presentation pathway by pyrimidine depletion mediated by CDK9/PTEFb was not validated by genetic KD or KO targeting by CDK9/PTEFb pathways. Finally, high concentrations of BQ have been reported to show off-target effects, sensitizing cancer cells to ferroptosis, and the authors should discuss whether the dose used in the in vivo study reached the ferroptotic sensitizing dose or not.</p>
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<article-id pub-id-type="doi">10.7554/eLife.87292.1.sa1</article-id>
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<p>In their manuscript entitled &quot;DHODH inhibition enhances the efficacy of immune checkpoint blockade by increasing cancer cell antigen presentation&quot;, Mullen et al. describe an interesting mechanism of inducing antigen presentation. The manuscript includes a series of experiments that demonstrate that blockade of pyrimidine synthesis with DHODH inhibitors (i.e. brequinar (BQ)) stimulates the expression of genes involved in antigen presentation. The authors provide evidence that BQ mediated induction of MHC is independent of interferon signaling. A subsequent targeted chemical screen yielded evidence that CDK9 is the critical downstream mediator that induces RNA Pol II pause release on antigen presentation genes to increase expression. Finally, the authors demonstrate that BQ elicits strong anti-tumor activity in vivo in syngeneic models, and that combination of BQ with immune checkpoint blockade (ICB) results in significant lifespan extension in the B16-F10 melanoma model. Overall, the manuscript uncovers an interesting and unexpected mechanism that influences antigen presentation and provides an avenue for pharmacological manipulation of MHC genes, which is therapeutically relevant in many cancers. However, a few key experiments are needed to ensure that the proposed mechanism is indeed functional in vivo.</p>
<p>The combination of DHODH inhibition with ICB reflects more of an additive response instead of a synergistic combination. Moreover, the temporal separation of BQ and ICB raises the question of whether the induction of antigen presentation with BQ is persistent during the course of delayed ICB treatment. To confidently conclude that induction of antigen presentation is a fundamental component of the in vivo response to DHODH inhibition, the authors should examine whether depletion of immune cells can reduce the therapeutic efficacy of BQ in vivo. Moreover, they should examine whether BQ treatment induces antigen presentation in non-malignant cells and APCs to determine the cancer specificity. Finally, although the authors show that DHODH inhibition induces expression of both MHC-I and MHC-II genes at the RNA level, only MHC-I is validated by flow cytometry given the importance of MHC-II expression on epithelial cancers, including melanoma, MHC-II should be validated as well.</p>
<p>Overall, the paper is clearly written and presented. With the additional experiments described above, especially in vivo, this manuscript would provide a strong contribution to the field of antigen presentation in cancer. The distinct mechanisms by which DHODH inhibition induces antigen presentation will also set the stage for future exploration into alternative methods of antigen induction.</p>
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<article-id pub-id-type="doi">10.7554/eLife.87292.1.sa0</article-id>
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<p>Mullen et al present an important study describing how DHODH inhibition enhances efficacy of immune checkpoint blockade by increasing cell surface expression of MHC I in cancer cells. DHODH inhibitors have been used in the clinic for many years to treat patients with rheumatoid arthritis and there has been a growing interest in repurposing these inhibitors as anti-cancer drugs. In this manuscript, the Singh group build on their previous work defining combinatorial strategies with DHODH inhibitors to improve efficacy. The authors identify an increase in expression of genes involved in the antigen presentation pathway and MHC I after BQ treatment and they narrow the mechanism to be strictly pyrimidine and CDK9/P-TEFb dependent. The authors rationalize that increased MHC I expression induced by DHODH inhibition might favor efficacy of dual immune checkpoint blockade. This combinatorial treatment prolonged survival in an immunocompetent B16F10 melanoma model.</p>
<p>Previous studies have shown that DHODH inhibitors can increase expression of innate immunity-related genes but the role of DHODH and pyrimidine nucleotides in antigen presentation has not been previously reported. A strength of the manuscript is the use of multiple controls across a panel of cell lines to exclude off-target effects and to confirm that effects are exclusively dependent on pyrimidine depletion. Overall, the authors do a thorough characterization of the mechanism that mediates MHC I upregulation using multiple strategies. Furthermore, the in vivo studies provide solid evidence for combining DHODH inhibitors with immune checkpoint blockade.</p>
<p>However, despite the use of multiple cell lines, most experiments are only performed in one cell line, and it is hard to understand why particular gene sets, cell lines or time points are selected for each experiment. It would be beneficial to standardize experimental conditions and confirm the most relevant findings in multiple cell lines. The differential in vivo survival depending on dosing schedule is interesting. However, this section could be strengthened with a more thorough evaluation of the tumors at endpoint.</p>
<p>Overall, this is an interesting manuscript proposing a mechanistic link between pyrimidine depletion and MHC I expression and a novel therapeutic strategy combining DHODH inhibitors with dual checkpoint blockade. These results might be relevant for the clinical development of DHODH inhibitors in the treatment of solid tumors, a setting where these inhibitors have not shown optimal efficacy yet.</p>
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