Biology subjects

Coppes, R. P.

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

5 recordsLinked to original sources

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↗