Unlocking the potential of organoids in cancer treatment and translational research: An application of cytologic techniques.

Patient-derived organoid models hold promise for advancing clinical cancer research, including diagnosis and personalized and precision medicine approaches, and cytology, in particular, plays a pivotal role in this process. These three-dimensional multicellular structures are heterogeneous, potentially maintain the cancer phenotype, and conserve the genomic, transcriptomic, and epigenomic patterns of the parental tumors. To ensure that only tumor tissue is used for organoid development, cytologic validation is necessary before initiating the process of organoid generation. Here, we explore the technology of tumor organoids and discuss the fundamental application of cytology as a simple and cost-effective approach toward organoid development. We also underscore the potential application of organoid development in drug efficacy studies for lung cancer and head and neck tumors. Additionally, we stress the importance of using fine-needle aspiration to generate tumoroids.

Optimal carcinoembryonic antigen (CEA) cutoff values in the diagnosis of neoplastic mucinous pancreatic cysts differ among assays.

AIM: Pancreatic cyst fluid carcinoembryonic antigen (CEA) is a pivotal test in the diagnosis and management of neoplastic mucinous cysts (NMC) of the pancreas. Cyst fluid CEA levels of 192 ng/mL have been widely used to identify NMC. However, CEA values are unique to and significantly differ between individual assays with various optimal cutoffs reported in the literature for NMC. Here, we investigate the optimal CEA cut-off value of pancreatic cysts from two different assays to identify differences in thresholds. METHODS: Pancreatic cyst fluid CEA levels, CEA assay platform (Beckman Dxl (BD) or Siemens Centaur XP (SC)), and clinical/pathological information were retrospectively collected. Cases were categorised into either NMC or non-NMC. Optimal CEA cut-off values were calculated via a receiver operator characteristic curve. Cut-off values were then identified separately by assay platform. RESULTS: In total, 149 pancreatic cystic lesions with concurrent CEA values (SC: n=47; BD: n=102) were included. Histological correlation was available for 26 (17%) samples. The optimal CEA cut-off value for all samples at the study institution was 45.9 ng/mL (area under the curve (AUC)=86, Sn=85.7%, Sp=73.8%). When analysed separately by CEA assay, the cut-off values were 45.9 ng/mL (AUC=84.27, Sn=89.7%, Sp=71.4%) for BD and 24.4 ng/mL (AUC=77, Sn=81.8%, Sp=75%) for SC (p=0.48). CONCLUSIONS: This study showed an optimal pancreas cyst CEA cut-off threshold of 45.9 ng/mL, which is lower than commonly cited literature with different cutoffs on the two separate platforms (BD: 45.9 ng/mL, SC: 24.4 ng/mL).

Diagnostic implication of extracellular mucin in pancreatic/biliary brushing and stent cytology.

BACKGROUND: Pancreatic and/or biliary (PB) brushing is commonly used to rule out malignant strictures. Many studies have attempted to characterize cytomorphologic characteristics of brushing and stent cytology. However, scant literature exists on the diagnostic implication (DI) of thick extracellular mucin (ECM) indicative of neoplasm in these samples. This study was aimed at reviewing the DI of thick ECM in PB brushing and stent cytology. METHODS: A retrospective search of consecutive cytologic samples of PB brushings/stents with corresponding surgical pathology or relevant clinical information over a 1-year period was performed. Blinded review of the slides was performed by two cytopathologists. The slides were assessed for the presence, quantity, and quality of ECM. The results were analyzed for statistical significance with the Fisher exact and χ2 tests. RESULTS: One hundred ten cases were identified from 63 patients. Twenty-two cases (20%) were PB brushings only without a prior stent. The remaining 88 cases (80%) had a preexisting stent for symptomatic obstruction. Fourteen of 22 cases (63%) without prior stents and 67 of 88 poststented cases (76%) were nonneoplastic (NN) upon follow-up. ECM was present more frequently in neoplastic cases than in NN cases (p = .03). Among NN cases (n = 87), poststented samples showed more evidence of ECM than prestented samples (15% vs. 45%, p = .045). Identical thick ECM was observed in NN poststent and main-duct intraductal papillary neoplasm samples. CONCLUSIONS: Although ECM was frequently seen in neoplastic cases, NN cases showed increased evidence of thick ECM among poststented samples. Thick ECM may be common in stent cytology, regardless of the underlying biologic process.

