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<front>
<journal-meta>
<journal-id journal-id-type="publisher-id">Front. Cell Dev. Biol.</journal-id>
<journal-title>Frontiers in Cell and Developmental Biology</journal-title>
<abbrev-journal-title abbrev-type="pubmed">Front. Cell Dev. Biol.</abbrev-journal-title>
<issn pub-type="epub">2296-634X</issn>
<publisher>
<publisher-name>Frontiers Media S.A.</publisher-name>
</publisher>
</journal-meta>
<article-meta>
<article-id pub-id-type="publisher-id">843297</article-id>
<article-id pub-id-type="doi">10.3389/fcell.2022.843297</article-id>
<article-categories>
<subj-group subj-group-type="heading">
<subject>Cell and Developmental Biology</subject>
<subj-group>
<subject>Original Research</subject>
</subj-group>
</subj-group>
</article-categories>
<title-group>
<article-title>Transcriptome Profiles of IncRNA and mRNA Highlight the Role of Ferroptosis in Chronic Neuropathic Pain With Memory Impairment</article-title>
<alt-title alt-title-type="left-running-head">Tang et al.</alt-title>
<alt-title alt-title-type="right-running-head">Ferroptosis in Pain With Memory Impairment</alt-title>
</title-group>
<contrib-group>
<contrib contrib-type="author">
<name>
<surname>Tang</surname>
<given-names>Yidan</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/624318/overview"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Liu</surname>
<given-names>Changliang</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/1270694/overview"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Zhu</surname>
<given-names>Tao</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Chen</surname>
<given-names>Hai</given-names>
</name>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Sun</surname>
<given-names>Yalan</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Zhang</surname>
<given-names>Xueying</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/536836/overview"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Zhao</surname>
<given-names>Qi</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Wu</surname>
<given-names>Jiahui</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Fei</surname>
<given-names>Xuejie</given-names>
</name>
<xref ref-type="aff" rid="aff3">
<sup>3</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/1144487/overview"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Ye</surname>
<given-names>Shixin</given-names>
</name>
<xref ref-type="aff" rid="aff4">
<sup>4</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/1460683/overview"/>
</contrib>
<contrib contrib-type="author" corresp="yes">
<name>
<surname>Chen</surname>
<given-names>Chan</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="corresp" rid="c001">&#x2a;</xref>
<uri xlink:href="https://loop.frontiersin.org/people/739120/overview"/>
</contrib>
</contrib-group>
<aff id="aff1">
<sup>1</sup>
<institution>Department of Anesthesiology and National Clinical Research Center for Geriatrics</institution>, <institution>Laboratory of Anesthesia and Critical Care Medicine</institution>, <institution>Translational Neuroscience Center</institution>, <institution>West China Hospital</institution>, <institution>The Research Units of West China</institution>, <institution>Chinese Academy of Medical Science</institution>, <institution>Sichuan University</institution>, <addr-line>Chengdu</addr-line>, <country>China</country>
</aff>
<aff id="aff2">
<sup>2</sup>
<institution>Precision Medicine Research Center</institution>, <institution>West China Hospital</institution>, <institution>Sichuan University</institution>, <addr-line>Chengdu</addr-line>, <country>China</country>
</aff>
<aff id="aff3">
<sup>3</sup>
<institution>Department of Anesthesiology and Perioperative Medicine</institution>, <institution>Shanghai Fourth People&#x2019;s Hospital Affiliated to Tongji University School of Medicine</institution>, <addr-line>Shanghai</addr-line>, <country>China</country>
</aff>
<aff id="aff4">
<sup>4</sup>
<institution>Unit&#xe9; INSERM U1195</institution>, <institution>H&#xf4;pital de Bic&#xea;tre</institution>, <institution>Le Kremlin-Bic&#xea;tre</institution>, <institution>Universit&#xe9; Paris-Saclay</institution>, <addr-line>Paris</addr-line>, <country>France</country>
</aff>
<author-notes>
<fn fn-type="edited-by">
<p>
<bold>Edited by:</bold> <ext-link ext-link-type="uri" xlink:href="https://loop.frontiersin.org/people/1082613/overview">Jun Ren</ext-link>, Fudan University, China</p>
</fn>
<fn fn-type="edited-by">
<p>
<bold>Reviewed by:</bold> <ext-link ext-link-type="uri" xlink:href="https://loop.frontiersin.org/people/1265078/overview">Li Tan</ext-link>, Fudan University, China</p>
<p>
<ext-link ext-link-type="uri" xlink:href="https://loop.frontiersin.org/people/902787/overview">Haixia Xu</ext-link>, Fudan University, China</p>
</fn>
<corresp id="c001">&#x2a;Correspondence: Chan Chen, <email>xychenchan@gmail.com</email>
</corresp>
<fn fn-type="other">
<p>This article was submitted to Cell Death and Survival, a section of the journal Frontiers in Cell and Developmental Biology</p>
</fn>
</author-notes>
<pub-date pub-type="epub">
<day>25</day>
<month>04</month>
<year>2022</year>
</pub-date>
<pub-date pub-type="collection">
<year>2022</year>
</pub-date>
<volume>10</volume>
<elocation-id>843297</elocation-id>
<history>
<date date-type="received">
<day>25</day>
<month>12</month>
<year>2021</year>
</date>
<date date-type="accepted">
<day>21</day>
<month>03</month>
<year>2022</year>
</date>
</history>
<permissions>
<copyright-statement>Copyright &#xa9; 2022 Tang, Liu, Zhu, Chen, Sun, Zhang, Zhao, Wu, Fei, Ye and Chen.</copyright-statement>
<copyright-year>2022</copyright-year>
<copyright-holder>Tang, Liu, Zhu, Chen, Sun, Zhang, Zhao, Wu, Fei, Ye and Chen</copyright-holder>
<license xlink:href="http://creativecommons.org/licenses/by/4.0/">
<p>This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.</p>
</license>
</permissions>
<abstract>
<p>
<bold>Background:</bold> Chronic neuropathic pain is commonly associated with memory loss, which increases the risk of dementia, lowers life quality and spending. On the other hand, the molecular processes are unknown, and effective therapies have yet to be discovered. Long non-coding RNAs (lncRNAs) are emerging potential therapeutic targets for chronic pain, but their role in chronic pain-induced memory impairment is unknown.</p>
<p>
<bold>Methods:</bold> We established a CCI-induced memory impairment rat model. To investigate and validate the gene expression alterations in the hippocampus of CCI-induced memory impairment, we used RNA-Seq, bioinformatics analysis, qRT-PCR, western blot, immunostaining, Nissl staining, and Diaminobenzidine-enhanced Perls&#x2019; stain.</p>
<p>
<bold>Results:</bold> CCI rats displayed long-term memory deficits in the Y maze and novel objective recognition tests, and chronic mechanical and thermal pain hypersensitivity in the hind paws. We found a total of 179 differentially expressed mRNAs (DEmRNAs) (81 downregulated and 98 upregulated) and 191 differentially expressed long noncoding RNAs (DElncRNAs) (87 downregulated and 105 upregulated) between the hippocampus CA1 of CCI-induced memory impairment model and the sham control, using RNA-Seq expression profiles. The most enriched pathways involving oxidation and iron metabolism were explored using a route and function pathway analysis of DEmRNAs and DElncRNAs. We also discovered that ATF3 was considerably overexpressed in the hippocampal CA1 area, and gene markers of ferroptosis, such as GPX4, SLC7A11, SLC1A5, and PTGS2, were dysregulated in the CCI-induced memory impairment paradigm. Furthermore, in the hippocampus CA1 of CCI-induced memory impairment, lipid peroxidation and iron overload were considerably enhanced. Fer-1 treatment reversed ferroptosis damage of CCI with memory impairment model. Finally, in CCI-induced memory impairment, a competing RNA network analysis of DElncRNAs and DEmRNAs was performed to investigate the putative regulatory link of DElncRNAs on DEmRNAs via miRNA sponging.</p>
<p>
<bold>Conclusion:</bold> Using RNA-Seq, we created a genome-wide profile of the whole hippocampus of a rat model of CCI-induced memory impairment. In the hippocampus, pathways and function analyses revealed numerous intriguing genes and pathways involved in ferroptosis and memory impairment in response to chronic pain stress. As a result, our research may aid in the identification of potential and effective treatments for CCI-induced memory impairment.</p>
</abstract>
<kwd-group>
<kwd>pain</kwd>
<kwd>memory impairment</kwd>
<kwd>RNA-seq</kwd>
<kwd>ferroptosis</kwd>
<kwd>ATF3</kwd>
</kwd-group>
</article-meta>
</front>
<body>
<sec id="s1">
<title>1 Introduction</title>
<p>Memory impairment is one of the most common problems in the context of chronic pain stress, mainly manifesting as impairments in attention, learning memory, information processing speed, and executive capacity, and its long-term progression raises the risk of dementia (<xref ref-type="bibr" rid="B9">Dick and Rashiq, 2007</xref>; <xref ref-type="bibr" rid="B26">Moriarty et al., 2011</xref>; <xref ref-type="bibr" rid="B47">Whitlock et al., 2017</xref>; <xref ref-type="bibr" rid="B25">Mazza et al., 2018</xref>; <xref ref-type="bibr" rid="B51">Zhang et al., 2021</xref>). Working memory problems are present in 70% of people with chronic pain worldwide (<xref ref-type="bibr" rid="B3">Berryman et al., 2013</xref>). In recent clinical investigations, patients with peripheral neuropathic pain have objective cognitive deficits (<xref ref-type="bibr" rid="B29">Ojeda et al., 2018</xref>; <xref ref-type="bibr" rid="B41">Tyrtyshnaia and Manzhulo, 2020</xref>). Furthermore, chronic pain with memory loss has been linked to a lower quality of life and increased spending (<xref ref-type="bibr" rid="B47">Whitlock et al., 2017</xref>). However, the cause of pain-related cognitive impairment is unknown, and there is no effective prevention or treatment for chronic pain-related cognitive impairment. Analgesic medications routinely used in clinics can help with pain relief, but they can also cause and/or exacerbate the cognitive dysfunction that comes with it (<xref ref-type="bibr" rid="B26">Moriarty et al., 2011</xref>). Therefore, exploring the etiology and preventative strategies of chronic pain accompanied by cognitive impairment is crucial in therapeutic practice.</p>
<p>Apoptosis, autophagy, and ferroptosis are cell death processes with diverse morphologies and molecular properties that play an essential role in the pathology of neurodegenerative disorders (<xref ref-type="bibr" rid="B28">Moujalled et al., 2021</xref>). The accumulation of lipid peroxidation products and fatal reactive oxygen species characterizes ferroptosis, an iron-dependent, programmed form of cell death (<xref ref-type="bibr" rid="B11">Dixon et al., 2012</xref>). A growing body of evidence suggests that aberrant iron metabolism plays a crucial role in Parkinson&#x2019;s disease, Alzheimer&#x2019;s disease, Huntington&#x2019;s disease, amyotrophic lateral sclerosis, and cerebral hemorrhage models (<xref ref-type="bibr" rid="B37">Stockwell et al., 2017</xref>). A growing body of evidence suggests that aberrant iron metabolism plays a crucial role in Parkinson&#x2019;s disease, Alzheimer&#x2019;s disease, Huntington&#x2019;s disease, amyotrophic lateral sclerosis, and cerebral hemorrhage models (<xref ref-type="bibr" rid="B37">Stockwell et al., 2017</xref>). Moreover, researchers discovered a decreased GPX4 level and an increased ACSL4 expression level (markers of ferroptosis) in the spinal cords of chronic pain model rats and mice and aberrant iron deposition (<xref ref-type="bibr" rid="B45">Wang H et al., 2021</xref>). Furthermore, the ferroptosis inhibitors were revealed to effectively reduce pain behavior, implying that ferroptosis may play a role in chronic pain. Moreover, the ferroptosis inhibitors were found to effectively reduce pain behavior, indicating that ferroptosis may play a role in chronic pain (<xref ref-type="bibr" rid="B15">Guo et al., 2021</xref>). However, it is unclear whether ferroptosis is associated with memory impairment in patients suffering from chronic pain.</p>
