A metabolic perspective to sleep genetics.

The metabolic signals that regulate sleep and the metabolic functions that occur during sleep are active areas of research. Prior studies have focused on sugars and nucleotides but new genetic evidence suggests novel functions of lipid and amino acid metabolites in sleep. Additional genetic studies of energetic signaling pathways and the circadian clock transcription factor network have increased our understanding of how sleep responds to changes in the metabolic state. This review focuses on key recent insights from genetic experiments in humans and model organisms to improve our understanding of the interrelationship between metabolism and sleep.

The Genetics of Human Sleep and Sleep Disorders.

Healthy sleep is vital for humans to achieve optimal health and longevity. Poor sleep and sleep disorders are strongly associated with increased morbidity and mortality. However, the importance of good sleep continues to be underrecognized. Mechanisms regulating sleep and its functions in humans remain mostly unclear even after decades of dedicated research. Advancements in gene sequencing techniques and computational methodologies have paved the way for various genetic analysis approaches, which have provided some insights into human sleep genetics. This review summarizes our current knowledge of the genetic basis underlying human sleep traits and sleep disorders. We also highlight the use of animal models to validate genetic findings from human sleep studies and discuss potential molecular mechanisms and signaling pathways involved in the regulation of human sleep.

Nutrient Abundance Signals the Changing of the Seasons by Phosphorylating PER2.

The circadian clock synchronizes metabolic and behavioral cycles with the rotation of the Earth by integrating environmental cues, such as light. Nutrient content also regulates the clock, though how and why this environmental signal affects the clock remains incompletely understood. Here, we elucidate a role for nutrient in regulating circadian alignment to seasonal photoperiods. High fat diet (HFD) promoted entrainment to a summer light cycle and inhibited entrainment to a winter light cycle by phosphorylating PER2 on serine 662. PER2-S662 phospho-mimetic mutant mice were incapable of entraining to a winter photoperiod, while PER2-S662 phospho-null mutant mice were incapable of entraining to a summer photoperiod, even in the presence of HFD. Multi-omic experimentation in conjunction with isocaloric hydrogenated-fat feeding, revealed a role for polyunsaturated fatty acids in nutrient-dependent seasonal entrainment. Altogether, we identify the mechanism whereby nutrient content shifts circadian rhythms to anticipate seasonal photoperiods in which that nutrient state predominates. HIGHLIGHTS: High fat diet promotes entrainment to summer but inhibits entrainment to winter.Calorie restriction promotes entrainment to winter but inhibits entrainment to summer.PER2-S662 phosphorylation is required for nutritional regulation of seasonal circadian entrainment.Dietary polyunsaturated fatty acids regulate seasonal circadian entrainment.

Diverse roles of pontine NPS-expressing neurons in sleep regulation.

Neuropeptide S (NPS) was postulated to be a wake-promoting neuropeptide with unknown mechanism, and a mutation in its receptor (NPSR1) causes the short sleep duration trait in humans. We investigated the role of different NPS+ nuclei in sleep/wake regulation. Loss-of-function and chemogenetic studies revealed that NPS+ neurons in the parabrachial nucleus (PB) are wake-promoting, whereas peri-locus coeruleus (peri-LC) NPS+ neurons are not important for sleep/wake modulation. Further, we found that a NPS+ nucleus in the central gray of the pons (CGPn) strongly promotes sleep. Fiber photometry recordings showed that NPS+ neurons are wake-active in the CGPn and wake/REM-sleep active in the PB and peri-LC. Blocking NPS-NPSR1 signaling or knockdown of Nps supported the function of the NPS-NPSR1 pathway in sleep/wake regulation. Together, these results reveal that NPS and NPS+ neurons play dichotomous roles in sleep/wake regulation at both the molecular and circuit levels.

Adaptive Long-Read Sequencing Reveals GGC Repeat Expansion in ZFHX3 Associated with Spinocerebellar Ataxia Type 4.

