Biology subjects

Gerber, A.

Publications and source records attributed to Gerber, A..

16 recordsLinked to original sources

bioRxiv2026

Targeted CRISPRi screening reveals unexpected resilience across the RNA polymerase III transcriptome

Increased RNA polymerase III (Pol III) activity and tRNA abundance are widely linked to cancer cell growth, yet the functional requirement for individual Pol III genes and core components remains unclear, in part due to the difficulty of achieving gene-specific perturbation of highly conserved loci. Here, we developed an inducible CRISPR interference platform and a custom single-guide RNA (sgRNA) library enabling gene-specific targeting of Pol III-transcribed genes and Pol III machinery. Genome-wide screening identified several Pol III dependencies in diploid fibroblasts and HEK293T cells, including multiple initiator methionine tRNA genes among the strongest fitness dependencies. Unexpectedly, glioblastoma models remained largely insensitive to repression of both individual Pol III genes and core Pol III components, despite efficient target repression. These findings establish a general strategy for gene-specific interrogation of conserved Pol III genes and indicate that glioblastoma models tolerate extensive perturbation of Pol III genes and machinery.

genomics↗

bioRxiv2026

EGFR upregulation drives signaling reactivation during EGFR inhibition in glioblastoma without broad kinome rewiring

BackgroundEpidermal growth factor receptor (EGFR) amplification occurs in [~]50% of IDH-wildtype glioblastoma (GBM) cases, frequently accompanied by expression of the oncogenic EGFRvIII variant. Although EGFR represents an attractive therapeutic target, EGFR-directed therapies have shown limited clinical efficacy in GBM. Resistance to kinase inhibitors is frequently attributed to activation of compensatory signaling pathways ("kinome rewiring"). We therefore investigated whether EGFR inhibition in GBM induces broad adaptive kinase responses that could be co-targeted to overcome resistance. MethodsWe molecularly profiled 29 patient-derived GBM cell lines for EGFR status and selected five representative models spanning EGFR amplification states for functional analyses. Cells were treated with EGFR inhibitors and responses were assessed using viability assays, time-resolved immunoblotting, and phosphoproteomics (LC-MS/MS) with kinase activity inference. ResultsEGFR inhibitors preferentially impaired viability in EGFR-driven models and transiently reduced EGFR phosphorylation during the initial response. However, partial restoration of EGFR phosphorylation and downstream signaling occurred after 24 hours of inhibitor exposure. Phosphoproteomics revealed no evidence of broad kinome rewiring within this timeframe but instead identified increased EGFR abundance, associated with partial restoration of EGFR pathway activity. The phosphorylated-to-total EGFR ratio remained stable, indicating that increased EGFR abundance may enable persistent residual kinase activity despite continued, but incomplete, target inhibition. ConclusionsEarly responses to EGFR inhibition in GBM were not characterized by broad kinome rewiring but by restoration of EGFR signaling associated with increased EGFR abundance. These findings suggest that adaptive signaling remains largely EGFR-dependent despite inhibitor exposure, identifying regulation of EGFR abundance as a potential contributor to therapeutic resistance. Key points- Early responses to EGFR inhibition occur without evidence of broad kinome rewiring. - EGFR signaling is restored during sustained inhibitor exposure. - Increased EGFR abundance is associated with restoration of pathway activity. Importance of the studyAdaptive resistance to EGFR-targeted therapies in GBM is commonly attributed to activation of alternative signaling pathways. Using patient-derived GBM models and phosphoproteomic profiling, we show that early adaptive responses to EGFR inhibition are not characterized by broad kinome signaling rewiring but instead remain centered on reactivation of EGFR signaling. Our findings suggest that increased EGFR abundance in response to inhibitor exposure may enhance residual EGFR signaling sufficiently to partially restore downstream pathway activity. These results indicate that early adaptive responses to EGFR inhibition may remain largely EGFR-dependent, potentially limiting the effectiveness of strategies primarily aimed at co-targeting alternative signaling pathways. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=105 SRC="FIGDIR/small/744581v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@8d4ea3org.highwire.dtl.DTLVardef@125e3eeorg.highwire.dtl.DTLVardef@9742c0org.highwire.dtl.DTLVardef@9f4fa8_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2026

