Biology subjects

Koronowski, K. B.

Publications and source records attributed to Koronowski, K. B..

8 recordsLinked to original sources

bioRxiv2026

Co-expression network analysis reveals repression of Igf2bp2 by REV-ERBβ in skeletal muscle

The circadian clock genes Bmal1 and Nr1d1/2 (REV-ERB/{beta}) regulate skeletal muscle metabolism and homeostasis, yet the precise genes and mechanisms involved remain incompletely understood. Here, we perform Weighted Gene Co-expression Network Analysis (WGCNA) on skeletal muscle circadian transcriptomes with varying Bmal1 operational status to identify genes central to muscle circadian function. The largest WGCNA module, potentially under Bmal1 regulation, contains clock and muscle-specific output genes governed hierarchically by hub genes including Igf2bp2, an RNA-binding protein involved in muscle progenitor growth and maintenance. Igf2bp2 expression is rhythmic in mouse and human muscle and functional experiments in muscle-specific Bmal1 knockout mice show that Igf2bp2 is upregulated by loss of Bmal1 at ZT8 and negatively correlated with Nr1d2, suggesting de-repression through REV-ERB{beta} as a regulatory mechanism. Luciferase reporter experiments in cultured myotubes show that REV-ERB{beta}, but not REV-ERB, represses Igf2bp2 transcription and that repression is mediated by non-canonical GCC motifs in the Igf2bp2 promoter region. Together, these findings uncover a circadian Nr1d2-Igf2bp2 regulatory axis linking transcriptional and post-transcriptional regulation in skeletal muscle, with implications for muscle homeostasis. HighlightsO_LIIgf2bp2 clusters with Nr1d2 (Rev-erb{beta}) in circadian co-expression network C_LIO_LIBmal1 or Rev-erb[a]/{beta} knockout upregulates Igf2bp2 in muscle C_LIO_LIIgf2bp2 is rhythmic in WT muscle but arrhythmic in clock mutant muscle C_LIO_LIREV-ERB{beta} represses Igf2bp2 transcription in myotubes C_LIO_LIREV-ERB{beta} repression requires GCC motifs in the Igf2bp2 promoter C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/724827v1_ufig1.gif" ALT="Figure 1"> View larger version (89K): org.highwire.dtl.DTLVardef@1716a34org.highwire.dtl.DTLVardef@f3a5b1org.highwire.dtl.DTLVardef@33f58org.highwire.dtl.DTLVardef@133e3db_HPS_FORMAT_FIGEXP M_FIG C_FIG

systems biology↗

bioRxiv2025

Protein Secretion From Liver Ex Vivo Reveals Regulation of Hepatokines by Sex and Circadian Rhythm

Here, we use an ex vivo approach compatible with the circadian timescale to interrogate protein secretion from liver, revealing several findings. Proteomic analyses in male and female mice identify hundreds of proteins that exhibit time-of-day-dependent or clock-dependent secretion involved in extracellular matrix, immune, redox, xenobiotic, and fatty acid functions. Among these, the liver secretes more endostatin, a cleavage product of collagen type XVIII alpha 1 (COL18A1), during the inactive, fasting phase of the diurnal cycle. Temporal regulation of COL18A1/endostatin is dysregulated upon loss of Bmal1 through combined effects on Col18a1 transcriptional repression and proteolytic processing. Functional experiments in vivo and in vitro reveal that endostatin suppresses mitochondrial gene expression in white adipose tissue in a time-dependent manner and reduces mitochondrial respiration in adipocytes, while enhancing lipolysis. These results support a mechanism of inter-organ crosstalk whereby hepatically derived, temporally-restricted endostatin tunes adipocytes toward metabolic activities required during the fasting phase.

molecular biology↗

bioRxiv2025

The liver clock tunes transcriptional rhythms in skeletal muscle to regulate mitochondrial function

Circadian clocks present throughout the brain and body coordinate diverse physiological processes to support daily homeostasis and respond to changing environmental conditions. The local dependencies within the mammalian clock network are not well defined. We previously demonstrated that the skeletal muscle clock controls transcript oscillations of genes involved in fatty acid metabolism in the liver, yet whether the liver clock also regulates the muscle was unknown. Here, we use hepatocyte-specific Bmal1 KO mice (Bmal1hep-/-) and reveal that approximately one third of transcriptional rhythms in skeletal muscle are regulated by the liver clock vivo. Treatment of myotubes with serum harvested from Bmal1hep-/- mice inhibited expression of genes involved in metabolic pathways, including oxidative phosphorylation. Overall, the transcriptional changes induced by liver clock-driven endocrine-communication revealed from our in vitro system were small in magnitude, leading us to surmise that the liver clock acts to fine-tune metabolic gene expression in muscle. Strikingly, treatment of myotubes with serum from Bmal1hep-/- mice inhibited mitochondrial ATP production compared to WT and this effect was only observed with serum harvested during the active phase. Overall, our results reveal communication between the liver clock and skeletal muscle-uncovering a bidirectional endocrine communication pathway dependent on clocks in these two key metabolic tissues. Targeting liver and muscle circadian clocks may represent a potential avenue for exploration for diseases associated with dysregulation of metabolism in these tissues.

