This report documents the outcomes of the EFSA procurement (OC/EFSA/NIF/2022/01) aimed at identifying in vitro toxicity testing approaches for (novel) proteins in the context of food and feed safety assessment. In the present report, we present an integrated testing strategy for the evaluation of toxicity of novel/toxic proteins. A text‐mining approach was used to create a literature database of toxic outcomes associated with toxic proteins retrieved from the UniProt KB database using the search term “Toxin activity”. It was shown that toxic proteins are produced by a relatively limited phylogenetic subset, including, among others, bacteria, insects, serpents, molluscs, and fungi. Toxicological effects of these proteins are generally conserved within phylogenetic groups. Analysis of toxic effects from these proteins was performed using GO term analysis as well as a text‐mining based approach. Relevant tests to address and quantify these toxicity effects were identified and evaluated for their applicability in an in vitro based toxicity testing strategy. A stepwise approach was developed. As a first step, an initial in silico prediction of toxicity is carried out (Step 1). This is followed by a battery of in vitro assays to address the primary mechanisms of toxicity associated with toxic proteins (Step 2). If concern arises in the Step 2 battery of tests, the use of relevant in vitro model systems to explore potential target organ toxicity are required (Step 3). Knowledge gaps have been identified and recommendations are provided in in vitro toxicity testing strategies, in particular for (novel) proteins. Some of these gaps involve the selection and integration of a standardized, relevant in vitro digestion step, reflective of passage through the digestive tract, within the testing strategy, as well as a thorough assessment of the suitability and applicability of in vitro tests and new approach methodologies for regulatory toxicity assessment of (novel) proteins. To accelerate the incorporation of NAMs in the assessment of protein safety, case studies and proof of concept projects are needed to demonstrate the utility and effectiveness of in vitro toxicity testing strategies in the safety assessment of (novel) proteins.