Progressive neuronal network reorganisation in glioblastoma drives pathological activity in vitro

Glioblastoma (GBM) is the most aggressive primary brain tumour and is frequently accompanied by severe neurological symptoms, including epilepsy and cognitive impairment. Neurological symptoms often persist after surgical resection, indicating that GBM induces durable and self-sustaining changes in the surrounding neuronal networks. However, the mechanisms by which GBM reshapes network structure and function in the tumour periphery remain poorly understood. We present a compartmentalised in vitro platform enabling long-term coculture of iPSC-derived neurons and primary GBM cells to investigate these changes. Placed on high-density microelectrode arrays, the platform permits longitudinal electrophysiological recordings at single-neuron resolution. Using effective network inference, we find that GBM drives a reproducible structural progression: first toward a hyperconnected, hub-dominated architecture, then a collapse of community structure accompanied by a widespread neuron loss. This evolving structure shapes population dynamics, constraining features such as network burst rate and instantaneous synchrony. The reorganisation also carries computational consequences: signal propagation becomes progressively redundant and synergistic rather than unique. As a result, neurons lose the capacity to encode distinct input combinations independently, and the repertoire of accessible network states contracts. Together, these findings reframe GBM as a driver of neuronal network reorganisation rather than uniform hyperexcitability, and establish a compartmentalised, single-neuron-resolution platform for the longitudinal observation, dissection, and ultimately targeting of the network processes that underlie disease progression.

neuroscience↗

bioRxiv2026

The brain-meningeal interface functions as a reservoir and entry site for brain parenchymal macrophages

Microglia are regarded as self-maintaining brain parenchymal macrophages without contribution from adult hematopoiesis. Nevertheless, peripheral macrophage engraftment into the brain has been reported, but the biological variables governing central nervous system (CNS) macrophage niche access remain unclear. We show that CNS macrophage engraftment is determined by the balance between tissue-resident macrophage (TRM) self-renewal and the temporal alignment of niche opening with the availability of engraftment-competent cells and proximity to the vacated niche, rather than prolonged niche vacancy. Fate mapping revealed that monocytes entering the subdural space undergo border-associated macrophage (BAM)-like differentiation, clonal expansion, and transpial migration into the parenchyma, whereas mature BAMs directly repopulate selectively vacated parenchymal niches. We further identify a parenchymal macrophage population with a peripheral BAM-like transcriptional program in aged and neurodegenerative human brains, challenging the dogma of MG-exclusivity. Together, these findings establish a predictive framework for interpreting macrophage maintenance and replacement and for developing macrophage-based therapies.

neuroscience↗

bioRxiv2026

'Zipper' Grammar of CTD Governs the Spatial Programing of the Transcription Cycle of RNA Polymerase II

RNA polymerase II transcribes all protein-coding genes in eukaryotes, with its C-terminal domain (CTD) acting as a regulatory platform throughout the transcription cycle. Despite its simple sequence, the conserved heptad repeats encode a regulatory grammar critical for transcription initiation, elongation, and termination. Using structural analysis, single-molecule imaging, and synthetic CTD-engineered Pol II constructs, we defined the minimal sequence requirements across transcriptional stages. We show that while SP motifs are essential phosphorylation sites, flanking residues tolerate variability. In contrast, the periodic positioning of tyrosine residues is indispensable for pre-initiation complex (PIC) assembly through interactions with the Mediator, which are disrupted upon Ser5 phosphorylation triggering promoter escape. This supports a "zipper" model where sequential tyrosine engagement stabilizes PIC assembly and progressive phosphorylation propels Pol II escape. Site-specific Ser2/5 phosphorylation orchestrates 3-end processing factor recruitment. These findings redefine the functional grammar of the Pol II CTD and explain how a low-complexity sequence achieves regulatory specificity.

