Autonomous circadian rhythms in the human hepatocyte regulate hepatic drug metabolism and inflammatory responses

Circadian attributes of neurological and psychiatric disorders as basis for their medication chronotherapy

This review focuses on (i) 24 h patterns in the symptom intensity of common neurologic and psychiatric disorders and (ii) medications prescribed for their management that have a recommended administration time or schedule, presumably to potentiate desired and minimize undesired effects and by definition qualify them as chronotherapies. Predictable-in-time patterning of symptoms is exhibited by many neurologic -- headaches, multiple sclerosis, neurogenic orthostatic hypotension, neuropathic pain, Parkinson's disease, epileptic seizure, attention deficit hyperactivity, Alzheimer's disease - and psychiatric - eating, depressive, obsessive-compulsive, post-traumatic stress, anxiety, and panic - disorders, due either to circadian rhythms of disease pathophysiology or inadequacies of medication-delivery systems. Circadian disruption and circadian misalignment of the sleep-wake and other 24 h rhythms plus late chronotype are characteristic of many of these disorders, suggesting involvement in the mechanisms or consequence of their pathology or as an adverse effect of therapy, especially when administered at an inappropriate biological time. The Prescribers' Digital Reference, a compendium of all prescription medications approved for marketing in the US, reveals 65 of them are utilized to manage neurologic and psychiatric disorders by a specified time-of-day or an asymmetrical interval or strength of dose schedule, presumably to optimize beneficial and minimize adverse effects, thereby qualifying them as chronotherapies. Overall, the contents of this review are intended to inform the development of future chronotherapies that incorporate state-of-the-art drug-delivery systems to improve management of neurologic and psychiatric disorders and associated circadian malalignment and disruption.

Implantable systems for neurological chronotherapy

Implantable systems for neurological chronotherapy are poised to revolutionize the treatment of central nervous system diseases and disorders. These devices enable precise, time-controlled drug delivery aligned with the body's circadian rhythms, optimizing therapeutic outcomes. By bypassing the blood-brain barrier, they achieve high local drug concentrations while minimizing systemic side effects, offering significant advantages for conditions where traditional therapies often fall short. Platforms like SynchroMed II and CraniUS showcase this innovation, providing programmable delivery for conditions such as epilepsy and glioblastoma, with customizable profiles ranging from continuous infusion to timed bolus administration. Preclinical and clinical studies underscore the efficacy of aligning drug delivery with circadian rhythms, enhancing outcomes in chrono-chemotherapy and anti-epileptic treatments. Despite their promise, challenges remain, including the invasiveness of implantation within the brain, device longevity, synchronization complexities, and cost(s). Accordingly, this review explores the current state of implantable neurological systems that may be leveraged for chronotherapy, their applications, limitations, and potential to transform neurological disease/disorder management.

Circadian rhythm disruption by PARP inhibitors correlates with treatment toxicity in patients with ovarian cancer and is a predictor of side effects

BACKGROUND

Ovarian cancer is among the most lethal malignancies in women. The advent of PARP inhibitors (PARPi) has improved outcomes. However, treatment-related toxicity remains a critical challenge, impacting patient quality of life and treatment adherence.

METHODS

In a circadian sub-study of the MAMOC trial-a double-blind, phase III study-42 patients (FIGO stage IIIA-IV) were randomised in a 2:1 ratio to receive rucaparib or placebo. In a subset of these patients, we performed differential gene expression and rhythmicity analysis on up to 800 genes, including clock and clock-controlled genes. Machine learning algorithms and mathematical modelling were employed to simulate patient-specific toxicity profiles and to explore correlations between gene expression patterns and treatment-related side effects.

FINDINGS

Our analysis revealed significant disruptions in circadian rhythms, specifically in the expression of the core clock genes BMAL1 and PER2, following treatment. These disruptions strongly correlated with the severity and frequency of side effects, including nausea and fatigue, displaying opposite trends between the placebo and rucaparib-treated groups. K-means clustering successfully distinguished rucaparib-treated patients from those receiving placebo based on BMAL1 phase and gene expression profiles. In addition, rucaparib therapy also altered the expression of several clock-controlled genes, including SIRT1, BRCA1, BRCA2, and TP53. Notably, our data suggest that individual differences in circadian rhythms may lead to distinct 24-h toxicity profiles among patients.

INTERPRETATION

These findings suggest that circadian rhythm dysregulation may contribute to the toxicity of PARPi therapy. Aligning treatment timing with circadian rhythms could mitigate these adverse effects, and improve patient outcomes.

