Ossifying fibromyxoid tumor presenting EP400-PHF1 fusion gene

Functional Classification of Fusion Proteins in Sarcoma

Sarcomas comprise a heterogeneous group of malignant tumors of mesenchymal origin. More than 80 entities are associated with different mesenchymal lineages. Sarcomas with fibroblastic, muscle, bone, vascular, adipocytic, and other characteristics are distinguished. Nearly half of all entities contain specific chromosomal translocations that give rise to fusion proteins. These are mostly pathognomonic, and their detection by various molecular techniques supports histopathologic classification. Moreover, the fusion proteins act as oncogenic drivers, and their blockade represents a promising therapeutic approach. This review summarizes the current knowledge on fusion proteins in sarcoma. We categorize the different fusion proteins into functional classes, including kinases, epigenetic regulators, and transcription factors, and describe their mechanisms of action. Interestingly, while fusion proteins acting as transcription factors are found in all mesenchymal lineages, the others have a more restricted pattern. Most kinase-driven sarcomas belong to the fibroblastic/myofibroblastic lineage. Fusion proteins with an epigenetic function are mainly associated with sarcomas of unclear differentiation, suggesting that epigenetic dysregulation leads to a major change in cell identity. Comparison of mechanisms of action reveals recurrent functional modes, including antagonism of Polycomb activity by fusion proteins with epigenetic activity and recruitment of histone acetyltransferases by fusion transcription factors of the myogenic lineage. Finally, based on their biology, we describe potential approaches to block the activity of fusion proteins for therapeutic intervention. Overall, our work highlights differences as well as similarities in the biology of fusion proteins from different sarcomas and provides the basis for a functional classification.

Polycomb-like Proteins in Gene Regulation and Cancer

Polycomb-like proteins (PCLs) are a crucial group of proteins associated with the Polycomb repressive complex 2 (PRC2) and are responsible for setting up the PRC2.1 subcomplex. In the vertebrate system, three homologous PCLs exist: PHF1 (PCL1), MTF2 (PCL2), and PHF19 (PCL3). Although the PCLs share a similar domain composition, they differ significantly in their primary sequence. PCLs play a critical role in targeting PRC2.1 to its genomic targets and regulating the functionality of PRC2. However, they also have PRC2-independent functions. In addition to their physiological roles, their dysregulation has been associated with various human cancers. In this review, we summarize the current understanding of the molecular mechanisms of the PCLs and how alterations in their functionality contribute to cancer development. We particularly highlight the nonoverlapping and partially opposing roles of the three PCLs in human cancer. Our review provides important insights into the biological significance of the PCLs and their potential as therapeutic targets for cancer treatment.

Identification of key gene signatures for the overall survival of ovarian cancer

BACKGROUND

The five-year overall survival (OS) of advanced-stage ovarian cancer remains nearly 25-35%, although several treatment strategies have evolved to get better outcomes. A considerable amount of heterogeneity and complexity has been seen in ovarian cancer. This study aimed to establish gene signatures that can be used in better prognosis through risk prediction outcome for the survival of ovarian cancer patients. Different studies' heterogeneity into a single platform is presented to explore the penetrating genes for poor or better survival. The integrative analysis of multiple data sets was done to determine the genes that influence poor or better survival. A total of 6 independent data sets was considered. The Cox Proportional Hazard model was used to obtain significant genes that had an impact on ovarian cancer patients. The gene signatures were prepared by splitting the over-expressed and under-expressed genes parallelly by the variable selection technique. The data visualisation techniques were prepared to predict the overall survival, and it could support the therapeutic regime.

RESULTS

We preferred to select 20 genes in each data set as upregulated and downregulated. Irrespective of the selection of multiple genes, not even a single gene was found common among data sets for the survival of ovarian cancer patients. However, the same analytical approach adopted. The chord plot was presented to make a comprehensive understanding of the outcome.

CONCLUSIONS

This study helps us to understand the results obtained from different studies. It shows the impact of the heterogeneity from one study to another. It shows the requirement of integrated studies to make a holistic view of the gene signature for ovarian cancer survival.

