P–272 The aneuploid embryo secretome

2021 ◽  
Vol 36 (Supplement_1) ◽  
Author(s):  
M Piccolomini ◽  
C Garcia ◽  
E L Turco ◽  
I Massaia ◽  
M Orteiro ◽  
...  

Abstract Study question Does the metabolomic analysis of the embryonic culture medium predict the embryo aneuploidy? Summary answer The presence and quantity of some metabolites in the culture medium can select euploid embryos for transfer. What is known already Advances in analytical techniques for metabolomics have brought the possibility of better tools for the characterization of molecules. Embryonic metabolism can be used as a good indicator of viability, regardless of the morphology of the blastocysts, since differences were observed in the metabolic activities between the days of embryo development and in the rates of live births. Study design, size, duration 17 patients had their embryos biopsied between January to July 2019 in a human reproduction laboratory. All cases had PGT-A indication and after the biopsy, the embryos were frozen. The culture medium samples were individually prepared for metabolites extraction according to the Bligh and Dyer protocol. Controlled ovarian stimulation and dose adjustments according to the response of each patient. The metabolomics analysis was performed by mass spectrometry. Participants/materials, setting, methods Ovum pick up will be performed 35 hours after r-hCG administration. The embryos were kept in individual 50ul drops until the blastocyst stage. The biopsy was performed in 26 blastocysts. The samples were sent to the 337 metabolites analysis by mass spectrometry. 15 molecules with the highest score on the PLS-Da was submitted the ROC curves to illustrate the power of the metabolic ploidy analysis. Besides, we performed the functional enrichment analysis for each group. Main results and the role of chance After the genetic analysis by PGT-a, 10 aneuploid embryos and 16 euploid embryos were found. Comparing the quantitative target metabolomic analysis of the 337 metabolites in the embryo culture medium, we observed the L-Alanine, Cytosine, Guanosine monophosphate, Homocysteine, Hypoxanthine, and Xanthine hiperrepresented in the aneuploid embryos, and the Citrulline, L-Glutamic acid, Kynurenine, L-Leucine, Methionine, Ornithine, L-Phenylalanine, L-Tyrosine, L-Valine were hiperrepresented in the euploid embryos. Through the ROC curve, we can verify AUC = 0.987. This result suggests that the analysis of euploid embryos through the metabolomic analysis of the culture medium is valid to be used as a noninvasive aneuploid diagnostic. The functional enrichment analysis shows the urea cycle and the glycine and serine metabolism as the principal function alter by aneuploid. Limitations, reasons for caution Small number of samples and not validate sample group. Wider implications of the findings: Further studies are needed to validate these findings for the diagnostic of embryo euploidy. Trial registration number N/A

2021 ◽  
Vol 36 (Supplement_1) ◽  
Author(s):  
M Orteiro ◽  
M Piccolomini ◽  
C Garcia ◽  
I Massaia ◽  
A Alvarenga ◽  
...  

Abstract Study question Does the analysis of the metabolites of the embryonic culture medium can predict the sex of the embryo? Summary answer The presence and quantity of some metabolites in the culture medium can predict the sex of the human embryos. What is known already Advances in analytical techniques for metabolomics have brought the possibility of better tools for the characterization of molecules. Embryonic metabolism can be used as a good indicator of viability, regardless of the morphology of the blastocysts, since differences were observed in the metabolic activities between the days of embryo development and in the rates of live births. Study design, size, duration 16 patients had their embryos biopsied between the months of January to July 2019 in a human reproduction laboratory. All cases had PGT-A indication and after the biopsy, the embryos were frozen. The culture medium samples were individually prepared for metabolites extraction according to the Bligh and Dyer protocol. Controlled ovarian stimulation and dose adjustments according to the response of each patient. The metabolomics analysis was performed by mass spectrometry. Participants/materials, setting, methods Follicular puncture were performed 35 hours after r-hCG. The eggs were kept in individual culture until the blastocyst stage. The blastocysts biopsy was performed (20). After the culture medium was sent to the 337 metabolites analysis by mass spectrometry. 14 molecules with the highest score on the PLS-Da was submitted to the ROC curves showing the power of metabolic analysis to predict the sex of euploid embryos. Besides, we performed the functional enrichment analysis. Main results and the role of chance After the genetic analysis by PGT-a, we obtain 20 euploid embryos, being 12 female embryos and 08 male embryos. Comparing the quantitative target metabolomic analysis of the 337 metabolites in the embryo culture medium, we observed the Asymmetric dimethylarginine, FAD, Malic Acid, Serotonin, increased in female embryos and Adenosine monophosphate, L-Alanine, L-Arginine, Cysteamine, DL-Dopa, Flavin Mononucleotide, Methionine sulfone, Nicotinic acid, L-Tyrosine, Uracil in male embryos. Through the ROC curve, we can verify AUC = 0.937. This result suggests that the metabolomic analysis of the culture medium is valid to be used as a complement of PGT-A to know embryo sex diagnostic. The functional enrichment analysis shows the Asymmetric dimethylarginine and Malic Sulfone metabolism as the principal function alter by female embryos. Limitations, reasons for caution Small number of samples Wider implications of the findings: Further studies are needed to validate these findings for the diagnostic of sex embryos Trial registration number N/A