cell biology↗

bioRxiv2025

Inflammatory cytokines promote interferon regulatory factor (IRF) transcriptional activity in human pulmonary epithelial cells through the induction of IRF1 by nuclear factor-κB

Transcription factors of the interferon regulatory factor (IRF) family play key roles during viral and bacterial infections. However, IRF regulation by inflammatory cytokines, including interleukin (IL)-1{beta} and tumor necrosis factor (TNF) , remains underexplored. Since airway epithelial cells (AECs) modulate lung inflammation, IRF expression was characterized in pulmonary A549 and bronchial BEAS-2B epithelial cells, plus primary human AECs grown in submersion or highly differentiated air-liquid interface culture. Whereas most IRF mRNAs were expressed across models, IRF4 and IRF8 showed consistently low expression, and IRF6 was only expressed highly in primary cells. IRF3 and IRF9 were highly expressed in each model, and while protein expression was confirmed in A549 cells, this remained primarily cytoplasmic post-IL-1{beta} treatment. IRF2 was constitutively nuclear in A549 cells and showed moderate/high mRNA expression in each model. IRF1 mRNA was induced by IL-1{beta}-in primary and A549 cells, where IL-1{beta} and TNF dramatically increased IRF1 protein expression. TNF also increased IRF1 protein in BEAS-2B cells. In A549 cells, an IRF reporter system combined with RNA silencing did not support transcriptional roles for IRF2 or IRF3 but suggested a modest role for IRF9 following IL-1{beta} stimulation. IL-1{beta}-induced IRF1 localized to the nucleus of A549 cells revealing a major transcriptional role. IRF1 expression induced by IL-1{beta}/TNF required NF-{kappa}B and four novel 5' enhancer regions to IRF1 bound the NF-{kappa}B subunit, p65. These regions drove IL-1{beta}/TNF-inducible reporter activity via consensus NF-{kappa}B motifs. Three such regions recruited RNA polymerase-2 and were flanked by the active chromatin mark, histone 3 lysine 27 acetylation which, given the high levels of genetic conservation, support involvement in IRF1 transcription. Finally, IRF1 expression, transcription rate, and enhancer activity induced by IL-1{beta}/TNF were relatively unaffected by glucocorticoid co-treatment. IRF1-dependent gene expression could therefore be insensitive to glucocorticoid and may contribute to glucocorticoid-resistant diseases such as severe asthma.

molecular biology↗

bioRxiv2024

Full-length tRNAs lacking a functional CCA tail are selectively sorted into the lumen of extracellular vesicles

Small extracellular vesicles (sEVs) are heterogenous lipid membrane particles typically less than 200 nm in size and secreted by most cell types either constitutively or upon activation signals. sEVs isolated from biofluids contain RNAs, including small non-coding RNAs (ncRNAs), that can be either encapsulated within the EV lumen or bound to the EV surface. EV-associated microRNAs (miRNAs) are, despite a relatively low abundance, extensively investigated for their selective incorporation and their role in cell-cell communication. In contrast, the sorting of highly-structured ncRNA species is understudied, mainly due to technical limitations of traditional small RNA sequencing protocols. Here, we adapted ALL-tRNAseq to profile the relative abundance of highly structured and potentially methylated small ncRNA species, including transfer RNAs (tRNAs), small nucleolar RNAs (snoRNAs), and Y RNAs in bulk EV preparations. We determined that full-length tRNAs, typically 75 to 90 nucleotides in length, were the dominant small ncRNA species (>60% of all reads in the 18-120 nucleotides size-range) in all cell culture-derived EVs, as well as in human plasma-derived EV samples, vastly outnumbering 21 nucleotides-long miRNAs. Nearly all EV-associated tRNAs were protected from external RNAse treatment, indicating a location within the EV lumen. Strikingly, the vast majority of luminal-sorted, full-length, nucleobase modification-containing EV-tRNA sequences, harbored a dysfunctional 3 CCA tail, 1 to 3 nucleotides truncated, rendering them incompetent for amino acid loading. In contrast, in non-EV associated extracellular particle fractions (NVEPs), tRNAs appeared almost exclusively fragmented or nicked into tRNA-derived small RNAs (tsRNAs) with lengths between 18 to 35 nucleotides. We propose that in mammalian cells, tRNAs that lack a functional 3 CCA tail are selectively sorted into EVs and shuttled out of the producing cell, offering a new perspective into the physiological role of secreted EVs and luminal cargo-selection.

