Journal: bioRxiv

Article Title: Biofilm-Derived Curli and Z-DNA Shape Anti-DNA Antibody Responses During Salmonella Infections

doi: 10.64898/2026.03.02.708989

Figure Lengend Snippet: (A-B) 129X1/SvJ mice were intragastrically infected with STm IR715 or an isogenic non-invasive mutant STm ( invAspiB ). The serum was collected 13 weeks post-infection, diluted 1:600, and assayed by ELISA for (A) anti-Z-DNA and (B) anti-B-DNA antibodies. (C-E) 129X1/SvJ mice were fed a lithogenic (high-cholesterol) diet for 8 weeks, then switched to a normal diet for 1 week before i.p. infection with STm. (C) Serum from 3 weeks post-infection was diluted 1:250 and analyzed by ELISA for anti-dsDNA autoantibodies. (D-E) Cecal tissue was stained with antibodies against Salmonella (green) and Z-DNA (blue), EBBA Biolight 680 bacterial amyloid dye for curli (red), and DAPI for host nuclei (cyan). Representative images were taken at 63X magnification on the confocal microscope and processed via ImageJ.

Article Snippet: The following commercial antibodies were used: 5μg/mL rabbit IgG isotype control (AC042), 5μg/mL mouse IgG2b isotype control (02-6300), 5μg/mL mouse anti-Z-DNA/anti-Z-RNA antibody [Z22] (Absolute Antibodies Ab00783-3.0) (Z-DNA), 5μg/mL rabbit anti-dsDNA antibody [DSD/4054R] (Novus Biologicals NBP3-07302-100ug) (B-DNA).

Techniques: Infection, Mutagenesis, Enzyme-linked Immunosorbent Assay, Staining, Microscopy

Journal: Genetics

Article Title: A novel role for the E2F transcription factor and the ER stress sensor IRE1 in cytoplasmic DNA accumulation

doi: 10.1093/genetics/iyaf190

Figure Lengend Snippet: DNA accumulates in the cytoplasm of de2f1b SGs. a) Control ( w 1118 ) and de2f1b SGs ( de2f1b/Df ) are stained with an antibody against double-stranded DNA (anti-dsDNA) and DAPI. Lower panels show magnified views of the box area (scale bars: 50 and 20 μm for magnified images). Arrowheads mark anti-dsDNA signals that overlap with cytoplasmic DAPI. b) de2f1b SGs expressing mitochondrially localized GFP (Mito-GFP) are stained with anti-dsDNA. Arrowheads mark anti-dsDNA signals that overlap with cytoplasmic DAPI and asterisks indicate anti-dsDNA signals that demark mitochondria (scale bars: 10 μm) (c) Antimicrobial peptide gene (AMP) expression levels were measured by RT-qPCR. Relative fold difference of indicated AMPs between control and de2f1b SGs are shown (**** P < 0.0001, *** P < 0.001, ** P < 0.01, * P < 0.05). d) The relative fold differences of the expression of previously identified STING-regulated genes between control and de2f1b SGs is determined by RT-qPCR (**** P < 0.0001).

Article Snippet: The anti- γ H2Av (UNC93-5.2.1) and anti-double-stranded dsDNA (autoanti-dsDNA) antibodies were obtained from the Developmental Studies Hybridoma Bank ( https://dshb.biology.uiowa.edu ).

Techniques: Control, Staining, Expressing, Quantitative RT-PCR

Journal: Genetics

Article Title: A novel role for the E2F transcription factor and the ER stress sensor IRE1 in cytoplasmic DNA accumulation

