In this thesis, we hypothesized that microRNAs (miRNAs) with deregulated expression in lung fibroblasts, are crucial players in the impaired lung tissue repair and remodelling as observed in chronic obstructive pulmonary disease (COPD). To explore this, we focused on miRNA expression changes in the lung, and in particular in fibroblasts in relation to the effects of TGF-β, and current smoking and associations with COPD and ageing. We identified 106 TGF-β-regulated miRNAs in control and/or in COPD lung fibroblasts. Of these, three miRNAs responded differently to TGF-β in COPD compared to control lung fibroblasts. Only one miRNA was higher expressed in COPD compared to control lung fibroblasts. Furthermore, we identified one miRNA that was lower expressed in lung fibroblasts from current compared to ex-smokers. We identified >960 genes that are actively regulated by miRNAs in lung fibroblasts, which were used to identify fibroblast-specific targets of the differentially expressed miRNAs. Our studies indicate that the identified miRNAs may affect the function of lung fibroblasts through these genes, and affect tissue repair and remodelling, and thus are implicated in COPD pathogenesis. In bronchial biopsies of healthy control subjects, 285 age-related genes and 27 age-related miRNAs were identified. Genes with lower expression with increasing age included several hallmarks of ageing whereas genes with higher expression with increasing age were amongst others involved in synapse-related processes. These studies provide a good stepping stone for further studies aiming to clarify the complex role of these miRNAs in relation to abnormal tissue repair in COPD and ageing.

In this thesis, we studied the role of microRNAs (miRNAs) in the pathogenesis of Hodgkin lymphoma (HL). Small RNA sequencing revealed 84 significantly differentially expressed miRNAs between HL cell lines and normal germinal center B cells. Inhibition of the in HL significantly overexpressed miR-24-3p resulted in decreased growth which was at least in part caused by an increase in apoptotic cells. MiRNA target gene identification using Ago2-IP in HL cell lines revealed 1,142 miRNA target genes of which 52 were predicted to be targeted by miR-24-3p. Western blotting analysis confirmed increased CDKN1B/P27kip1 upon miR-24-3p inhibition, possibly explaining the effect on cell growth. We next set up a next generation sequencing based high throughput loss- and gain-of-function screening approach to identify miRNAs that influence HL cell growth. The overexpression screen revealed that miR-19b-1 may enhance while miR-141 may repress HL cell growth. The inhibition screen revealed that inhibition of miR-449a-5p, miR-625-5p, let-7f-2-3p and miR-21-5p has a negative effect on HL cell growth. The highly abundant miR-21-5p showed significantly higher expression levels in HL. We confirmed the negative effects of miR-21-5p inhibition on cell growth and observed a concomitant significant increase in apoptotic cells. Among the in HL Ago2-IP enriched target genes, we identified 36 predicted miR-21-5p targets. We confirmed targeting of BTG2 and PELI1 by miR-21-5p using reporter assays and Western blot. Overall, we set up the technology for functional miRNA studies in HL and identified two miRNAs and their target genes relevant for the pathogenesis of HL.

While RNA was long thought to act as a mere intermediary between DNA and protein, we now know RNA transcripts can have diverse cellular functions themselves. The major class of long noncoding (lncRNAs) thus represent a missing piece in the puzzle of human cell biology. A variety of transcriptional as well as posttranscriptional regulatory mechanisms have been described for lncRNAs. This thesis addresses the relevance of lncRNAs in normal B cell development and B cell malignancies. Specifically, we study lncRNA expression changes in normal B cells before, during and after the maturation process using naive, germinal center [GC] and memory B cells, respectively. Vast lncRNA expression changes are observed in the highly proliferative GC B cells, indicating significant lncRNA involvement in the B cell maturation process. Furthermore we identify multiple lncRNAs overexpressed in Hodgkin lymphoma cell lines compared to their cell-of-origin, which show cancer cell specific expression in primary patient tissue. We defined lncRNAs regulated by the oncogenic transcription factor Myc and putatively involved in its proliferation-supportive effects. We observe deregulation of hundreds of lncRNAs in response to Myc, thus identifying lncRNAs as a major component of the Myc transcriptional network. Myc-induced lncRNA KTN1-AS1 is studied in more detail and shown to affect Burkitt lymphoma cell growth by reinforcing high Myc expression. In summary, our studies provide novel insights into the role of lncRNAs in normal B cells and B cell malignancies. The individual lncRNAs we identified can potentially serve as biomarkers or therapeutic targets for lymphoma detection and treatment.

The role of non-coding RNAs in B-cells lymphoma
In this thesis we explored the role of long non-coding (lnc)RNAs in B cell lymphoma. This very large family of non-coding RNA transcripts are mostly uncharacterized and their role in disease states such as cancer and B cell lymphoma is mainly unknown. The overall aim of this thesis was to characterize expression profiles of normal B cell subsets and to identify and functionally study lncRNAs relevant to the pathogenesis of Burkitt lymphoma and Hodgkin lymphoma, two germinal center B-cell-derived malignancies. The studies described in this thesis showed that lncRNA expression is actively regulated during normal B-cell maturation. In Burkitt lymphoma we showed that knockdown of MYC significantly altered expression of a substantial number of lncRNAs. In Hodgkin lymphoma we showed altered expression of lncRNAs compared to their normal counterparts. For part of the deregulated lncRNAs we have preliminary data to support a regulation in cis. In addition, we observed that a substantial proportion of the lncRNAs interacted with miRNAs, although the overall percentage was lower than the percentage of protein-coding genes interacting with miRNAs. For three lncRNAs we showed a role in growth of B-cell lymphoma cells. No eQTL effects were observed for lncRNAs mapping at Hodgkin lymphoma susceptibility loci, whereas we did find eQTL effects for some of the protein-coding genes at these loci. Together, our data provides comprehensive overviews on the lncRNAs that are expressed and deregulated in normal and malignant B-cells and pinpoints several lncRNAs that contribute to lymphomagenesis.

Kidney cancer of the clear cell type is often lethal and causes more than 100,000 deaths worldwide every year. Understanding the biology of this cancer type may help to develop better ways to diagnose and treat it. Damage in DNA (genes) is present in all cancer cells and clear cell kidney cancer is no exception. Exactly how these DNA changes contribute to the development of kidney cancer is still mostly unclear. The PhD study undertaken by Jun Li (Genetics department, UMCG) looked at the effects of damage in 2 genes that appear to be important in kidney cancer: SETD2 and PBRM1. Normal kidney cells cannot be grown in culture for many days, but after silencing the SETD2 gene the growth potential of these cells in became abnormally large. This suggests that damage to SETD2 can contribute to the change from normal kidney cells into cancer cells. In contrast, silencing the PBRM1 gene did not show this effect. However, it did cause changes in the activity of other genes, especially of some involved in immune response. These changes were, more strongly, also observed in kidney cancer cells. Together, these findings contribute to our further understanding of the biology of kidney cancer and may help in improving diagnostics and treatment of this aggressive cancer type.