Intrinsic genomic differences between african American and white patients with clear cell renal cell carcinoma

Bhavani Krishnan, Tracy L. Rose, Jordan Kardos, Matthew I. Milowsky, William Y. Kim

Research output: Research - peer-reviewArticle

  • 4 Citations

Abstract

IMPORTANCE There are well-documented racial disparities in outcomes for African American patients with clear cell renal cell carcinoma (ccRCC). Despite a dramatic improvement in overall survival in white patients since the advent of targeted therapy, survival for African Americans with advanced ccRCC has not changed. There is little known about potential racial differences in tumor biology of ccRCC. OBJECTIVE To determine if there are racial differences in the somatic mutation rate and gene expression of ccRCC tumors from white and African American patients. DESIGN, SETTING, AND PARTICIPANTS Overall, 438 patients with ccRCCwere identified through The Cancer Genome Atlas (TCGA) clear cell kidney (KIRC) dataset (419 white and 19 African American patients). The GSE25540 dataset containing 135 patients (125 white and 10 African American patients) was used for validation. Tumor samples were collected from numerous cancer centers and were examined for racial differences in somatic mutation rates and RNA expression. Racial differences in somatic mutation rates and RNA expression were examined. MAIN OUTCOMES AND MEASURES The comparison of somatic mutation rates and differences in RNA expression in white and African American patients with ccRCC. RESULTS Overall, 419 ccRCC tumor data sets from non-Hispanic white patients and 19 from non-Hispanic African American patients were identified through the publically available TCGA KIRC data set, and a validation set of 125 white and 10 African American ccRCC patient tumors was identified from the publicly available GSE25540 data set. African American patients were significantly less likely than white patients to have VHL mutations (2 of 12 [17%] vs 175 of 351 [50%], respectively; P = .04) and were enriched in the ccB molecular subtype (79% in African American vs 45%in white patients ; P = .005), a molecular subtype that carries a worse prognosis. It was found that RNA expression analysis revealed relative down-regulation of hypoxia-inducible factor (HIF) and vascular endothelial growth factor (VEGF)-associated pathways in African American patients compared with white patients. CONCLUSIONS AND RELEVANCE African American patients have less frequent VHL inactivation, are enriched in the ccB molecular subtype, and have decreased up-regulation of HIF-associated gene signatures than white patients. These genomic differences would predict decreased responsiveness to VEGF-targeted therapy and are a biologically plausible contributing factor to the worse survival of African American patients with ccRCC, even in the targeted therapy era.

LanguageEnglish (US)
Pages664-667
Number of pages4
JournalJAMA Oncology
Volume2
Issue number5
DOIs
StatePublished - May 1 2016

Fingerprint

Renal Cell Carcinoma
African Americans
Neoplasms
Datasets
Mutation Rate
RNA
Survival
Therapeutics
Atlases
Vascular Endothelial Growth Factor A
Genome
Hypoxia
Up-Regulation
Down-Regulation
Kidney
Gene Expression
Mutation
Genes

ASJC Scopus subject areas

  • Medicine(all)

Cite this

Intrinsic genomic differences between african American and white patients with clear cell renal cell carcinoma. / Krishnan, Bhavani; Rose, Tracy L.; Kardos, Jordan; Milowsky, Matthew I.; Kim, William Y.

In: JAMA Oncology, Vol. 2, No. 5, 01.05.2016, p. 664-667.

