Biology subjects

Alekseenko, A.

Publications and source records attributed to Alekseenko, A..

5 recordsLinked to original sources

bioRxiv2026

Identifying cancer cell-state transitions from multimodal single-cell data

Phenotypic plasticity allows cancer cells to evade therapy, yet the transient nature of state transitions has made their molecular drivers difficult to define. Here, we present a single-cell framework that leverages the temporal delays between mRNA and protein accumulation to directly capture cells undergoing phenotypic switching. We show that differentiation-associated delays between transcript and protein accumulation are detectable in multimodal single-cell data as discordant mRNA and surface-protein levels. Applying this strategy to the K562 leukemia model, which alternates between differentiated CD24- and progenitor-like CD24+ states, we identify transitioning cells and derive a transcriptional signature linking cell-cycle progression and mitochondrial remodeling to plasticity. Genome-wide CRISPR screening confirms key regulators of plasticity, including BCR-ABL1 and mitochondrial homeostasis genes. We summarize the transition-associated program into a score that predicts imatinib response in chronic myeloid leukemia, stratifies survival in acute myeloid leukemia, and retains prognostic value across 31 TCGA tumor types. Spatial transcriptomics reveals localized plasticity hotspots in solid tumors. Together, this framework exposes the molecular basis of cancer plasticity and enables its quantification across tumors.

cancer biology↗

bioRxiv2022

A palmitate-rich metastatic niche enables metastasis growth via p65 acetylation

Cancer cells outgrowing in distant organs of metastasis rewire their metabolism to fuel on the available nutrients. While this is often considered an adaptive pressure limiting metastasis formation, some nutrients available at the metastatic site naturally or through changes in organ physiology may inherently promote metastatic growth. We find that the lung, a frequent site of metastasis, is a lipid-rich environment. Moreover, we observe that pathological conditions such as pre-metastatic niche formation and obesity further increase the availability of the fatty acid palmitate in the lung. We find that targeting palmitate processing inhibits spheroid growth in vitro and metastasis formation in lean and obese mice. Mechanistically, we discover that breast cancer cells use palmitate to synthesize acetyl-CoA in a carnitine palmitoyltransferase 1a (CPT1a)-dependent manner. Lysine acetyltransferase 2a (KAT2a), whose expression is promoted by palmitate availability, relies on the available acetyl-CoA to acetylate the NF-{kappa}B subunit p65. This favors nuclear location of p65 and activates a pro-metastatic transcriptional program. Accordingly, deletion of KAT2a phenocopies CPT1a silencing in vitro as well as in vivo and patients with breast cancer show co-expression of both proteins in metastases across palmitate-rich metastatic sites. In conclusion, we find that palmitate-rich environments foster metastasis growth by increasing p65 acetylation resulting in elevated NF-{kappa}B signaling.

cancer biology↗

bioRxiv2022

Differential regulation of mRNA stability modulates transcriptional memory and facilitates environmental adaptation

Transcriptional memory, by which cells respond faster to repeated stimuli, is key for cellular adaptation and organism survival. Factors related to chromatin organization and activation of transcription have been shown to play a role in the faster response of those cells previously exposed to a stimulus (primed). However, the contribution of post-transcriptional regulation is not yet explored. Here, combining flow cytometry and high throughput sequencing, we perform a genome-wide screen to identify novel factors modulating transcriptional memory in S. cerevisiae in response to galactose nutrition sources. In addition to the well-known chromatin factors modulating transcriptional memory, we find that depletion of the nuclear RNA exosome increases GAL1 expression in primed cells. We perform a genome-wide characterisation of this process and show that changes in nuclear surveillance factor association can enhance both gene induction and repression in primed cells. Finally, we show that in addition to nuclear mRNA degradation, differences in cytoplasmic mRNA decay also modulate transcriptional memory and contribute to faster gene expression remodelling in primed cells. Our results demonstrate that mRNA post-transcriptional regulation, and not only transcription regulation, should be considered when investigating gene expression memory.

genomics↗

bioRxiv2020

Rpb4 and Puf3 imprint and post-transcriptionally control the stability of a common set of mRNAs in yeast

Gene expression involving RNA polymerase II is regulated by the concerted interplay between mRNA synthesis and degradation, crosstalk in which mRNA decay machinery and transcription machinery respectively impact transcription and mRNA stability. Rpb4, and likely dimer Rpb4/7, seem the central components of the RNA pol II governing these processes. In this work we unravel the molecular mechanisms participated by Rpb4 that mediate the posttranscriptional events regulating mRNA imprinting and stability. By RIP-Seq, we analyzed genome-wide the association of Rpb4 with mRNAs and demonstrated that it targeted a large population of more than 1400 transcripts. A group of these mRNAs was also the target of the RNA binding protein, Puf3. We demonstrated that Rpb4 and Puf3 physically, genetically, and functionally interact and also affect mRNA stability, and likely the imprinting, of a common group of mRNAs. Furthermore, the Rpb4 and Puf3 association with mRNAs depends on one another. We also demonstrated, for the first time, that Puf3 associates with chromatin in an Rpb4-dependent manner. Our data also suggest that Rpb4 could be a key element of the RNA pol II that coordinates mRNA synthesis, imprinting and stability in cooperation with RBPs.

molecular biology↗

bioRxiv2019

Improved Modeling of Peptide-Protein Binding through Global Docking and Accelerated Molecular Dynamics Simulations

Peptides mediate up to 40% of known protein-protein interactions in higher eukaryotes and play a key role in cellular signaling, protein trafficking, immunology and oncology. However, it is challenging to predict peptide-protein binding with conventional computational modeling approaches, due to slow dynamics and high peptide flexibility. Here, we present a prototype of the approach which combines global peptide docking using ClusPro PeptiDock and all-atom enhanced simulations using Gaussian accelerated molecular dynamics (GaMD). For three distinct model peptides, the lowest backbone root-mean-square deviations (RMSDs) of their bound conformations relative to X-ray structures obtained from PeptiDock were 3.3 [A] - 4.8 [A], being medium quality predictions according to the Critical Assessment of PRediction of Interactions (CAPRI) criteria. GaMD simulations refined the peptide-protein complex structures with significantly reduced peptide backbone RMSDs of 0.6 [A] - 2.7 [A], yielding two high quality (sub-angstrom) and one medium quality models. Furthermore, the GaMD simulations identified important low-energy conformational states and revealed the mechanism of peptide binding to the target proteins. Therefore, PeptiDock+GaMD is a promising approach for exploring peptide-protein interactions.

biophysics↗