Journal: Human Mutation

Article Title: A Novel Missense Variant in Ultrarare SLC35A1-CDG Alters Cellular Glycosylation, Lipid, and Energy Metabolism Without Affecting CDG Serum Markers

doi: 10.1155/humu/6290620

Figure Lengend Snippet: Effect of p.Thr45Ala on SLC35A1 expression and transporter activity. (a) Illustration of the cellular route of Neu5Ac. CMP-Neu5Ac is generated by the bifunctional UDP- N -acetylglucosamine 2-epimerase/ N -acetylmannosamine kinase (GNE) converting UDP-GlcNAc to ManNAc and then to ManNAc-6-phosphate. Next, sialic acid synthase (NANS) and N -acetylneuraminate-9-phosphatase (NANP) convert ManNAc-6-phosphate to Neu5Ac via Neu5Ac-9-phosphate. The final step of CMP-Neu5Ac synthesis occurs in the nucleus, where Neu5Ac is linked to the nucleotide CMP by cytidine monophosphate N -acetylneuraminic acid synthetase (CMAS). CMP-Neu5Ac can also be generated through an alternative synthesis pathway, where sialic acid molecules that have been cleaved from glycoconjugates by the lysosomal neuraminidases NEU1-4 are recycled and subsequently reactivated with CMP in the nucleus. (b) Top: variant c.133A>G of Patient 6 localizes to Exon 2 of the SLC35A1 gene. Bottom: electropherogram (Sanger sequencing) of Exon 2 showing homozygosity for variant c.133A>G; p.Thr45Ala in fibroblasts of Patient 6. (c) Transcript and protein expression determined by qPCR and SLC35A1-ELISA revealed a normal mRNA level but significantly reduced SLC35A1 protein level in the patient's cells. (d) Measurement of the import activity of radioactively labelled sugar substrates into Golgi vesicles isolated from control and patient fibroblasts and normalisation of the CMP-[ 14 C]-Neu5Ac import to the import of control sugars GDP-[ 14 C]-fucose and UDP-[ 14 C]-galactose. (e) Protein structure analysis. Left: visualization was performed by PROTTER (Version 1.0; http://wlab.ethz.ch/protter/start/ ). Highlighted in different colours are variants of the six known SLC35A1-CDG patients and of amino acid residues which are important for substrate binding and activity. Threonine 45 (blue circle) of Patient 6 is predicted to be located at the border of the first luminal loop to the second transmembrane domain. Right: due to the p.Thr45Ala variant (Patient 6), an interhelical H-bond is predicted to get lost. Simulation based on the murine Slc35a1 structure generated by DynaMut (PDB: 6XBO). (f) Cycloheximide (CHX) treatment of SLC35A1 K.o. HEK293 cells expressing the wild-type (WT) or the mutated (p.Thr45Ala) SLC35A1-HA protein revealed a shorter half-life of the mutated SLC35A1. The relative amount of SLC35A1-HA was determined by quantification of the Western blot signals where the start of treatment was set to 100%. The regression lines were used to calculate the protein half-life ( y = 50%).

Article Snippet: Primary antibodies for detection of SLC35A1 (Proteintech, BIOZOL, MyBioSource), ADAMTS13, ATP5H, GP130 (all Thermo Fisher), GAPDH, histone 2B (H2B), H2B-GlcNAc (all Abcam), ICAM1 (Sigma), OGA, OGT, TGN46 (all Proteintech), O-GlcNAcylation (Santa Cruz), and HA-Tag (Sigma) were used in 1:1000 dilution, β -ACTIN (Sigma) in 1:10,000 dilution, and incubated overnight at 4°C under constant movement.

Techniques: Expressing, Activity Assay, Generated, Variant Assay, Sequencing, Enzyme-linked Immunosorbent Assay, Isolation, Control, Binding Assay, Western Blot

Journal: Human Mutation

Article Title: A Novel Missense Variant in Ultrarare SLC35A1-CDG Alters Cellular Glycosylation, Lipid, and Energy Metabolism Without Affecting CDG Serum Markers

doi: 10.1155/humu/6290620

Figure Lengend Snippet: Effect of SLC35A1 deficiency on glycosylation in fibroblasts. (a) Lectin binding studies showed a significant increase of nonsialylated structures (RCAI) and a significant decrease in α -2,3 sialylated glycans (MAL-I) in the patient, whereas the amount of α -2,6 sialylated residues (SNA) in SLC35A1-CDG was comparable to controls. (b) Expression of ICAM1 and GP130 is significantly reduced in the patient's cells (Pat.) compared to controls (Ctrl.). For quantification, the fully glycosylated protein forms (glyco., black arrows) were compared to the hypoglycosylated forms (nonglyco, grey arrows). (c) LC-MS analysis of N-glycans in fibroblasts revealed a deviating amount of individual N-glycans in the patient's cells (indicated by black boxes and arrows).

