Molecular diagnosis of Ewing's sarcoma/primitive neuroectodermal tumor in formalin-fixed paraffin-embedded tissues by RT-PCR and fluorescence in situ hybridization

Renal Ewing sarcoma with inferior vena cava (IVC) tumor thrombosis; A case report

Ewing sarcoma (ES) is a rare group of undifferentiated tumors that originate from neuroectoderm. Although the overall prognosis is poor, early diagnosis and treatment by a multidisciplinary team with multimodal therapy can improve outcomes. Therefore, we present a 22-year-old female patient with primary renal ES with tumor thrombosis up to the vena cava who had radical nephrectomy and IVC tumor thrombectomy followed by adjuvant chemotherapy because a preoperative percutaneous biopsy was confirmed the diagnosis.

PAX8-positive, Cytokeratin-positive Intra-abdominal Ewing Sarcoma Masquerading as a Mullerian Carcinoma in a Postmenopausal Female

Extraskeletal Ewing sarcoma presenting as intra-abdominal or pelvic disease in adult female patients is very rare and may lead to diagnostic difficulty due to clinical and histologic overlap with Mullerian adenocarcinomas, which are far more common. We report a case of an intra-abdominal Ewing sarcoma in a postmenopausal female patient whose clinical and radiological presentation closely resembled that of peritoneal carcinomatosis. Biopsy of an omental nodule revealed numerous histologic features suggestive of a Mullerian carcinoma, including gland-like rosettes, strong, diffuse PAX8 immunoreactivity and cytokeratin expression. After excluding other differential diagnostic considerations, the possibility that this might represent an intra-abdominal Ewing sarcoma was entertained. Reverse transcriptase polymerase chain reaction testing demonstrated the presence of an EWSR1-ERG fusion transcript, confirming the diagnosis. The differential diagnostic considerations when dealing with this unusual clinical scenario and the uncommon yet important pitfall of PAX8 immunoreactivity in Ewing sarcoma are discussed.

Ewing Sarcoma in Older Adults: A Clinicopathologic Study of 50 Cases Occurring in Patients Aged ≥40 Years, With Emphasis on Histologic Mimics

Objective. We explore the clinicopathologic features of Ewing sarcoma (ES) presenting in older adulthood. Methods. Cases of molecularly confirmed ES arising in patients aged ≥40 years were evaluated. Results. Fifty patients were identified (33 males/17 females; 41-86 years). The majority of tumors (41) arose at extraskeletal sites, while 9 were bone primaries. Twenty-eight cases showed nested architecture, while the remaining cases showed sheet-like growth. Tumor cytology was categorized as conventional (n = 39), crushed (n = 5), clear cell (n = 4), rhabdoid (n = 3), and epithelioid (n = 2). Fifty percent had necrosis, while rosettes were noted in 1 case. Immunostains performed ranged from 1 to 28 (median = 10). Follow-up (n = 43, 1-147 months) revealed 15 patients with metastasis. Conclusion. Although rare, ES should be considered in the differential diagnosis for round cell malignancies in older adult patients. In this cohort, ES is most often extraskeletal, and may show unusual morphologic features, closely simulating more common neoplasms in this age group.

Molecular cytogenetic characterization of two established ESFT cell lines

Ewing's sarcoma/primitive neuroectodermal tumor/Askin's tumor (Ewing`s sarcoma family of tumors: ESFT) is the most common type of malignant tumor of bone and soft tissue in children and young adults, and morphologically is a member of a group of small round cell tumors. We report, here, on the establishment of two human ESFT cell lines, FU-PNET-3 and FU-PNET-4, from the iliac and the chest wall, respectively, the cells of both cell lines were tumorigenic in immunodeficient mice. Histologically, both original and xenograft tumors and cultured cells were composed of small round cells with positive immunoreactivity for CD99 and Nkx2.2. Molecular biological examination demonstrated chimeric transcripts of EWSR1 exon 7 to FLI1 exon 6 in FU-PNET-3 cells, and EWSR1 exon 10 to FLI1 exon 6 in FU-PNET-4 cells. Cytogenetic analysis revealed chromosome translocation t(11;22)(q24;q12) and some secondary changes in both cultured cells. These histological, molecular biological, and cytogenetical findings indicate ESFT in both cell lines. ESFT is well studied, but its recurrent fusion genes are heterogeneous and its biological behaviors are unclear. The FU-PNET-3 and FU-PNET-4 cell lines have been well examined and may become useful tools for studying the genetic and biological behavioral properties of ESFT.

Primary angiomatoid fibrous histiocytoma of the lung with mediastinal lymph node metastasis

Angiomatoid fibrous histiocytoma (AFH), a rare soft tissue tumor of borderline malignancy, typically occurs in the subcutis of the accessible soft tissues, most often in children and young adults. Lymph node and/or distant metastasis is seen in less than 2% of patients with AFH. Exceptionally rare examples of AFH have been reported in visceral locations, including the lung. We report a genetically confirmed primary pulmonary AFH in a 70-year-old woman with mediastinal lymph node metastasis, representing to the best of our knowledge the first report of metastases from a visceral AFH.

ChildSeq-RNA: A next-generation sequencing-based diagnostic assay to identify known fusion transcripts in childhood sarcomas

Childhood sarcomas can be extremely difficult to accurately diagnose on the basis of morphological characteristics alone. Ancillary methods, such as RT-PCR or fluorescence in situ hybridization, to detect pathognomonic gene fusions can help to distinguish these tumors. Two major deficiencies of these assays are their inability to identify gene fusions at nucleotide resolution or to detect multiple gene fusions simultaneously. We developed a next-generation sequencing-based assay designated ChildSeq-RNA that uses the Ion Torrent platform to screen for EWSR1-FLI1 and EWSR1-ERG, PAX3-FOXO1 and PAX7-FOXO1, EWSR1-WT1, and ETV6-NTRK3 fusions of Ewing sarcoma (ES), alveolar rhabdomyosarcoma, desmoplastic small round cell tumor, and congenital fibrosarcoma, respectively. To rapidly analyze resulting data, we codeveloped a bioinformatics tool, termed ChildDecode, that operates on a scalable, cloud-computing platform. Total RNA from four ES cell lines plus 33 clinical samples representing ES, alveolar rhabdomyosarcoma, desmoplastic small round cell tumor, and congenital fibrosarcoma tumors was subjected to ChildSeq-RNA. This accurately identified corresponding gene fusions in each tumor type, with no examples of false positive fusion detection in this proof-of-concept study. Comparison with previous RT-PCR findings demonstrated high sensitivity (96.4%; 95% CI, 82.3%-99.4%) and specificity (100%; 95% CI, 56.6%-100%) of ChildSeq-RNA to detect gene fusions. Herein, we propose ChildSeq-RNA as a novel tool to detect gene fusions in childhood sarcomas at single-nucleotide resolution.

