Whole-genome sequencing of a malignant granular cell tumor with metabolic response to pazopanib

Granular cell tumor of the breast: A case report and review of literature

BACKGROUND

Granular cell tumor (GCT) of the breast (GCTB) is a rare neoplasm that can exhibit malignant characteristics both clinically and radiologically. This tumor can also coexist and colocalize with breast carcinoma.

CASE SUMMARY

We present a patient with this uncommon tumor and discuss the diagnostic and therapeutic approaches in order to further the knowledge of GCTB and prevent misdiagnosis and overtreatment. The characteristics of the tumor, methods of diagnosis, therapy and postoperative pathological outcomes were analyzed, and relevant literatures of GCTs were reviewed. The patient underwent surgery after core needle biopsy, and the excised neoplasm was sent for pathological examination. Histological analysis revealed nests of cells with abundant pink granular cytoplasm, confirming the diagnosis of GCTB.

CONCLUSION

As manifestations of GCT and malignancy can mimic each other, a careful histological examination is essential before major surgery. Treatment consisting of complete excision with close clinical follow-up is recommended.

Antiangiogenics in Malignant Granular Cell Tumors: Review of the Literature

Granular cell tumors (GCT) represent 0.5% of all soft tissue sarcomas (STS), and when metastatic, they exhibit aggressive behavior and determine limited survival. Metastatic GCTs are relatively chemo-resistant; however, there is growing evidence of the benefit of using pazopanib and other targeted therapies in this histology. This is a review of the role of pazopanib and other targeted therapies in the treatment of GCTs, along with some insights on pathology and molecular biology described in GCTs. From 256 articles found in our search, 10 case-report articles met the inclusion criteria. Pazopanib was the most employed systemic therapy. The median reported time on therapy with pazopanib was seven months. Eight out of ten patients (80%) experienced disease control with pazopanib, while four out of ten (40%) patients achieved an objective RECIST response. Molecular studies suggested that antitumoral effects of pazopanib in GCT might be due to a loss-of-function of ATP6AP1/2 genes which consequently enhance signaling through several molecular pathways, such as SFKs, STAT5a/b, and PDGFR-β. Other reported targeted therapies for malignant GCTs included pazopanib in combination with crizotinib, which showed disease control for four months in one patient, and a PI3K inhibitor which achieved disease control for nine months in another patient. Dasatinib and megestrol were ineffective in two other different patients. Pazopanib has been demonstrated to be active in advanced GCTs and may be considered as a preferable treatment option.

Molecular Characterization of Multifocal Granular Cell Tumors

Granular cell tumors (GrCT) were recently found to be driven by inactivating mutations in vacuolar H + -ATPase (V-ATPase) genes, most frequently ATP6AP1 and ATP6AP2 . Multifocal presentation is present in ~10% of cases; however, the relationship between multifocal tumors in a given patient has not been elucidated. We hypothesized that benign-appearing multifocal GrCT are molecularly distinct whereas paired primary and metastatic malignant GrCT share identical mutations. To test this, we conducted targeted next-generation sequencing of the V-ATPase genes in multifocal GrCT and whole exome and Sanger sequencing in paired primary and metastatic malignant GrCT. Thirteen patients with≥2 GrCT were identified (total of 43 tumors). Forty-two tumors were successfully sequenced. Tumors showed somatic mutations in 3 of the 10 targeted genes in 32 of 42 samples (76%). Twenty tumors showed mutations in ATP6AP1 (48%), 10 tumors had mutations in ATP6AP2 (24%), and 2 tumors showed mutations in ATP6V0A4 (5%). Predicted loss-of-function mutations were found in ATP6AP1 in 17 tumors (40%), in ATP6AP2 in 10 tumors (24%), and in ATP6V0A4 in 1 tumor (2%). In 8 patients, mutually exclusive mutations were detected in at least 2 tumors per patient. Two patients were identified with malignant GrCT with material available from both primary and metastatic sites. Identical frameshift insertions were found in ATP6AP1 in 1 case and the second case showed identical nonsense mutations in ATP6AP1 . In conclusion, multifocal GrCT within an individual patient are molecularly distinct, while paired primary and metastatic GrCT share identical mutations.

