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<front>
<journal-meta>
<journal-id journal-id-type="publisher-id">Front. Genet.</journal-id>
<journal-title>Frontiers in Genetics</journal-title>
<abbrev-journal-title abbrev-type="pubmed">Front. Genet.</abbrev-journal-title>
<issn pub-type="epub">1664-8021</issn>
<publisher>
<publisher-name>Frontiers Media S.A.</publisher-name>
</publisher>
</journal-meta>
<article-meta>
<article-id pub-id-type="publisher-id">783799</article-id>
<article-id pub-id-type="doi">10.3389/fgene.2022.783799</article-id>
<article-categories>
<subj-group subj-group-type="heading">
<subject>Genetics</subject>
<subj-group>
<subject>Original Research</subject>
</subj-group>
</subj-group>
</article-categories>
<title-group>
<article-title>Identification of Novel Mutations in Chinese Infants With Citrullinemia</article-title>
<alt-title alt-title-type="left-running-head">Cheng et&#x20;al.</alt-title>
<alt-title alt-title-type="right-running-head">Genetic Analysis with Citrullinemia</alt-title>
</title-group>
<contrib-group>
<contrib contrib-type="author">
<name>
<surname>Cheng</surname>
<given-names>Zhi</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>He</surname>
<given-names>Xiwen</given-names>
</name>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Zou</surname>
<given-names>Fa</given-names>
</name>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/1503742/overview"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Xu</surname>
<given-names>Zhen-E</given-names>
</name>
<xref ref-type="aff" rid="aff3">
<sup>3</sup>
</xref>
<xref ref-type="aff" rid="aff4">
<sup>4</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/1191948/overview"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Li</surname>
<given-names>Chun</given-names>
</name>
<xref ref-type="aff" rid="aff3">
<sup>3</sup>
</xref>
<xref ref-type="aff" rid="aff4">
<sup>4</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/1575412/overview"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Liu</surname>
<given-names>Hao</given-names>
</name>
<xref ref-type="aff" rid="aff5">
<sup>5</sup>
</xref>
</contrib>
<contrib contrib-type="author" corresp="yes">
<name>
<surname>Miao</surname>
<given-names>Jingkun</given-names>
</name>
<xref ref-type="aff" rid="aff5">
<sup>5</sup>
</xref>
<xref ref-type="corresp" rid="c001">&#x2a;</xref>
<uri xlink:href="https://loop.frontiersin.org/people/1492766/overview"/>
</contrib>
</contrib-group>
<aff id="aff1">
<sup>1</sup>
<institution>Key Laboratory of Birth Defects and Reproductive Health of the National Health and Family Planning Commission (Chongqing Population and Family Planning Science and Technology Research Institute)</institution>, <addr-line>Chongqing</addr-line>, <country>China</country>
</aff>
<aff id="aff2">
<sup>2</sup>
<institution>College of Basic Medical Sciences</institution>, <institution>Chongqing Medical University</institution>, <addr-line>Chongqing</addr-line>, <country>China</country>
</aff>
<aff id="aff3">
<sup>3</sup>
<institution>Department of Neonatology</institution>, <institution>Children&#x2019;s Hospital of Chongqing Medical University</institution>, <addr-line>Chongqing</addr-line>, <country>China</country>
</aff>
<aff id="aff4">
<sup>4</sup>
<institution>National Clinical Research Center for Child Health and Disorders</institution>, <institution>Ministry of Education Key Laboratory of Child Development and Disorders</institution>, <institution>Chongqing Key Laboratory of Pediatrics</institution>, <addr-line>Chongqing</addr-line>, <country>China</country>
</aff>
<aff id="aff5">
<sup>5</sup>
<institution>Neonatal Disease Screening Center</institution>, <institution>Chongqing Health Center for Women and Children</institution>, <addr-line>Chongqing</addr-line>, <country>China</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/396023/overview">Chen Huei Leo</ext-link>, Singapore University of Technology and Design, Singapore</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/949480/overview">Dario Ronchi</ext-link>, University of Milan, Italy</p>
<p>
<ext-link ext-link-type="uri" xlink:href="https://loop.frontiersin.org/people/1110111/overview">Liang Li</ext-link>, Southern Medical University, China</p>
</fn>
<corresp id="c001">&#x2a;Correspondence: Jingkun Miao, <email>jennamiao99@sina.com</email>
</corresp>
<fn fn-type="other">
<p>This article was submitted to Human and Medical Genomics, a section of the journal Frontiers in Genetics</p>
</fn>
</author-notes>
<pub-date pub-type="epub">
<day>03</day>
<month>03</month>
<year>2022</year>
</pub-date>
<pub-date pub-type="collection">
<year>2022</year>
</pub-date>
<volume>13</volume>
<elocation-id>783799</elocation-id>
<history>
<date date-type="received">
<day>27</day>
<month>09</month>
<year>2021</year>
</date>
<date date-type="accepted">
<day>15</day>
<month>02</month>
<year>2022</year>
</date>
</history>
<permissions>
<copyright-statement>Copyright &#xa9; 2022 Cheng, He, Zou, Xu, Li, Liu and Miao.</copyright-statement>
<copyright-year>2022</copyright-year>
<copyright-holder>Cheng, He, Zou, Xu, Li, Liu and Miao</copyright-holder>
<license xlink:href="http://creativecommons.org/licenses/by/4.0/">
