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  <front>
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      <journal-id journal-id-type="publisher-id">oaai</journal-id>
      <journal-title-group>
        <journal-title>OAAI Biology</journal-title>
        <abbrev-journal-title>OAAI Biol</abbrev-journal-title>
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      <title-group>
        <article-title>Plac1 Ablation Disrupts Signaling Pathways Essential for Prenatal Development and Induces a Preeclampsia-Associated Transcriptomic Signature</article-title>
      </title-group>
      <pub-date date-type="pub" publication-format="electronic" iso-8601-date="2026-05-05T14:49:08.444+00:00">
        <year>2026</year>
        <month>05</month>
        <day>05T14:49:08.444+00:00</day>
      </pub-date>
      
      <abstract>
<p>Plac1 is an X-linked gene essential for placental and embryonic development. A knockout (KO) mouse model was used to identify Plac1-regulated gene expression at E16.5 and E18.5 using gene expression microarray. Genes exhibiting at least 1.5-fold change in expression and FDR &lt; .05 were considered significant. At E16.5, 717 genes were downregulated and 798 were upregulated in male KO placentas versus wild type (WT), whereas at E18.5, 1122 genes were downregulated and 1149 were upregulated. GO, KEGG, and IPA analyses revealed downregulated genes were enriched for Rho GTPase-mediated and actin-cytoskeleton based processes that transmit extracellular cues through canonical signaling pathways, including Integrin, GPCR, Wnt, Notch, VEGF, BMP and TGF-beta, documented to impact trophoblast development, vasculogenesis, vascular tone, branching morphogenesis, and immunomodulation. Furthermore, a preeclampsia-associated transcriptomic signature was induced that strengthened over time. By contrast, upregulated genes reflected immune activation and adaptations to oxidative stress resulting from impaired placental function. These findings indicate that Plac1 supports signaling required to maintain placental structure and regulatory function. Its absence disrupts essential regulatory processes and triggers cellular stress and immune activation, contributing to fetal growth restriction, increased risk for embryopathy and preeclampsia, consistent with the Developmental Origins of Health and Disease (DOHaD) framework.</p>
<p>Key Words: Plac1; placental development; Rho GTPase signaling; fetal growth restriction (FGR); birth defects; cardiovascular disease; preeclampsia; brain development; Developmental Origins of Health and Disease (DOHaD)</p>
</abstract>
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  <body>
<sec id="plac1-ablation-disrupts-signaling-pathways-essential-for-prenatal-development-and-induces-a-preeclampsia-associated-transcriptomic-signature">
<title>Plac1 Ablation Disrupts Signaling Pathways Essential for Prenatal Development and Induces a Preeclampsia-Associated Transcriptomic Signature</title>
<p>Suzanne Jackman¹*, Xiaoyuan Kong¹*, Yulan Piao², Alexei Sharov², Elin Lehrmann², Andrew Varshine², Ramaiah Nagaraja², David Schlessinger² and Michael E. Fant¹‡</p>
<p>¹Department of Pediatrics, University of South Florida, Morsani College of Medicine, Tampa, FL ²Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, Maryland</p>
<p>*S. Jackman and X. Kong contributed equally to this work. ‡ Correspondence – mfant@usf.edu</p>

</sec>

<sec id="1-introduction">
<title>1. Introduction</title>
<p>Plac1 is an X-linked gene that maps to a chromosomal locus previously shown to be important for placental and embryonic development <xref ref-type="bibr" rid="1">1</xref>. Its expression is particularly high in the placenta, hence its name Placenta-specific 1, as the placenta was initially thought to be the only locus of its expression <xref ref-type="bibr" rid="1">1</xref><xref ref-type="bibr" rid="2">2</xref>. Subsequent studies, however, have demonstrated that it is also expressed throughout the developing embryo, albeit at 1-10% of placental expression levels, suggesting a broader role in embryonic development. Its expression in adult animals, however, diminishes to essentially undetectable levels <xref ref-type="bibr" rid="3">3</xref>. The human PLAC1 gene encodes a putative protein of 212 amino acids, whereas the mouse ortholog has 173 amino acids with 65% homology <xref ref-type="bibr" rid="1">1</xref>. The protein is predicted to exist as a membrane-associated or extracellular peptide (PSORT: psort.ims.u-tokyo.ac.jp ). Consistent with targeting to a membranous compartment, a predicted transmembrane ™ domain lies at aa 23 – 40 from the N-terminus. Within the placenta, PLAC1 is expressed exclusively in the trophoblast, where its expression is tightly linked to differentiation of the syncytiotrophoblast <xref ref-type="bibr" rid="1">1</xref><xref ref-type="bibr" rid="2">2</xref><xref ref-type="bibr" rid="4">4</xref>. Immunohistochemical analysis of cytotrophoblasts has demonstrated distribution throughout the cytosolic region as well as near the plasma membrane. By contrast, its localization in the differentiated syncytiotrophoblast is highly restricted to the apical cytosolic region in proximity to the maternal-facing microvillous membrane surface <xref ref-type="bibr" rid="5">5</xref>.</p>
<p>An essential role for Plac1 in placental and embryonic development has been demonstrated in a mutant mouse model <xref ref-type="bibr" rid="6">6</xref>. Placentas in Plac1-null mice exhibit placentomegaly with an enlarged and disorganized junctional zone (JZ), characterized by spongiotrophoblast (SpT) hyperplasia and associated with mild fetal growth restriction. Consistent with preferential paternal X chromosome inactivation in murine extraembryonic tissue <xref ref-type="bibr" rid="7">7</xref><xref ref-type="bibr" rid="8">8</xref>, genetic analyses revealed that placentas derived from maternal (X^m^X) heterozygotes (Hets) were phenotypically similar (but not identical) to knockout (KO) placentas whereas paternal (XX^p^-) Hets were phenotypically identical to wild type (WT). Further analysis suggested that the paternal Plac1 allele is not completely inactivated, with approximately 10-15% residual activity remaining, providing some degree of functional activity in the X^m^X Het not observed in the KO.</p>
<p>A functional role for Plac1 was also shown to extend to the embryo proper. Surviving Plac1 mutants (Plac1-null males and X^m^X females) developed postnatal hydrocephalus with increased frequency, 22% and 11% respectively, suggesting Plac1 plays an important role in fetal brain development. The changes in the placental phenotype were later supported by Muto, et al, using a mutant mouse model derived using a different targeting vector and bred against a different mouse strain <xref ref-type="bibr" rid="9">9</xref>. By employing Lentivirus-mediated Plac1 expression, they were also able to show that Plac1 rescue failed to reverse the overgrowth of the spongiotrophoblast layer but did ameliorate changes in the labyrinth, pointing to temporal aspect(s) of Plac1 function.</p>
<p>PLAC1 expression has also been shown to be reactivated in a wide range of human cancers and cell lines in which it influences cell proliferation and migration in vitro . Its in vivo expression in tumors has been linked to increased metastasis risk and decreased survival [reviewed in 10].</p>
<p>We applied our mutant mouse model to the identification of genes and signaling pathways regulated by Plac1 that drive placental development and embryogenesis. Given the high degree of conservation of Plac1 between mouse and human, and its highly restricted, trophoblast-specific expression, Plac1 is likely to occupy an upstream position within regulatory hierarchies that coordinate placental growth, differentiation, and maternal–fetal exchange. Accordingly, the objective of this study was not to resolve the full regulatory cascade downstream of Plac1, but rather to establish a framework describing the physiological and signaling landscapes perturbed by its loss. By integrating gene-level expression changes with pathway and systems-level analyses, we aimed to identify the core biological processes dependent on Plac1 during late gestation and to generate a cohesive, hypothesis-generating model of its role in placental development and pregnancy maintenance. Accordingly, this study combines gene-centric analysis of highly dysregulated transcripts and reciprocally regulated genes with complementary GO, KEGG, and IPA analyses. This integrative strategy was designed to facilitate interpretation by multidisciplinary groups of investigators and to establish a biologically coherent framework upon which future mechanistic studies can build.</p>

