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<front>
<journal-meta>
<journal-id journal-id-type="publisher-id">Front. Pharmacol.</journal-id>
<journal-title-group>
<journal-title>Frontiers in Pharmacology</journal-title>
<abbrev-journal-title abbrev-type="pubmed">Front. Pharmacol.</abbrev-journal-title>
</journal-title-group>
<issn pub-type="epub">1663-9812</issn>
<publisher>
<publisher-name>Frontiers Media S.A.</publisher-name>
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<article-meta>
<article-id pub-id-type="publisher-id">1782458</article-id>
<article-id pub-id-type="doi">10.3389/fphar.2026.1782458</article-id>
<article-version article-version-type="Version of Record" vocab="NISO-RP-8-2008"/>
<article-categories>
<subj-group subj-group-type="heading">
<subject>Systematic Review</subject>
</subj-group>
</article-categories>
<title-group>
<article-title>Novel roles of SETD2 in tumor metabolism and immunotherapy: a systematic review and meta-analysis</article-title>
<alt-title alt-title-type="left-running-head">Liu et al.</alt-title>
<alt-title alt-title-type="right-running-head">
<ext-link ext-link-type="uri" xlink:href="https://doi.org/10.3389/fphar.2026.1782458">10.3389/fphar.2026.1782458</ext-link>
</alt-title>
</title-group>
<contrib-group>
<contrib contrib-type="author">
<name>
<surname>Liu</surname>
<given-names>Chunhui</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/2954051"/>
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</contrib>
<contrib contrib-type="author">
<name>
<surname>Lin</surname>
<given-names>Lei</given-names>
</name>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
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</contrib>
<contrib contrib-type="author" corresp="yes">
<name>
<surname>Fan</surname>
<given-names>Yonggang</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="corresp" rid="c001">&#x2a;</xref>
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<aff id="aff1">
<label>1</label>
<institution>The First Affiliated Hospital, College of Clinical Medicine of Henan University of Science and Technology.</institution>, <city>Luoyang</city>, <country country="CN">China</country>
</aff>
<aff id="aff2">
<label>2</label>
<institution>Luoyang Central Hospital Affiliated to Zhengzhou University</institution>, <city>Luoyang</city>, <country country="CN">China</country>
</aff>
<author-notes>
<corresp id="c001">
<label>&#x2a;</label>Correspondence: Yonggang Fan, <email xlink:href="mailto:1481108059@qq.com">1481108059@qq.com</email>
</corresp>
</author-notes>
<pub-date publication-format="electronic" date-type="pub" iso-8601-date="2026-02-27">
<day>27</day>
<month>02</month>
<year>2026</year>
</pub-date>
<pub-date publication-format="electronic" date-type="collection">
<year>2026</year>
</pub-date>
<volume>17</volume>
<elocation-id>1782458</elocation-id>
<history>
<date date-type="received">
<day>07</day>
<month>01</month>
<year>2026</year>
</date>
<date date-type="rev-recd">
<day>14</day>
<month>02</month>
<year>2026</year>
</date>
<date date-type="accepted">
<day>19</day>
<month>02</month>
<year>2026</year>
</date>
</history>
<permissions>
<copyright-statement>Copyright &#xa9; 2026 Liu, Lin and Fan.</copyright-statement>
<copyright-year>2026</copyright-year>
<copyright-holder>Liu, Lin and Fan</copyright-holder>
<license>
<ali:license_ref start_date="2026-02-27">https://creativecommons.org/licenses/by/4.0/</ali:license_ref>
<license-p>This is an open-access article distributed under the terms of the <ext-link ext-link-type="uri" xlink:href="https://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution License (CC BY)</ext-link>. The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.</license-p>
</license>
</permissions>
<abstract>
<sec>
<title>Background</title>
<p>SET domain-containing 2 (SETD2), the sole histone H3 lysine 36 trimethyltransferase, has emerged as a critical tumor suppressor across multiple cancer types. Recent evidence suggests SETD2 orchestrates complex interactions between metabolic reprogramming and immune evasion in the tumor microenvironment.</p>
</sec>
<sec>
<title>Methods</title>
<p>Following Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA)2020 guidelines, we systematically searched PubMed, EMBASE, Web of Science, and Cochrane databases from inception through April 2024. We included studies investigating SETD2&#x2019;s role in tumor metabolism and immunotherapy response. Meta-analysis was performed using random-effects models to assess the association between SETD2 status and clinical outcomes. Protocol was developed <italic>a priori</italic> but not registered due to the exploratory nature of this emerging field.</p>
</sec>
<sec>
<title>Results</title>
<p>Of 2,847 initially identified records, 78 studies met inclusion criteria, encompassing approximately 12,400 patients across 12 cancer types. SETD2 loss was associated with metabolic reprogramming (pooled OR: 2.34, 95% confidence interval (CI): 1.89&#x2013;2.89, p &#x3c; 0.001) and decreased immunotherapy response (hazard ratio (HR): 1.56, 95% CI: 1.32&#x2013;1.84, p &#x3c; 0.001). Substantial heterogeneity was observed (I-squared heterogeneity statistic (I<sup>2</sup>) &#x3d; 52&#x2013;68%) and explored through subgroup and sensitivity analyses. Mechanistically, SETD2 deficiency promoted glycolytic shift, lipid metabolism dysregulation, and immunosuppressive metabolite accumulation. Furthermore, SETD2 loss correlated with reduced CD8<sup>&#x2b;</sup> T cell infiltration and increased regulatory T cell presence.</p>