Discovery of an H3K36me3-Derived Peptidomimetic Ligand with Enhanced Affinity for Plant Homeodomain Finger Protein 1 (PHF1)

Plant homeodomain finger protein 1 (PHF1) is an accessory component of the gene silencing complex polycomb repressive complex 2 and recognizes the active chromatin mark, trimethylated lysine 36 of histone H3 (H3K36me3). In addition to its role in transcriptional regulation, PHF1 has been implicated as a driver of endometrial stromal sarcoma and fibromyxoid tumors. We report the discovery and characterization of UNC6641, a peptidomimetic antagonist of the PHF1 Tudor domain which was optimized through in silico modeling and incorporation of non-natural amino acids. UNC6641 binds the PHF1 Tudor domain with a K_d value of 0.96 ± 0.03 μM while also binding the related protein PHF19 with similar potency. A crystal structure of PHF1 in complex with UNC6641, along with NMR and site-directed mutagenesis data, provided insight into the binding mechanism and requirements for binding. Additionally, UNC6641 enabled the development of a high-throughput assay to identify small molecule binders of PHF1.

Primary malignant ossifying fibromyxoid tumour of the bone. A clinicopathologic and molecular report of two cases

Objective

To report the exceptional occurrence of ossifying fibromyxoid tumour (OFMT) as a primary bone lesion. OFMT is a rare soft tissue tumour of uncertain differentiation and variable malignant potential, that occurs in adults with a slight male predominance. It is typically located in the subcutis or in the skeletal muscles of the extremities, followed by trunk or head and neck.

Methods

Two cases of OFMT proven to arise from bone are presented. The first is a 65-year old female with a history of rib "osteosarcoma", presenting with an inferior lobe left lung mass. The second is a man with a lytic lesion of the 5th cervical vertebra that recurred shortly after resection. Following H&E and immunohistochemical examination, tumour samples were analysed by NGS and by break-apart FISH to detect rearrangement of the PHF1 and TFE3 genes.

Results

PHF1 gene-rearrangement was identified by FISH on both the primary and the metastatic lesion of first patient. NGS identified a PHF1(intron1) and EPC1 (exon 10) fusion transcript later confirmed by positive PHF1 rearrangement on FISH in the second case.

Conclusions

The demonstration of PHF1 gene rearrangements represents a fundamental ancillary diagnostic test when presented with challenging examples of OFMT.

Detection of MEAF6-PHF1 translocation in an endometrial stromal nodule

Endometrial stromal nodule (ESN) and low-grade endometrial stromal sarcoma (LG-ESS) are rare uterine tumors known as endometrial stromal tumors (ESTs). In addition to their similarity in morphological features, recent studies have shown that these two tumors share common genetic alterations. In particular, JAZF1-SUZ12 fusion is found with high frequency in both ESN and LG-ESS. In LG-ESS, some minor fusions have also been described, which include rearrangements involving PHF1 and its partner genes, such as JAZF1, EPC1, MEAF6, BRD8, EPC2, and MBTD1. Because of the rarity of ESN, genetic alterations other than JAZF1 fusion have not been investigated in detail. In this study, we performed a next-generation sequencing-based analysis in a case of ESN with peripheral metaplastic bone formation and detected MEAF6-PHF1 fusion, which has been reported in a small subset of uterine LG-ESSs and soft tissue ossifying fibromyxoid tumors. The finding that MEAF6-PHF1 fusion is a background genetic abnormality detected both in ESN and LG-ESS, along with JAZF1-SUZ12, provides further support for the similarity and continuum between these two types of ESTs. Furthermore, the association between metaplastic bone formation and MEAF6-PHF1 fusion may not be limited to soft tissue tumors.