Diagnostic features of low- and high-grade mucinous neoplasms in pancreatic cyst FNA cytology.

BACKGROUND: Pancreatic cyst cytology evaluates for neoplastic mucin and epithelial grade. This study describes cytological features of low- and high-grade mucinous neoplasms (MNs) using gastrointestinal contaminants for comparison. METHODS: Histologically confirmed pancreatic cystic neoplasms were reviewed by a panel of cytopathologists to identify which, among 26 selected cytologic features, correlate significantly with low- and high-grade MN. A test for greater than or equal to four of eight high-grade features (three-dimensional architecture, high nuclear:cytoplasmic ratio, moderate nuclear membrane abnormalities, loss of nuclear polarity, hyperchromasia, >4:1 nuclear size variation in one cluster, karyorrhexis, and necrosis) was assessed for identifying a high-grade neoplasms. Additional characteristics of the cohort such as cyst fluid carcinoembryonic antigen results, molecular testing, Papanicolaou Society of Cytopathology classification, and select high-risk clinical features are described. RESULTS: Endoscopic ultrasound fine-needle aspirations from 134 MN and 17 serous cystadenomas containing gastrointestinal contaminants were included. The MN consisted of 112 (84%) intraductal papillary MNs (low-grade = 69, 62%; high-grade = 24, 21%; and invasive = 19, 17%) and mucinous cystic neoplasms (low-grade = 20, 90%; high-grade = 2, 10%). Half had greater than five clusters of epithelium for analysis. Compared with gastrointestinal contaminants, mucin from MN was thick and colloid-like (40% vs. 6%, p < .01), covered >20% of the smear area (32% vs. none, p < .01), and contained histiocytes (46% vs. 18%, p = .04). Greater than or equal to four of eight select high-grade features was present in 36% of high-grade MN with sensitivity 37% and 98% specificity. CONCLUSION: Colloid-like features, >20% of smear, and histiocytes correlated with MN. Testing for greater than or equal to four high-grade features had low sensitivity and high specificity for high-grade MN.

Analysis of a pre-2017 follicular variant papillary thyroid carcinoma cohort reclassified as noninvasive follicular thyroid neoplasm with papillary-like features (NIFTP): an 11-year retrospective single institution experience.

INTRODUCTION: Noninvasive follicular thyroid neoplasm with papillary-like features (NIFTP), represents a distinct class of thyroid neoplasms with very low risk of adverse outcome and a set of strict histologic criteria. Introduction of NIFTP as a non-cancer has had an appreciable decrease in risk of malignancy and body of literature on this entity continues to grow. In this study, we reviewed clinical, fine-needle aspiration cytology (FNAC), imaging, and molecular findings of histologically proven NIFTPs at our institution. MATERIALS AND METHODS: Thyroid resections during an 11-year period, with histologic diagnosis of follicular variant of papillary thyroid carcinoma (FVPTC), were retrospectively reviewed to identify NIFTP. Ultrasonographic appearance, FNA findings, and molecular findings were also reviewed. RESULTS: Of 244 cases of FVPTC identified, 74 (30%) cases were reclassified as NIFTP. Mean tumor size was 2.5 cm. Of 33 patients with lymph node dissection, none had lymph node metastases. On imaging, 36 NIFTP (49%) showed vascularity, 25 (33%) were isoechoic to hypoechoic, there were calcifications in 14 cases (19%), and 7 cases (9%) showed a hypoechoic rim. Bethesda III/IV was the most common interpretation rendered on FNAC (31%). Seven cases had NRAS mutations and 1 case had BRAF V600E mutation. The remaining cases were either negative for BRAF V600E or had no identifiable molecular alterations. CONCLUSIONS: A significant percentage of tumors previously diagnosed as FVPTC were reclassified as NIFTP. This tumor cannot be reliably diagnosed preoperatively on FNAC, shows no characteristic features on ultrasound and has low suspicion of malignancy. BRAF V600E mutations are infrequent in NIFTP.