A Rare Case of Multifocal Asynchronous Benign Granular Cell Tumors with PIK3CA Subclonal Mutation Identified in One Tumor by Next-Generation Sequencing

Granular cell tumor (GCT) is a benign neuroectodermal tumor typically in the dermis or subcutis, although deep soft tissues and organs are occasionally involved. Multifocal GCTs are estimated to occur as many as 10% of patients. A 40-year-old female presented with multiple GCTs asynchronously involving various body sites including gastrointestinal, gynecologic, breast, urinary, and soft tissue systems. Pathologic examinations suggested benign GCTs. TruSight Tumor 170 next-generation sequencing (NGS) analysis performed on four resected tumors revealed subclonal mutation of PIK3CA p.H1047R identified in the esophageal GCT but not in the right vulva or the two cecal GCTs, suggesting that each is a primary tumor with a distinct genetic profile, rather than metastasis. PIK3CA p.H1047R is a common mutation in many cancers. Our benign GCT case demonstrates PIK3CA mutation with a low mutant allele frequency of 7%, which may represent an evolving subclone and might confer a more aggressive behavior.

Granular cell tumors of the urethra

Granular cell tumors (GCTs) are a rare type of mesenchymal tumors that are histologically derived by Schwann cells and rise within soft tissues such as skin and mucosal surfaces. Differentiation between benign and malignant GCTs is often difficult and relies on their biological behavior and metastatic potential. While there are no standard guidelines for management, upfront surgical resection, whenever feasible, is key as a definitive measure. Systemic therapy is often limited by poor chemosensitivity of these tumors; however, accumulating knowledge of their underlying genomic landscape has opened some opportunities for targeted approaches, for example, the vascular endothelial growth factor tyrosine kinase inhibitor pazopanib, which is already in clinical use for the treatment of many types of advanced soft tissue sarcomas.

Malignant granular cell tumors: Combining cytological and pathological findings for a definitive diagnosis

Malignant granular cell tumors (GCTs) account for less than 2% of all GCTs and mainly occur in the deep soft tissue of the thigh or trunk. Malignant GCTs are highly aggressive tumors with high rates of recurrence and metastasis. In this brief report, we describe a rare case of malignant GCT in a 64-year-old Japanese man who presented with a 14 × 20 cm mass in the left inguinal region. The cytologic findings of fine-needle aspiration (FNA) revealed atypical epithelial-like granular cells with granular substance in the background, which was difficult to differentiate from apocrine carcinoma or melanoma. The immunohistochemistry (IHC) findings of the needle biopsy revealed that the tumor cells were positive for S-100 and lysosomal marker CD68 which was suggestive of a GCT. However, the presence of crush artifacts made it challenging to identify cellular atypia, which is a characteristic of malignant tumor. Taken together, the FNA and needle biopsy results were suggestive of malignant GCT. The importance of preoperative diagnosis of malignant GCT is well known, but few reports have described its cytological findings. In our brief report, we show that combining cytological FNA and biopsy findings with IHC findings achieves an accurate diagnosis of malignant GCT.

Atypical granular cell tumor of the urinary bladder: A case report

BACKGROUND

Granular cell tumor (GCT) is a neurogenic tumor mainly occurring in the head and neck. GCT in the genitourinary system is extremely rare and only sporadic cases of urinary bladder GCT have been reported. Most urinary bladder GCT cases are benign and only two malignant cases have been reported. Due to its rarity, no consensus criteria for the treatment of urinary bladder GCT are available at present.

CASE SUMMARY

A 62-year-old Chinese woman was found to have a urinary bladder tumor without any clinical manifestations on physical examination. Cystoscopy revealed a semispherical shaped lesion measuring approximately 4.0 cm in diameter at the junction of the left wall and roof of the bladder, which was covered with normal bladder mucosa. Computed tomography scan demonstrated a high-density lesion on the left wall of the bladder, measuring approximately 2.9 cm × 2.4 cm with clear boundaries. Contrast-enhanced pelvic magnetic resonance imaging revealed a space-occupying lesion on the left wall of the bladder (non-mucosal origin/ external pressure), which was preliminarily suspected to be a desmoplastic fibroma or leiomyoma. In the context of the above findings, a pre-operative diagnosis of bladder leiomyoma was made. The patient consequently underwent a laparoscopic partial cystectomy. The resected bladder mass looked yellowish and well-demarcated, measuring 4.0 cm × 3.5 cm and infiltrated the muscular layer. The diagnosis of urinary bladder GCT was finally made by postoperative pathology, with positive immunohistochemical S-100 staining and negative pancytokeratin. The patient has been followed for 6 mo so far, with no tumor recurrence detected.

