Sarcomas: genetics, signalling, and cellular origins. Part 2: TET-independent fusion proteins and receptor tyrosine kinase mutations

Intracranial Myxoid Mesenchymal Tumor/Myxoid Subtype Angiomatous Fibrous Histiocytoma: Diagnostic and Prognostic Challenges

BACKGROUND AND IMPORTANCE

In the setting of intracranial neoplasms, EWSR1-cAMP Response Element-Binding Protein (CREB) transcription factor family fusions have been described in myxoid mesenchymal tumors, extremely rare entities with a close histopathologic and immunologic resemblance to myxoid subtype angiomatoid fibrous histiocytomas (AFH). Controversy exists on whether these central nervous system lesions are a subtype of myxoid AFH or a completely separate entity, which entitles a distinct clinical behavior and, consequently, a different approach to management. Upon review of the literature, only 14 cases of intracranial tumors harboring an EWSR1-CREB family fusion were identified, with only 3 cases presenting in middle-aged adults, none of which reported an EWSR1-CREM fusion mutation. Significant variability in reported radiographic and histopathological characteristics, as well as in clinical outcomes, was noted. Their similarity with other soft tissue tumors, added to the scarce information on its clinical behavior, represents a great diagnostic and therapeutic challenge to the treating physician.

CLINICAL PRESENTATION

We present a rare case of EWSR1-CREM mutated intracranial myxoid mesenchymal tumor/myxoid subtype AFH presenting as persistent headaches in a 36-yr-old woman with radiographic evidence of rapid growth and extensive vasogenic edema, for which she underwent surgical resection.

CONCLUSION

This represents a unique case of EWSR1-CREM mutated intracranial myxoid mesenchymal tumor presenting in adulthood, with evidence of aggressive behavior.

Diagnostic Utility of a Custom 34-Gene Anchored Multiplex PCR-Based Next-Generation Sequencing Fusion Panel for the Diagnosis of Bone and Soft Tissue Neoplasms With Identification of Novel USP6 Fusion Partners in Aneurysmal Bone Cysts

CONTEXT.—

Bone and soft tissue tumors are heterogeneous, diagnostically challenging, and often defined by gene fusions.

OBJECTIVE.—

To present our experience using a custom 34-gene targeted sequencing fusion panel.

DESIGN.—

Total nucleic acid extracted from formalin-fixed, paraffin-embedded (FFPE) tumor specimens was subjected to open-ended, nested anchored multiplex polymerase chain reaction and enrichment of 34 gene targets, thus enabling detection of known and novel fusion partners.

RESULTS.—

During a 12-month period, 147 patients were tested as part of routine clinical care. Tumor percentage ranged from 10% to 100% and turnaround time ranged from 3 to 15 (median, 7.9) days. The most common diagnostic groups were small round blue cell tumors, tumors of uncertain differentiation, fibroblastic/myofibroblastic tumors, and adipocytic tumors. In-frame fusion transcripts were identified in 64 of 142 cases sequenced (45%): in 62 cases, the detection of a disease-defining fusion confirmed the morphologic impression; in 2 cases, a germline TFG-GPR128 polymorphic fusion variant was detected. Several genes in the panel partnered with multiple fusion partners specific for different diagnoses, for example, EWSR1, NR4A3, FUS, NCOA2, and TFE3. Interesting examples are presented to highlight how fusion detection or lack thereof was instrumental in establishing accurate diagnoses. Novel fusion partners were detected for 2 cases of solid aneurysmal bone cysts (PTBP1-USP6, SLC38A2-USP6).

CONCLUSIONS.—

Multiplex detection of fusions in total nucleic acid purified from FFPE specimens facilitates diagnosis of bone and soft tissue tumors. This technology is particularly useful for morphologically challenging entities and in the absence of prior knowledge of fusion partners, and has the potential to discover novel fusion partners.

Development and potential applications of CRISPR-Cas9 genome editing technology in sarcoma

Sarcomas include some of the most aggressive tumors and typically respond poorly to chemotherapy. In recent years, specific gene fusion/mutations and gene over-expression/activation have been shown to drive sarcoma pathogenesis and development. These emerging genomic alterations may provide targets for novel therapeutic strategies and have the potential to transform sarcoma patient care. The RNA-guided nuclease CRISPR-Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated protein-9 nuclease) is a convenient and versatile platform for site-specific genome editing and epigenome targeted modulation. Given that sarcoma is believed to develop as a result of genetic alterations in mesenchymal progenitor/stem cells, CRISPR-Cas9 genome editing technologies hold extensive application potentials in sarcoma models and therapies. We review the development and mechanisms of the CRISPR-Cas9 system in genome editing and introduce its application in sarcoma research and potential therapy in clinic. Additionally, we propose future directions and discuss the challenges faced with these applications, providing concise and enlightening information for readers interested in this area.

Molecular diagnosis of soft tissue neoplasia: clinical applications and recent advances

Sarcomas are rare and heterogeneous neoplasms of mesenchymal tissues with diverse morphologies and clinical behavior. In the last few years, the discovery of specific genetic aberrations in these tumors has allowed better classification and understanding of mechanisms driving their pathogenesis. While the majority of sarcomas are still treated by traditional modalities, molecular markers driving the pathogenesis have paved the way for more accurate diagnosis and opportunity to explore other therapeutic strategies. This review discusses the available molecular tools in sarcoma diagnostics and highlight some of the biological significance of the recent discoveries and their clinical applications.

