Analysis of molecular mechanism for acceleration of polyembryony using gene functional annotation pipeline in Copidosoma floridanum

Abstract Background: Polyembryony is defined as the formation of several embryos from a single egg. This phenomenon can occur in humans, armadillo, and some endoparasitoid insects. However, the mechanism underlying polyembryogenesis in animals remains to be elucidated. The polyembryonic parasitoid wasp Copidosoma floridanum oviposits its egg into an egg of the host insect; eventually, over 2,000 individuals will arise from one egg. Previously, we reported that polyembryogenesis is enhanced when the juvenile hormone (JH) added to the culture medium in the embryo culture. Hence, in the present study, we performed RNA sequencing (RNA-Seq) analysis to investigate the molecular mechanisms controlling polyembryogenesis of C. floridanum . Functional annotation of genes is not fully available for C.floridanum ; however, whole genome assembly has been archived. Hence, we constructed a pipeline for gene functional annotation in C. floridanum and performed molecular network analysis. We analyzed differentially expressed genes between control and JH-treated molura after 48 h of culture, then used the tblastx program to assign whole C. floridanum transcripts to human gene. Results: We obtained 11,117 transcripts in the JH treatment group and identified 217 differentially expressed genes compared with the control group. As a result, 76% of C. floridanum transcripts were assigned to human genes. Gene enrichment analysis revealed genes associated with platelet degranulation, fatty acid biosynthesis, cell morphogenesis in the differentiation and integrin signaling pathways were fluctuated following JH treatment. Furthermore, Cytoscape analysis revealed a molecular interaction that was possibly associated with polyembryogenesis . Conclusions: We have constructed a pipeline for gene functional annotation of C. floridanum , and identified transcripts with high similarity to human genes during early embryo developmental. Additionally, this study reveals new molecular interactions associated with polyembryogenesis; these interactions could indicate the molecular mechanisms underlying polyembryony. Our results highlight the potential utility of molecular interaction analysis in human twins.

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Analysis of molecular mechanism for acceleration of polyembryony using gene functional annotation pipeline in Copidosoma floridanum

10.21203/rs.2.9609/v2 ◽

2019 ◽

Author(s):

Takuma Sakamoto ◽

Maaya Nishiko ◽

Hidemasa Bono ◽

Takeru Nakazato ◽

Jin Yoshimura ◽

...

Keyword(s):

Differentially Expressed Genes ◽

Molecular Interaction ◽

Functional Annotation ◽

Molecular Mechanisms ◽

Interaction Analysis ◽

Gene Annotation ◽

Differentially Expressed ◽

Control Group ◽

Copidosoma Floridanum ◽

Human Genes

Abstract Background: Polyembryony is defined as the formation of several embryos from a single egg. This phenomenon can occur in humans, armadillo, and some endoparasitoid insects. However, the mechanism underlying polyembryogenesis in animals remains to be elucidated. The polyembryonic parasitoid wasp Copidosoma floridanum oviposits its egg into an egg of the host insect; eventually, over 2,000 individuals will arise from one egg. Previously, we reported that polyembryogenesis is enhanced when the juvenile hormone (JH) added to the culture medium in the embryo culture. Hence, in the present study, we performed RNA sequencing (RNA-Seq) analysis to investigate the molecular mechanisms controlling polyembryogenesis of C. floridanum . Functional gene annotation is not available for C. floridanum because whole-genome sequencing has not been achieved. Hence, we constructed a pipeline for gene functional annotation in C. floridanum and performed molecular network analysis. We analyzed differentially expressed genes between control and JH-treated molura after 48 h of culture, then used the tblastx program to assign whole C. floridanum transcripts to human gene. Results: We obtained 11,117 transcripts in the JH treatment group and identified 217 differentially expressed genes compared with the control group. As a result, 76% of C. floridanum transcripts were assigned to human genes. Gene enrichment analysis revealed genes associated with platelet degranulation and fatty acid biosynthesis to be upregulated, while cell morphogenesis in the differentiation and integrin signaling pathways were suppressed following JH treatment. Furthermore, Cytoscape analysis revealed a molecular interaction that was possibly associated with polyembryogenesis . Conclusions: We have constructed a pipeline for gene functional annotation of C. floridanum , and identified transcripts with high homology to human genes during early embryo developmental. Additionally, this study reveals new molecular interactions associated with polyembryogenesis; these interactions could indicate the molecular mechanisms underlying polyembryony. Our results highlight the potential utility of molecular interaction analysis in human twins.

