Spindle Cell Tumors of the Sinonasal Tract: A Diagnostic Update with Focus on Ancillary Workup

Spindle cell neoplasms arising in the head and neck may be challenging to recognize due to their relative rarity. While underlying molecular alterations are increasingly elucidated, testing for these features may not be readily available. In most cases, combinations of key morphologic features and diagnostic immunohistochemical markers can be used to replace molecular diagnostics. Conversely, some molecular alterations and expression of their surrogate biomarkers are not specific for any one entity, and it is important to recognize these to avoid diagnostic pitfalls. In this review, we discuss both old and new spindle cell tumors of the sinonasal tract, with an emphasis on histologic features and clinically relevant immunohistochemical markers serving as surrogate markers for underlying genomic alterations.

CSF1 expression in xanthogranulomatous epithelial tumor/keratin-positive giant cell-rich tumor

"Xanthogranulomatous epithelial tumor" (XGET) and "keratin-positive giant cell-rich soft tissue tumor" (KPGCT), two recently described mesenchymal neoplasms, likely represent different aspects of a single entity. Both tumors are composed of only a small minority of tumor cells surrounded by large numbers of non-neoplastic inflammatory cells and histiocytes, suggesting production of a paracrine factor with resulting "landscape effect," as seen in tenosynovial giant cell tumor. Recent evidence suggests that the paracrine factor in XGET/KPGCT may be CSF1, as in tenosynovial giant cell tumor. We hypothesized that CSF1 is overexpressed in XGET/KPGCT. To test our hypothesis, we performed quantitative real time PCR (qPCR) for CSF1 expression and CSF1 RNAscope chromogenic in situ hybridization (CISH) on 6 cases of XGET/KPGCT. All cases were positive with CSF1 CISH and showed increased expression of CSF1 by qPCR. Our findings provide additional evidence that the CSF1/CSF1R pathway is involved in the pathogenesis of XGET/KPGCT. These findings suggest a possible role for CSF1R inhibition in the treatment of unresectable or metastatic XGET/KPGCT.

Biphasic synovial sarcoma with myoepithelial features: a distinctive variant with a predilection for the foot

Synovial sarcoma (SS) is a tumor known for its classic monophasic spindle cell or biphasic morphology. However, it exhibits a wide range of histologic variations, leading to diagnostic challenges. Here, we present four cases of molecularly confirmed, biphasic SS originating in the feet and displaying myoepithelial differentiation. The patients were two men and two women with an age range from 19 to 71 years (mean, 45 years). Each tumor showed foci with conventional spindle cell morphology. The epithelial components included areas with nests and cords of epithelioid cells set within a hyalinized and sclerotic stroma. The cytoplasm was clear to pale and eosinophilic. The nuclei were ovoid-round with fine chromatin and small to inconspicuous nucleoli. Mitotic figures were present (2-13 per 10 high-power fields; mean, 6.5). Immunohistochemical studies showed variable staining of the myoepithelial-like regions for low molecular weight keratins, EMA, p63, and S100 protein. Molecular studies confirmed the presence of SS18::SSX1/2 fusion in all four tumors. These cases highlight an unusual variant of synovial sarcoma with an apparent predilection for the distal lower extremity and suggest that differentiation of biphasic synovial sarcoma may be impacted by the anatomic site. Awareness of this variant is important to avoid misclassification and potential treatment and prognostic implications.

Deep learning integrates histopathology and proteogenomics at a pan-cancer level

We introduce a pioneering approach that integrates pathology imaging with transcriptomics and proteomics to identify predictive histology features associated with critical clinical outcomes in cancer. We utilize 2,755 H&E-stained histopathological slides from 657 patients across 6 cancer types from CPTAC. Our models effectively recapitulate distinctions readily made by human pathologists: tumor vs. normal (AUROC = 0.995) and tissue-of-origin (AUROC = 0.979). We further investigate predictive power on tasks not normally performed from H&E alone, including TP53 prediction and pathologic stage. Importantly, we describe predictive morphologies not previously utilized in a clinical setting. The incorporation of transcriptomics and proteomics identifies pathway-level signatures and cellular processes driving predictive histology features. Model generalizability and interpretability is confirmed using TCGA. We propose a classification system for these tasks, and suggest potential clinical applications for this integrated human and machine learning approach. A publicly available web-based platform implements these models.

Proteogenomic insights suggest druggable pathways in endometrial carcinoma

We characterized a prospective endometrial carcinoma (EC) cohort containing 138 tumors and 20 enriched normal tissues using 10 different omics platforms. Targeted quantitation of two peptides can predict antigen processing and presentation machinery activity, and may inform patient selection for immunotherapy. Association analysis between MYC activity and metformin treatment in both patients and cell lines suggests a potential role for metformin treatment in non-diabetic patients with elevated MYC activity. PIK3R1 in-frame indels are associated with elevated AKT phosphorylation and increased sensitivity to AKT inhibitors. CTNNB1 hotspot mutations are concentrated near phosphorylation sites mediating pS45-induced degradation of β-catenin, which may render Wnt-FZD antagonists ineffective. Deep learning accurately predicts EC subtypes and mutations from histopathology images, which may be useful for rapid diagnosis. Overall, this study identified molecular and imaging markers that can be further investigated to guide patient stratification for more precise treatment of EC.

Integrative multi-omic cancer profiling reveals DNA methylation patterns associated with therapeutic vulnerability and cell-of-origin

DNA methylation plays a critical role in establishing and maintaining cellular identity. However, it is frequently dysregulated during tumor development and is closely intertwined with other genetic alterations. Here, we leveraged multi-omic profiling of 687 tumors and matched non-involved adjacent tissues from the kidney, brain, pancreas, lung, head and neck, and endometrium to identify aberrant methylation associated with RNA and protein abundance changes and build a Pan-Cancer catalog. We uncovered lineage-specific epigenetic drivers including hypomethylated FGFR2 in endometrial cancer. We showed that hypermethylated STAT5A is associated with pervasive regulon downregulation and immune cell depletion, suggesting that epigenetic regulation of STAT5A expression constitutes a molecular switch for immunosuppression in squamous tumors. We further demonstrated that methylation subtype-enrichment information can explain cell-of-origin, intra-tumor heterogeneity, and tumor phenotypes. Overall, we identified cis-acting DNA methylation events that drive transcriptional and translational changes, shedding light on the tumor's epigenetic landscape and the role of its cell-of-origin.

VIM::KMT2A-rearranged sarcomas: A report of two new cases confirming an entity with distinct histologic features

The recently described KMT2A-rearranged sarcomas are rare emerging entities where the KMT2A gene fuses with YAP1 and, less commonly, VIM, resulting in two distinct morphologies. Unlike the sclerosing epithelioid fibrosarcoma-like features that characterize tumors with KMT2A::YAP1 fusions, VIM::KMT2A-rearranged sarcomas are more uniformly cellular and lack the extensively sclerotic background seen in the former. Most tumors behave aggressively with metastases on presentation. Here, we describe the clinicopathologic and molecular findings in two additional cases of VIM::KMT2A rearranged sarcomas that arose in the deep soft tissues of adult males. Both tumors were composed of hypercellular fascicles of uniform spindle cells with pale eosinophilic cytoplasm and ovoid nuclei. The stroma had scant delicate collagen with occasional thin-walled ectatic blood vessels and perivascular hyalinization. Immunohistochemical studies showed an unspecific staining pattern with diffuse positivity for CD99 and BCL2 and variable staining for S100 protein. RNA-sequencing detected the presence of VIM::KMT2A gene fusion involving VIM exon 4 and KMT2A exon 2 in both cases. Sarcomas with VIM::KMT2A gene fusions seem to have sufficient morphologic features to warrant distinction from KMT2A-rearranged sarcomas with YAP1 partner. Without the benefit of molecular testing, these tumors pose a diagnostic challenge due to their lack of specific immunohistochemical profile and great morphologic overlap with other monomorphic spindle cell neoplasms.

