Analysis Of Gene Expression Profile In SUDHL6 Cells Of siRNA-Mediated BCL11A Downregulation

Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 3780-3780
Author(s):  
Hong Wu ◽  
He Dongmei ◽  
Ding Li ◽  
Yangqiu Li
Keyword(s):  
Gene Expression ◽  
B Cell ◽  
Signaling Pathway ◽  
Gene Expression Profile ◽  
Differentially Expressed Genes ◽  
Expression Profile ◽  
B Cell Lymphoma ◽  
Negative Control ◽  
Differentially Expressed ◽  
Qrt Pcr

Abstract Background The B-cell chronic lymphocytic leukemia (CLL)/lymphoma 11A gene (BCL11A) was associated with hematopoietic malignancies. However, the precise function of this transcription factor in B-cell malignancies still remain poorly characterized. Previous work from our laboratory has shown that BCL11A gene by small interfering RNA (siRNA) resulted in the growth inhibition and apoptosis of the B cell lymphoma cell line (i.e., SUDHL6 and EB1). The aim of this study was to further elucidate the molecular mechanism of this process by analyzing the gene expression profile in SUDHL6 cells after BCL11A knockdown. Methods FBCL11A siRNA was transfected into SUDHL6 cells to knock down BCL11A expression. Cells were collected, and RNA isolated for transcriptional profiling using the Affymetrix HG-U133 Plus 2.0 array. The global gene expression profile of the BCL11A siRNA-treated SUDHL6 cells was identified and analyzed. Twenty-one differentially expressed genes were further validated and analyzed from the BCL11A siRNA-treated SUDHL6 cells by real-time quantitative reverse transcript-polymerase chain reaction (qRT-PCR). Results FThere were 659 genes differentially expressed between the BCL11A siRNA- and negative control-transfected cells. These included 294 upregulated genes and 365 downregulated genes. The differentially expression genes are involved in various signaling pathways including metabolic pathways, focal adhesion, the MAPK signaling pathway, the cell cycle, the JAK-STAT signaling pathway, the TGF-beta signaling pathway, the WNT signaling pathway, apoptosis, and BCR signaling. qRT-PCR validation of the selected differentially expressed genes demonstrated agreement with the microarray analysis. There was a significant difference in the relative expression level of most of the selected genes differentially expressed between the BCL11A siRNA- and negative control siRNA-treated cells (P<0.05). After the transfection of BCL11A siRNA, among the apoptosis-related genes in the BCL-2 family, BCL2L11 was upregulated 7.24-fold, and BCL-2 was downregulated 3.23-fold. Conclusions Our results indicate that BCL11A is involved in gene networks with cancer related functions. BCL11A may play a role in gene expression events related to apoptosis. Disclosures: Li: This work was supported by Grants from National Natural Science Foundation of China (30871091 and 91129720), the Collaborated grant for HK-Macao-TW of Ministry of Science and Technology (2012DFH30060), the Guangdong Science & Technology Project (2012B0506: Research Funding.

scholarly journals Gene Expression Profile of HCAEC Cells Exposed to Serum From Chronic Kidney Disease Patients: Role of MAPK Signaling Pathway

2021 ◽  
Author(s):  
Angélica Rangel-López ◽  
Oscar Pérez-González ◽  
Sergio Juárez-Méndez ◽  
Ricardo López-Romero ◽  
Minerva Mata-Rocha ◽  
...  
Keyword(s):  
Gene Expression ◽  
Endothelial Dysfunction ◽  
Signaling Pathway ◽  
Gene Expression Profile ◽  
Differentially Expressed Genes ◽  
Pathway Analysis ◽  
Expression Profile ◽  
Differentially Expressed ◽  
Uremic Serum ◽  
Esrd Patients

