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Application of molecular testing in clinical practice has led to significant advances in the classification of soft tissue sarcomas. Despite remarkable progress, there are still challenging cases that remain unclassified. In this study, we present an unusual spindle cell sarcoma arising in the abdominal cavity of a 37-year-old female. An extensive panel of immunostains was nonspecific for a line of differentiation and the tumor was subjected to targeted RNA sequencing for further classification. The findings showed a novel WWTR1::AFF2 fusion, which was further confirmed by break-apart FISH analysis for WWTR1 gene rearrangement. The tumor was attached to the wall of sigmoid colon and showed a highly cellular proliferation of plump spindle to epithelioid cells arranged in intersecting fascicles. Areas of extensive endometriosis were identified adjacent to the tumor. The immunoprofile was significant for reactivity with desmin, calponin, WT-1, ER, and PR, while negative for CD10, SMA, caldesmon, pan-keratin, ALK, CD117, and S100. The patient is alive and well after 11 months of follow-up. The exact histogenesis of this sarcoma remains unclear, however, the presence of adjacent endometriosis and coexpression of WT1/ER/PR raises the possibility of an unusual endometrioid stromal sarcoma, occurring outside the GYN tract. Additional cases are needed to establish the recurrent potential of this fusion event and to better define its pathogenesis and clinical behavior.

Aims: Recently, a novel isoform of anaplastic lymphoma kinase, with alternative transcription initiation (ALKATI ), has been described in melanoma and is susceptible to targeted ALK-inhibitor therapy. Clinical outcomes of patients with ALKATI mutated melanoma as well as correlation with immunohistochemical (IHC) methods has not yet been described. Methods and results: Clinicopathologic characteristics were abstracted for 324 patients with metastatic melanoma (MM). IHC, fluorescence in situ hybridization, and RNA based digital molecular analysis (NanoString Technologies) assays were performed on archival tissue from 173 stage III and 192 stage IV tumors. ALKATI was identified in 12.7% and 4.8% stage III and IV tumors, respectively. Discrete presentations of the ALKATI are seen: isolated ALKATI (N=20) and mixed ALKATI (combined ALKATI and ALKWT ; N=7). Isolated ALKWT expression (N=4) was seen with no ALK fusions. Stage III patients showed improved survival with ALKATI expression as compared to those with ALKWT or no expression [5-year survival 80% (95% CI: 57%-100%) versus 43% (95% CI: 34%-55%), p=0.013]. Clinicopathologic characteristics were not statistically significant. Strong diffuse cytoplasmic staining of ALK IHC (N=12), has a sensitivity of 52.2%, specificity 100%, PPV of 100% and NPV of 92.5% of detecting isolated ALKATI . Conclusion: Presence of ALKATI is a good prognostic indicator in MM. ALK IHC and digital molecular analysis can be incorporated into MM evaluation to identify patients with ALKATI for targeted therapy.

Primary aneurysmal bone cyst (ABC) is a benign multiloculated cystic lesion of bone that is defined cytogenetically by USP6 gene rearrangements. Rearrangements involving USP6 are promoter swaps, usually generated by fusion of the noncoding upstream exons of different partner genes with exon 1 or 2 of USP6, thus leading to transcriptional upregulation of full-length USP6 coding sequence. Testing for USP6 rearrangements is used diagnostically to distinguish it from secondary ABC and other giant cell-rich primary bone tumors. In this report, we present a case of a 16-year-old male with a primary ABC of the left distal femur. USP6 break apart fluorescence in situ hybridization was positive for a rearrangement and conventional chromosome analysis identified a reciprocal X;17 translocation. In order to identify the putative USP6 fusion partner, we performed RNA sequencing and uncovered a novel USP9X-USP6 promoter swap fusion. This result was confirmed by reverse transcription-polymerase chain reaction (RT-PCR) and by mate pair sequencing thus showing the utility of these alternative methodologies in identifying novel fusion candidates. Ubiquitin-specific protease 9X (USP9X), like USP6, encodes a highly conserved substrate-specific deubiquitylating enzyme. USP9X is highly expressed in a number of tissue types and acts as both an oncogene and tumor suppressor in several human cancers. We conclude that oncogenic activation of USP6 via USP9X promoter exchange represents a novel driver of primary ABC formation.

