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RBPJ::ALK : a novel fusion gene amplified in a metastatic sarcomatoid chromophobe renal cell carcinoma

ABSTRACT: RBPJ::ALK : a novel fusion gene amplified in a metastatic sarcomatoid chromophobe renal cell carcinoma

PROVIDER: PRJNA930896 | ENA |

REPOSITORIES: ENA

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RBPJ::ALK : a novel fusion gene amplified in a metastatic sarcomatoid chromophobe renal cell carcinoma

Project description:Using Fluorescence in situ hybridization (FISH), Comparative genomic hybridization on array (aCGH) and Targeted RNA sequencing (RNASeq), we observed a novel fusion of ALK with RPBJ that was amplified and immunohistochemically overexpressed in both the small sarcomatoid component of a chromophobe renal cell carcinoma (chRCC) and in its lymph node metastasis. The amplified RBPJ::ALK fusion was not detected in the chromophobe component of the primary tumour that harbored chRCC-typical losses of chromosomes 1, 2, 6, 10, 13 and 17. In contrast, the same mutations of PTEN, TP53 and TERT promoter were observed together in the three analyzed samples from chRCC, sarcomatoid component of the chRCC and metastasis.

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Project description:Kinase gene fusions are critical oncogenic drivers and key targets in precision oncology. Here, we report a previously undescribed out-of-frame CBX3::ALK fusion identified in metastatic melanoma. Remarkably, this fusion generates a biologically active ALK protein. In this study, we performed RNA-seq to compare the transcriptional profile of CBX3::ALK with the well-characterized EML4-ALK fusion. Our goal is to evaluate the similarities between these fusions and investigate potential therapeutic targets for CBX3::ALK.

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Transcription analysis of CBX3::ALK Fusion and EML4-ALK Fusion that drives ALK Activation

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Genome wide transcriptomic analysis of sarcomatoid (E/S), rhabdoid (E/R) and non-sarcomatoid (E*) clear cell renal cell carcinoma

Project description:An analysis of the biphasic epithelioid (E-) and sarcomatoid(S-) components of sarcomatoid RCC and advanced stage non-sarcomatoid RCC (E*) showed that: the E- and S- components shared a similar transcriptomic signature, despite morphologic differences; and that the transcriptome of sarcomatoid RCC was sharply distinct from non-sarcomatoid RCC. The E- and R- components of rhabdoid RCC were also transcriptomically similar but distinct from RCC lacking rhabdoid/sarcomatoid features (E*). Total RNA processed and spotted on Illumina microarrays from the following patient samples: 38 sarcomatoid RCC (37 paired E- and S and 1 unpaired S-), 4 rhabdoid RCC (paired E- and R-) and 56 non-sarcomatoid RCC. There are 8 replicate samples (7 sarcomatoid RCC and 1 rhabdoid RCC).

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Project description:The biphasic epithelioid (E-) and sarcomatoid(S-) components of sarcomatoid RCC and epithelioid (E-) and rhabdoid (R-) components of rhabdoid RCC shared a similar transcriptomic signature, despite morphologic differences; by contrast, the transcriptome of sarcomatoid and rhabdoid RCC was sharply distinct from non-sarcomatoid RCC. Total RNA was processed for RNA-seq from the following patient samples: 7 sarcomatoid RCC (E- and S- pairs), 4 rhabdoid RCC (E- and R- pairs) and 15 non-sarcomatoid RCC.

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Project description:High anaplastic lymphoma kinase (ALK) protein levels may be correlated with an unfavorable prognosis in neuroblastoma (NBL) patients, regardless of ALK mutation status. We therefore examined the correlation between levels of ALK, phosphorylated ALK (pALK) and downstream signaling proteins and response to ALK inhibition in a large panel of both ALK mutated (MUT) and wild type (WT) NBL cell lines. Six of the nineteen NBL cell lines had a point mutation and four an amplification of the ALK gene. ALK amplified cell lines showed similar ALK levels and ALK inhibitor sensitivity as WT cell lines and were therefore co-analyzed. The ALK mRNA (p=0.043), ALK 220 kDa (p=0.009) and ALK 140 kDa (p=0.025) protein levels were higher in ALK mutant (n=6) than WT cell lines (n=13). ALK mRNA and protein levels significantly correlated with ERK1 and ERK2 protein levels, and also with PHOX2B mRNA levels, a neural differentiation marker which is mutated in NBL. Response to ALK inhibitor TAE684 was also significantly correlated with ALK levels. ALK mutant cell lines (n=4) demonstrated a higher sensitivity towards ALK inhibitor TAE684 (14.9 fold more sensitive, p=0.004) than eight WT cell lines. These results underline the importance of ALK mutations but also ALK levels for response to ALK inhibitors in NBL cell lines. Furthermore, the strong correlation of PHOX2B and ALK suggests that neural differentiation stage may be correlated with ALK levels in neuroblastoma. These data will enhance understanding of ALK inhibitor response in future patient trials.

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Identifying the intergenic ALK fusion LOC388942-ALK as a driver of non-small cell lung cancer

Project description:ALK fusions, such as the classic EML4-ALK, are known drivers of lung cancer and effective therapeutic targets. However, variant ALK fusions, including intergenic fusions like LOC388942-ALK (LA), have been detected in increasing numbers of patients, with their roles in tumorigenesis and ALK inhibitor resistance remaining unclear. Using CRISPR/Cas9, we generated the LA fusion in A549 and H441 cells, confirming elevated ALK expression via qRT-PCR and immunohistochemistry (IHC) staining. Functional analyses showed that LA significantly promoted tumor growth in vitro and in vivo while conferring increased resistance to alectinib. RNA-seq revealed upregulation of the FOS pathway in LA tumors, identifying FOS as a potential therapeutic target. Subsequently, we demonstrated that FOS disruption and inhibition sensitized LA tumors to treatment. RNA-seq profiling demonstrated that FOS depletion in LOC388942-ALK tumor significantly downregulated multiple oncogenic pathways related to cell cycle progression, DNA replication fidelity, and extracellular matrix remodeling, suggesting a pivotal role of FOS in maintaining tumor growth. These findings establish LOC388942-ALK as a novel oncogenic driver in lung cancer, highlighting its role in tumor growth and ALK inhibitor resistance. Targeting FOS may provide a promising therapeutic strategy for tumors harboring this intergenic fusion.

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