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Murphy Lab







The long-term goal of my research is to help unravel the complex interplay between recruited immune cells and the endothelial lining of the vasculature in chronic inflammation, with a focus on alternative splicing and changes in the sub-endothelial matrix as critical determinants of that interaction. Our research uses in vivo and in vitro models of the effects of low and disturbed flow on arterial endothelium, the physical forces of which drive vascular disease underlying heart attack and stroke.

As a postdoctoral fellow in Dr. Richard Hynes' lab at MIT, I examined the regulation of Fibronectin, an extracellular matrix protein found in abundance at sites of vascular injury. Analysis of Fibronectin mRNA expression in response to low and disturbed flow in the arterial endothelium revealed a splicing switch that resulted in the inclusion of two widely conserved alternative exons.

Splicing image

Using genetic models I showed that this splicing switch protects against hemorrhagic dissection of the arterial vessel wall under low and disturbed flow.

Splicing is increasingly recognized as an important contributor to human disease. Variations resulting from changes in splicing can produce proteins with entirely new functions. Although a number of critical endothelial proteins are alternatively spliced, little is known about the regulation and function of alternative splicing in the endothelium.

Our work applies in vivo and in vitro models for examining the signaling interactions between immune cells and the arterial wall under disturbed flow, and the alternative splicing events that regulate these interactions.

We work closely with a group of talented researchers in Vascular Biology and Immunology to achieve our objectives, within the Center for Vascular Biology and the Calhoun Cardiology Center and the collaborators in the Immuno-Cardiovascular Group.

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Project 1: Analysis of alternative splicing in flow-driven arterial inflammation


RNA splicing event regulated by disturbed flow across the endothelium
RNA regulation in endothelium under disturbed flow

Figure shows the consistency in gene expression and in splicing response among different biological replicates of endothelium exposed to low flow in vivo

Using an established model of flow-induced arterial injury, we have recently performed large scale RNA-sequencing analysis of an endothelial enriched fraction in normal and disturbed flow conditions. We have identified thousands of changes in alternative splicing, and a handful of potential upstream regulatory splice-factors. A large portion of these splicing changes are responsive to the recruitment of innate immune cells. We have mouse lines for the conditional deletion of three of these splice factors from the endothelium, allowing us to assess their functions in vivo.

This project involves phenotypic analysis of the consequences of perturbing these splice factors in vivo, with an emphasis on understanding the effects on immune response.


Project 2: Alternative splicing in cross-talk with myeloid cell

macrophages co-cultured with splicing-mutated endothelial cells

Macrophages co-cultured with splicing-mutated endothelial cells

Figure shows a DIC image of an aortic endothelial cell monolayer, which is overlaid with bone marrow derived monocytes from a reporter mouse (red). Profiling of the co-cultured monocytes and their differentiated progeny has revealed striking differences in phenotype, depending on the alternative splicing status of the endothelial cells they are cultured on.

We have developed methods for the conditional expansion of aortic endothelial cells in culture. These cells, and versions of these cells with alterations in specific splice factors or alternatively spliced genes are being used in co-culture experiments with myeloid cells. Pilot experiments have shown strong effects on the phenotype of wild-type myeloid cells cultured with endothelial cells altered in either the expression of the splice factors we have identified in vivo, or the alternative splicing events they regulate. This interesting result suggests how splicing responses in the endothelium, which are responsive to innate immune cell recruitment, shape chronic inflammation in arterial injury and likely other inflammatory processes as well.

This project involves in vitro culture of endothelial cells with mutations in the alternative splicing response, and the isolation and characterization of immune cells by FACs and molecular biology.

Project 3: Identification of splice regulators by candidate screen

Figure shows the relative level of alternative exon inclusion (increasing from left to right) by flow cytometry. Red=baseline, yellow=mutant cells, with impaired inclusion, blue=wild-type cells, with normal inclusion.

The list of regulatory splice factors identified in vivo was done by bioinformatics – specifically an enrichment in the regulatory motifs they bind to among the regulated splicing events. While this has revealed a clear role for the splice factors we are testing in Project 1, we have a handful of other factors which have been less characterized are therefore very interesting. We have established a method to screen the function of these factors in the regulation of a few key splicing events by flow cytometry. This screen will allow us to identify factors that result in either the increased or the decreased inclusion of specific exons in the final RNA in primary and cultured aortic endothelial cells.

