Biology subjects

Coppes, R. P.

Publications and source records attributed to Coppes, R. P..

9 recordsLinked to original sources

bioRxiv2026

A two-step organoid screen identifies transient p53 activation as a senolytic strategy for radiation-induced salivary gland dysfunction

Radiotherapy significantly improves the survival of head and neck cancer patients. However, it frequently damages the salivary glands, causing persistent hyposalivation and xerostomia. Radiation-induced cellular senescence within the salivary gland stem/progenitor cell niche contributes to hyposalivation, suggesting that selective elimination of senescent cells could promote tissue recovery. However, the effectiveness of senolytic compounds is strongly context dependent, varying with tissue of origin and potentially impairing regenerative cells required for functional restoration. Here, we developed a two-step organoid-based screening methodology that integrates the preferential induction of apoptosis in irradiated, senescence enriched, salivary gland organoids with the preservation of stem/progenitor cell regenerative capacity. As a first step, the senolytic activity of candidate drugs was tested to identify drugs that induced apoptosis in senescent cells of irradiated organoids but were not or less toxic to unirradiated organoids. As a second step, the confirmed senolytic compounds were tested for effects on stem cell self-renewal potential. Using this approach, we identified Nutlin3a, an MDM2 inhibitor and p53 activator, as the compound with the most favorable toxicity profile in salivary glands. Last, we confirmed the anti-senescence and pro-regenerative potential of Nutlin3a in an in vivo mouse model of radiation-induced hyposalivation, where localized Nutlin3a delivery resulted in a robust increase in saliva production, as early as two weeks after administration. These findings establish an organoid-based strategy for identifying tissue-adapted senolytic interventions and propose transient local p53 activation with Nutlin3a as a potential approach to mitigate radiation-induced salivary gland dysfunction.

cell biology↗

bioRxiv2026

Radiation-induced interferon-I response impairs thyroid organoid function

Background and AimRadiotherapy is a standard cancer treatment, but radiation exposure to surrounding healthy tissues may lead to adverse side effects that compromise patient quality of life. In patients with head and neck cancer treated with radiotherapy, thyroid damage is a frequent complication, resulting in hypothyroidism or secondary thyroid malignancies. Although clinically recognized, the molecular mechanisms underlying these side effects remain mostly unexplored. This study aims to characterize the radiation-induced molecular alterations in thyroid organoids. MethodsBulk RNA sequencing was performed to investigate transcriptomic changes in tissue-derived thyroid organoids following gamma-irradiation. Observed changes were further validated and explored using qPCRs, western blotting, immunofluorescence, caspase 3/7 activity and organoid forming efficiency. ResultsOur findings identify interferon-{beta} (IFN-{beta}) signaling as a key mediator of radiation-induced inflammation in the thyroid. Additionally, the intrinsic apoptotic pathway was found to be the predominant mechanism of radiation-induced thyroid cell death. Notably, while IFN-{beta} exhibited a protective effect against apoptosis, it concurrently reduced thyroid stem progenitor cell potential. ConclusionsThese results highlight the dual role of IFN-{beta} signaling in modulating thyroid cell fate after irradiation, potentially promoting survival upon injury at the expense of regenerative potential.

cell biology↗

bioRxiv2025

Role of Klhl14 in senescence and epithelial-to-mesenchymal transition via TGF- modulation

KLHL14, a component of an E3-ubiquitin ligase complex, has emerged as a context-dependent oncogene or tumor suppressor, particularly important for thyroid development. Yet its role in thyroid biology remains largely unexplored. In this study, we uncover a central function for KLHL14 in maintaining thyroid epithelial identity and regulating tissue homeostasis. Using a thyroid organoid model, we show that KLHL14 is essential for the proper growth and maturation of thyroid cells. Reduction of KLHL14 expression disrupts organoid development and triggers a dual cellular response involving features of both senescence and epithelial-to-mesenchymal transition. These phenotypic changes are accompanied by increased cellular plasticity and migratory capacity. Mechanistically, we identify TGF-{beta} signaling as a key pathway activated upon KLHL14 depletion, contributing to the observed cellular reprogramming. Inhibiting TGF-{beta} restores growth and reduces markers of senescence and EMT, positioning KLHL14 as an upstream modulator of this signaling axis. These findings reveal a previously unrecognized role for KLHL14, suggesting that its dysfunction may contribute to disease progression in aggressive thyroid cancers. This work broadens our understanding of thyroid epithelial biology and provides molecular insights extendable to other tissues, highlighting KLHL14 as a potential target for therapeutic interventions in malignancies displaying the herein explored features.

