The Murray Lab

My lab is interested in understanding the developmental mechanisms of morphogenesis and structural birth defects using both forward and reverse genetic approaches. We use genome editing technology to engineer precise models of rare disease and, when feasible, explore genome editing strategies for therapeutic intervention.

My group also leads or co-leads multiple large-scale resource programs, including the Knockout Mouse Phenotyping Program (KOMP2), our JAX Center for Precision Genetics (JCPG), and our Center in the Somatic Cell Genome Editing (SCGE) consortium.

Genetics of congenital anomalies

My lab has long been interested in using mouse genetics to understand the mechanisms that govern the development and differentiation of the neural crest, a unique cell population that gives rise to many adult tissues including cephalic smooth muscle, cranial ganglia, and the craniofacial skeleton. Our forward genetic approach takes advantage of the numerous spontaneous mutants that arise at JAX, providing an unbiased means to identify novel genes and pathways involved in neural crest and craniofacial development. In addition, we take advantage novel gene discoveries in the KOMP2 screen to dissect novel genes in craniofacial development and other developmental systems such as skeletal, heart, and respiratory development. We use variety of genetic and genomic approaches to understand the complex systems-level dynamics of morphogenesis, including bulk and single-cell RNA-seq and natural genetic diversity available in different mouse strain backgrounds. We also collaborate with investigators around the world to develop novel mouse models of rare, syndromic and non-syndromic birth defects, including orofacial clefts, congenital diaphragmatic hernia, and congenital heart disease.

Rapid modeling human structural birth defects

Advances in high-throughput sequencing have led to an acceleration in the pace of discovery of novel variants associated with structural birth defects. Because many of these mutations are de novo, functional validation and ultimately biological investigation of these mutations lags far behind. While the mouse is an ideal, and in some cases essential, system to characterize these variants, typical modeling approaches are slow and lack the scalability to address the growing backlog. To address this, we have been developing and applying methods to use CRISPR/Cas9 genome editing to validate and model human structural birth defects directly in “founder” (F0) embryos, drastically reducing the time required to prove the causality of new human genetic discoveries (Gumier et al., 2015, Nat. Genetics; Wang et al., 2023, PNAS). This approach takes full advantage of the scale and imaging capabilities developed for the KOMP2 screen. Our current work focuses on optimization of the efficiency of homology directed repair (HDR) to improve our ability to model precise, orthologous human mutations in F0 embryos, while continuing our collaborations to validate the causal etiology of novel disease gene variants for a number of conditions including, orofacial clefting and craniofacial dysmorphology, lethal skeletal dysplasia, congenital diaphragmatic hernia, and congenital heart defect

Resource Development

The Knockout Mouse Phenotyping program (KOMP2)

The overarching goal of the KOMP2 and its partners in the International Mouse Phenotyping Consortium (IMPC) is to generate and phenotype a genome-wide set of knockout mice to build a catalogue of gene function (www.mousephenotype.org). We are in the final phase of the program and have generated over 2,000 single gene knockouts to date for phenotyping, including assessment of viability. In addition to production, my lab led the development of a broad, high-throughput embryonic phenotyping pipeline of lethal lines that includes high-resolution 3D imaging to ascertain both the time of and phenotypes associated with lethality in these lines. We’ve found that roughly 1/3 of all genes are essential, and that these genes are highly enriched for disease-causing variants in the human population (Dickinson et al., 2016, Nature). We select from the large number of novel, interesting developmental phenotypes for more extensive mechanistic characterization.

Modeling human rare disease

There are over 7,000 individual rare diseases that affect, as a group, between 25 and 30 million people in the US alone. Despite recent progress in genetic diagnoses driven by advances in sequencing technology, our understanding of the basic biological mechanisms of disease is limited and progress in developing therapeutic interventions lags far behind. The overall mission of the JAX Center for Precision Genetics (JCPG) is to address this unmet need and generate novel mouse models of rare disease, characterize clinically relevant phenotypes, explore mechanisms of pathophysiology and when possible deploy these models in preclinical studies of novel therapeutics. We work closely with patient-driven foundations, clinicians and researchers to design and engineer precise, complex models frequently including extensive humanization around the disease-causing mutation in order to provide a more useful preclinical platform for therapeutic intervention. We are specifically interested in designing and testing genome editing strategies to precisely correct mutations to achieve therapeutic benefit, and have been recently awarded a collaborative U19 Center to conduct IND-enabling studies to treat rare neurological diseases including Spinal Muscular Atrophy, Friedreich’s Ataxia, Huntington’s Disease and Rett Syndrome. We are working to extend and generalize these strategies to many of the models of rare and ultra-rare disease developed in the JCPG.

Resources for somatic cell genome editing

With the approval of the first genome editing treatment for Sickle Cell Disease in 2023, genome editing has achieved a key milestone in its evolution from a research tool to a viable therapeutic strategy. Despite this success and several more promising candidate treatments in the clinic, key challenges remain including the development of technology to deliver genome editors effectively and specifically to disease relevant cells and tissues. The overall goal of the first Phase of the NIH Common Fund-supported Somatic Cell Genome Editing (SCGE) Consortium (Saha et al., 2021)  was to support collaborative programs to address these challenges, and to provide results as a data resource “toolkit” to the scientific community (https://scge.mcw.edu/). As part of this consortium, we established a Small Animal Testing Center that had two primary goals: generation of novel mouse reporter lines to reliably indicate different types of genome editing activity with single-cell resolution, and to work closely with other consortium members to validate the efficiency and specificity of novel delivery technologies in mice. We implemented novel delivery methods, refined and applied quantitation tools, and assured rigor and reproducibility by independently replicating key findings of SCGE partners. All data are available as part of the SCGE toolkit and mouse strains are all available through JAX (https://www.jax.org/strain/034033) and the Mutant Mouse Resource and Research Centers (MMRRC) (https://www.mmrrc.org/). Our tools, methods, and resources are now being utilized by the JCPG (above) to design and deploy genome editing therapeutic strategies for rare disease models developed in that program.

Cre Driver Resources

Cre/loxP technology is a critical tool for the spatial and temporal manipulation of genes to understand their function in development and disease. With the large number of cre driver strains produced over the past three decades, there is a strong need for a centralized data resource that includes both intended and non-specific activity of these lines. Through a partnership with Mouse Genome Informatics (MGI) at The Jackson Laboratory, we have established a one-stop shop for both cre strains and functionality data (https://www.informatics.jax.org/home/recombinase). This includes our broad characterization pipeline that extends functional data for the scientific community, including both on-target and off-target activity. More recently, we have focused our efforts on identifying and characterizing the integration sites of transgenic cre lines (Goodwin et al., 2019, Genome Research), demonstrating that many are accompanied by structural variation at the integration site that disrupt coding genes, highlighting the importance of study design and control strategy for proper interpretation of results.