Current Approaches for Personalized Therapy of Soft Tissue Sarcomas

Soft tissue sarcomas (STS) are a highly heterogeneous group of cancers of mesenchymal origin with diverse morphologies and clinical behaviors. While surgical resection is the standard treatment for primary STS, advanced and metastatic STS patients are not eligible for surgery. Systemic treatments, including standard chemotherapy and newer chemical agents, still play the most relevant role in the management of the disease. Discovery of specific genetic alterations in distinct STS subtypes allowed better understanding of mechanisms driving their pathogenesis and treatment optimization. This review focuses on the available targeted drugs or drug combinations based on genetic aberration involved in STS development including chromosomal translocations, oncogenic mutations, gene amplifications, and their perspectives in STS treatment. Furthermore, in this review, we discuss the possible use of chemotherapy sensitivity and resistance assays (CSRA) for the adjustment of treatment for individual patients. In summary, current trends in personalized management of advanced and metastatic STS are based on combination of both genetic testing and CSRA.

Fusion of the Genes PHF1 and TFE3 in Malignant Chondroid Syringoma

BACKGROUND/AIM

Malignant chondroid syringoma is a rare tumor of unknown pathogenesis.

MATERIALS AND METHODS

Genetic analyses were performed on a malignant chondroid syringoma.

RESULTS

G-banding analysis of short-term cultured tumor cells yielded the karyotype 46,Y,t(X;6)(p11;p21)[15]/46,XY[2]. RNA sequencing detected an in-frame fusion of PHF1 from 6p21 with TFE3 from Xp11, verified by RT-PCR and Sanger sequencing. Genomic PCR showed that the PHF1-TFE3 junction was identical to the fusion found by RNA sequencing and RT-PCR.

CONCLUSION

Malignant chondroid syringoma is genetically related to tumors with PHF1 rearrangements such as low-grade endometrial sarcoma and ossifying fibromyxoid tumor, but also with tumors having TFE3 rearrangements such as renal cell carcinoma, alveolar soft part sarcoma, PEComa, and epithelioid hemangioendothelioma. Further investigations on malignant chondroid syringomas are needed in order to determine whether genetic heterogeneity exists among them and the clinical impact of the PHF1-TFE3 fusion.

Diagnosis and Management of Subcutaneous Soft Tissue Sarcoma

OPINION STATEMENT

The proper diagnosis and treatment planning for subcutaneous soft tissue sarcoma is very important. Soft tissue tumors can occur anywhere in the body, but if they occur subcutaneously, patients can easily notice a subcutaneous soft tissue mass. Therefore, it is possible to determine through recording, the growth speed of the mass, which is often difficult to obtain with deep-situated soft tissue masses. Palpation can also provide information about the firmness and mobility of the mass. Thus, history taking and physical examinations are informative for subcutaneous soft tissue tumors, compared to tumors that occur deeply. Because subcutaneous soft tissue tumors are easily recognized, they are often resected, without sufficient imaging analyses or thorough treatment planning. An operation performed based on such an inadequate preoperative plan is called a "whoops surgery." In the case of "whoops surgeries," subsequent radical surgery is required to remove additional areas, including hematomas that result from the initial surgery, that require a wider range of resection and soft tissue reconstruction. Therefore, as with deep-seated soft tissue tumors, it is important to conduct careful imaging examinations and make appropriate preoperative plans for subcutaneous soft tissue tumors. Subcutaneous soft tissue sarcomas often show an invasive pattern, and such tumors require a more careful assessment to prevent local recurrence after surgery. During surgery, it is necessary to remove the entire infiltration area along the fascia. Sometimes, an adequately wide excision is necessary, which is considered the minimum necessary procedure to eradicate the lesion. As noted above, clinicians who see patients with subcutaneous soft tissue tumors are encouraged to have sufficient knowledge and experience regarding the diagnosis and treatment. This article is intended for all doctors who deal with subcutaneous soft tissue tumors and focuses on essential points regarding their diagnosis and management.

Identification of an EPC2-PHF1 fusion transcript in low-grade endometrial stromal sarcoma

Recurrent chromosomal translocations leading to gene fusion formation have been described in uterine sarcomas, including low-grade endometrial stromal sarcoma (LG-ESS). Involvement of the PHF1 gene in chromosomal rearrangements targeting band 6p21 has been found in LG-ESS with different partners from JAZF1 mapping in 7p15, to EPC1 from 10p11, MEAF6 from 1p34, and BRD8 from 5q31.

