The dihydropyrimidine dehydrogenase gene contributes to heritable differences in sleep in mice

Some unanswered questions about the pyrimidine catabolic pathway: The human macrophage perspective

Pyrimidine catabolism has attracted attention in relation to pyrimidine analogs used as anticancer drugs but the absence of a severe phenotype associated with pyrimidine catabolism byproducts did not favor to pursue these efforts. Recently, the discovery that dihydropyrimidine dehydrogenase (DPD) has an oxygen-dependent expression in human macrophages brings the aforementioned pathway to the forefront. Moreover, the finding that thymidine phosphorylase, the direct upstream enzyme to DPD in the pathway, also has a huge expression level in macrophages puts a new perspective on this pathway suggesting to look again at the physiology of intracellular pyrimidine bases catabolism revealing some unanswered questions. In this review, we propose to reassess the known and unknown of the catabolism of pyrimidine base in the light of these new results obtained in human macrophages.

Novel predictive biomarkers for atonic postpartum hemorrhage as explored by proteomics and metabolomics

BACKGROUND

Postpartum hemorrhage (PPH) is the leading cause of maternal mortality worldwide, with uterine atony accounting for approximately 70% of PPH cases. However, there is currently no effective prediction method to promote early management of PPH. In this study, we aimed to screen for potential predictive biomarkers for atonic PPH using combined omics approaches.

METHODS

Collection of cervicovaginal fluid (CVF) samples from 27 women with atonic PPH and 32 women with normal delivery was performed for metabolomic (LC-MS/MS) and proteomic (LC-MS/MS) detection and subsequent confirmation experiments in this nested case-control study. Mass spectrum and enzyme-linked immunosorbent assays (ELISA) were used to validate significantly different metabolites and proteins for screening potential biomarkers of atonic PPH. Furthermore, multivariate logistic regressions were performed for the prediction of PPH using the identified biomarkers mentioned above, and the area under the curve (AUC) was computed.

RESULTS

We identified 216 and 311 metabolites under positive and negative ion modes, respectively, as well as 1974 proteins. The PPH group had significant differences in metabolites and proteins belonging to the β-alanine metabolic pathway. Specifically, the PPH group had downregulation of critical metabolites, including histidine and protein dihydropyrimidine dehydrogenase (DPYD). Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) functional enrichment analysis of significantly differentially expressed proteins revealed that atonic PPH was associated with T cell- and macrophage-related immune inflammatory responses. Furthermore, we verified that concentrations of histidine (350.85 ± 207.87 vs. 648.33 ± 400.87) and DPYD (4.01 ± 2.56 vs. 10.96 ± 10.71), and immune cell-related proteins such as CD163 (0.29 ± 0.19 vs. 1.51 ± 0.83) and FGL2 (5.98 ± 4.23 vs. 11.37 ± 9.42) were significantly lower in the PPH group. Finally, the AUC for independent prediction of PPH using CD163, histidine, DPYD, and FGL2 are 0.969 (0.897-1), 0.722 (0.536-0.874), 0.719 (0.528-0.864), and 0.697 (0.492-0.844), respectively. A relatively high predictive efficiency was obtained when using joint histidine, DPYD, CD163, and FGL2, with AUC = 0. 964 (0.822-1).

CONCLUSIONS

This study suggested that immune inflammation may play a role in the occurrence of PPH. The metabolite histidine and proteins of DPYD, CD163, and FGL2 in CVF were associated with uterine atony and could be used as predictive biomarkers for atonic PPH.

Into the Wild: A novel wild-derived inbred strain resource expands the genomic and phenotypic diversity of laboratory mouse models

The laboratory mouse has served as the premier animal model system for both basic and preclinical investigations for over a century. However, laboratory mice capture only a subset of the genetic variation found in wild mouse populations, ultimately limiting the potential of classical inbred strains to uncover phenotype-associated variants and pathways. Wild mouse populations are reservoirs of genetic diversity that could facilitate the discovery of new functional and disease-associated alleles, but the scarcity of commercially available, well-characterized wild mouse strains limits their broader adoption in biomedical research. To overcome this barrier, we have recently developed, sequenced, and phenotyped a set of 11 inbred strains derived from wild-caught Mus musculus domesticus. Each of these "Nachman strains" immortalizes a unique wild haplotype sampled from one of five environmentally distinct locations across North and South America. Whole genome sequence analysis reveals that each strain carries between 4.73-6.54 million single nucleotide differences relative to the GRCm39 mouse reference, with 42.5% of variants in the Nachman strain genomes absent from current classical inbred mouse strain panels. We phenotyped the Nachman strains on a customized pipeline to assess the scope of disease-relevant neurobehavioral, biochemical, physiological, metabolic, and morphological trait variation. The Nachman strains exhibit significant inter-strain variation in >90% of 1119 surveyed traits and expand the range of phenotypic diversity captured in classical inbred strain panels. These novel wild-derived inbred mouse strain resources are set to empower new discoveries in both basic and preclinical research.

