Day-night and seasonal variation of human gene expression across tissues

Non-human primate seasonal transcriptome atlas reveals seasonal changes in physiology and diseases

The metabolic, immune, and endocrine systems show profound seasonal changes in animals, including humans. In addition, morbidity from cardiovascular and psychiatric diseases is more severe and mortality rate is higher in winter. However, their molecular mechanisms remain unknown. Here we report the seasonal transcriptome of 80 tissues collected over 1 year from male and female rhesus macaques kept in a semi-natural outdoor environment. We find seasonal changes in plasma metabolites and hormones. Transcriptome analysis identifies sex differences in seasonally oscillating genes (SOGs) in all tissues studied, and we generate the web database 'Non-Human Primate Seasonal Transcriptome Atlas (NHPSTA).' Transcriptional regulatory network analysis, siRNA knockdown, and mutant mouse analyses reveal regulation of SOGs by GA-binding protein (GABP). We also demonstrate seasonal oscillations in the expression of disease risk factor genes and drug interacting genes. NHPSTA provides a molecular resource for seasonally regulated physiology and targets for therapeutic interventions for seasonally regulated diseases.

Biomarkers in headaches as a potential solution to simplify differential diagnosis of primary headache disorders: a systematic review

BACKGROUND

According to the International Classification of Headache Disorders, 3rd edition (ICHD-3), headache disorders can be divided into two main groups: primary, which are not caused by any other disease, and secondary, which are symptomatic of underlying disease. Differentiating between both groups is crucial for the patient's prognosis. The diagnosis of primary headache disorders relies solely on official clinical criteria, with no additional diagnostic tools available. Therefore, they usually remain underdiagnosed, decreasing the patient's quality of life.

METHODS

This systematic review aimed to analyse the available literature on the topic of biomarkers in the differentiation between different types of headaches. To be included, a primary study had to cover the abovementioned topic. Studies comparing one type of headache to healthy controls were excluded since the review focused on differential diagnosis. Articles to be considered had to describe original research and be written in English or Polish. No publication year limits were applied. A selection process was performed between October 19th, 2024, and January 1st, 2025, through six databases (PubMed, Embase, Scopus, Cochrane, Web of Science, Medline Ultimate), according to the PRISMA 2020. The risk of bias was assessed accordingly using the Prediction Model Risk of Bias Assessment Tool (PROBAST), and data synthesis was performed narratively. The review was registered in PROSPERO.

FINDINGS

The findings from 21 included studies (with a wide range of publication years between 1990 and 2023) demonstrated several biomarkers, mainly comparing migraine to other primary headaches, tension-type headaches and cluster headaches, and some secondary headaches: medication-overuse headaches and post-traumatic headaches. The main types of biomarkers were blood biomarkers and imaging biomarkers. Among the former, molecules such as magnesium and calcitonin gene-related peptide (CGRP) or inflammatory markers could be found. The latter group focused mainly on assessing volumes or functional connections in brain magnetic resonance imaging and seem to have a significant impact in the nearest future. Saliva analyses were covered only by two research groups, showing the putative role of magnesium and CGRP. Similarly, two research groups described evoked potentials' value only in the paediatric population.

CONCLUSIONS

There is a clear gap in the literature regarding biomarkers for the differential diagnosis of headaches. However, an analysis of the most recent studies suggests that imaging biomarkers are the most promising group since they have gained the most attention in the past few years. Finding high-value biomarkers can simplify differential diagnosis of headaches, especially when clinical presentation is atypical. Nevertheless, more research on biomarkers of all types is highly needed.

PROSPERO

Registration ID: CRD42024603632.

