Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

DNAJB1-PRKACA fusion protein-regulated LINC00473 promotes tumor growth and alters mitochondrial fitness in fibrolamellar carcinoma

ABSTRACT: Fibrolamellar carcinoma (FLC) is a rare liver cancer that disproportionately affects adolescents and young adults. Currently, no standard of care is available and there remains a dire need for new therapeutics. Most patients harbor the fusion oncogene DNAJB1-PRKACA (DP fusion), but clinical inhibitors are not yet developed and it is critical to identify downstream mediators of FLC pathogenesis. Here, we identify long non-coding RNA LINC00473 among the most highly upregulated genes in FLC tumors and determine that it is strongly suppressed by RNAi-mediated inhibition of the DP fusion in FLC tumor epithelial cells. We show by loss- and gain-of-function studies that LINC00473 suppresses apoptosis, increases the expression of FLC marker genes, and promotes FLC growth in cell-based and in vivo models of disease. Mechanistically, LINC00473 plays an important role in promoting glycolysis and altering mitochondrial activity. Specifically, LINC00473 knockdown leads to increased spare respiratory capacity, an indicator of mitochondrial fitness. Overall, we propose that LINC00473 could be a viable target for this devastating disease.

ORGANISM(S): Homo sapiens

PROVIDER: GSE253465 | GEO | 2024/01/19

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

DNAJB1-PRKACA fusion protein-regulated LINC00473 promotes tumor growth and alters mitochondrial fitness in fibrolamellar carcinoma

Project description:Fibrolamellar carcinoma (FLC) is a rare liver cancer that disproportionately affects adolescents and young adults. Currently, no standard of care is available and there remains a dire need for new therapeutics. Most patients harbor the fusion oncogene DNAJB1-PRKACA (DP fusion), but clinical inhibitors are not yet developed and it is critical to identify downstream mediators of FLC pathogenesis. Here, we identify long non-coding RNA LINC00473 among the most highly upregulated genes in FLC tumors and determine that it is strongly suppressed by RNAi-mediated inhibition of the DP fusion in FLC tumor epithelial cells. We show by loss- and gain-of-function studies that LINC00473 suppresses apoptosis, increases the expression of FLC marker genes, and promotes FLC growth in cell-based and in vivo models of disease. Mechanistically, LINC00473 plays an important role in promoting glycolysis and altering mitochondrial activity. Specifically, LINC00473 knockdown leads to increased spare respiratory capacity, an indicator of mitochondrial fitness. Overall, we propose that LINC00473 could be a viable target for this devastating disease.

2023-05-27 | GSE233148 | GEO

Effects of fibrolamellar carcinoma-associated DNAJB1-PRKACA in HEK293T cells

Project description:Fibrolamellar carcinoma (FLC) is a type of primary liver cancer that commonly arises in adolescents and young adults in a background of normal liver tissue and has an overall poor prognosis due to lack of effective chemotherapeutic agents. The DNAJB1-PRKACA gene fusion (DP) has been reported in the majority of FLC tumors, however its exact oncogenic mechanisms are unclear. Given the paucity of cellular models, in particular FLC tumor cell lines, we hypothesized that engineering the DP fusion gene in HEK293T cells will provide insight into the oncogenic mechanism of the fusion gene. We used CRISPR/Cas9 to engineer HEK293T clones expressing DP fusion gene (HEK-DP) and performed transcriptomic, proteomic, and mitochondrial studies to characterize this cellular model. Transcriptomic analysis of HEK-DP cells revealed a significant increase in LINC00473 expression similar to primary FLC samples. Proteomic analysis identified mitochondrial proteins as well as proteins in other subcellular compartments which interact with DP. HEK-DP cells demonstrated significant mitochondrial fission which suggests a role for DP in altering mitochondrial dynamics. Our results support the use of the HEK-DP cells as a novel model for elucidating the oncogenic mechanisms underlying DNAJB1-PRKACA-associated FLC pathogenesis and as a platform for high-throughput drug targeting of DNAJB1-PRKACA protein.

2022-04-05 | GSE161932 | GEO

The oncogenic fusion protein DNAJB1-PRKACA can be specifically targeted by peptide-based immunotherapy in fibrolamellar hepatocellular carcinoma

Project description:The DNAJB1-PRKACA fusion transcript is the oncogenic driver in fibrolamellar hepatocellular carcinoma, a lethal disease lacking specific therapies. This study reports on the identification, characterization, and immunotherapeutic application of HLA-presented neoantigens specific for the DNAJB1-PRKACA fusion transcript in fibrolamellar hepatocellular carcinoma. DNAJB1-PRKACA-derived HLA class I and HLA class II ligands induce multifunctional cytotoxic CD8+ and T-helper 1 CD4+ T cells, and their cellular processing and presentation in DNAJB1-PRKACA expressing tumor cells is demonstrated by mass spectrometry-based immunopeptidome analysis. Single-cell RNA sequencing further identifies multiple T cell receptors from DNAJB1-PRKACA-specific T cells. Vaccination of a fibrolamellar hepatocellular carcinoma patient, suffering from recurrent short interval disease relapses, with DNAJB1-PRKACA-derived peptides under continued Poly (ADP-ribose) polymerase inhibitor therapy induces multifunctional CD4+ T cells, with an activated T-helper 1 phenotype and high T cell receptor clonality. Vaccine-induced DNAJB1-PRKACA-specific T cell responses persist over time and, in contrast to various previous treatments, are accompanied by durable relapse free survival of the patient for more than 21 months post vaccination. Our preclinical and clinical findings identify the DNAJB1-PRKACA protein as source for immunogenic neoepitopes and corresponding T cell receptors and provide efficacy in a single-patient study of T cell-based immunotherapy specifically targeting this oncogenic fusion.

