Gender-specific differences in gene expression profiles in gynogenetic Pengze crucian carp

Gynogenesis is a form of asexual reproduction that is used to obtain all-female fish stocks. In this study, we were interested in studying gender-specific differences in gene expression profiles in gynogenetic teleosts, using a carp species. The four-month old gynogenetic Pengze crucian carp F1 (Carassius auratus var. pengzensis, Pcc) showed a high ratio of males under laboratory culture condition. The present study aimed to investigate the differences between males and females. The gonadosomatic index of the females was significantly higher than that of the males. Moreover, the hepatosomatic index of the females was significantly lower than that of the males. Vitellogenin B mRNA was abnormally highly expressed in male hepatopancreas and testes compared to females. Similarly, zona pellucida 2 expressed at a significantly high level in the testes. For the sex related genes, dosage-sensitive sex reversal, adrenal hypoplasia congenital critical region on the X-chromosome gene 1, doublesex and mab-3 related transcription factor 1a, nuclear receptor subfamily 5, group A, member 1b and SRY-box containing gene 9a had significantly higher expression levels in the males than in the females, whereas there was no difference in expression of anti-Müllerian hormone, cytochrome P450 family 19 subfamily A member 1A and forkhead box L2 transcripts between the two genders. The females showed higher levels of estrogen but no significant difference in testosterone compared to the males. The data suggest remarkable differences between the two genders of the Pengze crucian carp.

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High expression of RRM2 promotes the pathogenesis of malignant ovarian endometriosis.

10.21203/rs.3.rs-342433/v1 ◽

2021 ◽

Author(s):

Binkai Yang ◽

Yuanjing Hu ◽

Tian Wang ◽

Na Li ◽

Wenwen Zhang

Keyword(s):

Gene Expression ◽

Ovarian Cancer ◽

Malignant Transformation ◽

Expression Profiles ◽

Quantitative Polymerase Chain Reaction ◽

Gene Expression Profiles ◽

High Expression ◽

Ovarian Endometriosis ◽

Ki 67 ◽

Significant Difference

Abstract Objective: Our objective was to investigate the upregulated expression of ribonucleotide reductase M2 (RRM2) in the ectopic endometrium (EC) of ovarian endometriosis (OE) patients that may indicate malignant transformation. RRM2 may be used as a marker of OE, which contribute to the research of the mechanism of the malignant transformation of OE.Methods: The gene expression profiles of ovarian cancer and OE were downloaded from Gene Expression Omnibus (GEO), and a common hub gene, RRM2, was identified. The expression of RRM2 was low in OE and high in ovarian cancer. A total of 44 patients with endometriosis-associated ovarian cancers (EAOC) and 44 with OE were enrolled in this study. Immunohistochemistry (IHC) and real-time quantitative polymerase chain reaction (RT-qPCR) were used to detect the expression of RRM2, while the relationship between RRM2 and Ki-67 was analyzed by IHC co-localization. Results: There was no significant difference in the expression of RRM2 in the eutopic endometrium (EU), EC, and cancer tissues of EAOC patients. Compared with OE patients, the mRNA and protein expression levels of RRM2 were higher in the EC of EAOC patients (p＜0.01). Moreover, the high expression of RRM2 was consistent with the expression of Ki-67 in EC of EAOC patients.Conclusions: The upregulated expression of RRM2 in the EC of OE patients may indicate malignant transformation. RRM2 may be used as a marker of OE, which allows the investigation of the mechanism of the malignant transformation of OE.

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Identification of prognosis-related genes in the cervical cancer immune microenvironment

10.21203/rs.3.rs-16157/v1 ◽

2020 ◽

Author(s):

Lirong Yang ◽

Yang Yang ◽

Mingyao Meng ◽

Wenju Wang ◽

Shan He ◽

...

Keyword(s):

Gene Expression ◽

Cervical Cancer ◽

Tumor Microenvironment ◽

Clinical Data ◽

Immune Cells ◽

Stromal Cells ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Malignant Tumours ◽

Significant Difference

Abstract Background Cervical cancer is the fourth most common cancer in women worldwide. The metastasis and invasion of this type of cancer are closely related to the tumor microenvironment. Immune cells and stromal cells dominate the tumor microenvironment in cervical cancer. Therefore, we should further understand the association between tumor progress and immune cells or stromal cells.Methods we downloaded the gene expression profiles and clinical data of 307 patients with cervical cancers based on the TCGA database. Subsequently the Estimation of Stromal and Immune cells in Malignant Tumours using Expression data (ESTIMATE) algorithm was used to calculate the scores of stromal cells and immune cells to find differential genes, and analyzed the correlation between their scores and patient survival. Moreover, we also used R language packs and network tools to analyze GO term, gene enrichment pathway, and protein-protein relationship to find genes related to inflammation and immune regulation.Results The gene expression profiles and corresponding clinical data of 307 patients were obtained from TCGA datasets. The results showed that there was a statistically significant difference between the high immunescore group and the low immunescore group. And the low immunescore group had shorter lifetimes than the high scores group (P = 0.035).Moreover, PPI network analysis CCR5 and CXCL9, -10, -11 / CXCR3 axis might be new target for cervical cancer treatment. Finally, Kaplan-Meier survival curves found out nine representative genes significantly related to survival including BTNL8 , CCR7 , CD1E , CD6 , CD27 , CD79A , GRAP2 , SP1B , LY9 .Conclusions These genes can be used as markers for the prognosis and diagnosis of cervical cancer and also might be used as treatment targets.