BACKGROUND: Spinocerebellar ataxia type 4 (SCA4) is an autosomal dominant ataxia with invariable sensory neuropathy originally described in a family with Swedish ancestry residing in Utah more than 25 years ago. Despite tight linkage to the 16q22 region, the molecular diagnosis has since remained elusive. OBJECTIVES: Inspired by pathogenic structural variation implicated in other 16q-ataxias with linkage to the same locus, we revisited the index SCA4 cases from the Utah family using novel technologies to investigate structural variation within the candidate region. METHODS: We adopted a targeted long-read sequencing approach with adaptive sampling on the Oxford Nanopore Technologies (ONT) platform that enables the detection of segregating structural variants within a genomic region without a priori assumptions about any variant features. RESULTS: Using this approach, we found a heterozygous (GGC)n repeat expansion in the last coding exon of the zinc finger homeobox 3 (ZFHX3) gene that segregates with disease, ranging between 48 and 57 GGC repeats in affected probands. This finding was replicated in a separate family with SCA4. Furthermore, the estimation of this GGC repeat size in short-read whole genome sequencing (WGS) data of 21,836 individuals recruited to the 100,000 Genomes Project in the UK and our in-house dataset of 11,258 exomes did not reveal any pathogenic repeats, indicating that the variant is ultrarare. CONCLUSIONS: These findings support the utility of adaptive long-read sequencing as a powerful tool to decipher causative structural variation in unsolved cases of inherited neurological disease. © 2024 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.

The characteristics of excitatory lineage differentiation and the developmental conservation in Reeler neocortex.

The majority of neocortical projection neurons are generated indirectly from radial glial cells (RGCs) mediated by intermediate progenitor cells (IPCs) in mice. IPCs are thought to be a great breakthrough in the evolutionary expansion of the mammalian neocortex. However, the precise ratio of neuron production from IPCs and characteristics of RGC differentiation process are still unclear. Our study revealed that direct neurogenesis was seldom observed and increased slightly at late embryonic stage. Besides, we conducted retrovirus sparse labelling combined carboxyfluorescein diacetate succinimide ester (CFSE) and Tbr2-CreER strain to reconstruct individual lineage tree in situ. The lineage trees simulated the output of RGCs at per round of division in sequence with high temporal, spatial and cellular resolution at P7. We then demonstrated that only 1.90% of neurons emanated from RGCs directly in mouse cerebral neocortex and 79.33% of RGCs contributed to the whole clones through IPCs. The contribution of indirect neurogenesis was underestimated previously because approximately a quarter of IPC-derived neurons underwent apoptosis. Here, we also showed that abundant IPCs from first-generation underwent self-renewing division and generated four neurons ultimately. We confirmed that the intermediate proliferative progenitors expressed higher Cux2 characteristically at early embryonic stage. Finally, we validated that the characteristics of neurogenetic process in lineages and developmental fate of neurons were conserved in Reeler mice. This study contributes to further understanding of neurogenesis in neocortical development.

Mutant ß1-adrenergic receptor improves REM sleep and ameliorates tau accumulation in a mouse model of tauopathy.

Sleep is essential for our well-being, and chronic sleep deprivation has unfavorable health consequences. We recently demonstrated that two familial natural short sleep (FNSS) mutations, DEC2-P384R and Npsr1-Y206H, are strong genetic modifiers of tauopathy in PS19 mice, a model of tauopathy. To gain more insight into how FNSS variants modify the tau phenotype, we tested the effect of another FNSS gene variant, Adrb1-A187V, by crossing mice with this mutation onto the PS19 background. We found that the Adrb1-A187V mutation helped restore rapid eye movement (REM) sleep and alleviated tau aggregation in a sleep-wake center, the locus coeruleus (LC), in PS19 mice. We found that ADRB1+ neurons in the central amygdala (CeA) sent projections to the LC, and stimulating CeAADRB1+ neuron activity increased REM sleep. Furthermore, the mutant Adrb1 attenuated tau spreading from the CeA to the LC. Our findings suggest that the Adrb1-A187V mutation protects against tauopathy by both mitigating tau accumulation and attenuating tau spreading.

