Makoto Ishitobi

A strategy for large-scale phosphoproteomics and SRM-based validation of human breast cancer tissue samples

Protein phosphorylation is a key mechanism of cellular signaling pathways and aberrant phosphorylation has been implicated in a number of human diseases. Thus, approaches in phosphoproteomics can contribute to the identification of key biomarkers to assess disease pathogenesis and drug targets. Moreover, careful validation of large-scale phosphoproteome analysis, which is lacking in the current protein-based biomarker discovery, significantly increases the value of identified biomarkers. Here, we performed large-scale differential phosphoproteome analysis using IMAC coupled with the isobaric tag for relative quantification (iTRAQ) technique and subsequent validation by selected/multiple reaction monitoring (SRM/MRM) of human breast cancer tissues in high- and low-risk recurrence groups. We identified 8309 phosphorylation sites on 3401 proteins, of which 3766 phosphopeptides (1927 phosphoproteins) were able to be quantified and 133 phosphopeptides (117 phosphoproteins) were differentially expressed between the two groups. Among them, 19 phosphopeptides were selected for further verification and 15 were successfully quantified by SRM using stable isotope peptides as a reference. The ratio of phosphopeptides between high- and low-risk groups quantified by SRM was well correlated with iTRAQ-based quantification with a few exceptions. These results suggest that large-scale phosphoproteome quantification coupled with SRM-based validation is a powerful tool for biomarker discovery using clinical samples.

Strategy for SRM-based Verification of Biomarker Candidates Discovered by iTRAQ Method in Limited Breast Cancer Tissue Samples

Since LC-MS-based quantitative proteomics has become increasingly applied to a wide range of biological applications over the past decade, numerous studies have performed relative and/or absolute abundance determinations across large sets of proteins. In this study, we discovered prognostic biomarker candidates from limited breast cancer tissue samples using discovery-through-verification strategy combining iTRAQ method followed by selected reaction monitoring/multiple reaction monitoring analysis (SRM/MRM). We identified and quantified 5122 proteins with high confidence in 18 patient tissue samples (pooled high-risk (n=9) or low-risk (n=9)). A total of 2480 proteins (48.4%) of them were annotated as membrane proteins, 16.1% were plasma membrane and 6.6% were extracellular space proteins by Gene Ontology analysis. Forty-nine proteins with >2-fold differences in two groups were chosen for further analysis and verified in 16 individual tissue samples (high-risk (n=9) or low-risk (n=7)) using SRM/MRM. Twenty-three proteins were differentially expressed among two groups of which MFAP4 and GP2 were further confirmed by Western blotting in 17 tissue samples (high-risk (n=9) or low-risk (n=8)) and Immunohistochemistry (IHC) in 24 tissue samples (high-risk (n=12) or low-risk (n=12)). These results indicate that the combination of iTRAQ and SRM/MRM proteomics will be a powerful tool for identification and verification of candidate protein biomarkers.

Mutational analysis of BARD1 in familial breast cancer patients in Japan.

Since BRCA1,which is a breast cancer susceptibility gene, form heterodimers with BARD1, it is speculated that BARD1 mutations might affect the function of BRCA1, contributing to breast carcinogenesis. Thus, in the present study, we have conducted mutational analysis of BARD1 in familial breast cancer patients (n=60) who were tested negative for both BRCA1 and BRCA2 germline mutations. We have been unable to show any clearly deleterious mutations but identified four missence mutations (Ser/Cys 241, Arg/Ser 378, Asn/Ser 470, Val/Met 507), one silent mutation (His/His 506), and one frameshift (in-frame) mutation (1139del21bp). Of these six mutations, one (Asn/Ser 470) was considered as a putative germline mutation since such a mutation was not observed in any of the healthy controls (n=152) but the other five mutations were considered as common genetic polymorphisms since they were frequently observed in the healthy controls. These genetic polymorphisms were further analyzed in their association with breast cancer risk by a case-control study using the population-based breast cancers (n=143) and healthy controls (n=155), which showed that carriers of the variant allele Met at codon 507 are significantly associated with the increased risk of breast cancer (adjusted odds ratio=2.05, 95% confidential interval=1.01-4.16) in postmenopausal women and that the other genetic polymorphisms are not associated with breast cancer risk. These results suggest that BARD1 mutations are responsible for, if any, a very small number of familial breast cancers. Genetic polymorphism of BARD1 (Val/Met 507) could be useful in the selection of postmenopausal women at a high risk for developing breast cancer.

