Personalized Functional Genomics for Mitochondrial Encephalopathy Gene Discovery

Project Summary
Mitochondrial disease is a commonly occurring inherited condition, incidence 1/5000, which can affect every
organ system and thus exhibits a broad range of clinical phenotypes. The most common are neurological and
neuromuscular dysfunction that manifest as neurodegeneration, seizures, ataxia, chronic progressive
external opthalmoplegia (CPEO), and hypotonia. Childhood-onset mitochondrial disease most often results
from mutations in the nuclear genome; however, the majority of cases remain without a molecular diagnosis
and no effective treatments thus underscoring the critical need to identify the genetic aberrations driving these
disorders. We propose a personalized functional genomics approach combining genome-wide sequencing,
transcriptomics, metabolomics and mitochondrial functional profiling in cells to identify validated novel
mitochondrial disease genes and variants. We will leverage a multi-omic strategy for identifying the
pathogenic genes and elucidating pathomechanisms: 1. Genome-wide sequencing of patients coupled with
transcriptomics and metabolomics 2. Cell-based functional studies of genes and pathways identified in
patients. Through our international network of collaborators we have collected patients with clinically
confirmed primary mitochondrial encephalopathy who do not have a molecular diagnosis. For patients who
have already had WES/WGS but no molecular diagnosis we will re-interpret these data and leverage our
ability to interpret beyond ABMGG guidelines for diagnosis. Additionally, we have a parallel effort to identify
disease genes through datamining the clinical exome database at Baylor Genetics diagnostic laboratory
wherein genes that are known to be essential for mitochondrial function but are not yet demonstrated as
disease causing are analyzed for mutations in patients. Gene causality will be determined through a series of
cell-based disease modeling experiments of mitochondrial functional profiling that include strategies of gene
knock down, high-throughput mutagenesis knock-in, and cDNA complementation studies. We will utilize this
technology to test the functionality of variants of uncertain significance identified in our sequencing efforts as
well as those obtained through collaborators, diagnostic laboratories, and the public domain. This work will
generate an unprecedented resource of systematic profiling of cellular mitochondrial function and functionally-
confirmed pathogenic molecular defects. The elucidation of these pathogenic genes and variants will
immediately improve the molecular diagnostic potential for children with suspected mitochondrial disease.
Moreover, by identifying the pathogenic genes for primary mitochondrial encephalopathy we will empower the
scientific community focused on neurological and neurodegenerative disorders, which have a more complex
etiology, by delivering genes and pathways for further study of the pathogenetic mechanisms of these global
health problems.

Grant Number: 5R01NS083726-10
NIH Institute/Center: NIH
Principal Investigator: Penelope Bonnen