In the present study, RNA sequencing of a LG-ESS showed a novel recombination of PHF1 with the Enhancer of Polycomb homolog 2 (EPC2). RT-PCR followed by Sanger sequencing and FISH analysis confirmed the EPC2-PHF1 fusion transcript.

Oncogenic roles of SMARCB1/INI1 and its deficient tumors

SMARCB1/INI1 is one of the core subunit proteins of the ATP-dependent SWI/SNF chromatin remodeling complex, and is identified as a potent and bona fide tumor suppressor. Interactions have been demonstrated between SMARCB1/INI1 and key proteins in various pathways related to tumor proliferation and progression: the p16-RB pathway, WNT signaling pathway, sonic hedgehog signaling pathway and Polycomb pathway. Initially, no detectable SMARCB1/INI1 protein expression was found in malignant rhabdoid tumor cells, whereas all other kinds of tumor cells and non-tumorous tissue showed SMARCB1/INI1 protein expression. Therefore, immunohistochemical testing for the SMARCB1/INI1 antibody has been considered useful in confirming the histologic diagnosis of malignant rhabdoid tumors. However, recently, aberrant expression of SMARCB1/INI1 has been found in various tumors such as epithelioid sarcomas, schwannomatosis, synovial sarcomas, and so on. In addition, it has been reported that aberrant expression can be classified into three patterns: complete loss, mosaic expression and reduced expression. Although the various pathways related to mechanisms of tumorigenesis and tumor proliferation are complexly intertwined, the clarification of these mechanisms may contribute to therapeutic strategies in SMARCB1/INI1-deficient tumors. In terms of pathological classifications, SMARCB1/INI1-deficient tumors may be re-classified by genetic backgrounds.

The Multiple Facets of PRC2 Alterations in Cancers

Genome sequencing of large cohorts of tumors has revealed that mutations in genes encoding chromatin regulators are frequent in cancer. However, the precise contribution of these mutations to tumor development often remains elusive. Here, we review the current knowledge concerning the alterations of the Polycomb machinery in cancer, with a particular focus on the Polycomb repressive complex 2 (PRC2), a key chromatin modifier involved in the maintenance of transcriptional silencing. A broad variety of alterations can impair PRC2 activity; yet, overall, only one type of alteration is found in a given class of tumor. We discuss the potential impact of the various types of PRC2 alterations on gene expression. We propose that the distinct set of genes regulated by PRC2, depending on tumor etiology, constrain the type of alteration of PRC2 that can fuel tumor development. Beyond this specificity, we propose that PRC2 and, more generally, chromatin regulators act as gatekeepers of transcriptional integrity, a role that often confers a tumor-suppressive function.

Cytogenetic and molecular profile of endometrial stromal sarcoma

Recent cytogenetic and molecular investigations have improved our understanding of endometrial stromal tumors, including sarcomas (ESS), and helped redefine their classification into more pathogenetically meaningful categories. Because much more can be gained through such studies, we add information on another 22 ESS examined by karyotyping, PCR analysis, expression array analysis, and transcriptome sequencing. In spite of the known preference for certain pathogenetic pathways, we found considerable genetic heterogeneity in high‐grade (HG) as well as in low‐grade (LG) ESS. Not all HG tumors showed a YWHAE‐NUTM chimeric transcript and as many as six LGESS showed no hitherto known ESS‐related fusions. Among the transcripts identified by transcriptome sequencing and verified by Sanger sequencing, new variants of ZC3H7‐BCOR and its reciprocal BCOR‐ZC3H7 were identified as was involvement of the CREBBP and MLLT4 genes (both well known leukemia‐related genes) in two new fusions. FISH analysis identified a known EPC1‐PHF1 fusion which led to the identification of a new variant at the molecular level. The fact that around 70 genes were found differentially expressed, by microarray analysis, when comparing LGESS showing ESS‐related fusions with LGESS without such transcripts, underscores the biochemical importance of the observed genetic heterogeneity and hints that new subgroups/entities in LGESS still remain undiscovered. © 2016 The Authors. Genes, Chromosomes & Cancer Published by Wiley Periodicals, Inc.