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Analysis of molecular mechanism for acceleration of polyembryony using gene functional annotation pipeline in Copidosoma floridanum

10.21203/rs.2.9609/v1 ◽

2019 ◽

Author(s):

Takuma Sakamoto ◽

Maaya Nishiko ◽

Hidemasa Bono ◽

Takeru Nakazato ◽

Jin Yoshimura ◽

...

Keyword(s):

Treatment Group ◽

Molecular Mechanism ◽

Molecular Interaction ◽

Functional Annotation ◽

Molecular Mechanisms ◽

Gene Annotation ◽

Control Group ◽

Annotation Pipeline ◽

Copidosoma Floridanum ◽

Human Genes

Abstract Background: Polyembryony, when several embryos are clonally produced from a single egg, is found in humans, armadillo, and some endoparasitoid insects. Thus, although polyembryony is conserved through insects to mammals, the polyembryogenesis progress remains obscure in these animals. The polyembryonic parasitoid wasp Copidosoma floridanum oviposits its egg into the host insect egg, and, eventually, >2000 individuals occur from one egg. We reported previously that polyembryogenesis was enhanced by juvenile hormone (JH) treatment under the culture condition. Hence, we performed RNA-Seq analysis to elucidate the molecular mechanisms in controlling polyembryogenesis using C. floridanum. Nevertheless, C. floridanum genes do not have a functional gene annotation because of partial whole-genome sequence elucidation. Hence, we constructed a gene functional annotation pipeline for C. floridanum and performed a molecular network analysis in C. floridanum. Results: We extracted fluctuated genes from control and JH treatment molura after 48-h culture to assess molecular mechanisms in polyembryogenesis. Consequently, we obtained 11,117 transcripts and 217 differentially expressed genes in the JH treatment group compared with the control group. Whereas, we used the blastp program to assign whole C. floridanum transcripts to human gene. Remarkably, 76% of C. floridanum transcripts were assigned to human genes. Moreover, we determined platelet degranulation and fatty acid biosynthetic process, suppressing cell morphogenesis involved in the differentiation and integrin signaling pathway by the gene enrichment analysis in the JH treatment group compared with the control group. Furthermore, we noted that molecular interaction possibly associated with polyembryogenesis using Cytoscape. Conclusions: In this study, we constructed C. floridanum gene functional annotation pipeline and C. floridanum transcripts shared with homology to human genes during early embryo developmental stage. Additionally, this study establishes new molecular interactions associated with polyembryogenesis; these molecules could elucidate molecular mechanism in polyembryony, suggesting a possibility of using the molecular interaction in twinning of humans.

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Uncovering Potential Roles of Differentially Expressed Genes, Upstream Regulators, and Canonical Pathways in Endometriosis Using an In Silico Genomics Approach

Diagnostics ◽

10.3390/diagnostics10060416 ◽

2020 ◽

Vol 10 (6) ◽

pp. 416

Author(s):

Zeenat Mirza ◽

Umama A. Abdel-dayem

Keyword(s):

Gene Expression ◽

Differentially Expressed Genes ◽

Molecular Mechanisms ◽

Interaction Analysis ◽

Meta Analysis ◽

Cell Cycle Checkpoint ◽

Reproductive Age ◽

Differentially Expressed ◽

Checkpoint Control ◽

Canonical Pathways

Endometriosis is characterized by ectopic endometrial tissue implantation, mostly within the peritoneum, and affects women in their reproductive age. Studies have been done to clarify its etiology, but the precise molecular mechanisms and pathophysiology remain unclear. We downloaded genome-wide mRNA expression and clinicopathological data of endometriosis patients and controls from NCBI’s Gene Expression Omnibus, after a systematic search of multiple independent studies comprising 156 endometriosis patients and 118 controls to identify causative genes, risk factors, and potential diagnostic/therapeutic biomarkers. Comprehensive gene expression meta-analysis, pathway analysis, and gene ontology analysis was done using a bioinformatics-based approach. We identified 1590 unique differentially expressed genes (129 upregulated and 1461 downregulated) mapped by IPA as biologically relevant. The top upregulated genes were FOS, EGR1, ZFP36, JUNB, APOD, CST1, GPX3, and PER1, and the top downregulated ones were DIO2, CPM, OLFM4, PALLD, BAG5, TOP2A, PKP4, CDC20B, and SNTN. The most perturbed canonical pathways were mitotic roles of Polo-like kinase, role of Checkpoint kinase proteins in cell cycle checkpoint control, and ATM signaling. Protein–protein interaction analysis showed a strong network association among FOS, EGR1, ZFP36, and JUNB. These findings provide a thorough understanding of the molecular mechanism of endometriosis, identified biomarkers, and represent a step towards the future development of novel diagnostic and therapeutic options.

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Identification and Interaction Analysis of Significant Genes and MicroRNAs in Pterygium

BioMed Research International ◽

10.1155/2019/2767512 ◽

2019 ◽

Vol 2019 ◽

pp. 1-12 ◽

Cited By ~ 2

Author(s):

Siying He ◽

Hui Sun ◽

Yifang Huang ◽

Shiqi Dong ◽

Chen Qiao ◽

...

Keyword(s):

Differentially Expressed Genes ◽

Molecular Mechanisms ◽

Interaction Analysis ◽

Interaction Network ◽

Enrichment Analysis ◽

Functional Enrichment Analysis ◽

Gene Expression Omnibus ◽

Functional Enrichment ◽

Differentially Expressed ◽

Differentially Expressed Mirnas

Purpose. MiRNAs have been widely analyzed in the occurrence and development of many diseases, including pterygium. This study aimed to identify the key genes and miRNAs in pterygium and to explore the underlying molecular mechanisms. Methods. MiRNA expression was initially extracted and pooled by published literature. Microarray data about differentially expressed genes was downloaded from Gene Expression Omnibus (GEO) database and analyzed with the R programming language. Functional and pathway enrichment analyses were performed using the database for Annotation, Visualization and Integrated Discovery (DAVID). The protein-protein interaction network was constructed with the STRING database. The associations between chemicals, differentially expressed miRNAs, and differentially expressed genes were predicted using the online resource. All the networks were constructed using Cytoscape. Results. We found that 35 miRNAs and 301 genes were significantly differentially expressed. Functional enrichment analysis showed that upregulated genes were significantly enriched in extracellular matrix (ECM) organization, while downregulated genes were mainly involved in cell death and apoptotic process. Finally, we concluded the chemical-gene affected network, miRNA-mRNA interacted networks, and significant pathway network. Conclusion. We identified lists of differentially expressed miRNAs and genes and their possible interaction in pterygium. The networks indicated that ECM breakdown and EMT might be two major pathophysiological mechanisms and showed the potential significance of PI3K-Akt signalling pathway. MiR-29b-3p and collagen family (COL4A1 and COL3A1) might be new treatment target in pterygium.

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Transcriptional Insights into Key Genes and Pathways Underlying Muscovy Duck Subcutaneous Fat Deposition at Different Developmental Stages

Animals ◽

10.3390/ani11072099 ◽

2021 ◽

Vol 11 (7) ◽

pp. 2099

Author(s):

Liping Guo ◽

Congcong Wei ◽

Li Yi ◽

Wanli Yang ◽

Zhaoyu Geng ◽

...

