The human body consists of many different cell types. Cell types can be defined by the genes expressed, and unique cell-type-specific transcriptional mechanisms control these expressions. Single... Show moreThe human body consists of many different cell types. Cell types can be defined by the genes expressed, and unique cell-type-specific transcriptional mechanisms control these expressions. Single nucleotide polymorphisms (SNPs) in the DNA can be associated with diseases, but approximately 95% fall in the non-coding region. Usually, it is unknown whether these variants are causal, and which gene and cell type they affect.Advances in single-cell RNA-sequencing improved our understanding of heterogeneous tissues and led to the discovery of many new cell types. This new technology also presents computational challenges including consistent cell-type annotations. It is essential to annotate cells using classification instead of currently practiced clustering methods. To facilitate this transition, we benchmarked cell-type classification methods and developed computational methods to automatically build reference atlases using multiple already labeled single-cell datasets.Next, we establish a relationship between mutations and their effect on gene or isoform expression. We study sequence-to-expression models that can predict an alteration in expression when a mutation is observed. Given that gene expression mechanisms are cell-type specific, we introduce sequence-to-expression models based on single-cell data to make cell-type-specific predictions. We use these models to show that certain mutations are indeed changing expression, increasing our understanding of transcriptional regulation. Show less
Tienhoven, R. van; Kracht, M.J.L.; Slik, A.R. van der; Thomaidou, S.; Wolters, A.H.G.; Giepmans, B.G.; ... ; Roep, B.O. 2023
Aims/hypothesis Transcriptome analyses revealed insulin-gene-derived transcripts in non-beta endocrine islet cells. We studied alternative splicing of human INS mRNA in pancreatic islets. Methods:... Show moreAims/hypothesis Transcriptome analyses revealed insulin-gene-derived transcripts in non-beta endocrine islet cells. We studied alternative splicing of human INS mRNA in pancreatic islets. Methods: Alternative splicing of insulin pre-mRNA was determined by PCR analysis performed on human islet RNA and single-cell RNA-seq analysis. Antisera were generated to detect insulin variants in human pancreatic tissue using immunohistochemistry, electron microscopy and single-cell western blot to confirm the expression of insulin variants. Cytotoxic T lymphocyte (CTL) activation was determined by MIP-1 beta release. Results: We identified an alternatively spliced INS product. This variant encodes the complete insulin signal peptide and B chain and an alternative C-terminus that largely overlaps with a previously identified defective ribosomal product of INS. Immunohistochemical analysis revealed that the translation product of this INS-derived splice transcript was detectable in somatostatin-producing delta cells but not in beta cells; this was confirmed by light and electron microscopy. Expression of this alternatively spliced INS product activated preproinsulin-specific CTLs in vitro. The exclusive presence of this alternatively spliced INS product in delta cells may be explained by its clearance from beta cells by insulin-degrading enzyme capturing its insulin B chain fragment and a lack of insulin-degrading enzyme expression in delta cells. Conclusions/interpretation: Our data demonstrate that delta cells can express an INS product derived from alternative splicing, containing both the diabetogenic insulin signal peptide and B chain, in their secretory granules. We propose that this alternative INS product may play a role in islet autoimmunity and pathology, as well as endocrine or paracrine function or islet development and endocrine destiny, and transdifferentiation between endocrine cells. INS promoter activity is not confined to beta cells and should be used with care when assigning beta cell identity and selectivity. Show less