GAB1::ABL1 fusions define a distinctive soft tissue neoplasm, with variable perineurial differentiation, and a predilection for children and young adults

Although well known as a fusion partner in hematological malignancies, fusion genes involving the ABL proto-oncogene 1 (ABL1), mapping to chromosomal region 9q34.12, have only been anecdotally reported in five soft tissue tumors. These neoplasms have been variously reported as perineurioma, angiofibroma, and solitary fibrous tumor, and all have harbored a GAB1::ABL1 gene fusion; however, the nosology and clinicopathological characteristics of soft tissue tumors carrying this rare fusion have not been delineated. We herein describe eight tumors containing the GAB1::ABL1 fusion and review previously reported cases in a series to define their morphological spectrum, address immunohistochemical evidence for a line of differentiation, with special reference to the presence or absence of a perineurial immunophenotype, and gather insight into their behavior. The patients included four females and four males, aged 13-37 years (median, 24 years). Two cases each originated in the shoulder area, trunk, hands, and lower extremities, with a size range of 1.5-8 cm (median, 3.4 cm). Four tumors were deep and four superficial. All tumors were morphologically similar, being composed of bland fibroblast-like spindle to ovoid cells diffusely arranged in a paucivascular fibrous to fibromyxoid stroma with variable resemblance to soft tissue perineurioma. Mitotic activity was generally low (0-8 mitoses in 10 high-power fields [HPFs]; median, 1). All lesions had at least focally infiltrative margins, but they otherwise lacked pleomorphism and necrosis. Immunohistochemistry showed focal reactivity for CD34 (5/7), epithelial membrane antigen (EMA) (3/8), claudin1 (2/3), GLUT1 (4/6), and S100 (2/7); other markers, including MUC4 (0/7), desmin (0/9), and smooth muscle actin (SMA) (0/4), were negative. RNA sequencing revealed a GAB1::ABL1 fusion in all cases with exon 6 of GAB1 fused to exon 2 of ABL1. Treatments included various forms of surgical intervention in seven cases; one tumor was biopsied only. Limited follow-up was available for five patients. One tumor regrew rapidly within 1 month to 1.5 cm after an initial marginal excision and was re-excised with close margins. Four patients were disease-free at 1, 3, 14, and 25 months of follow-up. Metastases have not, to date, been observed. This series characterizes "GAB1::ABL1 fusion-positive spindle cell neoplasm" as a distinct entity, with overlapping features with soft tissue perineurioma and predilection for children and young adults.

ZFP64::NCOA3 gene fusion defines a novel subset of spindle cell rhabdomyosarcoma

Spindle cell rhabdomyosarcoma represents a rare neoplasm characterized by monomorphic spindle cells with a fascicular architecture and variable skeletal muscle differentiation. Following incidental identification of a ZFP64::NCOA3 gene fusion in an unclassified spindle cell sarcoma resembling adult-type fibrosarcoma, we performed a retrospective archival review and identified four additional cases with a similar histology and identical gene fusion. All tumors arose in adult males (28-71 years). The neoplasms were found in the deep soft tissues, two were gluteal, and one each arose in the thigh, abdominal wall, and chest wall. Morphologically, the tumors were characterized by spindle cells with a distinctive herringbone pattern and variable collagenous to myxoid stroma. The nuclei were relatively monomorphic with variable mitotic activity. Three tumors had immunoreactivity for MyoD1, and four contained variable expression of desmin and smooth muscle actin. All cases tested for myogenin, CD34, S100, pankeratin, and epithelial membrane antigen were negative. Targeted RNA sequencing revealed a ZFP64::NCOA3 fusion product in all five tumors. Three patients developed distant metastases, and two ultimately succumbed to their disease within 2 years of initial diagnosis. This study suggests ZFP64::NCOA3 fusions define a novel subtype of rhabdomyosarcoma with a spindle cell morphology and aggressive clinical behavior. The potential for morphologic and immunohistochemical overlap with several other sarcoma types underscores the value of molecular testing as a diagnostic adjunct to ensure accurate classification and management of these neoplasms.

Xanthogranulomatous epithelial tumors and keratin-positive giant cell-rich soft tissue tumors: two aspects of a single entity with frequent HMGA2-NCOR2 fusions

Xanthogranulomatous epithelial tumor (XGET) and keratin-positive giant cell-rich soft tissue tumor with HMGA2-NCOR2 fusion (KPGCT) are two recently described neoplasms with both distinct and overlapping clinical and histopathologic features. We hypothesized that XGET and KPGCT may be related and represent a histologic spectrum of a single entity. To test this, we sought to characterize the clinical, radiographic, immunohistochemical, ultrastructural and molecular features of additional tumors with features of XGET and/or KPGCT, which we refer to descriptively as keratin-positive xanthogranulomatous/giant cell-rich tumors (KPXG/GCT). The archives were searched for potential cases of KPXG/GCT. Clinical and imaging features were noted. Slides were assessed for histologic and immunohistochemical findings. Ultrastructural and next generation RNA sequencing-based analysis were also performed. Nine cases were identified arising in seven women and two men [median age of 33 years (range: 12-87)]. Median tumor size was 4 cm (range: 2.4-14.0 cm) and tumors presented in the thigh (2), buttock (1), forearm (2), groin (1), cranial fossa (1), ilium (1), and tibia (1). Morphologically, tumors were most frequently characterized by a fibrous capsule, with associated lymphoid reaction, enclosing a polymorphous proliferation of histiocytes, giant cells (Touton and osteoclast-types), mixed inflammatory infiltrate, hemorrhage and hemosiderin deposition, which imparted a variably xanthogranulomatous to giant cell tumor-like appearance. One case clearly showed mononuclear cells with eosinophilic cytoplasm characteristic of XGET. All cases expressed keratin and 7 of 9 were found to harbor HMGA2-NCOR2 fusions including cases with xanthogranulomatous appearance. One patient developed local recurrence and multifocal pulmonary lesions, which were radiographically suspicious for metastases. Shared clinical, histologic and immunohistochemical features, and the shared presence of HMGA2-NCOR2 fusions supports interpretation of KPXG/GCT as a single entity which includes XGET and KPGCT. Given limited clinical follow-up to date and rare cases with apparently aggressive findings, we provisionally regard these tumors as having uncertain biologic potential.

Mesenchymal chondrosarcoma of the head and neck with HEY1::NCOA2 fusion: A clinicopathologic and molecular study of 13 cases with emphasis on diagnostic pitfalls

BACKGROUND

Mesenchymal chondrosarcoma (MCS) is a rare translocation-associated sarcoma, driven by a canonical HEY1::NCOA2 fusion. The tumors typically have a biphasic phenotype of primitive small blue round cells intermixed with hyaline cartilage. The head and neck (HN) region is a common site for MCS, accounting for 12-45% of all cases reported.

AIMS

We assembled a relatively large cohort of 13 molecularly confirmed HN MCS for a detailed clinicopathologic analysis. The underlying fusion events were determined using fluorescence in situ hybridization and/or targeted RNA sequencing.

RESULTS

The median age of presentation was 19 years. Five MCSs (39%) had an intraosseous presentation (skull, maxilla, palate, and mandible), while the remaining eight cases occurred in the brain/meninges, orbit, and nasal cavity. Microscopically, HN MCSs were characterized by primitive round cells arranged in a distinctive nested architecture and a rich staghorn vasculature. A cartilaginous component of hyaline cartilage islands and/or single chondrocytes were present in 69% cases. A combined immunoprofile of CD99(+)/SATB2(+)/CD34(-)/STAT6(-) was typically noted. As this immunoprofile is non-specific, the referral diagnoses in cases lacking a cartilaginous component included Ewing sarcoma family and osteosarcoma. Among the seven patients with follow-up data, three developed distant metastasis and one died of disease.

CONCLUSION

HN MCS may arise at intra- or extra-osseous sites. The HN MCS appears to have a more prolonged survival compared other MCS sites. Testing for HEY1::NCOA2 fusion is recommended in HN tumors with nested round cell morphology and staghorn vasculature that lack a distinctive cartilaginous component.

