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Mutations in SGOL1 cause a novel cohesinopathy affecting heart and gut rhythm

Abstract

The pacemaking activity of specialized tissues in the heart and gut results in lifelong rhythmic contractions. Here we describe a new syndrome characterized by Chronic Atrial and Intestinal Dysrhythmia, termed CAID syndrome, in 16 French Canadians and 1 Swede. We show that a single shared homozygous founder mutation in SGOL1, a component of the cohesin complex, causes CAID syndrome. Cultured dermal fibroblasts from affected individuals showed accelerated cell cycle progression, a higher rate of senescence and enhanced activation of TGF-β signaling. Karyotypes showed the typical railroad appearance of a centromeric cohesion defect. Tissues derived from affected individuals displayed pathological changes in both the enteric nervous system and smooth muscle. Morpholino-induced knockdown of sgol1 in zebrafish recapitulated the abnormalities seen in humans with CAID syndrome. Our findings identify CAID syndrome as a novel generalized dysrhythmia, suggesting a new role for SGOL1 and the cohesin complex in mediating the integrity of human cardiac and gut rhythm.

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Figure 1: Synopsis of families and electrocardiographic features.
Figure 2: Cellular phenotypes of CAID.
Figure 3: Synopsis of the gastrointestinal histology of CAID.
Figure 4: Spatiotemporal expression and function of sgol1 in zebrafish.

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Acknowledgements

We are deeply indebted to all participating families and patients. We thank L. Gosselin, L. L'Écuyer, M.-F. Boudreault, C. Faure, F. LeDeist, L. D'Aoust and the McGill Genome Québec Innovation Centre (D. Vincent) for expert assistance. We gratefully acknowledge the contribution of all referring physicians and supporting staff to this project. We would like to thank J. Marcadier (clinical coordinator) and C. Beaulieu (project manager) for their contributions to the infrastructure of the FORGE Canada Consortium. The FORGE (Finding of Rare Disease Genes) Consortium Steering Committee includes Kym Boycott (University of Ottawa), Jan Friedman (University of British Columbia), Jacques Michaud (Université de Montréal), François Bernier (University of Calgary), Michael Brudno (University of Toronto), Bridget Fernandez (Memorial University), Bartha Knoppers (McGill University) and Steve Scherer (University of Toronto). FORGE Canada was funded by the Canadian government through Genome Canada, the Canadian Institutes of Health Research and the Ontario Genomics Institute (OGI-049). Additional funding was provided by Génome Québec, Genome British Columbia, Foundation Nussia and André Aisenstadt, La Fondation du Grand défi Pierre Lavoie, Fondation CHU Sainte-Justine, Fondation Leducq, Association des Pseudo Obstructions Intestinales Chroniques (France), the Netherlands Organization for Scientific Research (NWO) and ZonMw (91212086). G.A. holds a Senior Scholarship from the Fonds de Recherche du Québec–Santé and holds the Banque Nationale Research Chair in Cardiovascular Genetics. We thank G. Rouleau for sharing whole-exome data for control purposes and M. Samuels for critical reading of the manuscript.

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P.C., J.-M.C. and G.A. identified the novel CAID syndrome in the families. Functional experiments were performed by F.W., N.G., J.P., S.L., C.G., E.L., I.B., J.B., S.B., A.G., E.T., S.F., M.C., N.E.A., E.G.-M., S.H.Z., Y.S., M.J. and S.J.M.J. Further patient recruitment and enrollment was performed by P.C., J.-M.C., C.H., J.C., A.J., P.d.S.B., M.T., D.W.B. and G.A. C.P. performed and supervised the genotyping and the haplotype and population genetic analysis. G.R.H., G.A., J.P. and N.E.A. performed confocal microscopy for the cell lines and analyzed the data. S.B. and J.B. established the zebrafish model. C.G., J.P. and E.G.-M. performed the functional cell line experiments. Genealogical analysis was provided by M.J., D.L. and C.M. H.C.D. provided advice on the analysis of the functional data derived from the cell lines. P.C., C.P., J.B., S.J.M.J. and G.A. wrote the manuscript with contributions and input from all authors. G.A. designed and supervised the study.

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Correspondence to Gregor Andelfinger.

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The authors declare no competing financial interests.

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Membership of the Steering Committee for the Consortium is given in the Acknowledgments

Integrated supplementary information

Supplementary Figure 1 Representative manometries in two CAID patients.

(a) Antroduodenal manometry showing visceral neuropathy with abnormal response (normal amplitude, no phase III–like contractions) to IV erythromycin (antrum, channels 1–3; duodenum, channels 4 and 5; jejunum, channels 6 and 7). (b) Colonic manometry showing visceral myopathy with low-amplitude propagated contractions after stimulation (intracolonic bisacodyl) (right colon, channels 1 and 2; transverse, channels 3 and 4; sigmoid rectum, channels 5–7).

Supplementary Figure 2 Results of sequencing.

(a) Venn diagram indicating the number of genes with homozygous nonsynonymous variants in three sequenced patients. In parentheses are the numbers of genes after filtering for rare alleles (MAF < 1%). (b) Examples of Sanger sequencing results for the screening of the exon 1 c.67A>G mutation (red arrow) showing the wild-type allele (top), a heterozygous parent (middle) and a homozygous CAID patient (bottom). One-letter amino acid code is used for the translation of individual codons. (c) The lysine (K) at position 23 is highly conserved in all vertebrates.

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Supplementary Figure 3 Results from homozygosity and haplotype mapping.

