scholarly journals Screening and identifcation of differentially expressed microRNAs in diffuse large B-cell lymphoma based on microRNA microarray

2020 ◽  
Author(s):  
Hai-Xia Gao ◽  
Xinxia Li
Keyword(s):  
Target Gene ◽  
Target Genes ◽  
Cell Lymphoma ◽  
B Cell Lymphoma ◽  
Signal Pathway ◽  
Differentially Expressed ◽  
Potential Target ◽  
Large B Cell Lymphoma ◽  
Differentially Expressed Mirnas ◽  
Microrna Microarray

Abstract We aimed to screen and identify differentially expressed microRNAs (miRNAs) between diffuse large B-cell lymphoma (DLBCL) and control (lymph node reactive hyperplasia, LRH) groups, investigate whether miRNAs associated with DLBCL and could serve as potential therapeutic targets. Five DLBCL experimental samples and five control samples were obtained from fresh tissues. The exclusion criteria were expressed as follows: patients with other lymphoid diseases and patients undergoing chemical treatment. Firstly, fresh samples were analyzed using microRNA microarray to identify differentially expressed miRNAs. Next, three databases (Targetscan, microRNAorg, PITA) were used to intersection predict the potential target gene of the 204 differential miRNAs and performed Venn diagram of the results. Then, target genes of differential miRNAs were performed by Gene ontology (GO) and Kyoto Encyclopedia of Gene and Genome (KEGG) pathway analysis. Finally, to validate the microRNA microarray data, we performed Real-time reverse transcription PCR (qRT-PCR) for eight differentially expressed miRNAs (miR-193a-3p, miR-19a-3p, miR-19b-3p, miR-370-3p, miR-1275, miR-490-5p, miR-630 and miR-665) using DLBCL and LRH fresh samples. Two hundred and four miRNAs showed differential expression, including 105 down-regulated and 54 up-regulated miRNAs. The cut-off criterion was set as P value ≤0.05 and fold change (FC) ≥2. A total of 7522 potential target genes for the 204 miRNAs were predicted. Potential target genes were enriched in pathway in cancers, MAPK signal pathway, regulation of actin cytoskeleton, focal adhesion, endocytosis, Wnt signal pathway, axon guidance, calcium signal pathway, and PI3K/AKT signal pathway. Eight miRNAs validation by qRT-PCR, four miRNAs (miR-19b-3p, miR-193a-3p, miR-370-3p and miR-490-5p) were low expression in DLBCL (P< 0.05). The high expression of miR-630 in DLBCL was statistically significant (P< 0.05). Our results of identification of differentially expressed miRNAs, predicted the target gene of the differential miRNAs, enrichment of target gene biological functions and signaling pathway, will provide basis for researchers in identifying the pathogenesis of DLBCL, could serve as reliable biomarkers for precise diagnosis and as therapeutic target for improvement of therapeutic efficacy in DLBCL in the future.

scholarly journals Differentially Expressed Trfs in Relapsed & Refractory Diffuse Large B Cell Lymphoma and the Bioinformatic Analysis for Their Potential Clinical Use

Blood ◽  
2018 ◽  
Vol 132 (Supplement 1) ◽  
pp. 5121-5121
Author(s):  
Qingyuan Qu ◽  
Yujie Jiang ◽  
Ying Li ◽  
Yiqing Cai ◽  
Ya Zhang ◽  
...  
Keyword(s):  
Cell Proliferation ◽  
B Cell ◽  
Target Genes ◽  
Cell Lymphoma ◽  
B Cell Lymphoma ◽  
Differentially Expressed ◽  
Biological Processes ◽  
Potential Target ◽  
Large B Cell Lymphoma ◽  
Large B Cell