</sec>

<sec id="2-results">
<title>2. Results</title>

</sec>

<sec id="2-1-developmental-dynamics-of-placental-growth-in-plac1-mutants">
<title>2.1 Developmental dynamics of placental growth in Plac1 mutants</title>
<p>We focused this analysis on the period of pregnancy when the growth trajectory of Plac1-null placentas exhibit maximal divergence from WT placentas. Placentas associated with Plac1-null embryos and maternal Hets (X^m^X) exhibit placentomegaly and a disorganized junctional zone (JZ) <xref ref-type="bibr" rid="6">6</xref>. Placental weights of X^m^X Hets diverge from KO littermates between E16.5 and E18.5, likely because the paternal allele escapes complete inactivation. As we previously reported <xref ref-type="bibr" rid="6">6</xref> and summarize in Figure 1, X^m^X Het placental weight peaks at E16.5 and decreases slightly thereafter. By contrast, the weight of Plac1-null placentas continues to accelerate until E17.5 and then plateaus. These observations guided our transcriptomic analysis of the developmental span bordered by E16.5 and E18.5.</p>
<fig id="fig1">
  <label>Figure 1</label>
  <caption><p>Growth trajectories of placentas from Plac-1 mutants compared to WT placentas. Placental weights were determined throughout gestation representing WT, X^m^X, and KO mice and presented in graphical form summarizing previously published data [6]. Each point represents the mean of age-specific samples for each genotype (n = 1-10 per data point). WT and KO data include both male and female placentas.</p></caption>
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</fig>

</sec>

<sec id="2-2-gene-expression-microarray-analysis">
<title>2.2 Gene Expression Microarray Analysis</title>
<p>The Agilent 4x44k gene chip, representing the entire mouse genome, was used to identify Plac1-dependent gene expression at E16.5 and E18.5. KO male placentas were compared to WT male placentas in duplicate samples. At E16.5, 717 known or putative genes were downregulated and 798 genes were upregulated at least 1.5-fold (FDR &lt; .05) in KO placentas compared to WT. Similarly, at E18.5, 1122 genes were downregulated and 1149 genes were upregulated. (See supplemental materials, Tables S1-S7, for processed data and complete gene lists).</p>
<p>Principal Component Analysis (PCA) (Supplemental Table, S3) revealed that the first three components explained 79.1% of the variance (PC1: 41.7%, PC2: 25.33%, PC3:12.07%). Visual inspection of PC1 and PC2 (Figure 2) indicates that PC1 primarily separated samples by gestational age (E16.5 versus E18.5, whereas PC2 distinguished genotypes (WT from KO). Female samples are included to provide reassurance regarding the overall coherence and quality of the expression data derived from the male samples and are shown for qualitative visualization only. No statistical or comparative conclusions were drawn due to the lack of biological replication. The WT female sample appeared modestly separated from the KO female, suggesting a potential female specific expression pattern (possibly contributing to PC3). Because Plac-1 is X-linked, subtle sex dependent effects are not unexpected. However, this observation should be interpreted cautiously given the lack of female replicates.</p>
<fig id="fig2">
  <label>Figure 2</label>
  <caption><p>PCA of normalized expression data: E16.5 and E18.5 placentas (WT and KO). PC1 and PC2 explain [41.70%] and [25.33%] of the variance, respectively. PC1 separates E16.5 vs E18.5, PC2 separates WT vs KO. Points are labeled by age, sex, genotype, and replicate. Color = genotype (WT = blue, KO = red); Shape = age (E16.5 = circles, E18.5 = triangles); Black outline = female. Note there is only one female replicate per genotype and are shown for descriptive purposes only. No statistical or comparative conclusions were drawn due to the lack of biological replication.</p></caption>
  <graphic xlink:href="https://qzydlaimdnpogmrslkea.supabase.co/storage/v1/object/public/manuscripts/figures/upload-1777992173558/fig-02-p6.png" />
</fig>
<p>KO versus WT scatter plots are shown for each age/sex group (Figure 3). Most genes lie near the diagonal reference line, indicating broadly similar expression between KO and WT. Colored points denote differentially expressed genes (DEGs) meeting our threshold (≥1.5-fold change, FDR &lt; 0.05). Red indicates upregulated genes in the Plac1 KO and green indicates downregulated KO genes. Grey points indicate genes not significantly dysregulated. Axes show log₁₀ expression values. Panel A and panel B display replicate means for males, whereas panel C shows values from one female per genotype.</p>
<fig id="fig3">
  <label>Figure 3</label>
  <caption><p>KO vs WT scatter plots by age and sex. Pairwise scatter plots compare KO (yaxis) versus WT (xaxis) log₁₀ expression within (A) E16.5 males (replicate means), (B) E18.5 males (replicate means), and © E16.5 females. Single female samples are shown for descriptive purposes only. No statistical or comparative conclusions were drawn due to lack of biological replication. Each point represents a gene/probe; the diagonal line indicates y = x (equal expression in KO and WT). Red points represent upregulated genes in the KO; green points represent downregulated genes in the KO; grey points represent no significant dysregulation, based on ≥1.5fold change and FDR &lt; 0.05.</p></caption>
  <graphic xlink:href="https://qzydlaimdnpogmrslkea.supabase.co/storage/v1/object/public/manuscripts/figures/upload-1777992173558/fig-03-p7.png" />
</fig>
<p>The heatmap of DEGs meeting our cutoff criteria of ≥1.5 fold change and FDR &lt; 0.05 is shown in Figure 4. Differential expression was assessed using linear mixed-effects model with subjects treated as a random effect. Expression values are visualized, with genes (rows) ordered by hierarchical clustering. Although hierarchical clustering was applied only to genes and not to samples, several gene clusters exhibit expression patterns that appear to align with trends observed in the PCA. Specifically, a subset of genes revealed slightly divergent expression in WT versus KO females. However, again because of the lack of female replicates, a possible sex-associated trend should be interpreted cautiously.</p>
<fig id="fig4">
  <label>Figure 4</label>
  <caption><p>Heatmap of differentially expressed genes across samples. Heatmap displays relative gene expression patterns for DEGs identified at each developmental stage. For visualization, log₁₀-transformed expression values were row-centered such that each gene’s mean expression across all samples equals zero. Color indicates expression relative to that gene’s mean level (blue, lower than average; yellow/brown, higher than average). Values were not variance-scaled. Genes (rows) are ordered by hierarchical clustering.</p></caption>
  <graphic xlink:href="https://qzydlaimdnpogmrslkea.supabase.co/storage/v1/object/public/manuscripts/figures/upload-1777992173558/fig-04-p8.png" />
</fig>