The results from homozygosity mapping1 in 12 French-Canadian CAID patients, 3 unaffected family members (family 4) and the Swedish patient are displayed. (a,b) Graphic depiction of homozygosity scores (a) across the genome and (b) for chromosome 3 providing mapping evidence for the SGOL1 locus in CAID. (c) Reconstruction of the founder haplotype in the SGOL1 region based on the largest window of consecutive homozygous variant calls obtained from high-density genotyping. The haplotype is displayed on the UCSC Genome Browser, showing that a 650-kb interval overlapping the SGOL1 locus is identical by descent. Graphic depiction of haplotypes on the UCSC Genome Browser for the region between 20 Mb and 20.65 Mb on chromosome 3 harboring the following four genes: SGOL1, RAB5A, C3orf48 and PCAF.

Supplementary Figure 4 Haplotype gradients.

(a) The distribution of haplotype frequencies across a world map highlights the absence of the disease-associated haplotype outside of Europe and North America. The haplotype gradients follow a migration pattern from northern European populations across the Atlantic. (b) For simplicity, a set of seven rare tagging SNPs for three haplotype combinations of different length is shown. Recombination breaks down the haplotypes over time within a population2. The presence of the longest haplotype in northern European populations and in North America combined with the absence of this haplotype in southern Europeans undermines the idea of a transatlantic founder effect. (c) Overview of allele frequencies and genotype counts for the rare tagging SNPs from the 1000 Genomes Project panel. Colors highlight the higher frequencies of variants in the European population compared to the Asian and African populations.

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Supplementary Figure 5 Genealogical analysis.

(a) The genealogy of the French-Canadian CAID patients linking all of them to their most likely founder couple married in France in 1620. (b) The corresponding genealogy of only one of the patients, illustrating details of the familial relationships along generations. The proposed founder couple is more than 100 times more likely to be the founder than other potential founders (posterior probability P = 0.993, estimated by gene dropping). Duplicated individuals are indicated by dashed lines. (c) Haplotype alignment. A schematic representation of the haplotypes around the CAID mutation (vertical line) found in nine patients, each representing an independent nuclear family, compared with two haplotypes for the Swedish patient. The consensus haplotype is represented by a solid line that is interrupted by empty spaces representing recombination break points. Notably, the Swedish patient shares about 0.5 cM with the Quebec haplotypes. We estimated the age of the founder haplotype to be between 9 and 17 generations, given proportions of 78% and 50% for the non-recombined mutation-carrying haplotypes at lengths of 0.28 and 0.41 cM, respectively. This is in line with the genealogical evidence pointing to the founder couple arriving in Nouvelle France around 1620 (ref. 3).

Supplementary Figure 6 Confocal analysis of SGOL1 during mitosis.

Comparison of a control wild-type cell line and two cell lines homozygous for the SGOL1 K23E mutant is shown. SGOL1 K23E localizes correctly to the centromeric regions during pro-metaphase and anaphase but retains an abnormal cytosolic localization pattern. Left: green, SGOL1 staining. Right: green and blue, SGOL1 plus Hoechst. Scale bar, 10 µm.

Supplementary Figure 7 Quantitative analysis of confocal microscopy.

Quantitative analysis of the distribution of nuclear SGOL1 pixel intensities reveals altered SGOL1 organization in fibroblasts from homozygous CAID patients (red) compared to controls (blue). Data are the mean ± s.e.m. from 12 cells from 3 individuals per genotype. In control nuclei, the distribution partially overlaps that of adjacent cell-free regions (background, green), reflecting nuclear domains of negligible SGOL1 signal intensity among domains of higher intensity. In patient nuclei, the SGOL1 (K23E) intensity distribution does not overlap the background, showing that, in fibroblasts from three different patients, nuclear SGOL1 is reproducibly delocalized compared to three different controls, consistent with the more diffuse staining patterns observed.

Supplementary Figure 8 SGOL1 expression in normal human colon.

SGOL1 expression in normal human colon. Immunohistochemistry shows that SGOL1 expression in the intestinal wall is very strong in enteric neuronal cells and interstitial cells of Cajal networks (black and red arrows, respectively). SGOL1 is expressed to a lower extent in smooth muscle cells. Antibodies used (left to right): SGOL1, TMEM16A (a calcium channel expressed in the network of interstitial cells of Cajal), TUJ1 (neuron-specific β III tubulin, a neuronal marker expressed in intestinal ganglial cells) and αSMA (α smooth muscle actin, a smooth muscle cell marker).

Supplementary Figure 9 Antisense morpholino knockdown of sgol1 analyzed at 3 d.p.f.

(a) Schematic of the morpholino target site location in the sgol1 gene transcript. (b) Representative images of control and sgol1 morpholino-injected embryos (3 d.p.f.). Arrows point to cardiac edema. (c) Analysis of cardiac cycle length by high-speed video imaging (n = 15 per group). *P < 0.05, **P < 0.01.

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Supplementary Text and Figures

Supplementary Figures 1–9 and Supplementary Note. (PDF 6175 kb)

Supplementary Table 1

Summary of patient characteristics. (XLSX 10 kb)

Supplementary Table 2

Full characterization of patient cohort. (XLSX 15 kb)

Supplementary Table 3

In silico prediction of the deleterious SGOL1 mutation. (XLSX 12 kb)

Supplementary Table 4

Primer design and PCR. (XLSX 10 kb)

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Chetaille, P., Preuss, C., Burkhard, S. et al. Mutations in SGOL1 cause a novel cohesinopathy affecting heart and gut rhythm. Nat Genet 46, 1245–1249 (2014). https://doi.org/10.1038/ng.3113

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