Retrospective observational studies in ultra-rare sarcomas: A consensus paper from the Connective Tissue Oncology Society (CTOS) community of experts on the minimum requirements for the evaluation of activity of systemic treatments

BACKGROUND

In ultra-rare sarcomas (URS) the conduction of prospective, randomized trials is challenging. Data from retrospective observational studies (ROS) may represent the best evidence available. ROS implicit limitations led to poor acceptance by the scientific community and regulatory authorities. In this context, an expert panel from the Connective Tissue Oncology Society (CTOS), agreed on the need to establish a set of minimum requirements for conducting high-quality ROS on the activity of systemic therapies in URS.

METHODS

Representatives from > 25 worldwide sarcoma reference centres met in November 2020 and identified a list of topics summarizing the main issues encountered in ROS on URS. An online survey on these topics was distributed to the panel; results were summarized by descriptive statistics and discussed during a second meeting (November 2021).

RESULTS

Topics identified by the panel included the use of ROS results as external control data, the criteria for contributing centers selection, modalities for ensuring a correct pathological diagnosis and radiologic assessment, consistency of surveillance policies across centers, study end-points, risk of data duplication, results publication. Based on the answers to the survey (55 of 62 invited experts) and discussion the panel agreed on 18 statements summarizing principles of recommended practice.

CONCLUSIONS

These recommendations will be disseminated by CTOS across the sarcoma community and incorporated in future ROS on URS, to maximize their quality and favor their use as control data when results from prospective studies are unavailable. These recommendations could help the optimal conduction of ROS also in other rare tumors.

Human and machine: Better at pathology together?

Meaningful integration of artificial intelligence (AI) will transform the application of "big data" for patient care, diagnosis, and research. In this issue of Cancer Cell, Chen et al. describe a transparent system to integrate histopathology and molecular data to predict outcomes and identify novel biomarkers in cancer.

Toward Better Understanding and Management of Solitary Fibrous Tumor

Solitary fibrous tumor (SFT) comprises a histologic spectrum of soft tissue neoplasms that are characterized by the unique NAB2-STAT6 gene fusion. Changes in diagnostic terminology and site-specific classification over the past few decades have resulted in a disjointed literature. Complete surgical excision with preservation of function remains the mainstay of treatment. New risk stratification systems including risk factors such as mitotic rate, age, tumor size, and presence of necrosis, among others, can be used to predict risk of recurrence or metastasis. Long-term follow-up after surgical resection is recommended. The clinical manifestations, diagnosis, management, and prognosis of SFT are reviewed here.

Leiomyosarcoma: Current Clinical Management and Future Horizons

Leiomyosarcomas are soft tissue tumors that are derived from smooth muscle mainly in the pelvis and retroperitoneum. Percutaneous biopsy is paramount to confirm diagnosis. Imaging is necessary to complete clinical staging. Multimodal treatment should be directed by expert sarcoma multidisciplinary teams that see a critical volume of these rare tumors. Surgery is the mainstay of curative intent treatment; however due to its high metastatic progression, there may be a benefit for neoadjuvant systemic treatment. Adjuvant systemic treatment has no proven disease-free survival, and its main role is in the palliative setting to potentially prolong overall survival.

Clear cell stromal tumor of the lung with YAP1::TFE3 fusion: four cases including case with highly aggressive clinical course

Clear cell stromal tumor of the lung (CCST-L) is a rare, recently recognized neoplasm, which has been found to express TFE3 and harbor YAP1::TFE3 fusions. Initial data suggested a benign process, however a single reported case gave rise to distant metastases. We sought to describe the clinicopathologic and molecular features of additional cases of CCST-L. Pathology and molecular archives were searched for cases of CCST-L or tumors with YAP1::TFE3 fusions. Clinical features were noted. Available slides, including immunohistochemical studies, were re-reviewed for diagnosis confirmation and assessment of pathologic features. Results of molecular studies were also recorded. Four tumors were identified, all occurring in women [median age 61 years (range: 24-69)]. Median tumor size was 4.4 cm (range: 1-9.5 cm); three tumors were unifocal and one was multifocal. Tumors were composed of epithelioid to spindled cells with eosinophilic to clear cytoplasm and grew in sheets, vague nests and short fascicles. Nuclear atypia was predominately mild, however two cases showed scattered atypical cells. Mitotic activity was generally low, though one case showed a mitotic count of 6/2 mm² . All tumors expressed TFE3 and harbored YAP1::TFE3 fusions. One case was unresectable and was treated with chemotherapy, and two underwent complete resection. One patient died of disease 7 months following diagnosis, while a second patient is alive with no evidence of disease after 43 months. Follow-up was not available for two cases. CCST-L expresses TFE3, harbors YAP1::TFE3 fusions and at least rare cases behave in an aggressive manner.

Soft tissue solitary fibrous tumors of the musculoskeletal system: spectrum of MRI appearances and characteristic imaging features

OBJECTIVE

Solitary fibrous tumors (SFTs) uncommonly occur in the musculoskeletal system, with limited available data on their MRI appearance. This study was performed to assess the MRI features of SFTs in the musculoskeletal system (MSK-SFTs).

MATERIALS AND METHODS

Pre-treatment MRI in 39 patients with pathologically proven SFTs in the trunk or extremities was evaluated. Patient demographics, clinical management and follow-up, and lesion histology were reviewed. MRI features including lesion location, size, morphology, signal characteristics, vascularity, and relationship to major neurovascular structures were assessed.

RESULTS

MSK-SFTs most frequently occurred in the lower extremity (23/39 cases, 59%), deep to fascia (29/39, 74%), and intermuscular (22/29, 76%) in location. The majority of deep lesions were located along a major neurovascular bundle (20/29, 69%). Lesions had well-defined margins (39/39, 100%), multilobulated contours (27/39, 69%), and measured mean 6.9 ± 2.8 cm. The majority of lesions had slightly hyperintense T1 signal (34/39, 87%) and heterogenous intermediate-to-high T2/STIR signal (28/38, 74%). A "pseudo-cerebriform" internal architectural pattern on fluid-sensitive sequences, with internal lobulations and low signal bands/septations, was observed in 63% (24/38) of lesions. Lesions commonly demonstrated prominent intra-lesional (30/39, 75%) and peripheral juxta-lesional flow voids. Local invasion of surrounding structures was uncommon (3/39, 8%). Mitotically active lesions (p = 0.02) and lesions with tumor necrosis (p < 0.01) were larger in size. Tumor necrosis was associated with T1 heterogeneity (p = 0.04). Distant metastasis occurred in 10% (4/39) of patients, all in mitotically active lesions pre-operatively considered at least at intermediate risk of metastasis.

CONCLUSION

MSK-SFTs commonly present as well-defined, hypervascular masses deep to fascia along major neurovascular bundles, with heterogeneous slightly hyperintense T1 signal, intermediate-to-high T2/STIR signal, and prominent macroscopic flow voids.

Update from the 5th Edition of the World Health Organization Classification of Head and Neck Tumors: Soft Tissue Tumors

The fifth (5th) edition of the World Health Organization (WHO) Classification of Head and Neck Tumors introduces a new chapter dedicated to soft tissue neoplasms commonly affecting the head and neck. While the diversity, rarity, and wide anatomic range of soft tissue tumors precludes a discussion of all entities that may be found in the head and neck, the addition of this new chapter to the head and neck "blue book" aims to provide a more comprehensive and uniform reference text, including updated diagnostic criteria, of mesenchymal tumor types frequently (or exclusively) arising at head and neck sites. Since publication of the previous edition in 2017, there have been numerous advances in our understanding of the pathogenesis of many soft tissue tumors which have facilitated refinements in tumor classification, identification of novel entities, development of diagnostic markers, and improved prognostication. This review will provide a focused discussion of the soft tissue tumors included in the 5th edition WHO Head and Neck classification, with an emphasis on updates.

