Anatomical Structure Development Research Articles

Mayfly developmental atlas: developmental temporal expression atlas of the mayfly, Ephemera vulgata, reveals short germ-specific hox gene activation

BackgroundOver the course of evolution, insects have seen drastic changes in their mode of development. While insects with derived modes of development have been studied extensively, information on ancestral modes of development is lacking. To address this, we selected a member of one of the earliest lineages of extant flying insects, serving as an outgroup to the modern winged insects, the short germ, non-model mayfly Ephemera vulgata Linnaeus (Insecta: Ephemeroptera, Ephemeridae). We document the embryonic morphology throughout its development and establish a global temporal expression atlas.ResultsDAPI staining was used to visualise developmental morphology to provide a frame of reference for the sequenced timepoints. A transcriptome was assembled from 3.2 billion Illumina RNAseq reads divided in 12 timepoints with 3 replicates per timepoint consisting of 35,091 putative genes. We identified 6,091 significantly differentially expressed genes (DEGs) and analysed them for broad expression patterns via gene ontology (GO) as well as for specific genes of interest. This revealed a U-shaped relationship between the sum of DEGs and developmental timepoints, over time, with the lowest number of DEGs at 72 hours after egg laying (hAEL). Based on a principal component analysis of sequenced timepoints, overall development could be divided into four stages, with a transcriptional turning point around katatrepsis. Expression patterns of zld and smg showed a persistent negative correlation and revealed the maternal-to-zygotic transition (MZT), occurring 24 hAEL. The onset of development of some major anatomical structures, including the head, body, respiratory system, limb, muscle, and eye, are reported. Finally, we show that the ancestral short germ sequential mode of segmentation translates to a sequential Hox gene activation and find diverging expression patterns for lab and pb. We incorporate these patterns and morphological observations to an overview of the developmental timeline.ConclusionsWith our comprehensive differential expression study, we demonstrate the versatility of our global temporal expression atlas. It has the capacity to contribute significantly to phylogenetic insights in early-diverging insect developmental biology and can be deployed in both molecular and genomic applications for future research.

A Study of Sperm DNA Damage Mechanism Based on miRNA Sequencing.

To analyze the differential expression profiles of microRNAs (miRNAs) in spermatozoa of patients with sperm DNA damage and to investigate the role of miRNAs in sperm DNA damage. Male infertility patients with sperm DNA damage who attended the First Affiliated Hospital of Henan University of Chinese Medicine from October 2023 to December 2023 were selected and included in this study as a case group. Fertile healthy men who were seen at the health check-up center during the same period and diagnosed by examination were also included as a control group. Sperm miRNA expression was detected in patients with sperm DNA damage (case group, n = 5) and healthy medical check-ups (control group, n = 5) using high-throughput sequencing technology. The differentially expressed miRNAs between the two groups were bioinformatically analyzed to explore the main biological functions of the target genes. We found that 63 miRNAs were significantly changed in the spermatozoa of patients with sperm DNA damage,|log2 (foldchange)| ≥ 1, p < .05. Gene Ontology (GO) enrichment analysis indicated that these differential miRNAs might be involved in developmental process, anatomical structure development, cellular macromolecule metabolic process, multicellular organism development, system development, and so on. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that that they mainly affect the PI3K-AKT signaling pathway. The present study suggests that the altered expression of miR-1255a, miR-921, and miR-3156-5p may play an important role in the sperm DNA damage process, and the mechanism may involve the phosphatidylinositol-3'-kinase-AKT (PI3K-AKT) signaling pathway.

Phenotype identification and genome-wide association study of ear-internode vascular bundles in maize (Zea mays).

The vascular bundle in the ear-internode of maize is a key conduit for transporting photosynthetic materials between "source" and "sink", making it critically important to examine its micro-phenotypes and genetic architecture to identify advantageous characteristics and cultivate high-yielding and high-quality varieties. Unfortunately, the limited observation methods and scope of study precludes any comprehensive and systematic investigations into the microscopic phenotypes and genetic mechanisms of vascular bundle in maize ear-internode. In this study, 47 phenotypic traits were extracted in 495 maize inbred lines using micro computed tomography (Micro-CT) scanning technology and a deep learning-based phenotype acquisition method for stem vascular bundle, which included stem slice-related, epidermis zone-related, periphery zone-related, inner zone-related and vascular bundles-related traits. Phenotypic analysis indicated that there was extensive phenotypic variation of vascular bundle traits in ear-internode, especially that in the inner zone. Of these, 30 phenotypic traits with heritability greater than 0.70 were conducted for GWAS, and a total of 4,225 significant SNPs and 416 candidate genes with detailed functional annotations were identified. Furthermore, 20 genes were highly expressed in stem-related tissues, especially in maize internodes. Functional analysis of candidate genes indicated that the pathways obtained for candidate genes of different trait groups were distinct, mainly involved in vitamin synthesis and metabolism, transport of substances, carbohydrate derivative catabolic process, protein transport and localization, and anatomical structure development. The results of this study will help to further understand the phenotypic traits of stem vascular bundles and provide a reference for revealing the genetic mechanism of maize ear-internode vascular bundles.