molecular biology↗

bioRxiv2023

Enhancing anti-EGFRvIII CAR T cell therapy against glioblastoma with a paracrine SIRPγ-derived CD47 blocker

A major challenge for chimeric antigen receptor (CAR) T cell therapy against glioblastoma (GBM) is its immunosuppressive tumor microenvironment (TME), which is densely populated and supported by protumoral glioma-associated microglia and macrophages (GAMs). Targeting of CD47, a "dont-eat-me" signal overexpressed by tumor cells, disrupts the CD47-SIRP axis and induces GAM phagocytic function. However, antibody-mediated CD47 blockade monotherapy is associated with toxicity and low bioavailability in solid tumors. To overcome these limitations, we combined local CAR T cell therapy with paracrine GAM modulation for more effective elimination of GBM. To this end, we engineered a new CAR T cell against epidermal growth factor receptor variant III (EGFRvIII) that constitutively secretes a SIRP{gamma}-related protein (SGRP) with high affinity to CD47. Anti-EGFRvIII-SGRP CAR T cells eliminated EGFRvIII+ GBM in a dose-dependent manner in vitro and eradicated orthotopically xenografted EGFRvIII-mosaic GBM by locoregional application in vivo. This resulted in significant tumor-free long-term survival, followed by partial tumor control upon tumor re-challenge. The combination of anti-CD47 antibodies with anti-EGFRvIII CAR T cells failed to achieve a similar therapeutic effect, underscoring the importance of sustained paracrine GAM modulation. Multidimensional brain immunofluorescence microscopy and in-depth spectral flow cytometry on GBM-xenografted brains showed that anti-EGFRvIII-SGRP CAR T cells accelerated GBM clearance, increased CD68+ cell trafficking to tumor scar sites, and induced myeloid-mediated tumor cell uptake. Additionally, in a peripheral lymphoma mouse xenograft model, anti-CD19-SGRP CAR T cells had superior efficacy compared to conventional anti-CD19 CAR T cells. Validation on human GBM explants revealed that anti-EGFRvIII-SGRP CAR T cells had similar tumor-killing capacity to anti-EGFRvIII CAR monotherapy, but showed a slight improvement in maintenance of tumor-infiltrated CD14+ myeloid cells. Thus, local anti-EGFRvIII-SGRP CAR T cell therapy combines the potent antitumor effect of engineered T cells with the modulation of the surrounding innate immune TME, resulting in the additive elimination of bystander EGFRvIII- tumor cells in a manner that overcomes major mechanisms of CAR T cell therapy resistance, including tumor innate immune suppression and antigen escape.

cancer biology↗

bioRxiv2023

Multidimensional analysis of matched primary and recurrent glioblastoma identifies Fcgamma receptors upregulation on microglia as a contributor of tumor recurrence.