Keyword(s):

Fatty Acid ◽

Differentially Expressed Genes ◽

Molecular Mechanisms ◽

Fatty Acid Biosynthesis ◽

Developmental Stages ◽

Subcutaneous Fat ◽

Fat Deposition ◽

Differentially Expressed ◽

Muscovy Duck ◽

Key Genes

Subcutaneous fat is a crucial trait for waterfowl, largely associated with meat quality and feed conversion rate. In this study, RNA-seq was used to identify differentially expressed genes of subcutaneous adipose tissue among three developmental stages (12, 35, and 66 weeks) in Muscovy duck. A total of 138 and 129 differentially expressed genes (DEGs) were identified between 35 and 12 weeks (wk), and 66 and 35 wk, respectively. Compared with 12 wk, subcutaneous fat tissue at 35 wk upregulated several genes related to cholesterol biosynthesis and fatty acid biosynthesis, including HSD17B7 and MSMO1, while it downregulated fatty acid beta-oxidation related genes, including ACOX1 and ACSL1. Notably, most of the DEGs (92.2%) were downregulated in 66 wk compared with 35 wk, consistent with the slower metabolism of aging duck. Protein network interaction and function analyses revealed GC, AHSG, FGG, and FGA were the key genes for duck subcutaneous fat from adult to old age. Additionally, the PPAR signaling pathway, commonly enriched between the two comparisons, might be the key pathway contributing to subcutaneous fat metabolism among differential developmental stages in Muscovy duck. These results provide several candidate genes and pathways potentially involved in duck subcutaneous fat deposition, expanding our understanding of the molecular mechanisms underlying subcutaneous fat deposition during development.

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Comprehensive analysis of differential expression profiles via transcriptome sequencing in SH-SY5Y cells infected with CV-A16

PLoS ONE ◽

10.1371/journal.pone.0241174 ◽

2020 ◽

Vol 15 (11) ◽

pp. e0241174

Author(s):

Yajie Hu ◽

Zhen Yang ◽

Shenglan Wang ◽

Danxiong Sun ◽

Mingmei Zhong ◽

...

Keyword(s):

Differentially Expressed Genes ◽

Transcriptome Sequencing ◽

Molecular Mechanisms ◽

Expression Profiles ◽

Transcriptome Profiling ◽

Differentially Expressed ◽

Control Group ◽

Protein Coding ◽

Qrt Pcr ◽

Protein Coding Genes

Coxsackievirus A16 (CV-A16) is one of the viruses that is most frequently associated with hand-foot-and-mouth disease (HFMD). Previous studies have shown that CV-A16 infections are mostly self-limiting, but in recent years, it has been gradually found that CV-A16 infections can also induce neurological complications and eventually cause death in children with HFMD. Moreover, no curative drugs or preventative vaccines have been developed for CV-A16 infection. Therefore, it is particularly important to investigate the mechanism of CV-A16 infection-induced neuropathy. In the current study, transcriptome sequencing technology was used to identify changes in the transcriptome of SH-SY5Y cells infected with CV-A16, which might hide the mechanism of CV-A16-induced neuropathology. The transcriptome profiling showed that 82,406,974, 108,652,260 and 97,753,565 clean reads were obtained in the Control, CV-A16-12 h and CV-A16-24 h groups, respectively. And it was further detected that a total of 136 and 161 differentially expressed genes in CV-A16-12 h and CV-A16-24 h groups, respectively, when compared with Control group. Then, to explore the mechanism of CV-A16 infection, we focused on the common differentially expressed genes at different time points of CV-A16 infection and found that there were 34 differentially expressed genes based on which clustering analysis and functional category enrichment analysis were performed. The results indicated that changes in oxidation levels were particularly evident in the GO term analysis, while only the “Gonadotropin-releasing hormone receptor pathway” was enriched in the KEGG pathway analysis, which might be closely related to the neurotoxicity caused by CV-A16 infection. Meanwhile, the ID2 closely related to nervous system has been demonstrated to be increased during CV-A16 infection. Additionally, the data on differentially expressed non-protein-coding genes of different types within the transcriptome sequencing results were analyzed, and it was speculated that these dysregulated non-protein-coding genes played a pivotal role in CV-A16 infection. Ultimately, qRT-PCR was utilized to validate the transcriptome sequencing findings, and the results of qRT-PCR were in agreement with the transcriptome sequencing data. In conclusion, transcriptome profiling was carried out to analyze response of SH-SY5Y cells to CV-A16 infection. And our findings provide important information to elucidate the possible molecular mechanisms which were linked to the neuropathogenesis of CV-A16 infection.