Molecular Cytogenetic Analysis of JAZF1, PHF1, and YWHAE in Endometrial Stromal Tumors: Discovery of Genetic Complexity by Fluorescence in Situ Hybridization

Diagnosis of endometrial stromal tumors (ESTs) can be challenging, particularly endometrial stromal sarcomas (ESSs) because of variable histologic appearance, long latency to recurrence, frequent metastases with unknown primary, and overlap with endometrial stromal nodules and undifferentiated uterine sarcomas. To enhance EST diagnosis, a break-apart strategy fluorescence in situ hybridization panel to detect JAZF1, PHF1, and YWHAE rearrangements was applied to a cohort of primary or metastatic endometrial stromal nodules, ESSs, or undifferentiated uterine sarcomas (36 cases for JAZF1, 24 of which were also assessed for PHF1 and YWHAE), 24 myometrium/endometrium controls, and 37 non-ESTs in the differential diagnosis. JAZF1 was the most frequently altered gene and occurred in all EST types, JAZF1 and/or PHF1 were mutually exclusive from YWHAE involvement, and uterine and extrauterine ESTs have a shared pathogenesis. We further defined frequency of these rearrangements and provided a resource demonstrating the signal complexity that can manifest when evaluating JAZF1. Rearrangement of JAZF1 occurred in 47% of ESTs, most (70%) of which had atypical patterns representing multiple structural alterations and/or more than one clone. YWHAE and PHF1 rearrangements each occurred in 8% of ESTs. An exceptional case was an ESS without JAZF1 or MEAF6 disruption that further disputes correlation of PHF1 involvement with the sex cord-like variant. These results expand our understanding of the genetic heterogeneity that defines ESTs.

Primary pulmonary clear cell sarcoma-the first two reported cases

We report two cases (male patients 50 and 55 years old) of clear cell sarcoma ("melanoma of soft parts") arising in the lung, of which one case showed regional lymph node metastases. Histologically, both tumors displayed varying clear epithelioid and spindle neoplastic cells arranged in storiform and nested growth patterns, separated by thin fibrovascular septa. Immunohistochemical studies demonstrated positive expression of S-100 protein, HMB-45 and Melan-A in one case and S-100 protein only in the other. Fluorescence in situ hybridization showed positive EWSR1 gene rearrangement, and a presence of EWS-ATF1 fusion transcript was confirmed by RT-PCR and sequencing in one case.

Ossifying Fibromyxoid Tumor: An Update

Ossifying fibromyxoid tumor (OFMT) is a rare soft tissue neoplasm of uncertain differentiation, initially described by Enzinger and colleagues. Until now, nearly 300 such cases have been reported worldwide. The histogenesis of these tumors remains controversial. These tumors show characteristic imaging findings and exhibit a spectrum of histopathologic features, including classical and atypical subtypes. Local recurrences and, occasionally, distant metastases have also been reported. A complete tumor resection forms the preferred treatment modality for these tumors, along with follow-up, as these tumors have an uncertain malignant potential. Lately, certain “molecular signatures” underlying OFMTs have been described that can further aid in reaching an accurate diagnosis for these tumors and unraveling their pathogenesis. This article is a review of the clinical, radiologic, histopathologic, and molecular features of OFMTs.

