Development of a new expanded next‐generation sequencing panel for genetic diseases involved in dyslipidemia

Marmontel, Oriane; Rollat‐Farnier, Pierre Antoine; Wozny, Anne-Sophie; Charrière, Sybil; Vanhoye, Xavier; Simonet, Thomas; Chatron, Nicolas; Collin‐Chavagnac, Delphine; Nony, Séverine; Dumont, Sabrina; Mahl, Muriel; Jacobs, Chantal; Janin, Alexandre; Caussy, Cyrielle; Poinsot, Pierre; Tauveron, Igor; Bardel, Claire; Millat, Gilles; Peretti, Noël; Moulin, Philippe; Marçais, Christophe; Filippo, Mathilde Di

doi:10.1111/cge.13832

Cited by 19 publications

(11 citation statements)

References 23 publications

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“…After genomic DNA extraction, DNA from the proband and patient IV.2 was sequenced and analyzed as previously detailed with the DysliSEQ custom design. 10 This panel includes coding exons and intron/exon junctions of 311 genes selected from published literature: (1) genes identified in monogenic dyslipidemia, (2) genes identified in genome-wide association studies in lipid metabolism through direct or indirect effects, (3) genes associated with dyslipidemia in mice, and (4) single-nucleotide polymorphisms already described in familial hypercholesterolemia genetic risk scores and in genome-wide association studies (with P >5.10 -8 ). Among these genes, a first intention panel was defined for FHBL ( APOB, PCSK9, ANGPTL3 ), abetalipoproteinemia ( ABL , OMIM 200100; MTTP ), and chylomicron retention disease ( CMRD , OMIM No.…”

Section: Methodsmentioning

confidence: 99%

“…246700; SAR1B ). In the absence of a variant in the first intention panel, relevant variants were selected as previously described 10 ( Table S1.3 ). The only relevant variant common to the proband and his granddaughter and that cosegregated with the combined hypocholesterolemia observed in the family after Sanger sequencing was the E97G variant in the LIPC gene.…”

Section: Methodsmentioning

confidence: 99%

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Identification of a Gain-of-Function LIPC Variant as a Novel Cause of Familial Combined Hypocholesterolemia

et al. 2022

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Background: Atherosclerotic cardiovascular disease is the main cause of mortality worldwide and is strongly influenced by circulating low-density lipoprotein (LDL) cholesterol levels. Only a few genes causally related to plasma LDL cholesterol levels have been identified so far, and only 1 gene, ANGPTL3 , has been causally related to combined hypocholesterolemia. Here, our aim was to elucidate the genetic origin of an unexplained combined hypocholesterolemia inherited in 4 generations of a French family. Methods: Using next-generation sequencing, we identified a novel dominant rare variant in the LIPC gene, encoding for hepatic lipase, which cosegregates with the phenotype. We characterized the impact of this LIPC -E97G variant on circulating lipid and lipoprotein levels in family members using nuclear magnetic resonance–based lipoprotein profiling and lipidomics. To uncover the mechanisms underlying the combined hypocholesterolemia, we used protein homology modeling, measured triglyceride lipase and phospholipase activities in cell culture, and studied the phenotype of APOE*3.Leiden.CETP mice after LIPC -E97G overexpression. Results: Family members carrying the LIPC -E97G variant had very low circulating levels of LDL cholesterol and high-density lipoprotein cholesterol, LDL particle numbers, and phospholipids. The lysophospholipids/phospholipids ratio was increased in plasma of LIPC -E97G carriers, suggestive of an increased lipolytic activity on phospholipids. In vitro and in vivo studies confirmed that the LIPC -E97G variant specifically increases the phospholipase activity of hepatic lipase through modification of an evolutionarily conserved motif that determines substrate access to the hepatic lipase catalytic site. Mice overexpressing human LIPC -E97G recapitulated the combined hypocholesterolemic phenotype of the family and demonstrated that the increased phospholipase activity promotes catabolism of triglyceride-rich lipoproteins by different extrahepatic tissues but not the liver. Conclusions: We identified and characterized a novel rare variant in the LIPC gene in a family who presents with dominant familial combined hypocholesterolemia. This gain-of-function variant makes LIPC the second identified gene, after ANGPTL3 , causally involved in familial combined hypocholesterolemia. Our mechanistic data highlight the critical role of hepatic lipase phospholipase activity in LDL cholesterol homeostasis and suggest a new LDL clearance mechanism.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Identification of a Gain-of-Function LIPC Variant as a Novel Cause of Familial Combined Hypocholesterolemia

et al. 2022

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“…DNA from peripheral blood leucocytes was amplified using the Multiplicom ADH MASTR assay v2.0 multiplexing kit (Agilent, Santa Clara, CA, USA) or libraries were prepared using Ampliseq, a SeqCapEZ Solution-Based Enrichment strategy (Roche NimbleGen Madison, WI, USA). Sequencing was performed on coding DNA sequences and flanking introns (exon padding +/−30 bp) of the LDLR , PCSK9 , APOB , and APOE genes and SNPs included in the wPRS as described [ 43 , 44 ].…”

