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1.  The expression patterns of gremlin 1 and noggin in normal adult and tumor tissues 
Gremlin 1 and noggin are inhibitors of bone morphogenetic protein (BMP) signaling. They are vital during early development but their role in adult tissues has remained largely unresolved. The BMP signaling pathway has also been implicated in tumorigenesis, however with emphasis on the role of the ligands and receptors. We performed a concurrent survey of gremlin 1 and noggin protein expression in multiple normal and cancer samples, using immunohistochemistry on tissue microarrays containing 96 samples from 34 different normal organs/tissue sites and 208 samples of 34 different tumor types. In majority of both normal and tumor samples, gremlin 1 and noggin expression was negative or weak. However, normal stomach and skin demonstrated distinct gremlin 1 and noggin expression indicating a role in adult tissues. Likewise, strong expression of both antagonists was detected in Leydig cells of testis. In the tumor panel, the expression patterns were more variable but elevated BMP antagonist expression was detected for the first time in few cases, such as glioblastoma, hepatocellular carcinoma and diffuse B-cell lymphoma for gremlin 1 and renal granular cell tumor and thyroid papillary carcinoma for noggin. Even though gremlin 1 and noggin were not widely expressed in adult tissues, in a subset of organs their expression pattern indicated a potential role in normal tissue homeostasis as well as in malignancies.
PMCID: PMC3693206  PMID: 23826422
Gremlin 1; noggin; cancer; normal tissue; immunohistochemistry
2.  Analysis of and prognostic information from disseminated tumour cells in bone marrow in primary breast cancer: a prospective observational study 
BMC Cancer  2012;12:403.
Background
Disseminated tumour cells (DTCs) in the bone marrow of patients with breast cancer have been identified as an independent predictor of poor prognosis in patients with non-metastatic disease. This prospective study aimed to evaluate the presence and prognostic value of DTCs in the bone marrow of female patients with primary breast cancer.
Methods
Between 1999 and 2003, bone marrow aspirates were obtained from patients at the time of surgery for primary invasive breast cancer. DTCs in bone marrow were identified using monoclonal antibodies against cytokeratins for detection of epithelial cells. The detection of DTCs was related to clinical follow-up with distant disease-free survival (DDFS) and breast cancer-specific survival as endpoints. Bone marrow aspirates from adult healthy bone marrow donors were analysed separately.
Results
DTCs were analysed in 401 patients, and cytokeratin-positive cells were found in 152 of these (38%). An immunofluorescence (IF) staining procedure was used in 327 patients, and immunocytochemistry (IC) was performed in 74 patients. The IF-based method resulted in 40% DTC-positive cases, whereas 30% were positive using IC (p = 0.11). The presence of DTCs in bone marrow was not significantly related to patient or tumour characteristics. The presence of DTCs was not a prognostic factor for DDFS (IF: hazards ratio [HR], 2.2; 95% confidence interval [CI], 0.63–2.2; p = 0.60; IC: HR, 0.84; 95% CI, 0.09–8.1; p = 0.88). Significant prognostic factors were lymph node metastases, oestrogen receptor positivity, Nottingham histological grade, and tumour size using Cox univariate analysis. The analyses were positive for epithelial cells in bone marrow from adult healthy donors in 19 (25%) samples.
Conclusions
The detection of DTCs in bone marrow in primary breast cancer was previously shown to be a predictor of poor prognosis. We were not able to confirm these results in a prospective cohort including unselected patients before the standard procedure was established. Future studies with a standardised patient protocol and improved technique for isolating and detecting DTCs may reveal the clinical applications of DTC detection in patients with micrometastases in the bone marrow.
doi:10.1186/1471-2407-12-403
PMCID: PMC3488538  PMID: 22963449
Breast cancer; Disseminated tumour cells; Cytokeratin-positive cells; Micrometastases; Prognosis
3.  Long-term prognosis of breast cancer detected by mammography screening or other methods 
Breast Cancer Research : BCR  2011;13(6):R134.
Introduction
Previous studies of breast cancer have shown that patients whose tumors are detected by mammography screening have a more favorable survival. Little is known, however, about the long-term prognostic impact of screen detection. The purpose of the current study was to compare breast cancer-specific long-term survival of patients whose tumors were detected in mammography screening compared with those whose tumors were detected by other methods.
Methods
Breast cancer patients diagnosed within five specified geographical areas in Finland in 1991 and 1992 were identified (N = 2,936). Detailed clinical, treatment and outcome data, as well as tissue samples, were collected. Women with in situ carcinoma, distant metastases at the time of primary diagnosis and women who were not treated surgically were excluded. The main analyses were performed after excluding patients with other malignancy or contralateral breast cancer, followed by sensitivity analyses with different exclusion criteria. Median follow-up time was 15.4 years. Univariate and multivariate analyses of breast cancer-specific survival were performed.