Epigenetic Control of Adamantinomatous Craniopharyngiomas.

Studies addressing the methylation pattern in adamantinomatous craniopharyngioma (ACP) are lacking. To identify methylation signatures in ACPs regarding clinical presentation and outcome. Clinical and pathology data were collected from 35 patients with ACP (54% male; 18.1 years [2-68]). CTNNB1 mutations and methylation profile (MethylationEPIC/Array-Illumina) were analyzed in tumoral DNA. Unsupervised machine learning analysis of this comprehensive methylome sample was achieved using hierarchical clustering and multidimensional scaling. Statistical associations between clusters and clinical features were achieved using the Fisher test and global biological process interpretations were aided by Gene Ontology enrichment analyses. Two clusters were revealed consistently by all unsupervised methods (ACP-1: n = 18; ACP-2: n = 17) with strong bootstrap statistical support. ACP-2 was enriched by CTNNB1 mutations (100% vs 56%, P = .0006), hypomethylated in CpG island, non-CpG Island sites, and globally (P < .001), and associated with greater tumor size (24.1 vs 9.5 cm3, P = .04). Enrichment analysis highlighted pathways on signaling transduction, transmembrane receptor, development of anatomical structures, cell adhesion, cytoskeleton organization, and cytokine binding, and cell type-specific biological processes as regulation of oligodendrocytes, keratinocyte, and epithelial cells differentiation. Two clusters of patients with ACP were consistently revealed by unsupervised machine learning methods, with one of them significantly hypomethylated, enriched by CTNNB1 mutated ACPs, and associated with increased tumor size. Enrichment analysis reinforced pathways involved in tumor proliferation and in cell-specific tumoral microenvironment.

Dietary encapsulated fennel seed (Foeniculum vulgare Mill.) essential oil supplementation improves performance, modifies the intestinal microflora, morphology, and transcriptome profile of broiler chickens.

Global antimicrobial resistance has led to a ban on the use of antibiotics as growth promoters (AGPs) in poultry farming, encouraging the use of natural phytogenic feed additives that provide similar effects to AGPs without causing resistance. The aim of this study was to determine the effects of the addition of encapsulated fennel seed (Foeniculum vulgare Mill.) essential oil (FEO) into the diets on the performance, intestinal microflora, morphology, and transcriptomic profiling of broiler chickens. In the study, 400 one-d-old male chicks of the Ross-308 genotype were randomly distributed into five groups, each with 16 replicates of five birds. The experiment included a control group fed on basal diets without the addition of FEO and treatment groups supplemented with 50 (FEO50), 100 (FEO100), 200 (FEO200), or 400 (FEO400) mg of encapsulated FEO/kg. Body weight and the European Production Efficiency Factor values were higher in the FEO100, FEO200, and FEO400 groups (P < 0.05). The feed conversion ratio significantly improved at all FEO levels (P < 0.05). FEO supplementation improved duodenum, jejunum, and ileum morphologies. It enhanced mucosal layer thickness in the duodenum and jejunum, and muscular layer thickness in the jejunum and ileum (P < 0.05). It also increased the number of Lactobacillus spp. in the jejunum and ileum (P < 0.05). According to the transcriptome profile obtained from the microarray analysis of samples taken from small intestine tissues, the mRNA expression levels of 261 genes in the FEO50 group (206 upregulated and 55 downregulated), 302 genes in the FEO100 group (218 upregulated and 84 downregulated), 292 genes in the FEO200 group (231 upregulated and 61 downregulated), and 348 genes in the FEO400 group (268 upregulated and 80 downregulated) changed compared to the control group. Most upregulated genes were associated with catalytic activity, binding, transcription regulators and transcription factors, anatomical structure and cellular development, and protein binding activity modulators. The downregulated genes mostly belonged to the transporter, carrier, and protein-modifying enzyme classes. Besides, the anti-inflammatory IL-10 gene (4.41-fold) increased significantly in the FEO100 group compared to the control group (P < 0.05). In conclusion, FEO improved the performance of broiler chickens by regulating biological processes such as performance and intestinal health, with the 100mg FEO/kg supplementation being the most prominent.

