HistoEM: A Pathologist-Guided and Explainable Workflow Using Histogram Embedding for Gland Classification.

Pathologists have, over several decades, developed criteria for diagnosing and grading prostate cancer. However, this knowledge has not, so far, been included in the design of convolutional neural networks (CNN) for prostate cancer detection and grading. Further, it is not known whether the features learned by machine-learning algorithms coincide with diagnostic features used by pathologists. We propose a framework that enforces algorithms to learn the cellular and subcellular differences between benign and cancerous prostate glands in digital slides from hematoxylin and eosin-stained tissue sections. After accurate gland segmentation and exclusion of the stroma, the central component of the pipeline, named HistoEM, utilizes a histogram embedding of features from the latent space of the CNN encoder. Each gland is represented by 128 feature-wise histograms that provide the input into a second network for benign vs cancer classification of the whole gland. Cancer glands are further processed by a U-Net structured network to separate low-grade from high-grade cancer. Our model demonstrates similar performance compared with other state-of-the-art prostate cancer grading models with gland-level resolution. To understand the features learned by HistoEM, we first rank features based on the distance between benign and cancer histograms and visualize the tissue origins of the 2 most important features. A heatmap of pixel activation by each feature is generated using Grad-CAM and overlaid on nuclear segmentation outlines. We conclude that HistoEM, similar to pathologists, uses nuclear features for the detection of prostate cancer. Altogether, this novel approach can be broadly deployed to visualize computer-learned features in histopathology images.

Histologic patterns in prostatic adenocarcinoma are not predictive of mutations in the homologous recombination repair pathway.

Somatic or germline homologous recombination repair (HRR) pathway gene mutations are commonly detected in prostate cancer, especially in advanced disease, and are associated with response to poly (ADP-ribose) polymerase (PARP) inhibitors. In this study, we evaluated whether histological patterns are predictive of HRR pathway gene mutations. The study population comprised 130 patients with advanced prostate carcinoma who underwent comprehensive genomic profiling (CGP) of tumor tissue at a CLIA-certified laboratory. HRR genes in the study included BRCA1, BRCA2, ATM, BARD1, BRIP, CHEK2, MRE11A, NBN, PALB2, RAD51C, RAD51D, EMSY, ATR, CHEK1, and FAM175A. Overall, 38 patients had mutations in BRCA1/2, 36 in other HRR genes, and 56 were negative for HRR mutations. All cases were re-reviewed and quantified by two genitourinary pathologists blinded to mutational status for the following histological patterns of prostate carcinoma: cribriform, ductal, intraductal carcinoma (IDC), small cell carcinoma, signet ring-like pattern, and lobular carcinoma-like pattern. Discordances were resolved by consensus review. Histologic patterns were analyzed for any correlation with mutations in HRR pathway genes (grouped as BRCA1/2 mutated or non-BRCA1/2 mutated) compared to tumors without mutations in HRR genes by Chi-square testing. Patterns with >20 % and >30 % of tumor volume were additionally evaluated for correlation with mutational status. We found no significant association between HRR pathway mutations and cribriform pattern, IDC, ductal carcinoma, small cell carcinoma, signet ring-like pattern, or lobular carcinoma-like patterns. Tumors with >20 % or >30 % histologic patterns by volume also demonstrated no significant association with mutational status. This study suggests that histopathologic examination alone is insufficient to distinguish prostate cancer with germline or somatic mutations in HRR pathway genes, highlighting the continuing importance of ancillary molecular diagnostics in guiding therapy selection for prostate cancer patients who may benefit from PARP inhibitors.

Quantitative Imaging Analysis Fluorescence In Situ Hybridization Validation for Clinical HER2 Testing in Breast Cancer.

CONTEXT.­: Quantitative imaging is a promising tool that is gaining wide use across several areas of pathology. Although there has been increasing adoption of morphologic and immunohistochemical analysis, the adoption of evaluation of fluorescence in situ hybridization (FISH) on formalin-fixed, paraffin-embedded tissue has been limited because of complexity and lack of practice guidelines. OBJECTIVE.­: To perform human epidermal growth factor receptor 2 (HER2) FISH validation in breast carcinoma in accordance with the American Society of Clinical Oncology/College of American Pathologists (ASCO/CAP) 2018 guideline. DESIGN.­: Clinical validation of HER2 FISH was performed using the US Food and Drug Administration-approved dual-probe HER2 IQFISH (Dako, Carpinteria, California) with digital scanning performed on a PathFusion (Applied Spectral Imaging, Carlsbad, California) system. Validation parameters evaluated included z-stacking, classifier, accuracy, precision, software, and hardware settings. Finally, we evaluated the performance of digital enumeration on clinical samples in a real-world setting. RESULTS.­: The accuracy samples showed a final concordance of 95.3% to 100% across HER2 groups 1 to 5. During clinical implementation for HER2 groups 2, 3, and 4, we achieved a final concordance of 76% (95 of 125). Of these cases, only 8% (10 of 125) had discordances with clinical impact that could be identified algorithmically and triaged for manual review. CONCLUSIONS.­: Digital FISH enumeration is a useful tool to improve the efficacy of HER2 FISH enumeration and capture genetic heterogeneity across HER2 signals. Excluding cases with high background or poor image quality and manual review of cases with ASCO/CAP group discordances can further improve the efficiency of digital HER2 FISH enumeration.

