PIK3CA exon 20 mutation is independently associated with a poor prognosis in breast cancer patients.

BACKGROUND: Prognostic factors that could select breast cancer patients with poor survival, and influence clinical trials of targeted therapy, are needed. However, the reported observations regarding the impact of PI3KCA mutation on breast cancers are controversial. METHODS: We analyzed exons 4, 7, 9, and 20 of PI3KCA on a series of 158 patients. Clinicopathological characteristics were correlated with the mutation data. RESULTS: Among 152 patients who were available for follow-up (median follow-up time, 6.57 years), 26% had PIK3CA mutations, more than half of which occurred in exon 20. The five-year survival rate of patients with exon 20 mutations (46%) was significantly lower than that of patients without (75%) (p = 0.0054). Multivariate analysis showed that PIK3CA exon 20 mutations and nodal involvement were independent risk factors for overall survival. The relative risk of death in patients with PIK3CA exon 20 mutations was 2.881 (95% CI, 1.406-5.900; p = 0.0038). CONCLUSIONS: PIK3CA mutations are common in invasive ductal carcinomas of the breast. Our result suggests that PIK3CA exon 20 mutation is an independent risk factor for poor prognosis in breast cancer patients, indicating that differences in patient numbers with PIK3CA exon 20 mutations in study and control arms should be avoided in clinical trials of PI3K inhibitors.

ND4 mutation in transitional cell carcinoma: Does mitochondrial mutation occur before tumorigenesis?

To investigate how mitochondrial mutation occurs in cancers, we analyzed ND4 mutation in 53 transitional cell carcinomas (TCCs) of the upper urinary tract and the normal counterpart (perirenal soft tissue). Three methods, i.e., DNA sequencing, restriction fragment length polymorphism (RFLP), and denaturing high-performance liquid chromatography (DHPLC), were employed because of their different sensitive of detecting mutation. The results of sequencing and RFLP showed that ND4 mutations were only found in 24.5% (13/53) of tumor. However, 11 of these mutations could also be identified in the normal tissue by DHPLC, indicating that most mitochondrial mutations identified in tumors preexist as minor components, which are too low in quantity to be detected by less sensitive methods such as DNA sequencing. The result suggests that mtDNA mutation occurs before tumorigenesis and become apparent in cancer cells.

Analysis of disease-associated ND4 mutations: how do we know which mutation is pathogenic?

It is not uncommon to identify more than one mtDNA replacement mutations in the specimens from patients. However, we usually do not know if the identified mtDNA mutation is pathogenic or not. Even functional assays are available to use, we would not know which mutation(s) is to be tested. To provide a rapid method for initial evaluation for the pathogenicity of the replacement mutation, we compared three evolutional analyses: primate conservation index (PCI), mammalian conservation index (MCI), and conservation index across a wide spectrum of species (CI). After analyzing 35 so-called diseases-associated replacement mutations of ND4, we found 8 pathogenic mutations, 15 nonpathogenic mutations, and 12 mutations of undetermined significance. The MCI classification appears to be the best one among the three systems. This study demonstrates that evolutional analysis can serve as a rapid evaluation for the pathogenicity of mtDNA replacement mutations.

Identification of human-specific adaptation sites of ATP6.

Mitochondria play an essential role in forming ATP and generating heat. The proportion of these two depends on the coupling efficiency of electrochemical gradient to synthesize ATP. Therefore, an increased basal metabolic rate caused by partial uncoupling of the mitochondria can be balanced by a high caloric intake provided by a high-fat diet. The recent study by Mishmar et al. (Proc. Natl. Acad. Sci. USA 2003; 100: 171-176) suggested that ATP6 was the most variable gene among human mitochondrial DNAs and probably resulted from the adaptation of Homo sapiens to the colder climate during the migration out of Africa. According to this adaptation theory, the ATP6 of Homo sapiens (omnivorous animals consuming fat-containing diet) should be significantly different from that of other primates for permitting human adaptation to the dietary conditions. On the basis of this rationale, we analyzed ATP6 sequences of 136 unrelated Taiwanese subjects, which then were compared with 1,130 reported sequences. The obtained human consensus from 1,266 individuals was compared with that derived from 42 species of primates other than human. The alignment showed that human ATP6 harbored 80 variable residues, among which 25 amino acids were conserved in other primates, suggesting that adaptation constraints operating at the amino acid level results in the species-specific difference of ATP6. Therefore, these 25 amino acids are probably the human-specific adaptation residues of ATP6.

Analysis of CD117-negative gastrointestinal stromal tumors.

AIM: To identify the gastrointestinal stromal tumors (GISTs) that are negative for CD117 expression by immunohistochemistry and to characterize their malignant potential. METHODS: A total of 108 primary mesenchymal tumors of the gastrointestinal tract were screened to select CD117-negative tumors, from which KIT (exons 9, 11, 13, and 17) and PDGFRA (exons 10, 12, 14, and 18) were sequenced to identify GISTs. Tumor recurrence and distant metastasis were used as the criteria of malignancy. RESULTS: The result showed that approximately 25% (29/108) of the gastrointestinal mesenchymal tumors were negative for CD117 and approximately 6% (7/108) of the tumors were CD117-negative GISTs. All these CD117-negative tumors had a mutated KIT and a wild-type PDGFRA. All CD117-negative GISTs with mutations at codons 557/558 of KIT had mitotic counts >10/50 high power field, and 75% (3/4) of them showed multiple recurrence or distant metastasis. CONCLUSION: CD117-negative KIT mutated GISTs account for approximately 6% of the gastrointestinal mesenchymal tumors. Tumor recurrence or distant metastasis correlates to both the KIT mutations at codons 557/558 and the mitotic counts, but not to the tumor size.