<p>Long non-coding RNAs (lncRNAs) are a type of non-coding transcript that is longer than 200 nucleotides (<xref ref-type="bibr" rid="B4">Bhat et al., 2016</xref>), exhibited a potential and multifunctional regulation in gene expression (<xref ref-type="bibr" rid="B42">Ulitsky and Bartel, 2013</xref>). Following peripheral nerve injury, lncRNA expression was found to be dysregulated in nerves (<xref ref-type="bibr" rid="B7">Chen Y et al., 2021</xref>), the dorsal root ganglion (DRG) (<xref ref-type="bibr" rid="B31">Pan et al., 2021</xref>), and the spinal cord (<xref ref-type="bibr" rid="B48">Wu et al., 2021</xref>). While researchers are increasingly focused on the role of lncRNA in chronic pain, the significance of lncRNA in the comorbidity of chronic pain and cognitive impairment remains unknown.</p>
<p>To learn more about the biological pathways that cause chronic pain-induced memory impairment. In a chronic constriction injury (CCI)-induced memory impairment rat paradigm, we performed a genome-wide RNA-Seq (mRNAs and lncRNAs). We also looked into the critical pathological pathways in which differentially expressed genes (DEGs) have a role. Our findings could lead to more research into the intriguing genes or signaling pathways that protect against memory loss caused by prolonged stress.</p>
</sec>
<sec id="s2">
<title>2 Materials and Methods</title>
<sec id="s2-1">
<title>2.1 Animals Preparation and Groups</title>
<p>Male Sprague&#x2013;Dawley rats (5&#x2013;8&#xa0;weeks, 180&#x2013;220&#xa0;g) were purchased from Chengdu Dossy Experimental Animals CO., LTD. (Chengdu, Sichuan, China) and maintained under controlled conditions with no restrictions on food or water on a 12&#xa0;h light/dark cycle. The rats were given some time to adjust to their new surroundings before the experiment. The Animal Care and Use Committee at Sichuan University approved all of the experimental techniques. The experiments <italic>in vivo</italic> were performed in 3 parts. In the first part, rats were randomly divided into Sham and CCI groups for the behavior tests, RNA-seq, and molecular and biochemical analysis. In the second part, rats received CCI induction for validation of transcriptome profiles, detection of iron content, and lipid peroxidation levels. In the third part, rats were divided into the Sham &#x2b; vehicle group, CCI group, CCI &#x2b; vehicle group, CCI &#x2b; Ferrostatin-1 (Fer-1) group. Fer-1 was dissolved in 1% dimethyl sulfoxide (DMSO). For CCI &#x2b; Fer-1, rats were administered with Fer-1 2&#xa0;h after model establishment (intraperitoneal injections (i.p.), 2&#xa0;mg/kg), followed three times a week for 21&#xa0;days. For the Sham &#x2b; vehicle group and CCI &#x2b; vehicle group, rats receive an equal volume of 1% DMSO solvent.</p>
</sec>
<sec id="s2-2">
<title>2.2 Model Establishment</title>
<p>The CCI model was established based on the findings of a prior study (<xref ref-type="bibr" rid="B2">Bennett and Xie, 1988</xref>). Briefly, the left sciatic nerve was exposed at mid-thigh level after rats were sedated and maintained with 2&#x2013;3% isoflurane. The nerve trunk was then loosely tied four times using 4-O gut sutures near the branching site. Only anesthesia, incision, and nerve exposure were given to the sham rats. The rats eventually recovered on a heating pad and were returned to their cages.</p>
</sec>
<sec id="s2-3">
<title>2.3 Behavior Tests</title>
<sec id="s2-3-1">
<title>2.3.1 Mechanical allodynia</title>
<p>As previously reported, von Frey filaments were used to assess mechanical allodynia. Before the experiment, the rats were placed for 30&#xa0;min in a transparent glass frame (22 &#xd7; 10 &#xd7; 14&#xa0;cm). The up-down method used six precisely calibrated von Frey filaments to test the paw withdrawal thresholds (PWTs). Von Frey fiber filaments stimulated the plantar of the rat hind paw in a perpendicular manner (range from 0.008 to 300&#xa0;g). Retraction of the foot, withdrawal or paw licking were all considered positive responses.</p>
</sec>
<sec id="s2-3-2">
<title>2.3.2 Thermal Hyperalgesia</title>
<p>Thermodynamic hyperalgesia was measured using the approach previously described. In addition, the paw withdrawal latencies (PWLs) were measured using a thermal pain stimulator (Ugo Basile business). Three trials with a 5-min gap were given to each rat. The 20&#xa0;s were selected as a stimulation cut-off time to avoid tissue damage.</p>
</sec>
<sec id="s2-3-3">
<title>2.3.3 Cold Test</title>
<p>As described previously, the cold test was carried out (<xref ref-type="bibr" rid="B49">You et al., 2018</xref>), with acetone as the solvent. A hind paw&#x2019;s lateral plantar surface was treated with 50&#xa0;&#x3bc;l of acetone. Bisk foot removal was considered a positive response. Both the paw withdrawal score and the length of the withdrawal were recorded.</p>
</sec>
<sec id="s2-3-4">
<title>2.3.4 Y Maze Test</title>
<p>The Y maze test was used to examine spontaneous modification behavior. The equipment consisted of three identical arms with a 120&#xb0; angle, designated arm A, B, and C (50&#xa0;cm in length, 10&#xa0;cm in width, 25&#xa0;cm in height). Each animal was carefully placed in the maze&#x2019;s center, then tracked and filmed for 8&#xa0;min using a video-tracking device. A spontaneous alternation was defined as entering all three arms in the consecutive order as ABC, BCA, and CAB. The following calculation was used to calculate the percentage of spontaneous alternation: percent spontaneous alternation &#x3d; number of spontaneous alternations/(total arm entries&#x2014;2) &#x2a;100.</p>
</sec>
<sec id="s2-3-5">
<title>2.3.5 Novel Objective Recognition Test</title>
<p>The NOR test was carried out in a box measuring 60 &#xd7; 60 &#xd7; 50&#xa0;cm. The experiment was split into two parts: training and testing. Each animal was placed in a quiet experimental area for at least 30&#xa0;min before the test. For the training step, each rat was placed in a box with two identical objects for 10&#xa0;minutes. Each rat was placed in the box for 5&#xa0;min after a 24-h intertrial interval in the home cage, where one of the familiar objects was swapped with a novel object. Exploratory activity was characterized as sniffing or touching the object, and the total time spent investigating within 1.5&#xa0;cm for each object was recorded. As a result, the new item recognition index is calculated as follows: new object recognition index &#x3d; (time spent investigating the novel object/total time spent exploring the novel and familiar objects).</p>
</sec>
</sec>
<sec id="s2-4">
<title>2.4 Tissue Collection and RNA Extraction</title>
<p>The rats were sedated with sodium pentobarbital (40&#xa0;mg/kg, i. p.) on day 21, and the rat&#x2019;s entire hippocampus was promptly collected under the ice. According to the manufacturer&#x2019;s protocol, the mirVanaTM miRNA ISOlation Kit (Ambion) was used to extract total RNA from the hippocampus of the CCI and sham groups. The Agilent 2,100 Bioanalyzer assessed RNA integrity (Agilent Technologies, Santa Clara, CA, United States). The samples with an RNA Integrity Number (RIN) of 7 were sent for further testing.</p>
</sec>
<sec id="s2-5">
<title>2.5 RNA-Seq Library Establishment and RNA-Seq</title>
<p>The libraries were built using TruSeq Stranded Total RNA with Ribo-Zero Gold, as directed by the manufacturer. To Ribo-Zero deplete and fragment RNA, about 1&#xa0;g total RNA was processed using TruSeq Stranded Total RNA with Ribo-Zero Gold Kit. After that, the first-strand cDNA synthesis was treated with Act D Mix, followed by the second-strand cDNA synthesis. The 3&#x2032;ends of cDNA were then adenylated, and the adapters were ligated to the 3&#x2032;adenylated ends. The PCR Primer Cocktail and PCR Master Mix were also employed to enrich cDNA fragments. The size and purity of the sample were checked using an Agilent Technologies 2,100 Bioanalyzer. Finally, these libraries were sequenced on an Illumina sequencing device (HiSeqTM 2,500 platform), and paired-end reads of 150&#xa0;bp/125 bp were generated.</p>
</sec>
<sec id="s2-6">
<title>2.6 Bioinformatics Analysis and Differentially Expressed Genes Analysis</title>
<p>Quality control (QC) was performed on the primary sequencing data generated by RNA-Seq (raw reads). <xref ref-type="table" rid="T1">Table 1</xref> summarizes the details of total readings and mapping ratio reads. By deleting the adaptor, low-quality bases, low-quality reads, and reads with unknown N bases, Trimmomatic software (<xref ref-type="bibr" rid="B5">Bolger et al., 2014</xref>) filtered the raw reads into high-quality clean reads. HISAT2 (version 2.2.1.0) (<xref ref-type="bibr" rid="B19">Kim et al., 2015</xref>) was used to align the clean reads to the reference genome and the RSeQC (version 2.6.4) (<xref ref-type="bibr" rid="B43">Wang et al., 2012</xref>) technique was used to count the proportions of various comparison types and evaluate the comparison results. Stringtiew2 software (version 1.3.3b) (<xref ref-type="bibr" rid="B32">Pertea et al., 2015</xref>) was used to assemble the reads and splice the new transcript after getting the SAM file with the comparison findings. The candidate lncRNA transcripts were then chosen by comparing the gene annotation information of the reference sequence obtained by Cuffcompare software (version 2.2.1) to the gene annotation information of the candidate lncRNA transcripts (<xref ref-type="bibr" rid="B40">Trapnell et al., 2012</xref>). Finally, to acquire lncRNA predicted sequences, transcripts with coding potential were screened out using CPC (<xref ref-type="bibr" rid="B20">Kong et al., 2007</xref>), Pfam (version v30) (<xref ref-type="bibr" rid="B13">Finn et al., 2006</xref>), and PLEK (version 1.2) (<xref ref-type="bibr" rid="B22">Li et al., 2014</xref>). The sequencing reads were aligned with the sequence of mRNA transcript sequences using Bowtie (version 2.2.9) (<xref ref-type="bibr" rid="B21">Langmead and Salzberg, 2012</xref>). And then, eXpress (version 1.5.1) (<xref ref-type="bibr" rid="B33">Roberts and Pachter, 2013</xref>) was applied to make quantitative gene analysis, the FPKM value, and counts value. Finally, differential expression analysis was done using DESeq2 (version 1.18.0) (<xref ref-type="bibr" rid="B8">Delhomme et al., 2012</xref>) with a <italic>p</italic>-value of 0.05 and &#x7c;Log2 (fold change)&#x7c; of 0.58.</p>
<table-wrap id="T1" position="float">
<label>TABLE 1</label>
<caption>
<p>The total reads and mapping ratio for sham and CCI with memory impairment groups by RNA-Seq.</p>
</caption>
<table>
<thead valign="top">
<tr>
<th align="left">Sample</th>
<th align="center">Total raw reads (Mb)</th>
<th align="center">Total clean reads (Mb)</th>
<th align="center">Clean reads Q30 (30%)</th>
<th align="center">Valid bases (%)</th>
<th align="center">Total mapped reads (%)</th>
</tr>
</thead>
<tbody valign="top">
<tr>
<td align="left">Sham 1</td>
<td align="char" char=".">94.89</td>
<td align="char" char=".">93.35</td>
<td align="char" char=".">93.33</td>
<td align="char" char=".">92.78</td>
<td align="char" char=".">96.61</td>
</tr>
<tr>
<td align="left">Sham 2</td>
<td align="char" char=".">99.48</td>
<td align="char" char=".">97.87</td>
<td align="char" char=".">93.32</td>
<td align="char" char=".">93.03</td>
<td align="char" char=".">96.52</td>
</tr>
<tr>
<td align="left">Sham 3</td>
<td align="char" char=".">97.62</td>
<td align="char" char=".">96</td>
<td align="char" char=".">93.31</td>
<td align="char" char=".">92.22</td>
<td align="char" char=".">96.46</td>
</tr>
<tr>
<td align="left">CCI 1</td>
<td align="char" char=".">95.85</td>
<td align="char" char=".">94.25</td>
<td align="char" char=".">93.01</td>
<td align="char" char=".">92.92</td>
