Search

Alternative splicing (AS) is a major regulatory process underpinning the development and function of the immune system. 29% of alternatively spliced genes are specific to immune cells, yet the regulation and function of AS during B cell activation remain largely unknown. The activation of naive B cells and the subsequent germinal centre (GC) reaction drive the cascade of reactions resulting in short- and long-term antibody responses, making the GC crucial for adaptive immunity. However, abnormal function of GC B cells contributes to autoimmune disease and the development of lymphomas. Hence, GC reaction needs to be tightly regulated. Previous studies have linked individual AS events in GC B cells to B cell malignancies using short-read sequencing; however, this methodology is limited in defining the complete sequence of transcript variants generated by AS. Therefore, many transcript variants remain undefined. During my PhD, I have developed a long-read sequencing methodology Oxford Nanopore Technologies (ONT) workflow to understand post-transcriptional regulation at both gene and isoform levels in human and mouse GC B cells. Because one of the challenges of ONT is the accurate computational analysis of isoforms, we developed the ‘Nexons’ pipeline to identify the differentially spliced transcript variants. Transcriptome characterisation using ONT allowed us to detect differentially expressed transcripts during antigen-mediated activation of GC B cells in human and mouse. Moreover, identification of individual isoforms with Nexons revealed differential splicing of transcripts, including potentially novel splice variants, as well as changes which were undetectable in short-read sequencing data. An in-depth analysis revealed the differential regulation of poison exons (PE) in serine/arginine-rich splicing factors (SRSF) (e.g., SRSF3 and SRSF7). Naive B cells preferentially expressed isoforms carrying PE, leading to nonsense-mediated mRNA decay, whilst the PE were preferentially removed in activated and GC B cells. Notably, we found this regulation of PE in splicing factors is conserved between human and mouse. We validate an ONT/Nexons workflow as a suitable method for the identification and quantification of transcript isoforms and highlight the SRSF family as important candidates for regulating the GC reaction.

International audience; The extracellular matrix (ECM) is a fundamental component of the tissue of multicellular organisms that is comprised of an intricate network of multidomain proteins and associated factors, collectively known as the matrisome. The ECM creates a biophysical environment that regulates essential cellular processes such as adhesion, proliferation and migration and impacts cell fate decisions. The composition of the ECM varies across organs, developmental stages and diseases. Interestingly, most ECM genes generate transcripts that undergo extensive alternative splicing events, producing multiple protein variants from one gene thus enhancing ECM complexity and impacting matrix architecture. Extensive studies over the past several decades have linked ECM remodeling and expression of alternatively spliced ECM isoforms to cancer, and reprogramming of the alternative splicing patterns in cells has recently been proposed as a new hallmark of tumor progression. Indeed, tumor-associated alternative splicing occurs in both malignant and non-malignant cells of the tumor environment and growing evidence suggests that expression of specific ECM splicing variants could be a key step for stromal activation. In this review, we present a general overview of alternative splicing mechanisms, featuring examples of ECM components. The importance of ECM variant expression during essential physiological processes, such as tissue organization and embryonic development is discussed as well as the dysregulation of alternative splicing in cancer. The overall aim of this review is to address the complexity of the ECM by highlighting the importance of the yet-to-be-fully-characterized "alternative" matrisome in physiological and pathological states such as cancer.

Hepatocellular carcinoma (HCC) is one of the most prevalent malignancies worldwide and the second leading cause of death among all cancer types. Deregulation of the networks of tissue-specific transcription factors (TFs) observed in HCC leads to profound changes in the hepatic transcriptional program that facilitates tumor progression. In addition, recent reports suggest that substantial aberrations in the production of TF isoforms occur in HCC. In vitro experiments have identified distinct isoform-specific regulatory functions and related biological effects of liver-specific TFs that are implicated in carcinogenesis, which may be relevant for tumor progression and clinical outcome. This study reviews available data on the expression of isoforms of liver-specific and ubiquitous TFs in the liver and HCC and their effects, including HNF4α, C/EBPs, p73 and TCF7L2, and indicates that assessment of the ratio of isoforms and targeting specific TF variants may be beneficial for the prognosis and treatment of HCC.

