Biology subjects

Wolfrum, E.

Publications and source records attributed to Wolfrum, E..

8 recordsLinked to original sources

bioRxiv2026

NF1 splicing reprograms ERα signaling to promote luminal breast cancer progression

Alternative splicing is an emerging driver of cancer progression, yet its role in modulating tumor suppressor function remains incompletely understood. Here, we identify an alternatively spliced NF1 isoform lacking the nuclear localization sequence (NLS; NLS SE) as a clinically and functionally relevant regulator of breast cancer progression. Analysis of TCGA and AURORA cohorts revealed that NF1 NLS SE is enriched in metastatic tumors, preferentially occurs in luminal subtypes, and is associated with decreased overall survival independent of NF1 genomic alterations. Using a CRISPR-engineered MCF7 model, we show that NLS SE expression abolishes nuclear localization of neurofibromin, enhances ERK signaling, and promotes proliferation and resistance to endocrine and MAPK-targeted therapies. Despite increased ER protein levels, transcriptomic analysis revealed suppression of canonical estrogen response programs and activation of KRAS, EMT, and inflammatory pathways. Mechanistically, NLS SE expression increased RNA-bound ER and reprogrammed RNA binding protein networks, including CELF, ESRP1, and SRSF family members, leading to widespread alternative splicing. Together, these findings define NF1 NLS exon skipping as a luminal breast cancer-associated, isoform-level mechanism that disrupts nuclear neurofibromin function, rewires ER signaling towards post-transcriptional regulation, and promotes endocrine-resistant disease. Targeting splicing regulatory networks may represent a therapeutic strategy in NF1-dysregulated breast cancer. O_FIG O_LINKSMALLFIG WIDTH=192 HEIGHT=200 SRC="FIGDIR/small/726647v1_ufig1.gif" ALT="Figure 1"> View larger version (59K): org.highwire.dtl.DTLVardef@d507dborg.highwire.dtl.DTLVardef@1f6f6c9org.highwire.dtl.DTLVardef@c42e1corg.highwire.dtl.DTLVardef@1af38dd_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical Abstract.C_FLOATNO NF1 NLS exon skipping drives cytoplasmic retention of neurofibromin and reprograms ER toward post-transcriptional regulatory functions. (A) In cells expressing NLS-containing NF1 isoforms, neurofibromin localizes to the nucleus and constrains ER activity. (B-C) Alternative splicing of the NF1 NLS exon generates the NLS SE isoform, resulting in cytoplasmic retention of neurofibromin. This shift disrupts canonical ER signaling and is associated with increased ER phosphorylation and enhanced RNA-binding activity. ER engages RNA and cooperates with splicing machinery, including phosphorylated SF3B1, to promote transcriptomic remodeling. These changes support a therapy-resistant state characteristic of aggressive, endocrine-resistant breast cancer. C_FIG

cancer biology↗

bioRxiv2025

YAP signaling promotes resistance to MEK and AKT inhibition in NF1-related MPNSTs

Neurofibromatosis type 1 (NF1) is a tumor predisposition syndrome caused by loss of function of the neurofibromin protein. Malignant peripheral nerve sheath tumors (MPNSTs) are a rare and deadly sarcoma with few therapeutic options that are the leading cause of death for patients with NF1. To date, no targeted therapies have been approved for MPNST treatment, highlighting the need for an understanding of adaptive signaling mechanisms that drive resistance. We developed a preclinical model of drug resistance using a cross-over drug holiday design and evaluated patterns of response and resistance to MEK and AKT inhibitors, two pathways that are dysregulated by loss of neurofibromin. We show that the mTOR and YAP/TEAD pathways are activated by MEK inhibitor exposure, yet blockade of these pathways in resistant MPNST PDX models does not significantly reduce tumor growth, despite strong in vitro synergy between trametinib and the novel TEAD inhibitor, GNE-7883. Using spatial transcriptomics, we uncovered phenotypic inertia as a key mechanism of drug resistance in MPNST, in addition to signaling plasticity. Further, we found that resistance is mediated by sustained ERK, YAP, and MYC driven transcriptional programs. In the future, preclinical studies should focus on addressing intratumoral heterogeneity and how it evolves over time.

