Jose Mcfaline

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This week we profile a recent publication in Nature Genetics from José
(pictured) in the laboratory of Dr. Cole Trapnell at UW.

Can you provide a brief overview of your lab’s current research focus?

My laboratory studies cellular differentiation, reprogramming and other biological processes. Specifically, we focus on identifying the regulators of these transitions. My laboratory develops and applies single-cell genomic assays to answer these fundamental questions in biology. As these assays generate data of great complexity and scale, we routinely develop algorithms by which to analyze these complex datasets.

What is the significance of the findings in this publication?

This study delves into the nature of the epithelial to mesenchymal transition (EMT). The process by which an epithelial cell, normally found in very organized sheets and is generally non-motile, transitions into a mesenchymal cell affording it increased mobility and the ability to invade surrounding tissues. EMT is fundamental to normal development and has been implicated in disease as a mechanism that can lead to fibrosis and the dissemination of tumor cells. Despite its central role in normal and disease physiology, it is still unclear whether EMT consists of a sequence of discrete steps or a continuous spectrum of molecular states. Determining its nature has the potential to unlock strategies to target EMT in disease. Our results, as well as recent work from other groups, support that EMT is continuous in nature and further posits that the transition is different depending on how EMT is induced. Our study then incorporates a single-cell CRISPR/Cas9 screen to identify factors that determine a cell’s position along the EMT continuum. We identify various cell surface receptors and transcription factors whose loss impedes or slows a cell’s progression along EMT. Interestingly, these results imply that the diversity of EMT states identified in vivo may be a consequence of a lack of a key signal that leads to the accumulation of cells somewhere along the EMT continuum. On a conceptual level, the observation that interrupting a signaling pathway can lead to cells “arresting” along a continual process has important implications in ongoing debates regarding the definition of cell types and cell states.

What are the next steps for this research?

EMT is far from the only example of a continuous biological process. Biological continua are common in development and there is a need for methods that can dissect the regulation of these processes. Our methodology provides a blueprint as to how to combine single-cell trajectory analysis and high-throughput pooled genetic screens. What we hope will be a powerful approach to identify the molecular regulators of many cellular processes in both normal and disease contexts.

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