Biology subjects

Kovatcheva, M.

Publications and source records attributed to Kovatcheva, M..

5 recordsLinked to original sources

bioRxiv2026

SENOMORPHIC EFFECT OF GENETIC AND CHEMICAL PARTIAL REPROGRAMMING

Partial reprogramming has emerged as a promising strategy to ameliorate aging phenotypes, yet its cellular targets and mechanisms remain poorly defined. Cellular senescence is a central hallmark of aging and a plausible mediator of reprogramming-induced rejuvenation. Here we show that genetic and chemical partial reprogramming act directly on senescent cells without restoring proliferative capacity. OSKM expression or a reduced two-compound regimen, tranylcypromine and RepSox (2c), attenuates senescence-associated secretory activity, restores mitochondrial homeostasis and apoptotic priming, and improves functional and inflammatory parameters in aged mice, establishing senomorphic, identity-preserving reprogramming as a potentially safer aging intervention.

cell biology↗

bioRxiv2024

Persister cancer cells are characterized by H4K20me3 heterochromatin that defines a low inflammatory profile

Anti-cancer therapies may induce proliferative arrest in cancer cells in the form of senescence or drug-tolerant persistency, the latter being a reversible arrest with similarities to embryonic diapause. Here, we use mTOR/PI3K inhibition to develop and characterize a model of persistency/diapause-like arrest in human cancer cells of various origins. We show that persister and senescent cancer cells share an expanded lysosomal compartment and hypersensitivity to BCL-XL inhibition. However, persister cells do not exhibit other features of senescence, such as the loss of Lamin B1, senescence-associated b-galactosidase activity, and an inflammatory phenotype. Compared to senescent cells, persister cells have a profoundly diminished senescence-associated secretory phenotype (SASP), low activation of interferon signaling pathways and lack upregulation of MHC-I presentation. Based on a genome-wide CRISPR/Cas9 screen performed in diapause mouse embryonic stem cells (mESC), we discover that persister human cancer cells are hypersensitive to the inhibition of one-carbon metabolism. This finding led us to uncover that the repressive heterochromatic mark H4K20me3 is enriched at promoters of SASP and interferon response genes in persister cells, but not in senescent cells. Collectively, we define novel features and vulnerabilities of persister cancer cells and we provide insight into the epigenetic mechanisms underlying their low inflammatory and immunogenic activity.

cancer biology↗

bioRxiv2023

A targeted metabolomic method to detect epigenetically relevant metabolites

Metabolites play a central role in the chemical crosstalk between metabolism and epigenetic marks. Epigenetically relevant metabolites are substrates, products and cofactors that can act as activators or inhibitors of epigenetic enzymes, which control gene expression by adding or removing chemical marks in the DNA, RNA and histones. Diet composition, and biosynthetic pathways encoded in the gut microbiome and the host genome are the main sources of these metabolites for mammals. Despite the increasing interest in the study of the microbiota-nutrient metabolism-host epigenetic axis to understand health and disease, there is a lack of a sensitive and easy analytical method to detect epigenetically relevant metabolites simultaneously. Here, we show an straightforward biphasic extraction where the organic phase is directly analyzed by GC-EI MS to detect short-chain fatty acids and formate without chemical derivatization, and the aqueous phase is analyzed by HILIC coupled to ESI-MS/MS, which together can cover >30 epigenetically relevant metabolites in biological samples such as liver, plasma or feces. In addition, we propose a stable isotope tracing method based on multiple-reaction monitoring (MRM) transitions by LC-QqQ MS to understand how 13C-labeled glucose or glutamine are used to build SAM and acetyl-CoA, the main methyl and acetyl group donors in epigenetic modifications, respectively. We anticipate that our methods will complement epigenomic and proteomic analyses adding another layer of molecular information towards mechanistic insights. HighlightsO_LIHost and microbiota metabolites link metabolism with epigenetic regulation. C_LIO_LIChemical structure diversity in epigenetically relevant metabolites challenges its analysis with a single method. C_LIO_LIA biphasic extraction with no chemical derivatization is able to recover SCFAs and other epigenetically relevant metabolites. C_LIO_LIA novel isotope trace experiment approach allows isotopomer resolution using MS2 data. C_LI

biochemistry↗

bioRxiv2022

Induction of senescence renders cancer cells highly immunogenic

Cellular senescence is a stress response that activates innate immunity. However, the interplay between senescent cells and the adaptive immune system remains largely unexplored. Here, we show that senescent cells display enhanced MHC class I (MHC-I) antigen processing and presentation. Immunization of mice with senescent syngeneic fibroblasts generates CD8 T cells reactive against both normal and senescent fibroblasts, some of them targeting senescence-associated MHC-I-peptides. In the context of cancer, we demonstrate that senescent cancer cells trigger strong anti-tumor protection mediated by antigen-presenting cells and CD8 T cells. This response is superior to the protection elicited by cells undergoing immunogenic cell death. Finally, induction of senescence in patient-derived cancer cells exacerbates the activation of autologous tumor-reactive CD8 tumor-infiltrating lymphocytes (TILs) with no effect on non-reactive TILs. Our study indicates that immunization with senescent cancer cells strongly activates anti-tumor immunity, and this can be exploited for cancer therapy. STATEMENT OF SIGNIFICANCEOur study shows that senescent cells are endowed with a high immunogenic potential, superior to the gold standard of immunogenic cell death. The induction of senescence in cancer cells can be exploited to develop efficient and protective CD8-dependent anti-tumor immune responses.

cancer biology↗

bioRxiv2022

Deciphering the roadmap of in vivo reprogramming towards pluripotency

Differentiated cells can be converted to pluripotent stem cells (iPSCs) upon ectopic expression of transcription factors OCT4, SOX2, KLF4 and MYC (OSKM) in a process known as reprogramming. Great efforts have been made to dissect intermediate states of in vitro reprogramming and how they are affected by culture conditions, while the roadmap of in vivo reprogramming remains unexplored. Here, we use single cell RNA sequencing to capture cells undergoing reprogramming in the adult pancreas. We identify markers along the trajectory from acinar identity to pluripotency, which allow in situ visualization of the intermediate states of reprogramming. Importantly, different tissues expressing OSKM, such as pancreas, stomach and colon, share markers of intermediate reprogramming, suggesting a conserved in vivo reprogramming path. Our in vivo roadmap defines landmarks along in vivo reprogramming that could be useful for applications in tissue regeneration and cellular rejuvenation based on intermediate reprogramming states.

developmental biology↗