Two Stages of Dynamic Metabolic and Transcriptomic Remodeling During the Adaptation to Caloric Restriction in Male C57BL/6J

The molecular basis of caloric restriction (CR) has been defined primarily at a metabolic steady state, leaving the initiating events that drive the transition from ad libitum feeding to an adapted CR state largely unresolved. Here, we combine continuous indirect calorimetry with longitudinal bulk RNA-seq of liver and inguinal white adipose tissue (iWAT) sampled at six circadian timepoints across four stages of adaptation to 30% CR in male C57BL/6J mice. We show that whole-body metabolic adaptation proceeds through two discrete adaptive phases separated by a threshold at approximately 14 days; during this initial transition, consolidated feeding attenuates ketogenesis, establishing a distinct whole-body metabolic phenotype prior to long-term adaptation. To elucidate the molecular mechanisms underlying these physiological shifts, weighted gene co-expression network analysis (WGCNA) was performed, revealing that hepatic transcriptional remodeling is organized proportionally to fasting duration, whereas iWAT remodeling remains restricted to specific circadian timepoints. Because systemic adaptation requires coordinated inter-tissue communication, we conducted a cartographic analysis to evaluate network topology and inter-modular connectivity. This approach identifies restricted populations of early kinless and connector hub genes, nucleated by Casp3 in the liver and Lpl in iWAT, whose structural integration is established prior to the broader transcriptional remodeling observed at later timepoints. Functional annotation indicates the hepatic hub network is enriched for mitochondrial bioenergetics and FOXO/TP53-mediated transcription, while the iWAT hub network exhibits a bifurcated enrichment spanning ribosomal biosynthesis and immune-regulatory signaling. Although these tissues exhibit distinct transcriptional profiles, projecting both datasets onto a shared phenotypic eigenspace reveals a unified systemic response; as CR is maintained, dynamically regulated transcripts in both liver and iWAT converge on an adiponectin-coupled state. Ultimately, the identification of adiponectin as an integrative signal coordinating chronic adaptation across metabolically distinct tissues delineates the temporal sequence of early CR adaptation; furthermore, it establishes a mechanistic framework defining how early molecular and physiological shifts converge to achieve steady-state metabolic homeostasis.