Research output: Research - peer-reviewArticle

Krishnan, Bhavani ; Rose, Tracy L. ; Kardos, Jordan ; Milowsky, Matthew I. ; Kim, William Y./ Intrinsic genomic differences between african American and white patients with clear cell renal cell carcinoma. In: JAMA Oncology. 2016 ; Vol. 2, No. 5. pp. 664-667
@article{3c3001cfd57c4f688a0965a79103f6c0,
title = "Intrinsic genomic differences between african American and white patients with clear cell renal cell carcinoma",
abstract = "IMPORTANCE There are well-documented racial disparities in outcomes for African American patients with clear cell renal cell carcinoma (ccRCC). Despite a dramatic improvement in overall survival in white patients since the advent of targeted therapy, survival for African Americans with advanced ccRCC has not changed. There is little known about potential racial differences in tumor biology of ccRCC. OBJECTIVE To determine if there are racial differences in the somatic mutation rate and gene expression of ccRCC tumors from white and African American patients. DESIGN, SETTING, AND PARTICIPANTS Overall, 438 patients with ccRCCwere identified through The Cancer Genome Atlas (TCGA) clear cell kidney (KIRC) dataset (419 white and 19 African American patients). The GSE25540 dataset containing 135 patients (125 white and 10 African American patients) was used for validation. Tumor samples were collected from numerous cancer centers and were examined for racial differences in somatic mutation rates and RNA expression. Racial differences in somatic mutation rates and RNA expression were examined. MAIN OUTCOMES AND MEASURES The comparison of somatic mutation rates and differences in RNA expression in white and African American patients with ccRCC. RESULTS Overall, 419 ccRCC tumor data sets from non-Hispanic white patients and 19 from non-Hispanic African American patients were identified through the publically available TCGA KIRC data set, and a validation set of 125 white and 10 African American ccRCC patient tumors was identified from the publicly available GSE25540 data set. African American patients were significantly less likely than white patients to have VHL mutations (2 of 12 [17%] vs 175 of 351 [50%], respectively; P = .04) and were enriched in the ccB molecular subtype (79% in African American vs 45%in white patients ; P = .005), a molecular subtype that carries a worse prognosis. It was found that RNA expression analysis revealed relative down-regulation of hypoxia-inducible factor (HIF) and vascular endothelial growth factor (VEGF)-associated pathways in African American patients compared with white patients. CONCLUSIONS AND RELEVANCE African American patients have less frequent VHL inactivation, are enriched in the ccB molecular subtype, and have decreased up-regulation of HIF-associated gene signatures than white patients. These genomic differences would predict decreased responsiveness to VEGF-targeted therapy and are a biologically plausible contributing factor to the worse survival of African American patients with ccRCC, even in the targeted therapy era.",
author = "Bhavani Krishnan and Rose, {Tracy L.} and Jordan Kardos and Milowsky, {Matthew I.} and Kim, {William Y.}",
year = "2016",
month = "5",
doi = "10.1001/jamaoncol.2016.0005",
volume = "2",
pages = "664--667",
journal = "JAMA oncology",
issn = "2374-2437",
publisher = "American Medical Association",
number = "5",

}

TY - JOUR

T1 - Intrinsic genomic differences between african American and white patients with clear cell renal cell carcinoma

AU - Krishnan,Bhavani

AU - Rose,Tracy L.

AU - Kardos,Jordan

AU - Milowsky,Matthew I.

AU - Kim,William Y.

