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

Autores
Lardone, Ricardo Dante; Plaisier, Seema; Navarrete, Marian S.; Shamonki, Jaime M.; Jalas, John R.; Sieling, Peter A; Lee, Delphine J.
Año de publicación
2016
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
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<0.05) and their relative proximity (p<0.05) were detected in FO-to-PO tumor comparisons from an independent MM patients cohort. Finally, expression of FOS in two independent Stage III MM tumor datasets correctly predicted clinical outcome in 12/14 and 44/70 patients using a weighted gene voting classifier (area under the curve values 0.96 and 0.75, respectively). This RRHO-based, cross-study analysis emphasizes the RRHO approach power, confirms T cells relevance for prolonged MM survival, supports a favorable role for B cells in anti-melanoma immunity, and suggests B cells potential as means of intervention in melanoma treatment.
Fil: Lardone, Ricardo Dante. The John Wayne Cancer Institute; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Plaisier, Seema. The John Wayne Cancer Institute; Estados Unidos
Fil: Navarrete, Marian S.. The John Wayne Cancer Institute; Estados Unidos
Fil: Shamonki, Jaime M.. California Cryobank; Estados Unidos
Fil: Jalas, John R.. Providence Saint John’s Health Center; Estados Unidos
Fil: Sieling, Peter A. The John Wayne Cancer Institute; Estados Unidos
Fil: Lee, Delphine J.. The John Wayne Cancer Institute; Estados Unidos
Materia
B CELLS
BIOINFORMATICS
METASTATIC MELANOMA
RANK-RANK HYPERGEOMETRIC OVERLAP
TUMOR IMMUNOLOGY
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/52094

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oai_identifier_str oai:ri.conicet.gov.ar:11336/52094
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Cross-platform comparison of independent datasets identifies an immune signature associated with improved survival in metastatic melanomaLardone, Ricardo DantePlaisier, SeemaNavarrete, Marian S.Shamonki, Jaime M.Jalas, John R.Sieling, Peter ALee, Delphine J.B CELLSBIOINFORMATICSMETASTATIC MELANOMARANK-RANK HYPERGEOMETRIC OVERLAPTUMOR IMMUNOLOGYhttps://purl.org/becyt/ford/3.2https://purl.org/becyt/ford/3https://purl.org/becyt/ford/1.2https://purl.org/becyt/ford/1https://purl.org/becyt/ford/3.1https://purl.org/becyt/ford/3Platform 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<0.05) and their relative proximity (p<0.05) were detected in FO-to-PO tumor comparisons from an independent MM patients cohort. Finally, expression of FOS in two independent Stage III MM tumor datasets correctly predicted clinical outcome in 12/14 and 44/70 patients using a weighted gene voting classifier (area under the curve values 0.96 and 0.75, respectively). This RRHO-based, cross-study analysis emphasizes the RRHO approach power, confirms T cells relevance for prolonged MM survival, supports a favorable role for B cells in anti-melanoma immunity, and suggests B cells potential as means of intervention in melanoma treatment.Fil: Lardone, Ricardo Dante. The John Wayne Cancer Institute; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Plaisier, Seema. The John Wayne Cancer Institute; Estados UnidosFil: Navarrete, Marian S.. The John Wayne Cancer Institute; Estados UnidosFil: Shamonki, Jaime M.. California Cryobank; Estados UnidosFil: Jalas, John R.. Providence Saint John’s Health Center; Estados UnidosFil: Sieling, Peter A. The John Wayne Cancer Institute; Estados UnidosFil: Lee, Delphine J.. The John Wayne Cancer Institute; Estados UnidosImpact Journals2016-02info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/52094Lardone, Ricardo Dante; Plaisier, Seema; Navarrete, Marian S.; Shamonki, Jaime M.; Jalas, John R.; et al.; Cross-platform comparison of independent datasets identifies an immune signature associated with improved survival in metastatic melanoma; Impact Journals; Oncotarget; 7; 12; 2-2016; 14415-144281949-2553CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.18632/oncotarget.7361info:eu-repo/semantics/altIdentifier/url/https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4924725/info:eu-repo/semantics/altIdentifier/url/http://www.oncotarget.com/index.php?journal=oncotarget&page=article&op=view&path[]=7361&path[]=21094info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-03T09:54:32Zoai:ri.conicet.gov.ar:11336/52094instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-03 09:54:32.711CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Cross-platform comparison of independent datasets identifies an immune signature associated with improved survival in metastatic melanoma
title Cross-platform comparison of independent datasets identifies an immune signature associated with improved survival in metastatic melanoma
spellingShingle Cross-platform comparison of independent datasets identifies an immune signature associated with improved survival in metastatic melanoma
Lardone, Ricardo Dante
B CELLS
BIOINFORMATICS
METASTATIC MELANOMA
RANK-RANK HYPERGEOMETRIC OVERLAP
TUMOR IMMUNOLOGY
title_short Cross-platform comparison of independent datasets identifies an immune signature associated with improved survival in metastatic melanoma
title_full Cross-platform comparison of independent datasets identifies an immune signature associated with improved survival in metastatic melanoma
title_fullStr Cross-platform comparison of independent datasets identifies an immune signature associated with improved survival in metastatic melanoma
title_full_unstemmed Cross-platform comparison of independent datasets identifies an immune signature associated with improved survival in metastatic melanoma
title_sort Cross-platform comparison of independent datasets identifies an immune signature associated with improved survival in metastatic melanoma
dc.creator.none.fl_str_mv Lardone, Ricardo Dante
Plaisier, Seema
Navarrete, Marian S.