Detection of common chromosomal translocations in small round blue cell pediatric tumors

BACKGROUND AND AIMS

Recurrent and specific chromosomal translocations have been described in four pediatric sarcomas belonging to the small round blue cell (SRBC) group of tumors. Identification of mRNA chimeras using RT-PCR discriminates among alveolar rhabdomyosarcoma (ARMS), Ewing's sarcoma (ES/pPNET), synovial sarcoma (SS) and desmoplastic small round cell tumor (DSRCT); however, frequencies of these translocations are variable. We present a retrospective study comparing histological examination and occurrence of major chromosomal translocations to validate the diagnosis and to assess the frequency of these molecular markers in a group of 92 small round blue cell (SRBC) tumor samples from Hospital Infantil de Mexico.

METHODS

We tested a panel of RT-PCR assays to each RNA tumor sample from formalin-fixed, paraffin-embedded tumors to detect specific mRNA chimeras in 47 ES/pPNET, 19 ARMS, four SS, three DSRCT, and 19 other SRBC tumors.

RESULTS

After excluding poor RNA quality samples, we found translocations in 17/31 ES/pPNET (54.8%), 10/19 ARMS (52.6%), 4/4 SS (100%) and 4/4 DSRCT (100%). We found disagreement in only three samples: one ES/pPNET and one embryonal rhabdomyosarcoma harbor a PAX3-FOXO1 translocation (for ARMS), and one neuroepithelioma harboring a EWS-WT1 (for DSRCT). Unsuitable RNA was found in 20/92 samples (21.7%) and was related to necrosis, small amount of tumor tissue, and use of nitric acid in bone biopsies, but was not related to age of the block.

CONCLUSIONS

We found a significantly lower occurrence of chromosomal translocations in ES/pPNET compared to reports from other groups. Differences may exist in the frequencies of these molecular markers among different populations.

Usefulness of a monoclonal ERG/FLI1 antibody for immunohistochemical discrimination of Ewing family tumors

Ewing family tumors (EFTs) and prostate carcinomas are characterized by rearrangement of ETS genes, most commonly FLI1 (EFTs) and ERG (prostate carcinomas). Previously, we characterized an antibody against ERG (EPR3864) for detecting ERG-rearranged prostate carcinoma. Because EPR3864 also cross-reacts with FLI1, we evaluated the usefulness of EPR3864 for discriminating EFTs from other small round blue cell tumors (SRBCTs) with immunohistochemistry. Of 57 evaluable EFTs, 47 (82%) demonstrated at least moderate, diffuse, nuclear ERG/FLI1 staining (including 89% and 100% of cases with confirmed EWSR1:FLI1 and EWSR1:ERG fusions, respectively), of which 1, 3, and 43 showed negative, cytoplasmic, or membranous CD99 staining, respectively. Among other SRBCTs (61 cases, 7 types), at least moderate, diffuse, nuclear EPR3864 staining was seen in all precursor B-lymphoblastic lymphomas/leukemias and subsets of Burkitt lymphomas (10%) and synovial sarcomas (45%). In summary, EPR3864 may be useful in detecting EWSR1:FLI1 and EWSR1:ERG rearranged EFTs in addition to prostate carcinomas.

Molecular detection and targeting of EWSR1 fusion transcripts in soft tissue tumors

Soft tissue tumors are a heterogeneous group of tumors, traditionally classified according to morphology and histogenesis. Molecular classification divides sarcomas into two main categories: (a) sarcomas with specific genetic alterations and (b) sarcomas showing multiple complex karyotypic abnormalities without any specific pattern. Most chromosomal alterations are represented by translocations which are increasingly detected. The identification of fusion transcripts, in fact, not only support the diagnosis but also provides the basis for the development of new therapeutic strategies aimed at blocking aberrant activity of the chimeric proteins. One of the genes most susceptible to breakage/translocation in soft tissue tumors is represented by Ewing sarcoma breakpoint region 1 (EWSR1). This gene has a large number of fusion partners, mainly associated with the pathogenesis of Ewing's sarcoma but with other soft tissue tumors too. In this review, we illustrate the characteristics of this gene/protein, both in normal cellular physiology and in carcinogenesis. We describe the different fusion partners of EWSR1, the molecular pathways in which is involved and the main molecular biology techniques for the identification of fusion transcripts and for their inhibition.

Molecular Pathology of Sarcoma

The rapid growth of tissue-based molecular pathology has changed the practice of the surgical pathologist signing out soft tissue tumors. This information is presented in a practical and succinct manner focusing on clinically validated findings that have diagnostic or therapeutic relevance. The approach is morphologically based and focuses on differential diagnoses and clinical scenarios. Molecular techniques can be an invaluable ancillary tool.

IDH mutation and neuroglial developmental features define clinically distinct subclasses of lower grade diffuse astrocytic glioma

PURPOSE

Diffuse gliomas represent the most prevalent class of primary brain tumor. Despite significant recent advances in the understanding of glioblastoma [World Health Organization (WHO) IV], its most malignant subtype, lower grade (WHO II and III) glioma variants remain comparatively understudied, especially in light of their notable clinical heterogeneity. Accordingly, we sought to identify and characterize clinically relevant molecular subclasses of lower grade diffuse astrocytic gliomas.

