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

The standard paradigm of developmental and synthetic biology focuses on gene expression driving changes in morphology. 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 the basal (no engineering, no sculpting) form of Xenobots – autonomously motile constructs derived from Xenopus embryo ectodermal cell explants. We compared transcriptomes of these Xenobots with age-matched Xenopus embryos. These Xenobots showed significantly larger inter-individual gene variability than age-matched embryos, suggesting increased exploration of the transcriptional space. We identified at least 537 (non-epidermal) transcripts uniquely upregulated in these 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 transcriptomic shifts in these 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.