Divergent local and systemic antitumor response in primary uveal melanomas
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1046093 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR26972229_1.fastq.gz | Fastqsanger.gz | |||
| SRR26972229_2.fastq.gz | Fastqsanger.gz | |||
| SRR26972230_1.fastq.gz | Fastqsanger.gz | |||
| SRR26972230_2.fastq.gz | Fastqsanger.gz | |||
| SRR26972231_1.fastq.gz | Fastqsanger.gz |
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Project description:Uveal melanoma (UM) is the most common cancer of the eye. The loss of chromosome-3 (M3) is associated with high risk of metastases. M3-tumors are more infiltrated by T-lymphocytes than low-risk disomic-3 (D3) tumors, contrasting with other tumor types in which T-cell infiltration correlates with better prognosis. Whether these T-cells represent an anti-tumor response and how these T-cells would be primed in the eye are both unknown. Herein, we characterized the T-cells infiltrating primary UMs. CD8+ and Treg cells were more abundant in M3- than in D3-tumors. CD39+PD-1+CD8+ T-cells were enriched in M3-tumors suggesting specific responses to tumor-antigen (Ag) as confirmed using HLA-A2:Melan-A tetramers. ScRNAseq-VDJ analysis of T-cells evidenced high numbers of proliferating CD39+PD1+CD8+ clonal expansions suggesting in-situ anti-tumor Ag responses. TCRseq and tumor-Ag tetramer staining characterized the recirculation pattern of the anti-tumor responses in M3- and D3-tumors. Thus, tumor-Ag responses occur in localized UMs raising the question of the priming mechanisms in the absence of known lymphatic drainage.
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Project description:Primary uveal melanomas show multiple genetic alterations. To determine mutational status of six human primary uveal melanomas, we performed whole exome sequencing (WES) and called Single Nucleotide Polimorphism (SNPs) to identify somatic mutations in these human primary uveal melanomas.
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Project description:Primary uveal melanomas show multiple chromosomal aberrations. To identify genome variation in six human primary uveal melanomas, genome wide copy number variation (CNV) analyses were carried out in human primary uveal melanoma samples using array comparative genome hybridization.
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Project description:SF3B1 is coding an essential splicing factor. This gene was found recurrently mutated in uveal melanoma. To understand the consequences of these hotspot SF3B1 mutations, we performed high coverage RNA-seq on 74 primary uveal melanomas, which were treated by primary enucleation. We analyzed data for aberrant splicing in relation with SF3B1 status.
2016-07-03 | E-MTAB-4097 | biostudies-arrayexpress
Project description:Uveal melanoma is the most common cancer of the eye arising from melanocytes within the choroid, ciliary bodies and iris. Almost half of uveal melanomas metastasize hematogenously to distant organs, most often the liver, where the disease becomes fatal. One of the first genetic alterations to be identified in primary uveal melanomas was monosomy 3, which was found to be strongly associated with metastasis. We used gene expression profiling to identify two phenotypically distinct classes of uveal melanomas: class 1 tumors with low-grade morphology and low metastatic risk; and class 2 tumors with aggressive morphology and high metastatic risk. Our initial studies suggested that gene expression profiling was a better predictor of metastasis than monosomy 3. For this study, BAC-array comparative genomic hybridization was used to assay genomic DNA isolated from fresh frozen primary uveal melanoma samples of known molecular class based on gene expression profiling. Independent samples were sent to the aCGH cores at the University of California, San Francisco and the Roswell Park Cancer Institute for hybridization, and log2 ratios were reported. Total genomic DNA was obtained from tumor samples that were collected at the time of treatment. Samples were analyzed by the Microarray Shared Resource at the Comprehensive Cancer Center, University of California, San Francisco or by the Microarray and Genomics Facility of the Roswell Park Cancer Institute.
