{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,28]],"date-time":"2026-07-28T10:37:39Z","timestamp":1785235059210,"version":"3.55.0"},"reference-count":55,"publisher":"MDPI AG","issue":"1","license":[{"start":{"date-parts":[[2025,1,12]],"date-time":"2025-01-12T00:00:00Z","timestamp":1736640000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Eye Institute","award":["R01 EY032539"],"award-info":[{"award-number":["R01 EY032539"]}]},{"name":"Boston Children\u2019s Hospital Office of Sponsored Programs Internal Pilot Funding","award":["R01 EY032539"],"award-info":[{"award-number":["R01 EY032539"]}]},{"name":"Boston Children\u2019s Hospital Translational Research Program","award":["R01 EY032539"],"award-info":[{"award-number":["R01 EY032539"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>Background\/Objectives: Strabismus is the most common ocular disorder of childhood. Three rare, recurrent genetic duplications have been associated with both esotropia and exotropia, but the mechanisms by which they contribute to strabismus are unknown. This work aims to investigate the mechanisms of the smallest of the three, a 23 kb duplication on chromosome 4 (hg38|4:25,554,985-25,578,843). Methods: Using CRISPR and bridging oligos, we introduced the duplication into the Kolf2.1J iPSC line. We differentiated the parent line and the line with the duplication into cortical neurons using a three-dimensional differentiation protocol, and performed bulk RNASeq on neural progenitors (day 14) and differentiated neurons (day 63). Results: We successfully introduced the duplication into Kolf2.1J iPSCs by nucleofecting a bridging oligo for the newly formed junction along with cas9 ribonucleoparticles. We confirmed that the cells had a tandem duplication without inversion or deletion. The parent line and the line with the duplication both differentiated into neurons reliably. There were a total of 37 differentially expressed genes (DEGs) at day 63, 25 downregulated and 12 upregulated. There were 55 DEGs at day 14, 18 of which were also DEGs at day 63. The DEGs included a number of protocadherins, several genes involved in neuronal development, including SLITRK2, CSMD1, and VGF, and several genes of unknown function. Conclusions: A copy number variant (CNV) that confers risk for strabismus affects gene expression of several genes involved in neural development, highlighting that strabismus most likely results from abnormal neural development, and identifying several new genes and pathways for further research into the pathophysiology of strabismus.<\/jats:p>","DOI":"10.3390\/genes16010080","type":"journal-article","created":{"date-parts":[[2025,1,13]],"date-time":"2025-01-13T09:49:17Z","timestamp":1736761757000},"page":"80","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":7,"title":["Chromosome 4 Duplication Associated with Strabismus Leads to Gene Expression Changes in iPSC-Derived Cortical Neurons"],"prefix":"10.3390","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0470-8642","authenticated-orcid":false,"given":"Mayra","family":"Martinez-Sanchez","sequence":"first","affiliation":[{"name":"Department of Ophthalmology, Boston Children\u2019s Hospital, Boston, MA 02115, USA"},{"name":"Department of Ophthalmology, Harvard Medical School, Boston, MA 02115, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8334-3329","authenticated-orcid":false,"given":"William","family":"Skarnes","sequence":"additional","affiliation":[{"name":"Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ashish","family":"Jain","sequence":"additional","affiliation":[{"name":"Research Computing, Department of Information Technology, Boston Children\u2019s Hospital, Boston, MA 02115, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4052-4218","authenticated-orcid":false,"given":"Sampath","family":"Vemula","sequence":"additional","affiliation":[{"name":"Department of Ophthalmology, Boston Children\u2019s Hospital, Boston, MA 02115, USA"},{"name":"Department of Ophthalmology, Harvard Medical School, Boston, MA 02115, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0321-9222","authenticated-orcid":false,"given":"Liang","family":"Sun","sequence":"additional","affiliation":[{"name":"Research Computing, Department of Information Technology, Boston Children\u2019s Hospital, Boston, MA 02115, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shira","family":"Rockowitz","sequence":"additional","affiliation":[{"name":"Research Computing, Department of Information Technology, Boston Children\u2019s Hospital, Boston, MA 02115, USA"},{"name":"Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children\u2019s Hospital, Boston, MA 02115, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6297-7499","authenticated-orcid":false,"given":"Mary C.","family":"Whitman","sequence":"additional","affiliation":[{"name":"Department of Ophthalmology, Boston Children\u2019s Hospital, Boston, MA 02115, USA"},{"name":"Department of Ophthalmology, Harvard Medical School, Boston, MA 02115, USA"},{"name":"F.M. Kirby Neurobiology Center, Boston Children\u2019s Hospital, Boston, MA 02115, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,1,12]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"138","DOI":"10.1034\/j.1600-0420.2003.00024.x","article-title":"Negative social bias against children with strabismus","volume":"81","author":"Uretmen","year":"2003","journal-title":"Acta Ophthalmol. 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