Biology subjects

van de Werken, H. J.

Publications and source records attributed to van de Werken, H. J..

5 recordsLinked to original sources

bioRxiv2021

ProteoDisco: A flexible R approach to generate customized protein databases for extended search space of novel and variant proteins in proteogenomic studies

SummaryWe present an R-based open-source software termed ProteoDisco that allows for flexible incorporation of genomic variants, fusion-genes and (aberrant) transcriptomic variants from standardized formats into protein variant sequences. ProteoDisco allows for a flexible step-by-step workflow allowing for in-depth customization to suit a myriad of research approaches in the field of proteogenomics, on all organisms for which a reference genome and transcript annotations are available. Availability and ImplementationProteoDisco (R package version [≥] 0.99) is available from https://github.com/ErasmusMC-CCBC/ProteoDisco/. Contacth.vandewerken@erasmusmc.nl Supplementary informationSupplementary table, figures and data files available.

bioinformatics↗

bioRxiv2020

FASTAFS: file system virtualisation of random access compressed FASTA files

BackgroundThe FASTA file format used to store polymeric sequence data has become a bioinformatics file standard used for decades. The relatively large files require additional files beyond the scope of the original format, to identify sequences and provide random access. Currently, multiple compressors have been developed to archive FASTA files back and forth, but these lack direct access to targeted content or metadata of the archive. Moreover, these solutions are not directly backwards compatible to FASTA files, resulting in limited software integration. ResultsWe designed linux based a toolkit using Filesystem in Userspace (FUSE) that virtualises the content of DNA, RNA and protein FASTA archives into the filesystem. This guarantees in-sync virtualised metadata files and offers fast random-access decompression using Zstandard (zstd). The toolkit, FASTAFS, can track all system wide running instances, allows file integrity verification and can provide, instantly, scriptable access to sequence files and is easy to use and deploy. ConclusionsFASTAFS is a user-friendly and easy to deploy backwards compatible generic purpose solution to store and access compressed FASTA files, since it offers file system access to FASTA files as well as in-sync metadata files through file virtualisation. Using virtual filesystems as in-between layer offers the possibility to design format conversion without the need to rewrite code into different languages while preserving compatibility. Code Availabilityhttps://github.com/yhoogstrate/fastafs

bioinformatics↗

bioRxiv2020

Phenotypic plasticity and partial EMT underlie local invasion and distant metastasis in colon cancer

Phenotypic plasticity represents the most relevant hallmark of the carcinoma cell as it bestows it with the capacity of transiently altering its morphologic and functional features while en route to the metastatic site. However, the study of phenotypic plasticity is hindered by the rarity of these events within primary lesions and by the lack of experimental models. Here, we identified a subpopulation of phenotypic plastic colon cancer cells: EpCAMlo cells are motile, invasive, chemo-resistant, and highly metastatic. EpCAMlo bulk and single-cell RNAseq analysis indicated 1. enhanced Wnt/{beta}-catenin signaling, 2. a broad spectrum of degrees of EMT activation including hybrid E/M states (partial EMT) with highly plastic features, and 3. high correlation with the CMS4 subtype, accounting for colon cancer cases with poor prognosis and a pronounced stromal component. Of note, a signature of genes specifically expressed in EpCAMlo cancer cells is highly predictive of overall survival in tumors other than CMS4, thus highlighting the relevance of quasi-mesenchymal tumor cells across the spectrum of colon cancers. Enhanced Wnt and the downstream EMT activation represent key events in eliciting phenotypic plasticity along the invasive front of primary colon carcinomas. Distinct sets of epithelial and mesenchymal genes define transcriptional trajectories through which state transitions arise. pEMT cells, often earmarked by the extracellular matrix glycoprotein SPARC together with nuclear ZEB1 and {beta}-catenin along the invasive front of primary colon carcinomas, are predicted to represent the origin of these (de)differentiation routes through biologically-distinct cellular states, and to underlie the phenotypic plasticity of colon cancer cells.

cancer biology↗

bioRxiv2018

The mouse Klf1 Nan variant impairs nuclear condensation and erythroid maturation

Kruppel-like factor 1 (KLF1) is an essential transcription factor for erythroid development, as demonstrated by Klf1 knockout mice which die around E14 due to severe anemia. In humans, >65 KLF1 variants, causing different erythroid phenotypes, have been described. The Klf1 Nan variant, a single amino acid substitution (p.E339D) in the DNA binding domain, causes hemolytic anemia and is dominant over wildtype KLF1. Here we describe the effects of the Nan variant during fetal development. We show that Nan embryos have defects in erythroid maturation. RNA-sequencing of the Nan fetal liver cells revealed that Exportin 7 (Xpo7) was among the ~780 deregulated genes. This nuclear exportin is implicated in terminal erythroid differentiation; in particular it is involved in nuclear condensation. Indeed, KLF1 Nan fetal liver cells had larger nuclei and reduced chromatin condensation. Knockdown of XPO7 in wildtype erythroid cells caused a similar phenotype. We conclude that reduced expression of XPO7 is partially responsible for the erythroid defects observed in Nan erythroid cells.

developmental biology↗

bioRxiv2018

Molecular Heterogeneity and Early Metastatic Clone Selection in Testicular Germ Cell Cancer Development

BackgroundTesticular germ cell cancer (TGCC), being the most frequent malignancy in young Caucasian males, is initiated from an embryonic germ cell. This study determines intratumor heterogeneity to unravel tumor progression from initiation till metastasis.\n\nMethodsIn total 42 purified samples of four treatment-resistant nonseminomatous TGCC (NS) were investigated, including the precursor germ cell neoplasia in situ (GCNIS) and metastatic specimens, using whole genome- and targeted sequencing. Their evolution was reconstructed.\n\nResultsIntratumor molecular heterogeneity did not correspond to the supposed primary tumor histological evolution. Metastases after systemic treatment could be derived from cancer stem cells not identified in the primary cancer. GCNIS mostly lacked the molecular marks of the primary NS and comprised dominant clones that failed to progress. A BRCA-like mutational signature was observed without evidence for direct involvement of BRCA1 and BRCA2 genes.\n\nConclusionsOur data strongly support the hypothesis that NS is initiated by whole genome duplication, followed by chromosome copy number alterations in the cancer stem cell population, and accumulation of low numbers of somatic mutations. These observations of heterogeneity at all stages of tumorigenesis should be considered when treating patients with GCNIS-only disease, or with clinically overt NS.

cancer biology↗