cancer biology↗

bioRxiv2025

Oocyte mitochondria link maternal environment to offspring phenotype

During oogenesis and maturation oocytes undergo a recently discovered mitochondrial electron transport chain (ETC) remodeling in flies1, frogs1, and humans2. This conserved oocyte ETC remodeling is regulated by maternal insulin signaling, but its role in biology remains unclear. In the model animal Caenorhabditis elegans, we previously found that insulin signaling to oocytes regulates offsprings ability to adapt to future osmotic stress by altering offspring metabolism. However, the molecular mechanisms that function in oocytes to mediate this intergenerational stress response are similarly unknown. Here, we developed a low-input oocyte proteomics workflow and combined it with our C. elegans intergenerational stress response model to find that both a mothers environment and maternal insulin signaling regulate the abundance of ETC proteins in oocytes - particularly the abundance of proteins involved in the transfer of electrons from QH2 to cytochrome C by ETC Complex III. Using genetic perturbations of ETC function we further found that promoting ETC Complex III function in oocytes was both necessary and sufficient to link a mothers environment to adaptive changes in offspring metabolism. Lastly, we found that the effects of Complex III dysfunction in oocytes on offspring were mediated via an AMP-kinase (AAK-2) dependent mechanism and that AAK-2 functions in offspring to promote ATP preservation and glycerol metabolism in response to stress. Collectively, our data suggest that the role of oocyte ETC remodeling in biology includes linking maternal environments to changes in offspring metabolism that promote offspring survival in the environment experienced by their mother.

genetics↗

bioRxiv2024

Engineering ERα degraders with pleiotropic ubiquitin ligase ligands maximizes therapeutic efficacy by co-opting distinct effector ligases

Proximity-inducing compounds that modulate target protein homeostasis are an emerging therapeutic strategy [1]. While the inherent complexity of these bifunctional compounds poses challenges for rational design and bioavailability, their composition also provides opportunities to co-opt specific cellular proteins to maximize therapeutic impact. Here, we systematically evaluate the cellular efficacy, biophysical mechanisms, and therapeutic benefits of a series of bifunctional degrader compounds, that are all engineered with the Estrogen Receptor-alpha (ER)-inhibitor endoxifen linked to different bioactive ubiquitin ligase ligands. Bifunctional ER degraders that incorporate CRL4-CRBN-binding ligands promoted the most potent ER degradation, whereas those incorporating either CRL2-VHL- or IAP-binding ligands maximized the depth of ER degradation. Notably, ER degraders containing pan-IAP antagonist ligands significantly decreased the proliferation of ER-dependent cells relative to clinical-stage ER-degraders, including the SERDs fulvestrant and GDC-9545 and the bifunctional degrader ARV-471. Mechanistic studies revealed that pan-IAP antagonist-based ER degraders uniquely promote TNF-dependent cell death, unlike the clinical-stage comparators. Remarkably, the pan-IAP antagonist-ER-degraders co-opt distinct effector ligases to achieve dual therapeutic effects: they harness XIAP within tumor cells to promote ER degradation, and activate cIAP1/2 within tumor and immune cells to induce TNF that drives tumor cell death. Our studies demonstrate a broader concept that co-opting the discrete functions of a selected set of cellular effectors, while simultaneously modulating therapeutic target protein homeostasis, are dual strategies that can be leveraged to maximize the efficacy of induced proximity therapeutics.

cancer biology↗

bioRxiv2023

A diverse proteome is present and enzymatically active in metabolite extracts

Metabolomics, a foundational tool in metabolism research, relies on the accurate transmittal of biochemical profiles underlying biological phenotypes. Over the years, workflows used in metabolomics have been assumed to remove enzymes to preserve metabolite levels during processing. Here, we uncover a diverse landscape of over 1,000 proteins, strongly enriched for metabolic enzymes, within metabolite extracts generated using common extraction workflows. Moreover, by combining in-extract stable isotope additions and enzyme inhibitors, we demonstrate transaminase activity, which is preventable by protein removal by 3 kDa filtration. We extend these findings to untargeted metabolomics, revealing that both post-extraction formation of glutamate dipeptide and depletion of total glutathione can also be prevented by removing proteins. Finally, we present a simple yet novel workflow that integrates passive filtration for protein removal of crude metabolite extracts as a superior method for broad-coverage metabolomics. Our findings have broad-reaching experimental implications across all fields that use metabolomics and molecular metabolism, especially cancer, immunology, and diabetes research.

