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<front>
<journal-meta>
<journal-id journal-id-type="publisher-id">Front. Immunol.</journal-id>
<journal-title>Frontiers in Immunology</journal-title>
<abbrev-journal-title abbrev-type="pubmed">Front. Immunol.</abbrev-journal-title>
<issn pub-type="epub">1664-3224</issn>
<publisher>
<publisher-name>Frontiers Media S.A.</publisher-name>
</publisher>
</journal-meta>
<article-meta>
<article-id pub-id-type="doi">10.3389/fimmu.2023.1231543</article-id>
<article-categories>
<subj-group subj-group-type="heading">
<subject>Immunology</subject>
<subj-group>
<subject>Original Research</subject>
</subj-group>
</subj-group>
</article-categories>
<title-group>
<article-title>Construction of an m6A- and neutrophil extracellular traps-related lncRNA model to predict hepatocellular carcinoma prognosis and immune landscape</article-title>
</title-group>
<contrib-group>
<contrib contrib-type="author">
<name>
<surname>Zhan</surname>
<given-names>Tian</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="author-notes" rid="fn003">
<sup>&#x2020;</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Wang</surname>
<given-names>Wei</given-names>
</name>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
<xref ref-type="author-notes" rid="fn003">
<sup>&#x2020;</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/2060323"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Guan</surname>
<given-names>Xiao</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="author-notes" rid="fn003">
<sup>&#x2020;</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/1887325"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Bao</surname>
<given-names>Wei</given-names>
</name>
<xref ref-type="aff" rid="aff3">
<sup>3</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/1837842"/>
</contrib>
<contrib contrib-type="author" corresp="yes">
<name>
<surname>Lu</surname>
<given-names>Na</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="author-notes" rid="fn001">
<sup>*</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/1888463"/>
</contrib>
<contrib contrib-type="author" corresp="yes">
<name>
<surname>Zhang</surname>
<given-names>Jianping</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="author-notes" rid="fn001">
<sup>*</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/1134030"/>
</contrib>
</contrib-group>
<aff id="aff1">
<sup>1</sup>
<institution>Department of General Surgery, The Second Affiliated Hospital of Nanjing Medical University</institution>, <addr-line>Nanjing, Jiangsu</addr-line>, <country>China</country>
</aff>
<aff id="aff2">
<sup>2</sup>
<institution>Department of Clinical Laboratory, Lianshui County People&#x2019;s Hospital</institution>, <addr-line>Huai&#x2019;an</addr-line>, <country>China</country>
</aff>
<aff id="aff3">
<sup>3</sup>
<institution>Department of Urology, The Second Affiliated Hospital of Nanjing Medical University</institution>, <addr-line>Nanjing</addr-line>, <country>China</country>
</aff>
<author-notes>
<fn fn-type="edited-by">
<p>Edited by: Jadwiga Jablonska, Essen University Hospital, Germany</p>
</fn>
<fn fn-type="edited-by">
<p>Reviewed by: Jichun Sun, Central South University, China; Junxian Du, Fudan University, China</p>
</fn>
<fn fn-type="corresp" id="fn001">
<p>*Correspondence: Jianping Zhang, <email xlink:href="mailto:drzhangjp@njmu.edu.cn">drzhangjp@njmu.edu.cn</email>; Na Lu, <email xlink:href="mailto:ln2248457306@163.com">ln2248457306@163.com</email>
</p>
</fn>
<fn fn-type="equal" id="fn003">
<p>&#x2020;These authors have contributed equally to this work</p>
</fn>
</author-notes>
<pub-date pub-type="epub">
<day>05</day>
<month>10</month>
<year>2023</year>
</pub-date>
<pub-date pub-type="collection">
<year>2023</year>
</pub-date>
<volume>14</volume>
<elocation-id>1231543</elocation-id>
<history>
<date date-type="received">
<day>30</day>
<month>05</month>
<year>2023</year>
</date>
<date date-type="accepted">
<day>21</day>
<month>09</month>
<year>2023</year>
</date>
</history>
<permissions>
<copyright-statement>Copyright &#xa9; 2023 Zhan, Wang, Guan, Bao, Lu and Zhang</copyright-statement>
<copyright-year>2023</copyright-year>
<copyright-holder>Zhan, Wang, Guan, Bao, Lu and Zhang</copyright-holder>
<license xlink:href="http://creativecommons.org/licenses/by/4.0/">
<p>This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.</p>
</license>
</permissions>
<abstract>
<sec>
<title>Purpose</title>
<p>To investigate the impact of N6-methyladenosine- (m6A) and neutrophil extracellular traps- (NETs) related lncRNAs (MNlncRNAs) on the prognosis of hepatocellular carcinoma (HCC).</p>
</sec>
<sec>
<title>Methods</title>
<p>We collected m6A and NETs-related genes from published studies. We identified the MNlncRNAs by correlation analysis. Cox regression and the least absolute selection operator (LASSO) method were used to select predictive MNlncRNAs. The expressions of predictive MNlncRNAs were detected by cell and tissue experiments. Survival, medication sensitivity, and immunological microenvironment evaluations were used to assess the model&#x2019;s prognostic utility. Finally, we performed cellular experiments to further validate the model&#x2019;s prognostic reliability.</p>
</sec>
<sec>