<p>This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these&#x20;terms.</p>
</license>
</permissions>
<abstract>
<p>Citrullinemia is a rare autosomal recessive disorder characterized by elevated concentrations of citrulline in the blood resulting from malfunction of the urea cycle. It is categorized into two types, types I and II, which are caused by argininosuccinate synthase 1 (<italic>ASS1</italic>), and citrin (<italic>SLC25A13</italic>) gene mutations, respectively. In this study, we performed genetic analysis on nine Chinese infants with citrullinemia using next-generation sequencing, which identified a novel mutation (p.Leu313Met) and a rare mutation (p.Thr323Ile, rs1250895424) of <italic>ASS1</italic>. We also found a novel splicing mutation of <italic>SLC25A13</italic>: c.1311 &#x2b; 4_&#x2b;7del. Functional analysis of the <italic>ASS1</italic> missense mutations showed that both significantly impaired the enzyme activity of ASS1, with the p. Thr323Ile mutation clearly affecting the interaction between ASS1 and protein arginine methyltransferase 7 (PRMT7). These findings expand the mutational spectrum of <italic>ASS1</italic> and <italic>SLC25A13</italic>, and further our understanding of the molecular genetic mechanism of citrullinemia in the Chinese population.</p>
</abstract>
<kwd-group>
<kwd>citrullinemia</kwd>
<kwd>genetic analysis</kwd>
<kwd>mutation</kwd>
<kwd>ASS1</kwd>
<kwd>SLC25A13</kwd>
</kwd-group>
</article-meta>
</front>
<body>
<sec id="s1">
<title>Introduction</title>
<p>Citrullinemia is a rare autosomal recessive disorder characterized by elevated concentrations of citrulline in the blood from malfunctions of the urea cycle (<xref ref-type="bibr" rid="B27">Saheki et&#x20;al., 1987</xref>). It is categorized into two types according to the molecular pathogenesis. Type I citrullinemia (CTLN1, OMIM&#x23; 2,15,700) is caused by argininosuccinate synthase 1 gene (<italic>ASS1</italic>) mutations, while type II citrullinemia is caused by citrin gene (<italic>SLC25A13</italic>) mutations (<xref ref-type="bibr" rid="B33">Woo et&#x20;al., 2014</xref>).</p>
<p>Classic CTLN1 often presents early in the neonatal period in affected individuals with acute hyperammonemia and neurologic manifestations. If untreated, it can lead to life-threatening encephalopathy, metabolic coma, and death (<xref ref-type="bibr" rid="B9">H&#xe4;berle et&#x20;al., 2002</xref>). Late-onset forms of CTLN1 can also occur. These usually have milder phenotypes, including neurodisability, somnolence, and chronic intermittent hyperammonemia during childhood and adulthood (<xref ref-type="bibr" rid="B10">H&#xe4;berle et&#x20;al., 2003</xref>).</p>
<p>Type II citrullinemia has two main clinical phenotypes: neonatal intrahepatic cholestatic hepatitis caused by citrin deficiency (NICCD; OMIM&#x23; 6,05,814) and adult-onset type II citrullinemia (CTLN2; OMIM&#x23; 6,03,471) (<xref ref-type="bibr" rid="B26">Saheki and Kobayashi, 2002</xref>). NICCD is clinically characterized by intrahepatic cholestasis and metabolic abnormalities including multiple aminoacidemia, galactosemia, hypoglycemia, and hypoproteinemia. Most patients improve spontaneously without medical treatment before 1&#xa0;year of age. However, some develop severe CTLN2 one or more decades later (<xref ref-type="bibr" rid="B22">Liu et&#x20;al., 2014</xref>). Patients with CTLN2 suffer from various neuropsychological symptoms including disorientation, delirium, seizures, and coma because of hyperammonemia. Death from brain edema occurs in some cases (<xref ref-type="bibr" rid="B31">Tabata et&#x20;al., 2008</xref>).</p>
<p>
<italic>ASS1</italic> is located at chromosome 9q24.11&#x2013;9q23.12 and contains 16 exons. It encodes the argininosuccinate synthetase enzyme, which catalyzes the synthesis of argininosuccinate from citrulline, and aspartate. It is mainly expressed in the periportal hepatocytes of the liver, but also in most other body tissues (<xref ref-type="bibr" rid="B7">Engel et&#x20;al., 2009</xref>). At least 153&#x20;<italic>ASS1</italic> CTLN1&#x20;disease-causing mutations have been reported, of which most are missense mutations distributed within exons 3&#x2013;15 (<xref ref-type="bibr" rid="B6">Diez-Fernandez et&#x20;al., 2017</xref>).</p>
<p>
<italic>SLC25A13</italic> is located at chromosome 7q21.3. It encodes citrin, which functions as a calcium (Ca<sup>2&#x2b;</sup>)-stimulated aspartate-glutamate carrier. Citrin is expressed in many tissues but most abundantly in the liver, and is localized to the mitochondrial inner membrane (<xref ref-type="bibr" rid="B14">Iijima et&#x20;al., 2001</xref>). The first <italic>SLC25A13</italic> disease-causing mutation was identified in a Japanese family with CTLN2 (<xref ref-type="bibr" rid="B16">Kobayashi et&#x20;al., 1999</xref>). Later, some NICCD patients were also shown to carry homozygous and compound heterozygous mutations of <italic>SLC25A13</italic> (<xref ref-type="bibr" rid="B34">Yamaguchi et&#x20;al., 2002</xref>). To date, more than 110 pathogenic mutations of <italic>SLC25A13</italic> have been reported, of which most are point mutations or short insertions/deletions (InDels). These were mainly identified in east Asian populations, including Japanese, Korean, and Chinese (<xref ref-type="bibr" rid="B35">Zhang et&#x20;al., 2017</xref>).</p>