</sec>
<sec>
<title>Conclusion</title>
<p>This meta-analysis identifies SETD2 as an epigenetic regulator linking tumor metabolic reprogramming to antitumor immunity. SETD2 loss was associated with altered metabolic states and reduced clinical benefit from immune checkpoint inhibitors, with the strongest translational relevance observed in ccRCC and substantial evidence in NSCLC and CRC. These findings support further prospective validation and standardized assessment of SETD2, as well as exploration of rational metabolic&#x2013;immunotherapy combination strategies in SETD2-deficient tumors.</p>
</sec>
</abstract>
<kwd-group>
<kwd>epigenetics</kwd>
<kwd>H3K36me3</kwd>
<kwd>immunotherapy</kwd>
<kwd>SETD2</kwd>
<kwd>systematic review</kwd>
<kwd>tumor metabolism</kwd>
</kwd-group>
<funding-group>
<funding-statement>The author(s) declared that financial support was not received for this work and/or its publication.</funding-statement>
</funding-group>
<counts>
<fig-count count="4"/>
<table-count count="2"/>
<equation-count count="0"/>
<ref-count count="25"/>
<page-count count="9"/>
</counts>
<custom-meta-group>
<custom-meta>
<meta-name>section-at-acceptance</meta-name>
<meta-value>Pharmacology of Anti-Cancer Drugs</meta-value>
</custom-meta>
</custom-meta-group>
</article-meta>
</front>
<body>
<sec sec-type="intro" id="s1">
<title>Introduction</title>
<p>The epigenetic landscape of cancer has undergone profound reconceptualization with the recognition that chromatin modifiers act as master regulators orchestrating cellular state decisions beyond conventional growth-control paradigms (<xref ref-type="bibr" rid="B12">Valencia and Kadoch, 2019</xref>; <xref ref-type="bibr" rid="B4">Davies et al., 2023</xref>; <xref ref-type="bibr" rid="B6">Gu et al., 2024</xref>). Among these epigenetic gatekeepers, SET domain-containing 2 (SETD2) has emerged as a tumor suppressor whose inactivation produces multi-layered consequences extending beyond its canonical role in transcriptional elongation (<xref ref-type="bibr" rid="B7">He et al., 2023</xref>; <xref ref-type="bibr" rid="B18">Yu et al., 2023</xref>). SETD2 is the sole mammalian enzyme responsible for trimethylation of histone H3 at lysine 36 (H3K36me3), a chromatin mark tightly coupled to active transcription, RNA processing, and DNA damage repair (<xref ref-type="bibr" rid="B7">He et al., 2023</xref>; <xref ref-type="bibr" rid="B18">Yu et al., 2023</xref>). Accordingly, SETD2 loss promotes genome instability and widespread transcriptional and post-transcriptional defects (<xref ref-type="bibr" rid="B7">He et al., 2023</xref>; <xref ref-type="bibr" rid="B18">Yu et al., 2023</xref>).</p>
<p>Clinically, SETD2 alterations are recurrent across several solid tumors, with particularly high prevalence in clear cell renal cell carcinoma (ccRCC) and appreciable frequencies in non-small cell lung cancer (NSCLC) and colorectal cancer (CRC) (<xref ref-type="bibr" rid="B7">He et al., 2023</xref>; <xref ref-type="bibr" rid="B18">Yu et al., 2023</xref>). Across the studies included in this review, the pooled frequency of SETD2 loss was highest in ccRCC (&#x223c;11%), followed by NSCLC (&#x223c;7%) and CRC (&#x223c;5%), whereas other tumor types collectively showed lower frequencies (<xref ref-type="table" rid="T1">Table 1</xref>). These three cancers therefore represent the most informative clinical settings for evaluating the translational relevance of SETD2 as a biomarker.</p>
<table-wrap id="T1" position="float">
<label>TABLE 1</label>
<caption>
<p>Characteristics of included studies.</p>
</caption>
<table>
<thead valign="top">
<tr>
<th align="left">Cancer type</th>
<th align="left">No. Studies</th>
<th align="left">Total patients</th>
<th align="left">SETD2 loss frequency (95% CI)</th>
<th align="left">Assessment method</th>
<th align="left">Quality score&#x2a;</th>
</tr>
</thead>
<tbody valign="top">
<tr>
<td align="left">ccRCC</td>
<td align="left">22</td>
<td align="left">&#x223c;3,500</td>
<td align="left">11.2% (8.4&#x2013;14.0)</td>
<td align="left">Next-generation sequencing (NGS) (59%), immunohistochemistry (IHC) (41%)</td>
<td align="left">7.2 &#xb1; 1.1</td>
</tr>
<tr>
<td align="left">NSCLC</td>
<td align="left">19</td>
<td align="left">&#x223c;3,200</td>
<td align="left">6.8% (4.9&#x2013;8.7)</td>
<td align="left">NGS (63%), IHC (37%)</td>
<td align="left">7.4 &#xb1; 0.9</td>
</tr>
<tr>
<td align="left">CRC</td>
<td align="left">12</td>
<td align="left">&#x223c;2,200</td>
<td align="left">5.1% (3.2&#x2013;7.0)</td>
<td align="left">NGS (50%), IHC (50%)</td>
<td align="left">6.9 &#xb1; 1.2</td>
</tr>
<tr>
<td align="left">Other&#x2a;&#x2a;</td>
<td align="left">25</td>
<td align="left">&#x223c;3,500</td>
<td align="left">4.7% (2.8&#x2013;6.6)</td>
<td align="left">NGS (56%), IHC (44%)</td>
<td align="left">7.0 &#xb1; 1.0</td>
</tr>
</tbody>
</table>
<table-wrap-foot>
<fn>
<p>&#x2a;Mean &#xb1; SD, Newcastle-Ottawa Scale score (0&#x2013;9).</p>
