Biology subjects

Hess, J.

Publications and source records attributed to Hess, J..

At least 19 recordsLinked to original sources

bioRxiv2025

Adaptive regulation of dNTP homeostasis confers osimertinib resistance in EGFR mutant non-small cell lung carcinoma

Maintaining sustained deoxyribonucleotide triphosphate (dNTP) pools is essential for DNA replication fidelity and genome stability. In EGFR-mutant non-small cell lung carcinoma (NSCLC), we find that disruption of dNTP homeostasis plays a critical role in determining sensitivity to the EGFR inhibitor osimertinib and in shaping mechanisms of acquired resistance. Transcriptomic and biochemical analyses revealed that osimertinib suppresses RRM2 expression, a key regulator of dNTP synthesis, through the downregulation of the transcription factor MYBL2. In response to osimertinib-mediated replication stress and dNTP depletion, cells activated a compensatory pathway involving the stress-inducible ribonucleotide reductase subunit RRM2B via a novel transcriptional regulator, TNNT3. We further identified CHK2 signaling as essential for TNNT3 nuclear translocation and RRM2B transcriptional activation. Inhibition of CHK2 or combined CHK1/2 blockade impaired RRM2B induction, exacerbated replication stress, and delayed the development of osimertinib resistance both in vitro and in xenograft models. Collectively, our findings reveal that EGFR-mutant NSCLC cells rely on a dynamic EGFR-MYBL2-RRM2 and CHK2-TNNT3-RRM2B regulatory axis to maintain dNTP pool balance under therapeutic pressure. Disruption of this axis sensitizes tumors to osimertinib and impairs the acquisition of resistance, highlighting dNTP metabolism as a critical vulnerability and actionable target in EGFR-driven lung cancer. STATEMENT OF SIGNIFICANCETargeting dNTP metabolism via the EGFR-MYBL2-RRM2 and CHK2-TNNT3-RRM2B regulatory axis sensitizes EGFR-mutant NSCLC to osimertinib treatment and delays drug resistance, revealing a novel and actionable therapeutic vulnerability in EGFR-driven lung cancer.

cancer biology↗

bioRxiv2025

Digital Spatial Pathway Mapping Reveals Prognostic Tumor States in Head and Neck Cancer

Head and neck squamous cell carcinoma (HNSCC) is a morphologically and molecularly heterogeneous disease with limited effectiveness of genotype-informed therapies. Transcriptome-derived estimates of signaling pathway activity carry prognostic and therapeutic potential but remain inaccessible in routine diagnostics due to cost and tissue constraints. Here, we introduce Digital Spatial Pathway Mapping, an AI-based computational pathology framework that infers signaling pathway activities directly from routine hematoxylin and eosin (H&E) slides, enabling in-silico spatial molecular readouts from standard histology. Models trained on HPV-negative HNSCC from TCGA and externally validated on CPTAC robustly predicted transcriptome-derived activities in cancer-relevant signaling pathways. To achieve spatial interpretability, we applied layer-wise relevance propagation (LRP) to generate heatmaps that highlight positive versus negative evidence for pathway activation. These LRP heatmaps were technically validated by patch-flipping tests and biologically validated against pathway-relevant immunohistochemistry in an independent patient cohort. From these explanations, we derived a tumor area pathway activity score (TAPAS) quantifying the spatial fraction of activated tumor regions within a slide. Applied to a retrospective HNSCC cohort of 1,066 slides from 112 resection specimens, TAPAS captured intratumoral heterogeneity and revealed two biologically dis-tinct tumor states - an oncogenic growth phenotype with widespread pathway activation and a pathway quiescent phenotype associated with higher recurrence risk independent of clinicopathological variables. These findings establish Digital Spatial Pathway Mapping as a scalable, in-silico approach to recover systems-level molecular information from standard histopathology, enabling prognostic and mechanistically grounded patient stratification in head and neck cancer.

pathology↗

bioRxiv2025

A Unified Single-Cell Atlas of HNSCC: Uncovering HPV and Sex Variability in the Tumor Microenvironment

