Biology subjects

Sigaeva, A.

Publications and source records attributed to Sigaeva, A..

3 recordsLinked to original sources

bioRxiv2024

A PERTURBATION CELL ATLAS OF HUMAN INDUCED PLURIPOTENT STEM CELLS

Towards comprehensively investigating the genotype-phenotype relationships governing the human pluripotent stem cell state, we generated an expressed genome-scale CRISPRi Perturbation Cell Atlas in KOLF2.1J human induced pluripotent stem cells (hiPSCs) mapping transcriptional and fitness phenotypes associated with 11,739 targeted genes. Using the transcriptional phenotypes, we created a minimum distortion embedding map of the pluripotent state, demonstrating rich recapitulation of protein complexes, such as strong co-clustering of MRPL, BAF, SAGA, and Ragulator family members. Additionally, we uncovered transcriptional regulators that are uncoupled from cell fitness, discovering potential novel pluripotency (JOSD1, RNF7) and metabolic factors (ZBTB41). We validated these findings via phenotypic, protein-interaction, and metabolic tracing assays. Finally, we propose a contrastive human-cell engineering framework (CHEF), a machine learning architecture that learns from perturbation cell atlases to predict perturbation recipes that achieve desired transcriptional states. Taken together, our study presents a comprehensive resource for interrogating the regulatory networks governing pluripotency.

bioengineering↗

bioRxiv2024

Dissecting autonomous enzyme variability in single cells

Metabolic enzymes perform life-sustaining functions in various cellular compartments. Anecdotally, metabolic activity is observed to vary between genetically identical cells, which impacts drug resistance, differentiation, and immune cell activation. However, no large-scale resource systematically reporting metabolic cellular heterogeneity exists. Here, we leverage imaging-based single-cell spatial proteomics to reveal the extent of non-genetic variability of the human enzymatic proteome, as a proxy for metabolic states. Nearly two fifths of enzymes exhibit cell-to-cell variable expression, and half localize to multiple cellular compartments. Metabolic heterogeneity arises largely autonomously of cell cycling, and individual cells reestablish these myriad metabolic phenotypes over several cell divisions. Multiplexed imaging revealed that metabolic states are continuous and that the correlation between metabolic pathways is metabolic state dependent. These results establish cell-to-cell enzymatic heterogeneity as an organizing principle of cell biology that may rewire our understanding of drug resistance, treatment design, and other aspects of medicine.

cell biology↗

bioRxiv2023

Evolution of intracellular free radical load in colon adenocarcinoma cells over the course of butyrate-induced redifferentiation

Fluorescent nanodiamonds have exceptional optical properties and are highly biocompatible, which allows to use them as labels for long-term tracking of the cells. The research fields that make use of this application of nanodiamonds include stem cell biology and cancer biology, where quiescent and differentiating cells can be traced in vitro and in vivo. However, these studies focus on using nanodiamonds as simple labels, whereas they can serve as highly sensitive intracellular sensors for free radical species. In this study, we aimed to bring the two approaches together and to assess the free radical production in the cells over the course of their differentiation. We report on the successful enterocytic differentiation of HT-29 colon adenocarcinoma cells, pre-loaded with fluorescent nanodiamonds. The cells were cultured in butyrate-free or butyrate-supplemented medium for 13 days. Butyrate-treated cells developed the morphological and molecular traits, characteristic for normal enterocytes. Fluorescent nanodiamonds did not have a negative effect on the process of differentiation. Moreover, the particles could be found in the cytoplasm of both undifferentiated and re-differentiated cells even after 13 days of culture. The internalized nanodiamonds were used to assess the free radical load in the undifferentiated and re-differentiated HT-29 cells at different stages of the experiment. Consistently with previous findings, re-differentiated HT-29 cells showed higher free radical load than undifferentiated ones.

cell biology↗