</fn>
<fn>
<p>&#x2a;&#x2a;Includes bladder, endometrial, gastric, and hepatocellular carcinomas.</p>
</fn>
</table-wrap-foot>
</table-wrap>
<p>Beyond genome maintenance, emerging experimental evidence suggests that SETD2/H3K36me3 participates in regulating tumor metabolism (<xref ref-type="bibr" rid="B18">Yu et al., 2023</xref>; <xref ref-type="bibr" rid="B10">Liu et al., 2019</xref>). SETD2 deficiency can reshape metabolic gene programs through altered chromatin accessibility and transcriptional control, and through RNA processing/splicing defects that rewire enzyme isoforms and pathway flux (<xref ref-type="bibr" rid="B7">He et al., 2023</xref>; <xref ref-type="bibr" rid="B18">Yu et al., 2023</xref>). These changes converge on hallmark metabolic phenotypes observed across tumors, including enhanced glycolysis, altered mitochondrial oxidative phosphorylation, and dysregulated lipid metabolism (<xref ref-type="bibr" rid="B18">Yu et al., 2023</xref>; <xref ref-type="bibr" rid="B10">Liu et al., 2019</xref>). Such metabolic remodeling is not only permissive for tumor growth but may also generate exploitable vulnerabilities (<xref ref-type="bibr" rid="B13">Walter et al., 2023</xref>).</p>
<p>Importantly, tumor metabolism and antitumor immunity are mechanistically coupled (<xref ref-type="bibr" rid="B20">Zhao et al., 2021</xref>). Metabolites such as lactate, altered lipid species, and amino-acid depletion can directly suppress effector T-cell function while favoring the survival and activity of regulatory T cells, thereby shifting the tumor microenvironment toward immune evasion (<xref ref-type="bibr" rid="B14">Wang et al., 2021</xref>; <xref ref-type="bibr" rid="B20">Zhao et al., 2021</xref>). Thus, metabolic rewiring induced by epigenetic alterations may represent a plausible route by which tumor-intrinsic SETD2 loss shapes tumor&#x2013;immune interactions and therapeutic response (<xref ref-type="bibr" rid="B19">Zeng et al., 2023</xref>; <xref ref-type="bibr" rid="B21">Zheng et al., 2023a</xref>; <xref ref-type="bibr" rid="B22">Zheng et al., 2023b</xref>).</p>
<p>Immune checkpoint inhibitors (ICIs) have transformed cancer therapy, yet durable responses occur in only a subset of patients, underscoring the need for robust biomarkers and rational combination strategies (<xref ref-type="bibr" rid="B5">Goswami et al., 2024</xref>). Because SETD2 loss can simultaneously affect transcriptional programs, genome stability, and metabolic states that influence immune surveillance, SETD2 status has been proposed as a candidate determinant of ICI efficacy (<xref ref-type="bibr" rid="B19">Zeng et al., 2023</xref>; <xref ref-type="bibr" rid="B21">Zheng et al., 2023a</xref>; <xref ref-type="bibr" rid="B22">Zheng et al., 2023b</xref>). However, the available evidence is dispersed across cancer types and study designs, and the interconnected roles of SETD2 in metabolism and immunity have not been quantitatively synthesized.</p>
<p>Therefore, we performed a PRISMA 2020-guided systematic review and meta-analysis to quantitatively evaluate: (i) the association between SETD2 alterations and tumor metabolic reprogramming, (ii) the relationship between SETD2 status and clinical outcomes following ICI therapy, and (iii) integrated evidence linking metabolic changes to immune microenvironment features in SETD2-deficient tumors. To address context dependence, we emphasize findings from tumor types with the strongest evidence base and highest SETD2 alteration frequency (ccRCC, NSCLC, and CRC), while treating results from other cancers as exploratory (<xref ref-type="bibr" rid="B11">Page et al., 2021</xref>).</p>
</sec>
<sec sec-type="methods" id="s2">
<title>Methods</title>
<sec id="s2-1">
<title>Protocol development and reporting standards</title>
<p>This systematic review and meta-analysis was conducted according to a pre-specified protocol (<xref ref-type="sec" rid="s12">Supplementary Material S1</xref>) following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) 2020 guidelines (<xref ref-type="bibr" rid="B11">Page et al., 2021</xref>) (<xref ref-type="sec" rid="s12">Supplementary Table S1</xref>). While PROSPERO registration was considered, the rapidly evolving nature of this field and exploratory scope of our analysis led us to proceed without formal registration, acknowledging this limitation. As this study involved analysis of published literature only, ethical approval was not required.</p>
</sec>
<sec id="s2-2">
<title>Search strategy</title>
<p>A comprehensive literature search was performed across PubMed/MEDLINE, EMBASE, Web of Science Core Collection, and Cochrane Central Register of Controlled Trials from database inception through 30 April 2024. The search strategy combined controlled vocabulary (MeSH terms, Emtree) and free-text terms encompassing three conceptual domains: (1) SETD2 and related terms, (2) metabolism and metabolic processes, and (3) immunotherapy and immune response. No language restrictions were applied.</p>
</sec>
<sec id="s2-3">
<title>Eligibility criteria</title>
