KOBAS-i: intelligent prioritization and exploratory visualization of biological functions for gene enrichment analysis

Inheritance of perturbed methylation and metabolism caused by uterine malnutrition via oocytes

BACKGROUND

Undernourishment in utero has deleterious effects on the metabolism of offspring, but the mechanism of the transgenerational transmission of metabolic disorders is not well known. In the present study, we found that undernourishment in utero resulted in metabolic disorders of female F1 and F2 in mouse model.

RESULTS

Undernutrition in utero induced metabolic disorders of F1 females, which was transmitted to F2 females. The global methylation in oocytes of F1 exposed to undernutrition in utero was decreased compared with the control. KEGG analysis showed that genes with differential methylation regions (DMRs) in promoters were significantly enriched in metabolic pathways. The altered methylation of some DMRs in F1 oocytes located at the promoters of metabolic-related genes were partially observed in F2 tissues, and the expressions of these genes were also changed. Meanwhile, the abnormal DNA methylation of the validated DMRs in F1 oocytes was also observed in F2 oocytes.

CONCLUSIONS

These results indicate that DNA methylation may mediate the transgenerational inheritance of metabolic disorders induced by undernourishment in utero via female germline.

Clocking Epilepsies: A Chronomodulated Strategy-Based Therapy for Rhythmic Seizures

Epilepsy is a neurological disorder characterized by hypersynchronous recurrent neuronal activities and seizures, as well as loss of muscular control and sometimes awareness. Clinically, seizures have been reported to display daily variations. Conversely, circadian misalignment and circadian clock gene variants contribute to epileptic pathogenesis. Elucidation of the genetic bases of epilepsy is of great importance because the genetic variability of the patients affects the efficacies of antiepileptic drugs (AEDs). For this narrative review, we compiled 661 epilepsy-related genes from the PHGKB and OMIM databases and classified them into 3 groups: driver genes, passenger genes, and undetermined genes. We discuss the potential roles of some epilepsy driver genes based on GO and KEGG analyses, the circadian rhythmicity of human and animal epilepsies, and the mutual effects between epilepsy and sleep. We review the advantages and challenges of rodents and zebrafish as animal models for epileptic studies. Finally, we posit chronomodulated strategy-based chronotherapy for rhythmic epilepsies, integrating several lines of investigation for unraveling circadian mechanisms underpinning epileptogenesis, chronopharmacokinetic and chronopharmacodynamic examinations of AEDs, as well as mathematical/computational modeling to help develop time-of-day-specific AED dosing schedules for rhythmic epilepsy patients.

Genome-Wide Association Analysis Identified Variants Associated with Body Measurement and Reproduction Traits in Shaziling Pigs

With the increasing popularity of genomic sequencing, breeders pay more attention to identifying the crucial molecular markers and quantitative trait loci for improving the body size and reproduction traits that could affect the production efficiency of pig-breeding enterprises. Nevertheless, for the Shaziling pig, a well-known indigenous breed in China, the relationship between phenotypes and their corresponding genetic architecture remains largely unknown. Herein, in the Shaziling population, a total of 190 samples were genotyped using the Geneseek Porcine 50K SNP Chip, obtaining 41857 SNPs for further analysis. For phenotypes, two body measurement traits and four reproduction traits in the first parity from the 190 Shaziling sows were measured and recorded, respectively. Subsequently, a genome-wide association study (GWAS) between the SNPs and the six phenotypes was performed. The correlation between body size and reproduction phenotypes was not statistically significant. A total of 31 SNPs were found to be associated with body length (BL), chest circumference (CC), number of healthy births (NHB), and number of stillborns (NSB). Gene annotation for those candidate SNPs identified 18 functional genes, such as GLP1R, NFYA, NANOG, COX7A2, BMPR1B, FOXP1, SLC29A1, CNTNAP4, and KIT, which exert important roles in skeletal morphogenesis, chondrogenesis, obesity, and embryonic and fetal development. These findings are helpful to better understand the genetic mechanism for body size and reproduction phenotypes, while the phenotype-associated SNPs could be used as the molecular markers for the pig breeding programs.

De Novo Assembly and Characterization of the Transcriptome of an Omnivorous Camel Cricket (Tachycines meditationis)

Tachycines meditationis (Orthoptera: Rhaphidophoridae: Tachycines) is a widely distributed insect in eastern Asia. This species is common in urban environments, and its unique omnivorous diet may contribute to its success in various habitats. However, molecular studies on the species are scarce. Here, we obtained the first transcriptome sequence of T. meditationis and performed preliminary analyses to test whether the evolution of coding sequences fits the expectations based on the species' ecology. We retrieved 476,495 effective transcripts and annotated 46,593 coding sequences (CDS). We analysed the codon usage and found that directional mutation pressure was the leading cause of codon usage bias in this species. This genome-wide relaxed codon usage pattern in T. meditationis is surprising, given the potentially large population size of this species. Moreover, despite the omnivorous diet, the chemosensory genes of this species do not exhibit codon usage deviating significantly from the genome-level pattern. They also do not seem to experience more gene family expansion than other cave cricket species do. A thorough search for rapidly evolved genes using the dN/dS value showed that genes associated with substance synthesis and metabolic pathways, such as retinol metabolism, aminoacyl-tRNA biosynthesis, and fatty acid metabolism, underwent species-specific positive selection. While some results seem to contradict the species ecology, our transcriptome assembly provides a valuable molecular resource for future studies on camel cricket evolution and molecular genetics for feeding ecology in insects, in general.

Genomic analysis reveals a KIT-related chromosomal translocation associated with the white coat phenotype in yak

White coat pigmentation is a striking phenotype of many domesticated species and has various genetic controls. The Tianzhu White yak, an indigenous breed with a complete white coat, has fascinated Tibetans for centuries. However, the genetic basis of this trait remains unknown. Here, we conducted population genomics analysis and genome-wide association study based on the whole-genome sequencing data of 38 white and 59 non-white-coated yak. The results revealed the presence of KIT-linked Cs alleles characterized by the translocations between chromosomes 6 and 29 in all-white yak. Furthermore, structural variations showed additional duplications of the Cs alleles in white yak compared with colour-sidedness cattle. Interestingly, the Cs alleles associated with the white coat phenotype in yak were found to have introgressed from taurine cattle. Our findings unveil the shared genetic control of the white coat phenotype and its evolution in closely related bovine species.

Global transcriptional and translational regulation of Sphingomonas melonis TY in response to hyperosmotic stress

Hyperosmotic stress is one of the most ubiquitous stress factors in microbial habitats and impairs the efficiency of bacteria performing vital biochemical tasks. Sphingomonas serves as a 'superstar' of plant defense and pollutant degradation, and is widely existed in the environment. However, it is still unclear that how Sphingomonas sp. survives under hyperosmotic stress conditions. In this study, multiomics profiling analysis was conducted with S. melonis TY under hyperosmotic conditions to investigate the intracellular hyperosmotic responses. The transcriptome and proteome revealed that sensing systems, including most membrane protein coding genes were upregulated, genes related to two-component systems were tiered adjusted to reset the whole system, other stress response regulators such as sigma-70 were also significantly tiered upregulated. In addition, transport systems together with compatible solute biosynthesis related genes were significantly upregulated to accumulate intracellular nutrients and compatible solutes. When treated with hyperosmotic stress, redox-stress response systems were triggered and mechanosensitive channels together with ion transporters were induced to maintain cellular ion homeostasis. In addition, cellular concentration of c-di-guanosine monophosphate synthetase (c-di-GMP) was reduced, followed by negative influences on genes involved in flagellar assembly and chemotaxis pathways, leading to severe damage to the athletic ability of S. melonis TY, and causing detachments of biofilms. Briefly, this research revealed a comprehensive response mechanism of S. melonis TY exposure to hyperosmotic stress, and emphasized that flagellar assembly and biofilm formation were vulnerable to hyperosmotic conditions. Importance. Sphingomonas, a genus with versatile functions survives extensively, lauded for its prominent role in plant protection and environmental remediation. Current evidence shows that hyperosmotic stress as a ubiquitous environmental factor, usually threatens the survival of microbes and thus impairs the efficiency of their environmental functions. Thus, it is essential to explore the cellular responses to hyperosmotic stress. Hence, this research will greatly enhance our understanding of the global transcriptional and translational regulation of S. melonis TY in response to hyperosmotic stress, leading to broader perspectives on the impacts of stressful environments.

Gapless Genome Assembly of Puccinia triticina Provides Insights into Chromosome Evolution in Pucciniales

Chromosome evolution drives species evolution, speciation, and adaptive radiation. Accurate genome assembly is crucial to understanding chromosome evolution of species, such as dikaryotic fungi. Rust fungi (Pucciniales) in dikaryons represent the largest group of plant pathogens, but the evolutionary process of adaptive radiation in Pucciniales remains poorly understood. Here, we report a gapless genome for the wheat leaf rust fungus Puccinia triticina determined using PacBio high-fidelity (HiFi) sequencing. This gapless assembly contains two sets of chromosomes, showing that one contig represents one chromosome. Comparisons of homologous chromosomes between the phased haplotypes revealed that highly frequent small-scale sequence divergence shapes haplotypic variation. Genome analyses of Puccinia triticina along with other rusts revealed that recent transposable element bursts and extensive segmental gene duplications synergistically highlight the evolution of chromosome structures. Comparative analysis of chromosomes indicated that frequent chromosomal rearrangements may act as a major contributor to rapid radiation of Pucciniales. This study presents the first gapless, phased assembly for a dikaryotic rust fungus and provides insights into adaptive evolution and species radiation in Pucciniales. IMPORTANCE Rust fungi (Pucciniales) are the largest group of plant pathogens. Adaptive radiation is a predominant feature in Pucciniales evolution. Chromosome evolution plays an important role in adaptive evolution. Accurate chromosome-scale assembly is required to understand the role of chromosome evolution in Pucciniales. We took advantage of HiFi sequencing to construct a gapless, phased genome for Puccinia triticina. Further analyses revealed that the evolution of chromosome structures in rust lineage is shaped by the combination of transposable element bursts and segmental gene duplications. Chromosome comparisons of Puccinia triticina and other rusts suggested that frequent chromosomal arrangements may make remarkable contributions to high species diversity of rust fungi. Our results present the first gapless genome for Pucciniales and shed light on the feature of chromosome evolution in Pucciniales.