2021 ◽  
Vol 12 ◽  
Author(s):  
Decai Xiang ◽  
Baoyu Jia ◽  
Jianxiong Guo ◽  
Qingyong Shao ◽  
Qionghua Hong ◽  
...  

Cryopreservation of porcine cloned zygotes has important implications for biotechnology and biomedicine research; however, lower embryo developmental potential remains an urgent problem to be resolved. For exploring the sublethal cryodamages during embryo development, this study was designed to acquire the mRNA and long non-coding RNA (lncRNA) profiles of 2-cells, 4-cells and blastocysts derived from vitrified porcine cloned zygotes using transcriptome sequencing. We identified 167 differentially expressed (DE) mRNAs and 516 DE lncRNAs in 2-cell stage, 469 DE mRNAs and 565 lncRNAs in 4-cell stage, and 389 DE mRNAs and 816 DE lncRNAs in blastocyst stage. Functional enrichment analysis revealed that the DE mRNAs during embryo development were involved in many regulatory mechanisms related to cell cycle, cell proliferation, apoptosis, metabolism and others. Moreover, the target genes of DE lncRNAs in the three embryonic stages were also enriched in many key GO terms or pathways such as “defense response”, “linoleic acid metabolic process”, “embryonic axis specification”, “negative regulation of protein neddylation”, etc., In conclusion, the present study provided comprehensive transcriptomic data about mRNAs and lncRNAs for the vitrified porcine cloned zygotes during different developmental stages, which contributed to further understand the potential cryodamage mechanisms responsible for impaired embryo development.


2019 ◽  
Vol 14 (7) ◽  
pp. 591-601 ◽  
Author(s):  
Aravind K. Konda ◽  
Parasappa R. Sabale ◽  
Khela R. Soren ◽  
Shanmugavadivel P. Subramaniam ◽  
Pallavi Singh ◽  
...  

Background: Chickpea is a nutritional rich premier pulse crop but its production encounters setbacks due to various stresses and understanding of molecular mechanisms can be ascribed foremost importance. Objective: The investigation was carried out to identify the differentially expressed WRKY TFs in chickpea in response to herbicide stress and decipher their interacting partners. Methods: For this purpose, transcriptome wide identification of WRKY TFs in chickpea was done. Behavior of the differentially expressed TFs was compared between other stress conditions. Orthology based cofunctional gene networks were derived from Arabidopsis. Gene ontology and functional enrichment analysis was performed using Blast2GO and STRING software. Gene Coexpression Network (GCN) was constructed in chickpea using publicly available transcriptome data. Expression pattern of the identified gene network was studied in chickpea-Fusarium interactions. Results: A unique WRKY TF (Ca_08086) was found to be significantly (q value = 0.02) upregulated not only under herbicide stress but also in other stresses. Co-functional network of 14 genes, namely Ca_08086, Ca_19657, Ca_01317, Ca_20172, Ca_12226, Ca_15326, Ca_04218, Ca_07256, Ca_14620, Ca_12474, Ca_11595, Ca_15291, Ca_11762 and Ca_03543 were identified. GCN revealed 95 hub genes based on the significant probability scores. Functional annotation indicated role in callose deposition and response to chitin. Interestingly, contrasting expression pattern of the 14 network genes was observed in wilt resistant and susceptible chickpea genotypes, infected with Fusarium. Conclusion: This is the first report of identification of a multi-stress responsive WRKY TF and its associated GCN in chickpea.


BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Zhenyang Liao ◽  
Xunxiao Zhang ◽  
Shengcheng Zhang ◽  
Zhicong Lin ◽  
Xingtan Zhang ◽  
...  

Abstract Background Structural variations (SVs) are a type of mutations that have not been widely detected in plant genomes and studies in animals have shown their role in the process of domestication. An in-depth study of SVs will help us to further understand the impact of SVs on the phenotype and environmental adaptability during papaya domestication and provide genomic resources for the development of molecular markers. Results We detected a total of 8083 SVs, including 5260 deletions, 552 tandem duplications and 2271 insertions with deletion being the predominant, indicating the universality of deletion in the evolution of papaya genome. The distribution of these SVs is non-random in each chromosome. A total of 1794 genes overlaps with SV, of which 1350 genes are expressed in at least one tissue. The weighted correlation network analysis (WGCNA) of these expressed genes reveals co-expression relationship between SVs-genes and different tissues, and functional enrichment analysis shows their role in biological growth and environmental responses. We also identified some domesticated SVs genes related to environmental adaptability, sexual reproduction, and important agronomic traits during the domestication of papaya. Analysis of artificially selected copy number variant genes (CNV-genes) also revealed genes associated with plant growth and environmental stress. Conclusions SVs played an indispensable role in the process of papaya domestication, especially in the reproduction traits of hermaphrodite plants. The detection of genome-wide SVs and CNV-genes between cultivated gynodioecious populations and wild dioecious populations provides a reference for further understanding of the evolution process from male to hermaphrodite in papaya.


Open Medicine ◽  
2020 ◽  
Vol 15 (1) ◽  
pp. 672-688
Author(s):  
Yanbo Dong ◽  
Siyu Lu ◽  
Zhenxiao Wang ◽  
Liangfa Liu

AbstractThe chaperonin-containing T-complex protein 1 (CCT) subunits participate in diverse diseases. However, little is known about their expression and prognostic values in human head and neck squamous cancer (HNSC). This article aims to evaluate the effects of CCT subunits regarding their prognostic values for HNSC. We mined the transcriptional and survival data of CCTs in HNSC patients from online databases. A protein–protein interaction network was constructed and a functional enrichment analysis of target genes was performed. We observed that the mRNA expression levels of CCT1/2/3/4/5/6/7/8 were higher in HNSC tissues than in normal tissues. Survival analysis revealed that the high mRNA transcriptional levels of CCT3/4/5/6/7/8 were associated with a low overall survival. The expression levels of CCT4/7 were correlated with advanced tumor stage. And the overexpression of CCT4 was associated with higher N stage of patients. Validation of CCTs’ differential expression and prognostic values was achieved by the Human Protein Atlas and GEO datasets. Mechanistic exploration of CCT subunits by the functional enrichment analysis suggests that these genes may influence the HNSC prognosis by regulating PI3K-Akt and other pathways. This study implies that CCT3/4/6/7/8 are promising biomarkers for the prognosis of HNSC.


2021 ◽  
Vol 28 (1) ◽  
pp. 20-33
Author(s):  
Lydia-Eirini Giannakou ◽  
Athanasios-Stefanos Giannopoulos ◽  
Chrissi Hatzoglou ◽  
Konstantinos I. Gourgoulianis ◽  
Erasmia Rouka ◽  
...  

