title: Crowd-Sourced Verification of Computational Methods and Data in Systems Toxicology: A Case Study with a Heat-Not-Burn Candidate Modified Risk Tobacco Product.
abstract: Systems toxicology intends to quantify the effect of toxic molecules in biological systems and unravel their mechanisms of toxicity. The development of advanced computational methods is required for analyzing and integrating high throughput data generated for this purpose as well as for extrapolating predictive toxicological outcomes and risk estimates. To ensure the performance and reliability of the methods and verify conclusions from systems toxicology data analysis, it is important to conduct unbiased evaluations by independent third parties. As a case study, we report here the results of an independent verification of methods and data in systems toxicology by crowdsourcing. The sbv IMPROVER systems toxicology computational challenge aimed to evaluate computational methods for the development of blood-based gene expression signature classification models with the ability to predict smoking exposure status. Participants created/trained models on blood gene expression data sets including smokers/mice exposed to 3R4F (a reference cigarette) or noncurrent smokers/Sham (mice exposed to air). Participants applied their models on unseen data to predict whether subjects classify closer to smoke-exposed or nonsmoke exposed groups. The data sets also included data from subjects that had been exposed to potential modified risk tobacco products (MRTPs) or that had switched to a MRTP after exposure to conventional cigarette smoke. The scoring of anonymized participants' predictions was done using predefined metrics. The top 3 performers' methods predicted class labels with area under the precision recall scores above 0.9. Furthermore, although various computational approaches were used, the crowd's results confirmed our own data analysis outcomes with regards to the classification of MRTP-related samples. Mice exposed directly to a MRTP were classified closer to the Sham group. After switching to a MRTP, the confidence that subjects belonged to the smoke-exposed group decreased significantly. Smoking exposure gene signatures that contributed to the group separation included a core set of genes highly consistent across teams such as AHRR, LRRN3, SASH1, and P2RY6. In conclusion, crowdsourcing constitutes a pertinent approach, in complement to the classical peer review process, to independently and unbiasedly verify computational methods and data for risk assessment using systems toxicology.
authors.affiliation: PMI R&D, Philip Morris Products S.A. , Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland (Part of Philip Morris International group of companies).
authors.forename: Carine
authors.identifier: 0000-0001-9729-6853
authors.initials: C
authors.lastname: Poussin
authors.affiliation: PMI R&D, Philip Morris Products S.A. , Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland (Part of Philip Morris International group of companies).
authors.forename: Vincenzo
authors.initials: V
authors.lastname: Belcastro
authors.affiliation: PMI R&D, Philip Morris Products S.A. , Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland (Part of Philip Morris International group of companies).
authors.forename: Florian
authors.initials: F
authors.lastname: Martin
authors.affiliation: PMI R&D, Philip Morris Products S.A. , Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland (Part of Philip Morris International group of companies).
authors.forename: Stéphanie
authors.initials: S
authors.lastname: Boué
authors.affiliation: PMI R&D, Philip Morris Products S.A. , Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland (Part of Philip Morris International group of companies).
authors.forename: Manuel C
authors.initials: MC
authors.lastname: Peitsch
authors.affiliation: PMI R&D, Philip Morris Products S.A. , Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland (Part of Philip Morris International group of companies).
authors.forename: Julia
authors.initials: J
authors.lastname: Hoeng
mesh_terms: D000818:Animals; D015415:Biomarkers / Q000097:blood; D063045:Crowdsourcing; D006358:Hot Temperature; D006801:Humans; D008562:Membrane Glycoproteins; D008565:Membrane Proteins / Q000097:blood; D051379:Mice; D008962:Models, Theoretical; D009363:Neoplasm Proteins / Q000097:blood; D018336:Receptors, Aryl Hydrocarbon / Q000097:blood; D018048:Receptors, Purinergic P2 / Q000097:blood; D012306:Risk; D012907:Smoking; D059467:Transcriptome / Q000187:drug effects*; D025521:Tumor Suppressor Proteins / Q000097:blood; D014026:Nicotiana
chemical_list: D015415:Biomarkers; C494422:LRRN3 protein, human; D008562:Membrane Glycoproteins; D008565:Membrane Proteins; D009363:Neoplasm Proteins; D018336:Receptors, Aryl Hydrocarbon; D018048:Receptors, Purinergic P2; C474743:SASH1 protein, human; D025521:Tumor Suppressor Proteins