<td align="char" char=".">96.42</td>
</tr>
<tr>
<td align="left">CCI 2</td>
<td align="char" char=".">94.85</td>
<td align="char" char=".">93.36</td>
<td align="char" char=".">93.13</td>
<td align="char" char=".">92.84</td>
<td align="char" char=".">96.4</td>
</tr>
<tr>
<td align="left">CCI 3</td>
<td align="char" char=".">96.6</td>
<td align="char" char=".">94.98</td>
<td align="char" char=".">93.38</td>
<td align="char" char=".">92.66</td>
<td align="char" char=".">96.33</td>
</tr>
</tbody>
</table>
</table-wrap>
</sec>
<sec id="s2-7">
<title>2.7 Functional Enrichment Analysis of Differentially Expressed Genes</title>
<p>The detected DEGs were subjected to gene ontology (GO) (<ext-link ext-link-type="uri" xlink:href="http://geneontology.org/">http://geneontology.org/</ext-link>) and Kyoto Encyclopedia of Gene and Genomes (KEGG) (<ext-link ext-link-type="uri" xlink:href="http://www.genome.jp/kegg/">http://www.genome.jp/kegg/</ext-link>) enrichment analysis based on the hypergeometric distribution test. Biological process (BP), cellular component (CC), and molecular function were all included in the GO study (MF). The enrichment scores were used to rank the KEGG analysis pathways.</p>
</sec>
<sec id="s2-8">
<title>2.8 Real-Time qPCR</title>
<p>Rather than using total RNA from the hippocampus for RNA-Seq, HiScript<sup>&#xae;</sup> III-RT SuperMix (Vazyme Biotech Co., Ltd., China) was used to reverse transcribe total RNA from the hippocampus into cDNA according to the manufacturer&#x2019;s instructions. <xref ref-type="table" rid="T2">Table 2</xref> lists all of the primer sequences used. As an internal reference gene, 18sRNA was employed. The qRT-PCR was performed using a Taq Pro Universal SYBR qPCR Master Mix (Vazyme Biotech Co., Ltd., China) kit with a 20L reaction system and a CFX96 Real-Time System (Bio-Rad Laboratories Inc., Hercules, CA, United States). The expression of the 18sRNA gene was normalized to each reaction of a single sample. The &#x394;&#x394;CT method was applied for the relative gene expression.</p>
<table-wrap id="T2" position="float">
<label>TABLE 2</label>
<caption>
<p>All primers sequence for qRT-PCR analysis.</p>
</caption>
<table>
<thead valign="top">
<tr>
<th align="left">Gene name</th>
<th align="center">Forward</th>
<th align="center">Reverse</th>
</tr>
</thead>
<tbody valign="top">
<tr>
<td align="left">18sRNA</td>
<td align="left">GAC&#x200b;ACG&#x200b;GAC&#x200b;AGG&#x200b;ATT&#x200b;GAC&#x200b;AG</td>
<td align="left">GCT&#x200b;CCA&#x200b;CCA&#x200b;ACT&#x200b;AAG&#x200b;AAC&#x200b;GG</td>
</tr>
<tr>
<td align="left">NFS1</td>
<td align="left">GGA&#x200b;GGC&#x200b;CCT&#x200b;ACA&#x200b;AAG&#x200b;TGG&#x200b;AG</td>
<td align="left">CCA&#x200b;TCT&#x200b;CCC&#x200b;AGA&#x200b;GAG&#x200b;GAC&#x200b;TCA</td>
</tr>
<tr>
<td align="left">CARTPT</td>
<td align="left">GGA&#x200b;CAT&#x200b;CTA&#x200b;CTC&#x200b;TGC&#x200b;CGT&#x200b;GG</td>
<td align="left">CAA&#x200b;TCT&#x200b;GCA&#x200b;ACA&#x200b;CAG&#x200b;CGC&#x200b;C</td>
</tr>
<tr>
<td align="left">APH1B</td>
<td align="left">GGGTACCATGACAGCGCC</td>
<td align="left">CCA&#x200b;GCG&#x200b;TCA&#x200b;TGA&#x200b;AAG&#x200b;CTG&#x200b;AAT&#x200b;TA</td>
</tr>
<tr>
<td align="left">NDUFA10</td>
<td align="left">GCC&#x200b;TTG&#x200b;AGG&#x200b;TTG&#x200b;CTG&#x200b;AGA&#x200b;CT</td>
<td align="left">GAT&#x200b;GGA&#x200b;ACG&#x200b;CTC&#x200b;CAA&#x200b;GAC&#x200b;CA</td>
</tr>
<tr>
<td align="left">MRPL53</td>
<td align="left">GTG&#x200b;GAG&#x200b;TCA&#x200b;ACA&#x200b;AGG&#x200b;ACC&#x200b;TTT&#x200b;C</td>
<td align="left">TGG&#x200b;TTA&#x200b;AGC&#x200b;AGT&#x200b;GAG&#x200b;AAA&#x200b;GAA&#x200b;AAA</td>
</tr>
<tr>
<td align="left">ATF3</td>
<td align="left">CGACCAACCCGCGCTC</td>
<td align="left">CTC&#x200b;TCC&#x200b;AGT&#x200b;TTC&#x200b;TCT&#x200b;GAC&#x200b;TCC&#x200b;TTC&#x200b;T</td>
</tr>
<tr>
<td align="left">CBLN1</td>
<td align="left">AGA&#x200b;CCA&#x200b;TCC&#x200b;AGG&#x200b;TGA&#x200b;GCC&#x200b;T</td>
<td align="left">AGG&#x200b;AAC&#x200b;CAT&#x200b;AAT&#x200b;GAC&#x200b;AAG&#x200b;GCA</td>
</tr>
<tr>
<td align="left">MT1</td>
<td align="left">CTG&#x200b;CTG&#x200b;CCC&#x200b;TCA&#x200b;GGT&#x200b;GTA&#x200b;AA</td>
<td align="left">ATG&#x200b;CTC&#x200b;GGT&#x200b;AGA&#x200b;AAA&#x200b;CGG&#x200b;GG</td>
</tr>
<tr>
<td align="left">OXTR</td>
<td align="left">CTG&#x200b;CTG&#x200b;TGT&#x200b;CGT&#x200b;CTG&#x200b;GTC&#x200b;AA</td>
<td align="left">GCT&#x200b;TGA&#x200b;CAC&#x200b;TAC&#x200b;TGA&#x200b;CCC&#x200b;GT</td>
</tr>
<tr>
<td align="left">LOC102549072</td>
<td align="left">GTC&#x200b;CTT&#x200b;TCA&#x200b;GTC&#x200b;TTG&#x200b;CGG&#x200b;GA</td>
<td align="left">CCT&#x200b;AAG&#x200b;TCC&#x200b;TCC&#x200b;GAC&#x200b;CCA&#x200b;GA</td>
</tr>
<tr>
<td align="left">LOC103693876</td>
<td align="left">GTA&#x200b;GAA&#x200b;CCC&#x200b;ACA&#x200b;CGC&#x200b;AGG&#x200b;AA</td>
<td align="left">AGA&#x200b;AGC&#x200b;AGG&#x200b;CAA&#x200b;ATT&#x200b;CCC&#x200b;GA</td>
</tr>
<tr>
<td align="left">LOC102550954</td>
<td align="left">ACC&#x200b;ATG&#x200b;GTC&#x200b;AAT&#x200b;GGC&#x200b;ACT&#x200b;GT</td>
<td align="left">TCT&#x200b;GGA&#x200b;ACC&#x200b;AGG&#x200b;ACT&#x200b;GAC&#x200b;CA</td>
</tr>
<tr>
<td align="left">LOC108351425</td>
<td align="left">TGG&#x200b;GAA&#x200b;CCA&#x200b;GAA&#x200b;CCC&#x200b;AAA&#x200b;TGT</td>
<td align="left">TGG&#x200b;CAG&#x200b;TGA&#x200b;TTG&#x200b;GTA&#x200b;TTG&#x200b;AGG</td>
</tr>
<tr>
<td align="left">LOC103691475</td>
<td align="left">TGA&#x200b;GGG&#x200b;GGT&#x200b;TAA&#x200b;TCA&#x200b;GGT&#x200b;GT</td>
<td align="left">TGC&#x200b;ACT&#x200b;CTT&#x200b;TTG&#x200b;GTG&#x200b;TCA&#x200b;GT</td>
</tr>
<tr>
<td align="left">LOC108352208</td>
<td align="left">GAG&#x200b;GTT&#x200b;CAG&#x200b;GAA&#x200b;GAG&#x200b;CAC&#x200b;CAG</td>
<td align="left">AAC&#x200b;AGG&#x200b;AGC&#x200b;TAC&#x200b;CCA&#x200b;CCA&#x200b;AGA&#x200b;G</td>
</tr>
<tr>
<td align="left">LOC103694103</td>
<td align="left">GGC&#x200b;TTC&#x200b;AAA&#x200b;AGG&#x200b;CTG&#x200b;TGG&#x200b;TG</td>
<td align="left">GTG&#x200b;GAG&#x200b;GTG&#x200b;TGT&#x200b;CAG&#x200b;CAG&#x200b;TT</td>
</tr>
<tr>
<td align="left">LOC103693799</td>
<td align="left">TGA&#x200b;TGA&#x200b;ACA&#x200b;GGG&#x200b;GCA&#x200b;TCT&#x200b;GAA</td>
<td align="left">GCA&#x200b;CAC&#x200b;CCT&#x200b;ACA&#x200b;TCT&#x200b;CAA&#x200b;GCA</td>
</tr>
<tr>
<td align="left">GPX4</td>
<td align="left">CAA&#x200b;AGT&#x200b;CCT&#x200b;AGG&#x200b;AAG&#x200b;CGC&#x200b;CC</td>
<td align="left">GCA&#x200b;TCG&#x200b;TCC&#x200b;CCA&#x200b;CTT&#x200b;ACA&#x200b;CA</td>
</tr>
<tr>
<td align="left">SLC7A11</td>
<td align="left">GTG&#x200b;TTT&#x200b;GCT&#x200b;GTC&#x200b;TCC&#x200b;AGG&#x200b;TTA&#x200b;T</td>
<td align="left">TCT&#x200b;TTA&#x200b;GAG&#x200b;TCT&#x200b;TCT&#x200b;GGT&#x200b;ACA&#x200b;ACT&#x200b;T</td>
</tr>
<tr>
<td align="left">SLC1A5</td>
<td align="left">GGG&#x200b;CTG&#x200b;TAG&#x200b;GAT&#x200b;GAC&#x200b;AGG&#x200b;AAT</td>
<td align="left">GTC&#x200b;CCG&#x200b;AAA&#x200b;GCT&#x200b;GTA&#x200b;GCC&#x200b;AG</td>
</tr>
<tr>
<td align="left">PTGS2</td>
<td align="left">ACG&#x200b;TGT&#x200b;TGA&#x200b;CGT&#x200b;CCA&#x200b;GAT&#x200b;CA</td>
<td align="left">ACG&#x200b;TGG&#x200b;GGA&#x200b;GGG&#x200b;TAG&#x200b;ATC&#x200b;AT</td>
</tr>
</tbody>
</table>
</table-wrap>
</sec>
<sec id="s2-9">
<title>2.9 Western Blot</title>
<p>Western blot was used to determine the protein expression levels in the hippocampus corresponding to the identified genes. The tissues were suspended in lysis buffer containing 50&#xa0;mM Tris (pH 8.0), 150&#xa0;mM NaCl, and protease inhibitors and further sonicated for 30&#xa0;s at 10% amplitude (ultrasonic cell crusher, Ningbo) to sufficiently dissolve the total proteins. The total proteins in the supernatant were collected using a 16,000&#xa0;g centrifuge at 4&#xb0;C for 20&#xa0;min. The protein concentration of supernatants was determined using a BCA assay kit (Beyotime, Nanjing, China). Protein samples were separated on polyacrylamide gels with a 15% polyacrylamide content and then transferred to PVDF membranes (0.45 mm, Millipore, Bedford, MA, United States). The membranes were blocked for 1&#xa0;hour at room temperature with 5 percent nonfat milk (BD Biosciences) in Tris-buffered saline with 0.1 percent Tween (TBST), then incubated overnight at 4&#xb0;C with the primary antibodies anti-ATF3 (abs136180, Absin), anti-GPX4 (A1933, ABclonal), and anti-SLC7A11 (PA1-16893, Thermo Fisher, United States). The membranes were treated in TBST containing 5% nonfat milk for 1&#xa0;hour at room temperature with horseradish peroxidase-conjugated anti-Rabbit IgG (Goat mAb, Abcam, ab6721). The Enhanced Chemiluminescence Kit (Thermo Pierce, Waltham, MA, United States) was used to detect the immunoreactivity, which was then viewed using ImageJ (BIO-RAD, United States). The -tubulin expression levels were used to normalize the sample&#x2019;s expression levels.</p>
</sec>
<sec id="s2-10">
<title>2.10 Protein-Protein Interaction Network Analysis</title>
<p>The DEGs&#x2019; interactive network was built using the STRING database (<ext-link ext-link-type="uri" xlink:href="http://string-db.org/">http://string-db.org/</ext-link>). The interactions score &#x3e;0.4 was used as the reliability threshold value (<xref ref-type="bibr" rid="B30">Otasek et al., 2019</xref>). The Cytoscape program (version 3.8.2) was used to view further and analyze the PPI network (<xref ref-type="bibr" rid="B34">Shannon et al., 2003</xref>). Finally, the relevance of this network was determined by calculating the connectivity degree of each protein, which is the number of proteins with which it interacts.</p>
</sec>
<sec id="s2-11">
<title>2.11 Competing Endogenous RNA Analysis of DElncRNAs and DEmRNAs</title>
<p>The miRanda database was used to predict interactions between lncRNA and miRNAs. The OmicStudio tools (<ext-link ext-link-type="uri" xlink:href="https://www.omicstudio.cn/tool">https://www.omicstudio.cn/tool</ext-link>) were then used to determine the likely target binding of miRNA and mRNA interactions using the TargetScan and miRanda databases.</p>
</sec>
<sec id="s2-12">
<title>2.12 Rat Reactive Oxygen Species ELISA Assessment</title>
<p>Following the instructions, ROS was assessed via the ROS ELISA kit (Beyotime, Nanjing, China). The rats were sedated with sodium pentobarbital (40&#xa0;mg/kg, i. p.) on day 21, and the rat&#x2019;s entire hippocampus was promptly collected. The rats were sedated with sodium pentobarbital (40&#xa0;mg/kg, i. p.) on day 21, and the rat&#x2019;s entire hippocampus was promptly collected. The entire hippocampal tissue was then crushed with a sufficient amount of normal saline to create tissue homogenate. The tissue homogenate was centrifuged at 3,000&#xa0;rpm for 10&#xa0;min to obtain the supernatant. ROS, malondialdehyde (MDA), superoxide dismutase (SOD), and reduced glutathione (GSH) were all measured in the supernatant. For ROS detection, all reagents were prepared before starting the assay procedure according to the manufacturer&#x2019;s instructions. Standards and sample diluent were added into standard and testing sample wells, respectively. After that, 100&#xa0;&#x3bc;l of HRP-conjugate reagent was added to each test well and incubated for 60&#xa0;min at 37&#xb0;C. Following that, chromogen solutions A and B were added to each well, and all of the wells were incubated at 37&#xb0;C for 15&#xa0;min. Finally, a stop solution was applied to each well, and the Optical Density (OD) at 450&#xa0;nm was determined within 15&#xa0;min using a microplate reader.</p>
</sec>
<sec id="s2-13">
<title>2.13 Lipid Peroxidation Determination</title>
<p>The MDA level of the hippocampus was evaluated using an MDA assay kit as a marker of lipid peroxidation (A003-1, Nanjing Jiancheng Bioengineering Institute, Nanjing, China). According to the manufacturer&#x2019;s instructions, standards, anhydrous alcohol, sample diluent, reagents, and 50% glacial acetic acid were all put to corresponding centrifugal tubes. After mixing, all centrifugal tubes were incubated at 95&#xb0;C for 40&#xa0;min before centrifuging for 10&#xa0;min at 3,000&#xa0;rpm to extract the supernatant. The ODs were measured at 532&#xa0;nm using a microplate reader.</p>