This project involves pooled screens, using shRNA and CRISPR depletion approaches, to determine which factors affect the splicing response. We will be using FACs as the screen, and NextGen sequencing enrichment as the readout. "Hits," or novel regulators of splicing, will then be further interrogated in vitro and potentially in vivo.

Project 4: Regulation of NF-kappa B signaling by alternative splicing

Regulation of NF-kappa B signaling by alternative splicing

For the vast majority of alternative splicing events we have identified, the function remains unknown. However, many of them target key processes in endothelial cells. One of the processes we are most interested in is NF-kappaB signaling. This pathway has a pivotal role in the response of the vascular endothelium to low and disturbed flow, and thus alterations of this pathway induced by changes in splicing are likely to impact the response of the vasculature to chronic flow-induced injury. We will examine these splice variants in our in vitro model, to determine which impact NF-kappaB induction, and then define the mechanism for this regulation.

This project involves the expression cDNA encoding the splice variants, and shRNA or CRISPR mediated suppression of specific splice isoforms. Outcomes will be assessed in a pooled fashion, using murine and human aortic endothelial cells engineered to express NF-kappaB reporters.


<--Molecular components of the NF-kappa B signaling pathway.

Figure reprinted by permission from Macmillan Publishers Ltd: Nature Reviews Molecular Cell Biology, 8, 49-62 (doi:10.1038/nrm2083), copyright 2007

Patrick Murphy
Principal Investigator

Amy Kimble
Research Assistant II

Amy Kimble

Jess Hensel
Graduate Student


Sarah-Anne Nicholas
Graduate Student


We are looking for talented researchers to join our team at all levels.


Lab News

September 2016 - the Murphy lab is up and running! 

July 2018 - Congratulations Jess on passing your qualifying exam with flying colors.

October 2018 - Thanks to the North American Vascular Biology Organization, for recognizing Sarah-Anne's work with a Travel Award to the 2018 meeting.

October 2018 - Nice work Jess, on winning a poster prize at the 2018 North American Vascular Biology Organization meeting in Newport!

April 2019 - Congratulations Maria Xu, on your graduation from the Ph.D. phase of your program. I look forward to hearing about your next accomplishments, it was a pleasure working with you and Dr. Vella to uncover new ways in which activated T cells are retained and re-activated within atherosclerotic plaque.

May 2019 - Thank you, to the American Heart Association, for the 2019 Innovative Project Award to apply our screening approach to identify endothelial RNA-binding proteins involved in the regulation of inflammatory responses.

June 2019 - Congratulations Sarah-Anne on passing your qualifying exam, I'm looking forward to your outstanding PhD work!

September 2019 - Happy to share my thoughts on the post-doc to faculty transition through the North American Vascular Biology Organization "Lessons Learned"; NAVBO has been a key component of my success in research and I am happy to have a chance to give back!

September 2019 - We appreciate the recognition by the North American Vascular Biology Organization as "Lab of the Month".

Dec 2019 - Thank you, to the American Heart Association, for funding Sarah-Anne's graduate work on endothelial Elavl1 functions in adaptive immune responses.

Dec 2019 - Thank you, to the American Heart Association, for funding Jess's graduate work on the regulation of NFkB responses by RNA-binding proteins.

May 2020 - We were honored to be considered a finalist for the Irvine H. Page Junior Faculty Research Award from the American Heart Association, and congratulations to Hanrui Zhang of Colombia on winning the award.

May 2020 - Thank you, American Heart Association, for the Paul Dudley White International Scholar Award for the top ranked submitted abstract from a United States lab to the 2020 Vascular Discovery Meeting.

August 2020 - We are grateful for RF1 funding ($2.2M) from the NIH's National Institute of Neurological Disorders and Stroke, to support our work on splice factor function in the endothelial cells of the blood brain barrier in Alzheimer's and related diseases. We are incredibly enthusiastic about pushing boundaries over the next five years in work with our collaborators Riqiang Yan (UCONN Health), Li Gan (Weill Cornell) and Chris Schaffer (Cornell). Watch this space!

September 2020 - excited to present three different projects at the North American Vascular Biology conference, and to hear about other exciting work on immune cell interactions with the endothelium, and endothelial contributions to atherosclerosis and neurodegenerative disease.

October 2020 - congratulations Sarah-Anne, on a great talk at the 2020 NAVBO meeting, and congratulations Jess on a great poster presentation, and a poster award!