Fig 2: The E/I imbalance in the Chd8+/− mice is associated with abnormalities in both the brain and intestine.a, b Representative traces (top), cumulative distribution plots (bottom) and bar graphs (bottom) showing the amplitude and frequency of mEPSCs (a) and mIPSCs (b) of pyramidal cells in neocortical layer V of adult mice (weeks 8–9). n = 3 mice per group. Four to six data points per mouse. n = 13 (mEPSCs/Chd8+/+), 12 (mEPSCs/Chd8+/−), 14 (mIPSCs/Chd8+/+), and 15 (mIPSCs/Chd8+/−) data points, respectively. c Levels of L-glutamate (μg/g), glutamate/GABA, and L-glutamine (μg/g) in the cerebrum of 12-week-old mice detected by the targeted metabolomics assay. n = 13 and 12 mice, respectively. d Level of L-glutamine (μg/ml) in the serum of 12-week-old mice detected by the targeted metabolomics assay. n = 12 and 10 mice, respectively. e GSEA plot showing the enrichment of the amino acid transmembrane transporter activity pathway in small intestinal cells. f UMAP plot of single-cell transcriptome profiles of intestines from 12-week-old mice. g, h Highlights of enterocyte cells expressing Slc6a19 (g) and Slc7a8 (h) in the UMAP plot (left), and comparison of the expression levels of Slc6a19 and Slc7a8 between the Chd8+/+ and Chd8+/− mice (right) (n = 4 mice). The bar plots represent the mean of abundance of Slc6a19 (top) and Slc7a8 (bottom) in enterocyte cells (n = 1527 and 3445 cells in Chd8+/+ and Chd8+/− mice, respectively). Error bars represent 95% confidence interval (CI) of mean value. i Immunofluorescence staining of SLC6A19 and SLC7A8 in the ileum of the mice at week 12. Scale bar, 20 μm. Each symbol represents one image; six to seven images per mouse. n = 17 and 22 symbols, respectively. j Western blotting analysis of SLC6A19 and SLC7A8 protein levels in the small intestine of mice at week 12 (n = 6 mice). Source data are provided as a Source Data file. Quantitative data are shown as the mean ± SEM. Statistical analysis was determined by the two-tailed Mann–Whitney test (a–d, g–j). Significance was indicated by P value (a–d, g–j). n.s. means no significant difference.

Fig 3: Proposed SARS-CoV-2 cell entry mechanism regulated by PDZ-mediated interaction(A) β-Arrestin 1 or β-arrestin 2 binds to ACE2 with nearly equivalent affinity. FLAG-β-arrestin 1 or 2 was transiently coexpressed in HEK293 GnTI cells with Myc-ACE2. The cleared cell lysates were incubated with anti-c-Myc agarose beads. Proteins are eluted by 2x Laemmli sample buffer (Bio-Rad) supplemented with β-mercaptoethanol and detected by western blotting using the indicated specific antibodies (left panel). β-Actin was used as a loading control. The molecular markers are indicated in kDa on the right. Given the equivalent expression of myc-ACE2 observed in the cell lysate and immunoprecipitates, pull-down of β-arrestin 1 or β-arrestin 2 by myc-ACE2 was quantified by normalizing the signal intensities to their individual lysate expression, respectively (right panel). Error bars indicate SD.(B) NHERF1 is not required to promote ACE2 dimerization. FLAG-NHERF1 and Myc-ACE2 were transiently transfected into HK2 cells. Forty-eight hours post transfection, the cell lysates were cleared by centrifugation and incubated with anti-c-Myc agarose beads (only the sample in the lower left panel was prepared using anti-FLAG agarose beads and therefore eluted by 3x FLAG peptide). Purified proteins by c-Myc peptide elution were detected by the indicated antibodies. The boxed blots in red are from SDS-PAGE (top panel) and the blots in the lower panel are from blue native PAGE performed as described before (Dewson, 2015). Molecular weights are indicated at the right side of the blots. In the lower right panel, the same samples were loaded in the first and third lane to better show the slight difference of protein size from different samples.(C) Sequence alignment of ACE2 and NRP1 from SARS-CoV-2 hosts human (Protein ID: NP_001358344.1 for ACE2 and ADN93470.1 for NRP1) and bat (Protein ID: NP_001231902.2 for ACE2 and KAF6372190.1 for NRP1). Human and bat ACE2/Ace2 and NRP1/Nrp1 are used because they are primary hosts of SARS-CoV-2 (Burki, 2020). Both identified SARS-CoV-2 receptors are single-pass transmembrane proteins and have a typical type I PDZ-binding motif (QTSF and YSEA) implying a possible common mechanism by which NHERF1 regulates SARS-CoV-2 receptor internalization. The single-pass transmembrane regions are colored in red, and the intracellular C-terminal tail is colored in blue. The conserved serine and threonine residues are indicated by asterisks and are likely to be potential phosphorylation sites denoted by an encircled P. These sites may mediate SARS-CoV-2 receptor binding to β-arrestin as in the case of β2AR, where the phosphorylated receptor C terminus is required for binding to β-arrestin and receptor internalization (Nobles et al., 2011).(D) NHERF1 functions in ACE2-mediated SARS-CoV-2 cell entry in lung, kidney, and intestine and possibly NRP1-mediated virus entry in brain. NHERF1 enhances plasma membrane localization of B0AT1-stabilized ACE2 receptor and regulates its internalization and hence, ACE2-mediated SARS-CoV-2 cell entry. Except NHERF1, the virion-receptor complex also requires β-arrestin to facilitate its internalization process in which clathrin is involved. Once internalized, SAS-CoV-2 is either degraded in lysosomes (pink arrow) or released into the cytosol where the viral genomic RNA is released and immediately translated into viral RNA polymerase. The ACE2 receptor may be recycled back to the plasma membrane. Viral RNA genome and its structural nucleocapsid protein is replicated and synthesized in the cytoplasm. Other viral structural proteins are translated in the endoplasmic reticulum and further glycosylated in the Golgi. Mature progeny virions are then formed and bud out from plasma by exocytosis.