Section: Methodsmentioning

confidence: 99%

APOE Molecular Spectrum in a French Cohort with Primary Dyslipidemia

Abou-Khalil

Marmontel

Ferrières

et al. 2022

IJMS

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Primary hypercholesterolemia is characterized by elevated LDL-cholesterol (LDL-C) levels isolated in autosomal dominant hypercholesterolemia (ADH) or associated with elevated triglyceride levels in familial combined hyperlipidemia (FCHL). Rare APOE variants are known in ADH and FCHL. We explored the APOE molecular spectrum in a French ADH/FCHL cohort of 5743 unrelated probands. The sequencing of LDLR, PCSK9, APOB, and APOE revealed 76 carriers of a rare APOE variant, with no mutation in LDLR, PCSK9, or APOB. Among the 31 APOE variants identified here, 15 are described in ADH, 10 in FCHL, and 6 in both probands. Five were previously reported with dyslipidemia and 26 are novel, including 12 missense, 5 synonymous, 2 intronic, and 7 variants in regulatory regions. Sixteen variants were predicted as pathogenic or likely pathogenic, and their carriers had significantly lower polygenic risk scores (wPRS) than carriers of predicted benign variants. We observed no correlation between LDL-C levels and wPRS, suggesting a major effect of APOE variants. Carriers of p.Leu167del were associated with a severe phenotype. The analysis of 11 probands suggests that carriers of an APOE variant respond better to statins than carriers of a LDLR mutation. Altogether, we show that the APOE variants account for a significant contribution to ADH and FCHL.

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“…The coding exons of LRP6 , CYP7A1, and LDLRAP1 and their flanking exon–intron boundaries (100 pb surrounding each exon boundary) were sequenced by Sanger or by next-generation sequencing [ 49 ]. The coverage was >99% for the coding bases of the LRP6 and CYP7A1 genes and 90% for LDLRAP1 , in the 160 unrelated ADH probands.…”

Section: Methodsmentioning

confidence: 99%

Whole Exome/Genome Sequencing Joint Analysis of a Family with Oligogenic Familial Hypercholesterolemia

et al. 2022

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Autosomal Dominant Hypercholesterolemia (ADH) is a genetic disorder caused by pathogenic variants in LDLR, APOB, PCSK9 and APOE genes. We sought to identify new candidate genes responsible for the ADH phenotype in patients without pathogenic variants in the known ADH-causing genes by focusing on a French family with affected and non-affected members who presented a high ADH polygenic risk score (wPRS). Linkage analysis, whole exome and whole genome sequencing resulted in the identification of variants p.(Pro398Ala) in CYP7A1, p.(Val1382Phe) in LRP6 and p.(Ser202His) in LDLRAP1. A total of 6 other variants were identified in 6 of 160 unrelated ADH probands: p.(Ala13Val) and p.(Aps347Asn) in CYP7A1; p.(Tyr972Cys), p.(Thr1479Ile) and p.(Ser1612Phe) in LRP6; and p.(Ser202LeufsTer19) in LDLRAP1. All six probands presented a moderate wPRS. Serum analyses of carriers of the p.(Pro398Ala) variant in CYP7A1 showed no differences in the synthesis of bile acids compared to the serums of non-carriers. Functional studies of the four LRP6 mutants in HEK293T cells resulted in contradictory results excluding a major effect of each variant alone. Within the family, none of the heterozygous for only the LDLRAP1 p.(Ser202His) variant presented ADH. Altogether, each variant individually does not result in elevated LDL-C; however, the oligogenic combination of two or three variants reveals the ADH phenotype.

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Development of a new expanded next‐generation sequencing panel for genetic diseases involved in dyslipidemia

Cited by 19 publications

References 23 publications

Identification of a Gain-of-Function LIPC Variant as a Novel Cause of Familial Combined Hypocholesterolemia

Identification of a Gain-of-Function LIPC Variant as a Novel Cause of Familial Combined Hypocholesterolemia

APOE Molecular Spectrum in a French Cohort with Primary Dyslipidemia

Whole Exome/Genome Sequencing Joint Analysis of a Family with Oligogenic Familial Hypercholesterolemia

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