Targeted RNA sequencing in the routine clinical detection of fusion genes in salivary gland tumors

Salivary gland tumors represent a diverse group of neoplasms that occasionally pose a diagnostic challenge for pathologists, particularly with limited sampling. Gene fusions, which may reflect genetic drivers, are increasingly recognized in a subset of these neoplasms, and can be leveraged for diagnostic purposes. We performed a retrospective analysis on a cohort of 80 benign and malignant salivary gland tumors, enriched for subtypes known to harbor recurrent fusion events, to validate the diagnostic use of a targeted RNA sequencing assay to detect fusion transcripts. Testing identified fusion genes in 71% (24/34) of pleomorphic adenoma and carcinoma-ex-pleomorphic adenoma, with 56% of cases showing rearrangement of PLAG1 and 15% HMGA2. In addition to confirming known partners for these genes, novel PLAG1 fusion partners were identified, including DSTN, NTF3, and MEG3; CNOT2 was identified as a novel fusion partner for HMGA2. In adenoid cystic carcinoma, 95% of cases (19/20) were positive for a fusion event. MYB was rearranged in 60% (12/20), MYBL1 in 30% (6/20), and NFIB in 5% (1/20); two tumors exhibited novel fusion products, including NFIB-TBPL1 and MYBL1-VCPIP1. Fusion genes were identified in 64% (9/14) of cases of mucoepidermoid carcinoma; MAML2 was confirmed to partner with either CRTC1 (43%) or CRTC3 (21%). One salivary duct carcinoma was found to harbor a novel RAPGEF6-ACSL6 fusion gene. Finally, as anticipated, gene fusions were not detected in any of the five acinic cell carcinomas included in the cohort. In summary, targeted RNA sequencing represents a diagnostically useful ancillary technique for identifying a variety of existing, and novel, fusion transcripts in the classification of salivary gland neoplasms.

Hybrid schwannoma-perineurioma frequently harbors VGLL3 rearrangement

Benign peripheral nerve tumors include schwannoma, neurofibroma, and perineurioma, as well as a recently recognized group of tumors with dual patterns of differentiation. The molecular pathogenesis of these so-called "hybrid" tumors remains poorly understood. Following identification of a novel CHD7-VGLL3 fusion gene in a hybrid schwannoma-perineurioma, we evaluated an expanded cohort of this tumor-type-as well as tumors with VGLL3 rearrangement identified from a curated molecular database-to characterize the prevalence of fusion genes among these tumors. Eighteen tumors met the inclusion criteria for this study. RNA sequencing identified VGLL3 rearrangement in 14 of these cases; the partner genes included CHD7 (ten cases), CHD9 (two cases), and MAMLD1 (two cases). Two cases possessed altogether unrelated fusions, including: DST-BRAF and SQSTM1-CDX1 fusion genes. Finally, two cases lacked identifiable fusion products. These findings highlight the molecular diversity of these neoplasms, with frequent rearrangement of VGLL3. More importantly, despite their dual pattern of differentiation, our results reveal the pathogenesis of hybrid schwannoma-perineurioma is unrelated to conventional schwannoma and perineurioma, thereby implying this tumor represents an altogether pathologically distinct entity.

RNA expression profiling reveals PRAME, a potential immunotherapy target, is frequently expressed in solitary fibrous tumors

Solitary fibrous tumors are a type of translocation-associated sarcoma with up to 30% rates of metastasis and poor response to conventional chemotherapy. Other translocation-associated sarcomas have been shown to display elevated expression of various cancer-testis antigens which may render them susceptible to immunotherapy strategies such as cancer vaccines and adoptive T-cell therapy. After an RNA sequencing assay brought the cancer-testis antigen Preferentially Expressed Antigen In Melanoma (PRAME) to our attention as possibly being upregulated in aggressive TERT promoter-mutated solitary fibrous tumors, we used tissue microarrays to asses PRAME expression in a large series of previously characterized solitary fibrous tumors, with correlation to various clinicopathologic features, as well as with tumor-infiltrating macrophages and the associated signal regulatory protein α (SIRPα)-CD47 regulatory checkpoint. We found that PRAME was expressed in 165/180 solitary fibrous tumors, with high expression seen in 58%, irrespective of TERT promoter status. Elevated PRAME expression was more frequent in primary intrathoracic solitary fibrous tumors and correlated with older age at primary diagnosis. Elevated PRAME was also associated with features suggestive of immune evasion, including lower numbers of antigen-presenting CD163+ and CD68+ macrophages, and expression of the "don't eat me" receptor CD47 on tumor cells. Taken together, these features suggest that strategies targeting PRAME with or without concomitant SIRPα-CD47 axis inhibition may represent a potential future therapeutic option in aggressive solitary fibrous tumor.

Relationships between highly recurrent tumor suppressor alterations in 489 leiomyosarcomas

BACKGROUND

Leiomyosarcoma (LMS) is the most common soft tissue and uterine sarcoma, but no standard therapy is available for recurrent or metastatic LMS. TP53, p16/RB1, and PI3K/mTOR pathway dysregulations are recurrent events, and some LMS express estrogen receptor (ER) and/or progesterone receptor (PR). To characterize relationships between these pathway perturbations, the authors evaluated protein expression in soft tissue and uterine nonprimary leiomyosarcoma (np-LMS), including local recurrences and distant metastases.

METHODS

TP53, RB1, p16, and PTEN expression aberrations were determined by immunohistochemistry (IHC) in tissue microarrays (TMAs) from 227 np-LMS and a comparison group of 262 primary leiomyosarcomas (p-LMS). Thirty-five of the np-LMS had a matched p-LMS specimen in the TMAs. Correlative studies included differentiation scoring, ER and PR IHC, and CDKN2A/p16 fluorescence in situ hybridization.

RESULTS

Dysregulation of TP53, p16/RB1, and PTEN was demonstrated in 90%, 95%, and 41% of np-LMS, respectively. PTEN inactivation was more common in soft tissue np-LMS than uterine np-LMS (55% vs 31%; P = .0005). Moderate-strong ER expression was more common in uterine np-LMS than soft tissue np-LMS (50% vs 7%; P < .0001). Co-inactivation of TP53 and RB1 was found in 81% of np-LMS and was common in both soft tissue and uterine np-LMS (90% and 74%, respectively). RB1, p16, and PTEN aberrations were nearly always conserved in p-LMS and np-LMS from the same patients.

CONCLUSIONS

These studies show that nearly all np-LMS have TP53 and/or RB1 aberrations. Therefore, therapies targeting cell cycle and DNA damage checkpoint vulnerabilities should be prioritized for evaluations in LMS.

SS18 Break-Apart Fluorescence In Situ Hybridization is a Practical and Effective Method for Diagnosing Microsecretory Adenocarcinoma of Salivary Glands

Molecular analysis has allowed for refinement of salivary gland tumor classification and, in some cases, the recognition of entirely new tumor types. Microsecretory adenocarcinoma (MSA) is a salivary gland tumor described in 2019 characterized by microcystic growth, bland cytomorphology, luminal secretions, fibromyxoid stroma, and S100/p63 positivity with negative p40. Most important, MSA is defined by MEF2C-SS18 fusion. While this fusion has, to this point, been detected by next-generation sequencing, this is a technique that is currently inaccessible in most diagnostic laboratories. On the other hand, SS18 break-apart fluorescence in situ hybridization (FISH) is widely available and frequently used as an adjunct for diagnosing synovial sarcoma. It is not known if SS18 break-apart FISH is positive in tumors with MEF2C-SS18, or if it is entirely specific for MSA. Break apart FISH for SS18 was performed on 4 cases of MSA, as well as 8 tissue microarrays (TMAs) containing 423 various salivary gland carcinomas: 26 acinic cell carcinomas, 35 adenocarcinomas not otherwise specified, 96 adenoid cystic carcinomas, 3 basal cell adenocarcinomas, 20 epithelial-myoepithelial carcinomas, 15 hyalinizing clear cell carcinomas, 3 intraductal carcinomas, 12 myoepithelial carcinomas, 117 mucoepidermoid carcinomas, 30 polymorphous adenocarcinomas, 45 salivary duct carcinomas, 19 secretory carcinomas, and 2 undifferentiated carcinomas. SS18 break-apart FISH was also performed on whole slides of 2 tumors from the TMAs. All MSA cases demonstrated classic split patterns on SS18 break-apart FISH. On the TMAs, 374 cases were evaluable by FISH, and 372 cases were clearly negative for SS18 rearrangement. Two cases, both mucoepidermoid carcinomas, had rare split signals below the positivity threshold of 12% on their TMA cores, so FISH was performed on whole sections. On the whole sections both tumors were unequivocally negative for SS18 rearrangement. Taken together, SS18 break-apart FISH was 100% sensitive and 100% specific for a diagnosis of MSA. SS18 break-apart FISH, a diagnostic tool widely available in pathology laboratories, appears to be a highly accurate method for diagnosing MSA of salivary glands. Accordingly, this new tumor type may be molecularly confirmed without needing to resort to highly specialized techniques like next-generation sequencing.

