Biology subjects

Niepel, M.

Publications and source records attributed to Niepel, M..

10 recordsLinked to original sources

bioRxiv2025

Integrative multi-omics reveals PARP14 as a key IFNγ-regulated mediator of metastatic progression in Ewing sarcoma.

Metastatic Ewing sarcoma (EwS) remains a major clinical challenge, highlighting the need to identify molecular drivers of disease dissemination. Through integrated transcriptomic, functional, and mechanistic analyses, we identify PARP14 as a key regulator of EwS metastatic progression. PARP14 is consistently upregulated in metastatic lesions across spontaneous and xenograft mouse models as well as in patient samples. Genetic and pharmacologic depletion of PARP14 (via siRNA knockdown, CRISPR-Cas9 knockout, or PROTAC-mediated degradation) significantly impaired EwS cell migration and invasion in vitro, without affecting proliferation or clonogenic capacity. In vivo, PARP14 loss delayed tumor growth and reduced metastatic burden, supporting a functional role in disease progression. Conversely, IFN{gamma}-induced PARP14 upregulation and stable overexpression enhanced EwS cell migration and increased lung metastasis formation. Transcriptomic profiling of PARP14-deficient cells revealed downregulation of invasive signatures and enrichment of inflammatory and p53-related pathways, together with gene sets associated with chromatin remodeling. Subcellular fractionation and interactome analyses showed that PARP14 localizes to cytoplasmic, nuclear, and chromatin-associated compartments, and interacts with chromatin, cytoskeletal and ECM regulators. ChlP analyses further demonstrated PARP14 binding to promoters enriched for NRF1 motifs, suggesting a role as a transcriptional co-regulator influencing gene networks relevant to EwS progression. Together, our results establish PARP14 as a contributor to EwS dissemination and uncover a previously unappreciated chromatin-associated role for this protein, supporting its potential as both a biomarker and therapeutic target in metastatic EwS. STATEMENT OF SIGNIFICANCEWe identify PARP14 as a novel driver of Ewing sarcoma metastasis through integrated multi-omics profiling. Genetic and pharmacological interrogation establishes PARP14 as a promising therapeutic target for this understudied malignancy.

cancer biology↗

bioRxiv2024

Combined PARP14 Inhibition and PD-1 Blockade Promotes Cytotoxic T Cell Quiescence and Modulates Macrophage Polarisation in Relapsed Melanoma

Programmed Cell Death 1 (PD-1) signaling blockade effectively restores immune surveillance to treat melanoma. However, chronic interferon-gamma (IFN{gamma}) -driven immune homeostatic mechanisms in melanoma cells contribute to immune evasion and acquired resistance. We previously demonstrated that poly ADP ribosyl polymerase 14 (PARP14), an IFN{gamma}-responsive gene product, in part mediates IFN{gamma}-driven resistance, as its inhibition prolonged PD-1 blockade responses in preclinical models. Nevertheless, PARP14 inhibition alone could not achieve full tumor clearance, indicating additional resistance mechanisms. Herein, we identify a robust PARP14 catalytic inhibitor (PARP14i) gene signature associated with improved patient survival. We elucidate immune and tumor cell adaptations to PARP14 inhibition combined with PD-1 blockade using preclinical models. This combination therapy suppressed tumor-associated macrophages while increasing pro-inflammatory memory macrophages. Notably, it preserved cytotoxic T cell function by inducing a quiescent state, mitigating terminal exhaustion. Despite enhancing immune responses, adaptive resistance mechanisms emerged in tumor cells, engaging alternative immune evasion pathways. These findings indicate that this combination therapy primes immune cells for further therapeutic intervention, providing a promising strategy to overcome resistance and optimize treatment outcomes. SummaryWhile immune checkpoint inhibitors, such as -PD-1 therapy, provide significant clinical benefits, many tumors develop resistance and relapse. Re-treatment with -PD-1 often fails because T cells lose their function (a process called exhaustion), and immune-suppressing cells like tumor-associated macrophages (TAMs) increase in the tumor environment, enabling tumors to evade immune attack. Recent studies have shown that a small molecule inhibitor of PARP14 can restore sensitivity to -PD-1 therapy by remodeling the tumor environment. This includes increasing immune cell infiltration and improving antigen presentation, which helps the immune system recognize tumor cells. Using single-cell RNA sequencing, we discovered that this therapy induces a new state of T cell dormancy, where cytotoxic T cells temporarily stop attacking but retain the potential to be reactivated by additional treatments. This finding opens new opportunities to sustain immune responses and improve outcomes for patients who relapse after immunotherapy. Graphical Summary O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=133 SRC="FIGDIR/small/615178v2_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@1e6dcf4org.highwire.dtl.DTLVardef@1b44548org.highwire.dtl.DTLVardef@309cb1org.highwire.dtl.DTLVardef@17f6202_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2022