Article Snippet: Primary antibodies for detection of SLC35A1 (Proteintech, BIOZOL, MyBioSource), ADAMTS13, ATP5H, GP130 (all Thermo Fisher), GAPDH, histone 2B (H2B), H2B-GlcNAc (all Abcam), ICAM1 (Sigma), OGA, OGT, TGN46 (all Proteintech), O-GlcNAcylation (Santa Cruz), and HA-Tag (Sigma) were used in 1:1000 dilution, β -ACTIN (Sigma) in 1:10,000 dilution, and incubated overnight at 4°C under constant movement.

Techniques: Glycoproteomics, Binding Assay, Expressing, Liquid Chromatography with Mass Spectroscopy

Journal: Human Mutation

Article Title: A Novel Missense Variant in Ultrarare SLC35A1-CDG Alters Cellular Glycosylation, Lipid, and Energy Metabolism Without Affecting CDG Serum Markers

doi: 10.1155/humu/6290620

Figure Lengend Snippet: Metabolic measurements and GlcNAc supplementation assay in fibroblasts. (a) Measurement of very long-chain fatty acids (VLCFAs) in the lysate of patient fibroblasts normalized to the mean values of the control cell lysate revealed partially increased levels. (b) Staining of lipids in control and patient fibroblasts with Oil Red O presented with an increase in pronounced coloration in the case of the patient's cells indicating an accumulation of neutral lipids. (c) Nanoelectrospray ionization tandem mass spectrometry of cellular lipids revealed significant alterations concerning ceramide (Cer), phosphatidylethanolamine plasmalogen (PE-P), and triacylglycerol (TAG) within the main lipid classes. Abbreviations: CE, cholesteryl ester; Chol, cholesterol; DAG, diacylglycerol; PC, phosphatidylcholine; PE, phosphatidylethanolamine; PI, phosphatidylinositol; PS, phosphatidylserine; SM, sphingomyelin; Hex2Cer, dihexosylceramide; HexCer, hexosylceramide; LPC, lysophosphatidylcholine; PA, phosphatidic acid; PG, phosphatidylglycerol. (d) Reduced expression of ATP5H combined with a decreased ATP level (e) hint to a general mitochondrial impairment in SLC35A1-CDG. (f) Reduced proliferation due to decreased growth rate and increased doubling time in the patient's cells can be improved by 10 mM GlcNAc as a cell culture supplement.

Article Snippet: Primary antibodies for detection of SLC35A1 (Proteintech, BIOZOL, MyBioSource), ADAMTS13, ATP5H, GP130 (all Thermo Fisher), GAPDH, histone 2B (H2B), H2B-GlcNAc (all Abcam), ICAM1 (Sigma), OGA, OGT, TGN46 (all Proteintech), O-GlcNAcylation (Santa Cruz), and HA-Tag (Sigma) were used in 1:1000 dilution, β -ACTIN (Sigma) in 1:10,000 dilution, and incubated overnight at 4°C under constant movement.

Techniques: Control, Staining, Mass Spectrometry, Expressing, Cell Culture

Journal: EBioMedicine

Article Title: LRH1-driven transcription factor circuitry for hepatocyte identity: Super-enhancer cistromic analysis

doi: 10.1016/j.ebiom.2018.12.056

Figure Lengend Snippet: The core TFs identified in the liver. (A) H3K27Ac ChIP-seq and DNase-seq profiles at the Hnf4a (left) and the Sec62 (right) loci in mouse liver. Gray bars indicate enhancer regions. (B) Distribution of H3K27Ac ChIP-seq signal intensities across 9891 enhancers in the liver. H3K27Ac occupancy was not evenly distributed across the enhancer regions, with a subset of 460 enhancers containing exceptionally high amounts of H3K27Ac (i.e., super-enhancers) (left). A box plot of H3K27Ac ChIP-seq densities at constituent enhancers within 9431 typical enhancers or 460 super-enhancers (right). (C) Gene ontology (GO) functional categories regarding molecular functions for super-enhancer-associated genes. Genes encoding for the factors controlling transcription were enriched. (D) A protein-protein interaction network of super-enhancer-associated transcription factors (TFs) according to STRING database. LRH1 (also known as Nr5a2 ), HNF4α, PPARα, and RXRα make a core network. The TFs were divided into two groups (multiple interactions with quadruple evidences and multiple interactions with double or triple evidences) according to the number of evidences in the above network. The red dotted line designates the cutoff dividing core and second-tier TFs. (E) A network displaying interactions between GO categories. Each node indicates GO term. The thickness of node colour represents the degree of statistical significance for enrichment. Node sizes show the number of gene counts assigned to each GO term. The network was generated by analysis of Cytoscape plugin BiNGO. (F) H3K27Ac ChIP-seq data at the loci of Nr5a2 (LRH1), Hnf4a , Ppara, and Rxra . (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

Article Snippet: The plasmids encoding mouse LRH1 (#16342, RRID: Addgene_16,342) and mouse PPARα (#22751, RRID: Addgene_22,751) were supplied from Addgene (Cambridge, MA).