Primary superficial synovial sarcoma: clinical and histopathological characteristics in eight cases with molecular confirmation

BACKGROUND AND AIMS

Synovial sarcoma (SS) is a spindled cell sarcoma demonstrating varying degrees of epithelial differentiation and characterized by a pathognomonic t(X;18) translocation. SS most frequently involves deep soft tissue of the extremities in young adults. Superficial SS involving dermis and/or subcutaneous tissue is exceedingly rare.

METHODS AND RESULTS

We identified eight cases of primary superficial synovial sarcomas across three tertiary institutions. All cases were confined to the dermis/subcutis based on imaging or gross and microscopic examination. The average patient age was 36 years (range 14-50). The average tumor size was 2.4 cm (range 0.9-3.9 cm) and lesions showed classic monophasic (n = 4) or biphasic (n = 4) morphology. All tumors expressed keratin AE1/AE3 and/or epithelial membrane antigen (EMA), but were negative for CD34. The diagnosis for each case was confirmed by molecular detection of t(X;18). Six of the eight cases were treated with curative excision while the other two received additional radiotherapy. Follow-up was available for six patients (mean 68 months, range 2-108 months) and no patient experienced recurrence or metastatic disease.

CONCLUSIONS

We present the largest series to date of primary superficial SS with molecular confirmation for all cases. SS should be considered when evaluating a cutaneous monomorphic spindle cell neoplasm.

Curability of patients with lymph node metastases from extremity soft-tissue sarcoma

BACKGROUND

Lymph node metastases (LNM) rarely occur in adult extremity soft-tissue sarcoma (STS), affecting approximately 5% of patients. To the authors' knowledge, few studies to date have evaluated the prognosis and survival of patients with LNM.

METHODS

A retrospective review was performed of a single-center, prospectively collected STS database. Demographic, treatment, and oncologic data for patients with STS of the extremity with LNM were obtained from clinical and radiographic records.

RESULTS

Of 2689 patients with extremity STS, a total of 120 patients (4.5%) were diagnosed with LNM. LNM occurred most frequently among patients diagnosed with clear cell sarcoma (27.6%), epithelioid sarcoma (21.9%), rhabdomyosarcoma (17.3%), angiosarcoma (14.0%), and extraskeletal myxoid chondrosarcoma (9.3%). A total of 98 patients (81.7%) underwent LNM surgical resection. Patients with isolated LNM had a greater 5-year overall survival (57.3%) compared with patients with American Joint Committee on Cancer (AJCC) eighth edition stage IV STS with only systemic metastases (14.6%) or both LNM and systemic disease (0%; P < .0001). Patients with isolated LNM had an overall survival rate (52.9%) similar to that of patients with localized AJCC stage III tumors (ie, large, high-grade tumors) (49.3%) (P = .8). Patients with late, isolated, metachronous LNM had a 5-year overall survival rate (61.2%) that was similar to that of patients with isolated synchronous LNM at the time of presentation (53.6%) (P = .4).

CONCLUSIONS

Many different types of STS develop LNM. Patients with extremity STS with isolated LNM should not be considered as having stage IV disease as they are according to the current AJCC eighth edition classification because they have significantly better survival than those with systemic metastases. Patients with isolated, late, metachronous LNM have a survival similar to that of patients with isolated synchronous LNM at the time of presentation.

LAY SUMMARY

The results of the current study demonstrated that patients diagnosed with isolated lymph node metastases have a prognosis similar to that of patients diagnosed with localized American Joint Committee on Cancer stage III soft-tissue sarcomas, which also equates to a significantly better overall survival compared with patients with systemic metastases. Therefore, the authors recommend modifications to the most recent eighth edition of the American Joint Committee on Cancer staging system to clearly distinguish patients with isolated lymph node metastases to acknowledge their better prognosis compared with those with systemic metastases.

Epithelioid and spindle cell rhabdomyosarcoma with FUS-TFCP2 or EWSR1-TFCP2 fusion: report of two cases

The WHO Classification of Tumors of Soft Tissue and Bone divides rhabdomyosarcoma (RMS) into alveolar, embryonal, pleomorphic, and spindle cell/sclerosing types. Advances in molecular diagnostics have allowed for further refinement of RMS classification including the identification of new subtypes. Very rare RMS with epithelioid and spindle cell morphology, female predominance, marked osseous predilection, ALK expression, EWSR1/FUS-TFCP2 gene fusions, and highly aggressive clinical behavior have recently been recognized with only 23 cases reported in the English language literature. Herein, we report two additional cases with detailed clinicopathologic description and molecular confirmation. In brief, two young women presented each with a primary bone tumor-one with a frontal bone tumor and another with an osseous pelvic tumor. Both tumors showed epithelioid to spindle cell morphology, ALK expression, and EWSR1/FUS-TFCP2 gene fusions. Both patients died of disease less than 17 months from diagnosis despite administration of multiple lines of aggressive treatment. In addition, we review the literature and discuss differential diagnostic and potential treatment considerations.

Epithelioid and spindle cell rhabdomyosarcoma with FUS-TFCP2 or EWSR1-TFCP2 fusion: report of two cases

The WHO Classification of Tumors of Soft Tissue and Bone divides rhabdomyosarcoma (RMS) into alveolar, embryonal, pleomorphic, and spindle cell/sclerosing types. Advances in molecular diagnostics have allowed for further refinement of RMS classification including the identification of new subtypes. Very rare RMS with epithelioid and spindle cell morphology, female predominance, marked osseous predilection, ALK expression, EWSR1/FUS-TFCP2 gene fusions, and highly aggressive clinical behavior have recently been recognized with only 23 cases reported in the English language literature. Herein, we report two additional cases with detailed clinicopathologic description and molecular confirmation. In brief, two young women presented each with a primary bone tumor-one with a frontal bone tumor and another with an osseous pelvic tumor. Both tumors showed epithelioid to spindle cell morphology, ALK expression, and EWSR1/FUS-TFCP2 gene fusions. Both patients died of disease less than 17 months from diagnosis despite administration of multiple lines of aggressive treatment. In addition, we review the literature and discuss differential diagnostic and potential treatment considerations.

Tumor-associated macrophages and macrophage-related immune checkpoint expression in sarcomas

Early trials for immune checkpoint inhibitors in sarcomas have delivered mixed results, and efforts to improve outcomes now look to combinatorial strategies with novel immunotherapeutics, including some that target macrophages. To enhance our understanding of the sarcoma immune landscape, we quantified and characterized tumor-associated macrophage infiltration and expression of the targetable macrophage-related immune checkpoint CD47/SIRPα across sarcoma types. We surveyed immunohistochemical expression of CD68, CD163, CD47, and SIRPα in tissue microarrays of 1242 sarcoma specimens (spanning 24 types). Non-translocation sarcomas, particularly undifferentiated pleomorphic sarcoma and dedifferentiated liposarcoma, had significantly higher counts of both CD68+ and CD163+ macrophages than translocation-associated sarcomas. Across nearly all sarcoma types, macrophages outnumbered tumor-infiltrating lymphocytes and CD163+ (M2-like) macrophages outnumbered CD68+ (M1-like) macrophages. These findings were supported by data from The Cancer Genome Atlas, which showed a correlation between increasing macrophage contributions to immune infiltration and several measures of DNA damage. CD47 expression was bimodal, with most cases showing either 0% or >90% tumor cell staining, and the highest CD47 scores were observed in chordoma, angiosarcoma, and pleomorphic liposarcoma. SIRPα scores correlated well with CD47 expression. Given the predominance of macrophage infiltrates over tumor-infiltrating lymphocytes, the bias toward M2-like (immunosuppressive) macrophage polarization, and the generally high scores for CD47 and SIRPα, macrophage-focused immunomodulatory agents, such as CD47 or IDO-1 inhibitors, may be particularly worthwhile to pursue in sarcoma patients, alone or in combination with lymphocyte-focused agents.