Abstract End-stage renal disease (ESRD) patients have an elevated risk of cardiovascular (CV) complications including acute myocardial infarction (AMI); endothelial dysfunction and accumulation of uremic toxins have been associated with such CV-events. To explore which molecular pathways are involved in this CV-complication and the effects of the uremic serum on gene expression, an endothelial dysfunction model was studied through microarrays and pathway analysis. mRNA was isolated of human coronary arterial endothelial cells (HCAEC) primary cultures supplemented with 20% uremic serum from two groups of patients, USI: ESRD-patients; UCI: ESRD-AMI-patients. Affymetrix GeneChip® microarray and the LIMMA-package (Linear Models for Microarray Data) of the Bioconductor sofware17 was implemented to identify relevant DEGs between the two groups of uremic patients. Protein-protein interaction networks and pathway analysis were made to analyze the interaction and expression tendency of differentially expressed genes. 100 differentially expressed genes were identified from two data sets triggered by uremic state using bioinformatics, from 16,607. After in a new cohort, 30 genes were overexpressed in UCI group, which we identified 500 ontological genetic terms and one KEGG-pathway with p < 0.05. The metabolic pathway significantly represented was the MAPK signaling pathway. Network analysis showed six genes (PTGS2, SELE, ICAM1, HMOX1, EGR1, and TLR2) that represent potential markers for ESRD with AMI, as an approximation to their underlying mechanisms. The results obtained suggest that uremic toxins in patients with ESRD can alter HCAEC and modify the gene expression profile, which could have an impact on the development of cardiovascular complications in these patients.

scholarly journals Gene Expression Profiles of Papillary Thyroid Microcarcinoma

2017 ◽  
Vol 102 (1-2) ◽  
pp. 39-46 ◽  
Author(s):  
Woo Young Kim ◽  
Jae Bok Lee ◽  
Seung Pil Jung ◽  
Hoon Yub Kim ◽  
Sang Uk Woo ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Expression Profile ◽  
Differentially Expressed Genes ◽  
Expression Profile ◽  
Expression Profiles ◽  
Differentially Expressed ◽  
Papillary Thyroid Microcarcinoma ◽  
Papillary Thyroid ◽  
Normal Thyroid ◽  
Thyroid Microcarcinoma

The objective was to identify gene expression profile of papillary thyroid microcarcinoma. To help improve diagnosis of papillary thyroid microcarcinoma, we performed gene expression profiling and compared it to pair normal thyroid tissues. We performed microarray analysis with 6 papillary thyroid microcarcinoma and 6 pair normal thyroid tissues. Differentially expressed genes were selected using paired t test, linear models for microarray data, and significance analysis of microarrays. Real-time quantitative reverse transcription–polymerase chain reaction was used to validate the representative 10 genes (MET, TIMP1, QPCT, PROS1, LRP4, SDC4, CITED1, DPP4, LRRK2, RUNX2). We identified 91 differentially expressed genes (84 upregulated and 7 downregulated) in the gene expression profile and validated 10 genes of the profile. We identified a significant genetic difference between papillary thyroid microcarcinoma and normal tissue by 10 upregulated genes greater than 2-fold (P &lt; 0.05).

Gene Expression Profile Analysis According to Recurrent Gene Copy Number Abnormalities Defines a Diffuse Large B-Cell Lymphoma Subgroup Characterized by 9p21 Locus Deletion, Ribosome Machinery Deregulation and Poor Prognosis. A GELA Study

Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 803-803
Author(s):  
Fabrice Jardin ◽  
Jean-Philippe Jais ◽  
Thierry Jo Molina ◽  
Francoise Parmentier ◽  
Jean-Michel Picquenot ◽  
...  
Keyword(s):  
Gene Expression ◽  
B Cell ◽  
Gene Expression Profile ◽  
Expression Profile ◽  
Copy Number ◽  
Gene Copy Number ◽  
B Cell Lymphoma ◽  
Gene Copy ◽  
Bar Code ◽  
9P21 Locus