Aims Rhabdomyosarcomas of bone are extremely rare, with fewer than 10 reported cases. A very rare subtype of spindle cell/sclerosing rhabdomyosarcoma harbouring a FUS-TFCP2 fusion and involving both soft tissue and bone locations has been reported very recently. We report only the fourth case of this unusual, clinically aggressive rhabdomyosarcoma. Material and results A previously well 72-year-old male presented with a destructive lesion of the mandible. Morphological and immunohistochemical study of a needle biopsy and the subsequent resection showed a spindle cell rhabdomyosarcoma. RNA-seq, RT-PCR and FISH confirmed the presence of the FUS-TFCP2 fusion. Conclusions Spindle cell rhabdomyosarcomas carrying the FUS-TFCP2 fusion are very rare rhabdomyosarcoma variants with osseous predilection. The classification and differential diagnosis of this unusual molecular variant of spindle cell/sclerosing rhabdomyosarcoma are discussed.

BACKGROUND The cytologic diagnosis of urothelial carcinoma (UC) of the upper urothelial tract (UT) is challenging. Using the UroVysion probe set adds diagnostic value for the detection of bladder cancer in voided urine. In instrumented UT specimens, the authors encountered positive UT cytology and fluorescence in situ hybridization (FISH) cases that did not demonstrate subsequent UT carcinoma. METHODS The performance of cytology and FISH in the presence or absence of concomitant bladder cancer within 2 years was compared in 61 patients (112 samples) from 2003 through 2009. The mean follow-up was 3.2 years. The authors also compared the performance of near-tetrasomy versus hypertetrasomy. Biopsy confirmation of UTUC in 21 patients was considered the gold standard. RESULTS Cytology alone was found to be poorly sensitive (38%) but highly specific (89%) for the detection of UTUC. FISH was found to increase the sensitivity of cytology and decrease specificity. Tetrasomy FISH resulted in many false-positive cases. Other false-positive FISH results were likely due to the presence of bladder cancer cells contaminating the UT specimen. CONCLUSIONS Caution should be used when evaluating instrumented urine specimens of the UT from patients with a previous history of bladder carcinoma, and tetrasomy FISH results should not be interpreted as abnormal because it significantly lowers the specificity of the test. The combination of cytology and FISH appears to have good specificity while maintaining good sensitivity in evaluating UTUC when using modified scoring criteria for the appropriate patient population. Cancer (Cancer Cytopathol) 2014;122:459–467. © 2014 American Cancer Society.

BACKGROUND Patients diagnosed with primary sclerosing cholangitis (PSC) and dominant strictures often undergo endoscopic retrograde cholangiopancreatography with brush cytology to exclude or confirm the development of malignancy. Equivocal (atypical or suspicious) routine cytologic results may confound patient management decisions, especially in the absence of a mass on imaging. The objective of the current study was to identify independent predictors of malignancy in patients with PSC with an equivocal cytology diagnosis. METHODS Patients with PSC underwent brush cytology for routine cytology and fluorescence in situ hybridization (FISH) during endoscopy as per standard care. FISH slides were classified as polysomy if at least 5 cells displayed a gain of ≥ 2 probes. A retrospective search identified 102 patients without a mass lesion noted on initial imaging studies, an equivocal routine cytology, and ≥ 2 years of follow-up. RESULTS Of 102 patients, 30 (29%) with an equivocal cytology result developed cancer within 2 years. Serum carbohydrate antigen 19-9 (CA 19-9) levels ≥ 129 U/mL (hazard ratio [HR] 3.19; P = .001) and polysomy (HR 8.70; P