cell biology↗

bioRxiv2024

Notch Signaling Drives Pro-Regenerative and Migratory Traits in Glandular Stem/Progenitor Cells

Organoid models have advanced our understanding of adult stem/progenitor cell dynamics and function. However, uncovering the regulatory mechanisms of scarce and often quiescent stem cells in organs like the salivary glands remains challenging. Using single-cell RNA sequencing and bulk ATAC and RNA-sequencing analysis, we conducted in-depth profiling of the cellular populations and key signaling pathways characterizing a mouse submandibular salivary gland organoid (mSGO) model at different temporal stages and in response to radiation damage. We identified Sox9- and Itgb1-expressing cells as the most primitive adult stem/progenitor populations and uncover novel stemness and migratory roles for Cd44-expressing cells. Moreover, we revealed that Notch signaling is essential for maintaining self-renewal and migration potential of these stem/progenitor cells post-irradiation. Extending these findings to patient-derived mSGOs, as well as murine and patient-derived mammary and thyroid gland organoids, we confirmed Notch signaling as a conserved regulator of stem/progenitor cell function under migrative and regenerative conditions.

cell biology↗

bioRxiv2024

The Mayo Clinic Salivary Tissue-Organoid Biobanking: A Resource for Salivary Regeneration Research

The salivary gland (SG) is an essential organ that secretes saliva, which supports versatile oral function throughout life, and is maintained by elusive epithelial stem and progenitor cells (SGSPC). Unfortunately, aging, drugs, autoimmune disorders, and cancer treatments can lead to salivary dysfunction and associated health consequences. Despite many ongoing therapeutic efforts to mediate those conditions, investigating human SGSPC is challenging due to lack of standardized tissue collection, limited tissue access, and inadequate purification methods. Herein, we established a diverse and clinically annotated salivary regenerative biobanking at the Mayo Clinic, optimizing viable salivary cell isolation and clonal assays in both 2D and 3D-matrigel growth environments. Our analysis identified ductal epithelial cells in vitro enriched with SGSPC expressing the CD24/EpCAM/CD49f+ and PSMA-phenotype. We identified PSMA expression as a reliable SGSPC differentiation marker. Moreover, we identified progenitor cell types with shared phenotypes exhibiting three distinct clonal patterns of salivary differentiation in a 2D environment. Leveraging innovative label-free unbiased LC-MS/MS-based single-cell proteomics, we identified 819 proteins across 71 single cell proteome datasets from purified progenitor-enriched parotid gland (PG) and sub-mandibular gland (SMG) cultures. We identified distinctive co-expression of proteins, such as KRT1/5/13/14/15/17/23/76 and 79, exclusively observed in rare, scattered salivary ductal basal cells, indicating the potential de novo source of SGSPC. We also identified an entire class of peroxiredoxin peroxidases, enriched in PG than SMG, and attendant H2O2-dependent cell proliferation in vitro suggesting a potential role for PRDX-dependent floodgate oxidative signaling in salivary homeostasis. The distinctive clinical resources and research insights presented here offer a foundation for exploring personalized regenerative medicine.

cell biology↗

bioRxiv2024

Derepression of transposable elements enhances interferon beta signaling and stem/progenitor cell activity after proton irradiation.

Radiotherapy is a mainstay in cancer treatment, aiming to maximize DNA damage in tumors while minimizing harm to surrounding healthy tissues. However, the collateral damage to normal tissues, especially stem/progenitor cells essential for tissue regeneration and organ function, remains a significant challenge. Here, we investigate the molecular responses to photon and proton irradiation, two key modalities in head and neck cancer treatment, using organoids. Multiomics analysis reveals a stronger double-stranded RNA (dsRNA)-induced type I interferon (IFN-I) response following proton irradiation, driven by loss of heterochromatin regulators and derepression of transposable elements (TEs). This response, mediated by the cytoplasmic sensor RIG-I, enhances the inflammatory signaling initiated by the canonical dsDNA sensors cGAS and ZBP1. Genetic and pharmacological modulation of IFN-I signaling in vitro and in vivo demonstrates its critical role in enhancing stem/progenitor cell activity post-irradiation. Our findings reveal a pro-regenerative role of TE derepression-mediated IFN-I response suggesting this pathway as a promising therapeutic target to mitigate radiation-induced side effects. TeaserTransposable element-mediated type I interferon signaling enhances stem/progenitor cell activity after irradiation.

cell biology↗

bioRxiv2023

Patient-Derived Medullary Thyroid Cancer Organoids; a Model for Patient-tailored Drug and PET-Tracer Screening