CONCLUSION

This case highlights the biological feature and differential diagnosis of urinary bladder GCT at the pathological and molecular levels. Transurethral resection of the bladder tumor and partial cystectomy are recommended in most urinary bladder GCT cases, while radical cystectomy is recommended in malignant cases.

Granular cell tumor of the cecum: Case report of mini invasive surgical resection and review of the literature

Introduction and importance

Granular Cell Tumor (GCT) is a rare lesion with unclear histogenesis, predominantly described as a skin lesion. Visceral localization of GCT is even more rare with few cases reported in the literature. Nowadays GCT guidelines are not available.

Case presentation

A 45-year-old Caucasian woman was visited in our surgical department for significant weight loss (about 30 kg) during the previous 6 months. Colonoscopy showed a caecal polypoid lesion that was resected with a diatermic loop and classified as GCT. Microscopically, the neoplasm partially involved the mucosa and diffusely the submucosa, extending to the endoscopic resection margins. Because of the high risk of perforation during endoscopic radicalisation attempt, the patient underwent ileocecal resection. The postoperative course was uneventful.

Clinical discussion

GCT is a rare soft tissue neoplasm probably deriving from Schwann cells. The main treatment for GCT is an endoscopic mucosal/submucosal resection. Nevertheless, a radicalization of the lesion through a surgical attempt should be preferred when the endoscopic procedure is linked to a high risk of perforation.

It is important to distinguish GCT from other polypoid lesions of the colon, due to its malignant potential (about 2%) and its relapsing capacity when margins are involved.

Conclusion

GTC is a rare neoplasm and as its diagnosis is made only histologically, it should be included in differential diagnosis of colonic polypoid lesions. Surgery can be considered the best choice when an endoscopic attempt of GCT lesions is linked to a high risk of colon perforation.

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Granular Cell Tumor (GCT) is a rare lesion with unclear histogenesis.

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Visceral localizations are even more rare that skin lesions.

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GCT should be distinguished from all other polypoid lesions.

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GCT epidemiology is limited due to its unknown origin and rare occurrence.

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Some specialists recommend a surgical resection for lesions >2–5 cm.

Recent developments in gastroesophageal mesenchymal tumours

The pathologist's approach to gastroesophageal mesenchymal tumours has changed dramatically during the last 25 years. In particular, gastrointestinal stromal tumour (GIST) has evolved from a wastebasket mesenchymal tumour category to a precisely defined entity with an increasingly detailed genetic subclassification. This subclassification has brought gastrointestinal mesenchymal neoplasia into the realm of precision medicine, with specific treatments optimised for particular genetic subtypes. Molecular genetic data have also greatly improved our understanding of oesophageal mesenchymal tumours, including the discovery that so-called 'giant fibrovascular polyps' in fact represent a clinically distinctive presentation of well-differentiated liposarcoma. Here, we will focus on gastroesophageal mesenchymal tumours for which there have been recent developments in classification, molecular genetics or tumour biology: granular cell tumour, 'giant fibrovascular polyp'/well-differentiated liposarcoma, plexiform fibromyxoma, gastroblastoma and, of course, GIST.

Whole-exome sequencing reveals novel vacuolar ATPase genes' variants and variants in genes involved in lysosomal biology and autophagosomal formation in oral granular cell tumors

BACKGROUND

Granular cell tumors (GCTs) are rare neuroectodermal soft tissue neoplasms that mainly affect the skin of the upper limbs and trunks and the oral cavity. GCTs are derived from Schwann cells and, ultrastructurally, their intracytoplasmic granules are considered autophagosomes or autophagolysosomes and are consistent with myelin accumulation.

METHODS

In this study, a convenience set of 22 formalin-fixed, paraffin-embedded samples of oral GCTs, all but one sample located at the tongue, was screened for mutations by whole-exome (WES) or targeted sequencing.