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Large-scale tissue-specific and temporal gene expression profiles in Pengze crucian carp

Genetics and Molecular Research ◽

10.4238/gmr.15017642 ◽

2016 ◽

Vol 15 (1) ◽

Cited By ~ 1

Author(s):

Y. Zheng ◽

J.Z. Chen ◽

H.P. Wang ◽

M. Li ◽

H.W. Liang ◽

...

Keyword(s):

Gene Expression ◽

Large Scale ◽

Crucian Carp ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Tissue Specific ◽

Temporal Gene Expression

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Activation of intracellular signaling pathways as a new type of biomarkers for selection of target anticancer drugs.

Journal of Clinical Oncology ◽

10.1200/jco.2017.35.15_suppl.e23142 ◽

2017 ◽

Vol 35 (15_suppl) ◽

pp. e23142-e23142 ◽

Cited By ~ 8

Author(s):

Anton Buzdin ◽

Maxim Sorokin ◽

Alexander Glusker ◽

Andrew Garazha ◽

Elena Poddubskaya ◽

...

Keyword(s):

Gene Expression ◽

Cancer Patients ◽

Intracellular Signaling ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Molecular Targets ◽

Signalling Pathways ◽

Pathway Activation ◽

Significant Difference ◽

Selection Of

e23142 Background: Anticancer target drugs (ATDs) specifically bind and inhibit molecular targets that play important roles in tumorigenesis. More than 150 different ATDs have been approved for clinical use worldwide, and the clinicians are faced with the problem of choosing the best therapeutic solution for each patient. The problem of efficient ATD selection remains largely unsolved and personalized approaches are needed to select the best ATD candidates for individual patients. Methods: We propose a new approach termed OncoFinder. It is based on digesting gene expression profiles for the analysis of activation of intracellular signalling pathways as a marker for the selection of target therapies. The original bioinformatic algorithms were integrated with the databases featuring molecular drug targets, compositions of signalling pathways, including the functional role of each gene product, for more than 1700 pathways (Buzdin, Front.Genet 2014; Ozerov, Nature Communications 2016). Results: We showed that pathway activation strengths are more stable and reliable biomarkers of cancer than the expressions of individual genes. OncoFinder allows to detect changes at the level of pathway activation and to predict the effectiveness of drugs based on the knowledge of their molecular targets. We applied it to find new biomarkers of clinical response to the ATD cetuximab; for modelling the combined chemotherapy of acute myeloid leukemia and combined anti-VEGF/BRAF therapy of melanoma. For two unrelated datasets obtained for colon cancer patients before treatment with the ATD bevacizumab, we were able to distinguish between those who responded to treatment and not (p < 0.01). We next assayed biopsies for kidney cancer patients with known responses to the ATD sorafenib. The responders and non-responders showed a significant difference (p = 0.02). Finally, the OncoFinder platform was prospectively used for decision making support to patients with advanced metastatic solid tumors (n = 23). The efficiency of the ATD treatment was 61% (complete + partial response, RECIST). Conclusions: OncoFinder method may be effective for predicting response to ATD based on high throughput gene expression profiles.

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The prognostic value of gene expressions of ERCC1 and RRM1 in non-small cell lung cancer.

Journal of Clinical Oncology ◽

10.1200/jco.2013.31.15_suppl.e19071 ◽

2013 ◽

Vol 31 (15_suppl) ◽

pp. e19071-e19071

Author(s):

Serap Hasturk ◽

Ozlem Olgunus ◽

Abdullah Tuli ◽

Ebru Dundar ◽

Emine Ozgur Unlu

Keyword(s):

Gene Expression ◽

Lung Cancer ◽

Survival Analysis ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Small Cell ◽

