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Article ; Online: Multi-Omics Analysis and Machine Learning Prediction Model for Pregnancy Outcomes After Intracytoplasmic Sperm Injection-

Chen, Fangying / Chen, Yixin / Mai, Qinyun

2022 Volume 10, Page(s) 924539

Abstract: Background: To explore the methylation profiles in cumulus cells (CCs) of women undergoing intracytoplasmic sperm injection-: Methods: Methylation data were retrieved from the Gene Expression Omnibus (GEO) database, and differentially methylated ... ...

Abstract	Background: To explore the methylation profiles in cumulus cells (CCs) of women undergoing intracytoplasmic sperm injection- Methods: Methylation data were retrieved from the Gene Expression Omnibus (GEO) database, and differentially methylated genes (DMGs) were subjected to gene set analyses. Support vector machine (SVM), random forest (RF), and logistic regression (LR) were used to establish the prediction model, and microarray data from GEO was analyzed to identify differentially expressed genes (DEGs) associated with the dichotomous outcomes of clinical pregnancy (pregnant vs. non-pregnant). Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis provided multi-dimensional validation for selected DMGs. Results: A total of 338 differentially methylated CpG sites associated with 146 unique genes across the genome were identified. Among the identified pathways, the prominent ones were involved in the regulation of cell growth and oocyte development (hsa04340, hsa04012, hsa04914, hsa04614, hsa04913, hsa04020, and hsa00510). The area under the curve (AUC) of machine learning classifiers was 0.94 (SVM) vs. 0.88 (RF) vs. 0.97 (LR). 196 DEGs were found in transcriptional microarray. Mapped genes were selected through overlapping enriched pathways in transcriptional profiles and methylated data of CCs, predictive of successful pregnancy. Conclusions: Methylated profiles of CCs were significantly different between women receiving ICSI-IVF procedures that conceived successfully and those that did not conceive. Machine learning approaches are powerful tools that may provide crucial information for prognostic assessment. Pathway analysis may be another way in multiomics analysis of cumulus cells.
MeSH term(s)	Female ; Fertilization in Vitro ; Humans ; Machine Learning ; Male ; Pregnancy ; Pregnancy Outcome ; Semen ; Sperm Injections, Intracytoplasmic
Language	English
Publishing date	2022-06-30
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2711781-9
ISSN	2296-2565 ; 2296-2565
ISSN (online)	2296-2565
ISSN	2296-2565
DOI	10.3389/fpubh.2022.924539
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Absence of complementary sex determination in two Leptopilina species (Figitidae, Hymenoptera) and a reconsideration of its incompatibility with endosymbiont‐induced thelytoky

Chen, Fangying / Schenkel, Martijn / Geuverink, Elzemiek / van de Zande, Louis / Beukeboom, Leo W.

Insect science. 2022 June, v. 29, no. 3

2022

Abstract: Complementary sex determination (CSD) is a widespread sex determination mechanism in haplodiploid Hymenoptera. Under CSD, sex is determined by the allelic state of one or multiple CSD loci. Heterozygosity at one or more loci leads to female development, ... ...

Abstract	Complementary sex determination (CSD) is a widespread sex determination mechanism in haplodiploid Hymenoptera. Under CSD, sex is determined by the allelic state of one or multiple CSD loci. Heterozygosity at one or more loci leads to female development, whereas hemizygosity of haploid eggs and homozygosity of diploid eggs results in male development. Sexual (arrhenotokous) reproduction normally yields haploid male and diploid female offspring. Under asexual reproduction (thelytoky), diploidized unfertilized eggs develop into females. Thelytoky is often induced by bacterial endosymbionts that achieve egg diploidization by gamete duplication. As gamete duplication leads to complete homozygosity, endosymbiont‐induced thelytokous reproduction is presumed to be incompatible with CSD, which relies on heterozygosity for female development. Previously, we excluded CSD in four Asobara (Braconidae) species and proposed a two‐step mechanism for Wolbachia‐induced thelytoky in Asobara japonica. Here, we conclusively reject CSD in two cynipid wasp species, Leptopilina heterotoma and Leptopilina clavipes. We further show that thelytoky in L. clavipes depends on Wolbachia titer but that diploidization and feminization steps cannot be separated, unlike in A. japonica. We discuss what these results reveal about the sex determination mechanism of L. clavipes and the presumed incompatibility between CSD and endosymbiont‐induced thelytoky in the Hymenoptera.
Keywords	Asobara ; Cynipidae ; Figitidae ; Leptopilina heterotoma ; Wolbachia ; asexual reproduction ; diploidy ; eggs ; females ; feminization ; haploidy ; hemizygote ; heterozygosity ; homozygosity ; males ; microsymbionts ; progeny ; sex determination ; thelytoky ; wasps
Language	English
Dates of publication	2022-06
Size	p. 900-914.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	2179775-4
ISSN	1744-7917 ; 1672-9609
ISSN (online)	1744-7917
ISSN	1672-9609
DOI	10.1111/1744-7917.12969
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Article: Signature based on RNA-binding protein-related genes for predicting prognosis and guiding therapy in non-small cell lung cancer.

