Transcriptomic analysis of DHODH inhibition in PIK3CA-mutant colorectal cancer
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ABSTRACT:
ORGANISM(S): Homo
PROVIDER: GSE335693 | GEO | 2026/06/19
REPOSITORIES: GEO
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Project description:Dihydroorotate dehydrogenase (DHODH), a key enzyme in de novo pyrimidine biosynthesis, has recently emerged as a therapeutic target in various cancers. We have previously identified a pivotal role of DHODH in initiation of cutaneous squamous cell carcinoma (cSCC), the second most common type of non-melanoma skin cancer. However, the key mechanisms driving the anticancer activity of DHODH inhibition remain unexplored in cSCC. To evaluate the impact of DHODH inhibition on cSCC growth, we employed three complementary approaches: (1) pharmacological inhibition of DHODH in mice bearing xenografts of A431 and SCC13 cells through oral administration of leflunomid (LFN) or PTC299 (PTC), and (2) genetic silencing of DHODH via transduction of cells with a lentiviral vector expressing shRNA targeting DHODH (shDHODH) prior to transplantation into NSG mice. After transplantation of A431 or SCC13 cells and once tumors reached an average volume of 150 to 200 mm3, mice were divided into two groups that receiving either vehicle alone or LFN administrated orally on a daily basis. The same procedure was applied for treatment with PTC299. To further investigate, DHODH expression was downregulated in A431 and SCC13 cells using shDHODH. Cells transduced with shCtrol used as control. Six days after transduction, the cells were subcutaneously engrafted into NSG mice. To investigate the molecular consequences of DHODH inhibition across distinct cSCC models, label-free quantitative proteomic analyses were performed on A431 and SCC13 xenografts treated with LFN or PTC299, as well as on tumors transduced with shDHODH (6 xenografts per group).
2026-06-15 | PXD070860 | Pride
Project description:Oncogenic PIK3CA mutations activate phosphoinositide 3-kinase (PI3K) and are among the commonest somatic mutations in cancer and mosaic, developmental overgrowth disorders. We recently demonstrated that the ‘hotspot’ variant PIK3CAH1047R exerts striking allele dose-dependent effects on stemness in human induced pluripotent stem cells (iPSCs), and moreover demonstrated multiple oncogenic PIK3CA copies in a substantial subset of human cancers. To identify the molecular mechanism underpinning PIK3CAH1047R allele dose-dependent stemness, we profiled isogenic wild-type, PIK3CAWT/H1047R and PIK3CAH1047R/H1047R iPSCs by high-depth transcriptomics, proteomics and reverse-phase protein arrays (RPPA). PIK3CAH1047R/H1047R iPSCs exhibited altered expression of 5644 genes and 248 proteins, whereas heterozygous hPSCs showed 492 and 54 differentially-expressed genes and proteins, respectively, confirming a nearly deterministic phenotypic effect of homozygosity for PIK3CAH1047R. Pathway and network-based analyses predicted a strong association between self-sustained TGFb/NODAL signaling and the ‘locked’ stemness phenotype induced by homozygosity for PIK3CAH1047R. This stemness gene signature was maintained without exogenous NODAL in PIK3CAH1047R/H1047R iPSCs and was reversed by pharmacological inhibition of TGFb/NODAL signaling but not by PIK3CA-specific inhibition. Analysis of PIK3CA-associated human breast cancers revealed increased expression of the stemness markers NODAL and POU5F1 as a function of disease stage and PIK3CAH1047R allele dosage. Together with emerging realization of the link between NODAL re-expression and aggressive cancer behavior, our data suggest that TGFb/NODAL inhibitors warrant testing in advanced breast tumors with multiple oncogenic PIK3CA copies.