Gene expression plasticity in response to rapid and extreme elevation changes in Perdix hodgsoniae (Tibetan Partridge)

Phenotypic plasticity is a vital biological process facilitating the persistence of organisms amid rapid environmental changes. Investigating the genetic basis of plastic traits necessitates transplantation experiments, but much of the existing research has focused on laboratory model systems. Transplant experiments in the wild may provide better understanding of how plasticity operates in the context of real-world challenges. However, performing transplantation experiments in non-model systems, such as birds, could be challenging. In this study, we aim to develop Perdix hodgsoniae (Tibetan Partridge) inhabiting the highlands of the Tibetan Plateau as a suitable system to study genetic basis underlying short-term plastic response to rapid changes in elevation. We did a first attempt of field-based transplantation experiment by exposing P. hodgsoniae individuals to extreme change in elevation from their native elevation (3,623 m) to a low elevation outside their natural distribution range (500 m). We compared changes in gene expression in these birds at different time points, pre-transplant (day 0), and post-transplant (days 3 and 22). The birds successfully survived transplantation and exhibited well-being after 22 days. We identified a total of 715 differentially expressed genes (DEGs) across these time points. Our analysis revealed a genome-wide decrease in expression following the transplantation, indicating that the birds possibly exhibited stress-induced transcriptional attenuation (SITA) because of the extreme change in elevation, suggesting a broader response at the transcriptional level, possibly as a mechanism to cope with extreme changes in the environment. Our analysis further suggested that heat stress posed an immediate challenge for the birds following the transplant, as we identified changes in expression in many genes associated with heat stress response. Our findings affirm the viability of conducting transplant experiments in the P. hodgsoniae and provides initial insights into gene expression changes associated with the plastic response to rapid changes in elevation in these birds.

The neurobiological mechanisms of photoperiod impact on brain functions: a comprehensive review

Variations in day length, or photoperiodism, whether natural or artificial light, significantly impact biological, physiological, and behavioral processes within the brain. Both natural and artificial light sources are environmental factors that significantly influence brain functions and mental well-being. Photoperiodism is a phenomenon, occurring either over a 24 h cycle or seasonally and denotes all biological responses of humans and animals to these fluctuations in day and night length. Conversely, artificial light occurrence refers to the presence of light during nighttime hours and/or its absence during the daytime (unnaturally long and short days, respectively). Light at night, which is a form of light pollution, is prevalent in many societies, especially common in certain emergency occupations. Moreover, individuals with certain mental disorders, such as depression, often exhibit a preference for darkness over daytime light. Nevertheless, disturbances in light patterns can have negative consequences, impacting brain performance through similar mechanisms albeit with varying degrees of severity. Furthermore, changes in day length lead to alterations in the activity of receptors, proteins, ion channels, and molecular signaling pathways, all of which can impact brain health. This review aims to summarize the mechanisms by which day length influences brain functions through neural circuits, hormonal systems, neurochemical processes, cellular activity, and even molecular signaling pathways.

Seasonality in regional brain glucose metabolism

BACKGROUND

Daylength and the rates of changes in daylength have been associated with seasonal fluctuations in psychiatric symptoms and in cognition and mood in healthy adults. However, variations in human brain glucose metabolism in concordance with seasonal changes remain under explored.

METHODS

In this cross-sectional study, we examined seasonal effects on brain glucose metabolism, which we measured using 18F-fluorodeoxyglucose-PET in 97 healthy participants. To maximize the sensitivity of regional effects, we computed relative metabolic measures by normalizing the regional measures to white matter metabolism. Additionally, we explored the role of rest-activity rhythms/sleep-wake activity measured with actigraphy in the seasonal variations of regional brain metabolic activity.

RESULTS

We found that seasonal variations of cerebral glucose metabolism differed across brain regions. Glucose metabolism in prefrontal regions increased with longer daylength and with greater day-to-day increases in daylength. The cuneus and olfactory bulb had the maximum and minimum metabolic values around the summer and winter solstice respectively (positively associated with daylength), whereas the temporal lobe, brainstem, and postcentral cortex showed maximum and minimum metabolic values around the spring and autumn equinoxes, respectively (positively associated with faster daylength gain). Longer daylength was associated with greater amplitude and robustness of diurnal activity rhythms suggesting circadian involvement.

CONCLUSIONS

The current findings advance our knowledge of seasonal patterns in a key indicator of brain function relevant for mood and cognition. These data could inform treatment interventions for psychiatric symptoms that peak at specific times of the year.

One seasonal clock fits all?

