High-throughput sequencing reveals hub genes for human early embryonic development arrest in vitro fertilization: a pilot study
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ABSTRACT:
SUBMITTER: Zhang W
PROVIDER: S-EPMC10684309 | biostudies-literature | 2023 Jan
REPOSITORIES: biostudies-literature
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Project description:Parthenogenesis activation (PA), as an important artificial breeding method, can stably preserve the dominant genotype of a species. However, the delayed development of PA embryos is still overly severe and largely leads to pre-implantation failure in pigs. The mechanisms underlying the deficiencies of PA embryos have not been completely understood. For further understanding of the molecular mechanism behind PA embryo failure, we performed transcriptome analysis among pig oocytes (meiosis II, MII) and early embryos at three developmental stages (zygote, morula, and blastocyst) in vitro fertilization (IVF) and PA group. Totally, 11,110 differentially expressed genes (DEGs), 4694 differentially expressed lincRNAs (DELs) were identified, and most DEGs enriched the regulation of apoptotic processes. Through cis- and trans-manner functional prediction, we found that hub lincRNAs were mostly involved in abnormal parthenogenesis embryonic development. In addition, twenty DE imprinted genes showed that some paternally imprinted genes in IVF displayed higher expression than that in PA. Notably, we identified that three DELs of imprinted genes (MEST, PLAGL1, and DIRAS3) were up regulated in IVF, and there was no significant change in PA group. Disordered expression of key genes for embryonic development might play key roles in abnormal parthenogenesis embryonic development. Our study indicates that embryos derived from different production techniques have varied in vitro development to the blastocyst stage, and they also affect the transcription level of corresponding genes, such as imprinted genes. This work will help future research on these genes and molecular-assisted breeding for pig parthenotes.
| S-EPMC8535918 | biostudies-literature
Project description:Demand for in vitro fertilization (IVF) treatment is growing; however, success rates remain low partly due to difficulty in selecting the best embryo to be transferred. Current manual assessments are subjective and may not take advantage of the most informative moments in embryo development. Here, we apply convolutional neural networks (CNNs) to identify key windows in pre-implantation human development that can be linked to embryo viability and are therefore suitable for the early grading of IVF embryos. We show how machine learning models trained at these developmental time points can be used to refine overall embryo viability assessment. Exploiting the well-known capabilities of transfer learning, we illustrate the performance of CNN models for very limited datasets, paving the way for the use on a clinic-by-clinic basis, catering for local data heterogeneity.
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Project description:Research in model organisms relies on unspoken assumptions about the conservation of protein-protein interactions across species, yet several analyses suggest such conservation is limited. Fortunately, for many purposes the crucial issue is not global conservation of interactions, but preferential conservation of functionally important ones. An observed bias towards essentiality in highly-connected proteins implies the functional importance of such "hubs". We therefore define the notion of degree-conservation and demonstrate that hubs are preferentially degree-conserved. We show that a protein is more likely to be a hub if it has a high-degree ortholog, and that once a protein becomes a hub, it tends to remain so. We also identify a positive correlation between the average degree of a protein and the conservation of its interaction partners, and we find that the conservation of individual hub interactions is surprisingly high. Our work has important implications for prediction of protein function, computational inference of PPIs, and interpretation of data from model organisms.
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Project description:As a vital metabolic and immune organ in animals, the liver plays an important role in protein synthesis, detoxification, metabolism, and immune defense. The primary research purpose of this study was to reveal the effect of breast-feeding, weaning transition, and weaning on the gene expression profile in the goat kid liver and to elucidate the transcriptome-level signatures associated with liver metabolic adaptation. Therefore, transcriptome sequencing was performed on liver tissues, which was collected at 1 day (D1), 2 weeks (W2), 4 weeks (W4), 8 weeks (W8), and 12 weeks (W12) after birth in Laiwu black goats at five different time-points, with five goats at each time point. From 25 libraries, a total of 37497 mRNAs were found to be expressed in goat kid livers, and 1271 genes were differentially expressed between at least two of the five time points. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses revealed that these genes were annotated as an extracellular region fraction, exhibiting monooxygenase activity, positive regulation of T cell activation, mitotic spindle mid-region assembly, cytokinesis, cytoskeleton-dependent cytokinesis, regulation of cytokinesis, regulation of lymphocyte proliferation, and so on. In addition, it mainly deals with metabolism, endocrine, cell proliferation and apoptosis, and immune processes. Finally, a gene regulatory network was constructed, and a total of 14 key genes were screened, which were mainly enriched for cell growth and development, endocrine, immune, and signal transduction-related pathways. Our results provide new information on the molecular mechanisms and pathways involved in liver development, metabolism, and immunity of goats.