Mechanisms analysis for Formononetin counteracted-Osimertinib resistance in non-small cell lung cancer cells: From the insight into the gene transcriptional level.

Formononetin is one of the main isoflavone components, which has strong anti-cancer effects in non-small cell lung cancer (NSCLC). However, the potentials and the mechanisms of Formononetin to counteract the Osimertinib resistance in NSCLC are unclear. In this study, Formononetin-induced cell apoptosis, cell proliferation, and clonal formation were detected in Osimertinib-resistant NSCLC cells (H1975_OR). RNA sequencing analysis was conducted to study the gene expression profiles of Formononetin-induced H1975_OR cells. The results indicated that Formononetin could significantly induce cell apoptosis, whereas dramatically inhibited cell proliferation and clonal formation on H1975_OR cells. Furthermore, a total of 4309 differentially expressed genes (DEGs) between Formononetin-treated and nontreated H1975_OR cells were had been detected. Gene Ontology (GO) annotation enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis and the Gene Set Enrichment Analysis (GSEA) showed that Formononetin affected the expression of genes involving in anatomical structure morphogenesis, anatomical structure development, and multicellular organism development via regulating inflammation- and metabolism-related signaling pathways. Taken together, our study preliminarily revealed the mechanisms of Formononetin to counteract the Osimertinib resistance in NSCLC cells from the transcriptional level and provided a potential treatment method for Osimertinib-resistant NSCLC patients.

New progress in diagnosis and treatment of congenital laryngomalacia in infants

Congenital laryngomalacia is the most common disease causing laryngeal stridor in infants. The pathogenesis has not yet been clearly concluded. It may be related to abnormal development of laryngeal cartilage anatomical structure, neuromuscular dysfunction, gastroesophageal and laryngeal reflux disease, etc. The typical manifestations of the disease are inspiratory laryngeal stridor and feeding difficulties, which can be divided into mild, moderate and severe according to the severity of symptoms. The diagnosis is mainly based on clinical symptoms, signs and endoscopy, among which endoscopy is an important diagnostic basis. The treatment of laryngomalacia depends on the severity of symptoms. Mild and some moderate congenital laryngomalacia children can be relieved by conservative treatment, and severe and some moderate congenital laryngomalacia children should be treated by surgery. Supraglottic plasty is the main surgical method, which can effectively improve the symptoms of laryngeal stridor, dyspnea, feeding difficulties and growth retardation in most children, and the surgical effect is good.

Maternal diet during gestation affect prostatic tissue component in SHR/Izm offspring.

Numerous studies have investigated the associations between maternal nutritional status and various diseases, with the underlying mechanism often attributed to epigenetic changes. However, limited research has been conducted on the relationship between maternal nutrition and benign prostatic hyperplasia (BPH). In this study, we aimed to explore the potential association between maternal nutrition and BPH using an animal experiment and evaluating the findings through fluorescent immunostaining and genetic analysis. Female spontaneously hypertensive rats (SHR/Izm) were randomly assigned to three groups at the start of pregnancy: a standard diet group (SD; 17% protein, 7% fat), a low-protein diet group (LPD; 6% protein, 7% fat), and a high-fat diet group (HFD; 22% protein, 35% fat). The diets were maintained throughout gestation. After giving birth, both the mothers and their pups were exclusively fed a standard diet. Male pups were euthanized at 48 weeks, and their prostates were removed. The composition of the ventral prostate (VP) was evaluated using fluorescent immunostaining with antibodies for cytokeratin, vimentin, and Ki-67. Microarray analysis, real-time RT-PCR, and DNA methylation analysis using pyrosequencing were performed. Statistical analysis was conducted using one-way ANOVA and Tukey's multiple comparison test, with a significance level set at p < 0.05. Pups in the LPD group exhibited significant underweight from birth (1 day; SD vs.LPD vs.HFD: 4.46 vs. 4.08 vs. 4.35, p = 0.04) until weaning (21 days; SD vs.LPD vs.HFD: 30.8 vs. 27.4 vs. 29.2, p = 0.03). However, they exhibited catch-up growth, and there was no significant difference at 48 weeks (p = 0.84). The epithelial area in the ventral prostate was significantly increased in the LPD group (SD vs.LPD vs.HFD: 39% vs. 48% vs. 37%, p = 0.01), while the stromal area was significantly increased in the HFD group (SD vs.LPD vs.HFD: 11% vs. 11% vs. 15%, p < 0.01). Gene ontology analysis of the gene expression microarray showed increased activity in developmental processes (SD vs.LPD: p = 6.3E-03, SD vs.HFD: p = 7.2E-03), anatomical structure development (SD vs.LPD: p = 6.3E-03, SD vs.HFD: p = 5.3E-03), and cell differentiation (SD vs.LPD: p = 0.018, SD vs.HFD: p = 0.041) in both the LPD and HFD groups. Real-time RT-PCR revealed high expression levels of the transcription factors NFκB (p < 0.01) and Smad3 (p < 0.01) in both the LPD and HFD groups. XIAP, an apoptosis inhibitor, was increased in the LPD group (p = 0.02). The TGF beta pathway, associated with epithelial mesenchymal transition (EMT), and vimentin (p < 0.01) were upregulated in the HFD group. Pyrosequencing DNA methylation analysis of the TGF beta pathway indicated hypomethylation of TGFb1, TGFbR1, and Smad3 in all groups, although there were no significant differences. Our findings suggest that both maternal undernutrition and obesity influence the prostatic development of offspring. Maternal consumption of a low protein diet promotes epithelial hyperplasia through the upregulation of apoptosis inhibitors, while a high fat diet leads to increased stromal growth through the induction of EMT.

