Here are some interesting recently published papers from our community. If you have published an interesting article in the field of in silico medicine, send it to us: we will insert it in this section of the newsletter!
We open the "in the literature" section of January with a special contribution from the EUStands4PM consortium:
Computational Models for Clinical Applications in Personalized Medicine—Guidelines and Recommendations for Data Integration and Model Validation
Authors: Catherine Bjerre Collin et al.
The future development of personalized medicine depends on a vast exchange of data from different sources, as well as harmonized integrative analysis of large-scale clinical health and sample data. Computational-modelling approaches play a key role in the analysis of the underlying molecular processes and pathways that characterize human biology, but they also lead to a more profound understanding of the mechanisms and factors that drive diseases; hence, they allow personalized treatment strategies that are guided by central clinical questions. However, despite the growing popularity of computational-modelling approaches in different stakeholder communities, there are still many hurdles to overcome for their clinical routine implementation in the future. Especially the integration of heterogeneous data from multiple sources and types are challenging tasks that require clear guidelines that also have to comply with high ethical and legal standards. Here, we discuss the most relevant computational models for personalized medicine in detail that can be considered as best-practice guidelines for application in clinical care. We define specific challenges and provide applicable guidelines and recommendations for study design, data acquisition, and operation as well as for model validation and clinical translation and other research areas.
Read the full paper: https://www.mdpi.com/2075-4426/12/2/166
Animal models and animal-free innovations for cardiovascular research: current status and routes to be explored. Consensus document of the ESC Working Group on Myocardial Function and the ESC Working Group on Cellular Biology of the Heart
Authors: Jolanda van der Velden et al.
Cardiovascular diseases represent a major cause of morbidity and mortality, necessitating research to improve diagnostics, and to discover and test novel preventive and curative therapies, all of which warrant experimental models that recapitulate human disease. The translation of basic science results to clinical practice is a challenging task, in particular for complex conditions such as cardiovascular diseases, which often result from multiple risk factors and comorbidities. This difficulty might lead some individuals to question the value of animal research, citing the translational ‘valley of death’, which largely reflects the fact that studies in rodents are difficult to translate to humans. This is also influenced by the fact that new, human-derived in vitro models can recapitulate aspects of disease processes. However, it would be a mistake to think that animal models do not represent a vital step in the translational pathway as they do provide important pathophysiological insights into disease mechanisms particularly on an organ and systemic level. While stem cell-derived human models have the potential to become key in testing toxicity and effectiveness of new drugs, we need to be realistic, and carefully validate all new human-like disease models. In this position paper, we highlight recent advances in trying to reduce the number of animals for cardiovascular research ranging from stem cell-derived models to in situ modelling of heart properties, bioinformatic models based on large datasets, and state-of-the-art animal models, which show clinically relevant characteristics observed in patients with a cardiovascular disease. We aim to provide a guide to help researchers in their experimental design to translate bench findings to clinical routine taking the replacement, reduction, and refinement (3R) as a guiding concept.
Arrhythmogenic Effects of Genetic Mutations Affecting Potassium Channels in Human Atrial Fibrillation: A Simulation Study
Authors: Rebecca Belletti et al.
