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Luthfi M, Pandey RB, Su YC, Sompornpisut P. Deciphering molecular basis of pesticide-induced recurrent pregnancy loss: insights from transcriptomics analysis. Toxicol Mech Methods 2024; 34:527-544. [PMID: 38294000 DOI: 10.1080/15376516.2024.2307975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 01/15/2024] [Indexed: 02/01/2024]
Abstract
Recent studies have revealed a notable connection between pesticide exposure and Recurrent Pregnancy Loss (RPL), yet the precise molecular underpinning of this toxicity remains elusive. Through the alignment of Differentially Expressed Genes (DEGs) of healthy and RPL patients with the target genes of 9 pesticide components, we identified a set of 12 genes responsible for RPL etiology. Interestingly, biological process showed that besides RPL, those 12 genes also associated with preeclampsia and cardiovascular disease. Enrichment analysis showed the engagement of these genes associated with essential roles in the molecular transport of small molecules, as well as the aldosterone-regulated sodium reabsorption, endocrine and other factor-regulated calcium reabsorption, mineral absorption, ion homeostasis, and ion transport by P-type ATPases. Notably, the crosstalk targets between pesticide components played crucial roles in influencing RPL results, suggesting a role in attenuating pesticide agents that contribute to RPL. It is important to note that non-significant concentration of the pesticide components observed in both control and RPL samples should not prematurely undermine the potential for pesticides to induce RPL in humans. This study emphasizes the complexity of pesticide induced RPL and highlights avenues for further research and precautionary measures.
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Affiliation(s)
- Muhammad Luthfi
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, Thailand
- Center of Excellence in Computational Chemistry, Department of Chemistry, Chulalongkorn University, Bangkok, Thailand
| | - R B Pandey
- School of Mathematics and Natural Sciences, University of Southern Mississippi, Hattiesburg, MS, USA
| | - Yong-Chao Su
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Pornthep Sompornpisut
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, Thailand
- Center of Excellence in Computational Chemistry, Department of Chemistry, Chulalongkorn University, Bangkok, Thailand
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Liu Y, Liu S, Yan L, Zhang Q, Liu W, Huang X, Liu S. Contribution of m5C RNA Modification-Related Genes to Prognosis and Immunotherapy Prediction in Patients with Ovarian Cancer. Mediators Inflamm 2023; 2023:1400267. [PMID: 38022687 PMCID: PMC10661868 DOI: 10.1155/2023/1400267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 09/03/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023] Open
Abstract
Background 5-Methylcytosine (m5C) RNA modification is closely implicated in the occurrence of a variety of cancers. Here, we established a novel prognostic signature for ovarian cancer (OC) patients based on m5C RNA modification-related genes and explored the correlation between these genes with the tumor immune microenvironment. Methods Methylated-RNA immunoprecipitation sequencing helped us to identify candidate genes related to m5C RNA modification at first. Based on TCGA database, we screened the differentially expressed candidate genes related to the prognosis and constructed a prognostic model using LASSO Cox regression analyses. Notably, the accuracy of the model was evaluated by Kaplan-Meier analysis and receiver operator characteristic curves. Independent prognostic risk factors were investigated by Cox proportional hazard model. Furthermore, we also analyzed the biological functions and pathways involved in the signature. Finally, the immune response of the model was visualized in great detail. Results Totally, 2,493 candidate genes proved to be involved in m5C modification of RNA for OC. We developed a signature with prognostic value consisting of six m5C RNA modification-related genes. Specially, samples have been split into two cohorts with low- and high-risk scores according to the model, in which the low-risk OC patients exhibited dramatically better overall survival time than those with high-risk scores. Besides, not only was this model a prognostic factor independent of other clinical characteristics but it predicted the intensity of the immune response in OC. Significantly, the accuracy and availability of the signature were verified by ICGC database. Conclusions Our study bridged the gap between m5C RNA modification and the prognosis of OC and was expected to provide an effective breakthrough for immunotherapy in OC patients.