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Identification and Verification of Candidate Genes Regulating Human Umbilical Vein Endothelial Cells Behavior Under Hyperglycemia

10.21203/rs.3.rs-26855/v1 ◽

2020 ◽

Author(s):

XIAOYE MA ◽

YUCHEN ZHOU ◽

JUNCHAO XIE ◽

GUILIN MENG ◽

YICHEN ZHAO ◽

...

Keyword(s):

Endothelial Cells ◽

Differentially Expressed Genes ◽

Molecular Mechanisms ◽

Umbilical Vein ◽

Life Quality ◽

Differentially Expressed ◽

Therapeutic Interventions ◽

Control Group ◽

Human Umbilical Cord ◽

Qrt Pcr

Abstract Background: Diabetes is a metabolic disease that has been widely demonstrated to be correlated with many microvascular and macrovascular diseases that seriously damage the patient’s life quality. This study intended to investigate the underlying molecular mechanisms of endothelial dysfunction under hyperglycemia. Methods: The gene expression profile of GSE49524 was downloaded and differentially expressed genes (DEGs) in hyperglycemia human umbilical cord endothelial cells (HUVECs) samples compared with normoglycemia HUVECs samples were identified by R software. Afterward, we analyzed the data by applying a combination of the bioinformatics method and used the microRNAs (miRNAs) databases to predict microRNAs that target key genes. The expression of the top 10 differentially expressed genes was validated through quantitative real-time PCR (qRT-PCR). Results: A total of 65 genes were distinguished as DEGs. The dominant GO (gene ontology) terms and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways which were significantly overrepresented in the hyperglycemia HUVECs were identified. The results of the protein-protein interaction networks demonstrated that fibronectin 1 (FN1) is of the highest degree. In addition, several predicted miRNAs that target FN1 were obtained too. The further verification of the top 10 DEGs through qRT-PCR illustrated that nine of the up-regulated DEGs were up-regulated significantly in the hyperglycemia group when compared to the control group. Conclusions:This exploratory study may help to prompt an understanding of the underlying molecular mechanisms of the effect of hyperglycemia on the behavior of HUVECs and contribute to the production of effective therapeutic interventions.

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Transcriptome analysis of fasting caecotrophy on hepatic lipid metabolism in New Zealand rabbits

10.1101/493957 ◽

2018 ◽

Author(s):

yadong wang ◽

Huifen Xu ◽

Guirong Sun ◽

Mingming Xue ◽

Shuaijie Sun ◽

...

Keyword(s):

Growth Rate ◽

Lipid Metabolism ◽

Growth Performance ◽

Differentially Expressed Genes ◽

Molecular Mechanisms ◽

Effective Means ◽

Differentially Expressed ◽

Control Group ◽

Rna Seq ◽

Final Body Weight

Background: Rabbit produce two kinds of feces: hard and soft feces, and they have a preference for consuming the latter. Although this habit of rabbits has been reported for many years, little is known on whether this behavior will impact growth performance and metabolism. The RNA-Seq technology is an effective means of analyzing transcript groups to clarify molecular mechanisms. The aim of the present study was to investigate the effects of fasting caecotrophy on growth performance and lipid metabolism in rabbits. Results: Our results indicated that, compared with the control group, the final body weight, weight gain, liver weight, specific growth rate and feed conversion ratio were all decreased in the experimental group (P<0.05). Oil red staining of the liver tissue indicated that fasting caecotrophy resulted in decrease of lipid droplet accumulation. RNA sequencing (RNA-seq) analysis revealed a total of 301.2 million raw reads approximately 45.06 Gb of high-quality clean data. The data were mapped to the rabbit genome (http://www.ensembl.org/Oryctolagus_cuniculus). After a five step filtering process, 14964 genes were identified, including 444 differentially expressed genes (P<0.05, foldchange≥1). Especially for remarkable changes of genes related to lipid metabolism, RT-PCR further validated the remarkable decrease of these genes in fasting caecotrophy group, including CYP7A1, PPARG, ABCA1, ABCB1, ABCG1, GPAM, SREBP, etc. KEGG annotation of the differentially expressed genes indicated that the main pathways affected were retinol metabolism, pentose and glucuronide interactions, starch and sucrose metabolism, fatty acid degradation, steroid hormone biosynthesis. Conclusion: In conclusion, the present study revealed that banning caecotrophy reduced growth rate and altered lipid metabolism, our results laid instructive basis for rabbit feeding and production. These data also provides a reference for studying the effects of soft feces on other small herbivores.