Mutational analysis of the class I β-tubulin gene in human breast cancer

Non‐small cell lung cancers have a high incidence of somatic mutations of the β‐tubulin (class I) gene, suggesting involvement in the acquisition of resistance to taxanes, which exert their effects through binding to β‐tubulin. Since taxanes are often used in the treatment of breast cancer, we carried out a mutational analysis of the class I β‐tubulin (GenBank accession AF070600) gene in breast cancer. We paid special attention to the primer design so as not to amplify the pseudogenes. We identified 1 somatic mutation, codon 306 [Arg (CGC) to Cys (TGC)], and 2 genetic polymorphisms, codon 217 [Leu (CTG) to Leu (CTA)] and (C to T) at 57 bases downstream from exon 4. Our results suggest that acquisition of resistance to taxanes is unlikely to be explained by somatic mutations of the class I β‐tubulin gene in most breast cancers. In addition, the overestimation of the incidence of somatic mutations of the class I β‐tubulin gene due to the pseudogenes is discussed.

SPIO-Enhanced Magnetic Resonance Imaging for the Detection of Metastases in Sentinel Nodes Localized by Computed Tomography Lymphography in Patients with Breast Cancer

BackgroundSuperparamagnetic nanoparticle-enhanced magnetic resonance (MR) imaging has been reported to be a promising improvement for diagnostic imaging of lymph node metastases from various tumors. Moreover, sentinel nodes have been reported to be well identified using computed tomography (CT) lymphography (CT-LG) in patients with breast cancer. The aim of this study was to evaluate MR imaging with superparamagnetic iron oxide (SPIO) enhancement for the detection of metastases in sentinel nodes localized by CT-LG in patients with breast cancer.MethodsThis study included 102 patients with breast cancer and clinically negative nodes. Sentinel nodes were identified by CT-LG, and SPIO-enhanced MR imaging of the axilla was performed to detect metastases in the sentinel nodes. A node was considered nonmetastatic if it showed a homogenous low signal intensity and metastatic if the entire node or a focal area did not show low signal intensity on MR imaging. Sentinel node biopsy was performed, and imaging results were correlated with histopathologic findings.ResultsThe mean number of sentinel nodes identified by CT-LG was 1.1 (range, 1–3). The sensitivity, specificity, and accuracy of MR imaging for the diagnosis of sentinel node metastases were 84.0%, 90.9%, and 89.2%, respectively. In 4 of 10 patients with micrometastases, metastases were not detected, but all 15 patients with macrometastases were successfully identified.ConclusionsSPIO-enhanced MR imaging is a useful method of detecting metastases in sentinel nodes localized by CT-LG in patients with breast cancer and may avoid sentinel node biopsy when the sentinel node is diagnosed as disease-free.Superparamagnetic nanoparticle-enhanced magnetic resonance (MR) imaging has been reported to be a promising improvement for diagnostic imaging of lymph node metastases from various tumors. Moreover, sentinel nodes have been reported to be well identified using computed tomography (CT) lymphography (CT-LG) in patients with breast cancer. The aim of this study was to evaluate MR imaging with superparamagnetic iron oxide (SPIO) enhancement for the detection of metastases in sentinel nodes localized by CT-LG in patients with breast cancer. This study included 102 patients with breast cancer and clinically negative nodes. Sentinel nodes were identified by CT-LG, and SPIO-enhanced MR imaging of the axilla was performed to detect metastases in the sentinel nodes. A node was considered nonmetastatic if it showed a homogenous low signal intensity and metastatic if the entire node or a focal area did not show low signal intensity on MR imaging. Sentinel node biopsy was performed, and imaging results were correlated with histopathologic findings. The mean number of sentinel nodes identified by CT-LG was 1.1 (range, 1–3). The sensitivity, specificity, and accuracy of MR imaging for the diagnosis of sentinel node metastases were 84.0%, 90.9%, and 89.2%, respectively. In 4 of 10 patients with micrometastases, metastases were not detected, but all 15 patients with macrometastases were successfully identified. SPIO-enhanced MR imaging is a useful method of detecting metastases in sentinel nodes localized by CT-LG in patients with breast cancer and may avoid sentinel node biopsy when the sentinel node is diagnosed as disease-free.

Repeat Lumpectomy for Ipsilateral Breast Tumor Recurrence after Breast-Conserving Treatment

Objectives: There are limited data on the outcomes of patients treated with repeat lumpectomy at the time of ipsilateral breast tumor recurrence (IBTR). Methods: We retrospectively analyzed 78 patients who underwent repeat lumpectomy after IBTR. The risk factors for second IBTR were assessed. Results: The median follow-up period was 40 months. The 5-year second IBTR-free survival rate was 78.8%. Patients with estrogen receptor (ER)-positive or unknown tumors at IBTR had a significantly better second IBTR-free survival rate than those with ER-negative tumors at IBTR (88.3 vs. 55.4%, respectively; p = 0.0022). Multivariate analysis revealed that the ER status of IBTR was a significantly independent predictive factor for second IBTR-free survival (p = 0.0177). The low-risk group for second IBTR was detected using the ER status, disease-free interval, margin status of IBTR, and age at diagnosis (5-year cumulative incidence, 7.0%). Conclusion: The ER status of IBTR was a significantly independent predictive factor for second IBTR-free survival. Some patients could safely undergo repeat lumpectomy for IBTR.