Copy Number Variation Analysis Revealed the Evolutionary Difference between Chinese Indigenous Pigs and Asian Wild Boars

Copy number variation (CNV) has been widely used to study the evolution of different species. We first discovered different CNVs in 24 Anqingliubai pigs and 6 Asian wild boars using next-generation sequencing at the whole-genome level with 10× depth to understand the relationship between genetic evolution and production traits in wild boars and domestic pigs. A total of 97,489 CNVs were identified and divided into 10,429 copy number variation regions (CNVRs), occupying 32.06% of the porcine genome. Chromosome 1 had the most CNVRs, and chromosome 18 had the least. Ninety-six CNVRs were selected using VST 1% based on the signatures of all CNVRs, and sixty-five genes were identified in the selected regions. These genes were strongly correlated with traits distinguishing groups by enrichment in Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathways, such as growth (CD36), reproduction (CIT, RLN), detoxification (CYP3A29), and fatty acid metabolism (ELOVL6). The QTL overlapping regions were associated with meat traits, growth, and immunity, which was consistent with CNV analysis. Our findings increase the understanding of evolved genome structural variations between wild boars and domestic pigs, and provide new molecular biomarkers to guide breeding and the efficient use of available genetic resources.

Exploration of Candidate Genes Involved in the Biosynthesis, Regulation and Recognition of the Male-Produced Aggregation Pheromone of Halyomorpha halys

The aggregation pheromone of the brown marmorated stink bug, Halyomorpha halys (Stål), is produced by adult males, and plays an important role in the behavioral regulation of H. halys. However, information on the molecular mechanisms underlying this pheromone's biosynthesis is limited. In this study, HhTPS1, a key candidate synthase gene in the aggregation pheromone biosynthesis pathway of H. halys, was identified. Then, through weighted gene co-expression network analysis, the candidate P450 enzyme genes in the biosynthetic downstream of this pheromone and the related candidate transcription factor in this pathway were also identified. In addition, two olfactory-related genes, HhCSP5 and HhOr85b, involved in the recognition of the aggregation pheromone of H. halys, were detected. We further identified the key amino acid sites of HhTPS1 and HhCSP5 that interact with substrates by using molecular docking analysis. This study provides basic information for further investigations into the biosynthesis pathways and recognition mechanisms of aggregation pheromones in H. halys. It also provides key candidate genes for bioengineering bioactive aggregation pheromones necessary for the development of technologies for the monitoring and control of H. halys.

Study on Neuroprotective Mechanism of Houshiheisan in Ischemic Stroke Based on Transcriptomics and Experimental Verification

Houshiheisan (HSHS), a classic prescription in traditional Chinese medicine (TCM), has shown outstanding efficacy in treating stroke. This study investigated various therapeutic targets of HSHS for ischemic stroke using mRNA transcriptomics. Herein, rats were randomly separated into the sham, model, HSHS 5.25 g/kg (HSHS5.25), and HSHS 10.5 g/kg (HSHS10.5) groups. Rats suffering from stroke were induced by permanent middle cerebral artery occlusion (pMCAO). After seven days of HSHS treatment, behavioral tests were conducted, and histological damage was examined with hematoxylin-eosin (HE). The mRNA expression profiles were identified using microarray analysis and quantitative real-time PCR (qRT-PCR) validated gene expression changes. An analysis of gene ontology and pathway enrichment was conducted to analyze potential mechanisms confirmed using immunofluorescence and western blotting. HSHS5.25 and HSHS10.5 improved neurological deficits and pathological injury in pMCAO rats. The intersections of 666 differentially expressed genes (DEGs) were chosen using transcriptomics analysis in the sham, model, and HSHS10.5 groups. The enrichment analysis suggested that the therapeutic targets of HSHS might regulate the apoptotic process and ERK1/2 signaling pathway, which was related to neuronal survival. Moreover, TUNEL and immunofluorescence analysis indicated that HSHS inhibited apoptosis and enhanced neuronal survival in the ischemic lesion. Western blot and immunofluorescence assay indicated that HSHS10.5 decreased Bax/Bcl-2 ratio and suppressed caspase-3 activation, while the phosphorylation of ERK1/2 and CREB was upregulated in a stroke rat model after HSHS treatment. Effective inhibition of neuronal apoptosis by activating the ERK1/2-CREB signaling pathway may be a potential mechanism for HSHS in the treatment of ischemic stroke.

Blood transcriptome reveals immune and metabolic-related genes involved in growth of pasteurized colostrum-fed calves

The quality of colostrum is a key factor contributing to healthy calf growth, and pasteurization of colostrum can effectively reduce the counts of pathogenic microorganisms present in the colostrum. Physiological changes in calves fed with pasteurized colostrum have been well characterized, but little is known about the underlying molecular mechanisms. In this study, key genes and functional pathways through which pasteurized colostrum affects calf growth were identified through whole blood RNA sequencing. Our results showed that calves in the pasteurized group (n = 16) had higher body height and daily weight gain than those in the unpasteurized group (n = 16) in all months tested. Importantly, significant differences in body height were observed at 3 and 4 months of age (p < 0.05), and in daily weight gain at 2, 3, and 6 months of age (p < 0.05) between the two groups. Based on whole blood transcriptome data from 6-months old calves, 630 differentially expressed genes (DEGs), of which 235 were upregulated and 395 downregulated, were identified in the pasteurized compared to the unpasteurized colostrum groups. Most of the DEGs have functions in the immune response (e.g., CCL3, CXCL3, and IL1A) and metabolism (e.g., PTX3 and EXTL1). Protein-protein interaction analyses of DEGs revealed three key subnetworks and fifteen core genes, including UBA52 and RPS28, that have roles in protein synthesis, oxidative phosphorylation, and inflammatory responses. Twelve co-expression modules were identified through weighted gene co-expression network analysis. Among them, 17 genes in the two modules that significantly associated with pasteurization were mainly involved in the tricarboxylic acid cycle, NF-kappa B signaling, and NOD-like receptor signaling pathways. Finally, DEGs that underwent alternative splicing in calves fed pasteurized colostrum have roles in the immune response (SLCO4A1, AKR1C4, and MED13L), indicative of potential roles in immune regulation. Results from multiple analytical methods used suggest that differences in calf growth between the pasteurized and unpasteurized groups may be due to differential immune activity. Our data provide new insights into the impact of pasteurization on calf immune and metabolic-related pathways through its effects on gene expression.

Transcriptome diversity assessment of Gossypium arboreum (FDH228) leaves under control, drought and whitefly infestation using PacBio long reads

Alternative splicing (AS) and alternative polyadenylation (APA) are common mechanisms in eukaryotes to increase the complexity of transcriptomes and subsequently proteomes. Analysis of long reads transcriptomics data can result in the discovery of novel transcripts, splice sites, AS or APA events. Gossypium arboreum is an important cultivated cotton species and a putative contributor of the A sub-genome to the modern tetraploid cotton; and inherently tolerant to several biotic and abiotic stresses. Specifically, its variety 'FDH228' is considered to be an important resistance source. In this study, we sequenced the G. arboreum (var. FDH228) transcriptome using PacBio IsoSeq and illumina short read sequencing under three different conditions i.e. untreated/healthy, treated with biotic stress through whitefly infestation, and treated with abiotic stress via water deprivation, for the discovery and surveying of canonical and non-canonical AS, APA and transcript fusion events. We were able to obtain 15,419 unique transcripts from all samples representing 11,343 genes, out of which 10,832 were annotated and 520 were novel with respect to the published reference genome. These transcripts were grouped into different structural categories including 60 Antisense, 11,959 having a full-splice match, 999 with incomplete-splice match, 30 fusion transcripts, 177 genic, 479 intergenic, 771 novels in the catalog, and 944 Novel but not found in the catalog. Subsequently, randomly selected candidate transcripts were experimentally validated using qRT-PCR. Our comprehensive identification of canonical and non-canonical splicing events, and novel and fusion transcripts aids in the understanding of the resistance mechanisms for this specific germplasm.

RNA-seq analysis reveals the critical role of the novel lncRNA BIANCR in intramuscular adipogenesis through the ERK1/2 signaling pathway

BACKGROUND

Long non-coding RNAs (lncRNAs) regulate numerous biological processes, including adipogenesis. Research on adipogenesis will assist in the treatment of human metabolic diseases and improve meat quality in livestock, such as the content of intramuscular fat (IMF). However, the significance of lncRNAs in intramuscular adipogenesis remains unclear. This research aimed to reveal the lncRNAs transcriptomic profiles in the process of bovine intramuscular adipogenesis and to identify the lncRNAs involved in the adipogenesis of bovine intramuscular adipocytes.