Results
Of patients included in the main analyses (n = 1,884), 22% (n = 408) of cancers were screen-detected and 78% (n = 1,476) were detected by other methods. Breast cancer-specific 15-year survival was 86% for patients with screen-detected cancer and 66% for patients diagnosed using other methods (P < 0.0001, HR = 2.91). Similar differences in survival were observed in women at screening age (50 to 69 years), as well as in clinically important subgroups, such as patients with small tumors (≤ 1 cm in diameter) and without nodal involvement (N0). Women with breast cancer diagnosed on the basis of screening mammography had a more favorable prognosis than those diagnosed outside screening programs, following adjustments according to patient age, tumor size, axillary lymph node status, histological grade and hormone receptor status. Significant differences in the risk of having future contralateral breast cancer according to method of detection were not observed.
Conclusions
Breast cancer detected by mammography screening is an independent prognostic factor in breast cancer and is associated with a more favorable survival rate as well as in long-term follow-up.
doi:10.1186/bcr3080
PMCID: PMC3326576  PMID: 22204661
screening; mammography; prognosis; survival analysis
4.  Characterization of Non-Specific Cytotoxic Cell Receptor Protein 1: A New Member of the Lectin-Type Subfamily of F-Box Proteins 
PLoS ONE  2011;6(11):e27152.
Our previous microarray study showed that the non-specific cytotoxic cell receptor protein 1 (Nccrp1) transcript is significantly upregulated in the gastric mucosa of carbonic anhydrase IX (CA IX)-deficient (Car9−/−) mice. In this paper, we aimed to characterize human NCCRP1 and to elucidate its relationship to CA IX. Recombinant NCCRP1 protein was expressed in Escherichia coli, and a novel polyclonal antiserum was raised against the purified full-length protein. Immunocytochemistry showed that NCCRP1 is expressed intracellularly, even though it has previously been described as a transmembrane protein. Using bioinformatic analyses, we identified orthologs of NCCRP1 in 35 vertebrate genomes, and up to five paralogs per genome. These paralogs are FBXO genes whose protein products are components of the E3 ubiquitin ligase complexes. NCCRP1 proteins have no signal peptides or transmembrane domains. NCCRP1 has mainly been studied in fish and was thought to be responsible for the cytolytic function of nonspecific cytotoxic cells (NCCs). Our analyses showed that in humans, NCCRP1 mRNA is expressed in tissues containing squamous epithelium, whereas it shows a more ubiquitous tissue expression pattern in mice. Neither human nor mouse NCCRP1 expression is specific to immune tissues. Silencing CA9 using siRNAs did not affect NCCRP1 levels, indicating that its expression is not directly regulated by CA9. Interestingly, silencing NCCRP1 caused a statistically significant decrease in the growth of HeLa cells. These studies provide ample evidence that the current name, “non-specific cytotoxic cell receptor protein 1,” is not appropriate. We therefore propose that the gene name be changed to FBXO50.
doi:10.1371/journal.pone.0027152
PMCID: PMC3210139  PMID: 22087255
5.  Overall and worst gleason scores are equally good predictors of prostate cancer progression 
BMC Urology  2011;11:21.
Background
Gleason scoring has experienced several modifications during the past decade. So far, only one study has compared the prognostic abilities of worst (WGS) and overall (OGS) modified Gleason scores after the ISUP 2005 conference. Prostatic needle biopsies are individually paraffin-embedded in 57% of European pathology laboratories, whereas the rest of laboratories embed multiple (2 - 6) biopsies per one paraffin-block. Differences in the processing method can have a far-reaching effect, because reporting of the Gleason score (GS) is different for individually embedded and pooled biopsies, and GS is one of the most important factors when selecting treatment for patients.
Methods
The study material consisted of needle biopsies from 236 prostate cancer patients that were endocrine-treated in 1999-2003. Biopsies from left side and right side were embedded separately. Haematoxylin-eosin-stained slides were scanned and analyzed on web-based virtual microscopy. Worst and overall Gleason scores were assessed according to the modified Gleason score schema after analyzing each biopsy separately. The compound Gleason scores (CGS) were obtained from the original pathology reports. Two different grade groupings were used: GS 6 or less vs. 7 vs. 8 or above; and GS 7(3 + 4) or less vs. 7(4 + 3) and 8 vs. 9-10. The prognostic ability of the three scoring methods to predict biochemical progression was compared with Kaplan-Meier survival analysis and univariate and multivariate Cox regression analyses.
Results
The median follow-up time of the patients was 64.5 months (range 0-118). The modified GS criteria led to upgrading of the Gleason sums compared to the original CGS from the pathology reports 1999-2003 (mean 7.0 for CGS, 7.5 for OGS, 7.6 for WGS). In 43 cases WGS was > OGS. In a univariate analysis the relative risks were 2.1 (95%-confidence interval 1.8-2.4) for CGS, 2.5 (2.1-2.8) for OGS, and 2.6 (2.2-2.9) for WGS. In a multivariate analysis, OGS was the only independent prognostic factor.
Conclusions
All of the three Gleason scoring methods are strong predictors of biochemical recurrence. The use of modified Gleason scoring leads to upgrading of GS, but also improves the prognostic value of the scoring. No significant prognostic differences between OGS and WGS could be shown, which may relate to the apparent narrowing of the GS scale from 2-10 to 5-10 due to the recent modifications.
doi:10.1186/1471-2490-11-21
PMCID: PMC3193164  PMID: 21978318
6.  Breast cancer biological subtypes and protein expression predict for the preferential distant metastasis sites: a nationwide cohort study 
Introduction
Some molecular subtypes of breast cancer have preferential sites of distant relapse. The protein expression pattern of the primary tumor may influence the first distant metastasis site.
