Resistance to host defense peptides is required for AIEC expansion in the inflamed gut and immunopathology.

<p>129e mice were colonized with wild type AIEC or the peptide-sensitive ΔPI-6 mutant and then infected with <i>Salmonella</i>. Survival was assessed over 35 days and the tissue burden of AIEC was determined in the cecum (A) and the ileum (B). Each point represents one animal and the data represents 3 independent experiments. ***p< 0.001 (Mann-Whitney test). 129e mice were colonized with AIEC and then infected with either wild type <i>Salmonella</i> or a mutant that is less proinflammatory, <i>S</i>.<i>tm</i>^<i>avir</i>. Tissue burden of AIEC (blue circles) and <i>Salmonella</i> (yellow circles) was determined in the cecum (C) and the ileum (D). Each point represents one animal and the data represents 2 independent experiments. *p<0.05; **p<0.01; ***p< 0.001 (Mann-Whitney test). (E) H&E-stained tissue samples from cecal tips are shown for the indicated infection groups. Original magnification 200x. (F) Quantification of histopathology from part E. Data are the means ± SEM of 5 mice per group from 2–3 separate experiments and 5 views per mouse. ***p<0.001 (one way ANOVA with Tukey). (G) TNFα levels determined from explanted cecal supernatants by ELISA. (H) Fecal lipocalin-2 levels determined from fecal pellets on day 5 after <i>Salmonella</i> infection. Data are means with SEM from 2–3 experiments. **p<0.01, ***p< 0.001 (Mann-Whitney test).</p

Tissue-associated expansion of AIEC following <i>Salmonella gastroenteritis</i>.

<p>(A) Fecal <i>Salmonella</i> loads on day 2, 4, and 5 after infection. Each data point is from one animal and represents 3–4 independent experiments. (B) Tissue-associated <i>Salmonella</i> burdens in the cecum, ileum, and spleen on day 5 after <i>Salmonella</i> infection. Each point is from one animal and data represents 3–4 independent experiments. (C) Tissue-associated AIEC burden in feces, cecum and ileum on day 5 after <i>Salmonella</i> infection. Each point is from one animal and data represent 3–4 independent experiments. (D) Tissue-associated <i>E</i>. <i>coli</i> K12 in feces, cecum and ileum on day 5 after <i>Salmonella</i> infection. Each point is from one animal. <i>ns</i> not significantly different between comparison groups, *p<0.05, **p<0.01, ***p< 0.001 (Mann-Whitney test).</p

Acute Infectious Gastroenteritis Potentiates a Crohn's Disease Pathobiont to Fuel Ongoing Inflammation in the Post-Infectious Period

<div><p>Crohn’s disease (CD) is a chronic inflammatory condition of diverse etiology. Exposure to foodborne pathogens causing acute gastroenteritis produces a long-term risk of CD well into the post-infectious period but the mechanistic basis for this ongoing relationship to disease onset is unknown. We developed two novel models to study the comorbidity of acute gastroenteritis caused by <i>Salmonella</i> Typhimurium or <i>Citrobacter rodentium</i> in mice colonized with adherent-invasive <i>Escherichia coli</i> (AIEC), a bacterial pathobiont linked to CD. Here, we show that disease activity in the post-infectious period after gastroenteritis is driven by the tissue-associated expansion of the resident AIEC pathobiont, with an attendant increase in immunopathology, barrier defects, and delays in mucosal restitution following pathogen clearance. These features required AIEC resistance to host defense peptides and a fulminant inflammatory response to the enteric pathogen. Our results suggest that individuals colonized by AIEC at the time of acute infectious gastroenteritis may be at greater risk for CD onset. Importantly, our data identify AIEC as a tractable disease modifier, a finding that could be exploited in the development of therapeutic interventions following infectious gastroenteritis in at-risk individuals.</p></div

Mucosal epithelial restitution is delayed by AIEC following infectious colitis.

<p>(A) H&E staining of colonic sections from C57BL/6 mice infected as indicated, on day 14 and day 21 after <i>C</i>. <i>rodentium</i> infection. Images are representative of 2 experiments with 5 mice per group per time point. Arrows indicate submucosa edema, desquamation, hyperplasia, inflammatory cellular infiltrates and epithelial sloughing. Original magnification 200x. Quantification of colonic pathology on day 14 (B) and day 21 (C) after <i>C</i>. <i>rodentium</i> infection. Measurements represent an average of at least 5 views per section and are the means with SEM from 5 mice. Quantification of crypt length (D) and goblet cell numbers (E) on day 14 and day 21 after <i>C</i>. <i>rodentium</i> infection. Measurements are from at least 5 views per section. Data are expressed as the means ±SEM of 5 mice per group/time point from 2 separate experiments. *p<0.05, **p<0.01, and ***p<0.001 (one way ANOVA with Tukey).</p

AIEC modifies disease outcome following acute gastroenteritis.

