Biology subjects

Van Nieuwerburgh, F.

Publications and source records attributed to Van Nieuwerburgh, F..

At least 19 recordsLinked to original sources

bioRxiv2026

PERTURBATION OF THE AMINO ACID STRESS RESPONSE PATHWAY EXPOSES A METABOLIC VULNERABILITY IN MULTIPLE AGGRESSIVE CANCER SUBTYPES

Cancer cells frequently experience nutrient limitation and depend on adaptive stress-response pathways to maintain metabolic homeostasis. Here, we show that pharmacological perturbation of amino acid stress signaling exerts broad anti-tumor activity across multiple aggressive malignancies, including acute lymphoblastic leukemia, acute myeloid leukemia, triple-negative breast cancer, ovarian cancer, and neuroblastoma. Sensitivity to pathway modulation is associated with a chronic stress-adapted metabolic state marked by constitutive amino acid response signaling, elevated NFE2L2 expression, and reduced mitochondrial abundance despite evidence of efficient oxidative metabolism. Mechanistically, we demonstrate that the ATP-competitive compound GCN2-IN-6 does not phenocopy genetic GCN2 suppression and exhibits context-dependent effects on the amino acid stress response. Nevertheless, tumors experiencing chronic metabolic stress remain exquisitely sensitive to disruption of this adaptive network, regardless of whether signaling is perturbed through canonical inhibition or paradoxical activation. Collectively, our findings identify chronic metabolic stress adaptation as an actionable vulnerability and establish off-balancing amino acid stress signaling as a therapeutic strategy across multiple cancer types

cancer biology↗

bioRxiv2026

Recombinase polymerase amplification: characterization and mitigation of undescribed multimeric artefacts

Recombinase polymerase amplification (RPA) enables rapid nucleic acid testing in low-resource environments, but poorly characterized byproducts can compromise assay specificity and cause false-positive results. Here, we amplified the thirteen original CODIS core loci and Amelogenin to characterize recurrent RPA artefacts and establish conditions that reduce their formation. First, RPA products were analyzed for two reference samples by Oxford Nanopore Technologies sequencing. This revealed two distinct classes of multimeric products: primer multimers and amplicon multimers, consisting of repeated primer or amplicon sequences, respectively. Individual artefacts contained up to 281 primer copies or 22 amplicon copies, demonstrating the extensive range of these products. Next, we performed an optimization study to evaluate the effects of reaction temperature and reagent concentrations at two representative loci, D3S1358 and D5S818. Among the conditions tested, temperature had the most pronounced effect. Reducing the temperature from 42{degrees}C to 34{degrees}C increased the relative target amplicon fraction from 15% to 83% for D3S1358 and from 84% to 98% for D5S818, while maintaining or increasing absolute target concentration. Lower primer concentrations and higher T4 UvsX concentrations also reduced multimer formation, although lower primer concentrations reduced target yield and caused allelic dropout. Finally, amplification at 34{degrees}C was evaluated across all fourteen loci by sequencing. Relative to 42{degrees}C, the target read fraction increased by more than 5 percentage points for 7/14 loci in one reference sample and 9/14 loci in the other, with the largest improvements at multimer-prone loci. These findings identify multimers as an important class of RPA artefacts and establish reaction temperature and T4 UvsX concentration as promising conditions to improve RPA specificity.

biochemistry↗

bioRxiv2026

Equi-depth pooling for standardized and cost-effective Adaptive Immune Receptor Repertoire sequencing (AIRRseq)