EXPERIMENTAL DESIGN

We conducted multidimensional molecular profiling, including global transcriptional analysis, on 101 lower grade diffuse astrocytic gliomas collected at our own institution and validated our findings using publically available gene expression and copy number data from large independent patient cohorts.

RESULTS

We found that IDH mutational status delineated molecularly and clinically distinct glioma subsets, with IDH mutant (IDH mt) tumors exhibiting TP53 mutations, platelet-derived growth factor receptor (PDGFR)A overexpression, and prolonged survival, and IDH wild-type (IDH wt) tumors exhibiting EGFR amplification, PTEN loss, and unfavorable disease outcome. Furthermore, global expression profiling revealed three robust molecular subclasses within lower grade diffuse astrocytic gliomas, two of which were predominantly IDH mt and one almost entirely IDH wt. IDH mt subclasses were distinguished from each other on the basis of TP53 mutations, DNA copy number abnormalities, and links to distinct stages of neurogenesis in the subventricular zone. This latter finding implicates discrete pools of neuroglial progenitors as cells of origin for the different subclasses of IDH mt tumors.

CONCLUSION

We have elucidated molecularly distinct subclasses of lower grade diffuse astrocytic glioma that dictate clinical behavior and show fundamental associations with both IDH mutational status and neuroglial developmental stage.

Small Round Cell Tumors of Bone

Diagnosing small round cell tumors (SCRTs) can be a difficult task for pathologists due to overlapping clinicopathologic features. This review highlights the clinical, radiographic, histologic, immunohistochemical, and genetic features of the most common SRCTs involving bone with an emphasis on differential diagnosis. SRCTs are a heterogeneous group of neoplasms characterized by poorly differentiated cells with small, blue, round nuclei and scant cytoplasm. They can occur as primary tumors in bone or soft tissue.

R1507, an anti-insulin-like growth factor-1 receptor (IGF-1R) antibody, and EWS/FLI-1 siRNA in Ewing's sarcoma: convergence at the IGF/IGFR/Akt axis

A subset of patients with Ewing's sarcoma responds to anti-insulin-like growth factor-1 receptor (IGF-1R) antibodies. Mechanisms of sensitivity and resistance are unknown. We investigated whether an anti-IGF-1R antibody acts via a pathway that could also be suppressed by small interfering (si) RNA against the EWS/FLI-1 fusion protein, the hallmark of Ewing's sarcoma. The growth of two Ewing's sarcoma cell lines (TC-32 and TC-71) was inhibited by the fully human anti-IGF-1R antibody, R1507 (clonogenic and MTT assays). TC-32 and TC-71 cells express high levels of IGF-2, while RD-ES and A4573 Ewing's cell lines, which were less responsive to R1507 in our assays, express low or undetectable IGF-2, respectively. TC-71 cells also expressed high levels of IGF-1R, and R1507 decreased steady-state levels of this receptor by internalization/degradation, an effect which was associated with a decrease in p-IGF-1R, p-IRS-1, and p-Akt. EWS/FLI-1 siRNA also decreased p-Akt, due to its ability to increase IGF-BP3 levels and subsequently decrease IGF-1 and IGF-2 levels, thus inhibiting signaling through p-IGF-1R. This inhibition correlated with growth suppression and apoptosis. The attenuation of Akt activation was confirmed in TC-71 and HEK-293 (human embryonic kidney) cells by transfecting them with IGF-1R siRNA. We conclude that antibodies and siRNA to IGF-1R, as well as siRNA to EWS/FLI-1, act via intersecting IGF/IGF-1R signals that suppress a common point in this pathway, namely the phosphorylation of Akt.

Nodular fasciitis: a novel model of transient neoplasia induced by MYH9-USP6 gene fusion

Nodular fasciitis (NF) is a relatively common mass-forming and self-limited subcutaneous pseudosarcomatous myofibroblastic proliferation of unknown pathogenesis. Due to its rapid growth and high mitotic activity, NF is often misdiagnosed as a sarcoma. While studying the USP6 biology in aneurysmal bone cyst and other mesenchymal tumors, we identified high expression levels of USP6 mRNA in two examples of NF. This finding led us to further examine the mechanisms underlying USP6 overexpression in these lesions. Upon subsequent investigation, genomic rearrangements of the USP6 locus were found in 92% (44 of 48) of NF. Rapid amplification of 5'-cDNA ends identified MYH9 as the translocation partner. RT-PCR and direct sequencing revealed the fusion of the MYH9 promoter region to the entire coding region of USP6. Control tumors and tissues were negative for this fusion. Xenografts of cells overexpressing USP6 in nude mice exhibited clinical and histological features similar to human NF. The identification of a sensitive and specific abnormality in NF holds the potential to be used diagnostically. Considering the self-limited nature of the lesion, NF may represent a model of 'transient neoplasia', as it is, to our knowledge, the first example of a self-limited human disease characterized by a recurrent somatic gene fusion event.

Primary Ewing's sarcoma/primitive neuroectodermal tumor of the kidney: Report of a case diagnosed by fine needle aspiration cytology and confirmed by immunocytochemistry and RT-PCR along with review of literature

Primary Ewing's sarcoma/primitive neuroectodermal tumor (ES/PNET) of the kidney is a distinct entity that can be mistaken for variety of round cell tumors. We report a rare case of ES/PNET of the kidney in a 35-year-old female patient diagnosed by fine needle aspiration cytology (FNAC) and confirmed by immunohistochemistry (IHC) and reverse-transcriptase polymerase chain reaction (RT-PCR). Ultrasound guided FNAC smears from the kidney mass showed a population of malignant small round cells with perivascular arrangement and focal rosette formation. IHC performed on the cell block, showed strong immunopositivity for CD99 (MIC2) and vimentin. Molecular analysis of the aspirate by RT-PCR confirmed the EWS-FLI type1 transcript. The application of RT-PCR on FNAC material for establishing a diagnosis of renal ES/PNET is being reported for the first time. FNAC also confirmed metastases in the right level I cervical lymph node. The utility of IHC and molecular techniques in diagnosis of such a rare case is stressed and relevant literature is discussed.