<p>There are currently no well-recognized clinical/biochemical diagnostic criteria for either type of citrullinemia, yet molecular genetic analysis is critical for the diagnosis of patients. In this study, we performed genetic analysis of Chinese infants with citrullinemia using next-generation sequencing (NGS). We also carried out a functional investigation of <italic>ASS1</italic> mutations identified in this study to better understand the genetic mechanism of this disease in the Chinese population.</p>
</sec>
<sec sec-type="materials|methods" id="s2">
<title>Materials and Methods</title>
<sec id="s2-1">
<title>Subjects</title>
<p>From June 2014 to December 2020, nine infants with citrullinemia were enrolled in this study. The patients were diagnosed based on clinical findings and biochemical characterization. Clinical and biochemical data were recorded. Whole blood samples were collected for genetic analysis. A cohort of 100 healthy men was studied as a control&#x20;group.</p>
</sec>
<sec id="s2-2">
<title>Genetic Analysis</title>
<p>Genomic DNA was extracted from the whole blood of all recruited subjects using DNA isolation kits (Tiangen, Beijing, China). A total of 3&#xa0;&#xb5;g genomic DNA of affected infants was used to prepare indexed Illumina libraries according to the manufacturer&#x2019;s protocol (Illumina, San Diego, CA, United&#x20;States). Coding exons and flanking regions of 165 genes reported to be mutated in disorders of amino acid, organic acid, and fatty acid metabolism were selected and captured using the Agilent SureSelect Target Enrichment System (Agilent, Santa Clara, CA, United&#x20;States). A list of the targeted genes is provided in <xref ref-type="sec" rid="s11">Supplementary Table S1</xref>. The enriched libraries were sequenced on an Illumina HiSeq 2500 sequencer.</p>
<p>After sequencing, low-quality reads and adaptor sequences were filtered out using the Solexa QA package and the cutadapt program (<ext-link ext-link-type="uri" xlink:href="https://cutadapt.readthedocs.org/">https://cutadapt.readthedocs.org/</ext-link>), respectively (<xref ref-type="bibr" rid="B3">Cox et&#x20;al., 2010</xref>). Clean reads were aligned to the human reference genome (hg19) using the SOAPaligner program (<xref ref-type="bibr" rid="B20">Li et&#x20;al., 2009</xref>), which was also used to identify single nucleotide polymorphisms (SNPs). To detect InDels, reads were realigned to the reference genome using the Burrows-Wheeler alignment tool, and InDels were identified with the Genome Analysis Toolkit (<xref ref-type="bibr" rid="B19">Li and Durbin, 2009</xref>; <xref ref-type="bibr" rid="B5">DePristo et&#x20;al., 2011</xref>). The impact of non-synonymous mutations was assessed <italic>in silico</italic> using Polyphen2 and SIFT (<xref ref-type="bibr" rid="B18">Kumar et&#x20;al., 2009</xref>; <xref ref-type="bibr" rid="B1">Adzhubei et&#x20;al., 2010</xref>), while the effect of splice site mutation was predicted by MutationTaster (<xref ref-type="bibr" rid="B29">Schwarz et&#x20;al., 2014</xref>). The novelty of the mutations was confirmed by searching in dbSNP (<ext-link ext-link-type="uri" xlink:href="http://www.ncbi.nlm.nih.gov/snp/">http://www.ncbi.nlm.nih.gov/snp/</ext-link>), the 1,000 Genomes Project (<ext-link ext-link-type="uri" xlink:href="https://www.internationalgenome.org/">https://www.internationalgenome.org/</ext-link>), and the HGMD Professional (<ext-link ext-link-type="uri" xlink:href="http://www.hgmd.cf.ac.uk/ac/index.php">http://www.hgmd.cf.ac.uk/ac/index.php</ext-link>) databases. The novel mutations were also confirmed by Sanger sequencing. Conservation analysis was performed using CLC Main Workbench Software.</p>
</sec>
<sec id="s2-3">
<title>Plasmid Construction</title>
<p>The open reading frame (ORF) of human <italic>ASS1</italic> was amplified by PCR from cDNA and inserted into the <italic>Bgl</italic> II- and <italic>Bam</italic>H I-digested pEGFP-N1 vector. p. Leu313Met and p. Thr323Ile mutations were introduced into wild-type (WT) expression plasmids by PCR-based site-directed mutagenesis. Then, the ORFs of WT and mutant <italic>ASS1</italic> were amplified and inserted into the <italic>Nde</italic> I- and <italic>Xba</italic> I-digested pCMV5-FLAG vector to create FLAG-tagged expression plasmids. The ORF of human <italic>PRMT7</italic> was also PCR-amplified and inserted into <italic>Nde</italic> I and <italic>Xba</italic> I sites of the pCMV5-FLAG vector to create expression plasmids. All plasmids were verified by sequencing. The sequences of primers used in plasmid construction are shown in <xref ref-type="sec" rid="s11">Supplementary Table&#x20;S2</xref>.</p>
</sec>
<sec id="s2-4">
<title>Cell Culture and Transient Transfection</title>
<p>Human embryonic kidney cells (HEK 293) were purchased from Shanghai cell bank (Chinese Academy of Sciences) and were cultured in Dulbecco&#x2019;s modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum, 100&#xa0;U/ml penicillin, and 100&#xa0;&#x3bc;g/ml streptomycin in a humidified incubator containing 5% CO<sub>2</sub> at 37&#xb0;C. Transient transfection was carried out using Lipofectamine 2000 (Invitrogen, Carlsbad, CA, United&#x20;States) according to the manufacturer&#x2019;s instructions.</p>