Bulk B- and T-cell adaptive immune receptor (BCR/TCR) repertoire sequencing (AIRRseq) enables comprehensive analysis of adaptive immune diversity, but achieving balanced sequencing depth across heterogeneous clinical samples remains a major cost driver. Standard equimolar pooling prior to sequencing disproportionately allocates reads, leading to undersequencing of libraries with high sequence abundance and oversampling of those with few sequences. Here, a quantitative pooling strategy is described in which libraries are pooled based on estimated target-specific unique molecular identifier (UMI) counts rather than library molarity, ensuring a uniform number of supporting reads per target sequence UMI across samples. Libraries were prepared from human RNA using the NEBNext Immune Sequencing (IS) kit and quantified by qPCR during the second amplification (PCR2) step. Deeply sequenced samples from a dengue 1 human infection model (DHIM1) clinical study were used to model the log-linear relationship between PCR2 cycle threshold (Ct) values and detected sequence counts. This model was then applied to a second, independent batch of samples from a dengue 3 human infection model (DHIM3) clinical study to predict UMI abundance and guide equi-depth pooling prior to sequencing. Sequencing of these equi-depth pools demonstrated a near-uniform reads-per-sequence ratio across samples, confirming that this approach achieves balanced depth without oversampling and at reduced cost. Simulations across a range of between-sample UMI-count distributions reflecting real-world sample pools showed that equi-depth pooling is expected to reduce the total number of required sequencing reads by approximately 70% compared with equimolar pooling, with savings increasing as the spread of library sizes grows. Beyond cost efficiency, equi-depth pooling eliminates the complexity-dependent sampling bias inherent to equimolar pooling, ensuring uniform sequencing depth and comparable UMI recovery across small and large libraries. For new workflows or sample types, implementation requires either an existing calibration dataset or a pilot sequencing experiment to establish the relationship between PCR2 Ct values and relative UMI abundance. The equi-depth method thus provides a robust, scalable, and cost-efficient strategy for bulk AIRRseq studies where library sizes vary widely.

bioinformatics↗

bioRxiv2026

Predicting subclonal TP53 mutations from tumor spatial transcriptomics data using a graph convolutional neural network

Spatial transcriptomics (ST) has revolutionized our understanding of tumor biology but inherently lacks information on the upstream somatic driver mutations. We developed a spatially-aware graph convolutional neural network (MuT-GCNN) that infers TP53 clones directly from ST data. MuT-GCNN was trained on virtual ST slides with clones simulated from a large collection of existing RNA and matched DNA sequencing data. The model is highly performant with precision and recall values exceeding 95% in most analysed cancer types. It is sensitive for single hit mutations and is primarily informed by the expression of p53 signalling genes in cancer cells. After demonstrating the potential of the model on publicly available squamous cell carcinoma (SCC) data, a direct validation was performed using ST and matched DNA sequencing from serial slices obtained from 4 cutaneous SCC samples. With the increasing availability of ST data and upcoming ST atlases, MuT-GCNN can unveil the location of (sub)clonal alterations in TP53, the most frequently mutated gene in human cancer.

cancer biology↗

bioRxiv2026

Salt-induced osmotic stress remodels osmoadaptive gene expression and physiology in the polyhydroxyalkanoate-accumulating thermophilic bacterium Caldimonas thermodepolymerans

Caldimonas thermodepolymerans is a thermophilic polyhydroxyalkanoate (PHA)-producing bacterium with strong potential for sustainable bioplastic production. Besides serving as intracellular carbon and energy storage compounds, PHAs are increasingly associated with bacterial stress resistance and cellular robustness. This study aimed to investigate the physiological and transcriptomic response of C. thermodepolymerans to osmotic stress induced by elevated NaCl concentrations. Growth analysis demonstrated tolerance up to a supplementation of 2% NaCl, while moderate salt concentrations enhanced PHA accumulation, reaching 65% cell dry weight at 1.5% NaCl supplementation. To better understand the bacterial response to osmotic stress, RNA sequencing was performed under sublethal salt stress conditions. Differential expression analysis revealed major changes in genes related to osmoprotection, trehalose metabolism and type VI secretion systems, whereas motility and chemotaxis genes were strongly repressed. Phenotypic assays confirmed increased biofilm formation and reduced swarming motility under salt-induced osmotic stress. Although canonical PHA biosynthesis genes were not significantly differentially expressed, increased polymer accumulation suggests other underlying mechanisms linked to osmoadaptation. Together, these findings demonstrate that osmotic stress induces metabolic, physiological and regulatory responses in C. thermodepolymerans, highlighting the importance of PHA in stress adaptation besides its industrial applicability.

microbiology↗

bioRxiv2026

Integrated single-cell analysis reveals interferon-driven immune signatures in a DENV1 human infection model.