Methods
We identified from the files of the Finnish Cancer Registry patients diagnosed with breast cancer in five geographical regions Finland in 1991-1992, reviewed the hospital case records, and collected primary tumor tissue. Out of the 2,032 cases identified, 234 developed distant metastases after a median follow-up time of 2.7 years and had the first metastatic site documented (a total of 321 sites). Primary tumor microarray (TMA) cores were analyzed for 17 proteins using immunohistochemistry and for erbB2 using chromogenic in situ hybridization, and their associations with the first metastasis site were examined. The cancers were classified into luminal A, luminal B, HER2+ enriched, basal-like or non-expressor subtypes.
Results
A total of 3,886 TMA cores were analyzed. Luminal A cancers had a propensity to give rise first to bone metastases, HER2-enriched cancers to liver and lung metastases, and basal type cancers to liver and brain metastases. Primary tumors that gave first rise to bone metastases expressed frequently estrogen receptor (ER) and SNAI1 (SNAIL) and rarely COX2 and HER2, tumors with first metastases in the liver expressed infrequently SNAI1, those with lung metastases expressed frequently the epidermal growth factor receptor (EGFR), cytokeratin-5 (CK5) and HER2, and infrequently progesterone receptor (PgR), tumors with early skin metastases expressed infrequently E-cadherin, and breast tumors with first metastases in the brain expressed nestin, prominin-1 and CK5 and infrequently ER and PgR.
Conclusions
Breast tumor biological subtypes have a tendency to give rise to first distant metastases at certain body sites. Several primary tumor proteins were associated with homing of breast cancer cells.
doi:10.1186/bcr2944
PMCID: PMC3262199  PMID: 21914172
7.  Carbonic anhydrase II. A novel biomarker for gastrointestinal stromal tumors 
Gastrointestinal stromal tumors are clinically distinct mesenchymal tumors, which generally result from expression of mutant KIT or PDGFRA receptor tyrosine kinase oncogenes. Most gastrointestinal stromal tumors feature strong expression of KIT that serves as a crucial diagnostic adjunct. However, a subset of tumors lacks KIT expression and otherwise may also be difficult to distinguish from other sarcomas, including leiomyosarcoma. Because various carbonic anhydrase isozymes have been identified as potential treatment targets against different cancers, we evaluated carbonic anhydrase II expression in 175 gastrointestinal stromal tumors. Western blotting experiments indicated that carbonic anhydrase II is highly expressed in gastrointestinal stromal tumor cell lines. Immunohistochemically, 95% of gastrointestinal stromal tumors showed positive signal. The carbonic anhydrase II expression in gastrointestinal stromal tumors did not correlate with particular KIT or PDGFRA mutation types. Carbonic anhydrase II immunoreactivity was absent or low in other mesenchymal tumor categories analyzed. High carbonic anhydrase II expression was associated with a better disease-specific survival rate than low or no expression (Mantel-Cox test, p<0.0001). The present results indicate that carbonic anhydrase II is overexpressed in most gastrointestinal stromal tumors, is quite selective to this tumor type among mesenchymal tumors, and therefore might be a useful biomarker in diagnostics.
doi:10.1038/modpathol.2009.189
PMCID: PMC2900582  PMID: 20081808
biomarker; cancer; carbonic anhydrase; GIST; sarcoma
8.  Trastuzumab-DM1 causes tumour growth inhibition by mitotic catastrophe in trastuzumab-resistant breast cancer cells in vivo 
Introduction
Trastuzumab is widely used for the treatment of HER2-positive breast cancer. Despite encouraging clinical results, a significant fraction of patients are, or become, refractory to the drug. To overcome this, trastuzumab-DM1 (T-DM1), a newer, more potent drug has been introduced. We tested the efficacy and mechanisms of action of T-DM1 in nine HER2-positive breast cancer cell lines in vitro and in vivo. The nine cell lines studied included UACC-893, MDA-453 and JIMT-1, which are resistant to both trastuzumab and lapatinib.
Methods
AlamarBlue cell-proliferation assay was used to determine the growth response of breast cancer cell lines to trastuzumab and T-DM1 in vitro. Trastuzumab- and T-DM1-mediated antibody-dependent cellular cytotoxicity (ADCC) was analysed by measuring the lactate dehydrogenase released from the cancer cells as a result of ADCC activity of peripheral blood mononuclear cells. Severe Combined Immunodeficient (SCID) mice were inoculated with trastuzumab-resistant JIMT-1 cells to investigate the tumour inhibitory effect of T-DM1 in vivo. The xenograft samples were investigated using histology and immunohistochemistry.
