Interpretable deep learning reveals the role of an E-box motif in suppressing somatic hypermutation of AGCT motifs within human immunoglobulin variable regions.

Introduction: Somatic hypermutation (SHM) of immunoglobulin variable (V) regions by activation induced deaminase (AID) is essential for robust, long-term humoral immunity against pathogen and vaccine antigens. AID mutates cytosines preferentially within WRCH motifs (where W=A or T, R=A or G and H=A, C or T). However, it has been consistently observed that the mutability of WRCH motifs varies substantially, with large variations in mutation frequency even between multiple occurrences of the same motif within a single V region. This has led to the notion that the immediate sequence context of WRCH motifs contributes to mutability. Recent studies have highlighted the potential role of local DNA sequence features in promoting mutagenesis of AGCT, a commonly mutated WRCH motif. Intriguingly, AGCT motifs closer to 5' ends of V regions, within the framework 1 (FW1) sub-region1, mutate less frequently, suggesting an SHM-suppressing sequence context. Methods: Here, we systematically examined the basis of AGCT positional biases in human SHM datasets with DeepSHM, a machine-learning model designed to predict SHM patterns. This was combined with integrated gradients, an interpretability method, to interrogate the basis of DeepSHM predictions. Results: DeepSHM predicted the observed positional differences in mutation frequencies at AGCT motifs with high accuracy. For the conserved, lowly mutating AGCT motifs in FW1, integrated gradients predicted a large negative contribution of 5'C and 3'G flanking residues, suggesting that a CAGCTG context in this location was suppressive for SHM. CAGCTG is the recognition motif for E-box transcription factors, including E2A, which has been implicated in SHM. Indeed, we found a strong, inverse relationship between E-box motif fidelity and mutation frequency. Moreover, E2A was found to associate with the V region locale in two human B cell lines. Finally, analysis of human SHM datasets revealed that naturally occurring mutations in the 3'G flanking residues, which effectively ablate the E-box motif, were associated with a significantly increased rate of AGCT mutation. Discussion: Our results suggest an antagonistic relationship between mutation frequency and the binding of E-box factors like E2A at specific AGCT motif contexts and, therefore, highlight a new, suppressive mechanism regulating local SHM patterns in human V regions.

A Time-Embedding Network Models the Ontogeny of 23 Hepatic Drug Metabolizing Enzymes.

Pediatric patients are at elevated risk of adverse drug reactions, and there is insufficient information on drug safety in children. Complicating risk assessment in children, there are numerous age-dependent changes in the absorption, distribution, metabolism, and elimination of drugs. A key contributor to age-dependent drug toxicity risk is the ontogeny of drug metabolism enzymes, the changes in both abundance and type throughout development from the fetal period through adulthood. Critically, these changes affect not only the overall clearance of drugs but also exposure to individual metabolites. In this study, we introduce time-embedding neural networks in order to model population-level variation in metabolism enzyme expression as a function of age. We use a time-embedding network to model the ontogeny of 23 drug metabolism enzymes. The time-embedding network recapitulates known demographic factors impacting 3A5 expression. The time-embedding network also effectively models the nonlinear dynamics of 2D6 expression, enabling a better fit to clinical data than prior work. In contrast, a standard neural network fails to model these features of 3A5 and 2D6 expression. Finally, we combine the time-embedding model of ontogeny with additional information to estimate age-dependent changes in reactive metabolite exposure. This simple approach identifies age-dependent changes in exposure to valproic acid and dextromethorphan metabolites and suggests potential mechanisms of valproic acid toxicity. This approach may help researchers evaluate the risk of drug toxicity in pediatric populations.