Molecular diagnosis in Ewing family tumors: the Rizzoli experience--222 consecutive cases in four years

The Ewing's family of tumors (EFTs) are characterized by chimeric transcripts generated by specific chromosomal rearrangements. The most common fusions are between the EWSR1 gene on chromosome 22 and the ETS family of transcription factors; rarely, FUS (on chromosome 16) substitutes for EWSR1. The detection of specific translocations using molecular analysis is now a routine part of the pathological examination of EFT. Here, we report our experience with molecular diagnosis of EFT during the 4 years (2006-2009) at the Rizzoli Institute. We analyzed 222 consecutive tumors with a presumptive diagnosis of EFT using molecular techniques and IHC. We found five distinct types of EWSR1-FLI1 fusion transcripts resulting from translocation t(11;22), three types of EWSR1-ERG transcripts resulting from t(21;22), and one type of t(2;22) resulting in EWSR1-FEV fusion. Molecular investigation validated 92% of cases ultimately diagnosed as EFT; IHC validated 76% of the cases. Thus, despite the difficulties and limitations associated with both molecular and IHC analysis on fresh and formalin-fixed, paraffin-embedded tissue, a combination of these techniques is the best approach to enhancing the accuracy of EFT diagnosis. We also present our method for choosing which molecular techniques to apply. Finally, we collected the most prevalent breakpoints reported in the literature, indicating which exons are involved, the sequence breakpoints, and the NCBI reference sequences.

Diagnostic utility of IMP3 expression in thyroid neoplasms: a quantitative RT-PCR study

The capability of molecular markers to differentiate between benign and malignant well-differentiated thyroid tumors remains unclear. The aim of this study was to evaluate the use of insulin-like growth factor II mRNA binding protein-3 (IMP3) mRNA expression to distinguish benign from malignant thyroid tumors. RNA samples from 80 formalin-fixed, paraffin-embedded thyroid tissues, including 22 usual papillary thyroid carcinomas (PTCs), 18 follicular variants of PTC, 5 follicular thyroid carcinomas, 33 follicular adenomas, and 2 hyperplastic nodules, were used for quantitative reverse transcription-polymerase chain reaction (qRT-PCR) analysis. IMP3 mRNA expression levels in thyroid tumors were expressed as relative fold change (fold) after normalization with normal thyroid RNA. The results showed that thyroid carcinomas including PTC, follicular variants of PTC, and follicular thyroid carcinomas have significantly higher IMP3 expression levels with 48.3, 35.3, and 43.8 fold, respectively, compared with benign thyroid lesions (2.8 fold). Using the IMP3 expression value of 5 fold as a cutoff point to separate benign and malignant thyroid tumors, IMP3 qRT-PCR analysis had a 91.4% clinical specificity and 86.7% clinical sensitivity for the diagnosis of well-differentiated thyroid carcinomas. Conventional RT-PCR and immunohistochemical analysis for IMP3 in a subset of cases supported the qRT-PCR results. These results indicate that detection of IMP3 mRNA expression levels by qRT-PCR may be a useful molecular marker to assist in the diagnosis of well-differentiated thyroid carcinomas.

Detection of SYT and EWS gene rearrangements by dual-color break-apart CISH in liquid-based cytology samples of synovial sarcoma and Ewing sarcoma/primitive neuroectodermal tumor

To improve cytologic diagnostic accuracy for translocation-associated sarcomas, we explored dual-color break-apart (dc) chromogenic in situ hybridization (CISH) on liquid-based cytology (LBC) samples of 2 prototypic sarcomas: synovial sarcoma (SS) and Ewing sarcoma/primitive neuroectodermal tumor (ES/PNET). LBC samples of 10 cases of SS and 9 cases of ES/PNET were subjected to dc-CISH using probes for the specifically rearranged genes in each tumor entity: SYT in SS and EWS in ES/PNET. Rearranged SYT was successfully detected in all SSs but not in any ES/PNETs. In contrast, EWS rearrangement was identified in all ES/PNETs but not in any SSs. These results were validated by dc-fluorescence in situ hybridization and reverse transcription-polymerase chain reaction. dc-CISH on LBC samples is a reliable modality to detect gene rearrangements in sarcomas. This system has a clear advantage over other methods, enabling simultaneous visualization of the genetic abnormality and well-preserved, nonoverlapping cytomorphologic features with clear background under bright-field microscope.

Pathology of Ewing's sarcoma/PNET: Current opinion and emerging concepts

Ewing's sarcoma/PNET are small round cell tumors showing a varying degree of neuroectodermal differentiation. They are one of the commonest tumors of childhood and occur in bone and within soft tissues. Traditionally, light microscopy with the aid of immunohistochemical stains was suitable for diagnosis. But now translocation analyses are being used not only for the diagnosis and classification of small round cell tumors, but to ascertain their prognostic significance, detect micrometastasis, and monitor minimal residual disease, with potential for targeted therapy. This article analyzes the pathology, biology, and molecular aspects of Ewing's sarcoma/PNET and discusses their clinical and therapeutic implications.

Primary vulvar Ewing sarcoma/primitive neuroectodermal tumor: a report of 2 cases and review of the literature

Ewing sarcoma/primitive neuroectodermal tumor (ES/PNET) family of tumor is a very aggressive malignant round cell tumor characterized by translocations involving EWS-FLI1 genes. They are increasingly recognized in extraosseous sites as a result of improvements in diagnostic tools. In this paper, we report 2 additional cases arising in vulva of young adults who have been treated aggressively and have survived fore more than 7 and 4 years successively. Histologic examination showed small round (blue) cell morphology in both cases. The tumor cells contained glycogen and were positive for CD99 and vimentin and negative for keratins, lymphoid markers, S-100, synaptophysin, chromogranin, and desmin. Reverse transcriptase polymerase chain reaction analysis from paraffin-embedded tissue revealed EWS-FLI1 fusion product in 1 case. Collectively, 13 cases of vulvar ES/PNET have been reported in the literature. Only 8 cases have detailed follow-up information with an average follow-up data of 28 months. Ewing sarcoma/PNET should be considered in the differential diagnosis of any undifferentiated tumors involving the lower gynecologic tract and all axillary tests including molecular tests should be performed for correct diagnosis because prolonged survival is possible for this dreadful disease after complete surgical resection, followed by adjuvant therapy.