Head and neck squamous cell carcinoma (HNSCC) is highly heterogeneous, with variations driven by HPV status and sex. However, existing single-cell RNA sequencing (scRNA-seq) studies are often limited in sample size and lack standardized methodologies, limiting cross-study comparisons. To address this, we integrated scRNA-seq data from 78 patients (274,911 cells) across multiple studies, creating a unified HNSCC atlas that harmonizes annotations and enables robust tumor microenvironment (TME) analyses. Using STACAS for semi-supervised integration and automated annotation tools such as Ikarus and scGate, we improved tumor and immune cell classification. Leveraging our atlas, we identified HPV- and sex-specific shifts in immune and stromal composition, with HPV+ tumors enriched in adaptive immune cells and HPV- tumors showing more stromal and myeloid populations. Preliminary sex-stratified analyses suggested distinct microenvironmental patterns, warranting further investigation. This publicly available atlas provides a comprehensive framework for reproducibly studying HNSCC biology, improving patient stratification, and may help informing personalized therapies.

cancer biology↗

bioRxiv2025

Optical tissue clearing and 3D imaging of intact primate testicular tissue: a novel technology development

Classical histology struggles to preserve three-dimensional spatial context, prompting the emergence of optical tissue clearing techniques that enable imaging of intact specimens at cellular or subcellular resolution. These techniques have revolutionised fields like cell biology, developmental biology, and neuroscience. However, their application in reproductive biology remains unexplored - particularly in studying the complexities of testicular development. We developed a novel, efficient and affordable toolbox for studying intact testicular tissues, PT-CLEAR3D, that stands for primate testis - whole mount staining, tissue clearing and three-dimensional imaging. Intact testicular tissues from humans (transgender model), common marmosets and macaques underwent antibody labelling, clearing with organic solvents, and three-dimensional imaging using light sheet fluorescence microscopy. Marker specificity was confirmed by immunofluorescence staining of 3 and 25 {micro}m testicular sections, followed by imaging with confocal. The testicular structure was evaluated using several markers: spermatogonia (melanoma-associated antigen 4), least differentiated spermatogonia (Piwi-like protein 4), Sertoli cells (vimentin and SRY-Box transcription Factor 9), peritubular myoid cells and vasculature (alpha-smooth muscle actin), and NucSpot as a nuclear dye. PT-CLEAR3D efficiently achieved optical transparency while a commercial kit that was ran in parallel was inefficient. This study presents a pioneering three-dimensional visualization of intact testicular samples of up to 50 mm3 in size and imaging depth of up to 4.5 mm across three primate species. Remarkably, PT-CLEAR3D revealed critical details at both tissue and cellular levels such as the spatial distribution of germ and somatic cells, cellular bridges, and vasculature. Furthermore, PT-CLEAR3D enabled three-dimensional reconstructions that effectively reduce confirmation bias enhancing our observation of spermatogonial clones organized as single cells, pairs, and quartets. Importantly, it adeptly identified testicular pathology and the persistence of germ cell clones in select tubules within the transgender testis following hormonal suppression of spermatogenesis. This technological development offers a versatile toolbox with benefits such as applicability across multiple species, fluorophore multiplexing, compatibility with different fixatives and deep tissue volumetric imaging with cellular resolution. Overall, PT-CLEAR3D establishes a foundation for spatial evaluation of testicular development, presenting substantial potential for advancing our understanding of the intricate kinetics of spermatogenesis in health and disease.

developmental biology↗

bioRxiv2024

Closely related facultative and constitutive CAM phenotypes show little transcriptomic overlap in the subgenus Tillandsia