<title>Results</title>
<p>We obtained a total of 209 MNlncRNAs. 7 MNlncRNAs comprised the prognostic model, which successfully stratifies HCC patients, with the area under the curve (AUC) ranging from 0.7 to 0.8. <italic>In vitro</italic> tests confirmed that higher risk patients had worse prognosis. Risk score, immunological microenvironment, and immune checkpoint gene expression were all significantly correlated with each other in HCC. In the group at high risk, immunotherapy could be more successful. Cellular assays confirmed that HCC cells with high risk scores have a higher proliferation and invasive capacity.</p>
</sec>
<sec>
<title>Conclusion</title>
<p>The MNlncRNAs-related prognostic model aided in determining HCC prognosis, revealing novel therapeutic options, notably immunotherapy.</p>
</sec>
</abstract>
<kwd-group>
<kwd>long non-coding RNA</kwd>
<kwd>N6-methyladenosine</kwd>
<kwd>neutrophil extracellular traps</kwd>
<kwd>hepatocellular carcinoma</kwd>
<kwd>bioinformatics</kwd>
</kwd-group>
<contract-num rid="cn001">81874058</contract-num>
<contract-sponsor id="cn001">National Natural Science Foundation of China<named-content content-type="fundref-id">10.13039/501100001809</named-content>
</contract-sponsor>
<counts>
<fig-count count="8"/>
<table-count count="0"/>
<equation-count count="0"/>
<ref-count count="68"/>
<page-count count="11"/>
<word-count count="4143"/>
</counts>
<custom-meta-wrap>
<custom-meta>
<meta-name>section-in-acceptance</meta-name>
<meta-value>Cancer Immunity and Immunotherapy</meta-value>
</custom-meta>
</custom-meta-wrap>
</article-meta>
</front>
<body>
<sec id="s1" sec-type="intro">
<label>1</label>
<title>Introduction</title>
<p>Liver cancer has a poor prognosis and ranks third in the list of tumor-related causes of death (<xref ref-type="bibr" rid="B1">1</xref>). The most frequent kind of liver cancer is hepatocellular carcinoma (HCC) (<xref ref-type="bibr" rid="B2">2</xref>). With the development of medicine, great progress has been made in the treatment of HCC (<xref ref-type="bibr" rid="B3">3</xref>). Surgery and liver transplantation are currently the common treatment options for HCC (<xref ref-type="bibr" rid="B4">4</xref>, <xref ref-type="bibr" rid="B5">5</xref>). However, the prognosis of HCC patients does not increase with the progression of treatment. Five-year survival for patients with advanced HCC is only 10%, with a median survival of fewer than 10 months (<xref ref-type="bibr" rid="B6">6</xref>). HCC is a rather complex disease with a high degree of heterogeneity that poses a challenge to the prognostic assessment of patients (<xref ref-type="bibr" rid="B7">7</xref>). For immunotherapy of HCC, the identification and validation of predictive biomarkers remain a major unresolved challenge (<xref ref-type="bibr" rid="B8">8</xref>).</p>
<p>Long non-coding RNAs (lncRNAs), which are usually not translated into proteins, regulate gene expression involved in cell growth and proliferation (<xref ref-type="bibr" rid="B9">9</xref>). According to research, lncRNA is a potential biomarker that plays a critical function in tumor formation (<xref ref-type="bibr" rid="B10">10</xref>). Meanwhile, the lncRNA model can reliably predict the outcome of cancer patients and recommend therapeutic therapy (<xref ref-type="bibr" rid="B11">11</xref>). Therefore, it is practical to study lncRNA to evaluate the outcome of patients with HCC (<xref ref-type="bibr" rid="B12">12</xref>).</p>
<p>N6-methyladenosine (m6A) is the most common RNA modification and a hot issue in the field of cancer research and is abundantly represented in the transcriptome (<xref ref-type="bibr" rid="B13">13</xref>, <xref ref-type="bibr" rid="B14">14</xref>). M6A affects almost all aspects of RNA metabolism, providing new ideas for cancer diagnosis, treatment, and prognosis assessment (<xref ref-type="bibr" rid="B15">15</xref>). The tumor immune microenvironment is an important element in the growth and spread of malignancies (<xref ref-type="bibr" rid="B16">16</xref>). The majority of immune system cells in humans are neutrophils, which serve as tumor patients&#x2019; biomarkers for risk classification (<xref ref-type="bibr" rid="B17">17</xref>, <xref ref-type="bibr" rid="B18">18</xref>). Especially in HCC, the presence of tumor-associated neutrophils is linked to poor prognosis (<xref ref-type="bibr" rid="B19">19</xref>). Neutrophil extracellular traps (NETs) are reticulations whose function is mainly to kill harmful microorganisms (<xref ref-type="bibr" rid="B20">20</xref>). Classical NETs are formed by a process known as &#x201c;NETosis&#x201d;, which is distinct from programmed cell death and is a certain type of controlled cell death (<xref ref-type="bibr" rid="B21">21</xref>). NETs are important for tumor development. By stimulating the immune system, NETs prevent tumor development, whereas tumors can instruct neutrophils to undergo NETosis in order to promote metastasis (<xref ref-type="bibr" rid="B22">22</xref>).</p>