Abstract Introduction Diffuse large B-cell lymphoma (DLBCL) is an aggressive but potentially curable malignancy in some low-risk patients. However, patients with high-risk factors or diagnosed as some special subtypes often have a poor prognosis although they received intensive combine chemotherapy or bio-target treatment. The exact mechanism of the anti-chemotherapy is unknown and it may be related to multiple oncogene mutations and signal pathways. tRFs is reported stability in almost all types of cells and organisms ranging from humans to bacteria. They are highly conserved, tissue-specific and time-specific tRNA fragments and can be detected in body fluid. Their precise sequence structure located at the end of tRNA or nearby. The length of them has a close relationship with the nucleotide composition at cleavage junctions, indicating that the tRFs are derived from tRNA cleavage in a specific manner. tRFs is a group of abundant non-coding RNAs secondly only to miRNAs. It has been proved that tRFs participate in many biological processes including cell proliferation, viral reverse transcriptases activation, gene expression, RNA procession regulation, DNA damage response modulation and tumor suppression. In this study, we aimed to investigate the potential function of associated tRFs in patients with relapsed & refractory (R/R) DLBCL. Materials and Methods Peripheral blood mononuclear cells (PBMCs) were separated from patients with R/R DLBCL and control groups, respectively. Next-generation sequencing and quantitative real-time reverse transcription-PCR were used to determine the expression profiles of tRFs in the two groups. Two databases of tRFs, tRFs2Cancer and tRFdb were utilized to analyse the similarity and dissimilarity of homologous tRNA fragment. Results Among the sequences with significant difference value, ten tRFs were picked, four (sequence 1- sequence 4) were up-regulated and six (sequence 5- sequence 10) were down-regulated (Figure1). To investigate the content of the differentially expressed tRF in patients group, we performed quantitative PCR to verify three tRFs. The PCR result was consistent with the sequencing analysis. Combined with the results of qRT-PCR and database searching (Figure2,3), we finally chose three sequences (sequence 2, sequence 4 and sequence 10) for further study. With the help of TargetScan, miRanda and other target gene predicting tools, we identified the associated target genes for the three tRFs (sequence 2:497, sequence 10: 9114, sequence 4: 730). The regulatory relationship of sequence 4 is shown in figure 4, the color of each line corresponds to the chromosome which the tRNA comes from. Because sequence 10 has a large number of potential regulatory target genes and it is difficult to obtain satisfying results, we made a functional enrichment analysis for the other tRFs to get their potential regulatory genes. The results showed that the potential target genes of sequence 4 tend to be enriched in multiple ways, including plasma membrane-bounded cell projection morphogenesis, nervous system development, and sensory organ development, etc. The potential target genes of sequence 2 tend to be enriched in FCGR-dependent phagocytosis, Ras signaling pathway, and cellular component regulation(Figure 5). The results of protein interactions analysis showed that the potential regulatory target genes of sequence 4 and sequence 2 can be constructed to gene-protein interaction networks. In this network, several biological processes such as alternative splicing, endosomal transport, and endocytosis might play important roles in tumorigenesis(Figure 6). Conclusion In this study, we analyzed the differently expressed tRFs profiles in patients with R/R DLBCL and the results are consistent with the database data analysis. We also predicted the possible mechanism of the up- or down-regulated tRFs which might be used in clinical although they are unexploited yet. Up or down-regulated tRFs is common in many types of tumors. It is well known that knockdown of the overexpressed tRF may inhibit tumor cell proliferation and the recovery of the downregulated tRFs may reverse the sensitivity to chemotherapy. We hyperthesis that the associated tRFs can be used as fluid-based biomarkers for diagnosis and prognosis assessment. Future investigation on them may help to develop new methods to repair the disordered biological signaling pathways associated with the DLBCL. Disclosures No relevant conflicts of interest to declare.

A BCL6 Target Gene Signature Predicts the Biological Behavior and Classification of Diffuse Large B-Cell Lymphoma.

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 616-616
Author(s):  
Jose M. Polo ◽  
Przemyslaw Juszczynski ◽  
Leandro Cerchietti ◽  
Stefano Monti ◽  
Kenny Ye ◽  
...  
Keyword(s):  
B Cell ◽  
Cell Lines ◽  
Target Gene ◽  
Target Genes ◽  
Cell Lymphoma ◽  
B Cell Lymphoma ◽  
Gene Signature ◽  
Transcriptional Profiles ◽  
Large B Cell Lymphoma ◽  
Large B Cell