</sec>
<sec id="s2-14">
<title>2.14 Superoxide Dismutase Activity and GSH Content Measurement</title>
<p>The SOD activity was measured using the SOD test kit (A001-3; Nanjing Jiancheng Bioengineering Institute, Nanjing, China). The GSH assay kit was used to determine the amount of GSH in the body (A006-2-1, Nanjing Jiancheng Bioengineering Institute, Nanjing, China). The assay was performed according to the manufacturer&#x2019;s instructions.</p>
</sec>
<sec id="s2-15">
<title>2.15 Immunofluorescence Staining</title>
<p>On day 21, the rats were anesthetized with sodium pentobarbital (40&#xa0;mg/kg, i. p.) and perfused with 0.9 percent saline (4&#xb0;C) and 4 percent paraformaldehyde in PBS (4&#xb0;C) via the ascending aorta. The hippocampus was then removed, fixed for 24&#xa0;h in 4% paraformaldehyde, and dehydrated in a 30% sucrose solution. A frozen microtome was used to cut transverse brain sections (40&#xa0;&#x3bc;m). The sections were first blocked in 5% normal donkey serum in PBS with 0.1% triton for 1&#xa0;hour at room temperature. Next, they were treated overnight with rabbit anti-ATF3 (abs136180, Absin), anti-NeuN (66836-1-1g, Proteintech), and anti-GFAP primary antibodies (BSM-33065M, Bioss). After washing with PBS, the sections were incubated for 1&#xa0;hour at room temperature with the second Cy3-, Cy5-, or fluorescein isothiocyanate (FITC)-conjugated secondary antibodies. The sections were then incubated in DAPI for 10&#xa0;min at room temperature. Finally, an automatically inverted fluorescent microscope (Olympus, Japan) was used to view the sections blindly. The percentage of the stained area of each selected image was calculated using ImageJ software. Three to five images were randomly selected per rat tissue.</p>
</sec>
<sec id="s2-16">
<title>2.16 Nissl Staining</title>
<p>Transverse brain sections (20&#xa0;&#x3bc;m) were prepared with a frozen microtome. The staining was performed following the manufacturer&#x2019;s directions using Nissl Staining Solution (C0117, Beyotime, Nanjing, China). The sections were fixed with 4% paraformaldehyde for more than 10&#xa0;min before staining and then rinsed twice with distilled water. Next, the sections were stained for 10&#xa0;min with Nissl staining and then rinsed twice with distilled water. All of the sections were dehydrated with 95 percent ethanol and then treated with xylene for transparency. Finally, an automatically inverted fluorescent microscope (Olympus, Japan) was used to view the sections blindly.</p>
</sec>
<sec id="s2-17">
<title>2.17 Diaminobenzidine-Enhanced Perls&#x2019; Stain</title>
<p>DAB-enhanced Perls&#x2019; stain was applied as specific ferric staining. Transverse brain sections (10&#xa0;&#x3bc;m) were prepared with a frozen microtome. The staining procedure was followed exactly as described previously (<xref ref-type="bibr" rid="B27">Moroishi et al., 2011</xref>). Briefly, the tissue slices were rinsed with distilled water and treated for 30&#xa0;min with Perls reagent (5% potassium ferrocyanide, 5% HCl), then washed again in distilled water before incubation for 15&#xa0;min with DAB (0.05% DAB in distilled water). An automatically inverted fluorescent microscope (Olympus, Japan) was then used to observe the sections blindly.</p>
</sec>
<sec id="s2-18">
<title>2.18 Iron Content Measurement</title>
<p>The iron content of the hippocampus and serum were measured to see if there was any evidence of iron overproduction. The measurements were performed using the tissue iron assay kit (A039-2-1, Nanjing Jiancheng Bioengineering Institute, Nanjing, China) and the serum iron assay kit (A039-1-1, Nanjing Jiancheng Bioengineering Institute, Nanjing, China). The tests were carried out under the manufacturer&#x2019;s instructions. The ODs were measured at 532&#xa0;nm using a microplate reader.</p>
</sec>
<sec id="s2-19">
<title>2.19 Statistical Analysis</title>
<p>GraphPad prism 9.0 was used for statistical analysis. For comparisons between two groups, the Student&#x2019;s t test was used. When comparing the population mean of various related groups, ANOVA tests are acceptable. In graphs, all data is provided as means &#xb1; SD. If <italic>p</italic> &#x3c; 0.05, the comparison is regarded as statistically significant.</p>
</sec>
</sec>
<sec id="s3">
<title>3 Results</title>
<sec id="s3-1">
<title>3.1 Establishment of the Rat Model of Chronic Constriction Injury Induced Memory Impairment</title>
<p>We started by establishing a CCI rat model with memory impairment. After that, the flowchart was used to look at nociceptive thresholds and cognitive activities after CCI (<xref ref-type="fig" rid="F1">Figure 1A</xref>). PWT and PWL decreased dramatically and consistently in the CCI group (<xref ref-type="fig" rid="F1">Figures 1B,C</xref>). In addition, the CCI group developed prolonged cold hyperalgesia (<xref ref-type="fig" rid="F1">Figures 1D,E</xref>). In the Y maze test, spontaneous alternation was considerably reduced on day 7 after CCI compared to the sham group and continued until the conclusion of the observation period (day 21) (<xref ref-type="fig" rid="F1">Figure 1F</xref>). After CCI, the discrimination index in the NOR test was considerably lower on day 21 (<xref ref-type="fig" rid="F1">Figure 1G</xref>). These findings revealed that a successful model of CCI with a memory problem had been established.</p>
<fig id="F1" position="float">
<label>FIGURE 1</label>
<caption>
<p>The rat model of CCI exhibits persistent mechanical and thermal hypersensitivities and accompanied by long-term memory deficit. <bold>(A)</bold>: The flowchart of the establishment of the CCI-induced memory impairment rat model. <bold>(B)</bold>: 50% paw withdrawal thresholds (PWTs) of the left hind paw of sham and CCI-induced memory impairment rats. <bold>(C)</bold>: 50% paw withdrawal latencies (PWLs) of the left hind paw of sham and CCI-induced memory impairment rats. <bold>(D,E)</bold>: Mean withdrawal scores and duration of cold hyperalgesia. <bold>(F)</bold>: %spontaneous alternation in the Y maze test. <bold>(G)</bold>: Recognition index in the NOR test. n &#x3d; 6&#x2013;9 rats/group. &#x2a;<italic>p</italic> &#x3c; 0.05, &#x2a;&#x2a;<italic>p</italic> &#x3c; 0.01, &#x2a;&#x2a;&#x2a;<italic>p</italic> &#x3c; 0.001, &#x2a;&#x2a;&#x2a;&#x2a;<italic>p</italic> &#x3c; 0.0001 vs sham group. Student&#x2019;s t and ANOVA tests were used for comparisons.</p>
</caption>
<graphic xlink:href="fcell-10-843297-g001.tif"/>
</fig>
</sec>
<sec id="s3-2">
<title>3.2 Transcriptome Profiling of Hippocampus of Chronic Constriction Injury Rats With Memory Impairment by RNA-Seq</title>
<p>We harvested the hippocampus of CCI with memory impairment rats and sham rats to investigate the causes of CCI-induced memory impairment. RNA-Seq was then used to examine the mRNA and lncRNA expression profiles. The sequencing yielded over 95&#xa0;million raw reads per sample, with a clean reads Q30 ratio of almost 93.0% (<xref ref-type="table" rid="T1">Table 1</xref>). RNA-Seq resulted in the mapping and identification of 22,601 mRNAs and 15,683 lncRNAs. We then set the filtering criterion for the DEGs to be <italic>p</italic>-value 0.05 and &#x7c;Log2 (fold change)&#x7c; 0.58, as seen in the volcano figure (<xref ref-type="sec" rid="s12">Supplementary Figure S1A, B</xref>). As a result, 179 DEmRNAs and 191 DElncRNAs have been discovered (<xref ref-type="sec" rid="s12">Supplementary Figure S1A, B</xref> and <xref ref-type="sec" rid="s12">Supplementary Table S1, B</xref>). We next used a heat map to describe the DEGs we found, followed by hierarchical clustering analysis. There was a substantial distinction between the sham and the CCI groups with memory impairment. In addition, the results showed clear segregation between the sham and CCI with memory impairment groups (<xref ref-type="sec" rid="s12">Supplementary Figure S1C,D</xref>).</p>
</sec>
<sec id="s3-3">
<title>3.3 Analysis of DEmRNAs and DElncRNAs in the Hippocampus of Chronic Constriction Injury With Memory Impairment Model Rats</title>
<p>Some of the DEmRNAs and DElncRNAs we found have been linked to oxidative stress or cognitive disorders, such as <italic>SLC27A2</italic> (solute carrier family 27 member 2, fold change &#x3d; 2.332164385), <italic>LOC108348106</italic> (alpha-ketoglutarate-dependent dioxygenase alkB homolog 6, fold change &#x3d; 3.135245512), <italic>SLC18A1</italic> (solute carrier family 18 member A1, fold change &#x3d; 0.590955033), <italic>NDUFA10</italic> (NADH dehydrogenase (ubiquinone) 1 alpha subcomplex 10-like 1, fold change &#x3d; 0.480971719), <italic>BMP4</italic> (bone morphogenetic protein 4, fold change &#x3d; 0.607791806), <italic>GDF7</italic> (growth differentiation factor 7, fold change &#x3d; 0.194844902), <italic>OXTR</italic> (oxytocin receptor, fold change &#x3d; 2.250338978), <italic>CBLN1</italic> (cerebellin 1 precursor, fold change &#x3d; 2.247821962). There were 25 DEmRNAs with expression changes greater than 5-fold, with 13 upregulated mRNAs (such as <italic>LOC100911730</italic> with 54.98731663 of fold change) and 12 downregulated mRNAs (such as <italic>LOC685716</italic> with 0.025834514 of fold change). <italic>TCONS_00012750</italic> (fold change &#x3d; 288.6572008), <italic>TCONS_00012029</italic> (fold change &#x3d; 226.3665341), <italic>TCONS_00030575</italic> (fold change &#x3d; 0.004728013), <italic>TCONS_00026782</italic> (fold change &#x3d; 0.00562614) were among the 46 upregulated genes and 32 downregulated genes identified in the DElncRNA profile. <xref ref-type="table" rid="T3">Tables 3</xref>, <xref ref-type="table" rid="T4">4</xref>, <xref ref-type="table" rid="T5">5</xref> and <xref ref-type="table" rid="T6">6</xref> describe the Top 20 up- and down-regulated genes in further detail.</p>
<table-wrap id="T3" position="float">
<label>TABLE 3</label>
<caption>
<p>The detail of the top 20-upregulated DEmRNAs.</p>
</caption>
<table>
<thead valign="top">
<tr>
<th align="left">Upregulated gene name</th>
<th align="center">Gene ID</th>
<th align="center">Location</th>
<th align="center">Log2 (fold change) (CCI/Sham)</th>
<th align="center">
<italic>p</italic> value</th>
</tr>
</thead>
<tbody valign="top">
<tr>
<td align="left">LOC100911730</td>
<td align="char" char=".">64315</td>
<td align="char" char="ndash">196564744&#x2013;196568753</td>
<td align="char" char=".">5.78102698</td>
<td align="center">0.01230071</td>
</tr>
<tr>
<td align="left">Tsen34l1</td>
<td align="char" char=".">100909510</td>
<td align="char" char="ndash">63242432&#x2013;63250265</td>
<td align="char" char=".">5.57491881</td>
<td align="center">0.00877734</td>
</tr>
<tr>
<td align="left">Six2</td>
<td align="char" char=".">366542</td>
<td align="char" char="ndash">8974859&#x2013;8981345</td>
<td align="char" char=".">4.97072558</td>
<td align="center">0.02731944</td>
</tr>
<tr>
<td align="left">LOC100912573</td>
<td align="char" char=".">293749</td>
<td align="char" char="ndash">208243561&#x2013;208255400</td>
<td align="char" char=".">4.5235508</td>
<td align="center">0.03086266</td>
</tr>
<tr>
<td align="left">Yipf7</td>
<td align="char" char=".">364147</td>
<td align="char" char="ndash">38571045&#x2013;38599070</td>
<td align="char" char=".">4.3849271</td>
<td align="center">0.03951931</td>
</tr>
<tr>
<td align="left">Adam5</td>
<td align="char" char=".">498654</td>
<td align="char" char="ndash">67223095&#x2013;67298733</td>
<td align="char" char=".">3.96381527</td>
<td align="center">0.02477011</td>
</tr>
<tr>
<td align="left">Fkbp6</td>
<td align="char" char=".">288597</td>
<td align="char" char="ndash">21318251&#x2013;21390350</td>
<td align="char" char=".">3.25554386</td>
<td align="center">0.00830697</td>
</tr>
<tr>
<td align="left">Tnnt1</td>