<p>Studies had demonstrated that the expression of m6A-related genes was closely related to the immune microenvironment of malignant tumors and can guide patient immunotherapy (<xref ref-type="bibr" rid="B23">23</xref>). Meanwhile, m6A genes were mainly enriched in the formation of extracellular traps in neutrophils, suggesting that probing the m6A patterns of tumors can help to understand the diversity and complexity of the tumor microenvironment (<xref ref-type="bibr" rid="B23">23</xref>). It has been shown that models that integrate multiple markers into a single model outperform those constructed using a single marker, facilitating individualized patient management (<xref ref-type="bibr" rid="B24">24</xref>). Consequently, combining several kinds of biomarkers is acceptable to create a more accurate model.</p>
<p>Hence, we first identified a set of m6A- and NETs-related lncRNAs (MNlncRNAs) linked to m6A genes and NETs-related genes. We developed a predictive model that can reliably predict patients&#x2019; survival from HCC based on these MNlncRNAs. Also, the immune microenvironment and drug sensitivity of HCC were correlated with MNlncRNAs. This research lays the groundwork for an HCC treatment plan.</p>
</sec>
<sec id="s2" sec-type="materials|methods">
<label>2</label>
<title>Materials and methods</title>
<sec id="s2_1">
<label>2.1</label>
<title>Data acquisition</title>
<p>Transcriptome and clinical data were obtained from the TCGA database. Counts was the workflow type utilized. All data were log2 transformed. All the HCC tissues and adjacent tissues were gathered from 20 HCC patients who had received curative surgery at Second Affiliated Hospital of Nanjing Medical University between 2020 and 2021. The utilization of human tissues was granted ethical approval by the ethics committee of the Second Affiliated Hospital of Nanjing Medical University. Meanwhile, we collected 23 m6A-related genes and 69 NETs-related genes from the published studies. 23 m6A genes were m6A regulators, including 13 readers, 8 writers and 2 erasers (<xref ref-type="bibr" rid="B25">25</xref>). The NETs-related gene set composed of 69 genes summarized the research progress of NETs in immunity and various diseases, mainly covering the ligands and receptors that stimulate the formation of NETs, downstream-related signals, and the molecules identified to adhere to the framework of NETs (<xref ref-type="bibr" rid="B26">26</xref>, <xref ref-type="bibr" rid="B27">27</xref>).</p>
</sec>
<sec id="s2_2">
<label>2.2</label>
<title>Identification of MNlncRNAs</title>
<p>By Pearson correlation analysis, we identified a set of m6A-related lncRNAs and NETs-related lncRNAs. The p-value was set to 0.001 and the correlation coefficient was set at 0.40. Then, We obtained a set of MNlncRNAs by taking the intersection of these two sets of lncRNAs. These MNlncRNAs were used for subsequent analysis.</p>
</sec>
<sec id="s2_3">
<label>2.3</label>
<title>TCGA data process</title>
<p>Before obtaining the count file, the downloaded data were combined and preprocessed with the Perl programming language. The lncRNA symbols were changed using Perl. The TCGA transcriptome data were then matched to MNlncRNAs. Patients with insufficient clinical data and no follow-up days were eliminated. We performed differential analysis (p&lt;0.001) of normal and tumor samples to screen out MNlncRNAs with differential, which were matched to the survival data. In addition, to reduce the effect of noise, patients with zero expression of MNlncRNAs were removed, and a 7:3 ratio of training cohorts (218) to test cohorts (98) was generated from the TCGA dataset at random.</p>
</sec>
<sec id="s2_4">
<label>2.4</label>
<title>Prognostic model construction and evaluation</title>
<p>After matching the MNlncRNAs expression data and clinical data, the univariate COX analysis was performed (p &lt;0.001). Then, the LASSO regression method was utilized to narrow down the list of MNlncRNAs with prognostic significance. The risk score was computed according to the model formula. After that, the prognostic model was built. The prognostic model&#x2019;s performance was validated using the test cohorts.</p>
<p>We divided them into high- and low-risk categories based on the median. Following that, we ran a survival analysis to check if there was any difference in prognosis between the training and test cohorts. Meanwhile, we displayed the sample distribution between the two cohorts to assess the efficacy of stratifying samples. Heatmaps were utilized to compare the expression levels of the model MNlncRNAs. The AUC was used to validate the model&#x2019;s prediction capabilities. In addition, we compared the predictive performance of risk scores with clinical factors.</p>
</sec>
<sec id="s2_5">
<label>2.5</label>
<title>Functional analysis</title>
<p>The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway studies were performed using the &#x201c;clusterProfiler&#x201d; package. To do gene set variation analysis (GSVA), we used the &#x201c;GSVA&#x201d; package. The results were shown using bar charts (p&lt;0.05).</p>
</sec>
<sec id="s2_6">
<label>2.6</label>
<title>Cell culture</title>
<p>HCC cell lines, including PLC, SK, LM3, HepG2 and HuH-7, and human liver cell LO2 were obtained from the American Type Culture Collection (ATCC) and cultured in DMEM medium containing 10% FBS.</p>
</sec>
<sec id="s2_7">
<label>2.7</label>
<title>Quantitative real-time polymerase chain reaction (qRT-PCR)</title>