Results
T-DM1 was strongly growth inhibitory on all investigated HER2-positive breast cancer cell lines in vitro. T-DM1 also evoked antibody-dependent cellular cytotoxicity (ADCC) similar to that of trastuzumab. Outgrowth of JIMT-1 xenograft tumours in SCID mice was significantly inhibited by T-DM1. Histologically, the cellular response to T-DM1 consisted of apoptosis and mitotic catastrophe, the latter evidenced by an increased number of cells with aberrant mitotic figures and giant multinucleated cells.
Conclusions
Our results suggest mitotic catastrophe as a previously undescribed mechanism of action of T-DM1. T-DM1 was found effective even on breast cancer cell lines with moderate HER2 expression levels and cross-resistance to trastuzumab and lapatinib (MDA-453 and JIMT-1).
doi:10.1186/bcr2868
PMCID: PMC3219209  PMID: 21510863
9.  Development and evaluation of a virtual microscopy application for automated assessment of Ki-67 expression in breast cancer 
Background
The aim of the study was to develop a virtual microscopy enabled method for assessment of Ki-67 expression and to study the prognostic value of the automated analysis in a comprehensive series of patients with breast cancer.
Methods
Using a previously reported virtual microscopy platform and an open source image processing tool, ImageJ, a method for assessment of immunohistochemically (IHC) stained area and intensity was created. A tissue microarray (TMA) series of breast cancer specimens from 1931 patients was immunostained for Ki-67, digitized with a whole slide scanner and uploaded to an image web server. The extent of Ki-67 staining in the tumour specimens was assessed both visually and with the image analysis algorithm. The prognostic value of the computer vision assessment of Ki-67 was evaluated by comparison of distant disease-free survival in patients with low, moderate or high expression of the protein.
Results
1648 evaluable image files from 1334 patients were analysed in less than two hours. Visual and automated Ki-67 extent of staining assessments showed a percentage agreement of 87% and weighted kappa value of 0.57. The hazard ratio for distant recurrence for patients with a computer determined moderate Ki-67 extent of staining was 1.77 (95% CI 1.31-2.37) and for high extent 2.34 (95% CI 1.76-3.10), compared to patients with a low extent. In multivariate survival analyses, automated assessment of Ki-67 extent of staining was retained as a significant prognostic factor.
Conclusions
Running high-throughput automated IHC algorithms on a virtual microscopy platform is feasible. Comparison of visual and automated assessments of Ki-67 expression shows moderate agreement. In multivariate survival analysis, the automated assessment of Ki-67 extent of staining is a significant and independent predictor of outcome in breast cancer.
doi:10.1186/1472-6890-11-3
PMCID: PMC3040126  PMID: 21262004
10.  Recurrent gross mutations of the PTEN tumor suppressor gene in breast cancers with deficient DSB repair 
Nature genetics  2007;40(1):102-107.
Basal-like breast cancer (BBC) is a subtype of breast cancer with poor prognosis1–3. Inherited mutations of BRCA1, a cancer susceptibility gene involved in double-strand DNA break (DSB) repair, lead to breast cancers that are nearly always of the BBC subtype3–5; however, the precise molecular lesions and oncogenic consequences of BRCA1 dysfunction are poorly understood. Here we show that heterozygous inactivation of the tumor suppressor gene Pten leads to the formation of basal-like mammary tumors in mice, and that loss of PTEN expression is significantly associated with the BBC subtype in human sporadic and BRCA1-associated hereditary breast cancers. In addition, we identify frequent gross PTEN mutations, involving intragenic chromosome breaks, inversions, deletions and micro copy number aberrations, specifically in BRCA1-deficient tumors. These data provide an example of a specific and recurrent oncogenic consequence of BRCA1-dependent dysfunction in DNA repair and provide insight into the pathogenesis of BBC with therapeutic implications. These findings also argue that obtaining an accurate census of genes mutated in cancer will require a systematic examination for gross gene rearrangements, particularly in tumors with deficient DSB repair.
doi:10.1038/ng.2007.39
PMCID: PMC3018354  PMID: 18066063
11.  PDK1 potentiates upstream lesions on the PI3K pathway in breast carcinoma 
Cancer research  2009;69(15):6299-6306.
Lesions of ERBB2, PTEN, and PIK3CA activate the PI3K pathway during cancer development by increasing levels of phosphatidylinositol-3,4,5-triphosphate (PIP3). 3-phosphoinositide-dependent kinase 1 (PDK1) is the first node of the PI3K signal output and is required for activation of AKT. PIP3 recruits PDK1 and AKT to the cell membrane through interactions with their PH domains, allowing PDK1 to activate AKT by phosphorylating it at residue threonine 308. We show that total PDK1 protein and mRNA was over-expressed in a majority of human breast cancers and that 21% of tumors had five or more copies of the gene encoding PDK1, PDPK1. We found that increased PDPK1 copy number was associated with upstream pathway lesions (ERBB2 amplification, PTEN loss, or PIK3CA mutation), as well as patient survival. Examination of an independent set of breast cancers and tumor cell lines derived from multiple forms of human cancers also found increased PDK1 protein levels associated with such upstream pathway lesions. In human mammary cells, PDK1 enhanced the ability of upstream lesions to signal to AKT, stimulate cell growth and migration, and rendered cells more resistant to PDK1 and PI3K inhibition. After orthotopic transplantation, PDK1 overexpression was not oncogenic but dramatically enhanced the ability of ERBB2 to form tumors. Our studies argue that PDK1 overexpression and increased PDPK1 copy number are common occurrences in cancer that potentiate the oncogenic effect of upstream lesions on the PI3K pathway. Therefore, we conclude that alteration of PDK1 is a critical component of oncogenic PI3K signaling in breast cancer.