Miao, Ti-Wei / Chen, Fang-Ying / Du, Long-Yi / Xiao, Wei / Fu, Juan-Juan

Frontiers in genetics

2022 Volume 13, Page(s) 930826

Abstract: Background: ...

Abstract	Background:
Language	English
Publishing date	2022-09-02
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2606823-0
ISSN	1664-8021
ISSN	1664-8021
DOI	10.3389/fgene.2022.930826
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Article ; Online: Microbiome composition is shaped by geography and population structure in the parasitic wasp Asobara japonica, but not in the presence of the endosymbiont Wolbachia.

Brinker, Pina / Chen, Fangying / Chehida, Yacine Ben / Beukeboom, Leo W / Fontaine, Michael C / Salles, Joana Falcao

Molecular ecology

2022 Volume 32, Issue 23, Page(s) 6644–6658

Abstract: The microbial community composition is crucial for diverse life-history traits in many organisms. However, we still lack a sufficient understanding of how the host microbiome is acquired and maintained, a pressing issue in times of global environmental ... ...

Abstract	The microbial community composition is crucial for diverse life-history traits in many organisms. However, we still lack a sufficient understanding of how the host microbiome is acquired and maintained, a pressing issue in times of global environmental change. Here we investigated to what extent host genotype, environmental conditions, and the endosymbiont Wolbachia influence the bacterial communities in the parasitic wasp Asobara japonica. We sampled multiple wasp populations across 10 locations in their natural distribution range in Japan and sequenced the host genome (whole genome sequencing) and microbiome (16S rRNA gene). We compared the host population structure and bacterial community composition of wasps that reproduce sexually and are uninfected with Wolbachia with wasps that reproduce asexually and carry Wolbachia. The bacterial communities in asexual wasps were highly similar due to a strong effect of Wolbachia rather than host genomic structure. In contrast, in sexual wasps, bacterial communities appear primarily shaped by a combination of population structure and environmental conditions. Our research highlights that multiple factors shape the bacterial communities of an organism and that the presence of a single endosymbiont can strongly alter their compositions. This information is crucial to understanding how organisms and their associated microbiome will react in the face of environmental change.
MeSH term(s)	Animals ; Wasps/genetics ; Wasps/microbiology ; Wolbachia/genetics ; RNA, Ribosomal, 16S/genetics ; Microbiota/genetics ; Bacteria/genetics ; Geography
Chemical Substances	RNA, Ribosomal, 16S
Language	English
Publishing date	2022-09-30
Publishing country	England
Document type	Journal Article
ZDB-ID	1126687-9
ISSN	1365-294X ; 0962-1083
ISSN (online)	1365-294X
ISSN	0962-1083
DOI	10.1111/mec.16699
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Article ; Online: DNA Methylation Profiling in a Cigarette Smoke-Exposed Mouse Model of Airway Inflammation.

Li, Ping / Peng, Junjie / Chen, Guangxi / Chen, Fangying / Shen, Yongchun / Liu, Lin / Chen, Lei

International journal of chronic obstructive pulmonary disease

2022 Volume 17, Page(s) 2443–2450

Abstract: Purpose: DNA methylation, a major epigenetic modification, has been documented to play an important role in chronic obstructive pulmonary disease (COPD). In this study, we aimed to profile the DNA methylation patterns in a mouse model of airway ... ...

