Molecular mechanism of a new cardiac syndrome associated with an enhancer deletion – LEARN

Genetic study has been performed using whole genome sequencing (WGS). Based on transgenic mouse strains, we assessed the impact of Family#1 mutation on the phenotype and on gene expression. Then, we generated human cardiomyocytes derived iPS cells (CM-iPS) isogenic models to evaluate the epigenome (CUT&RUN and ATAC-seq), transcriptome (RNA-seq) and topological associated domain (TAD) remodelling (Hi-C).

By WGS we uncovered a deletion of 15kb in a gene desert area on 4q25, segregating in all affected relatives of Family#1. The 6 other families present overlapping deletions. Mouse model recapitulates the cardiac phenotype and exhibit a dysregulation of Pitx2 expression in cardiac specific compartments. Based on human CM-iPS models, epigenetic data highlight among the 15kb deletion a unique open region containing a CTCF binding site, crucial for delimiting TAD boundaries. Hi-C assay reveals the fusion of 2 TADs and highlights new interactions between PITX2 and atrial specific regulatory elements.

We describe a new molecular mechanism implying a yet unidentified non-coding regulatory element of PITX2 and responsible for a new complex electrical and developmental cardiac syndrome.
The datasets generated for this project and the molecualr mechanism uncovered are relevant for a broader spectrum of (cardiac) disease.

1. Multimodality imaging and transciptomics to phenotype mitral valve dystrophy in a unique ki filamin-a rat model
Delwarde C, Toquet C, Aumond P, Kayvanjoo AH, Foucal A, Le Vely B, Baudic M, Lauzier B, Blandin S, Véziers J, Paul-Gilloteaux P, Lecointe S, Baron E, Massaiu I, Poggio P, Rémy S, Anegon I, Le Marec H, Monassier L, Schott JJ, Mass E, Barc J, Le Tourneau T, Merot J, Capoulade R
Cardiovasc Res. 2022, Accepted

2. Genome-wide association analyses identify new Brugada syndrome risk loci and highlight a new mechanism of sodium channel regulation in disease susceptibility.
Barc J, Tadros R, Glinge C, Chiang DY, Jouni M, Simonet F, Jurgens SJ, Baudic M, Nicastro M, Potet F, Offerhaus JA, Walsh R, Choi SH, Verkerk AO, Mizusawa Y, Anys S, Minois D, Arnaud M, Duchateau J, Wijeyeratne YD, Muir A, Papadakis M, Castelletti S, Torchio M, Ortuño CG, Lacunza J, Giachino DF, Cerrato N, Martins RP, Campuzano O, Van Dooren S, Thollet A, Kyndt F, Mazzanti A, Clémenty N, Bisson A, Corveleyn A, Stallmeyer B, Dittmann S, Saenen J, Noël A, Honarbakhsh S, Rudic B, Marzak H, Rowe MK, Federspiel C, Le Page S, Placide L, Milhem A, Barajas-Martinez H, Beckmann BM, Krapels IP, Steinfurt J, Winkel BG, Jabbari R, Shoemaker MB, Boukens BJ, Škoric-Milosavljevic D, Bikker H, Manevy F, Lichtner P, Ribasés M, Meitinger T, Müller-Nurasyid M; KORA-Study Group, Veldink JH, van den Berg LH, Van Damme P, Cusi D, Lanzani C, Rigade S, Charpentier E, Baron E, Bonnaud S, Lecointe S, Donnart A, Le Marec H, Chatel S, Karakachoff M, Bézieau S, London B, Tfelt-Hansen J, Roden D, Odening KE, Cerrone M, Chinitz LA, Volders PG, van de Berg MP, Laurent G, Faivre L, Antzelevitch C, Kääb S, Arnaout AA, Dupuis JM, Pasquie JL, Billon O, Roberts JD, Jesel L, Borggrefe M, Lambiase PD, Mansourati J, Loeys B, Leenhardt A, Guicheney P, Maury P, Schulze-Bahr E, Robyns T, Breckpot J, Babuty D, Priori SG, Napolitano C; Nantes Referral Center for inherited cardiac arrhythmia, de Asmundis C, Brugada P, Brugada R, Arbelo E, Brugada J, Mabo P, Behar N, Giustetto C, Molina MS, Gimeno JR, Hasdemir C, Schwartz PJ, Crotti L, McKeown PP, Sharma S, Behr ER, Haissaguerre M, Sacher F, Rooryck C, Tan HL, Remme CA, Postema PG, Delmar M, Ellinor PT, Lubitz SA, Gourraud JB, Tanck MW, George AL Jr, MacRae CA, Burridge PW, Dina C, Probst V, Wilde AA, Schott JJ, Redon R, Bezzina CR.
Nat Genet. 2022 Mar;54(3):232-239. doi: 10.1038/s41588-021-01007-6.

3. Sex matters? Sex matters!
Barc J, Erdmann J.
Cardiovasc Res. 2022 Jan 7;118(1):e1-e3. doi: 10.1093/cvr/cvab356.

4. From polygenic risk scores to integrative epigenomics: the dawn of a new era for cardiovascular precision medicine.
Barc J, Kovacic JC.Cardiovasc Res. 2021 May 25;117(6):e73-e75. doi: 10.1093/cvr/cvab146.

We identified 6 families presenting a new syndrome associating cardiac electrical disorders and developmental defects. All affected members of the 6 families present large overlapping deletions located in a 4q25 gene desert area suggesting the crucial role of this region and its likely key regulatory function in gene expression. Our project LEARN will conduct a translational research combining multi-omics approach and phenotype characterization to decipher the molecular mechanism leading to this severe and complex cardiac disorder. Based on human cardiomyocytes derived from iPSC deleted for the regulatory element, we will characterize the role and the transcription factor binding on the regulatory element, its targeted genes, the transcriptomic, proteomic, electrophysiological and morphological consequences. LEARN is in full accordance with the actual challenge of translating genetic variants located in non-coding region to molecular mechanism and with a personalized medicine. LEARN is in full accordance with the Investments for the Future Programme of the French government on rare diseases: solve the diagnostic impasses.