scholarly journals Transcriptomic Analysis of Rice Plants Overexpressing PsGAPDH in Response to Salinity Stress

Genes ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 641
Author(s):  
Hyemin Lim ◽  
Hyunju Hwang ◽  
Taelim Kim ◽  
Soyoung Kim ◽  
Hoyong Chung ◽  
...  
Keyword(s):  
Salt Stress ◽  
Abiotic Stress ◽  
Salinity Stress ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Pathway Enrichment Analysis ◽  
Sequencing Data ◽  
Illumina Hiseq ◽  
Rice Plants ◽  
Significant Difference

In plants, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a main enzyme in the glycolytic pathway. It plays an essential role in glycerolipid metabolism and response to various stresses. To examine the function of PsGAPDH (Pleurotus sajor-caju GAPDH) in response to abiotic stress, we generated transgenic rice plants with single-copy/intergenic/homozygous overexpression PsGAPDH (PsGAPDH-OX) and investigated their responses to salinity stress. Seedling growth and germination rates of PsGAPDH-OX were significantly increased under salt stress conditions compared to those of the wild type. To elucidate the role of PsGAPDH-OX in salt stress tolerance of rice, an Illumina HiSeq 2000 platform was used to analyze transcriptome profiles of leaves under salt stress. Analysis results of sequencing data showed that 1124 transcripts were differentially expressed. Using the list of differentially expressed genes (DEGs), functional enrichment analyses of DEGs such as Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were performed. KEGG pathway enrichment analysis revealed that unigenes exhibiting differential expression were involved in starch and sucrose metabolism. Interestingly, trehalose-6-phosphate synthase (TPS) genes, of which expression was enhanced by abiotic stress, showed a significant difference in PsGAPDH-OX. Findings of this study suggest that PsGAPDH plays a role in the adaptation of rice plants to salt stress.

scholarly journals De-novo transcriptome analysis unveils differentially expressed genes regulating drought and salt stress response in Panicum sumatrense

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Rasmita Rani Das ◽  
Seema Pradhan ◽  
Ajay Parida
Keyword(s):  
Gene Expression ◽  
Salt Stress ◽  
Abiotic Stress ◽  
Stress Tolerance ◽  
Differentially Expressed Genes ◽  
Salinity Stress ◽  
Abiotic Stress Tolerance ◽  
Differentially Expressed ◽  
Little Millet ◽  
Drought And Salt Stress

AbstractScreening the transcriptome of drought tolerant variety of little millet (Panicum sumatrense), a marginally cultivated, nutritionally rich, susbsistent crop, can identify genes responsible for its hardiness and enable identification of new sources of genetic variation which can be used for crop improvement. RNA-Seq generated ~ 230 million reads from control and treated tissues, which were assembled into 86,614 unigenes. In silico differential gene expression analysis created an overview of patterns of gene expression during exposure to drought and salt stress. Separate gene expression profiles for leaf and root tissue revealed the differences in regulatory mechanisms operating in these tissues during exposure to abiotic stress. Several transcription factors were identified and studied for differential expression. 61 differentially expressed genes were found to be common to both tissues under drought and salinity stress and were further validated using qRT-PCR. Transcriptome of P. sumatrense was also used to mine for genic SSR markers relevant to abiotic stress tolerance. This study is first report on a detailed analysis of molecular mechanisms of drought and salinity stress tolerance in a little millet variety. Resources generated in this study can be used as potential candidates for further characterization and to improve abiotic stress tolerance in food crops.

scholarly journals Integration of mRNA and miRNA Analysis Reveals the Molecular Mechanism of Cotton Response to Salt Stress

2021 ◽  
Vol 12 ◽  
Author(s):  
Jingjing Zhan ◽  
Yangyang Diao ◽  
Guo Yin ◽  
Muhammad Sajjad ◽  
Xi Wei ◽  
...  
Keyword(s):  
Salt Stress ◽  
Differential Expression ◽  
Signal Transduction Pathway ◽  
Differentially Expressed ◽  
Sequencing Data ◽  
Regulatory Relationship ◽  
Significant Differential Expression ◽  
Amplification Bias ◽  
Before And After ◽  
Increased Sensitivity

