Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA353380 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Retinoblastoma (RB) is an intraocular childhood tumor which, if left untreated, leads to blindness and mortality. Nucleolin (NCL) protein which is differentially expressed on the tumor cell surface, binds ligands and regulates carcinogenesis and angiogenesis. We found that NCL is over expressed in RB tumor tissues and cell lines compared to normal retina. We studied the effect of nucleolin-aptamer (NCL-APT) to reduce proliferation in RB tumor cells. Aptamer treatment on the RB cell lines (Y79 and WERI-Rb1) led to significant inhibition of cell proliferation. Locked nucleic acid (LNA) modified NCL-APT administered subcutaneously (s.c.) near tumor or intraperitoneally (i.p.) in Y79 xenografted nude mice resulted in 26 and 65% of tumor growth inhibition, respectively. Downregulation of inhibitor of apoptosis proteins, tumor miRNA-18a, altered serum cytokines, and serum miRNA-18a levels were observed upon NCL-APT treatment. Desorption electrospray ionization mass spectrometry (DESI MS)-based imaging of cell lines and tumor tissues revealed changes in phosphatidylcholines levels upon treatment. Thus, our study provides proof of concept illustrating NCL-APT-based targeted therapeutic strategy and use of DESI MS-based lipid imaging in monitoring therapeutic responses in RB.
2016-11-15 | GSE89818 | GEO
Project description:AS1411 is a G-rich DNA aptamer that targets the multifunctional RNA-binding protein nucleolin. AS1411 has both antiproliferative and cell size-regulating activities and has been evaluated for clinical utility, reaching phase II trials as an anticancer agent. The mechanisms underlying the different activities of AS1411 are not completely understood and broad characterization of its molecular effects is lacking. Here, we used a multi-omics approach to profile transcriptome, proteome and lipidome changes in AS1411-treated NIH-3T3 cells, which increase in size in response to the aptamer. We found that AS1411 caused downregulation of cholesterol biosynthesis pathway enzymes at both mRNA and protein levels, without an accompanying drop in cellular cholesterol levels. In addition, AS1411 induced changes in several lipid classes, including increases in phospatidylethanolamine levels. Thus, nucleolin regulates lipid biosynthesis and homeostasis, potentially underlying its roles in cell proliferation and size control.
2025-10-27 | GSE274745 | GEO
Project description:Intratumoral heterogeneity (ITH) challenges the molecular characterization of clear cell renal cell Carcinoma (ccRCC) with percutaneous biopsies and is a confounding factor in selection of molecular-targeted versus immune-based therapy. Magnetic Resonance (MR) Imaging can noninvasively assess the spatial landscape of the entire tumor. To validate MRI for ITH assessment, we implemented a radiogenomic platform through a systematic imaging based co-localization approach for multi region tissue acquisition from single tumors. We investigated if the spatial changes in imaging can predict the molecular changes using transcriptome and histopathological correlatives. Our study confirmed imaging heterogeneity as a predictor of molecular heterogeneity in ccRCC.
| EGAS00001003846 | EGA
Project description:Purpose The heterogeneity of squamous cell carcinoma tissue complicates diagnosis and an individualized therapy to a great extent. Therefore it is of utmost importance to spatially characterize this tissue heterogeneity and to identify appropriate biomarkers. Matrix assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) can analyze spatially resolved tissue biopsies on a molecular level. Experimental design MALDI MSI of snap frozen tissues as well as of formalin-fixed and paraffin-embedded (FFPE) tissue samples from patients with head and neck cancer (HNC) were used to analyze m/z values localized in tumor and non-tumor regions. Peptide identification was performed by using liquid chromatography (LC)-MS/MS and immunohistochemistry (IHC). Results In both FFPE and frozen tissue specimen seven characteristic masses of the tumor epithelial region were found identified. Using LC-MS/MS, the peaks were identified as Vimentin, Keratin type II, Nucleolin, Heat shock protein 90, Prelamin-A/C, Junction plakoglobin and PGAM1. Finally, Vimentin, Nucleolin and PGAM1 were verified with IHC. Conclusions and Clinical Relevance The combination of MALDI MSI, LC-MS/MS and subsequent IHC is an appropriate tool to characterize the molecular heterogeneity of tissue as well as to identify new representative biomarkers for a more individualized therapy.