Ossifying fibromyxoid tumor: morphology, genetics, and differential diagnosis

Ossifying fibromyxoid tumor (OFMT) is a soft tissue neoplasm of uncertain differentiation and intermediate (rarely metastasizing) biologic potential, with typical morphologic features, of an encapsulated, lobulated tumor comprising uniform polygonal cells within fibromyxoid stroma, which is surrounded by or contains metaplastic bone, classically as a peripheral rim of lamellar bone. Ossifying fibromyxoid tumor can arise at almost any site, although most frequently occurs within the extremities and trunk. Although most behave in a benign fashion, tumors can rarely show atypical or malignant features. It is now established that OFMTs represent translocation-associated tumors, with up to 85% associated with recurrent gene rearrangements, mostly involving the PHF1 gene (including in typical, atypical, and malignant neoplasms), with EP400-PHF1 in approximately 40% of tumors, and ZC3H7B-BCOR, MEAF6-PHF1, and EPC1-PHF1 fusions also described. Correct diagnosis is clinically important to ensure correct treatment and prognostication, both to avoid overdiagnosing OFMT as a malignant neoplasm such as osteosarcoma and also because of the propensity for aggressive behavior in a small number of OFMT. We review OFMT, with emphasis on the morphologic spectrum, recent molecular genetic findings, and the differential diagnosis.

The New Kids on the Block: Recently Characterized Soft Tissue Tumors

Soft tissue pathology is a rapidly changing subspecialty. New entities are described relatively often, and new molecular findings for soft tissue tumors are reported in the literature almost every month. This article summarizes the major features and diagnostic approach to several recently characterized entities: superficial CD34-positive fibroblastic tumor, fibrosarcoma-like lipomatous neoplasm, angiofibroma of soft tissue, low-grade sinonasal sarcoma with neural and myogenic features, malignant gastrointestinal neuroectodermal tumor, hemosiderotic fibrolipomatous tumor, and epithelioid inflammatory myofibroblastic sarcoma. Additionally, the article also provides a summary table of recent molecular findings in soft tissue tumors.

Ossifying fibromyxoid tumor: a clinicopathologic analysis of 26 subcutaneous tumors with emphasis on differential diagnosis and prognostic factors

INTRODUCTION

Ossifying fibromyxoid tumor (OFMT) is rare and may present diagnostic difficulty. We describe 26 subcutaneous examples of OFMT emphasizing differential diagnosis and prognostic features.

METHODS

Histopathology and follow-up data from archival/consultation cases were reviewed. Prognostic features were assessed according to proposed criteria.

RESULTS

Patients (16 female, 10 male) ranged from 26 to 88 years (median 54). The tumors (median 2.3 cm, range 0.8-8.5) involved lower limb (11), trunk (7), head/neck (4), or arm (4). All showed combinations of corded, nested and trabecular patterns in a fibromyxoid stroma. Out of 26 cases 13 had peripheral ossification. Sixteen of 22 cases showed S100 protein expression. Nuclear grade was low (14); intermediate (8) and high (4) while cellularity was low (14); moderate (7) and high (5), with overall good interobserver agreement. Median mitotic rate was 3/50HPF (0-61). Five met criteria for malignant OFMT showing high nuclear grade or high cellularity and mitotic rate >2/50HPF or both. Thirteen OFMTs were atypical. Follow-up (16/26, median 45.5 months, range 8-108) showed that patients with typical OFMT (3) and atypical OFMT (9) remained disease-free. Three malignant examples of OFMT recurred and one metastasized to the lung. No deaths were recorded.

CONCLUSIONS

Our results validate proposed prognostic classification of OFMT. Dermatopathologists should be aware of this unusual superficial tumor given its potentially aggressive behavior.

Promiscuous genes involved in recurrent chromosomal translocations in soft tissue tumours