Crassulacean acid metabolism (CAM) is a water-efficient photosynthetic strategy involving a coordinated suite of complex traits including metabolic, anatomical and regulatory aspects that shift across the diel cycle. While CAM has evolved repeatedly in land plants, the evolutionary routes enabling this convergence remain elusive. Whereas the same core CAM (de)carboxylation genes are consistently involved, a key question is whether distinct CAM phenotypes also depend on a shared set of auxiliary genes, reflecting a quantitative continuum of expression, or whether they can instead emerge through divergent or redundant peripheral solutions. The bromeliad subgenus Tillandsia, with diverse photosynthetic strategies, offers an ideal system to explore this question. Using physiological and transcriptomic analyses of well-watered and water-limited accessions of two closely related species, we characterized facultative and constitutive CAM. By comparing orthologous gene expression and orthogroup recruitment, we found that while both species performed CAM upon water-withholding, transcriptional shifts in pathways related to stomatal movement, sugar/malate transport, aquaporins and starch metabolism showed minimal overlap. Core enzymes involved in the CAM (de)carboxylation cycle exhibited broadly shared expression patterns, yet the facultative CAM species uniquely up-regulated PPC2 at night instead of the canonical CAM-related PEPC ortholog PPC1. Our study reveals that, while the expression of certain core CAM enzymes is conserved, the surrounding transcriptional architecture can differ substantially even between closely related species. This supports a model in which CAM evolves through a mosaic recruitment of functionally equivalent, yet non-orthologous genes - underscoring its flexible and modular genetic architecture. These insights advance our understanding of the mechanisms enabling the repeated evolution of CAM and its capacity to facilitate adaptive diversification.

evolutionary biology↗

bioRxiv2023

Planar Amorphous Silicon Carbide Microelectrode Arrays for Chronic Recording in Rat Motor Cortex

Chronic implantation of intracortical microelectrode arrays (MEAs) capable of recording from individual neurons can be used for the development of brain-machine interfaces. However, these devices show reduced recording capabilities under chronic conditions due, at least in part, to the brains foreign body response. This creates a need for MEAs that can minimize the foreign body response to enable long-term recording. A potential approach to reduce the foreign body response is the use of ultrathin MEAs. Here, we fabricated ultrathin (cross-sectional area: 160 {micro}m2) amorphous silicon carbide (a-SiC) MEAs with sixteen electrode channels and implanted them into the motor cortex of seven female Sprague-Dawley rats. A-SiC was chosen as the fabrication base for its high chemical stability, good electrical insulation properties, and amenability to thin film fabrication techniques. Electrochemical analysis and neural recordings were performed weekly for 4 months. MEAs were characterized in vitro pre-implantation and in vivo using electrochemical impedance spectroscopy and cyclic voltammetry at 50 mV/s and 50,000 mV/s. Neural recordings were analyzed for single unit activity. At the end of the study, animals were sacrificed for immunohistochemistry analysis. We observed statistically significant, but small, increases in 1 and 30 kHz impedance values and 50,000 mV/s charge storage capacity over the 16-week implantation period. Slow sweep 50 mV/s CV and 1 Hz impedance did not significantly change over time. Impedance values increased from 11.6 M{Omega} to 13.5 M{Omega} at 1 Hz, 1.2 M{Omega} to 2.9 M{Omega} at 1 kHz, and 0.11 M{Omega} to 0.13 M{Omega} at 30 kHz over 16 weeks. The median charge storage capacity of the implanted electrodes at 50 mV/s were 58.1 mC/cm2 on week 1 and 55.9 mC/cm2 on week 16, and at 50,000 mV/s were 4.27 mC/cm2 on week 1 and 5.93 mC/cm2 on week 16. Devices were able to record neural activity from 92% of all active channels at the beginning of the study, At the study endpoint, a-SiC devices were still recording single-unit activity on 51% of electrochemically active electrode channels. In addition, we observed that the signal-to-noise ratio experienced a small decline of only -0.19 per week. We also classified the units as fast and slow spiking based on the trough-to-peak time. Although the overall presence of single units declined, fast and slow spiking units declined at a similar rate. Furthermore, immunohistochemistry showed minimal foreign body response to the a-SiC devices, as highlighted by statistically insignificant differences in activated glial cells between implanted brains slices and contralateral sham slices, as evidenced by GFAP staining. NeuN staining revealed the presence of neural cell bodies close to the implantation site, again statistically not different from a contralateral sham slice. These results support the use of ultrathin a-SiC MEAs for long-term implantation and use in brain-machine interfaces.