Ameloblastoma with adenoid features: Case report with cyto-histopathologic correlation and molecular findings.

Ameloblastomas are benign but locally aggressive odontogenic tumors that commonly present as expansile lesions in the tooth-bearing areas. Fine-needle aspiration (FNA) biopsies of ameloblastomas are rare in clinical practice, and only a handful of case reports and series have described their cytologic features. We present the case of a 70-year-old woman with a large and disfiguring maxillary sinus soft tissue mass sampled via transcutaneous FNA. Aspirate smears were composed of small clusters of cohesive and monotonous basaloid cells. The accompanying cellblock showed similar clusters of basaloid cells in gland-like, or "adenoid," configurations, eliciting a differential diagnosis that included sinonasal and salivary gland neoplasms. Excisional surgery material was consistent with ameloblastoma with adenoid morphology. Next-generation sequencing (NGS) analysis demonstrated FGFR2 and SMO pathogenic variants. This case exemplifies several uncommonly described features of ameloblastomas in cytology, including cyto-histologic correlation, adenoid morphology, and NGS findings. Awareness of the cytologic features of this neoplasm are important for cytopathologists confronted with maxillary sinus lesions.

NR4A3 Immunostain Is a Highly Sensitive and Specific Marker for Acinic Cell Carcinoma in Cytologic and Surgical Specimens.

OBJECTIVES: Salivary gland acinic cell carcinoma (AciCC) has recognizable cytomorphologic features that can overlap with benign and malignant entities, creating a diagnostic challenge. AciCC harbors a t(4;9) translocation increasing nuclear receptor subfamily 4 group A member 3 (NR4A3) expression, detectable by immunohistochemistry (IHC) on surgical resection (SR). NR4A3 IHC cytology data are limited. Here, we examine NR4A3 IHC on smears, cell blocks (CBs), and SRs of AciCC and its mimickers. METHODS: Our cohort comprised AciCC (including high-grade transformation), secretory carcinoma, mucoepidermoid carcinoma (MEC), Warthin tumor, pleomorphic adenoma (PA), cellular PA, carcinoma ex-PA, oncocytic carcinoma, oncocytoma, and nodular oncocytosis. NR4A3 IHC (Santa Cruz Biotechnology and Origene antibodies) was positive if more than 5% tumor cells showed nuclear staining. RESULTS: Among CBs, 90% of AciCC cases and none of the mimickers expressed NR4A3. Among SRs, 100% of AciCC cases showed diffuse NR4A3, whereas one high-grade MEC expressed focal NR4A3. Concordance was 95% with two antibody clones. Sensitivity, specificity, positive predictive value, and negative predictive value were 90%, 100%, 100%, and 94.7% for CBs and 100%, 98.8%, 92.3%, and 100% for SRs, respectively. NR4A3 immunostaining was demonstrable on smears from an AciCC case. CONCLUSIONS: NR4A3 IHC can be a robust diagnostic tool to identify AciCC, especially for cytology specimens.

Fine-needle aspiration biopsy of growing teratoma syndrome as a diagnostic pitfall of metastatic adenocarcinoma.

Growing teratoma syndrome (GTS) is a rare clinical entity that can occur in patients with a history of treatment for germ cell tumors (GCTs) and normalized serum tumor markers. Owing to the assortment of tissue types found in teratomas that may exhibit atypical features, distinguishing GTS from metastatic cancer in extragonadal masses can be challenging. Fine-needle aspiration biopsy (FNAB) can be useful for the rapid diagnosis of metastatic masses and has been effective in distinguishing GCTs from one another. However, discrepancies in cytologic and histologic diagnoses have been reported in the evaluation of GCTs by FNAB. The potential incomplete sampling of metastatic teratomas in GTS by FNAB along with features of cellular atypia commonly found in teratomas can lead to a misdiagnosis of metastatic carcinoma and drastically affect treatment. Correlation of cytologic, histologic, clinical, and radiographic findings are essential in evaluating metastatic masses in patients with a history of GCT. We report a case of a 46-year-old man with GTS originally diagnosed on FNAB as metastatic adenocarcinoma compatible with a colorectal primary tumor.