To identify the regulatory network of known and novel microRNAs (miRNAs) and their targets responding to salt stress, a combined analysis of mRNA libraries, small RNA libraries, and degradome libraries were performed. In this study, we used unique molecular identifiers (UMIs), which are more sensitive, accurate, and reproducible than traditional methods of sequencing, to quantify the number of molecules and correct for amplification bias. We identified a total of 312 cotton miRNAs using seedlings at 0, 1, 3, and 6 h after NaCl treatment, including 80 known ghr-miRNAs and 232 novel miRNAs and found 155 miRNAs that displayed significant differential expression under salt stress. Among them, fifty-nine differentially expressed miRNAs were simultaneously induced in two or three tissues, while 66, 11, and 19 were specifically expressed in the roots, leaves, and stems, respectively. It is indicated there were different populations of miRNAs against salt stress in roots, leaves and stems. 399 candidate targets of salt-induced miRNAs showed significant differential expression before and after salt treatment, and 72 targets of 25 miRNAs were verified by degradome sequencing data. Furthermore, the regulatory relationship of miRNA-target gene was validated experimentally via 5′RLM-RACE, proving our data reliability. Gene ontology and KEGG pathway analysis found that salt-responsive miRNA targets among the differentially expressed genes were significantly enriched, and mainly involved in response to the stimulus process and the plant hormone signal transduction pathway. Furthermore, the expression levels of newly identified miRNA mir1 and known miRNAs miR390 and miR393 gradually decreased when subjected to continuous salt stress, while overexpression of these miRNAs both increased sensitivity to salt stress. Those newly identified miRNAs and mRNA pairs were conducive to genetic engineering and better understanding the mechanisms responding to salt stress in cotton.

PD-L1 expression and TOP3A mutation as prognostic factors for adjuvant chemotherapy in triple negative breast cancer.

2021 ◽  
Vol 39 (15_suppl) ◽  
pp. 541-541
Author(s):  
Xue Wang ◽  
Peng Yuan ◽  
Feng Du ◽  
Lina Cui ◽  
Fangchao Zheng ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Adjuvant Chemotherapy ◽  
Triple Negative Breast Cancer ◽  
Triple Negative ◽  
Disease Free Survival ◽  
Genetic Alterations ◽  
Functional Enrichment ◽  
Pathway Enrichment Analysis ◽  
Genetic Characteristics ◽  
Significant Difference

541 Background: Triple negative breast cancer (TNBC) is a highly aggressive subtype of breast cancer that is markedly heterogeneous and lacks specific targets. The aim of this study is to explore potential predictors and therapeutic targets based on clinical and genetic characteristics. Methods: 138 patients with triple-negative breast cancer after surgical treatment were 1:1 randomly assigned to the paclitaxel combined with carboplatin (TCb) group or the epirubicin combined with cyclophosphamide sequential paclitaxel (EC-T) adjuvant chemotherapy group. PD-L1 was retrospectively analyzed by surgically resected specimens, and 733 cancer-related genes were detected by NGS. Pathway enrichment analysis was performed using DAVID for functional enrichment genetic alterations. Cox regression models and Kaplan-Meier were used to evaluate disease-free survival (DFS). Results: In this study, there was no significant difference in DFS between the TCb and EC-T groups. 31 (22.5%) of 138 TNBC patients were positive for PD-L1 expression, including 15 (10.9%) patients positive for PD-L1 in tumor cells (TCs) and 29 (21.0%) patients positive for PD-L1 in tumor-infiltrating immune cells (TICs). Patients with positive PD-L1 expression, either in TCs or TICs, achieved better DFS [HR=0.13 (95% CI: 0.02-0.93), p=0.016], the difference was also shown in the EC-T group [HR=0 (95% CI: 0- inf), p=0.037], but not in the TCb group [HR=0 (95% CI: 0.04-2.1), p=0.189]. In addition, we identified 7 patients with mutations in DNA topoisomerase IIIα(TOP3A), a homologous recombination (HR)-related gene, and patients with mutations in this gene had worse DFS than those without mutations [HR=4]. However, there was no statistically significant association between BRCA mutation and response to either therapeutic regimens. Conclusions: In this TNBC patient population, immunohistochemistry (IHC) and NGS analyses identified potential prognostic markers. PD-L1 positive and TOP3A mutation were significantly associated with early triple-negative breast cancer prognosis.