Tacrolimus improved the pregnancy outcomes of patients with refractory recurrent spontaneous abortion and immune bias disorders: a randomized controlled trial.

OBJECTIVE: To investigate the effect of tacrolimus treatment on refractory recurrent spontaneous abortion (RSA) patients with elevated serum IL-33/ST2 levels. METHODS: This study was a randomized controlled trial (RCT) of refractory RSA patients with elevated peripheral blood IL-33/ST2 levels or an elevated Th1/Th2 cell ratio. A total of 149 women were enrolled, each of whom had had at least 3 serial miscarriages and was confirmed to have elevated peripheral blood IL-33/ST2 levels or an elevated Th1/Th2 cell ratio. These women were randomly divided into two groups. The tacrolimus group (n = 75) received basic therapy with the addition of tacrolimus (Prograf). Tacrolimus was administered at a dose of 0.05 ~ 0.1 mg/kg/day from the end of the menstrual period to the beginning of the next menstrual period or to the 10th week of pregnancy. In contrast, basic therapy with the addition of placebo was given to the placebo group (n = 74). The main study outcome was the delivery of healthy newborns without deformities. RESULTS: A total of 60 (80.00%) patients in the tacrolimus group and 47 (63.51%) patients in the placebo group delivered healthy newborns [P = 0.03, odds ratio = 2.30; 95% confidence interval (1.10 ~ 4.81)]. The peripheral blood IL-33/ST2 levels and Th1/Th2 cell ratio of the tacrolimus group were much lower than those of the placebo group (P < 0.05). CONCLUSION: We validated our previous finding that serum IL-33 and sST2 concentrations are related to RSA. Immunosuppressive treatment with tacrolimus was demonstrated to be a promising method to treat refractory RSA with immune bias disorders.

Correlation Analysis of Molecularly-Defined Cortical Interneuron Populations with Morpho-Electric Properties in Layer V of Mouse Neocortex.

Cortical interneurons can be categorized into distinct populations based on multiple modalities, including molecular signatures and morpho-electrical (M/E) properties. Recently, many transcriptomic signatures based on single-cell RNA-seq have been identified in cortical interneurons. However, whether different interneuron populations defined by transcriptomic signature expressions correspond to distinct M/E subtypes is still unknown. Here, we applied the Patch-PCR approach to simultaneously obtain the M/E properties and messenger RNA (mRNA) expression of >600 interneurons in layer V of the mouse somatosensory cortex (S1). Subsequently, we identified 11 M/E subtypes, 9 neurochemical cell populations (NCs), and 20 transcriptomic cell populations (TCs) in this cortical lamina. Further analysis revealed that cells in many NCs and TCs comprised several M/E types and were difficult to clearly distinguish morpho-electrically. A similar analysis of layer V interneurons of mouse primary visual cortex (V1) and motor cortex (M1) gave results largely comparable to S1. Comparison between S1, V1, and M1 suggested that, compared to V1, S1 interneurons were morpho-electrically more similar to M1. Our study reveals the presence of substantial M/E variations in cortical interneuron populations defined by molecular expression.

Circ_0001777 Affects Triple-negative Breast Cancer Progression Through the miR-95-3p/AKAP12 Axis.