Cytomorphologic features of intraductal salivary gland carcinoma: A multi-institutional study of 13 FNA cases with histologic, molecular, and clinical correlations.

BACKGROUND: Intraductal carcinoma of the salivary gland (IDC) is a rare cancer with potential actionable targets, including RET fusions. Histologic and molecular features of IDC were recently reported, but cytomorphologic data are limited. In the largest multi-institutional fine-needle aspiration (FNA) series, the authors describe the cytomorphologic features of 13 IDC cases with available clinical, radiologic, histopathologic, and molecular data. METHODS: The cases included 13 FNAs for 9 low-grade (LG) IDCs and 4 high-grade (HG) IDCs with corresponding histopathology and available molecular, imaging, and clinical data. Smears and liquid-based preparations available for 12 FNAs were semiquantitatively scored for key cytomorphologic findings and correlated with the corresponding resection. RESULTS: LG IDC FNAs showed a cellular, biphasic population of large, atypical ductal cells with mildly pleomorphic nuclei in a clean background and a minor population of small, uniform myoepithelial cells. In contrast, all HG IDC FNAs showed predominantly ductal cells with marked nuclear pleomorphism, coarse chromatin, and necrosis. With the Milan system, most LG and HG IDC FNAs were classified as either salivary gland neoplasms of uncertain malignant potential (54%) or malignant (31%). Immunohistochemistry showed ductal epithelial reactivity with mammaglobin, androgen receptor, and S100, whereas myoepithelial cells were positive for p63 and/or calponin. Among cases with next-generation sequencing, 4 LG IDCs showed NCOA4-RET gene fusions, whereas an HG IDC showed HRAS and PIK3CA mutations. CONCLUSIONS: The cytomorphology of IDC overlaps with other benign and malignant salivary gland neoplasms. Immunohistochemistry limits the differential diagnosis, but definitive classification requires molecular analysis. A diagnosis of IDC has potential implications for patient management.

Histoplasmosis in an off-trail Hiker receiving ustekinumab: Implications for Preventive and diagnostic strategies for patients receiving anti-IL-12/23 therapy.

Ustekinumab, an IL-12/23 inhibitor, is an important agent in treatment of inflammatory bowel disease and psoriasis. Clinical trials have not demonstrated significantly increased infection risk with ustekinumab. We report a case of disseminated histoplasmosis in the setting of ustekinumab and methotrexate following a hike in the Catskill Mountains, a region not commonly associated with Histoplasma encapsulatum. To our knowledge, this is the first reported case of newly acquired histoplasmosis complicating treatment with ustekinumab.

Incorporating cytologic adequacy assessment into precision oncology workflow using telepathology: An institutional experience.

BACKGROUND: Tumor sample quality and quantity determine the success of somatic mutation analysis. Thus, a rapid on-site evaluation (ROSE) tumor cytology adequacy assessment was incorporated into the workflow of precision oncology at Weill Cornell Medicine in New York City. Optimal samples were obtained from 68 patients with metastatic cancer. METHODS: Cytopathologists performed ROSE on fine-needle aspirate samples via telepathology, and subsequently core-needle biopsies were obtained. In a retrospective manner, the concordance between adequacy assessment and the success rate of the procedure was evaluated to obtain sufficient tumor tissue for next-generation sequencing (NGS). RESULTS: Out of the 68 procedures, 43 were documented as adequate and 25 were documented as inadequate. The diagnostic yield of adequate procedures was 100%. Adequacy evaluation predicted the success rate of molecular profiling in 40 of 43 procedures (93%; 95% CI, 80.9-98.5 procedures). The success rate of molecular testing was significantly higher in the adequate group: 93% compared with 32% in the inadequate group (P < .0005). Seven procedures that failed to provide quality material for mutational analysis and pathological diagnosis were evaluated as inadequate. Cell block provided sufficient DNA for NGS in 6 cases. In 2 cases, a core biopsy could not be performed; hence, the fine-needle aspirate material confirmed the diagnosis and was used for NGS testing. CONCLUSION: These results support the incorporation of ROSE into the workflow of precision oncology to obtain high-quality tissue samples from metastatic lesions. In addition, NGS testing of concurrent cytology specimens with adequate cellularity can be a surrogate for NGS testing of biopsy specimens.