Dengue virus infection triggers complex innate and adaptive immune responses, yet the molecular mechanisms that shape early antiviral immunity remain incompletely defined. We performed longitudinal single-cell multi-omics profiling of peripheral blood mononuclear cells from four flavivirus-naive adults experimentally infected with DENV-1, integrating 5' scRNA-seq with paired surface proteomics. Across 95,841 high-quality cells collected at baseline and on days 8 and 10 post-infection, we observed a strong interferon-driven transcriptional response accompanied by marked immune-cell redistribution, including expansion of monocytes and transient reductions in dendritic cells and double-negative T cells. Cytotoxic and helper lymphocyte populations, particularly naive, central memory, and effector memory CD8 T cells, showed extensive crosstalk with monocytes and NK cells, reflecting coordinated cytokine production and cytotoxic activation. Early B cell activation was evident through increased immunoglobulin gene expression. Innate sensing pathways, including RIG-I and Toll-like signaling, were activated across NK, T, and B cell subsets, while also demonstrating enrichment of antigen processing and apoptosis programs. Pro-inflammatory and cytotoxic signatures peaked at day 8, supported by broad upregulation of interferon-stimulated, pro-apoptotic, and regulatory genes. Together, these findings define a robust IFN-driven antiviral state and coordinated activation of immune cell subsets, providing new insights into the immune dynamics of primary dengue infection. ImportanceDengue virus infects millions of people each year, but the early immune events that shape disease outcomes are still unclear. Most studies measure average responses across all blood cells, which hides how individual cell types react. By tracking thousands of single immune cells from volunteers infected with dengue virus under controlled conditions, we show how the immune system rapidly reorganizes during the first days of infection. Many cell types activate antiviral programs, communicate with one another, and shift their behavior in a coordinated way, driven by strong interferon activity. These results provide a clearer view of how early immune responses unfold in humans and identify cellular processes that may influence who develops more severe illness.

microbiology↗

bioRxiv2025

Widespread DNA off-targeting confounds studies of RNA chromatin occupancy

The importance of long noncoding RNA (lncRNA) functions is recognized across biological systems, but their modes of action remain poorly understood. One mechanism proposed to be particularly common is gene expression regulation via recruitment to specific genomic regions. Several high-throughput sequencing methods were developed for studying the genome-wide chromatin occupancy of lncRNAs, including ChIRP-seq, CHART-seq, and RAP-seq. These methods utilize biotin-labeled probes targeting the RNA of interest to isolate and recover the chromatin associated with it. Many of the datasets obtained with these methods contain thousands of binding sites, which appears to be in contradiction with the low abundance of the interrogated lncRNAs. We studied the chromatin interactome of NESPR lncRNA in cells with varying levels of endogenous expression and then performed a meta-analysis using dozens of RNA-chromatin interaction datasets in human and mouse cells. We demonstrate that thousands of regions reported to bind lncRNAs most likely arise from the spurious recovery of DNA elements, where the ends of the recovered DNA fragments exhibit partial complementarity with the probes used for the pulldown. In addition, crucial controls were rarely used in studies profiling RNA-chromatin interactions. Therefore, most chromatin regions reported as bound by trans-acting RNAs in recent studies in mammalian cells appear to be technical artifacts. We provide suggestions for assessing the quality of RNA-chromatin datasets and their improvement.

molecular biology↗

bioRxiv2025

A laser capture microdissection-based method for high-sensitivity transcriptomics from archived FFPE tissue slides with single-cell resolution using LCM-FFPEseq

Understanding gene expression within its spatial context is essential for unravelling biological processes. Laser Capture Microdissection (LCM) has emerged as a transformative technology, enabling targeted isolation of individual cells or regions from tissue sections while preserving spatial context. However, its application to formalin-fixed, paraffin-embedded (FFPE) tissues has been limited by RNA degradation, leaving the vast repository of clinical FFPE samples underutilized. To address this, we introduce LCM-FFPEseq, a novel method combining LCM with the advanced Smart-seq3xpress protocol and FFPE-specific adaptations for spatial transcriptomics of FFPE sections. Unlike traditional protocols requiring thousands of cells to generate high-quality libraries, LCM-FFPEseq achieves high sensitivity, reproducibility, and transcript coverage. With as few as 30 FFPE-embedded K562 cells and Sertoli cells, we detected over 14,000 protein-coding genes per sample, with no substantial gains when a higher number of cells were isolated. Even individual LCM-isolated cells yielded an average of 7,353 or 6,490 protein-coding genes per K562 or Sertoli single cell, respectively. To demonstrate its clinical utility, we applied LCM-FFPEseq to archived testicular FFPE samples from transgender females receiving gender-affirming hormone therapy. Transcriptomic profiling of isolated seminiferous tubules revealed tubular hyalinization to be associated with greater upregulation of extracellular matrix remodelling and inflammatory pathways, alongside stronger downregulation of spermatogenesis-associated pathways. These findings suggest that testicular fibrosis and/or tubular hyalinization may contribute to germ cell loss following inappropriate hormonal exposure. By enabling high-resolution transcriptomics in archived FFPE samples, LCM-FFPEseq unlocks new possibilities for investigating rare cell types, spatial heterogeneity, and therapy-induced tissue remodelling in vast FFPE repositories.