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Project description:This is a method for zebrafish sperm cryopreservation that is an adaptation of the Harvey method (Harvey et al., 1982). We have introduced two changes to the original protocol that both streamline the procedure and increase sample uniformity. First, we normalize all sperm volumes using freezing media that does not contain the cryoprotectant. Second, cryopreserved sperm are stored in cryovials instead of capillary tubes. The rates of sperm freezing and thawing (delta degrees C/time) are probably the two most critical variables to control in this procedure. For this reason, do not substitute different tubes for those specified. Working in teams of 2 it is possible to freeze the sperm of 100 males per team in approximately 2 hrs. Sperm cryopreserved using this protocol has an average of 25% fertility (measured as the number of viable embryos generated in an in vitro fertilization divided by the total number of eggs fertilized) and this percent fertility is stable over many years.
| S-EPMC2785217 | biostudies-literature
Project description:Age-related cataract (ARC) is a major cause of blindness. Long non-coding RNAs (lncRNAs) are a heterogeneous class of RNAs that are non-protein-coding transcripts >200 nucleotides in length. LncRNAs are involved in various critical biological processes, such as chromatin remodeling, gene transcription, and protein transport and trafficking. Furthermore, the dysregulation of lncRNAs causes a number of complex human diseases, including coronary artery diseases, autoimmune diseases, neurological disorders and various cancers. However, the role of lncRNA in cataract remains unclear. Therefore, in the present study, lens anterior capsular membrane was collected from normal subjects and patients with ARC and total RNA was extracted. High-throughput sequencing was applied to detect differentially expressed lncRNAs and mRNAs. The analysis identified a total of 42,556 candidate differentially expressed mRNAs (27,447 +15,109) and a total of 7,041 candidate differentially expressed lncRNAs (4,146 + 2,895). Through bioinformatics analysis, the significant differential expression of novel lincRNA was observed and its possible molecular mechanism was explored. Reverse transcription-quantitative polymerase chain reaction was used to validate the different expression levels of selected lncRNAs. These findings may lead to the development of novel strategies for genetic diagnosis and gene therapy.
| S-EPMC5716429 | biostudies-other
Project description:BackgroundEsophageal squamous cell carcinoma (ESCA) is a type of cancer that starts in the cells lining the esophagus, the tube connecting the throat to the stomach. It is known for its aggressive nature and poor prognosis. Understanding the key factors that drive this cancer is crucial for developing better diagnostic tools and treatments.MethodsGene expression profiles of ESCA were analyzed using Gene Expression Omnibus (GEO) datasets (GSE23400, GSE29001, GSE92396, and GSE1420) from the GEO database. Differentially expressed genes (DEGs) were identified using the limma package, and a protein-protein interaction (PPI) network was constructed using the STRING database. Hub genes were identified based on the degree method. Further validation was performed through reverse transcription quantitative PCR (RT-qPCR), mutational and copy number variation (CNV) analysis via the cBioPortal database, promoter methylation analysis using the OncoDB and GSCA databases, survival analysis, immune infiltration analysis through the GSCA database, and functional assays, including knockdown of key genes.ResultsWe identified four key hub genes, COL3A1, COL4A1, COL5A2, and CXCL8 that play significant roles in ESCA. These genes were highly expressed in ESCA tissues and cell lines, with expression levels significantly (p-value < 0.001) elevated compared to normal controls. Receiver operating characteristic (ROC) curve analysis revealed exceptional diagnostic performance for all four genes, with area under the curve (AUC) values of 1.0, indicating perfect sensitivity and specificity in distinguishing ESCA from normal controls. Mutational analysis revealed that COL3A1 was altered in 67% of ESCA samples, primarily through missense mutations, while COL5A2 exhibited alterations in 50% of the samples, including splice site and missense mutations. Additionally, gene amplification patterns were observed in all four hub genes, further validating their oncogenic potential in ESCA progression. A significant (p-value < 0.05) promoter hypomethylation was detected in these genes, suggesting a potential regulatory role in their expression. Functional assays demonstrated that knocking down COL3A1 and COL4A1 led to decreased cell proliferation, colony formation, and migration, indicating their critical roles in tumor progression. Additionally, these genes were involved in pathways related to the extracellular matrix and immune system modulation.ConclusionCOL3A1, COL4A1, COL5A2, and CXCL8 are crucial in ESCA development and progression, particularly in remodeling the extracellular matrix, modulating the immune system, and promoting metastasis. These findings suggest that these genes could serve as potential biomarkers for diagnosing ESCA and targets for future therapies. Future research should focus on in vivo validation of these findings and clinical testing to assess the therapeutic potential of targeting these genes in ESCA treatment.