296 Comparison of Dna Methylation Patterns in Sperm Collected from Brahman Bulls with Differences in Embryo Development

Abstract The objective was to determine if methylation patterns in sperm differed between bulls with good vs poor embryo development. Semen collected from sexually mature Brahman bulls was purified from frozen-thawed straws using a gradient [50% (vol/vol) and 90% (vol/vol)] of Isolate (Irvine Scientific, Santa Ana, CA), and used to fertilize abattoir-derived cumulus oocyte complexes (n = 81-100/bull in 2 wells). Number of blastocysts were recorded on d 8, and bulls were classified as Good (GD; &amp;gt;35% blastocyst rate; n = 5) or Poor (PD; &amp;lt; 35% blastocyst rate; n = 4) embryo development. Methylation of sperm DNA was assessed by reduced representation sodium bisulfite sequencing. Differences in methylation were determined with the Dispersion Shrinkage for Sequencing method in conjunction with Wald test. Differentially methylated cytosines and regions located in promoters of genes and gene bodies were analyzed to reveal gene ontology terms associated with them. Proportion of sperm cells that were viable (before and after a three-hour stress test), with inceased reactive oxygen species (ROS), and with damaged chromatin was determined. Statistical analysis (PROC GLIMMIX; SAS 9.4) included the fixed effect of embryo development classification which was considered significant at P &amp;lt; 0.05. Mean separation was performed using LSmeans. The proportion of viable (P &amp;gt; 0.21; GD = 46 ± 5%; PD = 36 ± 5%) sperm cells did not differ before the stress test. Post-stress test, PD bulls had more viable sperm cells (P &amp;lt; 0.02; 37 ± 3%) than GD (25 ± 2%) bulls. There was no difference between GD and PD for ROS (H2O2; P &amp;gt; 0.16 and •O2; P &amp;gt; 0.59). Proportion of sperm cells with damaged chromatin was greater (P &amp;lt; 0.01) in PD (3 ± 0.3%) than GD bulls (1 ± 0.01%). There were 1,742 differentially methylated cytosines and 343 differentially methylated regions when GD bulls were compared with PD bulls. Genes whose promoters were differentially methylated included DDC, GTSF1L, PPP1R27, NTM, HCK, GPR173, and TNFRSF1A. Functionally enriched pathways for differentially methylated promoters included apoptosis and amyotrophic lateral sclerosis while some of the significant biological processes were regulation of apoptotic process involved in morphogenesis, negative regulation of neuron migration, pyrimidine nucleoside catabolic process, and regulation of cardiac muscle tissue development. Differentially methylated gene bodies were significantly related to cellular components such as cell surface, endomembrane system, synapse, and cell periphery while molecular functions included binding, protein binding, and transmembrane receptor protein tyrosine kinase activity. Biological processes impacted by differentially methylated gene bodies included system development, neurogenesis, animal organ development, anatomical structure development, generation of neurons, nervous system development, and multicellular organism development. In summary, differences in embryo development are likely due to differences in methylation patterns impacting developmental processes, as semen characteristics were mainly similar between bulls with good versus poor embryo development.