doi: 10.1093/genetics/iyaf190

Figure Lengend Snippet: The endoplasmic reticulum (ER) homeostasis is deregulated in de2f1b SGs. a) RNA-seq was performed to compare the gene expression profile between control and de2f1b SGs. Volcano plot of differentially expressed genes in de2f1b SGs is shown. Each point represents a gene plotted by log 2 fold change (x-axis) and –log 10 adjusted P -value ( y -axis). Significantly upregulated and significantly downregulated genes are shown (genes with adjusted P -value < 0.05). Five genes that belongs to the category “protein processing in the ER” are highlighted and labeled. b) Ontology analysis was performed with genes whose expressions are downregulated in de2f1b SGs. The top 5 biological processes identified from the ontology analysis are shown. The intensity of the color depicts the false discovery rate, and the size of the circles depicts the fold enrichment. c) A GFP construct tagged with ER localization and retention signals is used to visualize ER morphology (ER:GFP). Anti-dsDNA was also used to determine the abundance of cytoDNA. Magnified view of the boxed area is also shown (scale bars: 50 and 25 μm for magnified images). (d) A genomic construct, in which the coding region of the SGS3 gene is fused with the GFP sequence (SGS:GFP), is used to monitor the expression of “glue proteins” in control and de2f1b SGs. Anti-dsDNA was also used to determine the abundance of cytoDNA. White arrowheads point to cells with a high level of cytoDNA (scale bars: 50 and 25 μm for magnified images). FB: Fat body.

Article Snippet: The anti- γ H2Av (UNC93-5.2.1) and anti-double-stranded dsDNA (autoanti-dsDNA) antibodies were obtained from the Developmental Studies Hybridoma Bank ( https://dshb.biology.uiowa.edu ).

Techniques: RNA Sequencing, Gene Expression, Control, Labeling, Construct, Sequencing, Expressing

Journal: Genetics

Article Title: A novel role for the E2F transcription factor and the ER stress sensor IRE1 in cytoplasmic DNA accumulation

doi: 10.1093/genetics/iyaf190

Figure Lengend Snippet: IRE-1 is required for proper ER development and preventing cytoDNA accumulation. a) Ire1 was depleted in the SG and their effect on the ER was visualized by ER-localized GFP (ER:GFP). A control SG ( sg-G4 ) and a representative image of ire1 -depleted SGs are shown ( sg-G4 > ire1 RNAi ). b) Xbp1 was depleted in the SG ( sg-G4 > xbp1 RNAi ) and their effect on the ER network was visualized. c) Ire1 was depleted in the SG ( sg-G4 > ire1 RNAi ) and cytoDNA was visualized by anti-dsDNA. d) The SGS:GFP genomic construct was used to monitor the expression of glue proteins in control and ire-1 depleted SGs at 110–120 h AEL. cytoDNA was also visualized by anti-dsDNA (scale bars for all the images: 50 and 20 μm for magnified images).

Article Snippet: The anti- γ H2Av (UNC93-5.2.1) and anti-double-stranded dsDNA (autoanti-dsDNA) antibodies were obtained from the Developmental Studies Hybridoma Bank ( https://dshb.biology.uiowa.edu ).

Techniques: Control, Construct, Expressing

Journal: Genetics

Article Title: A novel role for the E2F transcription factor and the ER stress sensor IRE1 in cytoplasmic DNA accumulation

doi: 10.1093/genetics/iyaf190

Figure Lengend Snippet: IRE1 overexpression differently affects the ER in de2f1b SGs. a) XBP1 or IRE1 was overexpressed in control ( sg-G4 ) and de2f1b SGs ( sg-G4; de2f1b/Df ), and the ER was visualized by ER:GFP. Magnified images of the boxed area are shown in the lower panels. b) The effect of overexpressing XBP1 or IRE1 on cytoDNA accumulation in wild-type SGs is determined. The presence of cytoDNA was visualized by anti-dsDNA. Arrowheads point to cytoDNA. Magnified images of the boxed area are shown in the lower panels (scale bars for all the images: 50 and 20 μm for magnified images).

Article Snippet: The anti- γ H2Av (UNC93-5.2.1) and anti-double-stranded dsDNA (autoanti-dsDNA) antibodies were obtained from the Developmental Studies Hybridoma Bank ( https://dshb.biology.uiowa.edu ).

