Johns Hopkins University

The United States of America, As Represented by the Secretary, Department of Health and Human Services

Yardena Samuels

Bert Vogelstein

Kenneth W Kinzler

Victor E Velculescu

Alberto Bardelli

Todd D Prickett

Tian-li Wang

Donald William Parsons

Christopher Lengauer

Wei Xiaomu

Phosphatidylinositol 3-kinases (PI3Ks) are known to be important regulators of signaling pathways. To determine whether PI3Ks are genetically altered in cancers, we analyzed the sequences of the PI3K gene family and discovered that one family member, PIK3CA, is frequently mutated in cancers of the colon and other organs. The majority of mutations clustered near two positions within the PI3K helical or kinase domains. PIK3CA represents one of the most highly mutated oncogenes yet identified in human cancers and is useful as a diagnostic and therapeutic target.

Treatment of cancers having mutations of the PIK3CA gene

Mutations of the PIK3CA gene in human cancers

Given the important role of protein kinases in pathways affecting cellular growth and invasion, we have analyzed 340 serine/threonine kinases for genetic mutations in colorectal cancers. Mutations in eight genes were identified, including three members of the phosphatidylinositol-3-kinase (PI3K) pathway; the alterations in the latter genes each occurred in different tumors and did not overlap with mutations in PIK3CA or other non-serine-threonine kinase (STK) members of the PI3K pathway, suggesting that mutations in any of these genes had equivalent tumorigenic effects. These data demonstrate that the PI3K pathway is a major target for mutational activation in colorectal cancers and provide new opportunities for therapeutic intervention.

P13K pathway mutations in cancer

Described herein is the identification of 68 genes with an elevated frequency of somatic mutations in melanoma. Nine genes were identified that exhibited recurring mutations in melanoma. The TRRAP gene was mutated at nucleotide 2165 (C2165T) in six different melanoma tumor samples. In addition, 16 genes were identified that were highly mutated in melanoma samples. The most highly mutated gene identified was GRIN2A, which was mutated in 34% of melanoma tumor samples. The study disclosed herein identified 34 different nonsynonymous somatic mutations in GRIN2A among 36 melanoma tumor samples. Provided is a method of diagnosing a subject as having melanoma or susceptible to developing melanoma by detecting one or more mutations in the TRRAP or GRIN2A genes. Further provided is a method of selecting an appropriate therapy for a subject diagnosed with melanoma by detecting the presence or absence of a mutation in TRRAP or GRIN2A.

GRIN2A mutations and use thereof for the diagnosis of melanoma

It is disclosed herein that members of the protein tyrosine kinase (PTK) family are highly mutated in patients with melanoma. Described herein are novel somatic mutations in the ERBB4 gene that result in increased kinase activity, transformation ability and anchorage-independent growth. These ERBB4 mutations contribute to the tumorogenicity of melanoma. Thus, provided herein is a method of predicting the prognosis of a patient with melanoma by detecting the presence or absence of a mutation in the ERBB4 gene. In some examples, the ERBB4 mutation is selected from G949A, G1354A, G1624A, C1630T, G1687A, G2506A and G2614A (numbering based on SEQ ID NO: 1). Also provided are methods of selecting a patient as a candidate for treatment with an ERBB4 and/or PI3K/AKT pathway inhibitor, and a method of identifying a therapeutic agent for the treatment of a subject diagnosed with melanoma. Oligonucleotides that specifically hybridize with an ERBB4 nucleic acid molecule comprising a novel mutation, and arrays comprising such oligonucleotides, are also provided.

Use of ERBB4 as a prognostic and therapeutic marker for melanoma

Phosphatidylinositol 3-kinases (PI3Ks) are known to be important regulators of signaling pathways. To determine whether PI3Ks are genetically altered in cancers, we analyzed the sequences of the P13K gene family and discovered that one family member, PIK3CA, is frequently mutated in cancers of the colon and other organs. The majority of mutations clustered near two positions within the P13K helical or kinase domains. PIK3CA represents one of the most highly mutated oncogenes yet identified in human cancers and is useful as a diagnostic and therapeutic target.

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Potomac, MD, United States of America

Yardena Samuels