Possible Contexts of Use for In Silico trials methodologies: a consensus- based review

The term In Silico Trial indicates the use of computer modelling and simulation to evaluate the safety and efficacy of a medical product, whether a drug, a medical device, a diagnostic product or an advanced therapy medicinal product. Predictive models are positioned as new methodologies for the development and the regulatory evaluation of medical products. New methodologies are qualified by regulators such as FDA and EMA through formal processes, where a first step is the definition of the Context of Use (CoU), which is a concise description of how the new methodology is intended to be used in the development and regulatory assessment process. As In Silico Trials are a disruptively innovative class of new methodologies, it is important to have a list of possible CoUs highlighting potential applications for the development of the relative regulatory science. This review paper presents the result of a consensus process that took place in the InSilicoWorld Community of Practice, an online forum for experts in in silico medicine. The experts involved identified 46 descriptions of possible CoUs which were organised into a candidate taxonomy of nine CoU categories. Examples of 31 CoUs were identified in the available literature; the remaining 15 should, for now, be considered speculative

GPR61 anchoring of PKA consolidates GPCR and cAMP signaling

Scaffolding proteins organize the information flow from activated G protein-coupled receptors (GPCRs) to intracellular effector cascades both spatially and temporally. By this means, signaling scaffolds, such as A-kinase anchoring proteins (AKAPs), compartmentalize kinase activity and ensure substrate selectivity. Using a phosphoproteomics approach we identified a physical and functional connection between protein kinase A (PKA) and Gpr161 (an orphan GPCR) signaling. We show that Gpr161 functions as a selective high-affinity AKAP for type I PKA regulatory subunits (RI). Using cell-based reporters to map protein–protein interactions, we discovered that RI binds directly and selectively to a hydrophobic protein–protein interaction interface in the cytoplasmic carboxyl-terminal tail of Gpr161. Furthermore, our data demonstrate that a binary complex between Gpr161 and RI promotes the compartmentalization of Gpr161 to the plasma membrane. Moreover, we show that Gpr161, functioning as an AKAP, recruits PKA RI to primary cilia in zebrafish embryos. We also show that Gpr161 is a target of PKA phosphorylation, and that mutation of the PKA phosphorylation site affects ciliary receptor localization. Thus, we propose that Gpr161 is itself an AKAP and that the cAMP-sensing Gpr161:PKA complex acts as cilium-compartmentalized signalosome, a concept that now needs to be considered in the analyzing, interpreting, and pharmaceutical targeting of PKA-associated functions

Scientific and regulatory evaluation of mechanistic in silico drug and disease models in drug development: building model credibility

The value of in silico methods in drug development and evaluation has been demonstrated repeatedly and convincingly. While their benefits are now unanimously recognized, international standards for their evaluation, accepted by all stakeholders involved, are still to be established. In this white paper, we propose a risk-informed evaluation framework for mechanistic model credibility evaluation. To properly frame the proposed verification and validation activities, concepts such as context of use, regulatory impact and risk-based analysis are discussed. To ensure common understanding between all stakeholders, an overview is provided of relevant in silico terminology used throughout this paper. To illustrate the feasibility of the proposed approach, we have applied it to three real case examples in the context of drug development, using a credibility matrix currently being tested as a quick-start tool by regulators. Altogether, this white paper provides a practical approach to model evaluation, applicable in both scientific and regulatory evaluation contexts

The SysteMHC Atlas project.

Mass spectrometry (MS)-based immunopeptidomics investigates the repertoire of peptides presented at the cell surface by major histocompatibility complex (MHC) molecules. The broad clinical relevance of MHC-associated peptides, e.g. in precision medicine, provides a strong rationale for the large-scale generation of immunopeptidomic datasets and recent developments in MS-based peptide analysis technologies now support the generation of the required data. Importantly, the availability of diverse immunopeptidomic datasets has resulted in an increasing need to standardize, store and exchange this type of data to enable better collaborations among researchers, to advance the field more efficiently and to establish quality measures required for the meaningful comparison of datasets. Here we present the SysteMHC Atlas (https://systemhcatlas.org), a public database that aims at collecting, organizing, sharing, visualizing and exploring immunopeptidomic data generated by MS. The Atlas includes raw mass spectrometer output files collected from several laboratories around the globe, a catalog of context-specific datasets of MHC class I and class II peptides, standardized MHC allele-specific peptide spectral libraries consisting of consensus spectra calculated from repeat measurements of the same peptide sequence, and links to other proteomics and immunology databases. The SysteMHC Atlas project was created and will be further expanded using a uniform and open computational pipeline that controls the quality of peptide identifications and peptide annotations. Thus, the SysteMHC Atlas disseminates quality controlled immunopeptidomic information to the public domain and serves as a community resource toward the generation of a high-quality comprehensive map of the human immunopeptidome and the support of consistent measurement of immunopeptidomic sample cohorts