biochemistry↗

bioRxiv2023

Developmental priming of cancer susceptibility

DNA mutations are necessary drivers of cancer, yet only a small subset of mutated cells go on to cause the disease. To date, the mechanisms that determine which rare subset of cells transform and initiate tumorigenesis remain unclear. Here, we take advantage of a unique model of intrinsic developmental heterogeneity (Trim28+/D9) and demonstrate that stochastic early life epigenetic variation can trigger distinct cancer-susceptibility states in adulthood. We show that these developmentally primed states are characterized by differential methylation patterns at typically silenced heterochromatin, and that these epigenetic signatures are detectable as early as 10 days of age. The differentially methylated loci are enriched for genes with known oncogenic potential. These same genes are frequently mutated in human cancers, and their dysregulation correlates with poor prognosis. These results provide proof-of-concept that intrinsic developmental heterogeneity can prime individual, life-long cancer risk.

cancer biology↗

bioRxiv2023

Nf1 Deficiency Increases Mammary Collagen Deposition and Restricts Adipocyte Differentiation Before Tumor Formation

BACKGROUNDNeurofibromin, coded by the NF1 tumor suppressor gene, is the main negative regulator of the RAS pathway and is frequently mutated in various cancers. Women with Neurofibromatosis Type I (NF1) - a tumor predisposition syndrome caused by a germline NF1 mutation - have an increased risk of developing aggressive breast cancer with poorer prognosis. The mechanism by which NF1 mutations lead to breast cancer tumorigenesis is not well understood. Therefore, the objective of this work was to identify stromal alterations before tumor formation that result in the increased risk and poorer outcome seen among NF1 patients with breast cancer. METHODSTo accurately model the germline monoallelic NF1 mutations in NF1 patients, we utilized an Nf1-deficient rat model with accelerated mammary development before presenting with highly penetrant breast cancer. RESULTSWe identified increased collagen content in Nf1-deficient rat mammary glands before tumor formation that correlated with age of tumor onset. Additionally, gene expression analysis revealed that Nf1-deficient mature adipocytes in the rat mammary gland have increased collagen expression and shifted to a fibroblast and preadipocyte expression profile. This alteration in lineage commitment was also observed with in vitro differentiation, however, flow cytometry analysis did not show a change in mammary adipose-derived mesenchymal stem cell abundance. CONCLUSIONCollectively, these studies uncovered the previously undescribed role of Nf1 in mammary collagen deposition and regulating adipocyte differentiation. In addition to unraveling the mechanism of tumor formation, further investigation of adipocytes and collagen modifications in preneoplastic mammary glands will create a foundation for developing early detection strategies of breast cancer among NF1 patients. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=158 SRC="FIGDIR/small/539442v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@d4aeeforg.highwire.dtl.DTLVardef@128d9a5org.highwire.dtl.DTLVardef@e8f9e0org.highwire.dtl.DTLVardef@16d0164_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2023

p53 modulates kinase inhibitor resistance and lineage plasticity in NF1-related MPNSTs

Malignant peripheral nerve sheath tumors (MPNSTs) are chemotherapy resistant sarcomas that are a leading cause of death in neurofibromatosis type 1 (NF1). Although NF1-related MPNSTs derive from neural crest cell origin, they also exhibit intratumoral heterogeneity. TP53 mutations are associated with significantly decreased survival in MPNSTs, however the mechanisms underlying TP53-mediated therapy responses are unclear in the context of NF1-deficiency. We evaluated the role of two commonly altered genes, MET and TP53, in kinome reprograming and cellular differentiation in preclinical MPNST mouse models. We previously showed that MET amplification occurs early in human MPNST progression and that Trp53 loss abrogated MET-addiction resulting in MET inhibitor resistance. Here we demonstrate a novel mechanism of therapy resistance whereby p53 alters MET stability, localization, and downstream signaling leading to kinome reprogramming and lineage plasticity. Trp53 loss also resulted in a shift from RAS/ERK to AKT signaling and enhanced sensitivity to MEK and mTOR inhibition. In response to MET, MEK and mTOR inhibition, we observed broad and heterogeneous activation of key differentiation genes in Trp53-deficient lines suggesting Trp53 loss also impacts lineage plasticity in MPNSTs. These results demonstrate the mechanisms by which p53 loss alters MET dependency and therapy resistance in MPNSTS through kinome reprogramming and phenotypic flexibility.

cancer biology↗