<p>Utilizing the TRIzol method (Invitrogen, Carlsbad, CA, USA) to extract total RNA from cells or tissues. Reverse transcription followed the instructions of PrimeScriptTM RT reagent kit (TaKaRa, Kyoto, Japan) and qRT-PCR followed the instructions of the CHAMQ SYBR qPCR Master Mix kit (Vazyme, Nanjing, China). The relative gene expression was calculated using the 2<sup>-&#x25b3;&#x25b3;CT</sup> method. All primers sequences in our research are listed in <xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Table&#xa0;1</bold>
</xref>.</p>
</sec>
<sec id="s2_8">
<label>2.8</label>
<title>Transwell migration and invasion assay</title>
<p>Utilizing transwell chambers (8 &#x3bc;m PET; Millipore Corporation, Burlington, MA, USA) to perform transwell assay. Cells (2&#xd7;105/ml) were resuspended in serum-free DMEM medium. For the migration assay, 200&#xb5;l of the cell suspension was added to the upper chamber, and 800&#xb5;l of DMEN medium supplemented with 10% serum was added to lower chamber. For the invasion assay, 200&#xb5;l of the cell suspension was added to the upper chamber precoated with 0.5 mg/L Matrigel (BD Biosciences, Franklin Lakes, NJ, USA), and 800&#xb5;l medium containing with 10% serum was added to lower chamber. After 24 hours of incubation, cells were fixed with methanol for 30 minutes and stained with 0.4% crystal violet for an hour at room temperature. The upper layers of cells were gently erased with cotton swabs, and the chambers were washed 3 times with PBS. The cells were counted in 5 random fields.</p>
</sec>
<sec id="s2_9">
<label>2.9</label>
<title>Colony formation assay</title>
<p>200 untreated cells were seeded in six-well plate and cultivated for 2 weeks. Afterwards, cells were fixed with methanol for 15 minutes and stained with 0.4% crystal violet for 30 minutes at room temperature, and the colonies were analyzed.</p>
</sec>
<sec id="s2_10">
<label>2.10</label>
<title>EDU proliferation assay</title>
<p>20,000 untreated cells were seeded in 96-well plate and cultivated for 24 hours. EDU proliferation assay was performed following the instruction of BeyoClick&#x2122; EdU Cell Proliferation Kit with DAB (Beyotime, Nanjing, China), and the cells were then observed using fluorescent microscope.</p>
</sec>
<sec id="s2_11">
<label>2.11</label>
<title>Immunoassay analysis</title>
<p>Utilizing heatmaps for immune infiltration and correlation maps, the degree of tumor invasion was compared to the model. CIBERSORT and XCELL methods were mainly refered (<xref ref-type="bibr" rid="B28">28</xref>, <xref ref-type="bibr" rid="B29">29</xref>). A list of genes related to immune checkpoints was discovered (<xref ref-type="bibr" rid="B30">30</xref>&#x2013;<xref ref-type="bibr" rid="B33">33</xref>). The boxplots depicted the results of the analyses.</p>
</sec>
<sec id="s2_12">
<label>2.12</label>
<title>Drug sensitivity analysis</title>
<p>We received expression matrices and medication processing data from the Cancer Genome Project. The drugs associated with the prognosis model were derived using the &#x201c;pRROpheticPredict&#x201d; tool (p&lt;0.001) (<xref ref-type="bibr" rid="B34">34</xref>).</p>
</sec>
</sec>
<sec id="s3" sec-type="results">
<label>3</label>
<title>Results</title>
<sec id="s3_1">
<label>3.1</label>
<title>Data processing</title>
<p>After screening, 365 patients with HCC were included in the study. Using Pearson correlation analysis, we obtained 415 m6A-associated lncRNAs and 488 NETs-related lncRNAs. Then, we obtained a total of 209 MNlncRNAs for subsequent analysis after taking the intersection of the two sets of lncRNAs.</p>
</sec>
<sec id="s3_2">
<label>3.2</label>
<title>Prognostic model construction</title>
<p>First, we performed a different analysis and 148 MNlncRNAs with differences in the normal and tumor groups were screened out. After matching the MNlncRNAs expression data and clinical data, we performed the univariate COX analysis and selected 17 MNlncRNAs (<xref ref-type="fig" rid="f1">
<bold>Figure&#xa0;1A</bold>
</xref>). Then through Lasso regression analysis, we selected out 7 MNlncRNAs and built the prognostic model (<xref ref-type="fig" rid="f1">
<bold>Figures&#xa0;1B, C</bold>
</xref>). The model was calculated as follows: risk score = AC074117.1* 0.10679103 + AC026401.3* 0.00817401 + AL355574.1* 0.08725795 + ZEB1.AS1* 0.11541016 + AL031985.3* 0.24377726 + NRAV* 0.11141409 + AC107959.3* 0.03665612.</p>
<fig id="f1" position="float">
<label>Figure&#xa0;1</label>
<caption>
<p>Prognostic model construction. <bold>(A)</bold> Univariate COX analysis. 17 predictive N6-methyladenosine- and neutrophil extracellular traps- related long non-coding RNA (MNlncRNAs) were chosen. MNlncRNAs in red are classified as high risk. <bold>(B, C)</bold> The least absolute selection operator (LASSO) regression analysis. LASSO regression analysis was used to select additional predictive MNlncRNAs.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fimmu-14-1231543-g001.tif"/>
</fig>
<p>
<xref ref-type="fig" rid="f2">
<bold>Figures&#xa0;2A, B</bold>
</xref> demonstrated how we classified HCC samples as high- or low-risk. The risk score increased the percentage of patients who died (<xref ref-type="fig" rid="f2">
<bold>Figures&#xa0;2C, D</bold>