BACKGROUND: Triple Negative Breast Cancer (TNBC) is 1 of the most serious cancer. Circular RNA_0001777 (circ_0001777) expression was decreased in TNBC tissues. However, the molecular mechanism of circ_0001777 remains unknown. METHODS: The expression of circ_0001777, microRNA-95-3p (miR-95-3p) and A-kinase anchor protein 12 (AKAP12) were detected by quantitative real-time fluorescence polymerase chain reaction (qRT-PCR). A series of in vitro experiments were designed to explore the function of circ_0001777 in TNBC cells and the regulatory mechanism between circ_0001777 and miR-95-3p and AKAP12 in TNBC cells. Western blot examined the relative protein levels in TNBC cells. Bioinformatics prediction site predicted the relationship between miR-95-3p and circ_0001777 or AKAP12 and was verified by Dual-luciferase reporter assays. The xenotransplantation model was established to study the role of circ_0001777 in vivo. RESULTS: The expression of circ_0001777 and AKAP12 was decreased in TNBC tissues, while the expression of miR-95-3p was increased. Circ_0001777 can sponge miR-95-3p, and AKAP12 is the target of miR-95-3p. In vitro complement experiments, overexpression of circ_0001777 significantly decreased the malignant behavior of TNBC, while co-transfection of miR-95-3p partially up-regulated this change. In addition, AKAP12 knockdown increased the proliferation, migration, and invasion of TNBC cells inhibited by overexpression of circ_0001777. Mechanically, circ_0001777 regulates AKAP12 expression in TNBC cells by sponge miR-95-3p. In addition, in vivo studies have shown that overexpression of circ_0001777 inhibits tumor growth. CONCLUSION: Overexpression of circ_0001777 decreased proliferation, migration, and invasion of TNBC cells by regulating the miR-95-3p/AKAP12 axis, suggesting that circ_0001777/miR-95-3p/AKAP12 axis may be a potential regulatory mechanism for the treatment of TNBC.

mvPPT: A Highly Efficient and Sensitive Pathogenicity Prediction Tool for Missense Variants.

Next-generation sequencing technologies both boost the discovery of variants in the human genome and exacerbate the challenges of pathogenic variant identification. In this study, we developed Pathogenicity Prediction Tool for missense variants (mvPPT), a highly sensitive and accurate missense variant classifier based on gradient boosting. mvPPT adopts high-confidence training sets with a wide spectrum of variant profiles, and extracts three categories of features, including scores from existing prediction tools, frequencies (allele frequencies, amino acid frequencies, and genotype frequencies), and genomic context. Compared with established predictors, mvPPT achieves superior performance in all test sets, regardless of data source. In addition, our study also provides guidance for training set and feature selection strategies, as well as reveals highly relevant features, which may further provide biological insights into variant pathogenicity. mvPPT is freely available at http://www.mvppt.club/.

Sncg, Mybpc1, and Parm1 Classify subpopulations of VIP-expressing interneurons in layers 2/3 of the somatosensory cortex.

Neocortical vasoactive intestinal polypeptide-expressing (VIP+) interneurons display highly diverse morpho-electrophysiological and molecular properties. To begin to understand the function of VIP+ interneurons in cortical circuits, they must be clearly and comprehensively classified into distinct subpopulations based on specific molecular markers. Here, we utilized patch-clamp RT-PCR (Patch-PCR) to simultaneously obtain the morpho-electric properties and mRNA profiles of 155 VIP+ interneurons in layers 2 and 3 (L2/3) of the mouse somatosensory cortex. Using an unsupervised clustering method, we identified 3 electrophysiological types (E-types) and 2 morphological types (M-types) of VIP+ interneurons. Joint clustering based on the combined electrophysiological and morphological features resulted in 3 morpho-electric types (ME-types). More importantly, we found these 3 ME-types expressed distinct marker genes: ~94% of Sncg+ cells were ME-type 1, 100% of Mybpc1+ cells were ME-type 2, and ~78% of Parm1+ were ME-type 3. By clarifying the properties of subpopulations of cortical L2/3 VIP+ interneurons, this study establishes a basis for future investigations aiming to elucidate their physiological roles.

An excitatory peri-tegmental reticular nucleus circuit for wake maintenance.