Histone Deacetylase Inhibition Has Targeted Clinical Benefit in ARID1A-Mutated Advanced Urothelial Carcinoma.

Histone deacetylase (HDAC) inhibition has sporadic clinical efficacy in urothelial carcinoma; the genomic basis for clinical response is not known. In two separate phase I clinical trials testing pharmacokinetic aspects of HDAC inhibitors in advanced solid tumors, we identified one patient with advanced urothelial carcinoma who had a complete response to belinostat, and one patient with advanced urothelial carcinoma who had a partial response to panobinostat. The archived tumors of the responders were genomically characterized in comparison to others with urothelial carcinoma on the trials. Urothelial carcinoma cell lines treated with panobinostat and belinostat were studied to elucidate the mechanisms of benefit. Notably, the urothelial carcinoma tumors that responded to HDAC inhibition had ARID1A mutations. ARID1A mutations were also noted in the tumors of three patients who had stable disease as their best response to HDAC inhibition. Corroborating the basis of sensitivity, transcriptional profiling of platinum-resistant ARID1A-mutated HT1197 cells treated with panobinostat reveals negative enrichment for both cyto-proliferative (MYC and E2F targets) and DNA repair gene sets, and positive enrichment for TP53 and inflammatory gene sets. Our study identifies ARID1A loss as a basis for clinical response to pan HDAC inhibition and offers avenues for potential rational therapeutic combinations with HDAC inhibitors in advanced urothelial carcinoma.

Demographics, stage distribution, and relative roles of surgery and radiotherapy on survival of persons with primary prostate sarcomas.

BACKGROUND: Primary prostate sarcomas (PPS) are rare. Outcomes for this cancer have not been well characterized. MATERIALS AND METHODS: Subjects with a PPS diagnosed between 1973 and 2014 were identified in the SEER database. Subjects were stratified by disease stage and types of therapies received. Disease-specific survival (DSS) and Overall survival (OS) was estimated by Kaplan-Meier analysis and cohorts were compared with a univariate and multivariable Cox regression. RESULTS: The incidence of PPS among all prostate cancer diagnoses was 0.02%. Subjects younger than age 26 years at diagnosis represented 29% of cases, and 32% of primary prostate sarcomas were rhabdomyosarcoma histology. RHABDOMYOSARCOMA HISTOLOGIES: The median age at diagnosis was 9 years. Between age 0-25 years rhabdomyosarcoma accounted for 96.4% of primary prostate sarcoma diagnoses, after age 25 rhabdomyosarcoma represented 15% of new diagnoses. The 10-year DSS and OS for rhabdomyosarcoma was 47% and 44%. NON-RHABDOMYOSARCOMA HISTOLOGIES: The median age at diagnosis was 71 years. The most common diagnoses were leiomyosarcoma (33%) and carcinosarcoma (28%). Localized, regional, or distant disease occurred in 40%, 34%, and 26% of cases. The 10-year DSS and OS were 26% and 14%. In locally advanced cases, RT added to surgery trended toward improved DSS (P = 0.10). CONCLUSIONS: Disease-specific survival and OS for non-rhabdomyosarcoma histologies appear inferior to those of rhabdomyosarcoma. The addition of RT to surgical resection may improve DSS in locally advanced non-rhabdomyosarcoma. This is the largest report of the incidence, stage distribution, and survival for this extremely rare urologic malignancy providing valuable prognostic information.

Patterns and Significance of PIM Kinases in Urothelial Carcinoma.

BACKGROUND: The Provirus integrating site Moloney murine leukemia virus (Pim) family are proteins with serine/threonine kinase activity. Studies have demonstrated overexpression of Pims in cancer. To our knowledge, only a single study has examined Pim-1 in urothelial carcinoma. The aim of this investigation was to evaluate Pim-1, Pim-2, and Pim-3 in urothelial carcinoma and assess for expression that may contribute to disease progression and serve as a site for targeted therapy. METHODS: This retrospective study included 137 cases taken from specimens from the University of Utah, Department of Pathology (2008 to 2011). Tissue was stained with antibodies against Pim-1, Pim-2, and Pim-3. Cases were classified into 3 groups, based upon current World Health Organization criteria (invasive high-grade urothelial carcinoma [IHG] [n=84], noninvasive high-grade urothelial carcinoma/carcinoma in situ [n=32], and noninvasive low-grade urothelial carcinoma [NILG] [n=21]). Cases were scored and recorded as positive or negative on the basis of the percentage of cells with cytoplasmic and/or nuclear staining. RESULTS: NILG showed higher expression of Pim-1 (relative expression rate [RER]=2.28; 95% confidence interval [CI], 0.183-0.764) and Pim-3 (RER=3.06; 95% CI, 0.423-0.816) compared with other lesions. IHG had lower expression of Pim-1 (RER=0.31; 95% CI, 0.401-0.844) and Pim-3 (RER=0.354; 95% CI, 0.322-0.816) and noninvasive high-grade urothelial carcinoma (NIHG) demonstrated increased expression of Pim-1 and (RER=2.09; 95% CI, 0.124-0.739) and Pim-2 (RER=1.70; 95% CI, 0.151-0.591). At least 1 Pim kinase protein was expressed at the following rates: 49% in IHG, 66% in NIHG, and 76% in NILG. CONCLUSION: A high percentage of urothelial carcinomas express Pim kinases. Pim expression differs in NILG, NIHG, and IHG lesions.

