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Kukhta, T.

Publications and source records attributed to Kukhta, T..

3 recordsLinked to original sources

Distinct metabolic states of yeast and pseudohyphae differentially prime innate immune responsiveness

Pseudohyphal growth in skin-associated fungi is often considered a morphological response to environmental stress, but whether it represents a coordinated metabolic state that influences host immunity remains unclear. Using Malassezia furfur, we combined synchronized morphogenesis, temporal metabolomics, stable-isotope tracing, targeted metabolite measurements, transcriptional profiling, and functional immune assays to compare yeast and pseudohyphal states. Yeast cells maintained an active tryptophan-aldehyde metabolic program that partitioned carbon between oxidative and reductive branches associated with redox balance and methylation potential. Pseudohyphal cells attenuated this program and instead underwent sequential metabolic remodeling, characterized by early changes in one-carbon and amino acid metabolism followed by sulfur-pathway remodeling and increased glutathione biosynthesis. These distinct fungal states generated extracellular environments that altered THP-1 innate immune responsiveness without directly inducing canonical macrophage polarization. Yeast-conditioned cells responded preferentially to tissue-repair signals, whereas pseudohypha-conditioned cells displayed enhanced responses to inflammatory stimuli. Individual metabolites did not reproduce these effects, suggesting that immune conditioning depends on the integrated extracellular milieu. Together, these findings identify pseudohyphal growth as an organized adaptive metabolic state and establish a framework linking fungal morphogenetic potential to context-dependent host immune responses.

microbiology↗

CpG island density predicts CBP/p300 dependency across 3D chromatin clusters

RNA Polymerase II (Pol2) organizes transcription through higher-ordered chromatin clusters that integrate promoter and enhancer interactions to coordinate gene expression. Nevertheless, the features that distinguish unique classes of Pol2-mediated clusters remain to be defined. Here, we identify two distinct classes of Pol2-mediated clusters: one enriched for CpG islands, promoter-promoter interactions, and housekeeping gene expression, and another characterized by high CBP/p300 occupancy, enhancer-promoter looping, and lineage-defining (LD) transcriptional programs. Acute inhibition of CBP/p300 catalytic activity leads to rapid loss of acetylation at enhancers and preferential downregulation of LD genes, resulting in impaired cellular proliferation and activation of apoptotic programs. Integrative machine learning modeling reveals that cluster strength, RNA half-life, and CpG island content as strong predictors of genes sensitive to CBP/p300 inhibition. Together, these findings clarify enhancer-addiction and vulnerability to CBP/p300 inhibition.

cancer biology↗

Occurrence and classification of T-shaped interactions between nucleobases in RNA structures

Understanding the frequency and structural context of discrete noncovalent interactions between nucleotides is of pivotal significance in establishing the rules that govern RNA structure and dynamics. Although T-shaped contacts (i.e., perpendicular stacking contacts) between aromatic amino acids and nucleobases at the nucleic acid-protein interface have recently garnered attention, the analogous contacts within the nucleic acid structures have not been discussed. In this work, we have developed an automated method for identifying and unambiguously classifying T-shaped interactions between nucleobases. Using this method, we identified a total of 3262 instances of T-shaped (perpendicular stacking) contacts between two nucleobases in an array of RNA structures from an up-to-date dataset of high-resolution crystal structures deposited in the Protein Databank. These analyses add to the understanding of the physicochemical forces that are responsible for structure and dynamics of RNA.

biophysics↗