FUNDING

This study was funded by the Dr. Rolf Schwiete Stiftung and the MSH Medical School Hamburg, Germany. The MAMOC trial (ClinicalTrials.gov: NCT04227522) was funded by Clovis Oncology, United States.

The Relationship Between Biological Noise and Its Application: Understanding System Failures and Suggesting a Method to Enhance Functionality Based on the Constrained Disorder Principle

The Constrained Disorder Principle (CDP) offers a new framework for understanding how biological systems use and manage noise to maintain optimal functionality. This review explores the relationship between noise and biological systems at various scales, including genetic, cellular, and organ levels, and its implications for system malfunctions. According to the CDP, all systems require an optimal range of noise to function appropriately, and disease states can arise when these noise levels are disrupted. This review presents evidence supporting this principle across different biological contexts, such as genetic variability, cellular behavior, brain functions, human behavior, aging, evolution, and drug administration. For accurate clinical assessments, it is essential to distinguish between technical variability and intrinsic biological variability. When noise is adequately constrained, it serves as a fundamental mechanism for system adaptation and optimal functioning rather than simply a source of disruption. These findings have important implications for developing more effective therapeutic strategies and understanding biological systems' dynamics. CDP-based second-generation artificial intelligence systems can help regulate noise levels to address malfunctions. These systems have improved clinical outcomes in various conditions by incorporating controlled randomness. Understanding these patterns of variability has significant implications for diagnosis, treatment monitoring, and the development of more effective therapeutic strategies across various medical conditions.

Roles of Gut Microbiota Metabolites and Circadian Genes in the Improvement of Glucose and Lipid Metabolism in KKAy Mice by Theabrownin

Theabrownin (TB), a prominent pigment in fermented dark tea, exhibits beneficial effects on adiposity reduction. Our study revealed that TB derived from Fu brick tea significantly lowered fasting blood glucose levels and insulin resistance in obese/diabetic KKAy mice. Furthermore, TB demonstrated potent anti-inflammatory effects in the liver, adipose tissue, and intestines, as well as enhancing intestinal integrity. Additionally, TB was found to inhibit hepatic gluconeogenesis and promote fatty acid oxidation. Notably, TB altered gut metabolites, particularly l-palmitoylcarnitine, which showed an elevation in serum, liver, and adipose tissue following TB intervention. l-Palmitoylcarnitine reduced gluconeogenesis in primary hepatocytes and decreased lipid deposition in both primary hepatocytes and 3T3-L1 adipocytes in vitro. However, these effects were abolished when the circadian gene Period 3 (Per3) was knocked down. Our findings suggest that l-palmitoylcarnitine may play a crucial role in improving TB-mediated glucose homeostasis and lipid metabolism by regulating Per3.

Dual-approach co-expression analysis framework (D-CAF) enables identification of novel circadian co-regulation from multi-omic timeseries data

BACKGROUND

The circadian clock is a central driver of many biological and behavioral processes, regulating the levels of many genes and proteins, termed clock controlled genes and proteins (CCGs/CCPs), to impart biological timing at the molecular level. While transcriptomic and proteomic data has been analyzed to find potential CCGs and CCPs, multi-omic modeling of circadian data, which has the potential to enhance the understanding of circadian control of biological timing, remains relatively rare due to several methodological hurdles. To address this gap, a dual-approach co-expression analysis framework (D-CAF) was created to perform co-expression analysis that is robust to Gaussian noise perturbations on time-series measurements of both transcripts and proteins.

RESULTS

Applying this D-CAF framework to previously gathered transcriptomic and proteomic data from mouse macrophages gathered over circadian time, we identified small, highly significant clusters of oscillating transcripts and proteins in the unweighted similarity matrices and larger, less significant clusters of of oscillating transcripts and proteins using the weighted similarity network. Functional enrichment analysis of these clusters identified novel immunological response pathways that appear to be under circadian control.

CONCLUSIONS

Overall, our findings suggest that D-CAF is a tool that can be used by the circadian community to integrate multi-omic circadian data to improve our understanding of the mechanisms of circadian regulation of molecular processes.

