Organoid-based drug screening reveals neddylation as therapeutic target for malignant rhabdoid tumors

Calandrini, Camilla; Hooff, Sander R. van; Paassen, Irene; Ayyildiz, Dilara; Derakhshan, Sepide; Dolman, M. Emmy M.; Langenberg, Karin P.S.; Ven, Marieke van de; Heus, Cecilia de; Liv, Nalan; Kool, Marcel; Krijger, Ronald R. de; Tytgat, Godelieve A.M.; Heuvel‐Eibrink, Marry M. van den; Molenaar, Jan J.; Drost, Jarno

doi:10.1016/j.celrep.2021.109568

Cited by 29 publications

(23 citation statements)

References 59 publications

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“…In future studies, the transfection conditions and methods will be optimized to replicate the current findings in more cell lines. MLN4924 (pevonedistat) is an inhibitor of NAE, which has been widely studied in various solid tumors [33][34][35][36][37][38][39][42][43][44][45]. MLN4924 inhibited NEDDylation to play an antitumor role, and induced apoptosis, senescence, autophagy, angiogenesis inhibition, inflammatory response and chemosensitization/radiosensitization [46].…”

Section: Discussionmentioning

confidence: 99%

Inhibition of NEDD8 NEDDylation induced apoptosis in acute myeloid leukemia cells via p53 signaling pathway

Chen

Sun

2022

Bioscience Reports

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MLN4924 is a potent and selective small-molecule inhibitor of NEDD8-activating enzyme, which showed anti-tumor effect in several types of malignant tumor types. However, the mechanism of action of MLN4924 in acute myeloid leukemia (AML) requires further investigation. Real-time fluorescent quantitative polymerase chain reaction (RT-qPCR) was conducted to detect the mRNA levels of genes. Gene expression was knocked down by short hairpin RNA (shRNA). Moreover, the protein expression was detected by Western blotting (WB) assay. The proliferation and apoptosis of AML cells were measured by cell counting kit-8 (CCK8) assay and flow cytometry (FCM). In the present study, we observed that the mRNA expression levels of NEDD8, UBA3, UBE2M and RBX1 in AML patients were up-regulated compared with healthy controls, which were correlated with worse overall survival (OS) of patients. Besides, knockdown of UBA3, UBE2M and RBX1 inhibited the NEDDylation of CULs and increased the protein expression of p53 and p21 in MOLM-13 cell line. In AML cells, MLN4924 inhibited cell proliferation, promoted cell apoptosis, and induced cell cycle arrest at the G2/M phase. As revealed by experiments in vivo and in vitro, the NEDDylation of CULs was significantly inhibited and the p53 signaling pathway was activated after MLN4924 treatment. So we concluded that NEDD8, UBA3, UBE2M and RBX1 may serve as the prognostic biomarkers and novel therapeutic targets for AML. Inhibition of the NEDDylation pathway resulted in an anti-leukemia effect by activating the p53 signaling pathway.

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Section: Discussionmentioning

confidence: 99%

Inhibition of NEDD8 NEDDylation induced apoptosis in acute myeloid leukemia cells via p53 signaling pathway

Chen

Sun

2022

Bioscience Reports

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“…However, differences were also observed in the comparative analysis, which suggests future protocol optimizations are needed 9 . Previous studies have demonstrated the wide application of organoids as experimental models for drug-screening of neuro-diseases 13 and other diseases, e.g., cancer 48,49 . Other studies have also shown using patient-derived organoid (PDO) platforms to improve preclinical drug discovery in personalized medicine 50 .…”

Section: Discussionmentioning

confidence: 99%

Brain and Organoid Manifold Alignment (BOMA), a machine learning framework for comparative gene expression analysis across brains and organoids

Kalafut

Sandoval

et al. 2022

Preprint

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Organoids have become valuable models for understanding cellular and molecular mechanisms in human development including brains. However, whether developmental gene expression programs are preserved between human organoids and brains, especially in specific cell types, remains unclear. Importantly, there is a lack of effective computational approaches for comparative data analyses between organoids and developing humans. To address this, by considering the public data availability and research significance, we developed a machine learning framework, Brain and Organoid Manifold Alignment (BOMA) for comparative gene expression analysis of brains and organoids, to identify conserved and specific developmental trajectories as well as developmentally expressed genes and functions, especially at cellular resolution. BOMA first performs a global alignment and then uses manifold learning to locally refine the alignment, revealing conserved developmental trajectories between brains and organoids. Using BOMA, we found that human cortical organoids better align with certain brain cortical regions than other non-cortical regions, implying organoid-preserved developmental gene expression programs specific to brain regions. Additionally, our alignment of non-human primate and human brains reveals highly conserved gene expression around birth. Also, we integrated and analyzed developmental scRNA-seq data of human brains and organoids, showing conserved and specific cell trajectories and clusters. Further identification of expressed genes of such clusters and enrichment analyses reveal brain- or organoid-specific developmental functions and pathways. Finally, we experimentally validated important specific expressed genes using immunofluorescence. BOMA is open-source available as a web tool for general community use.

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“…Bulk RNA sequencing data from pediatric renal tumor tissue and organoids as well as normal kidney organoids were used to determine RNA expression of CD70 45 .…”

Section: Bulk Rna Sequencing Analysismentioning

confidence: 99%

Knocking out CD70 rescues CD70-specific nanoCAR T cells from antigen induced exhaustion

Munter

Buhl

Cock

et al. 2023

Preprint

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CD70 is an attractive target for chimeric antigen receptor (CAR) T cell therapy as treatment for both solid and liquid malignancies. However, functionality of CD70-specific CARs is only modest. Here, we optimized a CD70-specific VHH based CAR (nanoCAR). We evaluated the nanoCARs in clinically relevant models in vitro, using co-cultures of CD70-specific nanoCAR T cells with malignant rhabdoid tumor organoids, and in vivo by using a diffuse large B cell lymphoma (DLBCL) patient-derived xenograft (PDX) model. Whereas the nanoCAR T cells were highly efficient in organoid co-cultures, they showed only modest efficacy in the PDX model. Knocking out CD70 expression by the nanoCAR T cells resulted in dramatically enhanced functionality in the PDX model, suggesting that endogenous CD70 interaction with the nanoCAR induces exhaustion. Through single-cell transcriptomics, we obtained evidence that CD70KO CD70-specific nanoCAR T cells are protected from antigen induced exhaustion. Our data shows that CARs targeted to endogenous T cell antigens, negatively affect CAR T cell functionality by inducing an exhausted state which can be overcome by knocking out the specific target, in this case CD70.

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Organoid-based drug screening reveals neddylation as therapeutic target for malignant rhabdoid tumors

Cited by 29 publications

References 59 publications

Inhibition of NEDD8 NEDDylation induced apoptosis in acute myeloid leukemia cells via p53 signaling pathway

Inhibition of NEDD8 NEDDylation induced apoptosis in acute myeloid leukemia cells via p53 signaling pathway

Brain and Organoid Manifold Alignment (BOMA), a machine learning framework for comparative gene expression analysis across brains and organoids

Knocking out CD70 rescues CD70-specific nanoCAR T cells from antigen induced exhaustion

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