Xenobot Transcriptomics: Gene Expression Changes in wild-type cells forming a synthetic biobot

The standard paradigm of developmental and synthetic biology focuses on changes in morphology driven by gene expression. Here, we investigated the reverse relationship: would transcriptomes change if cell collectives acquired a novel morphogenetic and behavioral phenotype in the absence of genomic editing, transgenes, heterologous materials, or drugs? We investigated the effects of morphology and nascent emergent life history on gene expression in Xenobots – motile, autonomous constructs that self-assemble from frog embryo epidermal progenitor cells. We compared transcriptomes of Xenobots with age-matched frog embryos, identifying at least 537 transcripts uniquely upregulated in the Xenobots. Pathway analyses indicated shifts in the categories of motility machinery, pattern formation and multicellularity, stress and immune response, metabolism, and sensory perception of sound and mechanical stimuli. Phylostratigraphic analysis showed that the majority of these shifts in Xenobots were towards evolutionarily ancient transcripts and systems. Lastly, we found enrichment of thanatotranscriptomic genes, shedding light on the distinction between death of an organism and that of its cells. These data on the relationship between genotype and phenotype may have implications for evolution, biomedicine, and synthetic morphoengineering. Overall design: Comparative gene expression profiling analysis of RNA-seq data for Xenobots and age-matched Xenopus embryos. Xenobots and age-matched Xenopus embryo samples are in triplicates