<p>Studies were included if they met the following criteria: (1) original research articles published in peer-reviewed journals; (2) investigated SETD2 function in human cancers; (3) examined metabolic alterations and/or immunotherapy response in relation to SETD2 status; (4) provided sufficient data for effect size calculation. Exclusion criteria comprised: (1) reviews, editorials, or conference abstracts without full data; (2) non-human studies without clinical correlation; (3) studies lacking appropriate controls; (4) duplicate publications. For studies with overlapping patient cohorts, we included the most recent or most comprehensive report.</p>
</sec>
<sec id="s2-4">
<title>Study selection and data extraction</title>
<p>Two independent reviewers (C.L. and L.L.) screened titles/abstracts and subsequently full texts, with discrepancies resolved through consensus or third-reviewer arbitration (Y.F.). Inter-rater reliability was assessed using Cohen&#x2019;s kappa (&#x3ba; &#x3d; 0.82 for title/abstract screening, &#x3ba; &#x3d; 0.89 for full-text review). Data extraction utilized a standardized form capturing study characteristics, patient demographics, SETD2 assessment methods, metabolic parameters, immunotherapy regimens, and clinical outcomes. The pilot-tested extraction form is provided in <xref ref-type="sec" rid="s12">Supplementary Table S2</xref>.</p>
</sec>
<sec id="s2-5">
<title>Quality assessment</title>
<p>Methodological quality was evaluated using the Newcastle-Ottawa Scale (NOS) for observational studies and the Cochrane Risk of Bias tool (RoB 2) for randomized trials (<xref ref-type="bibr" rid="B23">Wells et al., 2011</xref>; <xref ref-type="bibr" rid="B24">Sterne et al., 2019</xref>). Studies scoring &#x2265;7 on NOS or with low risk of bias in &#x2265;4 domains of RoB 2 were considered high quality. Publication bias was assessed through funnel plot inspection and Egger&#x2019;s regression test when &#x2265;10 studies were available for a given outcome (<xref ref-type="sec" rid="s12">Supplementary Table S3</xref>).</p>
</sec>
<sec id="s2-6">
<title>Statistical analysis</title>
<p>Meta-analyses were conducted using random-effects models (DerSimonian-Laird method) to account for anticipated heterogeneity. Effect sizes were expressed as odds ratios (OR) for dichotomous outcomes and hazard ratios (HR) for time-to-event data, with 95% confidence intervals (CI). Heterogeneity was quantified using I<sup>2</sup> statistics and Cochran&#x2019;s Q test. We considered I<sup>2</sup> values of 25%, 50%, and 75% as low, moderate, and substantial heterogeneity, respectively (<xref ref-type="sec" rid="s12">Supplementary Figure S1</xref>). Subgroup analyses examined cancer type, SETD2 assessment method, and treatment modality (<xref ref-type="sec" rid="s12">Supplementary Table S4</xref>). Meta-regression was performed to explore sources of heterogeneity when I<sup>2</sup> exceeded 50%. Sensitivity analyses excluded studies with high risk of bias. All analyses were performed using R version 4.3.2 with the meta and metafor packages. Statistical significance was set at p &#x3c; 0.05 (two-tailed).</p>
<p>We used the PRISMA 2020 reporting guideline (<xref ref-type="bibr" rid="B11">Page et al., 2021</xref>) to draft this manuscript, and the PRISMA 2020 reporting checklist (<xref ref-type="bibr" rid="B25">Page et al., 2025</xref>) when editing.</p>
</sec>
</sec>
<sec sec-type="results" id="s3">
<title>Results</title>
<sec id="s3-1">
<title>Study selection and characteristics</title>
<p>The systematic search yielded 2,847 records after duplicate removal. Following title/abstract screening, 312 articles underwent full-text review, with 78 studies meeting inclusion criteria (<xref ref-type="fig" rid="F1">Figure 1</xref>). These comprised 52 retrospective cohort studies, 18 prospective observational studies, 6 clinical trials with biomarker analysis, and 2 case-control studies, collectively encompassing approximately 12,400 patients across 12 cancer types. The most common reasons for exclusion were: lack of metabolic or immunotherapy outcome data (n &#x3d; 134), insufficient data for meta-analysis (n &#x3d; 67), and non-human studies without clinical validation (n &#x3d; 33).</p>
<fig id="F1" position="float">
<label>FIGURE 1</label>
<caption>
<p>Prisma 2020 Flow Diagram.</p>
</caption>
<graphic xlink:href="fphar-17-1782458-g001.tif">
<alt-text content-type="machine-generated">PRISMA flow diagram outlining systematic review process: 3,929 records identified, 1,082 duplicates removed, 2,847 screened, 2,535 excluded, 312 reports sought, none not retrieved, 312 assessed for eligibility, 234 excluded for reasons such as lacking metabolic or immune data, insufficient data, or non-human studies. Seventy-eight studies were included in the final review.</alt-text>
</graphic>
</fig>
<p>The predominant cancer types included clear cell renal cell carcinoma (n &#x3d; 22 studies, &#x223c;3,500 patients), non-small cell lung cancer (n &#x3d; 19 studies, &#x223c;3,200 patients), and colorectal cancer (n &#x3d; 12 studies, &#x223c;2,200 patients). SETD2 status was assessed through next-generation sequencing (58%), immunohistochemistry for H3K36me3 (31%), or combined approaches (11%). Study characteristics are summarized in <xref ref-type="table" rid="T1">Table 1</xref>. Notably, ccRCC, NSCLC, and CRC collectively accounted for the majority of included studies and patients. These three tumor types also showed the highest pooled frequencies of SETD2 loss across the included datasets (<xref ref-type="table" rid="T1">Table 1</xref>). Accordingly, we prioritize these cancers when interpreting clinical relevance and biomarker implications; evidence from other tumor types is summarized as exploratory due to smaller numbers and lower event rates.</p>
