BE Seminars & Events

TBA

TBA

TBA

We engineer proteins as therapeutics and diagnostic agents for biomedical applications including cancer and regenerative medicine. I will discuss the discovery and development of novel therapeutic approaches to targeted cancer treatment, spanning a broad range of efforts in the areas of protein engineering, biochemical and biophysical analyses, and preclinical testing.

We also create technologies for protein analysis and engineering, including a high-throughput screening platform that enables massively parallel, quantitative biochemical measurements to be performed on millions of protein variants expressed in yeast or bacteria. My presentation will highlight examples of engineered proteins with translational impact, as well as protein engineering applications performed with this new technology platform.

Protein clustering is a hallmark of genome regulation in mammalian cells. However, the dynamic molecular processes involved make it difficult to correlate clustering with functional consequences in vivo. We developed a live-cell super-resolution approach to uncover the correlation between mRNA synthesis and the dynamics of RNA Polymerase II (Pol II) clusters at a gene locus. For endogenous β-actin genes in mouse embryonic fibroblasts, we observe that short-lived (~8 s) Pol II clusters correlate with basal mRNA output. During serum stimulation, a stereotyped increase in Pol II cluster lifetime correlates with a proportionate increase in the number of mRNAs synthesized. Our findings suggest that transient clustering of Pol II may constitute a pre-transcriptional regulatory event that predictably modulates nascent mRNA output.

TBA

TBA

As part of our ongoing studies into lug tissue engineering we have been focusing on optimizing the efficiency of directed in vitro differentiation of murine embryonic stem cells (mESCs) into lung alveolar epithelial cells. In this presentation I will describe how this differentiative process can be modulated by two microenvironmental cues: oxygen tension and substrate stiffness. Specifically, both these factors, using distinct signaling pathways that involve HIF-1α and Rho/Rock, respectively, independently enhance differentiation of mESCs into definitive endoderm, and subsequently into alveolar epithelium. Augmentation of endodermal differentiation and subsequent alveolar differentiation depend strikingly on the duration of exposure to hypoxia.  Of note is also the marked biphasic nature of the effect of substrate stiffness on endoderm induction. The results of our study will be important in advancing the production of differentiated alveolar cells necessary for cell based therapies of lung diseases and/or for whole lug tissue engineering.

TBA

Biological tissues are an exciting system to study because they are non-equilibrium materials that consist of self-propelled, interacting agents (cells) and as such exhibit interesting phenomena not observed in passive materials. In my talk I will present our recent work on two
examples of active violent morphological restructuring in biological tissues.

The first study explains how Hydra, a simple freshwater animal, opens its mouth to eat. In contrast to humans and most other animals, Hydra does not have a permanent mouth. Instead, it rips a hole in its skin every time it wants to eat. For a preview, see:
http://shows.howstuffworks.com/now/hydra-mouth-video.htm

The second study explains how freshwater planarians rip themselves apart during asexual reproduction using only substrate adhesion and their own musculature. How this feat can be achieved is a complex biomechanics problem which reportedly already bugged the great Michael Faraday, but has
remained a mystery for centuries.

Each study solves a longstanding puzzle about a fundamental biological phenomenon which remained unsolved due to a lack of experimental tools and quantitative measurements. These examples further illustrate how complex biological phenomena can be described by relatively simple physics and
that our quantitative approach provides new insights into the biological mechanisms underlying these phenomena.

Reactivation of telomerase reverse transcriptase (TERT) expression enables cells to overcome replicative senescence and escape apoptosis, which are fundamental steps in the initiation of human cancer. Multiple cancer types, including up to 83% of glioblastomas (GBMs), harbor highly recurrent TERT promoter mutations specific to two nucleotide positions. I will describe how we have recently identified the functional consequence of these mutations in GBMs to be recruitment of the multimeric GA-binding protein (GABP) transcription factor specifically to the mutant promoter. Allelic recruitment of GABP is consistently observed across four cancer types, highlighting a shared mechanism underlying TERT reactivation. Tandem flanking native E26 transformation-specific motifs critically cooperate with these mutations to activate TERT by facilitating GABP heterotetramer binding. GABP thus directly links TERT promoter mutations to aberrant TERT activation in multiple cancers and provides an opportunity for targeting these highly recurrent non-coding mutations.

The recent advent of RNA-guided effectors derived from clustered regularly interspaced short palindromic repeats (CRISPR)–CRISPR-associated (Cas) systems have dramatically transformed our ability to engineer the genomes of diverse organisms. As unique factors capable of co-localizing RNA, DNA, and protein, tools and techniques based on these are paving the way for unprecedented control over cellular organization, regulation, and behavior. Here I will describe some of our ongoing efforts towards engineering this system for enabling therapeutic applications.