Large-scale analysis of peptide sequence variants : the case for high-field asymmetric waveform ion mobility spectrometry

[Image: see text] Large scale analysis of proteins by mass spectrometry is becoming increasingly routine; however, the presence of peptide isomers remains a significant challenge for both identification and quantitation in proteomics. Classes of isomers include sequence inversions, structural isomers, and localization variants. In many cases, liquid chromatography is inadequate for separation of peptide isomers. The resulting tandem mass spectra are composite, containing fragments from multiple precursor ions. The benefits of high-field asymmetric waveform ion mobility spectrometry (FAIMS) for proteomics have been demonstrated by a number of groups, but previously work has focused on extending proteome coverage generally. Here, we present a systematic study of the benefits of FAIMS for a key challenge in proteomics, that of peptide isomers. We have applied FAIMS to the analysis of a phosphopeptide library comprising the sequences GPSGXVpSXAQLX(K/R) and SXPFKXpSPLXFG(K/R), where X = ADEFGLSTVY. The library has defined limits enabling us to make valid conclusions regarding FAIMS performance. The library contains numerous sequence inversions and structural isomers. In addition, there are large numbers of theoretical localization variants, allowing false localization rates to be determined. The FAIMS approach is compared with reversed-phase liquid chromatography and strong cation exchange chromatography. The FAIMS approach identified 35% of the peptide library, whereas LC–MS/MS alone identified 8% and LC–MS/MS with strong cation exchange chromatography prefractionation identified 17.3% of the library

Enhanced decomposition and nitrogen mineralization sustain rapid growth of Eucalyptus regnans after wildfire

1. Eucalyptus regnans grows rapidly from seed after wildfires, out-competing other species, thereby forming pure stands of mature forests that rank amongst the world\u27s most carbon dense. By global standards, these forests grow on infertile soils. It is unclear how E. regnans is able to obtain large amounts nitrogen (N) from these infertile soils to support its rapid growth after fire. 2. We measured carbon (C) and N stored in plant biomass and photosynthetic rates of E. regnans 2 years after a wildfire and examined whether E. regnans stimulated its own N supply through rootinduced increases in microbial decomposition and N mineralization. We compared microbial biomass, gross N mineralization rates and soil C in trenched and rooted plots. 3. Photosynthetic rates of E. regnans seedlings were high and comparable to photosynthetic rates observed in fertilized crops. Presence of roots of E. regnans and allied microflora enhanced gross N mineralization more than fivefold compared to soil without roots present. Soil microbial biomass was more than doubled by root presence. The soil N pulse caused by the fire and N mineralization rates in the absence of roots were too small to account for the large amount of N stored in E. regnans 2 years after the fire. 4. Our results suggest that E. regnans facilitated its rapid growth by enhancing microbial activity and N mineralization. This enhanced microbial activity also contributed to a substantial loss of soil C (~62% of carbon gained in plant biomass was concurrently lost from soil). 5. Synthesis. At the ecosystem scale, the synergistic effects of plant growth and soil N mineralization need to be carefully assessed against costs to soil C for forests regenerating after disturbance

Data from: Enhanced decomposition and nitrogen mineralisation sustain rapid growth of Eucalyptus regnans after wildfire

Eucalyptus regnans grows rapidly from seed after wildfires, out-competing other species, thereby forming pure stands of mature forests that rank amongst the world's most carbon dense. By global standards, these forests grow on infertile soils. It is unclear how E. regnans is able to obtain large amounts nitrogen (N) from these infertile soils to support its rapid growth after fire. We measured carbon (C) and N stored in plant biomass and photosynthetic rates of E. regnans 2 years after a wildfire and examined whether E. regnans stimulated its own N supply through root-induced increases in microbial decomposition and N mineralization. We compared microbial biomass, gross N mineralization rates and soil C in trenched and rooted plots. Photosynthetic rates of E. regnans seedlings were high and comparable to photosynthetic rates observed in fertilized crops. Presence of roots of E. regnans and allied microflora enhanced gross N mineralization more than fivefold compared to soil without roots present. Soil microbial biomass was more than doubled by root presence. The soil N pulse caused by the fire and N mineralization rates in the absence of roots were too small to account for the large amount of N stored in E. regnans 2 years after the fire. Our results suggest that E. regnans facilitated its rapid growth by enhancing microbial activity and N mineralization. This enhanced microbial activity also contributed to a substantial loss of soil C (˜62% of carbon gained in plant biomass was concurrently lost from soil). Synthesis. At the ecosystem scale, the synergistic effects of plant growth and soil N mineralization need to be carefully assessed against costs to soil C for forests regenerating after disturbance

Dijkstra et al 2016

Dijkstra et al 201