<td align="char" char=".">171409</td>
<td align="char" char="ndash">69306362&#x2013;69316721</td>
<td align="char" char=".">3.20696783</td>
<td align="center">0.00022016</td>
</tr>
<tr>
<td align="left">RGD1562652</td>
<td align="char" char=".">499402</td>
<td align="char" char="ndash">2632898&#x2013;2635694</td>
<td align="char" char=".">2.64444974</td>
<td align="center">0.0097335</td>
</tr>
<tr>
<td align="left">LOC103690118</td>
<td align="char" char=".">83836</td>
<td align="char" char="ndash">839788&#x2013;883946</td>
<td align="char" char=".">2.63854731</td>
<td align="center">0.0103477</td>
</tr>
<tr>
<td align="left">LOC100909392</td>
<td align="char" char=".">292944</td>
<td align="char" char="ndash">12698107&#x2013;12775561</td>
<td align="char" char=".">2.60782392</td>
<td align="center">0.0000251</td>
</tr>
<tr>
<td align="left">Ces1d</td>
<td align="char" char=".">113902</td>
<td align="char" char="ndash">13873490&#x2013;13912035</td>
<td align="char" char=".">2.48941746</td>
<td align="center">0.04505145</td>
</tr>
<tr>
<td align="left">Tbcb</td>
<td align="char" char=".">292777</td>
<td align="char" char="ndash">85477639&#x2013;85483488</td>
<td align="char" char=".">2.35883642</td>
<td align="center">0.0000165</td>
</tr>
<tr>
<td align="left">Phykpl</td>
<td align="char" char=".">100169747</td>
<td align="char" char="ndash">35839965&#x2013;35863631</td>
<td align="char" char=".">2.25983594</td>
<td align="center">0.0000411</td>
</tr>
<tr>
<td align="left">Prg4</td>
<td align="char" char=".">289104</td>
<td align="char" char="ndash">62487257&#x2013;62504657</td>
<td align="char" char=".">2.25639342</td>
<td align="center">0.02979234</td>
</tr>
<tr>
<td align="left">LOC100912228</td>
<td align="char" char=".">24604</td>
<td align="char" char="ndash">78881294&#x2013;78888495</td>
<td align="char" char=".">2.24267013</td>
<td align="center">4.61E-08</td>
</tr>
<tr>
<td align="left">LOC100911186</td>
<td align="char" char=".">140547</td>
<td align="char" char="ndash">194895036&#x2013;194903863</td>
<td align="char" char=".">2.20391882</td>
<td align="center">0.00244014</td>
</tr>
<tr>
<td align="left">Pnpla2</td>
<td align="char" char=".">361676</td>
<td align="char" char="ndash">196552723&#x2013;196557805</td>
<td align="char" char=".">2.1788874</td>
<td align="center">0.000012</td>
</tr>
<tr>
<td align="left">Hprt1</td>
<td align="char" char=".">24465</td>
<td align="char" char="ndash">132736175&#x2013;132768149</td>
<td align="char" char=".">2.08657003</td>
<td align="center">0.00037877</td>
</tr>
<tr>
<td align="left">LOC685933</td>
<td align="char" char=".">685933</td>
<td align="char" char="ndash">236603597&#x2013;236685859</td>
<td align="char" char=".">2.02708822</td>
<td align="center">0.03049839</td>
</tr>
</tbody>
</table>
</table-wrap>
<table-wrap id="T4" position="float">
<label>TABLE 4</label>
<caption>
<p>The detail of the top 20-downregulated DEmRNAs.</p>
</caption>
<table>
<thead valign="top">
<tr>
<th align="left">Down-regulated gene name</th>
<th align="center">Gene ID</th>
<th align="center">Location</th>
<th align="center">Log2 (fold change) (CCI/Sham)</th>
<th align="center">
<italic>p</italic> value</th>
</tr>
</thead>
<tbody valign="top">
<tr>
<td align="left">LOC685716</td>
<td align="char" char=".">685716</td>
<td align="center">55279853&#x2013;55326753</td>
<td align="char" char=".">&#x2212;5.2745565</td>
<td align="center">0.00383337</td>
</tr>
<tr>
<td align="left">Slc24a5</td>
<td align="char" char=".">311387</td>
<td align="center">112319305&#x2013;112339231</td>
<td align="char" char=".">&#x2212;5.140615</td>
<td align="center">0.01109464</td>
</tr>
<tr>
<td align="left">LOC100912034</td>
<td align="char" char=".">64199</td>
<td align="center">32023003&#x2013;32028443</td>
<td align="char" char=".">&#x2212;4.9495918</td>
<td align="center">0.0065692</td>
</tr>
<tr>
<td align="left">P2ry10</td>
<td align="char" char=".">317219</td>
<td align="center">72121558&#x2013;72207174</td>
<td align="char" char=".">&#x2212;3.8438431</td>
<td align="center">0.03376527</td>
</tr>
<tr>
<td align="left">LOC100910278</td>
<td align="char" char=".">64040</td>
<td align="center">79505738..79522539</td>
<td align="char" char=".">-3.6968195</td>
<td align="center">0.00012598</td>
</tr>
<tr>
<td align="left">LOC102557478</td>
<td align="char" char=".">102557478</td>
<td align="center">68443437&#x2013;68505774</td>
<td align="char" char=".">&#x2212;3.2566427</td>
<td align="center">0.01336716</td>
</tr>
<tr>
<td align="left">Mrpl53</td>
<td align="char" char=".">362388</td>
<td align="center">115615329&#x2013;115616219</td>
<td align="char" char=".">&#x2212;2.6079781</td>
<td align="center">1.58E-05</td>
</tr>
<tr>
<td align="left">NEWGENE_1308196</td>
<td align="char" char=".">301352</td>
<td align="center">40125352&#x2013;40136189</td>
<td align="char" char=".">&#x2212;2.596599</td>
<td align="center">0.00038693</td>
</tr>
<tr>
<td align="left">Lipg</td>
<td align="char" char=".">291437</td>
<td align="center">68514923&#x2013;68536105</td>
<td align="char" char=".">&#x2212;2.5262274</td>
<td align="center">0.03772631</td>
</tr>
<tr>
<td align="left">LOC100911814</td>
<td align="char" char=".">309312</td>
<td align="center">227883247..227962119</td>
<td align="char" char=".">&#x2212;2.4137944</td>
<td align="center">0.02360257</td>
</tr>
<tr>
<td align="left">Gimap4</td>
<td align="char" char=".">286938</td>
<td align="center">77636401&#x2013;77643315</td>
<td align="char" char=".">&#x2212;2.3785594</td>
<td align="center">0.0379737</td>
</tr>
<tr>
<td align="left">Gdf7</td>
<td align="char" char=".">252833</td>
<td align="center">31171495&#x2013;31182447</td>
<td align="char" char=".">&#x2212;2.3596019</td>
<td align="center">0.04450489</td>
</tr>
<tr>
<td align="left">RT1-T24-1</td>
<td align="char" char=".">361787</td>
<td align="center">2761541&#x2013;2774749</td>
<td align="char" char=".">-2.2627501</td>
<td align="center">0.0416867</td>
</tr>
<tr>
<td align="left">Kif14</td>
<td align="char" char=".">360849</td>
<td align="center">47926975&#x2013;47990598</td>
<td align="char" char=".">-2.2606806</td>
<td align="center">0.03106551</td>
</tr>
<tr>
<td align="left">Mgat2</td>
<td align="char" char=".">94273</td>
<td align="center">87656360&#x2013;87658849</td>
<td align="char" char=".">&#x2212;2.1608588</td>
<td align="center">0.00867277</td>
</tr>
<tr>
<td align="left">LOC100909709</td>
<td align="char" char=".">89821</td>
<td align="center">96263322&#x2013;96314197</td>
<td align="char" char=".">&#x2212;2.1581355</td>
<td align="center">0.00638393</td>
</tr>
<tr>
<td align="left">Rpl39l</td>
<td align="char" char=".">497860</td>
<td align="center">5455712&#x2013;5459828</td>
<td align="char" char=".">&#x2212;2.0308892</td>
<td align="center">0.02228026</td>
</tr>
<tr>
<td align="left">Romo1</td>
<td align="char" char=".">679572</td>
<td align="center">144659709&#x2013;144661310</td>
<td align="char" char=".">&#x2212;2.0164828</td>
<td align="center">0.00390799</td>
</tr>
<tr>
<td align="left">LOC100911994</td>
<td align="char" char=".">312083</td>
<td align="center">31484424&#x2013;31585617</td>
<td align="char" char=".">&#x2212;1.9809055</td>
<td align="center">0.00040545</td>
</tr>
<tr>
<td align="left">RT1-Db1</td>
<td align="char" char=".">294270</td>
<td align="center">4548664&#x2013;4558237</td>
<td align="char" char=".">&#x2212;1.9316996</td>
<td align="center">0.00064276</td>
</tr>
</tbody>
</table>
</table-wrap>
<table-wrap id="T5" position="float">
<label>TABLE 5</label>
<caption>
<p>The detail of the top 20-upregulated DElncRNAs.</p>
</caption>
<table>
<thead valign="top">
<tr>
<th align="left">Upregulated gene</th>
<th align="center">Gene ID</th>
<th align="center">Location</th>
<th align="center">Log2 Fold change (CCI/Sham)</th>
<th align="center">
<italic>p</italic> value</th>
</tr>
</thead>
<tbody valign="top">
<tr>
<td colspan="2" align="left">ENSRNOT00000076561</td>
<td align="center">&#x2014;</td>
<td align="char" char=".">5.78512442</td>
<td align="center">0.01730266</td>
</tr>
<tr>
<td colspan="2" align="left">ENSRNOT00000077876</td>
<td align="center">&#x2014;</td>
<td align="char" char=".">2.20373049</td>
<td align="center">0.02111258</td>
</tr>
<tr>
<td colspan="2" align="left">ENSRNOT00000079282</td>
<td align="center">&#x2014;</td>
<td align="char" char=".">2.09798552</td>
<td align="center">0.04796722</td>
</tr>
<tr>
<td colspan="2" align="left">ENSRNOT00000081463</td>
<td align="center">&#x2014;</td>
<td align="char" char=".">6.06317183</td>
<td align="center">0.04165964</td>
</tr>
<tr>
<td colspan="2" align="left">ENSRNOT00000083718</td>
<td align="center">&#x2014;</td>
<td align="char" char=".">2.66877138</td>
<td align="center">0.03800823</td>
</tr>
<tr>
<td colspan="2" align="left">ENSRNOT00000084042</td>
<td align="center">&#x2014;</td>
<td align="char" char=".">3.53248432</td>
<td align="center">0.00746108</td>
</tr>
<tr>
<td colspan="2" align="left">ENSRNOT00000086466</td>
<td align="center">&#x2014;</td>
<td align="char" char=".">2.90999256</td>
<td align="center">0.00483471</td>
</tr>
<tr>
<td colspan="2" align="left">ENSRNOT00000088572</td>
<td align="center">&#x2014;</td>
<td align="char" char=".">1.63653171</td>
<td align="center">0.00185723</td>
</tr>
<tr>
<td colspan="2" align="left">ENSRNOT00000088984</td>
<td align="center">&#x2014;</td>
<td align="char" char=".">3.06189614</td>
<td align="center">0.04935497</td>
</tr>
<tr>
<td colspan="2" align="left">ENSRNOT00000089993</td>
<td align="center">&#x2014;</td>
<td align="char" char=".">0.94690101</td>
<td align="center">0.01452598</td>
</tr>
<tr>
<td colspan="2" align="left">ENSRNOT00000092488</td>
<td align="center">&#x2014;</td>
<td align="char" char=".">7.59302524</td>
<td align="center">0.00000197</td>
</tr>
<tr>
<td align="left">NR_126572.1</td>
<td align="char" char=".">102554851</td>
<td align="char" char="ndash">107727772&#x2013;107739795</td>
<td align="char" char=".">2.04684063</td>
<td align="center">0.03806143</td>
</tr>
<tr>
<td colspan="2" align="left">TCONS_00000046</td>
<td align="center">&#x2014;</td>
<td align="char" char=".">3.67510588</td>
<td align="center">4.54E-10</td>
</tr>
<tr>
<td colspan="2" align="left">TCONS_00000063</td>
<td align="center">&#x2014;</td>
<td align="char" char=".">3.6221488</td>
<td align="center">0.00521153</td>
</tr>
<tr>
<td colspan="2" align="left">TCONS_00000066</td>
<td align="center">&#x2014;</td>
<td align="char" char=".">5.01538596</td>
<td align="center">0.0000116</td>
</tr>
<tr>
<td colspan="2" align="left">TCONS_00000072</td>
<td align="center">&#x2014;</td>
<td align="char" char=".">3.72144139</td>
<td align="center">7.83E-08</td>
</tr>
<tr>
<td colspan="2" align="left">TCONS_00003409</td>
<td align="center">&#x2014;</td>
<td align="char" char=".">6.19777226</td>
<td align="center">0.03438166</td>
</tr>
<tr>
<td colspan="2" align="left">TCONS_00004570</td>
<td align="center">&#x2014;</td>
<td align="char" char=".">5.26965975</td>
<td align="center">0.00385247</td>
</tr>
<tr>
<td colspan="2" align="left">TCONS_00007059</td>
<td align="center">&#x2014;</td>
<td align="char" char=".">1.97880803</td>
<td align="center">0.00534686</td>
</tr>
<tr>
<td colspan="2" align="left">TCONS_00008373</td>
<td align="center">&#x2014;</td>
<td align="char" char=".">6.35884856</td>
<td align="center">0.0057876</td>
</tr>
</tbody>
</table>
</table-wrap>
<table-wrap id="T6" position="float">
<label>TABLE 6</label>
<caption>
<p>The detail of the top 20-downregulated DElncRNAs.</p>
</caption>
<table>
<thead valign="top">
<tr>
<th align="left">Down-regulated gene name</th>
<th align="left">Gene ID</th>
<th align="center">Location</th>
<th align="center">Log2 (fold change) (CCI/Sham)</th>
<th align="center">
<italic>p</italic> value</th>
</tr>
</thead>
<tbody valign="top">
<tr>
<td colspan="2" align="left">ENSRNOT00000079308</td>
<td align="center">&#x2014;</td>
<td align="char" char=".">&#x2212;6.4901256</td>
<td align="center">0.00389627</td>
</tr>
<tr>