Abstract Diffuse large B-cell lymphoma (DLBCL), the most common lymphoid malignancy, is a heterogeneous disease. These tumors are thought to arise from normal antigen-exposed B-cells that have migrated to or through the germinal center (GC). Structural abnormalities of the BCL6 locus (chromosomal translocation and aberrant somatic hypermutation) are the most common genetic abnormalities in DLBCL, occurring in over a third of these tumors. We recently developed a potent and specific BCL6 peptide inhibitor (BPI) that disrupts the interaction between BCL6 and the SMRT co-repressor complex. BPI was cytotoxic against some, but not all, BCL6 positive primary DLBCLs and DLBCL cell lines, indicating that a subset of DLBCLs was particularly dependent on BCL6 for their survival. We predicted that such cases might be identified through a specific BCL6-dependent gene signature and utilized ChIP on chip and a 24,000 promoter genomic microarray to identify BCL6 target genes. In these studies, BCL6 bound to 431 loci. Eighty percent of these candidate target genes contained a canonical BCL6 binding site and 85% of analyzed candidates were confirmed using quantitative single-locus CHIP. GO term enrichment revealed that BCL6 targets were significantly more likely to be genes associated with transcription, ubiquitylation, response to DNA damage, cell cycle and chromatin assembly/disassembly (FDR &lt;.05). We predicted that coordinate regulation of the BCL6 targets would serve as a signature of BCL6 activity. For this reason, we asked whether the BCL6 target gene set was differentially expressed in the recently described DLBCL comprehensive clusters, “B-cell Receptor/Proliferation (BCR),” “Oxidative Phosphorylation (OxPhos),” and Host Response (HR),” using 2 large series of primary DLBCLs with available transcriptional profiles. Since HR tumors are largely defined by infiltrating host inflammatory cells, we focused on BCR and OxPhos DLBCLs. Of interest, BCR tumors more frequently exhibit BCL6 chromosomal translocations and increased BCL6 expression. Consistent with these observations, gene set enrichment analysis (GSEA) revealed highly significant differential expression of BCL6 target genes in BCR vs. OxPhos tumors (p &lt;.0001). In contrast, GSEA of the BCL6 targets in the same DLBCLs sorted into developmental cell-of-origin groups was not significant (“GC” vs. “ABC”/”Other”, p =.25 and “GC” vs. “ABC” only, p =.082). To assess the functional significance of the BCL6 signature in the DLBCL consensus clusters, we generated a predictive algorithm based on the transcriptional profiles of a series of DLBCL cell lines to assign the lines to BCR, OxPhos or HR comprehensive clusters. Five BCR and 3 OxPhos DLBCL cell lines were selected for additional blinded functional analyses. BPI treatment upregulated BCL6 target gene expression in BCR, but not OxPhos, DLBCLs. Furthermore, BPI was significantly more effective in BCR lines than OxPhos DLBCLs (BPI IC50s of BCR vs. Ox Phos lines, 12.7±1.7 μM vs 48.9±2.6 μM, respectively, p&lt;. 0001). Taken together, the data indicate that BCR DLBCLs are significantly more dependent on BCL6 transcriptional repression and more sensitive to targeted BCL6 inhibition. More generally, these studies suggest that DLBCL comprehensive cluster designation will help guide the targeted therapy of biologically discrete DLBCL subsets.

Identification of FOXP1 Transcriptional Targets in Diffuse Large B Cell Lymphoma

Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 5119-5119
Author(s):  
Emily T Camilleri ◽  
Carlos A Aya-Bonilla ◽  
Philip J Brown ◽  
Alison Banham ◽  
Paula Marlton ◽  
...  
Keyword(s):  
Cell Line ◽  
Differentially Expressed Genes ◽  
Target Genes ◽  
Cell Lymphoma ◽  
Prognostic Significance ◽  
B Cell Lymphoma ◽  
Differentially Expressed ◽  
Large B Cell Lymphoma ◽  
Truncated Isoforms ◽  
Large B Cell