</sec>
<sec id="s3-2">
<title>SETD2 loss and metabolic reprogramming</title>
<p>Meta-analysis of 45 studies showed that SETD2 loss was significantly associated with tumor metabolic reprogramming (pooled odds ratio (OR): 2.34, 95% CI: 1.89&#x2013;2.89, p &#x3c; 0.001), with moderate heterogeneity (I<sup>2</sup> &#x3d; 56%). Meta-regression suggested that cancer type (p &#x3d; 0.023) and SETD2 assessment method (p &#x3d; 0.041) were significant contributors to between-study variability. Nevertheless, subgroup analyses demonstrated a consistent direction and magnitude of effect across key metabolic subdomains, including glycolytic enhancement (OR: 2.56, 95% CI: 1.98&#x2013;3.31), mitochondrial dysfunction (OR: 2.21, 95% CI: 1.67&#x2013;2.93), and lipid metabolism dysregulation (OR: 2.08, 95% CI: 1.54&#x2013;2.81) (<xref ref-type="fig" rid="F2">Figure 2</xref>). Although publication-bias diagnostics indicated potential small-study effects, trim-and-fill adjustment only modestly attenuated the pooled estimate, supporting the robustness of the association.</p>
<fig id="F2" position="float">
<label>FIGURE 2</label>
<caption>
<p>Forest plot of SETD2 loss and metabolic alterations.</p>
</caption>
<graphic xlink:href="fphar-17-1782458-g002.tif">
<alt-text content-type="machine-generated">Forest plot displaying odds ratios and confidence intervals from multiple studies, grouped into glycolytic enhancement, mitochondrial dysfunction, and lipid metabolism subgroups. Pooled models indicate overall effect sizes: 2.53, 2.20, and 2.08, respectively. Subgroup and overall heterogeneity are low.</alt-text>
</graphic>
</fig>
<p>Mechanistic investigations identified recurrent metabolic signatures associated with SETD2 deficiency:<list list-type="order">
<list-item>
<p>Glycolytic reprogramming: Upregulation of hexokinase 2(HK2), pyruvate kinase M2(PKM2), and lactate dehydrogenase A (LDHA) (n &#x3d; 18 studies).</p>
</list-item>
<list-item>
<p>Mitochondrial alterations: Reduced oxidative phosphorylation capacity by 35%&#x2013;45% and complex I/III activity (n &#x3d; 14 studies).</p>
</list-item>
<list-item>
<p>Lipid metabolism: Enhanced fatty acid synthesis with 1.8-fold increase in FASN expression and altered cholesterol homeostasis (n &#x3d; 11 studies).</p>
</list-item>
<list-item>
<p>Amino acid metabolism: Disrupted serine/glycine pathway flux and glutamine metabolism (n &#x3d; 8 studies).</p>
</list-item>
</list>
</p>
</sec>
<sec id="s3-3">
<title>SETD2 status and immunotherapy response</title>
<p>Among 48 studies evaluating immunotherapy outcomes, SETD2 loss significantly correlated with decreased response rates (HR: 1.56, 95% CI: 1.32&#x2013;1.84, p &#x3c; 0.001; I<sup>2</sup> &#x3d; 52%) and shorter progression-free survival (median difference: -3.2 months, 95% CI: -4.1 to &#x2212;2.3, p &#x3c; 0.001) (<xref ref-type="fig" rid="F3">Figure 3</xref>). The association remained significant in sensitivity analysis excluding studies with high risk of bias (HR: 1.48, 95% CI: 1.26&#x2013;1.74, p &#x3c; 0.001). Given the heterogeneity in ICI regimens, clinical endpoints, and SETD2 assessment methods across studies, we employed a random-effects model with prespecified sensitivity analyses. Notably, the association between SETD2 loss and poorer immunotherapy outcomes remained significant after exclusion of studies at high risk of bias (HR: 1.48, 95% CI: 1.26&#x2013;1.74, p &#x3c; 0.001), supporting the robustness of the findings. Nevertheless, the presence of residual heterogeneity indicates potential context dependence, underscoring the need for prospective validation in tumor types with higher SETD2 alteration frequencies, particularly ccRCC, NSCLC, and CRC.</p>
<fig id="F3" position="float">
<label>FIGURE 3</label>
<caption>
<p>Kaplan-meier curves of PFS stratified by SETD2 status.</p>
</caption>
<graphic xlink:href="fphar-17-1782458-g003.tif">
<alt-text content-type="machine-generated">Kaplan-Meier survival curve comparing progression-free survival between SETD2 wild-type (blue) and SETD2 mutant/loss (red) groups shows shorter median survival for the mutant group at 8.0 months versus 11.2 months for wild-type, with significant difference by log-rank p less than 0.001; shaded regions represent confidence intervals, and a table below displays the number at risk over time for each group.</alt-text>
</graphic>
</fig>
<p>The immune microenvironment analysis revealed:<list list-type="bullet">
<list-item>
<p>Reduced CD8<sup>&#x2b;</sup> T cell infiltration (standardized mean difference (SMD): -0.52, 95% CI: -0.68 to &#x2212;0.36).</p>
</list-item>
<list-item>
<p>Increased regulatory T cells (SMD: 0.48, 95% CI: 0.32&#x2013;0.64).</p>
</list-item>
<list-item>
<p>Elevated lactate levels (mean difference: 2.3&#xa0;mmol/L, 95% CI: 1.8&#x2013;2.8).</p>
</list-item>
<list-item>
<p>Decreased interferon-gamma (IFN-&#x3b3;) signature scores (mean z-score difference: -0.73, 95% CI: -0.91 to &#x2212;0.55).</p>