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Affiliation(s)
- Yibin Liu
- Department of Gynecology, The Second Hospital of Hebei Medical University, 215 Heping West Road, Shijiazhuang, Hebei 050011, China
| | - Shouze Liu
- Department of Gynecology, The Second Hospital of Hebei Medical University, 215 Heping West Road, Shijiazhuang, Hebei 050011, China
- Department of Gynecology III, Cangzhou Central Hospital, Cangzhou, Hebei 061000, China
| | - Lu Yan
- Department of Gynecology, The Second Hospital of Hebei Medical University, 215 Heping West Road, Shijiazhuang, Hebei 050011, China
| | - Qianqian Zhang
- Department of Gynecology and Obstetrics, Beijing Tsinghua Changgung Hospital, Beijing 102218, China
| | - Wenhua Liu
- Department of Pain, Cangzhou Hospital of Integrated TCM-WM Hebei, Cangzhou, Hebei 061001, China
| | - Xianghua Huang
- Department of Gynecology, The Second Hospital of Hebei Medical University, 215 Heping West Road, Shijiazhuang, Hebei 050011, China
| | - Shikai Liu
- Department of Gynecology III, Cangzhou Central Hospital, Cangzhou, Hebei 061000, China
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Zhao J, Han H, Wang R, Wang Y, Zhang Y, Li N, Wang B, Chu Z, Zhang Y, Zhang H. Identification of N1 methyladenosine-related biomarker predicting overall survival outcomes and experimental verification in ovarian cancer. J Obstet Gynaecol Res 2023; 49:2457-2467. [PMID: 37435915 DOI: 10.1111/jog.15745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 07/04/2023] [Indexed: 07/13/2023]
Abstract
AIM This study aimed to construct a N1-methyladenosine (m1A)-related biomarker model for predicting the prognosis of ovarian cancer (OVCA). METHODS OVCA samples were clustered into two subtypes using the Non-Negative Matrix Factorization (NMF) algorithm, including TCGA (n = 374) as the training set and GSE26712 (n = 185) as the external validation set. Hub genes, which were screened to construct a risk model, and nomogram to predict the overall survival of OVCA were explored and validated through various bioinformatic analysis and quantitative real-time PCR. RESULTS Following bootstrap correction, the C-index of nomogram was 0.62515, showing reliable performance. The functions of DEGs in the high- and low-risk groups were mainly enriched in immune response, immune regulation, and immune-related diseases. The immune cells relevant to the expression of hub genes were explored, for example, Natural Killer (NK) cells, T cells, activated dendritic cells (aDC). CONCLUSIONS AADAC, CD38, CACNA1C, and ATP1A3 might be used as m1A-related biomarkers for OVCA, and the nomogram labeled with m1A for the first time had excellent performance for predicting overall survival in OVCA.
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Affiliation(s)
- Jing Zhao
- Department of Obstetrics and Gynecology, The First Hospital of Hebei Medical University, Shijiazhuang, China
- Department of Gynecology, Hebei General Hospital, Shijiazhuang, China
| | - Hua Han
- Department of Gynecology, Hebei General Hospital, Shijiazhuang, China
| | - Runfang Wang
- Department of Obstetrics, Hebei General Hospital, Shijiazhuang, China
| | - Yazhuo Wang
- Department of Gynecology, Hebei General Hospital, Shijiazhuang, China
| | - Yuan Zhang
- Department of Gynecology, Hebei General Hospital, Shijiazhuang, China
| | - Na Li
- Department of Oncology, Hebei General Hospital, Shijiazhuang, China
| | - Bei Wang
- Department of Gynecology, Hebei General Hospital, Shijiazhuang, China
| | - Zhaoping Chu
- Department of Gynecology, Hebei General Hospital, Shijiazhuang, China
| | - Yunxia Zhang
- Department of Gynecology, Hebei General Hospital, Shijiazhuang, China
| | - Hongzhen Zhang
- Department of Obstetrics and Gynecology, The First Hospital of Hebei Medical University, Shijiazhuang, China
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Huang K, Chen X, Geng Z, Xiong X, Cong Y, Pan X, Liu S, Ge L, Xu J, Jia X. LncRNA SLC25A21-AS1 increases the chemosensitivity and inhibits the progression of ovarian cancer by upregulating the expression of KCNK4. Funct Integr Genomics 2023; 23:110. [PMID: 36995496 DOI: 10.1007/s10142-023-01035-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/20/2023] [Accepted: 03/21/2023] [Indexed: 03/31/2023]
Abstract
Owing to high mortality rate, ovarian cancer seriously threatens women's health. Extensive abdominal metastasis and chemoresistance are the leading causes of ovarian cancer deaths. Through lncRNA sequencing, our previous study identified lncRNA SLC25A21-AS1, which was significantly downregulated in chemoresistant ovarian cancer cells. In this study, we aimed to evaluate the role and mechanism of SLC25A21-AS1 in ovarian cancer. The expression of SLC25A21-AS1 was analyzed by qRT-PCR and online database GEPIA. The biological functions of SLC25A21-AS1 and KCNK4 were analyzed by CCK-8, transwell, and flow cytometry. The specific mechanism was analyzed by RNA-sequencing, RNA binding protein immunoprecipitation, rescue experiments, and bioinformatic analysis. SLC25A21-AS1 was decreased in ovarian cancer tissues and cell lines. Overexpression of SLC25A21-AS1 enhanced the sensitivity of ovarian cancer cells to paclitaxel and cisplatin, and inhibited cell proliferation, invasion, and migration, while SLC25A21-AS1-silencing showed the opposite effect. Potassium channel subfamily K member 4 (KCNK4) was significantly up-regulated upon enforced expression of SLC25A21-AS1. Overexpression of KCNK4 inhibited cell proliferation, invasion, migration ability, and enhanced the sensitivity of ovarian cancer cells to paclitaxel and cisplatin. Meanwhile, KNCK4-overexpression rescued the promotive effect of SLC25A21-AS1-silencing on cell proliferation, invasion and migration. In addition, SLC25A21-AS1 could interact with the transcription factor Enhancer of Zeste Homolog 2 (EZH2), while EZH2 knockdown increased the expression of KCNK4 in some of the ovarian cancer cell lines. SLC25A21-AS1 enhanced the chemosensitivity and inhibited the proliferation, migration, and invasion ability of ovarian cancer cells at least partially by blocking EZH2-mediated silencing of KCNK4.
