[Show abstract][Hide abstract] ABSTRACT: Osteosarcomas are aggressive bone tumours with a high degree of genetic heterogeneity, which has historically complicated driver gene discovery. Here we sequence exomes of 31 tumours and decipher their evolutionary landscape by inferring clonality of the individual mutation events. Exome findings are interpreted in the context of mutation and SNP array data from a replication set of 92 tumours. We identify 14 genes as the main drivers, of which some were formerly unknown in the context of osteosarcoma. None of the drivers is clearly responsible for the majority of tumours and even TP53 mutations are frequently mapped into subclones. However, >80% of osteosarcomas exhibit a specific combination of single-base substitutions, LOH, or large-scale genome instability signatures characteristic of BRCA1/2-deficient tumours. Our findings imply that multiple oncogenic pathways drive chromosomal instability during osteosarcoma evolution and result in the acquisition of BRCA-like traits, which could be therapeutically exploited.
Full-text · Article · Dec 2015 · Nature Communications
[Show abstract][Hide abstract] ABSTRACT: Purpose:
To evaluate utility of magnetic resonance (MR) imaging in local staging of soft-tissue sarcoma, with an emphasis on assessment of neurovascular encasement.
Materials and methods:
Institutional review board approval was obtained; informed consent requirement was waived. Preoperative MR images in 174 patients with soft-tissue sarcoma were analyzed by two readers. Tumor staging according to the American Joint Committee on Cancer/Union International Contre le Cancer and Enneking staging systems and analysis of osseous and articular invasion were performed. To assess neurovascular encasement, contact between tumor and arteries, between tumor and veins, and between tumor and nerves was classified (no contact, contact ≤90°, 91°-180°, 181°-270°, >271°). Interobserver agreement was determined; imaging findings were correlated with intraoperative findings and/or histopathologic findings (Pearson correlation coefficient [r] and Cohen κ coefficient).
Intraoperative evaluation and/or histopathologic evaluation confirmed osseous, articular, and neurovascular invasion in 8.6%, 2.9%, and 25.3% of patients. Interobserver agreement was excellent for tumor staging (American Joint Committee on Cancer/Union International Contre le Cancer staging, κ = 0.811; Enneking staging, κ = 0.943) and osseous invasion (κ = 1.000). It was substantial for articular invasion (κ = 0.794). Sensitivity and specificity for osseous invasion were 100% and 98.7%, respectively (both readers). For articular invasion, sensitivity was 80% (both readers); specificities were 100% and 98.8% for readers 1 and 2, respectively. Interobserver agreement in quantifying contact between tumor and vessels and between tumor and nerves was excellent for arteries, veins, and nerves (κ = 0.845, 0.892, 0.893, respectively). Receiver operating characteristic analysis revealed optimal threshold of greater than 180° for prediction of arterial and venous encasement (both readers). For neural encasement, optimal threshold was greater than 180° (reader 1) and greater than 270° (reader 2). Sensitivities in diagnosing encasement for arteries, veins, and nerves were 84.6%, 84.6%, and 77.8% (reader 1) and 84.6%, 84.6%, and 72.2% (reader 2). Specificities for encasement of arteries, veins, and nerves, respectively, were 97.5%, 97.5%, and 93.2% (reader 1) and 93.8%, 94.7%, 97.3% (reader 2).
MR imaging allows reliable and accurate local staging of soft-tissue sarcoma. Encasement of arteries, veins, and nerves should be diagnosed, if the contact between tumor and vascular or neural circumference exceeds 180°.
[Show abstract][Hide abstract] ABSTRACT: Detection of anaplastic lymphoma kinase (ALK)-gene rearrangements in non-small-cell lung cancer (NSCLC) is mainly performed by fluorescence in-situ hybridization (FISH). The question was raised if FISH might be replaced by immunohistochemistry (IHC) in a reliable and reproducible manner across different laboratories.
After calibration of the staining instruments and training of the observers to binary interpretation (positive versus negative), 15 NSCLC were independently tested for ALK protein expression by IHC only in a multicenter setting (16 institutes). Each laboratory utilized the VENTANA ALK-D5F3 IHC assay. As demonstrated by FISH the samples displayed unequivocal ALK break-positivity (6×) and negativity (7×), as well as ALK positive-"borderline" character (2×), which is challenging for FISH diagnosis and thus was RT-PCR-confirmed.
All seven ALK FISH-negative cases were homogenously scored as ALK-IHC negative. All 16 participants scored the two ALK positive-"borderline" samples as unequivocally positive according to their protein expression. Concordant IHC interpretation was also noticed in four of six unequivocal ALK break positive cases. In two of six some observers described a weak/heterogeneous ALK-IHC staining. This would have resulted in a subsequent ALK-testing (FISH/PCR) in a routine diagnostic setting.
