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Whole exome sequencing identifies a recurrent RQCD1 P131L mutation in cutaneous melanoma.

Wong SQ, Behren A, Mar VJ, Woods K, Li J, Martin C, Sheppard KE, Wolfe R, Kelly J, Cebon J, Dobrovic A, McArthur GA - Oncotarget (2015)

Bottom Line: Compared to tumors without the mutation, the P131L mutant positive tumors were associated with increased thickness (p = 0.02), head and neck (p = 0.009) and upper limb (p = 0.03) location, lentigo maligna melanoma subtype (p = 0.02) and BRAF V600K (p = 0.04) but not V600E or NRAS codon 61 mutations.Mutant RQCD1 was predicted to bind strongly to HLA-A0201 and HLA-Cw3 MHC1 complexes.From thirteen patients with mutant RQCD1, an anti-tumor CD8⁺ T cell response was observed from a single patient's peripheral blood mononuclear cell population stimulated with mutated peptide compared to wildtype indicating a neoantigen may be formed.

View Article: PubMed Central - PubMed

Affiliation: Division of Cancer Research, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia.

ABSTRACT
Melanoma is often caused by mutations due to exposure to ultraviolet radiation. This study reports a recurrent somatic C > T change causing a P131L mutation in the RQCD1 (Required for Cell Differentiation1 Homolog) gene identified through whole exome sequencing of 20 metastatic melanomas. Screening in 715 additional primary melanomas revealed a prevalence of ~4%. This represents the first reported recurrent mutation in a member of the CCR4-NOT complex in cancer. Compared to tumors without the mutation, the P131L mutant positive tumors were associated with increased thickness (p = 0.02), head and neck (p = 0.009) and upper limb (p = 0.03) location, lentigo maligna melanoma subtype (p = 0.02) and BRAF V600K (p = 0.04) but not V600E or NRAS codon 61 mutations. There was no association with nodal disease (p = 0.3). Mutually exclusive mutations of other members of the CCR4-NOT complex were found in ~20% of the TCGA melanoma dataset suggesting the complex may play an important role in melanoma biology. Mutant RQCD1 was predicted to bind strongly to HLA-A0201 and HLA-Cw3 MHC1 complexes. From thirteen patients with mutant RQCD1, an anti-tumor CD8⁺ T cell response was observed from a single patient's peripheral blood mononuclear cell population stimulated with mutated peptide compared to wildtype indicating a neoantigen may be formed.

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Recurrent hotspot RQCD1 P131L mutation(A) Representative melting peak curve from a high resolution melting analysis of the RQCD1 P131L region. Three wildtype patients are shown in blue with one RQCD1 P131L positive sample shown in pink. Validation of aberrant melt curves from the high resolution melting analysis was performed using Sanger sequencing (Shown are sequencing chromatograms from a positive RQCD1 P131L patient and a wildtype patient). (B) Conservation of RQCD1 at the P131 residue across various species (C) Location of P131 residue on crystal structure of RQCD1. Zoomed view: Rendered spherical chemical structures of the wildtype proline at position 131 and mutant leucine residue. The protein crystal structure of the Human RQCD1 was generated using PyMOL software 3.0.
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Figure 2: Recurrent hotspot RQCD1 P131L mutation(A) Representative melting peak curve from a high resolution melting analysis of the RQCD1 P131L region. Three wildtype patients are shown in blue with one RQCD1 P131L positive sample shown in pink. Validation of aberrant melt curves from the high resolution melting analysis was performed using Sanger sequencing (Shown are sequencing chromatograms from a positive RQCD1 P131L patient and a wildtype patient). (B) Conservation of RQCD1 at the P131 residue across various species (C) Location of P131 residue on crystal structure of RQCD1. Zoomed view: Rendered spherical chemical structures of the wildtype proline at position 131 and mutant leucine residue. The protein crystal structure of the Human RQCD1 was generated using PyMOL software 3.0.

Mentions: We validated the RQCD1 P131L mutations by screening an additional 715 cases of primary cutaneous melanoma by high resolution melting analysis (HRM) screening and Sanger sequencing of samples with heteroduplexes (Figure 2a). Of the 715 cases, 29 (4%) had the RQCD1 P131L mutation. Eleven cases with the RQCD1 mutation were female and 18 male (p = 0.7) (Table 2). The median age of patients with RQCD1 mutant melanomas was 61 years compared to 58 years for patients without the mutation (p = 0.6).


