Fourth European stroke science workshop

Rare Sequence Variation Underlying Suspected Familial Cerebral Small-Vessel Disease

BACKGROUND

Cerebral small-vessel disease (cSVD) is the leading monogenic cause of stroke. Despite genetic screening in routine diagnosis, many cases remain without a known causative variant. Using a cohort with suspected familial cSVD and whole-genome sequencing, we screened for variants in genes associated with monogenic cSVD and searched for novel variants associated with the disease.

METHODS AND RESULTS

Rare variants were identified in whole-genome sequencing data from the NBR (National Institute for Health Research BioResource Rare Disease) study. Pathogenic variants in known monogenic cSVD genes were identified. Gene-based burden tests and family analysis were performed to identify novel variants associated with familial cSVD. A total of 257 suspected cSVD cases (mean ± SD age, 56.2 ± 16.1 years), and 13 086 controls with other nonstroke diseases (5874 [44.9%] men) were studied. A total of 8.9% of the cases carried a variant in known cSVD genes. Excluding these known causes, 23.6% of unrelated subjects with cSVD carried predicted deleterious variants in the Genomics England gene panel, but no association was found with cSVD in burden tests. We identified potential associations with cSVD in noncoding genes, including RP4-568F9.3 (adjusted P = 7.1 × 10-25), RP3-466I7.1 (adjusted P = 8.9 × 10-16), and ZNF209P (adjusted P = 1.0 × 10-15), and matrisomal genes (adjusted P = 5.1 × 10-6), including FAM20C, INHA, LAMC1, and VWA5B2.

CONCLUSIONS

Predicted deleterious variants in known cSVD genes were present in 23.6% of unrelated cases with cSVD, but none of the genes were associated with the disease. Rare variants in noncoding and matrisomal genes could potentially contribute to cSVD development. These genes could play a role in tissue development and brain endothelial cell function. However, further studies are needed to confirm their pathophysiological roles.

An AluYa5 Insertion in the 3'UTR of COL4A1 and Cerebral Small Vessel Disease

Importance

Cerebral small vessel diseases (CSVDs) account for one-fifth of stroke cases. Numerous familial cases remain unresolved after routine screening of known CSVD genes.

Objective

To identify novel genes and mechanisms associated with familial CSVD.

Design, Setting, and Participants

This 2-stage study involved linkage analysis and a case-control study; linkage analysis and whole exome and genome sequencing were used to identify candidate gene variants in 2 large families with CSVD (9 patients with CSVD). Then, a case-control analysis was conducted on 246 unrelated probands, including probands from these 2 families and 244 additional probands. All probands (clinical onset

Main Outcomes and Measures

A pathogenic AluYa5 insertion was identified within the COL4A1 3'UTR in the 2 large families with CSVD. Reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR), Western blot, and long-read RNA sequencing were used to investigate outcomes associated with the insertion using patient fibroblasts. Clinical and magnetic resonance imaging features of probands with variants and available relatives were assessed.

Results

Among 246 probands (141 females [57.3%]; median [IQR] age at referral, 56 [49-64] years), 7 patients of French ancestry carried the insertion. This insertion was absent in 467 healthy French individuals in a control group (odds ratio, ∞; 95% CI, 2.78 to ∞; P = 5 × 10-4) and 10 847 individuals from the gnomAD structural variant database (odds ratio, ∞; 95% CI, 64.77 to ∞; P = 2.42 × 10-12). In these 7 patients' families, 19 family members with CSVD carried the insertion. RT-qPCR and Western blot showed an upregulation of COL4A1 mRNA (10.6-fold increase; 95% CI, 1.4-fold to 17.1-fold increase) and protein levels (2.8-fold increase; 95% CI, 2.1-fold to 3.5-fold increase) in patient vs control group fibroblasts. Long-read RNA sequencing data showed that the insertion was associated with perturbation in the use of canonical COL4A1 polyadenylation signals (approximately 87% of isoforms transcribed from the wild type allele vs 5% of isoforms transcribed from the allele with the insertion used the 2 distal canonical polyadenylation signals). The main clinical feature of individuals with CSVD was the recurrence of pontine ischemic lesions starting at an early age (17 of 19 patients [89.5%]).

