Genes, variant genes, and pseudogenes of the human tRNAValgene family are differentially expressed in HeLa cells and in human placenta

ABSTRACT Adherence of enterohemorrhagic Escherichia coli (EHEC) to the intestinal epithelium is essential for initiation of infection. Intimin is the only factor demonstrated to play a role in intestinal colonization by EHEC O157:H7. Other attempts to identify additional adhesion factors in vitro have been unsuccessful, suggesting that expression of these factors is under tight regulation. We sought to identify genes involved in the control of adherence of EHEC O157:H7 to cultured epithelial cells. A total of 5,000 independent transposon insertion mutants were screened for their ability to adhere to HeLa cells, and 7 mutants were isolated with a markedly enhanced adherence. The mutants adhered at levels 113 to 170% that of the wild-type strain, and analysis of the protein profiles of these mutants revealed several proteins differentially expressed under in vitro culture conditions. We determined the sequence of the differentially expressed proteins and further investigated the function of OmpA, whose expression was increased in a mutant with an insertionally inactivated tcdA gene. An isogenic ompA mutant showed reduced adherence compared to the parent strain. Disruption of the ompA gene in the tdcA mutant strain abolished the hyperadherent phenotype, and anti-OmpA serum inhibited adhesion of wild-type and tdcA mutant strains to HeLa cells. Enhanced adhesion mediated by OmpA was also observed with Caco-2 cells, and anti-OmpA serum blocked adherence to HeLa cells of other EHEC O157:H7 strains. Our results indicate that multiple elements control adherence and OmpA acts as an adhesin in EHEC O157:H7.

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Identification of differentially expressed circular RNAs in HeLa cells infected with Chlamydia trachomatis

Pathogens and Disease ◽

10.1093/femspd/ftz062 ◽

2019 ◽

Vol 77 (7) ◽

Author(s):

Yuanjun Liu ◽

Chunmin Hu ◽

Yina Sun ◽

Haoqing Wu ◽

Xiaojun Chen ◽

...

Keyword(s):

Chlamydia Trachomatis ◽

Signaling Pathways ◽

Hela Cells ◽

Expression Profiles ◽

Quantitative Polymerase Chain Reaction ◽

Host Cells ◽

Differentially Expressed ◽

Chlamydia Infection ◽

Circular Rnas ◽

Mrna Microarray

ABSTRACT Non-coding circular RNAs (circRNAs) have been shown to have important roles in many diseases; however, no study has indicated circRNAs are involved in Chlamydia trachomatis infection. In this study, we used circRNA microarray to measure the global circRNA expression profiles in HeLa cells with or without C. trachomatis serovar E (Ct.E) infection. CircRNA/miRNA/mRNA interactions were predicted and bioinformatics analyses were performed. The differentially expressed circRNAs were selected according to our criterion for validation by reverse-transcription and quantitative polymerase chain reaction (RT-qPCR). The mRNA microarray was used to detect the mRNA expression profiles after Ct.E infection. Among 853 differentially expressed circRNAs, 453 were upregulated and 400 were downregulated after Ct.E infection. Target miRNAs and miRNA-targeted mRNAs of these circRNAs were predicted. RT-qPCR analysis indicated hsa_circRNA_001226, hsa_circRNA_007046 and hsa_circRNA_400027 were elevated similar to those determined in the circRNA microarray analysis. The mRNA microarray results showed 915 genes were upregulated and 619 genes were downregulated after Ct.E infection. Thirty-four differentially expressed genes overlapped in the bioinformatics and mRNA microarray results. KEGG pathway analysis revealed several signaling pathways, including endocytosis, MAPK and PI3P-Akt signaling pathways, that were targeted by circRNAs may play important roles in Chlamydia infection. This study provides evidence that circRNAs in host cells are involved in the process of Chlamydia infection.

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Construction of miRNA-target networks using microRNA profiles of CVB3-infected HeLa cells

Scientific Reports ◽

10.1038/s41598-019-54188-w ◽

2019 ◽

Vol 9 (1) ◽

Author(s):

Hai Lan Yao ◽

Mi Liu ◽

Wen Jun Wang ◽

Xin Ling Wang ◽

Juan Song ◽

...