doi:10.1158/0008-5472.CAN-09-0820
PMCID: PMC2727605  PMID: 19602588
PDK1; PI3K; ERBB2; PTEN; breast
12.  ImmunoRatio: a publicly available web application for quantitative image analysis of estrogen receptor (ER), progesterone receptor (PR), and Ki-67 
Introduction
Accurate assessment of estrogen receptor (ER), progesterone receptor (PR), and Ki-67 is essential in the histopathologic diagnostics of breast cancer. Commercially available image analysis systems are usually bundled with dedicated analysis hardware and, to our knowledge, no easily installable, free software for immunostained slide scoring has been described. In this study, we describe a free, Internet-based web application for quantitative image analysis of ER, PR, and Ki-67 immunohistochemistry in breast cancer tissue sections.
Methods
The application, named ImmunoRatio, calculates the percentage of positively stained nuclear area (labeling index) by using a color deconvolution algorithm for separating the staining components (diaminobenzidine and hematoxylin) and adaptive thresholding for nuclear area segmentation. ImmunoRatio was calibrated using cell counts defined visually as the gold standard (training set, n = 50). Validation was done using a separate set of 50 ER, PR, and Ki-67 stained slides (test set, n = 50). In addition, Ki-67 labeling indexes determined by ImmunoRatio were studied for their prognostic value in a retrospective cohort of 123 breast cancer patients.
Results
The labeling indexes by calibrated ImmunoRatio analyses correlated well with those defined visually in the test set (correlation coefficient r = 0.98). Using the median Ki-67 labeling index (20%) as a cutoff, a hazard ratio of 2.2 was obtained in the survival analysis (n = 123, P = 0.01). ImmunoRatio was shown to adapt to various staining protocols, microscope setups, digital camera models, and image acquisition settings. The application can be used directly with web browsers running on modern operating systems (e.g., Microsoft Windows, Linux distributions, and Mac OS). No software downloads or installations are required. ImmunoRatio is open source software, and the web application is publicly accessible on our website.
Conclusions
We anticipate that free web applications, such as ImmunoRatio, will make the quantitative image analysis of ER, PR, and Ki-67 easy and straightforward in the diagnostic assessment of breast cancer specimens.
doi:10.1186/bcr2615
PMCID: PMC2949645  PMID: 20663194
13.  The Application of JPEG2000 in Virtual Microscopy 
Virtual microscopy (i.e., the viewing of entire microscope specimens on a computer display) is becoming widely applied in microscopy teaching and clinical laboratory medicine. Despite rapidly increasing use, virtual microscopy currently lacks of a universally accepted image format. A promising candidate is JPEG2000, which has potential advantages for handling gigabyte-sized virtual slides. To date, no JPEG2000-based software has been specifically suited for virtual microscopy. To study the utility of JPEG2000 in virtual microscopy, we first optimized JPEG2000 code-stream parameters for virtual slide viewing (i.e., fast navigation, zooming, and use of an overview window). Compression using ratios 25:1–30:1 with the irreversible wavelet filter were found to provide the best compromise between file size and image quality. Optimal code-stream parameters also consisted of 10 wavelet decomposition levels, progression order Resolution-Position-Component-Layer (RPCL), a precinct size of 128 × 128, and code-block size of 64 × 64. Tiling and the use of multiple quality layers were deemed unnecessary. A compression application (JVScomp) was developed for creating optimally parameterized JPEG2000 virtual slides. A viewing application (JVSview) was developed specifically for virtual microscopy, offering all of the basic viewing functions. JVSview also supports viewing of focus stacks, embedding of textual descriptions, and defining regions of interest as metadata. Combined with our server application (JVSserv), virtual slides can be viewed over networks by employing the JPEG2000 Interactive Protocol (JPIP). The software can be tested using virtual slide examples located on our public JPIP server (http://jvsmicroscope.uta.fi/). The software package is freely downloadable and usable for noncommercial purposes.
doi:10.1007/s10278-007-9090-z
PMCID: PMC3043697  PMID: 17999112
JPEG2000; JPIP; telepathology; digital pathology; virtual slide
14.  HER-2 positive breast cancer: decreasing proportion but stable incidence in Finnish population from 1982 to 2005 
Introduction
Classification of breast cancers according to the HER-2 oncogene status is of central importance in the selection of post-surgical therapies. A decrease in the proportion of HER-2-positive breast cancer has been suspected, but no data on the incidence trends at population level have been reported.
Methods
We studied the proportion of HER-2-positive breast cancers by chromogenic in situ hybridization (CISH) in three cohorts (years 1982 to 1986 (n = 310), 1989 to 1992 (n = 108), and 2004 to 2005 (n = 713)) in the population of the Pirkanmaa hospital district (approximately 220,000 women). Cancer incidence rates were age-adjusted to the world standard population.