Abstract Abstract 5119 Introduction Diffuse Large B cell Lymphoma (DLBCL) is a clinically and biologically heterogeneous lymphoid malignancy, where complete response is achieved in up to 60% of patients, though over half of all patients relapse (Hunt and Reichard, 2007). The prognostic significance of the expression of FOXP1 transcription factor in DLBCL has been highly controversial with some studies describing immunohistochemical FOXP1 expression as a poor prognostic marker (Banham et. all. 2005). Recent transcript analysis has identified over 10 FOXP1 isoforms where some exhibit COOH- or NH3- truncations and also the absence of regulatory domains. These truncated isoforms are highly expressed in ABC-DLBCL (Brown et. al. 2008) and it is suggested that truncated isoforms may aberrantly regulate FOXP1 target genes. Although there have been many studies debating the prognostic significance of FOXP1 overexpression in DLBCL, there has been little examination of the function of FOXP1 in DLBCL, specifically the genes targeted by FOXP1, and how the function of FOXP1 isoforms may contribute to a more aggressive phenotype. Methods Expression constructs for 4 FOXP1 isoforms (isoforms 1, 2, 3 and 8) were kindly provided by Dr. Philip Brown and Dr. Alison Banham. Stable cell lines were established by transfecting the BJAB cell line with either FOXP1 isoform 1 or the empty pBKCMV construct, and selection with G418 antibiotic. Total RNA was extracted from both cell lines and 4 DLBCL tumours (with low to high FOXP1 expression), and gene expression was analysed using Illumina HT12v4 microarray. Genes with >2-fold changes in expression between pBKCMV and Isoform 1 stable cell line were investigated. VisANT analysis and Gene set enrichment was performed on differentially expressed genes and candidates were validated by qRT-PCR. Promoter analysis using MatInspector revealed forkhead-binding sites in the promoter region of candidate genes, and dual luciferase reporter gene assays were performed to ascertain promoter regulation by FOXP1 isoforms. Western blot was also performed to validate translational changes in expression. Results In the gene expression microarray analysis of FOXP1 isoform 1 expression compared to baseline levels, 271 genes were identified with >2-fold differential expression. High versus low FOXP1 expressing DLBCL patients were also compared, where it was found that 2472 genes were differentially expressed over the 2-fold level. Significantly, comparison of differentially expressed genes in both the cell line and patient samples revealed all 271 genes differentially expressed in the cell line overlapped with the patient genes, indicating these results are translatable to FOXP1 function in DLBCL tumours. Pathway analysis was performed on the differentially expressed genes, and unexpectedly there were no significant enrichment of curated pathways. Alternatively visANT was used to examine interactive networks of the 271 candidate genes, and an integrative analysis using the FOXP1 microarray expression data was used to enrich the interactions. This analysis revealed critical interactions that could not be revealed by pathway analysis, and also identified genes that are likely FOXP1 targets. The promoter regions of 5 genes were investigated using reporter gene assays, and FOXP1 isoforms 3 and 8 were found to be significantly stronger transcriptional repressors compared to isoforms 1 and 2. For example, one of the genes identified, heterogeneous nuclear ribonucleoprotein U (HNRNPU) was highly expressed in the presence of isoform 1, however in the presence of isoform 3 was greatly downregulated. Although this gene has not previously been associated with DLBCL, HNRNPU is a potent regulator of snRNP's thereby having global effects on mRNA production and protein synthesis (Xiao et. al. 2012 Cell Vol. 45(5) 656–668). We are currently investigating the biological significance of other novel FOXP1 target genes, and how the truncated isoforms are involved in the differential regulation of these genes. Conclusion We have identified 271 genes that are differentially expressed in both a cell line model and DLBCL patient tissues with high versus low FOXP1 expression. These are novel genes in DLBCL pathogenesis that also show differential expression in the presence of truncated isoforms, indicating truncated isoforms may have aberrant functions and may contribute to a more pathogenic phenotype. Disclosures: No relevant conflicts of interest to declare.

NFκB Activation in Primary Mediastinal Large B-Cell Lymphoma: Nuclear Localization of c-REL and Coordinate Upregulation of NFκB Target Genes.