Haemophilus influenzae (Hi), Moraxella catarrhalis (MorCa) and Pseudomonas aeruginosa (Psa) are three of the most common gram-negative bacteria responsible for human respiratory diseases. In this study, we aimed to identify, using the functional enrichment analysis (FEA), the human gene interaction network with the aforementioned bacteria in order to elucidate the full spectrum of induced pathogenicity. The Human Pathogen Interaction Database (HPIDB 3.0) was used to identify the human proteins that interact with the three pathogens. FEA was performed via the ToppFun tool of the ToppGene Suite and the GeneCodis database so as to identify enriched gene ontologies (GO) of biological processes (BP), cellular components (CC) and diseases. In total, 11 human proteins were found to interact with the bacterial pathogens. FEA of BP GOs revealed associations with mitochondrial membrane permeability relative to apoptotic pathways. FEA of CC GOs revealed associations with focal adhesion, cell junctions and exosomes. The most significantly enriched annotations in diseases and pathways were lung adenocarcinoma and cell cycle, respectively. Our results suggest that the Hi, MorCa and Psa pathogens could be related to the pathogenesis and/or progression of lung adenocarcinoma via the targeting of the epithelial cellular junctions and the subsequent deregulation of the cell adhesion and apoptotic pathways. These hypotheses should be experimentally validated.


AMB Express ◽  
2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Zhiyong Liu ◽  
Kai Dang ◽  
Cunzhi Li ◽  
Junhong Gao ◽  
Hong Wang ◽  
...  

Abstract Hexanitrohexaazaisowurtzitane (CL-20) is a compound with a polycyclic cage and an N-nitro group that has been shown to play an unfavorable role in environmental fate, biosafety, and physical health. The aim of this study was to isolate the microbial community and to identify a single microbial strain that can degrade CL-20 with desirable efficiency. Metagenomic sequencing methods were performed to investigate the dynamic changes in the composition of the community diversity. The most varied genus among the microbial community was Pseudomonas, which increased from 1.46% to 44.63% during the period of incubation (MC0–MC4). Furthermore, the new strain was isolated and identified from the activated sludge by bacterial morphological and 16s rRNA sequencing analyses. The CL-20 concentrations decreased by 75.21 μg/mL and 74.02 μg/mL in 48 h by MC4 and Pseudomonas sp. ZyL-01, respectively. Moreover, ZyL-01 could decompose 98% CL-20 of the real effluent in 14 day’s incubation with the glucose as carbon source. Finally, a draft genome sequence was obtained to predict possible degrading enzymes involved in the biodegradation of CL-20. Specifically, 330 genes that are involved in energy production and conversion were annotated by Gene Ontology functional enrichment analysis, and some of these candidates may encode enzymes that are responsible for CL-20 degradation. In summary, our studies indicate that microbes might be a valuable biological resource for the treatment of environmental contamination caused by CL-20 and that Pseudomonas sp. ZyL-01 might be a promising candidate for eradicating CL-20 to achieve a more biosafe environment and improve public health.


2020 ◽  
Vol 2020 ◽  
pp. 1-8
Author(s):  
Yuntao Shi ◽  
Yingying Zhuang ◽  
Jialing Zhang ◽  
Mengxue Chen ◽  
Shangnong Wu

Objective. Although noncoding RNAs, especially the microRNAs, have been found to play key roles in CRC development in intestinal tissue, the specific mechanism of these microRNAs has not been fully understood. Methods. GEO and TCGA database were used to explore the microRNA expression profiles of normal mucosa, adenoma, and carcinoma. And the differential expression genes were selected. Computationally, we built the SVM model and multivariable Cox regression model to evaluate the performance of tumorigenic microRNAs in discriminating the adenomas from normal tissues and risk prediction. Results. In this study, we identified 20 miRNA biomarkers dysregulated in the colon adenomas. The functional enrichment analysis showed that MAPK activity and MAPK cascade were highly enriched by these tumorigenic microRNAs. We also investigated the target genes of the tumorigenic microRNAs. Eleven genes, including PIGF, TPI1, KLF4, RARS, PCBP2, EIF5A, HK2, RAVER2, HMGN1, MAPK6, and NDUFA2, were identified to be frequently targeted by the tumorigenic microRNAs. The high AUC value and distinct overall survival rates between the two risk groups suggested that these tumorigenic microRNAs had the potential of diagnostic and prognostic value in CRC. Conclusions. The present study revealed possible mechanisms and pathways that may contribute to tumorigenesis of CRC, which could not only be used as CRC early detection biomarkers, but also be useful for tumorigenesis mechanism studies.


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