</sec>

<sec id="2-3-rt-qpcr-validation-of-differentially-expressed-genes">
<title>2.3 RT-qPCR Validation of Differentially Expressed Genes</title>
<p>A panel of genes were selected to validate the original microarray results when it was first carried out. Five downregulated genes (Cnn1, Elavl4, Nppb, Slc6a15, Zbtb4) and one upregulated gene (Cer1) were assessed in placentas at E18.5 (Figure 5). The results were qualitatively consistent (directional change) with the current (2026) microarray analysis. These data represent the mean of two biological replicates assayed in triplicate per genotype (See Supplemental Data, S8).</p>
<p>Diminishing availability of mutant placentas due to colony attrition limited the number of genes that could be assayed. While these results are supportive of our microarray expression data, we acknowledge the limitations imposed by the small sample size on performing a robust statistical analysis. Surveying a larger sample of genes derived from multiple placentas will be necessary to establish a statistically powered qPCR validation in future studies.</p>
<fig id="fig5">
  <label>Figure 5</label>
  <caption><p>Real time - qPCR of selected placental genes. Two biological replicates per genotype were assayed in triplicate. The bars represent the mean of the two biological replicates per genotype (n = 2), + SEM. Values for each gene were rescaled, independently, to permit visualization on a shared panel. Absolute values cannot be compared between genes. The original single gene plots with their native scales are provided in Supplementary Data, S8.</p></caption>
  <graphic xlink:href="https://qzydlaimdnpogmrslkea.supabase.co/storage/v1/object/public/manuscripts/figures/upload-1777992173558/fig-05-p9.png" />
</fig>

</sec>

<sec id="2-4-gene-level-curation-of-dysregulated-genes">
<title>2.4 Gene-Level Curation of Dysregulated Genes</title>
<p>Given the complexity of placental development and its sensitivity to temporal and physiological context, we initially approached the Plac1-regulated transcriptomic changes by manually curating a limited subset of highly dysregulated and developmentally informative genes. Importantly, these uniquely dysregulated subsets represent the unbiased identification of genes likely to play significant roles in the pathophysiological responses to Plac1’s absence. This gene-centric approach provides a time-resolved physiological perspective, highlighting directionality, adaptation, and potential compensatory programs that can otherwise be obscured when transcripts are immediately aggregated into higher-order categories. We then applied GO, KEGG, and IPA analyses to gain a systems-level interpretation, allowing pathway-level structure to be layered onto a biologically grounded narrative derived from the most salient gene-level changes.</p>
<p>DEGs exhibiting the highest fold-change at E16.5 and E18.5 were examined for potential relevance to the Plac1-null phenotype (See Supplemental Tables, S4–S7, for complete gene lists). Their hierarchical order differed at each gestational age, reflecting the placenta’s intrinsic developmental program and its adaptations to deficits resulting from Plac1’s absence. We also identified small subsets of DEGs showing reciprocal directional dysregulation over time (e.g., downregulation at E16.5 followed by upregulation at E18.5) and examined these patterns as possible indicators of evolving pathophysiology. Functional inferences that emerged are intended to suggest plausible interpretations based on known or inferred gene function as well as placental physiology. Definitive interpretation will require experimental validation in the future.</p>

</sec>

<sec id="2-4-1-downregulated-genes-inferred-functional-deficits">
<title>2.4.1 Downregulated Genes: Inferred Functional Deficits</title>
<p>To provide biological context for the most prominent transcriptional changes, we first focused on a small subset of the most strongly downregulated genes at E16.5 and E18.5. Many of these genes are linked to immune–trophoblast interactions, membrane or vesicular processes, endocrine signaling, and transcriptional programs associated with late placental maturation. Discussion of these genes individually offers insight into potential functional consequences of Plac1 loss at the level of specific cellular programs, prior to the broader pathway-based analyses.</p>
<p>At E16.5, KO placentas showed marked decreases in granzymes ( Gzmc, Gzmf, Gzmg; and Gzmd ~13-fold) versus WT (Table 1). Granzymes are produced by uterine natural killer cells (uNKs), not trophoblasts. uNKs promote spiral artery remodeling by facilitating invasive trophoblast differentiation and depth (11–13). Their reduction therefore suggests either fewer uNKs or reduced uNK–trophoblast encounters needed to induce granzyme expression. Pertinent to this, PLAC1 has been shown to interact directly with NK activating proteins (NKG2D, NKp30, NKp44, DNAM-1) and can modulate NK cytotoxicity <xref ref-type="bibr" rid="14">14</xref>. If reduced trophoblast invasion occured early in placentation, consistent with PLAC1’s role in trophoblast invasion/migration in culture <xref ref-type="bibr" rid="15">15</xref>, uNK activation would be limited, impairing spiral artery remodeling and contributing to later placental insufficiency.</p>
<table-wrap id="">
  <label>Table</label>
  
