Novel CTNNB1-USP6 fusion in intravascular fasciitis of the large vein identified by next-generation sequencing

Physiological roles and therapeutic implications of USP6

Ubiquitin-specific protease 6 (USP6) is a member of deubiquitinating enzyme family, recognized for its essential roles in physiological and pathological processes. USP6 is initially identified as a hominoid-specific enzyme residing on chromosome 17p13. USP6 is involved in regulating cellular functions, signaling pathways, protein degradation, intracellular trafficking, tumorigenesis and immune responses. USP6 is pivotal in signaling pathways, including NF-κB, JAK-STAT, and Wnt, which are fundamental for maintaining cellular homeostasis and mediating stress responses. Dysregulation of USP6 has been implicated in a spectrum of diseases, including bone tumors, breast and colorectal cancers, cranial fasciitis, and neurological disorders such as memory dysfunction. Furthermore, USP6 is involved in emerging therapeutic strategies highlighting its implications for drug development. A number of potential small molecule inhibitors are known to be responsible for suppression of USP6, such as Momelotinib (CYT387), FT385, USP30 Inh-1, -2 and -3, 2,6-Diaminopyridine-3,5-bis(thiocyanate) (PR-619) and so on. This review explores the emerging role of USP6 as a key regulator of cellular signaling pathways, its involvement in disease progression, its physiological functions, and the inhibitors that effectively suppress USP6 activity in detail. The comprehensive study provides insight to enhance our understanding of biological importance and therapeutic interventions of USP6 in drug development.

A Rare Tumor of Intravascular Myopericytoma in the Right Renal Vein

Myopericytoma, a perivascular myoid neoplasm, is commonly found in the dermis or subcutaneous tissues; however, its occurrence in visceral organs is unusual. Here, we present an extremely rare tumor of intravascular myopericytoma of the right renal vein. A 44-year-old man was incidentally diagnosed with a mass in the right kidney during a routine checkup. A nephrectomy was performed because the urologist suspected renal cancer. A gross examination of the resected specimen revealed a well-circumscribed brown mass in the renal hilum. Histologically, the tumor showed a concentric multilayered proliferation of spindle cells surrounding blood vessels. Immunohistochemical staining showed that the spindle-shaped tumor cells were negative for desmin but positive for α-smooth muscle actin and h-caldesmon, indicating their myoid nature. We confirmed that the tumor was located in the right renal vein because it was encased within a thick wall that was desmin-positive and contained elastic fibers, as shown by Elastica van Gieson staining. The patient was diagnosed with an intravascular myopericytoma of the right renal vein. There are several differential diagnoses for renal mesenchymal tumors, including angiomyolipoma. This emphasizes the importance of considering these uncommon tumors when examining nephrectomy specimens.

Unusual fusion gene rearrangements in patients with nodular fasciitis: a study of rare and novel USP6 fusion partners with a review of the literature

AIMS

This retrospective non-randomised study aims to identify new and rare fusion partners with USP6 in the setting of nodular fasciitis. It has been proven, that nodular fasciitis can harbour different variants of USP6 fusions, which can be used in routine diagnostics and even determine the biological behaviour of the process.

METHODS

A total of 19 cases of nodular fasciitis examined between 2011 and 2022 at Motol University Hospital in Prague were included into this study. Next to the histopathological evaluation, all cases were assessed using immunohistochemistry, RT-PCR and Anchored multiplex RNA methods. Patient's main demographic characteristics and corresponding clinical data were also analysed.

RESULTS

This study presents one novel (KIF1A) and five rare examples (TMP4, SPARC, EIF5A, MIR22HG, COL1A2) of fusion partners with USP6 among 19 cases of nodular fasciitis.

CONCLUSION

Identification of USP6 fusion partners in nodular fasciitis helps to understand the biology of such lesions. Moreover, it can be useful in routine histopathological practice of soft-tissues diagnostics, especially in preventing possible misdiagnosis of malignancy.

Intravascular fasciitis of the scalp as a complication of ICP monitor placement: a case report and review of the literature

BACKGROUND/IMPORTANCE

There are only 56 documented cases of intravascular fasciitis, a rare variant of nodular fasciitis. Of these cases, only 2 involved the scalp. This lesion is amenable to surgical resection, making it important to differentiate it from soft tissue malignancies of the scalp.

