Unveiling new insights into mitochondrial–nuclear interactions
Exploring recent breakthroughs uncovering how nuclear DNA (nuDNA) variations impact mitochondrial DNA (mtDNA) dynamics, offers new insights into understanding human genetic diversity and its implications. Would you like to learn about mtDNA, the role of NGS in diagnosis of these disorders and what the varvis® software offers for mtDNA analysis?
The powerhouses of life
Mitochondria, often referred to as the powerhouses of life, are cellular organelles that house their own DNA. Each DNA molecule is built from 16,569 nucleotides — a stark contrast to the 3 billion nucleotides needed to build each copy of the nuDNA [1]. The structure and function of mitochondria are under dual genetic control. Most of the mitochondrial proteins are encoded by nuDNA, with merely 13 proteins in oxidative phosphorylation (OXPHOS) pathways encoded by mtDNA.
In contrast to nuDNA, mtDNA is maternally inherited. Most human nucleated cells have 500 ~ 2000 mitochondria, and there are multiple copies of mtDNA in each mitochondrion. Due to this multicopy nature, mtDNA mutations might be present in all mtDNA copies (homoplasmy) or in a subset of all copies (heteroplasmy). In addition, the heteroplasmy of mitochondrial genomes with a specific variant may differ greatly between tissues.
Mitochondrial diseases
Mitochondrial diseases (MDs) have revealed dramatic variability in the phenotype even when patients carry the same variant. The dosage of mutated variants affected the type and severity of symptoms in MD patients. Studying mutations associated with mitochondrial disorders is extremely challenging due to phenotypic variability and genetic heterogeneity among individuals. Nowadays, next-generation sequencing (NGS) techniques are used to address the challenges of mitochondrial variant identification. Apart from detecting common and uncommon point mutations and deletions, NGS enables a sensitive measurement of the level of heteroplasmy.
Mitochondrial variation
Thanks to the latest sequencing technologies, recent studies [2] involving over 270,000 individuals have shed light on the interplay between nuDNA variations and mtDNA changes. Firstly, they discovered that as we grow older, the number of copies of this mitochondrial DNA tends to decrease gradually. This seems to be linked with our aging process. Even more interesting was the discovery that certain differences in our nuDNA seem to play a role in how much mtDNA we have.
The team also found that heteroplasmy follows two patterns over a person’s life. Some single-nucleotide variants of DNA predominantly accumulate somatically with age, whereas some heteroplasmic indels are maternally inherited as mixtures with relative levels associated with 42 nuclear loci involved in mtDNA replication, maintenance, and novel pathways. These loci may act by conferring a replicative advantage to certain mtDNA alleles.
For example, they identified an Indel carried by more than half of humans at position chrM:302 within a G-quadruplex previously proposed to mediate mtDNA transcription/replication switching. This variant exerts cis-acting genetic control over mtDNA abundance and is itself associated in-trans with nuclear loci encoding machinery for this regulatory switch, suggesting that common variation in the nuclear genome can shape variation in mtCN and heteroplasmy dynamics across the human population.
Implications for rare diseases
The study also has implications for rare MDs. The genome wide association in fact, nominates candidate genes for unsolved MD. PNP is an excellent example because it has not previously been linked to mtDNA disease. Understanding the synergistic relationship between nuDNA and mtDNA could pave the way for future therapies aiming to replace disease-causing mtDNA with healthy donor DNA [3,4].
Despite the advancements in sequencing technologies, challenges persist in studying mtDNA and MDs due to the complexity MDs of symptoms and genotype-phenotype correlations. To address these challenges, accurate interpretation tools like varvis® software are indispensable.
Mitochondrial DNA analysis with varvis® software
The varvis® software offers mitochondrial DNA analysis services, requiring the upload of raw data generated from whole-genome or targeted sequencing with mitochondrial DNA spike-in for adequate coverage. The software processes samples, aligning them with a reference genome and conducting variant calling. It utilizes sensitive somatic variant callers for detecting low-frequency, heteroplasmic variants. This is particularly useful for whole-exome sequencing (WES) analysis to inspect genes involved in mtDNA maintenance.
varvis® mtDNA service
- Offered as an additional service to CNV and SNV analysis for sample.
- Validation of the assay.
- The limit of the detection (LOD) of 2% with 1200x average coverage.
- Cost-effectiveness as the BAM file generated previously in the NGS analysis is used.
- Mitochondrial analysis is visible in varvis® software as separate analysis but mitochondrial variants are shown along with other nuclear variants in the variant grid.
- The varvis® software uses the Ensembl transcripts and specific genetic code. Annotation from ClinVar are incorporated.
- MtDNA specific ACMG criteria are available for variant interpretation according to internationally accepted standards.
In conclusion, understanding mtDNA dynamics and its relationship with nuDNA is crucial for unraveling disease mechanisms and developing effective therapies. The innovative varvis® software plays a pivotal role in advancing mtDNA analysis, providing researchers and clinicians with valuable insights into mitochondrial disorders.
About the varvis® software
The varvis® software is a clinical decision support system designed by Limbus Medical Technologies GmbH, a medical device manufacturer and software development company. The cloud-based genomics platform is tailored to support the entire NGS workflow, from raw data processing to genomics data management and variant interpretation.
Automated CNV and SNV analyses are completely integrated into the NGS workflow and clinically validated for panels of all sizes including WES. Our services comprise first class support, training, automated quality control and validation compliant with relevant international guidelines. The varvis® software is a registered CE-IVD device and specifically made to aid in the diagnosis of patients.
See for yourself
If you want to learn more how varvis® software can help you navigating, please get in touch with us to schedule your personal varvis® software demo (https://www.varvis.com/schedule-a-demo.html) or check our varvis® Academy courses (https://varvis.learnworlds.com).
References
1. Stewart JB, Chinnery PF. Extreme heterogeneity of human mitochondrial DNA from organelles to populations. Nat Rev Genet. 2021 Feb;22(2):106–118. doi: 10.1038/s41576–020–00284-x. Epub 2020 Sep 28. PMID: 32989265.
2. Gupta, R., Kanai, M., Durham, T.J. et al. Nuclear genetic control of mtDNA copy number and heteroplasmy in humans. Nature 620, 839–848 (2023).
3. Ertl, H. Nuclear genome influences mitochondrial DNA. Nat Rev Genet 24, 803 (2023).
4. Davis RL, Kumar KR, Puttick C, Liang C, Ahmad KE, Edema-Hildebrand F, Park JS, Minoche AE, Gayevskiy V, Mallawaarachchi AC, Christodoulou J, Schofield D, Dinger ME, Cowley MJ, Sue CM. Use of Whole-Genome Sequencing for Mitochondrial Disease Diagnosis. Neurology. 2022 Aug 16;99(7):e730-e742. doi: 10.1212/WNL.0000000000200745. Epub 2022 May 31. PMID: 35641312; PMCID:PMC9484606.
