Discrete-to-analog signal conversion in human pluripotent stem cells

Prochazka, L.; Zandstra, P. W.; Michaels, Y. S.; Lau, C.; Siu, M.; Yin, T.; Wu, D.; Jang, E.; Jones, R. D.; Vazquez-Cantu, M.; Gilbert, P. M.; Kaul, H.; Benenson, Y.

doi:10.1101/2021.11.05.467377

bioRxiv · 10.1101/2021.11.05.467377

Discrete-to-analog signal conversion in human pluripotent stem cells

Prochazka, L.·Zandstra, P. W.·Michaels, Y. S.·Lau, C.·Siu, M.·Yin, T.·Wu, D.·Jang, E.·Jones, R. D.·Vazquez-Cantu, M.·Gilbert, P. M.·Kaul, H.·Benenson, Y.

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Abstract

During development, state transitions are coordinated through changes in the identity of molecular regulators in a cell state- and dose specific manner. The ability to rationally engineer such functions in human pluripotent stem cells (hPSC) will enable numerous applications in regenerative medicine. Herein we report the generation of synthetic gene circuits that can detect a discrete cell state, and upon state detection, produce fine-tuned effector proteins in a programmable manner. Effectively, these gene circuits convert a discrete (digital-like) cell state into an analog signal by merging AND-like logic integration of endogenous miRNAs (classifiers) with a miRNA-mediated output fine-tuning technology (miSFITs). Using an automated miRNA identification and model-guided circuit optimization approach, we were able to produce robust cell state specific and graded output production in undifferentiated hPSC. We further finely controlled the levels of endogenous BMP4 secretion, which allowed us to document the effect of endogenous factor secretion in comparison to exogenous factor addition on early tissue development using the hPSC-derived gastruloid system. Our work provides the first demonstration of a discrete-to-analog signal conversion circuit operating in living hPSC, and a platform for customized cell state-specific control of desired physiological factors, laying the foundation for programming cell compositions in hPSC-derived tissues and beyond. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=141 SRC="FIGDIR/small/467377v2_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@150da71org.highwire.dtl.DTLVardef@135554borg.highwire.dtl.DTLVardef@72b5b3org.highwire.dtl.DTLVardef@f70f84_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Prochazka, L., Zandstra, P. W., Michaels, Y. S., Lau, C., Siu, M., Yin, T., Wu, D., Jang, E., Jones, R. D., Vazquez-Cantu, M., Gilbert, P. M., Kaul, H., Benenson, Y.. 2021-11-06. Discrete-to-analog signal conversion in human pluripotent stem cells. https://doi.org/10.1101/2021.11.05.467377

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