genomics↗

bioRxiv2025

Recombinase Polymerase Amplification of Forensic Short Tandem Repeat Loci

Short tandem repeats (STRs) are highly polymorphic repetitive DNA sequences extensively used in forensic science for identification of individuals. STR genotyping is usually performed by capillary electrophoresis (CE) or next-generation sequencing (NGS) in centralized laboratories. However, there is an increasing need for a low cost, portable and rapid STR genotyping method. Multiple methods for miniaturization have been explored, all relying on polymerase chain reaction (PCR) for generating amplicons. PCR requires precise thermal cycling, which complicates the design of the STR genotyping microfluidic device. Recombinase Polymerase Amplification (RPA) is an isothermal DNA amplification method that operates between 37{degrees}C and 42{degrees}C and completes within 40 minutes. This, along with the robustness of reagents and reduced stutter rate compared to PCR makes RPA a suitable candidate for implementation in an STR genotyping microfluidics device as well as a part of the established STR genotyping work flows. In this proof-of-concept study, we evaluate RPA assay for amplification of forensically relevant STR loci. Thirteen core STR loci of the Combined DNA Index System (CODIS) were amplified using RPA in both singleplex and multiplex formats. The amplicons were then analyzed using three different methods: CE, Illumina and Oxford Nanopore Technologies (ONT). A subset of 5 loci was used for CE analysis. CE, Illumina and ONT sequencing of singleplex RPA each resulted in complete and correct STR profiles across all samples. Sensitivity assessment demonstrated that complete and correct genotypes were achieved with DNA inputs of 62 pg and above for all but locus D8S1179. Attempts at multiplex RPA amplification resulted in incomplete or incorrect STR profiles. This outcome highlights a challenge in adapting RPA for simultaneous amplification of multiple STR loci, which is a standard requirement in forensic DNA profiling.

genomics↗

bioRxiv2025

On the edge of extinction: Delayed plant genetic response to forest edge dynamics

Understanding genetic responses to forest dynamics is essential for predicting the long-term viability of understory plant populations and for developing effective conservation strategies. This study investigates genetic extinction debt and colonization credit in Circaea lutetiana, a clonal forest understory species, across its European range. Using pooled genotype-by-sequencing data from 40 forest edge and core populations, we examined to what extent population size, latitude and historical changes in forest configuration predict genetic diversity. Our findings reveal that the historical forest configuration profoundly shapes present-day genetic diversity. Long-established forest edge populations exhibit significantly reduced allelic richness (-9%) compared to core populations, indicating the partial pay-off of a genetic extinction debt. In contrast, populations from recently established forest edges maintain comparable allelic richness to core populations, suggesting delayed population genetic responses to land use changes. Finally, populations established in areas that were afforested during the past 250 years exhibit lower genetic diversity than historical forest core populations, indicating a delay in genetic recovery and thus a potential genetic colonization credit. Our results highlight that C. lutetiana populations are not at equilibrium with the current forest configuration, underscoring the role of lagged genetic responses across very long time scales. Connectivity and population size further moderate genetic diversity, with smaller, isolated populations particularly vulnerable to genetic erosion. Given the limited research on delayed evolution in forest understory species, our results improve the understanding of extinction risk dynamics and underscore the need for history-informed restoration efforts.

ecology↗

bioRxiv2025

Harnessing machine learning to predict antibiotic susceptibility in Pseudomonas aeruginosa biofilms

