Joost Kluiver

BIC and miR-155 are highly expressed in Hodgkin, primary mediastinal and diffuse large B cell lymphomas.

In a previous study we demonstrated high expression of the non‐coding BIC gene in the vast majority of Hodgkins lymphomas (HLs). Evidence suggesting that BIC is a primary microRNA transcript containing the mature microRNA‐155 (miR‐155) as part of a RNA hairpin is now accumulating. We therefore analysed HL cell lines and tissue samples to determine whether miR‐155 is also expressed in HL. High levels of miR‐155 could be demonstrated, indicating that BIC is processed into a microRNA in HL. Most non‐HL subtypes were negative for BIC as determined by RNA‐ISH. However, in diffuse large B cell lymphoma (DLBCL) and primary mediastinal B cell lymphoma (PMBL), significant percentages of positive tumour cells were observed in 12/18 and 8/8 cases. A higher proportion of tumour cells were positive for BIC in DLBCL with activated B cell‐like phenotype than in DLBCL with germinal centre B cell‐like phenotype. Differential BIC expression was confirmed by qRT‐PCR analysis. Northern blot analysis showed expression of miR‐155 in all DLBCL and PMBL derived cell lines and tissue samples analysed. In summary, we demonstrate expression of primary microRNA BIC and its derivative miR‐155 in HL, PMBL and DLBCL. Copyright

High expression of B-cell receptor inducible gene BIC in all subtypes of Hodgkin lymphoma.

In a search for genes specifically expressed in Reed–Sternberg (RS) cells of Hodgkin lymphoma (HL), we applied the serial analysis of gene expression (SAGE) technique on the HL‐derived cell line DEV. Genes highly expressed in DEV were subjected to an RT‐PCR analysis to confirm the SAGE results. For one of the genes, a high expression was observed in DEV and other HL‐derived cell lines but not in non‐Hodgkin lymphoma (NHL)–derived cell lines and normal controls, suggesting an HL‐specific expression. This gene corresponds to the human BIC gene, a member of the noncoding mRNA‐like molecules. RNA in situ hybridization (ISH) indicated an exclusive nucleolar localization of BIC transcripts in all RS cells in 91% of HL cases, including nodular lymphocyte predominance (NLP) HL and classical HL. Analyses of normal human tissues revealed BIC transcripts in only a small number of CD20‐positive B‐cells in lymph node and tonsil tissue, albeit at a much lower level compared to that of RS cells. BIC RT‐PCR in the Burkitt lymphoma–derived cell line Ramos demonstrated a significant up‐regulation upon cross‐linking of the B‐cell receptor (BcR). IκBα‐mediated blocking of NF‐κB translocation in Ramos did not effect the up‐regulation of BIC expression upon BcR triggering, suggesting that activation of NF‐κB is not involved in regulation of BIC expression. In summary, our data show that expression of BIC is specific for RS cells of HL. In normal tissue, BIC is expressed weakly in a minority of germinal center B cells. Expression of BIC can be modified/influenced by BcR triggering, indicating that BIC might play a role in the selection of B cells.

Lack of BIC and microRNA miR-155 expression in primary cases of Burkitt lymphoma.

We previously demonstrated high expression of primary‐microRNA BIC (pri‐miR‐155) in Hodgkin lymphoma (HL) and lack of expression in most non‐Hodgkin lymphoma subtypes including some Burkitt lymphoma (BL) cases. Recently, high expression of BIC was reported in BL in comparison to pediatric leukemia and normal peripheral‐blood samples. In this study, we extended our series of BL cases and cell lines to examine expression of BIC using RNA in situ hybridization (ISH) and quantitative RT‐PCR (qRT‐PCR) and of miR‐155 using Northern blotting. Both BIC RNA ISH and qRT‐PCR revealed no or low levels of BIC in 25 BL tissue samples [including 7 Epstein–Barr virus (EBV)–positive cases] compared to HL and normal controls. In agreement with these findings, no miR‐155 was observed in BL tissues. EBV‐negative and EBV latency type I BL cell lines also showed very low BIC and miR‐155 expression levels as compared to HL cell lines. Higher levels of BIC and miR‐155 were detected in in vitro transformed lymphoblastoid EBV latency type III BL cell lines. An association of latency type III infection and induction of BIC was supported by consistent expression of BIC in 11 and miR‐155 in 2 posttransplantation lymphoproliferative disorder (PTLD) cases. In summary, we demonstrated that expression of BIC and miR‐155 is not a common finding in BL. Expression of BIC and miR‐155 in 3 latency type III EBV–positive BL cell lines and in all primary PTLD cases suggests a possible role for EBV latency type III specific proteins in the induction of BIC expression.

