National Academy of Medical Sciences of Ukraine
 
Біологія старіння, Лабораторії

Epigenetics Laboratory

Dmytro Krasnienkov
Oleksandr M. Vaiserman

Laboratory Head
Dmytro Krasnienkov, Candidate of Biological Sciences (PhD equivalent)

The Epigenetics Laboratory was established in 2010 on the basis of the former Molecular Genetics Laboratory, previously headed by Dr. Oleksandr Yakovych Litoshenko, Doctor of Biological Sciences. Until 2021 the laboratory was led by Dr. Oleksandr Mykhailovych Vaiserman, Doctor of Medical Sciences and Professor.

Main Research Areas

  • Studying the role of epigenetic processes (changes in gene expression not linked to changes in DNA sequence) in aging.
  • Searching for functional relationships between genetic factors involved in the control of lifespan.
  • Using spectral methods (Raman and IR spectroscopy) to identify and analyze markers of aging and stemness.
  • Studying OSKM factors (Sox2, Klf4, Oct-4, c-Myc) in young and old animals.
  • Studying telomere length and telomerase activity.
  • Studying markers of oxidative stress.
  • Research aimed at reducing the number of somatic mutations that arise during in vitro cell culturing.
  • Active participation in developing SARS-CoV-2 genotyping methods, alongside testing of cellular immunity and antibody avidity to SARS-CoV-2.
  • Studying the role of miRNA in atherosclerosis.
  • Using whole-genome sequencing to identify significant sex-linked and somatic mutations.
  • Genetic engineering and gene therapy experiments related to aging.
  • Applying machine learning methods to build biological age models.

Laboratory staff have demonstrated that the lifespan of Drosophila melanogaster can be extended using histone deacetylase inhibitors, which affect gene expression through histone modification. It has also been shown that insect lifespan can be extended by modifying developmental conditions — specifically, reducing nutrient concentration in food and increasing larval population density. These changes are associated with substantial shifts in the expression levels of longevity-associated genes.

The laboratory identified associations between polymorphic variants of certain genes and the risk of Parkinson’s and Alzheimer’s disease in the Ukrainian population. It was established that disorders of carbohydrate metabolism in elderly people are associated with shortened peripheral blood leukocyte telomere length. An elevated risk of type 2 diabetes was found in a cohort of people born during the Holodomor (1932–1933 famine). Further research into the long-term epigenetic consequences of the Holodomor is planned, along with future work on telomere length and telomerase activity in elderly people with various age-related diseases.

Equipment

The laboratory is equipped with modern instrumentation from leading global manufacturers, including an Olympus fluorescence microscope, a confocal Raman microscope, a Thermo Fisher Nicolet iS50 FTIR spectrometer, a Bio-Rad real-time PCR amplifier, electrophoresis equipment, a Thermo Scientific Varioskan Flash plate spectrofluorometer (for DNA/RNA/protein concentration measurement and ELISA detection), G-Force centrifuges, incubators and laminar flow cabinets for cell culture, a −80°C freezer, a liquid-nitrogen dewar and containers for sample/reagent storage, a Millipore water purification system, and a dedicated room equipped for DNA and RNA extraction.

Cell Culture Research Group

Cellular- and tissue-level research plays a major role in contemporary science, and the laboratory has built a well-equipped, effective cell culture facility to meet current research and practical demands. It includes a sterile clean room with an airlock and HEPA-filtered ventilation and air intake system, an inverted light microscope for observing live cell populations, a Class 2A laminar flow cabinet with full sample protection, modern gas-controlled incubators, a high-capacity centrifuge, and other supporting equipment. The clean room is preceded by a base laboratory equipped with light microscopes and analytical balances, and a cryostorage facility for various cell culture and line samples. Working space can be quickly scaled up by bringing additional rooms and reserved equipment into use.

Our laboratory is organized and equipped to the high standards of leading research institutions. Creative, high-technology solutions have let us combine compact spaces with high ergonomics, ensuring high-quality aseptic working conditions. The equipment allows work with almost any cell line, and our resourceful, talented team has experience successfully applying methods on the boundary between contemporary science and science fiction.

Our facilities include a full sterile clean room with an airlock and supply/exhaust ventilation through HEPA filters, fitted with an inverted light microscope for observing live cell populations, a Class 2A laminar flow cabinet with full sample protection, state-of-the-art incubators with full gas-composition control, a high-capacity centrifuge, and many other useful instruments. The clean room is preceded by a base laboratory with light microscopes, analytical balances and other equipment, and a cryostorage facility holding samples of various cell cultures and lines. Working space can be rapidly scaled up by bringing additional rooms and reserved equipment into use.

