2015 Beckman Symposium   

Alex Shalek

Presentation Date:

Alex Shalek

Micro- and Nanoscale Tools for "Bottom Up" Profiling of Interacting Cellular Systems

Massachusetts Institute of Technology

Chemistry & Institute for Medical and Engineering Sciences

We consist of trillions of interacting cells, but our understanding of how they work together is limited. This is because we have traditionally divided organisms from the 'top-down' into broad cell types or iteratively-refined 'homogeneous' subsets and then studied each such population separately. Yet recent studies have shown that even 'identical' cells can exhibit functionally important differences and that cellular behaviors are strongly influenced by both the microenvironment and cellular interactions. Illustratively, for immune dendritic cells (DCs) and T cells – collectively responsible for recognizing pathogens and inducing adaptive immune responses – cellular subtype, signaling milieu, and physical contacts all impact the balance between proinflammatory and regulatory responses. Unfortunately, our inability to thoroughly measure and analyze each of these influences within the context of a complex system has limited our ability to grasp how proper immune function is achieved. Here, I will discuss our efforts to leverage recent advances in nanotechnology and molecular biology to develop broadly applicable platforms for systematically manipulating and deeply profiling many interacting single cells so that we can dissect how they work from the 'bottom-up'. Using the mouse and human immune systems as our model, we are developing five broadly-applicable, core, cross-disciplinary platforms to: (a) culture and monitor individual cells in isolation; (b) examine specific single cells within an ensemble; (c) perform targeted manipulations; (d) detect many different types of molecular entities in the same cell (e.g., RNA and protein); and, (e) profile, genome-wide, gene expression in many single cells, in vitro and ex-vivo. Collectively, we hope that our work will help identify the cellular players and the strategies they use to execute systems-level behaviors, radically altering our understanding of cellular response, communication, disease, and therapeutics, as well as enabling us to design and build functionality for therapeutic aims.

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