Standard antibiotic susceptibility tests (ASTs) often fail to accurately predict treatment outcomes because they do not account for biofilm-specific mechanisms of reduced susceptibility. In the present study, we explored alternative approaches to predict tobramycin susceptibility of Pseudomonas aeruginosa biofilms that were experimentally evolved in physiologically relevant conditions. To this end, we used four analytical methods - whole-genome sequencing (WGS), matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS), isothermal microcalorimetry (IMC) and multi-excitation Raman spectroscopy (MX-Raman). Machine learning models were trained on data outputs from these methods to predict tobramycin susceptibility of our evolved strains and subsequently validated with a collection of clinical isolates. For minimal inhibitory concentration (MIC) predictions of the evolved strains, the highest accuracy{+/-}1 was achieved with MALDI-TOF MS (97.83 %), while for biofilm prevention concentration (BPC) predictions, Raman spectroscopy performed best with an accuracy{+/-}1 of 80.43 %. Overall, all analytical methods demonstrated comparable predictive performance, showing their potential for improving biofilm AST.

microbiology↗

bioRxiv2023

A spatial human thymus cell atlas mapped to a continuous tissue axis

T cells develop from circulating precursors, which enter the thymus and migrate throughout specialised sub-compartments to support maturation and selection. This process starts already in early fetal development and is highly active until the involution of the thymus in adolescence. To map the micro-anatomical underpinnings of this process in pre- vs. post-natal states, we undertook a spatially resolved analysis and established a new quantitative morphological framework for the thymus, the Cortico-Medullary Axis. Using this axis in conjunction with the curation of a multimodal single-cell, spatial transcriptomics and high-resolution multiplex imaging atlas, we show that canonical thymocyte trajectories and thymic epithelial cells are highly organised and fully established by post-conception week 12, pinpoint TEC progenitor states, find that TEC subsets and peripheral tissue genes are associated with Hassalls Corpuscles and uncover divergence in the pace and drivers of medullary entry between CD4 vs. CD8 T cell lineages. These findings are complemented with a holistic toolkit for spatial analysis and annotation, providing a basis for a detailed understanding of T lymphocyte development.

immunology↗

bioRxiv2023

Non-random polymorphisms near transposable elements facilitate evolution across the genome of Arabidopsis thaliana

Evolution is a key characteristic of all life on earth, and is achieved mainly through mutation and recombination. To facilitate evolutionary rates in the absence of recombination, increased mutagenesis could provide essential opportunities for evolution. Here, we harness the genomes of 973 wild accessions of Arabidopsis thaliana, a self-fertilizing species characterized by reduced recombination rates, to study the role of transposable elements (TEs) as mutagenic drivers of non-random genetic variation. We found that multiple TE superfamilies accumulate large numbers of genetic variants in gene-rich regions of the genome. Moreover, TEs were enriched in genes underpinning key molecular processes, including fertilization and mRNA cis-splicing, suggesting that TEs generate genetic variation that is fundamental to organismal functioning and reproduction. An excess of common genetic variants (maf>0.4) flanking TEs, despite the extreme degree of self-fertilization, further corroborates the notion that TEs can generate substantial evolutionary potential in the absence of outcrossing. Nevertheless, while other studies point to TE mobilization as a strategy to facilitate adaptive evolution, we find that only a fraction (4.8%) of TE families was linked to genetic variants involved in climate adaptation to a significantly larger extent than background genomic variation, possibly because the high mutation rates near TEs dilute adaptive signals. Overall, all TE superfamilies but one (Gypsy) were significantly associated with evolutionary processes through their association with genes, functional molecular processes, flanking common variants and/or climate adaptation. We conclude that non-random mutations flanking TEs provide substantial evolutionary potential in a self-fertilizing species.