  <table><tbody>
<tr><th></th><th>E16.5</th><th></th><th>E18.5</th><th></th></tr>
<tr><td>Downregulated</td><td>Fold Change</td><td>Upregulated</td><td>Fold Change</td><td>Downregulated</td></tr>
<tr><td>Plac1</td><td>-73.063</td><td>Igfbp1</td><td>+15.174</td><td>Plac1</td></tr>
<tr><td>Tff3</td><td>-22.146</td><td>Khdc1b</td><td>+13.586</td><td>Krt6a</td></tr>
<tr><td>Gzmg</td><td>-21.952</td><td>Minar1</td><td>+9.727</td><td>Elavl4</td></tr>
<tr><td>Angptl3</td><td>-19.512</td><td>Syt15</td><td>+9.467</td><td>Bhlhe22</td></tr>
<tr><td>Gzmf</td><td>-17.179</td><td>Farp1</td><td>+9.12</td><td>Ntrk2</td></tr>
<tr><td>Gzmc</td><td>-16.634</td><td>Ifi203</td><td>+7.984</td><td>Ceacam18</td></tr>
<tr><td>Vmn1r17</td><td>-16.118</td><td>Tcra</td><td>+7.912</td><td>Dio2</td></tr>
<tr><td>Ehd4</td><td>15.531</td><td>C730014E05Rik</td><td>+7.248</td><td>Or51e2</td></tr>
<tr><td>Neurod4</td><td>-14.461</td><td>Gabrq</td><td>+6.871</td><td>Isx</td></tr>
<tr><td></td><td></td><td>9330162B11Rik</td><td>+6.634</td><td>Gzmc</td></tr>
  </tbody></table>
</table-wrap>
<disp-quote><p><p>Table 1. Top Up- and Downregulated Genes at E16.5 and E18.5 (P-value and FDR &lt; 0.05)</p>
</p></disp-quote>
<p>A second potential explanation is impaired recruitment of uNKs to the maternal–placental interface. Cxcr4 , a GPCR for Cxcl12, mediates uNK homing to decidua, and Cxcr4 deficiency reduces uNK numbers, disrupts placental vasculature, and causes pregnancy loss <xref ref-type="bibr" rid="16">16</xref>. Although neither gene is dysregulated in our study, the E16.5–E18.5 window occurs well after early placentation and would not be expected to capture earlier recruitment signatures. Interestingly, Tff3 (second most downregulated) can also bind Cxcr4 and promote epithelial recruitment in retina <xref ref-type="bibr" rid="17">17</xref>, but there is no evidence it acts as a gestational chemoattractant. Instead, Tff3 protein is expressed across multiple mouse epithelia at E14–E18, contributing to maturation and barrier formation <xref ref-type="bibr" rid="18">18</xref>. Thus, its downregulation more likely reflects collapse of secretory epithelial maturation in the placenta, consistent with labyrinth expression reported in Bgee <xref ref-type="bibr" rid="19">19</xref> and syncytiotrophoblast/JZ/sTGC expression in STAMP <xref ref-type="bibr" rid="20">20</xref>.</p>
<p>Evidence of early vascular impairment is further strengthened by disruption of the trophoblast–vascular interface. Angptl3 downregulation suggests impaired nutrient delivery and labyrinthine function [21–23]. Its C-terminal domain binds integrin αvβ3 to promote endothelial adhesion/migration/vessel formation. Reduced expression would therefore limit migration and capillary branching. Angptl3 also inhibits endothelial lipase and LPL, potentially affecting lipid availability and essential fatty-acid delivery to the fetus. In parallel, Ehd4 , an intracellular trafficking protein, participates in a PACSIN2/EHD4/MICALL1 complex controlling VE-cadherin recycling during sprouting angiogenesis <xref ref-type="bibr" rid="24">24</xref>. Together, these changes point to the possible loss of regulatory integrity between trophoblasts and the endothelium.</p>
<p>Stress-related compromise was suggested by the profound downregulation of Krt6a , typically induced in stratified epithelia in response to stress <xref ref-type="bibr" rid="25">25</xref> and implicated in abnormal placentation (placenta accreta) <xref ref-type="bibr" rid="26">26</xref>. Here Krt6a is ~45-fold reduced, consistent with decompensated stress, and is accompanied by reduction of additional keratins, Krt8 and Krt18 , suggesting late-gestation trophoblast instability. Downregulation of Ceacam18 , expressed in decidua, spongiotrophoblasts, sTGCs, and labyrinthine trophoblasts, further suggests membrane disruption. While its placental function is unknown, other Ceacam family members support roles in adhesion and immunomodulation <xref ref-type="bibr" rid="27">27</xref>.</p>
<p>Genes affecting fetoplacental metabolism are also dysregulated. Dio2 converts T4 to the active form, T3. T3 supports neuronal differentiation and trophoblast cell cycle progression, migration, and invasion. Early Dio2 downregulation has been linked to shallow invasion and miscarriage <xref ref-type="bibr" rid="28">28</xref>. Because fetal thyroid output is still increasing during this time, reduced placental Dio2 at E18.5 implies reduced fetal T3 availability during a critical neurodevelopmental window. Placental Isx is also profoundly reduced, likely disrupting β-carotene–dependent regulation of Mtp and ApoB transcription <xref ref-type="bibr" rid="29">29</xref>, impairing lipoprotein-mediated provitamin A transfer. Since β-carotene supports in situ retinoic acid essential for organogenesis, impaired transfer may constrain retinoic acid during late gestation when fetal demand peaks, potentially compromising maturation of pulmonary, renal, and neural systems.</p>
<p>Notably, several downregulated genes ( Elavl4, Bhlhe22, Ntrk2, Neurod4, Vmn1r17 ) are typically linked to neurological development. Elavl4 is an early marker of neuronal differentiation and contributes to synaptic plasticity <xref ref-type="bibr" rid="30">30</xref>. Its placental expression is supported by STAMP (parietal endoderm; labyrinth/JZ trophoblasts) <xref ref-type="bibr" rid="20">20</xref> and Bgee (labyrinth) <xref ref-type="bibr" rid="19">19</xref>. Ntrk2 (TrkB), classically the high-affinity receptor for BDNF in nervous system development <xref ref-type="bibr" rid="31">31</xref>, is also expressed in trophoblasts along with its ligands throughout gestation <xref ref-type="bibr" rid="32">32</xref>. Trk inhibition in pregnancy suppresses placental development, increases trophoblast apoptosis, reduces labyrinth area at mid-gestation, and decreases fetal weight later in gestation. Bhlhe22 , involved in sensory specification (33,34), and Neurod4 <xref ref-type="bibr" rid="35">35</xref> lack established placental roles but are reported in placental compartments (Bgee; STAMP), raising the possibility they contribute to lineage-specific differentiation programs affected by Plac1 loss. Finally, Or51e2 (mouse ortholog Olfr78) is expressed in smooth muscle cells of resistance vessels, sensing small-chain fatty acids (SCFA) and metabolites to regulate vascular tone <xref ref-type="bibr" rid="36">36</xref> and renin secretion <xref ref-type="bibr" rid="37">37</xref>. Its placental downregulation may therefore contribute to impaired regulation of vascular resistance. Vmn1r17 , a pheromone-related receptor, lacks clear evidence for placental expression <xref ref-type="bibr" rid="38">38</xref>. Given Plac1 is expressed in both the fetal brain and placenta and the KO is not placenta-specific, its apparent dysregulation could reflect brain-derived transcripts or extracellular vesicles (EVCs) entering placental circulation <xref ref-type="bibr" rid="39">39</xref>, although mapping artifacts/noise remain possible and require validation.</p>
<p>Taken together, the coordinated downregulation of these genes suggests that Plac1 deficiency disrupts multiple late-gestational programs required for placental maturation, including immune signaling, membrane trafficking, and endocrine and differentiation-linked regulatory processes. Rather than reflecting isolated gene-level effects, these changes point to a broader impairment in the functional specialization of the placenta that will help contextualize pathway-level signatures.</p>