</xref>). Besides, among those at high risk, all the model MNlncRNAs were substantially expressed in both cohorts (<xref ref-type="fig" rid="f2">
<bold>Figures&#xa0;2E, F</bold>
</xref>). The results of the survival research showed that the high-risk group&#x2019;s outcome was much poorer (<xref ref-type="fig" rid="f3">
<bold>Figures&#xa0;3A, B</bold>
</xref>). For the training cohort, the AUCs were 0.740, 0.755, and 0.749 at 1, 3, and 5 years, respectively (<xref ref-type="fig" rid="f3">
<bold>Figure&#xa0;3C</bold>
</xref>). For the test cohort, the AUCs were 0.795, 0.775, and 0.863 at 1, 3, and 5 years, respectively (<xref ref-type="fig" rid="f3">
<bold>Figure&#xa0;3D</bold>
</xref>). Finally, to further evaluate the prognostic value of the model, we compared it with clinical characteristics (TNM stage, age, grade and gender) and found that the model had the highest predictive accuracy (<xref ref-type="fig" rid="f3">
<bold>Figures&#xa0;3E, F</bold>
</xref>).</p>
<fig id="f2" position="float">
<label>Figure&#xa0;2</label>
<caption>
<p>Prognostic model evaluation. <bold>(A, B)</bold> The risk score of training <bold>(A)</bold> and test <bold>(B)</bold> cohorts. <bold>(C, D)</bold> The correlation between survival status and riskscore. <bold>(E, F)</bold> Expression heatmap of 7 model MNlncRNAs.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fimmu-14-1231543-g002.tif"/>
</fig>
<fig id="f3" position="float">
<label>Figure&#xa0;3</label>
<caption>
<p>Prognostic model evaluation. <bold>(A, B)</bold> High-risk patients did poorly in both the training <bold>(A)</bold> and test cohorts <bold>(B)</bold>. <bold>(C, D)</bold> The AUC in both cohorts was essentially in the 0.7&#x2013;0.9 range. <bold>(E, F)</bold> Risk score had the highest predictive accuracy compared with clinical characteristics in both cohorts.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fimmu-14-1231543-g003.tif"/>
</fig>
</sec>
<sec id="s3_3">
<label>3.3</label>
<title>Functional analysis</title>
<p>The key roles of these genes, as determined by the results of the GO enrichment study, were stimulation of mononuclear migration and leukocyte migration in BP, tertiary granule and secretory granule membrance in CC, and immune receptor activity and receptor activity in MF (<xref ref-type="fig" rid="f4">
<bold>Figure&#xa0;4A</bold>
</xref>). Besides, they mostly contributed to neutrophil extracellular trap formation, immune-related signaling pathways, and cytokine&#x2212;cytokine receptor interaction by the KEGG analysis (<xref ref-type="fig" rid="f4">
<bold>Figure&#xa0;4B</bold>
</xref>). The GSVA analysis showed that they also contributed to leukocyte migration, signal transmission, and apoptosis (<xref ref-type="fig" rid="f4">
<bold>Figure&#xa0;4C</bold>
</xref>).</p>
<fig id="f4" position="float">
<label>Figure&#xa0;4</label>
<caption>
<p>Functional analysis. <bold>(A)</bold> The Gene Ontology (GO) analysis. These genes functions were stimulation of mononuclear migration and leukocyte migration in BP, tertiary granule and secretory granule membrance in CC, and immune receptor activity and receptor activity in MF. <bold>(B)</bold> The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. They were mainly involved in cytokine&#x2212;cytokine receptor interaction, neutrophil extracellular trap formation, and immune-related signaling pathways. <bold>(C)</bold> The gene set variation analysis (GSVA). They were mainly involved in leukocyte migration, signal transmission, and apoptosis.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fimmu-14-1231543-g004.tif"/>
</fig>
</sec>
<sec id="s3_4">
<label>3.4</label>
<title>Model validation <italic>in vitro</italic> and <italic>vivo</italic>
</title>
<p>To further verify the reliability of the risk model, we detected the expression of the 7 genes by using qRT-PCR. The results showed significantly increased expression of these genes in HCC cells (PLC, SK, LM3, HepG2 and HuH-7) (<xref ref-type="fig" rid="f5">
<bold>Figures&#xa0;5A&#x2013;G</bold>
</xref>) and tumor tissues from 20 patients diagnosed with hepatocellular carcinoma (<xref ref-type="fig" rid="f5">
<bold>Figures&#xa0;5H&#x2013;N</bold>
</xref>), consistent with these of the bioinformatics analysis. Afterwards, we calculated the risk score of hepatocellular carcinoma cell lines according above calculation method. As shown in <xref ref-type="fig" rid="f6">
<bold>Figure&#xa0;6A</bold>
</xref>, the risk scores of HepG2 (2.4662) and LM3 (2.655) were relatively close. Similarly, the risk scores of PLC (1.5669), SK (1.5028) and HuH-7 (1.3849) were also relatively close. Based on our model, we believe that cells with similar risk scores have little difference in biological characteristics, so we selected cells with the highest and lowest risk scores for functional experiments. Subsequently, we further compared the ability of proliferation and metastasis of LM3 and HuH-7. Colony formation and EDU proliferation assay indicted that LM3 cells proliferation rate was significantly higher than HuH-7 cells (<xref ref-type="fig" rid="f6">
<bold>Figures&#xa0;6B, C</bold>
</xref>). Meanwhile transwell migration and invasion assay was performed, which showed that LM3 cells had higher metastatic potential (<xref ref-type="fig" rid="f6">