O_LIBackground: Glioblastoma (GBM) is a lethal brain tumor without effective treatment options. The aim of this study was to characterize longitudinal tumor immune microenvironment (iTME) changes in order to find potential actionable targets to prevent GBM-induced immune evasion mechanisms. C_LIO_LIMethods: This study included 15 patient-matched treatment-naive WHO grade 4 primary (pGBM) and recurrent (rGBM) tumors. RNA and proteins extracted from fresh frozen tumor samples from matched pGBM and rGBM were profiled via transcriptomics and proteomics, respectively. A tissue microarray containing paired formalin-fixed paraffin-embedded tumor samples was processed for spatial transcriptomics analysis. C_LIO_LIResults: Differentially expressed genes and proteins between pGBM and rGBM were involved in pathways responsible for synapse development and myelination which have been shown to play a role in GBM recurrence. By categorizing patients into short and long time-to-relapse (STTR vs LTTR), we identified genes positively or negatively associated with TTR. Expression of Fc{gamma} receptors and complement system genes such as FCGR1A (CD64), FCGR3A and C3 in rGBM samples were negatively correlated with TTR, whereas expression of DNMT1/3A, and SMARCA4, involved in DNA methylation, were positively correlated with TTR. Spatial transcriptomic analysis of the tumor cell compartment showed enrichment of oligodendrocytes in rGBM, whereas the myeloid cell compartment switched from quiescent to activated microglia, was enriched in B and T cells, specifically in rGBM with STTR. C_LIO_LIConclusions: Our results uncover a role for CD64-expressing activated microglia in GBM recurrence and suggest that interfering with these cells may represent a therapeutic option for hindering GBM relapse. C_LI Key pointsO_LITranscriptomic and proteomic differences exist between patient-paired primary and recurrent GBM tumors C_LIO_LIHigh expression of Fcy receptors genes on activated microglia at tumor recurrence is associated with shorter time to relapse. C_LI Importance of this studyIn glioblastoma (GBM), the tumor recurs in almost all cases after standard treatment such as surgery and chemo-radiotherapy. In this study, we longitudinally evaluated the immune- and neoplastic compartments using transcriptomic, proteomic, and spatial transcriptomics in patient-matched treatment-naive and recurrent tumor samples. By correlating gene expression with time-to-relapse, we identified a geneset associated with treatment resistance and faster tumor recurrence. Moreover, this study highlighted the plasticity of the myeloid compartment during disease progression and an unfavorable role of activated microglia in tumor recurrence.

cancer biology↗

bioRxiv2021

Microthrombocytopenia caused by impaired microtubule stability in RhoB-deficient mice

Megakaryocytes are large cells in the bone marrow, which give rise to blood platelets. Platelet biogenesis involves megakaryocyte maturation, the localization of mature cells in close proximity to bone marrow sinusoids and the formation of protrusions, which are shed into the circulation. Rho GTPases play important roles in platelet biogenesis and function. RhoA-deficient mice display macrothrombocytopenia and a striking mislocalization of megakaryocytes into bone marrow sinusoids and a specific defect in G-protein signaling in platelets. However, the role of the closely related protein RhoB in megakaryocytes or platelets remains unknown. In this study, we show that, in contrast to RhoA deficiency, genetic ablation of RhoB in mice results in microthrombocytopenia (decreased platelet count and size). RhoB-deficient platelets displayed mild functional defects predominantly upon induction of the collagen/glycoprotein VI pathway. Megakaryocyte maturation and localization within the bone marrow, as well as actin dynamics were not affected in the absence of RhoB. However, in vitro generated proplatelets revealed pronouncedly impaired microtubule organization. Furthermore, RhoB-deficient platelets and megakaryocytes displayed selective defects in microtubule dynamics/stability, correlating with pronouncedly reduced levels of acetylated -tubulin. Our findings imply that absence of this tubulin posttranslational modification results in decreased microtubule stability leading to microthrombocytopenia in RhoB-deficient mice. Our data thus points to specifically impaired microtubule - but not actin - dynamics as a general mechanism underlying the manifestation of microthrombocytopenia in vivo. We furthermore demonstrate that RhoA and RhoB have specific, non-redundant functions in the megakaryocyte lineage. KEY POINTSO_LIRhoB-deficient mice display microthrombocytopenia C_LIO_LIRhoB has different functions in the megakaryocyte lineage than RhoA and regulates microtubule dynamics C_LI

cell biology↗

bioRxiv2021

Quality-preserving low-cost probabilistic 3D denoising with applications to Computed Tomography