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Identification of Potential Biomarkers for Progression and Prognosis of Bladder Cancer by Comprehensive Bioinformatics Analysis. JOURNAL OF ONCOLOGY 2022; 2022:1802706. [PMID: 35498536 PMCID: PMC9042640 DOI: 10.1155/2022/1802706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 03/22/2022] [Indexed: 11/23/2022]
Abstract
Background. Bladder cancer (BLCA) is a highly malignant tumor that develops in the urinary system. Identification of biomarkers in progression and prognosis is crucial for the treatment of BLCA. BLCA-related differentially expressed genes (DEGs) were authenticated by screening the DEGs and weighted gene coexpression network analysis (WGCNA). LASSO and SVM-RFE algorithms were utilized to screen the feature genes in BLCA. Survival analysis was performed using the Kaplan–Meier curve provided by the ‘survival' R package. The BLCA samples were clustered by hclust based on the immune score matrix calculated by the single-sample GSEA (ssGSEA) algorithm. The immune, stromal, and ESTIMATE scores of each BLCA patient were calculated by applying the ESTIMATE algorithm. ssGSEA was conducted to explore the function of characteristic genes in BLCA. The expression of characteristic genes in clinical cancer tissue, and the pericancerous tissue of BLCA patients was verified using qRT-PCR assays. A total of 189 BLCA-related DEGs were identified. Fourteen feature genes were defined by LASSO and SVM-RFE algorithms. Five characteristic genes, including SMYD2, GAPDHP1, ATP1A2, CILP, and THSD4, were related to the OS of BLCA. The correlation analysis of five characteristic genes and clinicopathological factors showed that five genes played a role in the progression of BLCA. Additionally, the expression of five characteristic genes in clinical cancer tissues and pericarcinomatous tissues from BLCA patients was verified by qRT-PCR, which was consistent with the result from the public database. Finally, we discovered five prognostic genes linked to BLCA progression, which might serve as a theoretical basis for prognosis and treatment targets for BLCA patients.
