Dynamical and combinatorial coding by MAPK p38 and NFκB in the inflammatory response of macrophages.

Macrophages sense pathogens and orchestrate specific immune responses. Stimulus specificity is thought to be achieved through combinatorial and dynamical coding by signaling pathways. While NFκB dynamics are known to encode stimulus information, dynamical coding in other signaling pathways and their combinatorial coordination remain unclear. Here, we established live-cell microscopy to investigate how NFκB and p38 dynamics interface in stimulated macrophages. Information theory and machine learning revealed that p38 dynamics distinguish cytokine TNF from pathogen-associated molecular patterns and high doses from low, but contributed little to information-rich NFκB dynamics when both pathways are considered. This suggests that immune response genes benefit from decoding immune signaling dynamics or combinatorics, but not both. We found that the heterogeneity of the two pathways is surprisingly uncorrelated. Mathematical modeling revealed potential sources of uncorrelated heterogeneity in the branched pathway network topology and predicted it to drive gene expression variability. Indeed, genes dependent on both p38 and NFκB showed high scRNAseq variability and bimodality. These results identify combinatorial signaling as a mechanism to restrict NFκB-AND-p38-responsive inflammatory cytokine expression to few cells.

Co-imaging of RelA and c-Rel reveals features of NF-κB signaling for ligand discrimination.

Individual cell sensing of external cues has evolved through the temporal patterns in signaling. Since nuclear factor κB (NF-κB) signaling dynamics have been examined using a single subunit, RelA, it remains unclear whether more information might be transmitted via other subunits. Using NF-κB double-knockin reporter mice, we monitored both canonical NF-κB subunits, RelA and c-Rel, simultaneously in single macrophages by quantitative live-cell imaging. We show that signaling features of RelA and c-Rel convey more information about the stimuli than those of either subunit alone. Machine learning is used to predict the ligand identity accurately based on RelA and c-Rel signaling features without considering the co-activated factors. Ligand discrimination is achieved through selective non-redundancy of RelA and c-Rel signaling dynamics, as well as their temporal coordination. These results suggest a potential role of c-Rel in fine-tuning immune responses and highlight the need for approaches that will elucidate the mechanisms regulating NF-κB subunit specificity.

Pneumococcal Vaccination Recommendation and Completion Rates Among Patients With Inflammatory Bowel Disease and Barriers to Vaccination.

BACKGROUND: Guidelines for inflammatory bowel disease (IBD) patients receiving immunosuppression encouraged both the pneumococcal polysaccharide vaccine (PPSV23) and the pneumococcal conjugate vaccine (PCV13). We aimed to evaluate which pneumococcal vaccines are recommended and administered, and to understand provider and IBD patient knowledge regarding pneumococcal vaccinations. METHODS: We performed a retrospective, cross-sectional analysis of 357 adult IBD patients on immunosuppression in our health care system. Patient demographics and clinical characteristics were collected. The primary outcome was rate of documented vaccinations recommended by providers; the secondary outcome was rate of receipt of the vaccines. We identified factors associated with receipt of any pneumococcal vaccine through multivariable logistic regression. We also performed provider and IBD patient surveys to understand provider and patient knowledge regarding pneumococcal vaccines. We used χ 2 and Fisher exact tests to assess survey responses. RESULTS: Fifty seven percent of IBD patients had any pneumococcal vaccination recommended and 35% had recommendations for both PPSV23 and PCV13. Forty percent received any pneumococcal vaccine and 18% received both vaccines. In multivariable analyses, increasing age (adjusted odds ratio: 1.03, 95% CI: 1.01-1.05) was associated with receipt of any pneumococcal vaccine, after adjusting for gender, race, insurance, disease activity, and time seen in our gastroenterology clinics. In the survey study, on average, 59% of providers correctly answered questions regarding pneumococcal vaccination indications. CONCLUSION: In our health care system, while recommendation for any pneumococcal vaccination was >50%, receipt of both PPSV23 and PCV13 was low. Simplified vaccine regimens (ie, PCV20) will likely improve vaccination rates.

Declining Rates of Surgery for Inflammatory Bowel Disease in the Era of Biologic Therapy.

