Biology subjects

Deryagin, O.

Publications and source records attributed to Deryagin, O..

4 recordsLinked to original sources

bioRxiv2025

The central clock drives metabolic rhythms in muscle stem cells

Circadian rhythms are essential for organismal health. Satellite cells (SCs), the muscle resident stem cells, maintain a state of quiescence yet exhibit robust circadian oscillations at the transcriptional level. Although peripheral clocks have been extensively studied in various tissues, how the intrinsic clock of stem cells interacts with the central, distal clock is largely unknown. We used SC-specific reconstitution of the essential clock gene Bmal1 to elucidate the role of the local SC clock and its interplay with the central clock in the mouse brain and found that daily transcriptional control of metabolic processes in SCs depend on central clock input, independent of the SC clock. Central clock-driven genes were involved in lipid metabolism, functionally important for SC-mediated muscle repair, and autophagy was required for their oscillation. In summary, we provide the first evidence of circadian coordination of central and local clocks for control of rhythmic gene expression in quiescent stem cells. HighlightsO_LIBrain:satellite cell clock communication restores rhythms of core clock machinery in quiescent satellite cells C_LIO_LIBrain inputs are the dominant regulator of transcript rhythms in SCs, driving the oscillation of lipid metabolic genes. C_LIO_LIAutophagy in satellite cells is required for the oscillation of lipid metabolic genes. C_LIO_LIEarly phases of muscle regeneration depend on brain-driven circadian signals. C_LI

cell biology↗

bioRxiv2024

Network-community analysis of cellular senescence

Most cellular phenotypes are genetically complex. Identifying the set of genes that are most closely associated with a specific cellular state is still an open question in many cases. Here we study the transcriptional profile of cellular senescence using a combination of network-based approaches, which include eigenvector centrality feature selection and community detection. We apply our method to cell-type-resolved RNA sequencing data obtained from injured muscle tissue in mice. The analysis identifies some genetic markers consistent with previous findings, and other previously unidentified ones, which are validated with previously published single-cell RNA sequencing data in a different type of tissue. The key identified genes, both those previously known and the newly identified ones, are transcriptional targets of factors known to be associated with established hallmarks of senescence, and can thus be interpreted as molecular correlates of such hallmarks. The method proposed here could be applied to any complex cellular phenotype even when only bulk RNA sequencing is available, provided the data is resolved by cell type.

systems biology↗

bioRxiv2022

Interrogating Metabolic Interactions Between Skeletal Muscle and Liver Circadian Clocks In Vivo

Expressed throughout the body, the circadian clock system achieves daily metabolic homeostasis at every level of physiology, with clock disruption associated with metabolic disease (1, 2). Molecular clocks present in the brain, liver, adipose, pancreas and skeletal muscle each contribute to glucose homeostasis (3). However, it is unclear; 1) which organ clocks provide the most essential contributions, and 2) if these contributions depend on inter-organ communication. We recently showed that the liver clock alone is insufficient for most aspects of daily liver glucose handling and requires connections with other clocks (4). Considering the pathways that link glucose metabolism between liver and skeletal muscle, we sought to test whether a clock connection along this axis is important. Using our previous published methodology for tissue-specific rescue of Bmal1 in vivo (4, 5), we now show that in the absence of feeding-fasting cycles, liver and muscle clocks are not sufficient for systemic glucose metabolism, nor do they form a functional connection influencing local glucose handling or daily transcriptional rhythms in each tissue. However, the introduction of a daily feeding-fasting rhythm enables a synergistic state between liver and muscle clocks that leads to restoration of systemic glucose tolerance. These findings reveal limited autonomous capabilities of liver and muscle clocks and highlight the need for inter-organ clock communication for glucose homeostasis which involves at least two peripheral metabolic organs.

cell biology↗

bioRxiv2022

Brain-keratinocyte communication suffices for epidermal daily homeostasis

In mammals, an integrated network of molecular oscillators drives daily rhythms of tissue-specific homeostatic processes. This circadian clock network is required for maintaining health and is compromised by disease and lifestyle choices, such as diet and exercise. However, critical properties of this systemic network, such as which tissues communicate to coordinate their respective programs of daily physiology, and the exact homeostatic processes requiring each communication pathway, remain undefined. To dissect daily inter-tissue communication, we have constructed in mice a minimal clock network comprising only two nodes: the peripheral epidermal clock and the central brain clock. By circadian transcriptomic and functional characterization of this isolated connection, we have identified a previously unknown gatekeeping function of the peripheral tissue clock with respect to systemic inputs. That is, the epidermal clock concurrently integrates and corrects brain signals to ensure timely execution of epidermal daily physiology. Specifying the integrative arm of the clock, we identify that timely cell cycle termination in the epidermal stem cell compartment is dependent upon incorporation of clock-driven signals originating from the brain. Unexpectedly, and in contrast, the epidermal clock corrects potentially disruptive feeding-related signals to ensure that DNA replication occurs at the optimum time of day. Together, we present a novel approach for cataloguing the systemic dependencies of a given tissue, and in turn identify an essential gate-keeping function of peripheral circadian clocks that guarantees tissue homeostasis.

cell biology↗