</sec>
<sec id="s2-5">
<title>ASS1 Immunoprecipitation and Activity Assay</title>
<p>ASS1 immunoprecipitation was performed as described previously with minor modifications (<xref ref-type="bibr" rid="B11">Herrera Sanchez et&#x20;al., 2017</xref>; <xref ref-type="bibr" rid="B23">Miyamoto et&#x20;al., 2017</xref>). Briefly, FLAG-tagged expression plasmids of ASS1 (WT or mutant) and empty vector were transfected into HEK 293 cells. Two days after transfection, cells were collected and lysed in NP-40 lysis buffer (Beyotime, Shanghai, China). The supernatants were collected after centrifugation at 10,000&#x20;<underline>&#xd7;</underline> <italic>g</italic> for 15&#xa0;min at 4&#xb0;C and incubated with anti-FLAG M2 Beads (Sigma-Aldrich, Shanghai, China) at 4&#xb0;C for 4&#xa0;h. The beads were then washed three times with lysis buffer. Bound proteins were eluted by adding 100&#xa0;&#x3bc;g/ml 3&#x20;<underline>&#xd7;</underline> FLAG peptide, and eluted proteins were used for ASS1 activity assays.</p>
<p>For these assays, equal amounts of eluted proteins were resuspended in reaction buffer (20&#xa0;mM Tris-HCl, pH 7.8, 2&#xa0;mM ATP, 2&#xa0;mM citrulline, 2&#xa0;mM aspartate, 6&#xa0;mM MgCl<sub>2</sub>, 20&#xa0;mM KCl, and 0.1 U pyrophosphatase) to a final volume of 100&#xa0;&#xb5;l. Samples were incubated for 30&#xa0;min at 37&#xb0;C, then the reactions were stopped by the addition of 100&#xa0;&#xb5;l molybdate buffer (10&#xa0;mM ascorbic acid, 2.5&#xa0;mM ammonium molybdate, and 2% sulfuric acid). The accumulation of pyrophosphate was determined at 660&#xa0;nm by spectrophotometry. Experiments were performed in triplicate and repeated three&#x20;times.</p>
</sec>
<sec id="s2-6">
<title>Co-Immunoprecipitation and Western Blotting</title>
<p>Expression plasmid pCMV5-FLAG-PRMT7 was co-transfected with pEGFP-ASS1, pEGFP-ASS1-Leu313Met, pEGFP-ASS1-Thr323Ile, or pEGFP-N1 empty vector into HEK293 cells. Immunoprecipitation was carried out as described above. For western blotting, cell lysates and immunoprecipitates were separated by sodium dodecyl sulfate polyacrylamide gel electrophoresis and transferred to nitrocellulose membranes. The membranes were blocked overnight with 5% (w/v) non-fat milk in Tris-buffered saline with 0.1% Tween 20, then probed with anti-green fluorescent protein (GFP) (Sungene, Tianjin, China), anti-&#x3b2;-actin (Sungene), or anti-FLAG M2 (Sigma-Aldrich, Shanghai, China) primary antibodies. They were then incubated with horseradish peroxidase-conjugated goat anti-mouse or goat anti-rabbit secondary antibodies and visualized by enhanced chemiluminescence (Sigma-Aldrich).</p>
</sec>
</sec>
<sec sec-type="results" id="s3">
<title>Results</title>
<sec id="s3-1">
<title>Patient Characteristics</title>
<p>A total of nine patients (three females, six males) were included in this study. All had high plasma citrulline levels (&#x3e;1,00&#xa0;&#x3bc;mol/L), and most had elevated levels of blood arginine, methionine, and threonine. Five patients presented with hyperammonemia. Patient clinical and biochemical characteristics are summarized in <xref ref-type="table" rid="T1">Table&#x20;1</xref>.</p>
<table-wrap id="T1" position="float">
<label>TABLE 1</label>
<caption>
<p>Clinical and Biochemical characteristics of patients.</p>
</caption>
<table>
<thead valign="top">
<tr>
<th rowspan="2" align="left">Patients ID</th>
<th rowspan="2" align="center">Gender</th>
<th rowspan="2" align="center">Age&#x20;of onset</th>
<th rowspan="2" align="center">Blood ammonia (9&#x2013;33&#xa0;&#x3bc;mol/l)<sup>&#x2a;</sup>
</th>
<th colspan="7" align="center">Initial plasma amino acids (&#x3bc;mol/l)</th>
</tr>
<tr>
<th align="center">Arginine (1.5&#x2013;25)<sup>&#x2a;</sup>
</th>
<th align="center">Citrulline (7&#x2013;40)<sup>&#x2a;</sup>
</th>
<th align="center">Methionine (8&#x2013;35)<sup>&#x2a;</sup>
</th>
<th align="center">Serine (20&#x2013;100)<sup>&#x2a;</sup>
</th>
<th align="center">Threonine (15&#x2013;100)<sup>&#x2a;</sup>
</th>
<th align="center">Tyrosine (20&#x2013;100)<sup>&#x2a;</sup>
</th>
<th align="center">Ornithine (15&#x2013;80)<sup>&#x2a;</sup>
</th>
</tr>
</thead>
<tbody valign="top">
<tr>
<td align="left">P1</td>
<td>Male</td>
<td>18&#xa0;months</td>
<td align="char" char=".">60</td>
<td align="char" char=".">89.1</td>
<td align="char" char=".">416.9</td>
<td align="char" char=".">58.6</td>
<td align="char" char=".">32.3</td>
<td align="char" char=".">119.9</td>
<td align="char" char=".">168.3</td>
<td align="char" char=".">39.6</td>
</tr>
<tr>
<td align="left">P2</td>
<td>Male</td>
<td>1&#xa0;month</td>
<td align="char" char=".">29</td>
<td align="char" char=".">63.2</td>
<td align="char" char=".">248.9</td>
<td align="char" char=".">312.6</td>
<td align="char" char=".">58.0</td>
<td align="char" char=".">233.9</td>
<td align="char" char=".">283.1</td>
<td align="char" char=".">58.5</td>
</tr>
<tr>
<td align="left">P3</td>
<td>Male</td>
<td>12&#x20;months</td>