RESULTS

In this research, a landscape of lncRNAs was identified with RNA-seq in bovine intramuscular adipocytes at four adipogenesis stages (0 d, 3 d, 6 d, and 9 d after differentiation). A total of 7035 lncRNAs were detected, including 3396 novel lncRNAs. Based on the results of differential analysis, co-expression analysis, and functional prediction, we focused on the bovine intramuscular adipogenesis-associated long non-coding RNA (BIANCR), a novel lncRNA that may have an important regulatory function. The knockdown of BIANCR inhibited proliferation and promoted apoptosis of intramuscular preadipocytes. Moreover, BIANCR knockdown inhibited intramuscular adipogenesis by regulating the ERK1/2 signaling pathway.

CONCLUSION

This study obtained the landscape of lncRNAs during adipogenesis in bovine intramuscular adipocytes. BIANCR plays a crucial role in adipogenesis through the ERK1/2 signaling pathway. The results are noteworthy for improving beef meat quality, molecular breeding, and metabolic disease research.

Identification of candidate genes related to highland adaptation from multiple Chinese local chicken breeds by whole genome sequencing analysis

Understanding the genetic mechanism of highland adaptation is of great importance for breeding improvement of Tibetan chickens (TBC). Some studies of TBC have identified some candidate genes and pathways from multiple subgroups, but the related genetic mechanisms remain largely unknown. Different genetic backgrounds and the independent genetic basis of highland adaptation make it difficult to identity the selective region of highland adaptation with all TBC samples. In this study, we conducted pre-analysis in a large-scale population to select a TBC subgroup with the purest and highest level of highland-specific lineage for the further analysis. Finally, the 37 samples from a TBC subgroup and 19 Lahsa White chickens were used to represent the highland group for further analysis with 80 samples from five Chinese local lowland breeds as controls. Population structure analysis revealed that highland adaptation significantly affected population stratification in Chinese local chicken breeds. Genome-wide selection signal analysis identified 201 candidate genes associated with highland adaptation of TBC, and these genes were significantly enriched in calcium signaling, vascular smooth muscle contraction and the cellular response to oxidative stress pathways. Additionally, we identified a narrow 1.76 kb region containing an overlapping region between HBZ and an active enhancer, and our identified region showed a highly significant signal. The highland group selected the haplotype with high activity to improve the oxygen-carrying capacity, thus being adapted to a hypoxic environment. We also found that STX2 was significantly selected in the highland group, thus potentially reducing the oxidative stress caused by hypoxia, and that STX2 exhibited the opposite effects on highland adaptation and reproductive traits. Our findings advance our understanding of extreme environment adaptation of highland chickens, and provide some variants and genes beneficial to TBC genetic breeding improvement.

Exploration of microRNA-106b-5p as a therapeutic target in intervertebral disc degeneration: a preclinical study

MicroRNA (miRNA) has emerge as a vital regulator in the pathogenesis of intervertebral disc degeneration (IDD). However, miR-106b-5p expression in the human nucleus pulposus (NP) and potential mechanisms remain to be elucidated. In this study, the aim was to verify the potential therapeutic mechanisms of miR-106b-5p for IDD. Key miRNAs were screened for in degenerative and normal human intervertebral disc samples. qRT-PCR and fluorescence in situ hybridization (FISH) were used to verify the miR-106b-5p differential expression. The targeting link between miR-106b-5p and Sirtuin 2 (SIRT2) was identified using the luciferase reporter assay and bioinformatics. Flow cytometry, EdU method, and cell scratching were all performed to determine the NP cell function and IDD models were constructed for in vivo experiments. SIRT2, MMP13, ADAMTS5, Col II, Aggrecan, Ras, ERK1/2, and p-ERK1/2 protein levels were assayed by western blotting. Overexpression of miR-106b-5p in NP cells decreased cell growth, induced apoptosis, hindered extracellular matrix formation, and increased the expression of matrix-degrading enzymes through the SIRT2/MAPK/ERK signaling pathway. Importantly, intradiscal delivery of antagomiR-106b-5p significantly attenuated IDD development. Our findings demonstrate that targeting miR-106b-5p in intervertebral disc has therapeutic effects on IDD.

Spatial multi-omics revealed the impact of tumor ecosystem heterogeneity on immunotherapy efficacy in patients with advanced non-small cell lung cancer treated with bispecific antibody

BACKGROUND

Immunotherapy for malignant tumors has made great progress, but many patients do not benefit from it. The complex intratumoral heterogeneity (ITH) hindered the in-depth exploration of immunotherapy. Conventional bulk sequencing has masked intratumor complexity, preventing a more detailed discovery of the impact of ITH on treatment efficacy. Hence, we initiated this study to explore ITH at the multi-omics spatial level and to seek prognostic biomarkers of immunotherapy efficacy considering the presence of ITH.

METHODS

Using the segmentation strategy of digital spatial profiling (DSP), we obtained differential information on tumor and stromal regions at the proteomic and transcriptomic levels. Based on the consideration of ITH, signatures constructed by candidate proteins in different regions were used to predict the efficacy of immunotherapy.

RESULTS

Eighteen patients treated with a bispecific antibody (bsAb)-KN046 were enrolled in this study. The tumor and stromal areas of the same samples exhibited distinct features. Signatures consisting of 11 and 18 differentially expressed DSP markers from the tumor and stromal areas, respectively, were associated with treatment response. Furthermore, the spatially resolved signature identified from the stromal areas showed greater predictive power for bsAb immunotherapy response (area under the curve=0.838). Subsequently, our stromal signature was validated in an independent cohort of patients with non-small cell lung cancer undergoing immunotherapy.

CONCLUSION

We deciphered ITH at the spatial level and demonstrated for the first time that genetic information in the stromal region can better predict the efficacy of bsAb treatment.

TRIAL REGISTRATION NUMBER

NCT03838848.

Electroacupuncture ameliorates surgery-induced spatial memory deficits by promoting mitophagy in rats

Background

This study sought to explore the mechanism underlying the therapeutic effects of electroacupuncture (EA) on spatial memory deficits caused by surgery.

Methods

Hepatic apex resection was performed under propofol-based total intravenous anesthesia. Male Sprague-Dawley rats were subjected to EA treatment or EA + mitochondrial division inhibitor-1 (mdivi-1) treatment once a day for three consecutive days after surgery. The Morris water maze test was used to evaluate the spatial memory of the rats after surgery. Tissue from the hippocampus of each rat was frozen and used for transcriptomic and proteomic analyses to identify potential targets for EA treatment. Western blotting was used to confirm the protein expression levels. The levels of reactive oxygen species (ROS) and adenosine triphosphate (ATP) were detected using commercial kits. The rat mitochondria were then isolated, and the activity of mitochondrial complex V was assessed.

Results

EA attenuated surgery-induced spatial memory deficits on postoperative day 3, while these effects were reversed by treatment with the mdivi-1 (P<0.05). Ribonucleic acid (RNA)-sequencing revealed that EA upregulated multiple metabolic pathways and the phosphatidylinositol 3‑kinas/protein kinase B signaling pathway. The proteomic and western blotting results suggested that the EA treatment substantially downregulated coiled-coil-helix-coiled-coil-helix domain containing 3 (ChChd3) expression in the hippocampus. The EA treatment significantly increased the autophagy-related protein levels, including phosphatase and tensin homolog-induced kinase 1, Parkin, MAP1LC3 (LC3), and Beclin1, and inhibited the production of ROS and inflammatory cytokine interleukin-1β in the hippocampus (P<0.05).

Conclusions

These results suggest that EA ameliorates postoperative spatial memory deficits and protects hippocampus from oxidative stress and inflammation through enhanced autophagy in an animal model of perioperative neurocognitive disorders (PNDs).

Genome-wide study and functional characterization elucidates the potential association of late embryogenesis abundant (LEA) genes with lotus seed development

Late embryogenesis abundant (LEA) proteins are extremely hydrophilic proteins imperatively associated with plant growth and development, as well as cell protection from abiotic stress. However, the genome-wide characterization of LEA gene family remains limited, especially in aquatic species such as lotus (Nelumbo spp.). Here, 57 putative LEA genes, including 28 NnLEAs and 29 NlLEAs were identified in the N.nucifera and N.lutea genomes, respectively. A total of 27 homologous LEA gene pairs were identified, indicating high degree of sequence homologies between the two Nelumbo species. Secondary structure prediction indicated high prevalence of alpha (α) helix structure among LEA proteins in the LEA_1, LEA_4, and SMP groups. Screening of putative promoter cis-elements revealed that NnLEA genes were involved in diverse biological processes. Most NnLEA genes were predominantly expressed in the late cotyledons and plumules development stages, suggesting their potential vital roles in lotus seed maturation. In addition, genes co-expressed with NnLEAs were involved in ABA signaling, seed maturation, and development processes. Overall, this study provides new insights for the in-depth understanding of the functions of NnLEA proteins in lotus seed development, and could act as a useful reference for the molecular breeding of seeds with prolonged lifespan.

Whole-transcriptome profiling across different developmental stages of Aedes albopictus (Diptera: Culicidae) provides insights into chitin-related non-coding RNA and competing endogenous RNA networks

BACKGROUND

The Asian tiger mosquito, Aedes albopictus, is one of the most invasive species and a vector of numerous arboviruses. The deleterious effects of long-term and inappropriate use of chemical pesticides have stimulated the exploration of new, environmentally friendly control strategies. Non-coding RNAs (ncRNAs) have been proven to participate in almost all biological processes of insects.