Abstract Genomic gains and losses play a crucial role in the development and progression of DLBCL. Some gains or losses are associated with particular morphologic or clinical manifestations and correlate with the “germinal center B-cell like” (GCB)/non-GCB phenotype, as defined by gene expression profiles (GEP). We previously developed a reliable and routinely single applicable PCR assay, which provided information regarding gain/loss of relevant genes, and prognosis in DLBCL, termed QMPSF (Multiplex PCR of Short Fluorescent Fragments). Here, we combined GEP and QMPSF approaches to delineate molecular pathways related to recurrent gene copy number abnormalities (GCNA) and assess their prognosis value in patients treated by R-CHOP. For this purpose a series of 69 newly diagnosed DLBCL, included in the 98–5 GELA trial with available tumor DNA was studied (median age = 69 years [59–79], IPI2–3: 64%; 4–5: 36%, 40 treated by R-CHOP and 29 by CHOP). A single QMPSF assay, validated by CGH array, to detect GCNA of 8 relevant genes including SIM1 (6q16), MYC (8q24), CDNK2A (9p21), RB1 (13q14), REL (2p13), BCL2 (18q21), TP53 (17p13), and CDKN1B (12p13) was performed. In addition a dedicated QMPSF assay that provides a “bar code” of the 9p21 locus containing CDKN2A (p16INK4a and p14ARF) and CDKN2B (p15INK4b) was designed. To delineate specific gene expression profile according to recurrent GCNA a subset of 52 patients were studied by both GEP (Affymetrix U133A) and QMPSF technologies. Gains of MYC, BCL2, and REL were observed in 13, 28 and 20 % respectively. DNA copy losses of TP53, CDNK2A, RB1 and SIM1 were observed in 9, 40, 6 and 17 % of cases respectively. Using supervised analysis, we delineated specific GEP according to the most frequent GCNA detected by QMPSF. Interestingly, a signature related to 9p21 locus (CDKN2A/CDKN2B) deletion was associated with an overexpression of several ribosome machinery coding genes and the involvement of distinct antiapoptotic molecular mechanisms. Subsequent genomic analysis with the dedicated assay indicated that in most of cases deletions were homozygous and abolished simultaneously p14arf and p16INK4a expression. With a median follow-up of 81 months, CDKN2A deletion, strongly correlates to a poor outcome in the entire cohort (5y OS=25% respectively vs.60% for patients in germline configuration, p=.003) and in the subgroup of patients treated by R-CHOP (5y OS=40% vs.70%, p=.04). Furthermore, prognosis impact of GCNA involving CDKN2A was validated in an independent set of 35 patients treated by R-CHOP. To conclude, combination of QMPSF and GEP may constitute a powerful approach to delineate new genomic pathways with prognosis impact in DLBCL. Notably, CDKN2A/CDKN2B loss, detected in more than one third of DLBCL patients constitutes a strong factor of chemoresistance that is not overcome by R combination. GEP indicates that this may be a consequence of an independent p14arf/p53 pathway, involving the well-established p14arf related ribosome regulation function.

scholarly journals Immune polychemotherapy regimen choice in B-cell non-Hodgkin lymphoma of high and low malignancy based on the identification of the mutational c-myc and BCL 2 genes

2021 ◽  
Author(s):  
Dilyara R. Kaidarova ◽  
Raiymkul K. Karakulov ◽  
Saule T. Gabbasova ◽  
Meruert K. Karazhanova ◽  
Svetlana A. Lyubko
Keyword(s):  
Gene Expression ◽  
B Cell ◽  
Gene Expression Profile ◽  
Expression Profile ◽  
B Cell Lymphoma ◽  
Response To Therapy ◽  
High Dose ◽  
Molecular Subgroups ◽  
Proliferative Index ◽  
Ki 67

Introduction: The relevance of research is conditioned by the study of the gene expression profile for the identification of molecular subgroups of non-Hodgkin B-cell lymphomas (NHBCLs) in haematology. Aim: The aim of this research was to study the gene expression profile with the identification of molecular subgroups in patients with NHBCLs for personalised treatment. Material and methods: This paper is aimed at analysing the frequency and role of expression of c-myc, B-cell lymphoma 2 (BCL 2) proteins and the Ki 67 proliferative index in patients with NHBCLs and conducting personalised therapy to improve the immediate effectiveness and immediate treatment results. Results and discussion: The paper presents the results of the use of high-dose polychemotherapy (PCT) in 9 patients out of 80 with NHBCL during co-expression of the c-myc, BCL 2 mutational gene and with high values of the Ki 67 proliferative index. High-dose chemotherapy (HDCT) was performed according to the R+HyperCVAD scheme (6 courses) and hematopoietic stem cell (HSC) autotransplantation improved the immediate effectiveness of therapy, with a complete remission rate of 80% and an event-free survival of 28 months. Conclusions: The study of molecular genetic characteristics in 80 patients with NHBCLs revealed co-expression of the c-myc and BCL 2 mutational gene in 9 out of 80 patients, and they differed in the aggressive course, ‘poor’ response to therapy, which predetermined the use of high-dose PCT with transplantation of autologous stem cells.

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