The ontogenesis of the circadian clock in the suprachiasmatic nuclei of the hypothalamus (SCN) and its sensitivity to maternal signals are not fully understood. Here, we investigated the development of the clock in the rat SCN from the fetal to the postweaning period and identified rhythmic metabolic signals from the mother to the fetal SCN. We determined daily expression profiles of clock genes (Per2, Nr1d1, Bmal1) and clock- and metabolism-related genes (Dbp, E4bp4) and performed time-resolved analysis of the metabolome and lipidome in the SCN and plasma of 19-day-old embryos (E19) and 2-, 10-, 20-, and 28-day-old pups (P02-28). Our data show that rhythms in the expression of canonical clock genes are absent at E19 and develop gradually until P10, but the Dbp rhythm was still developing between P20 and P28. Expression of the metabolism-sensitive gene E4bp4 and levels of essential amino acids and other metabolites supplied by maternal food are rhythmic in the fetal SCN, which is lost after birth at P02 and reappears later in the postnatal period. Maternal food-derived metabolites were also rhythmic in fetal plasma. The temporal coherence of the fetal SCN metabolome and lipidome declines markedly and its rhythmicity disappears immediately after birth. The results revealed previously unforeseen pathways by which the fetal SCN may receive rhythmic information from the mother before its clock develops.

• MeSH
• Circadian Clocks * physiology   genetics   MeSH
• Period Circadian Proteins genetics   metabolism   MeSH
• Circadian Rhythm physiology   MeSH
• Rats MeSH
• Metabolome MeSH
• Suprachiasmatic Nucleus * metabolism   embryology   physiology   MeSH
• CLOCK Proteins genetics   metabolism   MeSH
• Pregnancy MeSH
• ARNTL Transcription Factors genetics   metabolism   MeSH
• Gene Expression Regulation, Developmental MeSH
• Animals MeSH
• Check Tag
• Rats MeSH
• Male MeSH
• Pregnancy MeSH
• Female MeSH
• Animals MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• Period Circadian Proteins MeSH
• CLOCK Proteins MeSH
• ARNTL Transcription Factors MeSH

Circadian rhythms regulate key physiological processes through clock genes in central and peripheral tissues. While circadian gene expression during development has been well studied, the temporal dynamics of metabolism across tissues remain less understood. Here, we present the Circadian Ontogenetic Metabolomics Atlas (COMA), which maps circadian metabolic rhythms across 16 rat anatomical structures. The brain (suprachiasmatic nuclei, medial prefrontal cortex) and periphery (liver, plasma) span developmental stages from embryonic E19 to postnatal P2, P10, P20, and P28. Fecal samples include all four postnatal stages, while additional peripheral tissues were analyzed at P20 and P28. Using a multiplatform liquid chromatography-mass spectrometry approach, we annotated 851 metabolites from 1610 samples. We identified distinct circadian shifts, particularly during the transition from nursing to solid food intake (P10-P20), with an average of 24% of metabolites exhibiting circadian oscillations across sample types, as determined by JTK_CYCLE. Our study also underscores the importance of standardized sampling, as metabolite intensities fluctuate with both circadian rhythms and development. COMA serves as an open-access resource ( https://coma.metabolomics.fgu.cas.cz ) for exploring circadian metabolic regulation and its role in developmental biology.

• Keywords
• Atlas, Circadian rhythm, Lipidomics, Metabolomics, Resource,
• MeSH
• Chromatography, Liquid MeSH
• Circadian Rhythm * physiology   MeSH
• Feces * chemistry   MeSH
• Liver metabolism   MeSH
• Rats MeSH
• Metabolome * MeSH
• Metabolomics * methods   MeSH
• Animals MeSH
• Check Tag
• Rats MeSH
• Male MeSH
• Female MeSH
• Animals MeSH
• Publication type
• Journal Article MeSH

Choroid plexus (ChP), the brain structure primarily responsible for cerebrospinal fluid production, contains a robust circadian clock, whose role remains to be elucidated. The aim of our study was to [1] identify rhythmically controlled cellular processes in the mouse ChP and [2] assess the role and nature of signals derived from the master clock in the suprachiasmatic nuclei (SCN) that control ChP rhythms. To accomplish this goal, we used various mouse models (WT, mPer2Luc, ChP-specific Bmal1 knockout) and combined multiple experimental approaches, including surgical lesion of the SCN (SCNx), time-resolved transcriptomics, and single cell luminescence microscopy. In ChP of control (Ctrl) mice collected every 4 h over 2 circadian cycles in darkness, we found that the ChP clock regulates many processes, including the cerebrospinal fluid circadian secretome, precisely times endoplasmic reticulum stress response, and controls genes involved in neurodegenerative diseases (Alzheimer's disease, Huntington's disease, and frontotemporal dementia). In ChP of SCNx mice, the rhythmicity detected in vivo and ex vivo was severely dampened to a comparable extent as in mice with ChP-specific Bmal1 knockout, and the dampened cellular rhythms were restored by daily injections of dexamethasone in mice. Our data demonstrate that the ChP clock controls tissue-specific gene expression and is strongly dependent on the presence of a functional connection with the SCN. The results may contribute to the search for a novel link between ChP clock disruption and impaired brain health.

• Keywords
• mPer2 Luc mouse, Choroid plexus, Circadian clock, Circadian transcriptome, Glucocorticoid, Mouse, Suprachiasmatic nuclei,
• MeSH
• Circadian Clocks * physiology   MeSH
• Circadian Rhythm physiology   MeSH
• Mice, Inbred C57BL MeSH
• Mice, Knockout MeSH
• Mice MeSH
• Suprachiasmatic Nucleus * metabolism   physiology   MeSH
• Choroid Plexus * metabolism   physiology   MeSH
• ARNTL Transcription Factors metabolism   genetics   MeSH
• Animals MeSH
• Check Tag
• Male MeSH
• Mice MeSH
• Animals MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• Bmal1 protein, mouse MeSH Browser
• ARNTL Transcription Factors MeSH

Liquid chromatography with mass spectrometry (LC-MS)-based metabolomics detects thousands of molecular features (retention time-m/z pairs) in biological samples per analysis, yet the metabolite annotation rate remains low, with 90% of signals classified as unknowns. To enhance the metabolite annotation rates, researchers employ tandem mass spectral libraries and challenging in silico fragmentation software. Hydrogen/deuterium exchange mass spectrometry (HDX-MS) may offer an additional layer of structural information in untargeted metabolomics, especially for identifying specific unidentified metabolites that are revealed to be statistically significant. Here, we investigate the potential of hydrophilic interaction liquid chromatography (HILIC)-HDX-MS in untargeted metabolomics. Specifically, we evaluate the effectiveness of two approaches using hypothetical targets: the post-column addition of deuterium oxide (D2O) and the on-column HILIC-HDX-MS method. To illustrate the practical application of HILIC-HDX-MS, we apply this methodology using the in silico fragmentation software MS-FINDER to an unknown compound detected in various biological samples, including plasma, serum, tissues, and feces during HILIC-MS profiling, subsequently identified as N1-acetylspermidine.

• Keywords
• hydrogen/deuterium exchange, liquid chromatography, mass spectrometry, metabolomics, unknown identification,
• MeSH
• Chromatography, Liquid methods   MeSH
• Deuterium MeSH
• Hydrophobic and Hydrophilic Interactions MeSH
• Metabolomics * methods   MeSH
• Hydrogen Deuterium Exchange-Mass Spectrometry * MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• Deuterium MeSH