Atypical lipomatous tumour/well-differentiated liposarcoma and de-differentiated liposarcoma in patients aged ≤ 40 years: a study of 116 patients

AIMS

Limited data exist on atypical lipomatous tumour (ALT)/well-differentiated liposarcoma (WDL) and de-differentiated liposarcoma (DDLPS) in children and young adults.

METHODS AND RESULTS

Cases of ALT/WDL/DDLPS arising in patients aged ≤ 40 years were collected from multiple institutional and consultation archives. A total of 116 cases of ALT/WDL (75) and DDLPS (41) were identified, representing fewer than 5% of these tumours seen at our institutions during this time-period. The patients (59 male/57 female) ranged in age from 8 to 40 years. Sites included deep central (abdomen/retroperitoneum/pelvis/groin) (n = 60), extremity (n = 42), trunk (n = 5), head/neck (n = 8) and mediastinum (n = 1). De-differentiated patterns included: high-grade pleomorphic sarcoma, myxofibrosarcoma-like, heterologous rhabdomyoblastic differentiation, low-grade spindle cell sarcoma and homologous lipoblastic differentiation. Forty-one patients experienced a local recurrence and 11 patients with DDLPS developed metastasis. ALT arising in the extremities had lower recurrence rates than deep central WDL (5-year recurrence-free survival 88.9% versus 59.0%; P = 0.002), while patients with deep central DDLPS experienced significantly more adverse events compared to WDL at this site (5-year event-free survival 11.9% versus 59.0%) (P < 0.0001). Seven (of eight) head/neck tumours had follow-up available; five recurred, and one patient (DDLPS) with recurrence also experienced a metastasis. The single mediastinal tumour (DDLPS) recurred and metastasised.

CONCLUSION

ALT/WDL and DDLPS occurring in patients aged ≤ 40 years is rare, but exhibits similar morphological features to its counterparts in older adults, including potential for heterologous and homologous de-differentiation in the latter. Although case numbers are limited, tumours arising in the head and neck exhibit high rates of adverse events, suggesting that classification as WDL rather than ALT is more appropriate.

Expression of lymphocyte immunoregulatory biomarkers in bone and soft-tissue sarcomas

Despite advances in our understanding of the underlying molecular drivers of sarcomas, few treatments are available with proven benefit for advanced metastatic sarcomas. Immunotherapy has value in this setting for some types of cancers, but sarcomas, with their multiplicity of rare types, have not been characterized in detail for their expression of targetable immune biomarkers. This study provides the most systematic evaluation to date of tumor-infiltrating lymphocytes and immune checkpoint biomarker expression in sarcomas. We examined by morphology and immunohistochemistry 1072 sarcoma specimens representing 22 types, in addition to 236 benign bone and soft-tissue tumors. Genomically-complex sarcoma types-those driven by mutations and/or copy-number alterations-had much higher numbers of tumor-infiltrating lymphocytes than translocation-associated sarcomas. Prior exposure to radiotherapy was associated with increased immune infiltrates. Higher lymphocytic infiltration was associated with better overall survival among the non-translocation-associated sarcomas. Expression of PD-1 and CD56 were associated with worse overall survival. LAG-3 and TIM-3, two emerging immune checkpoints, were frequently expressed in most sarcoma types. Indeed, most cases positive for PD-(L)1 coexpressed one or both of these novel biomarkers, providing a potential rationale in support for trials targeting LAG-3 and/or TIM-3 in conjunction with PD-1 inhibition.

Infiltrating Myeloid Cells Drive Osteosarcoma Progression via GRM4 Regulation of IL23

The glutamate metabotropic receptor 4 (GRM4) locus is linked to susceptibility to human osteosarcoma, through unknown mechanisms. We show that Grm4^-/- gene-targeted mice demonstrate accelerated radiation-induced tumor development to an extent comparable with Rb1^+/- mice. GRM4 is expressed in myeloid cells, selectively regulating expression of IL23 and the related cytokine IL12. Osteosarcoma-conditioned media induce myeloid cell Il23 expression in a GRM4-dependent fashion, while suppressing the related cytokine Il12. Both human and mouse osteosarcomas express an increased IL23:IL12 ratio, whereas higher IL23 expression is associated with worse survival in humans. Consistent with an oncogenic role, Il23 ^-/- mice are strikingly resistant to osteosarcoma development. Agonists of GRM4 or a neutralizing antibody to IL23 suppressed osteosarcoma growth in mice. These findings identify a novel, druggable myeloid suppressor pathway linking GRM4 to the proinflammatory IL23/IL12 axis. SIGNIFICANCE: Few novel systemic therapies targeting osteosarcoma have emerged in the last four decades. Using insights gained from a genome-wide association study and mouse modeling, we show that GRM4 plays a role in driving osteosarcoma via a non-cell-autonomous mechanism regulating IL23, opening new avenues for therapeutic intervention.See related commentary by Jones, p. 1484.This article is highlighted in the In This Issue feature, p. 1469.

Comparison of published risk models for prediction of outcome in patients with extrameningeal solitary fibrous tumour

AIMS

Solitary fibrous tumours (SFTs) are fibroblastic mesenchymal tumours with a 10-30% metastatic rate. Several risk models have been proposed for extrameningeal SFT, but they have not been evaluated in direct comparison with each other. The aim of this study is to compare the utility of published risk models in a multi-institutional SFT cohort.

METHODS AND RESULTS

Clinicopathological data were evaluated for a cohort of extrameningeal SFTs, and used to stratify tumours by the use of five proposed risk models designed for soft tissue and/or pleural SFT [modified Demicco, Pasquali, Salas overall survival (OS), Salas metastasis, and Salas local recurrence (LR)]. Kaplan-Meier and Cox proportional hazards models were used to assess OS, time to first metastasis, time to first LR, and recurrence-free survival (RFS). The study included 303 patients (109 from a referral cancer treatment centre; previously described in the original Demicco model) and an independent cohort from two large hospitals (n = 194). The median patient age was 54 years, and the median clinical follow-up (available for 220 patients) was 37 months. The independent cohort had a 13% risk of metastasis at 5 years and a 16% risk of metastasis at 10 years. In this cohort, the modified Demicco, Salas OS, and Salas metastasis models predicted metastasis and RFS, whereas the Pasquali model had the best correlation with OS.

CONCLUSIONS

Multivariate risk models that include mitotic rate and patient age can more accurately predict aggressive behaviour in SFTs, with the modified Demicco and Salas OS risk models showing the best correlation with metastasis and RFS.

Abstract 1184: Comprehensive analysis with interactive exploration of immune response signatures in 10,000 tumor samples

In recent years, analysis of cancer genomics data using methods of immunogenomics has yielded valuable insight into how cancer cells interact with immune cells in the tumor microenvironment. A recent analysis of the multiple molecular platforms by The Cancer Genome Atlas (TCGA) of over 10,000 tumors comprising 33 cancer types identified six immune subtypes, spanning multiple tumor types, that are characterized by differences in: macrophage vs. lymphocyte signatures; Th1:Th2 cell ratio; extent of intratumoral heterogeneity; aneuploidy; extent of neoantigen load; signatures of cell proliferation; expression of immunomodulatory genes; and disease outcome [1]. Particular driver mutations correlate with variation in leukocyte levels across all cancers or with the fraction of individual immune cell types. Intracellular and extracellular networks (involving transcription, microRNAs, copy number and epigenetic processes) are predicted to play a role in establishing the observed tumor-immune cell interactions, both across and within immune subtypes. Additionally, machine learning methods have been applied to H&E images to extract information on which tissue regions contain tumor infiltrating lymphocytes (TILs), yielding TIL maps of whole slide images from digital pathology[2]. Spatial patterns of TILs are associated with a variety of genomic alterations, including cancer subtypes.