Phase I, Pharmacokinetic, and Pharmacodynamic Study of AMG 479, a Fully Human Monoclonal Antibody to Insulin-Like Growth Factor Receptor 1

Purpose

To determine the maximum-tolerated dose (MTD) and to assess the safety, pharmacokinetics, and evidence of antitumor activity of AMG 479, a fully human monoclonal antibody to insulin-like growth factor receptor 1 (IGF-1R).

Patients and Methods

Patients with advanced solid malignancies or non-Hodgkin's lymphoma received escalating doses of AMG 479 intravenously (IV) every 2 weeks (Q2W). Blood samples were assayed to determine pharmacokinetic parameters and IGF-1R occupancy on neutrophils; fluorodeoxyglucose–positron emission tomography scans were used to assess tumor metabolic effects.

Results

Fifty-three patients received 312 infusions of AMG 479 Q2W. Overall, the most common grades 1 to 2 toxicities were fatigue, thrombocytopenia, fever, rash, chills, and anorexia. One dose-limiting toxicity (ie, grade 3 thrombocytopenia) occurred in a patient at 20 mg/kg during course 1; grade 3 thrombocytopenia (n = 8) and grade 3 transaminitis elevations (n = 1) also were reported but not in the escalation phase. The maximum-planned dose of 20 mg/kg was safely administered; thus, an MTD was not reached. High levels of neutrophil IGF-1R binding and increases from baseline in serum IGF-1 levels were observed in the 12- and 20-mg/kg cohorts. Tumor responses included one durable complete response (CR) and one unconfirmed partial response (PR) in two patients with Ewing/primitive neuroectodermal tumors and included one PR and one minor response in two patients with neuroendocrine tumors. The patients with Ewing/PNET who had a CR have remained disease free on therapy after 28 months.

Conclusion

AMG 479 can be administered safely at 20 mg/kg IV Q2W. The absence of severe toxicities, attainment of serum concentrations associated with high levels of IGF-1R binding on neutrophils, and provocative antitumor activity warrant additional studies of this agent.

Ewing sarcoma-peripheral neuroectodermal tumor of the kidney with a FUS-ERG fusion transcript

The Ewing family of tumors (EFTs) represents a neoplastic entity characterized by specific chromosomal rearrangements. The most commonly detected translocation involves fusion of EWSR1 to one of the genes encoding ETS family of transcription factors, usually FLI1 or ERG. In rare cases, FUS or FEV has been shown to substitute for EWSR1. The detection of specific translocations by fluorescence in situ hybridization (FISH), reverse transcription-polymerase chain reaction (RT-PCR), or both has become a diagnostic hallmark for the EFTs. We report here a case of small round blue cell tumor detected in the kidney of a 3-year-old girl. The use of FISH in combination with RT-PCR led to identification of a novel FUS-ERG fusion transcript in the tumor, with FUS exons 1-5 fused in-frame to ERG exons 6-9. The results from the molecular analyses were critical for reaching a final diagnostic conclusion of Ewing tumor-peripheral neuroectodermal tumor and hence had important therapeutic implications for the patient.

Desmoplastic small round cell tumor of the central nervous system: report of two cases and review of the literature

Desmoplastic small round cell tumor (DSRCT) is a malignant tumor often involving the abdominal and/or pelvic peritoneum. Only one fully documented example has arisen in the central nervous system (CNS). Herein, we describe two additional examples, fulfilling the morphologic, immunohistochemical, and molecular criteria (EWS/WT1 translocation) of DSRCT. Both arose in the cerebellopontine angle (CPA) and underwent spinal dissemination. Patient 1, a 37-year-old male, underwent a subtotal resection, and 2 years later died of recurrent disease with spinal dissemination. Patient 2, a 39-year-old man, presented with cerebellar and CPA lesions as well as spinal leptomeningeal deposits. After 27 months of adjuvant therapy, he is alive with progressive disease. In conclusion, CNS DSRCT follows a similar aggressive course as do peritoneal examples. Although rare, DSRCT warrants consideration in the differential diagnosis of "malignant small blue cell tumors" of the CNS.

Molecular and phenotypic analysis of poorly differentiated sinonasal neoplasms: an integrated approach for early diagnosis and classification

Primary poorly differentiated (small round and non-small) sinonasal neoplasms comprise histogenetically and biologically diverse entities with overlapping morphologic features. Because of the limited initial biopsy tissue materials, differential diagnostic difficulties may arise and complicate timely management of some cases. We used immunohistochemical and molecular marker analyses in a large cohort of these tumors to optimize their early diagnosis and classification. Fifty-two tumors of the skull base and sinonasal regions and, for comparison, 19 poorly differentiated neoplasms of other head and neck sites were analyzed by a panel of immunohistochemical markers including those of epithelial, mesenchymal, melanocytic, and neuroectodermal origin using tissue microarray. Reverse transcriptase-polymerase chain reaction analysis of messenger RNA for EWS-FLI1 and PAX-FKHR fusion transcripts and the human achaete-scute homolog-1 gene was performed on 24 of the 52 sinonasal tumors and the 19 tumors of other sites for comparison. The immunohistochemical results substantiated the phenotypic assessment and the initial diagnosis in 49 of the 52 tumors. In 4 instances the integrated markers and phenotypic analyses led to reclassification of 3 tumors and confirmed the histogenesis of a mesenchymal tumor with aberrant cytokeratin expression. Molecular analysis of the EWS-FLI1 fusion gene transcript revealed 4 (9.3%) of the 43 tumors to be positive; all were Ewing sarcomas. The human achaete-scute homolog-1 gene transcript was identified in 10 (23.8%) of 42 tumors: 3 of 6 neuroblastomas, all 4 neuroendocrine carcinomas, and 1 each in sinonasal undifferentiated carcinoma, rhabdomyosarcoma, and melanoma. The PAX-FKHR fusion transcript was not detected in any tumors. We conclude that (1) an integrated morphologic and biomarker algorithm may better optimize the early diagnosis of poorly differentiated sinonasal and skull-base tumors; (2) molecular analysis may assist in future biological stratification of certain classes of these tumors; and (3) the human achaete-scute homolog-1 gene transcript is a nonspecific marker for the diagnosis of neuroblastoma.

