Genetically defined human GBM organoids reveal principles of GBM development and actionable targets
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE213835 | GEO | 2024/01/26
REPOSITORIES: GEO
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Project description: Not available
| ST002284 | MetabolomicsWorkbench
Project description:Genetically defined human GBM organoids reveal principles of GBM development and actionable targets
| PRJNA882668 | ENA
Project description:Cerebral organoids have emerged as faithful humanoid avatars for modeling neurodevelopmental and pathological processes. Additionally, they serve as powerful discovery platforms for less characterized neurobiological programs. Towards this prospect, we leveraged mass spectrometry-based proteomics to molecularly profile precursor and neural compartments of both human-derived organoids and mid-gestation fetal brain tissue, to define overlapping programs. Our analysis included precursor-enriched transcriptional regulatory proteins that were not found to be differentially expressed in previous transcriptomic datasets. To highlight the discovery potential of this resource, we show that RUVBL2 is preferentially expressed in the SOX2-positive compartment of organoids and chemical inactivation leads to precursor cell displacement and apoptosis. To explore clinicopathological correlates of this cytoarchitectural disruption, we interrogated clinical datasets, and identified rare de novo genetic variants involving RUVBL2 in patients with neurodevelopmental impairments. Together, our study demonstrates how cell-type specific profiling of organoids can help nominate previously unappreciated genes in neurodevelopment and disease.
2022-04-07 | PXD033012 | Pride
Project description:Cardiovascular diseases are the leading cause of death worldwide, with heart failure being a complex condition that affects millions of individuals. Single-nucleus RNA sequencing has recently emerged as a powerful tool for unraveling the molecular mechanisms behind cardiovascular diseases. This cutting-edge technology enables the identification of molecular signatures, intracellular networks, and spatial relationships among cardiac cells, including cardiomyocytes, mast cells, lymphocytes, macrophages, lymphatic endothelial cells, endocardial cells, endothelial cells, epicardial cells, adipocytes, fibroblasts, neuronal cells, pericytes, and vascular smooth muscle cells. Despite these advancements, the discovery of essential therapeutic targets and drugs for precision cardiology remains a challenge. To bridge this gap, we conducted comprehensive in silico analyses of single-nucleus RNA sequencing data, functional enrichment, protein interactome network, and identification of the shortest pathways to physiological phenotypes. This integrated multi-omics analysis generated CardiOmics signatures, which allowed us to pinpoint three therapeutically actionable targets (ADRA1A1, PPARG, and ROCK2) and 15 effective drugs, including adrenergic receptor agonists, adrenergic receptor antagonists, norepinephrine precursors, PPAR receptor agonists, and Rho-associated kinase inhibitors, involved in late-stage cardiovascular disease clinical trials.
| S-EPMC10770621 | biostudies-literature
Project description:Autosomal Recessive Renal Tubular Dysgenesis (AR-RTD) is a fatal genetic disorder affecting proximal tubule (PT) development in patients harboring mutations in genes comprising the Renin–Angiotensin–Aldosterone System (RAAS). To uncover the pathomechanism of AR-RTD, we differentiated ACE and AGTR1 deficient pluripotent stem cells and reprogrammed AR-RTD patient cells into kidney organoids. Marker analyses confirmed that all mutant and control organoids generated PT in room air (21% O2) or under hypoxic conditions (2% O2). Mature (d24) AGTR1-/- and control organoids transplanted under the kidney capsule of immunodeficient mice engrafted and differentiated well, as did renal vesicle stage (d14) control organoids. By contrast, d14 AGTR1-/- organoids failed to engraft due to insufficient pro-angiogenic VEGF-A expression. When grown under hypoxic conditions VEGF-A expression was stimulated and organoids engrafted. Thus, PT dysgenesis in AR-RTD is a non-autonomous consequence of a developmental delay in VEGF-A induction linking ANGII pro angiogenic role to PT dysgenesis.