METHODS

In this study, circular RNAs (circRNAs) and microRNAs (miRNAs) covering five developmental stages [egg, early larvae, late larvae, pupae, adult (female and male)] of A. albopictus were obtained using whole-transcriptome sequencing technology. Combined with long non-coding RNAs (lncRNAs) from previous research, circRNA/lncRNA‒miRNA‒mitochondrial RNA (mRNA) networks were constructed.

RESULTS

A total of 1434 circRNAs and 208 miRNAs were identified. More differentially expressed circRNAs (DE circRNAs) and miRNAs (DE miRNAs) were found in the egg versus early larvae comparison group. Functional enrichment analysis demonstrated that most of the circRNA/lncRNA‒miRNA‒mRNA networks were involved in chitin metabolism. Hub genes of each circRNA/lncRNA‒miRNA‒mRNA network were screened out, which can be used as novel targets to disturb the molting process of A. albopictus.

CONCLUSIONS

Regulatory relationships obtained from competing endogenous RNA (ceRNA) networks provide more information to manipulate the metamorphosis process and are helpful for developing effective and sustainable methods to control mosquitoes.

Whole-exome sequencing identified recurrent and novel variants in benzene-induced leukemia

BACKGROUND

Genome-wide sequencing may extensively identify potential pathogenic variants, which helps to understand mechanisms of tumorigenesis, but such study has not been reported in benzene-induced leukemia (BIL).

METHODS

We recruited 10 BIL patients and conducted the whole-exome sequencing on their peripheral blood samples. The obtained sequencing data were screened for potential pathogenic and novel variants, then the variants-located genes were clustered to identify cancer-related pathways. Shared or recurrent variants among the BIL cases were also identified and evaluated for their potential functional impact.

RESULTS

We identified 48,802 variants in exons in total, 97.3% of which were single nucleotide variants. After filtering out variants with minor allele frequency ≥ 1%, we obtained 8667 potentially pathogenic variants, of which 174 were shared by all the BIL cases. The identified variants located in genes that could be significantly enriched into certain cancer-related pathways such as PI3K-AKT signaling pathway and Ras signaling pathway. We also identified 1010 novel variants with no record in the Genome Aggregation Database and in dbSNP, and one of them was shared by 90% cases. The recurrent and novel variant caused a missense mutation in SESN3.

CONCLUSIONS

We examined variations of the whole exome in BIL patients for the first time. The commonly shared variants implied a relation with BIL, and the recurrent and novel variant might be specifically related to BIL. The related variants may help unravel the carcinogenic mechanisms of BIL.

The Chromosome-Level Genome of Hestina assimilis (Lepidoptera: Nymphalidae) Reveals the Evolution of Saprophagy-Related Genes in Brush-Footed Butterflies

Most butterflies feed on nectar, while some saprophagous butterflies forage on various non-nectar foods. To date, little is known about the genomic and molecular shifts associated with the evolution of the saprophagous feeding strategy. Here, we assembled the high-quality chromosome-level genome of Hestina assimilis to explore its saprophagous molecular and genetic mechanisms. This chromosome-level genome of H. assimilis is 412.82 Mb, with a scaffold N50 of 15.70 Mb. In total, 98.11% of contigs were anchored to 30 chromosomes. Compared with H. assimilis and other Nymphalidae butterflies, the genes of metabolism and detoxification experienced expansions. We annotated 80 cytochrome P450 (CYP) genes in the H. assimilis genome, among which genes belonging to the CYP4 subfamily were significantly expanded (p < 0.01). These P450 genes were unevenly distributed and mainly concentrated on chromosomes 6-9. We identified 33 olfactory receptor (OR), 20 odorant-binding protein (OBP), and six gustatory receptor (GR) genes in the H. assimilis genome, which were fewer than in the nectarivorous Danaus plexippus. A decreased number of OBP, OR, and GR genes implied that H. assimilis should resort less to olfaction and gustation than their nectarivorous counterparts, which need highly specialized olfactory and gustatory functions. Moreover, we found one site under positive selection occurred in residue 996 (phenylalanine) of GR genes exclusive to H. assimilis, which is conservative in most lineages. Our study provides support for the adaptive evolution of feeding habits in butterflies.

Identification of PLATZ genes in Malus and expression characteristics of MdPLATZs in response to drought and ABA stresses

Plant AT-rich sequences and zinc-binding proteins (PLATZ) play crucial roles in response to environmental stresses. Nevertheless, PLATZ gene family has not been systemically studied in Rosaceae species, such as in apple, pear, peach, or strawberry. In this study, a total of 134 PLATZ proteins were identified from nine Rosaceae genomes and were classified into seven phylogenetic groups. Subsequently, the chromosomal localization, duplication, and collinearity relationship for apple PLATZ genes were investigated, and segmental duplication is a major driving-force in the expansion of PLATZ in Malus. Expression profiles analysis showed that PLATZs had distinct expression patterns in different tissues, and multiple genes were significantly changed after drought and ABA treatments. Furthermore, the co-expression network combined with RNA-seq data showed that PLATZ might be involved in drought stress by regulating ABA signaling pathway. In summary, this study is the first in-depth and systematic identification of PLATZ gene family in Rosaceae species, especially for apple, and provided specific PLATZ gene resource for further functional research in response to abiotic stress.

Transcriptomic and metabolic regulatory network characterization of drought responses in tobacco

Drought stress usually causes huge economic losses for tobacco industries. Drought stress exhibits multifaceted impacts on tobacco systems through inducing changes at different levels, such as physiological and chemical changes, changes of gene transcription and metabolic changes. Understanding how plants respond and adapt to drought stress helps generate engineered plants with enhanced drought resistance. In this study, we conducted multiple time point-related physiological, biochemical,transcriptomic and metabolic assays using K326 and its derived mutant 28 (M28) with contrasting drought tolerance. Through integrative analyses of transcriptome and metabolome,we observed dramatic changes of gene expression and metabolic profiles between M28 and K326 before and after drought treatment. we found that some of DEGs function as key enzymes responsible for ABA biosynthesis and metabolic pathway, thereby mitigating impairment of drought stress through ABA signaling dependent pathways. Four DEGs were involved in nitrogen metabolism, leading to synthesis of glutamate (Glu) starting from NO-3 /NO-2 that serves as an indicator for stress responses. Importantly, through regulatory network analyses, we detected several drought induced TFs that regulate expression of genes responsible for ABA biosynthesis through network, indicating direct and indirect involvement of TFs in drought responses in tobacco. Thus, our study sheds some mechanistic insights into how plant responding to drought stress through transcriptomic and metabolic changes in tobacco. It also provides some key TF or non-TF gene candidates for engineering manipulation for breeding new tobacco varieties with enhanced drought tolerance.

Genetic screening of MMP1 as a potential pathogenic gene in chronic obstructive pulmonary disease

BACKGROUND

Chronic obstructive pulmonary disease (COPD) is a complex and heterogeneous syndrome. Airway inflammation and remodeling are the two key processes involved in COPD pathogenesis. However, the key pathogenic genes driving COPD development have not been revealed. This study aims to identify and validate hub gene(s) underlying COPD development through bioinformatics analysis and experimental validation.

METHODS

Three lung tissue sequencing datasets of the COPD (including GSE38974, GSE103174, and GSE106986) were analyzed. Further, differentially expressed genes (DEGs) were used to compare patients with COPD with non-COPD individuals, and the Robust Rank Aggregation (RRA) analysis was also performed. Results revealed a series of potential pathogenic genes of COPD. DEGs were subjected to KEGG, GO, and GSEA analyses. The scRNA dataset of human lung tissues (Human Lung Cell Atlas), and human primary airway epithelial cells (GSE134147) were used to identify the cell subtype localization. The qRT-PCR assay was performed in the human lung tissues, COPD mice model, and primary bronchial epithelial cells at the air-liquid interface (ALI) under cigarette smoke extract (CSE) stimulation to verify the expression of the hub genes. LASSO and GLM analysis with the hub genes were performed to identify the most critical gene. RNA-seq was performed after knocking down the critical gene using siRNA in HBECs at ALI. The potential role of the critical gene was confirmed through qRT-PCR, Western blot, and Immunofluorescence (IF) assays.

RESULTS

A total of 98 genes were significantly and differently expressed in 3 GEO datasets. The KEGG and GO analyses showed that most of these genes are responsible for inflammation, immunity, and cell proliferation. The core gene set including 15 genes was screened out and consequently, the MMP1 was the most likely responsible for the progression of COPD. Moreover, we confirmed that MMP1 is significantly related to inflammatory effects and cilia function in human bronchial epithelial cells cultured at the air-liquid interface (ALI).

CONCLUSION

In summary, we confirmed that inflammation and cell proliferation are potentially critical processes in COPD occurrence and development. A total of 15 potential hub genes were identified among which MMP1 was the most likely gene responsible for the development of COPD. Therefore, MMP1 is a potential molecular target of COPD therapy.