<td colspan="2" align="left">ENSRNOT00000080318</td>
<td align="center">&#x2014;</td>
<td align="char" char=".">&#x2212;3.2237543</td>
<td align="center">0.04966201</td>
</tr>
<tr>
<td colspan="2" align="left">ENSRNOT00000080624</td>
<td align="center">&#x2014;</td>
<td align="char" char=".">&#x2212;5.5762886</td>
<td align="center">0.0226858</td>
</tr>
<tr>
<td colspan="2" align="left">ENSRNOT00000081988</td>
<td align="center">&#x2014;</td>
<td align="char" char=".">&#x2212;5.4100888</td>
<td align="center">0.00722821</td>
</tr>
<tr>
<td colspan="2" align="left">ENSRNOT00000083218</td>
<td align="center">&#x2014;</td>
<td align="char" char=".">&#x2212;1.3429282</td>
<td align="center">0.00913697</td>
</tr>
<tr>
<td colspan="2" align="left">ENSRNOT00000083980</td>
<td align="center">&#x2014;</td>
<td align="char" char=".">&#x2212;4.8410086</td>
<td align="center">0.02553616</td>
</tr>
<tr>
<td colspan="2" align="left">ENSRNOT00000085297</td>
<td align="center">&#x2014;</td>
<td align="char" char=".">&#x2212;3.4793701</td>
<td align="center">0.00869084</td>
</tr>
<tr>
<td colspan="2" align="left">ENSRNOT00000085430</td>
<td align="center">&#x2014;</td>
<td align="char" char=".">&#x2212;1.5983594</td>
<td align="center">0.00029936</td>
</tr>
<tr>
<td colspan="2" align="left">ENSRNOT00000086000</td>
<td align="center">&#x2014;</td>
<td align="char" char=".">&#x2212;5.2736508</td>
<td align="center">0.00650296</td>
</tr>
<tr>
<td colspan="2" align="left">ENSRNOT00000087909</td>
<td align="center">&#x2014;</td>
<td align="char" char=".">&#x2212;0.6072032</td>
<td align="center">0.00820781</td>
</tr>
<tr>
<td colspan="2" align="left">ENSRNOT00000090624</td>
<td align="center">&#x2014;</td>
<td align="char" char=".">&#x2212;0.9477649</td>
<td align="center">0.03438361</td>
</tr>
<tr>
<td align="left">NR_110678.1</td>
<td align="char" char=".">100910558</td>
<td align="char" char="ndash">96976181&#x2013;97014187</td>
<td align="char" char=".">&#x2212;1.9759649</td>
<td align="center">0.02172322</td>
</tr>
<tr>
<td align="left">TCONS_00000049</td>
<td align="center">&#x2014;</td>
<td align="center">&#x2014;</td>
<td align="char" char=".">&#x2212;1.6223783</td>
<td align="center">0.00036462</td>
</tr>
<tr>
<td align="left">TCONS_00000050</td>
<td align="center">&#x2014;</td>
<td align="center">&#x2014;</td>
<td align="char" char=".">&#x2212;0.6466528</td>
<td align="center">0.02698395</td>
</tr>
<tr>
<td align="left">TCONS_00002534</td>
<td align="center">&#x2014;</td>
<td align="center">&#x2014;</td>
<td align="char" char=".">&#x2212;1.3421975</td>
<td align="center">4.69E-08</td>
</tr>
<tr>
<td align="left">TCONS_00002535</td>
<td align="center">&#x2014;</td>
<td align="center">&#x2014;</td>
<td align="char" char=".">&#x2212;0.7819754</td>
<td align="center">0.00362422</td>
</tr>
<tr>
<td align="left">TCONS_00002540</td>
<td align="center">&#x2014;</td>
<td align="center">&#x2014;</td>
<td align="char" char=".">&#x2212;0.7632558</td>
<td align="center">0.00609918</td>
</tr>
<tr>
<td align="left">TCONS_00002547</td>
<td align="center">&#x2014;</td>
<td align="center">&#x2014;</td>
<td align="char" char=".">&#x2212;2.4841896</td>
<td align="center">0.02406492</td>
</tr>
<tr>
<td align="left">TCONS_00002551</td>
<td align="center">&#x2014;</td>
<td align="center">&#x2014;</td>
<td align="char" char=".">&#x2212;0.9798316</td>
<td align="center">0.00531827</td>
</tr>
<tr>
<td align="left">TCONS_00002552</td>
<td align="center">&#x2014;</td>
<td align="center">&#x2014;</td>
<td align="char" char=".">&#x2212;1.6084354</td>
<td align="center">0.00000503</td>
</tr>
</tbody>
</table>
</table-wrap>
</sec>
<sec id="s3-4">
<title>3.4 Validation of Expression Changes of DEmRNAs and DElncRNAs via Real-Time qPCR</title>
<p>We also randomly reselected 9 DEmRNAs (5 downregulated and 4 upregulated) and 8 DElncRNAs (5 downregulated and 3 upregulated) from the DEGs list for qRT-PCR validation to check the correctness and reproducibility of the RNA-Seq results (<xref ref-type="fig" rid="F2">Figure 2</xref>). The expression levels of <italic>NFS1, CARTPT, APH1B, NDUFA10,</italic> and <italic>MRPL53</italic> in the hippocampus of CCI with memory impairment model rats 21&#xa0;days were all significantly downregulated compared to the sham groups (<xref ref-type="fig" rid="F2">Figure 2A</xref>), while <italic>ATF3, CBLN1, MT1</italic>, and <italic>OXTR</italic> were all considerably upregulated (<xref ref-type="fig" rid="F2">Figure 2B</xref>), which is consistent with the RNA-Seq expression profiles. Furthermore, <italic>LOC102549072, LOC103693876, LOC102550954, LOC108351425,</italic> and <italic>LOC103691475</italic> were all strongly downregulated (<xref ref-type="fig" rid="F2">Figure 2C</xref>), whereas <italic>LOC108352208, LOC103694103,</italic> and <italic>LOC103693799</italic> were significantly upregulated (<xref ref-type="fig" rid="F2">Figure 2D</xref>), which was also consistent with the RNA-Seq expression profiles.</p>
<fig id="F2" position="float">
<label>FIGURE 2</label>
<caption>
<p>Randomly validation of DEGs from RNA-Seq via qRT-PCR. <bold>(A)</bold>: The expression of five randomly downregulated DEmRNAs via qRT-PCR. <bold>(B)</bold>: The expression of four randomly upregulated DEmRNAs via qRT-PCR. <bold>(C)</bold>: The expression of five randomly downregulated DElncRNAs via qRT-PCR. <bold>(D)</bold>: The expression of three randomly upregulated DElncRNAs via qRT-PCR. n &#x3d; 3&#x2013;6 rats/group. &#x2a;<italic>p</italic> &#x3c; 0.05, &#x2a;&#x2a;<italic>p</italic> &#x3c; 0.01, &#x2a;&#x2a;&#x2a;<italic>p</italic> &#x3c; 0.001 vs sham group. Student&#x2019;s t test was used for comparisons.</p>
</caption>
<graphic xlink:href="fcell-10-843297-g002.tif"/>
</fig>
</sec>
<sec id="s3-5">
<title>3.5 Function and Pathway Analysis of the Identified DEmRNAs and DElncRNAs</title>
<p>We used GO analysis of the discovered DEGs in the hippocampus in the sham group and CCI with the memory impairment group to discover more about the molecular process underlying CCI-induced memory impairment. The results showed that the significantly enriched BP of downregulated DEmRNAs were antigen processing and presentation, smooth muscle cell differentiation, etc. (<xref ref-type="fig" rid="F3">Figure 3A</xref>, <xref ref-type="sec" rid="s12">Supplementary Table S2</xref>). The significantly enriched CC of downregulated DEmRNAs was MHC class I protein complex, cell-cell junction, basement membrane, immunological synapse, mitochondrial large ribosomal subunit, etc. (<xref ref-type="fig" rid="F3">Figure 3C</xref>, <xref ref-type="sec" rid="s12">Supplementary Table S2</xref>). The significantly enriched MF of downregulated DEmRNAs were peptide antigen binding, signaling receptor binding, cytokine activity, etc. (<xref ref-type="fig" rid="F3">Figure 3E</xref>, <xref ref-type="sec" rid="s12">Supplementary Table S2</xref>). In addition, the most enriched BP of upregulated DEmRNAs were skeletal muscle cell differentiation, cholesterol biosynthetic process, regulation of long-term synaptic potentiation, etc. (<xref ref-type="fig" rid="F3">Figure 3B</xref>, <xref ref-type="sec" rid="s12">Supplementary Table S3</xref>). The most enriched CC of upregulated DEmRNAs was gap junction, chloride channel complex, an integral component of mitochondrial membrane, mitochondrial matrix, etc. (<xref ref-type="fig" rid="F3">Figure 3D</xref>, <xref ref-type="sec" rid="s12">Supplementary Table S3</xref>). The most enriched MF of upregulated DEmRNAs were pyridoxal phosphate binding, transaminase activity, lyase activity, ferrous iron-binding, etc. (<xref ref-type="fig" rid="F3">Figure 3F</xref>, <xref ref-type="sec" rid="s12">Supplementary Table S3</xref>).</p>
<fig id="F3" position="float">
<label>FIGURE 3</label>
<caption>
<p>GO analysis of DEmRNAs. <bold>(A,C,E)</bold>: The top 10 significant biological process, cellular components, and molecular functions of downregulated DEmRNAs. <bold>(B,D,F)</bold>: The top 10 significant biological processes, cellular components, and molecular functions of upregulated DEmRNAs.</p>
</caption>
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</fig>
<p>We then looked at the KEGG pathways of the DEmRNAs we found. The primarily enriched pathways of downregulated DEmRNAs were viral myocarditis, graft-versus-host disease, allograft rejection, etc. (<xref ref-type="fig" rid="F4">Figure 4A</xref>, <xref ref-type="sec" rid="s12">Supplementary Table S4</xref>). On the other hand, the primarily enriched pathways of upregulated DEmRNAs were mineral absorption, glycerophospholipid metabolism, sulfur relay system, etc. (<xref ref-type="fig" rid="F4">Figure 4C</xref>, <xref ref-type="sec" rid="s12">Supplementary Table S4</xref>). In addition, the potential targets of downregulated DElncRNAs mainly were enriched in the hedgehog signaling pathway, wnt signaling pathway, oxidative phosphorylation, etc. (<xref ref-type="fig" rid="F4">Figure 4B</xref>, <xref ref-type="sec" rid="s12">Supplementary Table S5</xref>). In contrast, the significantly enriched pathways of upregulated DElncRNAs were taste transduction, mitophagy, antigen processing, presentation, etc. (<xref ref-type="fig" rid="F4">Figure 4D</xref>, <xref ref-type="sec" rid="s12">Supplementary Table S5</xref>).</p>
<fig id="F4" position="float">
<label>FIGURE 4</label>
<caption>
<p>KEGG analysis of DEGs. <bold>(A,B)</bold>: The top 10 enriched pathways of downregulated DEmRNAs and DElncRNAs. <bold>(C,D)</bold>: The top 10 enriched pathways of upregulated DEmRNAs and DElncRNAs.</p>
</caption>
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</fig>
<p>Then, to analyze the hub genes of identified DEGs that are involved in CCI induced memory damage, we conducted the PPI network analysis and found the significant hub genes, including <italic>ALB, ATF3, NPY, CD3E, PIK3CA, GFAP, CD68, CFTR,</italic> and <italic>RT1-A2</italic> derived from PPI analysis (<xref ref-type="sec" rid="s12">Supplementary Figure S2</xref>).</p>
</sec>
<sec id="s3-6">
<title>3.6 Comparison of RNA-Seq Dataset of Chronic Constriction Injury With Memory Impairment Model Rats With Other Published Datasets of Neuropathic Pain Models and Cognitive Disorder Models</title>
<p>Firstly, we compared the CCI with memory impairment model rats&#x2019; RNA-Seq dataset with RNA-Seq datasets from SNI (GSE18803) and CCI models (<xref ref-type="bibr" rid="B36">Stephens et al., 2021</xref>). Total RNA for RNA-Seq was extracted from the spinal cord and the dorsal root ganglion. To detect DEmRNAs from SNI and CCI datasets, we used the same screening criteria as &#x7c;Log2 (fold change)&#x7c; &#x2265; 0.58<italic>, p</italic> &#x3c; 0.05. As a result, 3 DEmRNAs from CCI with memory impairment model rats (<italic>ATF3</italic>, <italic>C1QC</italic>, and <italic>CD68</italic>) and 13 DEmRNAs from SNI and CCI models (<italic>ADAMTS2</italic>, <italic>BCL6B</italic>, <italic>CLCF1</italic>, <italic>RBP1</italic>, and <italic>TPBG</italic>, among others) overlapped with SNI and CCI models, respectively (<xref ref-type="sec" rid="s12">Supplementary Figure S3A</xref>, <xref ref-type="sec" rid="s12">Supplementary Table S6</xref>). Besides, no overlapping genes were found in any of the three groups.</p>
<p>Furthermore, we compared the CCI with memory impairment model rats&#x2019; RNA-Seq dataset with RNA-Seq datasets from aging cognitive decline (GSE9990), various stages of Alzheimer&#x2019;s disease (GSE28146), and Huntington&#x2019;s disease (GSE1767), respectively. We set the same screening criteria as &#x7c;Log2 (fold change)&#x7c; &#x2265; 0.58 and <italic>p</italic> &#x3c; 0.05 to identify the DEmRNAs from the cognitive aging and AD datasets. These cognitive models did not have any genes in common (<xref ref-type="sec" rid="s12">Supplementary Figure S3A</xref>, <xref ref-type="sec" rid="s12">Supplementary Table S6</xref>). 11 DEmRNAs (<italic>APOC1, TMEM106A, TSC22D4, CYR61, BCL6B, MRVI1, LAMC3, BAIAP3, CTXN3, TPBG,</italic> and <italic>C4B</italic>) and 24 DEmRNAs (<italic>ABHD10, ARC, CARTPT, CD3E, CLCF1, KIF14, OXTR, RARRES1, SLC18A1,</italic> and <italic>SLC2A9</italic>, etc.) of CCI with memory impairment model rats overlapped with AD and HD model, respectively. There was no DEmRNA of CCI with memory impairment model rats overlapped with a cognitive aging model. 7 DEmRNAs (<italic>HEYL, NFS1, MKI67, MFF, OCLN, MGAT2,</italic> and <italic>HPRT1</italic>) of CCI with memory impairment model rats overlapped with both AD and HD models.</p>
