Resolving Incomplete Penetrance in Primary Immunodeficiencies

Primary Immunodeficiencies (PIDs) are monogenic disorders of the immune system. Phenotypic variability of PIDs provide clinical challenges in these inborn errors. Recent studies indicate that 10% of autosomal genes randomly commit to expression of a single allele, termed monoallelic expression (MAE). Unlike X-inactivation or imprinting, MAE is not specific to gene clusters or a single chromosome and leads to a diverse population of cells at the transcript level. Despite an increase in the understanding of MAE, both the functional and mechanistic impact in disease is unknown. MAE contributes to the phenotypic variability in individuals with PIDs. Single T cells from healthy donor PBMCs (n = 10) expanded into clonal populations. Donors examined for heterozygous single nucleotide polymorphisms (snps) in PID genes via WES. Bulk RNA-sequencing of clones used to identify expressed transcript. Allele specific read counts merged to snps across donors using custom computational pipeline. Gene candidates validated via digital droplet PCR (ddPCR). Single cell qPCR of family members with JAK1 mutation to assess MAE in patients, healthy carriers and healthy controls. Single-cell RNA-sequencing to examine MAE across various immune cell subtypes. WES identifies 350 PID genes with heterozygous snps that can be assessed in our system. Computational pipeline validated via allele specific expression of known imprinted genes. Analysis reveals monoallelic expression of numerous PID genes across 45 clonal T cell populations. Select gene candidates (4) validated in additional clones via ddPCR. Using this system of monoclonal T cells, genes which cause PIDs were found to undergo monoallelic expression. Mutations in a number of these genes are known to cause autosomal dominant inherited disease, facilitating further study in patient samples.