Faculty Investigator: Stas Shvartsman (Princeton)

Topic: Organoids

Contributing Trainees: Rocky Diegmiller, Caroline Doherty

The overarching goal of our work is to understand collective dynamics in clusters of cells joined by stable cytoplasmic bridges, which are critical for the growth of transcriptionally quiescent oocytes in multiple organisms. Fundamental studies and medical research motivated by human fertility defects continue to reveal molecular and cellular features of the germline cell clusters (cysts), but our understanding of the mechanisms essential for the ultimate success of their development is rudimentary at best. Capitalizing on the highly conserved nature of germline development, we are using Drosophila as a system amenable to highly integrated combination of genetic and imaging experiments and theory to establish predictive computational models accounting for multiple stages of germline development, from the first divisions of a single germline stem cell, to collective dynamics within growing cysts and their interactions with supporting soma.

Faculty Investigator: Ron Weiss (MIT)

Topic: Organoids

Contributing Trainee(s) and corresponding trainee projects: 

Graduate students:  Sebastian Palacios – “RNAi-based logic circuit engineering in hiPSCs,” Farimah Mapar – “Engineering of a neuronal toggle switch”. Postdoctoral researchers: Erez Pery – “3D Liver organoid formation and maturation,” Elvira Vitu – “Embedded synthetic biology for multistep organoid differentiation.”

Current technology for organoid and tissue engineering generally involves exposing a population of hiPSCs to chemical, mechanical or molecular signals that cause a response in the endogenous gene regulatory networks that control tissue formation. In many cases, these signals are the same that are observed during embryogenesis. Although appropriate in many cases to study development, this approach can exhibit significant challenges with reproducibility, control of cell fate, maturation, and custom tissue design. We develop engineering tools to precisely probe and control tissue formation. We focus on using the principles of synthetic biology to engineer synthetic gene regulatory networks that can precisely control tissue formation and the emergence of multicellular phenotypes. We develop these tools within a computational and engineering framework in the context of practical applications for Multi-Cellular Engineered Living Systems (M-CELS).

Figure 1. Biological devices for sensing and computation based on RNAi-based. (A) CRISPR/Cas9 technology was used to knockin an RMCE landing pad in the AAVS1 locus of hiPSCs. Engineered miRNA sensors were subsequently integrated into the landing pad. FACS data shows that the engineered miRNA sensor in AAVS1 locus can detect a miRNA that is transiently delivered into the cells. (B) Cells before transient delivery of the miRNA, and (C) three days after transient delivery of the miRNA. (D) hiPSCs with stable integration of miRNA sensors for miRNA FF4 and endogenous miRNA 25-3p, which is highly active in hiPCS. 

Faculty Investigator: Taher Saif (UIUC)

Topic: Biomachines (Motile Bots, Pump-bots), MPS (Neuron-Muscle)

Contributing Trainee(s) and corresponding trainee projects: Onur Aydin (Motile Bots, Neuron-Muscle), Zhengwei Li (Pump-bots).

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This is the first prototype of a bio-hybrid swimmer where a group of neurons innervate a band of muscle wrapping around two tails of the swimmer. The neurons fire collectively and synchronously. As a result, the tails bend like flagella and the swimmer can swim. Such biological machines may one day be used for intelligent drug delivery, environmental cleaning, and for sensing. 


O. Aydin, X. Zhang, S. Nuethong, G.J. Pagan-Diaz, R. Bashir, M. Gazzola, and M.T.A. Saif (2019). Neuromuscular actuation of biohybrid motile bots. PNAS, 116(40), 19841-19847.

Faculty Investigator: Kara McCloskey (UC Merced)

Topic: MPS

Contributing Trainee(s) and corresponding trainee projects: Nicole Madfis – Co-emergence of Endothelial Subphenotypes (graduated summer, 2018); Lian Wong –Microfluidic platforms for generating microvasculature and Role of Mechanical Forces in Endothelial Cell Fate from human ESC and iPS cells (graduated fall, 2018); Rachel Hatano – Towards integration of functional muscle with endothelial cells/vasculature (graduated summer, 2019); Edwin Shen – Modular 3D Bioprinting, Directing smooth muscle cells and pericytes from human ESC and iPS cells; Jose Zamora – Modeling Vascular Cell Fate.

