Biology subjects

Kiwimagi, K.

Publications and source records attributed to Kiwimagi, K..

3 recordsLinked to original sources

bioRxiv2025

Magnetized Cellbots to Spatiotemporally Control Differentiation of Human-Induced Pluripotent Stem Cells

Precise spatiotemporal control of gene expression and cellular differentiation is essential for engineering native-like multicellular structures. Current cell differentiation approaches typically rely on externally provided inputs whose effects are not targeted to distinct cells in the appropriate state and hence cannot spatially organize and mature tissue structures as needed. Our work introduces a magnetically controlled microrobot (MR) platform for guiding mammalian cells to desired locations that, combined with synthetic biology, delivers biological signals at precise locations and times, enabling spatiotemporal control of cell-fate decision-making. We use synNotch, a cell-cell contact-based biological signaling that induces relevant gene expression in receivers when the receiver cells contact sender cells through ligand-receptor binding. Magnetically driven MRs are then allowed to be internalized by sender cells, resulting in magnetized sender cellbots. Using a 3-pair orthogonal Helmholtz coil system, we guided magnetized sender cellbots to precise locations in a receiver cell culture, activating desired fluorescent protein expression in target Chinese Hamster Ovary (CHO) receiver cells. Next, we engineered Human-Induced Pluripotent Stem Cells (hiPSC) to function as receivers that can be instructed by senders to differentiate into endothelial cells (ECs) via overexpression of ETV2 (ETS variant transcription factor 2), a master transcriptional regulator of endothelial cell development. Using our magnetic platform, we guided multiple sender cellbots to target locations on a monolayer of hiPSC receivers, resulting in differentiation of receivers into ECs and possible onset of vascular formation. Our approach provides a foundation for the engineering spatial patterns by activating conditional triggers based on MR location and cell state at multiple time points, enabling several applications such as control of organoid architecture.

synthetic biology↗

bioRxiv2024

A Genetic Toggle Switch in Plants

In synthetic biology, genetic components are assembled to make transcriptional units, and transcriptional units are assembled into circuits to perform specific and predictable functions of a genetic device. Genetic devices have been described in bacteria, mammalian cell cultures and small organoids, yet development of programmable genetic circuits for devices in plants has lagged. Programmable genetic devices require defining the components quantitative functions. Because plants have long life spans, studies often use transient analysis to define quantitative functions while verification in stably engineered plants is often neglected and largely unknown. This raises a question if unique attributes of plants such as environmental sensitivity, developmental plasticity, or alternation of generations, adversely impacts predictability of plant genetic circuits and devices. Alternatively, it is also possible that genetic elements to produce predictable genetic devices for plants require rigorous characterization with detailed mathematical modeling. Here we use plant genetic elements with quantitatively characterized transfer functions and developed in silico models to guide their assembly into a genetic device: a toggle switch or a mutually inhibitory gene-regulatory device. Our approach allows computational selection of plant genetic components and iterative refinement of the circuit if the desired genetic functions are not initially achieved. We show that our computationally selected genetic circuit functions as predicted in stably engineered plants including through tissue and organ differentiation. Developing abilities to produce predictable and programmable plant genetic devices opens the prospect of predictably engineering plants unique abilities in sustainable human and environmental systems.

synthetic biology↗

bioRxiv2024

The restricted N-glycome of neurons is programmed during differentiation

The protein glycome of individual cell types in the brain is unexplored, despite the critical function of these modifications in development and disease. In aggregate, the most abundant asparagine (N-) linked glycans in the adult brain are high mannose structures, and specifically Man5GlcNAc2 (Man-5), which normally exits the ER for further processing in the Golgi. Mannose structures are uncommon in other organs and often overlooked or excluded in most studies. To understand cell-specific contributions to the unique brain N-glycome and its abundance of Man-5, we performed RNAseq and MALDI-MS TOF protein N-glycomics at several timepoints during differentiation of multiple cell types. To this end, homogeneous cultures of glutamatergic neurons, GABAergic neurons, and brain-specific endothelial cells were generated from monoclonal human inducible pluripotent stem cells (hiPSCs) through cellular reprogramming. Small molecule induction of stably integrated synthetic transcription units driving morphogen expression generated differentiated cells with distinct patterns mirroring intact tissue. Comparing uninduced hiPSCs for each cell type revealed identical transcriptomic and glycomic profiles before differentiation, with low quantities of Man-5. In differentiated glutamatergic and GABAergic neurons, the most abundant N-glycans became Man-5 and its immediate precursor Man-6, despite the presence of transcripts encoding enzymes for their subsequent modification. Differentiation to brain-specific endothelial cells showed an opposite effect, with the N-glycome displaying an abundance of complex N-glycans and terminal modifications of the late secretory pathway. These results confirm that the restricted N-glycome profile of brain is programmed into neuronal differentiation, with regulation independent of the transcriptome and under tight evolutionary constraint.

neuroscience↗