</list-item>
</list>
</p>
</sec>
<sec id="s3-4">
<title>Integrated analysis of metabolic-immune interactions</title>
<p>Cross-sectional analysis of 15 studies examining both metabolic and immune parameters revealed significant correlations between metabolic alterations and immune dysfunction in SETD2-deficient tumors (<xref ref-type="table" rid="T2">Table 2</xref>).</p>
<table-wrap id="T2" position="float">
<label>TABLE 2</label>
<caption>
<p>Correlations between metabolic and immune parameters.</p>
</caption>
<table>
<thead valign="top">
<tr>
<th align="left">Metabolic feature</th>
<th align="left">Immune parameter</th>
<th align="left">Correlation (r)</th>
<th align="left">95% CI</th>
<th align="left">p-value</th>
<th align="left">Studies (n)</th>
</tr>
</thead>
<tbody valign="top">
<tr>
<td align="left">Lactate accumulation</td>
<td align="left">CD8<sup>&#x2b;</sup> T cell exhaustion</td>
<td align="left">0.52</td>
<td align="left">0.38&#x2013;0.64</td>
<td align="left">&#x3c;0.001</td>
<td align="left">8</td>
</tr>
<tr>
<td align="left">Lipid peroxidation</td>
<td align="left">Regulatory T cell (Treg) infiltration</td>
<td align="left">0.46</td>
<td align="left">0.31&#x2013;0.59</td>
<td align="left">&#x3c;0.001</td>
<td align="left">6</td>
</tr>
<tr>
<td align="left">Glutamine depletion</td>
<td align="left">Natural killer (NK) cell dysfunction</td>
<td align="left">0.41</td>
<td align="left">0.24&#x2013;0.55</td>
<td align="left">0.002</td>
<td align="left">5</td>
</tr>
<tr>
<td align="left">ATP/AMP ratio</td>
<td align="left">Dendritic cell maturation</td>
<td align="left">&#x2212;0.49</td>
<td align="left">&#x2212;0.63 to &#x2212;0.32</td>
<td align="left">&#x3c;0.001</td>
<td align="left">7</td>
</tr>
</tbody>
</table>
</table-wrap>
</sec>
<sec id="s3-5">
<title>Clinical implications and biomarker performance</title>
<p>Pooled analysis of biomarker studies demonstrated SETD2/H3K36me3 status achieved:<list list-type="bullet">
<list-item>
<p>Sensitivity: 68% (95% CI: 61%&#x2013;74%) for predicting immunotherapy response.</p>
</list-item>
<list-item>
<p>Specificity: 72% (95% CI: 65%&#x2013;78%).</p>
</list-item>
<list-item>
<p>Area under receiver operating characteristic (ROC) curve: 0.73 (95% CI: 0.68&#x2013;0.78).</p>
</list-item>
<list-item>
<p>Positive predictive value: 64% (95% CI: 57%&#x2013;71%).</p>
</list-item>
<list-item>
<p>Negative predictive value: 75% (95% CI: 69%&#x2013;81%).</p>
</list-item>
</list>
</p>
<p>Combined metabolic-immune signatures incorporating SETD2 status improved predictive performance (area under the receiver operating characteristic curve (AUC): 0.79, 95% CI: 0.74&#x2013;0.84).</p>
</sec>
<sec id="s3-6">
<title>Quality assessment and publication bias</title>
<p>Quality assessment revealed 52 studies (67%) with low risk of bias, 21 (27%) with moderate risk, and 5 (6%) with high risk. The mean Newcastle-Ottawa Scale score was 7.1 &#xb1; 1.0. Funnel plot asymmetry and Egger&#x2019;s test (p &#x3d; 0.048) suggested potential publication bias for metabolic outcomes, though trim-and-fill analysis reduced the effect size only marginally (OR: 2.21, 95% CI: 1.78&#x2013;2.75). No significant publication bias was detected for immunotherapy outcomes (p &#x3d; 0.127) (<xref ref-type="fig" rid="F4">Figure 4</xref>).</p>
<fig id="F4" position="float">
<label>FIGURE 4</label>
<caption>
<p>Funnel plot for publication bias assessment.</p>
</caption>
<graphic xlink:href="fphar-17-1782458-g004.tif">
<alt-text content-type="machine-generated">Funnel plot displaying log odds ratio versus standard error for metabolic outcomes, with individual study points scattered symmetrically around a vertical red dashed line at log odds ratio one and gray dashed funnel limits; Egger&#x27;s test p-value is zero point three five one, suggesting low publication bias.</alt-text>
</graphic>
</fig>
</sec>
</sec>
<sec sec-type="discussion" id="s4">
<title>Discussion</title>
<p>This systematic review and meta-analysis synthesizes clinical and translational evidence supporting SETD2 as a key epigenetic determinant at the interface of tumor metabolism and antitumor immunity (<xref ref-type="bibr" rid="B15">Weng et al., 2024</xref>; <xref ref-type="bibr" rid="B3">Chen et al., 2025</xref>). Across 78 eligible studies (&#x223c;12,400 patients), SETD2 loss was associated with metabolic reprogramming (pooled OR: 2.34, 95% CI: 1.89&#x2013;2.89) and with inferior outcomes to immune checkpoint blockade (pooled HR: 1.56, 95% CI: 1.32&#x2013;1.84). Importantly, the evidence base is not evenly distributed across malignancies: ccRCC, NSCLC, and CRC comprise the majority of included studies and show the highest pooled frequencies of SETD2 loss (<xref ref-type="table" rid="T1">Table 1</xref>). Therefore, while our pooled estimates summarize multi-tumor evidence, the strongest translational inferences and near-term biomarker relevance are most directly applicable to these tumor types.</p>
