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Impact of Genetic Ancestry on Prognostic Biomarkers in Uveal Melanoma.

ABSTRACT: Uveal melanoma (UM) is the most common cancer of the eye and leads to metastatic death in up to half of patients. Genomic prognostic biomarkers play an important role in clinical management in UM. However, research has been conducted almost exclusively in patients of European descent, such that the association between genetic admixture and prognostic biomarkers is unknown. In this study, we compiled 1381 control genomes from West African, European, East Asian, and Native American individuals, assembled a bioinformatic pipeline for assessing global and local ancestry, and performed an initial pilot study of 141 UM patients from our international referral center that manages many admixed individuals. Global and local estimates were associated with genomic prognostic determinants. Expression quantitative trait loci (eQTL) analysis was performed on variants found in segments. Globally, after correction for multiple testing, no prognostic variable was significantly enriched in a given ancestral group. However, there was a trend suggesting an increased proportion of European ancestry associated with expression of the PRAME oncogene (q = 0.06). Locally enriched European haplotypes were associated with the poor prognosis class 2 gene expression profile and with genes involved in immune regulation (q = 4.7 × 10-11). These findings reveal potential influences of genetic ancestry on prognostic variables, implicate immune genes in prognostic differences based on ancestry, and provide a basis for future studies of admixed patients with UM using rigorous genetic ancestry methodology.

SUBMITTER: Rodriguez DA

PROVIDER: S-EPMC7693692 | biostudies-literature | 2020 Oct

REPOSITORIES: biostudies-literature

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Impact of Genetic Ancestry on Prognostic Biomarkers in Uveal Melanoma.

Rodriguez Daniel A DA Sanchez Margaret I MI Decatur Christina L CL Correa Zelia M ZM Martin Eden R ER Harbour J William JW

Cancers 20201031 11

Uveal melanoma (UM) is the most common cancer of the eye and leads to metastatic death in up to half of patients. Genomic prognostic biomarkers play an important role in clinical management in UM. However, research has been conducted almost exclusively in patients of European descent, such that the association between genetic admixture and prognostic biomarkers is unknown. In this study, we compiled 1381 control genomes from West African, European, East Asian, and Native American individuals, as ...[more]

PMID: 33142712

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Project description:BACKGROUND:The risk of metastases in uveal melanoma can accurately be estimated through genetic analysis of the tumor. A growing number of patients decide to receive information on their prognosis, although this can be extremely burdensome. Studies on the psychosocial impact of testing are sparse. The objective of this study was to examine traits of patients opting for prognostication, to investigate its psychosocial impact and the use of psycho-oncological services over time. We further examined characteristics of patients utilizing these services and risk factors of prolonged psychological distress. DESIGN AND METHODS:This study is a non-randomized controlled prospective clinical observational trial. Patients availing for prognostication formed the test group, while those who opted out constituted the observational group. The psychosocial impact of genetic testing was assessed with the following variables: resilience, social support, fear of tumor progression, depression, general distress, health-related quality of life, estimation of the perceived risk, and the utilization of psycho-oncological interventions. Data were assessed at five different time points over a period of 12?months. We applied binary logistic regression analysis, multiple linear regressions and a mixed model. RESULTS:Of 175 patients, 63 decided to obtain prognostic information. Treatment method (enucleation > brachytherapy), lower social support and higher general distress could significantly predict patient's choice for prognostic testing. After result announcement, perceived risk of metastases was significantly increased in patients with poor prognosis, while it decreased in those with good prognosis. Overall, a significant decrease over time appeared concerning fear of progression, general distress, depression and anxiety. Mental quality of life increased over time. The utilization of psycho-oncological interventions increased significantly after prognostication; however, this was equivalent in the test and observational groups. Female sex, higher general distress and higher anxiety predicted greater use of psycho-oncological interventions. DISCUSSION:Availing of prognostic testing is not associated with poorer subsequent psychological well-being. It rather may help to alleviate distress and promote a more realistic risk perception. However, psychological support should be available to all patients, independent of prognosis and treatment, especially considering that patients with low social support and high distress increasingly opt for prognostication.