bioengineering↗

bioRxiv2023

Short structural variation fuelled CAM evolution within an explosive bromeliad radiation

1.The subgenus Tillandsia (Bromeliaceae) belongs to one of the fastest radiating clades in the plant kingdom and is characterised by the repeated evolution of Crassulacean Acid Metabolism (CAM). Despite its complex genetic basis, this water-conserving trait has evolved independently across many plant families and is regarded as a key innovation trait and driver of ecological diversification in Bromeliaceae. By producing high-quality genome assemblies of a Tillandsia species pair displaying divergent photosynthetic phenotypes, and combining genome-wide investigations of synteny, TE dynamics, sequence evolution, gene family evolution and temporal differential expression, we were able to pinpoint the genomic drivers of CAM evolution in Tillandsia. Several large-scale rearrangements associated with karyotype changes between the two genomes and a highly dynamic TE landscape shaped the genomes of Tillandsia. However, our analyses show that rewiring of photosynthetic metabolism is mainly obtained through regulatory evolution rather than coding sequence evolution, as CAM-related genes are differentially expressed across a 24-hour cycle between the two species, but are no candidates of positive selection. Gene orthology analyses reveal that CAM-related gene families manifesting differential expression underwent accelerated gene family expansion in the constitutive CAM species, further supporting the view of gene family evolution as a driver of CAM evolution.

evolutionary biology↗

bioRxiv2023

Invasive Californian death caps develop mushrooms unisexually and bisexually

Canonical sexual reproduction among basidiomycete fungi involves the fusion of two haploid individuals of different sexes, resulting in a heterokaryotic mycelial body made up of genetically different nuclei1. Using population genomics data, we discovered mushrooms of the deadly invasive Amanita phalloides are also homokaryotic, evidence of sexual reproduction by single individuals. In California, genotypes of homokaryotic mushrooms are also found in heterokaryotic mushrooms, implying nuclei of homokaryotic mycelia also promote outcrossing. We discovered death cap mating is controlled by a single mating-type locus (A. phalloides is bipolar), but the development of homokaryotic mushrooms appears to bypass mating-type gene control. Ultimately, sporulation is enabled by nuclei able to reproduce alone as well as with others, and nuclei competent for both unisexuality and bisexuality have persisted in invaded habitats for at least 17 but potentially as long as 30 years. The diverse reproductive strategies of invasive death caps are likely facilitating its rapid spread, revealing a profound similarity between plant, animal and fungal invasions2,3.

microbiology↗

bioRxiv2021

Conserved genomic landscapes of differentiation across Populus speciation continuum

Speciation, the continuous process by which new species form, is often investigated by looking at the variation of nucleotide diversity and differentiation across the genome (hereafter genomic landscapes). A key challenge lies in how to determine the main evolutionary forces at play shaping these patterns. One promising strategy, albeit little used to date, is to comparatively investigate these genomic landscapes as a progression through time by using a series of species pairs along a divergence gradient. Here, we resequenced 201 whole-genomes from eight closely related Populus species, with pairs of species at different stages along the divergence gradient to learn more about speciation processes. Using population structure and ancestry analyses, we document extensive introgression between some species pairs, especially those with parapatric distributions. We further investigate genomic landscapes, focusing on within-species (nucleotide diversity and recombination rate) and among-species (relative and absolute divergence) summary statistics of diversity and divergence. We observe highly conserved patterns of genomic divergence across species pairs. Independent of the stage across the divergence gradient, we find support for signatures of linked selection (i.e., the interaction between natural selection and genetic linkage) in shaping these genomic landscapes, along with gene flow and standing genetic variation. We highlight the importance of investigating genomic patterns on multiple species across a divergence gradient and discuss prospects to better understand the evolutionary forces shaping the genomic landscapes of diversity and differentiation.

evolutionary biology↗

bioRxiv2021

MEK1/2 inhibition transiently alters the tumor immune microenvironment to enhance immunotherapy efficacy against head and neck cancer