Gene co-expression network identifies critical genes, pathways and regulatory motifs mediating the progression of rift valley fever in Bostaurus

Rift Valley Fever (RVF) is a mosquito-borne viral disease caused by the Rift Valley Fever Virus. The disease is a zoonosis that largely affects domestic animals, including sheep, goats, and cattle, resulting in severe morbidity and mortality marked by massive storm abortions. To halt human and livestock deaths due to RVF, the development of efficacious vaccines and therapeutics is a compelling and urgent priority. We sought to identify potential key modules (gene clusters), hub genes, and regulatory motifs involved in the pathogenesis of RVF in Bos taurus that are amenable to inhibition. We analyzed 39 Bos taurus RNA-Seq samples using the weighted gene co-expression network analysis (WGCNA) R package and uncovered significantly enriched modules containing genes with potential pivotal roles in RVF progression. Moreover, regulatory motif analysis conducted using the Multiple Expectation Maximization for Motif Elicitation (MEME) suite identified motifs that probably modulate vital biological processes. Gene ontology terms associated with identified motifs were inferred using the GoMo human database. The gene co-expression network constructed in WGCNA using 5000 genes contained seven (7) modules, out of which four were significantly enriched for terms associated with response to viruses, response to interferon-alpha, innate immune response, and viral defense. Additionally, several biological pathways implicated in developmental processes, anatomical structure development, and multicellular organism development were identified. Regulatory motifs analysis identified short, repeated motifs whose function(s) may be amenable to disruption by novel therapeutics. Predicted functions of identified motifs include tissue development, embryonic organ development, and organ morphogenesis. We have identified several hub genes in enriched co-expressed gene modules and regulatory motifs potentially involved in the pathogenesis of RVF in B. taurus that are likely viable targets for disruption by novel therapeutics.

Carcass composition, meat quality, leg muscle status, and its mRNA expression profile in broilers affected by valgus-varus deformity

Valgus-varus deformity (VVD) is a common leg disease in commercial broilers, which seriously affects animal welfare and causes economic losses. Up to now, most of the studies on VVD have been on skeleton, whereas there are fewer studies on VVD muscle. In this study, carcass composition and meat quality of 35-day-old normal and VVD Cobb broilers assess the effect of VVD on broiler growth. Molecular biology, morphology, and RNA sequencing (RNA-seq) were used to study the difference between normal and VVD gastrocnemius muscle. In comparison with the normal broilers, the breast muscle and leg muscle of the VVD broilers had lower shear force, notably lower crude protein, lower water content, cooking loss, and deeper meat color (P < 0.05). The morphological results showed that the weight of skeletal muscle was significantly higher in the normal broilers than that in the VVD broilers (P < 0.01), the diameter and area of myofibrils in the affected VVD were smaller than in the normal broilers (P < 0.01). Quantitative real-time PCR (qPCR) of gastrocnemius muscle revealed that the expression of myasthenic marker genes, fast myofiber marker genes, and apoptosis-related factors were significantly higher in the VVD broilers than in the normal broilers (P < 0.01). In total, 736 differentially expressed genes (DEGs) were identified firstly in the normal and VVD leg muscle by RNA-seq. Gene ontology (GO) enrichment indicated that these DEGs were mainly involved in the multicellular organismal process and anatomical structure development. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that DEGs are significantly enriched in proteasome. Protein interaction analysis obtained that DEGs with high interaction were proteasome-related coding genes and ubiquitin-related genes, these DEGs were closely associated with muscle atrophy. These show that VVD has an adverse effect on growth characteristics, slaughter characteristics, and meat quality in broilers, which may cause leg muscle atrophy. This study provides some reference values and basis for studying the pathogenesis of VVD in broilers.

Comparative analysis of phosphoproteomic in the intestine of Sepia lycidas under different salinity environments

Cuttlefish are sensitive to the breeding environment, and the low-salinity environment significantly impacts their growth and immunity. So far, it is difficult to breed this species artificially. This study was conducted in Sepia lycidas. And the aim was to investigate the differences in protein phosphorylation in the intestine of S. lycidas under different salinity conditions. Firstly, 999 phosphoproteins (specific peptide ≥ 1), 1928 phosphopeptides, and 2727 phosphorylation sites were identified. Among them were 284 down-regulated expression phosphorylation sites (corresponding to 115 phosphoproteins) and 674 up-regulated expression phosphorylation sites (corresponding to 408 phosphoproteins) in the intestine under a low salinity environment compared with that under a natural salinity environment. Next, GO analysis found that more phosphoproteins corresponding to differentially expressed phosphorylation sites were related to anatomical structure development, multicellular organism development, regulation of the cellular process, etc. The molecular functions of these proteins mainly contain protein binding, transferase activity, catalytic activity, and heterocyclic compound binding. And they are mainly involved in the cellular components of intracellular anatomical structure, organelle, and cytoplasm. KEGG enrichment analysis of the differential phosphoproteins suggested that many significantly enriched pathways were related to the phosphatidylinositol signaling system, cell junction (adherens junction and tight junction), and inositol phosphate metabolism. Finally, changes in environmental salinity can affect the intestinal structure, metabolism, and immune homeostasis of S. lycidas.