Conclusions and relevance

This study found a novel mechanism associated with COL4A1 upregulation and a highly penetrant adult-onset CSVD. These findings suggest that quantitative alterations of the cerebrovascular matrisome are associated with CSVD pathogenesis, with diagnostic and therapeutic implications.

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MESH Headings

• Adult
• Female
• Humans
• Middle Aged
• 3' Untranslated Regions/genetics
• Alleles
• Case-Control Studies
• Cerebral Small Vessel Diseases/genetics
• Collagen Type IV/metabolism
• Protein Isoforms
• Mutagenesis, Insertional

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Affiliation(s)

Chaker Aloui NeuroDiderot, Université Paris Cité, Institut National de la Santé Et de la Recherche Médicale, Unité Mixte de Recherche 1141, Paris, France
Lisa Neumann NeuroDiderot, Université Paris Cité, Institut National de la Santé Et de la Recherche Médicale, Unité Mixte de Recherche 1141, Paris, France
Françoise Bergametti NeuroDiderot, Université Paris Cité, Institut National de la Santé Et de la Recherche Médicale, Unité Mixte de Recherche 1141, Paris, France
Eric Sartori Service de Neurologie, Centre Hospitalier Bretagne Sud, Lorient, France
Marc Herbreteau Service de Neurologie, Centre Hospitalier Bretagne Sud, Lorient, France
Arnaud Maillard Assistance Publique-Hôpitaux de Paris, Service de Génétique Moléculaire Neurovasculaire, Hôpital Saint-Louis, Paris, France
Thibault Coste NeuroDiderot, Université Paris Cité, Institut National de la Santé Et de la Recherche Médicale, Unité Mixte de Recherche 1141, Paris, France Assistance Publique-Hôpitaux de Paris, Service de Génétique Moléculaire Neurovasculaire, Hôpital Saint-Louis, Paris, France
Hélène Morel NeuroDiderot, Université Paris Cité, Institut National de la Santé Et de la Recherche Médicale, Unité Mixte de Recherche 1141, Paris, France Assistance Publique-Hôpitaux de Paris, Service de Génétique Moléculaire Neurovasculaire, Hôpital Saint-Louis, Paris, France
Dominique Hervé NeuroDiderot, Université Paris Cité, Institut National de la Santé Et de la Recherche Médicale, Unité Mixte de Recherche 1141, Paris, France Assistance Publique-Hôpitaux de Paris, Service de Neurologie, Hôpital Lariboisière, Paris, France
Hugues Chabriat NeuroDiderot, Université Paris Cité, Institut National de la Santé Et de la Recherche Médicale, Unité Mixte de Recherche 1141, Paris, France Assistance Publique-Hôpitaux de Paris, Service de Neurologie, Hôpital Lariboisière, Paris, France
Serge Timsit Service de Neurologie Vasculaire, Centre Hospitalier Régional Universitaire de Brest, Brest, France
Irina Viakhireva Service de Neurologie Vasculaire, Centre Hospitalier Régional Universitaire de Brest, Brest, France
Yves Denoyer Service de Neurologie, Centre Hospitalier Bretagne Sud, Lorient, France Université de Rennes, Laboratoire Traitement du Signal et de l'Image, Institut National de la Santé Et de la Recherche Médicale Unité Mixte de Recherche 1099, Rennes, France
Rémi Allibert Service de Neurologie, Unité Neurovasculaire, Centre Hospitalier Universitaire de Saint Etienne, Saint Etienne, France
Florence Demurger Service de Neurologie, Unité Neurovasculaire, Centre Hospitalier Bretagne Atlantique, Vannes, France
Cedric Gollion Service de Neurologie, Centre Hospitalier Universitaire de Toulouse, Toulouse, France
Patrick Vermersch Univ. Lille, Institut National de la Santé Et de la Recherche Médicale Unité Mixte de Recherche 1172 LilNCog, Centre Hospitalier Universitaire Lille, Fédérations Hospitalo-Universitaire Precise, Lille, France
Florence Marchelli Assistance Publique-Hôpitaux de Paris, Service de Génétique Moléculaire Neurovasculaire, Hôpital Saint-Louis, Paris, France
Corinne Blugeon GenomiqueENS, Institut de Biologie de l’Ecole Normale Supérieur, Département de biologie, École Normale Supérieure, Centre National de la Recherche Scientifique, Institut National de la Santé Et de la Recherche Médicale, Université Paris Sciences et Lettres, Paris, France
Sophie Lemoine GenomiqueENS, Institut de Biologie de l’Ecole Normale Supérieur, Département de biologie, École Normale Supérieure, Centre National de la Recherche Scientifique, Institut National de la Santé Et de la Recherche Médicale, Université Paris Sciences et Lettres, Paris, France
Claire Tourtier-Bellosta Service de Neurologie, Centre Hospitalier Bretagne Sud, Lorient, France
Alexis Brouazin Service de neurologie, Centre Hospitalier de Cornouaille, Quimper, France
Anne-Louise Leutenegger NeuroDiderot, Université Paris Cité, Institut National de la Santé Et de la Recherche Médicale, Unité Mixte de Recherche 1141, Paris, France
Eva Pipiras NeuroDiderot, Université Paris Cité, Institut National de la Santé Et de la Recherche Médicale, Unité Mixte de Recherche 1141, Paris, France Assistance Publique-Hôpitaux de Paris, Hôpitaux Jean Verdier et Armand Trousseau, Université Sorbonne Paris Nord, Bobigny, France
Elisabeth Tournier-Lasserve NeuroDiderot, Université Paris Cité, Institut National de la Santé Et de la Recherche Médicale, Unité Mixte de Recherche 1141, Paris, France Assistance Publique-Hôpitaux de Paris, Service de Génétique Moléculaire Neurovasculaire, Hôpital Saint-Louis, Paris, France