PARP14 inhibition restores PD-1 immune checkpoint inhibitor response following IFNγ-driven adaptive resistance

Adaptive resistance limits immune checkpoint blockade therapy (ICBT) response duration and magnitude. Interferon {gamma} (IFN{gamma}), a critical cytokine that promotes cellular immunity, also induces adaptive resistance to ICBT. Using syngeneic mouse tumour models, we confirmed that chronic IFN{gamma} exposure confers resistance to anti-Programmed cell death protein 1 (-PD-1) therapy. We identified consistent upregulation of poly-ADP ribosyl polymerase 14 (PARP14) in both chronic IFN{gamma}-treated cancer cells and patient melanoma with elevated IFNG expression. Knockdown or pharmacological inhibition of PARP14 increased effector T cell infiltration into tumours derived from cells pre-treated with IFN{gamma} and decreased the presence of regulatory T cells, leading to restoration of -PD-1 sensitivity. Finally, we determined that tumours which spontaneously relapsed following -PD-1 therapy could be re-sensitised upon receiving PARP14 inhibitor treatment, establishing PARP14 as an actionable target to reverse IFN{gamma}-driven ICBT resistance.

cancer biology↗

bioRxiv2021

Multiplexed and reproducible high content screening of live and fixed cells using the Dye Drop method

High-throughput measurement of cells perturbed using libraries of small molecules, gene knockouts, or different microenvironmental factors is a key step in functional genomics and pre-clinical drug discovery. However, it remains difficult to perform accurate single-cell assays in 384-well plates, limiting many studies to well-average measurements (e.g. CellTiter-Glo(R)). Here we describe a public domain "Dye Drop" method that uses sequential density displacement and microscopy to perform multi-step assays on living cells. We use Dye Drop cell viability and DNA replication assays followed by immunofluorescence imaging to collect single-cell dose-response data for 67 investigational and clinical-grade small molecules in 58 breast cancer cell lines. By separating the cytostatic and cytotoxic effects of drugs computationally, we uncover unexpected relationships between the two. Dye Drop is rapid, reproducible, customizable, and compatible with manual or automated laboratory equipment. Dye Drop improves the tradeoff between data content and cost, enabling the collection of information-rich perturbagen-response datasets.

systems biology↗

bioRxiv2021

Selective pharmaceutical inhibition of PARP14 mitigates allergen-induced IgE and mucus overproduction in a mouse model of pulmonary allergic response

The type 2 cytokines IL-4 and IL-13, which share use of an IL-4 receptor alpha chain and its nuclear induction of the transcription factor STAT6, are crucial in elicitation and maintenance of allergic conditions that include asthma. Prior work has shown a physical and functional association of STAT6 with PARP14, an ADP-ribosyl monotransferase. Moreover, elimination of all PARP14 expression by gene targeting led to altered recall antibody responses and attenuation of ovalbumin-specific allergic lung inflammation with no apparent health issues for mice lacking this protein. However, an unanswered question is whether or not inhibition of the catalytic function has any biological consequence since PARP14 has multiple functional domains apart from the portion that catalyzes ADP-ribosylation. As reported separately, iterative structural analyses and medicinal chemistry fostered the generation of a compound, RBN2759, that is highly selective in its inhibition of PARP14 with negligible impact on other members of the PARP gene family. We show here that administration of this compound to mice previously sensitized to the allergen Alternaria alternata achieved biochemically active levels and altered physiological responses to the antigen. These results show for the first time that in vivo administration of a specific inhibitor of the ADP-ribosyltransferase activity encoded by PARP14 is sufficient to alter biological responses. Specifically, the orally absorbable pharmaceutical compound decreased allergen-induced mucus, blunted the induced increases in circulating IgE, and prevented suppression of IgG2a. We conclude that the catalytic activity can contribute to pathogenesis in allergic processes and propose that other biological endpoints that depend on ADP-ribosylation by PARP14 can be targeted using selective inhibition.

immunology↗

bioRxiv2019

Combined inhibition of mTOR and PIKKs exploits replicative and checkpoint vulnerabilities to induce death of PI3K-activated triple-negative breast cancer cells