This so-called "ALK-Harmonization-Study" shows for the first time that predictive semiquantitative IHC reveals reliable and reproducible results across several labs when methodology and interpretation are strictly defined and the pathologists are uniquely trained. The application of validated ALK IHC assays and its comparison to ALK-FISH is highly needed in future clinical trials. This might answer the question if ALK-IHC cannot only serve as a prescreening tool, but as a stand-alone test at least in cases displaying an unequivocally staining pattern as well as an alternative predictive test in samples with reduced FISH interpretability.
Full-text · Article · Nov 2014 · Journal of Thoracic Oncology
[Show abstract][Hide abstract] ABSTRACT: The aim of our study was to evaluate the quality of histo- and cytomorphological features of PAXgene-fixed specimens and their suitability for histomorphological classification in comparison to standard formalin fixation. Fifteen colon cancer tissues were collected, divided into two mirrored samples and either formalin fixed (FFPE) or PAXgene fixed (PFPE) before paraffin embedding. HE- and PAS-stained sections were scanned and evaluated in a blinded, randomised ring trial by 20 pathologists from Europe and the USA using virtual microscopy. The pathologists evaluated histological grading, histological subtype, presence of adenoma, presence of lymphovascular invasion, quality of histomorphology and quality of nuclear features. Statistical analysis revealed that the reproducibility with regard to grading between both fixation methods was rather satisfactory (weighted kappa statistic (k
w) = 0.73 (95 % confidence interval (CI), 0.41–0.94)), with a higher agreement between the reference evaluation and the PFPE samples (k
w = 0.86 (95 % CI, 0.67–1.00)). Independent from preservation method, inter-observer reproducibility was not completely satisfactory (k
w = 0.60). Histomorphological quality parameters were scored equal or better for PFPE than for FFPE samples. For example, overall quality and nuclear features, especially the detection of mitosis, were judged significantly better for PFPE cases. By contrast, significant retraction artefacts were observed more frequently in PFPE samples. In conclusion, our findings suggest that the PAXgene Tissue System leads to excellent preservation of histomorphology and nuclear features of colon cancer tissue and allows routine morphological diagnosis.
Full-text · Article · Aug 2014 · Archiv für Pathologische Anatomie und Physiologie und für Klinische Medicin
[Show abstract][Hide abstract] ABSTRACT: OBJECTIVES:
To test the hypothesis that bone marrow oedema (BME) observed on MRI in patients with avascular necrosis (AVN) of the femoral head represents an indicator of subchondral fracture.
Thirty-seven symptomatic hips of 27 consecutive patients (53 % women, mean age 49.2) with AVN of the femoral head and associated BME on magnetic resonance (MR) imaging were included. MR findings were correlated with computed tomography (CT) of the hip and confirmed by histopathological examination of the resected femoral head. Imaging studies were analysed by two radiologists with use of the ARCO classification.
On MR imaging a fracture line could be identified in 19/37 (51 %) cases, which were classified as ARCO stage 3 (n = 15) and stage 4 (n = 4). The remaining 18/37 (49 %) cases were classified as ARCO stage 2. However, in all 37/37 (100 %) cases a subchondral fracture was identified on CT, indicating ARCO stage 3/4 disease. The extent of subchondral fractures and the femoral head collapse was graded higher on CT as compared to MRI (P < 0.05). Histopathological analysis confirmed bone necrosis and subchondral fractures.
In patients with AVN, BME of the femoral head represents a secondary sign of subchondral fracture and thus indicates ARCO stage 3 disease.
Full-text · Article · May 2014 · European Radiology
[Show abstract][Hide abstract] ABSTRACT: In gastrointestinal stromal tumor (GIST), there is no biomarker available that indicates success or failure of therapy. We hypothesized that tumor specific CKIT or PDGFRA mutant DNA fragments can be detected and quantified in plasma samples of GIST patients.
We prospectively collected 291 plasma samples from 38 subjects with GIST harbouring activating mutations of CKIT or PDGFRA detected in tumor tissue, irrespective of current disease status or treatment. We used allele-specific Ligation PCR to detect mutant free circulating (fc)DNA.
We were able to detect fcDNA harbouring the tumor mutation in 15 out of 38 patients. Patients with active disease displayed significantly higher amounts of mutant fcDNA compared to patients in CR. The amount of mutant fcDNA correlated with disease course. We observed repeated positive test results or an increase of mutant fcDNA in five patients with progressive disease or relapse. A decline of tumor fcDNA or conversion from positive to negative was seen in five patients responding to treatment. A negative to positive conversion was seen in two patients with relapse and one patient with progression. In two cases, we aimed to identify additional mutations, and found four additional exchanges, including mutations not known from sequentially performed tumor biopsies.