<bold>Figure&#xa0;6D</bold>
</xref>). The results confirmed that LM3 had relatively higher malignancy than other cell lines, suggesting that patients with higher risk score had worse prognosis.</p>
<fig id="f5" position="float">
<label>Figure&#xa0;5</label>
<caption>
<p>Expression level analysis. <bold>(A&#x2013;G)</bold> The expression of AL355574.1, AL031985.3, NRAV, ZEB1.AS1, AC026401.3, AC074117.1 and AC107959.3 in normal liver cell and HCC cells were detected by RT-qPCR. <bold>(H&#x2013;N)</bold> Paired comparison of the differential expression of the 7 lncRNAs between 20 HCC tissues and adjacent tissues. *p&lt;0.05; **p&lt;0.01; ***p&lt;0.001; ns, not significant.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fimmu-14-1231543-g005.tif"/>
</fig>
<fig id="f6" position="float">
<label>Figure&#xa0;6</label>
<caption>
<p>Model validation <italic>in vitro</italic>. <bold>(A)</bold> Application of risk model to hepatocellular carcinoma (HCC) cell lines. <bold>(B&#x2013;D)</bold> Colony formation assay, EDU assay, and transwell migration and invasion assay (Scale bar: 100mm) showing that LM3 had relatively higher malignancy than HuH-7. **p&lt;0.01.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fimmu-14-1231543-g006.tif"/>
</fig>
</sec>
<sec id="s3_5">
<label>3.5</label>
<title>Immunoassay analysis</title>
<p>The immune microenvironment had a significant impact on tumor development. B cell, monocyte, T cell, and macrophage immunocorrelation research revealed a high correlation between risk scores and each of these cell types (<xref ref-type="fig" rid="f7">
<bold>Figure&#xa0;7A</bold>
</xref>). In the low-risk group, the Cytolytic_activity, the Type-II-IFN_Reponse, and Type-I-IFN-Response were more activate; In the high-risk group, the MHC_class-I were more activated (<xref ref-type="fig" rid="f7">
<bold>Figure&#xa0;7B</bold>
</xref>). Significant differences in immunological checkpoint gene expression were found between the two groups, as demonstrated by <xref ref-type="fig" rid="f7">
<bold>Figure&#xa0;7C</bold>
</xref>. In the low-risk group, the immune system was more active, indicating that immunotherapy could be beneficial for these individuals. Furthermore, the high-risk group had higher levels of the vast majority of immune checkpoint genes, which raises the possibility that the immunological milieu may differ between the two groups.</p>
<fig id="f7" position="float">
<label>Figure&#xa0;7</label>
<caption>
<p>Immunoassay analysis. <bold>(A)</bold> Significant correlations existed between risk scores and B cells, T cells, monocyte cells, and macrophage cells. <bold>(B)</bold> Low-risk populations have more active immune systems. <bold>(C)</bold> Most immune checkpoint genes had increased expression in the high-risk group. *p&lt;0.05; **p&lt;0.01; ***p&lt;0.001; ns, not significant.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fimmu-14-1231543-g007.tif"/>
</fig>
</sec>
<sec id="s3_6">
<label>3.6</label>
<title>Drug sensitivity analysis</title>
<p>We carry out drug susceptibility testing to find effective medications for targeted therapy. After analysis, in the high-risk group, Camptothecin and Mitomycin.C, were more sensitive (<xref ref-type="fig" rid="f8">
<bold>Figures&#xa0;8A, B</bold>
</xref>). Doxorubicin, Refametinib, and Sorafenib were more sensitive in the low-risk group (<xref ref-type="fig" rid="f8">
<bold>Figures&#xa0;8C&#x2013;E</bold>
</xref>).</p>
<fig id="f8" position="float">
<label>Figure&#xa0;8</label>
<caption>
<p>Drug sensitivity analysis. <bold>(A, B)</bold> Camptothecin <bold>(A)</bold> and Mitomycin.C <bold>(B)</bold> sensitivity was higher in the high-risk group. <bold>(C-E)</bold> Doxorubicin <bold>(C)</bold>, Refametinib <bold>(D)</bold>, and Sorafenib <bold>(E)</bold> were more toxic to the low-risk group.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fimmu-14-1231543-g008.tif"/>
</fig>
</sec>
</sec>
<sec id="s4" sec-type="discussion">
<label>4</label>
<title>Discussion</title>
<p>We used in-depth bioinformatics analysis to investigate the significance of lncRNAs associated with m6A and NETs in HCC in this work. Based on the TCGA database, we constructed a prognostic model based on MNlncRNAs expression, which can accurately predict their prognosis and stratify HCC patients. Additionally, our research revealed substantial variations in the function of MNlncRNAs in the immunological milieu of HCC, which may provide HCC patients a new therapy predictor. By finding more sensitive drugs, drug sensitivity analysis helps stratify the treatment of HCC.</p>