Systematic Metabolic Profiling of Mice with Sleep-Deprivation

Adequate sleep is essential for the biological maintenance of physical energy. Lack of sleep can affect thinking, lead to emotional anxiety, reduce immunity, and interfere with endocrine and metabolic processes, leading to disease. Previous studies have focused on long-term sleep deprivation and the risk of cancer, heart disease, diabetes, and obesity. However, systematic metabolomics analyses of blood, heart, liver, spleen, kidney, brown adipose tissue, and fecal granules have not been performed. This study aims to systematically assess the metabolic changes in the target organs caused by sleep deprivation in vivo, to search for differential metabolites and the involved metabolic pathways, to further understand the impact of sleep deprivation on health, and to provide strong evidence for the need for early intervention.

Into the Wild: A novel wild-derived inbred strain resource expands the genomic and phenotypic diversity of laboratory mouse models

The laboratory mouse has served as the premier animal model system for both basic and preclinical investigations for a century. However, laboratory mice capture a narrow subset of the genetic variation found in wild mouse populations. This consideration inherently restricts the scope of potential discovery in laboratory models and narrows the pool of potentially identified phenotype-associated variants and pathways. Wild mouse populations are reservoirs of predicted functional and disease-associated alleles, but the sparsity of commercially available, well-characterized wild mouse strains limits their broader adoption in biomedical research. To overcome this barrier, we have recently imported, sequenced, and phenotyped a set of 11 wild-derived inbred strains developed from wild-caught Mus musculus domesticus. Each of these "Nachman strains" immortalizes a unique wild haplotype sampled from five environmentally diverse locations across North and South America: Saratoga Springs, New York, USA; Gainesville, Florida, USA; Manaus, Brazil; Tucson, Arizona, USA; and Edmonton, Alberta, Canada. Whole genome sequence analysis reveals that each strain carries between 4.73-6.54 million single nucleotide differences relative to the mouse reference assembly, with 42.5% of variants in the Nachman strain genomes absent from classical inbred mouse strains. We phenotyped the Nachman strains on a customized pipeline to assess the scope of disease-relevant neurobehavioral, biochemical, physiological, metabolic, and morphological trait variation. The Nachman strains exhibit significant inter-strain variation in >90% of 1119 surveyed traits and expand the range of phenotypic diversity captured in classical inbred strain panels alone. Taken together, our work introduces a novel wild-derived inbred mouse strain resource that will enable new discoveries in basic and preclinical research. These strains are currently available through The Jackson Laboratory Repository under laboratory code NachJ.

Investigating Neuron Degeneration in Huntington's Disease Using RNA-Seq Based Transcriptome Study

Huntington's disease (HD) is a progressive neurodegenerative disorder caused due to a CAG repeat expansion in the huntingtin (HTT) gene. The primary symptoms of HD include motor dysfunction such as chorea, dystonia, and involuntary movements. The primary motor cortex (BA4) is the key brain region responsible for executing motor/movement activities. Investigating patient and control samples from the BA4 region will provide a deeper understanding of the genes responsible for neuron degeneration and help to identify potential markers. Previous studies have focused on overall differential gene expression and associated biological functions. In this study, we illustrate the relationship between variants and differentially expressed genes/transcripts. We identified variants and their associated genes along with the quantification of genes and transcripts. We also predicted the effect of variants on various regulatory activities and found that many variants are regulating gene expression. Variants affecting miRNA and its targets are also highlighted in our study. Co-expression network studies revealed the role of novel genes. Function interaction network analysis unveiled the importance of genes involved in vesicle-mediated transport. From this unified approach, we propose that genes expressed in immune cells are crucial for reducing neuron death in HD.

Synaptic dysfunction connects autism spectrum disorder and sleep disturbances: A perspective from studies in model organisms

Sleep disturbances (SD) accompany many neurodevelopmental disorders, suggesting SD is a transdiagnostic process that can account for behavioral deficits and influence underlying neuropathogenesis. Autism Spectrum Disorder (ASD) comprises a complex set of neurodevelopmental conditions characterized by challenges in social interaction, communication, and restricted, repetitive behaviors. Diagnosis of ASD is based primarily on behavioral criteria, and there are no drugs that target core symptoms. Among the co-occurring conditions associated with ASD, SD are one of the most prevalent. SD often arises before the onset of other ASD symptoms. Sleep interventions improve not only sleep but also daytime behaviors in children with ASD. Here, we examine sleep phenotypes in multiple model systems relevant to ASD, e.g., mice, zebrafish, fruit flies and worms. Given the functions of sleep in promoting brain connectivity, neural plasticity, emotional regulation and social behavior, all of which are of critical importance in ASD pathogenesis, we propose that synaptic dysfunction is a major mechanism that connects ASD and SD. Common molecular targets in this interplay that are involved in synaptic function might be a novel avenue for therapy of individuals with ASD experiencing SD. Such therapy would be expected to improve not only sleep but also other ASD symptoms.