The detection of aneuploidy by fluorescence in situ hybridization (FISH) has revolutionized how laboratories diagnose cholangiocarcinoma and pancreatic adenocarcinoma using cytology specimens. Numerous clinical studies have demonstrated that FISH increases the diagnostic sensitivity of routine cytology for detecting pancreatobiliary tract malignancy with minimal decreases in clinical specificity. FISH also provides useful information in difficult clinical scenarios, including the assessment of patients with biliary strictures who have equivocal cytology results and the assessment of patients with primary sclerosing cholangitis who have clinical features suggestive of malignancy. The improved ability to detect pancreatobiliary tract cancers offers the possibility of earlier detection when patients are amenable to surgical intervention and can decrease health care costs by reducing the amount of clinical evaluation required to arrive at a cancer diagnosis. Cytopathology personnel should maintain familiarity with molecular cytology testing methodologies, because morphologic and aneuploidy assessment of tumors will continue to be an integral part of large-scale genome analyses of individual tumors. Cancer (Cancer Cytopathol) 2013;121:610-9. © 2013 American Cancer Society.

Barrett esophagus (BE) predisposes patients to esophageal adenocarcinoma, a cancer with one of the fastest rising incidence rates over the past decade and a highly lethal malignancy once it is symptomatic.1,2 It is believed that esophageal adenocarcinoma arises as the final step of a postulated sequential change in the metaplastic epithelium, progressing from low-grade dysplasia (LGD), to high-grade dysplasia (HGD), and finally carcinoma. HGD on histologic samples has been used as the most reliable clinical biomarker of potential carcinogenesis, with studies reporting variable rates of progression to esophageal carcinoma (range, 16%–59%).3–5 Interruption of the metaplasia-dysplasia-carcinoma sequence by ablating or resecting this at-risk mucosa has been proposed as a strategy to reduce the incidence of esophageal adenocarcinoma and has served as the rationale for the recommendation of esophagectomy for patients with HGD. Over the past few years, endoscopic therapy has emerged as an alternative to esophagectomy because of the significant mortality and morbidity associated with esophagectomy.6,7 Multiple modalities, including photodynamic therapy (PDT),8 argon plasma coagulation,9 and multipolar electrocoagulation10 in isolation and in combination with endoscopic mucosal resection (EMR),11,12 have been reported in the treatment of HGD. Variable success rates have been reported (range, 75%–90%). A randomized multicenter trial compared PDT with surveillance and treatment with omeprazole in patients with HGD. After a 24-month follow-up, complete ablation of HGD was noted in 77% of patients versus 39% in the omeprazole group. Thirteen percent of patients who received PDT plus omeprazole progressed to cancer compared with 28% of patients in the omeprazole group.13 This led to U.S. Food and Drug Administration approval for the use of PDT for the treatment of HGD in BE. We recently reported that long-term outcomes (overall mortality and cancer-free survival) were comparable between patients who underwent esophagectomy and patients who received PDT.14 Several genetic alterations have been described in BE. These include loss of cell cycle checkpoint genes, such as p16 and p53. Loss of these genes by allelic loss (deletions or loss of heterozygosity [LOH]), point mutations, or promoter hypermethylation (for p16) have been observed in a substantial number of patients with BE.15,16 Several other genetic alterations that involve gains/amplifications of proto-oncogenes (and growth factors/growth factor receptors) as well as changes in DNA content (as assessed by flow cytometry and image cytometry) also have been described.17,18 Currently, histology is used as the endpoint to define success with ablative therapy in HGD. However, recurrences and/or progression to cancer despite ‘successful’ ablation/resection are common. To our knowledge, predictors of recurrent dysplasia have not been defined. Few studies have assessed genetic alterations after ablation of BE19–21: those studies primarily assessed patients with predominantly nondysplastic BE (a category for which ablation currently is not recommended) rather than HGD (in which endoscopic ablation is gaining acceptance as an alternative to esophagectomy) by using techniques that lack long-term data on successful ablation. Studies also have raised concern about the appearance of cancer-associated biomarkers after ablation (in patients with nondysplastic BE)20: however, data are lacking on the clinical implication of this phenomenon in terms of the recurrence or progression of dysplasia. The role of biomarkers in defining response to PDT remains unclear. The correlation between histologic response and ‘biomarker response’ also is unknown. We hypothesized that patients who remain positive for genetic alterations despite achieving a histologic response to PDT would be at risk for recurrence of dysplasia. In this study, we used fluorescence in situ hybridization (FISH) to characterize genetic alterations that were present in patients with HGD and mucosal cancer before treatment with PDT and compared them with the alterations observed after PDT. In addition, we assessed the recurrence of dysplasia after initial histologic response and correlated those findings with post-PDT genetic alterations assessed by FISH.