Keyword(s):

Hela Cells ◽

Regulatory Networks ◽

Cellular Differentiation ◽

High Throughput Sequencing ◽

Target Genes ◽

Expression Profiles ◽

Differentially Expressed ◽

Mirna Regulation ◽

Cvb3 Infection ◽

Differentially Expressed Mirnas

AbstractMicroRNAs (miRNAs) play an important role in regulating gene expression in multiple biological processes and diseases. Thus, to understand changes in miRNA during CVB3 infection, specific miRNA expression profiles were investigated at 3 h, 6 h, and 9 h postinfection in HeLa cells by small-RNA high-throughput sequencing. Biological implications of 68 differentially expressed miRNAs were analyzed through GO and KEGG pathways. Interaction networks between 34 known highly differentially expressed miRNAs and targets were constructed by mirDIP and Navigator. The predicted targets showed that FAM135A, IKZF2, PLAG1, ZNF148, PHC3, LCOR and DYRK1A, which are associated with cellular differentiation and transcriptional regulation, were recognized by 8 miRNAs or 9 miRNAs through interactional regulatory networks. Seven target genes were confirmed by RT-qPCR. The results showed that the expression of DYRK1A, FAM135A, PLAG1, ZNF148, and PHC3 were obviously inhibited at 3 h, 6 h, and 9 h postinfection. The expression of LCOR did not show a significant change, and the expression of IKZF2 increased gradually with prolonged infection time. Our findings improve the understanding of the pathogenic mechanism of CVB3 infection on cellular differentiation and development through miRNA regulation, which has implications for interventional approaches to CVB3-infection therapy. Our results also provide a new method for screening target genes of microRNA regulation in virus-infected cells.

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СONSECUTIVE INTEGRATION OF AVAILABLE MICROARRAY DATA FOR ANALYSIS OF DIFFERENTIAL GENE EXPRESSION IN HUMAN PLACENTA

Biotechnologia Acta ◽

10.15407/biotech14.01.38 ◽

2021 ◽

Vol 14 (1) ◽

pp. 38-45

Author(s):

O. Lykhenko ◽

Keyword(s):

Gene Expression ◽

Differential Gene Expression ◽

Differentially Expressed Genes ◽

Human Placenta ◽

Normal Pregnancy ◽

Integrative Analysis ◽

Differentially Expressed ◽

Second Trimester ◽

Placental Development ◽

Differential Gene

The purpose of the study was to provide the pipeline for processing of publicly available unprocessed data on gene expression via integration and differential gene expression analysis. Data collection from open gene expression databases, normalization and integration into a single expression matrix in accordance with metadata and determination of differentially expressed genes were fulfilled. To demonstrate all stages of data processing and integrative analysis, there were used the data from gene expression in the human placenta from the first and second trimesters of normal pregnancy. The source code for the integrative analysis was written in the R programming language and publicly available as a repository on GitHub. Four clusters of functionally enriched differentially expressed genes were identified for the human placenta in the interval between the first and second trimester of pregnancy. Immune processes, developmental processes, vasculogenesis and angiogenesis, signaling and the processes associated with zinc ions varied in the considered interval between the first and second trimester of placental development. The proposed sequence of actions for integrative analysis could be applied to any data obtained by microarray technology.

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The Immunomodulatory Proteins B7-DC, B7-H2, and B7-H3 Are Differentially Expressed across Gestation in the Human Placenta

American Journal Of Pathology ◽

10.1016/s0002-9440(10)62990-2 ◽

2005 ◽

Vol 167 (2) ◽

pp. 465-473 ◽

Cited By ~ 46

Author(s):

Margaret G. Petroff ◽

Elza Kharatyan ◽

Donald S. Torry ◽

Lesya Holets

Keyword(s):

Human Placenta ◽

Differentially Expressed

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Maspin, a Tumor Suppressor Gene, Is Differentially Expressed in Human Placenta

Fertility and Sterility ◽

10.1016/s0015-0282(00)00907-9 ◽

2000 ◽

Vol 74 (3) ◽

pp. S69

Author(s):