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Kushkevych I, Bychkov M, Bychkova S, Gajdács M, Merza R, Vítězová M. ATPase Activity of the Subcellular Fractions of Colorectal Cancer Samples under the Action of Nicotinic Acid Adenine Dinucleotide Phosphate. Biomedicines 2021; 9:biomedicines9121805. [PMID: 34944620 PMCID: PMC8698369 DOI: 10.3390/biomedicines9121805] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/23/2021] [Accepted: 11/29/2021] [Indexed: 11/30/2022] Open
Abstract
In tumor cells with defects in apoptosis, autophagy allows prolonged survival. Autophagy leads to an accumulation of damaged mitochondria by autophagosomes. An acidic environment is maintained in compartments of cells, such as autophagosomes, late endosomes, and lysosomes; these organelles belong to the “acid store” of the cells. Nicotinic acid adenine dinucleotide phosphate (NAADP) may affect the release of Ca2+ from these organelles and affect the activity of Ca2+ ATPases and other ion transport proteins. Recently, a growing amount of evidence has shown that the variations in the expression of calcium channels or pumps are associated with the occurrence, disease-presentation, and the prognosis of colorectal cancer. We hypothesized that activity of ATPases in cancer tissue is higher because of intensive energy metabolism of tumor cells. The aim of our study was to ascertain the effect of NAADP on ATPase activity on tissue samples of colorectal cancer patients’ and healthy individuals. We tested the effect of NAADP on the activity of Na+/K+ ATPase; Ca2+ ATPase of endoplasmic reticulum (EPR) and plasma membrane (PM) and basal ATPase activity. Patients’ colon mucus cancer samples were obtained during endoscopy from cancer and healthy areas (control) of colorectal mucosa of the same patients. Results. The mean activity of Na+/K+ pump in samples of colorectal cancer patients (n = 5) was 4.66 ± 1.20 μmol Pi/mg of protein per hour, while in control samples from healthy tissues of the same patient (n = 5) this value was 3.88 ± 2.03 μmol Pi/mg of protein per hour. The activity of Ca2+ ATPase PM in control samples was 6.42 ± 0.63 μmol Pi/mg of protein per hour and in cancer −8.50 ± 1.40 μmol Pi/mg of protein per hour (n = 5 pts). The mean activity of Ca2+ ATPase of EPR in control samples was 7.59 ± 1.21 μmol Pi/mg versus 7.76 ± 0.24 μmol Pi/mg in cancer (n = 5 pts). Basal ATPase activity was 3.19 ± 0.87 in control samples versus 4.79 ± 1.86 μmol Pi/mg in cancer (n = 5 pts). In cancer samples, NAADP reduced the activity of Na+/K+ ATPase by 9-times (p < 0.01) and the activity of Ca2+ ATPase EPR about 2-times (p < 0.05). NAADP caused a tendency to decrease the activity of Ca2+ ATPase of PM, but increased basal ATPase activity by 2-fold vs. the mean of this index in cancer samples without the addition of NAADP. In control samples NAADP caused only a tendency to decrease the activities of Na+/K+ ATPase and Ca2+ ATPase EPR, but statistically decreased the activity of Ca2+ ATPase of PM (p < 0.05). In addition, NAADP caused a strong increase in basal ATPase activity in control samples (p < 0.01). Conclusions: We found that the activity of Na+/K+ pump, Ca2+ ATPase of PM and basal ATPase activity in cancer tissues had a strong tendency to be higher than in the controls. NAADP caused a decrease in the activities of Na+/K+ ATPase and Ca2+ ATPase EPR in cancer samples and increased basal ATPase activity. In control samples, NAADP decreased Ca2+ ATPase of PM and increased basal ATPase activity. These data confirmed different roles of NAADP-sensitive “acidic store” (autophagosomes, late endosomes, and lysosomes) in control and cancer tissue, which hypothetically may be connected with autophagy role in cancer development. The effect of NAADP on decreasing the activity of Na+/K+ pump in cancer samples was the most pronounced, both numerically and statistically. Our data shows promising possibilities for the modulation of ion-transport through the membrane of cancer cells by influence on the “acidic store” (autophagosomes, late endosomes and lysosomes) as a new approach to the treatment of colorectal cancer.
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Affiliation(s)
- Ivan Kushkevych
- Department of Experimental Biology, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic
- Correspondence: (I.K.); (M.V.); Tel.: +420-549-495-315 (I.K.)
| | - Mykola Bychkov
- Department of Therapy No 1, Medical Diagnostic and Hematology and Transfusiology of Faculty of Postgraduate Education, Danylo Halytsky Lviv National Medical University, 79010 Lviv, Ukraine;
| | - Solomiia Bychkova
- Department of Human and Animal Physiology, Faculty of Biology, Ivan Franko National University of Lviv, 79005 Lviv, Ukraine;
| | - Márió Gajdács
- Department of Oral Biology and Experimental Dental Research, Faculty of Dentistry, University of Szeged, 6720 Szeged, Hungary;
- Faculty of Medicine, Institute of Medical Microbiology, Semmelweis University, Nagyvárad tér 4, 1089 Budapest, Hungary
| | - Romana Merza
- Department of Anesthesiology and Intensive Care, Faculty of Postgraduate Education, Danylo Halytsky Lviv National Medical University, 79010 Lviv, Ukraine;
| | - Monika Vítězová
- Department of Experimental Biology, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic
- Correspondence: (I.K.); (M.V.); Tel.: +420-549-495-315 (I.K.)