The diagnostic value of SYT-SSX detected by reverse transcriptase-polymerase chain reaction (RT-PCR) and fluorescence in situ hybridization (FISH) for synovial sarcoma: a review and prospective study of 255 cases

This study aimed to evaluate the diagnostic value of SYT-SSX detected by reverse transcriptase-polymerase chain reaction (RT-PCR) and fluorescence in situ hybridization (FISH) for synovial sarcoma (SS) in known and potential cases. SYT-SSX was analyzed in formalin-fixed, paraffin-embedded tissues of 62 known SS, 60 non-SS and 133 potential SS by RT-PCR and FISH. FISH was mainly performed on a tissue microarray with some modifications. SYT-SSX was detected in 94.7% (54/57) of known SS and 70.5% (86/122) of potential SS by RT-PCR and in 96.7% (58/60) of known SS and 78.1% (100/128) of potential SS by FISH. Moreover, SYT-SSX was negative in 100% (58/58) of non-SS by RT-PCR and in 100% (59/59) of non-SS by FISH. Accordingly, SYT-SSX was detected in 106 potential SS by RT-PCR or FISH, including 80 cases manifested by both methods, 20 specimens verified only by FISH and 6 samples confirmed only by RT-PCR. Clinical findings and immunohistochemistry data were analyzed in potential SS with final molecular diagnosis. The positive ratio of cytokeratin (CK) and epithelial membrane antigen (EMA) in finally diagnosed SS was 51.9% (55/106) and 61.3% (65/106), respectively. Except EMA, clinical parameters (age, sex, tumor size, tumor sites) and other immunohistochemistry indexes (CK, S-100, neurone specific enolase (NSE), CD99, myoglobin, smooth muscle actin (SMA), cluster of differentiation (CD) 68 and mesothelial cell) had no significant difference between finally diagnosed SS and non-SS. It is indicated that the efficiency of FISH is comparable to or even higher than that of RT-PCR for SYT-SSX detection. The detection of SYT-SSX by RT-PCR or FISH is very useful for the final diagnosis of potential synovial sarcomas.

Cytologic diagnosis of Ewing sarcoma/peripheral neuroectodermal tumor with paired prospective molecular genetic analysis

BACKGROUND

Ewing sarcoma/peripheral neuroectodermal tumor (EWS/PNET), since its characterization immunophenotypically and cytogenetically, has emerged as one of most common sarcomas of childhood. Currently, it is recognized that EWS/PNET can occur in any number of extraosseous sites and is one of several distinctive tumor types with an EWS translocation. In the past, the pathologic diagnosis of EWS/PNET relied on an open biopsy with the application of various ancillary studies, ranging from periodic acid-Schiff stain to molecular testing, but the tumor increasingly is diagnosed on the basis of cytologic specimens alone.

METHODS

The authors report 3 cases of EWS/PNET in patients aged 11 years to 53 years. These 3 patients had tumors that involved the parotid gland, cervical soft tissue, and pelvis, and were diagnosed by cytologic evaluation of fine-needle aspiration (FNA) biopsy material alone. The FNA materials also were evaluated prospectively by fluorescence in situ hybridization and/or reverse transcriptase-polymerase chain reaction.

RESULTS

The results emphasized the diagnostic utility of FNA biopsy material for morphologic and molecular analysis without compromising conventional cytologic and immunocytochemical analysis, and that prospective molecular testing of FNA specimens has utility in routine practice although it is subject to many of the same limitations that impact molecular analysis when applied to conventional tissue biopsy specimens.

CONCLUSIONS

The current results demonstrated that molecular genetic techniques can provide clinically useful ancillary information for FNA specimens when cytologic features and/or immunophenotype are equivocal on the basis of limited sampling or secondary changes, such as hemorrhage and/or necrosis.

Comparative analysis of routine histology, immunohistochemistry, reverse transcriptase polymerase chain reaction, and fluorescence in situ hybridization in diagnosis of Ewing family of tumors

CONTEXT

The Ewing family of tumors are often difficult to distinguish from other malignant small round cell tumors, but more than 90% have EWS-FLI1 chimeric transcript, which acts as a potential molecular diagnostic marker.

OBJECTIVE

To do a comparative analysis of 32 cases with EWS-FLI1: Ewing family of tumors (n = 30), desmoplastic small round cell tumor (n = 1), and undifferentiated sarcoma (n = 1).

DESIGN

The initial diagnosis was made on core biopsy (n = 22) and open biopsy (n = 4) specimens by using morphology and immunohistochemistry and on fine-needle aspiration cytology ([FNAC], n = 6) specimens. EWS-FLI1 was detected by reverse transcriptase polymerase chain reaction on all 32 fresh FNAC samples and by fluorescence in situ hybridization on 16 paraffin blocks.

RESULTS

The 19 male and 13 female patients had bone (n = 19) or soft tissue (n = 13) tumors. Histologic groups were typical Ewing sarcoma (n = 15), atypical Ewing sarcoma (n = 4), Askin Rosai tumors (n = 5), desmoplastic small round cell tumor (n = 1), undifferentiated sarcoma (n = 1), and cases diagnosed as malignant small round cell tumors on FNAC (n = 6). All tumors except desmoplastic small round cell tumor and undifferentiated sarcoma were CD99 positive. EWS-FLI1 by reverse transcriptase polymerase chain reaction was noted in 15 cases of typical Ewing sarcoma, 4 cases of atypical Ewing sarcoma, 5 cases of Askin Rosai tumor, and no cases of desmoplastic small round cell tumor or undifferentiated sarcoma. With use of fluorescence in situ hybridization, EWS break was detected in 10 of 11 paraffin blocks used and was negative in desmoplastic small round cell tumor.