Advanced Stage ◽

Small Cell Lung ◽

Gene Expressions ◽

Significant Difference

e19071 Background: Non small cell lung cancer is the most common cause of death due to cancer in the world. The role of ERCC1 and RRM1 genes has been researched in prediction of lung cancer prognosis and response of patients to chemotheraphy. We aimed to evaluate the effects of ERCC1 and RRM1 gene expressions profiles on the prediction of the prognosis and the treatment on bronchoscopy specimens of advanced stage NSCLC patients. Methods: The levels of ERCC1 and RRM1 gene expressions were studied for 76 patients which were diagnosed by bronchoscopic biopsy parafin embedded tissue samples. The RRM1 and ERCC1 gene expression profiles were examined by RT-PCR method. Forty were diagnosed with squamous cell cancer, 24 with adenocarcinoma, 12 with NOS NSCLC. Thirty patients were chemotherapy native, 33 were received gemcitabine-cisplatin and 13 were received docetaxel- cisplatin doublets chemotherapy. Results: The mean age of the patients in the study was 59.8±9.3 (years ± SD). The levels of gene expressions of ERCC1 and RRM1 were found to be 2-9 (median 4.9), and 1.3-17.7 (median 6.8). No significant difference was detected between ERCC1 and RRM1 levels and age, gender, histologic type, ECOG, weight loss when the median gene expression levels were used as cut off value. Also, no significant difference was observed for survival analysis among the patients that have low ERCC1 mRNA level (p=0.41). The level of gene expression of ERCC1 was lower in patients with advanced stage (p=0.06). In addition, no significant difference was detected for the survival analysis within the patients that have the low and high RRM1 mRNA levels (p=0.43). When the survival analyses were evaluated between the patients who had chemotherapy and the ones who did not; no significant difference was detected according to ERCC1 and RRM1 levels. Conclusions: We conclude that the analysis of ERCC1 and RRM1 gene expression profiles based on bronchoscopy obtained samples appeares feasible, but the methodology and cut off points that was used to classify expression level as ‘high’ or ‘low’ would require further optimization. These two gene signature proposed for advanced stage NSCLC may not be useful, particularly not ready for clinical application.

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Characteristics of SP600125 Induced Tetraploid Cells in Comparison With Diploid and Tetraploid Cells of Fish

Frontiers in Genetics ◽

10.3389/fgene.2021.781007 ◽

2021 ◽

Vol 12 ◽

Author(s):

Yunpeng Fan ◽

Guangjing Zhang ◽

Kaiyue Zhao ◽

Wen Fu ◽

Shujuan Chen ◽

...

Keyword(s):

Crucian Carp ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Mtdna Copy Number ◽

Chromosome Behavior ◽

Migration Ability ◽

Giant Mitochondria ◽

Ploidy Levels ◽

Significant Difference ◽

Cycle Regulation

In our previous research, SP600125 (Anthrapyrazolone) was used to induce autotetraploid of crucian carp cells (SP4N cells), and tetraploid fry was generated from the SP4N cells by somatic cell nuclear transfer technique. However, it is still unclear about biological characteristics of the SP4N cells. In this article, the cytological characteristic and gene expression profiles of the SP4N cells are investigated in comparison with the crucian carp cells (2N cells) and the tetraploid crucian carp cells (CC4N cells). The SP4N cells have tetraploid characteristics in terms of morphology and DNA ploidy levels, and their chromosome behavior is stable during the cell proliferation. The migration ability and the mtDNA copy number of SP4N cells are both lower than those in the CC4N cells and the 2N cells, but there exist giant mitochondria in the SP4N cells. The similar expression trends in the cell cycle regulation genes of the SP4N cells and 2N cells, while the corresponding expression profiles are clearly different between the SP4N cells and the CC4N cells. Moreover, the significant difference genes are associated with energy metabolism pathways among the SP4N cells, 2N cells and CC4N cells. These results can provide deeper understanding of SP600125 induction, as well as finding applications in polyploidization breeding of fish species.

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Bioinformatics Analysis of Genes Upregulating Poor Prognosis In Colorectal Cancer And Gastric Cancer

10.21203/rs.3.rs-635223/v1 ◽

2021 ◽

Author(s):

Ruizhi Dong ◽

Shaodong Li ◽

Bin Liang ◽

Zhenhua Kang

Keyword(s):

Gene Expression ◽

Colorectal Cancer ◽

Gastric Cancer ◽

Survival Rate ◽

Poor Prognosis ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Venn Diagram ◽

Expression Levels ◽

Significant Difference

Abstract Purpose : To analyze the up-regulated genes of poor prognosis in colorectal cancer and gastric cancer by bioinformatics. Methods: We searched the gene expression profiles GSE156355 and GSE64916 in colorectal cancer and gastric cancer tissues in NCBI-GEO. With P value < 0.05 and log2>1 as the standard, Venn diagram software was used to identify the common DEGs in the two data sets. Kaplan Meier plotter was used to analyze the survival rate data of common differentially expressed genes, draw and select survival curves, and analyze their expression levels. Results: A total of 97 genes were detected to be up-regulated in the two gene expression profiles. There were 19 genes in the prognosis of gastric cancer and 15 genes in the prognosis of colorectal cancer that had significant differences in the survival rate. Among them, KCNQ1, TRIM29, GART, MSX1, SNAI1, SUV39H2, LOXL2 and KCTD14 significantly decreased the survival rate of gastric cancer and colorectal cancer. The expression of MSX1 was the highest in gastric cancer. The expression level of KCTD14 was the highest in colorectal cancer, and there was no significant difference in the expression levels of other genes. Conclusion: There are 19 and 15 genes with significantly different prognostic viability in gastric cancer and colorectal cancer, respectively. The survival rates of KCNQ1, TRIM29, GART, Msx1, SNAI1, SUV39H2, LOXL2 and KCTD14 were significantly decreased in gastric cancer and colorectal cancer. The expression of MSX1 was the highest in gastric cancer. The expression of KCTD14 was the highest in colorectal cancer.

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