Soft tissue tumours represent a heterogeneous group of mesenchymal lesions and their classification continues to evolve as a result of incorporating advances in cytogenetic and molecular techniques. In the last decade, traditional diagnostic approaches were supplemented with a significant number of reliable molecular diagnostic tools, detecting tumour type specific genetic alterations. Additionally, the successful application of some of these techniques to formalin fixed, paraffin embedded tissue enabled a broader range of clinical material to be subjected to molecular analysis. However, despite all these remarkable advances, the realisation that some of the genetic abnormalities are not fully histotype specific and that certain gene aberrations can be shared among different sarcoma types, otherwise completely unrelated clinically or immunophenotypically, has introduced some drawbacks in surgical pathology practice. One such common example is the presence of EWSR1 gene rearrangements by fluorescence in situ hybridisation (FISH), a test now preferred over the elaborate RT-PCR testing, in a variety of benign and highly malignant soft tissue tumours, in addition to a subset of carcinomas. Furthermore, the presence of identical gene fusions in completely different sarcoma types (i.e., EWSR1-ATF1, EWSR1-CREB1) or in non-mesenchymal malignancies (epithelial or haematological) has raised skepticism as to their diagnostic utility, and their lack of specificity has been compared to the limitations of other ancillary techniques, in particular immunohistochemistry. This review catalogues the main groups of genes that behave in a promiscuous manner within recurrent fusion events in soft tissue tumours. Although we acknowledge that the present molecular classification of soft tissue tumours is much more complex than two decades ago, when EWSR1 gene rearrangements had been described as the hallmark of Ewing sarcoma, we make the strong argument that with very few exceptions, the prevalence of fusion transcripts in most sarcomas is such that they come to define these entities and can be used as highly specific molecular diagnostic markers in the right clinical and pathological context.

WHO classification of soft tissue tumours: an update based on the 2013 (4th) edition

The fourth edition of the World Health Organization (WHO) Classification of Tumours of Soft Tissue and Bone was published in February 2013, and serves to provide an updated classification scheme and reproducible diagnostic criteria for pathologists. Given the relative rarity of soft tissue tumours and the rapid rate of immunohistochemical and genetic/molecular developments (not infrequently facilitating recognition of new tumour entities), this updated text edited by a consensus group is important for both practising pathologists and oncologists. The 2013 WHO classification includes several changes in soft tissue tumour classification, including several new entities (e.g., pseudomyogenic haemangioendothelioma, haemosiderotic fibrolipomatous tumour, and acral fibromyxoma), three newly included sections for gastrointestinal stromal tumours, nerve sheath tumours, and undifferentiated/unclassified soft tissue tumours, respectively, various 'reclassified' tumours, and a plethora of new genetic and molecular data for established tumour types that facilitate better definition and are useful as diagnostic tools. This article briefly outlines these updates based on the 2013 WHO classification of soft tissue tumours.

Novel ZC3H7B-BCOR, MEAF6-PHF1, and EPC1-PHF1 fusions in ossifying fibromyxoid tumors--molecular characterization shows genetic overlap with endometrial stromal sarcoma

PHF1 gene rearrangements have been recently described in around 50% of ossifying fibromyxoid tumors (OFMT) including benign and malignant cases, with a small subset showing EP400-PHF1 fusions. In the remaining cases no alternative gene fusions have been identified. PHF1-negative OFMT, especially if lacking S100 protein staining or peripheral ossification, are difficult to diagnose and distinguish from other soft tissue mimics. In seeking more comprehensive molecular characterization, we investigated a large cohort of 39 OFMT of various anatomic sites, immunoprofiles and grades of malignancy. Tumors were screened for PHF1 and EP400 rearrangements by FISH. RNA sequencing was performed in two index cases (OFMT1, OFMT3), negative for EP400-PHF1 fusions, followed by FusionSeq data analysis, a modular computational tool developed to discover gene fusions from paired-end RNA-seq data. Two novel fusions were identified ZC3H7B-BCOR in OFMT1 and MEAF6-PHF1 in OFMT3. After being validated by FISH and RT-PCR, these abnormalities were screened on the remaining cases. With these additional gene fusions, 33/39 (85%) of OFMTs demonstrated recurrent gene rearrangements, which can be used as molecular markers in challenging cases. The most common abnormality is PHF1 gene rearrangement (80%), being present in benign, atypical and malignant lesions, with fusion to EP400 in 44% of cases. ZC3H7B-BCOR and MEAF6-PHF1 fusions occurred predominantly in S100 protein-negative and malignant OFMT. As similar gene fusions were reported in endometrial stromal sarcomas, we screened for potential gene abnormalities in JAZF1 and EPC1 by FISH and found two additional cases with EPC1-PHF1 fusions.