Cross-platform comparison of independent datasets identifies an immune signature associated with improved survival in metastatic melanoma

Autor: Ricardo D. Lardone, John R. Jalas, Jaime M. Shamonki, Seema B. Plaisier, Peter A. Sieling, Delphine J. Lee, Marian S. Navarrete
Jazyk: angličtina
Rok vydání: 2016
Předmět:
0301 basic medicine
Oncology
Medicina Clínica
purl.org/becyt/ford/1 [https]
0302 clinical medicine
Gene expression
Databases
Genetic
purl.org/becyt/ford/3.2 [https]
METASTATIC MELANOMA
tumor immunology
Melanoma
Regulation of gene expression
BIOINFORMATICS
Area under the curve
bioinformatics
purl.org/becyt/ford/1.2 [https]
purl.org/becyt/ford/3.1 [https]
Prognosis
3. Good health
Gene Expression Regulation
Neoplastic
Survival Rate
Medicina Básica
030220 oncology & carcinogenesis
Data Interpretation
Statistical
purl.org/becyt/ford/3 [https]
Medicina Critica y de Emergencia
CIENCIAS NATURALES Y EXACTAS
Algorithms
Research Paper
metastatic melanoma
rank-rank hypergeometric overlap
medicine.medical_specialty
CIENCIAS MÉDICAS Y DE LA SALUD
TUMOR IMMUNOLOGY
Inmunología
03 medical and health sciences
Immune system
Internal medicine
medicine
Biomarkers
Tumor
Humans
Gene
Survival rate
B cells
business.industry
Gene Expression Profiling
medicine.disease
Ciencias de la Computación
Gene expression profiling
030104 developmental biology
RANK-RANK HYPERGEOMETRIC OVERLAP
B CELLS
Ciencias de la Computación e Información
Immunology
business
Transcriptome
Biomarkers
Zdroj: CONICET Digital (CONICET)
Consejo Nacional de Investigaciones Científicas y Técnicas
instacron:CONICET
Oncotarget
Popis: // Ricardo D. Lardone 1 , Seema B. Plaisier 1 , Marian S. Navarrete 1 , Jaime M. Shamonki 2 , John R. Jalas 3 , Peter A. Sieling 1, * , Delphine J. Lee 1, * 1 Department of Translational Immunology, Dirks/Dougherty Laboratory for Cancer Research, John Wayne Cancer Institute, Santa Monica, CA 90404, USA 2 California Cryobank, Los Angeles, CA 90025, USA 3 Department of Pathology at Providence Saint John’s Health Center, Santa Monica, CA 90404, USA * These authors have contributed equally to this work Correspondence to: Delphine J. Lee, e-mail: leedj@jwci.org Ricardo D. Lardone, e-mail: rlardone@gmail.com Keywords: metastatic melanoma, tumor immunology, bioinformatics, rank-rank hypergeometric overlap, B cells Received: November 02, 2015 Accepted: January 29, 2016 Published: February 13, 2016 ABSTRACT Platform and study differences in prognostic signatures from metastatic melanoma (MM) gene expression reports often hinder consensus arrival. We performed survival/outcome-based pairwise comparisons of three independent MM gene expression profiles using the threshold-free algorithm rank-rank hypergeometric overlap analysis (RRHO). We found statistically significant overlap for genes overexpressed in favorable outcome (FO) groups, but no overlap for poor outcome (PO) groups. This “favorable outcome signature” (FOS) of 228 genes coinciding on all three overlapping gene lists showed immune function predominated in FO MM. Surprisingly, specific cell signature-enrichment analysis showed B cell-associated genes enriched in FO MM, along with T cell-associated genes. Higher levels of B and T cells (p
Databáze: OpenAIRE
Externí odkaz: