Biology subjects

Raaijmakers, J.

Publications and source records attributed to Raaijmakers, J..

6 recordsLinked to original sources

bioRxiv2025

Identification of critical factors of the replication stress response in human cells

High fidelity of replication is important to preserve genomic integrity and ensure healthy progeny. Perturbations of replication, also known as replication stress, is frequently observed in cancer cells and is considered a cancer cell-specific trait. Although replication stress drives genomic instability and tumor progression, it also generates a targetable cancer-specific vulnerability. In order to identify potential therapeutic targets in cancer cells that experience replication stress, we performed a genome wide genetic screen in human HAP1 cells challenged with low doses of replication stress-inducing drugs. We identified a large set of genes that specifically hamper cell survival in the context of replication stress. In addition to well-known players in the replication stress response and DNA repair, such as RNASEH1, BRIP1, and MDC1, we identified several genes with no prior described role in DNA replication, damage tolerance or repair. We validated that the loss of GIGYF2, HNRNPA2B1, and SUMO2 renders cells more vulnerable to replication stress. For GIGYF2 and SUMO2, we could implicate a role in homologous recombination. Taken together, our replication stress screen identified several known as well as some novel factors that protect against the toxic implications of replication stress. These factors could entail potential therapeutic targets for cancer cells experiencing replication stress.

cell biology↗

bioRxiv2023

A compendium of Amplification-Related Gain Of Sensitivity (ARGOS) genes in human cancer

Chromosomal gains are among the most frequent somatic genetic alterations occurring in cancer. While the effect of sustained oncogene expression has been characterized, the impact of copy-number gains affecting collaterally-amplified "bystander" genes on cellular fitness remains less understood. To investigate this, we built a comprehensive map of dosage compensations across human cancers by integrating expression and copy number profiles from over 8,000 TCGA tumors and CCLE cell lines. Further, we analyzed the effect of gene overexpression across 17 human cancer ORF screens to provide an overview of genes that prove toxic to cancer cells when overexpressed. Combining these two independent approaches we propose a class of Amplification-Related Gain Of Sensitivity (ARGOS) genes. These genes are located in commonly amplified regions of the genome, have lower expression levels than expected by their copy-number status, and are toxic to cancer cells when overexpressed. We experimentally validated CDKN1A and RBM14 as high-confidence pan-cancer ARGOS genes in lung and breast cancer cell line models. We additionally suggest that RBM14s mechanism of toxicity involves altered DNA damage response and innate immune signaling processes following gene overexpression. Finally, we provide a comprehensive catalog of compensated, toxic, and ARGOS genes as a community resource.

cancer biology↗

bioRxiv2023

Activity and diversity of prophages harbored by wheat phyllosphere bacteria

1.The plant microbiome harbors an enormous diversity of fungi, bacteria, and viruses, but little is known on the diversity and function of prophages harbored within plant-associated bacteria. Using "VIP-Seq", a novel method based on supernatant sequencing, we identified and quantified the activity of 120 spontaneously induced prophages in a collection of 63 Erwinia and Pseudomonas strains isolated from wheat flag leaves collected from the same field. These bacterial strains exhibited high levels of spontaneous prophage induction, with some producing > 108 virions/mL in overnight culture. Significant induction in planta also occurred from a lysogenic Erwinia strain inoculated on wheat seedlings. The potential of these active prophages in bacterial warfare was exhibited by their widespread killing of rival bacterial strains. Evidence of transduction was observed, and the prophages were shown to contribute a majority of the non-core genome of E. aphidicola isolates. Many additional prophages were predicted by bioinformatic tools, and we found that the predicted prophages that were not spontaneously induced had a significantly higher number of IS elements. Our results suggest that spontaneous induction of prophages may represent an unknown but wide-spread competition mechanism involved in phyllosphere microbiome assembly and function. This may also have implications for the design and resilience of synthetic bacterial communities used as biocontrol for certain plant diseases.

microbiology↗

bioRxiv2023

Paradoxical activation of oncogenic signaling as a cancer treatment strategy

Cancer homeostasis depends on a balance between activated oncogenic pathways driving tumorigenesis and engagement of stress-response programs that counteract the inherent toxicity of such aberrant signaling. While inhibition of oncogenic signaling pathways has been explored extensively, there is increasing evidence that overactivation of the same pathways can also disrupt cancer homeostasis and cause lethality. We show here that inhibition of Protein Phosphatase 2A (PP2A) hyperactivates multiple oncogenic pathways and engages stress responses in colon cancer cells. Genetic and compound screens identify combined inhibition of PP2A and WEE1 as synergistic in multiple cancer models by collapsing DNA replication and triggering premature mitosis followed by cell death. This combination also suppressed the growth of patient-derived tumors in vivo. Remarkably, acquired resistance to this drug combination suppressed the ability of colon cancer cells to form tumors in vivo. Our data suggest that paradoxical activation of oncogenic signaling can result in tumor suppressive resistance.

cancer biology↗

bioRxiv2022

baseLess: Lightweight detection of sequences in raw MinION data

AO_SCPLOWBSTRACTC_SCPLOWWith its candybar form factor and low initial investment cost, the MinION brought affordable portable nucleic acid analysis within reach. However, translating the electrical signal it outputs into a sequence of bases still requires high-end computer hardware, which remains a caveat when aiming for deployment of many devices at once or usage in remote areas. For applications focusing on detection of a target sequence, such as infectious disease or GMO monitoring, the computational cost of analysis may be reduced by directly detecting the target sequence in the electrical signal instead. Here we present baseLess, a computational tool that enables such target-detection-only analysis. BaseLess makes use of an array of small neural networks, each of which efficiently detects a fixed-size subsequence of the target sequence directly from the electrical signal. We show that baseLess can accurately determine the identity of reads between three closely related fish species and can classify sequences in mixtures of twenty bacterial species, on an inexpensive single-board computer. AvailabilitybaseLess and all code used in data preparation and validation is available on Github at https://github.com/cvdelannoy/baseLess, under an MIT license. Used validation data and scripts can be found at https://doi.org/10.4121/20261392, under an MIT license.

bioinformatics↗

bioRxiv2017

Inter- and intracellular colonization of Arabidopsis roots by endophytic actinobacteria and the impact of plant hormones on their antimicrobial activity

Many actinobacteria live in close association with eukaryotes like fungi, insects, animals and plants. Plant-associated actinobacteria display (endo)symbiotic, saprophytic or pathogenic life styles, and can make up a substantial part of the endophytic community. Here, we characterised endophytic actinobacteria isolated from root tissue of Arabidopsis thaliana (Arabidopsis) plants grown in soil from a natural ecosystem. Many of these actinobacteria belong to the family of Streptomycetaceae with Streptomyces olivochromogenes and Streptomyces clavifer as well represented species. When seeds of Arabidopsis were inoculated with spores of Streptomyces strain coa1, which shows high similarity to S. olivochromogenes, roots were colonised intercellularly and, unexpectedly, also intracellularly. Subsequent exposure of endophytic isolates to plant hormones typically found in root and shoot tissues of Arabidopsis led to altered antibiotic production against Escherichia coli and Bacillus subtilis. Taken together, our work reveals remarkable colonization patterns of endophytic streptomycetes with specific traits that may allow a competitive advantage inside root tissue.

microbiology↗