Adaptation of physiology and behavior to seasonal changes in the environment are for many organisms essential for survival. Most of our knowledge about the underlying mechanisms comes from research on photoperiodic regulation of reproduction in plants, insects and mammals. However, even humans, who mostly live in environments with minimal seasonal influences, show annual rhythms in physiology (e.g., immune activity, brain function), behavior (e.g., sleep-wake cycles) and disease prevalence (e.g., infectious diseases). As seasonal variations in environmental conditions may be drastically altered due to climate change, the understanding of the mechanisms underlying seasonal adaptation of physiology and behavior becomes even more relevant. While many species have developed specific solutions for dedicated tasks of photoperiodic regulation, we find a number of common principles and mechanisms when comparing insect and mammalian systems: (1) the circadian system contributes to photoperiodic regulation; (2) similar signaling molecules (VIP and PDF) are used for transferring information from the circadian system to the neuroendocrine system controlling the photoperiodic response; (3) the hormone melatonin participates in seasonal adaptation in insects as well as mammals; and (4) changes in photoperiod affect neurotransmitter function in both animal groups. The few examples of overlap elaborated in this perspective article, as well as the discussion on relevance for humans, should be seen as encouragement to unravel the machinery of seasonal adaptation in a multitude of organisms.

Seasonal tissue-specific gene expression in wild crown-of-thorns starfish reveals reproductive and stress-related transcriptional systems

Animals are influenced by the season, yet we know little about the changes that occur in most species throughout the year. This is particularly true in tropical marine animals that experience relatively small annual temperature and daylight changes. Like many coral reef inhabitants, the crown-of-thorns starfish (COTS), well known as a notorious consumer of corals and destroyer of coral reefs, reproduces exclusively in the summer. By comparing gene expression in 7 somatic tissues procured from wild COTS sampled on the Great Barrier Reef, we identified more than 2,000 protein-coding genes that change significantly between summer and winter. COTS genes that appear to mediate conspecific communication, including both signalling factors released into the surrounding sea water and cell surface receptors, are up-regulated in external secretory and sensory tissues in the summer, often in a sex-specific manner. Sexually dimorphic gene expression appears to be underpinned by sex- and season-specific transcription factors (TFs) and gene regulatory programs. There are over 100 TFs that are seasonally expressed, 87% of which are significantly up-regulated in the summer. Six nuclear receptors are up-regulated in all tissues in the summer, suggesting that systemic seasonal changes are hormonally controlled, as in vertebrates. Unexpectedly, there is a suite of stress-related chaperone proteins and TFs, including HIFa, ATF3, C/EBP, CREB, and NF-κB, that are uniquely and widely co-expressed in gravid females. The up-regulation of these stress proteins in the summer suggests the demands of oogenesis in this highly fecund starfish affects protein stability and turnover in somatic cells. Together, these circannual changes in gene expression provide novel insights into seasonal changes in this coral reef pest and have the potential to identify vulnerabilities for targeted biocontrol.

Circadian Regulation of Drug Responses: Toward Sex-Specific and Personalized Chronotherapy

Today's challenge for precision medicine involves the integration of the impact of molecular clocks on drug pharmacokinetics, toxicity, and efficacy toward personalized chronotherapy. Meaningful improvements of tolerability and/or efficacy of medications through proper administration timing have been confirmed over the past decade for immunotherapy and chemotherapy against cancer, as well as for commonly used pharmacological agents in cardiovascular, metabolic, inflammatory, and neurological conditions. Experimental and human studies have recently revealed sexually dimorphic circadian drug responses. Dedicated randomized clinical trials should now aim to issue personalized circadian timing recommendations for daily medical practice, integrating innovative technologies for remote longitudinal monitoring of circadian metrics, statistical prediction of molecular clock function from single-timepoint biopsies, and multiscale biorhythmic mathematical modelling. Importantly, chronofit patients with a robust circadian function, who would benefit most from personalized chronotherapy, need to be identified. Conversely, nonchronofit patients could benefit from the emerging pharmacological class of chronobiotics targeting the circadian clock.