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Monogenic causes of cerebral small vessel disease and stroke

Cerebral small vessel disease (cSVDs) account for 25% of stroke and are a frequent cause of cognitive or motor disability in adults. In a small number of patients, cSVDs result from monogenic diseases, the most frequent being cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL). An early disease onset, a suggestive family history, and a low vascular risk profile contrasting with a high load of cSVD imaging markers represent red flags that must trigger molecular screening. To date, a dozen of genes is involved in Mendelian cSVDs, most of them are responsible for autosomal dominant conditions of variable penetrance. Some of these mendelian cSVDs (CADASIL, HTRA1-related cSVD, pontine autosomal dominant microangiopathy and leukoencephalopathy (PADMAL), cathepsin-A related arteriopathy with strokes and leukoencephalopathy (CARASAL), and cSVD related to LAMB1 mutations) are causing ischemic stroke. Others (COL4A1/COL4A2-related angiopathy and hereditary cerebral amyloid angiopathy) preferentially lead to intracerebral hemorrhages. The clinical features of different Mendelian cSVDs can overlap. Therefore, the current approach is based on simultaneous screening of all genes involved in these conditions through a panel-targeted sequencing gene or exome sequencing. Nevertheless, a pathogenic variant is identified in less than 15% of patients with a suspected genetic cerebrovascular disease, suggesting that many additional genes remain to be identified.

End-Truncated LAMB1 Causes a Hippocampal Memory Defect and a Leukoencephalopathy

OBJECTIVE

The majority of patients with a familial cerebral small vessel disease (CSVD) referred for molecular screening do not show pathogenic variants in known genes. In this study, we aimed to identify novel CSVD causal genes.

METHODS

We performed a gene-based collapsing test of rare protein-truncating variants identified in exome data of 258 unrelated CSVD patients of an ethnically matched control cohort and of 2 publicly available large-scale databases, gnomAD and TOPMed. Western blotting was used to investigate the functional consequences of variants. Clinical and magnetic resonance imaging features of mutated patients were characterized.

RESULTS

We showed that LAMB1 truncating variants escaping nonsense-mediated messenger RNA decay are strongly overrepresented in CSVD patients, reaching genome-wide significance (p < 5 × 10^-8 ). Using 2 antibodies recognizing the N- and C-terminal parts of LAMB1, we showed that truncated forms of LAMB1 are expressed in the endogenous fibroblasts of patients and trapped in the cytosol. These variants are associated with a novel phenotype characterized by the association of a hippocampal type episodic memory defect and a diffuse vascular leukoencephalopathy.

INTERPRETATION

These findings are important for diagnosis and clinical care, to avoid unnecessary and sometimes invasive investigations, and also from a mechanistic point of view to understand the role of extracellular matrix proteins in neuronal homeostasis. ANN NEUROL 2021;90:962-975.