[Molecular biology of soft-tissue sarcomas]

Sarcomas represent a heterogeneous group of tumors with a complex and poorly reproducible classification. However, in the last ten years, several specific genetic alterations have been described allowing a molecular classification with: 1) sarcomas with a specific translocation which can be used as a diagnostic marker. These translocations can be demonstrated by RT-PCR or by FISH with commercially available break apart probes ; 2) sarcomas with simple genomic profile showing amplification of a few genes. Well differentiated liposarcomas, dedifferentiated liposarcomas and intimal sarcomas show a simple genomic profile characterised by MDM2 and CDK4 amplifications associated with amplification of other genes in dedifferentiated liposarcomas ; 3) sarcomas with activating mutations: about 90% of GIST show activating mutation of a receptor tyrosine kinase gene, either KIT or PDGFRA. The most frequent mutation involves exon 11 of KIT followed by exon 9 of KIT and exon 18 of PDGFRA. Demonstration of these mutations is useful for the diagnosis of CD117 negative GIST, for predicting response to imatinib and to explain secondary resistance to imatinib ; 4) sarcomas with inactivating mutations: malignant rhabdoid tumors show biallelic inactivation of INI1 gene with a lost of INI1 expression which can be demonstrated by immunohistochemistry ; 5) other sarcomas usually show a complex genomic profile characterised by numerous gains and losses of genes with a frequent loss of RB1 and alterations of P53. Leiomyosarcomas, pleomorphic rhabdomyosarcomas, pleomorphic liposarcomas, myxofibrosarcomas, poorly differentiated sarcomas (so-called MFH and fibrosarcomas) belong to this category and show no specific molecular abnormality.

Epigenetic features of human mesenchymal stem cells determine their permissiveness for induction of relevant transcriptional changes by SYT-SSX1

BACKGROUND

A characteristic SYT-SSX fusion gene resulting from the chromosomal translocation t(X;18)(p11;q11) is detectable in almost all synovial sarcomas, a malignant soft tissue tumor widely believed to originate from as yet unidentified pluripotent stem cells. The resulting fusion protein has no DNA binding motifs but possesses protein-protein interaction domains that are believed to mediate association with chromatin remodeling complexes. Despite recent advances in the identification of molecules that interact with SYT-SSX and with the corresponding wild type SYT and SSX proteins, the mechanisms whereby the SYT-SSX might contribute to neoplastic transformation remain unclear. Epigenetic deregulation has been suggested to be one possible mechanism.

METHODOLOGY/PRINCIPAL FINDINGS

We addressed the effect of SYT/SSX expression on the transcriptome of four independent isolates of primary human bone marrow mesenchymal stem cells (hMSC). We observed transcriptional changes similar to the gene expression signature of synovial sarcoma, principally involving genes whose regulation is linked to epigenetic factors, including imprinted genes, genes with transcription start sites within a CpG island and chromatin related genes. Single population analysis revealed hMSC isolate-specific transcriptional changes involving genes that are important for biological functions of stem cells as well as genes that are considered to be molecular markers of synovial sarcoma including IGF2, EPHRINS, and BCL2. Methylation status analysis of sequences at the H19/IGF2 imprinted locus indicated that distinct epigenetic features characterize hMSC populations and condition the transcriptional effects of SYT-SSX expression.

CONCLUSIONS/SIGNIFICANCE

Our observations suggest that epigenetic features may define the cellular microenvironment in which SYT-SSX displays its functional effects.

Benign cartilaginous tumors of bone: from morphology to somatic and germ-line genetics

Benign cartilaginous tumors of bones, intrinsic to their name, are tumors forming cartilaginous matrix with a clinically benign behavior. In this group, we recognize osteochondromas, (en)chondromas, chondroblastomas, and chondromyxoid fibromas. This group includes common tumors, that is, osteochondroma and (en)chondroma as well as rare tumors such as chondroblastoma and chondromyxoid fibroma. Several benign and malignant tumors may mimic benign cartilaginous tumors of bones. We reviewed the main morphologic features and the differential diagnosis is discussed. The genetics of these tumors is intriguing ranging from single gene event (ie, EXT mutation in multiple osteochondromas) to heterogeneous rearrangements with no recurrent involved chromosomal regions such as in chondroblastoma. The main genetic findings are hereby reviewed.

Role of trabectedin in the treatment of soft tissue sarcoma

Interest in marine natural products has allowed the discovery of new drugs and trabectedin (ET-743, Yondelis), derived from the marine tunicate Ecteinascidia turbinata, was approved for clinical use in 2007. It binds to the DNA minor groove leading to interferences with the intracellular transcription pathways and DNA-repair proteins. In vitro antitumor activity was demonstrated against various cancer cell lines and soft tissue sarcoma cell lines. In phase I studies tumor responses were observed also in osteosarcomas and different soft tissue sarcoma subtypes. The most common toxicities were myelosuppression and transient elevation of liver function tests, which could be reduced by dexamethasone premedication. The efficacy of trabectedin was established in three phase II studies where it was administered at 1.5 mg/m2 as a 24 h intravenous infusion repeated every three weeks, in previously treated patients. The objective response rate was 3.7%–8.3% and the tumor control rate (which included complete response, partial response and stable disease) was obtained in half of patients for a median overall survival reaching 12 months. In nonpretreated patients the overall response rate was 17%. Twenty-four percent of patients were without progression at six months. The median overall survival was almost 16 months with 72% surviving at one year. Predictive factors of response are being explored to identify patients who are most likely to respond to trabectedin. Combination with other agents are currently studied with promising results. In summary trabectedin is an active new chemotherapeutic agents that has demonstrated its role in the armamentarium of treatments for patients with sarcomas.