We propose a pipeline for a synthetic generation of personalized Computer Tomography (CT) images, with a radiation exposure evaluation and a lifetime attributable risk (LAR) assessment. We perform a patient-specific performance evaluation for a broad range of denoising algorithms (including the most popular Deep Learning denoising approaches, wavelets-based methods, methods based on Mumford-Shah denoising etc.), focusing both on accessing the capability to reduce the patient-specific CT-induced LAR and on computational cost scalability. We introduce a parallel probabilistic Mumford-Shah denoising model (PMS), showing that it markedly-outperforms the compared common denoising methods in denoising quality and cost scaling. In particular, we show that it allows an approximately 22-fold robust patient-specific LAR reduction for infants and a 10-fold LAR reduction for adults. Using a normal laptop the proposed algorithm for PMS allows a cheap and robust (with the Multiscale Structural Similartity index > 90%) denoising of very large 2D videos and 3D images (with over 107 voxels) that are subject to ultra-strong Gaussian and various non-Gaussian noises, also for Signal-to-Noise Ratios much below 1.0. The code is provided for open access. One-sentence summaryProbabilisitc formulation of Mumford-Shah principle (PMS) allows a cheap quality-preserving denoising of ultra-noisy 3D images and 2D videos.

bioinformatics↗

bioRxiv2021

The genome sequence of the cereal pest Sitophilus oryzae: an unprecedented transposable element content

BackgroundThe rice weevil Sitophilus oryzae is one of the most important agricultural pests, causing extensive damage to cereal in fields and to stored grains. S. oryzae has an intracellular symbiotic relationship (endosymbiosis) with the Gram-negative bacterium Sodalis pierantonius and is a valuable model to decipher host-symbiont molecular interactions. ResultsWe sequenced the Sitophilus oryzae genome using a combination of short and long reads to produce the best assembly for a Curculionidae species to date. We show that S. oryzae has undergone successive bursts of transposable element (TE) amplification, representing 72% of the genome. In addition, we show that many TE families are transcriptionally active, and changes in their expression are associated with insect endosymbiotic state. S. oryzae has undergone a high gene expansion rate, when compared to other beetles. Reconstruction of host-symbiont metabolic networks revealed that, despite its recent association with cereal weevils (30 Kyear), S. pierantonius relies on the host for several amino acids and nucleotides to survive and to produce vitamins and essential amino-acids required for insect development and cuticle biosynthesis. ConclusionsHere we present the genome of an agricultural pest beetle, which may act as a foundation for pest control. In addition, S. oryzae may be a useful model for endosymbiosis, and studying TE evolution and regulation, along with the impact of TEs on eukaryotic genomes.

genomics↗

bioRxiv2020

A histone-like motif in yellow fever virus contributes to viral replication

The mimicry of host proteins by viruses contributes to their ability to suppress antiviral immunity and hijack host biosynthetic machinery1. Host adaptation to evade this exploitation depends on host protein functional redundancy2. Non-redundant, essential host proteins have limited potential to adapt without severe consequences3. Histones, which are essential for genome architecture and control of gene expression, are among the most evolutionary conserved proteins4. Here we show that the capsid protein of the flavivirus yellow fever virus (YFV), mimics histone H4 and interferes with chromatin gene regulation by BRD4, a bromodomain and extraterminal domain (BET) protein. Two acetyl-lysine residues of YFV capsid are embedded in a histone-like motif that interacts with the BRD4 bromodomain, affecting gene expression and influencing YFV replication. These findings reveal histone mimicry as a strategy employed by an RNA virus that replicates in the cytosol5 and define convergent and distinct molecular determinants for motif recognition of the viral mimic versus histone H4.

microbiology↗

bioRxiv2019

Mapping the evolutionary landscape of Zika virus infection in immunocompromised mice.