<p>Mechanistically, our synthesis indicates that SETD2 deficiency is linked to coordinated remodeling of multiple metabolic networks rather than a single pathway shift. Subgroup analyses showed consistent associations with enhanced glycolysis (OR: 2.56), mitochondrial dysfunction (OR: 2.21), and lipid metabolism dysregulation (OR: 2.08). These phenotypes are biologically plausible given the role of H3K36me3 in transcriptional fidelity and RNA processing, and the observation that SETD2 loss can cause widespread RNA processing defects and altered chromatin accessibility at active gene bodies (<xref ref-type="bibr" rid="B3">Chen et al., 2025</xref>; <xref ref-type="bibr" rid="B16">Xie et al., 2022</xref>; <xref ref-type="bibr" rid="B15">Weng et al., 2024</xref>). Together, these mechanisms can reprogram metabolic enzyme expression and pathway flux, creating a tumor cell state characterized by increased glycolytic dependence, impaired oxidative phosphorylation capacity, and altered lipid homeostasis.</p>
<p>From an immunological perspective, the most clinically actionable finding is the association between SETD2 loss and reduced benefit from ICIs. At the tumor-microenvironment level, SETD2-deficient tumors showed reduced CD8<sup>&#x2b;</sup> T-cell infiltration (SMD: &#x2212;0.52) and increased regulatory T cells (SMD: 0.48), alongside higher lactate levels and lower IFN-&#x3b3; signature scores. These data support a model in which SETD2-linked metabolic rewiring produces an immunosuppressive metabolic milieu&#x2014;through lactate accumulation, nutrient competition, and oxidative/lipid stress&#x2014;that constrains effector T-cell function while favoring regulatory programs (<xref ref-type="bibr" rid="B1">Arner and Rathmell, 2023</xref>; <xref ref-type="bibr" rid="B9">Kumagai et al., 2022</xref>). Notably, our results do not exclude the possibility that SETD2 loss may also influence immunotherapy response through genome-instability-related mechanisms (e.g., altered neoantigen landscape) (<xref ref-type="bibr" rid="B15">Weng et al., 2024</xref>; <xref ref-type="bibr" rid="B3">Chen et al., 2025</xref>). However, the net clinical association observed across available studies is toward poorer ICI outcomes, suggesting that immunosuppressive metabolic and microenvironmental effects may dominate in many real-world contexts, particularly in ccRCC, NSCLC, and CRC.</p>
<p>In terms of biomarker development, the pooled diagnostic performance of SETD2/H3K36me3 status (AUC: 0.73; sensitivity 68%, specificity 72%) indicates moderate discrimination that is unlikely to be sufficient as a stand-alone clinical test (<xref ref-type="bibr" rid="B8">Holder et al., 2024</xref>; <xref ref-type="bibr" rid="B17">Yamaguchi et al., 2024</xref>). Nevertheless, the improvement observed with combined metabolic&#x2013;immune signatures incorporating SETD2 (AUC: 0.79) supports the concept that SETD2 could be a useful component of multiparametric biomarker panels (<xref ref-type="bibr" rid="B8">Holder et al., 2024</xref>; <xref ref-type="bibr" rid="B17">Yamaguchi et al., 2024</xref>). To translate these findings, standardization of SETD2 assessment is critical, because included studies used heterogeneous definitions (NGS-based mutation/copy-number status versus immunohistochemistry for H3K36me3) (<xref ref-type="bibr" rid="B8">Holder et al., 2024</xref>; <xref ref-type="bibr" rid="B17">Yamaguchi et al., 2024</xref>). Future clinical studies should pre-define assay platforms, cutoffs, and reporting standards to enable reproducible implementation.</p>
<p>Several limitations should temper interpretation. First, most included studies were retrospective, limiting causal inference and increasing susceptibility to confounding (e.g., disease stage, prior therapies, and co-occurring genomic alterations). Second, moderate heterogeneity was present for both metabolism (I<sup>2</sup> &#x3d; 56%) and immunotherapy outcomes (I<sup>2</sup> &#x3d; 52%), reflecting biological context dependence and methodological variation. Third, small-study effects were suggested for metabolic outcomes, although trim-and-fill analysis only modestly attenuated the pooled effect size. Fourth, the evidence base is concentrated in ccRCC, NSCLC, and CRC; results in other tumor types are based on fewer studies and should be considered hypothesis-generating. Finally, lack of individual patient data limited our ability to adjust for important covariates and to perform deeper subgroup analyses.</p>
<p>Despite these limitations, our analysis points to several actionable future directions. (i) <italic>In vivo</italic> validation: immune-competent models with SETD2 loss (including genetically engineered mouse models and syngeneic systems), as well as patient-derived xenografts with metabolic profiling, are needed to test whether SETD2-driven metabolic states causally shape immune infiltration and ICI response. (ii) Prospective clinical validation: SETD2-stratified cohorts and trials should incorporate pre-specified metabolic endpoints and standardized immune profiling to confirm biomarker utility in ccRCC, NSCLC, and CRC. (iii) Therapeutic hypothesis testing: rational combinations pairing ICIs with metabolic interventions (e.g., targeting glycolysis or lactate transport) merit prioritization in SETD2-deficient tumors (<xref ref-type="bibr" rid="B1">Arner and Rathmell, 2023</xref>; <xref ref-type="bibr" rid="B9">Kumagai et al., 2022</xref>; <xref ref-type="bibr" rid="B2">Babl et al., 2023</xref>). (iv) Multi-omic biomarkers: integrating SETD2 status with metabolic and immune signatures may provide clinically meaningful prediction beyond single markers (<xref ref-type="bibr" rid="B8">Holder et al., 2024</xref>; <xref ref-type="bibr" rid="B17">Yamaguchi et al., 2024</xref>).</p>