Integration of whole-exome and anchored PCR-based next generation sequencing significantly increases detection of actionable alterations in precision oncology.

BACKGROUND: Frequency of clinically relevant mutations in solid tumors by targeted and whole-exome sequencing is ∼30%. Transcriptome analysis complements detection of actionable gene fusions in advanced cancer patients. Goal of this study was to determine the added value of anchored multiplex PCR (AMP)-based next-generation sequencing (NGS) assay to identify further potential drug targets, when coupled with whole-exome sequencing (WES). METHODS: Selected series of fifty-six samples from 55 patients enrolled in our precision medicine study were interrogated by WES and AMP-based NGS. RNA-seq was performed in 19 cases. Clinically relevant and actionable alterations detected by three methods were integrated and analyzed. RESULTS: AMP-based NGS detected 48 fusions in 31 samples (55.4%); 31.25% (15/48) were classified as targetable based on published literature. WES revealed 29 samples (51.8%) harbored targetable alterations. TMB-high and MSI-high status were observed in 12.7% and 1.8% of cases. RNA-seq from 19 samples identified 8 targetable fusions (42.1%), also captured by AMP-based NGS. When number of actionable fusions detected by AMP-based NGS were added to WES targetable alterations, 66.1% of samples had potential drug targets. When both WES and RNA-seq were analyzed, 57.8% of samples had targetable alterations. CONCLUSIONS: This study highlights importance of an integrative genomic approach for precision oncology, including use of different NGS platforms with complementary features. Integrating RNA data (whole transcriptome or AMP-based NGS) significantly enhances detection of potential targets in cancer patients. In absence of fresh frozen tissue, AMP-based NGS is a robust method to detect actionable fusions using low-input RNA from archival tissue.

Assessing the diagnostic accuracy for pleomorphic adenoma and Warthin tumor by employing the Milan System for Reporting Salivary Gland Cytopathology: An international, multi-institutional study.

BACKGROUND: The Milan System for Reporting Salivary Gland Cytopathology (MSRSGC) has established distinct diagnostic categories for reporting cytopathological findings, and each is associated with a defined risk of malignancy (ROM). However, the ROM is applied at the overall category level and is not specific for particular morphological entities within a category. Here, the diagnostic performance of the MSRSGC for pleomorphic adenoma (PA) and Warthin tumor (WT) is reported. METHODS: The pathology archives of 11 institutions from 4 countries were retrospectively searched to identify all salivary gland fine-needle aspiration (FNA) biopsies with a differential or definitive diagnosis of PA or WT and all resection specimens with a diagnosis of PA or WT; only paired cases were included. All FNA diagnoses were retrospectively classified according to the MSRSGC. RESULTS: A total of 1250 cases met the inclusion criteria, and they included 898 PA cases and 352 WT cases. The ROM in the benign neoplasm category was 3.0% and 1.3% for cases with a differential or definitive diagnosis of PA and WT, respectively. The ROM in the salivary gland neoplasm with uncertain malignant potential (SUMP) category was 2.7% and 18.8% for PA and WT, respectively (P = .0277). The diagnostic accuracy for PA and WT was 95.1% and 96.1%, respectively. CONCLUSIONS: The diagnostic accuracy for PA and WT on FNA is high. Furthermore, these findings highlight the difference in the ROMs associated with 2 specific differential diagnoses in the SUMP category: basaloid neoplasms and oncocytoid neoplasms.

Next-generation sequencing of residual cytologic fixative preserved DNA from pancreatic lesions: A pilot study.