Expression characteristics of exosomal long non-coding RNA in abdominal aortic aneurysm

2020 ◽  
Author(s):  
Chuang Li ◽  
Yubo Zhao ◽  
Shuwei Wan ◽  
Yaming Guo ◽  
Mingli Han ◽  
...  
Keyword(s):  
Abdominal Aortic Aneurysm ◽  
Aortic Aneurysm ◽  
Calcium Signaling ◽  
Target Genes ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Abdominal Aortic ◽  
Wide Range ◽  
Significant Difference ◽  
Internal Mechanism

Abstract Background and objective:Abdominal aortic aneurysm(AAA) is one of the important causes of morbidity and mortality in middle-aged and elderly people. Although the understanding of the physiology and pathology of AAA has been improved, the potential molecular mechanism of AAA is still unclear. The existing evidence confirms that exosomal lncRNAs have a wide range of biological functions, and its regulatory disorders are related to the occurrence of diseases such as AAA, but the internal mechanism is not clear. The main purpose of this study is to screen the differentially expressed lncRNAs in exosomes between normal people and patients with AAA and to understand its internal mechanism.Materials and methods:The plasma of a healthy control group and patients with abdominal aortic aneurysm was collected, and the lncRNAs of exosomes were extracted and sequenced. Differential expression was assessed by DEseq using read counts as input and chosen according to the criteria of |log2(fold change)| > 1 and adjusted p-value < 0.05. Based on the Kyoto encyclopedia of genes and genomes (KEGG) and biological pathway and gene ontology (GO) functional enrichment analysis, the target genes were analyzed, and the correlation between lncRNA and target genes was analyzed.Result:We screened 45 species differentially expressed lncRNAs and found pathway significantly related to these genes, namely metabolic pathways, calcium signaling pathways and protein processing in endoplasmic reticulum and They play a significant and important role in the metabolic process and the cell signaling.Conclusion:There was significant difference in expression of exosomal lncRNAs between normal subjects and AAA patients. LncRNAs in exosomes regulate in the progress of AAA by activating metabolic pathway and calcium signaling pathway, but the specific mechanism is not clear and needs to be further explored.

scholarly journals Identification of novel genes and pathways in carotid atheroma using integrated bioinformatic methods

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Wenqing Nai ◽  
Diane Threapleton ◽  
Jingbo Lu ◽  
Kewei Zhang ◽  
Hongyuan Wu ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Transforming Growth Factor ◽  
Interaction Network ◽  
Enrichment Analysis ◽  
Functional Enrichment Analysis ◽  
Transforming Growth Factor Β ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Pathway Enrichment Analysis ◽  
Atheromatous Plaques

Abstract Atherosclerosis is the primary cause of cardiovascular events and its molecular mechanism urgently needs to be clarified. In our study, atheromatous plaques (ATH) and macroscopically intact tissue (MIT) sampled from 32 patients were compared and an integrated series of bioinformatic microarray analyses were used to identify altered genes and pathways. Our work showed 816 genes were differentially expressed between ATH and MIT, including 443 that were up-regulated and 373 that were down-regulated in ATH tissues. GO functional-enrichment analysis for differentially expressed genes (DEGs) indicated that genes related to the “immune response” and “muscle contraction” were altered in ATHs. KEGG pathway-enrichment analysis showed that up-regulated DEGs were significantly enriched in the “FcεRI-mediated signaling pathway”, while down-regulated genes were significantly enriched in the “transforming growth factor-β signaling pathway”. Protein-protein interaction network and module analysis demonstrated that VAV1, SYK, LYN and PTPN6 may play critical roles in the network. Additionally, similar observations were seen in a validation study where SYK, LYN and PTPN6 were markedly elevated in ATH. All in all, identification of these genes and pathways not only provides new insights into the pathogenesis of atherosclerosis, but may also aid in the development of prognostic and therapeutic biomarkers for advanced atheroma.

