Folon Lise, Baron Morgane, Toussaint Bénédicte, Vaillant Emmanuel, Boissel Mathilde, Scherrer Victoria, Loiselle Hélène, Leloire Audrey, Badreddine Alaa, Balkau Beverley, Charpentier Guillaume, Franc Sylvia, Marre Michel, Aboulouard Soulaimane, Salzet Michel, Canouil Mickaël, Derhourhi Mehdi, Froguel Philippe, Bonnefond Amélie
Inserm UMR1283, CNRS UMR8199, European Genomic Institute for Diabetes, Institut Pasteur de Lille, Lille University Hospital, Lille, France; Université de Lille, Lille, France.
Paris-Saclay University, Paris-Sud University, Université de Versailles Saint-Quentin-en-Yvelines, Center for Research in Epidemiology and Population Health, Inserm U1018 Clinical Epidemiology, Villejuif, France.
Lancet Diabetes Endocrinol. 2023 Mar;11(3):182-190. doi: 10.1016/S2213-8587(22)00392-8.
Rare biallelic pathogenic mutations in PCSK1 (encoding proprotein convertase subtilisin/kexin type 1 [PC1/3]) cause early-onset obesity associated with various endocrinopathies. Setmelanotide has been approved for carriers of these biallelic mutations in the past 3 years. We aimed to perform a large-scale functional genomic study focusing on rare heterozygous variants of PCSK1 to decipher their putative impact on obesity risk.
This case-control study included all participants with overweight and obesity (ie, cases) or healthy weight (ie, controls) from the RaDiO study of three community-based and one hospital-based cohort in France recruited between Jan 1, 1995, and Dec 31, 2000. In adults older than 18 years, healthy weight was defined as BMI of less than 25·0 kg/m, overweight as 25·0-29·9 kg/m, and obesity as 30·0 kg/m or higher. Participants with type 2 diabetes had fasting glucose of 7·0 mmol/L or higher or used treatment for hyperglycaemia (or both) and were negative for islet or insulin autoantibodies. Functional assessment of rare missense variants of PCSK1 was performed. Pathogenicity clusters of variants were determined with machine learning. The effect of each cluster of PCSK1 variants on obesity was assessed using the adjusted mixed-effects score test.
All 13 coding exons of PCSK1 were sequenced in 9320 participants (including 7260 adults and 2060 children and adolescents) recruited from the RaDiO study. We detected 65 rare heterozygous PCSK1 variants, including four null variants and 61 missense variants that were analysed in vitro and clustered into five groups (A-E), according to enzymatic activity. Compared with the wild-type, 15 missense variants led to complete PC1/3 loss of function (group A; reference) and rare exome variant ensemble learner (REVEL) led to 15 (25%) false positives and four (7%) false negatives. Carrying complete loss-of-function or null PCSK1 variants was significantly associated with obesity (six [86%] of seven carriers vs 1518 [35%] of 4395 non-carriers; OR 9·3 [95% CI 1·5-177·4]; p=0·014) and higher BMI (32·0 kg/m [SD 9·3] in carriers vs 27·3 kg/m [6·5] in non-carriers; mean effect π 6·94 [SE 1·95]; p=0·00029). Clusters of PCSK1 variants with partial or neutral effect on PC1/3 activity did not have an effect on obesity or overweight and on BMI.
Only carriers of heterozygous, null, or complete loss-of-function PCSK1 variants cause monogenic obesity and, therefore, might be eligible for setmelanotide. In silico tests were unable to accurately detect these variants, which suggests that in vitro assays are necessary to determine the variant pathogenicity for genetic diagnosis and precision medicine purposes.
Agence Nationale de la Recherche, European Research Council, National Center for Precision Diabetic Medicine, European Regional Development Fund, Hauts-de-France Regional Council, and the European Metropolis of Lille.
前蛋白转化酶枯草杆菌蛋白酶/kexin 1型（PCSK1）中罕见的双等位基因致病性突变会导致早发性肥胖，并伴有各种内分泌疾病。在过去3年中，司美格鲁肽已被批准用于这些双等位基因携带者。我们旨在进行一项大规模功能基因组学研究，重点关注PCSK1的罕见杂合变异，以解读其对肥胖风险的潜在影响。
这项病例对照研究纳入了来自法国三项社区队列研究和一项医院队列研究（RaDiO研究）的所有超重和肥胖参与者（即病例组）或健康体重参与者（即对照组），招募时间为1995年1月1日至2000年12月31日。在18岁以上的成年人中，健康体重定义为体重指数（BMI）小于25.0kg/m²，超重定义为25.0-29.9kg/m²，肥胖定义为30.0kg/m²或更高。2型糖尿病参与者的空腹血糖为7.0mmol/L或更高，或正在接受高血糖治疗（或两者兼有），且胰岛或胰岛素自身抗体检测为阴性。对PCSK1罕见错义变异进行功能评估。利用机器学习确定变异的致病性聚类。使用校正后的混合效应评分检验评估每组PCSK1变异对肥胖的影响。
对从RaDiO研究中招募的9320名参与者（包括7260名成年人和2060名儿童及青少年）的PCSK1的所有13个编码外显子进行了测序。我们检测到65个罕见的PCSK1杂合变异，包括4个无效变异和61个错义变异，这些变异在体外进行了分析，并根据酶活性分为五组（A-E）。与野生型相比，15个错义变异导致PC1/3功能完全丧失（A组；参照组），罕见外显子变异集成学习器（REVEL）导致15个（25%）假阳性和4个（7%）假阴性。携带功能完全丧失或无效的PCSK1变异与肥胖显著相关（7名携带者中的6名[86%]，而4395名非携带者中的1518名[35%]；比值比9.3[95%置信区间1.5-177.4]；p=0.014），且BMI更高（携带者为32.0kg/m²[标准差9.3]，非携带者为27.3kg/m²[6.5]；平均效应6.94[标准误1.95]；p=0.00029）。对PC1/3活性有部分或中性影响的PCSK1变异聚类对肥胖、超重及BMI均无影响。
只有杂合、无效或功能完全丧失的PCSK1变异携带者会导致单基因肥胖，因此可能符合使用司美格鲁肽的条件。计算机模拟测试无法准确检测到这些变异，这表明为了进行基因诊断和精准医学，有必要进行体外检测以确定变异的致病性。
法国国家研究机构、欧洲研究理事会、国家精准糖尿病医学中心、欧洲区域发展基金、上法兰西大区议会和里尔欧洲都会区。
