DeepScope: Nonintrusive Whole Slide Saliency Annotation and Prediction from Pathologists at the Microscope

Modern digital pathology departments have grown to produce whole-slide image data at petabyte scale, an unprecedented treasure chest for medical machine learning tasks. Unfortunately, most digital slides are not annotated at the image level, hindering large-scale application of supervised learning. Manual labeling is prohibitive, requiring pathologists with decades of training and outstanding clinical service responsibilities. This problem is further aggravated by the United States Food and Drug Administration's ruling that primary diagnosis must come from a glass slide rather than a digital image. We present the first end-to-end framework to overcome this problem, gathering annotations in a nonintrusive manner during a pathologist's routine clinical work: (i) microscope-specific 3D-printed commodity camera mounts are used to video record the glass-slide-based clinical diagnosis process; (ii) after routine scanning of the whole slide, the video frames are registered to the digital slide; (iii) motion and observation time are estimated to generate a spatial and temporal saliency map of the whole slide. Demonstrating the utility of these annotations, we train a convolutional neural network that detects diagnosis-relevant salient regions, then report accuracy of 85.15% in bladder and 91.40% in prostate, with 75.00% accuracy when training on prostate but predicting in bladder, despite different pathologists examining the different tissues. When training on one patient but testing on another, AUROC in bladder is 0.79±0.11 and in prostate is 0.96±0.04. Our tool is available at https://bitbucket.org/aschaumberg/deepscope.

Health Information Systems

This article provides surgical pathologists an overview of health information systems (HISs): what they are, what they do, and how such systems relate to the practice of surgical pathology. Much of this article is dedicated to the electronic medical record. Information, in how it is captured, transmitted, and conveyed, drives the effectiveness of such electronic medical record functionalities. So critical is information from pathology in integrated clinical care that surgical pathologists are becoming gatekeepers of not only tissue but also information. Better understanding of HISs can empower surgical pathologists to become stakeholders who have an impact on the future direction of quality integrated clinical care.

Translational Bioinformatics and Clinical Research (Biomedical) Informatics

Translational bioinformatics and clinical research (biomedical) informatics are the primary domains related to informatics activities that support translational research. Translational bioinformatics focuses on computational techniques in genetics, molecular biology, and systems biology. Clinical research (biomedical) informatics involves the use of informatics in discovery and management of new knowledge relating to health and disease. This article details 3 projects that are hybrid applications of translational bioinformatics and clinical research (biomedical) informatics: The Cancer Genome Atlas, the cBioPortal for Cancer Genomics, and the Memorial Sloan Kettering Cancer Center clinical variants and results database, all designed to facilitate insights into cancer biology and clinical/therapeutic correlations.

Coordinate loss of MAP3K7 and CHD1 promotes aggressive prostate cancer

Prostate cancer subtypes are poorly defined and functional validation of drivers of ETS rearrangement-negative prostate cancer has not been conducted. Here, we identified an ETS(-) subtype of aggressive prostate cancer (ERG(-)MAP3K7(del)CHD1(del)) and used a novel developmental model and a cell line xenograft model to show that cosuppression of MAP3K7 and CHD1 expression promotes aggressive disease. Analyses of publicly available prostate cancer datasets revealed that MAP3K7 and CHD1 were significantly codeleted in 10% to 20% of localized tumors and combined loss correlated with poor disease-free survival. To evaluate the functional impact of dual MAP3K7-CHD1 loss, we suppressed Map3k7 and/or Chd1 expression in mouse prostate epithelial progenitor/stem cells (PrP/SC) and performed tissue recombination experiments in vivo. Dual shMap3k7-shChd1 PrP/SC recombinants displayed massive glandular atypia with regions of prostatic intraepithelial neoplasia and carcinoma apparent. Combined Map3k7-Chd1 suppression greatly disrupted normal prostatic lineage differentiation; dual recombinants displayed significant androgen receptor loss, increased neuroendocrine differentiation, and increased neural differentiation. Clinical samples with dual MAP3K7-CHD1 loss also displayed neuroendocrine and neural characteristics. In addition, dual Map3k7-Chd1 suppression promoted E-cadherin loss and mucin production in recombinants. MAP3K7 and CHD1 protein loss also correlated with Gleason grade and E-cadherin loss in clinical samples. To further validate the phenotype observed in the PrP/SC model, we suppressed MAP3K7 and/or CHD1 expression in LNCaP prostate cancer cells. Dual shMAP3K7-shCHD1 LNCaP xenografts displayed increased tumor growth and decreased survival compared with shControl, shMAP3K7, and shCHD1 xenografts. Collectively, these data identify coordinate loss of MAP3K7 and CHD1 as a unique driver of aggressive prostate cancer development.