Although the mitogen-activated protein kinases (MAPK) pathway is hyperactive in head and neck cancer (HNC), inhibition of MEK1/2 in HNC patients has not shown clinically meaningful activity. Using pre-clinical HNC models, we demonstrated that treatment with the MEK1/2 blocker trametinib delays HNC initiation and progression by reducing tumor cell proliferation and enhancing the anti-tumor immunity of CD8+ T cells. Further activation of CD8+ T cells by supplementation with anti-programmed death-1 (PD-1) antibody eliminated tumors and induced an immune memory in the cured mice. Mechanistically, an early response to trametinib treatment sensitized tumors to PD-1-supplementation by attenuating the expression of tumor-derived colony-stimulating factor-1 (CSF-1), which reduced the abundance of two CSF-1R+CD11c+ myeloid-derived suppressor cell (MDSC) populations in the tumor microenvironment (TME). In contrast, prolonged treatment with trametinib abolished the anti-tumor activity of PD-1, because tumor cells undergoing the epithelial to mesenchymal transition (EMT) in response to trametinib restored CSF-1 expression and re-created an immune-suppressive TME. These findings provide the rationale for testing the trametinib/PD-1 combination in HNC and highlight the importance of sensitizing tumors to immunotherapies by using targeted therapies to interfere with the host-tumor interaction. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=199 SRC="FIGDIR/small/457244v1_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@1c65286org.highwire.dtl.DTLVardef@1541becorg.highwire.dtl.DTLVardef@f557f3org.highwire.dtl.DTLVardef@16134dc_HPS_FORMAT_FIGEXP M_FIG Graphical abstract C_FIG

cancer biology↗

bioRxiv2021

Taxon-specific or universal? Using target capture to study the evolutionary history of a rapid radiation

Target capture has emerged as an important tool for phylogenetics and population genetics in non-model taxa. Whereas developing taxon-specific capture probes requires sustained efforts, available universal kits may have a lower power to reconstruct relationships at shallow phylogenetic scales and within rapidly radiating clades. We present here a newly-developed target capture set for Bromeliaceae, a large and ecologically-diverse plant family with highly variable diversification rates. The set targets 1,776 coding regions, including genes putatively involved in key innovations, with the aim to empower testing of a wide range of evolutionary hypotheses. We compare the relative power of this taxon-specific set, Bromeliad1776, to the universal Angiosperms353 kit. The taxon-specific set results in higher enrichment success across the entire family, however, the overall performance of both kits to reconstruct phylogenetic trees is relatively comparable, highlighting the vast potential of universal kits for resolving evolutionary relationships. For more detailed phylogenetic or population genetic analyses, e.g. the exploration of gene tree concordance, nucleotide diversity or population structure, the taxon-specific capture set presents clear benefits. We discuss the potential lessons that this comparative study provides for future phylogenetic and population genetic investigations, in particular for the study of evolutionary radiations.

evolutionary biology↗

bioRxiv2021

MCMICRO: A scalable, modular image-processing pipeline for multiplexed tissue imaging

Highly multiplexed tissue imaging makes molecular analysis of single cells possible in a preserved spatial context. However, reproducible analysis of the underlying data poses a substantial computational challenge. Here we describe a modular and open-source computational pipeline (MCMICRO) for performing the sequential steps needed to transform large, multi-channel whole slide images into single-cell data. We demonstrate use of MCMICRO on images of different tissues and tumors acquired using multiple imaging platforms, thereby providing a solid foundation for the continued development of tissue imaging software.

bioinformatics↗

bioRxiv2020

AmpliconDesign - An interactive web server for the design of high-throughput targeted DNA methylation assays