Techniques: ChIP-sequencing, Functional Assay, Generated

Journal: EBioMedicine

Article Title: LRH1-driven transcription factor circuitry for hepatocyte identity: Super-enhancer cistromic analysis

doi: 10.1016/j.ebiom.2018.12.056

Figure Lengend Snippet: Correlation between identified core TF and each gene transcript levels. (A) Correlation analyses in a large cohort of cirrhosis patients (GSE25097) ( N = 46). Pearson's r correlation coefficients with corresponding P -values for co-variation between each core TF mRNA levels (x axis) and hepatocyte identity gene transcripts (y axis) show robust correlations. (B) Pearson correlation analyses in mice treated as in C. For single and multiple CCl 4 treatment models, group sizes (N) are 12 and 7, respectively. (C) Results of KEGG pathway analysis of the up- or down-regulated genes after hepatocyte-specific deletion of LRH1 (GSE68718). Enriched signaling pathways of each gene cluster were analyzed using DAVID.

Article Snippet: The plasmids encoding mouse LRH1 (#16342, RRID: Addgene_16,342) and mouse PPARα (#22751, RRID: Addgene_22,751) were supplied from Addgene (Cambridge, MA).

Techniques: Protein-Protein interactions

Journal: EBioMedicine

Article Title: LRH1-driven transcription factor circuitry for hepatocyte identity: Super-enhancer cistromic analysis

doi: 10.1016/j.ebiom.2018.12.056

Figure Lengend Snippet: LRH1 protection of the liver from toxicant-induced injury. (A) LRH1 protection of the liver from APAP-induced injury. H&E staining (upper left). At four days after a hydrodynamic injection of the plasmid encoding LRH1 or mock vector (pcDNA3.1), mice were fasted overnight and subjected to a single dose of APAP (300 mg/kg), and the liver tissues were obtained six h afterward. TUNEL staining (upper right). The scale bars represent 100 μm. Serum ALT and AST activities (lower left). Liver weight per body weight ratio (middle). Correlation between serum ALT activities and LRH1 transcript levels in the liver (lower right). (B) LRH1 protection of the liver from CCl 4 -induced injury. H&E staining (upper left). Mice were subjected to a single dose of CCl 4 (0.6 mL/kg) four days after a hydrodynamic injection of the plasmid encoding LRH1 or mock vector (pcDNA3.1), and the liver tissues were obtained two days afterward. TUNEL staining (upper right). TUNEL-stained tissues were separated to non-tissue, normal and apoptotic areas by blue, green and red colors, respectively. Insets showed true-colour images. The scale bars represent 100 μm. Serum ALT and AST activities (lower left). Correlation between serum ALT activities and LRH1 ( Nr5a2 ) mRNA levels in the liver (lower right). (C) Immunoblottings for apoptosis or liver regeneration markers (left). Values were obtained using scanning densitometry (right). Data information: For A, data represent the means ± SEM (Mock+Veh, n = 7; Mock+APAP, n = 8; LRH1 + APAP, n = 13; and non-injected control (Con), n = 5, significantly different as compared to vehicle control, ** P < .01; or APAP-treated control, # P < .05; ## P < .01). For B, data represent the means ± SEM (Mock+Veh, n = 6; Mock+CCl 4 , n = 14; LRH1 + CCl 4 , n = 4; and non-injected control (Con), n = 4, significantly different as compared to vehicle control, ** P < .01; or CCl 4 -treated control: # P < .05; ## P < .01). For C, data represent the means ± SEM (n = 4 each, significantly different as compared to vehicle control, * P < .05; ** P < .01; or CCl 4 -treated control: # P < .05; ## P < .01). (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

Article Snippet: The plasmids encoding mouse LRH1 (#16342, RRID: Addgene_16,342) and mouse PPARα (#22751, RRID: Addgene_22,751) were supplied from Addgene (Cambridge, MA).