<td align="char" char=".">26</td>
<td align="char" char=".">19.5</td>
<td align="char" char=".">115.6</td>
<td align="char" char=".">37.2</td>
<td align="char" char=".">46.7</td>
<td align="char" char=".">80.3</td>
<td align="char" char=".">93.8</td>
<td align="char" char=".">33.7</td>
</tr>
<tr>
<td align="left">P4</td>
<td>Female</td>
<td>2&#xa0;months</td>
<td align="char" char=".">39.8</td>
<td align="char" char=".">29.6</td>
<td align="char" char=".">100.4</td>
<td align="char" char=".">21.9</td>
<td align="char" char=".">21.7</td>
<td align="char" char=".">71.5</td>
<td align="char" char=".">31.3</td>
<td align="char" char=".">36.0</td>
</tr>
<tr>
<td align="left">P5</td>
<td>Female</td>
<td>1&#xa0;month</td>
<td align="char" char=".">10</td>
<td align="char" char=".">24.2</td>
<td align="char" char=".">359.1</td>
<td align="char" char=".">178.1</td>
<td align="char" char=".">21.2</td>
<td align="char" char=".">142.6</td>
<td align="char" char=".">107.6</td>
<td align="char" char=".">48.9</td>
</tr>
<tr>
<td align="left">P6</td>
<td>Male</td>
<td>3&#xa0;months</td>
<td align="char" char=".">60</td>
<td align="char" char=".">78.8</td>
<td align="char" char=".">171.9</td>
<td align="char" char=".">41.9</td>
<td align="char" char=".">19.6</td>
<td align="char" char=".">95.8</td>
<td align="char" char=".">326.0</td>
<td align="char" char=".">29.9</td>
</tr>
<tr>
<td align="left">P7</td>
<td>Male</td>
<td>2&#xa0;months</td>
<td align="char" char=".">43.2</td>
<td align="char" char=".">58.1</td>
<td align="char" char=".">331.2</td>
<td align="char" char=".">49.7</td>
<td align="char" char=".">54.1</td>
<td align="char" char=".">130.2</td>
<td align="char" char=".">125.5</td>
<td align="char" char=".">134.7</td>
</tr>
<tr>
<td align="left">P8</td>
<td>Male</td>
<td>1&#xa0;month</td>
<td align="char" char=".">119.7</td>
<td align="char" char=".">119.7</td>
<td align="char" char=".">671.3</td>
<td align="char" char=".">40.4</td>
<td align="char" char=".">26.2</td>
<td align="char" char=".">173.7</td>
<td align="char" char=".">52.2</td>
<td align="char" char=".">48.2</td>
</tr>
<tr>
<td align="left">P9</td>
<td>Female</td>
<td>1&#xa0;month</td>
<td align="char" char=".">23.3</td>
<td align="char" char=".">23.3</td>
<td align="char" char=".">1924.1</td>
<td align="char" char=".">51.8</td>
<td align="char" char=".">25.0</td>
<td align="char" char=".">16.8</td>
<td align="char" char=".">38.3</td>
<td align="char" char=".">39.3</td>
</tr>
</tbody>
</table>
<table-wrap-foot>
<fn>
<p>The symbol &#x201c;&#x2a;&#x201d; indicates reference&#x20;value.</p>
</fn>
</table-wrap-foot>
</table-wrap>
</sec>
<sec id="s3-2">
<title>Mutational Spectrum</title>
<p>Six mutations (15 mutated alleles) of <italic>SLC25A13</italic> were identified in the patients through NGS. The most common was c.851_854del (seven alleles, 47%), followed by c.1638_1660dup23 (four alleles, 27%). A novel splicing mutation of <italic>SLC25A13</italic> was identified: c.1311 &#x2b; 4_&#x2b;7del (<xref ref-type="sec" rid="s11">Supplementary Figure S1</xref>), which resulted in a deletion of &#x201c;AGUA&#x201d; at the 5<underline>&#x2032;</underline> splice site. This mutation was not observed in healthy controls, nor reported in dbSNP, 1,000 Genome Project, or the HGMD Professional databases. It was predicted to result in splice site changes and be disease-causing by MutationTaster.</p>
<p>Three <italic>ASS1</italic> mutations were detected in the patients, of which a missense mutation was novel: c.937C &#x3e; A (p.Leu313Met, shown in <xref ref-type="sec" rid="s11">Supplementary Figure S2</xref>). The c.968C &#x3e; T (p.Thr323Ile) mutation (rs1250895424, shown in <xref ref-type="sec" rid="s11">Supplementary Figure S3</xref>) was identified by Trans-Omics for Precision Medicine (TOPMed) program previously. The minor allele frequency (MAF) is 0.000008. In the Genome Aggregation Database (gnomAD), the MAF of this mutation is 0.00002 in Asian population. So it was a rare mutation. Both mutations were not detected in healthy controls. And both are located at sites that are highly conserved among species (<xref ref-type="fig" rid="F1">Figure&#x20;1</xref>). They were predicted to be pathogenic by Polyphen2 and SIFT (<xref ref-type="sec" rid="s11">Supplementary Table S3</xref>). The mutations identified in this study are summarized in <xref ref-type="table" rid="T2">Table&#x20;2</xref>.</p>
<fig id="F1" position="float">
<label>FIGURE 1</label>
<caption>
<p>Sequence alignment of ASS1 proteins among species.</p>
</caption>
<graphic xlink:href="fgene-13-783799-g001.tif"/>
</fig>
<table-wrap id="T2" position="float">
<label>TABLE 2</label>
<caption>
<p>Mutations detected in included infants.</p>
</caption>
<table>
<thead valign="top">
<tr>
<th align="left"/>
<th align="center">Mutations</th>
<th align="center">Gene</th>
<th align="center">Location</th>
<th align="left">rsID</th>
<th align="center">Type</th>
<th align="center">Patients ID</th>
</tr>
</thead>
<tbody valign="top">
<tr>
<td rowspan="3" align="left">Homozygotes (<italic>n</italic>&#x20;&#x3d; 3)</td>
<td align="left">c.851_854del (p.Met285Profs&#x2a;2)</td>
<td align="left">
<italic>SLC25A13</italic>
</td>