The aim of this thesis was to combine transcriptomics, genetics and human disease modelling to obtain further insight into molecular processes underlying osteoarthritis. More specifically, we aimed... Show moreThe aim of this thesis was to combine transcriptomics, genetics and human disease modelling to obtain further insight into molecular processes underlying osteoarthritis. More specifically, we aimed to elucidate the role of long noncoding RNAs expression changes as aberrant epigenetic mechanism in regulating gene expression in chondrocytes. We identified previously unknown long noncoding RNAs associated with the osteoarthritic process and showed enrichment for cis¬-regulation of these long noncoding RNAs with target messenger RNAs.To provide insight in the etiology of osteoarthritis, causal pathways can be identified by unravelling the substantial genetic component. To this end, we investigated the biological functionality of the high-impact, pathogenic mutation identified in the gene fibronectin1 in an early-onset osteoarthritis family. We demonstrated that the identified causal missense mutation in the gelatin-binding domain of the extracellular matrix protein fibronectin resulted in significant decreased binding capacity to collagen type II.Finally, the common function of fibronectin1 was investigated in cartilage and what changes occur at the transcript level of fibronectin1 with osteoarthritis. Down-regulation of full-length fibronectin was unbeneficial for in vitro chondrogenesis, we hypothesize that this was caused by decreased availability of the classical integrin binding site of fibronectin. Show less
Background During mammalian kidney development, nephron progenitors undergo a mesenchymal-to-epithelial transition and eventually differentiate into the various tubular segments of the nephron.... Show moreBackground During mammalian kidney development, nephron progenitors undergo a mesenchymal-to-epithelial transition and eventually differentiate into the various tubular segments of the nephron. Recently, Drop-seq single-cell RNA sequencing technology for measuring gene expression from thousands of individual cells identified the different cell types in the developing kidney. However, that analysis did not include the additional layer of heterogeneity that alternative mRNA splicing creates.Methods Full transcript length single-cell RNA sequencing characterized the transcriptomes of 544 individual cells from mouse embryonic kidneys.Results Gene expression levels measured with full transcript length single-cell RNA sequencing identified each cell type. Further analysis comprehensively characterized splice isoform switching during the transition between mesenchymal and epithelial cellular states, which is a key transitional process in kidney development. The study also identified several putative splicing regulators, including the genes Esrp1/2 and Rbfox1/2.Conclusions Discovery of the sets of genes that are alternatively spliced as the fetal kidney mesenchyme differentiates into tubular epithelium will improve our understanding of the molecular mechanisms that drive kidney development. Show less
Koedoot, E.; Wolters, L.; Water, B. van de; Dévédec, S.E.L. 2019
By regulating transcript isoform expression levels, alternative splicing provides an additional layer of protein control. Recent studies show evidence that cancer cells use different splicing... Show moreBy regulating transcript isoform expression levels, alternative splicing provides an additional layer of protein control. Recent studies show evidence that cancer cells use different splicing events to fulfill their requirements in order to develop, progress and metastasize. However, there has been less attention for the role of the complex catalyzing the complicated multistep splicing reaction: the spliceosome. The spliceosome consists of multiple sub-complexes in total comprising 244 proteins or splice factors and 5 associated RNA molecules. Here we discuss the role of splice factors in the oncogenic processes tumors cells need to fulfill their oncogenic properties (the so-called the hallmarks of cancer). Despite the fact that splice factors have been investigated only recently, they seem to play a prominent role in already five hallmarks of cancer: angiogenesis, resisting cell death, sustaining proliferation, deregulating cellular energetics and invasion and metastasis formation by affecting major signaling pathways such as epithelial-to-mesenchymal transition, the Warburg effect, DNA damage response and hormone receptor dependent proliferation. Moreover, we could relate expression of representative genes of four other hallmarks (enabling replicative mortality, genomic instability, avoiding immune destruction and evading growth suppression) to splice factor levels in human breast cancer tumors, suggesting that also these hallmarks could be regulated by splice factors. Since many splice factors are involved in multiple hallmarks of cancer, inhibiting splice factors might provide a new layer of oncogenic control and a powerful method to combat breast cancer progression. Show less