RESULTS

WES revealed two novel variants in genes of the vacuolar ATPase (V-ATPase) complex: ATP6AP1 frameshift c.746_749del, leading to p.P249Hfs*4, and ATP6V1A non-synonymous c.G868A, leading to p.D290N. Each of these mutations occurred in one case. With regard to the samples that were wild type for these V-ATPase variants, at least two samples presented variants in genes that are part of endosomal/lysosomal/autophagosomal networks including ABCA8, ABCC6, AGAP3, ATG9A, CTSB, DNAJC13, GALC, NPC1, SLC15A3, SLC31A2, and TMEM104.

CONCLUSION

Although the mechanisms involved in oral GCT initiation and progression remain unclear, our results suggest that oral GCTs have V-ATPase variants similarly to GCTs from other tissues/organs, and additionally show variants in lysosomes/endosomes/autophagosomal genes.

Recurrent Unresectable Malignant Granular Cell Tumor With Response to Pazopanib

Malignant granular cell tumors (MGCTs) are rare and aggressive variants of granular cell tumors. They usually involve the head and neck region, skin and soft tissues. There are no standard therapeutic guidelines for management; however, surgical resection, whenever feasible, is considered to be first line. We report a patient with recurrent unresectable MGCT of lower lip who responded to pazopanib monotherapy. This drug has been recently approved for the treatment of advanced soft tissue sarcomas. It is a potent oral tyrosine kinase inhibitor and acts on multiple receptors, including vascular endothelial growth factor receptor (VEGFR), epidermal growth factor receptor (EGFR), c-kit, platelet-derived growth factor receptor (PDGFR) and fibroblast growth factor receptor (FGFR). Due to the overexpression of multiple genes by the tumor and multiple targets of this drug, it is difficult to establish the mechanism of action responsible for disease response. 

Granular cell tumour of the cavernous sinus: A rare cause of secondary trigeminal neuralgia

Background: Cavernous sinus tumours comprise 0.1-0.2% of all intracranial tumours, and are most commonly meningiomas or schwannomas. Central nervous system and cranial nerve granular cell tumours (GCTs) are extremely rare. We report the tenth case of a GCT arising from a cranial nerve, and the second case reported in a cavernous sinus location, and review the literature. Clinical presentation: A 67-year-old man presented with right sided trigeminal neuralgia. Imaging findings suggested a trigeminal schwannoma and he was treated with CyberKnife radiosurgery. Over a period of 41 months follow up, there was a progression in both symptoms and imaging findings, requiring debulking surgery. Histopathology identified a GCT. Conclusions: This is the first case of a cranial nerve GCT treated with stereotactic radiosurgery. Trigeminal nerve GCTs are a rare differential in cases of presumed schwannomas.

Efficient identification of neoantigen-specific T-cell responses in advanced human ovarian cancer

Background

Efficient identification of neoantigen-specific T-cell responses in epithelial ovarian cancer (EOC) remains a challenge. Existing investigations of spontaneous T-cell response to tumor neoepitope in EOC have taken the approach of comprehensive screening all neoantigen candidates, with a validation rate of 0.5–2%.

Methods

Whole-exome and transcriptome sequencing analysis of treatment-naive EOC patients were performed to identify neoantigen candidates, and the immunogenicity of prioritized neoantigens was evaluated by analyzing spontaneous neoantigen-specfic CD4⁺ and CD8⁺ T-cell responses in the tumor and/or peripheral blood. The biological relevance of neoantigen-specific T-cell lines and clones were analyzed by evaluating the capacity of autologous ovarian tumor recognition. Genetic transfer of T-cell receptor (TCR) from these neoantigen-specific T-cell clones into peripheral blood T-cells was conducted to generate neoepitope-specific T-cells. The molecular signature associated with positive neoantigen T-cell responses was investigated, and the impacts of expression level and lymphocyte source on neoantigen identification were explored.

