A ONECUT1 regulatory, non-coding region in pancreatic development and diabetes [Nanopore-seq]

In a patient with permanent neonatal syndromic diabetes clinically similar to cases with ONECUT1 biallelic mutations, we identified a disease-causing deletion located upstream of ONECUT1. Through genetic, genomic and functional studies we identified a crucial regulatory region acting as an enhancer of ONECUT1 specifically during pancreatic development. This enhancer region contains a low-frequency variant showing strong association with type 2 diabetes and other glycemic traits, thus extending the contribution of this region to common forms of diabetes. Clinical relevance is provided by experimentally tailored therapy options for patients carrying ONECUT1 coding or regulatory mutations. Nanopore sequencing with adaptive sampling and 5hmC and 5mC methylation calling was conducted. Variant pahsing was performed with hESC (HUES) wildtype and in two knockout lines. The gene-edited hESCs consisted of a heterozygous 108kb deletion of Patient 1 (Pat1-del) and ONECUT1 heterozgyous knockout on the same allel (cis) or on different allels (trans). Methylation analysis was performed for HUES8 wildtype cells at hESC and differentiated pancreatic progenitors (PP).