Personalization of Cancer Treatment: Exploring the Role of Chronotherapy in Immune Checkpoint Inhibitor Efficacy

In the era of precision medicine, mounting evidence suggests that the time of therapy administration, or chronotherapy, has a great impact on treatment outcomes. Chronotherapy involves planning treatment timing by considering circadian rhythms, which are 24 h oscillations in behavior and physiology driven by synchronized molecular clocks throughout the body. The value of chronotherapy in cancer treatment is currently under investigation, notably in the effects of treatment timing on efficacy and side effects. Immune checkpoint inhibitor (ICI) therapy is a promising cancer treatment. However, many patients still experience disease progression or need to stop the therapy early due to side effects. There is accumulating evidence that the time of day at which ICI therapy is administered can have a substantial effect on ICI efficacy. Thus, it is important to investigate the intersections of circadian rhythms, chronotherapy, and ICI efficacy. In this review, we provide a brief overview of circadian rhythms in the context of immunity and cancer. Additionally, we outline current applications of chronotherapy for cancer treatment. We synthesize the 29 studies conducted to date that examine the impact of time-of-day administration on the efficacy of ICI therapy, its associated side effects, and sex differences in both efficacy and side effects. We also discuss potential mechanisms underlying these observed results. Finally, we highlight the challenges in this area and future directions for research, including the potential for a chronotherapeutic personalized medicine approach that tailors the time of ICI administration to individual patients' circadian rhythms.

The Impact of Toll-Like Receptor 5 on Liver Function in Age-Related Metabolic Disorders

Toll-like receptor 5 (TLR5) plays a critical role beyond its traditional function in innate immunity, significantly impacting metabolic regulation and liver health. Previously, we reported that TLR5 activation extends the healthspan and lifespan of aging mice. This study demonstrates that TLR5 deficiency leads to pronounced metabolic abnormalities with age, primarily affecting liver metabolic functions rather than intestinal inflammation. Comprehensive RNA sequencing analysis revealed that TLR5 deficiency induces gene expression changes in liver tissue similar to those caused by the methionine-choline deficient (MCD) diet, particularly affecting lipid metabolism and circadian rhythm-related genes. TLR5 knockout (TLR5 KO) mice displayed an increased propensity for liver fibrosis and lipid accumulation under the MCD diet, exacerbating liver pathology. Both hepatocytes and hepatic stellate cells in TLR5 KO mice were functionally impacted, leading to metabolic dysfunction and fibrosis. These findings suggest that TLR5 could be a significant target for addressing metabolic diseases that arise and worsen with aging. Furthermore, understanding the mechanisms by which TLR5 activation extends healthspan could provide valuable insights into therapeutic strategies for enhancing longevity and managing age-related metabolic disorders.

Unravelling malaria latency: parasite intrinsic and environmental factors influencing dormant liver stages

Hypnozoites - dormant Plasmodium parasites in the liver - can cause relapse infections and form a major obstacle to malaria eradication. The mechanisms controlling dormancy remain poorly understood, but hypnozoite formation and reactivation is likely regulated by a combination of parasite intrinsic factors and external stimuli. We reviewed current knowledge of Plasmodium dormancy and drew parallels with dormancy in other parasites and life-cycle stages. Epigenetic, post-transcriptional, or post-translational regulation probably jointly control hypnozoite dormancy at the intrinsic level. Additionally, environmental factors, such as vector availability, host wellbeing, and tissue microenvironment, could be instrumental to hypnozoite reactivation. A better understanding of how external stimuli influence the intrinsic reactivation switch at a mechanistic level will be required to expand the limited toolset to combat relapsing malaria.

Novel reduced heteropolyacid nanoparticles for effective treatment of drug-induced liver injury by manipulating reactive oxygen and nitrogen species and inflammatory signals

With the rapid advancements in biomedicine, the use of clinical drugs has surged sharply. However, potential hepatotoxicity limits drug exploitation and widespread usage, posing serious threats to patient health. Hepatotoxic drugs disrupt liver enzyme levels and cause refractory pathological damage, creating a challenge in the application of diverse first-line drugs. The activation and deterioration of reactive oxygen and nitrogen species (RONS) and inflammatory signals are key pathological mechanisms of drug-induced liver injury (DILI). Herein, a novel reduced heteropolyacid nanoparticle (RNP) has been developed, possessing high RONS-scavenging ability, strong anti-inflammatory activity, and excellent biosafety. These features enable it to swiftly restore the redox and immune balance of the liver. Intravenous administration of RNP effectively scavenged RONS storm, reversing liver oxidative stress and restoring normal mitochondrial membrane potential and function. Furthermore, by inhibiting c-Jun-N-terminal kinase phosphorylation, RNP facilitated the restoration of nuclear factor erythroid 2-related factor 2-mediated endogenous antioxidant signaling, ultimately rescuing the liver function and tissue morphology in acetaminophen-induced DILI mice. Crucially, the high biocompatible RNP exhibited superior efficacy in the DILI mouse model compared to the clinical antioxidant N-acetylcysteine. This targeted therapeutic approach, tailored to address the onset and progression of DILI, offers valuable new insights into controlling the condition and restoring liver structure and function.