Collaboration between Kara McCloskey and Yuhong Fan studying co-emergence of vascular smooth muscle and endothelial cells from a common progenitor cell. This data specifically examined the role of material stiffness in directing the fate of vascular progenitor cells. High stiffness hydrogels direct more smooth muscle cells while low stiffness hydrogels direct more cells towards the endothelial fate [2].

Faculty Investigator: Roger Kamm (MIT)

Topic: MPS

Contributing Trainee(s) and corresponding trainee projects: Tatsuya Osaki, Jean Carlos Serrano, Kristina Haase, Giovanni Offeddu, Yoojin Shin, Clare Ko

Microphysiological systems, or MPS, act as miniaturized versions of a human organ, and can be derived from induced pluripotent stem cells (iPSCs) obtained from a specific patient.  They enable development of models of disease that can be used for testing new drugs, or precision medicine applications by producing a model of the disease in a given patient.  Our EBICS research is addressing these needs through creating MPS for the central nervous system that include both cells of the brain tissue (neurons, astrocytes) and those comprising the brain vasculature.  By combining these different cell types within a single MPS, we have generated models for amyotrophic lateral sclerosis (ALS), Alzheimer’s disease, and the pathway for drugs entering into the brain from the vascular system.  In the ALS model, patient-derived cells from healthy donors and ALS patients were used to create a model of a neuromuscular junction that recreates the activation of a muscle strip by motor neurons.  The value of the model was demonstrated by showing differences between healthy and ALS cells in the ability of the muscle to generate force upon activation by the motor neurons, then showing that the functional benefits of two new drugs under development can be recapitulated in the model.

For drugs of this type to be effective, however, they must be capable of passing from the blood across the blood-brain barrier (BBB) into the tissue of the brain or nervous system.  To study transport across the BBB we developed a different MPS based entirely on human cells, including iPSC-derived vascular endothelial cells, pericytes, and astrocytes.  We demonstrated how, over time, the endothelial cells took on characteristics of the cells found in the brain, showing increased expression of junctional proteins that comprise the barrier, and transporter proteins that enable trancytosis (transport through the endothelial barrier cells) of substances that the brain requires.  This model and the results obtained from it will help us to identify ways in which we can ‘hijack’ these transporters to deliver new drugs for the treatment of ALS or other neurological diseases.

Figure Caption: Motor neurons on the left send out neurites (green) and connect with a strip of skeletal muscle (red) on the right. 

Faculty Investigator: Paula Hammond (MIT), Linda Griffith (MIT)

Topic: MPS

Microvascular Network Working Group (A Modular Polymer Microbead Angiogenesis Scaffold for Vascularizing Dense Epithelial Tissue, Synthetic Helical Modular Polypeptide Hydrogels for 3D Cell Culture)

Contributing Trainee(s) and corresponding trainee projects: Marianna Sofman

Proteoglycans are a broad, important class of biomacromolecules whose applications have been limited by the poor reproducibility of isolation from natural sources. Synthetic proteoglycans that capture generic compositional and biophysical features of the native counterparts offer a potential alternative as a reproducible and scalable source of proteoglycans, though many synthetic systems lack biological activity. We have developed a method to synthesize polypeptide-hyaluronic acid conjugates of various architectures that more closely mimic the composition of native proteoglycans. These conjugates exhibit biological activity distinct from constituent hyaluronic acid molecules. Furthermore, we have demonstrated an application of these conjugates in three-dimensional (3D) endothelial network formation.

Faculty Investigator: Linda Griffith (MIT)

Topic: Organoids & MPS

Contributing Trainee(s) and corresponding trainee projects: Alex Brown (MIT) – Engineering Synthetic Microenvironments for Vascularization and Organoid Morphogenesis, Marianna Sofmann (MIT) , joint with Paula Hammond– A facile approach to vascularization in dense tissue with microbeads (see Hammond Report), Alex Wang (MIT) – Biomaterials for morphogenesis of liver tissue

The primary focus of the Griffith Lab research in EBICS is design-based synthesis of synthetic biomaterials micro-environments for controlling tissue morphogenesis: vascularization, organoid growth, creation of complex mucosal barriers by morphogenesis approaches; these approaches are coupled with design of devices to control the fluidic microenvironment.  We have developed design principles for synthetic matrices that involve key properties as illustrated on the axes shown in the schematic below. The Figure shows human primary endometrial epithelial glands (stained green with EpCAM, an epithelial marker) forming by fusion of organoids and outgrowth along the synthetic matrix surface; stromal cells (red, vimentin) emerge over time.