Shamonki, Jaime M.
Jalas, John R.
Sieling, Peter A
Lee, Delphine J.
author Lardone, Ricardo Dante
author_facet Lardone, Ricardo Dante
Plaisier, Seema
Navarrete, Marian S.
Shamonki, Jaime M.
Jalas, John R.
Sieling, Peter A
Lee, Delphine J.
author_role author
author2 Plaisier, Seema
Navarrete, Marian S.
Shamonki, Jaime M.
Jalas, John R.
Sieling, Peter A
Lee, Delphine J.
author2_role author
author
author
author
author
author
dc.subject.none.fl_str_mv B CELLS
BIOINFORMATICS
METASTATIC MELANOMA
RANK-RANK HYPERGEOMETRIC OVERLAP
TUMOR IMMUNOLOGY
topic B CELLS
BIOINFORMATICS
METASTATIC MELANOMA
RANK-RANK HYPERGEOMETRIC OVERLAP
TUMOR IMMUNOLOGY
purl_subject.fl_str_mv https://purl.org/becyt/ford/3.2
https://purl.org/becyt/ford/3
https://purl.org/becyt/ford/1.2
https://purl.org/becyt/ford/1
https://purl.org/becyt/ford/3.1
https://purl.org/becyt/ford/3
dc.description.none.fl_txt_mv 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<0.05) and their relative proximity (p<0.05) were detected in FO-to-PO tumor comparisons from an independent MM patients cohort. Finally, expression of FOS in two independent Stage III MM tumor datasets correctly predicted clinical outcome in 12/14 and 44/70 patients using a weighted gene voting classifier (area under the curve values 0.96 and 0.75, respectively). This RRHO-based, cross-study analysis emphasizes the RRHO approach power, confirms T cells relevance for prolonged MM survival, supports a favorable role for B cells in anti-melanoma immunity, and suggests B cells potential as means of intervention in melanoma treatment.
Fil: Lardone, Ricardo Dante. The John Wayne Cancer Institute; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Plaisier, Seema. The John Wayne Cancer Institute; Estados Unidos
Fil: Navarrete, Marian S.. The John Wayne Cancer Institute; Estados Unidos
Fil: Shamonki, Jaime M.. California Cryobank; Estados Unidos
Fil: Jalas, John R.. Providence Saint John’s Health Center; Estados Unidos
Fil: Sieling, Peter A. The John Wayne Cancer Institute; Estados Unidos
Fil: Lee, Delphine J.. The John Wayne Cancer Institute; Estados Unidos
description 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<0.05) and their relative proximity (p<0.05) were detected in FO-to-PO tumor comparisons from an independent MM patients cohort. Finally, expression of FOS in two independent Stage III MM tumor datasets correctly predicted clinical outcome in 12/14 and 44/70 patients using a weighted gene voting classifier (area under the curve values 0.96 and 0.75, respectively). This RRHO-based, cross-study analysis emphasizes the RRHO approach power, confirms T cells relevance for prolonged MM survival, supports a favorable role for B cells in anti-melanoma immunity, and suggests B cells potential as means of intervention in melanoma treatment.
publishDate 2016
dc.date.none.fl_str_mv 2016-02
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/52094
Lardone, Ricardo Dante; Plaisier, Seema; Navarrete, Marian S.; Shamonki, Jaime M.; Jalas, John R.; et al.; Cross-platform comparison of independent datasets identifies an immune signature associated with improved survival in metastatic melanoma; Impact Journals; Oncotarget; 7; 12; 2-2016; 14415-14428
1949-2553
CONICET Digital
CONICET
url http://hdl.handle.net/11336/52094
identifier_str_mv Lardone, Ricardo Dante; Plaisier, Seema; Navarrete, Marian S.; Shamonki, Jaime M.; Jalas, John R.; et al.; Cross-platform comparison of independent datasets identifies an immune signature associated with improved survival in metastatic melanoma; Impact Journals; Oncotarget; 7; 12; 2-2016; 14415-14428
1949-2553
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/doi/10.18632/oncotarget.7361
info:eu-repo/semantics/altIdentifier/url/https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4924725/
info:eu-repo/semantics/altIdentifier/url/http://www.oncotarget.com/index.php?journal=oncotarget&page=article&op=view&path[]=7361&path[]=21094
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Impact Journals
publisher.none.fl_str_mv Impact Journals
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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