CLINICAL PRESENTATION

We report an unusual case of intravascular fasciitis involving the scalp at the site of an intracranial pressure (ICP) monitor of a 13-year-old male patient. The lesion was surgically excised with no recurrence upon 1-month follow-up.

CONCLUSION

Intravascular fasciitis is a benign, reactive proliferation of soft tissue that may arise at sites of prior trauma. It appears as a soft, painless, mobile lesion, and immunohistochemical studies are required to differentiate it from malignant lesions. The standard of care is surgical resection of the lesion.

Unravelling the USP6 gene: an update

Ubiquitin-specific protease 6 (USP6) rearrangements have been identified in aneurysmal bone cyst, nodular fasciitis, myositis ossificans, fibro-osseous pseudotumour of digits and cellular fibroma of tendon sheath. These entities show clinical as well as histological overlap, suggesting they are all clonal neoplastic belonging to the same biological spectrum and referred to as 'USP6-associated neoplasms'. They all show a characteristic gene fusion formed by juxtaposition of the USP6 coding sequences to the promoter regions of several partner genes, leading to USP6 transcriptional upregulation.

USP6-associated soft tissue tumors with bone metaplasia: Clinicopathologic and genetic analysis and the identification of novel USP6 fusion partners

Introduction

Among those tumors with consistent USP6 rearrangement, some arise from soft tissue and show bone metaplasia, including myositis ossificans (MO), fibro-osseous pseudotumor of digits (FOPD), soft tissue aneurysmal bone cyst (ST-ABC) and fasciitis ossificans (FO). These lesions are easily confused with malignancies because they show a rapid growth rate and brisk mitoses. Here, we aim to clarify the clinicopathologic and genetic characteristics of this entity and analyze the correlations among the different subtypes in one of the largest cohorts.

Materials and Methods

The clinicopathologic features of 73 cases of MO, FOPD, ST-ABC and FO diagnosed at West China Hospital, Sichuan University from January 2010 to December 2021 were retrospectively analyzed. Forty-three undecalcified samples were analyzed by systematic genetic studies, including fluorescence in situ hybridization (FISH), reverse transcription polymerase chain reaction (RT-PCR), Sanger sequencing and next-generation-based sequencing were performed.

Results

This series included 40 males and 33 females aged 2 to 80 years old (median: 31 years). FOPD occurred in extremal soft tissue, while lower extremities (38/58, 65.5%) were the most commonly involved lesions in the other three subgroups. Histologically, proliferative myofibroblasts/fibroblasts with varying degrees of osteoid tissue were present. Fluorescence in situ hybridization (FISH) results indicated that 22 cases (22/27, 81.5%) were positive for USP6 rearrangement, and 5 cases were negative. Among those cases with positive FISH results, 18 underwent reverse transcription-polymerase chain reaction (RT-PCR) detection that successfully detected common USP6 fusion types. Thirteen cases showed COL1A1::USP6 fusion, one showed MYH9::USP6 fusion, and 4 were negative for common fusion types. Next-generation-based sequencing technology was performed on two lesions with negative RT-PCR results and novel fusion partners SNHG3 and UBE2G1 were discovered.

Conclusions

Our findings revealed that COL1A1 is the most common fusion partner in this entity, unlike primary aneurysmal bone cysts and nodular fasciitis. Notably, we believed that FO may demonstrate more similar clinicopathologic and genetic manifestations with MO/FOPD and ST-ABC instead of nodular fasciitis for involving lower limbs most frequently and showing recurrent COL1A1::USP6 fusion. Additionally, this study also found two novel USP6 fusion partners, which further expanded our knowledge of this neoplastic spectrum.

