Neuropathologically-focused somatic genetic profiling of PRNP in Heidenhain variant, as a focal model for neurodegeneration, and across sporadic prion disease

Creutzfeldt-Jakob Disease (CJD), the most common human prion disease, is associated with pathologic misfolding of the prion protein (PrP), encoded by the PRNP gene (1). Of human prion disease cases, ~1% are transmitted by misfolded PrP, ~15% are inherited, and ~85% are sporadic (sCJD) (2). Familial cases are inherited through germline mutations in PRNP, while the cause of sCJD is unknown (3-8). Somatic mutations have been hypothesized as a cause of sCJD (9-10), and recent studies have revealed that somatic mutations accumulate in neurons during aging (11-12). To investigate the hypothesis that somatic mutations in PRNP may underlie sCJD, we sequenced PRNP in 205 sCJD cases and 170 age-matched non-disease controls. We included 5 cases of Heidenhain variant sporadic CJD (H-sCJD), where visual symptomatology and neuropathology implicate focal initiation of prion formation, and examined multiple regions across the brain including in the affected occipital cortex. We performed Multiple Independent Primer PCR Sequencing (MIPP-Seq) with a median depth of >5,000X across the PRNP coding region and analyzed for variants using MosaicHunter. An allele mixing experiment showed positive detection of variants in bulk DNA at a variant allele fraction as low as 0.2%. We identified multiple polymorphic germline variants among individuals in our cohort. However, we did not identify bona fide somatic variants in sCJD, including across multiple affected regions of H-sCJD, nor in control individuals. Beyond our stringent variant-identification pipeline, we also analyzed raw sequencing allele fractions, and observed no evidence of prion disease enrichment for the known germline pathogenic variants P102L, D178N, and E200K. In conclusion, ultra-deep PRNP sequencing did not identify pathogenic somatic mutations in H-sCJD or a broader cohort of sCJD, indicating that clonal somatic mutations in PRNP may not play a major role in sporadic prion disease.

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