<td align="left">Exon 9</td>
<td align="left">rs80338720</td>
<td align="left">Frameshift</td>
<td align="center">P1</td>
</tr>
<tr>
<td align="left">c.851_854del (p.Met285Profs&#x2a;2)</td>
<td align="left">
<italic>SLC25A13</italic>
</td>
<td align="left">Exon 9</td>
<td align="left">rs80338720</td>
<td align="left">Frameshift</td>
<td align="center">P2</td>
</tr>
<tr>
<td align="left">c.1638_1660dup23 (p.Ala554Glyfs&#x2a;17)</td>
<td align="left">
<italic>SLC25A13</italic>
</td>
<td align="left">Exon 16</td>
<td align="left">rs80338725</td>
<td align="left">Frameshift</td>
<td align="center">P3</td>
</tr>
<tr>
<td rowspan="12" align="left">Compound heterozygotes (<italic>n</italic> &#x3d; 6)</td>
<td align="left">c.615&#x2b;5G &#x3e; A (p.Ala206Valfs&#x2a;7)</td>
<td rowspan="2" align="left">
<italic>SLC25A13</italic>
</td>
<td align="left">Intron 6</td>
<td align="left">rs80338717</td>
<td align="left">Frameshift</td>
<td align="center">P4</td>
</tr>
<tr>
<td align="left">c.640C &#x3e; T (p.Gln214&#x2a;)</td>
<td align="left">Exon 7</td>
<td align="left">&#x2014;</td>
<td align="left">Nonsense</td>
<td align="left"/>
</tr>
<tr>
<td align="left">c.851_854del (p.Met285Profs&#x2a;2)</td>
<td rowspan="2" align="left">
<italic>SLC25A13</italic>
</td>
<td align="left">Exon 9</td>
<td align="left">rs80338720</td>
<td align="left">Frameshift</td>
<td align="center">P5</td>
</tr>
<tr>
<td align="left">c.1638_1660dup23 (p.Ala554Glyfs&#x2a;17)</td>
<td align="left">Exon 16</td>
<td align="left">rs80338725</td>
<td align="left">Frameshift</td>
<td align="left"/>
</tr>
<tr>
<td align="left">c.851_854del (p.Met285Profs&#x2a;2)</td>
<td rowspan="2" align="left">
<italic>SLC25A13</italic>
</td>
<td align="left">Exon 9</td>
<td align="left">rs80338720</td>
<td align="left">Frameshift</td>
<td align="center">P6</td>
</tr>
<tr>
<td align="left">c.1638_1660dup23 (p.Ala554Glyfs&#x2a;17)</td>
<td align="left">Exon 16</td>
<td align="left">rs80338725</td>
<td align="left">Frameshift</td>
<td align="left"/>
</tr>
<tr>
<td align="left">c.1311 &#x2b; 4_&#x2b;7del<sup>&#xa7;</sup>
</td>
<td rowspan="2" align="left">
<italic>SLC25A13</italic>
</td>
<td align="left">Intron 13</td>
<td align="left">&#x2014;</td>
<td align="left">Splicing</td>
<td align="center">P7</td>
</tr>
<tr>
<td align="left">c.1762C &#x3e; T (p.Arg588&#x2a;)</td>
<td align="left">Exon 17</td>
<td align="left">&#x2014;</td>
<td align="left">Nonsense</td>
<td align="left"/>
</tr>
<tr>
<td align="left">c.851_854del (p.Met285Profs&#x2a;2)</td>
<td align="left">
<italic>SLC25A13</italic>
</td>
<td align="left">Exon 9</td>
<td align="left">rs80338720</td>
<td align="left">Frameshift</td>
<td align="center">P8</td>
</tr>
<tr>
<td align="left">c.968C &#x3e; T (p.Thr323Ile)</td>
<td align="left">
<italic>ASS1</italic>
</td>
<td align="left">Exon 13</td>
<td align="left">rs1250895424</td>
<td align="left">Missense</td>
<td align="left"/>
</tr>
<tr>
<td align="left">c.937C &#x3e; A (p.Leu313Met)<sup>&#xa7;</sup>
</td>
<td rowspan="2" align="left">
<italic>ASS1</italic>
</td>
<td align="left">Exon 13</td>
<td align="left">&#x2014;</td>
<td align="left">Missense</td>
<td align="center">P9</td>
</tr>
<tr>
<td align="left">c.970&#x2b;5G &#x3e; A</td>
<td align="left">Intron 13</td>
<td align="left">&#x2014;</td>
<td align="left">Splicing</td>
<td align="left"/>
</tr>
</tbody>
</table>
<table-wrap-foot>
<fn>
<p>The symbol &#x201c;&#xa7;&#x201d; indicates novel mutation. And the symbol &#x201c;&#x2013;&#x201d; indicates no record. NM_014251.3 and NM_000050.4 were used as reference sequences for <italic>SLC25A13</italic> and <italic>ASS1</italic>, respectively. The italic values mean the numbers of homozygotes or heterozygotes.</p>
</fn>
</table-wrap-foot>
</table-wrap>
</sec>
<sec id="s3-3">
<title>Functional Analyses of Missense Mutations</title>
<p>Because splicing mutation can cause improper intron removal and alterations of the ORF, functional analyses were performed of the two <italic>ASS1</italic> missense mutations. WT and mutant ASS1 proteins were over-expressed and purified from HEK293 cells. Assays of enzyme activity showed that both p. Leu313Met and p. Thr323Ile mutant proteins had significantly decreased activity compared with WT (<xref ref-type="fig" rid="F2">Figure&#x20;2A</xref>).</p>
<fig id="F2" position="float">
<label>FIGURE 2</label>
<caption>
<p>Functional analysis of <italic>ASS1</italic> mutations. <bold>(A)</bold> Effect of p. Leu313Met and p. Thr323Ile mutations on ASS1 activity. The enzymatic activity of ASS1 immunoprecipitated from HEK293 cells expressing pCMV5-FLAG empty vector, ASS1-FLAG, ASS1-Leu313Met-FLAG, or ASS1-Thr323Ile-FALG was determined. Data are normalized to ASS1&#x20;wild-type protein (lane 2). Three independent experiments were performed. Statistical significance was determined by one-way ANOVA. <bold>(B)</bold> Effect of p. Leu313Met and p. Thr323Ile mutations on the ASS1&#x2013;PRMT7 interaction. HEK293 cells co-expressing PRMT7-FLAG and GFP, or PRMT7-FLAG with ASS1-GFP, ASS1-Leu313Met-GFP, or ASS1-Thr323Ile-GFP were harvested. PRMT7-FLAG was immunoprecipitated using anti-FLAG M2 Beads. Immunoprecipitates were analyzed by western blotting using anti-GFP and anti-FLAG M2 antibodies. Total cell lysates were analyzed by western blotting using anti-GFP, anti-FLAG M2, and anti-&#x3b2;-actin antibodies.</p>