Fig 4: B. uniformis reduces the expression of intestinal amino acid transporters in the Chd8+/− mice.a Serum levels of L-glutamine in of 12-week-old mice detected by targeted metabolomics assays. n = 18, 18, and 11 mice, respectively. b–d Bulk RNA-seq analysis of the small intestine of 12-week-old mice. There were n = 3, n = 3, and n = 5 mice in the KN, KB, and WN groups, respectively (WN: Chd8+/+ mice gavaged with PBS; KN: Chd8+/− mice gavaged with PBS; KB: Chd8+/− mice gavaged with B. uniformis). b Venn diagram illustrating the count of DE genes between KN_WN and DE genes between KB_WN. The DE genes were determined under a strict threshold of adjusted P < 0.01 and |log2(cf)| > 0.585. c Euclidean distance of KB_KN (Chd8+/− mice gavaged with PBS and Chd8+/− mice gavaged with B. uniformis), KB_WN, and KN_WN. The two-tailed Mann–Whitney test was used to calculate the significance. Box plots were based on 350 data points and showed center line as median, box limits as upper and lower quartiles, whiskers as 1.5 × interquartile range and dots as outliers. d GSEA plot shows the enrichment of the amino acid transmembrane transporter activity pathway in small intestinal cells of the Chd8+/− mice gavaged with PBS compared to the Chd8+/− mice gavaged with B. uniformis. e Immunofluorescence staining of SLC6A19 and SLC7A8 in the ileum of the mice at week 12. Scale bar, 20 μm. n = 3 mice per group. Each symbol represents one image; seven to nine images per mouse. n = 28, 26, and 21 symbols, respectively. f Western blotting analysis of the SLC6A19 and SLC7A8 protein levels in the small intestine of the mice at week 12. n = 9, 7, and 11 mice, respectively. Quantitative data are shown as the mean ± SEM. Statistical analysis was determined by one-way ANOVA with two-tailed Tukey’s multiple comparison test (a, e, f). Significance was indicated by P value.

Fig 5: Detection of host cell proteins and genes associated with SARS-CoV-2 viral infection.a–f Representative fluorescent confocal images (n = 3 independent experiments performed in duplicate) of human embryonic stem cell-derived cardiomyocytes (hESC-CMs) (upper) and representative fluorescent images (n = 6 from 6 different donors) of human left ventricle (human LV) tissue sections (lower). Both cells and tissue were fixed with 4% formaldehyde and immunolabelled with primary antibodies raised against ACE2 a, TMPRSS2 b, B0AT1 c, cathepsin B d, cathepsin L e, and furin f, before visualisation with secondary antibody conjugated to Alexa Fluor 555 (yellow) and Hoechst 33342 nuclear marker (blue). g shows control cells (upper) and tissue (lower) treated with secondary antibody only and Hoechst 33342 nuclear marker. Scale bars show 50 μm. h Graphical data showing the percentage of the observed hESC-CM population positively immunolabelled (above background) after visualisation with a secondary antibody targeting primary antibodies raised against the outlined protein targets. i Graphical data showing the reads per million (RPM) ± SEM for expression of viral entry and processing genes in hESC-CMs (n = 3 replicates across three distinct differentiations) and human left ventricle (n = 5 individuals). SLC6A19, CTSB, and CTSL are the genes that encode B0AT1, cathepsin B, and cathepsin L, respectively. All graphical data are mean±SEM, with individual data points indicated.