Changes in 3D genome organization can cause human disease

Novel pathological mechanism described for BOFS whereby an inversion physically disconnects TFAP2A from the enhancers that control its expression in the neural crest.

The CMMC team lead by Álvaro Rada Iglesias recently published a study in the prestigious journal Cell Stem Cell entitled "Modeling the pathological long-range regulatory effects of human structural variation with patient-specific hiPSCs" in which they describe a new experimental strategy to elucidate how changes in 3D genome organization can cause human disease. https://www.cell.com/cell-stem-cell/fulltext/S1934-5909 (19)30103-1

Each human cell contains up to 2 metres of DNA (i.e. the human genome) that need to be packed within tiny cellular structures called nuclei (around 10 um in diameter).

"Thanks to recent technical advances, we are starting to understand not only how the genome is folded within cellular nuclei but also how such 3D genome organization plays central roles in controlling the way genes are expressed. Furthermore, a number of recent studies have shown that alterations in the 3D genome organization due to structural variation (e.g. deletions, inversions) can cause human birth defects by disrupting the physical communication between genes and other DNA sequences that are in charge of controlling their expression, which are typically referred to as enhancers. However, these novel disease mechanisms can be sometimes difficult to study, since animal models, which have been instrumental to understand human disease, do not always recapitulate the way human cells respond to changes in 3D genome organization and gene expression" Alvaro Rada-Iglesias comments.

In a recent study lead by Magdalena Laugsch (Postdoc) and Michaela Bartusel (PhD student) the Rada-Iglesias laboratory has implemented a new experimental approach to investigate how changes in 3D genome organization can cause human disease.

Briefly, cells are first isolated from patients with structural variants and then reprogrammed towards a pluripotent state in which cells can be differentiated into any human cell type of interest. Subsequently, these differentiated cells derived from the patients are analysed with novel methods that can uncover how the structural variants alter 3D genome organization and, consequently, gene expression patterns.

To implement this experimental strategy, the Rada-Iglesias team, in collaboration with Julia Baptista, a geneticist at Exeter University (UK), focused on a patient with a rare disease called Branchio-Oculo-Facial Syndrome (BOFS). BOFS is characterized by a number of birth defects affecting facial structures such as the mouth, eyes and ears, which are caused by mistakes that occur during the development of a specific embryonic cell population called the neural crest.

Moreover, all BOFS cases reported to date are caused by mutations that directly affect one gene called TFAP2A. However, the new BOFS patient that the Rada-Iglesias has been investigating did not display any mutation within TFAP2A. Instead, what they found was a long inversion in one of the patient’s chromosomes.

Using the experimental strategy described above, they then showed that this inversion alters the 3D organization of the genome in the neural crest of the patient. As a result, the TFAP2A gene can not longer communicate with its enhancers, which reduces its expression and causes BOFS. Overall, this experimental approach could be broadly used to elucidate the pathological mechanisms by which certain structural variants cause birth defects, an essential step to improve the diagnosis and even the future treatment of this kind of disorders. Lastly, this approach offers an alternative that overcomes the ethical problems associated with the use of animal models in human research.

Publication
Modeling the Pathological Long-Range Regulatory Effects of Human Structural Variation with Patient-Specific hiPSCs.
Laugsch M, Bartusel M, Rehimi R, Alirzayeva H, Karaolidou A, Crispatzu G, Zentis P, Nikolic M, Bleckwehl T, Kolovos P, van Ijcken WFJ, Šarić T, Koehler K, Frommolt P, Lachlan K, Baptista J, Rada-Iglesias A.
Cell Stem Cell. 2019 Mar 21. pii: S1934-5909(19)30103-1. doi: 10.1016/j.stem.2019.03.004. [Epub ahead of print] - PMID:30982769
https://www.cell.com/cell-stem-cell/fulltext/S1934-5909 (19)30103-1

This recent work has been supported by the Else Kröner Fresenius Foundation fund and by the Junior Research Group Program of the Center for Molcular Medicine Cologne.

Contact
Prof. Dr. Alvaro Rada-Iglesias
aradaigl[at]uni-koeln.de