</caption>
<graphic xlink:href="fgene-13-783799-g002.tif"/>
</fig>
<p>PRMT7 was previously reported to interact with ASS1 (<xref ref-type="bibr" rid="B32">Verma et&#x20;al., 2017</xref>), so we next investigated the effect of the mutations on this interaction. Co-immunoprecipitation experiments using FLAG-tagged PRMT7 and GFP-tagged ASS1 revealed similar expression levels of the two mutant proteins with that of WT ASS1 in HEK293 cells. A similar amount of p. Leu313Met mutant protein to WT ASS1 was co-immunoprecipitated by PRMT7. However, less p. Thr323Ile mutant protein was co-immunoprecipitated by PRMT7 compared with WT (<xref ref-type="fig" rid="F2">Figure&#x20;2B</xref>), suggesting that the p. Thr323Ile mutant protein binds weakly to PRMT7.</p>
</sec>
</sec>
<sec sec-type="discussion" id="s4">
<title>Discussion</title>
<p>Although citrullinemia types I and II are caused by mutations in different genes, they exhibit partial similarities in clinical phenotypes. In the present study, we performed genetic analysis of nine Chinese infants with citrullinemia, and identified homozygous or compound heterozygous mutations of <italic>ASS1</italic> and <italic>SLC25A13</italic> (<xref ref-type="table" rid="T2">Table&#x20;2</xref>). This demonstrated that genetic analysis can help determine the subgroup of citrullinemia besides clinical and biochemical examinations.</p>
<p>Our study identified a novel splicing mutation of <italic>SLC25A13,</italic> which leads to the deletion of &#x201c;AGUA&#x201d; at the 5<underline>&#x2032;</underline> splice site. This mutation is very likely to affect pre-mRNA splicing for three main reasons. First, during the splicing process, the 5&#x2032; splice site (CAG/GUAAGU sequence) and 3&#x2032; splice site (NYAG/G sequence) are recognized by spliceosome components (<xref ref-type="bibr" rid="B25">Ohno et&#x20;al., 2018</xref>). While most common mutations affect &#x2b;1 and &#x2b;2 residues at the 5&#x2032; donor splice site and &#x2212;1 and &#x2212;2 residues at the 3&#x2032; acceptor splice site, any mutations in these canonical sequences could impair the interaction between pre-mRNA and the spliceosome, leading to abnormal pre-mRNA splicing (<xref ref-type="bibr" rid="B2">Anna and Monika, 2018</xref>). The <italic>OXCT1</italic> c.1248&#x2b;5G &#x3e; A mutation, <italic>IKBKAP</italic> c.2204&#x2b;6T &#x3e; C mutation, and <italic>CDHR1</italic> c.2040&#x2b;5G &#x3e; T mutation were previously found to cause exon skipping (<xref ref-type="bibr" rid="B13">Ibrahim et&#x20;al., 2007</xref>; <xref ref-type="bibr" rid="B12">Hori et&#x20;al., 2013</xref>; <xref ref-type="bibr" rid="B30">Stingl et&#x20;al., 2017</xref>). Moreover, the <italic>ATF6</italic> c.82&#x2b;5G &#x3e; T mutation led to intron retention (<xref ref-type="bibr" rid="B17">Kohl et&#x20;al., 2015</xref>), while <italic>ASS1</italic> mutations c.773&#x2b;4A &#x3e; C and c.970&#x2b;5G &#x3e; A were identified in patients with citrullinemia (<xref ref-type="bibr" rid="B15">Kobayashi et&#x20;al., 1995</xref>; <xref ref-type="bibr" rid="B21">Lin et&#x20;al., 2019</xref>). Second, the MutationTaster predicted that the mutation was disease-causing. Finally, high levels of plasma citrulline (331.2&#xa0;&#x3bc;mol/l; normal: 7&#x2013;40&#xa0;&#x3bc;mol/l) were detected in the patient carrying this mutation. Considering that he also carried a nonsense mutation of <italic>SLC25A13</italic> (p.Arg588&#x2a;), it is likely that these compound heterozygous mutations caused the production of defective citrin protein.</p>
<p>We also identified a novel mutation (p.Leu313Met) and a rare mutation (p.Thr323Ile) of <italic>ASS1</italic>, which are both located at highly conserved sites and were absent from the 100 healthy controls. Polyphen2 and SIFT predicted them to be damaging, and functional analyses showed that they significantly impaired the enzyme activity of ASS1. Furthermore, <italic>PRMT7</italic> encodes a protein arginine methyltransferase which catalyzes arginine methylation. A previous study showed that PRMT7 interacts with ASS1, and that several mutations associated with citrullinemia disrupt this interaction (<xref ref-type="bibr" rid="B32">Verma et&#x20;al., 2017</xref>). In this study, we found that the p. Thr323Ile mutation also considerably decreased the binding of ASS1 to PRMT7. Therefore, we believe that these two mutations are pathogenic for citrullinemia.</p>