A Cocktail of Polyherbal Bioactive Compounds and Regular Mobility Training as Senolytic Approaches in Age-dependent Alzheimer's: the In Silico Analysis, Lifestyle Intervention in Old Age

Alzheimer's is a principal concern globally. Machine learning is a valuable tool to determine protective and diagnostic approaches for the elderly. We analyzed microarray datasets of Alzheimer's cases based on artificial intelligence by R statistical software. This study provided a screened pool of ncRNAs and coding RNAs related to Alzheimer's development. We designed hub genes as cut points in networks and predicted potential microRNAs and LncRNA to regulate protein networks in aging and Alzheimer's through in silico algorithms. Notably, we collected effective traditional herbal medicines. A list of bioactive compounds prepared including capsaicin, piperine, crocetin, safranal, saffron oil, coumarin, thujone, rosmarinic acid, sabinene, thymoquinone, ascorbic acid, vitamin E, cyanidin, rhaponticin, isovitexin, coumarin, nobiletin, evodiamine, gingerol, curcumin, quercetin, fisetin, and allicin as an effective fusion that potentially modulates hub proteins and molecular signaling pathways based on pharmacophore model screening and chemoinformatics survey. We identified profiles of 21 mRNAs, 272 microRNAs, and eight LncRNA in Alzheimer's based on prediction algorithms. We suggested a fusion of senolytic herbal ligands as an alternative therapy and preventive formulation in dementia. Also, we provided ncRNAs expression status as novel monitoring strategies in Alzheimer's and new cut-point proteins as novel therapeutic approaches. Synchronizing fusion drugs and lifestyle could reverse Alzheimer's hallmarks to amelioration via an offset of the signaling pathways, leading to increased life quality in the elderly.

Integrative Proteomic and Phosphoproteomic Analyses Revealed the Regulatory Mechanism of the Response to Ultraviolet B Stress in Clematis terniflora DC

Clematis terniflora DC. (C. terniflora) has been used as an ancient Chinese traditional herbal medicine. The active substances in C. terniflora have been confirmed to be effective in treating diseases such as prostatitis. UV light radiation is a common environmental factor that damages plants and influences primary and secondary metabolism. Previous studies showed that ultraviolet B (UV-B) radiation followed by dark stress resulted in the accumulation of secondary metabolites in C. terniflora leaves. An in-depth understanding of how C. terniflora leaves respond to UV-B stress is crucial for improving C. terniflora value. Here, we conducted label-free proteomic and phosphoproteomic analyses to explore the protein changes under UV-B and UV-B combined with dark treatment. A total of 2839 proteins and 1638 phosphorylated proteins were identified. Integrative omics revealed that the photosynthetic system and carbohydrate balance were modulated under both stresses. The phosphoproteomic data indicated that the mitogen-activated protein kinase signaling pathway was triggered, while the abundance of phosphorylated proteins related to osmotic stress was increased under UV-B stress. Differentially abundant phosphoproteins from UV-B followed by dark treatment were mainly enriched in response to stimulus including calcium-mediated proteins. This study provides new insight into the impact of UV-B stress on C. terniflora and plant molecular resistance mechanisms through proteomic and phosphoproteomic analyses.

Transcriptome-wide characterization of bHLH transcription factor genes in Lycoris radiata and functional analysis of their response to MeJA

As one of the biggest plant specific transcription factor (TF) families, basic helix-loop-helix (bHLH) protein, plays significant roles in plant growth, development, and abiotic stress responses. However, there has been minimal research about the effects of methyl jasmonate (MeJA) treatment on the bHLH gene family in Lycoris radiata (L'Her.) Herb. In this study, based on transcriptome sequencing data, 50 putative L. radiata bHLH (LrbHLH) genes with complete open reading frames (ORFs), which were divided into 20 bHLH subfamilies, were identified. The protein motif analyses showed that a total of 10 conserved motifs were found in LrbHLH proteins and motif 1 and motif 2 were the most highly conserved motifs. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of LrbHLH genes revealed their involvement in regulation of plant growth, jasmonic acid (JA) mediated signaling pathway, photoperiodism, and flowering. Furthermore, subcellular localization revealed that most LrbHLHs were located in the nucleus. Expression pattern analysis of LrbHLH genes in different tissues and at flower developmental stages suggested that their expression differed across lineages and might be important for plant growth and organ development in Lycoris. In addition, all LrbHLH genes exhibited specific spatial and temporal expression patterns under MeJA treatment. Moreover, protein-protein interaction (PPI) network analysis and yeast two-hybrid assay showed that numerous LrbHLHs could interact with jasmonate ZIM (zinc-finger inflorescence meristem) domain (JAZ) proteins. This research provides a theoretical basis for further investigation of LrbHLHs to find their functions and insights for their regulatory mechanisms involved in JA signaling pathway.

Comprehensive Analysis of the lncRNA-miRNA-mRNA Regulatory Network for Intramuscular Fat in Pigs

Intramuscular fat (IMF) is an essential trait closely related to meat quality. The IMF trait is a complex quantitative trait that is regulated by multiple genes. In order to better understand the process of IMF and explore the key factors affecting IMF deposition, we identified differentially expressed mRNA, miRNA, and lncRNA in the longissimus dorsi muscle (LD) between Songliao Black (SL) pigs and Landrace pigs. We obtained 606 differentially expressed genes (DEGs), 55 differentially expressed miRNAs (DEMs), and 30 differentially expressed lncRNAs (DELs) between the SL pig and Landrace pig. Enrichment results from GO and KEGG indicate that DEGs are involved in fatty acid metabolism and some pathways related to glycogen synthesis. We constructed an lncRNA-miRNA-mRNA interaction network with 18 DELs, 11 DEMs, and 42 DEGs. Finally, the research suggests that ARID5B, CPT1B, ACSL1, LPIN1, HSP90AA1, IRS1, IRS2, PIK3CA, PIK3CB, and PLIN2 may be the key genes affecting IMF deposition. The LncRNAs MSTRG.19948.1, MSTRG.13120.1, MSTRG.20210.1, and MSTRG.10023.1, and the miRNAs ssc-miRNA-429 and ssc-miRNA-7-1, may play a regulatory role in IMF deposition through their respective target genes. Our research provides a reference for further understanding the regulatory mechanism of IMF.

Evaluating the Genetic Effects of Gut Microbiota on the Development of Neuroticism and General Happiness: A Polygenic Score Analysis and Interaction Study Using UK Biobank Data

Limited efforts have been invested in exploring the interaction effects between genetic factors and gut microbiota on neuroticism and general happiness. The polygenic risk scores (PRS) of gut microbiota were calculated from individual-level genotype data of the UK Biobank cohort. Linear regression models were then used to assess the associations between individual PRS of gut microbiota and mental traits and interaction analysis was performed by PLINK2.0. KOBAS-i was used to conduct gene ontology (GO) enrichment analysis of the identified genes. We observed suggestive significant associations between neuroticism and PRS for the genus Bifidobacterium (rank-normal transformation, RNT) (beta = -1.10, P = 4.16 × 10-3) and the genus Desulfovibrio (RNT) (beta = 0.54, P = 7.46 × 10-3). PRS for the genus Bifidobacterium (hurdle binary, HB) (beta = 1.99, P = 5.24 × 10-3) and the genus Clostridium (RNT) (beta = 1.26, P = 9.27 × 10-3) were found to be suggestive positively associated with general happiness. Interaction analysis identified several significant genes that interacted with gut microbiota, such as RORA (rs575949009, beta = -45.00, P = 1.82 × 10-9) for neuroticism and ASTN2 (rs36005728, beta = 19.15, P = 3.37 × 10-8) for general happiness. Our study results support the genetic effects of gut microbiota on the development of neuroticism and general happiness.

Convergent Genomic Signatures of Cashmere Traits: Evidence for Natural and Artificial Selection

Convergent evolution provides powerful opportunities to investigate the genetic basis of complex traits. The Tibetan antelope (Pantholops hodgsonii) and Siberian ibex (Capra sibirica) belong to different subfamilies in Bovidae, but both have evolved similar superfine cashmere characteristics to meet the cold temperature in plateau environments. The cashmere traits of cashmere goats underwent strong artificial selection, and some traces of domestication also remained in the genome. Hence, we investigated the convergent genomic signatures of cashmere traits between natural and artificial selection. We compared the patterns of convergent molecular evolution between Tibetan antelope and Siberian ibex by testing positively selected genes, rapidly evolving genes and convergent amino acid substitutions. In addition, we analyzed the selected genomic features of cashmere goats under artificial selection using whole-genome resequencing data, and skin transcriptome data of cashmere goats were also used to focus on the genes involved in regulating cashmere traits. We found that molecular convergent events were very rare, but natural and artificial selection genes were convergent enriched in similar functional pathways (e.g., ECM-receptor interaction, focal adhesion, PI3K-Akt signaling pathway) in a variety of gene sets. Type IV collagen family genes (COL4A2, COL4A4, COL4A5, COL6A5, COL6A6) and integrin family genes (ITGA2, ITGA4, ITGA9, ITGB8) may be important candidate genes for cashmere formation and development. Our results provide a comprehensive approach and perspective for exploring cashmere traits and offer a valuable reference for subsequent in-depth research on the molecular mechanisms regulating cashmere development and fineness.

MAEL gene contributes to bovine testicular development through the m5C-mediated splicing

Knowledge of RNA molecules regulating testicular development and spermatogenesis in bulls is essential for elite bull selection and an ideal breeding program. Herein, we performed direct RNA sequencing (DRS) to explore the functional characterization of RNA molecules produced in the testicles of 9 healthy Simmental bulls at three testicular development stages (prepuberty, puberty, and postpuberty). We identified 5,043 differentially expressed genes associated with testicular weight. These genes exhibited more alternative splicing at sexual maturity, particularly alternative 3' (A3) and 5' (A5) splice sites usage and exon skipping (SE). The expression of hub genes in testicular developmental stages was also affected by both m6A and m5C RNA modifications. We found m5C-mediated splicing events significantly (p < 0.05) increased MAEL gene expression at the isoform level, likely promoting spermatogenesis. Our findings highlight the complexity of RNA processing and expression as well as the regulation of transcripts involved in testicular development and spermatogenesis.