Sleep is a necessity for our survival, but its regulation remains incompletely understood. Here, we used a human sleep duration gene to identify a population of cells in the peri-tegmental reticular nucleus (pTRNADRB1) that regulate sleep-wake, uncovering a role for a poorly understood brain area. Although initial ablation in mice led to increased wakefulness, further validation revealed that pTRNADRB1 neuron stimulation strongly promotes wakefulness, even after stimulation offset. Using combinatorial genetics, we found that excitatory pTRNADRB1 neurons promote wakefulness. pTRN neurons can be characterized as anterior- or posterior-projecting neurons based on multiplexed analysis of projections by sequencing (MAPseq) analysis. Finally, we found that pTRNADRB1 neurons promote wakefulness, in part, through projections to the lateral hypothalamus. Thus, human genetic information from a human sleep trait allowed us to identify a role for the pTRN in sleep-wake regulation.

Familial natural short sleep mutations reduce Alzheimer pathology in mice.

Although numerous studies have demonstrated that poor sleep increases the development of AD, direct evidence elucidating the benefits of good sleep on the AD pathogenesis is lacking. Familial Natural Short Sleepers (FNSS) are genetically wired to have lifelong reduction in nightly sleep duration without evident consequence on cognitive demise, implying that they may have better sleep quality. Here we investigated two FNSS mutations, DEC2-P384R and Npsr1-Y206H, on the development of tau and amyloid pathology in AD-like mouse models. We found that the development of tau pathology is attenuated in the hippocampus of tau mice carrying FNSS mutations. We also found that DEC2-P384R;5XFAD and female Npsr1-Y206H;5XFAD mice exhibit significantly less amyloid plaques than control mice at 6 months of age. Together, these results reveal that these two FNSS alleles are strong genetic modifiers of AD pathology and may confer resilience to the progression of tau pathology and amyloid plaque formation in neurodegeneration.

Accuracy of optimized Sirius ray-tracing method in intraocular lens power calculation.

AIM: To evaluate the accuracy and predictability of ray tracing-assisted intraocular lens (IOL) calculation function in Sirius internal software and further improve the accuracy by optimizing the calculation of predicted lens position (PLP). METHODS: This retrospective study recruited 52 eyes of 49 patients. All of the cases with cataract had undergone phacoemulsification combined with IOL implantation. SRK-T, Haigis formula, and Sirius ray-tracing method were all used for each eye's IOL calculation. The mean absolute value of prediction error (prediction error=predicted refraction-postoperative refraction) was defined as mean absolute prediction error (MAPE) and was determined for each method. Calculation of PLP was optimized by effective lens position (ELP). Optimized PLP was entered to Sirius internal software again to verify whether the method was improved. RESULTS: Compared with SRK-T and Haigis formulas, less accuracy was shown in Sirius ray-tracing method (P=0.001). The ELP of the IOL moved forward compared to PLP (P<0.001). The MAPE of the ELP-inputted Sirius ray-tracing method was reduced. ELP and PLP were well correlated. Taking ELP as y and PLP given by Sirius soft as x, a linear regression formula y=0.1637x+3.1741 was concluded (R2 =0.1066, P=0.018). It was shown that the optimized Sirius ray-tracing method (optimized PLP entered), compared with SRK-T and Haigis formulas, worked with the same accuracy (P=0.038). CONCLUSION: The original Sirius ray tracing method is not satisfactory enough. However, in normal eyes, the optimized Sirius ray-tracing method in IOL calculation was as accurate as SRK-T and Haigis formulas.

Microglia are involved in the protection of memories formed during sleep deprivation.