Translational Bioinformatics and Clinical Research (Biomedical) Informatics

Translational bioinformatics and clinical research (biomedical) informatics are the primary domains related to informatics activities that support translational research. Translational bioinformatics focuses on computational techniques in genetics, molecular biology, and systems biology. Clinical research (biomedical) informatics involves the use of informatics in discovery and management of new knowledge relating to health and disease. This article details 3 projects that are hybrid applications of translational bioinformatics and clinical research (biomedical) informatics: The Cancer Genome Atlas, the cBioPortal for Cancer Genomics, and the Memorial Sloan Kettering Cancer Center clinical variants and results database, all designed to facilitate insights into cancer biology and clinical/therapeutic correlations.

Health Information Systems

This article provides surgical pathologists an overview of health information systems (HISs): what they are, what they do, and how such systems relate to the practice of surgical pathology. Much of this article is dedicated to the electronic medical record. Information, in how it is captured, transmitted, and conveyed, drives the effectiveness of such electronic medical record functionalities. So critical is information from pathology in integrated clinical care that surgical pathologists are becoming gatekeepers of not only tissue but also information. Better understanding of HISs can empower surgical pathologists to become stakeholders who have an impact on the future direction of quality integrated clinical care.

Lipid catabolism via CPT1 as a therapeutic target for prostate cancer

Prostate cancer is the most commonly diagnosed malignancy among Western men and accounts for the second leading cause of cancer-related deaths. Prostate cancer tends to grow slowly and recent studies suggest that it relies on lipid fuel more than on aerobic glycolysis. However, the biochemical mechanisms governing the relationships between lipid synthesis, lipid utilization, and cancer growth remain unknown. To address the role of lipid metabolism in prostate cancer, we have used etomoxir and orlistat, clinically safe drugs that block lipid oxidation and lipid synthesis/lipolysis, respectively. Etomoxir is an irreversible inhibitor of the carnitine palmitoyltransferase (CPT1) enzyme that decreases β oxidation in the mitochondria. Combinatorial treatments using etomoxir and orlistat resulted in synergistic decreased viability in LNCaP, VCaP, and patient-derived benign and prostate cancer cells. These effects were associated with decreased androgen receptor expression, decreased mTOR signaling, and increased caspase-3 activation. Knockdown of CPT1A enzyme in LNCaP cells resulted in decreased palmitate oxidation but increased sensitivity to etomoxir, with inactivation of AKT kinase and activation of caspase-3. Systemic treatment with etomoxir in nude mice resulted in decreased xenograft growth over 21 days, underscoring the therapeutic potential of blocking lipid catabolism to decrease prostate cancer tumor growth.

Significance of signet ring cells in high-grade mucinous adenocarcinoma of the peritoneum from appendiceal origin

Significance of signet ring cells in mucinous adenocarcinoma of the peritoneum from appendiceal origin has never been specifically studied. We retrospectively reviewed cases of mucinous adenocarcinoma of the peritoneum from appendiceal origin (n = 55) and collected clinical follow-up data. Signet ring cells were identified in 29 of 55 cases. No low-grade mucinous adenocarcinoma case (n = 11) had signet ring cells, whereas 29 of 44 high-grade mucinous adenocarcinoma cases did. Cases of high-grade mucinous adenocarcinoma were subdivided into 3 groups: (1) high-grade mucinous adenocarcinoma without signet ring cells (n = 15), (2) high-grade mucinous adenocarcinoma with signet ring cells only within mucin pools (n = 20), and (3) high-grade mucinous adenocarcinoma with signet ring cells invading tissue (n = 9). Overall survival (OS) and progression-free survival were subsequently evaluated. Five-year OS for cases of high-grade mucinous adenocarcinoma without signet ring cells and high-grade mucinous adenocarcinoma with signet ring cells within mucin pools were similar at 31.8% (SE, 14.4%) and 35.8% (SE, 13.9%), respectively. A significant survival difference was seen for cases of high-grade mucinous adenocarcinoma with signet ring cells invading tissue with a median OS of 0.5 years versus 2.9 and 2.4 years (P = .04 and P = .03), respectively, for cases of high-grade mucinous adenocarcinoma without signet ring cells and high-grade mucinous adenocarcinoma with signet ring cells within mucin pools. Finding signet ring cells floating in extracellular mucin pools made no prognostic difference when compared with cases of high-grade mucinous adenocarcinoma without signet ring cells. In contrast, high-grade mucinous adenocarcinoma with signet ring cells invading tissue was significant for worse survival, and thus, we propose reporting signet ring cell tissue invasion particularly when extensive.

