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Human DICER1+/- RMS tumors are enriched for neutrophils [bulk RNA-seq]

ABSTRACT: Human DICER1+/- RMS tumors are enriched for neutrophils [bulk RNA-seq]

PROVIDER: PRJNA1103162 | ENA |

REPOSITORIES: ENA

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Human DICER1+/- RMS tumors are enriched for neutrophils [bulk RNA-seq]

Project description:We used RNA-seq from to compare the transcriptome of human FFPE diagnostic DICER1+/+ and DICER1+/- RMS tumor samples. We observed that human DICER1+/- RMS tumor were enriched for neutrophil transcripts.

2025-07-29 | GSE264566 | GEO

microRNA expression in mouse oviduct and Dicer1 tumors

Project description:We developed a genetically engineered conditional compound heterozygous Dicer1 mouse strain that fully recapitulates the bi-allelic mutations of DICER1 in DICER1 syndrome-associated cancers. Embryonic activation of bi-allelic Dicer1 mutations, driven by the anti-Müllerian hormone receptor 2 (Amhr2)-driven Cre strain (Amhr2+/cre), drove cancer development from oviduct. Small RNA sequencing was performed to compare the microRNA expression profiles between tumor and normal oviduct.

2023-07-18 | GSE233398 | GEO

mRNA expression in mouse oviduct and Dicer1 tumors

Project description:We developed a genetically engineered conditional compound heterozygous Dicer1 mouse strain that fully recapitulates the bi-allelic mutations of DICER1 in DICER1 syndrome-associated cancers. Embryonic activation of bi-allelic Dicer1 mutations, driven by the anti-Müllerian hormone receptor 2 (Amhr2)-driven Cre strain (Amhr2+/cre), drove cancer development from oviduct. mRNA sequencing was performed to compare the mRNA expression profiles between tumor and normal oviduct.

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Gene expression profile at single cell level of purified "Tumor" and "Stroma" cells in ASD+/+ and ASD+/- murine RMS tumors [scRNA-seq]

Project description:We used scRNA-seq to compare intratumoral heterogeniety between ASD+/+ and ASD+/- tumors. We found that RMS populations were similar between genotypes and that neutrophils were strongly enriched in ASD+/- tumor stroma

2025-07-29 | GSE264567 | GEO

Transcription profiling of human Rhabdomyosarcoma biopsy samples (15 embryonal RMS, 10 translocation-positive alveolar RMS and 5 translocation-negative alveolar RMS)

Project description:We measured the expression profiles of a series of 30 Rhabdomyosarcoma biopsy samples (15 embryonal RMS, 10 translocation-positive alveolar RMS and 5 translocation-negative alveolar RMS). Expression data was used for unsupervised hierarchical clustering as well as supervised analysis to find gene expression signatures characteristic for the different histological RMS subgroups.

2004-06-30 | E-MEXP-121 | biostudies-arrayexpress

Liver-specific DICER1 syndrome model mice develop cystic liver tumors with defective primary cilia

Project description:DICER1 syndrome is a tumor predisposition syndrome caused by familial genetic mutations in DICER1. Pathogenic variants of DICER1 have been discovered in many rare cancers, including cystic liver tumors. However, the molecular mechanisms underlying liver lesions induced by these variants remain unclear. In the present study, we sought to gain a better understanding of the pathogenesis of these variants by generating a mouse model of liver-specific DICER1 syndrome. The mouse model developed bile duct hyperplasia with fibrosis, similar to congenital hepatic fibrosis, as well as cystic liver tumors resembling those in Caroli's syndrome, intrahepatic cholangiocarcinoma, and hepatocellular carcinoma. Interestingly, the mouse model of DICER1 syndrome showed abnormal formation of primary cilia in the bile duct epithelium, which is a known cause of bile duct hyperplasia and cyst formation. These results indicated that DICER1 mutations contribute to cystic liver tumors by inducing defective primary cilia. The mouse model generated in this study will be useful for elucidating the potential mechanisms of tumorigenesis induced by DICER1 variants and for obtaining a comprehensive understanding of DICER1 syndrome.

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Rhabdomyosarcoma surfaceome profiling with six fusion-positive (FP) RMS cell lines, five fusion-negative (FN) RMS cell lines, and three ARMS patient-derived xenografts (PDXs)

Project description:Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma in children. Prognosis for patients with high grade and metastatic disease is still very poor, and survivors are burdened with long-lasting side effects. Therefore, more effective and less toxic therapies are needed. Surface proteins are ideal targets for antibody-based therapies, like bispecific antibodies, antibody drug conjugates, or chimeric antigen receptor (CAR) T cell. Specific surface targets for RMS are scarce. Here, we performed a surfaceome profiling based on differential centrifugation enrichment of surface/membrane proteins and detection by LC-MS on six fusion-positive (FP) RMS cell lines, five fusion-negative (FN) RMS cell lines, and three RMS patient-derived xenografts (PDXs). 699 proteins were detected in the three RMS groups. Ranking based on expression levels and comparison to expression in normal MRC-5 fibroblasts and myoblasts, followed by statistical analysis, highlighted known RMS targets such as FGFR4, NCAM1, and CD276/B7-H3, and revealed AGRL2, JAM3, MEGF10, GPC4, CADM2, as potential targets for immunotherapies of RMS. L1CAM expression was investigated in RMS tissues and strong L1CAM expression was observed in more than 80% of alveolar RMS tumors, making it a practicable target for antibody-based therapies of alveolar RMS.

2023-03-11 | PXD039480 | Pride

Proximity Proteomics Revealed Dicer1 and Transporters as Client Proteins of Aha1

Project description:Co-chaperone Aha1 activates HSP90 ATPase to promote the folding of client proteins. However, the client proteins of Aha1 are largely unknown. By employing ascorbate peroxidase (APEX) based proximity labeling, we identified 32 proximity proteins of HSP90 that are modulated by genetic depletion of Aha1. Among them, Dicer1 is one of the top-ranked proteins, which were further confirmed by streptavidin pull-down followed by Western blot analysis, demonstrating the reliability of the approach. Flag pull-down result showed interactions between endogenous HSP90 and Dicer1 and Aha1. The Dicer1 level is regulated synergistically by Aha1 and HSP90. Maturation-dependent interaction results showed a preferential binding of Aha1 and HSP90 to nascently translated Dicer1. Reconstitution of Aha1-depleted cells with WT Aha1 restored Dicer1 level, while the HSP90-binding-defective E67K mutant exhibited partial restoration. Moreover, knockdown of Aha1 and inhibition of HSP90 can diminish the levels of mature miRNA, let-7b and mir-30a. Overall, our study uncovers, for the first time, Dicer1 and transporter proteins as clients of Aha1 and HSP90.

2022-11-19 | PXD028980 | Pride

Somatic mutations in DROSHA and DICER1 impair microRNA biogenesis in Wilms tumors

Project description:Through whole-exome sequencing we identified somatic missense mutations in DICER1 and DROSHA in Wilms tumor, a childhood kidney cancer. DICER1 and DROSHA are key enzymes in the microRNA biogenesis pathway. To determine the effect of these mutations on microRNA expression, we prepared small RNAs from Wilms tumors and used next-generation sequencing to determine the expression levels of microRNAs in the tumors. Comparison of miRNA expression in tumors with and without mutations in DICER1 or DROSHA.

2015-04-21 | E-GEOD-56955 | biostudies-arrayexpress