Detection of sarcoma fusions by a next-generation sequencing based-ligation-dependent multiplex RT-PCR assay

Morphological, immunohistochemical, and molecular methods often need to be combined for accurate diagnosis and optimal clinical management of sarcomas. Here, we have developed, a new molecular diagnostic assay, for the detection of gene fusions in sarcomas. This targeted multiplexed next-generation sequencing (NGS)-based method utilizes ligation dependent reverse-transcriptase polymerase chain reaction (LD-RT-PCR-NGS) to detect oncogenic fusion transcripts involving 137 genes, leading to 139 gene fusions known to be recurrently rearranged in soft-tissue and bone tumors. 158 bone and soft-tissue tumors with previously identified fusion genes by fluorescent in situ hybridization (FISH) or RT-PCR were selected to test the specificity and the sensitivity of this assay. RNA were extracted from formalin-fixed paraffin-embedded (n = 143) or frozen (n = 15) material (specimen; n = 42 or core needle biopsies; n = 116). Tested tumors encompassed 23 major translocation-related sarcomas types, including Ewing and Ewing-like sarcomas, rhabdomyosarcomas, desmoplastic small round-cell tumors, clear-cell sarcomas, infantile fibrosarcomas, endometrial stromal sarcomas, epithelioid hemangioendotheliomas, alveolar soft-part sarcomas, biphenotypic sinonasal sarcomas, extraskeletal myxoid chondrosarcomas, myxoid/round-cell liposarcomas, dermatofibrosarcomas protuberans and solitary fibrous tumors. In-frame fusion transcripts were detected in 98.1% of cases (155/158). Gene fusion assay results correlated with conventional techniques (FISH and RT-PCR) in 155/158 tumors (98.1%). These data demonstrate that this assay is a rapid, robust, highly sensitive, and multiplexed targeted RNA sequencing assay for the detection of recurrent gene fusions on RNA extracted from routine clinical specimens of sarcomas (formalin-fixed paraffin-embedded or frozen). It facilitates the precise diagnosis and identification of tumors with potential targetable fusions. In addition, this assay can be easily customized to cover new fusions.

Intraneural Nodular Fasciitis of the Femoral Nerve with A Unique CTNNB1::USP6 Gene Fusion: Apropos of a Case and Review of Literature

Nodular fasciitis (NF) is a benign proliferation of fibroblasts and myofibroblasts occurring most commonly in the upper extremities that can mimic a variety of mesenchymal tumors including sarcoma. Although reported in almost all anatomic locations, only 7 cases of intraneural nodular fasciitis have been reported in English literature. The CTNNB1::USP6 gene fusion has not been previously reported in intraneural nodular fasciitis, although it has been reported in three entities including aneurysmal bone cyst, nodular fasciitis, and intravascular fasciitis. We report a case of a 29-year-old female with a 6-month history of left leg weakness, myalgia, and paresthesia of the left foot prompting a clinical diagnosis of a peripheral nerve sheath tumor. Surgical resection was performed, and histologic sections revealed a circumscribed lesion composed of banal spindle cells with variable interstitial collagen and occasional mitotic figures. By immunohistochemistry, the lesional cells were positive for smooth muscle actin, smooth muscle heavy chain myosin, p16, and H-caldesmon and negative for desmin, S-100, SOX10, HMB45, CD34, and beta-catenin. Fluorescence in Situ Hybridization for USP6 gene rearrangement was positive and consistent with the diagnosis of nodular fasciitis. Next-generation sequencing uncovered the presence of a CTNNB1::USP6 gene fusion involving CTNNB1 gene in exon 1 at the genomic position chr3:41241161 and the USP6 gene in exon 1 at the genomic position chr17:5033231. This gene fusion was confirmed by Sanger sequencing. Herein, we report a case that underscores the rare incidence of intraneural nodular fasciitis and highlights the pitfalls associated with the clinical differential diagnoses of intraneural tumors.

Intravascular fasciitis involving the external jugular vein and subclavian vein: A case report

BACKGROUND

Intravascular fasciitis (IVF) is a rare nodular fasciitis that often involves the layers and lumens of blood vessels; therefore, it is easily misdiagnosed as a malignant tumor with invasion into blood vessels.

CASE SUMMARY

A 13-year-old boy was admitted due to a mass on the left side of his neck. Duplex ultrasonography revealed a circular solid hypoechoic mass in the external jugular vein, and magnetic resonance imaging revealed an enhanced longitudinal mass-like lesion in the left supraclavicular fossa. Surgical treatment was arranged and completed, histopathological analysis showed a large amount of spindle cell proliferation, and immunohistochemistry showed that the spindle cells were positive for the expression of vimentin, caldesmon, and smooth muscle actin and negative for the expression of S-100 protein, desmin, CD34, and c-kit; Ki-67 staining revealed a low proliferative index (5%-10%), which confirmed the differentiation characteristics of myofibroblasts. Fluorescence in situ hybridization detected the rearrangement of USP6. IVF was subsequently diagnosed.