Molecular Confirmation of Ewing Sarcoma in an 85-Year-Old Woman.

We report a case of a Ewing sarcoma/primitive neuroectodermal tumor in an 85-year-old woman who presented with an enlarging circumscribed left flank mass. Magnetic resonance imaging revealed a 3 × 5 × 10 cm heterogeneous mass arising from the 10th rib. Computed tomography demonstrated a small nodule in the right middle lobe and bilateral pleural effusions. The patient underwent computed tomography-guided biopsy followed by open biopsy. The tumor cells were characterized by loosely cohesive sheets of tumor cells with uniform nuclei, and scant, granular, eosinophilic cytoplasm with indistinct cell membranes. Frequent mitoses, apoptosis, and necrosis were present. The cells were positive for CD99 with a strong concentric staining pattern. Epithelial, hematopoietic, and neural markers were all negative. Fluorescence in situ hybridization was performed and demonstrated EWSR1 (22q12) gene rearrangement. Sanger sequencing of the reverse transcriptase polymerase chain reaction product from the patient's tumor demonstrated the EWSR1-FLI1 type 1 fusion. Following diagnosis the patient elected to proceed with localized radiation and declined chemotherapy. She developed progressive lung disease and subsequently died of her disease a year after her initial diagnosis. Ewing sarcoma is predominantly a pediatric disease and uncommon in patients older than 40 years of age. To the best of our knowledge, this is the oldest documented case of Ewing sarcoma, diagnosed using modern molecular techniques.

Use of in situ hybridization for HPV in head and neck tumors: experience from a national reference laboratory.

The human papillomavirus (HPV) status of head and neck squamous cell carcinomas (SCCs) is a frequent request for Anatomic Pathology labs. However, prognostic value of HPV status is limited to identification of high risk HPV in oropharyngeal SCCs. The purpose of this study is to investigate the ordering practices of in situ hybridization (ISH) for HPV in head and neck tissues at our national reference laboratory. All testing orders for low risk, high risk, and combined low and high risk HPV-ISH tests requested at ARUP Laboratories between January 2010 and November 2013 had their results reviewed and were grouped by anatomic location of the tested tissue. The H&E and HPV-ISH slides from a sample of the most recent 123 tests were reviewed by two pathologists. A total of 1,128 HPV-ISH tests were ordered during the study period. Testing for combined low and high risk HPV was the most commonly ordered test. The positivity rate for high risk HPV was highest in oropharyngeal tissues. 49 of 123 reviewed cases had testing requested on non-malignant tissue, 11 of which were non-neoplastic. Unnecessary HPV-ISH ordering is prevalent in head and neck tissues. Dual testing for low and high risk HPV, frequent testing outside of the oropharynx, and testing non-neoplastic tissues appear to be common practices.

A small-molecule inhibitor of PIM kinases as a potential treatment for urothelial carcinomas.

The proto-oncogene proviral integration site for moloney murine leukemia virus (PIM) kinases (PIM-1, PIM-2, and PIM-3) are serine/threonine kinases that are involved in a number of signaling pathways important to cancer cells. PIM kinases act in downstream effector functions as inhibitors of apoptosis and as positive regulators of G1-S phase progression through the cell cycle. PIM kinases are upregulated in multiple cancer indications, including lymphoma, leukemia, multiple myeloma, and prostate, gastric, and head and neck cancers. Overexpression of one or more PIM family members in patient tumors frequently correlates with poor prognosis. The aim of this investigation was to evaluate PIM expression in low- and high-grade urothelial carcinoma and to assess the role PIM function in disease progression and their potential to serve as molecular targets for therapy. One hundred thirty-seven cases of urothelial carcinoma were included in this study of surgical biopsy and resection specimens. High levels of expression of all three PIM family members were observed in both noninvasive and invasive urothelial carcinomas. The second-generation PIM inhibitor, TP-3654, displays submicromolar activity in pharmacodynamic biomarker modulation, cell proliferation studies, and colony formation assays using the UM-UC-3 bladder cancer cell line. TP-3654 displays favorable human ether-à-go-go-related gene and cytochrome P450 inhibition profiles compared with the first-generation PIM inhibitor, SGI-1776, and exhibits oral bioavailability. In vivo xenograft studies using a bladder cancer cell line show that PIM kinase inhibition can reduce tumor growth, suggesting that PIM kinase inhibitors may be active in human urothelial carcinomas.