The CRI iAtlas (www.cri-iatlas.org) is a cloud-based platform for data exploration and discovery, allowing researchers to study TCGA immune response characterizations, and the relationships among them in individual tumor types, tumor subtypes, and immune subtypes. iAtlas supports the adaptive exploration of correlations within the cellularity of the tumor microenvironment, immune expression signatures, tumor mutation burden, cancer driver mutations, adaptive cell clonality, patient survival, and expression of key immunomodulators. iAtlas was launched in April 2018, and has since been expanded to include new capabilities such as (1) user-defined loading of cohorts, (2) a tool for classifying expression data into immune subtypes, (3) integration of TIL mapping from digital pathology images, and (4) addition of annotated genomics datasets from immunotherapy clinical trials as comparative data sources. As the resource evolves, we expect that the CRI iAtlas will help to accelerate discovery and improve patient outcomes by providing researchers greater access to immunogenomics data to better understand the immunological characteristics of the tumor microenvironment and its potential impact on patient responses to immunotherapy.

[1] Thorsson, V, et al., The Immune Landscape of Cancer; Immunity 48, p812 - 830.e14 (2018)

[2] Saltz, J et al. Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images; Cell Reports 23 pp.181-193.e7 (2018)

Citation Format: Vesteinn Thorsson, David L. Gibbs, Mary L. Disis, Elizabeth G. Demicco, Alexander J. Lazar, Jonathan S. Serody, James A. Eddy, Ilya Shmulevich, Justin Guinney, Benjamin G. Vincent. Comprehensive analysis with interactive exploration of immune response signatures in 10,000 tumor samples [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1184.

PRRX-NCOA1/2 rearrangement characterizes a distinctive fibroblastic neoplasm

Fibroblastic/myofibroblastic neoplasms represent a broad, and occasionally diagnostically challenging, category of soft tissue neoplasms. A subset of these tumors defy conventional classification. However, with the advent of next-generation sequencing, the identification of disease-defining molecular alterations is gradually improving their subclassification. Following identification of two index cases of a distinctive fibroblastic neoplasm with a fusion gene involving PRRX1 and NCOA1, we performed a retrospective review to further characterize this entity. We identified two additional cases, including one with a fusion between PRRX1 and NCOA2. The average patient age was 38 years, and three patients were female. Two tumors occurred on the neck, and the others involved the groin and thigh. Tumors were centered in the subcutis and ranged from 2.3 to 14.0 cm (average 5.8 cm). Morphologically, they were predominantly hypocellular, with focal hypercellularity. They were composed of monomorphic spindle-stellate cells with a vague fascicular pattern. The nuclei were bland with only rare mitotic activity, and occasional multinucleation. The intervening stroma was typically abundant and ranged from myxoid to collagenous, with frequent rope-like collagen bundles. Three of the cases had a prominent vasculature ranging from numerous small curvilinear vessels to ectatic and branching staghorn-like vessels. Immunohistochemistry was negative for desmin, smooth muscle actin, S100, CD34, keratin, and epithelial membrane antigen. Each of the patients was treated by simple excision and none of the tumors were associated with local recurrence or metastasis. Based on their unique morphological and molecular attributes, we believe this represents a novel fibroblastic tumor for which we have tentatively proposed the name "PRRX-NCOAx-rearranged fibroblastic tumor."

Molecular updates in adipocytic neoplasms✰

Adipocytic neoplasms include a diversity of both benign tumors (lipomas) and malignancies (liposarcomas), and each tumor type is characterized by its own unique molecular alterations driving tumorigenesis. Work over the past 30 years has established the diagnostic utility of several of these characteristic molecular alterations (e.g. MDM2 amplification in well- and dedifferentiated liposarcoma, FUS/EWSR1-DDIT3 gene fusions in myxoid liposarcoma, RB1 loss in spindle cell/pleomorphic lipoma). More recent studies have focused on additional molecular alterations which may have therapeutic or prognostic impact. This review will summarize several of the important molecular findings in adipocytic tumors that have been described over the past 10 years.

TERT promoter mutations in solitary fibrous tumour

AIMS

TERT promoter mutations have been reported in 22% of solitary fibrous tumours (SFT) and have been associated with poor outcomes. We performed testing for TERT hot-spot mutations in a large series of SFT in order to confirm this finding and explore clinicopathological correlates of mutation status.

METHODS AND RESULTS

PCR for TERT hot-spot mutations C250T and C228T was performed on DNA extracted from 216 SFT and mutation status correlated with clinicopathological factors, including predicted risk for metastasis using a previously published model. Testing was successful in 189 tumours from 172 patients, and mutations were present in 29%. The presence of TERT promoter mutation was associated with larger primary tumour size, necrosis and older patient age. TERT promoter mutations were most common in high-risk tumours (nine of 20, 45%), and were present in 11 of 26 (42%) moderate-risk tumours and 14 of 67 (21%) low-risk tumours (P = 0.004). Overall, TERT mutations were associated with shorter time to first metastasis (P = 0.04), but had no impact on overall survival. TERT promoter mutation status was found not to provide additional prognostic information in low- and high-risk SFT, but did identify a group of patients with intermediate risk SFT who had an increased risk of metastasis.

CONCLUSIONS

TERT promoter mutations were more frequent in SFT with higher risk of metastasis, but TERT promoter mutation status was not a reliable predictor of clinical outcome by itself. However, mutations in the TERT promoter may be useful in further stratifying patients with intermediate risk tumours.

Dermatofibrosarcoma protuberans with a novel COL6A3-PDGFD fusion gene and apparent predilection for breast

Dermatofibrosarcoma protuberans is a locally aggressive superficial mesenchymal neoplasm. It typically occurs in adulthood, and has been reported to have a slight male predilection. Tumors have a characteristic histopathologic appearance, including: storiform architecture, infiltrative "honeycomb" growth within subcutaneous adipose tissue, and immunoreactivity for CD34. Virtually all molecularly characterized cases to date have been found to harbor a COL1A1-PDGFB fusion product. Following identification of an index patient with a novel COL6A3-PDGFD fusion gene, we undertook a molecular investigation, using a combination of RNA sequencing and fluorescence in situ hybridization (FISH), to assess the prevalence of PDGFD rearrangement in dermatofibrosarcoma protuberans (N = 63). Three additional patients were found to have balanced PDGFD rearrangements. Interestingly, all 4 tumors arose on the breast of females. As a result, we subsequently examined 16 additional cases of primary breast dermatofibrosarcoma protuberans, identifying 2 additional tumors with PDGFD rearrangement. The morphology and immunophenotype of all 6 cases was analogous to those with the canonical COL1A1-PDGFB fusion; none of the cases showed fibrosarcomatous transformation. This study illustrates that the COL6A3-PDGFD fusion product is rare in dermatofibrosarcoma protuberans, and associated with an apparent predilection for breast. An awareness of this variant is important for pathologists, as it will not be detected using conventional reverse transcription polymerase chain reaction or FISH-based diagnostic assays for dermatofibrosarcoma protuberans.

Abstract 5639: Changes in local and peripheral T cell diversity after HPV E7 antigen-expressing Listeria-based immunotherapy (ADXS11-001) prior to robotic surgery for HPV-positive oropharyngeal cancer

Human papilloma virus associated oropharyngeal cancers (HPVOPC) account for about one third of OPC and express foreign viral antigens such as the E6 and E7 oncogenes, which are suitable for immune targeting. We performed a “window of opportunity” trial of patients undergoing standard-of-care transoral surgery for HPVOPC to assess the effect of the HPV16-E7 targeting vaccine ADXS11-001 on the intratumoral and systemic immune response. We reported, in a prior abstract, that 5 of 8 ADXS11-treated patients showed increased E6 or E7-specific IFN-γ responses post-treatment and 4/8 patients demonstrated increased CD8 and CD4 tumor infiltrating lymphocytes (TILs) after vaccination. In the present study, we profiled peripheral blood immunocyte populations (PBMCs) pre-vaccination, post-vaccination and post-surgery via multicolor flow cytometry in 8 patients. Clonal expansion and diversification of PBMCs and tumor TILs post-treatment were determined via T cell receptor (TCR) DNA sequencing and correlated to HPV antigen specific immune responses determined by ELISPOT as well as tumor immune profile determined by quantitative immunofluorescence. While peripheral CD8 cytotoxic T cell (CTL) levels remained constant over the course of the study, we observed trends towards their increased expression of LAG-3 (1.6 fold, p=0.0821) and PD-1 (1.6 fold, p=0.0748) 6 weeks post-surgery, consistent with activation. We did not observe statistically significant changes in levels of CD4 T helper cells, MDSC or Tregs, although a modest trend towards decreased CD8/MDSC ratio was observed post-surgery (0.5 fold, p=0.0864). Overall TCR diversity/clonality of PBMCs and TILs did not change. However the comparison of similarity between T cell repertoires of the tumor and PBMCs (Morisita's index) demonstrated an increase of expanded clones post-vaccination limited to TILs in 5/6 patients, indicating clonal expansion in ADXS11-treated patients. When we analyzed T cell repertoire changes in individual patients, 4 of 8 patients demonstrated expansion of specific TCR clones post-vaccination. The two patients with the greatest increase in number of expanded TCR clones among both, PBMCs and TILs, also had the strongest increase of E6 or E7-specific IFN-γ responses post-treatment, and also had strongly increased CD8 TILs. Our results demonstrate that immunomodulatory effects of ADXS11-001 on the local and peripheral immune response vary among patients, with 2/8 treated patients demonstrating evidence of an integrated adaptive immune response in blood and tumor, consistent with selective clonal expansion in the context of a vaccine-induced anti-tumor T cell response. Profiling of additional patients will permit more detailed analysis of ADXS11-induced immune modulation and impact on TCR diversity.