Our results indicate that free circulating DNA harbouring tumor specific mutations in the plasma of patients with GIST can be used as tumor-specific biomarker. The detection of resistance mutations in plasma samples might allow earlier treatment changes and obviates the need for repeated tumor biopsies.
Preview · Article · Jul 2013 · Clinical Cancer Research
[Show abstract][Hide abstract] ABSTRACT: Intraductal papillary neoplasms of the bile duct are still poorly characterized regarding (1) their molecular alterations during the development to invasive carcinomas, (2) their subtype stratification and (3) their biological behavior. We performed a multicenter study that analyzed these issues in a large European cohort. Intraductal papillary neoplasms of the bile duct from 45 patients were graded and subtyped using mucin markers and CDX2. In addition, tumors were analyzed for common oncogenic pathways, and the findings were correlated with subtype and grade. Data were compared with those from 22 extra- and intrahepatic cholangiocarcinomas. Intraductal papillary neoplasms showed a development from preinvasive low- to high-grade intraepithelial neoplasia to invasive carcinoma. Molecular and immunohistochemical analysis revealed mutated KRAS, overexpression of TP53 and loss of p16 in low-grade intraepithelial neoplasia, whereas loss of SMAD4 was found in late phases of tumor development. Alterations of HER2, EGFR, β-catenin and GNAS were rare events. Among the subtypes, pancreato-biliary (36%) and intestinal (29%) were the most common, followed by gastric (18%) and oncocytic (13%) subtypes. Patients with intraductal papillary neoplasm of the bile duct showed a slightly better overall survival than patients with cholangiocarcinoma (hazard ratio (cholangiocarcinoma versus intraductal papillary neoplasm of the bile duct): 1.40; 95% confidence interval: 0.46-4.30; P=0.552). The development of biliary intraductal papillary neoplasms of the bile duct follows an adenoma-carcinoma sequence that correlates with the stepwise activation of common oncogenic pathways. Further large trials are needed to investigate and verify the finding of a better prognosis of intraductal papillary neoplasms compared with conventional cholangiocarcinoma.Modern Pathology advance online publication, 5 July 2013; doi:10.1038/modpathol.2013.112.
[Show abstract][Hide abstract] ABSTRACT: Truncated forms of HER2, previously identified in subsets of HER2-positive breast cancer, originate from proteolytic extracellular domain (ECD) cleavage or alternative translation initiation. They lack ECD but may retain intracellular domain functionality, potentially associated with unfavorable prognosis, metastasis, and decreased sensitivity to antibody-based HER2-targeted therapy. To study the distribution of truncated HER2 in breast cancer, we detected loss of membrane-bound ECD independently of its molecular origin in paraffin sections, combining multispectral unmixing of chromogenic duplex IHC for HER2 ECD and intracellular domain with advanced image analysis. HER2 C-terminal fragment 611-transfected MCF7 and 4-aminophenylmercuric acetate-treated SKBR3 cell lines were used as controls. Applying a prototype work flow to whole sections, paired surgical resection/core needle biopsy samples, and paired samples from 69 patients of a phase 2 neoadjuvant clinical trial, we observed unexpected heterogeneity of ECD loss at the single-cell level, and in different areas of individual tumors, indicating that extent and localization of HER2 ECD loss add relevant information to averaging truncated HER2 across whole sections. We show acceptable run-to-run variation (coefficient of variation, <0.15), image analysis results in moderate agreement with conventional slide assessment (Cohen's κ = 0.59), and no obvious interference with previous HER2-ECD-targeted therapy. We conclude that duplex IHC and digital image processing extend current approaches of truncated HER2 detection.
Full-text · Article · May 2013 · American Journal Of Pathology
[Show abstract][Hide abstract] ABSTRACT: Objective:
Primary hepatic angiosarcoma is a very rare and aggressive malignancy of vascular origin. We describe cross-sectional imaging findings of this entity with emphasis on dynamic contrast-enhanced (DCE) and diffusion-weighted (DWI) MR imaging.
Seven cases of pathologically confirmed hepatic angiosarcoma were retrospectively reviewed (CT and MRI examinations were available in seven and six patients, respectively). Two radiologists evaluated lesion growth patterns, attenuation, signal intensity characteristics, contrast enhancement patterns, and apparent diffusion coefficients (ADCs).