Differentiation of Follicular Thyroid Adenoma from Carcinoma by Means of Gene Expression Profiling with Adapter-Tagged Competitive Polymerase Chain Reaction

Objective: Since preoperative differentiation between follicular thyroid adenoma (FTA) and carcinoma (FTC) remains very difficult, the purpose of this study was to identify the genes differentially expressed in FTA and FTC in order to construct a diagnostic system based on such genes for differentiation of FTA and FTC. Methods:Gene expression profiles of 45 FTAs and 22 FTCs were analyzed by means of adapter-tagged competitive polymerase chain reaction (ATAC-PCR) with 2,516 genes (learning set). The genes differentially expressed in FTAs and FTCs were then used to construct a diagnostic system based on the weighted-voting algorithm. In addition, a validation study of this diagnostic system was conducted using 12 FTAs and 6 FTCs (validation set). Results: The diagnostic system for differentiation of FTA and FTC, constructed with the aid of the learning set samples, was based on 60 genes differentially expressed in FTA and FTC, which included several genes previously identified as overexpressed in FTC (DPP4, KRT19 and IGFBP3) or FTA (trefoil factor 3 and thyroid peroxidase).The leave-one-out cross-validation study showed that the accuracy of this diagnostic system was as high as 90% (sensitivity: 77.3% and specificity: 95.6%), and was confirmed by the validation study (diagnostic accuracy: 83.3%; 95% confidence interval: 62.8–95.4%, sensitivity: 66.7% and specificity: 91.2%). Conclusions: This diagnostic system using the ATAC-PCR assay is expected to be clinically useful for preoperative differentiation between FTA and FTC since ATAC-PCR can be used for the small amount of RNA obtained from fine needle aspiration biopsy.

Expression of Estrogen Receptor Beta and Phosphorylation of Estrogen Receptor Alpha Serine 167 Correlate with Progression-Free Survival in Patients with Metastatic Breast Cancer Treated with Aromatase Inhibitors

Aromatase inhibitor (AI) is widely used as an endocrine treatment in postmenopausal patients with hormone receptor-positive breast cancer. To identify useful prognostic factors for patients with metastatic breast cancer treated with AI therapy, we investigated the association between several hormone receptor-related factors and prognosis. The expressions of estrogen receptor-α (ERα), ERβ, progesterone receptor, the phosphorylation of ERα serine 118 (Ser118) and ERα Ser167 were examined using immunohistochemical techniques for the primary tumors of 41 patients with metastatic breast cancer who received first-line AI therapy after relapse. To assess the associations of protein expression and phosphorylation levels with progression-free survival (PFS), the levels of each factor were categorized into low and high values at optimal cutoff points. In univariate analysis, high ERα expression and high ERα Ser167 phosphorylation correlated with longer PFS (p = 0.016 and 0.013, respectively). In multivariate analysis, low ERβ expression and high ERα Ser167 phosphorylation correlated with longer PFS (p = 0.031 and 0.004, respectively). Patients with both low ERβ expression and high ERα Ser167 phosphorylation had longer PFS than the others (p = 0.0107). These data suggest that the expression of ERβ and phosphorylation of ERα Ser167 may be useful prognostic factors in patients with metastatic breast cancer who received first-line AI therapy.

Ipsilateral breast tumor recurrence (IBTR) in patients with operable breast cancer who undergo breast-conserving treatment after receiving neoadjuvant chemotherapy: risk factors of IBTR and validation of the MD Anderson Prognostic Index.

There is limited information about the risk factors for ipsilateral breast tumor recurrence (IBTR) after patients undergo breast‐conserving surgery plus radiotherapy (breast‐conserving treatment [BCT]) subsequent to neoadjuvant chemotherapy (NAC). The objective of the current study was to analyze these risk factors.

Prognostic significance of neutropenia on day one of anthracycline-based neoadjuvant chemotherapy in operable breast cancer.

Objectives: It is currently unknown whether neutropenia during neoadjuvant chemotherapy for early breast cancer is associated with prognosis. Methods: We retrospectively analyzed 103 breast cancer patients who were treated with neoadjuvant chemotherapy including epirubicin-based chemotherapy followed by docetaxel. The association between neutropenia due to epirubicin-based chemotherapy and distant disease-free survival (DDFS) was assessed. Results: Thirty-one patients (30%) demonstrated neutropenia during the epirubicin-based regimen. Patients without neutropenia showed a significantly (p = 0.004) lower 5-year DDFS rate (64%) than those with neutropenia (97%). In addition, multivariate analysis showed that neutropenia is an independent prognostic factor for DDFS (p = 0.02). Conclusion: Neutropenia occurring in early breast cancer patients during the initial neoadjuvant treatment is strongly associated with a better prognosis.