<p>LncRNAs are connected to carcinogenesis and metastasis through aberrant expression, and they are a hub in the area of cancer diagnosis, therapy, and prognosis evaluation (<xref ref-type="bibr" rid="B35">35</xref>, <xref ref-type="bibr" rid="B36">36</xref>). LncRNA can promote or inhibit tumor progression. There have been reports that certain lncRNAs might serve as biomarkers for HCC patients with high sensitivity or be involved in important pathways of tumor regulation (<xref ref-type="bibr" rid="B37">37</xref>). It was shown that lncRNA-PDPK2P promotes the progression of HCC by interacting with PDK1, thereby affecting the value-added and migration of HCC (<xref ref-type="bibr" rid="B38">38</xref>). Prognostic markers of lncRNAs can be used to differentiate immunotherapy responses in cancer patients (<xref ref-type="bibr" rid="B39">39</xref>). Although lncRNA-based prognostic models are beneficial for the prognostic assessment of HCC patients, they have the disadvantage of many variables and lack accuracy (<xref ref-type="bibr" rid="B37">37</xref>). To increase the precision of lncRNA prognostic models, we tried to combine m6A and NETs inspired by the study of Huang et&#xa0;al (<xref ref-type="bibr" rid="B24">24</xref>). Thus, we first identified a set of specific lncRNAs linked to m6A and NETs genes in our study, which were used to construct MNlncRNAs markers. After combining the two prognostic biomarkers, we constructed a prognostic model with superior accuracy, with an AUC value for survival prediction essentially greater than 0.7. In conclusion, the construction of MNlncRNAs-based prognostic models is a great innovation that has superior predictive power than common clinical prognostic models.</p>
<p>According to preliminary results, the prognostic model&#x2019;s model lncRNAs have been linked to the illness&#x2019;s onset and progression. AC074117.1 was regulated by super-enhancers, and its silencing significantly slowed the growth of lung cancer cells (<xref ref-type="bibr" rid="B40">40</xref>). Yao et&#xa0;al. constructed a 4-lncRNA model to estimate the prognosis of individuals with breast cancer in which AC026401.3 played a key role (<xref ref-type="bibr" rid="B41">41</xref>). In the 7-lncRNA prognostic model developed by Yuan et&#xa0;al., AL355574.1 was a key component to assess the prognosis of gastric cancer (<xref ref-type="bibr" rid="B42">42</xref>). It has been demonstrated that increased ZEB1.AS1 expression is linked to tumor development and metastasis (<xref ref-type="bibr" rid="B43">43</xref>). The study by Li et&#xa0;al. screened 15 lncRNAs to estimate the prognosis of individuals with colorectal cancer, and AL031985.3 played a key role in this (<xref ref-type="bibr" rid="B44">44</xref>). NRAV promoted pancreatic cancer progression by targeting miR-299-3p (<xref ref-type="bibr" rid="B45">45</xref>). Huang et&#xa0;al. constructed an 8-lncRNA model to estimate the prognosis of individuals with HCC in which AC107959.3 played an important role (<xref ref-type="bibr" rid="B46">46</xref>). These 7 lncRNAs were included in the prognostic model used in this work, which can help us better understand tumor development.</p>
<p>Death in patients with tumors is more often attributed to metastases than to the primary tumor. The majority of patients die as a result of organ failure, cancer-associated thrombosis, or other problems connected to tumor spread (<xref ref-type="bibr" rid="B47">47</xref>). There is growing evidence that heterogeneity remains between tumors in the same tissue. The energy and nourishment that the tumor microenvironment provides to sustain tumor development and spread is essential for tumor growth (<xref ref-type="bibr" rid="B48">48</xref>). Neutrophils, the most common cells in the human immune system, may serve as a bridge between the tumor parenchyma and the immunological microenvironment. Neutrophil extracellular traps are an important mechanism in innate immunity that is implicated in cancer development and has recently emerged as a hotspot (<xref ref-type="bibr" rid="B49">49</xref>). NETs are expected to play an important function in the tumor immune microenvironment. NETs are a distinct kind of neutrophil that protects tumor cells from immune assault, activates dormant tumor cells, and promotes tumor invasion and metastasis (<xref ref-type="bibr" rid="B50">50</xref>). The colocalization between tumor cells and NETs is closely linked, which would also promote tumor progression (<xref ref-type="bibr" rid="B50">50</xref>). Recent studies have provided a preliminary exploration of the mechanisms by which NETs promote tumor metastasis. NETs can upregulate the TLR9 pathway to promote the progression of diffuse large B lymphoma (<xref ref-type="bibr" rid="B51">51</xref>). CTSC enzymes released by breast cancer cells can control NET development, thus promoting lung metastasis of breast cancer (<xref ref-type="bibr" rid="B52">52</xref>). The tumor microenvironment of HCC can promote early metastasis of HCC by facilitating tumor cell invasion and migration (<xref ref-type="bibr" rid="B53">53</xref>). In recent years, advances in epigenetic techniques provide researchers with new insights into tumor research (<xref ref-type="bibr" rid="B54">54</xref>). An increasing number of studies have focused on tumorigenic progression and m6A modifications of lncRNAs in innate immunity (<xref ref-type="bibr" rid="B55">55</xref>). The most prevalent RNA modification, M6A, is crucial for many cellular processes and biological functions (<xref ref-type="bibr" rid="B56">56</xref>, <xref ref-type="bibr" rid="B57">57</xref>). Factors that affect m6A alteration are linked to both specific malignancies and abnormal immune regulation (<xref ref-type="bibr" rid="B58">58</xref>, <xref ref-type="bibr" rid="B59">59</xref>). The tumor microenvironment is highly correlated with M6A alterations (<xref ref-type="bibr" rid="B60">60</xref>). Additionally, tumor immunotherapy benefits from aspects of tumor microenvironment cell invasion mediated by m6A regulator (<xref ref-type="bibr" rid="B61">61</xref>). Our findings revealed a set of lncRNA signatures associated with m6A and NETs that helped us understand the progression of HCC. The risk score classified all HCC patients into two groups. The majority of cancer progression occurred in high-risk individuals, whereas other patients lived longer.</p>