<p>Digenic inheritance refers to mutations in two distinct genes causing a genetic phenotype or disease. With increasing exome and genome sequence data being generated through NGS, the number of human diseases exhibiting digenic inheritance continues to grow (<xref ref-type="bibr" rid="B8">Gazzo et&#x20;al., 2016</xref>; <xref ref-type="bibr" rid="B4">Deltas, 2018</xref>). It provides new insights into the genetics underlying many disorders classically considered monogenic (<xref ref-type="bibr" rid="B28">Sch&#xe4;ffer, 2013</xref>). Distal renal tubular acidosis (dRTA) is just one example (<xref ref-type="bibr" rid="B24">Nagara et&#x20;al., 2018</xref>). In the present study, we identified a patient (P8) harboring both a heterozygous mutation of <italic>ASS1</italic> (p.Thr323Ile) and a heterozygous mutation of <italic>SLC25A13</italic> (p.Met285Profs&#x2a;2). The patient had high levels of plasma citrulline (671.3&#xa0;&#x3bc;mol/l, normal: 7&#x2013;40&#xa0;&#x3bc;mol/l) and arginine (119.7&#xa0;&#x3bc;mol/l, normal: 1.5&#x2013;25&#xa0;&#x3bc;mol/l). Together, these results might implicate a putative digenic inheritance mechanism in citrullinemia. A mutated allele of <italic>ASS1</italic> may reduce the formation of argininosuccinate from citrulline and aspartate, while a mutated <italic>SLC25A13</italic> allele is likely to further inhibit the reaction by limiting the supply of aspartate from mitochondria. Thus, the compound mutations would be predicted to lead to the upstream accumulation of citrulline. Further analyses are required to investigate the effects of these compound mutations on cell metabolism.</p>
<p>The clinical presentation of citrullinemia is very heterogeneous. In our study, patient P9 with <italic>ASS1</italic> mutations displayed the most severe clinical symptoms. She had the highest plasma citrulline level (1924.1&#xa0;&#x3bc;mol/l; normal: 7&#x2013;40&#xa0;&#x3bc;mol/l), and died at 1&#xa0;year of age. This indicates that <italic>ASS1</italic> mutations might cause more severe clinical manifestations than <italic>SLC25A13</italic> mutations. Consistent with this, patient P8 carrying compound heterozygous mutations of <italic>ASS1</italic> and <italic>SLC25A13</italic> also showed more severe clinical manifestations than patients only harboring <italic>SLC25A13</italic> mutations. Most mutations of <italic>SLC25A13</italic> identified in this study led to truncated proteins. However, no firm genotype&#x2013;phenotype correlations could be observed in patients carrying <italic>SLC25A13</italic> mutations.</p>
<p>The present study had some limitations. First, we did not perform functional analysis of the c.1311 &#x2b; 4_&#x2b;7del mutation to support its predicted effect on <italic>SLC25A13</italic> splicing. Second, because of limited sample sources, genetic analysis of the patients&#x2019; parents was not carried out to determine if the identified novel mutations were <italic>de novo</italic>; additionally, the segregation test for identified mutations could not be performed.</p>
<p>In summary, we carried out genetic analysis and functional investigation in Chinese infants with citrullinemia. We identified a novel mutation of <italic>ASS1</italic> and a novel mutation of <italic>SLC25A13</italic>. These findings expand the mutational spectrum of <italic>ASS1</italic> and <italic>SLC25A13</italic>, and improve our understanding of the molecular genetic mechanism of citrullinemia in the Chinese population.</p>
</sec>
</body>
<back>
<sec id="s5">
<title>Data Availability Statement</title>
<p>The datasets for this article are not publicly available due to concerns regarding participant/patient anonymity. Requests to access the datasets should be directed to the corresponding author.</p>
</sec>
<sec id="s6">
<title>Ethics Statement</title>
<p>The studies involving human participants were reviewed and approved by the Ethics Committee of the Children&#x2019;s Hospital affiliated to Chongqing Medical University (No. 2021078) and Chongqing Health Center for Women and Children (No. 2020024). Written informed consent to participate in this study was provided by the participants&#x2019; legal guardian/next of kin. Written informed consent was obtained from the minor(s)&#x2019; legal guardian/next of kin for the publication of any potentially identifiable images or data included in this article.</p>
</sec>
<sec id="s7">
<title>Author Contributions</title>
<p>JM conceived the study. Z-EX, CL, and HL were responsible for recruiting patients and collection of blood samples. ZC performed the experimental work. XH and FZ participated in the experimental work. JM and ZC drafted the manuscript, tables, and figures. All authors read and approved the final manuscript.</p>
</sec>
<sec id="s8">
<title>Funding</title>
<p>This study was supported by Chongqing Health Center for Women and Children: (No. 2019YJMS08), the Fundamental Research Funds for Non-profit Public Scientific Research Institutions of Chongqing (No. 2016CSTC-jbky-01711).</p>
</sec>
<sec sec-type="COI-statement" id="s9">
<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="s10">
<title>Publisher&#x2019;s Note</title>
<p>All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.</p>
</sec>
<sec id="s11">
<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/fgene.2022.783799/full#supplementary-material">https://www.frontiersin.org/articles/10.3389/fgene.2022.783799/full&#x23;supplementary-material</ext-link>
</p>
<supplementary-material xlink:href="DataSheet1.PDF" id="SM1" mimetype="application/PDF" xmlns:xlink="http://www.w3.org/1999/xlink"/>
<supplementary-material xlink:href="DataSheet2.docx" id="SM2" mimetype="application/docx" xmlns:xlink="http://www.w3.org/1999/xlink"/>
</sec>
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