CONCLUSIONS

The excellent correlation of routine histologic findings in Ewing family of tumors with results on immunohistochemistry and fluorescence in situ hybridization on archival material and reverse transcriptase polymerase chain reaction on fresh FNAC specimens underscores that the traditional observation on routine histologic examination is a time-tested tool. The diagnosis of Ewing family of tumors can be validated on archival material or fresh biopsy samples, including those obtained by FNAC.

Diagnostic utility of FLI-1 monoclonal antibody and dual-colour, break-apart probe fluorescence in situ (FISH) analysis in Ewing's sarcoma/primitive neuroectodermal tumour (EWS/PNET). A comparative study with CD99 and FLI-1 polyclonal antibodies

AIMS

To compare the sensitivity and specificity of the recently commercially available FLI-1 monoclonal (FLI-1m) antibody with the currently used antibodies [CD99 and FLI-1 polyclonal (FLI-1p)] in the diagnosis of Ewing's sarcoma/primitive neuroectodermal tumour (EWS/PNET) and to determine the diagnostic value of the EWSR1 (22q12) dual-colour, break-apart rearrangement probe fluorescence in situ hybridization (FISH) technique.

MATERIALS AND METHODS

Forty-three cases of well-documented EWS/PNET and 15 non-EWS/PNET cases were retrieved from the archival files. Immunohistochemistry (IHC) for FLI-1p, FLI-1m and FISH analysis was performed.

RESULTS

The most sensitive and specific test panel for the diagnosis of EWS/PNET is the combination of CD99 and FLI-1p. FISH had a very high specificity (100%) but only a moderate sensitivity (50%).

CONCLUSION

The combination of CD99 and FLI-1p is the method of choice for the diagnosis of EWS/PNET. EWRS1 (22q12) dual-colour, break-apart rearrangement probe FISH should be used as a confirmatory test in addition to CD99 and FLI1-p due to its high specificity.

Ewing sarcoma family of tumors in unusual sites: confirmation by rt-PCR

Ewing sarcoma family tumors originating in the palate or adrenal gland are extremely rare and may cause difficulty in diagnosis. More common tumors primary to these sites need to be excluded before one arrives at the correct diagnosis. We have recently diagnosed 2 such cases. The 1st case was that of a 24-year-old woman who presented with a swelling in the right side of the hard palate. The 2nd case was diagnosed in a 28-year-old woman who presented with a mass in the right adrenal gland. In both cases, the diagnosis of Ewing sarcoma family of tumors was confirmed by immunohistochemical studies and reverse transcriptase-polymerase chain reaction (RT-PCR). The hard palate case is the 1st and the adrenal gland the 3rd case of Ewing sarcoma family of tumors arising in these sites, in which the diagnosis was confirmed by RT-PCR and/or cytogenetics. Accurate diagnosis of Ewing sarcoma family of tumors is crucial for the management of patients, and when found in such rare locations, diagnosis should be supported by immunohistochemical and/or molecular genetic studies.

Diagnostic Molecular Pathology: An Increasingly Indispensable Tool for the Practicing Pathologist

Context.—Diagnostic molecular pathology is rapidly becoming an indispensable tool for anatomic pathologists. Familiarity with some of the technologic principles and current, as well as upcoming, molecular diagnostic applications is greatly advantageous for today's practice of pathology.

Objectives.— To provide a discussion of the most common techniques currently used in molecular pathology laboratories and review their essential applications to diagnosis and management of neoplastic diseases.

Data Sources.—A literature review and illustrative cases from the authors' molecular diagnostic practices.

Conclusions.—Applications such as clonality assays, molecular cytogenetics, and chimerism analysis are providing us with accurate tools to resolve difficult diagnostic and management decisions in hemato-oncology. This should serve as a future model to expand molecular applications into the wider field of solid tumors.

Pitfalls in the detection of t(11;22) translocation by fluorescence in situ hybridization and RT-PCR: a single-blinded study

The t(11;22) translocation is a diagnostic hallmark of various small round-cell tumors. This study correlates the performance of fluorescence in situ hybridization (FISH) and reverse transcription polymerase chain reaction (RT-PCR) in the detection of this translocation analyzing paraffin-embedded tissue specimens. As negative control samples, 10 cases of normal colon mucosa and 10 cases of colon carcinoma tissue were analyzed by FISH to determine a valid cutoff value for the diagnosis of a t(11;22) translocation. The mean number of false-positive nuclei differed significantly between disomic and polysomic control group cases (P=0.002). Therefore, the cutoff value was determined considering the pitfall polysomy. The analysis group consisted of 20 cases from the University of Düsseldorf and 10 cases from the University of Bonn. These cases were analyzed using PCR (Düsseldorf) and FISH (Bonn) using a single-blinded approach. Twenty-two cases (73.3%) were concordant in both methods. Five cases (16.7%) were discrepant, showing a positive result in FISH whereas PCR was negative. Three cases (10.0%) were analyzed by FISH, and PCR failed for nonoptimized tissue preparation. In conclusion, the detection of t(11;22) translocation is critically dependent on a thoroughly defined cutoff value for FISH and on appropriate tissue preparation for both methods. We recommend FISH as a sensitive screening tool in the detection of t(11;22) followed by subsequent PCR amplification of the specific chimeric transcript.