Src-dependent Tks5 phosphorylation regulates invadopodia-associated invasion in prostate cancer cells

BACKGROUND

The Src tyrosine kinase substrate and adaptor protein Tks5 had previously been implicated in the invasive phenotype of normal and transformed cell types via regulation of cytoskeletal structures called podosomes/invadopodia. The role of Src-Tks5 signaling in invasive prostate cancer, however, had not been previously evaluated.

METHODS

We measured the relative expression of Tks5 in normal (n = 20) and cancerous (n = 184, from 92 patients) prostate tissue specimens by immunohistochemistry using a commercially available tumor microarray. We also manipulated the expression and activity of wild-type and mutant Src and Tks5 constructs in the LNCaP and PC-3 prostate cancer cell lines in order to ascertain the role of Src-Tks5 signaling in invadopodia development, matrix-remodeling activity, motility, and invasion.

RESULTS

Our studies demonstrated that Src was activated and Tks5 upregulated in high Gleason score prostate tumor specimens and in invasive prostate cancer cell lines. Remarkably, overexpression of Tks5 in LNCaP cells was sufficient to induce invadopodia formation and associated matrix degradation. This Tks5-dependent increase in invasive behavior further depended on Src tyrosine kinase activity and the phosphorylation of Tks5 at tyrosine residues 557 and 619. In PC-3 cells we demonstrated that Tks5 phosphorylation at these sites was necessary and sufficient for invadopodia-associated matrix degradation and invasion.

CONCLUSIONS

Our results suggest a general role for Src-Tks5 signaling in prostate tumor progression and the utility of Tks5 as a marker protein for the staging of this disease.

High-stage urachal adenocarcinoma can be associated with microsatellite instability and KRAS mutations

Urachal adenocarcinoma (UAC) is a rare tumor of the urinary bladder, which can show intestinal, mucinous, and signet ring cell histology. The morphology is similar to that of colorectal adenocarcinoma (CAC). Microsatellite instability (MSI), KRAS, and BRAF have been more extensively studied in CAC. What is not known is whether UAC in its morphologic similarity to CAC could show immunohistochemical features of MSI along with KRAS- and BRAF-activating mutations. A retrospective review of institutional archives for UAC cases found 7 cases, all of which were high stage. Most (6/7) of our UAC cases showed evidence of MSI or mutations of KRAS. No cases showed a BRAF mutation at codon 600. Of the cases that demonstrated MSI, 1 showed mutS homolog 2 and mutS homolog 6 loss, and 2 showed PMS2 (postmeiotic segregation increased 2) loss. Of the remaining 4 cases, 3 showed KRAS mutations at codon 12. Our UAC series showed mutual exclusivity of MSI and KRAS mutations. Furthermore, our UAC cases with KRAS mutations showed markedly better overall survival (mean, 101.7 versus 6.5 months; P = .035). Thus, our study justifies ancillary testing for MSI and KRAS in UAC, particularly when there is high-stage and mucinous histology, but a larger multi-institutional accruement of UAC cases is necessary to further validate our novel findings.

Oncolytic vesicular stomatitis virus as a treatment for neuroendocrine tumors

BACKGROUND

Therapeutic goals for neuroendocrine tumors (NETs) not amenable to operative cure are limited to relieving symptoms and slowing progression. Many malignancies acquire defective antiviral responses as they undergo unregulated proliferation. Therefore, we explored the abilities of recombinant wild-type vesicular stomatitis virus and an attenuated matrix protein mutant (M51R-VSV) to exploit defective antiviral pathways in NETs.

METHODS

Viral infectivity and lethality were evaluated in a panel of human NET cell lines H727, UMC-11, and CNDT2.5. We evaluated β-interferon pathways in these cells to define the acquired defect. Murine xenografts were treated with a single intratumoral injection of M51R-VSV to study viral efficacy in vivo.

RESULTS

VSV infected >99% of cells within 24 hours and killed >95% within 72 hours. NET cells did not produce relevant amounts of β-interferon after infection, but exogenous β-interferon protected cells from oncolysis. Treatment with M51R-VSV resulted in suppressed tumor growth (mean value ± standard error of the mean) compared with mock-infected xenografts for H727 (87 ± 72% vs. 2,197 ± 335%; P < .001), UMC-11 (13 ± 59% vs. 1,471 ± 324%; P < .001), and CNDT2.5 (81 ± 121% vs. 1,576 ± 349%; P = .001).

CONCLUSION

VSV infects and kills human NETs by exploiting their inability to produce a type I antiviral response. Therefore, M51R-VSV is an excellent candidate for the treatment of advanced NETs.