BACKGROUND. Endometrial cytology sampling devices for direct uterine sampling have been shown in previous studies to be a reliable and relatively painless method for detecting endometrial lesions. The purpose of the current study was to determine the performance characteristics of endometrial cytology for the detection of malignancy and atypical hyperplasia using liquid-based cytology specimens collected with the Tao brush sampler. METHODS. Brushings of the endometrial cavity were obtained from 139 hysterectomy specimens before routine histopathologic evaluation. Cytology specimens were fixed in PreservCyt and processed using ThinPrep technology. Cytology diagnoses were classified as nondiagnostic, negative, atypical, or positive for malignancy. Histopathologic findings were used as the gold standard for determining the performance characteristics of cytology. RESULTS. Histopathologic results from the 139 patients included 81 (58%) endometrial cancers, 7 (5%) complex hyperplasias with atypia, 2 (1%) complex hyperplasias without atypia, and 49 (35%) patients with benign histology. The number of specimens diagnosed cytologically as positive, atypical, negative, or nondiagnostic was 60 (43%), 40 (29%), 37 (27%), and 2 (1%) specimens, respectively. The overall sensitivity and specificity of cytology for detecting endometrial cancer and atypical hyperplasia were 95% and 66% when atypical cytology specimens were considered positive. CONCLUSIONS. The results of the current study indicate that direct endometrial sampling by liquid-based endometrial cytology collected with the Tao brush sampler produces specimens that contain cellular material that may be identified as endometrial cancer or atypical hyperplasia. Both atypical and positive cytology diagnoses are indicators for triage to more specific methods of diagnosis. Cancer (Cancer Cytopathol) 2008. © 2008 American Cancer Society

The purpose of this study was to assess the performance of ThinPrep UroCyte filters, which were designed specifically for the preparation of slides for fluorescence in situ hybridization (FISH) analysis of urine specimens. One hundred urine specimens were evenly split, and one portion was utilized to prepare a slide with the UroCyte filter method and the other portion was used to prepare a slide with a manual dropping method. All 17 of the 100 specimens identified as positive by the manual method were also identified as positive with the UroCyte method. No significant differences were noted in the percentage of chromosomally abnormal cells (P = 0.227), cellularity (P = 0.857), signal quality (P = 0.816), and DAPI counterstain quality (P = 0.369) between the two methodologies. The average time taken to prepare a batch of 10 slides using the UroCyte method, and that using manual method was 103 min (10.3 min/case) and 194 min (19.4 min/case), respectively. This study suggests that the UroCyte filter method of preparing slides for FISH analysis reduces the time required to prepare these slides with overall results that are similar to the currently utilized manual dropping method.

BACKGROUND. Interphase fluorescence in situ hybridization (FISH) is a powerful tool for detecting chromosome and locus-specific changes in tumor cells. We developed a FISH-based assay to detect genetic changes in bronchial washing specimens of lung carcinoma patients. METHODS. The assay uses a mixture of fluorescently labeled probes to the centromeric region of chromosome 1 and to the 5p15, 8q24 (site of the c-myc gene), and 7p12 (site of the EGFR gene) loci to assess cells in bronchial washing specimens for chromosomal abnormalities indicative of lung carcinoma. The FISH assay was performed on 74 specimens that had been assessed previously for evidence of malignancy by routine cytology with Pap staining. RESULTS. Forty-eight patients had histologically confirmed lung carcinoma and 26 patients had a clinical diagnosis that was negative for lung carcinoma. FISH analysis was performed without knowledge of the patient's clinical information. The finding of six or more epithelial cells with gains of two or more chromosome regions was considered a positive FISH result (i.e., evidence of malignancy). The sensitivity of FISH for the detection of lung carcinoma was 82% in this set of specimens compared with a 54% sensitivity by design for cytology (FISH vs. cytology, P = 0.007). FISH detected 15 of 18 specimens that were falsely negative by cytology. The specificities of FISH and cytology were 82% and 100%, respectively, and were not significantly different (P = 0.993). CONCLUSIONS. The data indicate a potential utility of the FISH assay as an adjunct to bronchial washing cytology in routine clinical practice.