Abstract	Purpose: DNA methylation, a major epigenetic modification, has been documented to play an important role in chronic obstructive pulmonary disease (COPD). In this study, we aimed to profile the DNA methylation patterns in a mouse model of airway inflammation induced by cigarette smoke (CS), a foremost risk factor of COPD. Material and methods: To establish a model of airway inflammation, wild-type mice were exposed to mainstream CS or room air for 2 hours twice daily, 6 days per week for consecutive 4 weeks. Lung tissues of the mice were collected for genome-wide DNA methylation analysis by liquid hybridization capture-based bisulfite sequencing, which were used for intersection analysis with gene expression by cDNA microarray to identify candidate methylated genes. Then, functional enrichment analyses with protein-protein interaction (PPI) network regarding these genes were conducted to explore the potential mechanisms. Results: After 4-week CS exposure, the level of DNA methylation accompanied by a subacute airway inflammation was markedly enhanced, and 2002 differentially methylated genes (DMGs) were annotated, including 565 DMGs contained methylations in gene promoters, which were used for intersection with the differentially expressed genes. Then, 135 candidate methylated genes were further selected by the intersection, among which 58 genes with functional methylated modification were finally identified. Further analyses revealed candidate methylated genes were significantly enriched in a complicated network of signals and processes, including interleukins, toll-like receptors, T-cells differentiation, oxidative stress, mast cells activation, stem cells proliferation, etc., as well as the 58 functional methylated genes were partially located at key positions in PPI network, especially CXCL1, DDX58 and JAK3. Conclusion: This study suggests CS exposure significantly enhances DNA methylated level, and the potential functional methylated genes are closely related to complicated inflammatory-immune responses, which may provide some new experimental evidence in understanding the epigenetic mechanisms of CS-induced airway inflammation in COPD.
MeSH term(s)	Animals ; Cigarette Smoking/adverse effects ; DNA Methylation ; Inflammation/complications ; Interleukins/genetics ; Lung/metabolism ; Mice ; Pulmonary Disease, Chronic Obstructive/complications ; Nicotiana
Chemical Substances	Interleukins
Language	English
Publishing date	2022-10-01
Publishing country	New Zealand
Document type	Journal Article
ZDB-ID	2212419-6
ISSN	1178-2005 ; 1176-9106
ISSN (online)	1178-2005
ISSN	1176-9106
DOI	10.2147/COPD.S369702
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Article ; Online: A ferroptosis-related gene signature for overall survival prediction and immune infiltration in lung squamous cell carcinoma.

Miao, Ti-Wei / Yang, De-Qing / Chen, Fang-Ying / Zhu, Qi / Chen, Xin

Bioscience reports

2022 Volume 42, Issue 8

Abstract: Background: Ferroptosis is associated with cancer initiation and progression. However, the molecular mechanism and prognostic value of ferroptosis-related genes in lung squamous cell carcinoma (LUSC) are poorly understood.: Methods: The mRNA ... ...

Abstract	Background: Ferroptosis is associated with cancer initiation and progression. However, the molecular mechanism and prognostic value of ferroptosis-related genes in lung squamous cell carcinoma (LUSC) are poorly understood. Methods: The mRNA expression profiles, methylation data, and clinical information of patients with LUSC were downloaded from TCGA and GEO database. Ferroptosis-related differentially expressed genes (DEGs) were identified between cancerous and non-cancerous tissues, and their prognostic value was systemically investigated by bioinformatic analyses. Results: A ferroptosis-related gene signature (ALOX5, TFRC, PHKG2, FADS2, NOX1) was constructed using multivariate Cox regression analysis and represented as a risk score. Overall survival (OS) probability was significantly lower in the high-risk group than in the low-risk group (P<0.001), and receiver operating characteristic curve showed a good predictive capacity (AUC = 0.739). The risk score was an independent prognostic factor for LUSC. A nomogram was constructed to predict the OS probabilities at 1, 3, and 5 years. High-risk score was associated with increased immune infiltration, lower methylation levels, higher immune checkpoint genes expression levels, and better chemotherapy response. Cell adhesion molecules, focal adhesion, and extracellular matrix receptor interaction were the main pathways in the high-risk group. The signature was validated using the TCGA test cohort, entire TCGA cohort, GSE30219, GSE157010, GSE73403, and GSE4573 datasets. The gene disorders in patients with LUSC were validated using real-time PCR and single-cell RNA sequencing analysis. Conclusions: A ferroptosis-related gene signature was constructed to predict OS probability in LUSC. This could facilitate novel therapeutic methods and guide individualized therapy.
MeSH term(s)	Biomarkers, Tumor/genetics ; Carcinoma, Non-Small-Cell Lung/genetics ; Carcinoma, Squamous Cell/pathology ; Ferroptosis/genetics ; Gene Expression Regulation, Neoplastic ; Humans ; Lung/pathology ; Lung Neoplasms/pathology
Chemical Substances	Biomarkers, Tumor
Language	English
Publishing date	2022-07-26
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	764946-0
ISSN	1573-4935 ; 0144-8463
ISSN (online)	1573-4935
ISSN	0144-8463
DOI	10.1042/BSR20212835
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Article ; Online: A prognostic model for ovarian neoplasms established by an integrated analysis of 1580 transcriptomic profiles.