CONCLUSION

IVF is characterized by intraluminal, intramural and extramural involvement of small to large arteries or veins. Unless the doctor has a deep understanding of the disease or suspects that there is an initial indicator, IVF may be confused with other intravascular malignancies, leading to unnecessary radical surgery. Imaging examination combined with histopathological examination can improve the diagnostic accuracy of this disease.

Intravascular Fasciitis of the Jugular Vein Mimicking Thrombosis and Sarcoma: A Case Report

Background: Intravascular fasciitis is a rare disease that is a reactive proliferative lesion of myofibroblasts. There are rare reports that intravascular fasciitis has invaded the jugular vein as seen in this case. Case Presentation: A 41-year-old female presented with right neck dull pain for 20 days. The appearance of the subcutaneous mass was oval, pink hyaline, well-demarcated, and measuring ~5 mm in diameter. Microscopically, the mass was composed of spindle cells arranged in intersecting fascicles. Immunohistochemical stains showed that the spindle cells were positive for smooth muscle actin and negative for S-100, Desmin, MyoD1, and elastin stains. The nuclei of the spindle cells were relatively uniform, and mitotic activity was observed. The overall morphological and immunohistochemical features are consistent with intravascular fasciitis. Conclusion: Due to the rapid growth and vascular invasion, intravascular fasciitis created a high risk of misdiagnosing it as a sarcoma or thrombosis. Reporting this uncommon case, we raise awareness of this non-neoplastic lesion, and careful, light microscopic examination combined with immunohistochemical staining aids in the diagnosis of intravascular fasciitis.

Unusual split green-orange signals in USP6 fluorescence in situ hybridization in a malignant peripheral nerve sheath tumor with a novel NF1-SCIMP fusion: a potential diagnostic pitfall

Deletion of the neurofibromatosis 1 (NF1) gene is common, but NF1 rearrangement or fusion has rarely been reported in peripheral nerve sheath tumors. Here, we present a case of malignant peripheral nerve sheath tumor (MPNST) in a 36-year-old Chinese female. Histologically, the lesion was composed of spindle cells with moderate atypia, immature bone, and atypical cartilage elements. Fluorescence in situ hybridization (FISH) for USP6 revealed green-orange split signals, strongly suggesting the presence of USP6 rearrangement. Subsequent next-generation sequencing-based technology analyses revealed t(17,17) (p13.2, q11.2) intrachromosomal translocation resulting in a novel NF1-SCIMP fusion gene along with NF1 deletion. However, USP6 fusion was not identified. To the best of our knowledge, this is the first case with a confirmed NF1 gene fusion partner in a peripheral nerve sheath tumor. Notably, rearrangement of the SCIMP may cause a pitfall in the interpretation of USP6 FISH results.

Intravascular Fasciitis in the Femoral Vein with Hypermetabolic Signals Mimicking a Sarcoma: The Role of Preoperative Imaging Studies with Review of Literature

Intravascular fasciitis (IVF) is a very rare disease that is difficult to diagnose preoperatively. Frequently, it can be misdiagnosed as a malignancy or deep vein thrombosis. A 26-year-old man presented with a 6-month history of intermittent cramping pain in the right calf. Duplex ultrasonography, computed tomography, magnetic resonance imaging, and positron emission tomography were performed in various hospitals. The work-up revealed a hypermetabolic mass in the femoral vein, suggestive of a malignancy, such as leiomyosarcoma. The tumor was located inside the femoral vein with no invasion, and the mass was resected en bloc with the vein wall. Intraoperative frozen section biopsy revealed no malignancy, and the final pathological diagnosis was IVF. Herein, we report a case of IVF and discuss the role of imaging studies in its preoperative diagnosis, with an extensive literature review.