</sec>

<sec id="2-4-2-upregulated-genes-adaptations-and-stress-responses-to-functional-deficits">
<title>2.4.2 Upregulated Genes: Adaptations and Stress Responses to Functional Deficits</title>
<p>In contrast to the genes suppressed in the Plac1-null placenta, the most strongly upregulated genes at E16.5 and E18.5 suggest activation of stress-responsive, immune-associated and compensatory developmental programs. These genes span transcriptional regulators, immune receptors, metabolic enzymes, and poorly characterized loci, consistent with adaptive responses to declining placental functional reserve. Consideration of these genes individually provides insight into how the placenta may be attempting to stabilize fetal support as structural and signaling integrity becomes compromised.</p>
<p>At E16.5, the KO placenta shows strong induction of oxidative stress and immune activation genes, including robust Igfbp1 upregulation, consistent with reduced oxygen/nutrient availability and compensatory IGF signaling <xref ref-type="bibr" rid="40">40</xref>. Increased Ifi203 suggests activation of type I interferon pathways under cellular stress <xref ref-type="bibr" rid="41">41</xref>. Upregulation of Tcra may reflect maternal immune cell infiltration as inflammatory pressure increases <xref ref-type="bibr" rid="42">42</xref>. Markers of lineage instability also emerge, notably ectopic expression of Khdc1b , an oocyte/early embryo KH-domain protein that regulates maternally stored mRNA stability/translation <xref ref-type="bibr" rid="43">43</xref>. Its induction in the placenta is consistent with stress-associated trophoblast dysfunction.</p>
<p>Induction of neuronal modules ( Syt15, Gabrq, Farp1 ) may reflect derepression of noncanonical placental programs in a stressed environment. Syt15 (synaptotagmin family) likely supports calcium-regulated membrane trafficking/exocytosis needed under increased transport demands (UnitPro: Syt15). Gabrq upregulation may mirror aberrant activation observed in cancer under hypoxic/metabolic stress <xref ref-type="bibr" rid="44">44</xref>. Farp1 , a cytoskeletal membrane linker and Rho GEF (Rac1 activator), promotes dendritic growth and motility <xref ref-type="bibr" rid="45">45</xref>. Its induction may represent an attempt to reinforce labyrinth structure and vascular architecture. Minar1 (Membrane Integral NOTCH2 Associated Receptor 1) may represent a compensatory mechanism to dampen growth/angiogenesis/metabolic load in a resource-limited environment by suppressing mTOR and inhibiting angiogenesis while stabilizing Notch2 <xref ref-type="bibr" rid="46">46</xref>.</p>
<p>Finally, the lncRNA C730014E05Rik lies ~17.3 kb downstream of Adipoq, placing it within an adiponectin-associated regulatory region (MGI:106675; MGI:2443371) <xref ref-type="bibr" rid="47">47</xref><xref ref-type="bibr" rid="48">48</xref>. Its stress-induced upregulation may influence transcriptional responsiveness within this domain <xref ref-type="bibr" rid="49">49</xref>. Adiponectin is anti-diabetic/anti-inflammatory/anti-atherogenic and activates AMPK and downstream p38 MAPK signaling [50–53]. Because the placenta expresses adiponectin and its receptors, AdipoR1/R2 <xref ref-type="bibr" rid="54">54</xref><xref ref-type="bibr" rid="55">55</xref>, these pathways are relevant to trophoblast physiology. Consistent with this, multiple genes linked to AMPK, p38 MAPK, and TGFβ signaling ( Tgfb3, Eif4ebp1, Eef2, Pfkl, Pfkm, Mapk11, Mapk13 ) were upregulated, raising the possibility that C730014E05Rik marks stress-related activation within the adiponectin locus aligned with AMPK/p38 and TGFβ induction.</p>
<p>By E18.5, disrupted trophoblast differentiation cues are suggested by elevated Ascl2 , essential for SpT development and GlyT expansion <xref ref-type="bibr" rid="56">56</xref><xref ref-type="bibr" rid="57">57</xref>, along with induction of Cer1 , a Nodal/BMP/Wnt antagonist influencing trophoblast lineage allocation <xref ref-type="bibr" rid="58">58</xref><xref ref-type="bibr" rid="59">59</xref>. Ascl2 upregulation aligns with the enlarged junctional zone in Plac1-null placentas and may reflect compensatory adjustment to altered lineage balance. Concordant upregulation of Spata21 , reported in placental Giant Cells (GC), GC precursors, JZ precursors, SpT, and syncytiotrophoblasts (SynT) by Bgee and STAMP) supports expansion of JZ-associated populations. Cer1 induction at E18.5 further supports continued SpT expansion in response, in part, to metabolic stress.</p>
<p>Metabolic rewiring and lipid-mediated inflammation are suggested by increased Aldh1a3 and Pla2g4d . Aldh1a3 is consistent with expanded GlyT populations <xref ref-type="bibr" rid="60">60</xref><xref ref-type="bibr" rid="61">61</xref>, contributes to RA production, and detoxifies aldehydes generated during lipid peroxidation. Increased Pla2g4d (OMIM 612864) reflects ongoing lipid-mediated inflammatory stress. Heightened innate immune signaling is suggested by the induction of C-type lectins Clec2m and Clec9a , and immunoproteasome subunit Psmb9 , reflecting interferon-mediated antigen processing and tissue injury. Because Clec9a senses F-actin from damaged cells and Psmb9 supports degradation of misfolded proteins, their induction is consistent with active cellular injury responses. Tissue-level stress is further supported by increased Lrfn2 , a synaptic adhesion molecule that may promote structural stabilization, consistent with broader stress-driven activation of neural genes. Finally, 1700027H10Rik , a chromosome 3 lncRNA (MGI:1919524) with unknown function, was also induced.</p>
<p>Taken together, the genes most strongly upregulated at E16.5 and E18.5 indicate emergence of immune-associated, stress-responsive, and alternative developmental transcriptional programs that differ from those associated with normal placental maturation, reflecting a progressively altered placental gene expression landscape as gestation advances.</p>