Techniques: Staining, Injection, Plasmid Preparation, TUNEL Assay, Control

Journal: EBioMedicine

Article Title: LRH1-driven transcription factor circuitry for hepatocyte identity: Super-enhancer cistromic analysis

doi: 10.1016/j.ebiom.2018.12.056

Figure Lengend Snippet: LRH1-dependent recovery of hepatocyte identity genes. (A) Principal component analysis of RNA-seq data. RNA-seq data was generated using liver of mice treated with APAP alone or APAP+LRH1 overexpression vector as in A. RNA-seq data are deposited in the GEO under accession number GSE104302. (B) Pie graphs showing the enhancer composition. Genes having P -values lower than 0.05 between APAP and LRH1 + APAP groups were defined as LRH1-dependent genes. (C) Heatmaps and hierarchical correlation analyses of differentially expressed genes (DEGs). DEGs were selected as the genes with independent t -test ( P -values < .05 with a fold-change of >1.5). The DEGs were hierarchically clustered and presented as heatmaps according to the row Z score. Super-enhancer- or typical enhancer (SE or TE)-associated DEGs represent significantly altered genes in the APAP group as compared to the vehicle group among the SE-associated or TE-associated genes. Not assigned DEGs are DEGs which are assigned neither to SE nor TE. Heatmaps of total DEGs (a), SE-associated DEGs (b), TE-associated DEGs (c), and not assigned DEGs (d) are presented in left. The proportions of the gene clusters depicted in the heatmaps (left) were shown as a graph (right). (D) Results of KEGG pathway analysis of the clustered DEGs. A schematic description of the gene clusters (a). Enriched signaling pathways of each gene cluster were analyzed using DAVID (b-d).

Article Snippet: The plasmids encoding mouse LRH1 (#16342, RRID: Addgene_16,342) and mouse PPARα (#22751, RRID: Addgene_22,751) were supplied from Addgene (Cambridge, MA).

Techniques: RNA Sequencing, Generated, Over Expression, Plasmid Preparation, Protein-Protein interactions

Journal: EBioMedicine

Article Title: LRH1-driven transcription factor circuitry for hepatocyte identity: Super-enhancer cistromic analysis

doi: 10.1016/j.ebiom.2018.12.056

Figure Lengend Snippet: LRH1 as a driver gene for the core TF circuitry. (A) Hepatic super-enhancer-associated TF network with gene expression changes in mice treated with APAP alone or APAP+LRH1 overexpression vector. The node colors reflect log2 gene expression ratio in mice treated with APAP alone (left) or APAP+LRH1 overexpression (right) as compared to vehicle treatment (red, upregulation; blue, downregulation). Log2 fold changes of the core TFs are presented as an inset table. (B) The core TF mRNA levels from the APAP model. (C) The core TF mRNA levels from the CCl 4 model. (D) The effect of each core TF overexpression on other core TFs. qRT-PCR assays were done on AML12 cells transfected with pcDNA3.1, LRH1, HNF4α, PPARα or RXRα for 48 h. The first lane of each graph is transfection reagent-treated control. Heatmap presents averages of core TF mRNA levels. O/E, overexpression. (E) Super-enhancer (SE)-luciferase reporter assays. Luciferase assays were done on AML12 cells co-transfected with each SE-luciferase reporter, and pcDNA3.1, LRH1, HNF4α, PPARα or RXRα overexpression vector for 24 h. Relative luciferase activities represent arbitrary units of luminescence normalized to the pcDNA3.1 group. The schematic illustrations showing each SE-luciferase construct are presented in the upper panel. The ChIP-seq signal peaks in the scheme are also shown in F. Red bars indicate the peaks excised for cloning of each SE-luciferase reporter construct. O/E, overexpression. (F) A proposed scheme showing auto-regulatory loops for the core TFs. In healthy liver, the core TFs form an interconnected feedback loop for gene expression. Upon injury, the signal circuitry loses its integrity with decrease of hepatocyte identity. LRH1 serves a driver for reconstitution of the signal circuitry. Data information: For B, data represent the means ± SEM (Mock+Veh, n = 7; Mock+APAP, n = 8; and LRH1 + APAP, n = 13, significantly different as compared to vehicle control, ** P < .01; or APAP-treated control, # P < .05; ## P < .01). For C, data represent the means ± SEM (Mock+Veh, n = 6; Mock+CCl 4 , n = 14; and LRH1 + CCl 4 , n = 4; significantly different as compared to vehicle control, * P < .05; ** P < .01; or CCl 4 -treated control: # P < .05; ## P < .01). For D and E, data represent the means ± SEM ( n = 3 each, significantly different as compared to pcDNA3.1 group, * P < .05; ** P < .01). (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

Article Snippet: The plasmids encoding mouse LRH1 (#16342, RRID: Addgene_16,342) and mouse PPARα (#22751, RRID: Addgene_22,751) were supplied from Addgene (Cambridge, MA).

Techniques: Gene Expression, Over Expression, Plasmid Preparation, Quantitative RT-PCR, Transfection, Control, Luciferase, Construct, ChIP-sequencing, Cloning