Sleep deprivation can generate inflammatory responses in the central nervous system. In turn, this inflammation increases sleep drive, leading to a rebound in sleep duration. Microglia, the innate immune cells found exclusively in the CNS, have previously been found to release inflammatory signals and exhibit altered characteristics in response to sleep deprivation. Together, this suggests that microglia may be partially responsible for the brain's response to sleep deprivation through their inflammatory activity. In this study, we ablated microglia from the mouse brain and assessed resulting sleep, circadian, and sleep deprivation phenotypes. We find that microglia are dispensable for both homeostatic sleep and circadian function and the sleep rebound response to sleep deprivation. However, we uncover a phenomenon by which microglia appear to be essential for the protection of fear-conditioning memories formed during the recovery sleep period following a period of sleep deprivation. This phenomenon occurs potentially through the upregulation of synaptic-homeostasis related genes to protect nascent dendritic spines that may be otherwise removed or downscaled during recovery sleep. These findings further expand the list of known functions for microglia in synaptic modulation.

Retrospective Analysis of Fondaparinux and Low-Molecular-Weight Heparin in the Treatment of Women With Recurrent Spontaneous Abortion.

Background: To compare the clinical efficacy of fondaparinux and LMWH and provide clinical evidence for the effectiveness of fondaparinux in the treatment of recurrent spontaneous abortion caused by PTS. Methods: A retrospective analysis was conducted for 120 patients diagnosed with a recurrent spontaneous abortion caused by PTS in Qingdao Jinhua Women's Hospital from March 2019 to April 2020. The patients were divided into two groups: 68 cases in the control group, treated with LMWH, 52 cases in the observational group, treated with fondaparinux. The pregnancy outcomes and adverse reactions between the two groups of recurrent miscarriage patients were compared. Results: No significant difference was detected in the general data between the two groups of patients before treatment (P>0.05). In the observational group, the R value was increased, and the α and MA values were decreased after three months of treatment compared to those before treatment (P<0.05). In the control group, the R value was increased, and the MA value was decreased after three months of treatment compared to those before treatment (P<0.05). After treatment, no significant difference was observed in the pregnancy outcome between the two groups (P>0.05). The total adverse reaction rate of the fondaparinux group was lower than that of the LMWH group (P<0.05). Conclusions: In this study, no significant difference was detected in the pregnancy outcome between fondaparinux and LMWH in the treatment of recurrent spontaneous abortion caused by PTS, but fondaparinux had a low occurrence rate of adverse reactions and high safety.

Corrigendum: Efficacy of Intrauterine Perfusion of Cyclosporin A for Intractable Recurrent Spontaneous Abortion Patients With Endometrial Alloimmune Disorders: A Randomized Controlled Trial.

[This corrects the article DOI: 10.3389/fphys.2021.737878.].

Efficacy of Intrauterine Perfusion of Cyclosporin A for Intractable Recurrent Spontaneous Abortion Patients With Endometrial Alloimmune Disorders: A Randomized Controlled Trial.

Objective: To explore the therapeutic efficacy of intrauterine perfusion of cyclosporin A (CsA) in intractable recurrent spontaneous abortion (RSA) patients with endometrial alloimmune dysfunction. Methods: This is a randomized controlled trial (RCT) of patients with intractable RSA with endometrial alloimmune disorders. A total of 201 women were enrolled, all of whom had at least 3 serial abortions and endometrial alloimmune dysfunction. Participants were randomly assigned to two groups. The CsA group (n = 101) received intrauterine infusion of 250 mg CsA on the 3rd and 7th days after menstruation for 2 menstrual cycles, while the placebo group (n = 100) received placebo. The birth of healthy, deformity-free babies was the main study outcome. Results: In total, 75 (74.26%) women in the CsA group and 59 (59.00%) women in the placebo group gave birth to healthy babies [P = 0.01, OR = 2.01; 95% CI (1.10∼3.65)]. Compared to the placebo group, the CsA group had dramatically lower endometrial CD56+ cell and CD57+ cell concentrations at the luteal phase of the second menstrual cycle (P < 0.05). Conclusion: Intrauterine perfusion of CsA was confirmed to be a promising approach for the treatment of intractable alloimmune RSA.