Ubiquitin-specific Peptidase 6 (USP6)-associated Fibroblastic/Myofibroblastic Tumors: Evolving Concepts

Ubiquitin-specific peptidase 6 (USP6) is a hominoid-specific gene residing on chromosome 17p13 and serves as a deubiquitinating enzyme with a diverse set of functions including intracellular trafficking, inflammatory signaling, cell transformation and protein turnover. USP6 rearrangements were first identified in aneurysmal bone cysts, resulting in promoter swapping and over-expression of wild type USP6. Several morphologically overlapping fibroblastic/myofibroblastic tumors are known to harbor USP6 rearrangements, including nodular fasciitis, cellular fibroma of tendon sheath, myositis ossificans and fibro-osseous pseudotumor of digits. Over the past few years, fusions involving the USP6 gene and various partner genes have been described in these neoplasms. The current World Health Organization Classification of Tumors of Soft Tissue suggests that USP6-rearranged lesions are typically benign and usually self-limited in their growth. This review provides an updated overview of the clinical, histological and molecular genetic features of USP6-associated fibroblastic/myofibroblastic tumors and discusses how these lesions should be best classified.

Clinicopathological and molecular characterisation of USP6-rearranged soft tissue neoplasms: the evidence of genetic relatedness indicates an expanding family with variable bone-forming capacity

AIMS

USP6 rearrangement underpins self-limiting fibroblastic/myofibroblastic neoplasms, including nodular fasciitis (NF), myositis ossificans (MO), aneurysmal bone cyst (ABC), and related variants. The aim of this study was to characterise UPS6 and fusion partners in order to delineate the clinicopathological, genetic and bone-forming features in such lesions of soft tissue (ST).

METHODS AND RESULTS

Break-apart fluorescence in-situ hybridisation (FISH) validated USP6 rearrangement in 31 of 35 NF [comprising three of three fasciitis ossificans (FO) cases, seven of eight cellular variant of fibroma of tendon sheath (C-FTS), four of six MO, three of three ST-ABC, and two of two fibro-osseous pseudotumours of digits (FOPD)]. As determined with FISH and reverse transcription polymerase chain reaction, MYH9-USP6 was the commonest fusion in four C-FTS and 20 NF, including one intravascular case and two infantile (one retroperitoneal) cases. The presence of MYH9-USP6 confirmed the diagnosis of two NFs> 50 mm with prominent ischaemic necrosis. COL1A1-USP6 was predominant in ossifying lesions, including all FO, MO, ST-ABC and FOPD with identified partner genes, and was also present in non-ossifying head and neck NF (HN-NF) and C-FTS in two cases each. A cervical NF of a 14-month-old girl harboured the novel COL1A2-USP6. Ossifying lesions showed considerable genetic and morphological overlaps. Sharing COL1A1-USP6, FO and FOPD showed similar central or haphazard bone matrix deposition. Besides zonation of outward bone maturation, four COL1A1-USP6-positive MO had incipient to sieve-like pseudocysts reminiscent of ST-ABC.

CONCLUSION

MYH9-USP6 is present in some C-FTS and most NF, including rare variants, but is unrelated to bone formation. All bone-forming USP6-rearranged lesions adopt COL1A1 as the 5' partner, indicating close genetic kinships. However, COL1A1/COL1A2 also contributes to the pathogenesis of minor subsets of non-ossifying USP6-rearranged HN-NF and C-FTS.

Atypical nodular fasciitis with a novel PAFAH1B1-USP6 fusion in a 22-month-old boy

Nodular fasciitis (NF) rarely occurs in infants aged < 2 years although cranial fasciitis develops predominantly in this age group. Histologically, NF may present high cellularity and brisk mitoses, but atypical forms are generally absent. Here, we report a NF in a 22-month-old Chinese boy. Microscopically, the lesion was manifested as cellular variant of NF. Notably, atypical mitotic figures including multipolar form were identified. Immunohistochemically, the neoplastic cells showed strong positivity for smooth muscle actin. Fluorescence in situ hybridization analysis revealed an unbalanced rearrangement of USP6, along with the USP6 increased copies. Subsequent next-generation sequencing-based technology revealed a novel PAFAH1B1-USP6 fusion gene as well as unusual fusion point on USP6 (exon 9). To the best of our knowledge, this is the only reported case with overt atypical mitosis. This case is also the first published example of genetically confirmed infant NF. Additionally, PAFAH1B1-USP6 fusion has never been described in NF.