The fundamental basis of how arboviruses evolve in nature and what regulates the adaptive process remain unclear. To address this problem, we established a Zika virus (ZIKV) vector-borne transmission system in immunocompromised mice that mimics evolutionary characteristics of ZIKV infection in humans. Using this system, we defined factors that influence the evolutionary landscape of ZIKV infection and show that transmission route and specific organ microenvironments impact viral diversity and defective viral genome (DVG) production. In addition, we identified in mice the emergence of ZIKV mutants previously seen in natural infections, including variants present in currently circulating strains, as well as mutations unique to the mouse infections. With these studies, we have established an insect-to-mouse transmission model to study ZIKV evolution. We also defined how organ microenvironments and infection route impact the ZIKV evolutionary landscape, providing a deeper understanding of the factors that regulate arbovirus evolution and emergence.

microbiology↗

bioRxiv2019

Beyond Conventional Models: Recreating the Initiation, Evolution, and Genome of GBM

BackgroundImagining ways to prevent or treat glioblastoma (GBM) have been hindered by a lack of understanding of its pathogenesis. Although PDGF-AA overexpression may be an early event, critical details of the core biology are lacking. Existing PDGF-driven models replicate its microscopic appearance but not the genomic architecture characteristic of the human disease. Here we report a new model of GBM that overcomes this barrier to authenticity. MethodsUsing a method developed to study neural stem cells, we investigated the effects of PDGF-AA on subventricular zone (SVZ) cells, the putative cell of origin of GBM. We micro-dissected SVZ tissue from p53-null and wild-type adult mice, established primary cultures in media supplemented with PDGF-AA, and assessed cell viability, proliferation, genome stability, and tumour forming potential. ResultsCounterintuitive to its canonical role as a growth factor, we observed immediate and massive death of SVZ cells in PDGF-AA. Wild-type cells did not survive in PDGF-AA. However, a small fraction of null cells evaded apoptosis, displayed attenuated proliferation, gradually accumulated whole chromosome gains and losses, and, signalled by sudden rapid proliferation and growth factor independence, became tumorigenic in immune-competent syngeneic mice. Transformed cells had an OPC-like profile, were resistant to PDGFR- inhibition, and harboured highly abnormal karyotypes similar to those seen in human GBMs. ConclusionThis model associates genome instability in SVZ cells with chronic exposure to PDGF-AA; it is the first model to replicate the genomic landscape of GBM and first in which the earliest phases of GBM can be directly observed. IMPORTANCE OF STUDYWe have developed a mouse model in which the initiation, evolution and genomic landscape of GBM can be thoroughly studied thus paving the way for ideas about how this deadly brain cancer might be prevented, interrupted at an occult stage, or treated with very different therapies.

cancer biology↗

bioRxiv2019

Induced RPB1 depletion reveals a direct gene-specific control of RNA Polymerase III function by RNA Polymerase II

Increasing evidence suggests that tRNA levels are dynamically and specifically regulated in response to internal and external cues to modulate the cellular translational program. However, the molecular players and the mechanisms regulating the gene-specific expression of tRNAs are still unknown. Using an inducible auxin-degron system to rapidly deplete RPB1 (the largest subunit of RNA Pol II) in living cells, we identified Pol II as a direct gene-specific regulator of tRNA transcription. Our data suggest that Pol II transcription robustly interferes with Pol III function at specific tRNA genes. This activity was further found to be essential for MAF1-mediated repression of a large set of tRNA genes during serum starvation, indicating that repression of tRNA genes by Pol II is dynamically regulated. Hence, Pol II plays a direct and central role in the gene-specific regulation of tRNA expression.

molecular biology↗