Using metabolic abnormalities of carriers in the neonatal period to evaluate the pathogenicity of variants of uncertain significance in methylmalonic acidemia

Dongfan Xiao; Congcong Shi; Yinchun Zhang; Sitao Li; Yuhao Ye; Guilong Yuan; Taohan Miu; Haiyan Ma; Shiguang Diao; Chaoyun Su; Zhitao Li; Haiyan Li; Guiying Zhuang; Yuanli Wang; Feiyan Lu; Xia Gu; Wei Zhou; Xin Xiao; Weiben Huang; Tao Wei; Hu Hao

doi:10.3389/fgene.2024.1403913

Using metabolic abnormalities of carriers in the neonatal period to evaluate the pathogenicity of variants of uncertain significance in methylmalonic acidemia

Front Genet. 2024 Jul 15:15:1403913. doi: 10.3389/fgene.2024.1403913. eCollection 2024.

Authors

Dongfan Xiao^#^{1

2

3}, Congcong Shi^#^{1

2

3}, Yinchun Zhang^#^{1

3}, Sitao Li^#^{1

2

3}, Yuhao Ye^#⁴, Guilong Yuan⁵, Taohan Miu⁶, Haiyan Ma⁷, Shiguang Diao⁸, Chaoyun Su⁹, Zhitao Li¹⁰, Haiyan Li¹¹, Guiying Zhuang¹², Yuanli Wang¹³, Feiyan Lu¹⁴, Xia Gu^{1

2

3}, Wei Zhou¹⁵, Xin Xiao^{1

2

3}, Weiben Huang¹⁶, Tao Wei⁴, Hu Hao^{1

2

3}

Affiliations

¹ Department of Pediatrics, The Sixth Affiliated Hospital, Sun Yat Sen University, Guangzhou, China.
² Inborn Errors of Metabolism Laboratory, The Sixth Affiliated Hospital, Sun Yat Sen University, Guangzhou, China.
³ Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.
⁴ Department of Bioengineering, College of Food Science, South China Agricultural University, Guangzhou, China.
⁵ Neonates Department, Nanhai Maternity and Child Healthcare Hospital of Foshan, Foshan, China.
⁶ Neonatology Departmen, Heyuan Women and Children's Hospital and Health Institute, Heyuan, China.
⁷ Department of Neonatology, Zhuhai Women and Children's Hospital, Zhuhai, China.
⁸ Department of Neonatology, Yuebei People's Hospital, Shaoguan, China.
⁹ Department of Neonatology, Maoming Huazhou People's Hospital, Huazhou, China.
¹⁰ Guangzhou Baiyun District Maternal and Child Health Hospital, Guangzhou, China.
¹¹ Department of Pediatrics, Huidong County Maternal and Child Health Hospital, Huidong, China.
¹² Department of Neonatology, The Maternal and Child Healthcare Hospital of Huadu, Guangzhou, China.
¹³ Precision Medicine Laboratory, The First People's Hospital of Qinzhou, Qinzhou, China.
¹⁴ Huizhou Huiyang District Maternal and Child Health Hospital, Huizhou, China.
¹⁵ Department of Neonatology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China.
¹⁶ Department of Neonatology, The Fifth Affiliated Hospital of Southern Medical University, Guangzhou, China.

^# Contributed equally.

Abstract

Objective: To accurately verify the pathogenicity of variants of uncertain significance (VUS) in MUT and MMACHC genes through mass spectrometry and silico analysis.

Methods: This multicenter retrospective study included 35 participating units (ClinicalTrials.gov ID: NCT06183138). A total of 3,071 newborns (within 7 days of birth) were sorted into carrying pathogenic/likely pathogenic (P/LP) variants and carrying VUS, non-variant groups. Differences in metabolites among the groups were calculated using statistical analyses. Changes in conservatism, free energy, and interaction force of MMUT and MMACHC variants were analyzed using silico analysis.

Results: The percentage of those carrying VUS cases was 68.15% (659/967). In the MMUT gene variant, we found that C3, C3/C2, and C3/C0 levels in those carrying the P/LP variant group were higher than those in the non-variant group (p < 0.000). The conservative scores of those carrying the P/LP variant group were >7. C3, C3/C0, and C3/C2 values of newborns carrying VUS (c.1159A>C and c.1286A>G) were significantly higher than those of the non-variant group and the remaining VUS newborns (p < 0.005). The conservative scores of c.1159A>C and c.1286A>G calculated by ConSurf analysis were 9 and 7, respectively. Unfortunately, three MMA patients with c.1159A>C died during the neonatal period; their C3, C3/C0, C3/C2, and MMA levels were significantly higher than those of the controls.

Conclusion: Common variants of methylmalonic acidemia in the study population were categorized as VUS. In the neonatal period, the metabolic biomarkers of those carrying the P/LP variant group of the MUT gene were significantly higher than those in the non-variant group. If the metabolic biomarkers of those carrying VUS are also significantly increased, combined with silico analysis the VUS may be elevated to a likely pathogenic variant. The results also suggest that mass spectrometry and silico analysis may be feasible screening methods for verifying the pathogenicity of VUS in other inherited metabolic diseases.

Keywords: mass spectrometry; methylmalonic acidemia; neonatal period; silico analysis; variants of uncertain significant.

Associated data

ClinicalTrials.gov/NCT06183138

Grants and funding

The authors declare that financial support was received for the research, authorship, and/or publication of this article. The project of uncovering the list and being in charge at the Sixth Affiliated Hospital of Sun Yet-sen University (2022JBGS11); Big-data multi-center study on the genome and metabolites of neonatal genetic diseases (2023-063).