BACKGROUND: Endoscopic ultrasound-guided fine needle aspiration (EUS-FNA) is a sensitive and specific tool in the risk stratification of pancreatic lesions, including cysts. The sensitivity and specificity of EUS-FNA has been shown to improve when cytology is combined with next-generation sequencing (NGS). Ideally, fresh cyst fluid is used for NGS. In this pilot study, we explore the possibility of sequencing DNA derived from residual alcohol-fixed pancreatic aspirates. METHODS: Residual cytologic fixatives (n = 42) from 39 patients who underwent EUS-FNA for pancreatic lesions were collected along with demographics, imaging, and laboratory studies. Samples were designated as nonneoplastic/nonmucinous benign (NB), mucinous cyst (MC), pancreatic ductal adenocarcinoma (PDAC), or well-differentiated neuroendocrine tumor (NET) on the basis of cytopathologic evaluation and sequenced on the Oncomine platform (ThermoFisher Scientific, Waltham, Massachusetts). RESULTS: Ten of 14 (71.4%) MCs exhibited clinically significant variants, including KRAS, GNAS, and TP53. Ten of 15 (66.7%) PDACs had KRAS alterations, and 9 of 15 (60%) showed variants in TP53. No variants were detected in any NETs. Only 1 of 9 (11.1%) NB aspirates showed variants in KRAS and MAP2K. Sequencing of formalin-fixed, paraffin-embedded tissue revealed variants identical to those detected in fixative-derived DNA in 4 of 5 cases (80%). CONCLUSION: Residual DNA from alcohol-fixed aspirates are an underutilized source for NGS. Sequencing residual fixative-derived DNA has the potential to be integrated into the workup of pancreatic aspirates, possibly impacting management.

Interobserver variability between cytopathologists and cytotechnologists upon application and characterization of the indeterminate category in the Milan System for Reporting Salivary Gland Cytopathology.

BACKGROUND: The indeterminate categories in the Milan System for Reporting Salivary Gland Cytopathology (MSRSGC) are diagnostically challenging because of inherent heterogeneity and complexity, with wide interobserver variability (IOV). Herein, the authors explore the concordance rate (CR) between cytopathologists (CPs) and cytotechnologists (CTs) in interpreting indeterminate salivary gland lesions using the MSRSGC. METHODS: Between 2011 and 2016, 86 indeterminate fine-needle aspirations had slides available for review, of which 48 had follow-up. Four CPs and 2 CTs performed an independent, blinded review of these slides and categorized them according to the MSRSGC. The CRs between CTs and CPs with the final sign-out cytopathologist (FCP) were assessed, and interobserver agreement was categorized into uniform, majority, divided, minimal, or no agreement. RESULTS: The overall CR with the FCP ranged from 48.8% to 60.5% for CPs and from 22.1% to 36% for CTs. IOV κ scores for the entire group were 0.314 and, with the FCP as the reference, ranged from 0.403 to 0.539 for CPs and from 0.091 to 0.254 for CTs. Uniform, majority, divided, minimal, and no agreement was noted in 12.8%, 31.4%, 38.4%, 10.5%, and 6.9%, respectively, of all cases and in 16.7%, 35.4%, 31.3%, 8.3%, and 6.3%, respectively, of the cases with follow-up. Diagnostic challenges included distinguishing lymphoma from a reactive process and distinguishing mucin from mucin-like material. CONCLUSIONS: CPs had modestly higher CRs compared with CTs; and, although the variable CRs highlight indeterminate IOV, the MSRSGC enables reproducibility. Characterizing larger cohorts in the indeterminate categories will further improve MSRSGC criteria. Moreover, education on the MSRSGC should include CTs and CPs to improve overall diagnostic accuracy.

Insulinoma-associated protein 1 (INSM1) is a robust marker for identifying and grading pancreatic neuroendocrine tumors.