Genetic mutations in genes encoding for potassium channel protein structures have been recently associated with episodes of atrial fibrillation in asymptomatic patients. The aim of this study is to investigate the potential arrhythmogenicity of three gain-of-function mutations related to atrial fibrillation—namely, KCNH2 T895M, KCNH2 T436M, and KCNE3-V17M—using modeling and simulation of the electrophysiological activity of the heart. A genetic algorithm was used to tune the parameters’ value of the original ionic currents to reproduce the alterations experimentally observed caused by the mutations. The effects on action potentials, ionic currents, and restitution properties were analyzed using versions of the Courtemanche human atrial myocyte model in different tissues: pulmonary vein, right, and left atrium. Atrial susceptibility of the tissues to spiral wave generation was also investigated studying the temporal vulnerability. The presence of the three mutations resulted in an overall more arrhythmogenic substrate. Higher current density, action potential duration shortening, and flattening of the restitution curves were the major effects of the three mutations at the single-cell level. The genetic mutations at the tissue level induced a higher temporal vulnerability to the rotor’s initiation and progression, by sustaining spiral waves that perpetuate until the end of the simulation. The mutation with the highest pro-arrhythmic effects, exhibiting the widest sustained VW and the smallest meandering rotor’s tip areas, was KCNE3-V17M. Moreover, the increased susceptibility to arrhythmias and rotor’s stability was tissue-dependent. Pulmonary vein tissues were more prone to rotor’s initiation, while in left atrium tissues rotors were more easily sustained. Re-entries were also progressively more stable in pulmonary vein tissue, followed by the left atrium, and finally the right atrium. The presence of the genetic mutations increased the susceptibility to arrhythmias by promoting the rotor’s initiation and maintenance. The study provides useful insights into the mechanisms underlying fibrillatory events caused by KCNH2 T895M, KCNH2 T436M, and KCNE3-V17M and might aid the planning of patient-specific targeted therapies.
Read the full paper: https://www.frontiersin.org/articles/10.3389/fphys.2021.681943/full
Local Soft Tissue and Bone Displacements Following Midfacial Bipartition Distraction in Apert Syndrome - Quantification Using a Semi-Automated Method
Authors: Lara Van De Lande et al.
Patients with Apert syndrome experience midfacial hypoplasia, hypertelorism, and downslanting palpebral fissures which can be corrected by midfacial bipartition distraction with rigid external distraction device. Quantitative studies typically focus on quantifying rigid advancement and rotation postdistraction, but intrinsic shape changes of bone and soft tissue remain unknown. This study presents a method to quantify these changes. Pre- and post-operative computed tomography scans from patients with Apert syndrome undergoing midfacial bipartition distraction with rigid external distraction device were collected. Digital Imaging and Communications in Medicine files were converted to three-dimensional bone and soft tissue reconstructions. Postoperative reconstructions were aligned on the preoperative maxilla, followed by nonrigid iterative closest point transformation to determine local shape changes. Anatomical point-to-point displacements were calculated and visualized using a heatmap and arrow map. Nine patients were included.Zygomatic arches and frontal bone demonstrated the largest changes. Mid-lateral to supra-orbital rim showed an upward, inward motion. Mean bone displacements ranged from 3.3 to 12.8 mm. Soft tissue displacements were relatively smaller, with greatest changes at the lateral canthi. Midfacial bipartition distraction with rigid external distraction device results in upward, inward rotation of the orbits, upward rotation of the zygomatic arch, and relative posterior motion of the frontal bone. Local movements were successfully quantified using a novel method, which can be applied to other surgical techniques/syndromes.
Read the full paper: https://pubmed.ncbi.nlm.nih.gov/34260460/
Recent applications of quantitative systems pharmacology and machine learning models across diseases
Authors: Sara Sadat Aghamiri et al.
Quantitative systems pharmacology (QSP) is a quantitative and mechanistic platform describing the phenotypic interaction between drugs, biological networks, and disease conditions to predict optimal therapeutic response. In this meta-analysis study, we review the utility of the QSP platform in drug development and therapeutic strategies based on recent publications (2019-2021). We gathered recent original QSP models and described the diversity of their applications based on therapeutic areas, methodologies, software platforms, and functionalities. The collection and investigation of these publications can assist in providing a repository of recent QSP studies to facilitate the discovery and further reusability of QSP models. Our review shows that the largest number of QSP efforts in recent years is in Immuno-Oncology. We also addressed the benefits of integrative approaches in this field by presenting the applications of Machine Learning methods for drug discovery and QSP models. Based on this meta-analysis, we discuss the advantages and limitations of QSP models and propose fields where the QSP approach constitutes a valuable interface for more investigations to tackle complex diseases and improve drug development.
Read the full paper: https://pubmed.ncbi.nlm.nih.gov/34671863/