Results
The proportion of HER-2-positive breast cancer declined from 21.6% (average in 1982 to 1986) to 13.6% (average in 2004 to 2005). However, during the same time period the age-adjusted incidence of all invasive breast cancers had increased by 40%. These opposite trends balanced each other and indicated that the incidence of HER-2-positive breast cancer has remained unchanged (Poisson regression coefficient for time trend 1.000; 95% CI = 0.989 to 1.012). In contrast, the incidence of HER-2-negative cancer showed 2% annual increase (Poisson regression coefficient 1.021, 95% CI = 1.016 to 1.026). Although HER-2-negative cancers were more likely to be diagnosed by mammography screening, the changes were more likely to be explained by etiological risk factors favoring HER-2-negative (and hormone receptor-positive) disease such as menopausal hormone therapy.
Conclusions
These results document a significant decrease in the proportion of HER-2-positive breast cancer. However, the incidence of HER-2-positive cancer at the population level was found to be unchanged.
doi:10.1186/bcr2322
PMCID: PMC2716505  PMID: 19538720
15.  Linking Whole-Slide Microscope Images with DICOM by Using JPEG2000 Interactive Protocol 
Journal of Digital Imaging  2009;23(4):454-462.
The use of digitized histopathologic specimens (also known as whole-slide images (WSIs)) in clinical medicine requires compatibility with the Digital Imaging and Communications in Medicine (DICOM) standard. Unfortunately, WSIs usually exceed DICOM image object size limit, making it impossible to store and exchange them in a straightforward way. Moreover, transmitting the entire DICOM image for viewing is ineffective for WSIs. With the JPEG2000 Interactive Protocol (JPIP), WSIs can be linked with DICOM by transmitting image data over an auxiliary connection, apart from patient data. In this study, we explored the feasibility of using JPIP to link JPEG2000 WSIs with a DICOM-based Picture Archiving and Communications System (PACS). We first modified an open-source DICOM library by adding support for JPIP as described in the existing DICOM Supplement 106. Second, the modified library was used as a basis for a software package (JVSdicom), which provides a proof-of-concept for a DICOM client–server system that can transmit patient data, conventional DICOM imagery (e.g., radiological), and JPIP-linked JPEG2000 WSIs. The software package consists of a compression application (JVSdicom Compressor) for producing DICOM-compatible JPEG2000 WSIs, a DICOM PACS server application (JVSdicom Server), and a DICOM PACS client application (JVSdicom Workstation). JVSdicom is available for free from our Web site (http://jvsmicroscope.uta.fi/), which also features a public JVSdicom Server, containing example X-ray images and histopathology WSIs of breast cancer cases. The software developed indicates that JPEG2000 and JPIP provide a well-working solution for linking WSIs with DICOM, requiring only minor modifications to current DICOM standard specification.
doi:10.1007/s10278-009-9200-1
PMCID: PMC2896636  PMID: 19415383
Digital pathology; telepathology; DICOM; JPEG2000; JPIP; virtual slide; whole-slide imaging; WSI
16.  Linking Whole-Slide Microscope Images with DICOM by Using JPEG2000 Interactive Protocol 
Journal of Digital Imaging  2009;23(4):454-462.
The use of digitized histopathologic specimens (also known as whole-slide images (WSIs)) in clinical medicine requires compatibility with the Digital Imaging and Communications in Medicine (DICOM) standard. Unfortunately, WSIs usually exceed DICOM image object size limit, making it impossible to store and exchange them in a straightforward way. Moreover, transmitting the entire DICOM image for viewing is ineffective for WSIs. With the JPEG2000 Interactive Protocol (JPIP), WSIs can be linked with DICOM by transmitting image data over an auxiliary connection, apart from patient data. In this study, we explored the feasibility of using JPIP to link JPEG2000 WSIs with a DICOM-based Picture Archiving and Communications System (PACS). We first modified an open-source DICOM library by adding support for JPIP as described in the existing DICOM Supplement 106. Second, the modified library was used as a basis for a software package (JVSdicom), which provides a proof-of-concept for a DICOM client–server system that can transmit patient data, conventional DICOM imagery (e.g., radiological), and JPIP-linked JPEG2000 WSIs. The software package consists of a compression application (JVSdicom Compressor) for producing DICOM-compatible JPEG2000 WSIs, a DICOM PACS server application (JVSdicom Server), and a DICOM PACS client application (JVSdicom Workstation). JVSdicom is available for free from our Web site (http://jvsmicroscope.uta.fi/), which also features a public JVSdicom Server, containing example X-ray images and histopathology WSIs of breast cancer cases. The software developed indicates that JPEG2000 and JPIP provide a well-working solution for linking WSIs with DICOM, requiring only minor modifications to current DICOM standard specification.
doi:10.1007/s10278-009-9200-1
PMCID: PMC2896636  PMID: 19415383
Digital pathology; telepathology; DICOM; JPEG2000; JPIP; virtual slide; whole-slide imaging; WSI
17.  Absence of polysialylated NCAM is an unfavorable prognostic phenotype for advanced stage neuroblastoma 
BMC Cancer  2009;9:57.