Faculty Investigator: Laurie Boyer (MIT)

Topic: Organoids

Image of human cardiac muscle cell visualizing the complex sarcomere organization and actin cytoskeleton. 

Contributing Trainee(s) and corresponding trainee projects: Vera Koledova: “Generation and application of hiPSCs with genetically encoded voltage sensors and tissue specific markers for analysis of emergent behavior in cardiac organoid models.” and “Determining the impact of microvascular networks on cardiac muscle cell behavior.” Vera will also focus efforts on continuing our previous collaboration with the Kamm lab on this project over the next year.

The Boyer lab at MIT works on learning how cells translate signaling cues into specific cellular behaviors in the context of multi-cellular systems. Human induced pluripotent stem cells (hiPSCs) are a powerful model for understanding the molecular basis of cell fate determination. Current approaches have employed the differentiation of hiPSCs to specific cell types to study cell behavior; however, this single cell systems are limited in their ability to model the multi-cellularity of typical organ systems.

Moreover, the lack of quantitative tools has limited our ability to measure emergent behaviors in the context of cell-based systems. Using cardiac muscle cells as a model, we are developing innovative approaches for quantifying how cell-cell interactions and mechanical cues impact cell state in cell clusters that include cardiac muscle cells, microvascular networks, and ultimately neurons. Our exacting tools will allow us to measure the dynamics of cell behavior as they emerge in real time. We expect that these studies can be used to improve the ability to differentiate human iPSCs into mature multi-cellular heart tissue that will serve as a better model for pharmacology and regenerative therapy, and to discover fundamental principles that can be broadly applied to improve stem cell based regenerative therapies. 

Faculty Investigator: Todd C. McDevitt (Gladstone)

Topic: Organoids

Contributing Trainee(s) and corresponding trainee projects: Ashley Libby (Ph.D. graduate student): “Regulation of Patterning, Morphogenesis & Lineage Fate Decisions in hPSCs”

David Joy (Ph.D. graduate student): “Tracking Collective Cell Motion in hPSC Morphogenesis”

Ivana Vasic (Ph.D. graduate student): “Examining the Role of Apical/Basolateral Polarity in Directing hPSC Fate.”

Faculty Investigator: Hang Lu (GT)

Topic: Organoids

Contributing Trainee(s) and corresponding trainee projects: Emily Jackson-Holmes, Seleipiri Charles

The Lu lab is interested in developing techniques based on microfluidics and quantitative microscopy for organoid culture to study development and model diseases.  By using microfluidics, the organoid culture is more likely to be better controlled; further, microfluidics also has the ability to deliver reagents at will and the ability to accommodate different modalities of imaging, which greatly enhances the quality and the temporal and spatial resolution of the data gathered about the organoids. 

Faculty Investigator: Rashid Bashir (UIUC)

Topic: Biomachines

Contributing Trainee(s) and corresponding trainee projects: Lauren Grant: Engineering Connexins in Skeletal Muscle Cells; Gelson Pagan-Diaz: Forward Design and Modulation of Neural Tissue Using Optogenetics; Jiao Jiao Wang: Higher Order Designs for Muscle Based Biobots

Research Description: Our research aims to forward design soft polymeric biological machines that are driven and controlled by cells. Muscle cells are used to propel and power the devices, and neuron cells are used to sense and compute. The machines could self-heal, self-organize, and learn. We expect these devices and machines would someday have many applications in biology, engineering, medicine, sustainability, and agriculture. 

Faculty Investigator: Harry Asada (MIT)

Topic: Biomachines

Computational modeling of multicellular interactions in viscoelastic ECM

Contributing Trainee(s) and corresponding trainee projects: Min-Cheol Kim

Publications: Mayalu MN, Kim M, Asada HH. Multi-Cell ECM compaction is predictable via superposition of nonlinear cell dynamics linearized in augmented state space. https://plos.io/2kyhRm7  

Social Media: https://twitter.com/PLOSCompBiol/status/1177655393570476039

The left figure indicates a block diagram of latent variable superposition model of multiple cells and extracellular matrix (ECM), and the right figure indicates a simulated result of gel compaction through the latent variable superposition simulation.