</sec>
<sec id="s3-7">
<title>3.7 Construction of Competing Endogenous RNA Analysis</title>
<p>Based on the ceRNA hypothesis, lncRNAs may intervene in the translation of mRNAs by sponging miRNA. The ceRNA regulation network was then built in the CCI with memory impairment rat model to highlight the probable processes of lncRNA-miRNA-mRNA. By counting the number of miRNA response elements, we discovered 106 DEmRNAs, 75 miRNAs, and 90 DElncRNAs in total (<xref ref-type="sec" rid="s12">Supplementary Figure S4</xref> and <xref ref-type="sec" rid="s12">Supplementary Table S7</xref>). We chose 8 DElncRNAs that were validated by our qRT-PCR to construct the network diagram involving 8 DElncRNAs, 12 miRNAs, and 58 DEmRNAs with 137 edges (<xref ref-type="sec" rid="s12">Supplementary Figure S5</xref>) because the figure could not display the complex interaction (<xref ref-type="sec" rid="s12">Supplementary Figure S6</xref>). The significant miRNAs competitively bound by ceRNA were rno-miR-330-5p, rno-miR-326-3p, rno-miR-326-5p, rno-miR-6334, rno-miR-540-3p, and others, according to the network analysis.</p>
</sec>
<sec id="s3-8">
<title>3.8 Chronic Constriction Injury With Memory Impairment Model Rats Showed Ferroptosis Damage in the Hippocampus</title>
<p>The expression level of ATF3 mRNA was shown to be highly elevated in the CA1 region of the hippocampus of CCI patients with memory impairment (<xref ref-type="fig" rid="F2">Figure 2B</xref>), and it has also been linked to the pathological process of pain (<xref ref-type="bibr" rid="B10">Ding et al., 2020</xref>). Furthermore, overexpression of ATF3 has recently been attributed to ferroptosis (<xref ref-type="bibr" rid="B44">Wang et al., 2020</xref>). Ferroptosis is also reported to be essential for the development of neuropathic pain (<xref ref-type="bibr" rid="B15">Guo et al., 2021</xref>; <xref ref-type="bibr" rid="B45">Wang H et al., 2021</xref>). However, it is unknown if ATF3 overproduction in the CA1 region of the hippocampus is related to memory impairment caused by CCI and the mechanism. We, therefore, performed immunostaining of hippocampus (CA1 region) using ATF3, combined with NeuN (a marker for neuron) and GFAP (a marker for astrocyte), respectively. We discovered ATF3 positively stained cells were considerably increased in the hippocampus CA1 area of CCI with memory impairment model rats 21 days compared to the sham group, as shown in <xref ref-type="fig" rid="F5">Figures 5A&#x2013;C</xref>. Furthermore, the number of ATF3-positive neurons rose noticeably (<xref ref-type="fig" rid="F5">Figure 5A</xref>). In contrast, astrocytes showed little <italic>ATF3</italic> positivity (<xref ref-type="fig" rid="F5">Figure 5B</xref>). We also used western blot to confirm <italic>ATF3</italic> expression and discovered that the level of <italic>ATF3</italic> expression in the hippocampus CA1 area of CCI with memory impairment model rats 21 days is considerably higher (<xref ref-type="fig" rid="F5">Figure 5D</xref>). These findings suggest that <italic>ATF3</italic> may be linked to memory loss caused by CCI. qRT-PCR was used to examine the expression of gene markers for ferroptosis. qRT-PCR revealed that <italic>GPX4</italic> and <italic>SLC7A11</italic> gene expression were dramatically downregulated in the hippocampus of CCI with memory impairment model rats 21 days. However, <italic>SLC1A5</italic> and <italic>PTGS2</italic> gene expression were significantly elevated (<xref ref-type="fig" rid="F6">Figure 6A</xref>), indicating ferroptosis damage (<xref ref-type="bibr" rid="B38">Tang et al., 2021</xref>).</p>
<fig id="F5" position="float">
<label>FIGURE 5</label>
<caption>
<p>ATF3 expression of Hippocampus CA1 area increased in the CCI-induced memory impairment rat model. <bold>(A)</bold>: Representative immunofluorescence image indicating ATF3 antibody staining of the hippocampus CA1 <bold>(A,B)</bold> from sham and CCI-induced hippocampus. DAPI (blue) was used for cell nucleus labeling. NeuN (red) was used for neuron labeling. Green was used for the ATF3 positive area. GFAP (red) was used for astrocyte labeling. <bold>(C)</bold>: Summary of ATF3 positively stained neurons per observation area in the hippocampus from two groups. <bold>(D)</bold>: Validation of ATF3 protein expression in the hippocampus via western blot. n &#x3d; 4&#x2013;6 rats/group, &#x2a;<italic>p &#x3c; 0.05</italic> vs sham group. The student&#x2019;s t test was used for comparisons.</p>
</caption>
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</fig>
<fig id="F6" position="float">
<label>FIGURE 6</label>
<caption>
<p>Validation of ferroptosis-associated gene markers. <bold>(A)</bold>: validation of gene marker mRNA levels in the hippocampus for ferroptosis by qRT-PCR. <bold>(B,C)</bold>: Validation of GPX4 and SLC7A11 protein expression level in the hippocampus by western blot. n &#x3d; 3&#x2013;6 rats/group, &#x2a;<italic>p &#x3c; 0.05</italic> vs sham group. The student&#x2019;s t test was used for comparisons.</p>
</caption>
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</fig>
<p>Furthermore, the protein expressions of <italic>GPX4</italic> and <italic>SLC7A11</italic> in the hippocampus of CCI with memory impairment model rats 21 days were all considerably reduced, according to the western blot (<xref ref-type="fig" rid="F6">Figures 6B,C</xref>). We then used DAB-enhanced Perl&#x2019;s staining to detect ferric iron (<xref ref-type="bibr" rid="B27">Moroishi et al., 2011</xref>). Perl&#x2019;s positive iron deposits were found in the hippocampus of CCI with memory impairment model mice after 21 days, implying that ferrous iron collected in the hippocampus (<xref ref-type="fig" rid="F7">Figure 7B</xref>). Interestingly, the iron level of the plasma and the hippocampus were both elevated in the CCI with memory impairment group (<xref ref-type="fig" rid="F7">Figure 7C</xref>).</p>
<fig id="F7" position="float">
<label>FIGURE 7</label>
<caption>
<p>Iron overload, lipid peroxidation, and neuronal damage in the hippocampus of the CCI-induced memory impairment rat model. <bold>(A,D)</bold>: Compared with sham rats, the number of Nissl positive bodies in the hippocampus of CCI-induced memory impairment was decreased, and the morphology of Nissl positive bodies was obviously changed. <bold>(B)</bold>: DAB-enhanced Perls stain showed Perls positive iron deposits in the hippocampus of CCI-induced memory impairment rat model. <bold>(C)</bold>: Iron content in hippocampus and plasma were significantly increased in the hippocampus of CCI-induced memory impairment. <bold>(E&#x2013;H)</bold>: showing the lipid peroxidation in the hippocampus of CCI-induced memory impairment as the following results: significantly increased ROS level <bold>(E)</bold> and MDA content <bold>(F)</bold>, significantly downregulated SOD activity <bold>(G)</bold> and GSH content <bold>(H)</bold> via corresponding detection kits. n &#x3d; 3&#x2013;6 rats/group, &#x2a;<italic>p &#x3c; 0.05</italic>, &#x2a;&#x2a;<italic>p &#x3c; 0.01</italic> vs sham group. The student&#x2019;s t test was used for comparisons.</p>
</caption>
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</fig>
<p>The hallmarks of ferroptosis, including ROS, MDA, GSH, and SOD in the hippocampus, were found to include lipid peroxidation and ROS buildup. As shown in <xref ref-type="fig" rid="F7">Figures 7E&#x2013;H</xref>, the level of ROS and SOD were dramatically raised, whereas the GSH content and SOD activity were clearly downregulated in the hippocampus of CCI rats compared to sham rats. In addition, the number of Nissl-body neurons was significantly decreased. The shape of Nissl positive bodies was modified in the hippocampus of CCI with memory impairment group compared to the sham group, according to the results of Nissl staining (<xref ref-type="fig" rid="F7">Figures 7A,D</xref>). These findings suggested that the CCI caused hippocampal ferroptosis damage.</p>
</sec>
<sec id="s3-9">
<title>3.9 Ferrostatin-1 Improved the Memory Impairment and Ferroptosis Damage of the CCI Rat Model</title>
<p>To verify whether ferroptosis is related to cognitive impairment induced by CCI, we employed the well-known ferroptosis inhibitor Fer-1 to treat rats. As expected, when compared to CCI or CCI &#x2b; vehicle groups, Fer-1 treatment could significantly reverse the hyperalgesia generated by CCI (<xref ref-type="fig" rid="F8">Figures 8A&#x2013;D</xref>). Moreover, Fer-1 treatment alleviated the CCI-induced memory impairment, evidenced by greater spontaneous alternation behavior in the Y maze test and improved capacity to detect novel items in the NOR Test (<xref ref-type="fig" rid="F8">Figures 8E,F</xref>).</p>
<fig id="F8" position="float">
<label>FIGURE 8</label>
<caption>
<p>Ferrostatin-1 significantly reversed the improved CCI-induced hyperalgesia and memory impairment. <bold>(A)</bold>: Representative scatter diagram showing the 50% paw withdrawal thresholds (PWTs) of the left hind paw in these above groups. <bold>(B)</bold>: Representative scatter diagram showing the 50% paw withdrawal latencies (PWLs) of the left hind paw in these above groups. <bold>(C,D)</bold>: Representative scatter diagram showing mean withdrawal scores and duration of cold hyperalgesia in these above groups. <bold>(E)</bold>: Representative scatter diagram showing %spontaneous alternation of Y maze test in these above groups. <bold>(F)</bold>: Representative scatter diagram showing the recognition index of NOR test (Day 21 after CCI) in these above groups. n &#x3d; 6 rats/group. &#x2a;<italic>p</italic> &#x3c; 0.05, &#x2a;&#x2a;<italic>p</italic> &#x3c; 0.01, &#x2a;&#x2a;&#x2a;<italic>p</italic> &#x3c; 0.001, &#x2a;&#x2a;&#x2a;&#x2a;<italic>p</italic> &#x3c; 0.0001 vs sham group or CCI &#x2b; Fer-1 group. One-way ANOVA test was used for comparisons.</p>
</caption>
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</fig>
<p>After Fer-1 treatment, we further observed the ferroptosis damage changes of CCI rats. As shown in <xref ref-type="fig" rid="F9">Figures 9A,B</xref>, Fer-1 markedly reduced the iron levels of hippocampus and plasma after CCI. Bedsides, the Fer-1 treatment reduced ROS production and lipid peroxidation while increasing GSH levels and SOD activity (<xref ref-type="fig" rid="F9">Figures 9C&#x2013;F</xref>). qRT-PCR revealed that in the hippocampus of CCI with memory impairment model rats 21 days after Fer-1 therapy, <italic>GPX4</italic> and <italic>SLC7A11</italic> gene expressions were dramatically increased. In contrast, <italic>SLC1A5</italic> and <italic>PTGS2</italic> gene expressions were significantly reduced (<xref ref-type="fig" rid="F9">Figures 9G&#x2013;J</xref>). Those results indicated that ferroptosis is involved in CCI-induced memory impairment.</p>
<fig id="F9" position="float">
<label>FIGURE 9</label>
<caption>
<p>Ferrostatin-1 significantly inhibited the ferroptotic damage. <bold>(A,B)</bold>: Representative scatter diagram showing the iron content of hippocampus and plasma in these above groups. <bold>(C&#x2013;F)</bold>: Representative scatter diagram showing the levels of ROS <bold>(C)</bold>, MDA <bold>(D)</bold>, GSH <bold>(E)</bold>, and SOD <bold>(F)</bold> of hippocampus in these above groups. <bold>(G&#x2013;J)</bold>: Representative scatter diagram showing validation of gene marker mRNA levels in the hippocampus for ferroptosis. n &#x3d; 3&#x2013;6 rats/group. &#x2a;<italic>p</italic> &#x3c; 0.05, &#x2a;&#x2a;<italic>p</italic> &#x3c; 0.01, &#x2a;&#x2a;&#x2a;<italic>p</italic> &#x3c; 0.001 vs sham group or CCI &#x2b; Fer-1 group. One-way ANOVA test was used for comparisons.</p>