Background
The expression of a neural crest stem cell marker, polysialic acid (polySia), and its main carrier, neural cell adhesion molecule (NCAM), have been detected in some malignant tumors with high metastatic activity and unfavorable prognosis, but the diagnostic and prognostic value of polySia-NCAM in neuroblastoma is unclear.
Methods
A tumor tissue microarray (TMA) of 36 paraffin-embedded neuroblastoma samples was utilized to detect polySia-NCAM expression with a polySia-binding fluorescent fusion protein, and polySia-NCAM expression was compared with clinical stage, age, MYCN amplification status, histology (INPC), and proliferation index (PI).
Results
PolySia-NCAM-positive neuroblastoma patients had more often metastases at diagnosis, and polySia-NCAM expression associated with advanced disease (P = 0.047). Most interestingly, absence of polySia-NCAM-expressing tumor cells in TMA samples, however, was a strong unfavorable prognostic factor for overall survival in advanced disease (P = 0.0004), especially when MYCN was not amplified. PolySia-NCAM-expressing bone marrow metastases were easily detected in smears, aspirates and biopsies.
Conclusion
PolySia-NCAM appears to be a new clinically significant molecular marker in neuroblastoma, hopefully with additional value in neuroblastoma risk stratification.
doi:10.1186/1471-2407-9-57
PMCID: PMC2661096  PMID: 19222860
18.  Correction: Web-Based Virtual Microscopy for Parasitology: A Novel Tool for Education and Quality Assurance 
PLoS Neglected Tropical Diseases  2008;2(10):10.1371/annotation/1f73ee39-9e3c-4ce4-9c35-2a6ab393de7d.
doi:10.1371/annotation/1f73ee39-9e3c-4ce4-9c35-2a6ab393de7d
PMCID: PMC2583279
19.  Web-Based Virtual Microscopy for Parasitology: A Novel Tool for Education and Quality Assurance 
Background
The basis for correctly assessing the burden of parasitic infections and the effects of interventions relies on a somewhat shaky foundation as long as we do not know how reliable the reported laboratory findings are. Thus virtual microscopy, successfully introduced as a histopathology tool, has been adapted for medical parasitology.
Methodology/Principal Findings
Specimens containing parasites in tissues, stools, and blood have been digitized and made accessible as a “webmicroscope for parasitology” (WMP) on the Internet (http://www.webmicroscope.net/parasitology).These digitized specimens can be viewed (“navigated” both in the x-axis and the y-axis) at the desired magnification by an unrestricted number of individuals simultaneously. For virtual microscopy of specimens containing stool parasites, it was necessary to develop the technique further in order to enable navigation in the z plane (i.e., “focusing”). Specimens were therefore scanned and photographed in two or more focal planes. The resulting digitized specimens consist of stacks of laterally “stiched” individual images covering the entire area of the sample photographed at high magnification. The digitized image information (∼10 GB uncompressed data per specimen) is accessible at data transfer speeds from 2 to 10 Mb/s via a network of five image servers located in different parts of Europe. Image streaming and rapid data transfer to an ordinary personal computer makes web-based virtual microscopy similar to conventional microscopy.
Conclusion/Significance
The potential of this novel technique in the field of medical parasitology to share identical parasitological specimens means that we can provide a “gold standard”, which can overcome several problems encountered in quality control of diagnostic parasitology. Thus, the WMP may have an impact on the reliability of data, which constitute the basis for our understanding of the vast problem of neglected tropical diseases. The WMP can be used also in the absence of a fast Internet communication. An ordinary PC, or even a laptop, may function as a local image server, e.g., in health centers in tropical endemic areas.
Author Summary
Here, we describe a novel tool to observe parasites by virtual microscopy on the Internet. Microscopy-based identification of parasites is the basis for both diagnostics and epidemiological assessment of parasite burden globally. Yet, quality assessment of diagnostic parasitology laboratories is difficult, as delivering identical educational specimens has been impossible. In this study, a series of parasite specimens on ordinary glass slides were digitized using a recently developed microscope scanner technique. Up to 50,000 images captured at high magnification are digitally stitched together to form a representation of the entire glass slide. These “virtual slides” digitized at a thousand-fold magnification can hold more than 60 gigabytes of data. Handling such large amounts of data was made possible because of efficient compression techniques and a viewing system adopted from the geospatial imaging industry. Viewing the samples on the Internet very much resembles, for example, the use of Google Maps, and puts only modest requirements on the viewer's computer. In addition, we captured image stacks at different focal planes, and developed a web-based viewing system for three-dimensional navigation in the specimens. This novel technique is especially valuable for detailed visualization of large objects such as helminth eggs in stool specimens.
doi:10.1371/journal.pntd.0000315
PMCID: PMC2565642  PMID: 18941514
20.  The calcium-binding protein S100P in normal and malignant human tissues 
Background
S100P is a Ca2+ binding protein overexpressed in a variety of cancers, and thus, has been considered a potential tumor biomarker. Very little has been studied about its normal expression and functions.