Hua, Yanjiao / Cai, Du / Shirley, Cole Andrea / Mo, Sien / Chen, Ruyun / Gao, Feng / Chen, Fangying

Scientific reports

2023 Volume 13, Issue 1, Page(s) 19429

Abstract: Even after debulking surgery combined with chemotherapy or new adjuvant chemotherapy paired with internal surgery, the average year of disease free survival in advanced ovarian cancer was approximately 1.7 ... ...

Abstract	Even after debulking surgery combined with chemotherapy or new adjuvant chemotherapy paired with internal surgery, the average year of disease free survival in advanced ovarian cancer was approximately 1.7 years
MeSH term(s)	Female ; Humans ; Neoplasm Recurrence, Local/genetics ; Neoplasm Recurrence, Local/pathology ; Neoplasm Staging ; Ovarian Neoplasms/pathology ; Prognosis ; Sulfur Compounds ; Transcriptome
Chemical Substances	Sulfur Compounds
Language	English
Publishing date	2023-11-08
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-023-45410-x
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Article ; Online: Tripterygium and its plant extraction for systemic lupus erythematosus: A protocol for systematic review and meta analysis.

Chen, Fangying / Liu, Junting / Zhao, Zhimin / Li, Ziping / Wu, Kuanyu

Medicine

2020 Volume 99, Issue 34, Page(s) e21909

Abstract: Background: Systemic Lupus Erythematosus (SLE) is a diffuse connetive tissue disease, which is difficult to be conquered. However, the traditional Chinese medicine is significant in the treatment. And the Chinese medicine tripterygium and its plant ... ...

Abstract	Background: Systemic Lupus Erythematosus (SLE) is a diffuse connetive tissue disease, which is difficult to be conquered. However, the traditional Chinese medicine is significant in the treatment. And the Chinese medicine tripterygium and its plant extraction can help us to overcome this disease, to some extent. Methods: The deadline should be from inception to February 2020 by computer from the databases: the Cochrane Library, Pubmed, Embase, Web of Science in English and the Chinese National Knowledge Infrastructure, Wanfang Database, Chinese Biomedical Literature Database and Chinese Science, Chinese Traditional Medicine Database, Chinese Science and Technology Periodical Database in Chinese. Included criteria are randomized controlled trials. The primary outcomes are the clinical symptoms, systemic lupus erythematosus disease activity index and quality of life questionnaire (the top 10 frequency). We will use RevMan 5.0 statistical software for data synthesis, sensitivity analysis, meta regression, subgroup analysis, and risk of bias assessment. The publish bias will be assessed by a funnel plot and the funnel plot symmetries will be evaluated by Begg and Egger tests. We will use the Grading of Recommendations Assessment, Development and Evaluation system to assess the quality of evidence. Results: This article will give a protocol for meta analysis which can make sure the efficacy and side effect of the tripterygium and its plant extraction for SLE. Conclusion: The efficacy and side effect of the tripterygium and its plant extraction for SLE will be evaluated. Ethics and dissemination: Without personal information involved, ethical approval and informed consent form is no need. The review will be submitted to a peer-reviewed journal prospectively to spread our findings. Prospero registration number: PROSPERO CRD42020176444.
MeSH term(s)	Drugs, Chinese Herbal/therapeutic use ; Humans ; Lupus Erythematosus, Systemic/drug therapy ; Lupus Erythematosus, Systemic/psychology ; Medicine, Chinese Traditional/methods ; Plant Extracts/therapeutic use ; Quality of Life ; Randomized Controlled Trials as Topic ; Treatment Outcome ; Tripterygium/adverse effects ; Tripterygium/chemistry ; Meta-Analysis as Topic ; Systematic Review as Topic
Chemical Substances	Drugs, Chinese Herbal ; Plant Extracts
Language	English
Publishing date	2020-08-27
Publishing country	United States
Document type	Journal Article
ZDB-ID	80184-7
ISSN	1536-5964 ; 0025-7974
ISSN (online)	1536-5964
ISSN	0025-7974
DOI	10.1097/MD.0000000000021909
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Article ; Online: The Association and Influencing Factors between Antipsychotics Exposure and the Risk of VTE and PE: A Systematic Review and Meta-analysis.

Dai, Luqi / Zuo, Qiunan / Chen, Fangying / Chen, Lei / Shen, Yongchun

Current drug targets

2020 Volume 21, Issue 9, Page(s) 930–942

Abstract: Background: Different clinical studies have given inconsistent results on whether the use of antipsychotics increases the risk of thromboembolism. In this paper, we reviewed all relevant literature to provide suggestions for clinical diagnosis and ... ...