2021-03-03 | PXD014719 | Pride
Project description:The small molecule QC6352, developed as an inhibitor of the histone demethylase KDM4, exhibits potent anti-cancer activity, and its derivative, zavondemstat, is currently being evaluated in cancer clinical trials. Here, we demonstrate that the anti-proliferative efficacy of QC6352 in glioblastoma models is independent of KDM4 inhibition. Transcriptomic analysis revealed that QC6352's gene expression signature in glioblastoma cells closely resembles that of drugs targeting dihydroorotate dehydrogenase (DHODH). Biochemical assays, protein crystallography, metabolomic analysis, and uridine rescue experiments confirmed that QC6352 inhibits DHODH and thereby disrupts the de novo pyrimidine biosynthesis pathway. Furthermore, we show that the therapeutic efficacy of zavondemstat is primarily driven by DHODH inhibition, rather than KDM4 inhibition. Lastly, by uncovering the mechanism of action of QC6352, we identify PRMT5 inhibitors as synergistic partners for DHODH inhibitors, providing the basis for maximising the therapeutic impact of DHODH inhibitors in cancer treatments.
2026-03-31 | GSE296933 | GEO
Project description:The small molecule QC6352, developed as an inhibitor of the histone demethylase KDM4, exhibits potent anti-cancer activity, and its derivative, zavondemstat, is currently being evaluated in cancer clinical trials. Here, we demonstrate that the anti-proliferative efficacy of QC6352 in glioblastoma models is independent of KDM4 inhibition. Transcriptomic analysis revealed that QC6352's gene expression signature in glioblastoma cells closely resembles that of drugs targeting dihydroorotate dehydrogenase (DHODH). Biochemical assays, protein crystallography, metabolomic analysis, and uridine rescue experiments confirmed that QC6352 inhibits DHODH and thereby disrupts the de novo pyrimidine biosynthesis pathway. Furthermore, we show that the therapeutic efficacy of zavondemstat is primarily driven by DHODH inhibition, rather than KDM4 inhibition. Lastly, by uncovering the mechanism of action of QC6352, we identify PRMT5 inhibitors as synergistic partners for DHODH inhibitors, providing the basis for maximising the therapeutic impact of DHODH inhibitors in cancer treatments.
2026-03-31 | GSE292934 | GEO
Project description:Despite intensive therapy, children with high-risk neuroblastoma are at risk of treatment failure. We applied a multi-omic system approach to evaluate metabolic vulnerabilities in human neuroblastoma. We combined metabolomics, CRISPR screening and transcriptomic data across >700 solid tumor cell lines and identified dihydroorotate dehydrogenase (DHODH), a critical enzyme in pyrimidine synthesis, as a potential treatment target. Of note, DHODH inhibition is currently under clinical investigation in patients with hematologic malignancies. In neuroblastoma, DHODH expression was identified as an independent risk factor for aggressive disease, and high DHODH levels correlated to worse overall and event-free survival. A subset of tumors with the highest DHODH expression was associated with a dismal prognosis, with a 5-year survival of <10%. In xenograft and transgenic neuroblastoma mouse models treated with the DHODH inhibitor brequinar, tumor growth was dramatically reduced, and survival was extended. Furthermore, brequinar treatment was shown to reduce the expression of MYC targets in three different neuroblastoma models in vivo. A combination of brequinar and temozolomide was curative in the majority of transgenic TH-MYCN neuroblastoma mice, indicating a highly active clinical combination therapy. Overall, DHODH inhibition combined with temozolomide has therapeutic potential in neuroblastoma and we propose this combination for clinical testing.
2022-07-27 | GSE209812 | GEO
Project description:Despite intensive therapy, children with high-risk neuroblastoma are at risk of treatment failure. We applied a multi-omic system approach to evaluate metabolic vulnerabilities in human neuroblastoma. We combined metabolomics, CRISPR screening and transcriptomic data across >700 solid tumor cell lines and identified dihydroorotate dehydrogenase (DHODH), a critical enzyme in pyrimidine synthesis, as a potential treatment target. Of note, DHODH inhibition is currently under clinical investigation in patients with hematologic malignancies. In neuroblastoma, DHODH expression was identified as an independent risk factor for aggressive disease, and high DHODH levels correlated to worse overall and event-free survival. A subset of tumors with the highest DHODH expression was associated with a dismal prognosis, with a 5-year survival of <10%. In xenograft and transgenic neuroblastoma mouse models treated with the DHODH inhibitor brequinar, tumor growth was dramatically reduced, and survival was extended. Furthermore, brequinar treatment was shown to reduce the expression of MYC targets in three different neuroblastoma models in vivo. A combination of brequinar and temozolomide was curative in the majority of transgenic TH-MYCN neuroblastoma mice, indicating a highly active clinical combination therapy. Overall, DHODH inhibition combined with temozolomide has therapeutic potential in neuroblastoma and we propose this combination for clinical testing.