BACKGROUND Defective DNA mismatch repair (MMR) appears to be rare in nonsmall cell carcinomas of the lung. Defective DNA MMR results from genetic or epigenetic alterations that inactivate the DNA MMR genes hMLH1 or hMSH2, and rarely hMSH6. The loss of normal DNA MMR is thought to promote tumorigenesis by accelerating the accumulation of mutations in oncogenes and tumor suppressor genes. Inactivation of hMLH1, hMSH2, and hMSH6 is observed as a loss of expression of these proteins by immunohistochemistry. Bronchioloalveolar carcinoma is a subtype of adenocarcinoma with distinctive clinical and pathologic features. MATERIALS AND METHODS. An immunohistochemical study was performed on paraffin embedded sections of 33 bronchioloalveolar carcinomas (20 nonmucinous and 13 mucinous) for hmlh1, hmsh2, and hmsh6 proteins. RESULTS All the tumors showed normal expression of hmlh1, hmsh2, and hmsh6. CONCLUSIONS These findings suggest that defective DNA MMR due to inactivation of hMLH1, hMSH2, or hMSH6 does not play a significant role in the pathogenesis of bronchioloalveolar carcinomas. Cancer 2001;92:2898–901. © 2001 American Cancer Society.

Endometrial cancer is the second most common malignancy in patients with hereditary nonpolyposis colorectal cancer (HNPCC). The age at diagnosis of HNPCC-associated endometrial cancer is approximately 15 years younger than for sporadic endometrial cancer. Our current study was undertaken to determine the frequency of microsatellite instability (MSI) and absence of hMLH1 or hMSH2 protein expression in young patients with endometrial carcinoma and to correlate these findings with histopathologic and clinical features. Endometrial carcinoma from 62 women (23-52 years, median age 46) were assessed for MSI. Twenty-one of the 62 (34%) tumors demonstrated MSI. Of the 21 tumors demonstrating MSI, 12 showed an absence of hMLH1 expression, 4 showed an absence of hMSH2 expression, and 5 demonstrated normal expression of both proteins. All 41 tumors without MSI demonstrated normal hMLH1 and hMSH2 expression. Two patients with MSI tumors fulfilled the Amsterdam criteria for HNPCC, while 2 had histories suggestive of HNPCC. None of the patients with tumors without MSI had a personal or family cancer history suggestive of HNPCC. The MSI phenotype was associated (p < 0.05) with high FIGO stage and grade, cribriform growth pattern, mucinous differentiation and necrosis. Our findings suggest that the frequency of HNPCC in young endometrial cancer patients is relatively low when compared with the frequency of HNPCC in young colorectal cancer patients. Defects of the MMR proteins hMSH2 or hMLH1 account for MSI in most but not all endometrial cancers from young patients.

Chromosomal abnormalities are frequent in most cervical cancers. Amplifications of both the 3q26 (TERC) and 8q24 (MYC) loci have been shown to be prevalent in both high-grade lesions and invasive cervical carcinoma. Most of these studies have looked at either the histological sample or at the entire cytological population of cells. We have developed a Papanicolaou (Pap) destaining method that allows for the accurate analysis of individual cells that were previously identified by cytopathology as dysplastic. The application of fluorescence in situ hybridization (FISH) was then implemented to determine the chromosomal status of the dysplastic cells in the samples and correlate the two events. Chromosomal abnormality is over a thousand times more frequent in dysplastic cells compared with their morphologically normal counterparts.