My research focuses on understanding the relationship between aneuploidy and mitochondrial DNA quality and quantity, and methods of oocyte rejuvenation by boosting mitochondria functioning. My current interests also include the modification of CRISPR/Cas systems for mitochondrial DNA editing. I also have a great collaboration in the field of human genetics with a focus on mitochondrial genetics.
2010 PhD in Molecular Genetics
Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia.
Thesis title: “Analysis of the variability of mitochondrial DNA of Tubalars of the Altai Mountains and the Evens tribes of Eastern Siberia.”
Thesis supervisor: Prof Rem Sukernik.
2006 MS in Biology
Chelyabinsk State University, Chelyabinsk, Russia
Thesis title: “The influence of radiation on the formation of left-handedness.”
Using low-coverage, whole-genome sequences of trophectoderm biopsies from human blastocyst-stage embryos, we analyzed the relationship between chromosomal abnormalities and mitochondrial (mt) DNA dynamics. Comparing aneuploid and euploid embryos in cohort studies, we found that mtDNA content in aneuploid embryos was significantly higher than that in euploid embryos. This outcome was confirmed through intrafamilial analyses of embryos with matched parents and in vitro fertilization cycles, and it occurred independent of maternal age. Additional human population-based studies uncovered a higher abundance of ultra-rare mtDNA variants located in never-altered positions in the human population in aneuploid compared to euploid embryos in both cohort- and family-based analyses. This maternal age-independent association of increased mtDNA content and aneuploidy in human embryos may reflect a novel mechanism of purifying selection against potentially deleterious mtDNA variants, which arise from germline or early developmental mtDNA damaging events, that occurs in human embryos prior to implantation (Ri et al. https://www.biorxiv.org/content/10.1101/2022.10.14.512116v2.full.pdf).
CRISPR RNAs (crRNAs) that direct target DNA cleavage by Type V Cas12a nucleases consist of constant repeat-derived 5′-scaffold moiety and variable 3′-spacer moieties. We demonstrated that removal of most of the 20-nucleotide scaffold has only a slight effect on in vitro target DNA cleavage by a Cas12a ortholog from Acidaminococcus sp. (As-Cas12a) (Shebanova et al. 2022, NAR). In fact, residual cleavage was observed even in the presence of a 20-nucleotide crRNA spacer moiety only. In addition to dsDNA target cleavage, AsCas12a programmed with split crRNAs also catalyzed specific ssDNA target cleavage and non-specific ssDNA degradation (collateral activity). V-A effector nucleases from Francisella novicida (Fn-Cas12a) and Lachnospiraceae bacterium (LbCas12a) were also functional with split crRNAs. Thus, the ability of V-A effectors to use split crRNAs appears to be a general property. Another discovery made during the project was the identification of a new ortholog, which we named CRISPR/RbCas12a. It turned out that the RbCas12a nuclease is a more effective editor compared to the commonly used AsCas12a (Vasilev et al. 2022, IJMS). The ability to split guide RNAs that program Cas12 into two parts, of which only one corresponds to the target, while the other one is constant, simplifies both genome editing and diagnostic applications and drastically increases the ability to multiplex. It also makes it possible to specifically target the editor to mitochondria, something that has not been achieved before (Nikitchina et al. 2023, Biochimie). This opens up ways to treat mitochondrial genetic diseases, including many age-associated diseases.
Despite its high mutation rate and its association with numerous diseases, the mutagenesis of the mtDNA is not well understood. We hypothesized that the mtDNA mutational spectrum is linked to species-specific life-history traits. We analyzed the mtDNA mutational spectra of hundreds of mammalian species and found that variations in the spectra are correlated with the species-specific generation length. Our findings suggest that the mtDNA mutational signature (A>G substitutions on the heavy chain of mtDNA) reflects oxidative damage associated with aging and longevity (Mikhailova et al. 2022, NAR). Further analysis of mtDNA mutagenesis in cold- and warm-blooded vertebrates, as well as different types of human cancer, supports the universality of our findings, indicating that the mtDNA mutational spectrum – previously not understood or interpretable – is a natural marker of the level of aerobic metabolism in different tissues and species.
Two related BioRxives are under review: “A mitochondrial mutational signature of temperature in ectothermic and endothermic vertebrates” (https://www.biorxiv.org/content/10.1101/2020.07.25.221184v2) and “Mammalian mitochondrial mutational spectrum as a hallmark of cellular and organismal aging” (https://www.biorxiv.org/content/10.1101/589168v3).
Mitochondrial direct nucleotide repeats are involved in the development of mitochondrial somatic deletions, which are associated with common age-related traits such as neurodegeneration and sarcopenia. Disrupting these nucleotide repeats can mitigate their harmful effect, reducing the rate of somatic mitochondrial deletions and promoting healthy aging. This mechanism may explain the higher prevalence of centenarians among Japanese individuals with the disrupted common repeat in the mitochondrial genome (Mikhailova et al., 2019). We suggest that the positive properties of certain mitochondrial haplogroups, such as D4a, could potentially be utilized in mitochondrial donation techniques.