Use of a novel FISH assay on paraffin-embedded tissues as an adjunct to diagnosis of alveolar rhabdomyosarcoma

A valuable diagnostic adjunct and important prognostic parameter in alveolar rhabdomyosarcoma (ARMS) is the identification of translocations t(2;13)(q35;q14) and t(1;13)(p36;q14), and the associated PAX3-FKHR and PAX7-FKHR fusion transcripts, respectively. Most RMS fusion gene type studies have been based on reverse transcriptase-polymerase chain reaction (RT-PCR) detection of the fusion transcript, a technique limited by RNA quality and failure of devised primer sets to detect unusual variants. As an alternative approach, we developed a fluorescence in situ hybridization (FISH) assay that can: (1) distinguish between the two most common ARMS-associated fusion genes; (2) identify potential unusual variant translocations; (3) assess histologic components in mixed alveolar/embryonal RMS; and (4) be performed on paraffinized tissue. FISH analyses of 75 specimens (40 ARMS, 16 ERMS, 8 mixed ARMS/ERMS, and 11 non-RMS tumors) using selected cosmid clone, bacterial, P1-derived, and yeast artificial chromosome probe sets were successful in all but two cases. Among specimens with informative results for both FISH and RT-PCR or standard karyotyping, PAX/FKHR classification results were concordant in 94.6% (53/56). The three discordant cases included one exhibiting a t(2;13) by FISH that was subsequently confirmed by repeat RT-PCR, a second showing a rearrangement of the PAX3 locus only (consistent with the presence of a PAX3 variant translocation), and a third revealing a t(2;13) by FISH that lacked this translocation cytogenetically. Both alveolar and embryonal components of the mixed ARMS/ERMS subtype were negative for PAX3, PAX7, and FKHR rearrangements, a surprising finding confirmed by RT-PCR and/or conventional karyotyping. These data demonstrate that FISH with newly designed probe sets is a reliable and highly specific method of detecting t(1;13) and t(2;13) in routinely processed tissue and may be useful in differentiating ARMS from other small round cell tumors. The findings also suggest that FISH may be a more sensitive assay than RT-PCR in some settings, capable of revealing variant translocations.

Ewing's sarcoma of bone: the detection of specific transcripts in a large, consecutive series of formalin-fixed, decalcified, paraffin-embedded tissue samples using the reverse transcriptase-polymerase chain reaction

AIMS

(i) To report on the routine use of the reverse transcriptase-polymerase chain reaction (RT-PCR) technique on decalcified or non-decalcified, formalin-fixed, paraffin-embedded tissue (FFPET) for translocation detection, with particular emphasis on improved RNA extraction methodology and the use of PCR primers designed to generate small amplicons. (ii) To report on the relative incidences of translocation types and transcript variants in a large, single institution series of Ewing's sarcoma of bone.

METHODS AND RESULTS

Using RT-PCR to detect specific transcript variants, we analysed FFPET from 54 consecutive cases of Ewing's sarcoma of bone. We used 'gold standard' detection methods on corresponding fresh and fresh frozen tissue to validate the technique. We have demonstrated the effective use of RT-PCR on decalcified and non-decalcified FFPET samples for sarcoma-specific translocation detection (96% sensitivity, 100% specificity). Tissue decalcification did not affect the detection rate. The relative incidence of Ewing's sarcoma-specific translocation types and transcript variants was entirely consistent with previously published data.

CONCLUSIONS

With equal effectiveness, RT-PCR can be applied to both acid decalcified and non-decalcified FFPET for (Ewing's sarcoma) translocation detection and the technique can be introduced into routine practice in histopathology departments.

Molecular diagnosis of Ewing sarcoma/primitive neuroectodermal tumor in routinely processed tissue: a comparison of two FISH strategies and RT-PCR in malignant round cell tumors

Ewing sarcoma/primitive neuroectodermal tumor (EWS/PNET) is a diagnostically challenging malignant round cell tumor with signature translocations involving the EWS gene. These translocations are detectable with both reverse transcriptase-polymerase chain reaction (RT-PCR) and fluorescence in situ hybridization (FISH) in formalin-fixed paraffin-embedded tissue. However, RT-PCR is less sensitive in formalin-fixed paraffin-embedded than frozen tissue. Similarly, commercial FISH probes have recently become available, but have yet to be rigorously tested in the clinical setting. Therefore, we have compared RT-PCR with FISH using 'home brew' fusion probes for Ewing sarcoma (EWS)-FLI1 and a commercial EWS break apart probe set in 67 archival round cell tumors, including 27 EWS/PNETs. Sensitivities and specificities for both FISH assays were 91 and 100%, respectively, whereas RT-PCR had a sensitivity of 54% and a specificity of 85%. The break apart strategy was easier to interpret than probe fusion approach. We conclude that FISH is a more sensitive and reliable ancillary technique than RT-PCR for the diagnosis of EWS/PNET in formalin-fixed paraffin-embedded tissue, although the latter provides additional information regarding fusion transcript subtype and prognosis. The commercial break apart probe set is both readily available and easy to interpret, making it particularly attractive. Nonetheless, complex round cell tumors often benefit from molecular testing with multiple methods.

EWS–ETS oncoproteins: The linchpins of Ewing tumors

Ewing tumors, which comprise Ewing's sarcoma and peripheral primitive neuroectodermal tumors, are highly aggressive and mostly affect children and adolescents. Their molecular signature is a chromosomal translocation leading to the generation of EWS-ETS (or very rarely FUS-ETS) fusion proteins that are capable of transforming cells. These oncoproteins act as aberrant transcription factors due to the fusion of an ETS DNA binding domain to a highly potent EWS (or FUS) transactivation domain. Accordingly, many EWS-ETS target genes have been identified whose dysregulation could contribute to the development of tumor formation. Furthermore, EWS-ETS oncoproteins may impact on RNA splicing or affect other proteins through disturbing their ability to form functional complexes. The molecular knowledge gained so far from studying EWS-ETS oncoproteins has not only broadened our understanding of Ewing tumors but also improved the diagnosis of these highly undifferentiated tumors. In addition, several potential prognostic markers have been uncovered and novel therapies are suggested that may improve the still dismal survival rate of Ewing tumor patients.

Detection of fusion genes in sarcomas using paraffin-embedded tissues

Many sarcomas are characterized by specific recurrent chromosomal translocations resulting in gene fusions. The genes involved in almost all of these translocations have been cloned, greatly changing sarcoma diagnosis. At the biological level, these chromosomal translocations produce highly specific fusion genes that encode key molecules for tumor development. The clinical correlation between these translocation-derived genetic markers and discrete histopathological entities has been remarkable. Today, detection of fusion genes plays a crucial role in the diagnosis of sarcomas that harbor atypical clinical or pathological presentations. The focus of this brief review is the recent impact that cytogenetic and molecular detection of these translocations has had on sarcoma diagnosis using paraffin-embedded sections.