Abstract	Background: Different clinical studies have given inconsistent results on whether the use of antipsychotics increases the risk of thromboembolism. In this paper, we reviewed all relevant literature to provide suggestions for clinical diagnosis and treatment. Methods: PubMed, Web of Science, EMBASE, MEDLINE, Cochrane and Scopus databases were thoroughly searched up to June 2019. Two researchers independently searched the literature, extracted data. Data were analyzed by Stata 12.0 software. Results: A total of 22 studies involving 31514226 subjects were included. This meta-analysis showed that patients taking the first- or second-generation antipsychotics had a higher risk of venous thromboembolism and pulmonary embolism than those who did not, and low potency first-generation agents increased the risk of venous thromboembolism more than high potency antipsychotics, and olanzapine, clozapine, haloperidol, perphenazine and risperidone also significantly increased the risk of it. The risk of venous thrombosis in obese people was higher than that in overweight people, patients not less than 65 years old had an increased risk compared with younger patients. In addition, women taking antipsychotics had a higher risk of pulmonary embolism than men. Conclusion: The use of antipsychotics will increase the risk of venous thromboembolism and pulmonary embolism, which will be affected by the type of antipsychotics and patient characteristics.
MeSH term(s)	Adolescent ; Adult ; Aged ; Aged, 80 and over ; Antipsychotic Agents/adverse effects ; Data Interpretation, Statistical ; Humans ; Middle Aged ; Observational Studies as Topic ; Pulmonary Embolism/chemically induced ; Risk Assessment ; Risk Factors ; Software ; Venous Thromboembolism/chemically induced ; Young Adult
Chemical Substances	Antipsychotic Agents
Language	English
Publishing date	2020-05-04
Publishing country	United Arab Emirates
Document type	Journal Article ; Meta-Analysis ; Research Support, Non-U.S. Gov't ; Systematic Review
ZDB-ID	2064859-5
ISSN	1873-5592 ; 1389-4501
ISSN (online)	1873-5592
ISSN	1389-4501
DOI	10.2174/1389450121666200422084414
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Article ; Online: Absence of complementary sex determination in two Leptopilina species (Figitidae, Hymenoptera) and a reconsideration of its incompatibility with endosymbiont-induced thelytoky.

Chen, Fangying / Schenkel, Martijn / Geuverink, Elzemiek / van de Zande, Louis / Beukeboom, Leo W

Insect science

2021 Volume 29, Issue 3, Page(s) 900–914

Abstract	Complementary sex determination (CSD) is a widespread sex determination mechanism in haplodiploid Hymenoptera. Under CSD, sex is determined by the allelic state of one or multiple CSD loci. Heterozygosity at one or more loci leads to female development, whereas hemizygosity of haploid eggs and homozygosity of diploid eggs results in male development. Sexual (arrhenotokous) reproduction normally yields haploid male and diploid female offspring. Under asexual reproduction (thelytoky), diploidized unfertilized eggs develop into females. Thelytoky is often induced by bacterial endosymbionts that achieve egg diploidization by gamete duplication. As gamete duplication leads to complete homozygosity, endosymbiont-induced thelytokous reproduction is presumed to be incompatible with CSD, which relies on heterozygosity for female development. Previously, we excluded CSD in four Asobara (Braconidae) species and proposed a two-step mechanism for Wolbachia-induced thelytoky in Asobara japonica. Here, we conclusively reject CSD in two cynipid wasp species, Leptopilina heterotoma and Leptopilina clavipes. We further show that thelytoky in L. clavipes depends on Wolbachia titer but that diploidization and feminization steps cannot be separated, unlike in A. japonica. We discuss what these results reveal about the sex determination mechanism of L. clavipes and the presumed incompatibility between CSD and endosymbiont-induced thelytoky in the Hymenoptera.
MeSH term(s)	Animals ; Diploidy ; Female ; Haploidy ; Hymenoptera/genetics ; Hymenoptera/microbiology ; Male ; Parthenogenesis ; Wasps/genetics ; Wasps/microbiology ; Wolbachia/genetics
Language	English
Publishing date	2021-10-25
Publishing country	Australia
Document type	Journal Article
ZDB-ID	2179775-4
ISSN	1744-7917 ; 1672-9609
ISSN (online)	1744-7917
ISSN	1672-9609
DOI	10.1111/1744-7917.12969
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