Whole exome sequencing identifies a recurrent RQCD1 P131L mutation in cutaneous melanoma.

Wong SQ, Behren A, Mar VJ, Woods K, Li J, Martin C, Sheppard KE, Wolfe R, Kelly J, Cebon J, Dobrovic A, McArthur GA - Oncotarget (2015)

Recurrent hotspot RQCD1 P131L mutation(A) Representative melting peak curve from a high resolution melting analysis of the RQCD1 P131L region. Three wildtype patients are shown in blue with one RQCD1 P131L positive sample shown in pink. Validation of aberrant melt curves from the high resolution melting analysis was performed using Sanger sequencing (Shown are sequencing chromatograms from a positive RQCD1 P131L patient and a wildtype patient). (B) Conservation of RQCD1 at the P131 residue across various species (C) Location of P131 residue on crystal structure of RQCD1. Zoomed view: Rendered spherical chemical structures of the wildtype proline at position 131 and mutant leucine residue. The protein crystal structure of the Human RQCD1 was generated using PyMOL software 3.0.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4359221&req=5

Figure 2: Recurrent hotspot RQCD1 P131L mutation(A) Representative melting peak curve from a high resolution melting analysis of the RQCD1 P131L region. Three wildtype patients are shown in blue with one RQCD1 P131L positive sample shown in pink. Validation of aberrant melt curves from the high resolution melting analysis was performed using Sanger sequencing (Shown are sequencing chromatograms from a positive RQCD1 P131L patient and a wildtype patient). (B) Conservation of RQCD1 at the P131 residue across various species (C) Location of P131 residue on crystal structure of RQCD1. Zoomed view: Rendered spherical chemical structures of the wildtype proline at position 131 and mutant leucine residue. The protein crystal structure of the Human RQCD1 was generated using PyMOL software 3.0.
Mentions: We validated the RQCD1 P131L mutations by screening an additional 715 cases of primary cutaneous melanoma by high resolution melting analysis (HRM) screening and Sanger sequencing of samples with heteroduplexes (Figure 2a). Of the 715 cases, 29 (4%) had the RQCD1 P131L mutation. Eleven cases with the RQCD1 mutation were female and 18 male (p = 0.7) (Table 2). The median age of patients with RQCD1 mutant melanomas was 61 years compared to 58 years for patients without the mutation (p = 0.6).

Bottom Line: Compared to tumors without the mutation, the P131L mutant positive tumors were associated with increased thickness (p = 0.02), head and neck (p = 0.009) and upper limb (p = 0.03) location, lentigo maligna melanoma subtype (p = 0.02) and BRAF V600K (p = 0.04) but not V600E or NRAS codon 61 mutations.Mutant RQCD1 was predicted to bind strongly to HLA-A0201 and HLA-Cw3 MHC1 complexes.From thirteen patients with mutant RQCD1, an anti-tumor CD8⁺ T cell response was observed from a single patient's peripheral blood mononuclear cell population stimulated with mutated peptide compared to wildtype indicating a neoantigen may be formed.

View Article: PubMed Central - PubMed

Affiliation: Division of Cancer Research, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia.

ABSTRACT
Melanoma is often caused by mutations due to exposure to ultraviolet radiation. This study reports a recurrent somatic C > T change causing a P131L mutation in the RQCD1 (Required for Cell Differentiation1 Homolog) gene identified through whole exome sequencing of 20 metastatic melanomas. Screening in 715 additional primary melanomas revealed a prevalence of ~4%. This represents the first reported recurrent mutation in a member of the CCR4-NOT complex in cancer. Compared to tumors without the mutation, the P131L mutant positive tumors were associated with increased thickness (p = 0.02), head and neck (p = 0.009) and upper limb (p = 0.03) location, lentigo maligna melanoma subtype (p = 0.02) and BRAF V600K (p = 0.04) but not V600E or NRAS codon 61 mutations. There was no association with nodal disease (p = 0.3). Mutually exclusive mutations of other members of the CCR4-NOT complex were found in ~20% of the TCGA melanoma dataset suggesting the complex may play an important role in melanoma biology. Mutant RQCD1 was predicted to bind strongly to HLA-A0201 and HLA-Cw3 MHC1 complexes. From thirteen patients with mutant RQCD1, an anti-tumor CD8⁺ T cell response was observed from a single patient's peripheral blood mononuclear cell population stimulated with mutated peptide compared to wildtype indicating a neoantigen may be formed.

Show MeSH
Related in: MedlinePlus