Efficacy of melatonin treatment in a cystic fibrosis mouse model of airway infection

Approaches to mitigate the severity of infections and of immune responses are still needed for the treatment of cystic fibrosis (CF) even with the success of highly effective modulator therapies. Previous studies identified reduced levels of melatonin in a CF mouse model related to circadian rhythm dysregulation. Melatonin is known to have immunomodulatory properties and it was hypothesized that treatment with melatonin would improve responses to bacterial infection in CF mice. Data demonstrate that CF mice (G542X/G542X) treated with melatonin (10 µg/mL) in drinking water for 10 weeks had improved responses to airway infection with a clinical isolate of Pseudomonas aeruginosa. Melatonin-treated mice exhibited improved bacterial clearance, reduced inflammatory markers. Mice treated in drinking water for 1 week had improved bacterial clearance but no improvement in inflammation. Wild type (WT) control mice showed no response to melatonin treatment suggesting melatonin is eliciting a CF-specific response in this model. The efficacy of direct melatonin (1 µM) treatment to the airways was also tested and found to be ineffective. In conclusion, long-term systemic treatment with melatonin is an effective therapy in a CF mouse model that normalizes the response to airway infection to a WT pattern.

Regulation of protein abundance in normal human tissues

We report a systematic quantification of 10,841 unique proteins from over 700 GTEx samples, representing five human tissues. Sex, age and genetic factors are associated with variation in protein abundance. In total, 1981 cis-protein quantitative trait loci (cis-pQTL) are identified, of which a majority of protein targets have not been assayed in the recent plasma-based proteogenomic studies. Integrating transcriptomic information from matching tissues delineates concordant as well as discordant expression patterns at RNA and protein levels. Juxtaposition of data from different tissues indicates both shared and tissue-specific genetic architecture that underlie protein abundance. Complementing genomic annotation, RNA-based eQTL studies, as well as the recent establishment of plasma-based proteogenomic characterization, tissue-pQTLs shed light on biology underlying genotype-phenotype association of complex traits and diseases.

Mapping Plasmodium transitions and interactions in the Anopheles female

The human malaria parasite, Plasmodium falciparum , relies on Anopheles mosquitoes for transmission. Once ingested during blood feeding, most parasites die in the mosquito midgut lumen or during epithelium traversal. How surviving ookinetes interact with midgut cells and form oocysts is unknown, yet these steps are essential to initiate a remarkable, similarly uncharacterized growth process culminating in the production of thousands of infectious sporozoites. Here, using single-cell RNA sequencing of both parasites and mosquito cells across four time points and two metabolic conditions, we unveil key processes shaping developmental transitions and mosquito-parasite interactions occurring in the midgut. In depth functional analyses reveal processes regulating oocyst growth and identify the transcription factor Pf SIP2 as essential for sporozoite infection of human hepatocytes. By combining the analysis of shared mosquito-parasite barcodes with confocal microscopy, we discover that parasites preferentially interact with midgut progenitor cells during epithelial crossing, potentially using their basal location as an exit landmark. Additionally, we unveil tight connections between extracellular late oocysts and surrounding muscle cells that may ensure parasites adhere to the midgut without damaging it. Ultimately, our study provides fundamental insight into the molecular events characterizing previously inaccessible biological transitions and mosquito-parasite interactions, and identifies candidates for transmission-blocking strategies.

Dual-Approach Co-expression Analysis Framework (D-CAF) Enables Identification of Novel Circadian Regulation From Multi-Omic Timeseries Data

The circadian clock is a central driver of many biological and behavioral processes, regulating the levels of many genes and proteins, termed clock controlled genes and proteins (CCGs/CCPs), to impart biological timing at the molecular level. While transcriptomic and proteomic data has been analyzed to find potential CCGs and CCPs, multi-omic modeling of circadian data, which has the potential to enhance the understanding of circadian control of biological timing, remains relatively rare due to several methodological hurdles. To address this gap, a Dual-approach Co-expression Analysis Framework (D-CAF) was created to perform perturbation-robust co-expression analysis on time-series measurements of both transcripts and proteins. Applying this D-CAF framework to previously gathered transcriptomic and proteomic data from mouse macrophages gathered over circadian time, we identified small, highly significant clusters of oscillating transcripts and proteins in the unweighted similarity matrices and larger, less significant clusters of of oscillating transcripts and proteins using the weighted similarity network. Functional enrichment analysis of these clusters identified novel immunological response pathways that appear to be under circadian control. Overall, our findings suggest that D-CAF is a tool that can be used by the circadian community to integrate multi-omic circadian data to improve our understanding of the mechanisms of circadian regulation of molecular processes.