Fighting Against the Clock: Circadian Disruption and Parkinson's Disease

Circadian disruption is being increasingly recognized as a critical factor in the development and progression of Parkinson's disease (PD). This review aims to provide an in-depth overview of the relationship between circadian disruption and PD by exploring the molecular, cellular, and behavioral aspects of this interaction. This review will include a comprehensive understanding of how the clock gene system and transcription-translation feedback loops function and how they are diminished in PD. The article also discusses the role of clock genes in the regulation of circadian rhythms, as well as the impact of clock gene dysregulation on mitochondrial function, oxidative stress, and neuroinflammation, including the microbiota-gut-brain axis, which have all been proposed as being crucial mechanisms in the pathophysiology of PD. Finally, this review highlights potential therapeutic strategies targeting the clock gene system and circadian rhythm for the treatment of PD.

2023 at PLOS Biology

2023 saw many important advances in the life sciences. In this editorial, we highlight research from across the breadth of PLOS Biology's scope.

CIRCUST: A novel methodology for temporal order reconstruction of molecular rhythms; validation and application towards a daily rhythm gene expression atlas in humans

The circadian system drives near-24-h oscillations in behaviors and biological processes. The underlying core molecular clock regulates the expression of other genes, and it has been shown that the expression of more than 50 percent of genes in mammals displays 24-h rhythmic patterns, with the specific genes that cycle varying from one tissue to another. Determining rhythmic gene expression patterns in human tissues sampled as single timepoints has several challenges, including the reconstruction of temporal order of highly noisy data. Previous methodologies have attempted to address these challenges in one or a small number of tissues for which rhythmic gene evolutionary conservation is assumed to be preserved. Here we introduce CIRCUST, a novel CIRCular-robUST methodology for analyzing molecular rhythms, that relies on circular statistics, is robust against noise, and requires fewer assumptions than existing methodologies. Next, we validated the method against four controlled experiments in which sampling times were known, and finally, CIRCUST was applied to 34 tissues from the Genotype-Tissue Expression (GTEx) dataset with the aim towards building a comprehensive daily rhythm gene expression atlas in humans. The validation and application shown here indicate that CIRCUST provides a flexible framework to formulate and solve the issues related to the analysis of molecular rhythms in human tissues. CIRCUST methodology is publicly available at https://github.com/yolandalago/CIRCUST/.

Day-night fluctuations in choroid plexus transcriptomics and cerebrospinal fluid metabolomics

The cerebrospinal fluid (CSF) provides mechanical protection for the brain and serves as a brain dispersion route for nutrients, hormones, and metabolic waste. The CSF secretion rate is elevated in the dark phase in both humans and rats, which could support the CSF flow along the paravascular spaces that may be implicated in waste clearance. The similar diurnal CSF dynamics pattern observed in the day-active human and the nocturnal rat suggests a circadian regulation of this physiological variable, rather than sleep itself. To obtain a catalog of potential molecular drivers that could provide the day-night-associated modulation of the CSF secretion rate, we determined the diurnal fluctuation in the rat choroid plexus transcriptomic profile with RNA-seq and in the CSF metabolomics with ultraperformance liquid chromatography combined with mass spectrometry. We detected significant fluctuation of 19 CSF metabolites and differential expression of 2,778 choroid plexus genes between the light and the dark phase, the latter of which encompassed circadian rhythm-related genes and several choroid plexus transport mechanisms. The fluctuating components were organized with joint pathway analysis, of which several pathways demonstrated diurnal regulation. Our results illustrate substantial transcriptional and metabolic light-dark phase-mediated changes taking place in the rat choroid plexus and its encircling CSF. The combined data provide directions toward future identification of the molecular pathways governing the fluctuation of this physiological process and could potentially be harnessed to modulate the CSF dynamics in pathology.

Seasonal effect-an overlooked factor in neuroimaging research

In neuroimaging research, seasonal effects are often neglected or controlled as confounding factors. However, seasonal fluctuations in mood and behavior have been observed in both psychiatric disorders and healthy participants. There are vast opportunities for neuroimaging studies to understand seasonal variations in brain function. In this study, we used two longitudinal single-subject datasets with weekly measures over more than a year to investigate seasonal effects on intrinsic brain networks. We found that the sensorimotor network displayed a strong seasonal pattern. The sensorimotor network is not only relevant for integrating sensory inputs and coordinating movement, but it also affects emotion regulation and executive function. Therefore, the observed seasonality effects in the sensorimotor network could contribute to seasonal variations in mood and behavior. Genetic analyses revealed seasonal modulation of biological processes and pathways relevant to immune function, RNA metabolism, centrosome separation, and mitochondrial translation that have a significant impact on human physiology and pathology. In addition, we revealed critical factors such as head motion, caffeine use, and scan time that could interfere with seasonal effects and need to be considered in future studies.