</sec>

<sec id="2-4-3-reciprocal-gene-dysregulation-over-time">
<title>2.4.3 Reciprocal Gene Dysregulation Over Time</title>
<p>A distinct gene subset exhibited reciprocal, gestational age-dependent dysregulation, being suppressed at E16.5 but induced by E18.5. These genes cluster into several functional categories related to protein homeostasis, endocrine and secretory activity, cytoskeletal organization, membrane architecture, and genome regulation. Examination of these reciprocal patterns provides insight into alterations in the temporal coordination of placental functional programs in the absence of Plac1, complementing the gene sets dysregulated at a single point in time.</p>
<p>Gestational age-dependent, reciprocally dysregulated genes reveal several functional modules in the KO placenta. As shown in Table 2A, downregulation of Dnajb11 and Dnajc3 at E16.5 suggests reduced unfolded-protein response (UPR) capacity during a critical growth window, whereas their coordinated upregulation at E18.5 likely reflects adaptive activation of proteostasis <xref ref-type="bibr" rid="62">62</xref>. Second, the downregulation of placenta-specific prolactins ( Prl2c3, Prl7a2, Prl8a8 ) and Rab27a implies diminished endocrine/secretory output followed by an attempt to restore hormonal signaling and exocytosis [63–66]. Notably, increased expression at E18.5 coincides with continued JZ expansion, where these genes are primarily expressed. Third, reciprocal regulation of Tmsb10 (actin filament organization) and Prom1 (epithelial stem cell marker organizing apical micro- domains, including microvilli) may reflect a late attempt to reinforce trophoblast integrity and microvillous architecture.</p>
<p>Noct regulates circadian metabolic control, NADP(H) phosphatase activity, and post-transcriptional control of metabolic mRNAs <xref ref-type="bibr" rid="67">67</xref>. Although expressed in placenta (Uniprot: 035710; STAMP) without a defined placental role, its directional shift could reflect reduced metabolic regulation followed by an attempted compensatory response. Finally, Asz1 , a germ cell-specific regulator essential for piRNA biogenesis, transposable element silencing, and meiotic progression while protecting germline genome integrity <xref ref-type="bibr" rid="68">68</xref><xref ref-type="bibr" rid="69">69</xref>. Similarly, Gm773 , an X-linked gene, contributes to spermatogenesis and is required for sperm penetration of the zona pellucida <xref ref-type="bibr" rid="70">70</xref>. Both are typically germline-restricted, yet show coordinated downregulation at E16.5 and upregulation at E18.5. This pattern may reflect progressive cellular stress followed by compensatory activation of genome-protection programs in response to worsening placental stress.</p>
<p>Collectively, the reciprocal expression patterns observed for this gene set indicate disrupted temporal regulation of multiple placental support programs rather than a uniform gain or loss of function. Early suppression followed by late induction of genes involved in proteostasis, endocrine signaling, vesicular trafficking, and cytoskeletal and membrane organization is consistent with perturbed engagement of late-gestational placental functions. Together, these data underscore altered temporal dynamics of placental gene regulation in the Plac1-null context, rather than simply magnitude-based changes in expression.</p>
<p>A second subset of genes exhibited the opposite reciprocal pattern, being upregulated at E16.5 but downregulated by E18.5. This group includes factors associated with extracellular matrix regulation, immune modulation, redox balance, and signaling pathways that act at the maternal–fetal interface. Analysis of this subset, shown in Table 2B, provides insight into placental programs that are engaged early but not sustained as gestation progresses in the absence of Plac1.</p>
<p>At E16.5, upregulation of Cnmd (anti-angiogenic ECM protein) <xref ref-type="bibr" rid="71">71</xref><xref ref-type="bibr" rid="72">72</xref> together with Spon1 (matrix/adhesion cues relevant to cell attachment/axon guidance) <xref ref-type="bibr" rid="73">73</xref> and Tfpi2 (protease inhibitor suppressing trophoblast invasion) <xref ref-type="bibr" rid="74">74</xref><xref ref-type="bibr" rid="75">75</xref> can be viewed as attempts to stabilize the maternal–fetal interface. Concomitant induction of immune modulatory/tolerance factors, Crispld2 (LPS-binding neutralizer), Gpnmb (inflammation-resolving glycoprotein) and Siglecg (inhibitory Siglec) suggests efforts to defend against inflammatory stress [76–79]. Upregulation of Gpx3, H6pd, and Sphk1 points to adaptations to oxidative and ER stress [80–84]. Finally, induction of growth/genome maintenance genes, Porcn (Wnt ligand activity), Trnp1 (progenitor proliferation) and Tatdn2 (R-loop–resolving nuclease), is consistent with attempts to preserve trophoblast remodeling while containing replication stress [85–90]. Their downregulation by E18.5 possibly reflects exhaustion of these adaptive responses in a failing placenta.</p>
<table-wrap id="">
  <label>Table</label>
  
  <table><tbody>
<tr><th>Genes</th><th>E16.5 Fold Change</th><th>E18.5 Fold Change</th></tr>
<tr><td>Asz1</td><td>-2.412</td><td>+2.537</td></tr>
<tr><td>Dnajb11</td><td>-1.648</td><td>+1.682</td></tr>
<tr><td>Dnajc3</td><td>-1.834</td><td>+1.582</td></tr>
<tr><td>Gm12618</td><td>-1.892</td><td>+1.604</td></tr>
<tr><td>Gm773</td><td>-3.337</td><td>+2.159</td></tr>
<tr><td>Noct</td><td>-2.221</td><td>+1.749</td></tr>
<tr><td>Prl2c3</td><td>-2.010</td><td>+1.549</td></tr>
<tr><td>Prl7a2</td><td>-4.394</td><td>+1.938</td></tr>
<tr><td>Prl8a8</td><td>-1.710</td><td>+1.995</td></tr>
<tr><td>Rab27a</td><td>-1.797</td><td>+2.143</td></tr>
<tr><td>Tmsb10</td><td>-2.877</td><td>+1.703</td></tr>
<tr><td>Prom1</td><td>-1.579</td><td>+1.558</td></tr>
  </tbody></table>
</table-wrap>
<table-wrap id="">
  <label>Table</label>
  