BACKGROUND: Medical therapy for inflammatory bowel disease (IBD) has markedly advanced since the introduction of biologic therapeutics, although surgery remains an important therapeutic strategy for both Crohn's disease (CD) and ulcerative colitis (UC). This study evaluated how rates of bowel resection surgery and post-operative mortality for IBD have changed over the last decade in the era of biologic therapies. METHODS: The Nationwide Readmission Database (NRD) was queried for patients with IBD (based on ICD-9 and -10 diagnosis and procedure codes) who were hospitalized between 2010 and 2017. Longitudinal trends in bowel resection surgery, urgent surgery, and post-operative mortality were analyzed. RESULTS: During the 8-year period, a total of 1795,266 IBD-related hospitalizations (1,072,110 with CD and 723,156 with UC) were evaluated. There was an increase in the annual number of IBD patients hospitalized, but a statistically significant decrease in the proportion of IBD patients undergoing surgery, from 10 to 8.8% (p < 0.001) for CD and 7.7 to 7.5% (p < 0.001) for UC. From 2014 through 2017, the proportion of urgent surgeries remained stable around 25% (p = 0.16) for CD and decreased from 21 to 14% (p < 0.001) for UC. For CD, the rate of post-operative 30-day mortality varied between 1.2 and 1.6% and for UC decreased from 5.8 to 2.3% (p < 0.001). CONCLUSIONS: Analysis of a nationwide dataset from 2010 to 2017 determined that despite an increase in total admissions for IBD, a smaller proportion of hospitalized patients underwent surgery. A greater proportion of surgeries for UC were performed on an elective basis, and overall the rates of post-operative mortality for CD and UC decreased. The growth of biologic medical therapy during the study period highlights a probable contributing factor for the observed changes.

A clinical and radiographic model to predict surgery for acute small bowel obstruction in Crohn's disease.

PURPOSE: For more than half of Crohn's disease patients, strictures will cause bowel obstructions that require surgery within 10 years of their initial diagnosis. This study utilizes computed tomography imaging and clinical data obtained at the initial emergency room visit to create a prediction model for progression to surgery in Crohn's disease patients with acute small bowel obstructions. METHODS: A retrospective chart review was performed for patients who presented to the emergency room with an ICD-10 diagnosis for Crohn's disease and visit diagnosis of small bowel obstruction. Two expert abdominal radiologists evaluated the CT scans for bowel wall thickness, maximal and minimal luminal diameters, length of diseased segment, passage of oral contrast, evidence of penetrating disease, bowel wall hyperenhancement or stratification, presence of a comb sign, fat hypertrophy, and small bowel feces sign. The primary outcome was progression to surgery within 6 months of presentation. The secondary outcome was time to readmission. RESULTS: Forty patients met the inclusion criteria, with 78% receiving medical treatment alone and 22% undergoing surgery within 6 months of presentation to the emergency room. Multivariable analysis produced a model with an AUC of 92% (95% CI 0.82-1.00), 78% sensitivity, and 97% specificity, using gender, body mass index, and the radiographic features of segment length, penetrating disease, and bowel wall hyperenhancement. CONCLUSIONS: The model demonstrates that routine clinical and radiographic data from an emergency room visit can predict progression to surgery, and has the potential to risk stratify patients, guide management in the acute setting, and predict readmission.

Sequential Immunization Elicits Broadly Neutralizing Anti-HIV-1 Antibodies in Ig Knockin Mice.

A vaccine that elicits broadly neutralizing antibodies (bNAbs) against HIV-1 is likely to be protective, but this has not been achieved. To explore immunization regimens that might elicit bNAbs, we produced and immunized mice expressing the predicted germline PGT121, a bNAb specific for the V3-loop and surrounding glycans on the HIV-1 spike. Priming with an epitope-modified immunogen designed to activate germline antibody-expressing B cells, followed by ELISA-guided boosting with a sequence of directional immunogens, native-like trimers with decreasing epitope modification, elicited heterologous tier-2-neutralizing responses. In contrast, repeated immunization with the priming immunogen did not. Antibody cloning confirmed elicitation of high levels of somatic mutation and tier-2-neutralizing antibodies resembling the authentic human bNAb. Our data establish that sequential immunization with specifically designed immunogens can induce high levels of somatic mutation and shepherd antibody maturation to produce bNAbs from their inferred germline precursors.