Recessive mutations in a distal PTF1A enhancer cause isolated pancreatic agenesis

Abstract

The contribution of cis-regulatory mutations to human disease remains poorly understood. Whole genome sequencing can identify all non-coding variants, yet discrimination of causal regulatory mutations represents a formidable challenge. We used epigenomic annotation in hESC-derived embryonic pancreatic progenitor cells to guide the interpretation of whole genome sequences from patients with isolated pancreatic agenesis. This uncovered six different recessive mutations in a previously uncharacterized ~400bp sequence located 25kb downstream of PTF1A (pancreas-specific transcription factor 1a) in ten families with pancreatic agenesis. We show that this region acts as a developmental enhancer of PTF1A and that the mutations abolish enhancer activity. These mutations are the most common cause of isolated pancreatic agenesis. Integrating genome sequencing and epigenomic annotation in a disease-relevant cell type can uncover novel non-coding elements underlying human development and disease.

Predicting enhancers using a small subset of high confidence examples and co-training

“…The importance of distal regulatory elements like enhancers in human disease was suggested years ago by the observation in many genome-wide association studies that causal variants are very often identified distant from transcribed genes (Helgadottir et al, 2007). This suggestion has been confirmed in more recent studies showing that the disruption of the function of these regulatory elements can lead to changes in gene expression and disease phenotypes (Weedon et al, 2014;Lupiáñez et al, 2015).…”

Variant Interpretation: Functional Assays to the Rescue

“…[16][17][18] Variation in transcriptional regulatory elements is also important, and pathogenic regulatory variants have been identified for a number of Mendelian disorders. [49][50][51][52] One specific example is the alteration of SORT1 (MIM: 602458) expression by a transcriptional regulatory variant that can increase the risk of myocardial infarction by 40%. 53 However, the relationship between variation and disease in transcriptional regulatory elements is poorly understood.…”

An N‐Ethyl‐N‐Nitrosourea (ENU) Mutagenized Mouse Model for Autosomal Dominant Nonsyndromic Kyphoscoliosis Due to Vertebral Fusion

“…Such mutations are frequently large deletions or duplications, but may also consist of single‐nucleotide mutations, similar to those most frequently induced by ENU, as found in isolated pancreatic agenesis, and recently described in the promoter region of ovo‐like zinc finger 2 ( OVOL2 ) in families with autosomal‐dominant corneal endothelial dystrophies 71. Mutations upstream of PTF1A were found to reduce the expression of PTF1A , whereas mutations in the OVOL2 promoter were able to induce OVOL2 expression, likely leading to aberrant ectopic OVOL2 expression in the developing cornea 70, 71. Either of these two molecular mechanisms could account for the dominant disease presentation in Hvf mice, eg, through a dosage effect due to a reduction in the level of a critical transcript, or through ectopic induction of a transcript, and either of these may be time and/or spatially specific.…”

“…These include triphalangeal thumb/preaxial polydactyly (autosomal dominant with variable penetrance), due to mutations in the ZPA regulatory sequence, a long‐range cis‐acting regulator of Sonic Hedgehog ( SHH ) gene expression67, 68, 69; and autosomal recessive isolated pancreatic agenesis due to noncoding mutations downstream of pancreas‐specific transcription factor 1a ( PTF1A ) 70. Such mutations are frequently large deletions or duplications, but may also consist of single‐nucleotide mutations, similar to those most frequently induced by ENU, as found in isolated pancreatic agenesis, and recently described in the promoter region of ovo‐like zinc finger 2 ( OVOL2 ) in families with autosomal‐dominant corneal endothelial dystrophies 71.…”

“…Either of these two molecular mechanisms could account for the dominant disease presentation in Hvf mice, eg, through a dosage effect due to a reduction in the level of a critical transcript, or through ectopic induction of a transcript, and either of these may be time and/or spatially specific. Future work to identify the Hvf causative mutation will focus on analyses of the six intergenic and three intronic noncoding variants in transcriptional assays, such as luciferase assays, similarly to those undertaken for PTF1A and OVOL2‐associated noncoding variants 70, 71. To determine the specific role of the variants in somitogenesis, these assays may need to be undertaken in a somite cell‐line, such as cells derived from pluripotent stem cells,72 or in bone‐specific cells such as chondrocytes.…”