  <table><tbody>
<tr><th>Genes</th><th>E16.5 (Fold Change)</th><th>E18.5 (Fold Change)</th></tr>
<tr><td>Cnmd</td><td>+2.715</td><td>-3.786</td></tr>
<tr><td>Crispld2</td><td>+2.418</td><td>-2.093</td></tr>
<tr><td>Gpx3</td><td>+2.748</td><td>-2.012</td></tr>
<tr><td>Tfpi2</td><td>+1.698</td><td>-1.550</td></tr>
<tr><td>Porcn</td><td>+1.893</td><td>-2.205</td></tr>
<tr><td>Gpnmb</td><td>+1.584</td><td>-1.919</td></tr>
<tr><td>H6pd</td><td>+2.003</td><td>-2.591</td></tr>
<tr><td>Siglecg</td><td>+1.592</td><td>-2.017</td></tr>
<tr><td>Sphk1</td><td>+2.080</td><td>-2.344</td></tr>
<tr><td>Trnp1</td><td>+1.667</td><td>-2.279</td></tr>
<tr><td>Tatdn2</td><td>+1.746</td><td>-2.165</td></tr>
<tr><td>Spon1</td><td>+2.820</td><td>-2.284</td></tr>
<tr><td>1700064E03Rik</td><td>+3.458</td><td>-2.949</td></tr>
  </tbody></table>
</table-wrap>
<disp-quote><p><p>Table 2. Genes Reciprocally Dysregulated at E16.5 and E18.5 (P-value and FDR &lt; 0.05) A. Dynamic Developmental Shift (E16.5 Downregulated – to – E18.5 Upregulated) B. Dynamic Developmental Shift (E16.5 Upregulated – to – E18.5 Downregulated)</p>
</p></disp-quote>
<p>Taken together, this reciprocal expression pattern suggests early engagement of multiple stabilizing and protective transcriptional programs that diminish by late gestation in the Plac1-null placenta. The coordinated downregulation of genes involved in extracellular matrix restraint, immune modulation, oxidative stress handling, and growth control at E18.5 is consistent with loss or attenuation of these early responses over time.</p>

</sec>

<sec id="2-4-4-functional-classes-of-degs">
<title>2.4.4 Functional Classes of DEGs</title>
<p>Examination of the DEGs also revealed a marked enrichment for membrane-associated receptors, solute transporters, and ion channels pointing to broad disruption of membrane-linked signaling and transport functions in the Plac1-null placenta. (Table 3). Notably, many of these genes are also annotated to brain development, consistent with shared placental and neurodevelopmental regulatory programs and with the CNS abnormalities observed in Plac1 knockout mice <xref ref-type="bibr" rid="3">3</xref>.</p>
<table-wrap id="">
  <label>Table</label>
  
  <table><tbody>
<tr><th>Brain development/function</th><th>Ntrk2, Elavl4, Gata4, Nog, Nefm, NeuroD4, Negr1, Cnrip1, Syt12, Dlx2, Fzd6, Slc26a4. Slc6a15, Amigo2, Hes1</th></tr>
<tr><td>Solute transporters</td><td>Slc26a4, Slc10a6, Slc28a3, Slc2a10, Slc45a3, Slc1a6, Slc22a23, Slc22a4, Slc43a3, Slc1a5, Slc39a4, Slc44a3, Slc7a14, Slc7a6, Slc66a3, Slc27a3, Slc40a1, Slc26a2, Slc5a2, Slc6a14, Slc5a6, Slc8a1, Slc20a2, Slc19a2, Slc16a5, Slc7a10</td></tr>
<tr><td>Ion channels</td><td>Trpv6, P2rx4, P2rx1, Orai1, Kcnmb1, Kcnk5, Kcnd3, Trpc4, Ano1, Scnn1a, Cacna1g, Kcnmb2</td></tr>
<tr><td>GPCR signaling (receptors and mediators)</td><td>Adora1, F2rl1, Gcgr, Or51e2, Cysltr2, Tbxa2r, Gprc5a, Gprc5b, Gpr146, Mrgprf, Mrgprg, Rxfp1, Adgra2, Adgrl4, Lgr4</td></tr>
<tr><td>Plasma Membrane Signal Transduction</td><td>Wnt2, Tspan1, Tspan2, Tspan4, Tspan6, Tspan7, Tspan12, Pdgfb, Pdgfc, Smo</td></tr>
  </tbody></table>
</table-wrap>
<disp-quote><p><p>Table 3. Functional Classes of Downregulated Genes (non-inclusive)</p>
</p></disp-quote>

</sec>

<sec id="2-4-5-systems-level-and-pathway-analyses-go-gene-ontology-kegg-kyoto-encyclopedia-of-genes-and-genomes-ingenuity-pathway-analysis-ipa">
<title>2.4.5 Systems-level and Pathway Analyses: GO (Gene Ontology), KEGG (Kyoto Encyclopedia of Genes and Genomes), Ingenuity Pathway Analysis (IPA)</title>
<p>While examination of individual genes provides insight into specific temporal and functional perturbations, a systems-level perspective is required to more fully understand how these changes may converge on broader biological processes. To this end, we next assessed global patterns of differential expression to identify shared functional themes and regulatory networks disrupted in the Plac1-null placenta using GO, KEGG, and IPA tools.</p>

</sec>

<sec id="go-analysis">
<title>GO Analysis</title>
<p>GO enrichment demonstrated predominant downregulation of cellular components associated with the membrane–cytoskeletal interface , including plasma membrane, sarcolemma, lysosome, extracellular matrix, adherens and tight junctions, and actin-based structures at both E16.5 and E18.5 (Figure 6A, B; See Supplementary Tables S9–S14 for complete lists). These findings are consistent with Plac1 localization to membranous compartments, particularly at the apical trophoblast surface. Enrichment of midbody and spindle-associated structures suggested impaired cytokinesis, while prominent involvement of Weibel–Palade bodies at E16.5 indicated endothelial-specific dysfunction. Given their role in regulated release of von Willebrand factor, angiopoietin-2, and endothelin-1, reduced WP-associated signaling would be expected to compromise hemostasis, vascular tone, angiogenesis, and immune regulation at the maternal–fetal interface [91–93].</p>
<p>In contrast, upregulated cellular components reflected stress-adaptive and compensatory responses, most notably enrichment of translational machinery, ribonucleoprotein complexes, and ER/Golgi compartments, particularly at E18.5. These changes indicate increased translational load, secretory activity, and proteostasis demand under nutrient and oxidative stress. Immune-related components also showed progressive enrichment, shifting from MHC class I and cytotoxic signaling at E16.5 toward MHC class II–associated antigen presentation, phagocytic vesicles, and adaptive immune activation by E18.5. Additional enrichment of extracellular matrix and synapse-annotated compartments, likely reflecting vesicle trafficking and cytoskeletal remodeling rather than neuronal specificity, further supported widespread disruption of membrane dynamics and cell–cell communication.</p>
<p>Downregulated GO biological process analysis revealed significant suppression of growth factor and developmental signaling pathways, including BMP, FGF, Wnt, TGF-β, and Jak–STAT, all critical regulators of placental development. In addition, genes dysregulated in our placental dataset were significantly enriched for GO annotations related to embryonic organogenesis. Cardiovascular, neurodevelopmental, pulmonary, renal, and skeletal pathways were disproportionately affected, consistent with Plac1 expression in both the placenta and embryo and with documented neurodevelopmental vulnerability in Plac1-deficient models (See Supplementary Data, Tables S9–S14 for complete GO terms). GO Biological Process enrichment for upregulated genes at both E16.5 and E18.5 was represented by generalized immune, stress, and metabolic response terms that overlapped extensively with KEGG and IPA pathway annotations and is presented in full in the Supplementary Data (Tables S10, S13).</p>
<fig id="fig6">
  <label>Figure 6</label>
  <caption><p>Developmental Stage-Specific Dysregulation of Cellular Components and Biological Processes in KO Placentas. Bars represent GO terms significantly enriched among the downregulated genes. The X-axis shows log₂(Enrichment), indicating fold enrichment relative to WT controls. The Y-axis lists individual GO terms. Bar colors correspond to –log₁₀(FDR), with warmer colors (yellow/orange) indicating higher statistical significance and cooler colors (blue/purple/black) indicating lower significance. Panel A: E16.5, showing downregulated (left) and upregulated (middle) Cellular Components, and downregulated Biological Processes (right). Panel B: E18.5, showing downregulated (left) and upregulated (middle) Cellular Components, and downregulated Biological Processes (right). * Note – For visualization purposes, the number of BPs and CCs were selectively limited to a maximum of 20 by reducing implied functional redundancy.</p></caption>
  <graphic xlink:href="https://qzydlaimdnpogmrslkea.supabase.co/storage/v1/object/public/manuscripts/figures/upload-1777992173558/fig-06-p17.png" />
</fig>