Multifocal hepatic disease was present in six patients by means of a mixed pattern of large dominant masses and multiple small nodules; one patient had a solitary large mass. Unenhanced images depicted hemorrhagic areas and a markedly heterogeneous internal architecture within large tumors. Contrast-enhanced early phase images showed variable patterns including patchy peripheral or bizarre shaped intralesional foci of enhancement, peripheral rim enhancement, and small lesions without enhancement. On DCE images, the majority of lesions presented with varying degrees of progressive enhancement. Small nodules frequently displayed homogeneous enhancement on delayed phase images due to complete fill-in. DWI revealed a high interlesional variability of ADC values (range 0.57-2.41 × 10(-3 )mm(2)/s, mean 1.37 × 10(-3 )mm(2)/s).
Cross-sectional imaging findings of hepatic angiosarcoma reflect the varied histopathological composition of the tumors. Multifocal disease, hemorrhage within large lesions, as well as progressive enhancement on DCE images are typical features of hepatic angiosarcoma. The mean ADC of lesions was found to be slightly elevated in comparison with other hepatic malignancies.
No preview · Article · Dec 2012 · Abdominal Imaging
[Show abstract][Hide abstract] ABSTRACT: Objectives
Ovarian borderline tumors (BOTs) generally have an excellent prognosis, although recurrences and malignant transformation can occur. Our aim was to compare clinicopathologic features of BOT with clinical outcome.Methods
In seventy consecutive BOTs clinicopathologic parameters, tumor cell proliferation (Ki67) and in selected cases KRAS, BRAF and p53 mutational status were analyzed with recurrence-free and overall survival as the endpoints.ResultsSixty-one (87%) patients presented with FIGO stage I, 3 stage II, and 6 stage III. Thirty-four patients had serous and 36 mucinous BOT (30 intestinal and 6 endocervical subtypes). Non-invasive peritoneal implants occurred in 9 patients, and no invasive implants were observed. Recurrence-free and overall survival rates were 91% and 99%, respectively, at a mean follow-up of 63 months.Disease recurrence occurred in 6 cases (all FIGO stage I) including 3 serous, 1 mucinous-intestinal, and 2 mucinous-endocervical subtypes. Mean time to recurrence was 27 months (range 8–68). The recurrence rate following fertility-conserving surgery was 31% (5/16) compared to 2% (1/54) after bilateral salpingo-oophorectomy. Neither peritoneal implants (9/70), micropapillary pattern (2/34), microinvasion (4/70), nor increased tumor cell proliferation was associated with a higher recurrence rate. The frequency of KRAS or BRAF mutations was 50% (3/6 recurrences and 3/6 controls; 4 KRAS, 2 BRAF mutations). No p53 mutations (0/12) were detected in primary or recurrent BOTs.Conclusions
Histopathologic parameters were not predictive of BOT recurrence including previously suggested risk factors such as micropapillary pattern and microinvasion. However, fertility-conserving surgery and incomplete surgical staging were associated with a higher risk for recurrence.
No preview · Article · Dec 2012 · Gynecologic Oncology
[Show abstract][Hide abstract] ABSTRACT: We report a case of subcutaneous sparganosis in a 68-year-old female Japanese immigrant in Germany. The patient complained of a painless erythema caudal of the umbilicus with a palpable subcutaneous cherry-sized lump. Polymerase chain reaction on formalin-fixed parasite tissue identified Spirometra erinaceieuropaei as the causative agent; the proliferative form of sparganosis, which is caused by the branching and disseminating Sparganum proliferum, could, thus, be excluded. From the excised sparganum, an immunofluorescence test was established and revealed an antibody response directed against the parasite's tegument. Histological key features of the plerocercoid that facilitate diagnosis with different stains are presented.
Full-text · Article · Nov 2012 · The American journal of tropical medicine and hygiene
[Show abstract][Hide abstract] ABSTRACT: The accuracy of common markers for PI3K/AKT and MAPK pathway activation in preclinical and clinical cancer biomarker studies depends on phosphoepitope stability and changes of phosphorylation under ischemia. Herein, we define conditions under which phosphoepitope-specific duplex immunohistochemistry (IHC) on formalin-fixed, paraffin-embedded tumor tissues reflects pathway activation in situ as accurately as possible, and identify activation patterns linked to mutational status, pathway dependency and tumor microenvironment in clinical tumor samples, cell culture and xenograft tissues. Systematically assessing robustness of pAKT, pERK1/2, pMEK1/2 and pmTOR detection and related markers in xenograft tissues exposed to ischemia, we show that control of preprocessing and ischemia times allows accurate interpretation of staining results. Phosphorylation patterns were then analyzed in 33 xenograft models and in 58 cases with breast cancer, including 21 paired samples of core-needle biopsies with corresponding mastectomy specimens, and 37 mastectomy samples obtained under rigorously controlled conditions minimizing ischemia time. Patterns of pAKT and pERK1/2 staining (predominant PI3K/AKT, predominant MAPK and concomitant activation) were associated with sensitivity to pathway inhibition and partially with the mutational status in cell lines and corresponding xenograft tumors. In contrast, no clear correlation between mutational status and staining patterns was observed in clinical breast cancer samples, suggesting that interaction with the human tumor microenvironment may interfere with the use of phosphoepitope-specific IHC as potential markers for pathway dependency. In contrast to core needle biopsies, surgically resected breast cancer samples showed evidence of severe signal changes comparable to those effects observed in xenograft tumors exposed to controlled ischemia.
