The Discovery of a LEMD2-Associated Nuclear Envelopathy with Early Progeroid Appearance Suggests Advanced Applications for AI-Driven Facial Phenotyping

Am J Hum Genet. 2019 Apr 4;104(4):749-757. doi: 10.1016/j.ajhg.2019.02.021. Epub 2019 Mar 21.

Abstract

Over a relatively short period of time, the clinical geneticist's "toolbox" has been expanded by machine-learning algorithms for image analysis, which can be applied to the task of syndrome identification on the basis of facial photographs, but these technologies harbor potential beyond the recognition of established phenotypes. Here, we comprehensively characterized two individuals with a hitherto unknown genetic disorder caused by the same de novo mutation in LEMD2 (c.1436C>T;p.Ser479Phe), the gene which encodes the nuclear envelope protein LEM domain-containing protein 2 (LEMD2). Despite different ages and ethnic backgrounds, both individuals share a progeria-like facial phenotype and a distinct combination of physical and neurologic anomalies, such as growth retardation; hypoplastic jaws crowded with multiple supernumerary, yet unerupted, teeth; and cerebellar intention tremor. Immunofluorescence analyses of patient fibroblasts revealed mutation-induced disturbance of nuclear architecture, recapitulating previously published data in LEMD2-deficient cell lines, and additional experiments suggested mislocalization of mutant LEMD2 protein within the nuclear lamina. Computational analysis of facial features with two different deep neural networks showed phenotypic proximity to other nuclear envelopathies. One of the algorithms, when trained to recognize syndromic similarity (rather than specific syndromes) in an unsupervised approach, clustered both individuals closely together, providing hypothesis-free hints for a common genetic etiology. We show that a recurrent de novo mutation in LEMD2 causes a nuclear envelopathy whose prognosis in adolescence is relatively good in comparison to that of classical Hutchinson-Gilford progeria syndrome, and we suggest that the application of artificial intelligence to the analysis of patient images can facilitate the discovery of new genetic disorders.

Keywords: LEM domain-containing protein 2”; “deep neuronal network” and “intra-syndromal similarity; “next-generation phenotyping”; “nuclear envelopathy”; “progeria-like”.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adolescent
  • Artificial Intelligence
  • Cell Line, Tumor
  • Cell Nucleus
  • Child
  • Child, Preschool
  • Diagnosis, Computer-Assisted
  • Face
  • Fibroblasts / metabolism
  • Humans
  • Male
  • Mass Screening / methods
  • Medical Informatics
  • Membrane Proteins / genetics*
  • Mutation*
  • Nuclear Proteins / genetics*
  • Phenotype
  • Progeria / genetics*
  • Prognosis
  • Syndrome

Substances

  • LEMD2 protein, human
  • Membrane Proteins
  • Nuclear Proteins