scholarly journals Combining Bioinformatics Techniques to Study the Key Immune-Related Genes in Abdominal Aortic Aneurysm

2020 ◽  
Vol 11 ◽  
Author(s):  
Han Nie ◽  
Jiacong Qiu ◽  
Si Wen ◽  
Weimin Zhou
Keyword(s):  
Immune Response ◽  
T Cells ◽  
Abdominal Aortic Aneurysm ◽  
Mast Cells ◽  
Aortic Aneurysm ◽  
Immune Cells ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Abdominal Aortic ◽  
Significant Difference

Approximately 13,000 people die of an abdominal aortic aneurysm (AAA) every year. This study aimed to identify the immune response-related genes that play important roles in AAA using bioinformatics approaches. We downloaded the GSE57691 and GSE98278 datasets related to AAA from the Gene Expression Omnibus database, which included 80 AAA and 10 normal vascular samples. CIBERSORT was used to analyze the samples and detect the infiltration of 22 types of immune cells and their differences and correlations. The principal component analysis showed significant differences in the infiltration of immune cells between normal vascular and AAA samples. High proportions of CD4+ T cells, activated mast cells, resting natural killer cells, and 12 other types of immune cells were found in normal vascular tissues, whereas high proportions of macrophages, CD8+ T cells, resting mast cells, and six other types of immune cells were found in AAA tissues. In the selected samples, we identified 39 upregulated (involved in growth factor activity, hormone receptor binding, and cytokine receptor activity) and 133 downregulated genes (involved in T cell activation, cell chemotaxis, and regulation of immune response mediators). The key differentially expressed immune response-related genes were screened using the STRING database and Cytoscape software. Two downregulated genes, PI3 and MAP2K1, and three upregulated genes, SSTR1, GPER1, and CCR10, were identified by constructing a protein–protein interaction network. Functional enrichment of the differentially expressed genes was analyzed, and the expression of the five key genes in AAA samples was verified using quantitative polymerase chain reaction, which revealed that MAP2K1 was downregulated in AAA, whereas SSTR1, GEPR1, and CCR10 were upregulated; there was no significant difference in PI3 expression. Our study shows that normal vascular and AAA samples can be distinguished via the infiltration of immune cells. Five genes, PI3, MAP2K1, SSTR1, GPER1, and CCR10, may play important roles in the development, diagnosis, and treatment of AAA.

scholarly journals The role of ARHGAP9: clinical implication and potential function in acute myeloid leukemia

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Caixia Han ◽  
Shujiao He ◽  
Ruiqi Wang ◽  
Xuefeng Gao ◽  
Hong Wang ◽  
...  
Keyword(s):  
Acute Myeloid Leukemia ◽  
Differentially Expressed Genes ◽  
Myeloid Leukemia ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Clinicopathological Parameters ◽  
Hub Genes ◽  
Significant Difference ◽  
Acute Myeloid

