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
- Institución
- Consejo Nacional de Investigaciones Científicas y Técnicas
- OAI Identificador
- oai:ri.conicet.gov.ar:11336/52094
Ver los metadatos del registro completo
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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 |
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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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13.13397 |