2023-10-18 | GSE229842 | GEO
Project description:Biliary tract cancer (BTC) represents a heterogeneous disease with dismal outcome. Herein, we examined genotype and angiogenesis features in BTC. We applied genotyping (Sanger, qPCR, 101-gene panel NGS), mRNA relative quantification methods, and β-catenin immunohistochemistry in 84 FFPE BTC (55 gallbladder [GBC], 14 intrahepatic [ICC], 15 extrahepatic [ECC] carcinomas). We identified 541 mutations in 68 (81%) tumors. Top mutated genes were CTNNB1 (36%); PTEN (33%); TP53 (31%); PIK3R1 (29%); PIK3CA (13%); BRCA2 and KRAS (12%); BRCA1 (11%). Six GBCs were hypermutated [hm] displaying a distinct mutational pattern. Mutations in TP53 and PI3K, Wnt and RAS components were prevalent among non-hypermutated tumors. All hmGBCs carried mutations in BRCA2 and other homologous recombination repair (HRR) genes, in PD1, but not in CTNNB1 and KRAS. None of the pathogenic BRCA2 p.D2723G and BRCA1 p.Q563* and c.5266dupC was present at frequencies expected for germline mutations. We observed copy gains (>6 copies) in EGFR (9% of informative tumors), PRKAR1A (7%), PIK3CA (6%), ERBB2 (5%) and MET (4%). TP53 mutations were prevalent in GBC (P<0.001) and PRKAR1A copy gains in ICC (P=0.007). PTEN was frequently co-mutated with CTNNB1 (P<0.001). Unrelated to CTNNB1 mutations, nuclear β-catenin was detected in 45% of tumors, among them in 5/6 hmGBC. We observed strong mRNA expression correlation of the two neuropilins (NRP1 and NRP2) with each other (Spearman's rho 0.59) and with the endothelin receptor (NRP2 rho 0.66; NRP2 rho 0.51), and between VEGFA and its receptors (FLT1 rho 0.49; KDR rho 0.45). All PIK3CA mutated tumors expressed endothelin 1 mRNA (P=0.010). Most tumors expressing nuclear β-catenin were negative for VEGFC (P=0.009) and FLT4 (P=0.002) mRNA expression. In conclusion, we confirmed the presence of known genomic aberrations in BTC and different genotypes between BTC subsets. Novel findings are the coexistence of PI3K and WNT pathway gene alterations in BTC, their association with angiogenesis, and the hypermutated GBCs with HRR gene mutations, all of which may be considered for new treatment options in this difficult to treat disease.
| S-EPMC5794717 | biostudies-literature
Project description:APC inactivation is the early process in the tumorigenesis of colorectal cancer. We established organoid cultures from intestines of genetically modifeid mice harboring Apcfl/fl and R26CreERT2 allele We used microarrays to determine the alterations in intestinal stem cells in response to APC inactivation. Organoids were treated with 4OHT to induce recombination of APC or left untreated, and collected at 4 or 6 days after treatment. RNA were extracted and hybridization on Affymetrix microarrays.
2016-03-31 | E-GEOD-76847 | biostudies-arrayexpress
Project description:We report the single-cell RNA sequencing of day 33±2 human iPSC derived cerebral organoids harboring a CRIPSR/CAS9 mediated, heterozygous knock-out of the gene EML1 or the respective isogenic control organoids. By microdissection of several ventricular zones per organoid from 3 different batches followed by dissociation into single cells we obtained transcriptomic data of several thousand cells and we were able to identify different cell populations including RG cells (RG1), RG cells transitioning to bRG cells (RG to bRG), RG cells transitioning to neurons (RG2), intermediate progenitors and young neurons based on known marker genes (Nowakowski et al., 2017; Fan et al., 2020; Velasco et al., 2019; Pollen et al., 2015; Liu et al., 2017). When comparing the cell type composition between EML1-heKO and isogenic control-derived organoids we found a clear decrease of RG1 cells and a striking increase in the abundance of RG to bRG cells in the EML1-heKO condition, while only minor variations in the other cell clusters were observed. We further investigated molecular characteristics of the EML1-heKO derived RG to bRG cluster compared to control. Here we found a set of differentially expressed genes in the EML1-heKO compared to control. When further investigating these genes, we identified a clear upregulation of ECM and bRG markers Our data suggest that the RG to bRG cell cluster in the EML1-heKO is composed of a rather perturbed progenitor population not found as such in control organoids and most likely not reflecting a cell population present during normal human brain development.
2022-01-31 | GSE195666 | GEO
Project description:Here we developed a method to incorporate a genetically engineered endothelial niche into an established protocol for generating human kidney organoids.
2023-05-22 | GSE232767 | GEO
Project description:Although most acute myeloid leukemia (AML) patients achieve complete remissions, the majority still eventually relapse and die of their disease. Rare primitive leukemia cells, so-called leukemia stem cells (LSCs), represent one potential type of resistant cell subpopulation responsible for this dissociation between response and cure. Several LSC targets have been described, but there is limited evidence about their relative utility or that targeting any can prevent relapse. LSCs not only appear to be biologically heterogeneous, but the classic immunocompromised mouse transplantation model also has serious shortcomings as an LSC assay. Out data suggest that the most immature cell phenotype that can be identified within a patient's leukemia may be clinically relevant and represent the de facto LSC. Moreover, although phenotypically heterogeneous, these putative LSCs show consistent phenotypes within individual genetically defined groups. Using this LSC definition, we studied several previously described putative LSC targets, CD25, CD26, CD47, CD96, CD123, and CLL-1, and all were expressed across heterogeneous LSC phenotypes. In addition, with the exception of CD47, there was at most low expression of these targets on normal hematopoietic stem cells (HSCs). CD123 and CLL-1 demonstrated the greatest expression differences between putative LSCs and normal HSCs. Importantly, CD123 monoclonal antibodies were cytotoxic in vitro to putative LSCs from all AML subtypes, while showing limited to no toxicity against normal HSCs and hematopoietic progenitors. Since minimal residual disease appears to be a more homogeneous population of cells responsible for relapse, targeting CD123 in this setting may be most effective.
| S-EPMC7969493 | biostudies-literature