Genetics and epigenetics in human disease
I. Autosomal-dominant hypertension with Brachydactyly Type E
The search led to a family in whom a severe form of autosomal-dominant hypertension is combined with Brachydactyly Type E (short fingers). The phenotypes are always concomitantly inherited. We have since identified six families with this syndrome around the world. Over the past few years we have very carefully worked up the syndromic features as vessel tortuousity, impaired baroreceptor function, increased skin fibroblast proliferation and hyperplasia of the arterial smooth muscle cell layer. We showed that all these families have a rearrangement syndrome on chromosome 12p. We discovered different genomic rearrangements with deletions, reinsertions and inversions in the single families. Since the inversion is a common feature of the syndrome, we suppose that it harbors the genetic cause. The inverted interval is a gene-free region with no protein-coding genes but encloses many tissue-specific splice variants of non-coding RNAs (ncRNAs). We focused on a novel potential microRNA.
We learned that the syndrome is also complex at the genomic level, and have initiated whole genome sequencing of four families to clarify it at the single base level. Pursuit of the brachydactyly phenotype has brought us to an understanding of the complex epigenetic regulation of the gene that encodes parathyroid hormone-like hormone (PTHLH), which resides close to our locus. We have made remarkable progress thanks to the identification of two more translocation families with brachydactyly type E (BDE) on chromosome 12p.
II. Epigenetic gene and ncRNA regulation in isolated forms of Brachydactyly Type E (BDE)
We have made remarkable progress concerning the brachydactyly phenotype. We studied two families with BDE carrying translocations t(8;12)(q13;p11.2) and t(4;12)(q13.2-13.3;p11.2), respectively. In a collaborative project we linked the gene PTHLH encoding the parathyroid hormone related peptide on chromosome 12p11.2 to BDE with short stature. We observed tissue-specific downregulated PTHLH expression in chondrogenically-differentiated fibroblasts of BDE-patients. Using chromosome conformation capture techniques, we identified the native PTHLH cis-regulatory elements for the first time and determined how they are altered in BDE. Additionally we identified and characterized an enhancer that encodes a regulatory long ncRNA.
This case broadens our understanding of classical enhancers and molecular regulatory genetics, showing the involvement of ncRNA in human disease. Interestingly the ncRNA was upregulated in BDE-patients, implying that the genomic architecture that is disturbed in the translocation caused dysregulation of the protein coding gene PTHLH and the ncRNA. To sum up, our work reveals a novel cis- and trans-chromosomal communicator, which acts through DNA and ncRNA on gene regulation.
We will continue to investigate the mechanisms responsible for our cases of autosomal-dominant hypertension and brachdactyly and will follow up on the unexpected epigenetic findings in humans and animal models. Currently, we are establishing a genome-wide method termed ChIA-PET to detect chromatin interactions using paired-end tag deep sequencing on chromatin of human mesenchymal stem cells (MSC) and primary chondrocytes. Our aim is to identify intra- and inter-chromosomal communication and chromatin interaction partners for all of the known chondrogenesis genes. Moreover we will identify by chromatin isolations through RNA purification (ChIRP) the ncRNA genomic binding sites to investigate the ncRNA-mediated mechanisms of “remote-controlled” gene regulation. We will contribute to the completion of the chondrogenic pathways dysregulated in human skeletal disorders.