Results

Using a small subset of prioritized neoantigen candidates, we were able to detect spontaneous CD4⁺ and/or CD8⁺ T-cell responses against neoepitopes from autologous lymphocytes in half of treatment-naïve EOC patients, with a significantly improved validation rate of 19%. Tumors from patients exhibiting neoantigen-specific T-cell responses exhibited a signature of upregulated antigen processing and presentation machinery, which was also associated with favorable patient survival in the TCGA ovarian cohort. T-cells specific against two mutated cancer-associated genes, NUP214 and JAK1, recognized autologous tumors. Gene-engineering with TCR from these neoantigen-specific T-cell clones conferred neoantigen-reactivity to peripheral T-cells.

Conclusions

Our study demonstrated the feasibility of efficiently identifying both CD4⁺ and CD8⁺ neoantigen-specific T-cells in EOC. Autologous lymphocytes genetically engineered with tumor antigen-specific TCR can be used to generate cells for use in the personalized adoptive T-cell transfer immunotherapy.

Electronic supplementary material

The online version of this article (10.1186/s40425-019-0629-6) contains supplementary material, which is available to authorized users.

Comparison of SureSelect and Nextera Exome Capture Performance in Single-Cell Sequencing

BACKGROUND

Advances in single-cell sequencing provide unprecedented opportunities for clinical examination of circulating tumor cells, cancer stem cells, and other rare cells responsible for disease progression and drug resistance. On the genomic level, single-cell whole exome sequencing (scWES) started to gain popularity with its unique potentials in characterizing mutational landscapes at a single-cell level. Currently, there is little known about the performance of different exome capture kits in scWES. Nextera rapid capture (NXT; Illumina, Inc.) has been the only exome capture kit recommended for scWES by Fluidigm C1, a widely accessed system in single-cell preparation.

RESULTS

In this study, we compared the performance of NXT following Fluidigm's protocol with Agilent SureSelectXT Target Enrichment System (AGL), another exome capture kit widely used for bulk sequencing. We created DNA libraries of 192 single cells isolated from spheres grown from a melanoma specimen using Fluidigm C1. Twelve high-yield cells were selected to perform dual-exome capture and sequencing using AGL and NXT in parallel. After mapping and coverage analysis, AGL outperformed NXT in coverage uniformity, mapping rates of reads, exome capture rates, and low PCR duplicate rates. For germline variant calling, AGL achieved better performance in overlap with known variants in dbSNP and transition-transversion ratios. Using calls from high coverage bulk sequencing from blood DNA as the golden standard, AGL-based scWES demonstrated high positive predictive values, and medium to high sensitivity. Lastly, we evaluated somatic mutation calling by comparing single-cell data with the matched blood sequence as control. On average, 300 mutations were identified in each cell. In 10 of 12 cells, higher numbers of mutations were identified using AGL than NXT, probably caused by coverage depth. When mutations are adequately covered in both AGL and NXT data, the two methods showed very high concordance (93-100% per cell).

CONCLUSIONS

Our results suggest that AGL can also be used for scWES when there is sufficient DNA, and it yields better data quality than the current Fluidigm's protocol using NXT.

Analysis of mutations in primary and metastatic synovial sarcoma

Synovial sarcoma is the most common pediatric non-rhabdomyosarcoma soft tissue sarcoma and accounts for about 8-10% of all soft tissue sarcoma in childhood and adolescence. The presence of a chromosomal translocation-associated SS18-SSX-fusion gene is causally linked to development of primary synovial sarcoma. Metastases occur in approximately 50-70% of synovial sarcoma cases with yet unknown mechanisms, which led to about 70-80% mortality rate in five years. To explore the possibilities to investigate metastatic mechanisms of synovial sarcoma, we carried out the first genome-wide search for potential genetic biomarkers and drivers associated with metastasis by comparative mutational profiling of 18 synovial sarcoma samples isolated from four patients carrying the primary tumors and another four patients carrying the metastatic tumors through whole exome sequencing. Selected from the candidates yielded from this effort, we examined the effect of the multiple missense mutations of ADAM17, which were identified solely in metastatic synovial sarcoma. The mutant alleles as well as the wild-type control were expressed in the mammalian cells harboring the SS18-SSX1 fusion gene. The ADAM17-P729H mutation was shown to enhance cell migration, a phenotype associated with metastasis. Therefore, like ADAM17-P729H, other mutations we identified solely in metastatic synovial sarcoma may also have the potential to serve as an entry point for unraveling the metastatic mechanisms of synovial sarcoma.