An endogenous amniotic fluid-derived 10-amino acid peptide improves lung development and hyperoxia injury.

Bronchopulmonary dysplasia (BPD) is a chronic lung disease that occurs in preterm infants and lacks effective treatment. We aim to reveal the relationship between amniotic fluid (AF) peptides and lung development by analyzing the differences in the composition of AF peptides at different gestational periods, thus providing a new means of prevention and treatment for BPD. Based on the stages of lung development, we collected AF by amniocentesis in two different gestational periods, using the 25th week of pregnancy as the cut-off. We conducted a peptide omics analysis of these AF samples using liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. Additionally, we verified the regulatory effects of hyperoxia and the peptide COL5A2 on BPD-related cells [(mouse lung epithelial (MLE-12) cells] by 5-Ethynyl-2'-deoxyuridine (EdU) staining, JC-1 staining, flow cytometry, and reactive oxygen species (ROS) assay. There were 131 differentially expressed peptides, including 85 up-regulated and 46 down-regulated [fold change (FC) ≥1.2 or ≤1/1.2, P<0.05], in the ≥25 weeks' gestation group compared to the <25 weeks' gestation group. Further bioinformatics analysis revealed that the precursor proteins of the differentially expressed peptides between these two groups were involved in the regulation of the developmental process, anatomical structure development, and other biological processes, suggesting that these differential peptides may play a key role in lung development. We found peptide COL5A2 with the sequence GPPGEPGPPG and verified the regulatory effects of COL5A2 on the proliferation, apoptosis, cell viability, and ROS levels of MLE-12 cells by cell assays. In this study, peptidomic studies using AF from different gestational periods revealed that peptides in AF may be involved in lung development. They could be used in the future to assist in the postnatal development of preterm infants and provide new therapeutic prospects for BPD.

Phylogenomics provides insights into the evolution of cactophily and host plant shifts in Drosophila

Cactophilic species of the Drosophila buzzatii cluster (repleta group) comprise an excellent model group to investigate genomic changes underlying adaptation to extreme climate conditions and host plants. In particular, these species form a tractable system to study the transition from chemically simpler breeding sites (like prickly pears of the genus Opuntia) to chemically more complex hosts (columnar cacti). Here, we report four highly contiguous genome assemblies of three species of the buzzatii cluster. Based on this genomic data and inferred phylogenetic relationships, we identified candidate taxonomically restricted genes (TRGs) likely involved in the evolution of cactophily and cactus host specialization. Functional enrichment analyses of TRGs within the buzzatii cluster identified genes involved in detoxification, water preservation, immune system response, anatomical structure development, and morphogenesis. In contrast, processes that regulate responses to stress, as well as the metabolism of nitrogen compounds, transport, and secretion were found in the set of species that are columnar cacti dwellers. These findings are in line with the hypothesis that those genomic changes brought about key mechanisms underlying the adaptation of the buzzatii cluster species to arid regions in South America.

Analysis of gene expression profile of peripheral blood in alveolar and cystic echinococcosis.

RNA-sequencing (RNA-seq) is a versatile, high-throughput technology that is being widely employed for screening differentially expressed genes (DEGs) in various diseases. Echinococcosis, a globally distributed zoonosis, has been reported to impose a heavy disease burden in pastoral areas of China. Herein we aimed to explore the molecular mechanisms underlying echinococcosis. In this study, peripheral blood samples were collected from six patients with alveolar echinococcosis (AE), six patients with cystic echinococcosis (CE), and six healthy controls. RNA-Seq (mRNA) was performed to detect gene transcript and expression levels, and DEGs were subjected to bioinformatic analyses. In comparison with healthy controls, 492 DEGs (270 upregulated, 222 downregulated) were found in the AE group and 424 DEGs (170 upregulated, 254 downregulated) were found in the CE group (|log2 (fold change)| > 1 and P < 0.05). Further, 60 genes were upregulated and 39 were downregulated in both the AE and CE groups. Gene ontology enrichment analysis indicated that DEGs were mainly involved in molecular functions, including extracellular space, extracellular region, organ and system development, and anatomical structure development. Protein–protein interaction (PPI) networks were constructed to depict the complex relationship between DEGs and interacting proteins.