Preeclampsia is a syndrome of pregnancy characterised by hypertension and proteinuria and occurs in up to 5 percent of pregnant women. The pathophysiology of preeclampsia has not been fully... Show morePreeclampsia is a syndrome of pregnancy characterised by hypertension and proteinuria and occurs in up to 5 percent of pregnant women. The pathophysiology of preeclampsia has not been fully elucidated yet. The endothelium is known to play a key role in the pathogenesis and levels of vascular endothelial growth factor are decreased due to an angiogenic imbalance. In the first part of this thesis, genes associated with preeclampsia were investigated through meta-analysis; genes within the coagulation and immunology domains remained significantly associated with preeclampsia after meta-analysis. In the second and third part of this thesis, the possible role of a key regulator of coagulation and immunology on the endothelium, thrombomodulin, in preeclampsia was investigated in the placenta and the kidney. Diminished placental thrombomodulin expression was associated with the angiogenic imbalance of preeclampsia. Next, in the fourth part of this thesis the interplay between podocytes and endothelial cells in the glomerulus during the anti-angiogenic conditions in preeclampsia was reviewed. In the final part of this thesis the splicing pattern of vascular endothelial growth factor was investigated throughout different examples of glomerular disease. Show less
Within this thesis, several diseases central in the field of cardiovascular disease will be outlined. First, the central dogma of molecular biology, RNA biology in general, RNA (alternative... Show moreWithin this thesis, several diseases central in the field of cardiovascular disease will be outlined. First, the central dogma of molecular biology, RNA biology in general, RNA (alternative)splicing and the role of RNA-binding proteins within these processes will be discussed to enhance the accessibility to non-molecular biologists. Subsequently, the current literature and insights into the RNA-binding protein Quaking will be outlined. Thereafter, a brief summary of the role of many distinct RNA-binding proteins (RBPs) in the cardiovascular system is provided, detailing their importance in the heart and cells of the blood vessels. This review provides some historical and biological perspectives, while simultaneously highlighting many recent advances in our understanding of RBP function in cardiovascular health and disease. By harnessing established and novel techniques, including RNA-sequencing, this thesis will describe the role of Quaking in vascular stenosis, atherosclerosis, inflammation and endothelial barrier function. Collectively, Quaking can be described as a genome-wide governor of RNA-processing that results in the proper translation into functional proteins. This thesis describes which RNA transcripts are under control of Quaking, which alternative transcripts are being generated through modulation by Quaking, while also describing the unique role for this protein in health and cardiovascular and renal disease. Show less
Bruin, R.G. de; Rabelink, T.J.; Zonneveld, A.J. van; Veer, E.P. van der 2017
Cortactine wordt gecodeerd door het gen EMS1 dat op het chromosoom 11q13 ligt. Het 11q13 gebied is geamplificeerd in een deel van de borsttumoren dat geassocieerd is met cortactine overexpressie en... Show moreCortactine wordt gecodeerd door het gen EMS1 dat op het chromosoom 11q13 ligt. Het 11q13 gebied is geamplificeerd in een deel van de borsttumoren dat geassocieerd is met cortactine overexpressie en de aanwezigheid van lymfeklier metastasen en een verhoogde sterfte. Cortactine is een F-actine bindend eiwit dat betrokken is bij de regulatie van het actine cytoskelet, dat belangrijk is bij cel migratie. Agnes van Rossum onderzocht de rol van cortactine (over)expressie op cel biologische processen die betrokken zijn bij de ontwikkeling en/of het gedrag van borstkanker. Zij ontdekte onder meer dat er cortactine varianten zijn die de cel migratie beïnvloeden. Verder lijkt cortactine een rol te spelen bij intercellulaire cel adhesie en cel spreiding. Een studie met cortactine transgene muizen toonde aan dat cortactine geen oorzakelijke rol heeft in het ontstaan van borstkanker. Van Rossum vermoedt dat cortactine de binding tussen cellen en hun omgeving dusdanig kan beïnvloeden dat deze gemakkelijker uit de oorspronkelijke tumor kunnen ontsnappen en gaan migreren. Show less