The role of microRNAs in normal hematopoiesis and hematopoietic malignancies.

Over the past few years, it has become evident that microRNAs (miRNAs) play an important regulatory role in various biological processes. Much effort has been put into the elucidation of their biogenesis, and this has led to the general concept that a number of key regulators are shared with the processing machinery of small interfering RNAs. Despite the recognition that several miRNAs play crucial roles in normal development and in diseases, little is known about their exact molecular function and the identity of their target genes. In this review, we report on the biological relevance of miRNAs for the differentiation of normal hematopoietic cells and on the contribution of deregulated miRNA expression in their malignant counterparts.

Rapid Generation of MicroRNA Sponges for MicroRNA Inhibition

MicroRNA (miRNA) sponges are transcripts with repeated miRNA antisense sequences that can sequester miRNAs from endogenous targets. MiRNA sponges are valuable tools for miRNA loss-of-function studies both in vitro and in vivo. We developed a fast and flexible method to generate miRNA sponges and tested their efficiency in various assays. Using a single directional ligation reaction we generated sponges with 10 or more miRNA binding sites. Luciferase and AGO2-immuno precipitation (IP) assays confirmed effective binding of the miRNAs to the sponges. Using a GFP competition assay we showed that miR-19 sponges with central mismatches in the miRNA binding sites are efficient miRNA inhibitors while sponges with perfect antisense binding sites are not. Quantification of miRNA sponge levels suggests that this is at least in part due to degradation of the perfect antisense sponge transcripts. Finally, we provide evidence that combined inhibition of miRNAs of the miR-17∼92 cluster results in a more effective growth inhibition as compared to inhibition of individual miRNAs. In conclusion, we describe and validate a method to rapidly generate miRNA sponges for miRNA loss-of-function studies.

Immuno-miRs: critical regulators of T-cell development, function and ageing

MicroRNAs (miRNAs) are instrumental to many aspects of immunity, including various levels of T‐cell immunity. Over the last decade, crucial immune functions were shown to be regulated by specific miRNAs. These ‘immuno‐miRs’ regulate generic cell biological processes in T cells, such as proliferation and apoptosis, as well as a number of T‐cell‐specific features that are fundamental to the development, differentiation and function of T cells. In this review, we give an overview of the current literature with respect to the role of miRNAs at various stages of T‐cell development, maturation, differentiation, activation and ageing. Little is known about the involvement of miRNAs in thymic T‐cell development, although miR‐181a and miR‐150 have been implicated herein. In contrast, several broadly expressed miRNAs including miR‐21, miR‐155 and miR‐17~92, have now been shown to regulate T‐cell activation. Other miRNAs, including miR‐146a, show a more T‐cell‐subset‐specific expression pattern and are involved in the regulation of processes unique to that specific T‐cell subset. Importantly, differences in the miRNA target gene repertoires of different T‐cell subsets allow similar miRNAs to control different T‐cell‐subset‐specific functions. Interestingly, several of the here described immuno‐miRs have also been implicated in T‐cell ageing and there are clear indications for causal involvement of miRNAs in immunosenescence. It is concluded that immuno‐miRs have a dynamic regulatory role in many aspects of T‐cell differentiation, activation, function and ageing. An important notion when studying miRNAs in relation to T‐cell biology is that specific immuno‐miRs may have quite unrelated functions in closely related T‐cell subsets.

