RGD Reference Report - Genetic variants in the genes encoding rho GTPases and related regulators predict cutaneous melanoma-specific survival. - Rat Genome Database

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Genetic variants in the genes encoding rho GTPases and related regulators predict cutaneous melanoma-specific survival.

Authors: Liu, Shun  Wang, Yanru  Xue, William  Liu, Hongliang  Xu, Yinghui  Shi, Qiong  Wu, Wenting  Zhu, Dakai  Amos, Christopher I  Fang, Shenying  Lee, Jeffrey E  Hyslop, Terry  Li, Yi  Han, Jiali  Wei, Qingyi 
Citation: Liu S, etal., Int J Cancer. 2017 Aug 15;141(4):721-730. doi: 10.1002/ijc.30785. Epub 2017 Jun 1.
RGD ID: 401901274
Pubmed: PMID:28510328   (View Abstract at PubMed)
PMCID: PMC5512872   (View Article at PubMed Central)
DOI: DOI:10.1002/ijc.30785   (Journal Full-text)

Rho GTPases control cell division, motility, adhesion, vesicular trafficking and phagocytosis, which may affect progression and/or prognosis of cancers. Here, we investigated associations between genetic variants of Rho GTPases-related genes and cutaneous melanoma-specific survival (CMSS) by re-analyzing a published melanoma genome-wide association study (GWAS) and validating the results in another melanoma GWAS. In the single-locus analysis of 36,018 SNPs in 129 Rho-related genes, 427 SNPs were significantly associated with CMSS (p < 0.050 and false-positive report probability <0.2) in the discovery dataset, and five SNPs were replicated in the validation dataset. Among these, four SNPs (i.e., RHOU rs10916352 G > C, ARHGAP22 rs3851552 T > C, ARHGAP44 rs72635537 C > T and ARHGEF10 rs7826362 A > T) were independently predictive of CMSS (a meta-analysis derived p = 9.04 × 10-4 , 9.58 × 10-4 , 1.21 × 10-4 and 8.47 × 10-4 , respectively). Additionally, patients with an increasing number of unfavorable genotypes (NUGs) of these loci had markedly reduced CMSS in both discovery dataset and validation dataset (ptrend =1.47 × 10-7 and 3.12 × 10-5 ). The model including the NUGs and clinical variables demonstrated a significant improvement in predicting the five-year CMSS. Moreover, rs10916352C and rs3851552C alleles were significantly associated with an increased mRNA expression levels of RHOU (p = 1.8 × 10-6 ) and ARHGAP22 (p = 5.0 × 10-6 ), respectively. These results may provide promising prognostic biomarkers for CM personalized management and treatment.

RGD Manual Disease Annotations    Click to see Annotation Detail View
TermQualifierEvidenceWithReferenceNotesSourceOriginal Reference(s)
skin melanoma severityIAGP 401901274DNA:SNP:intron: (rs72635537) (human)RGD 
skin melanoma severityISOARHGAP44 (Homo sapiens)401901274; 401901274DNA:SNP:intron: (rs72635537) (human)RGD 

Phenotype Annotations    Click to see Annotation Detail View

Manual Human Phenotype Annotations - RGD

TermQualifierEvidenceWithReferenceNotesSourceOriginal Reference(s)
Cutaneous melanoma severityIAGP 401901274DNA:SNP:intron: (rs72635537)RGD 
Objects Annotated

Genes (Rattus norvegicus)
Arhgap44  (Rho GTPase activating protein 44)

Genes (Mus musculus)
Arhgap44  (Rho GTPase activating protein 44)

Genes (Homo sapiens)
ARHGAP44  (Rho GTPase activating protein 44)


Additional Information