evolutionary biology↗

bioRxiv2023

Myeloid A20 is critical for type-2 immune mediated helminth resistance

Protective immunity against intestinal helminths requires induction of robust Type-2 immunity orchestrated by various cellular and soluble effectors which promote goblet cell hyperplasia, mucus production, epithelial proliferation and smooth muscle contractions to expel worms and reestablish immune homeostasis. Conversely, defects in type-2 immunity result in ineffective helminth clearance, persistent infection and chronic inflammation. We identify A20 as an essential myeloid factor for the induction of type-2 immune responses against the intestinal parasite Trichuris muris. Myeloid cell-specific loss of A20 in mice (A20myel-KO) results in chronic Trichuris muris infection and intestinal inflammation. Myeloid A20 deficient mice are not able to induce anti-helmith type-2 immune responses while instead mount detrimental Th1/Th17 polarized immune responses. Antibody-mediated neutralization of the type-1 cytokines IFN{gamma}, IL18 and IL12 prevents Th1/Th17 polarization and reestablishes Type-2 mediated protective immunity against Trichuris muris in A20myel-KO mice. In contrast, the strong Th1/Th17 biased immunity in A20myel-KO mice offers protection against Salmonella infection. We hereby identify A20 as an essential myeloid factor to initiate approriate adaptive immunity in response to infection, and to induce a balanced type-2 immune response against the intestinal parasite Trichuris muris. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=140 SRC="FIGDIR/small/556360v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@632052org.highwire.dtl.DTLVardef@1def1f2org.highwire.dtl.DTLVardef@1de8459org.highwire.dtl.DTLVardef@1c316ff_HPS_FORMAT_FIGEXP M_FIG C_FIG Graphical abstractThe clearance of gastrointestinal helmiths depends on type-2 immunity. Helminths interact with and damage intestinal tissue, which leads to the release of intracellular DAMPs and cytokines such as TSLP and IL33, and IL25 produced by epithelial cells. These factors may activate myeloid cells and ILCs, which further activate T and B cells to mount effective Th2 responses and the secretion of IL4, IL5 and IL13 cytokines, as well as helminth-specific IgG1 immunoglobulins, leading to effective expulsion of the helminths. Deletion of A20 in the myeloid cells leads to enhanced secretion of type-1 cytokines, including IL12, IL18 and IFN{gamma}, which impede type-2 immune-mediated helminth clearance and promotes chronic intestinal inflammation.

immunology↗

bioRxiv2023

Genome-wide methylome stability and parental effects in the worldwide distributed Lombardy poplar

BackgroundDespite the increasing number of epigenomic studies in plants, little is known about the forces that shape the methylome in long-lived woody perennials. The Lombardy poplar offers an ideal opportunity to investigate the impact of the individual environmental history of trees on the methylome. ResultsWe present the results of three interconnected experiments on Lombardy poplar. In the first experiment, we investigated methylome variability during a growing season and across vegetatively reproduced generations. We found that ramets collected over Europe and raised in common conditions have stable methylomes in symmetrical CG-contexts. In contrast, seasonal dynamics occurred in methylation patterns in CHH-context. In the second experiment, we investigated whether methylome patterns of plants grown in a non-parental environment correlate with the parental climate. We did not observe a biological relevant pattern that significantly correlates with the parental climate. Finally, we investigated whether the parental environment has persistent carry-over effects on the vegetative offsprings phenotype. We combined new bud set observations of three consecutive growing seasons with former published bud set data. Using a linear mixed effects analysis, we found a statistically significant but weak short-term, parental carry-over effect on the timing of bud set. However, this effect was negligible compared to the direct effects of the offspring environment. ConclusionsGenome-wide cytosine methylation patterns in symmetrical CG-context are stable in Lombardy poplar and appear to be mainly the result of random processes. In this widespread poplar clone, methylation patterns in CG-context can be used as bio-markers to infer a common ancestor and thus to investigate the recent environmental history of a specific Lombardy poplar. The Lombardy poplar shows high phenotypic plasticity in a novel environment which enabled this clonal tree to adapt and survive all over the temperate regions of the world.

genomics↗

bioRxiv2023

The chromatin reader PHF6 at the crossroad of the replication stress and DNA damage responses in neuroblastoma through interaction with RRM2