Citation Format: Rosemarie Krupar, Ravi R. Pathak, Naoko Imai, Eric Genden, Krzys Misiukiewicz, Elizabeth G. Demicco, Jigneshkumar Patel, Falguni Parikh, Michael Donovan, Seunghee Kim-Schulze, Sven Perner, Marshall Posner, Brett Miles, Sacha Gnjatic, Andrew G. Sikora. Changes in local and peripheral T cell diversity after HPV E7 antigen-expressing Listeria-based immunotherapy (ADXS11-001) prior to robotic surgery for HPV-positive oropharyngeal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5639.

The Immune Landscape of Cancer

We performed an extensive immunogenomic analysis of more than 10,000 tumors comprising 33 diverse cancer types by utilizing data compiled by TCGA. Across cancer types, we identified six immune subtypes-wound healing, IFN-γ dominant, inflammatory, lymphocyte depleted, immunologically quiet, and TGF-β dominant-characterized by differences in macrophage or lymphocyte signatures, Th1:Th2 cell ratio, extent of intratumoral heterogeneity, aneuploidy, extent of neoantigen load, overall cell proliferation, expression of immunomodulatory genes, and prognosis. Specific driver mutations correlated with lower (CTNNB1, NRAS, or IDH1) or higher (BRAF, TP53, or CASP8) leukocyte levels across all cancers. Multiple control modalities of the intracellular and extracellular networks (transcription, microRNAs, copy number, and epigenetic processes) were involved in tumor-immune cell interactions, both across and within immune subtypes. Our immunogenomics pipeline to characterize these heterogeneous tumors and the resulting data are intended to serve as a resource for future targeted studies to further advance the field.

PanCancer insights from The Cancer Genome Atlas: the pathologist's perspective

The Cancer Genome Atlas (TCGA) represents one of several international consortia dedicated to performing comprehensive genomic and epigenomic analyses of selected tumour types to advance our understanding of disease and provide an open-access resource for worldwide cancer research. Thirty-three tumour types (selected by histology or tissue of origin, to include both common and rare diseases), comprising >11 000 specimens, were subjected to DNA sequencing, copy number and methylation analysis, and transcriptomic, proteomic and histological evaluation. Each cancer type was analysed individually to identify tissue-specific alterations, and make correlations across different molecular platforms. The final dataset was then normalized and combined for the PanCancer Initiative, which seeks to identify commonalities across different cancer types or cells of origin/lineage, or within anatomically or morphologically related groups. An important resource generated along with the rich molecular studies is an extensive digital pathology slide archive, composed of frozen section tissue directly related to the tissues analysed as part of TCGA, and representative formalin-fixed paraffin-embedded, haematoxylin and eosin (H&E)-stained diagnostic slides. These H&E image resources have primarily been used to verify diagnoses and histological subtypes with some limited extraction of standard pathological variables such as mitotic activity, grade, and lymphocytic infiltrates. Largely overlooked is the richness of these scanned images for more sophisticated feature extraction approaches coupled with machine learning, and ultimately correlation with molecular features and clinical endpoints. Here, we document initial attempts to exploit TCGA imaging archives, and describe some of the tools, and the rapidly evolving image analysis/feature extraction landscape. Our hope is to inform, and ultimately inspire and challenge, the pathology and cancer research communities to exploit these imaging resources so that the full potential of this integral platform of TCGA can be used to complement and enhance the insightful integrated analyses from the genomic and epigenomic platforms. Copyright © 2017 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

Abstract B32: Lymphocytes and immune checkpoint biomarker expression in sarcomas

Recent clinical trials of immune checkpoint inhibitors have raised hopes for sarcoma therapy, but they have not taken into account the variability of the immune microenvironment in their design or interpretation. Here, we present a comprehensive analysis of tumor-infiltrating lymphocytes (TILs) across a spectrum of sarcoma types, in order to better identify sarcoma populations that are more likely to respond to specific immunotherapies.

Methods: From a tissue microarray database of 1918 formalin-fixed, paraffin-embedded sarcoma tissue samples spanning 24 subtypes, immunohistochemistry was performed to quantify TILs, to characterize major T-cell subsets (CD4, CD8, FOXP3), and to evaluate expression of targetable immune checkpoint ligand PDL1 (programmed death ligand 1) and its immune cell receptor PD1. PDL1 was scored by percentage of tumor cells exhibiting positive membranous staining; all other markers were quantified by counting positive-staining lymphocytes.

Results: Lymphocytes were present in 93% of samples (ranging from 1-1300 TILS/mm2), of which 63% were CD8+. Dedifferentiated liposarcoma (DDLPS) showed the greatest enrichment, with a median count of 103 TILs/mm2. Other subtypes with notably high TIL counts include undifferentiated pleomorphic sarcoma (UPS; 38 TILs/mm2), myxofibrosarcoma (35 TILs/mm2), well-differentiated liposarcoma (26 TILs/mm2), osteosarcoma (21 TILs/mm2), and leiomyosarcoma (19 TILs/mm2). Without exception, translocation-associated sarcoma subtypes had very low levels of infiltrating lymphocytes (median 9 TILs/mm2). The subtype with the lowest levels of TILs was chondrosarcoma (0 TILs/mm2). PDL1 was present (≥1% tumor cell staining cutpoint) in 7% of samples, and stained ≥10% of tumor cells in 5.3% of samples. The subtypes that account for the majority of this PDL1 positivity are UPS (15/72), osteosarcoma (12/224), malignant peripheral nerve sheath tumor (9/74), myxofibrosarcoma (8/52), and DDLPS (6/60). Angiosarcoma had the highest proportion of positive cases (60%), but this was based on a small number of samples (n=5). PD1 lymphocyte staining was also low overall, with 14% of samples having at least one PD1+ TIL per mm2. The subtypes with the highest proportions of PD1+ cases were DDLPS (36/79), UPS (23/80), leiomyosarcoma (8/19), and epithelioid sarcoma (4/8).

Conclusions: Lymphocyte infiltration is predominantly limited to complex karyotype sarcomas and is rarely seen in translocation-associated sarcomas. The very highest levels of infiltrates are observed in DDLPS and the very lowest in chondrosarcoma. CD8+ effector T cells are the predominant lymphocyte subset present in sarcomas. PDL1 and PD1 expression are low overall for sarcomas, but some subtypes (UPS, DDLPS) appear to employ PDL1 immune blockade in up to 20% of cases. Further studies are pending to determine the significance of these findings for immunotherapy response.

Citation Format: Amanda R. Dancsok, David Thomas, Jean-Yves Blay, Robert G. Maki, Torsten O. Nielsen, Elizabeth G. Demicco. Lymphocytes and immune checkpoint biomarker expression in sarcomas [abstract]. In: Proceedings of the AACR Conference on Advances in Sarcomas: From Basic Science to Clinical Translation; May 16-19, 2017; Philadelphia, PA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(2_Suppl):Abstract nr B32.