A Dokras ◽

D.A Kirschmann ◽

L.G Gardner ◽

E.A Seftor ◽

M.J.C Hendrix

Keyword(s):

Tumor Suppressor ◽

Tumor Suppressor Gene ◽

Human Placenta ◽

Suppressor Gene ◽

Differentially Expressed

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The profile analysis of circular RNAs in human placenta of preeclampsia

Experimental Biology and Medicine ◽

10.1177/1535370218813525 ◽

2018 ◽

Vol 243 (14) ◽

pp. 1109-1117 ◽

Cited By ~ 12

Author(s):

Wenbo Zhou ◽

Huiyan Wang ◽

Xian Wu ◽

Wei Long ◽

Fangxiu Zheng ◽

...

Keyword(s):

Pregnant Women ◽

Human Placenta ◽

Profile Analysis ◽

Placental Tissue ◽

Circular Rna ◽

Differentially Expressed ◽

Circular Rnas ◽

Qrt Pcr ◽

Potential Biomarker

A total of 70 pregnant women were recruited for this study, including 35 early onset preeclampsia (PE) and 35 normal pregnant women. By RNA sequencing, the circular RNA (circRNAs) in placenta were identified. Differentially expressed circRNAs were bioinformatics analyzed with gene ontology, Kyoto Encyclopedia of Genes and Genomes, and circRNA–miRNA interaction prediction. Quantitative real time polymerase chain reaction(qRT-PCR) assay was used to verify the results. Compared with the normal pregnant women, there were 49 circRNAs differentially expressed in the placental tissue of PE women, including two circRNAs were up-regulated and 47 were down-regulated. Ten differentially expressed circRNAs were selected for validation by qRT-PCR, among which results of three circRNAs, circRNA_3286, circRNA_5593, and circRNA_3800, were consistent with the sequencing. According to the bioinformatic prediction, we speculate that these circRNAs may be involved in some cellular regulatory functions in PE through their targeted miRNAs. We also evaluated the expression of circRNA_3286 in plasma to be used as a potential biomarker for PE; in vitro Transwell assay shown transfected with si-circ-3286 significantly reduced invasion in HTR8/Svneo cells. In conclusion, we displayed a preliminary landscape of circRNA differential expression in PE and discussed their possible regulatory mechanisms. This study revealed a new insight into the molecular mechanism of PE. Impact statement The abnormal expression of many regulatory factors may be involved in the development of PE. circRNAs are proved to have a series of important biological functions; however, reports about circRNA and PE are rare. In this work, we evaluated the profile analysis of circRNAs in human placenta of PE by RNA-seq and found some newly differentially expressed circRNAs which might be involved in PE. Combined with bioinformatics analysis, their possible functions were preliminarily discussed.

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Molecular Characterization of SRSF2 Mutation Identifies a Clinically Relevant Lncrna (MALAT1) in Chronic Myelomonocytic Leukemia (CMML)

Blood ◽

10.1182/blood.v126.23.1641.1641 ◽

2015 ◽

Vol 126 (23) ◽

pp. 1641-1641

Author(s):

Maria E. Balasis ◽

Jane Merelvede ◽

Sateesh Kunigal ◽

Xiaoyi Ren ◽

Yan Ma ◽

...

Keyword(s):