Comparative transcriptome analysis of skin color-associated genes in leopard coral grouper (Plectropomus leopardus)

BACKGROUND

The leopard coral grouper (Plectropomus leopardus) is an important economic species in East Asia-Pacific countries. To meet the market demand, leopard coral grouper is facing overfishing and their population is rapidly declining. With the improvement of the artificial propagation technique, the leopard coral grouper has been successfully cultured by Fisheries Research Institute in Taiwan. However, the skin color of farmed individuals is often lacking bright redness. As such, the market price of farmed individuals is lower than wild-type.

RESULTS

To understand the genetic mechanisms of skin coloration in leopard coral grouper, we compared leopard coral grouper with different skin colors through transcriptome analysis. Six cDNA libraries generated from wild-caught leopard coral grouper with different skin colors were characterized by using the Illumina platform. Reference-guided de novo transcriptome data of leopard coral grouper obtained 24,700 transcripts, and 1,089 differentially expressed genes (DEGs) were found between red and brown skin color individuals. The results showed that nine candidate DEGs (epha2, sema6d, acsl4, slc7a5, hipk1, nol6, timp2, slc25a42, and kdf1) significantly associated with skin color were detected by using comparative transcriptome analysis and quantitative real-time polymerase chain reaction (qRT-PCR).

CONCLUSIONS

The findings may provide genetic information for further skin color research, and to boost the market price of farmed leopard coral grouper by selective breeding.

Modification and Expression of mRNA m6A in the Lateral Habenular of Rats after Long-Term Exposure to Blue Light during the Sleep Period

Artificial lighting, especially blue light, is becoming a public-health risk. Excessive exposure to blue light at night has been reported to be associated with brain diseases. However, the mechanisms underlying neuropathy induced by blue light remain unclear. An early anatomical tracing study described the projection of the retina to the lateral habenula (LHb), whereas more mechanistic reports are available on multiple brain functions and neuropsychiatric disorders in the LHb, which are rarely seen in epigenetic studies, particularly N6-methyladenosine (m6A). The purpose of our study was to first expose Sprague-Dawley rats to blue light (6.11 ± 0.05 mW/cm2, the same irradiance as 200 lx of white light in the control group) for 4 h, and simultaneously provide white light to the control group for the same time to enter a sleep period. The experiment was conducted over 12 weeks. RNA m6A modifications and different mRNA transcriptome profiles were observed in the LHb. We refer to this experimental group as BLS. High-throughput MeRIP-seq and mRNA-seq were performed, and we used bioinformatics to analyze the data. There were 188 genes in the LHb that overlapped between differentially m6A-modified mRNA and differentially expressed mRNA. The Kyoto Encyclopedia of Genes and Genomes and gene ontology analysis were used to enrich neuroactive ligand-receptor interaction, long-term depression, the cyclic guanosine monophosphate-dependent protein kinase G (cGMP-PKG) signaling pathway, and circadian entrainment. The m6A methylation level of the target genes in the BLS group was disordered. In conclusion, this study suggests that the mRNA expression and their m6A of the LHb were abnormal after blue light exposure during the sleep period, and the methylation levels of target genes related to synaptic plasticity were disturbed. This study offers a theoretical basis for the scientific use of light.

The selected genes NR6A1, RSAD2-CMPK2, and COL3A1 contribute to body size variation in Meishan pigs through different patterns

The high-fertility Meishan pig is currently categorized into medium sized (MMS) and small sized (SMS) based on body size. To identify causal genes responsible for the variation in body size within the two categories, we sequenced individuals representing the entire consanguinity of the existing Meishan pig. This enabled us to conduct genome selective signal analysis. Our findings revealed the genomes of MMS and SMS are stratified, with selective sweep regions formed by differential genomic intervals between the two categories enriched in multiple pig body size related quantitative trait loci (QTLs). Furthermore, the missense mutation c.575T > C of candidate causal gene NR6A1, accounting for the variation in lumbar vertebrae number in pigs, was positively selected in MMS only, leading to an increase in body length of MMS at 6 months of age. To precisely identify causal genes accounting for body size variation through multi-omics, we collected femoral cartilage and liver transcription data from MMS and SMS respectively, and re-sequencing data from pig breeds exhibiting varying body sizes. We found that two selected regions where the RSAD2-CMPK2 and COL3A1 genes are located, respectively, showed different haplotypes in pig breeds of varying body size, and was associated with body or carcass length in hybridized Suhuai pig. Additionally, the above three hub genes, were significantly greater expressed in SMS femoral cartilage and liver tissues compared to MMS. These three genes could strengthen the pathways related to bone resorption and metabolism in SMS, potentially hindering bone and skeletal development and resulting in a smaller body size in SMS. These findings provide valuable insights into the genetic mechanism of body size variation in Meishan pig population.

Neoadjuvant therapy with immune checkpoint blockade, antiangiogenesis, and chemotherapy for locally advanced gastric cancer

Despite neoadjuvant/conversion chemotherapy, the prognosis of cT4a/bN+ gastric cancer is poor. Immune checkpoint inhibitors (ICIs) and antiangiogenic agents have shown activity in late-stage gastric cancer, but their efficacy in the neoadjuvant/conversion setting is unclear. In this single-armed, phase II, exploratory trial (NCT03878472), we evaluate the efficacy of a combination of ICI (camrelizumab), antiangiogenesis (apatinib), and chemotherapy (S-1 ± oxaliplatin) for neoadjuvant/conversion treatment of cT4a/bN+ gastric cancer. The primary endpoints are pathological responses and their potential biomarkers. Secondary endpoints include safety, objective response, progression-free survival, and overall survival. Complete and major pathological response rates are 15.8% and 26.3%. Pathological responses correlate significantly with microsatellite instability status, PD-L1 expression, and tumor mutational burden. In addition, multi-omics examination reveals several putative biomarkers for pathological responses, including RREB1 and SSPO mutation, immune-related signatures, and a peripheral T cell expansion score. Multi-omics also demonstrates dynamic changes in dominant tumor subclones, immune microenvironments, and T cell receptor repertoires during neoadjuvant immunotherapy. The toxicity and post-surgery complications are limited. These data support further validation of ICI- and antiangiogenesis-based neoadjuvant/conversion therapy in large randomized trials and provide candidate biomarkers.

Integrating sperm cell transcriptome and seminal plasma metabolome to analyze the molecular regulatory mechanism of sperm motility in Holstein stud bulls

Considering that artificial insemination is the most widely used assisted reproductive technique in the dairy industry, the semen quality of bulls is very important for selecting excellent stud bulls. Sperm motility is one of the important traits of semen quality, and related genes may be regulated by environmental factors. Seminal plasma can affect sperm cell transcriptome and further affect sperm motility through exosome or other processes. However, the molecular regulation mechanism of bull sperm motility has not been studied by combining the sperm cell transcriptome with seminal plasma metabolome. The number of motile sperm per ejaculate (NMSPE) is an integrated indicator for assessing sperm motility in stud bulls. In the present study, we selected 7 bulls with higher NMSPE (5,698.55 million +/- 945.40 million) as group H and 7 bulls with lower NMSPE (2,279.76 million +/- 1,305.69 million) as group L from 53 Holstein stud bulls. The differentially expressed genes (DEGs) in sperm cells were evaluated between the two groups (H vs. L). We conducted gene co-expression network analysis (WGCNA) on H and L groups of bulls, as well as two monozygotic twin Holstein bulls with different NMSPE values, to screen candidate genes for NMSPE. The regulatory effect of seminal plasma metabolome on the candidate genes of NMSPE was also investigated. A total of 1,099 DEGs were identified in the sperm cells of H and L groups. These DEGs were primarily concentrated in energy metabolism and sperm cell transcription. The significantly enriched Kyoto encyclopedia of genes and genomes (KEGG) pathways of the 57 differential metabolites were the aminoacyl-tRNA biosynthesis pathway and vitamin B6 metabolism pathway. Our study discovered 14 genes as the potential candidate markers for sperm motility, including FBXO39. We observed a broad correlation between transcriptome of sperm cells and seminal plasma metabolome, such as three metabolites, namely, mesaconic acid, 2-coumaric acid, and 4-formylaminoantipyrine, might regulate FBXO39 expression through potential pathways. The genes related to seminal plasma metabolites expressed in sperm cells are not only located near the quantitative trait loci of reproductive traits, but also enriched in the genome-wide association study signal of sire conception rate. Collectively, this study was the first to investigate the interplays among transcriptome of sperm cells and seminal plasma metabolome from Holstein stud bulls with different sperm motility.

Whole-genome resequencing reveals the genomic diversity and signatures of selection in Romanov sheep

Romanov sheep are adapted to the extremely cold and harsh environment and display a distinctive grey color. Herein, we analyzed the population structure, genetic diversity, and selection signatures of Romanov sheep based on whole-genome sequencing data of 17 Romanov sheep, 114 individuals from other 10 European breeds. The results of PCA, ADMIXTURE, and NJ-tree showed that the Romanov sheep was closely related to other northern European breeds. A relative high level of genetic diversity, low inbreeding coefficient, and large effective population size was observed in Romanov sheep when compared with other European breeds. We then screened the genomic selection signatures of Romanov sheep using FST, XP-XLP, and XP-EHH methods. The most significant region under selection (CHR14:14.2 to 14.3 Mb) harbored a haplotype that contained MC1R gene. Furthermore, this haplotype was also found in other grey-body breeds including Gotland sheep, Grey Tronder Sheep, and German grey heath sheep, suggesting that it was associated with the unique coat color of these breeds. We also found one region (CHR10:40.8Mb- 41.0Mb) harboring PCDH9 gene which was potentially associated with cold environmental adaptation. In summary, this study identified candidate genes that were associated with the unique grey color and environmental adaptation in Romanov sheep, which provided a basis for understanding the genetic background and utilization of this breed.