The era of “omics” has ushered in the hope for personalized medicine.  Proteomic and genomic strategies that allow unbiased identification of genes and proteins and their post-transcriptional and -translation modifications are an essential component to successful understanding of disease and the choice of imaging targets.  However, the enormity of the genome and proteome and limitations in data analysis make it difficult to determine the targets that are particularly relevant to human disease and will be good targets for molecular imaging and targeted drug therapies.  Methods are therefore needed that allow rational identification of targets based on function, relevance to disease, and suitability for molecular imaging and therapy.

Through this lecture, we will explore one clinical scenario: pancreatic ductal adenocarcinoma (PDAC) as an application for target identification, imaging and therapeutic agent development. PDAC is among the most lethal of human cancers due to its marked resistance to existing chemo- and radiotherapies.  Unlike a number of other solid tumors, which have robust methods for early detection, there have been no significant improvements in PDAC survival over the past 40 years despite a large number of clinical trials of both conventional and targeted therapies.  Like other solid cancers, early detection that allows complete surgical resection offers the best hope for longer survival, unfortunately, most patients are diagnosed with metastatic disease due to the lack of specific symptoms and absence of suitable biomarkers for early detection.

TBA

Identifying the spatial organization of tissues at cellular resolution from single cell
gene expression profiles is essential to understanding many biological systems. We have developed an in situ 3D multiplexed imaging method to quantify hundreds of genes with single cell resolution via Sequential barcoded Fluorescence in situ hybridization (seqFISH) (Lubeck et al., 2014). We used seqFISH to identify unique transcriptional states by quantifying and clustering up to 249 genes in 16,958 cells. By visualizing these clustered cells in situ, we identified regions within distinct composition of cells in different transcriptional states. Together, these results demonstrate the power of seqFISH in transcriptional profiling of complex tissues.  Lastly, I will discuss our work in writing lineages and cell event history into genome of cells by CRISPR/Cas9 genome editing and reading out the stored information in single cells by seqFISH. 

TBA

Changes in the shape of a material – be it rubber, concrete, cells, or tissue – requires the action of physical forces. Therefore during embryonic development, the dramatic transformation from a seemingly disorganized mass of cells into the fully patterned adult form necessitates stereotyped regulation of forces at the genetic and molecular level. While great progress has been made in understanding how gene expression and signaling events generate biological pattern, little is known about how molecular cues organize forces to sculpt physical patterns during development. How does the developing embryo ensure that tissues are shaped by the right forces, acting at the right time and location, and with the right orientation and magnitude?  My work begins to address this in two complementary contexts during gastrointestinal morphogenesis in the chick embryo: gut tube formation and intestinal looping. Together these studies demonstrate how secreted signals are converted into tissue-level forces that shape the developing embryo, and yield new insight into important gastrointestinal birth defects. The long-term goal of this work is to provide insight into the fundamental mechanisms of tissue formation, ultimately revealing a molecular-mechanical toolkit of embryonic development that can be redeployed in the context of regenerative medicine and tissue engineering.

TBA

A major goal of synthetic biology is to predictively reshape cellular phenotype by introducing artificial regulatory network connections. While the practice of constructing synthetic circuitry is relatively well established in model prokaryotic systems, the pace and progress of engineering has been much slower for eukaryotic cells. In this presentation, I will describe our recent efforts at creating network engineering frameworks for both synthetic transcriptional (genetic circuits) and post-translational (phosphorylation-based signaling circuits) networks that are both inspired by and compatible with native networks found in eukaryotic cells. In each case, we showcase modular, scalable solutions which utilize simple molecular components that can be assembled into circuits that exhibit sophisticated, natural-like behavior. Furthermore, we introduce strategies for rapidly sampling circuit design space to quickly converge on behaviors that fulfill a particular design goal. Our engineering strategies are broadly applicable, and point toward a universal toolkit for reprogramming the ability of eukaryotic cells to sense, process, and transmit information for important industrial or therapeutic purposes.

TBA

Despite decades of cell signaling studies, we have a limited understanding of the cell signaling code: how can cells make diverse and complex decisions using only a small set of intracellular signaling pathways? An intriguing hypothesis is that cells can decode the strength, dynamics, or combinations of intracellular signals. Optogenetic (light-activatable) tools now enable us to test this hypothesis through precise and tunable control over signaling inputs in living cells.  These tools allow us to reverse-engineer the cell, giving fundamental insight into both 1) the cellular machinery and 2) the cell’s ability to process and interpret its dynamic environment. In this talk, I will first describe the engineering of optogenetic proteins for cell signaling, as well as their high-throughput implementation. I will then show how these approaches are revealing principles by which signaling dynamics govern cell fate decisions from neurogenesis to cancer cell proliferation.