Cell Line ◽

Hela Cells ◽

Research Funding ◽

Rna Binding ◽

Binding Capacity ◽

Critical Role ◽

Differentially Expressed ◽

Leukemic Cells ◽

Nuclear Speckle ◽

Significant Difference

Abstract SRSF2 is mutated at proline 95 (P95) in approximately 45% of patients with CMML. The consequence of SRSF2 P95H mutations on splicing has been associated with change in target RNA motif preference compared to wild type that favors CCNG over GGNG resulting in aberrant splicing abnormalities. Although this has led to several downstream mis-spliced candidates that may contribute to SRSF2 leukemic pathogenesis, the biologic consequences of SRSF2 mutation have not been fully elucidated and its effect on non-splicing pathways has yet to be explored. SRSF2 has two major functions within the nucleus: (1) bind to cis elements on pre-mRNA transcripts that functionally redefines putative exon-intron boundaries and (2) interact with other members of the spliceosome complex at nuclear suborganelles known as speckles. To explore the effects of SRSF2 P95 mutation on nuclear speckle dynamics, we transfected HeLa cells with GFP-SRSF2 wildtype (WT) and mutant (MT) constructs and performed Fluorescent Recovery After Photo-bleaching (FRAP) to determine the mutant specific kinetics of SRSF2 molecules localized to the nuclear speckle. Using this approach, we confirmed that SRSF2 WTs are characterized by complete photo-recovery with a half-life of approximately 35 (30-42) seconds as previously reported. However, when we performed FRAP of GFP-SRSF2 MTs a statistically significant difference in photo-recovery was observed compared to WT cells (Fig. 1a). The difference between baseline fluorescence and maximal recovered fluorescence in SRSF2 MT cells, or the immobile fraction, suggests that trapped bleached SRSF2 molecules are sterically inhibiting the diffusion of unbleached SRSF2 molecules. We reasoned that the observed differences in RNA binding capacity and nuclear speckle dynamics could be related. This rationale identified MALAT1 as a link connecting both increased RNA binding and nuclear speckle trafficking abnormalities because it is a Long Non-Coding (lnc) RNA that localizes to and has a critical role in SR protein recruitment and retention to the nuclear speckle. MALAT1, which is highly enriched for CCNG motifs, has also been demonstrated to bind to SRSF2 directly and has been implicated in a wide spectrum of carcinomas making it an attractive intermediary to study in our system. To determine whether SRSF2 MTs have increased MALAT1 binding capacity compared to SRSF2 WT, we performed RNA IP of myc-his-SRSF2 WT and MT transfected HeLa cells. Using this approach, we demonstrated a 60% enrichment of MALAT1 in SRSF2 WT transfected cells and a 120-150% enrichment of MALAT1 in SRSF2 MT cells compared to the empty vector control (Fig. 1b-c). We next performed the above FRAP experiment in the context of MALAT1 depletion and demonstrated that observed immobile fraction seen in SRSF2 MT cells is rescued (Fig. 1d). To determine the clinical relevance of MALAT1 in CMML we profiled a cohort of 54 CMML cases for MALAT1 expression by PCR. As shown in Figure 2a-b and d-e, MALAT1 expression is statistically elevated in CMML BMNCs and is among the highest differentially expressed transcripts in CMML monocytes (CD14+). We additionally characterized SRSF2 expression in our CMML BMNCs and CD14+ cohort and identified a linear correlation (Pearson R=0.7 p<0.05) between SRSF2 expression and MALAT1 expression (Figure 2c). Further, CMML patients with high MALAT1 expression in the BMNC compartment had inferior overall and leukemia-free survival (Fig. 2f-g). Given its relevance in solid tumors and its over-expression in CMML, we explored the consequence of MALAT1 depletion on human monocytic leukemic cells. We first performed ultra-deep RNA sequencing of the THP-1 cell line treated with two MALAT-1 depleting ASOs or matched chemistry specific controls. IPA analysis of differentially expressed transcripts identified a c-Myc gene signature that was validated by western blot analysis demonstrating reduction of c-Myc in THP-1 MALAT1-depleted cells. Colony formation assays using the THP-1 cell line demonstrated that MALAT-1 depletion resulted in decreased colony-forming capacity (CFC). MALAT-1 ASOs were also capable of depleting MALAT-1 in primary CMML BMNCs and were associated with a decreased CFC suggesting that MALAT-1 is a potential therapeutic target. Taken together, our data identifies SRSF2 P95 mutation nuclear trafficking abnormalities and identifies a novel clinically relevant lncRNA in CMML. Figure 1. Figure 1. Figure 2. Figure 2. Disclosures Komrokji: Celgene: Consultancy, Research Funding; Incite: Consultancy; Novartis: Speakers Bureau; GSK: Research Funding. List:Celgene Corporation: Honoraria, Research Funding.

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