Emerging polyfluorinated compound Nafion by-product 2 disturbs intestinal homeostasis in zebrafish (Danio rerio)

Nafion by-product 2 (Nafion BP2), an emerging fluorinated sulfonic acid commonly used in polymer electrolyte membrane technologies, has been detected in various environmental and human matrices. To date, however, few studies have explored its toxicity. In this study, zebrafish embryos were exposed to Nafion BP2 at concentrations of 20, 40, 60, 80, 100, 120, 140, and 160 mg/L from fertilization to 120 post-fertilization (hpf), and multiple developmental parameters (survival rate, hatching rate, and malformation rate) were then determined. Results showed that Nafion BP2 exposure led to a significant decrease in survival and hatching rates and an increase in malformations. The half maximal effective concentration (EC₅₀) of Nafion BP2 for malformation at 120 hpf was 55 mg/L, which is higher than the globally important contaminant perfluorooctane sulfonate (PFOS, 6 mg/L). Furthermore, exposure to Nafion BP2 resulted in additional types of malformations compared to PFOS exposure. Pathologically, Nafion BP2 caused abnormal early foregut development, with exfoliation of intestinal mucosa, damage to lamina propria, and aberrant proliferation of lamina propria cells. Nitric oxide content also decreased markedly. In addition, embryos showed an inflammatory response following Nafion BP2 exposure, with significantly increased levels of pro-inflammatory factors C4 and IL-6. Acidic mucin in the hindgut increased more than two-fold. 16 S rRNA sequencing revealed a marked increase in the pathogen Pseudomonas otitidis. Furthermore, pathways involved in intestinal protein digestion and absorption, inflammatory response, and immune response were significantly altered. Our findings suggest that the intestine is a crucial toxicity target of Nafion BP2 in zebrafish, thus highlighting the need to evaluate its health risks.

Comparative functional analysis of macrophage phagocytosis in Dagu chickens and Wenchang chickens

Phagocytosis of macrophages constitutes a powerful barrier to innate immunity. Differences in the phagocytic function of macrophages among chicken breeds have rarely been reported, and the molecular mechanisms underlying phagocytosis remain poorly understood. This study compared functional difference of macrophages in Dagu chickens, originated in Zhuanghe, Liaoning Province, China, and Wenchang chickens, originated from Hainan Island in the South China Sea, and explored the potential molecular mechanisms by integrated analysis of mRNA expression profiles of macrophages and whole genome sequencing. Immunological parameters in peripheral blood indicated that Dagu chickens were more resistant to Salmonella challenge at 28 days old. Phagocytosis index and phagocytosis rate of macrophages displayed Dagu chickens performed a significantly higher phagocytic ability of macrophages at 14 and 28 days old. Furthermore, comparative analysis of mRNA expression profiles of macrophages of two breeds at 28 days old revealed that 1136 differentially expressed genes (DEGs), and 22 DEGs (e.g., H2AFZ, SNRPA1, CUEDC2, S100A12) were found to be hub genes regulating phagocytosis by participating in different immunological biological signaling pathways. In addition, many DEGs and hub genes were under strong differentiation in genome between two breeds, the H2AFZ gene was an intersection of DEGs and hub genes. These results provided a comprehensive functional comparison and transcriptomic profiles of macrophages in Chinese native chicken breeds, and deepened our understanding of the genetic mechanism of innate immunity.

Novel Biomarker Prediction for Lung Cancer Using Random Forest Classifiers

Lung cancer is considered the most common and the deadliest cancer type. Lung cancer could be mainly of 2 types: small cell lung cancer and non-small cell lung cancer. Non-small cell lung cancer is affected by about 85% while small cell lung cancer is only about 14%. Over the last decade, functional genomics has arisen as a revolutionary tool for studying genetics and uncovering changes in gene expression. RNA-Seq has been applied to investigate the rare and novel transcripts that aid in discovering genetic changes that occur in tumours due to different lung cancers. Although RNA-Seq helps to understand and characterise the gene expression involved in lung cancer diagnostics, discovering the biomarkers remains a challenge. Usage of classification models helps uncover and classify the biomarkers based on gene expression levels over the different lung cancers. The current research concentrates on computing transcript statistics from gene transcript files with a normalised fold change of genes and identifying quantifiable differences in gene expression levels between the reference genome and lung cancer samples. The collected data is analysed, and machine learning models were developed to classify genes as causing NSCLC, causing SCLC, causing both or neither. An exploratory data analysis was performed to identify the probability distribution and principal features. Due to the limited number of features available, all of them were used in predicting the class. To address the imbalance in the dataset, an under-sampling algorithm Near Miss was carried out on the dataset. For classification, the research primarily focused on 4 supervised machine learning algorithms: Logistic Regression, KNN classifier, SVM classifier and Random Forest classifier and additionally, 2 ensemble algorithms were considered: XGboost and AdaBoost. Out of these, based on the weighted metrics considered, the Random Forest classifier showing 87% accuracy was considered to be the best performing algorithm and thus was used to predict the biomarkers causing NSCLC and SCLC. The imbalance and limited features in the dataset restrict any further improvement in the model's accuracy or precision. In our present study using the gene expression values (LogFC, P Value) as the feature sets in the Random Forest Classifier BRAF, KRAS, NRAS, EGFR is predicted to be the possible biomarkers causing NSCLC and ATF6, ATF3, PGDFA, PGDFD, PGDFC and PIP5K1C is predicted to be the possible biomarkers causing SCLC from the transcriptome analysis. It gave a precision of 91.3% and 91% recall after fine tuning. Some of the common biomarkers predicted for NSCLC and SCLC were CDK4, CDK6, BAK1, CDKN1A, DDB2.

Genome-wide association study for the primary feather color trait in a native Chinese duck

Background: To reveal candidate genes and the molecular genetic mechanism underlying primary feather color trait in ducks, a genome-wide association study (GWAS) for the primary feather color trait was performed based on the genotyping-by-sequencing (GBS) technology for a native Chinese female duck, Longyan Shan-ma ducks. Methods: Blood genomic DNA from 314 female Longyan Shan-ma duck were genotyped using GBS technology. A GWAS for the primary feather color trait with genome variations was performed using an univariate linear mixed model based on all SNPs in autosomes. Results: Seven genome-wide significant single nucleotide polymorphisms (SNPs, Bonferroni-adjusted p-value <8.03 × 10^-7) within the introns of the genes STARD9, ZNF106, SLC7A5, and BANP genes were associated with the primary feather color trait. Twenty-two genome-wide suggestive SNPs (Bonferroni-adjusted p-value <1.61 × 10^-5) of 17 genes (besides ZNF106 and SLC7A5) were also identified. Seven SNPs were located at one 0.22 Mb region (38.65-38.87 Mb) on chromosome 5, and six SNPs were located at one 0.31 Mb region (19.53-19.84 Mb) on chromosome 11. The functions of STARD9, SLC7A5, BANP, LOC101798015, and IPMK were involved pigmentation and follicle development, especially, STARD9 upregulated expression in black feather (haplotype-CCCC) bulb tissue compared with in pockmarked feather (haplotype-TGTT) bulb tissue, implicating these genes as candidate genes for primary feather color trait. Conclusion: The preliminarily findings suggested candidate genes and regions, and the genetic basis of primary feather color trait in a female duck.

Transcriptomic and metabolomic integration to assess the response of gilthead sea bream (Sparus aurata) exposed to the most used insect repellent: DEET

DEET is one of the most frequently detected insect repellents in the environment reaching concentrations of several μg L^-1 in surface water. There is scarce information available regarding its mode of action in non-target organisms. Here, we have used an integrated metabolomic and transcriptomic approach to elucidate the possible adverse effects of DEET exposure in the marine fish gilthead sea bream (Sparus aurata). Individuals were exposed at an environmentally relevant concentration of DEET (10 μg L^-1) for 22 days in a continuous flow-through system. Transcriptomic analysis revealed 250 differentially expressed genes in liver, while metabolomic analysis identified 190 differentially modulated features in liver and 98 in plasma. Multi-omic data integration and visualization allowed elucidation of the modes of action of DEET exposure, including: energy depletion through the disruption of carbohydrate and amino acids metabolisms, oxidative stress leading to DNA damage, lipid peroxidation, and damage to cell membrane and apoptosis. Activation of xenobiotic pathway as well as the inmune-inflammatory reaction was evidenced in the present work.

Analysis of Fat Graft Survival and Platelet-Rich Plasma Effects: The Transcriptomic Differences

INTRODUCTION

Fat graft survival has been studied numerously but has not gone beyond hypothetical solutions. The molecular changes in survival of standard fat grafts and enhanced survival by platelet-rich plasma (PRP) are compared in this study to reveal the etiology that causes the loss of fat grafts after transplantation.

MATERIALS AND METHODS

A New Zealand rabbit's inguinal fat pads were excised and divided into three groups: Sham, Control (C), and PRP. Each weighing 1 g, C and PRP fat were placed into the bilateral parascapular area of the rabbit. After 30 days, the remaining fat grafts were harvested and weighed (C = 0.7 g, PRP = 0.9 g). All three specimens were put into transcriptome analysis. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes Analysis were done to compare the genetic pathways between the specimens.