</sec>

<sec id="kegg-analysis">
<title>KEGG Analysis</title>
<p>KEGG analysis at E18.5 reinforced these findings, identifying coordinated downregulation of pathways governing vascular smooth muscle contraction, calcium and cGMP–PKG signaling, apelin signaling, tight junction integrity, TGF-β signaling, and Hippo pathway components at E18.5 (Figure 7; Supplementary Data, Tables S15–S19), collectively indicating impaired vascular remodeling, cytoskeletal organization, trophoblast proliferation, and structural stability. No significant downregulated KEGG terms were identified at E16.5.</p>
<fig id="fig7">
  <label>Figure 7</label>
  <caption><p>Fold enrichment of KEGG terms represented by downregulated genes at E18.5. Bars represent KEGG pathways significantly enriched among downregulated genes at E18.5. The X-axis shows fold enrichment, and the Y-axis lists individual KEGG terms (FDR &lt; .05).</p></caption>
  <graphic xlink:href="https://qzydlaimdnpogmrslkea.supabase.co/storage/v1/object/public/manuscripts/figures/upload-1777992173558/fig-07-p19.png" />
</fig>
<p>Conversely, KEGG terms enriched among upregulated genes were dominated by cellular stress, metabolic adaptation, and immune activation , including Ribosome, Protein Processing in the Endoplasmic Reticulum, Glycolysis/Gluconeogenesis, Carbon Metabolism, Phagosome, and Antigen Processing and Presentation (Table 4; Supplementary Data, Tables S15–S19). Viral and inflammatory pathway annotations reflected heightened innate and adaptive immune signaling rather than pathogen-specific responses.</p>
<table-wrap id="">
  <label>Table</label>
  
  <table><tbody>
<tr><th>KEGG Term</th><th>E16.5 Fold Enrichment</th><th>E16.5 FDR</th><th>E18.5 Fold Enrichment</th><th>E18.5 FDR</th></tr>
<tr><td>Ribosome</td><td>6.36</td><td>4.16E-16</td><td>9.38</td><td>3.02E-45</td></tr>
<tr><td>Coronavirus Disease-COVID 19</td><td>4.87</td><td>3.26E-12</td><td>6.88</td><td>5.71E-36</td></tr>
<tr><td>Glycolysis/Gluconeoneogenesis</td><td>5.75</td><td>8.95E-04</td><td>—</td><td>—</td></tr>
<tr><td>Antigen processing/presentation</td><td>4.84</td><td>1.06E-03</td><td>—</td><td>—</td></tr>
<tr><td>Allograft rejection</td><td>5.55</td><td>1.60E-03</td><td>—</td><td>—</td></tr>
<tr><td>Graft versus host disease</td><td>5.55</td><td>1.60E-03</td><td>—</td><td>—</td></tr>
<tr><td>Type I diabetes mellitus</td><td>4.94</td><td>4.12E-03</td><td>—</td><td>—</td></tr>
<tr><td>Biosynthesis of amino acids</td><td>4.46</td><td>7.31E-03</td><td>—</td><td>—</td></tr>
<tr><td>Autoimmune thyroid disease</td><td>4.33</td><td>7.31E-03</td><td>—</td><td>—</td></tr>
<tr><td>Carbon metabolism</td><td>3.66</td><td>7.41E-03</td><td>—</td><td>—</td></tr>
<tr><td>Pentose phosphate pathway</td><td>6.51</td><td>7.41E-03</td><td>—</td><td>—</td></tr>
<tr><td>Viral myocarditis</td><td>3.82</td><td>1.42E-02</td><td>—</td><td>—</td></tr>
<tr><td>Amino and nucleotide sugar metabolism</td><td>5.67</td><td>1.76E-02</td><td>—</td><td>—</td></tr>
<tr><td>Phagosome</td><td>2.91</td><td>2.0E-02</td><td>—</td><td>—</td></tr>
<tr><td>Cell adhesion molecules</td><td>2.87</td><td>2.2E-02</td><td>—</td><td>—</td></tr>
<tr><td>HIF-1 signaling pathway</td><td>3.36</td><td>2.6E-02</td><td>—</td><td>—</td></tr>
<tr><td>VEGF signaling pathway</td><td>4.36</td><td>3.1E-02</td><td>—</td><td>—</td></tr>
<tr><td>Epstein-Barr virus infection</td><td>2.52</td><td>3.93E-02</td><td>—</td><td>—</td></tr>
<tr><td>Fructose and mannose metabolism</td><td>5.13</td><td>4.37E-02</td><td>—</td><td>—</td></tr>
<tr><td>Biosynthesis of nucleotide sugars</td><td>4.99</td><td>4.97E-02</td><td>4.63</td><td>4.98E-02</td></tr>
<tr><td>Protein Processing in ER</td><td>—</td><td>—</td><td>2.7</td><td>3.80E-02</td></tr>
<tr><td>Amoebiasis</td><td>—</td><td>—</td><td>3.09</td><td>4.98E-02</td></tr>
<tr><td>Cellular senescence</td><td>2.65</td><td>4.97E-02</td><td>—</td><td>—</td></tr>
  </tbody></table>
</table-wrap>
<disp-quote><p><p>Table 4. KEGG Analysis of Upregulated Genes</p>
</p></disp-quote>

</sec>

<sec id="references-continued">
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