The circadian clock is disrupted in pancreatic cancer

Disruption of the circadian clock is linked to cancer development and progression. Establishing this connection has proven beneficial for understanding cancer pathogenesis, determining prognosis, and uncovering novel therapeutic targets. However, barriers to characterizing the circadian clock in human pancreas and human pancreatic cancer-one of the deadliest malignancies-have hindered an appreciation of its role in this cancer. Here, we employed normalized coefficient of variation (nCV) and clock correlation analysis in human population-level data to determine the functioning of the circadian clock in pancreas cancer and adjacent normal tissue. We found a substantially attenuated clock in the pancreatic cancer tissue. Then we exploited our existing mouse pancreatic transcriptome data to perform an analysis of the human normal and pancreas cancer samples using a machine learning method, cyclic ordering by periodic structure (CYCLOPS). Through CYCLOPS ordering, we confirmed the nCV and clock correlation findings of an intact circadian clock in normal pancreas with robust cycling of several core clock genes. However, in pancreas cancer, there was a loss of rhythmicity of many core clock genes with an inability to effectively order the cancer samples, providing substantive evidence of a dysregulated clock. The implications of clock disruption were further assessed with a Bmal1 knockout pancreas cancer model, which revealed that an arrhythmic clock caused accelerated cancer growth and worse survival, accompanied by chemoresistance and enrichment of key cancer-related pathways. These findings provide strong evidence for clock disruption in human pancreas cancer and demonstrate a link between circadian disruption and pancreas cancer progression.

Circadian Oscillations in Skin and Their Interconnection with the Cycle of Life

Periodically oscillating biological processes, such as circadian rhythms, are carefully concerted events that are only beginning to be understood in the context of tissue pathology and organismal health, as well as the molecular mechanisms underlying these interactions. Recent reports indicate that light can independently entrain peripheral circadian clocks, challenging the currently prevalent hierarchical model. Despite the recent progress that has been made, a comprehensive overview of these periodic processes in skin is lacking in the literature. In this review, molecular circadian clock machinery and the factors that govern it have been highlighted. Circadian rhythm is closely linked to immunological processes and skin homeostasis, and its desynchrony can be linked to the perturbation of the skin. The interplay between circadian rhythm and annual, seasonal oscillations, as well as the impact of these periodic events on the skin, is described. Finally, the changes that occur in the skin over a lifespan are presented. This work encourages further research into the oscillating biological processes occurring in the skin and lays the foundation for future strategies to combat the adverse effects of desynchrony, which would likely have implications in other tissues influenced by periodic oscillatory processes.

Different levels of circadian (de)synchrony -- where does it hurt?

A network of cellular timers ensures the maintenance of homeostasis by temporal modulation of physiological processes across the day. These so-called circadian clocks are synchronized to geophysical time by external time cues (or zeitgebers). In modern societies, natural environmental cycles are disrupted by artificial lighting, around-the-clock availability of food or shift work. Such contradictory zeitgeber input promotes chronodisruption, i.e., the perturbation of internal circadian rhythms, resulting in adverse health outcomes. While this phenomenon is well described, it is still poorly understood at which level of organization perturbed rhythms impact on health and wellbeing. In this review, we discuss different levels of chronodisruption and what is known about their health effects. We summarize the results of disrupted phase coherence between external and internal time vs. misalignment of tissue clocks amongst each other, i.e., internal desynchrony. Last, phase incoherence can also occur at the tissue level itself. Here, alterations in phase coordination can emerge between cellular clocks of the same tissue or between different clock genes within the single cell. A better understanding of the mechanisms of circadian misalignment and its effects on physiology will help to find effective tools to prevent or treat disorders arising from modern-day chronodisruptive environments.