Methods
We examined S100P expression in normal human tissues by quantitative reverse transcription polymerase chain reaction and immunohistochemistry. S100P protein expression was also studied in a series of tumors, consisting of 74 ovarian, 11 pancreatic, 56 gastric, 57 colorectal, 89 breast and 193 prostate carcinomas using a novel anti-S100P monoclonal antibody.
Results
Among the normal tissues, the highest S100P mRNA levels were observed in the placenta and esophagus. Moderate signals were also detected in the stomach, duodenum, large intestine, prostate and leukocytes. At the protein level, the highest reactions for S100P were seen in the placenta and stomach. Immunostaining of tumor specimens showed that S100P protein is expressed in all the tumor categories included in the study, being most prevalent in gastric tumors.
Conclusion
Based on our observations, S100P is widely expressed in both normal and malignant tissues. The high expression in some tumors suggests that it may represent a potential target molecule for future diagnostic and therapeutic applications.
doi:10.1186/1472-6890-8-2
PMCID: PMC2254630  PMID: 18282279
21.  Basal-like phenotype is not associated with patient survival in estrogen-receptor-negative breast cancers 
Breast Cancer Research  2007;9(1):R16.
Introduction
Basal-phenotype or basal-like breast cancers are characterized by basal epithelium cytokeratin (CK5/14/17) expression, negative estrogen receptor (ER) status and distinct gene expression signature. We studied the clinical and biological features of the basal-phenotype tumors determined by immunohistochemistry (IHC) and cDNA microarrays especially within the ER-negative subgroup.
Methods
IHC was used to evaluate the CK5/14 status of 445 stage II breast cancers. The gene expression signature of the CK5/14 immunopositive tumors was investigated within a subset (100) of the breast tumors (including 50 ER-negative tumors) with a cDNA microarray. Survival for basal-phenotype tumors as determined by CK5/14 IHC and gene expression signature was assessed.
Results
From the 375 analyzable tumor specimens, 48 (13%) were immunohistochemically positive for CK5/14. We found adverse distant disease-free survival for the CK5/14-positive tumors during the first years (3 years hazard ratio (HR) 2.23, 95% confidence interval (CI) 1.17 to 4.24, p = 0.01; 5 years HR 1.80, 95% CI 1.02 to 3.15, p = 0.04) but the significance was lost at the end of the follow-up period (10 years HR 1.43, 95% CI 0.84 to 2.43, p = 0.19). Gene expression profiles of immunohistochemically determined CK5/14-positive tumors within the ER-negative tumor group implicated 1,713 differently expressed genes (p < 0.05). Hierarchical clustering analysis with the top 500 of these genes formed one basal-like and a non-basal-like cluster also within the ER-negative tumor entity. A highly concordant classification could be constructed with a published gene set (Sorlie's intrinsic gene set, concordance 90%). Both gene sets identified a basal-like cluster that included most of the CK5/14-positive tumors, but also immunohistochemically CK5/14-negative tumors. Within the ER-negative tumor entity there was no survival difference between the non-basal and basal-like tumors as identified by immunohistochemical or gene-expression-based classification.
Conclusion
Basal cytokeratin-positive tumors have a biologically distinct gene expression signature from other ER-negative tumors. Even if basal cytokeratin expression predicts early relapse among non-selected tumors, the clinical outcome of basal tumors is similar to non-basal ER-negative tumors. Immunohistochemically basal cytokeratin-positive tumors almost always belong to the basal-like gene expression profile, but this cluster also includes few basal cytokeratin-negative tumors.
doi:10.1186/bcr1649
PMCID: PMC1851391  PMID: 17263897
22.  Proteolytic Cleavage and Phosphorylation of a Tumor-associated ErbB4 Isoform Promote Ligand-independent Survival and Cancer Cell GrowthD⃞ 
Molecular Biology of the Cell  2006;17(1):67-79.
The ErbB1 and ErbB2 receptors are oncogenes with therapeutic significance in human cancer, whereas the transforming potential of the related ErbB4 receptor has remained controversial. Here, we have addressed whether four alternatively spliced ErbB4 isoforms differ in regulating cellular responses relevant for tumor growth. We show that the two tumor necrosis factor-α converting enzyme (TACE)-cleavable ErbB4 isoforms (the juxtamembrane [JM]-a isoforms) were overexpressed in a subset of primary human breast cancers together with TACE. The overexpression of the JM-a cytoplasmic (CYT)-2 ErbB4 isoform promoted ErbB4 phosphorylation, survival of interleukin-3-dependent cells, and proliferation of breast cancer cells even in the absence of ligand stimulation, whereas activation of the other three ErbB4 isoforms required ligand stimulation. Ligand-independent cellular responses to ErbB4 JM-a CYT-2 overexpression were regulated by both tyrosine kinase activity and a two-step proteolytic generation of an intracellular receptor fragment involving first a TACE-like proteinase, followed by γ-secretase activity. These data suggest a novel transforming mechanism for the ErbB4 receptor in human breast cancer that is 1) specific for a single receptor isoform and 2) depends on proteinase cleavage and kinase activity but not ligand activation of the receptor.
doi:10.1091/mbc.E05-05-0402
PMCID: PMC1345647  PMID: 16251361

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