<p>Overall, our findings support SETD2 as an epigenetic regulator that links metabolic programming to immune surveillance, with the clearest near-term relevance in ccRCC, NSCLC, and CRC (<xref ref-type="bibr" rid="B15">Weng et al., 2024</xref>; <xref ref-type="bibr" rid="B3">Chen et al., 2025</xref>; <xref ref-type="bibr" rid="B1">Arner and Rathmell, 2023</xref>). Prospective, standardized, and mechanistically informed studies are required before SETD2-based biomarkers can be implemented for routine immunotherapy stratification.</p>
</sec>
<sec sec-type="conclusion" id="s5">
<title>Conclusion</title>
<p>This meta-analysis provides evidence that SETD2 functions as an important epigenetic regulator coordinating tumor metabolism and antitumor immunity. Across available studies, SETD2 loss was associated with metabolic reprogramming and with reduced clinical benefit from immune checkpoint blockade. Because the evidence base and SETD2 loss frequency are highest in ccRCC and remain substantial in NSCLC and CRC, the translational implications are most directly applicable to these tumor types, while findings in other cancers should be considered exploratory.</p>
<p>Future work should prioritize: (i) <italic>in vivo</italic> validation in immune-competent models to establish causality between SETD2-driven metabolic states and immune evasion; (ii) prospective clinical studies and SETD2-stratified trials with standardized assays (NGS and/or H3K36me3 immunohistochemistry), predefined endpoints (objective response rate, progression-free survival, overall survival), and integrated metabolic and immune profiling; and (iii) evaluation of combination strategies pairing ICIs with metabolic interventions in SETD2-deficient tumors. Such studies are necessary to confirm the clinical utility of SETD2 as a biomarker and to translate SETD2-associated metabolic vulnerabilities into precision therapeutic strategies.</p>
</sec>
</body>
<back>
<sec sec-type="data-availability" id="s6">
<title>Data availability statement</title>
<p>The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.</p>
</sec>
<sec sec-type="author-contributions" id="s7">
<title>Author contributions</title>
<p>CL: Conceptualization, Data curation, Formal Analysis, Investigation, Methodology, Validation, Visualization, Writing &#x2013; original draft. LL: Conceptualization, Data curation, Formal Analysis, Investigation, Resources, Software, Supervision, Validation, Visualization, Writing &#x2013; original draft. YF: Data curation, Investigation, Project administration, Resources, Supervision, Visualization, Writing &#x2013; review and editing.</p>
</sec>
<sec sec-type="COI-statement" id="s9">
<title>Conflict of interest</title>
<p>The author(s) declared that this work was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.</p>
</sec>
<sec sec-type="ai-statement" id="s10">
<title>Generative AI statement</title>
<p>The author(s) declared that generative AI was not used in the creation of this manuscript.</p>
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</sec>
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<title>Publisher&#x2019;s note</title>
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</sec>
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<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.2026.1782458/full#supplementary-material">https://www.frontiersin.org/articles/10.3389/fphar.2026.1782458/full&#x23;supplementary-material</ext-link>
</p>
<supplementary-material xlink:href="DataSheet1.doc" id="SM1" mimetype="application/doc" xmlns:xlink="http://www.w3.org/1999/xlink"/>
</sec>
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<ext-link ext-link-type="uri" xlink:href="https://loop.frontiersin.org/people/1744320/overview">Fahad Khan</ext-link>, Saveetha Medical College &#x26; Hospital, India</p>
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<fn fn-type="abbr" id="abbrev1">
<label>Abbreviations:</label>
<p>AUC, area under the receiver operating characteristic curve; ccRCC, clear cell renal cell carcinoma; CI, confidence interval; CRC, colorectal cancer; DC, dendritic cell; H3K36me3, histone H3 lysine 36 trimethylation; HK2, hexokinase 2; HR, hazard ratio; ICI, immune checkpoint inhibitor; IHC, immunohistochemistry; IFN-&#x3b3;, interferon-gamma; I<sup>2</sup>, I-squared heterogeneity statistic; LDHA, lactate dehydrogenase A; NGS, next-generation sequencing; NOS, Newcastle-Ottawa Scale; NK, natural killer (cell); NSCLC, non-small cell lung cancer; OR, odds ratio; OS, overall survival; OXPHOS, oxidative phosphorylation; PFS, progression-free survival; PKM2, pyruvate kinase M2; PRISMA, Preferred Reporting Items for Systematic Reviews and Meta-Analyses; RoB 2, revised Cochrane risk-of-bias tool for randomized trials; ROC, receiver operating characteristic; SETD2, SET domain-containing protein 2; SMD, standardized mean difference; Treg, regulatory T cell.</p>
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