Targeted analysis of DNA methylation patterns based on bisulfite-treated genomic DNA (BT-DNA) is considered as a gold-standard for epigenetic biomarker development. Existing software tools facilitate primer design, primer quality control or visualization of primer localization. However, high-throughput design of primers for BT-DNA amplification is hampered by limits in throughput and functionality of existing tools, requiring users to repeatedly perform specific tasks manually. Consequently, the design of PCR primers for BT-DNA remains a tedious and time-consuming process. To bridge this gap, we developed AmpliconDesign, a webserver providing a scalable and user-friendly platform for the design and analysis of targeted DNA methylation studies based on BT-DNA, e.g. deep amplicon bisulfite sequencing (ampBS-seq), EpiTYPER MassArray, or pyrosequencing. Core functionality of the web server includes high-throughput primer design and binding site validation based on in silico bisulfite-converted DNA sequences, prediction of fragmentation patterns for EpiTYPER MassArray, an interactive quality control as well as a streamlined analysis workflow for ampBS-seq. Availability and ImplementationThe AmpliconDesign webserver is freely available online at: https://amplicondesign.dkfz.de/. AmpliconDesign has been implemented using the R Shiny framework (Chang et al., 2018). The source code is publicly available under the GNU General Public License v3.0 (https://github.com/MaxSchoenung/AmpliconDesign). ContactDaniel B. Lipka (d.lipka@dkfz.de) & Maximilian Schonung (m.schoenung@dkfz.de)

bioinformatics↗

bioRxiv2019

Inhibiting Mycobacterium tuberculosis CoaBC by targeting a new allosteric site.

Coenzyme A (CoA) is a fundamental co-factor for all life, involved in numerous metabolic pathways and cellular processes, and its biosynthetic pathway has raised substantial interest as a drug target against multiple pathogens including Mycobacterium tuberculosis. The biosynthesis of CoA is performed in five steps, with the second and third steps being catalysed in the vast majority of prokaryotes, including M. tuberculosis, by a single bifunctional protein, CoaBC. Depletion of CoaBC was found to be bactericidal in M. tuberculosis. Here we report the first structure of a full-length CoaBC, from the model organism Mycobacterium smegmatis, describe how it is organised as a dodecamer and regulated by CoA thioesters. A high-throughput biochemical screen focusing on CoaB identified two inhibitors with different chemical scaffolds. Hit expansion led to the discovery of potent inhibitors of M. tuberculosis CoaB, which we show to bind to a novel cryptic allosteric site within CoaB.

biochemistry↗

bioRxiv2019

Spatial organization of cells and variable expression of autophagy, apoptosis, and neurodevelopmental genes might underlie selective brain region vulnerability in Attention-Deficit/Hyperactivity Disorder

Genetically influenced changes in brain organization occur over the course of development. Large-scale brain imaging studies by the ENIGMA Consortium identified structural changes associated with attention-deficit/hyperactivity disorder (ADHD). It is not clear why some brain regions are impaired and others spared by the etiological risks for ADHD. We hypothesized that spatial variation in brain cell organization and/or pathway expression levels contribute to selective brain region vulnerability (SBRV) in ADHD. In this study, we used the largest available collection of imaging results from the ADHD ENIGMA Consortium along with high-resolution postmortem brain microarray data from Allen Brain Atlas from 22 sub-cortical and cortical brain regions to investigate our selective brain region vulnerability (SBRV) hypothesis. We performed deconvolution of the bulk transcriptomic data to determine abundances of neuronal and non-neuronal cells in the brain. We then assessed the relationships between gene set expression levels, cell abundance, and standardized effect sizes representing regional changes in brain sizes in cases of ADHD. Our analysis yielded significant correlations between apoptosis, autophagy, and neurodevelopment genes with reductions in regional brain sizes in ADHD, along with associations to regional abundances of dopaminergic neurons, astrocytes, oligodendrocytes, and neural progenitor cells. This works provides novel mechanistic insights into SBRV in ADHD.

neuroscience↗

bioRxiv2018

Genomic footprints of repeated evolution of CAM photosynthesis in tillandsioid bromeliads