Abstract Background Rho GTPase activating protein 9 (ARHGAP9) is expressed in various types of cancers and can inactivate Rho GTPases that mainly regulate cytoskeletal dynamics. However, the exact role of ARHGAP9 in acute myeloid leukemia (AML) has yet to be clarified. Methods We compared the transcriptional expression, prognosis, differentially expressed genes, functional enrichment, and hub genes in AML patients on the basis of the data published in the following databases: UALCAN, GEPIA, Gene Expression Omnibus, the Human Protein Atlas, Cancer Cell Line Encyclopedia, LinkedOmics, Metascape, and String. Data from the Cancer Genome Atlas database was used to evaluate the correlations between ARHGAP9 expression and various clinicopathological parameters, as well as the significantly different genes associated with ARHGAP9 expression. Results We found that ARHGAP9 expression was higher in the tissues and cell lines extracted from patients with AML than corresponding control tissues and other cancer types. ARHGAP9 overexpression was associated with decreased overall survival (OS) in AML. Compared with the ARHGAP9low group, the ARHGAP9high group, which received only chemotherapy, showed significantly worse OS and event-free survival (EFS); however, no significant difference was observed after treatment with autologous or allogeneic hematopoietic stem cell transplantation (auto/allo-HSCT). The ARHGAP9high patients undergoing auto/allo-HSCT also had a significantly better prognosis with respect to OS and EFS than those receiving only chemotherapy. Most overlapping genes of the significantly different genes and co-expression genes exhibited enriched immune functions, suggesting the immune regulation potential of ARHGAP9 in AML. A total of 32 hub genes were identified from the differentially expressed genes, within which the KIF20A had a significant prognostic value for AML. Conclusions ARHGAP9 overexpression was associated with poor OS in AML patients and can be used as a prognostic biomarker. AML patients with ARHGAP9 overexpression can benefit from auto/allo-HSCT rather than chemotherapy.

scholarly journals Identification of an autophagy-related gene expression prognostic model in endometrial carcinoma patients

2020 ◽  
Author(s):  
Pinping Jiang ◽  
Wei Sun ◽  
Ningmei Shen ◽  
Qiang Wang ◽  
Shouyu Wang ◽  
...  
Keyword(s):  
Clinical Features ◽  
Prognostic Model ◽  
Cox Regression ◽  
Expression Profiles ◽  
Enrichment Analysis ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Pathway Enrichment Analysis ◽  
Prognostic Signature ◽  
Cox Regression Analysis

Abstract Background Autophagy, as a lysosomal degradation pathway, has been reported to be involved in various pathologies, including cancer. However, the expression profiles of autophagy-related genes (ARGs) in endometrial cancer (EC) remain poorly understood. Methods In this study, we analyzed the expression of MRGs using The Cancer Genome Atlas (TCGA) data to screen differentially expressed MRGs (DE-MRGs) significantly correlated to EC patients’ prognosis. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of DE-MRGs were investigated. LASSO algorithm and Cox regression analysis were performed to select MRGs closely related to EC patients’ outcomes. A prognostic signature was developed and the efficacy were validated in part of and the entire TCGA EC cohort. Moreover, we developed a comprehensive nomogram including the risk model and clinical features to predict EC patients' survival probability. Results Ninety-four ARGs significantly dysregulated in EC samples compared with the normal control samples. Functional enrichment analysis showed these differentially expressed ARGs (DE-ARGs) were highly enriched in apoptosis, P53 signaling pathway, and various cancer development. Among the 94 DE-ARGs, we subsequently screen out four-ARGs closely related to EC patients outcomes, which are ERBB2, PTEN, TP73 and ARSA. Based on the expression and coefficiency of 4 DE-ARGs, we developed a prognostic signature and further validated its efficacy in part of and the entire TCGA EC cohort. The four ARGs signature was independent of other clinical features, and was proved to effectively distinguish high- or low-risk EC patients and predicted patients' OS accurately. Moreover, the nomogram showed the excellent consistency between the prediction and actual observation in terms of patients' 3- and 5-year survival rates. Conclusions It was suggested that the ARG prognostic model and the comprehensive nomogram may guide the precise outcome prediction and rational therapy in clinical practice.

scholarly journals Tumor microenvironment characterization in cervical cancer identifies prognostic relevant gene signatures