2022-07-27 | GSE209811 | GEO
Project description:Sensitive versus Resistant patient-derived colorectal cancer tumor xenografts with PIK3CA mutant against saracatinib (AZD0530) Sensitive versus Resistant patient-derived colorectal cancer tumor xenografts with PIK3CA mutant against saracatinib (AZD0530)
2012-02-24 | E-GEOD-36006 | biostudies-arrayexpress
Project description:Relapse continues to limit survival for patients with B-cell acute lymphoblastic leukemia (B-ALL). Previous studies have independently implicated activation of B-cell developmental signaling pathways and increased glucose consumption with chemo-resistance and relapse risk. Here, we connect these observations, demonstrating that B-ALL cells with active signaling, defined by high expression of phosphorylated ribosomal protein S6 (“pS6+ cells”), are metabolically unique and glucose dependent. Metabolic flux and carbon tracing confirms pS6+ cells to be highly glycolytic and notably sensitive to glucose deprivation, relying on glucose for de novo nucleotide synthesis. Uridine, but not purines or pyrimidines, rescues pS6+ cells from glucose deprivation, demonstrating uridine to be essential for their survival. Active signaling in pS6+ cells drives uridine production through activating phosphorylation of carbamoyl phosphate synthetase (CAD), the enzyme catalyzing the initial steps of uridine synthesis. Inhibition of signaling abolishes glucose dependency and CAD phosphorylation in pS6+ cells. Primary pS6+ cells demonstrate high expression of uridine synthesis proteins, including dihydroorotate dehydrogenase (DHODH), the rate-limiting catalyst of de novo uridine synthesis. Gene expression demonstrates that increased expression of DHODH is associated with relapse and inferior event-free survival after chemotherapy. Further, the majority of B-ALL genomic subtypes demonstrate activity of DHODH. Inhibiting DHODH using BAY2402232 effectively kills pS6+ cells in vitro with its IC50 correlated with the strength of pS6 signaling across 14 B-ALL cell lines and patient-derived xenografts (PDX). In vivo DHODH inhibition prolongs survival and decreases leukemia burden in pS6+ B-ALL cell line and PDX models. These findings link active signaling to uridine dependency in B-ALL cells and associate this with risk of relapse. Targeting uridine synthesis through DHODH inhibition offers a promising therapeutic strategy for chemo-resistant B-ALL as a novel therapeutic approach for relapsed disease.
2026-01-12 | GSE286115 | GEO
Project description:The ability of cancer cells to evade immune destruction is governed by various intrinsic factors including their metabolic state. Here we demonstrate that inactivation of dihydroorotate dehydrogenase (DHODH), a pyrimidine synthesis enzyme, increases cancer cell sensitivity to T cell cytotoxicity through induction of ferroptosis. Lipidomic and metabolomic analyses revealed that DHODH inhibition reduces CDP-choline level and attenuates the synthesis of phosphocholine (PC) via the CDP-choline-dependent Kennedy pathway. To compensate this loss, there was increased synthesis from phosphatidylethanolamine via the phospholipid methylation pathway resulting in increased generation of very long chain polyunsaturated fatty acid-containing PCs. Importantly, inactivation of Dhodh in cancer cells promoted the infiltration of interferong-secreting CD8+ T cells and enhanced the anti-tumor activity of PD-1 blockade in mouse models. Our findings reveal the importance of DHODH in regulating immune evasion through a CDP-choline dependent mechanism and implicate DHODH as a promising target to improve the efficacy of cancer immunotherapies.
2025-03-12 | GSE243486 | GEO