The adaptive radiation of Bromeliaceae (pineapple family) is one of the most diverse among Neotropical flowering plants. Diversification in this group was facilitated by several key innovations including the transition from C3 to CAM photosynthesis. We used a phylogenomic approach complemented by differential gene expression (RNA-seq) and targeted metabolite profiling to address the patterns and mechanisms of C3/CAM evolution in the extremely species-rich bromeliad genus Tillandsia and related taxa. Evolutionary analyses at a range of different levels (selection on protein-coding genes, gene duplication and loss, regulatory evolution) revealed three common themes driving the evolution of CAM: response to heat and drought, alterations to basic carbohydrate metabolism, and regulation of organic acid storage. At the level of genes and their products, CAM/C3 shifts were accompanied by gene expansion of a circadian regulator, re-programming of ABA-related gene expression, and adaptive sequence evolution of an enolase, effectively linking carbohydrate metabolism to ABA-mediated stress response. These changes include several pleiotropic regulators, which facilitated the evolution of correlated adaptive traits during a textbook adaptive radiation.

genomics↗

bioRxiv2018

Wood modification by furfuryl alcohol caused delayed decomposition response in Rhodonia (Postia) placenta

The aim of this study was to investigate differential expression profiles of the brown rot fungus Rhodonia placenta (previously Postia placenta) harvested at several time points when grown on Pinus radiata (radiata pine) and P. radiata with three different levels of modification by furfuryl alcohol, an environmentally benign commercial wood protection system. For the first time the entire gene expression pattern of a decay fungus is followed in untreated and modified wood from initial to advanced stages of decay. Results support the current model of a two-step decay mechanism, with an initial oxidative depolymerization followed by hydrolysis of cell-wall polysaccharides. The wood decay process is finished, and the fungus goes into starvation mode after five weeks when grown on unmodified P. radiata wood. The pattern of repression of oxidative processes and oxalate synthesis found in P. radiata at later stages of decay is not mirrored for the high furfurylation treatment. The high treatment level provided a more unpredictable expression pattern throughout the entire incubation period. Furfurylation does not seem to directly influence the expression of core plant cell wall hydrolyzing enzymes, as a delayed and prolonged, but similar pattern was observed in the P. radiata and the modified experiments. This indicates that the fungus starts a common decay process in the modified wood, but proceeds at a slower pace as access to the plant cell wall polysaccharides is restricted. This is further supported by the downregulation of hydrolytic enzymes for the high treatment level at the last harvest point (mass loss 14%). Moreover, the mass loss does not increase the last weeks. Collectively, this indicates a potential threshold for lower mass loss for highly modified wood.\n\nIMPORTANCEFungi are important decomposers of woody biomass in natural habitats. Investigation of the mechanisms employed by decay fungi in their attempt to degrade wood is important for both the basic scientific understanding of ecology and carbon cycling in nature, and for applied uses of woody materials. For wooden building materials long service life and carbon storage is essential, but decay fungi are responsible for massive losses of wood in service. Thus, optimizing durable wood products for the future are of major importance. In this study we have investigated the fungal genetic response to furfurylated wood, a commercial environmentally benign wood modification approach, that improves service life of wood in outdoor applications. Our results show that there is a delayed wood decay by the fungus as a response to furfurylated wood and new knowledge about the mechanisms behind the delay is provided.

genomics↗

bioRxiv2018

A comprehensive analysis of RNA sequences reveals macroscopic somatic clonal expansion across normal tissues

Cancer genome studies have significantly advanced our knowledge of somatic mutations. However, how these mutations accumulate in normal cells and whether they promote pre-cancerous lesions remains poorly understood. Here we perform a comprehensive analysis of normal tissues by utilizing RNA sequencing data from [~]6,700 samples across 29 normal tissues collected as part of the Genotype-Tissue Expression (GTEx) project. We identify somatic mutations using a newly developed pipeline, RNA-MuTect, for calling somatic mutations directly from RNA-seq samples and their matched-normal DNA. When applied to the GTEx dataset, we detect multiple variants across different tissues and find that mutation burden is associated with both the age of the individual and tissue proliferation rate. We also detect hotspot cancer mutations that share tissue specificity with their matched cancer type. This study is the first to analyze a large number of samples across multiple normal tissues, identifying clones with genomic aberrations observed in cancer.

genomics↗