High-throughput imaging of ATG9A distribution as a diagnostic functional assay for adaptor protein complex 4-associated hereditary spastic paraplegia

• Published in: Brain communications Vol. 3; no. 4; p. fcab221
• Main Authors: Ebrahimi-Fakhari, Darius, Alecu, Julian E, Brechmann, Barbara, Ziegler, Marvin, Eberhardt, Kathrin, Jumo, Hellen, D’Amore, Angelica, Habibzadeh, Parham, Faghihi, Mohammad Ali, De Bleecker, Jan L, Vuillaumier-Barrot, Sandrine, Auvin, Stéphane, Santorelli, Filippo M, Neuser, Sonja, Popp, Bernt, Yang, Edward, Barrett, Lee, Davies, Alexandra K, Saffari, Afshin, Hirst, Jennifer, Sahin, Mustafa
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01.01.2021
• Subjects: Original; high-throughput imaging; functional assay; adaptor protein complex 4; hereditary spastic paraplegia; biomarker
• ISSN: 2632-1297; 2632-1297
• DOI: 10.1093/braincomms/fcab221

Abstract Adaptor protein complex 4-associated hereditary spastic paraplegia is caused by biallelic loss-of-function variants in AP4B1, AP4M1, AP4E1 or AP4S1, which constitute the four subunits of this obligate complex. While the diagnosis of adaptor protein complex 4-associated hereditary spastic paraplegia relies on molecular testing, the interpretation of novel missense variants remains challenging. Here, we address this diagnostic gap by using patient-derived fibroblasts to establish a functional assay that measures the subcellular localization of ATG9A, a transmembrane protein that is sorted by adaptor protein complex 4. Using automated high-throughput microscopy, we determine the ratio of the ATG9A fluorescence in the trans-Golgi-network versus cytoplasm and ascertain that this metric meets standards for screening assays (Z′-factor robust >0.3, strictly standardized mean difference >3). The ‘ATG9A ratio’ is increased in fibroblasts of 18 well-characterized adaptor protein complex 4-associated hereditary spastic paraplegia patients [mean: 1.54 ± 0.13 versus 1.21 ± 0.05 (standard deviation) in controls] and receiver-operating characteristic analysis demonstrates robust diagnostic power (area under the curve: 0.85, 95% confidence interval: 0.849–0.852). Using fibroblasts from two individuals with atypical clinical features and novel biallelic missense variants of unknown significance in AP4B1, we show that our assay can reliably detect adaptor protein complex 4 function. Our findings establish the ‘ATG9A ratio’ as a diagnostic marker of adaptor protein complex 4-associated hereditary spastic paraplegia. Ebrahimi-Fakhari et al. establish the intracellular ATG9A distribution as a diagnostic marker for AP-4-associated hereditary spastic paraplegia using a novel high-throughput assay in patient-derived fibroblasts. This approach enables the functional validation of novel variants in AP4B1, AP4M1, AP4S1 and AP4E1 with robust diagnostic power and opens opportunities for biomarker discovery. Graphical Abstract Graphical Abstract