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Zhang X, Wei X, Bai G, Huang X, Hu S, Mao H, Liu P. Identification of Three Potential Prognostic Genes in Platinum-Resistant Ovarian Cancer via Integrated Bioinformatics Analysis. Cancer Manag Res 2021; 13:8629-8646. [PMID: 34824550 PMCID: PMC8607279 DOI: 10.2147/cmar.s336672] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 11/03/2021] [Indexed: 12/20/2022] Open
Abstract
Purpose Ovarian cancer is the most lethal gynecologic malignancy. Resistance to platinum-based chemotherapy affects the overall survival of patients. This study used an integrated bioinformatics to find the poorly understood molecular mechanisms underlying platinum resistance in ovarian cancer. Methods Based on the RNA-seq data of tissues in The Cancer Genome Atlas (TCGA) and RNA-seq data of cells from the Cancer Cell Encyclopedia (CCLE), we integrated differentially expressed genes (DEGs) in ovarian cancer tissue and cells. After screening for DEGs related to platinum resistance, we conducted survival analysis and built protein interaction networks to identify genes that may affect prognosis and interact with each other. Least absolute shrinkage and selection operator (Lasso) regression analysis was used to construct a predictive model. Immunohistochemistry and Western blot were used to validate the results. Finally, gene set enrichment analysis (GSEA) was performed on the expression of genes individually. Results We found that ATPase Na+/K+ transporting subunit alpha 2 (ATP1A2), calsequestrin 2 (CASQ2) and ryanodine receptor 2 (RYR2) interacted with each other and could predict resistance to platinum-based therapy, correlating negatively with prognosis. Moreover, we constructed a predictive model based on nine genes, including ATP1A2 and CASQ2. Immunohistochemistry and Western blot validated the upregulation of these genes in ovarian cancer tissue samples and cell lines. The immunohistochemistry results also confirmed the prognostic value of ATP1A2, CASQ2 and RYR2. GSEA predicted that ATP1A2, CASQ2 and RYR2 may act on the KRAS and mTORC1 pathways and participate in metabolic reprogramming and regulation of calcium homeostasis in platinum-resistant cells. Conclusion ATP1A2, CASQ2 and RYR2 were highly expressed in platinum-resistant ovarian cancer. ATP1A2 and CASQ2 were related to the prognosis of platinum-resistant ovarian cancer patients. These genes might act on KARS and mTORC1 pathways and participate in metabolic reprogramming and regulation of calcium homeostasis in platinum-resistant cells.
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Affiliation(s)
- Xue Zhang
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Jinan, Shandong, People's Republic of China.,Key Laboratory of Gynecology Oncology of Shandong Province, Qilu Hospital of Shandong University, Jinan, Shandong, People's Republic of China.,Shandong Engineering Laboratory for Urogynecology, Qilu Hospital of Shandong University, Jinan, Shandong, People's Republic of China
| | - Xuan Wei
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Jinan, Shandong, People's Republic of China.,Key Laboratory of Gynecology Oncology of Shandong Province, Qilu Hospital of Shandong University, Jinan, Shandong, People's Republic of China.,Shandong Engineering Laboratory for Urogynecology, Qilu Hospital of Shandong University, Jinan, Shandong, People's Republic of China
| | - Gaigai Bai
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Jinan, Shandong, People's Republic of China.,Key Laboratory of Gynecology Oncology of Shandong Province, Qilu Hospital of Shandong University, Jinan, Shandong, People's Republic of China.,Shandong Engineering Laboratory for Urogynecology, Qilu Hospital of Shandong University, Jinan, Shandong, People's Republic of China
| | - Xueyao Huang
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Jinan, Shandong, People's Republic of China.,Key Laboratory of Gynecology Oncology of Shandong Province, Qilu Hospital of Shandong University, Jinan, Shandong, People's Republic of China.,Shandong Engineering Laboratory for Urogynecology, Qilu Hospital of Shandong University, Jinan, Shandong, People's Republic of China
| | - Shunxue Hu
- Department of Pathology, Qilu Hospital of Shandong University, Jinan, Shandong, People's Republic of China
| | - Hongluan Mao
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Jinan, Shandong, People's Republic of China.,Key Laboratory of Gynecology Oncology of Shandong Province, Qilu Hospital of Shandong University, Jinan, Shandong, People's Republic of China.,Shandong Engineering Laboratory for Urogynecology, Qilu Hospital of Shandong University, Jinan, Shandong, People's Republic of China
| | - Peishu Liu
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Jinan, Shandong, People's Republic of China.,Key Laboratory of Gynecology Oncology of Shandong Province, Qilu Hospital of Shandong University, Jinan, Shandong, People's Republic of China.,Shandong Engineering Laboratory for Urogynecology, Qilu Hospital of Shandong University, Jinan, Shandong, People's Republic of China
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