Reinforcement learning-guided control strategies for CAR T-cell activation and expansion.

Reinforcement learning (RL), a subset of machine learning (ML), could optimize and control biomanufacturing processes, such as improved production of therapeutic cells. Here, the process of CAR T-cell activation by antigen-presenting beads and their subsequent expansion is formulated in silico. The simulation is used as an environment to train RL-agents to dynamically control the number of beads in culture to maximize the population of robust effector cells at the end of the culture. We make periodic decisions of incremental bead addition or complete removal. The simulation is designed to operate in OpenAI Gym, enabling testing of different environments, cell types, RL-agent algorithms, and state inputs to the RL-agent. RL-agent training is demonstrated with three different algorithms (PPO, A2C, and DQN), each sampling three different state input types (tabular, image, mixed); PPO-tabular performs best for this simulation environment. Using this approach, training of the RL-agent on different cell types is demonstrated, resulting in unique control strategies for each type. Sensitivity to input-noise (sensor performance), number of control step interventions, and advantages of pre-trained RL-agents are also evaluated. Therefore, we present an RL framework to maximize the population of robust effector cells in CAR T-cell therapy production.

Effects of Sequence Features on Machine-Learned Enzyme Classification Fidelity.

Assigning enzyme commission (EC) numbers using sequence information alone has been the subject of recent classification algorithms where statistics, homology and machine-learning based methods are used. This work benchmarks performance of a few of these algorithms as a function of sequence features such as chain length and amino acid composition (AAC). This enables determination of optimal classification windows for de novo sequence generation and enzyme design. In this work we developed a parallelization workflow which efficiently processes >500,000 annotated sequences through each candidate algorithm and a visualization workflow to observe the performance of the classifier over changing enzyme length, main EC class and AAC. We applied these workflows to the entire SwissProt database to date (n = 565245) using two, locally installable classifiers, ECpred and DeepEC, and collecting results from two other webserver-based tools, Deepre and BENZ-ws. It is observed that all the classifiers exhibit peak performance in the range of 300 to 500 amino acids in length. In terms of main EC class, classifiers were most accurate at predicting translocases (EC-6) and were least accurate in determining hydrolases (EC-3) and oxidoreductases (EC-1). We also identified AAC ranges that are most common in the annotated enzymes and found that all classifiers work best in this common range. Among the four classifiers, ECpred showed the best consistency in changing feature space. These workflows can be used to benchmark new algorithms as they are developed and find optimum design spaces for the generation of new, synthetic enzymes.

Optimization of E. Coli Tip-Sonication for High-Yield Cell-Free Extract using Finite Element Modeling.

Optimal tip sonication settings, namely tip position, input power, and pulse durations, are necessary for temperature sensitive procedures like preparation of viable cell extract. In this paper, the optimum tip immersion depth (20-30% height below the liquid surface) is estimated which ensures maximum mixing thereby enhancing thermal dissipation of local cavitation hotspots. A finite element (FE) heat transfer model is presented, validated experimentally with (R2 > 97%) and used to observe the effect of temperature rise on cell extract performance of E. coli BL21 DE3 star strain and estimate the temperature threshold. Relative yields in the top 10% are observed for solution temperatures maintained below 32°C; this reduces below 50% relative yield at temperatures above 47°C. A generalized workflow for direct simulation using the COMSOL code as well as master plots for estimation of sonication parameters (power input and pulse settings) is also presented.