Multiplexed mRNA analysis of brain-derived extracellular vesicles upon experimental stroke in mice reveals increased mRNA content with potential relevance to inflammation and recovery processes

Extracellular vesicles (EVs) are lipid bilayer-enclosed structures that represent newly discovered means for cell-to-cell communication as well as promising disease biomarkers and therapeutic tools. Apart from proteins, lipids, and metabolites, EVs can deliver genetic information such as mRNA, eliciting a response in the recipient cells. In the present study, we have analyzed the mRNA content of brain-derived EVs (BDEVs) isolated 72 h after experimental stroke in mice and compared them to controls (shams) using nCounter® Nanostring panels, with or without prior RNA isolation. We found that both panels show similar results when comparing upregulated mRNAs in stroke. Notably, the highest upregulated mRNAs were related to processes of stress and immune system responses, but also to anatomical structure development, cell differentiation, and extracellular matrix organization, thus indicating that regenerative mechanisms already take place at this time-point. The five top overrepresented mRNAs in stroke mice were confirmed by RT-qPCR and, interestingly, found to be full-length. We could reveal that the majority of the mRNA cargo in BDEVs was of microglial origin and predominantly present in small BDEVs (≤ 200 nm in diameter). However, the EV population with the highest increase in the total BDEVs pool at 72 h after stroke was of oligodendrocytic origin. Our study shows that nCounter® panels are a good tool to study mRNA content in tissue-derived EVs as they can be carried out even without previous mRNA isolation, and that the mRNA cargo of BDEVs indicates a possible participation in inflammatory but also recovery processes after stroke.

Identification of hub genes specific to pulmonary metastasis in osteosarcoma through integrated bioinformatics analysis.

Pulmonary metastasis is the most frequent cause of death in osteosarcoma (OS) patients. Recently, several bioinformatics studies specific to pulmonary metastatic osteosarcoma (PMOS) have been applied to identify genetic alterations. However, the interpretation and reliability of the results obtained were limited for the independent database analysis. The expression profiles and key pathways specific to PMOS remain to be comprehensively explored. Therefore, in our study, three original datasets of GEO database were selected. Initially, three microarray datasets (GSE14359, GSE14827, and GSE85537) were downloaded from the GEO database. Differentially expressed genes (DEGs) between PMOS and nonmetastatic osteosarcoma (NMOS) were identified and mined using DAVID. Subsequently, GO and KEGG pathway analyses were carried out for DEGs. Corresponding PPI network of DEGs was constructed based on the data collected from STRING datasets. The network was visualized with Cytoscape software, and ten hub genes were selected from the network. Finally, survival analysis of these hub genes also used the TARGET database. In total, 569 upregulated and 1238 downregulated genes were filtered as DEGs between PMOS and NMOS. Based on the GO analysis result, these DEGs were significantly enriched in the anatomical structure development, extracellular matrix, biological adhesion, and cell adhesion terms. Based on the KEGG pathway analysis result, these DEGs were mainly enriched in the pathways in cancer, PI3K-Akt signaling, MAPK signaling, focal adhesion, cytokine-cytokine receptor interaction, and IL-17 signaling. Hub genes (ANXA1 and CXCL12) were significantly associated with overall survival time in OS patient. Our results may provide new insight into pulmonary metastasis of OS. However, experimental studies remain necessary to elucidate the biological function and mechanism underlying PMOS.

Novel deoxyribonucleic acid methylation perturbations in workers exposed to vinyl chloride

To explore the epigenetic mechanism of deoxyribonucleic acid (DNA) damage induced by vinyl chloride (VC), we studied the micronuclei of peripheral blood lymphocytes in 193 subjects (92 in a VC exposure group employed in a chlorine-alkali plant; 101 in a control group employed in a power plant) and selected three pairs from the subjects (exposed and control) for whole-genome bisulfite sequencing (WGBS). The results showed that the rate ofmicronucleus formation in the VC exposure group was higher than that of control group (6.05 ± 3.28‰ vs. 2.01 ± 1.79‰). A total of 9534 differentially methylated regions (DMRs) were identified by WGBS, of which 4816 were hypomethylated and 4718 were hypermethylated. The Kyoto encyclopedia of genes and genomes (KEGG) pathway and gene ontology (GO) analyses showed the top three KEGG pathways were cancer , neuroactive ligand-receptor interaction, and axon guidance, and the top three GO-BP pathways enriched were multicellular organismal process, developmental process, and anatomical structure development. In the most enriched DMR pathway (pathways in cancer), we found that BCL2, TJP2, TAOK1, PFKFB3, LIPI, and LIPH were hypermethylated, and the methylation levels of BNIP1 and GRPEL2 were decreased. The methylation of differentially methylated genes (DMGs) mentioned above were verified by methylation-specific PCR (MSP) and agarose gel electrophoresis (AGE) in 50 pairs of subjects, where the coincidence rate was 60-100%. In conclusion, the epigenetic perturbations of specific DMGs (BCL2, TJP2, TAOK1, PFKFB3, LIPI, LIPH, BNIP1, and GRPEL2) may be associated with DNA damage from vinyl chloride exposure.

