Synthetic biology and metabolic engineering have expanded the possibilities for engineered cell-based systems. The addition of non-native biosynthetic and regulatory components can, however, overburden the reprogrammed cells. In order to avoid metabolic overload, an emerging area of focus is on engineering consortia, wherein cell subpopulations work together to carry out a desired function. This strategy requires regulation of the cell populations. Here, we design a synthetic co-culture controller consisting of cell-based signal translator and growth-controller modules that, when implemented, provide for autonomous regulation of the consortia composition. The system co-opts the orthogonal autoinducer AI-1 and AI-2 cell-cell signaling mechanisms of bacterial quorum sensing (QS) to enable cross-talk between strains and a QS signal-controlled growth rate controller to modulate relative population densities. We further develop a simple mathematical model that enables cell and system design for autonomous closed-loop control of population trajectories.

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The epigenetic landscape and the responses to pharmacological epigenetic regulators in each human are unique. Classes of epigenetic writers and erasers, such as histone acetyltransferases, HATs, and histone deacetylases, HDACs, control DNA acetylation/deacetylation and chromatin accessibility, thus exerting transcriptional control in a tissue- and person-specific manner. Rapid development of novel pharmacological agents in clinical testing—HDAC inhibitors (HDACi)—targets these master regulators as common means of therapeutic intervention in cancer and immune diseases. The action of these epigenetic modulators is much less explored for cardiac tissue, yet all new drugs need to be tested for cardiotoxicity. To advance our understanding of chromatin regulation in the heart, and specifically how modulation of DNA acetylation state may affect functional electrophysiological responses, human-induced pluripotent stem-cell-derived cardiomyocyte (hiPSC-CM) technology can be leveraged as a scalable, high-throughput platform with ability to provide patient-specific insights. This review covers relevant background on the known roles of HATs and HDACs in the heart, the current state of HDACi development, applications, and any adverse cardiac events; it also summarizes relevant differential gene expression data for the adult human heart vs. hiPSC-CMs along with initial transcriptional and functional results from using this new experimental platform to yield insights on epigenetic control of the heart. We focus on the multitude of methodologies and workflows needed to quantify responses to HDACis in hiPSC-CMs. This overview can help highlight the power and the limitations of hiPSC-CMs as a scalable experimental model in capturing epigenetic responses relevant to the human heart.

AbstractWe developed a bidirectional bioelectronic communication system that is enabled by a redox signal transduction modality to exchange information between a living cell-embedded bioelectronics interface and an engineered microbial network. A naturally communicating three-member microbial network is “plugged into” an external electronic system that interrogates and controls biological function in real time. First, electrode-generated redox molecules are programmed to activate gene expression in an engineered population of electrode-attached bacterial cells. These cells interpret and translate electronic signals and then transmit this information biologically by producing quorum sensing molecules that are, in turn, interpreted by a planktonic co-culture. The propagated molecular communication drives expression and secretion of a therapeutic peptide from one strain and, simultaneously, enables direct electronic feedback from the second strain thus enabling real time electronic verification of biological signal propagation. Overall, we show how this multi-functional bioelectronic platform, termed BioLAN, reliably facilitates on-demand bioelectronic communication and concurrently performs programmed tasks.

Epigenetic regulation is critical for cardiac electrophysiology and pathology. Epigenetic modulators, such as histone deacetylases (HDACs) and histone acetyltransferases (HATs) are known master regulators of gene expression. Recently, novel pharmacological agents, HDAC inhibitors, have been developed as treatments for cancer and immune diseases. The effects of HDAC inhibitors on cardiac ion channels (ICs) are of great interest. To exert specific gene modulation, we used small interfering RNAs against the known HDACs, including sirtuins, and deployed them in human induced pluripotent stem-cell-derived cardiomyocytes (hiPSC-CMs). Follow-up RNAseq data (n = 61) were compared to identically processed and normalized RNAseq data from human left ventricle (LV) from the GTEx database (n = 84). Gene expression of cardiac ICs displayed similar patterns, with some differences. For example, hiPSC-CMs showed upregulated CACNA1C, SLC8A1 and downregulated KCNJ2 and RYR2 compared to the adult LV, most of which are known distinctions (Fig. 1A). Correlative analysis (Fig. 1B) and partial least square regression models helped visualize links between HDACs/HATs, key transcription factors (TFs) and cardiac ICs. Powerful TFs, including MEF2A, GATA4, 6 exerted positive effect on ICs in hiPSC-CM and the adult LV. In the hiPSC-CMs, HDAC1, HDAC10 and SIRT6 were found to be the strongest predictors of the expression of individual cardiac ICs, as revealed by permutation importance. Further studies will involve determination of the role of different cell types using single-cell sequencing data from the adult LV. Our analysis offers new insights about the role of epigenetic modifiers on cardiac electrophysiology and informs the utility of hiPSC-CM as a scalable, experimental model for cardiotoxicity testing of HDAC inhibitors.