Spectrum of germline and somatic mitochondrial DNA variants in Tuberous Sclerosis Complex

Krinio Giannikou; Katie R Martin; Ahmad G Abdel-Azim; Kaila J Pamir; Thomas R Hougard; Shefali Bagwe; Yan Tang; Jeffrey P MacKeigan; David J Kwiatkowski; Elizabeth P Henske; Hilaire C Lam

doi:10.3389/fgene.2022.917993

Spectrum of germline and somatic mitochondrial DNA variants in Tuberous Sclerosis Complex

Front Genet. 2023 Jan 30:13:917993. doi: 10.3389/fgene.2022.917993. eCollection 2022.

Authors

Affiliations

¹ Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States.
² Division of Hematology/Oncology, Cancer and Blood Disease Institute, Children's Hospital Los Angeles, Los Angeles, CA, United States.
³ Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States.
⁴ Center for LAM Research and Clinical Care, Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States.

Abstract

Tuberous Sclerosis Complex (TSC) is caused by loss of function variants in either TSC1 or TSC2 and is characterized by broad phenotypic heterogeneity. Currently, there is limited knowledge regarding the role of the mitochondrial genome (mtDNA) in TSC pathogenesis. In this study, we aimed to determine the prevalence and spectrum of germline and somatic mtDNA variants in TSC and identify potential disease modifiers. Analysis of mtDNA amplicon massively parallel sequencing (aMPS) data, off-target mtDNA from whole-exome sequencing (WES), and/or qPCR, revealed mtDNA alterations in 270 diverse tissues (139 TSC-associated tumors and 131 normal tissue samples) from 199 patients and six healthy individuals. Correlation of clinical features to mtDNA variants and haplogroup analysis was done in 102 buccal swabs (age: 20-71 years). No correlation was found between clinical features and either mtDNA variants or haplogroups. No pathogenic variants were identified in the buccal swab samples. Using in silico analysis, we identified three predicted pathogenic variants in tumor samples: MT-ND4 (m.11742G>A, p. Cys328Tyr, VAF: 43%, kidney angiomyolipoma), MT-CYB (m.14775T>C, p. Leu10Pro, VAF: 43%, LAM abdominal tumor) and MT-CYB (m.15555C>T, p. Pro270Leu, VAF: 7%, renal cell carcinoma). Large deletions of the mitochondrial genome were not detected. Analysis of tumors from 23 patients with corresponding normal tissue did not reveal any recurrent tumor-associated somatic variants. The mtDNA/gDNA ratio between tumors and corresponding normal tissue was also unchanged. Overall, our findings demonstrate that the mitochondrial genome is highly stable across tissues and within TSC-associated tumors.

Keywords: angiomyolipoma; buccal swab; lymphangioleiomyomatosis; mTORC1; renal cell carcinoma.

Abstract

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