BackgroundMedullary thyroid carcinoma (MTC) is a neuroendocrine tumor derived from the parafollicular C-cells of the thyroid gland. PET imaging, with various PET tracers, is performed when distant metastatic disease is suspected. After the recognition of progressive disease on imaging, targeted therapy may be initiated to prolong survival. Mutations in the gene encoding the REarranged during Transfection (RET) tyrosine kinase play a key role in the development of MTC. It seems that tyrosine kinase inhibitors (TKIs) inhibit tumor proliferation, but it remains challenging to determine the best patient specific treatment option. Here, we aim to set up an in vitro MTC organoid model to study its potential for patient-tailored drug-screening and uptake of PET tracers. MethodsDispersed cells obtained from surgical MTC biopsies were suspended in Matrigel with defined medium allowing MTC organoid formation. To study putative MTC stem cells, the self-renewal potential of organoids was tested by dissociation to single cells and re-plating. To check MTC origin, MTC-specific gene expression and proteins were characterized by qPCR and immunofluorescent (IF) staining. To investigate cytotoxicity, MTC-organoids (MTOs) were exposed to various TKIs after which hormone (calcitonin and CEA) excretion levels were determined. Lastly, we evaluated cell-specific uptake of clinically used Positron Emission Tomography (PET) tracers. ResultsNine MTC biopsies were processed and cultured as MTOs. Eight MTO lines were used to determine organoid formation efficiency (OFE), which yielded a maximum OFE of 6.3% in passage 1 (p1), 5.9% in p2, and 9.4% in p3, indicating the presence of putative stem cells. IF staining showed expression of MTC-specific markers in both tissue and MTOs showing tissue resemblance. Tumor marker measurements in MTO medium showed MTC-specific production of calcitonin and CEA with changed concentrations after exposure to TKIs. Exposure to PET tracers showed significant uptake in the MTOs. ConclusionMTC organoids can be successfully cultured and resemble the tissue of origin in gene expression, protein expression and functionality. In addition, MTOs can take up PET tracers, and have the potential to be used as a prediction model for TKI treatment in the future.

cancer biology↗

bioRxiv2023

Radiotherapy induces persistent innate immune reprogramming of microglia into a primed state

More than half of all brain tumour survivors experience debilitating and often progressive cognitive decline after treatment with radiotherapy. Microglia, the resident macrophages in the brain, have been implicated in this decline. In response to various insults microglia can develop innate immune memory (IIM), which can either enhance (priming) or repress (tolerance) the response to subsequent inflammatory challenges. Here, we investigated whether radiation affects the IIM of microglia by irradiating the brains of rats and later exposing them to a secondary inflammatory stimulus. Comparative transcriptomic profiling and protein validation of microglia isolated from irradiated rats showed a stronger immune response to a secondary inflammatory insult demonstrating that radiation can lead to long-lasting molecular reprogramming of microglia. Transcriptomic analysis of post-mortem normal-appearing non-tumour brain tissue of glioblastoma patients indicates that radiation-induced microglial priming is conserved in humans. Targeting microglial priming after radiotherapy or avoiding further inflammatory insults could decrease radiotherapy-induced neurotoxicity.

neuroscience↗

bioRxiv2022

Patient-derived parathyroid organoids as tracer and drug-screening application model

Parathyroid diseases are characterized by dysregulation of calcium homeostasis and alterations in parathyroid hormone (PTH) excretion. The understanding of parathyroid hyperplastic growth and the development of parathyroid-targeted treatment and imaging tracers could benefit from in vitro models. Therefore, we aim to establish stem cell-derived, three-dimensional organoids representing human parathyroid tissue in vitro. Patient-derived hyperplastic parathyroid tissue was dispersed and parathyroid organoids (PTO) were cultured and characterized. PTO-derived cells were shown to exhibit in vitro self-renewal over several passages, indicative of the presence of putative stem cells. Immunofluorescence and RNA-sequencing confirm that PTO phenocopy hyperplastic parathyroid tissue. Exposure of PTO to increasing calcium concentrations and to PTH-lowering drugs resulted in a significantly reduced PTH excretion. Next to this, the PTO showed specific binding of 11C-methionine to the targeted receptor. Additionally, when organoids were incubated with 99mTc-sestamibi, we observed a higher uptake in PTOs from patients with a 99mTc-sestamibi positive scan compared to patients with a negative scan. These data show functionality of PTOs resembling the parathyroid. In conclusion, we present a patient-derived PTO culture, that recapitulates the originating tissue on gene and protein expression and functionality. This PTO model paves the way for future physiology studies and therapeutic target and tracer discovery.

cell biology↗