The biological machines we plan to build are composed of specialized cellular and molecular components that dynamically interact to coordinate the larger system functions of biological machines. Initially it is important to understand the characteristics of the plethora of cells and their components and how they behave upon differentiation leading to a coordinated functional machine and what roles they play in replacing worn parts within an active biological machine. We will determine in real time, using enabling technologies (reporter genes, matrices etc.), how stem cells and progenitor cells exposed to intrinsic and extrinsic cues behave and interact in a coordinated fashion. This new understanding will aid in the creation of the emerging cell clusters that form the individual systems and that are ultimately integrated to produce biological machines. Therefore it is important to understand how to make available differentiating cells that meet the machine’s specifications, and how to predict and control phenotypic changes. A unique aspect of this project is the use of emerging technologies and computational tools to understand in real time and eventually predict the complex nature of cell function(s) of differentiating cells in a defined and controlled microenvironment.
Cells perform their intended functions not individually but collectively by forming temporally evolving, three-dimensional structures comprised of clusters of cells, and through active or passive cell-cell and cell-matrix interactions. Despite extensive research focusing on behaviors of individual cells and the functions and properties of tissues and organs, little progress has been made to elucidate the complex functional behaviors of interacting cell clusters, or biological machines. While there is general recognition that cellular behaviors are guided by integrated biological, biochemical, and physical (geometrical, mechanical, electrical, thermal) cues, the fundamental processes involved in such integration are poorly understood. We will develop novel experimental and computational tools that are essential for understanding and actively controlling cellular and cell network behaviors.
EBICS will address the grand challenge of engineering multi-cellular biological machines that have desired functionalities and can perform prescribed tasks. These machines consist of sensing, information processing, actuation, protein expression, and transport elements that can be effectively combined to create functional units.
The broader scientific goals of EBICS are to establish a fundamental understanding of cell-cell and cell-environment interactions, and their control by biochemical and mechanical cues; assemble and characterize the properties and performance of multi-cellular machines, thereby creating the nascent discipline for building living, multi-cellular machines for a wide range of applications.
EBICS has initially focused on building two biological machines: an implantable cellular machine, BetaCell Factory, for glucose sensing and insulin release for the treatment of diabetes; and an autonomous cellular machine, BioBot, for detecting and neutralizing toxins in the environment. To build these complex machines we must understand how individual cells – neurons, myocytes, endothelial cells, and beta cells – integrate their internal temporal developmental program with various environmental cues and with other cells to determine their differentiated states and biological behaviors. We must also understand the complex behaviors and functionalities that emerge from homotypic cell clusters composed of a single cell type and heterotypic cell clusters composed of multiple cell types. By understanding the factors, signals, forces, and external microenvironments that mediate interactions between cells in nature, we can harness that knowledge to construct complex neuro-muscular systems coupled to artificial endothelial vessels that can perform multimodal logical operations in functional biological machines.
Pathways to a Biological Machine
EBICS is taking two fundamental approaches to developing biological machines. Using a classic engineering approach we define the specifications for cellular machines or machine components, with desired functional capabilities, and develop the necessary parts (cells and cell clusters) and machine assembly pathways to construct a machine. In parallel we are using a systems biology approach to understand the emergent properties of cells and cell clusters to harness those properties to evolve interacting cell clusters that function within a biological machine with specific capabilities.
Integration of EBICS Research Thrusts
The BetaCell Factory and BioBots Thrusts constitute the major machine efforts within the EBICS research program. The design specifications of these biological machines will be defined within the CellClusters and SourceCells Thrusts, which will develop unique and reusable machine components. Within the Thrusts the Center has defined the vertical dependencies (grey arrows) between groups working to generate various desired cells and cell clusters, as defined by design specifications, to build the biological machines. Research in emergent behaviors will permeate all research initiatives contributing to the building of biological machines and a fundamental unserstnding of basic biological development.
EBICS RESEARCH THRUSTS
The overall goal of this project is to develop fundamental understanding and control of the environments and behaviors of cell clusters that generate single and multiple functionalities. In this context, our first task is to understand conditions and modes of interaction among cells of the same type and how these factors influence the behaviors of that cell cluster in generating a specific type of functionality. Further, we seek to understand and control the behaviors and emergent properties of multicellular clusters formed from four cell types: neurons (sensors, signal processors), myocytes (actuators), fibroblasts (protein expression) and endothelial cells (transporters). This project lies at the interface of basic biological science and engineering. It thus addresses fundamental questions related to the cell-substrate interactions, and explores to influence these interactions by engineering the substrate with the ultimate goal of guiding the emergent behavior of cell clusters.
The long term goal of this project is to develop millimeter scale biological machines constructed with polymers and living cells that can achieve net motion towards a chemical toxin and subsequently release chemicals to neutralize the toxins. We propose to use muscle cells (cardiac or skeletal) and neurons to develop such systems. The realization of such machines and systems could eventually come about with the integration of ‘bottoms up’ emerging behavior of cells and cellular clusters, and ‘top down’ methods for bio-fabrication of cells. The development of such integrated cellular system has been a grand challenge due to many technical issues that remain unaddressed. These include; controlled 2 and 3 dimensional patterning of living cells in bio-instructive materials; development of these biomaterials that allow cell growth and proliferation in 3-D; alignment of cells to create muscle strips for desired actuation; development of in-vitro neuro-muscular junction; the neuronal circuit to control the actuation of the muscle strips; coordination of the biological actuators for net movement, sensing of the target neuro-toxins; release of the neutralization agents by cell-based factories embedded in the biomaterials; just to name a few. We plan to address these challenges over the course of the Center lifetime in collaboration with the other projects.
A general flexible machine for biological sensing and reporting is proposed, with an initial specific machine for glucose biosensing. The machine consists of a cellular biosensor cell engineered for a biologically relevant biomarker, such as glucose, as the first part. A second machine part is communication by an artificial “synapse” which can be varied according to desired control parameters, such as integration over time or damping high frequency responses. A reporter cell that can optimally be monitored by transdermal imaging/spectroscopy represents the third machine part.
In order to directly study the emergent behaviors of 3D multicellular structures, it will be necessary to be able to: (1) control uniform and reproducible multicellular assembly, (2) incorporate regulatory and sensory technologies within cell aggregates, (3) examine phenotype dynamics (in space and time), and (4) model cell-cell and cell-environment interactions. Multicellular aggregates can be formed and manipulated by microscale technologies and maintained as individual distinct clusters for prolonged periods of time in suspension culture and/or hydrogel encapsulation. The biochemical and biophysical properties of the extracellular environment within multicellular clusters can be manipulated by introducing different environmental cues capable of influencing cell fate decisions.
EBICS Research Director: Ron Weiss, Massachussetts Institute of Technology