Project description:Uveal melanoma (UM) is the most common malignant intraocular tumour in the adult population. It is a rare cancer with an incidence of nearly five cases per million inhabitants per year, which develops from the uncontrolled proliferation of melanocytes in the choroid (≈90%), ciliary body (≈6%) or iris (≈4%). Patients initially present either with symptoms like blurred vision or photopsia, or without symptoms, with the tumour being detected in routine eye exams. Over the course of the disease, metastases, which are initially dormant, develop in nearly 50% of patients, preferentially in the liver. Despite decades of intensive research, the only approach proven to mildly control disease spread are early treatments directed to ablate liver metastases, such as surgical excision or chemoembolization. However, most patients have a limited life expectancy once metastases are detected, since there are limited therapeutic approaches for the metastatic disease, including immunotherapy, which unlike in cutaneous melanoma, has been mostly ineffective for UM patients. Therefore, in order to offer the best care possible to these patients, there is an urgent need to find robust models that can accurately predict the prognosis of UM, as well as therapeutic strategies that effectively block and/or limit the spread of the metastatic disease. Here, we initially summarized the current knowledge about UM by compiling the most relevant epidemiological, clinical, pathological and molecular data. Then, we revisited the most important prognostic factors currently used for the evaluation and follow-up of primary UM cases. Afterwards, we addressed emerging prognostic biomarkers in UM, by comprehensively reviewing gene signatures, immunohistochemistry-based markers and proteomic markers resulting from research studies conducted over the past three years. Finally, we discussed the current hurdles in the field and anticipated the future challenges and novel avenues of research in UM.

Project description:BackgroundUveal melanoma (UM) is the most common primary intraocular malignancy in adults. Many previous studies have demonstrated that the infiltrating of immune and stromal cells in the tumor microenvironment contributes significantly to prognosis.MethodsDataset TCGA-UVM, download from TCGA portal, was taken as the training cohort, and GSE22138, obtained from GEO database, was set as the validation cohort. ESTIMATE algorithm was applied to find intersection differentially expressed genes (DEGs) among tumor microenvironment. Kaplan-Meier analysis and univariate Cox regression model were performed on intersection DEGs to initial screen for potential prognostic genes. Then these genes entered into the validation cohort for validation using the same methods as that in the training cohort. Moreover, we conducted correlation analyses between the genes obtained in the validation cohort and the status of chromosome 3, chromosome 8q, and tumor metastasis to get prognosis genes. At last, the immune infiltration analysis was performed between the prognostic genes and 6 main kinds of tumor-infiltrating immune cells (TICs) for understanding the role of the genes in the tumor microenvironment.Results959 intersection DEGs were found in the UM microenvironment. Kaplan-Meier and Cox analysis was then performed in the training and validation cohorts on these DEGs, and 52 genes were identified with potential prognostic value. After comparing the 52 genes to chromosome 3, chromosome 8q, and metastasis, we obtained 21 genes as the prognostic genes. The immune infiltration analysis showed that Neutrophil had the potential prognostic ability, and almost every prognostic gene we had identified was correlated with abundances of Neutrophil and CD8+ T Cell.ConclusionsIdentifying 21 prognosis genes (SERPINB9, EDNRB, RAPGEF3, HFE, RNF43, ZNF415, IL12RB2, MTUS1, NEDD9, ZNF667, AZGP1, WARS, GEM, RAB31, CALHM2, CA12, MYEOV, CELF2, SLCO5A1, ISM1, and PAPSS2) could accurately identify patients' prognosis and had close interactions with Neutrophil in the tumor environment, which may provide UM patients with personalized prognosis prediction and new treatment insights.

Dataset Information

Impact of Genetic Ancestry on Prognostic Biomarkers in Uveal Melanoma.

Publications

Impact of Genetic Ancestry on Prognostic Biomarkers in Uveal Melanoma.

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