Abstract：
BACKGROUND: Severe combined immunodeficiency (SCID) is the most fatal form of inherited primary immunodeficiency disease. Known molecular defect mutations occur in most children with SCID.
METHODS: Herein, we report Adenosine Deaminase-SCID (ADA-SCID) using whole-exome sequencing (WES), explore exome mutational landscape and significance for 17 SCID samples, and verify the mutated exon genes using the Gene Expression Omnibus (GEO) datasets. A total of 250 patients, who were hospitalized at the Neonatal Intensive Care Unit (NICU) of The Seventh Medical Center of the PLA General Hospital for 3 years (from 2017 to 2020), were screened for SCID. We collected mutated genes from the WES data of 17 SCID children. GSE609 and GSE99176 cohorts were used to identify the expressions of mutated exon genes and molecular features in SCID. Gene set variation analyses (GSVA) and correlation analyses were performed.
RESULTS: The detection rate with approximately 6.8 % (17/250) of SCID is high in the NICU. A total of 16 genes were identified among 17 SCID samples, of which the Top 2 genes (MUC6 and RP11-683L23.1) might be crucial in the progression of SCID with 94 % mutation frequency. Furthermore, CNN2 and SCGB1C1 had significant co-mutations and may cooperate to affect SCID development. Importantly, the phylogenetic tree classification results of 17 SCID samples are more correlated to MUC6 with the most significant mutations. Expression profiles of seven mutated genes and five mutated genes were documented in GSE609 and GSE99176 cohorts based on microarray, respectively. Several immune-related pathways were significantly enriched, and Foxd4, differing from the other four mutated genes, was inversely correlated with the GSVA-enriched pathway.
CONCLUSIONS: Due to its high detection rate (6.8%) and fatality rate (100%), the inclusion of SCID in newborn screening (NBS) is urgent for children in China. The WES successfully identified several common exonic variants (e.g., MUC6) and depicted the feature of mutations and evolution, which will help develop new diagnostic methods for SCID.
METHODS: Herein, we report Adenosine Deaminase-SCID (ADA-SCID) using whole-exome sequencing (WES), explore exome mutational landscape and significance for 17 SCID samples, and verify the mutated exon genes using the Gene Expression Omnibus (GEO) datasets. A total of 250 patients, who were hospitalized at the Neonatal Intensive Care Unit (NICU) of The Seventh Medical Center of the PLA General Hospital for 3 years (from 2017 to 2020), were screened for SCID. We collected mutated genes from the WES data of 17 SCID children. GSE609 and GSE99176 cohorts were used to identify the expressions of mutated exon genes and molecular features in SCID. Gene set variation analyses (GSVA) and correlation analyses were performed.
RESULTS: The detection rate with approximately 6.8 % (17/250) of SCID is high in the NICU. A total of 16 genes were identified among 17 SCID samples, of which the Top 2 genes (MUC6 and RP11-683L23.1) might be crucial in the progression of SCID with 94 % mutation frequency. Furthermore, CNN2 and SCGB1C1 had significant co-mutations and may cooperate to affect SCID development. Importantly, the phylogenetic tree classification results of 17 SCID samples are more correlated to MUC6 with the most significant mutations. Expression profiles of seven mutated genes and five mutated genes were documented in GSE609 and GSE99176 cohorts based on microarray, respectively. Several immune-related pathways were significantly enriched, and Foxd4, differing from the other four mutated genes, was inversely correlated with the GSVA-enriched pathway.
CONCLUSIONS: Due to its high detection rate (6.8%) and fatality rate (100%), the inclusion of SCID in newborn screening (NBS) is urgent for children in China. The WES successfully identified several common exonic variants (e.g., MUC6) and depicted the feature of mutations and evolution, which will help develop new diagnostic methods for SCID.
摘要：
背景：严重联合免疫缺陷（SCID）是遗传性原发性免疫缺陷疾病的最致命形式。已知的分子缺陷突变发生在大多数患有SCID的儿童中。
方法：这里，我们报告了使用全外显子组测序（WES）的腺苷脱氨酶-SCID（ADA-SCID），探索17个SCID样本的外显子组突变格局和意义，并使用基因表达综合（GEO）数据集验证突变的外显子基因。共250名患者，在解放军总医院第七医学中心新生儿重症监护病房（NICU）住院3年（2017年至2020年），进行了SCID筛查。我们从17个SCID儿童的WES数据中收集了突变基因。GSE609和GSE99176队列用于鉴定SCID中突变外显子基因的表达和分子特征。进行基因集变异分析（GSVA）和相关性分析。
结果：在NICU中，SCID的检出率约为6.8％（17/250）。在17个SCID样本中共鉴定出16个基因,其中前2个基因（MUC6和RP11-683L23.1）可能在SCID的进展中至关重要，突变频率为94％。此外，CNN2和SCGB1C1具有显著的共突变并且可能合作影响SCID发育。重要的是,17个SCID样本的系统发育树分类结果与MUC6的相关性更强，突变最显著。在基于微阵列的GSE609和GSE99176队列中记录了七个突变基因和五个突变基因的表达谱,分别。几个免疫相关的途径显著丰富，和Foxd4，不同于其他四个突变基因，与GSVA富集途径呈负相关。
结论：由于其高检出率（6.8％）和死亡率（100％），在中国,将SCID纳入新生儿筛查(NBS)对儿童来说迫在眉睫.WES成功鉴定了几种常见的外显子变体(例如，MUC6)并描绘了突变和进化的特征，这将有助于为SCID开发新的诊断方法。
方法：这里，我们报告了使用全外显子组测序（WES）的腺苷脱氨酶-SCID（ADA-SCID），探索17个SCID样本的外显子组突变格局和意义，并使用基因表达综合（GEO）数据集验证突变的外显子基因。共250名患者，在解放军总医院第七医学中心新生儿重症监护病房（NICU）住院3年（2017年至2020年），进行了SCID筛查。我们从17个SCID儿童的WES数据中收集了突变基因。GSE609和GSE99176队列用于鉴定SCID中突变外显子基因的表达和分子特征。进行基因集变异分析（GSVA）和相关性分析。
结果：在NICU中，SCID的检出率约为6.8％（17/250）。在17个SCID样本中共鉴定出16个基因,其中前2个基因（MUC6和RP11-683L23.1）可能在SCID的进展中至关重要，突变频率为94％。此外，CNN2和SCGB1C1具有显著的共突变并且可能合作影响SCID发育。重要的是,17个SCID样本的系统发育树分类结果与MUC6的相关性更强，突变最显著。在基于微阵列的GSE609和GSE99176队列中记录了七个突变基因和五个突变基因的表达谱,分别。几个免疫相关的途径显著丰富，和Foxd4，不同于其他四个突变基因，与GSVA富集途径呈负相关。
结论：由于其高检出率（6.8％）和死亡率（100％），在中国,将SCID纳入新生儿筛查(NBS)对儿童来说迫在眉睫.WES成功鉴定了几种常见的外显子变体(例如，MUC6)并描绘了突变和进化的特征，这将有助于为SCID开发新的诊断方法。