Techniques: Over Expression, Control

Journal: JCI Insight

Article Title: Type II alveolar epithelial cell–specific loss of RhoA exacerbates allergic airway inflammation through SLC26A4

doi: 10.1172/jci.insight.148147

Figure Lengend Snippet: ( A ) Schematic representation of HBECs expressing either a constitutively active RHOA (RHOA-L63) or dominant-negative (RHOA-N19) for SLC26A4 regulation by RhoA and subsequently TGF-β1 secretion. ( B ) qPCR analysis of relative SLC26A4 expression in HBECs expressing either RHOA-L63 or RHOA-N19 ( n = 4). ( C ) Level of TGF-β1 in supernatants of RHOA-L63– or RHOA-N19–transfected HBECs treated with CRE ( n = 4). ( D ) Representative immunofluorescence images of Slc26a4 (red) expression in lung tissue AT2 cells (Sftpc, green) of CRE-induced mouse model of asthma with RhoA fl/fl or Sftpc-cre;RhoA fl/fl mice. ( E ) Quantification of relative Slc26a4 expression in E ( n = 6). Data represent mean ± SEM. Group comparisons were made using 2-way ANOVA ( B , C , and E ). * P < 0.05, ** P < 0.01, and *** P < 0.001. Total original magnification, ×20.

Article Snippet: Human SLA26A4 in serum was detected by using Human SLC26A4 ELISA kit (orb562738, Biorbyt).

Techniques: Expressing, Dominant Negative Mutation, Transfection, Immunofluorescence

Journal: JCI Insight

Article Title: Type II alveolar epithelial cell–specific loss of RhoA exacerbates allergic airway inflammation through SLC26A4

doi: 10.1172/jci.insight.148147

Figure Lengend Snippet: ( A ) Representative immunofluorescence images of SLC26A4 (red) expression in lung tissue AT2 cells (SFTPC, green) of asthmatics and healthy controls. ( B ) Quantitative analysis of SLC26A4 expression in A ( n = 5). ( C ) Serum levels of SLC26A4 in healthy subjects ( n = 18) and patients with mild ( n = 31) and severe ( n = 24) asthma. ( D ) Correlation between serum levels of SLC26A4 (pendrin) and FEV 1 % among asthmatics ( n = 55). ( E and F ) Correlation between serum levels of SLC26A4 (pendrin) and FEV 1 % among the mild ( E , n = 31) and severe ( F , n = 23) asthmatics, respectively. ( G ) Representative images of SLC26A4 expression in HBECs after CRE treatment. ( H ) Quantification of SLC26A4 + staining in G ( n = 5). Data represent mean ± SEM. Group comparisons were made using 2-tailed Student’s t test ( B and H ) and 2-way ANOVA ( C ). * P < 0.05, ** P < 0.01, and *** P < 0.001. Scale bars: 25 μm.

Article Snippet: Human SLA26A4 in serum was detected by using Human SLC26A4 ELISA kit (orb562738, Biorbyt).

Techniques: Immunofluorescence, Expressing, Staining

Journal: JCI Insight

Article Title: Type II alveolar epithelial cell–specific loss of RhoA exacerbates allergic airway inflammation through SLC26A4

doi: 10.1172/jci.insight.148147

Figure Lengend Snippet: ( A ) Epithelial cell–derived cytokines in the BALF of NPPB treated mice ( n = 8–10). ( B ) Epithelial cell–derived cytokines in supernatants of CRE-treated HBECs in the presence or absence of NPPB treatment ( n = 4–6). ( C ) Epithelial cell–derived cytokines in supernatants of CRE-treated HBECs with or without SLC26A4 knockdown ( n = 4). Data represent mean ± SEM of 2 independent experiments. Group comparisons were made using 2-way ANOVA ( A – C ). * P <0.05, ** P < 0.01, and *** P < 0.001.

Article Snippet: Human SLA26A4 in serum was detected by using Human SLC26A4 ELISA kit (orb562738, Biorbyt).

Techniques: Derivative Assay, Knockdown