<p>HCC is a disease that is fueled by inflammation, and a sizable portion of HCC patients show indicators of the inflammatory response (<xref ref-type="bibr" rid="B62">62</xref>). Stromal and tumor cells can produce immunosuppression associated with chronic inflammatory factors (<xref ref-type="bibr" rid="B63">63</xref>). Cells of bone marrow origin, including tumor-associated neutrophils (TANs), promote tumor progression (<xref ref-type="bibr" rid="B64">64</xref>). It has been demonstrated that TANs encourage HCC development, progression, and sorafenib resistance by enlisting macrophages and T cells into the tumor&#x2019;s microenvironment (<xref ref-type="bibr" rid="B65">65</xref>). TAN-induced HCC stem-like cells are active in signaling, CXCL5 secretion, and recruitment of more TAN infiltration (<xref ref-type="bibr" rid="B66">66</xref>). Also, a poor prognosis is linked to the presence of neutrophils in the tumor microenvironment (<xref ref-type="bibr" rid="B67">67</xref>). Importantly, the knockdown of CXCR2, a key chemotactic receptor for neutrophils, to inhibit immune infiltration of neutrophils can lead to a T cell-dependent suppression of tumor growth (<xref ref-type="bibr" rid="B68">68</xref>). Therefore, understanding the immune infiltration of neutrophils is crucial to the diagnosis and management of HCC. Our study stratified patients according to modeled risk scores. The high-risk patients had more immune infiltrating cells, and the majority of immunological checkpoint-related genes have increased expression, indicating that immunotherapy may help the high-risk patients more. For patients in the two groups, we screened for drugs that are sensitive to their treatment, which helped to individualize the treatment for patients.</p>
<p>However, our study possesses certain limitations. The first limitation pertains to the inadequate elucidation of the mechanisms underlying the functionality of these m6A and neutrophil extracellular traps-related lncRNAs. Their role in shaping the tumor microenvironment and tumor growth and progression remains ambiguous, necessitating further investigation. Furthermore, this model is constructed based on the TCGA public database and lacks validation with a larger sample size. Despite these limitations, it is the initial model created incorporating lncRNAs associated with m6A and NETs. It provides information for studying the metabolism of HCC tumors and aids in the treatment of HCC patients.</p>
</sec>
<sec id="s5" sec-type="conclusions">
<label>5</label>
<title>Conclusion</title>
<p>Based on m6A- and NETs-related lncRNAs, a prognostic model of HCC was established. This model can accurately predict the immune microenvironment and prognosis of HCC patients. In addition, our findings could result in new approaches.</p>
</sec>
<sec id="s6" sec-type="data-availability">
<title>Data availability statement</title>
<p>The original contributions presented in the study are included in the article/<xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Material</bold>
</xref>. Further inquiries can be directed to the corresponding authors.</p>
</sec>
<sec id="s7" sec-type="ethics-statement">
<title>Ethics statement</title>
<p>The studies involving humans were approved by The Second Affiliated Hospital of Nanjing Medical University. The studies were conducted in accordance with the local legislation and institutional requirements. The participants provided their written informed consent to participate in this study.</p>
</sec>
<sec id="s8" sec-type="author-contributions">
<title>Author contributions</title>
<p>TZ, WW, and XG designed the study. XG and WB were involved in database search and statistical analyses. TZ and NL were involved in the writing of the manuscript. NL and JZ were responsible for the submission of the final version of the paper. All authors contributed to the article and approved the submitted version.</p>
</sec>
</body>
<back>
<sec id="s9" sec-type="COI-statement">
<title>Conflict of interest</title>
<p>The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.</p>
</sec>
<sec id="s10" sec-type="disclaimer">
<title>Publisher&#x2019;s note</title>
<p>All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.</p>
</sec>
<sec id="s11" sec-type="supplementary-material">
<title>Supplementary material</title>
<p>The Supplementary Material for this article can be found online at: <ext-link ext-link-type="uri" xlink:href="https://www.frontiersin.org/articles/10.3389/fimmu.2023.1231543/full#supplementary-material">https://www.frontiersin.org/articles/10.3389/fimmu.2023.1231543/full#supplementary-material</ext-link>
</p>
<supplementary-material xlink:href="DataSheet_1.pdf" id="SM1" mimetype="application/pdf"/>
</sec>
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