Novel biomarkers identified in triple-negative breast cancer through RNA-sequencing

Background and aimsTriple-negative breast cancer (TNBC) is a subtype of breast cancer with a poor prognosis due to its aggressive biological behavior and lack of therapeutic targets. Here, we aimed to identify specific biomarkers for TNBC by using RNA-sequencing and bioinformatics analysis. Materials and methodsFresh breast tumor tissues were obtained from 34 patients who were admitted to the Breast Center, Peking University People’s Hospital, from June 2020 to December 2020; the patients were pathologically diagnosed with primary breast cancer and underwent surgery for the resection of tumor tissues. Tumor-tissue RNA was extracted and the generated cDNA libraries were sequenced using the NextSeq platform, after which the differentially expressed genes (DEGs) between TNBC and other subtypes of breast cancer were identified and DEG functional-enrichment analysis was performed. Next, weighted gene co-expression network analysis (WGCNA) was used to identify the most significant module and hub genes in TNBC, and then the correlations between the hub genes and the prognosis of TNBC patients were analyzed through survival analysis. Lastly, qRT-PCR analysis was used to validate the expression levels of hub genes in tumor tissues from TNBC and other subtypes of breast cancer. ResultsComparison of TNBC tissues and tissues from other subtypes of breast cancer led to the identification of 273 DEGs in TNBC: 172 upregulated and 101 downregulated genes. In Gene Ontology analysis of the DEGs, five terms were significantly enriched, “developmental process,” “anatomical structure development,” “tissue development,” “cell cycle,” and “epithelium development,” and in Kyoto Encyclopedia of Genes and Genomes pathway analysis, the most significantly enriched pathways for all DEGs were “cell cycle,” “mitophagy-animal,” and “autophagy-animal.” Furthermore, we identified the core module related to TNBC and screened for hub genes by using WGCNA, and after verifying the top 100 genes based on survival analysis, we selected four genes as the hub genes: SERPINB4, SMR3A, FERMT1, and STARD4; elevated expression of these genes was associated with poor overall survival (OS) of TNBC patients. Notably, qRT-PCR results indicated that FERMT1 mRNA expression was significantly upregulated in TNBC samples. ConclusionThe DEG profiles between tissues from TNBC and other subtypes of breast cancer were identified using RNA-sequencing and bioinformatics analysis. FERMT1 was significantly upregulated in TNBC tumor tissues, and increased expression of FERMT1 was associated with poor OS of TNBC patients. FERMT1 could serve as a specific biomarker of and therapeutic target in TNBC.

Recognition of a Novel Gene Signature for Human Glioblastoma.

Glioblastoma (GBM) is one of the most common malignant and incurable brain tumors. The identification of a gene signature for GBM may be helpful for its diagnosis, treatment, prediction of prognosis and even the development of treatments. In this study, we used the GSE108474 database to perform GSEA and machine learning analysis, and identified a 33-gene signature of GBM by examining astrocytoma or non-GBM glioma differential gene expression. The 33 identified signature genes included the overexpressed genes COL6A2, ABCC3, COL8A1, FAM20A, ADM, CTHRC1, PDPN, IBSP, MIR210HG, GPX8, MYL9 and PDLIM4, as well as the underexpressed genes CHST9, CSDC2, ENHO, FERMT1, IGFN1, LINC00836, MGAT4C, SHANK2 and VIPR2. Protein functional analysis by CELLO2GO implied that these signature genes might be involved in regulating various aspects of biological function, including anatomical structure development, cell proliferation and adhesion, signaling transduction and many of the genes were annotated in response to stress. Of these 33 signature genes, 23 have previously been reported to be functionally correlated with GBM; the roles of the remaining 10 genes in glioma development remain unknown. Our results were the first to reveal that GBM exhibited the overexpressed GPX8 gene and underexpressed signature genes including CHST9, CSDC2, ENHO, FERMT1, IGFN1, LINC00836, MGAT4C and SHANK2, which might play crucial roles in the tumorigenesis of different gliomas.