RESEARCH – Weiner

OVERVIEW

Our lab seeks to define the molecular logic of complex cell behaviors— how cells go from sets of interacting molecules to the emergent properties of living systems.

We currently focus on three questions:

We study a diversity of cell types and behaviors. We believe that this makes it easier to identify the general principles of cellular decision-making. We often pair biosensors to visualize a quantitative dynamic of choice inside living cells with precision tools to control the regulators of these behaviors. This approach reveals the molecular logic of these complex cell decisions.

Transformative science often happens at interfaces. So we seek to borrow tools and concepts from other fields to address open questions in cell biology and frequently develop new tools when they are needed to accelerate progress.

Our approach opens up opportunities for cross pollination between different projects in the lab.

Neutrophil polarity and motility

Neutrophils are innate immune cells that use directed migration to hone to sites of injury and infection.

This behavior requires a seamless integration of many cellular sub-routines. The cell has to decide when and where to make a protrusion. The protrusion needs to have the appropriate shape and size to guide the cell through a complex environment. Each protrusion competes with the rest of the cell to enable a winner-take-all, and this process is biased by external chemoattractants. The neutrophils don’t migrate independently but rather communicate with one another for more efficient convergence at sites of injury and infection.

Some of the essential regulators of these processes are known, but we lack an understanding of how these components interact to generate complex behaviors. We have uncovered a number of self-organizing circuits and cellular subroutines that generate the emergent features of cell shape and movement. |Cell Polarity and Motility References|

We leverage several approaches to achieve this understanding. Biosensors reveal the spatiotemporal dynamics of the signals that organize these pathways. Optogenetics tests the functional relation between these signaling dynamics and cell physiology. |Optogenetics References|

By studying the quantitative functional interactions of many different signaling currencies—biochemical signals, cytoskeletal rearrangements, physical forces, |Mechanotransduction References| and changes in cell shape—our work reveals the integrating principles that link local molecular interactions to coordinated cell-wide behaviors.

Directional movement of white blood cells to a point source of attractant (center).

We are dissecting the molecular logic of how cells control their shape and movement during chemotaxis.

We generated a system for controlling T cell activation with light. We are using this approach to understand how T cells discriminate foreign peptides from self-peptides.

T cell activation

T cells are crucial regulators of the adaptive immune system. T cell recognition of a given antigen instructs the rest of the adaptive immune system to attack, so proper discrimination between foreign peptides and self-peptides is critical.

The T cell receptor is so sensitive that a single molecule of foreign peptide can trigger cell activation. And it is so specific that it can detect rare foreign antigens in a sea of self-peptide that can be >100,000x greater in abundance. The differences between self and foreign peptide can be subtle—they can differ by as little as ten-fold in affinity. How the T cell achieves this specificity and sensitivity is not fully understood.

Our approach is to replace the complexity of native ligands, which differ in a range of biophysical properties, with an optogenetic system that enables us to systematically and specifically alter the binding kinetics and concentration of bound ligand. |Reference| We are currently probing the molecular logic of this decoding event.

Gene activation by genome organization and transcription factor dynamics

Despite sharing the same genome, an immune cell is very different from a nerve cell or a skin cell. These differences arise from the distinct sets of transcriptionally active genes.

One important regulator of these transcriptional differences are non-coding DNA sequences known as enhancers. The textbook model of enhancer function is for direct looping-based contact of enhancers with promoters to drive gene activation.

We developed tools to visualize enhancer-promoter interactions and real-time transcription in living mouse embryonic stem cells. Our work revealed that direct enhancer-promoter interactions do not drive contemporaneous gene activation, challenging the conventional model of enhancer function.

We find that in addition to genome organization, when and where a given gene is activated depends on the suite of expressed transcription factors and, importantly, their dynamics.

Using optogenetic tools we are currently probing the mechanism of temporal decoding of transcription factor dynamics.

Visualization of enhancer/promoter interactions at the Sox2 locus and real-time transcription in mouse embryonic stem cells.
|Reference|
We used this approach to challenge the conventional model of enhancer function.