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 243-243
Author(s):  
Friedrich Feuerhake ◽  
Jeffery L. Kutok ◽  
Stefano Monti ◽  
Giorgio Cattoretti ◽  
Paul Kurtin ◽  
...  
Keyword(s):  
Subcellular Localization ◽  
B Cell ◽  
Target Gene ◽  
Target Genes ◽  
Cell Lymphoma ◽  
B Cell Lymphoma ◽  
Large B Cell Lymphoma ◽  
Nfkb Activation ◽  
Large B Cell

Abstract Primary mediastinal large B-cell lymphoma (MLBCL) is a clinically distinct entity that typically presents as localized, sclerotic disease in young, female patients. We previously characterized the transcriptional profiles of MLBCLs and identified important shared features with a clinically related disorder, classical Hodgkin lymphoma (cHL) (Blood 102:3871, 2003). Given the documented role of the NFkB survival pathway in Hodgkin Reed-Sternberg cells, we previously assessed NFkB activation in MLBCL by determining the subcellular location of the c-REL subunit of the NFkB heterodimer with a 2-color immunofluoresence assay. In a small pilot MLBCL series, c-REL was localized to the nucleus in the majority of examined cases, consistent with NFkB activation. In the current study, we evaluated c-REL subcellular localization in an additional series of MLBCLs and DLBCLs using a broadly applicable immunoperoxidase method. 100% of MLBCLs exhibited nuclear c-REL staining whereas DLBCL c-REL subcellular localization was more variable. Thereafter, we analyzed the transcription profiles of the 34 MLBCLs and 176 DLBCLs for coordinate expression of NFkB target genes, using literature-curated NFkB target gene lists from three independent sources and gene set enrichment analysis (GSEA). MLBCL signatures exhibited significant enrichment of 2 of the 3 NFkB target gene sets. In addition, 32 NFkB target genes from the combined set were significantly more abundant in MLBCLs than DLBCLs (&gt; 30% more abundant and &gt; 99th percentile in permutation analysis). Similar results were obtained in an independent series of MLBCLs and DLBCLs with available gene expression profiles (J. Exp. Med. 198:851, 2003). To assess the role of c-REL amplification in NFkB activation in our lymphoma series, we compared c-REL amplification, c-REL subcellular localization and coordinate expression of the identified NFkB target genes and classified the DLBCLs according to putative cell of origin. The majority of c-REL amplifications (67%) were found in DLBCLs of germinal center (GC) subtype, consistent with the observation that c-REL is part of the described GC signature. However, most (71%) of the examined GC DLBCLs had cytoplasmic c-REL expression and the GC DLBCLs did not have increased expression of NFkB target genes. Taken together with the MLBCL analyses, these studies indicate that: 1) NFkB is consistently activated in MLBCL; 2) c-REL amplification is not closely associated with NFkB activation in large cell lymphomas (LCLs); and 3) NFkB activation in LCL subtypes does not require amplification of the c-REL locus.

scholarly journals Clinical significance of metabolism-related biomarkers in non-Hodgkin lymphoma – MCT1 as potential target in diffuse large B cell lymphoma

2019 ◽  
Vol 42 (3) ◽  
pp. 303-318 ◽  
Author(s):  
Julieta Afonso ◽  
Tatiana Pinto ◽  
Susana Simões-Sousa ◽  
Fernando Schmitt ◽  
Adhemar Longatto-Filho ◽  
...  
Keyword(s):  
B Cell ◽  
Hodgkin Lymphoma ◽  
Clinical Significance ◽  
Cell Lymphoma ◽  
B Cell Lymphoma ◽  
Potential Target ◽  
Non Hodgkin Lymphoma ◽  
Large B Cell Lymphoma ◽  
Large B Cell

Abstract B38: FOXP1 truncated isoforms differentially regulate target genes in diffuse large B cell lymphoma.

