Modeling of mitochondrial genetic polymorphisms reveals induction of heteroplasmy by pleiotropic disease locus 10398A>G

Abstract

Mitochondrial (MT) dysfunction has been associated with several neurodegenerative diseases including Alzheimer’s disease (AD). While MT-copy number differences have been implicated in AD, the effect of MT heteroplasmy on AD has not been well characterized. Here, we analyzed over 1800 whole genome sequencing data from four AD cohorts in seven different tissue types to determine the extent of MT heteroplasmy present. While MT heteroplasmy was present throughout the entire MT genome for blood samples, we detected MT heteroplasmy only within the MT control region for brain samples. We observed that an MT variant 10398A>G (rs2853826) was significantly associated with overall MT heteroplasmy in brain tissue while also being linked with the largest number of distinct disease phenotypes of all annotated MT variants in MitoMap. Using gene-expression data from our brain samples, our modeling discovered several gene networks involved in mitochondrial respiratory chain and Complex I function associated with 10398A>G. The variant was also found to be an expression quantitative trait loci (eQTL) for the gene MT-ND3. We further characterized the effect of 10398A>G by phenotyping a population of lymphoblastoid cell-lines (LCLs) with and without the variant allele. Examination of RNA sequence data from these LCLs reveal that 10398A>G was an eQTL for MT-ND4. We also observed in LCLs that 10398A>G was significantly associated with overall MT heteroplasmy within the MT control region, confirming the initial findings observed in post-mortem brain tissue. These results provide novel evidence linking MT SNPs with MT heteroplasmy and open novel avenues for the investigation of pathomechanisms that are driven by this pleiotropic disease associated loci.

Reliable multiplex generation of pooled induced pluripotent stem cells

“…Using gene expression data obtained from RNA sequencing data for LCLs 37 (see STAR Methods ), we checked for association between gene expression and reprogramming ability across 58 different LCLs present in the pool of 120 donors. Of the 58 lines, one individual was stratified from the central population cluster after performing PCA.…”

“…For a subset of donor LCLs from the PGP, we have RNA sequencing data available that was generated from a different project ( https://www.synapse.org/#!Synapse:syn25927432 ). 37 The RNA sequencing was obtained by first culturing the LCLs overnight (2x10 6 cells per donor in 1 well of a 6 well plate) in RPMI medium supplemented with 10% Fetal Bovine Serum (FBS) and 1% penicillin-streptomycin (2mL of media per well of a 6-well plate). The following day, the LCLs were harvested and we performed total RNA extraction of the LCLs (Invitrogen PureLink RNA Mini Kit).…”