PLoS ONE ◽  
2021 ◽  
Vol 16 (4) ◽  
pp. e0249374
Author(s):  
Linyu Peng ◽  
Gati Hayatullah ◽  
Haiyan Zhou ◽  
Shuzhen Chang ◽  
Liya Liu ◽  
...  
Keyword(s):  
Cervical Cancer ◽  
Tumor Microenvironment ◽  
Expression Profiles ◽  
Prognostic Indicator ◽  
Hpv Infection ◽  
Functional Enrichment ◽  
Rank Test ◽  
Sequencing Data ◽  
Ppi Networks ◽  
Significant Difference

Objective The aim of this study is to systematically analyze the transcriptional sequencing data of cervical cancer (CC) to find an Tumor microenvironment (TME) prognostic marker to predict the survival of CC patients. Methods The expression profiles and clinical follow-up information of CC were downloaded from the TCGA and GEO. The RNA-seq data of TCGA-CESC samples were used for CIBERSORT analysis to evaluate the penetration pattern of TME in 285 patients, and construct TMEscore. Other data sets were used to validate and evaluate TMEscore model. Further, survival analysis of TMEscore related DEGs was done to select prognosis genes. Functional enrichment and PPI networks analysis were performed on prognosis genes. Results The TMEscore model has relatively good results in TCGA-CESC (HR = 2.47,95% CI = 1.49–4.11), TCGA-CESC HPV infection samples (HR = 2.13,95% CI = 1–4.51), GSE52903 (HR = 2.65, 95% CI = 1.06–6.6), GSE44001 (HR = 2.1, 95% CI = 0.99–4.43). Patients with high/low TMEscore have significant difference in prognosis (log-rank test, P = 0.00025), and the main difference between high TMEscore subtypes and low TMEscore subtypes is immune function-related pathways. Moreover, Kaplan-Meier survival curves found out a list of identified prognosis genes (n = 86) which interestingly show significant enrichment in immune-related functions. Finally, PPI network analysis shows that highly related nodes such as CD3D, CD3E, CD8A, CD27 in the module may become new targets of CC immunotherapy. Conclusions TMEscore may become a new prognostic indicator predicting the survival of CC patients. The prognostic genes (n = 86) may help provide new strategies for tumor immunotherapy.

scholarly journals Integrative analysis of microRNA and mRNA expression in response to salt stress by UMI

2019 ◽  
Author(s):  
Jing jing Zhan ◽  
Yang yang Diao ◽  
Yan yan Zhao ◽  
Chao Li ◽  
Xiao Han ◽  
...  
Keyword(s):  
Salt Stress ◽  
Abiotic Stress ◽  
Salinity Stress ◽  
Target Genes ◽  
Plant Responses ◽  
Tolerance Mechanism ◽  
Significant Differential Expression ◽  
Function Annotation ◽  
Functional Studies ◽  
Processing Stability

Abstract Background Small RNAs play an important role in regulating plant responses to abiotic stress through modulation of the processing, stability, and translation of larger RNAs. Plants employ complex mechanisms of gene regulation to respond to salinity stress. Results In this study, we constructed 12 small RNA libraries, 12 mRNA libraries, and a degradome library to systematically investigate the miRNAs response to salt stress. A total of 312 cotton miRNAs were identified and of these, 80 were known ghr-miRNAs. 144 genes showed significant differential expression under salt stress combined with the targeting relationship between the sRNA data and mRNA data. We found 56 miRNA-mRNA pairs which were positively correlated, and 91 pairs which were negatively correlated. Using degradome sequencing, 72 target genes were identified associated with 25 miRNA families. Gene ontology and KEGG analysis indicated some targets were involved in vital biological pathways of salinity stress tolerance: 14 were involved in responses to abiotic stress, two were associated with an environmental adaptation pathway, and a total of 16 NAC and MYB family transcription factors were related to salinity stress. Conclusions The present study identified a large number of cotton miRNAs and identified relationships between miRNA and mRNA, with function annotation revealing their possible biological roles in response to salt stress. Our findings will further functional studies of cotton miRNAs and the salt tolerance mechanism.

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