<p>(A). Infection scheme: NRAMP+ 129e mice were colonized with 2 x 10⁹ cfu of AIEC strain NRG857c for 14 days to establish chronic colonization and low-grade intestinal inflammation (Phase 1). Control mice remained AIEC-naïve. AIEC-colonized and control mice were exposed to acute infectious gastroenteritis with 0.8 x 10⁸ cfu of <i>Salmonella enterica</i> serovar Typhimurium (Phase 2). (B) Kaplan-Meier survival plots of 129e mice after <i>Salmonella</i> infection. <i>n</i> = 32 mice per group from 6 independent experiments (p<0.0001, log rank). (C) Percent change in body weight was monitored up to 27 days post-<i>Salmonella</i> infection. Data is expressed as a mean ± SEM of 5 mice per group from 8 independent experiments.</p

Prior AIEC colonization worsens pathology following <i>S</i>. <i>Typhimurium</i> infection.

<p>(A) Gross pathology in the small and large intestine of 129e mice 5 days after <i>Salmonella</i> infection. (B) H&E-stained cecal sections from 4 experimental groups of 129e mice (as indicated). Images are representative of 5 mice per group from 4 independent experiments. Arrows indicate submucosa edema, desquamation, epithelial sloughing, crypt hyperplasia, and inflammatory cellular infiltrates in the lumen and mucosa. Original magnification 40x. (C) Cecal pathology was scored from H&E stained sections taken from day 5. Data are the mean with ± SEM for 5 views per mouse and 5 mice per group. ***p<0.001 (Mann-Whitney). (D) Nitrite concentration in cecal samples on day 5 after <i>Salmonella</i> infection. Treatment groups are indicated. Data are the means with SEM. **p<0.01, ***p<0.001 (Mann-Whitney). (E) FITC-dextran concentration in the serum following oral gavage in the indicated groups. Data are the means with SEM. **p<0.01, ***p<0.001 (Mann-Whitney).</p

Infectious colitis by <i>C</i>. <i>rodentium</i> prevents convalescence from AIEC colonization.

<p>(A) Infection scheme. C57BL/6 mice colonized with 2 x 10⁹ cfu AIEC NRG857c for 7 days or treated with PBS and then infected with 1 x 10⁸ cfu <i>C</i>. <i>rodentium</i> or given PBS. (B) Fecal shedding of <i>C</i>. <i>rodentium</i> was monitored for 21 days. Data are means ± SEM of at least 5 mice per group/time point from 3 independent experiments. (C) Fecal shedding of AIEC after <i>C</i>. <i>rodentium</i> infection was monitored for 36 days. Data are means ± SEM of at least 5 mice per group/time point from 3 independent experiments. Tissue- associated AIEC was measured in the cecum (D) and colon (E) on day 14 and 21 after <i>C</i>. <i>rodentium</i> infection. Data are means ± SEM of at least 5 mice per group/time point from 3 independent experiments. **p<0.01 and ***p<0.001 (Mann-Whitney test).</p

Multiscale interactome analysis coupled with off‑target drug predictions reveals drug repurposing candidates for human coronavirus disease

  The COVID-19 pandemic has highlighted the urgent need for the identification of new antiviral drug therapies for a variety of diseases. COVID-19 is caused by infection with the human coronavirus SARS-CoV-2, while other related human coronaviruses cause diseases ranging from severe respiratory infections to the common cold. We developed a computational approach to identify new antiviral drug targets and repurpose clinically-relevant drug compounds for the treatment of a range of human coronavirus diseases. Our approach is based on graph convolutional networks (GCN) and involves multiscale host-virus interactome analysis coupled to off-target drug predictions. Cell-based experimental assessment reveals several clinically-relevant drug repurposing candidates predicted by the in silico analyses to have antiviral activity against human coronavirus infection. In particular, we identify the MET inhibitor capmatinib as having potent and broad antiviral activity against several coronaviruses in a MET-independent manner, as well as novel roles for host cell proteins such as IRAK1/4 in supporting human coronavirus infection, which can inform further drug discovery studies.  </p