| S-EPMC11908063 | biostudies-literature
Project description:Early embryonic arrest is one of the major causes of female infertility. However, because of difficulties in phenotypic evaluation, genetic determinants of human early embryonic arrest are largely unknown. With the development of assisted reproductive technology, the phenotype of early human embryonic arrest can now be carefully evaluated. Here, we describe a consanguineous family with a recessive inheritance pattern of female infertility characterized by recurrent early embryonic arrest in cycles of in vitro fertilization (IVF) and intracytoplasmic sperm injection (ICSI). We have identified a homozygous PADI6 nonsense mutation (c.1141C>T [p.Gln381(?)]) that is responsible for the phenotype. Mutational analysis of PADI6 in a cohort of 36 individuals whose embryos displayed developmental arrest identified two affected individuals with compound-heterozygous mutations (c.2009_2010del [p.Glu670Glyfs(?)48] and c.633T>A [p.His211Gln]; c.1618G>A [p.Gly540Arg] and c.970C>T [p.Gln324(?)]). Immunostaining indicated a lack of PADI6 in affected individuals' oocytes. In addition, the amount of phosphorylated RNA polymerase II and expression levels of seven genes involved in zygotic genome activation were reduced in the affected individuals' embryos. This phenotype is consistent with Padi6 knockout mice. These findings deepen our understanding of the genetic basis of human early embryonic arrest, which has been a largely ignored Mendelian phenotype. Our findings lay the foundation for uncovering other genetic causes of infertility resulting from early embryonic arrest.
| S-EPMC5010645 | biostudies-literature
Project description:Mouse E14 embryonic stem cells (ESCs) are the most used ESC line, often employed for genome-wide studies involving next generation sequencing analysis [1-5]. More than 2 × 10 E9 sequences made on Illumina platform derived from the genome of E14 embryonic stem cells cultured in our laboratory were used to build a database of about 2.7 × 10 E6 single nucleotide variant [6]. The database was validated using other two sequencing datasets from other laboratory and high overlap was observed. The identified variants are enriched on intergenic regions, but several thousands reside on gene exons and regulatory regions, such as promoters, enhancers, splicing site and untranslated regions of RNA, thus indicating high probability of an important functional impact on the molecular biology of these cells. We created a new E14 genome assembly including the new identified variants and used it to map reads from next generation sequencing data generated in our laboratory or in others on E14 cell line. We observed an increase in the number of mapped reads of about 5%. CpG dinucleotide showed the higher variation frequency, probably because it could be a target of DNA methylation. Data were deposited in GEO datasets under reference GSM1283021 and here: http://epigenetics.hugef-research.org/data.php.
| S-EPMC4535964 | biostudies-literature
Project description:BackgroundRecent evidence supports the proposal that the observed diversity of animal body plans has been produced through alterations to the complexity of the regulatory genome rather than increases in the protein-coding content of a genome. One significant form of gene regulation is the contribution made by the non-coding content of the genome. Non-coding RNAs play roles in embryonic development of animals and these functions might be expected to evolve rapidly. Using next-generation sequencing and in situ hybridization, we have examined the miRNA content of early honeybee embryos.ResultsThrough small RNA sequencing we found that 28% of known miRNAs are expressed in the early embryo. We also identified developmentally expressed microRNAs that are unique to the Apoidea clade. Examination of expression patterns implied these miRNAs have roles in patterning the anterior-posterior and dorso-ventral axes as well as the extraembryonic membranes. Knockdown of Dicer, a key component of miRNA processing, confirmed that miRNAs are likely to have a role in patterning these tissues.ConclusionsExamination of the expression patterns of novel miRNAs, some unique to the Apis group, indicated that they are likely to play a role in early honeybee development. Known miRNAs that are deeply conserved in animal phyla display differences in expression pattern between honeybee and Drosophila, particularly at early stages of development. This may indicate miRNAs play a rapidly evolving role in regulating developmental pathways, most likely through changes to the way their expression is regulated.
| S-EPMC3562263 | biostudies-literature