PY - 2016/5/1

Y1 - 2016/5/1

N2 - IMPORTANCE There are well-documented racial disparities in outcomes for African American patients with clear cell renal cell carcinoma (ccRCC). Despite a dramatic improvement in overall survival in white patients since the advent of targeted therapy, survival for African Americans with advanced ccRCC has not changed. There is little known about potential racial differences in tumor biology of ccRCC. OBJECTIVE To determine if there are racial differences in the somatic mutation rate and gene expression of ccRCC tumors from white and African American patients. DESIGN, SETTING, AND PARTICIPANTS Overall, 438 patients with ccRCCwere identified through The Cancer Genome Atlas (TCGA) clear cell kidney (KIRC) dataset (419 white and 19 African American patients). The GSE25540 dataset containing 135 patients (125 white and 10 African American patients) was used for validation. Tumor samples were collected from numerous cancer centers and were examined for racial differences in somatic mutation rates and RNA expression. Racial differences in somatic mutation rates and RNA expression were examined. MAIN OUTCOMES AND MEASURES The comparison of somatic mutation rates and differences in RNA expression in white and African American patients with ccRCC. RESULTS Overall, 419 ccRCC tumor data sets from non-Hispanic white patients and 19 from non-Hispanic African American patients were identified through the publically available TCGA KIRC data set, and a validation set of 125 white and 10 African American ccRCC patient tumors was identified from the publicly available GSE25540 data set. African American patients were significantly less likely than white patients to have VHL mutations (2 of 12 [17%] vs 175 of 351 [50%], respectively; P = .04) and were enriched in the ccB molecular subtype (79% in African American vs 45%in white patients ; P = .005), a molecular subtype that carries a worse prognosis. It was found that RNA expression analysis revealed relative down-regulation of hypoxia-inducible factor (HIF) and vascular endothelial growth factor (VEGF)-associated pathways in African American patients compared with white patients. CONCLUSIONS AND RELEVANCE African American patients have less frequent VHL inactivation, are enriched in the ccB molecular subtype, and have decreased up-regulation of HIF-associated gene signatures than white patients. These genomic differences would predict decreased responsiveness to VEGF-targeted therapy and are a biologically plausible contributing factor to the worse survival of African American patients with ccRCC, even in the targeted therapy era.

AB - IMPORTANCE There are well-documented racial disparities in outcomes for African American patients with clear cell renal cell carcinoma (ccRCC). Despite a dramatic improvement in overall survival in white patients since the advent of targeted therapy, survival for African Americans with advanced ccRCC has not changed. There is little known about potential racial differences in tumor biology of ccRCC. OBJECTIVE To determine if there are racial differences in the somatic mutation rate and gene expression of ccRCC tumors from white and African American patients. DESIGN, SETTING, AND PARTICIPANTS Overall, 438 patients with ccRCCwere identified through The Cancer Genome Atlas (TCGA) clear cell kidney (KIRC) dataset (419 white and 19 African American patients). The GSE25540 dataset containing 135 patients (125 white and 10 African American patients) was used for validation. Tumor samples were collected from numerous cancer centers and were examined for racial differences in somatic mutation rates and RNA expression. Racial differences in somatic mutation rates and RNA expression were examined. MAIN OUTCOMES AND MEASURES The comparison of somatic mutation rates and differences in RNA expression in white and African American patients with ccRCC. RESULTS Overall, 419 ccRCC tumor data sets from non-Hispanic white patients and 19 from non-Hispanic African American patients were identified through the publically available TCGA KIRC data set, and a validation set of 125 white and 10 African American ccRCC patient tumors was identified from the publicly available GSE25540 data set. African American patients were significantly less likely than white patients to have VHL mutations (2 of 12 [17%] vs 175 of 351 [50%], respectively; P = .04) and were enriched in the ccB molecular subtype (79% in African American vs 45%in white patients ; P = .005), a molecular subtype that carries a worse prognosis. It was found that RNA expression analysis revealed relative down-regulation of hypoxia-inducible factor (HIF) and vascular endothelial growth factor (VEGF)-associated pathways in African American patients compared with white patients. CONCLUSIONS AND RELEVANCE African American patients have less frequent VHL inactivation, are enriched in the ccB molecular subtype, and have decreased up-regulation of HIF-associated gene signatures than white patients. These genomic differences would predict decreased responsiveness to VEGF-targeted therapy and are a biologically plausible contributing factor to the worse survival of African American patients with ccRCC, even in the targeted therapy era.

UR - http://www.scopus.com/inward/record.url?scp=85010660540&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85010660540&partnerID=8YFLogxK

U2 - 10.1001/jamaoncol.2016.0005

DO - 10.1001/jamaoncol.2016.0005

M3 - Article

VL - 2

SP - 664

EP - 667

JO - JAMA oncology

T2 - JAMA oncology

JF - JAMA oncology

SN - 2374-2437

IS - 5

ER -