2012-12-06 | E-GEOD-42739 | biostudies-arrayexpress
Project description:Uveal melanoma is the most common cancer of the eye arising from melanocytes within the choroid, ciliary bodies and iris. Almost half of uveal melanomas metastasize hematogenously to distant organs, most often the liver, where the disease becomes fatal. One of the first genetic alterations to be identified in primary uveal melanomas was monosomy 3, which was found to be strongly associated with metastasis. We used gene expression profiling to identify two phenotypically distinct classes of uveal melanomas: class 1 tumors with low-grade morphology and low metastatic risk; and class 2 tumors with aggressive morphology and high metastatic risk. Our initial studies suggested that gene expression profiling was a better predictor of metastasis than monosomy 3. For this study, BAC-array comparative genomic hybridization was used to assay genomic DNA isolated from fresh frozen primary uveal melanoma samples of known molecular class based on gene expression profiling. Independent samples were sent to the aCGH cores at the University of California, San Francisco and the Roswell Park Cancer Institute for hybridization, and log2 ratios were reported. Total genomic DNA was obtained from tumor samples that were collected at the time of treatment. Samples were analyzed by the Microarray Shared Resource at the Comprehensive Cancer Center, University of California, San Francisco or by the Microarray and Genomics Facility of the Roswell Park Cancer Institute.
2012-12-06 | E-GEOD-42738 | biostudies-arrayexpress
Project description:Uveal melanoma is the most common cancer of the eye arising from melanocytes within the choroid, ciliary bodies and iris. Almost half of uveal melanomas metastasize hematogenously to distant organs, most often the liver, where the disease becomes fatal. One of the first genetic alterations to be identified in primary uveal melanomas was monosomy 3, which was found to be strongly associated with metastasis. We used gene expression profiling to identify two phenotypically distinct classes of uveal melanomas: class 1 tumors with low-grade morphology and low metastatic risk; and class 2 tumors with aggressive morphology and high metastatic risk. Our initial studies suggested that gene expression profiling was a better predictor of metastasis than monosomy 3. For this study, BAC-array comparative genomic hybridization was used to assay genomic DNA isolated from fresh frozen primary uveal melanoma samples of known molecular class based on gene expression profiling. Independent samples were sent to the aCGH cores at the University of California, San Francisco and the Roswell Park Cancer Institute for hybridization, and log2 ratios were reported.
2012-12-06 | GSE42738 | GEO
Project description:Uveal melanoma is the most common cancer of the eye arising from melanocytes within the choroid, ciliary bodies and iris. Almost half of uveal melanomas metastasize hematogenously to distant organs, most often the liver, where the disease becomes fatal. One of the first genetic alterations to be identified in primary uveal melanomas was monosomy 3, which was found to be strongly associated with metastasis. We used gene expression profiling to identify two phenotypically distinct classes of uveal melanomas: class 1 tumors with low-grade morphology and low metastatic risk; and class 2 tumors with aggressive morphology and high metastatic risk. Our initial studies suggested that gene expression profiling was a better predictor of metastasis than monosomy 3. For this study, BAC-array comparative genomic hybridization was used to assay genomic DNA isolated from fresh frozen primary uveal melanoma samples of known molecular class based on gene expression profiling. Independent samples were sent to the aCGH cores at the University of California, San Francisco and the Roswell Park Cancer Institute for hybridization, and log2 ratios were reported.
2012-12-06 | GSE42739 | GEO
Project description:Lack of specific markers for invasive uveal melanoma cells prevents early diagnosis of metastasis, while no systemic treatment options are available for patients with disseminated uveal melanomas. Intra-tumor heterogeneity has been recognized in numerous cancers as the main cause of metastasis development and therapy resistance. However, in uveal melanomas the specific subpopulations and their biological function which influence tumor behavior remained unknown. Here, using scRNA-seq analysis of six different primary uveal melanomas, we uncovered previously unrecognized intratumor heterogeneity. We localized diverse tumor-associated populations and transcriptional states in primary uveal melanomas. We also unraveled a gene regulatory network underlying a poor prognosis melanoma state. Heterogeneity was demonstrated in uveal melanoma tissue using the RNAscope assay. Thus, single-cell analysis offers an unprecedented view of intratumor heterogeneity in primary uveal melanoma, identified bona fide biomarkers for metastatic cells in the primary tumor, and unravel targetable modules driving metastase formation and growth, with critical implications for prognosis and therapeutic opportunity.
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Project description:Array CGH analysis of human uveal melanomas
| PRJNA575742 | ENA