Pancreatic Development Disrupted by Mutations in the Dark Genome

Nearly 98% of the human genome does not encode proteins but comprises noncoding sequences—the “dark genome”—such as regulatory sequences that control gene transcription (enhancer elements). Thousands of enhancer elements in the genome act as switches that activate or deactivate genes in the right tissues, at the right time.

Like mutations in protein-coding genes that cause diseases such as sickle cell anemia or Huntington’s disease, mutations in an enhancer element could also trigger genetic disease. But enhancer element mutations are often overlooked or under-estimated. This is because of the prevalent notion that built-in redundancy among enhancers that regulate the same gene mitigates their pathogenic effect.

However, in recent studies researchers have shown that mutations in an enhancer element called EnhP near a gene that encodes the transcription factor PTF1A result in congenital malformations of the pancreas and the cerebellum, together with diabetes in newborns. This indicates that inherited genetic diseases can be caused by mutations in dark genome sequences that do not encode a protein.

A new study (“Pancreas agenesis mutations disrupt a lead enhancer controlling a developmental enhancer cluster”) from the same team, published in Developmental Cell, shows that this lead enhancer activates a cluster of embryonic-stage enhancers that regulates PTF1A in immature progenitor cells of the pancreas. The leading role of EnhP overrides the existence of functional redundancy among other PTF1A enhancers. Using CRISPR-based mouse and human genetic models, the researchers at the Centre for Genomic Regulation (CRG) in Spain and the Imperial College London demonstrated that this fleeting expression of PTF1A in the immature pancreas controls early growth of the organ and primes it for differentiation by hormones through a series of epigenetic signatures.

Jorge Ferrer, PhD, a scientist at CRG and senior author of the study, said, “Clinical genetics is shifting from a focus on sequencing protein-coding genes to sequencing whole genomes. It is now theoretically possible to discover disease-causing mutations that lie outside of traditional areas of the genome, although it is still challenging to discern which parts of the genome are truly vulnerable to mutations.”

The findings of the current study reveal how genome regulatory mechanisms drive the development and differentiation of the pancreas. It also indicates loss-of-function mutations in master-regulator enhancers can trigger genetic diseases. EnhP is only one such regulator sequence. Uncovering the role of mutations in other enhancers could lead to treatments for various diseases.

In addition, Ferrer said, “EnhP sparks a molecular program that is needed for proper formation of human beta cells. This knowledge can be harnessed to improve laboratory conditions to create beta cells.”

In this study, the authors showed that mice lacking both copies of EnhP were born with a severely underdeveloped pancreas and insulin-deficient diabetes. They also studied EnhP function in human stem cells in vitro.

“We show that enhancers operate in a hierarchical manner, and this one sits straight at the top,” said Ferrer. “This is a new concept, and it solves a paradox of how mutations in a single enhancer can be catastrophic despite the existence of multiple other enhancers regulating the same gene. This is not just about this particular enhancer or disease, there are probably many other enhancers with this particular function in the human genome. Finding them will help us understand which enhancers are vulnerable to mutations that cause various other monogenic diseases.”