BACKGROUND: Pancreatic neuroendocrine tumor (PNET) is a diagnostic challenge with limited samples in not only identification but grading. Prior studies have shown insulinoma-associated protein 1 (INSM1) to be a robust marker in identifying PNETs from other solid pancreatic tumors on resection specimens. In this study, we investigated the utility of INSM1 not only for identifying PNETs but also for grading in cell blocks (CBs) and surgical resections (SRs). METHODS: A search for PNET cases between 2000 and 2019 identified 55 samples (26 CBs and 29 SRs) that were further separated into high (2 CBs, 3 SRs), intermediate (4 CBs, 7 SRs), and low (20 CBs, 19 SRs) grades based on their final pathology report and Ki-67 level. Immunohistochemical (IHC) staining for INSM1 (C-8, Santa Cruz Biotechnology [1:100]) was performed and quantified using an H score of 0 to 300. Non-PNET solid pancreatic tumors were compared and included acinar cell carcinoma, solid pseudopapillary neoplasm, and ductal adenocarcinoma. RESULTS: All 55 cases of PNET demonstrated nuclear INSM1 staining. The average H scores for INSM1 staining of PNET were 254 and 252 in CB and SR, respectively. The H scores decreased with increasing tumor grade, with low-grade (G1), intermediate-grade (G2), and high-grade (G3) tumors showing average INSM1 H scores of 229 and 253, 266 and 253, and 30 and 33 in both CB and SR, respectively. CONCLUSION: IHC with INSM1 plays a role in identifying and potentially grading PNETs.

Integrative Molecular Analysis of Patients With Advanced and Metastatic Cancer.

PURPOSE: We developed a precision medicine program for patients with advanced cancer using integrative whole-exome sequencing and transcriptome analysis. PATIENTS AND METHODS: Five hundred fifteen patients with locally advanced/metastatic solid tumors were prospectively enrolled, and paired tumor/normal sequencing was performed. Seven hundred fifty-nine tumors from 515 patients were evaluated. RESULTS: Most frequent tumor types were prostate (19.4%), brain (16.5%), bladder (15.4%), and kidney cancer (9.2%). Most frequently altered genes were TP53 (33%), CDKN2A (11%), APC (10%), KTM2D (8%), PTEN (8%), and BRCA2 (8%). Pathogenic germline alterations were present in 10.7% of patients, most frequently CHEK2 (1.9%), BRCA1 (1.5%), BRCA2 (1.5%), and MSH6 (1.4%). Novel gene fusions were identified, including a RBM47-CDK12 fusion in a metastatic prostate cancer sample. The rate of clinically relevant alterations was 39% by whole-exome sequencing, which was improved by 16% by adding RNA sequencing. In patients with more than one sequenced tumor sample (n = 146), 84.62% of actionable mutations were concordant. CONCLUSION: Integrative analysis may uncover informative alterations for an advanced pan-cancer patient population. These alterations are consistent in spatially and temporally heterogeneous samples.

Cancer-Specific Thresholds Adjust for Whole Exome Sequencing-based Tumor Mutational Burden Distribution.

PURPOSE: To understand the clinical context of tumor mutational burden (TMB) when comparing a pan-cancer threshold and a cancer-specific threshold. MATERIALS AND METHODS: Using whole exome sequencing (WES) data from primary tumors in The Cancer Genome Atlas (TCGA) (n=3,534) and advanced/metastatic tumors from Weill Cornell Medicine (WCM Advanced) (n=696), TMB status was determined using a pan-cancer and cancer-specific threshold. Survival curves, number of samples classified as TMB high, and predicted neoantigens were used to evaluate the differences between thresholds. RESULTS: The distribution of TMB varied dramatically between cancer types. A cancer-specific threshold was able to adjust for the different TMB distributions, while the pan-cancer threshold was often too stringent. The dynamic nature of the cancer-specific threshold resulted in more tumors being classified as TMB high compared to the static pan-cancer threshold. Additionally, no significant difference in survival outcomes was found with the cancer-specific threshold compared to the pan-cancer one. Further, the cancer-specific threshold maintains higher predicted neoantigen load for the TMB high samples compared to the TMB low samples, even when the threshold is lower than the pan-cancer threshold. CONCLUSION: TMB is relative to the context of cancer type, metastatic state, and disease stage. Compared to a pan-cancer threshold, a cancer-specific threshold classifies more patients as TMB high while maintaining clinical outcomes that were not significantly different. Furthermore, the cancer-specific threshold identifies patients with a high number of predicted neoantigens. Due to the potential impact in cancer patient care, TMB status should be determined in a cancer-specific manner.

