Biology subjects

Bakker, L.

Publications and source records attributed to Bakker, L..

4 recordsLinked to original sources

bioRxiv2026

Mutagenic bypass of uracil-derived abasic sites underlies the SBS17 mutational signature

Understanding how mutations arise is central to predicting and preventing cancer, yet most of the mutational signatures found in cancer genomes still have no known mechanistic cause. Among these, single-base-substitution signature 17 (SBS17) is the dominant mutational process in gastric and oesophageal adenocarcinoma. SBS17 has been linked to oxidative damage and to the chemotherapeutic agent 5-fluorouracil (5-FU), but the molecular events that generate it are unknown. Here we demonstrate that SBS17 causes driver mutations in gastrointestinal cancer. We then combine genetics in cell lines and organoids with whole-genome sequencing to define the mechanistic aetiology of SBS17 mutagenesis. We disprove the prevailing oxidative damage hypothesis and instead show that SBS17 arises through the misincorporation of dUTP during DNA replication, followed by uracil excision by the glycosylase UNG and mutagenic bypass of the resulting abasic (AP) sites by the translesion synthesis machinery. Importantly, we reveal that the same mechanism underlies both spontaneous and chemotherapy-induced mutations. Together, our results resolve the origin of gastric mutagenesis, opening therapeutic avenues for curbing ongoing mutagenesis, tumour evolution and drug resistance in gastrointestinal cancers.

molecular biology↗

bioRxiv2025

Tissue-specific mutagenesis from endogenous guanine damageis suppressed by Polκ and DNA repair

Knowledge of mutational patterns has expanded significantly, but a persistent challenge is to link these complex patterns to the underlying molecular mechanism or source of DNA damage, especially when that damage is endogenous and not driven by environmental mutagens. Technological advances now allow us to catalogue mutation across tissues or even closely related cell types, but the results are largely descriptive until we identify the endogenous sources of mutation and how they differ across tissues. Here, we combine mouse genetics, advanced sequencing, biochemistry and mass spectrometry to provide a detailed mechanistic understanding of endogenous mutagenesis. We reveal that endogenous guanine adducts are significant drivers of tissue-specific mutagenesis, while the interwoven actions of DNA polymerase Pol{kappa} and DNA repair mechanisms are pivotal in mitigating mutagenesis. For the first time, we use untargeted DNA adductomics to characterize new sources of endogenous DNA damage. Our novel approach to understanding endogenous mutational landscapes reveals previously unseen mutational processes and points to vast potential for new discoveries.

molecular biology↗

bioRxiv2022

Multi-omics analysis reveals distinct non-reversion mechanisms of PARPi resistance in BRCA1- versus BRCA2-deficient mammary tumors

BRCA1 and BRCA2 both function in DNA double-strand break repair by homologous recombination (HR). Due to their HR-defect, BRCA1/2-deficient cancers are sensitive to poly(ADP-ribose) polymerase inhibitors (PARPi) but they eventually acquire resistance. Preclinical studies yielded several PARPi resistance mechanisms that do not involve BRCA1/2 reactivation, but their relevance in the clinic remains elusive. To investigate which BRCA1/2-independent mechanisms drive spontaneous resistance in vivo, we combined molecular profiling with functional analysis of the HR status of matched PARPi-naive and PARPi-resistant mouse mammary tumors harboring large intragenic deletions that prevent functional restoration of BRCA1/2. We observed restoration of HR in 64% of PARPi-resistant BRCA1-deficient tumors but none in the PARPi-resistant BRCA2-deficient tumors. Moreover, we found that 53BP1 loss is the prevalent resistance mechanism in HR-proficient BRCA1-deficient tumors, whereas resistance in BRCA2-deficient tumors is mainly induced by the loss of PARG. Our combined multi-omics analysis catalogued additional genes and pathways potentially involved in modulating PARPi response.

cancer biology↗

bioRxiv2021

Genome and transcriptome architecture of allopolyploid okra (Abelmoschus esculentus)

We present the first annotated genome assembly of the allopolyploid okra (Abelmoschus esculentus). Analysis of telomeric repeats and gene rich regions suggested we obtained whole chromosome and chromosomal arm scaffolds. Besides long distal blocks we also detected short interstitial TTTAGGG telomeric repeats, possibly representing hallmarks of chromosomal speciation upon polyploidization of okra. Ribosomal RNA genes are organized in 5S clusters separated from the 18S-5.8S-28S units, clearly indicating an S-type rRNA gene arrangement. The assembly is consistent with cytogenetic and cytometry observations, identifying 65 chromosomes and 1.45Gb of expected genome size in a haploid sibling. Approximately 57% of the genome consists of repetitive sequence. BUSCO scores and A50 plot statistics indicated a nearly complete genome. Kmer distribution analysis suggests that approximately 75% has a diploid nature, and at least 15% of the genome is heterozygous. We did not observe aberrant meiotic configurations, suggesting there is no recombination among the sub-genomes. BUSCO configurations as well as k-mer clustering analysis pointed to the presence of at least 2 sub-genomes. These observations are indicative for an allopolyploid nature of the okra genome. Structural annotation, using gene models derived from mapped IsoSeq transcriptome data, generated over 130,000 putative genes. Mapped transcriptome data from public okra accessions of Asian origin confirmed the predicted genes, showing limited genetic diversity of 1SNP/2.1kb. The discovered genes appeared to be located predominantly at the distal ends of scaffolds, gradually decreasing in abundance toward more centrally positioned scaffold domains. In contrast, LTR retrotransposons were more abundant in centrally located scaffold domains, while less frequently represented in the distal ends. This gene and LTR-retrotransposon distribution is consistent with the observed heterochromatin organization of pericentromeric heterochromatin and distal euchromatin. The derived amino acid queries of putative genes were subsequently used for phenol biosynthesis pathway annotation in okra. Comparison against manually curated reference KEGG pathways from related Malvaceae species revealed the genetic basis for putative enzyme coding genes that likely enable metabolic reactions involved in the biosynthesis of dietary and therapeutic compounds in okra.

genomics↗