TBA

It has become apparent that the surrounding tumor microenvironment can promote the growth, drug resistance, and metastasis of malignant cells. In this talk, I will discuss how cells within the vascular and bone marrow microenvironments can be engineered and exploited for cancer therapy. I will first discuss an approach to engineer the surface of innate immune cells in the bloodstream with cancer therapeutics in vivo. Mimicking the cytotoxic activity of natural killer cells, the approach exploits the extensive surface area of circulating immune cells to display both the cancer-specific TNF-related apoptosis-inducing ligand (TRAIL) and E-selectin adhesion receptor to metastatic cells in the vascular microenvironment. The resulting “unnatural killer cells” neutralized tumor cells within the circulation in vivo, and prevented metastatic tumor formation in spontaneous metastasis mouse models of prostate cancer. I will then present our most recent work on the development of gene delivery materials that target the bone marrow microenvironment in vivo, as a means to treat cancers that colonize in marrow. Through the synthesis of a diverse library of polymer-lipid hybrids in combination with high throughput in vivo screening methods, we have identified novel biomaterials that efficiently deliver nucleic acid therapeutics to target cells in the bone marrow microenvironment at low dosages. By targeting physical interactions between tumor cells and the surrounding microenvironment, these materials disrupted multiple myeloma progression in clinically relevant, humanized mouse models of the disease.

TBA

Abstract
TAM (Tyro3, AXL, MerTK) receptor tyrosine kinases (TAMRs) are critical regulators of immune response and tissue homeostasis. Immunological dysregulation of the family contributes to a wide range of diseases including lupus, retinal dystrophy, infection, and cancer. TAMR activation in cancer cells serves as a mechanism of resistance to chemotherapies and targeted inhibitors. Further improving our understanding of the molecular events that lead to oncogenic TAMR function will enable rational design of more specific inhibitors with precise effects in vivo and help identify the patients who will benefit from these therapies. In this talk, I will describe our efforts to identify the molecular events leading to TAMR activation, and how these events are tied to the receptors’ physiological function. Using kinetic models of receptor activation, tied to inference techniques that rigorously consider model uncertainty, have helped us to identify new ways of rationally targeting the TAMR family. Using these tools, we are deconvolving the pleiotropic role these receptors play in tumor cell heterogeneity, metastasis, and immune suppression using combinations of these targeted treatments with data-driven modeling. Lastly, I will touch upon how these approaches can inform other areas of innate immune signaling, and opportunities for bioengineering technological development presented by what we have learned.

Droplet microfluidics, in which micro-droplets serve as individual reactors, has enabled a range of high-throughput biochemical processes. The talk will start with our recent application on using droplets to identify microbes, specifically methane-metabolizing bacteria, for the more efficient generation of bioplastics. Unlike solid wells typically used in current biochemical assays, droplets are subject to instability and can break especially at fast flow conditions. Although the physics of single drops has been studied extensively, the flow of crowded drops or concentrated emulsions—where droplet volume fraction exceeds ~80%—is relatively unexplored in microfluidics. Ability to leverage concentrated emulsions is critical for further increasing the throughput of droplet applications. Prior work on concentrated emulsions focused on their bulk rheological properties. The behavior of individual drops within the emulsion is not well understood, but is important as each droplet carries a different reaction.

This talk examines the collective behavior of drops in a concentrated emulsion by tracking the dynamics and the fate of individual drops within the emulsion. At the fast flow limit, we show that droplet breakup within the emulsion is stochastic. This contrasts the deterministic breakup in classical single-drop studies. We further demonstrate that the breakup probability is described by dimensionless numbers including the capillary number and confinement factor, and the stochasticity originates from the time-varying packing configuration of the drops. To mitigate breakup, we design novel amphiphilic nanoparticles, and show they are more effective than surfactant molecules as droplet stabilizers.

At the slow flow limit, we observe an unexpected order, where the velocity of individual drops in the emulsion exhibits spatiotemporal periodicity. Such periodicity is surprising from both fluid and solid mechanics point of view. We show the phenomenon can be explained by treating the emulsion as a soft crystal undergoing plasticity, in a nanoscale system comprising thousands of atoms as modeled by droplets. Our results represent a new type of collective order not described before, and have practical use in on-chip droplet manipulation. From the solid mechanics perspective, the phenomenon directly contrasts the stochasticity of dislocations in microscopic crystals, and suggests a new approach to control the mechanical forming of nanocrystals.

*Chaos stands for Crowded droplet breakup HydrodynAmics not Ordered but Stochastic

TBA

TBA