2013 ◽  
Author(s):  
Emily Camilleri ◽  
Carlos Aya-Bonilla ◽  
Jamie Nourse ◽  
Philip J. Brown ◽  
Alison H. Banham ◽  
...  
Keyword(s):  
B Cell ◽  
Target Genes ◽  
Cell Lymphoma ◽  
B Cell Lymphoma ◽  
Large B Cell Lymphoma ◽  
Truncated Isoforms ◽  
Large B Cell

scholarly journals Effect of miR-27b-5p on apoptosis of human vascular endothelial cells induced by simulated microgravity

APOPTOSIS ◽  
2019 ◽  
Vol 25 (1-2) ◽  
pp. 73-91 ◽  
Author(s):  
Yi-Kai Pan ◽  
Cheng-Fei Li ◽  
Yuan Gao ◽  
Yong-Chun Wang ◽  
Xi-Qing Sun
Keyword(s):  
Endothelial Cells ◽  
Western Blot ◽  
Target Gene ◽  
Simulated Microgravity ◽  
Target Genes ◽  
Expression Profiles ◽  
Differentially Expressed ◽  
Luciferase Assay ◽  
Qrt Pcr ◽  
Differentially Expressed Mirnas

AbstractWeightlessness-induced cardiovascular dysfunction can lead to physiological and pathological consequences. It has been shown that spaceflight or simulated microgravity can alter expression profiles of some microRNAs (miRNAs). Here, we attempt to identify the role of miRNAs in human umbilical vein endothelial cells (HUVECs) apoptosis under simulated microgravity. RNA-sequencing and quantitative real-time PCR (qRT-PCR) assays were used to identify differentially expressed miRNAs in HUVECs under simulated microgravity. Then we obtained the target genes of these miRNAs through target analysis software. Moreover, GO and KEGG enrichment analysis were performed. The effects of these miRNAs on HUVECs apoptosis were evaluated by flow cytometry, Western blot and Hoechst staining. Furthermore, we obtained the target gene of miR-27b-5p by luciferase assay, qRT-PCR and Western blot. Finally, we investigated the relationship between this target gene and miR-27b-5p in HUVECs apoptosis under normal gravity or simulated microgravity. We found 29 differentially expressed miRNAs in HUVECs under simulated microgravity. Of them, the expressions of 3 miRNAs were validated by qRT-PCR. We demonstrated that miR-27b-5p affected HUVECs apoptosis by inhibiting zinc fingers and homeoboxes 1 (ZHX1). Our results reported here demonstrate for the first time that simulated microgravity can alter the expression of some miRNAs in HUVECs and miR-27b-5p may protect HUVECs from apoptosis under simulated microgravity by targeting ZHX1.

Array CGH Analysis for Target Genes at 6p21 Amplification Region in Diffuse Large B-Cell Lymphoma.

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 1116-1116
Author(s):  
Yumiko Kasugai ◽  
Hiroyuki Tagawa ◽  
Yoshihiro Kameoka ◽  
Sivasundaram Karnan ◽  
Ritsuro Suzuki ◽  
...  
Keyword(s):  
B Cell ◽  
Target Genes ◽  
Array Cgh ◽  
Cell Lymphoma ◽  
B Cell Lymphoma ◽  
Cyclin D3 ◽  
Common Region ◽  
Bac Clones ◽  
Large B Cell Lymphoma ◽  
Large B Cell

Abstract Amplification of 6p21 has been detected in various solid tumor and hematological neoplasms. These include hepatoma, osteosarcoma, pancreatic cancer, bladder cancer, and mantle cell lymphoma . However, no candidate target genes in this amplified region have been identified. In diffuse large B-cell lymphoma (DLBCL), no amplification has been reported. Recently, we established genome-wide array comparative genomic hybridization (array CGH) consisting of 2300 BAC clones that can survey a whole genome at the density of an average size of 1.3 Mb. The array CGH detected amplification at 6p21 in 12 of 70 (24%) DLBCL patients (Tagawa et al., Cancer Res. in press) and one DLBCL cell line, SUDHL-9. We next made high density array glass for 6p21 region with 23 BAC clones covering 3 Mb. We found that the minimal common region of amplification was approximately 2Mb in size. In this region, there are 27 known genes including cyclin D3. The cyclin D3 has been reported to be overexpressed in a case of DLBCL with t(6;14)(p21.1;q32.3). We have analyzed expression level of those genes in the minimal common region of amplification, and found that five genes, BYSL, cyclin D3, TBN, KIAA0240, and TBCC were overexpressed. These results indicate that not only cyclin D3 but also other genes are also possible target genes for the 6p21 amplification.

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