Comprehensive analysis of miRNA expression in T-cell subsets of rheumatoid arthritis patients reveals defined signatures of naive and memory Tregs

Disturbed expression of microRNAs (miRNAs) in regulatory T cells (Tregs) leads to development of autoimmunity in experimental mouse models. However, the miRNA expression signature characterizing Tregs of autoimmune diseases, such as rheumatoid arthritis (RA) has not been determined yet. In this study, we have used a microarray approach to comprehensively analyze miRNA expression signatures of both naive Tregs (CD4+CD45RO-CD25++) and memory Tregs (CD4+CD45RO+CD25+++), as well as conventional naive (CD4+CD45RO−CD25−) and memory (CD4+CD45RO+CD25−) T cells (Tconvs) derived from peripheral blood of RA patients and matched healthy controls. Differential expression of selected miRNAs was validated by TaqMan-based quantitative reverse transcription-PCR. We found a positive correlation between increased expression of miR-451 in T cells of RA patients and disease activity score (DAS28), erythrocyte sedimentation rate levels and serum levels of interleukin-6. Moreover, we found characteristic, disease- and treatment-independent, global miRNA expression signatures defining naive Tregs, memory Tregs, naive Tconvs and memory Tconvs. The analysis allowed us to define miRNAs characteristic for a general naive phenotype (for example, miR-92a) and a general memory phenotype (for example, miR-21, miR-155). Importantly, the analysis allowed us to define miRNAs that are specifically expressed in both naive and memory Tregs, defining as such miRNA signature characterizing the Treg phenotype (that is, miR-146a, miR-3162, miR-1202, miR-1246 and miR-4281).

Generation of miRNA sponge constructs

MicroRNA (miRNA) sponges are RNA molecules with repeated miRNA antisense sequences that can sequester miRNAs from their endogenous targets and thus serve as a decoy. Stably expressed miRNA sponges are especially valuable for long-term loss-of-function studies and can be used in vitro and in vivo. We describe here a straightforward method to generate retroviral miRNA sponge constructs using a single directional ligation reaction. This approach allows generation of sponges containing more than 20 miRNA binding sites. We provide a basis for the design of the sponge constructs with respect to the sequence of the miRNA binding site and the sequences flanking the miRNA binding sites. In-silico validation approaches are presented to test the predicted efficiencies of the sponges in comparison to known target genes. In addition, we describe in vitro validation experiments to confirm the effectiveness of the miRNA sponges. Finally, we describe how the here described procedure can be adapted to easily generate sponges that target multiple miRNAs simultaneously. In summary, our approach allows rapid generation of single or combination miRNA sponges that can be used for long-term miRNA loss-of-function studies.

Dual Role of miR-21 in CD4+T-Cells: Activation-Induced miR-21 Supports Survival of Memory T-Cells and Regulates CCR7 Expression in Naive T-Cells

Immune cell-type specific miRNA expression patterns have been described but the detailed role of single miRNAs in the function of T-cells remains largely unknown. We investigated the role of miR-21 in the function of primary human CD4+ T-cells. MiR-21 is substantially expressed in T-cells with a memory phenotype, and is robustly upregulated upon αCD3/CD28 activation of both naive and memory T-cells. By inhibiting the endogenous miR-21 function in activated naive and memory T-cells, we showed that miR-21 regulates fundamentally different aspects of T-cell biology, depending on the differentiation status of the T-cell. Stable inhibition of miR-21 function in activated memory T-cells led to growth disadvantage and apoptosis, indicating that the survival of memory T-cells depends on miR-21 function. In contrast, stable inhibition of miR-21 function in activated naive T-cells did not result in growth disadvantage, but led to a significant induction of CCR7 protein expression. Direct interaction between CCR7 and miR-21 was confirmed in a dual luciferase reporter assay. Our data provide evidence for a dual role of miR-21 in CD4+ T cells; Regulation of T-cell survival is confined to activated memory T-cells, while modulation of potential homing properties, through downregulation of CCR7 protein expression, is observed in activated naive T-cells.

The mutational landscape of Hodgkin lymphoma cell lines determined by whole-exome sequencing

The mutational landscape of Hodgkin lymphoma cell lines determined by whole-exome sequencing