Human models of GLE1-associated LCCS1 reveal neural crest deficiency and multisystem developmental failure accompanied by altered RNA metabolism

Lethal congenital contracture syndrome 1 (LCCS1) is a neurodevelopmental disorder caused by GLE1 c.432-10A>G variant and presenting fetal akinesia, defects in anterior horn spinal cord, skin, skull, and skeletal muscle development. The uniform prenatal lethality of LCCS1 limits access to patient material, thereby hindering mechanistic studies in physiologically relevant models. To overcome this, human embryonic stem cells (hESCs) carrying the LCCS1 variant, patient-derived fetal fibroblasts, and transcriptomic and proteomic profiling were utilized to examine early GLE1 dysfunction in human cells and tissues. Across LCCS1 cell types, reduced global transcription and translation were observed, while nucleocytoplasmic poly(A)+ RNA distribution was unchanged. Despite its context-dependent effects on proliferation, LCCS1 variant altered mRNA decay kinetics and increased stress granule formation in differentiated cells. LCCS1 hESCs retained core pluripotency but reduced choline acetyltransferase and β tubulin III levels, together with increased neurofilament inclusion incidence, indicate functional immaturity in differentiated spinal motor neurons. Differentiation of LCCS1 hESC-derived gastruloids uncovered broad perturbations in neuromuscular and neural crest derivative development, results which were supported by phenotypes detected in ectodermal organoids and fetal LCCS1 tissue. These findings provide new mechanistic insight into LCCS1 pathogenesis and establish a robust human model framework for studying neurodevelopmental disorders.