Homeotic hotspot in the human genome for eye and brain disease

PROJECT SUMMARY Classical homeotic mutations (e.g. Drosophila Ubx) disrupt embryonic development, transforming one tissue type into another. We have discovered the molecular basis of four human X-linked disorders affecting the eye or brain – BASR syndrome, foveal dysgenesis, retinitis pigmentosa and spinocerebellar ataxia, which have a homeotic or degenerative basis. Each disorder is caused by insertion of a large autosomal DNA segment at the same Xq27 palindromic site near SOX3, which encodes a potent trans- cription factor homologous to SRY (testis determinant). The Xq insertions are predicted to disrupt chromatin architecture, activating SOX3 ectopically in tissues defined by newly juxtaposed enhancers, and altering cell fate (homeosis) via a gain-of-function (GOF). We propose that SOX3 changes retinal pigment epithelia (RPE) into neuroretina in BASR, reprograms cerebellar Purkinje cells in SCAX5, and triggers photoreceptor degeneration in RP24. Using a novel palinsert PCR assay, we defined the breakpoints and candidate enhancers for each insertion. We also identified >10 further Xq27 disorders affecting the eye, brain or other organs – including unsolved cases with a likely similar mechanism. We will define new Xq27 palindrome insertions and test our hypothesis for disease pathogenesis at chromatin and developmental levels, using [1] patient-derived iPSCs, 3D chromatin interaction assays (Hi-C), in vitro differentiation, serial scRNA-seq profiles; and [2] (homol informative mouse transgenes, including the binary CRISPR/Cas9 Hprt HoP-In ogy promoted integration) GOF system we pioneered – with Sox3HA expression activated in RPE, rods, Purkinje cells, or other tissues via established Cre drivers, in a constitutional (XY) or mosaic (XX) pattern, and in a sustained or Dox-inducible manner.