cell biology↗

bioRxiv2023

Impact of Bmal1 rescue and time-restricted feeding on liver and muscle proteomes during the active phase in mice

ObjectiveMolecular clocks and daily feeding cycles support metabolism in peripheral tissues. Although the roles of local clocks and feeding is well defined at the transcriptional level, their impact on governing protein abundances in peripheral tissues is unclear. Here, we determine the relative contributions of the local molecular clock and daily feeding cycles on liver and muscle proteomes during feeding. MethodsLC-MS/MS was performed on liver and skeletal muscle harvested four hours into the dark phase from wild-type (WT), Bmal1 knockout (KO), and liver- and muscle-Bmal1-rescued (LMRE) mice housed under 12-h light/12-h dark cycles with either ad libitum feeding or nighttime-restricted feeding. Additional molecular and metabolic analyses were performed on liver and cultured hepatocytes. ResultsFeeding-fasting cycles had only minimal effects on liver and none on muscle. In contrast, Bmal1 KO altered the abundance of 674 proteins in liver, and 80 in muscle. Rescue of liver and muscle Bmal1 restored 50% of proteins in liver and 25% in muscle. These included proteins involved in carbohydrate metabolism in muscle and in fatty acid oxidation in liver. For liver, proteins involved in de novo lipogenesis were largely dependent on Bmal1 function in other tissues (i.e., the wider clock system). Proteins regulated by BMAL1 were enriched for secreted proteins; we determined that the maintenance of FGF1 abundance requires liver BMAL1, and that autocrine signaling through FGF1 is necessary and sufficient for mitochondrial respiration in hepatocytes. ConclusionsBMAL1 in liver and muscle is a more potent regulator of dark phase proteomes than daily feeding cycles, highlighting the need to assess protein levels in addition to mRNA when investigating clock mechanisms. The proteome is more extensively regulated by BMAL1 in liver than in muscle, and numerous metabolic pathways in peripheral tissues are reliant on the function of the clock system as a whole.

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↗

bioRxiv2022

The central clock suffices to drive the majority of circulatory metabolic rhythms

Life on Earth anticipates recurring 24-h environmental cycles via genetically-encoded molecular clocks active in all mammalian organs. Communication between these clocks is believed to control circadian homeostasis. Metabolism can be considered a form of inter- tissue communication language that results in temporal coordination of systemic metabolism between tissues. Here we characterize the extent to which clocks in different organs employ this means of communication, an area which remains largely unexplored. For this, we analysed the metabolome of serum from mice with tissue-specific expression of the clock gene Bmal1. Notably, having functional hepatic and muscle clocks can only drive a minority (13%) of the oscillating metabolites in circulation. Conversely, limiting Bmal1 expression to Syt10- expressing neurons (which are enriched in the suprachiasmatic nucleus [SCN], the master pacemaker that regulates circadian rhythms) restores rhythms to 57% of circulatory metabolites and 28% of liver transcripts, and rescues glucose intolerance. Importantly, these parameters were also restored in clock-less mice upon rhythmic feeding, indicating that the central clock mainly regulates metabolic rhythms via behavior. These findings explicate the circadian communication between tissues and highlight the importance of the central clock in governing those signals.

physiology↗

bioRxiv2021

Ketogenesis Impact on Liver Metabolism Revealed by Proteomics of Lysine β-hydroxybutyrylation

Ketone bodies are evolutionarily conserved metabolites that function as energy substrates, signaling molecules and epigenetic regulators. {beta}-hydroxybutyrate ({beta}-OHB) is utilized in lysine {beta}-hydroxybutyrylation (Kbhb) of histones, which associates with starvation-responsive genes, effectively coupling ketogenic metabolism with gene expression. The emerging diversity of the lysine acylation landscape prompted us to investigate the full proteomic impact of Kbhb. Global protein Kbhb is induced in a tissue-specific manner by a variety of interventions that evoke {beta}-OHB. Mass spectrometry analysis of the {beta}-hydroxybutyrylome in mouse liver revealed 891 sites of Kbhb within 267 proteins enriched for fatty acid, amino acid, detoxification and 1-carbon metabolic pathways. Kbhb of S-adenosyl-L-homocysteine hydrolase (AHCY), a rate-limiting enzyme of the methionine cycle, results in inhibition of enzymatic activity. Our results illuminate the role of Kbhb on hepatic metabolism under ketogenic conditions and demonstrate the functional consequence of this modification on a central metabolic enzyme.

molecular biology↗