Preview · Article · Oct 2012 · International Journal of Cancer
[Show abstract][Hide abstract] ABSTRACT: Gene expression profiles provide important information about the biology of breast tumors and can be used to develop prognostic tests. However, the implementation of quantitative RNA-based testing in routine molecular pathology has not been accomplished, so far. The EndoPredict assay has recently been described as a quantitative RT-PCR-based multigene expression test to identify a subgroup of hormone-receptor-positive tumors that have an excellent prognosis with endocrine therapy only. To transfer this test from bench to bedside, it is essential to evaluate the test-performance in a multicenter setting in different molecular pathology laboratories. In this study, we have evaluated the EndoPredict (EP) assay in seven different molecular pathology laboratories in Germany, Austria, and Switzerland. A set of ten formalin-fixed paraffin-embedded tumors was tested in the different labs, and the variance and accuracy of the EndoPredict assays were determined using predefined reference values. Extraction of a sufficient amount of RNA and generation of a valid EP score was possible for all 70 study samples (100%). The EP scores measured by the individual participants showed an excellent correlation with the reference values, respectively, as reflected by Pearson correlation coefficients ranging from 0.987 to 0.999. The Pearson correlation coefficient of all values compared to the reference value was 0.994. All laboratories determined EP scores for all samples differing not more than 1.0 score units from the pre-defined references. All samples were assigned to the correct EP risk group, resulting in a sensitivity and specificity of 100%, a concordance of 100%, and a kappa of 1.0. Taken together, the EndoPredict test could be successfully implemented in all seven participating laboratories and is feasible for reliable decentralized assessment of gene expression in luminal breast cancer.
Full-text · Article · Feb 2012 · Archiv für Pathologische Anatomie und Physiologie und für Klinische Medicin
[Show abstract][Hide abstract] ABSTRACT: Chemotherapy for advanced colorectal cancer leads to improved survival; however, predictors of response to systemic treatment are not available. Genomic and epigenetic alterations of the gene encoding transcription factor AP-2 epsilon (TFAP2E) are common in human cancers. The gene encoding dickkopf homolog 4 protein (DKK4) is a potential downstream target of TFAP2E and has been implicated in chemotherapy resistance. We aimed to further evaluate the role of TFAP2E and DKK4 as predictors of the response of colorectal cancer to chemotherapy.
We analyzed the expression, methylation, and function of TFAP2E in colorectal-cancer cell lines in vitro and in patients with colorectal cancer. We examined an initial cohort of 74 patients, followed by four cohorts of patients (total, 220) undergoing chemotherapy or chemoradiation.
TFAP2E was hypermethylated in 38 of 74 patients (51%) in the initial cohort. Hypermethylation was associated with decreased expression of TFAP2E in primary and metastatic colorectal-cancer specimens and cell lines. Colorectal-cancer cell lines overexpressing DKK4 showed increased chemoresistance to fluorouracil but not irinotecan or oxaliplatin. In the four other patient cohorts, TFAP2E hypermethylation was significantly associated with nonresponse to chemotherapy (P<0.001). Conversely, the probability of response among patients with hypomethylation was approximately six times that in the entire population (overall estimated risk ratio, 5.74; 95% confidence interval, 3.36 to 9.79). Epigenetic alterations of TFAP2E were independent of mutations in key regulatory cancer genes, microsatellite instability, and other genes that affect fluorouracil metabolism.
TFAP2E hypermethylation is associated with clinical nonresponsiveness to chemotherapy in colorectal cancer. Functional assays confirm that TFAP2E-dependent resistance is mediated through DKK4. In patients who have colorectal cancer with TFAP2E hypermethylation, targeting of DKK4 may be an option to overcome TFAP2E-mediated drug resistance. (Funded by Deutsche Forschungsgemeinschaft and others.).
Preview · Article · Jan 2012 · New England Journal of Medicine