Biallelic null variants in PNPLA8 cause microcephaly by reducing the number of basal radial glia
Authors: Nakamura Yuji , Shimada Issei S , Maroofian Reza , Falabella Micol , Zaki Maha S , Fujimoto Masanori , Sato Emi , Takase Hiroshi , Aoki Shiho , Miyauchi Akihiko , Koshimizu Eriko , Miyatake Satoko , Arioka Yuko , Honda Mizuki , Higashi Takayoshi , Miya Fuyuki , Okubo Yukimune , Ogawa Isamu , Scardamaglia Annarita , Miryounesi Mohammad , Alijanpour Sahar , Ahmadabadi Farzad , Herkenrath Peter , Dafsari Hormos Salimi , Velmans Clara , Al Balwi Mohammed , Vitobello Antonio , Denommé-Pichon Anne-Sophie , Jeanne Médéric , Civit Antoine , Abdel-Hamid Mohamed S , Naderi Hamed , Darvish Hossein , Bakhtiari Somayeh , Kruer Michael C , Carroll Christopher J , Ghayoor Karimiani Ehsan , Khailany Rozhgar A , Abdulqadir Talib Adil , Ozaslan Mehmet , Bauer Peter , Zifarelli Giovanni , Seifi Tahere , Zamani Mina , Al Alam Chadi , Alvi Javeria Raza , Sultan Tipu , Efthymiou Stephanie , Pope Simon A S , Haginoya Kazuhiro , Matsunaga Tamihide , Osaka Hitoshi , Matsumoto Naomichi , Ozaki Norio , Ohkawa Yasuyuki , Oki Shinya , Tsunoda Tatsuhiko , Pitceathly Robert D S , Taketomi Yoshitaka , Houlden Henry , Murakami Makoto , Kato Yoichi , Saitoh Shinji 
Published: August 2024

Abstract
Patatin-like phospholipase domain-containing lipase 8 (PNPLA8), one of the calcium-independent phospholipase A2 enzymes, is involved in various physiological processes through the maintenance of membrane phospholipids. Biallelic variants in PNPLA8 have been associated with a range of paediatric neurodegenerative disorders. However, the phenotypic spectrum, genotype–phenotype correlations and the underlying mechanisms are poorly understood.
Here, we newly identified 14 individuals from 12 unrelated families with biallelic ultra-rare variants in PNPLA8 presenting with a wide phenotypic spectrum of clinical features. Analysis of the clinical features of current and previously reported individuals (25 affected individuals across 20 families) showed that PNPLA8-related neurological diseases manifest as a continuum ranging from variable developmental and/or degenerative epileptic–dyskinetic encephalopathy to childhood-onset neurodegeneration. We found that complete loss of PNPLA8 was associated with the more profound end of the spectrum, with congenital microcephaly.
Using cerebral organoids generated from human induced pluripotent stem cells, we found that loss of PNPLA8 led to developmental defects by reducing the number of basal radial glial cells and upper-layer neurons. Spatial transcriptomics revealed that loss of PNPLA8 altered the fate specification of apical radial glial cells, as reflected by the enrichment of gene sets related to the cell cycle, basal radial glial cells and neural differentiation. Neural progenitor cells lacking PNPLA8 showed a reduced amount of lysophosphatidic acid, lysophosphatidylethanolamine and phosphatidic acid. The reduced number of basal radial glial cells in patient-derived cerebral organoids was rescued, in part, by the addition of lysophosphatidic acid.
Our data suggest that PNPLA8 is crucial to meet phospholipid synthetic needs and to produce abundant basal radial glial cells in human brain development.