RESULTS

Transcriptome analysis showed similar differential expressions in Sham vs. PRP and Sham vs. C comparisons, indicating the dominance of the cellular immune response in both C and PRP specimens. C and PRP comparison resulted in inhibited migration and inflammation pathways in PRP.

CONCLUSION

Fat graft survival is more related to immune responses than any other physiological process. PRP enhances survival by attenuating cellular immune reactions.

Molecular characterization of sub-frontal recurrent medulloblastomas reveals potential clinical relevance

Background

Single recurrence in the sub-frontal region after cerebellar medulloblastoma (MB) resection is rare and the underlying molecular characteristics have not been specifically addressed.

Methods

We summarized two such cases in our center. All five samples were molecularly profiled for their genome and transcriptome signatures.

Results

The recurrent tumors displayed genomic and transcriptomic divergence. Pathway analysis of recurrent tumors showed functional convergence in metabolism, cancer, neuroactive ligand-receptor interaction, and PI3K-AKT signaling pathways. Notably, the sub-frontal recurrent tumors had a much higher proportion (50-86%) of acquired driver mutations than that reported in other recurrent locations. The acquired putative driver genes in the sub-frontal recurrent tumors functionally enriched for chromatin remodeler-associated genes, such as KDM6B, SPEN, CHD4, and CHD7. Furthermore, the germline mutations of our cases showed a significant functional convergence in focal adhesion, cell adhesion molecules, and ECM-receptor interaction. Evolutionary analysis showed that the recurrence could be derived from a single primary tumor lineage or had an intermediate phylogenetic similarity to the matched primary one.

Conclusion

Rare single sub-frontal recurrent MBs presented specific mutation signatures that might be related to the under-dose radiation. Particular attention should be paid to optimally covering the sub-frontal cribriform plate during postoperative radiotherapy targeting.

Transcriptomic and metabolomic analysis of autumn leaf color change in Fraxinus angustifolia

Fraxinus angustifolia is a type of street tree and shade tree with ornamental value. It has a beautiful shape and yellow or reddish purple autumn leaves, but its leaf color formation mechanism and molecular regulation network need to be studied. In this study, we integrated the metabolomes and transcriptomes of stage 1 (green leaf) and stage 2 (red-purple leaf) leaves at two different developmental stages to screen differential candidate genes and metabolites related to leaf color variation. The results of stage 1 and stage 2 transcriptome analysis showed that a total of 5,827 genes were differentially expressed, including 2,249 upregulated genes and 3,578 downregulated genes. Through functional enrichment analysis of differentially expressed genes, we found that they were involved in flavonoid biosynthesis, phenylpropanoid biosynthesis, pigment metabolism, carotene metabolism, terpenoid biosynthesis, secondary metabolite biosynthesis, pigment accumulation, and other biological processes. By measuring the metabolites of Fraxinus angustifolia leaves, we found the metabolites closely related to the differentially expressed genes in two different periods of Fraxinus angustifolia, among which flavonoid compounds were the main differential metabolites. Through transcriptome and metabolomics data association analysis, we screened nine differentially expressed genes related to anthocyanins. Transcriptome and qRT-PCR results showed that these nine genes showed significant expression differences in different stages of the sample, and we speculate that they are likely to be the main regulatory factors in the molecular mechanism of leaf coloration. This is the first time that we have analyzed the transcriptome combination metabolome in the process of leaf coloration of Fraxinus angustifolia, which has important guiding significance for directional breeding of colored-leaf Fraxinus species and will also give new insights for enriching the landscape.

High-resolution sequencing of nine elite upland cotton cultivars uncovers genic variations and breeding improvement targets

Structural variations (SVs) are critical factors affecting genome evolution and important traits. However, identification results and functional analyses of SVs in upland cotton are rare. Here, based on the genetic relationships, breeding history and cumulative planting area of upland cotton in China, nine predominant cultivars from the past 60 years (1950s-2010s) were selected for long read sequencing to uncover genic variations and breeding improvement targets for this crop. Based on the ZM24 reference genome, 0.88-1.47 × 10⁴ SVs per cultivar were identified, and an SV set was constructed. SVs affected the expression of a large number of genes during fiber elongation, and a transposable element insertion resulted in the glandless phenotype in upland cotton. Six widespread inversions were identified based on nine draft genomes and high-throughput chromosome conformation capture data. Multiple haplotype blocks that were always associated with aggregated SVs were demonstrated to play a pivotal role in the agronomic traits of upland cotton and drove its adaptation to the northern planting region. Exotic introgression was the source of these haplotype blocks and increased the genetic diversity of upland cotton. Our results enrich the genome resources of upland cotton, and the identified SVs will promote genetic and breeding research in cotton.

Effector protein Hcp2a of avian pathogenic Escherichia coli interacts with the endoplasmatic reticulum associated RPL23 protein of chicken DF-1 fibroblasts

The type VI secretion system (T6SS) is a secretion apparatus widely found in pathogenic Gram-negative bacteria and is important for competition among various bacteria and host cell pathogenesis. Hcp is a core component of functional T6SS and transports toxic effectors into target cells by assembling to form tube-like structures. Studies have shown that Hcp simultaneously acts as an effector to influence cellular physiological activities; however, the mechanism of its activity in host cells remains unclear. To investigate the target of effector protein Hcp2a in a chicken fibroblast cell line, we first detected the subcellular localization of Hcp2a in DF-1 cells by indirect immunofluorescence assay. The results showed that Hcp2a protein was localized in the endoplasmic reticulum of DF-1 cells. We also used a streptavidin-biotin affinity pull-down assay combined with LC-MS/MS to screen DF-1 cell lysates for proteins that interact with Hcp2a and analyze the cellular functional pathways affected by them. The results showed that Hcp2a interacted with 52 DF-1 cellular proteins that are involved in multiple intracellular pathways. To further explore the mechanism of Hcp2a protein targeting the endoplasmic reticulum of DF-1 cells, we screened three endoplasmic reticulum-associated proteins (RSL1D1, RPS3A, and RPL23) from 52 prey proteins of Hcp2a for protein-protein molecular docking analysis. The docking analysis showed that the effector protein Hcp2a and the RPL23 protein had good complementarity. Overall, we propose that Hcp2a has strong binding activity to the RPL23 protein in DF-1 cells and this may help Hcp2a anchor to the endoplasmic reticulum in DF-1 cells.

Monthly dynamics of microbial communities and variation of nitrogen-cycling genes in an industrial-scale expanded granular sludge bed reactor

Introduction

The expanded granular sludge bed (EGSB) is a major form of anaerobic digestion system during wastewater treatment. Yet, the dynamics of microbial and viral communities and members functioning in nitrogen cycling along with monthly changing physicochemical properties have not been well elucidated.

Methods

Here, by collecting the anaerobic activated sludge samples from a continuously operating industrial-scale EGSB reactor, we conducted 16S rRNA gene amplicon sequencing and metagenome sequencing to reveal the microbial community structure and variation with the ever-changing physicochemical properties along within a year.

Results

We observed a clear monthly variation of microbial community structures, while COD, the ratio of volatile suspended solids (VSS) to total suspended solids (TSS) (VSS/TSS ratio), and temperature were predominant factors in shaping community dissimilarities examined by generalized boosted regression modeling (GBM) analysis. Meanwhile, a significant correlation was found between the changing physicochemical properties and microbial communities (p <0.05). The alpha diversity (Chao1 and Shannon) was significantly higher (p <0.05) in both winter (December, January, and February) and autumn (September, October, and November) with higher organic loading rate (OLR), higher VSS/TSS ratio, and lower temperature, resulting higher biogas production and nutrition removal efficiency. Further, 18 key genes covering nitrate reduction, denitrification, nitrification, and nitrogen fixation pathways were discovered, the total abundance of which was significantly associated with the changing environmental factors (p <0.05). Among these pathways, the dissimilatory nitrate reduction to ammonia (DNRA) and denitrification had the higher abundance contributed by the top highly abundant genes narGH, nrfABCDH, and hcp. The COD, OLR, and temperature were primary factors in affecting DNRA and denitrification by GBM evaluation. Moreover, by metagenome binning, we found the DNRA populations mainly belonged to Proteobacteria, Planctomycetota, and Nitrospirae, while the denitrifying bacteria with complete denitrification performance were all Proteobacteria. Besides, we detected 3,360 non-redundant viral sequences with great novelty, in which Siphoviridae, Podoviridae, and Myoviridae were dominant viral families. Interestingly, viral communities likewise depicted clear monthly variation and had significant associations with the recovered populations (p <0.05).

Discussion

Our work highlights the monthly variation of microbial and viral communities during the continuous operation of EGSB affected by the predominant changing COD, OLR, and temperature, while DNRA and denitrification pathways dominated in this anaerobic system. The results also provide a theoretical basis for the optimization of the engineered system.

Identification of copy number variants contributing to hallux valgus

Hallux valgus is a common form of foot deformity, and genetic factors contribute substantially to the pathogenesis of hallux valgus deformity. We conducted a genetic study on the structural variants underlying familial hallux valgus using whole exome sequencing approach. Twenty individuals from five hallux valgus families and two sporadic cases were included in this study. A total of 372 copy number variations were found and passed quality control filtering. Among them, 43 were only present in cases but not in controls or healthy individuals in the database of genomic variants. The genes covered by these copy number variations were enriched in gene sets related to immune signaling pathway, and cytochrome P450 metabolism. The hereditary CNVs demonstrate a dominant inheritance pattern. Two candidate pathogenic CNVs were further validated by quantitative-PCR. This study suggests that hallux valgus is a degenerative joint disease involving the dysregulation of immune and metabolism signaling pathways.