Mammary analogue secretory carcinoma of the parotid gland as a secondary malignancy in a childhood survivor of atypical teratoid rhabdoid tumor

We report the first case of mammary analogue secretory carcinoma (MASC) arising as a secondary malignancy in a 14 years old child with a history of atypical teratoid rhabdoid tumor (ATRT). Although MASC and ATRT are both rare malignancies, they do not share the same genetic and molecular profiles. MASC is a salivary malignancy characterized by a t(12;15)(p13;q25) translocation, resulting in an ETV6-NTRK3 fusion product encoding for a tyrosine kinase. ATRT is a highly malignant pediatric tumor characterized by a chromosome 22 mutation in the hSNF5/INI1 gene, encoding for a chromatin remodeling protein. Additionally, although mucoepidermoid carcinoma has been described as a secondary malignancy post-therapy for head and neck tumors, MASC has only been reported as a primary malignancy. Our patient was treated with a complete resection of his left sided ATRT at age 3 followed postoperatively with chemoradiotherapy. At age 14 he underwent a parotidectomy for his 1 year history of a left sided preauricular mass and was subsequently diagnosed with MASC. We not only report a case of two rare malignancies in one patient, but also the first case of MASC arising as a secondary malignancy.

Surgeon-controlled robotic partial nephrectomy for a rare renal epithelioid angiomyolipoma using near-infrared fluorescence imaging using indocyanine green dye: A case report and literature review

Renal epithelioid angiomyolipoma (E-AML) is a rare variant of angiomyolipoma (AML). It is a mesenchymal tumour believed to originate from the perivascular epithelioid cell (PEC). Unlike conventional AML which are benign, E-AML has a rare aggressive behaviour. Conventional AML is typically triphasic containing adipose tissue, smooth muscle and dystrophic vessels in variable proportions, while E-AML are generally composed of plump spindled and polygonal-shaped “epithelioid cells” showing clear or eosinophilic cytoplasm and occasional pleomorphic multinucleated giant cells. E-AML can be misdiagnosed as renal cell carcinoma (RCC) when these “epithelioid cells” show clearing. Only a small number of cases of E-AML have been reported with the standard treatment being radical or partial nephrectomy. We report the first case report of a surgeon-controlled robotic partial nephrectomy using a near infrared fluorescence imaging using indocyanine green dye on a 25-year-old woman with a T1B (6.6 cm) right renal mass. The final pathology revealed the diagnosis of E-AML. There was no recurrence and metastases after the 6-month follow-up.

Surgeon-controlled robotic partial nephrectomy for a rare renal epithelioid angiomyolipoma using near-infrared fluorescence imaging using indocyanine green dye: A case report and literature review

Renal epithelioid angiomyolipoma (E-AML) is a rare variant of angiomyolipoma (AML). It is a mesenchymal tumour believed to originate from the perivascular epithelioid cell (PEC). Unlike conventional AML which are benign, E-AML has a rare aggressive behaviour. Conventional AML is typically triphasic containing adipose tissue, smooth muscle and dystrophic vessels in variable proportions, while E-AML are generally composed of plump spindled and polygonal-shaped "epithelioid cells" showing clear or eosinophilic cytoplasm and occasional pleomorphic multinucleated giant cells. E-AML can be misdiagnosed as renal cell carcinoma (RCC) when these "epithelioid cells" show clearing. Only a small number of cases of E-AML have been reported with the standard treatment being radical or partial nephrectomy. We report the first case report of a surgeon-controlled robotic partial nephrectomy using a near-infrared fluorescence imaging using indocyanine green dye on a 25-year-old woman with a T1B (6.6 cm) right renal mass. The final pathology revealed the diagnosis of E-AML. There was no recurrence and metastases after the 6-month follow-up.

Experience with voice recognition in surgical pathology at a large academic multi-institutional center

There are few reports of institutional use of voice recognition technology in clinical practice. We describe our experience with voice recognition-integrated synoptic-like dictation, associating templates with key spoken phrases, that we have used in gross examination of common specimens and as a major component of our workflow since 2001. The primary application is VoiceOver Enterprise (Voicebrook, Lake Success, NY), which uses Dragon NaturallySpeaking Medical Edition (Nuance Communications, Burlington, MA) as its speech engine. This integrates with the anatomic pathology laboratory information system (APLIS) and other applications, such as Microsoft Office (Microsoft, Redmond, WA). The largest user group, pathology assistants, mainly dictates biopsy reports, numbering approximately 210,000 specimens since 2001. The technology has been useful in our anatomic pathology workflow and provided a good return on investment, including marked improvements in turnaround time, results standardization, error reduction, and cost savings. The most helpful features of the software are templating, the seamless integration with APLIS, and the voice command creation tools.