2. Abstract Histone methylation plays an important role in almost all cellular processes and its homeostasis is maintained by histone methyltransferases and histone demethylases. Misregulation of histone methylation levels is associated with gene expression misregulation and consequently also with various developmental defects and diseases. In this thesis we focus on the lysine demethylases KDM2A and KDM2B and on their demethylation deficient isoforms KDM2A-SF and KDM2B-SF. The lysine specific demethylases KDM2A and KDM2B have been predominantly studied for their demethylation function on CpG island-rich gene promoters. However, KDM2A-SF and KDM2B-SF have not been studied in detail. Therefore, the main goal of this thesis was to characterize KDM2A-SF more in detail and to focus on the role that KDM2A/B-SF might potentially play in canonical Wnt signaling pathway. We found that the KDM2A-SF mRNA arises through the action of an alternative intronic promoter and not by alternative splicing. We showed that the KDM2A-SF start codon is located in the exon that corresponds to KDM2A exon 14 and we thus determined the exact amino acid sequence of the KDM2A-SF protein. Furthermore, using an isoform specific knockdown assay we showed that KDM2A-SF, unlike KDM2A-LF, forms distinct nuclear foci on pericentromeric...

The TCF/LEF transcriptional factors regulate the target genes of the Wnt signalling pathway - one of the key signalling mechanisms involved in development of multicellular organisms. The TCF/LEF genes produce a number of various protein isoforms, which consequently leads to a great functional diversity of the TCF/LEF proteins. In this diploma project we focused on the Caenorhabditis elegans gene pop-1, the ortholog of the TCF/LEF genes, whose isoforms have not been studied yet. Using the Northern blot analysis we tried to identify alternative isoforms of the pop-1 mRNA in C. elegans. Using quantitative RT-PCR we also analyzed the pop-1 mRNA levels during seven developmental stages of C. elegans. Further, we also determined the expression profile of two important partners of pop-1, the bar-1 and sys-1 genes, whose protein products function as transcriptional co-activators. Key words: canonical Wnt signaling pathway, TCF/LEF transcription factors, Caenorhabditis elegans, pop-1

Alternative splicing (AS) is a basic molecular phenomenon that increases the functional complexity of higher eukaryotic transcriptomes. Indeed, through AS individual gene loci can generate multiple RNAs from the same pre-mRNA. AS has been investigated in a variety of clinical and pathological studies, such as the transcriptome regulation in cancer. In human, recent works based on massive RNA sequencing indicate that >95 % of pre-mRNAs are processed to yield multiple transcripts. Given the biological relevance of AS, several computational efforts have been done leading to the implementation of novel algorithms and specifi c specialized databases. Here we describe the web application ASPicDB that allows the recovery of detailed biological information about the splicing mechanism. ASPicDB provides powerful querying systems to interrogate AS events at gene, transcript, and protein levels. Finally, ASPicDB includes web visualization instruments to browse and export results for further off-line analyses.

Two N-terminal isoforms characterize the p63 protein: the transactivating isoform TAp63 and the amino-terminal truncated isoform DeltaNp63. Two further N-terminal isoforms lacking exon 4 (d4TAp63 and DeltaNp73L) have been reported. Purpose of the study was to investigate the molecular expression of N-terminal p63 isoforms in benign and malignant breast tissues. Eighteen randomly selected cases of invasive breast carcinoma (IBC) of luminal type, two cases of in situ duct carcinoma (DCIS/DIN), and 20 specimens of normal and benign breast tissues were studied. All cases were immunostained for p63. Reverse polymerase chain reaction and nested PCR were performed to evaluate p63 N-terminal expression patterns. These isoforms whenever present were validated by sequencing. All cases of normal breast, benign lesions, and the two cases of DCIS/DIN expressed DeltaNp63 and TAp63 isoforms only. The two variants lacking exon 4 (DeltaNp73L and d4TAp63) were not found. All invasive carcinomas expressed the DeltaNp63 and TAp63 isoforms as well as the two short isoforms lacking exon 4 which were found in 11 (d4TAp63) and four (DeltaNp73L) cases. The present cases of luminal-type IBC showed p63 isoforms together with short variants lacking exon 4. These isoforms were not observed in non-neoplastic breast tissue. Presence of p63 in invasive breast carcinomas of luminal type, as seen at molecular level, suggests caution to include p63 as a marker of basal-like carcinomas.