Deep Learning-Based Identification of Intraocular Pressure-Associated Genes Influencing Trabecular Meshwork Cell Morphology

• Published in: Ophthalmology science (Online) 2024-07, Vol.4 (4), p.100504-100504, Article 100504
• Main Authors: Greatbatch, Connor J., Lu, Qinyi, Hung, Sandy, Tran, Son N., Wing, Kristof, Liang, Helena, Han, Xikun, Zhou, Tiger, Siggs, Owen M., Mackey, David A., Liu, Guei-Sheung, Cook, Anthony L., Powell, Joseph E., Craig, Jamie E., MacGregor, Stuart, Hewitt, Alex W.
• Format: Article
• Language: English
• Subjects: CRISPR; Genetics; Glaucoma; Morphological profiling; Transcriptomics
• ISSN: 2666-9145; 2666-9145
• DOI: 10.1016/j.xops.2024.100504

Genome-wide association studies have recently uncovered many loci associated with variation in intraocular pressure (IOP). Artificial intelligence (AI) can be used to interrogate the effect of specific genetic knockouts on the morphology of trabecular meshwork cells (TMCs) and thus, IOP regulation. Experimental study. Primary TMCs collected from human donors. Sixty-two genes at 55 loci associated with IOP variation were knocked out in primary TMC lines. All cells underwent high-throughput microscopy imaging after being stained with a 5-channel fluorescent cell staining protocol. A convolutional neural network was trained to distinguish between gene knockout and normal control cell images. The area under the receiver operator curve (AUC) metric was used to quantify morphological variation in gene knockouts to identify potential pathological perturbations. Degree of morphological variation as measured by deep learning algorithm accuracy of differentiation from normal controls. Cells where LTBP2 or BCAS3 had been perturbed demonstrated the greatest morphological variation from normal TMCs (AUC 0.851, standard deviation [SD] 0.030; and AUC 0.845, SD 0.020, respectively). Of 7 multigene loci, 5 had statistically significant differences in AUC (P