The PHF6 protein is a presumed chromatin reader implicated in disease through germline loss-of-function mutations causing cognitive disability syndromes and somatic mutations are predominantly observed in acute T-cell leukemia. Previous reports support a role for PHF6 in DNA damage repair, replication fork restart as well as hematopoietic precursor cell self-renewal capacity and lineage commitment. To explore better how PHF6 mediates these functions, we mapped the PHF6 interactome and identified RRM2 as a consistent binding partner across different normal and malignant cell types. Next, PHF6 knockdown imposed increased replicative stress/DNA damage and suggested possible binding of PHF6 to H3K56ac, a marker for nascent DNA at sites of DNA damage repair. Genome-wide mapping of PHF6 chromatin binding indeed revealed overlap with sites of active DNA damage, binding sites of replication fork proteins and functional crosstalk with the neuroblastoma transcription core regulatory circuitry. Altogether, we show a canonical PHF6-RRM2 interaction enabling active transport of RRM2 to genomic sites of PHF6 mediated fork restart and PHF6 localization to H3K56ac at highly transcribed genes facilitating fork restart following replication-transcription conflicts.

cancer biology↗

bioRxiv2023

Elucidating the combined toxicity of aflatoxin B1 and fumonisin B1 on HepG2 cells based on respirometry and transcriptome analyses

Aflatoxin B1 (AFB1) and fumonisin B1 (FB1) are two toxic mycotoxins widely found in food contaminants, and known for their hepatotoxicity in human. However, their combined toxicity still needs to be deeply investigated especially for their harmful effect. Therefore, the current work aimed at investigating the (combined) effect of AFB1 and FB1 on mitochondrial and glycolytic activity of HepG2 cell line, a well-recognized in vitro model system to study liver cell function. In our previous work, we studied the impact of a short term exposure to different doses of AFB1, FB1, and their binary mixture (MIX) on the bioenergetic status of HepG2 cells. Seahorse respirometry analysis revealed that the co-exposure, especially at high doses (8 {micro}g/mL for AFB1 and 160 {micro}g/mL for FB1), is more toxic as a result of more inhibition of all parameters of mitochondrial respiration. RNA transcriptome sequencing showed that the p53 signaling pathway, which is a major orchestrator of mitochondrial apoptosis, was differentially expressed. Moreover, the co-exposure has significantly downregulated Cx I, Cx II, Cx III, and Cx IV genes, which represent the onset of the suppressed mitochondrial respiration in HepG2 cells. It was found that FB1 is contributed more to the MIX effects than AFB1. Environmental ImplicationAflatoxin B1 (AFB1) and fumonisin B1 (FB1) are two main mycotoxins that frequently (co-)contaminate maize and maize-based ingredients in several parts of the world. Both toxins are well-known for their hepatotoxicity in humans as the liver is their main target organ. However, the combined toxicity of AFB1 and FB1 still needs to be deeply investigated especially for their effect on cellular respiration. In this study, we proved that a binary mixture of AFB1 and FB1 is more toxic on mitochondrial respiration, and disrupted the p53 signaling pathway to induce apoptosis, which promised a novel insight of hazardous materials-induced hepatic damage.

pharmacology and toxicology↗

bioRxiv2023

HIV-PULSE: A long-read sequencing assay for high-throughput near full-length HIV-1 proviral genome characterization

A deep understanding of the composition of the HIV-1 reservoir is necessary for the development of targeted therapies and the evaluation of curative efforts. However, current near full-length (NFL) HIV-1 proviral genome sequencing assays are based on labor-intensive and costly principles of repeated PCRs at limiting dilution, restricting their scalability. To address this, we developed a high-throughput, long-read sequencing assay called HIV-PULSE (HIV Proviral UMI-mediated Long-read Sequencing). This assay uses unique molecular identifiers (UMIs) to tag individual HIV-1 genomes, allowing for the omission of the limiting dilution step and enabling long-range PCR amplification of many NFL genomes in a single PCR reaction, while simultaneously overcoming poor single-read accuracy. We optimized the assay using HIV-infected cell lines and then applied it to blood samples from 18 individuals living with HIV on antiretroviral therapy, yielding a total of 1,308 distinct HIV-1 genomes. Benchmarking against the widely applied Full-Length Individual Proviral Sequencing assay revealed similar sensitivity (11% vs 18%) and overall good concordance, though at a significantly higher throughput. In conclusion, HIV-PULSE is a cost-efficient and scalable assay that allows for the characterization of the HIV-1 proviral landscape, making it an attractive method to study the HIV-1 reservoir composition and dynamics.

molecular biology↗