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cDNA-RDA of genes expressed in fetal and adult lungs identifies factors important in development and function

AJP Lung Cellular and Molecular Physiology ◽

10.1152/ajplung.2000.278.2.l284 ◽

2000 ◽

Vol 278 (2) ◽

pp. L284-L293 ◽

Cited By ~ 8

Author(s):

Paul Cooper ◽

Beatrice Mueck ◽

Shida Yousefi ◽

Suzanne Potter ◽

Gabor Jarai

Keyword(s):

Differentially Expressed Genes ◽

Lung Development ◽

Molecular Mechanisms ◽

Sequence Similarity ◽

Fetal Lung ◽

Differentially Expressed ◽

Representational Difference Analysis ◽

Lung Protection ◽

Human Genes ◽

And Function

The identification of genetic factors important in lung development and function will help in understanding the underlying molecular mechanisms of respiratory disease. Representational difference analysis of cDNA (cDNA-RDA) is a PCR-based subtractive enrichment procedure for the isolation of differentially expressed genes. We performed cDNA-RDA and isolated genes expressed more abundantly in fetal and adult lungs. Fifty-four clones potentially representing genes with higher transcript levels in the fetal lung were sequenced. Sequence similarity searches indicated that these clones included 12 known genes, a discoidin-like domain-containing gene, six expressed sequence tags (ESTs), and one novel sequence. Fifty-six clones potentially representing genes expressed more abundantly in the adult lung were also cloned and sequenced. Of these, 16 known human genes were represented along with two sequences significantly similar to known mouse genes and two novel sequences. Several of these known genes are implicated in stress response and lung protection. Thus cDNA-RDA was successfully used to isolate known and novel differentially expressed genes, which putatively play an important role in human lung development.

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Identification of Differentially Expressed Genes Associated with Papillary Thyroid Carcinoma

Combinatorial Chemistry & High Throughput Screening ◽

10.2174/1386207323666200402085832 ◽

2020 ◽

Vol 23 (6) ◽

pp. 546-553

Author(s):

Hongyuan Cui ◽

Mingwei Zhu ◽

Junhua Zhang ◽

Wenqin Li ◽

Lihui Zou ◽

...

Keyword(s):

Papillary Thyroid Carcinoma ◽

Thyroid Carcinoma ◽

Differentially Expressed Genes ◽

Molecular Mechanisms ◽

Cellular Proliferation ◽

Mrna Level ◽

Thyroid Tissue ◽

Differentially Expressed ◽

Thyroid Tumors ◽

Papillary Thyroid

Objective: Next-generation sequencing (NGS) was performed to identify genes that were differentially expressed between normal thyroid tissue and papillary thyroid carcinoma (PTC). Materials & Methods: Six candidate genes were selected and further confirmed with quantitative real-time polymerase chain reaction (qRT-PCR), and immunohistochemistry in samples from 24 fresh thyroid tumors and adjacent normal tissues. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis was used to investigate signal transduction pathways of the differentially expressed genes. Results: In total, 1690 genes were differentially expressed between samples from patients with PTC and the adjacent normal tissue. Among these, SFRP4, ZNF90, and DCN were the top three upregulated genes, whereas KIRREL3, TRIM36, and GABBR2 were downregulated with the smallest p values. Several pathways were associated with the differentially expressed genes and involved in cellular proliferation, cell migration, and endocrine system tumor progression, which may contribute to the pathogenesis of PTC. Upregulation of SFRP4, ZNF90, and DCN at the mRNA level was further validated with RT-PCR, and DCN expression was further confirmed with immunostaining of PTC samples. Conclusion: These results provide new insights into the molecular mechanisms of PTC. Identification of differentially expressed genes should not only improve the tumor signature for thyroid tumors as a diagnostic biomarker but also reveal potential targets for thyroid tumor treatment.

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