Development of immune-specific interaction potentials and their application in the multi-agent-system VaccImm

Peptide vaccination in cancer therapy is a promising alternative to conventional methods. However, the parameters for this personalized treatment are difficult to access experimentally. In this respect, in silico models can help to narrow down the parameter space or to explain certain phenomena at a systems level. Herein, we develop two empirical interaction potentials specific to B-cell and T-cell receptor complexes and validate their applicability in comparison to a more general potential. The interaction potentials are applied to the model VaccImm which simulates the immune response against solid tumors under peptide vaccination therapy. This multi-agent system is derived from another immune system simulator (C-ImmSim) and now includes a module that enables the amino acid sequence of immune receptors and their ligands to be taken into account. The multi-agent approach is combined with approved methods for prediction of major histocompatibility complex (MHC)-binding peptides and the newly developed interaction potentials. In the analysis, we critically assess the impact of the different modules on the simulation with VaccImm and how they influence each other. In addition, we explore the reasons for failures in inducing an immune response by examining the activation states of the immune cell populations in detail.In summary, the present work introduces immune-specific interaction potentials and their application to the agent-based model VaccImm which simulates peptide vaccination in cancer therapy.     

Monitoring Central Venous Catheter Resistance to Predict Imminent Occlusion: A Prospective Pilot Study

Background

Long-term central venous catheters are essential for the management of chronic medical conditions, including childhood cancer. Catheter occlusion is associated with an increased risk of subsequent complications, including bloodstream infection, venous thrombosis, and catheter fracture. Therefore, predicting and pre-emptively treating occlusions should prevent complications, but no method for predicting such occlusions has been developed.

Methods

We conducted a prospective trial to determine the feasibility, acceptability, and efficacy of catheter-resistance monitoring, a novel approach to predicting central venous catheter occlusion in pediatric patients. Participants who had tunneled catheters and were receiving treatment for cancer or undergoing hematopoietic stem cell transplantation underwent weekly catheter-resistance monitoring for up to 12 weeks. Resistance was assessed by measuring the inline pressure at multiple flow-rates via a syringe pump system fitted with a pressure-sensing transducer. When turbulent flow through the device was evident, resistance was not estimated, and the result was noted as “non-laminar.”

Results

Ten patients attended 113 catheter-resistance monitoring visits. Elevated catheter resistance (>8.8% increase) was strongly associated with the subsequent development of acute catheter occlusion within 10 days (odds ratio = 6.2; 95% confidence interval, 1.8–21.5; p <0.01; sensitivity, 75%; specificity, 67%). A combined prediction model comprising either change in resistance greater than 8.8% or a non-laminar result predicted subsequent occlusion (odds ratio = 6.8; 95% confidence interval, 2.0–22.8; p = 0.002; sensitivity, 80%; specificity, 63%). Participants rated catheter-resistance monitoring as highly acceptable.

Conclusions

In this pediatric hematology and oncology population, catheter-resistance monitoring is feasible, acceptable, and predicts imminent catheter occlusion. Larger studies are required to validate these findings, assess the predictive value for other clinical outcomes, and determine the impact of pre-emptive therapy.

Trial Registration

Clinicaltrials.gov NCT01737554     

Biomechanical Aspects of Compliant Airways due to Mechanical Ventilation

Without proper knowledge of mechanical ventilation effects, physicians can aggravate an existing lung injury. A better understanding of the interaction between airflow and airway tissue during mechanical ventilation will be helpful to physicians so that they can provide appropriate ventilator parameters for intubated patients. In this study, a computational model incorporating the interactions between airflow and airway walls was developed to investigate the effects of airway tissue flexibility on airway pressure and stress. Two flow rates, 30 and 60 l/min, from mechanical ventilation were considered. The transient waveform was active inhalation with a constant flow rate and passive exhalation. Results showed that airway tissue flexibility decreased airway pressure at bifurcation sites by approximately 25.06% and 16.91% for 30 and 60 l/min, respectively, and increased wall shear stress (WSS) by approximately 74.00% and 174.91% for 30 and 60 l/min, respectively. The results from the present study suggested that it is very important to consider the interaction between airflow and airway walls when computational models are developed. Results of this study help to better quantify how the airflow rate used in mechanical ventilation, in conjunction with airway tissue flexibility, affects airway pressure and stresses.     

Activating mutations of N-WASP alter Shigella pathogenesis

The pathogenesis of Shigella requires binding to the host protein N-WASP. To examine the roles of structural conformation and phospho-regulation of N-WASP during Shigella pathogenesis, mutant N-WASP constructs predicted to result in a constitutively open conformation (L229P and L232P) or either a phospho-mimicking (Y253E) or phospho-disruptive (Y253F) structure were constructed. Pyrene actin assays demonstrated that the N-WASP L229P and L232P constructs are constitutively active. Despite the increase in actin polymerization seen in vitro, cell lines expressing N-WASP L229P and L232P supported shorter actin tails when infected with Shigella.Shigella actin tails were unchanged in cells expressing N-WASP phospho-regulation mutant proteins. Shigella invasion, intracellular, and intercellular motility were not altered in cells expressing N-WASP L229P or L232P. However, plaque numbers were increased in cells expressing N-WASP L229P and L232P. These data demonstrate that N-WASP structural conformation is an important regulator of Shigella pathogenesis in distinct segments of its lifecycle.     

Binding of MutS protein to oligonucleotides containing a methylated or an ethylated guanine residue, and correlation with mutation frequency

The MutS-based mismatch repair (MMR) system has been conserved from prokaryotes to humans, and plays important roles in maintaining the high fidelity of genomic DNA. MutS protein recognizes several different types of modified base pairs, including methylated guanine-containing base pairs. Here, we looked at the relationship between recognition and the effects of methylating versus ethylating agents on mutagenesis, using a MutS-deficient strain of E. coli. We find that while methylating agents induce mutations more effectively in a MutS-deficient strain than in wild-type, this genetic background does not affect mutagenicity by ethylating agents. Thus, the role of E. coli MMR with methylation-induced mutagenesis appears to be greater than ethylation-induced mutagenesis. To further understand this difference an early step of repair was examined with these alkylating agents. A comparison of binding affinities of MutS with O⁶-alkylated guanine base paired with thymine, which could lead to transition mutations, versus cytosine which could not, was tested. Moreover, we compared binding of MutS to oligoduplexes containing different base pairs; namely, O⁶-MeG:T, O⁶-MeG:C, O⁶-EtG:T, O⁶-EtG:C, G:T and G:C. Dissociation constants (K_d), which reflect the strength of binding, followed the order G:T- > O⁶-MeG:T- > O⁶-EtG:T- = O⁶-EtG:C- ≥ O⁶-MeG:C- > G:C. These results suggest that a thymine base paired with O⁶-methyl guanine is specifically recognized by MutS and therefore should be removed more efficiently than a thymine opposite O⁶-ethylated guanine. Taken together, the data suggest that in E. coli, the MMR system plays a more significant role in repair of methylation-induced lesions than those caused by ethylation.