Application of the Milan System for Reporting Submandibular Gland Cytopathology: An international, multi-institutional study.

BACKGROUND: The Milan System for Reporting Salivary Gland Cytopathology (MSRSGC) is a 6-tier diagnostic category system with associated risks of malignancy (ROMs) and management recommendations. Submandibular gland fine-needle aspiration (FNA) is uncommon with a higher frequency of inflammatory lesions and a higher relative proportion of malignancy, and this may affect the ROM and subsequent management. This study evaluated the application of the MSRSGC and the ROM for each diagnostic category for 734 submandibular gland FNAs. METHODS: Submandibular gland FNA cytology specimens from 15 international institutions (2013-2017) were retrospectively assigned to an MSRSGC diagnostic category as follows: nondiagnostic, nonneoplastic, atypia of undetermined significance (AUS), benign neoplasm, salivary gland neoplasm of uncertain malignant potential (SUMP), suspicious for malignancy (SM), or malignant. A correlation with the available histopathologic follow-up was performed, and the ROM was calculated for each MSRSGC diagnostic category. RESULTS: The case cohort of 734 aspirates was reclassified according to the MSRSGC as follows: nondiagnostic, 21.4% (0%-50%); nonneoplastic, 24.2% (9.1%-53.6%); AUS, 6.7% (0%-14.3%); benign neoplasm, 18.3% (0%-52.5%); SUMP, 12% (0%-37.7%); SM, 3.5% (0%-12.5%); and malignant, 13.9% (2%-31.3%). The histopathologic follow-up was available for 333 cases (45.4%). The ROMs were as follows: nondiagnostic, 10.6%; nonneoplastic, 7.5%; AUS, 27.6%; benign neoplasm, 3.2%; SUMP, 41.9%; SM, 82.3%; and malignant, 93.6%. CONCLUSIONS: This multi-institutional study shows that the ROM of each MSRSGC category for submandibular gland FNA is similar to that reported for parotid gland FNA, although the reported rates for the different MSRSGC categories were variable across institutions. Thus, the MSRSGC can be reliably applied to submandibular gland FNA.

Mucoepidermoid carcinoma, acinic cell carcinoma, and adenoid cystic carcinoma on fine-needle aspiration biopsy and The Milan System: an international multi-institutional study.

BACKGROUND: We evaluated the diagnostic accuracy (DA), risk of neoplasm (RON), and risk of malignancy (ROM) for the commonly encountered malignant salivary gland tumors mucoepidermoid carcinoma (MECa), acinic cell carcinoma (ACCa), and adenoid cystic carcinoma (ADCa) applying The Milan System for Reporting Salivary Gland Cytology (MSRSGC). MATERIALS AND METHODS: The cytology archives from 2007 to 2017 of 9 academic institutions were searched for salivary gland FNAs for the following key words mentioned either in the principal and/or differential diagnosis: MEC, ACCa, and ADCa. The original cytology diagnosis was retrospectively classified according to the MSRSGC. Patient demographics, biopsy site, and available surgical follow-up were recorded. The final analysis included only cases with surgical follow-up. RESULTS: A total of 212 salivary gland FNAs were included. Based on retrospective reclassification according to MSRSGC, 97 of 212 (46%) FNA cases carried a diagnosis of malignancy specific for either MECa, ACCa, or ADCa. In the remaining 115 cases, 24 of 212 (11%) were reclassified as suspicious for malignancy (SM) and 91 of 212 (43%) as salivary gland neoplasm of uncertain malignant potential (SUMP). The DA for MECa, ACCa, and ADCa was 78.7%, 75% and 89%, respectively. The RON was 100% for all 3 tumors and the ROM was 93.6% for MECa, 96.8% for ACCa, and 94.4% for ADCa. CONCLUSIONS: The DA of 78.7% for MECa, 75% for ACCa, and 89% for ADCa is reasonable in FNA specimens. Although the management of definitive cases of malignancy remains unchanged, the MSRSGC provides a ROM for SM and SUMP categories, which can improve patient management.