2018-11-14 | PXD009144 | Pride
Project description:Background: Retinoblastoma is a rare pediatric eye cancer caused by mutations in the RB1 gene, which regulates retinal cell growth. Early detection and treatment are critical for pre-venting vision loss and improving survival outcomes. This study aimed to perform an inte-grated proteotranscriptomic characterization of human retinoblastoma to provide a deeper understanding of disease biology and to identify novel therapeutic targets. Methods: Paired tumor and adjacent retinal tissue samples were dissected from seven eyes affected by retinoblastoma. The global transcriptome and proteome were determined using RNA sequencing and liquid chromatography-mass spectrometry from the same samples. The spatially resolved cellular landscape was assessed using Imaging Mass Cytometry (IMC). Results: The correlation between RNA and protein level was moderate (Pearson’s R = 0.339, p < 10-16) with variations across different pathways. While biological processes like visual perception were similarly regulated on the RNA and protein level, others, such as cell cycle processes and glycolysis were predominantly active at the protein level. IMC identified more than 67,000 single cells in distinct clusters, including antigen presenting cells, T cells, stroma cells, vascular cells and two clusters of proliferating and CD44/c-Myc positive tumor cells. In retinoblastoma, we observed increased apoptotic signals in T cells and higher ex-pression of CD68 in antigen presenting cells compared to control tissue. Conclusions: Retinoblastoma's key biological processes are predominantly regulated at either the RNA or protein level, underscoring the value of an integrated proteotranscriptomic approach. Elevated caspase 3 activity in tumor-associated T cells may indicate potential im-mune escape mechanisms and CD44+ and high-c-Myc-expressing tumor cells may repre-sent cancer stem cells with possible involvement in metastasis, warranting further validation. Our multilayered approach could pave the way for enhanced molecular assessments and novel targeted therapies for human retinoblastoma.
2025-05-29 | GSE276895 | GEO
Project description:Alternative splicing (AS) is a key regulatory mechanism that expands transcriptomic diversity and is frequently hijacked by cancer cells to drive epithelial-mesenchymal transition (EMT), thereby promoting invasion and therapy resistance. However, therapeutic strategies to reprogram pathological AS networks remain limited. Here, we identified a circular RNA, MASCOT (hnRNP M-ASsociated Circular RNA Of TGFβ), that functions as an endogenous aptamer targeting the splicing factor hnRNP M, a central regulator of EMT-related AS reprogramming. As an endogenous repressor of hnRNP M, MASCOT maintains the epithelial status of cancer cells and suppresses tumor metastasis. Conversely, its downregulation by TGFβ releases hnRNP M to initiate EMT-associated splicing changes. Restoring MASCOT expression significantly reduces metastatic burden in mouse models. Mechanistically, MASCOT scaffolds hnRNP M to nucleolin within the nucleolus, spatially sequestering hnRNP M away from the spliceosome. Our findings reveal a novel regulatory circuit that controls EMT-linked splicing and identify MASCOT as a promising RNA-based therapeutic candidate against metastatic progression.
2026-08-04 | GSE335525 | GEO
Project description:Alternative splicing (AS) is a key regulatory mechanism that expands transcriptomic diversity and is frequently hijacked by cancer cells to drive epithelial-mesenchymal transition (EMT), thereby promoting invasion and therapy resistance. However, therapeutic strategies to reprogram pathological AS networks remain limited. Here, we identified a circular RNA, MASCOT (hnRNP M-ASsociated Circular RNA Of TGFβ), that functions as an endogenous aptamer targeting the splicing factor hnRNP M, a central regulator of EMT-related AS reprogramming. As an endogenous repressor of hnRNP M, MASCOT maintains the epithelial status of cancer cells and suppresses tumor metastasis. Conversely, its downregulation by TGFβ releases hnRNP M to initiate EMT-associated splicing changes. Restoring MASCOT expression significantly reduces metastatic burden in mouse models. Mechanistically, MASCOT scaffolds hnRNP M to nucleolin within the nucleolus, spatially sequestering hnRNP M away from the spliceosome. Our findings reveal a novel regulatory circuit that controls EMT-linked splicing and identify MASCOT as a promising RNA-based therapeutic candidate against metastatic progression.
2026-08-04 | GSE336555 | GEO
Project description:MMP qualitative and quantitative mass spectrometry
| PRJNA92213 | ENA
Project description:Cyanobacterial identification by native mass spectrometry
| PRJEB45336 | ENA