Since the cell culture laboratory began operating, numerous unique protocols have been established, original experiments conducted, and advanced projects completed — most of which the laboratory is able to carry out on a commercial basis, including:

Senescent cells
Fibroblasts
  1. Isolation of primary human dermal fibroblast cultures. Autologous fibroblasts introduced into culture can subsequently be used for various scientific, medical, and cosmetological purposes.
  2. Culturing human fibroblasts suitable for research use or for cosmetological injections aimed at treating scars and wrinkles.
  3. Studying the effects of various compounds on fibroblast cultures:
    • MTT assay in various forms and modifications, including determination of toxic or stimulatory effects, and cross-MTT assays for selecting optimal concentration combinations of two substances.
    • Wound-healing assay under various influencing factors, to study the effect of compounds on cell migratory capacity.
    • Cell adhesion assays and studies of compound effects on cell attachment to substrates; substrate toxicity and attachment testing (in triplicate with controls).
    • Clonogenic assay, to establish cell viability and proliferative capacity after exposure to specific substances (large Petri dish and plate variants).
  4. Isolation of primary autologous mesenchymal stem cell cultures from adipose tissue. Requires additional specialists and equipment; adipose-derived MSCs, like fibroblasts, can be used for both research and medical-cosmetological purposes — more complex and costly to isolate/culture, but with more promising applications.
  5. Culturing and selection of mesenchymal stem cell cultures — producing a biomass of 20 million cells from the primary culture obtained.
  6. Isolation of primary mesenchymal stem cell cultures from umbilical cord. Donor allogeneic umbilical MSCs have high proliferative potential, produce useful compounds, and carry good-quality genetic material; given their allogeneic origin, they can be effectively applied in isolated structures such as the joint capsule to combat osteoarthritis development. Isolation and biomass production yields approximately 25 million cells.
  7. Isolation of primary mesenchymal stem cell cultures from placenta — somewhat inferior characteristics to umbilical-derived MSCs, but obtainable in larger volumes.
  8. Obtaining senescent cells through natural means — a unique scientific methodology, primarily needed for research purposes.
  9. Obtaining senescent cells through stress-induced methods — a valuable rapid technique, providing material for cell stress-resistance research.
  10. Cytochemical detection of senescent (aged, damaged, non-functional) cells in tissues and cell cultures.
  11. Transdifferentiation of skin fibroblasts into adipose and bone tissue cells — interesting scientific methodologies.
  12. Differentiation of mesenchymal stem cells from various sources into adipose and bone tissue cells — interesting scientific methodologies.
  13. Automation of senescent cell analysis — a promising research project.
  14. Development of a contrast-detection method for senescent cells alongside cell population counterstaining — a methodology that improves the efficiency and quality of work for researchers studying cell senescence.
  15. Reconstruction of coarse-fibered bone tissue from collagen scaffolds and donor fibroblasts — a promising regenerative technology.
  16. Reconstruction of vascular elements from decellularized connective-tissue patches and donor cells — a promising project, currently paused.
  17. Studying the effect of gas concentrations on genomic stability of cell cultures — research that enables the laboratory to obtain the highest-quality cells.
  18. Studying the effect of culturing temperature on the growth dynamics of mesenchymal stem cells.
  19. Transfection of various cell types (primary and passaged cultures) with target genes (using chemical agents or electroporation) — a valuable method for creating cultures that produce desired compounds.
  20. Cell analysis using a Raman spectrometer — a unique methodology, currently paused.
  21. Work with immortalized cell lines (CHO, HepG2, HEK-293, SK-MEL, etc.) — research on such cultures is roughly 25% cheaper than on primary fibroblasts and MSCs.
  22. Development of cell-freezing protocols and selection of cryoprotectants.
  23. Development of tissue-fragment freezing protocols and selection of cryoprotectants — valuable, promising methodologies.
  24. Improving cell and tissue viability after freezing.
  25. Development of culture media and media supplements.

The laboratory is also able to provide educational training in cell culturing methods.

Top Publications

Additional publications co-authored with the laboratory are indexed on PubMed and Frontiers under “Dmytro Krasnienkov, Laboratory of Epigenetics, D.F. Chebotarev Institute of Gerontology.” Some earlier spectroscopy work appears under the transliteration “D. Krasnenkov.”

Contact
Dmytro Krasnienkov, Head of Laboratory
Email: krasnienkovd@geront.kiev.ua
Phone (mobile): +38 (050) 216-21-51