</caption>
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</fig>
</sec>
</sec>
<sec id="s4">
<title>4 Discussion</title>
<p>We used genome-wide RNA-Seq to assess gene expression profiles in the hippocampus of CCI-induced memory impairment model and sham rats. We identified several DEGs (mRNAs and lncRNAs) and randomly validated some of these via qRT-PCR. GO, and KEGG analysis further investigated molecular functions, cellular components, biological processes, and enriched pathways. We discovered that mitochondrial-associated processes and iron metabolism were considerably enriched in a large number of DEGs. Furthermore, ceRNA analysis was used to investigate the link between DEmRNAs and DElncRNAs. This is, to our knowledge, the first study to use RNA-Seq to look at gene expression profiles and putative pathways in the hippocampus of a CCI-induced memory impairment model.</p>
<p>Accumulating evidence revealed that ferroptosis was a critical factor in the development of chronic pain. Ferroptosis is a novel iron-dependent cell death marked by excessive iron buildup and lipid peroxidation. Currently, ferroptosis is linked to decreased cystine/glutamate reverse transporter activity (which reduces the synthesis of antioxidant GSH), lipid peroxide accumulation (such as excessive creation of ROS), decreased <italic>GPX4</italic> activity, and iron overload (<xref ref-type="bibr" rid="B6">Chen X et al., 2021</xref>). According to recent research, iron death plays a role in the development of chronic pain. Moreover, Nissl staining is a standard marker of neuronal injury (<xref ref-type="bibr" rid="B35">Shao et al., 2021</xref>). The number of Nissl positive bodies in the hippocampus of CCI-induced memory impairment rats was considerably reduced, and the form of Nissl positive bodies changed, indicating hippocampal neuron injury, as compared to sham rats in this study. Furthermore, iron accumulation in the hippocampus and plasma and lipid peroxidation (overproduction of ROS and MDA, decreased SOD activity, and decreased GSH content) were all disrupted. Similarly, lipid peroxidation and gene markers (<italic>GPX4, SLC7A11, SLC1A5,</italic> and <italic>PTGS2</italic>) dysregulation of ferroptosis were discovered in the CCI-induced memory impairment model. Fer-1 is a common ferroptosis inhibitor (<xref ref-type="bibr" rid="B11">Dixon et al., 2012</xref>). In the present study, treatment with Fer-1 markedly reversed the mechanical, thermal, and cold pain thresholds and CCI-induced memory impairment. Besides, Fer-1 significantly reduced the iron content and lipid peroxide level (ROS and MDA). In addition, the mRNA expression of <italic>GPX4</italic> and <italic>SLC7A11</italic> were upregulated, whereas the mRNA expression of <italic>SLC1A5</italic> and <italic>PTGS2</italic> were downregulated. These findings suggest ferroptosis may be implicated in CCI-induced memory impairment.</p>
<p>According to GO analysis, the overexpression of DEGs in the hippocampus of two groups was highly enriched in the control of the lipoxygenase pathway and long-term synaptic potentiation. Lipoxygenase is a multipurpose enzyme that may metabolize both endogenous and exogenous chemicals, affecting the formation of reactive oxygen species (ROS) and causing intracellular oxidative stress throughout the metabolism process (<xref ref-type="bibr" rid="B12">Faulkner et al., 2015</xref>). Furthermore, the cell component of GO analysis revealed that one of the most significantly enriched functions in the hippocampus was mitochondrial matrix and membrane. It suggested that oxidative metabolism disorders and synaptic dysfunction could be implicated in the fundamental pathogenic mechanism of CCI-induced memory impairment. The molecular function of GO analysis DEGs was also shown to be enriched in ferrous ion binding. Iron could react with H<sub>2</sub>O<sub>2</sub> in the Fenton reaction to form ROS due to its extensive ligand-binding and electron-transfer characteristics (<xref ref-type="bibr" rid="B17">Kajarabille and Latunde-Dada, 2019</xref>). Based on these findings, iron metabolism may be involved in CCI-induced learning and memory problems.</p>
<p>Antigen processing and presentation, mineral absorption, and the sulfur relay system were the most enriched pathways involving DEGs, according to KEGG analysis. We also discovered that one of the DEGs, <italic>NFS1</italic> mRNA, was drastically reduced. For the formation of mitochondrial iron-sulfur clusters, <italic>NFS1</italic>, an essential enzyme in eukaryotes, gets sulfur from cysteine (ISCs). In sensitive cells and certain parts of the nervous system, biogenic errors in mitochondrial ICSs cause aberrant intracellular iron distribution, mitochondrial iron buildup, oxidative phosphorylation deficiencies, and increased oxidative stress (<xref ref-type="bibr" rid="B17">Kajarabille and Latunde-Dada, 2019</xref>). The pathogenic process of neurodegenerative disorders such as Parkinson&#x2019;s disease, aging, and Alzheimer&#x2019;s disease may be influenced by a lack of iron-sulfur cluster formation and an accumulation of iron metabolism (<xref ref-type="bibr" rid="B50">Zecca et al., 2004</xref>; <xref ref-type="bibr" rid="B16">Isaya, 2014</xref>). Inhibition of <italic>NFS1</italic> expression was found to cause the loss of iron-responsive protein and ICSs, up-regulation of the iron hunger response (increased transferrin receptor and decreased ferritin), and an increase in intracellular free iron, all of which led to ferroptosis in a prior study (<xref ref-type="bibr" rid="B1">Alvarez et al., 2017</xref>). As a result, our research suggests that ferroptosis could be a critical factor in CCI-induced memory loss. The role of <italic>NFS1</italic> in the hippocampus in response to pain stress should be the focus of future research.</p>
<p>Cluster analysis revealed that the CCI-induced learning and memory impairment model was highly consistent with the sham group&#x2019;s dataset and that the two groups were significantly isolated. RNA-seq is a method for predicting preliminary genes or pathways. We also used qPCR and Western blot to validate our RNA-Seq dataset at random, and we were able to identify specific genes and targets consistent with the pattern of our RNA-Seq profiles. When we analyzed our data to other well-known published datasets, we discovered certain DEGs that may be implicated in neuropathic and cognitive common pathogenic processes (neuropathic pain models and cognitive disease models). Future RNA-Seq analyses are likely to include further RNA-Seq analyses of more samples, which will be combined with our current datasets.</p>
<p>Increased endoplasmic reticulum stress is linked to ferroptosis, which upregulates the production of activated transcription factors (ATFs). Recent research has discovered that <italic>ATF3</italic> can bind to the promoter of <italic>SLC7A11</italic>, suppressing its expression and system Xc&#x2013;transport function (which prevents lipid peroxidation and protects cells from nonapoptotic, iron-dependent death), resulting in reduced GSH production, increased free Fe<sup>2&#x2b;</sup>, and lipid peroxidation accumulation, and ultimately causing DNA, protein, and lipid membrane damage (<xref ref-type="bibr" rid="B44">Wang et al., 2020</xref>; <xref ref-type="bibr" rid="B23">Lu et al., 2021</xref>). Furthermore, <italic>ATF3</italic> is a well-known marker of sensory neuron injury, with up-regulated expression found in the DRG and spinal cord in chronic pain models (<xref ref-type="bibr" rid="B10">Ding et al., 2020</xref>; <xref ref-type="bibr" rid="B46">Wang K et al., 2021</xref>). <italic>ATF3</italic> was highly increased in the hippocampus DEGs of CCI-induced memory impairment rats compared to the sham group, according to our RNA-Seq profiles. Using qRT-PCR, Western blot, and immunofluorescent staining, we discovered that <italic>ATF3</italic> mRNA and protein levels were dramatically enhanced. Moreover, we found the expression of SLC7A11 and GPX4 in the hippocampus of CCI-induced memory impairment using western blot. These findings suggested that <italic>ATF3</italic> may play a role in the pathological process of CNPP with cognitive impairment by preventing system Xc&#x2013;and <italic>GPX4</italic> from causing ferroptosis.</p>
<p>Chronic constriction injury of the sciatic nerve is a classic neuropathic pain model (<xref ref-type="bibr" rid="B18">Kalman and Keay, 2014</xref>). Neuropathic pain is regarded to be a persistent stress factor that can influence alterations in various areas of the brain, including the hippocampus (<xref ref-type="bibr" rid="B39">Tracey and Mantyh, 2007</xref>). Neuro-immune interactions play a role in the pathophysiology of neuropathic pain caused by peripheral nerve damage. Peripheral inflammation is likely to be transferred to the brain following nerve injury via a set of well-defined immune-to-brain communication pathways (<xref ref-type="bibr" rid="B14">Fiore and Austin, 2016</xref>). According to a recent study, monocyte migration-mediated neuroimmune response may be linked to cognitive impairment produced by neuropathic pain (<xref ref-type="bibr" rid="B24">Mai et al., 2021</xref>). However, whether the occurrence of ferroptosis in the hippocampus is related to the inflammatory microenvironment, we will focus on it. In a broader sense, there are three non-exclusive channels for immune-to-brain signaling: 1) neurological transmission, 2) humoral transmission, and 3) molecular transmission (<xref ref-type="bibr" rid="B14">Fiore and Austin, 2016</xref>). Future studies are needed to determine if peripheral nerve damage caused ferroptosis in the hippocampus via these pathways.</p>
</sec>
<sec id="s5">
<title>5 Conclusion</title>
<p>The current study used RNA-Seq to provide a genome-wide profile of the hippocampus of a rat model of CCI-induced memory impairment. In addition, several DEGs and pathways in the hippocampus were also discovered by pathways and function analysis, which may alter ferroptosis and memory impairment in response to chronic pain stress. These findings could lead to a better understanding of the molecular mechanisms behind CCI-induced memory loss, leading to the development of new and effective treatments for CCI-induced memory impairment.</p>
</sec>
</body>
<back>
<sec id="s6">
<title>Data Availability Statement</title>
<p>The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: NCBI BioProject accession number: PRJNA796160.</p>
</sec>
<sec id="s7">
<title>Ethics Statement</title>
<p>The animal study was reviewed and approved by the National Institutes of Health Guide for the Care and Use of Laboratory Animals.</p>
</sec>
<sec id="s8">
<title>Author Contributions</title>
<p>YT, CL, JW, HC, YS, XZ, QZ, XF, SY, TZ, and CC performed the experiments and analyzed the data. YT and CL conducted the bioinformatics analysis. YT and XZ coordinated with model establishment. YT, CL, TZ, and CC designed the study. YT wrote the manuscript. All authors reviewed the manuscript and approved the final manuscript.</p>
</sec>
<sec id="s9">
<title>Funding</title>
<p>This study was supported by the National Natural Science Foundation of China (Nos. 82171185 and 81870858 to CC), the National Key R&#x26;D Program of China (No. 2018YFC2001800 to TZ), the National Natural Science Foundation of China (No. 81671062 to TZ).</p>
</sec>
<sec sec-type="COI-statement" id="s10">
<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 sec-type="disclaimer" id="s11">
<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="s12">
<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/fcell.2022.843297/full#supplementary-material">https://www.frontiersin.org/articles/10.3389/fcell.2022.843297/full&#x23;supplementary-material</ext-link>
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