SUMMARY SUMMARY HIGHLIGHTS INTRODUCTION RESULTS DISCUSSION FUNDING AUTHOR CONTRIBUTIONS STAR METHODS Cell lines METHOD DETAILS Western blotting Evaluation of drug sensitivity Immunofluorescence microscopy Primary antibodies and dilutions Single-stranded DNA ssDNA and... Live cell microscopy Extraction of polar metabolites Metabolomics profiling by... Isobolograms and analysis of... Cell cycle model and... QUANTIFICATION AND STATISTICAL... Viable cell counts ...

cancer biology↗

bioRxiv2017

A multi-center study on factors influencing the reproducibility of in vitro drug-response studies

Evidence that some influential biomedical results cannot be repeated has increased interest in practices that generate data meeting findable, accessible, interoperable and reproducible (FAIR) standards. Multiple papers have identified examples of irreproducibility, but practical steps for increasing reproducibility have not been widely studied. Here, seven research centers in the NIH LINCS Program Consortium investigate the reproducibility of a prototypical perturbational assay: quantifying the responsiveness of cultured cells to anti-cancer drugs. Such assays are important for drug development, studying cell biology, and patient stratification. While many experimental and computational factors have an impact on intra- and inter-center reproducibility, the factors most difficult to identify and correct are those with a strong dependency on biological context. These factors often vary in magnitude with the drug being analyzed and with growth conditions. We provide ways of identifying such context-sensitive factors, thereby advancing the conceptual and practical basis for greater experimental reproducibility.

cancer biology↗

bioRxiv2017

Rapid isolation of functionally intact nuclei from the yeast Saccharomyces

Most available methods for nuclear isolation entail lengthy procedures that are difficult to master and generally emphasize yield and enrichment over nuclear preservation, thus limiting their utility for further studies. Here we demonstrate a novel and robust method to rapidly isolate well-preserved yeast nuclei. The method can be easily adapted to multiple preparation scales depending on experimental need and it can readily be performed on multiple samples by a single researcher in one day. We show that the nuclei fraction is strongly enriched and that the resulting nuclei are free from contaminating endoplasmatic reticulum and other cell debris. EM studies show that preservation of nuclear morphology is exquisite, making it possible to study peripheral nuclear pore components such as the cytoplasmic filaments and the basket, whose structure is generally difficult to maintain ex vivo. In addition, incubation of isolated nuclei with bulk transport substrates of different sizes and with import cargo indicates that the nuclear envelope is intact and nuclear pores retain their capacity to bind transport substrates. Our results suggest that this preparation procedure will greatly facilitate studies of the yeast nucleus which have been difficult to establish and to multiplex to date.

cell biology↗

bioRxiv2017

Receptor-Based Mechanism of Relative Sensing in Mammalian Signaling Networks

Detecting relative rather than absolute changes in external signals enables cells to make decisions in fluctuating environments and diverse biological contexts. However, how mammalian signaling networks store the memories of past stimuli and use them to compute relative signals is not well understood. Using the growth factor-activated PI3K-Akt signaling pathway, we develop computational and analytical models, and experimentally validate a novel mechanism of relative sensing in mammalian cells. This non-transcriptional mechanism relies on a new form of cellular memory, where cells effectively encode past stimulation levels in the abundance of cognate receptors on the cell surface. We show the robustness and specificity of the relative sensing for two physiologically important ligands, epidermal growth factor (EGF) and hepatocyte growth factor (HGF), and across wide ranges of background stimuli. The described memory and sensing mechanism could play a role in multiple other sensory cascades where stimulation leads to a proportional reduction in the abundance of cell surface receptors.

systems biology↗

bioRxiv2017

Maximum Entropy Framework For Inference Of Cell Population Heterogeneity In Signaling Networks

Predictive models of signaling networks are essential tools for understanding cell population heterogeneity and designing rational interventions in disease. However, using network models to predict signaling dynamics heterogeneity is often challenging due to the extensive variability of signaling parameters across cell populations. Here, we describe a Maximum Entropy-based fRamework for Inference of heterogeneity in Dynamics of sIgAling Networks (MERIDIAN). MERIDIAN allows us to estimate the joint probability distribution over signaling parameters that is consistent with experimentally observed cell-to-cell variability in abundances of network species. We apply the developed approach to investigate the heterogeneity in the signaling network activated by the epidermal growth factor (EGF) and leading to phosphorylation of protein kinase B (Akt). Using the inferred parameter distribution, we also predict heterogeneity of phosphorylated Akt levels and the distribution of EGF receptor abundance hours after EGF stimulation. We discuss how MERIDIAN can be generalized and applied to problems beyond modeling of heterogeneous signaling dynamics.

systems biology↗