Molecular Pathology of the Genitourinary Tract: Molecular Pathology of Kidney and Testes

With the advent of newer molecular technologies, our knowledge of cellular mechanisms with tumors of the kidney and testis has grown exponentially. Molecular technologies have led to better understanding of interplay between the von Hippel-Lindau gene and angiogenic cytokines in renal cancer and isochromosome 12p in testicular neoplasms. The result has been development of antiangiogenic-targeted therapy within recent years that has become the mainstay treatment for metastatic renal cell cancer. In the near future, classification and diagnosis of renal and testicular tumors through morphologic analysis will be supplemented by molecular information correlating to prognosis and targeted therapy. This article outlines tumor molecular pathology of the kidney and testis encompassing current genomic, epigenomic, and proteonomic findings.

Molecular Pathology of the Genitourinary Tract: Prostate and Bladder

The knowledge of cellular mechanisms in tumors of the prostate and bladder has grown exponentially. Molecular technologies have led to the discovery of TMPRSS2 in prostate cancer and the molecular pathways distinguishing low- and high-grade urothelial neoplasms. UroVysion with fluorescence in situ hybridization is already commonplace as an adjunct to cytologic diagnosis of urothelial neoplasms. This trend portends the future in which classification and diagnosis of tumors of the prostate and bladder through morphologic analysis will be supplemented by molecular information correlating with prognosis and targeted therapy. This article outlines tumor molecular pathology of the prostate and bladder encompassing current genomic, epigenomic, and proteonomic findings.

Impact of lymphadenectomy and nodal burden in renal cell carcinoma: retrospective analysis of the National Surveillance, Epidemiology, and End Results database

OBJECTIVES

To analyze the additional impact of retroperitoneal lymphadenectomy on overall and cancer-specific survival (CSS) in patients with primary renal cell carcinoma (RCC) undergoing radical nephrectomy. The benefit of regional lymphadenectomy in patients with primary RCC remains controversial.

METHODS

Of 33,016 patients diagnosed with primary RCC between 1983 and 1998, a subset of 4453 underwent radical nephrectomy with or without regional lymphadenectomy. The extent of lymphadenectomy was assessed using the number of nodes examined, and the tumor burden was assessed using the number of positive nodes and the ratio of the number of positive nodes to the total number of nodes examined. Associations between CSS and the number of nodes examined, number of positive nodes, and ratio of the number of positive nodes to the total number of nodes examined were assessed.

RESULTS

An inverse correlation was found between the likelihood of CSS and the number of nodes examined, particularly for those with regional disease even after controlling for other factors. A correlation was noted between the number of nodes examined and the number of positive nodes. Significant differences in CSS were observed in node-negative patients with regional disease compared with node-positive patients. An increasing nodal burden was associated with worse CSS.

CONCLUSIONS

More extensive lymphadenectomy does not appear to increase further the probability of CSS in patients undergoing radical nephrectomy for RCC. An increased number of positive nodes, as well as an increasing nodal burden, although associated with a lower likelihood of survival, were not independent predictors of RCC-specific mortality.

Suppression of spinal and cortical somatosensory evoked potentials by desflurane anesthesia

The effect of the volatile anesthetic desflurane on spinal and cortical somatosensory evoked potentials (SEPs) was examined in 11 Sprague-Dawley male rats. Platinum recording electrodes were placed stereotactically over the left somatosensory cortex and dorsal midline of the T11-12 spinal cord while the right posterior tibial nerve was stimulated at twice motor threshold. The effect of desflurane was examined at various concentrations ranging from 0.7 to 11.4% (2 MAC). Mean arterial blood pressure (MAP) decreased (p = 0.001) progressively with increasing end-tidal desflurane concentrations. Concentrations of 1.4% (1/4 MAC) and 2.8% (1/2 MAC) did not significantly affect the spinal SEP (SSEP) amplitude or the latency. With higher concentrations, there was a progressive decrease in amplitude of the cortical SEPs (CSEPs; p = 0.002) and SSEPs (p = 0.008). However, CSEP and SSEP latencies did not change. At 5.7% (1 MAC), three animals (33%) lost CSEPs while SSEPs remained intact. At 11.4% (2 MAC), the CSEPs were lost in all animals. Only one rat lost the SSEPs at the 2 MAC concentration of desflurane, indicating the resistance of the SSEPs to desflurane anesthesia. We conclude that desflurane anesthesia significantly alters the amplitude of SSEPs and CSEPs without a significant change in the peak latency.