James Shepherdson

Program: Computational and Systems Biology

Current advisor: Barak A. Cohen, PhD

Undergraduate university: Johns Hopkins University, 2016

Enrollment year: 2017

Research summary
Deep mutational scanning of retinal transcription factors

The transcription factor Cone-Rod Homeobox (CRX) is a master regulator of photoreceptor cell fate. Sequence variants in CRX can cause Retinitis Pigmentosa, Cone-Rod Dystrophy, and Leber Congenital Amaurosis, all inherited causes of vision loss and blindness. Several CRX variants have been reported to cause severe dominant disease through antimorphic genetic interactions with wild-type CRX, and yet these mutations are adjacent to variants which are benign or only cause mild, recessive disease. Determining which mutations in CRX are pathogenic and quantifying their effect on functional activity is prerequisite to interpreting patient variation and predicting patient phenotypes.

However, most variants in CRX are “Variants of Uncertain Significance” (VUS), meaning that insufficient clinical or functional evidence exists to determine their pathogenicity. I am working to apply Deep Mutational Scanning (DMS) to CRX, using libraries of CRX variant sequences in multiplexed assays to simultaneously measure the functional consequence of thousands of variants in a single experiment. The direct product of this work will be a “look-up table” listing the functional consequence of every CRX variant on protein activity and stability, which will be directly applicable to clinical variant classification and decision making.

Graduate publications
Shepherdson JL, Zheng H, Amarillo IE, McAlinden A, Shinawi M. 2021 Delineation of the 1q24.3 microdeletion syndrome provides further evidence for the potential role of non-coding RNAs in regulating the skeletal phenotype. Bone, 142():115705. PMCID: PMC8020873

King DM, Hong CKY, Shepherdson JL, Granas DM, Maricque BB, Cohen B. 2020 Synthetic and Genomic Regulatory Elements Reveal Aspects of cis-regulatory Grammar in Mouse Embryonic Stem Cells. Elife, 9():e41279. PMCID: PMC7077988