2022-10-13 | PXD029882 | Pride

Single cell RNA-seq and TCR-seq of T cell responses against DNAJB1-PRKACA

Project description:The DNAJB1-PRKACA fusion transcript is the oncogenic driver in fibrolamellar hepatocellular carcinoma (FL-HCC), a lethal disease lacking specific therapies. Here, we report on the identification, characterization and first immunotherapeutic application of HLA-presented neoantigens specific for the DNAJB1-PRKACA fusion transcript in FL-HCC. To characterize the T cell response against DNAJB1-PRKACA-derived HLA class I and HLA class II ligands, single cell RNA sequencing (scRNA-seq) and single cell TCR profiling from CD4+ and CD8+ T cells were performed using 10x Genomics single cell immune profiling.

2022-09-12 | GSE210337 | GEO

Effects of fibrolamellar carcinoma-associated DNAJB1-PRKACA in HEK293T cells

Project description:Effects of fibrolamellar carcinoma-associated DNAJB1-PRKACA in HEK293T cells

| PRJNA679841 | ENA

Chemical, molecular, and single cell analysis reveal chondroitin sulfate proteoglycan aberrancy in fibrolamellar carcinoma

Project description:Fibrolamellar carcinoma (FLC) is an aggressive liver cancer that predominantly afflicts adolescents and young adults. Patients with FLC are characterized by a heterozygous deletion on chromosome 19 that creates an oncogenic gene fusion, DNAJB1-PRKACA. The extracellular environment of FLC tumors is poorly characterized and may contribute to cancer progression, metastasis, and/or drug resistance. To bridge this knowledge gap, we propose to assess pathways relevant to proteoglycans, a major component of the extracellular matrix. We leveraged single-cell ATAC-seq to analyze the diversity of VCAN accessibility across different cell types.

2022-05-20 | GSE202315 | GEO

Multi-omic analysis of microRNA-mediated regulation reveals a proliferative axis involving miR-10b in fibrolamellar carcinoma

Project description:Fibrolamellar carcinoma (FLC) is an aggressive liver cancer with low survival rates and no standard-of-care. The vast majority of FLC patients carry a causative somatic mutation that leads to the gene fusion, DNAJB1-PRKACA. To work toward novel therapeutic strategies, it is important to understand the mechanisms underlying FLC etiology and progression. To that end, in this study, we analyzed a large sample cohort (52 patients) using multiple genome-scale assays to define genes subject primarily to post-transcriptional regulation by microRNAs. These studies revealed a candidate master microRNA regulator in FLC, miR-10b. Functional experiments in cells established from a patient-derived xenograft model revealed that miR-10b contributes to FLC cell metabolic health and proliferation.

2021-11-03 | GSE181922 | GEO

Retinoic acid treatment suppresses fibrolamellar carcinoma growth

Project description:Fibrolamellar carcinoma (FLC) is a devastating, early-onset rare cancer for which there is no effective standard of care. FLC tumors are initiated and likely also maintained by the fusion oncoprotein DNAJ-PKAc (DP). Strategies to therapeutically target DP are underway but remain challenging. Alternate therapeutic approaches are needed in order to maximize the potential benefit for patients. In this study, to identify candidate compounds for drug repurposing, we re-analyzed publicly available RNA-seq data in FLC and non-malignant liver (NML) tissue. We noted that retinoid metabolism, a normal function of a healthy liver, is strikingly suppressed in FLC, which led to the hypothesis that FLC tumors may be responsive to all-trans retinoic acid (ATRA). To test this hypothesis, we treated FLC tumor cells in culture, established from a patient-derived xenograft (PDX) mouse model, with ATRA and found by RNA-seq that well-established molecular markers of PKA signaling and FLC tumors are significantly reduced. Moreover, ATRA treatment markedly diminished cell viability, proliferation, and colony forming capability. We also demonstrated that ATRA sensitizes FLC cells to apoptotic induction by the TLR3 ligand, poly(I:C). Next, using patient tissue slices, we confirmed that ATRA reduces cell viability only in tumors and not in adjacent NML tissue. Finally, we performed in vivo studies in PDX mice to show that ATRA significantly suppresses FLC tumor growth. These findings motivate a more expansive pre-clinical examination of ATRA, especially in conjunction with TLR3 ligands and possibly other adjuvants, to establish the safety and efficacy of ATRA for FLC clinical trials.

2023-02-13 | GSE224888 | GEO

Transcription profiling by array of Pure Fibrolamellar Hepatocellular carcinoma

Project description:A Cartes d'Identite des Tumeurs (CIT) project from the french Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net) | Affymetrix HG-U133 Plus 2.0 : 5 mixed fibrolamellar carcinoma (m-FLC), 17 pure fibrolamellar carcinoma (p-FLC), 7 hepatocelluar carcinoma arising in non-cirrhotic liver (nc-HCC) and 10 non-tumoral livers (NL).

2014-08-15 | E-MTAB-1503 | biostudies-arrayexpress