CAP-ACP Workload Model for Advanced Diagnostics in Precision Medicine

OBJECTIVES

In precision medicine, where oncologic management is tailored to the individual's clinical and genetic profiles, advanced diagnostic testing provides prognostic information and guides management in a growing number of malignancies. There is a need to capture the work pathologists perform to meet this demand by providing medically relevant, timely, and accurate testing results. This work includes not only direct patient consults (interpretation of results and issuing reports) but the administrative and medical oversight as well as the research needed to provide the necessary quality assurance, quality control, direction, and framework for the laboratory.

METHODS

An expert panel of Canadian pathologists involved in advanced diagnostics was convened to establish and beta test a model for workload assessment in advanced diagnostics.

RESULTS

All aspects of the advanced diagnostics workload were detailed and applied to models based on members' experience, including medical oversight, administration, and the introduction of new testing and platforms. Models for biomarker testing were developed for simple and complex or multiplexed assays, and a detailed model was developed to assess the workload for next-generation sequencing-based assays.

CONCLUSIONS

This paper provides the first detailed proposal for capturing an advanced diagnostic workload to enable appropriate pathologist allotment for performing all the steps required to run an advanced diagnostic service.

Developing a panel of biomarkers and miRNA in patients with myocardial infarction for early intervention strategies of heart failure in West Virginian population

Background

Myocardial infarction is the most common cause of heart failure. MI has been intricately linked to ventricular remodeling, subsequently leading to the reduction in the cardiac ejection fraction causing HF. The cumulative line of evidence suggests an important role of several biomarkers in modulating the cardiac vasculature, further contributing towards the progression of post-MI complications. Studies have demonstrated, yet not fully established, that an important biomarker, IL-10, has a causal relationship with MI and associated cardiac dysfunction.

Hypothesis

This study aims to establish the role of IL-10 as a prognostic marker for the cardiovascular outcomes and to develop a panel of biomarkers and circulating miRNAs that could potentially result in the early detection of HF resulting from MI, allowing for early intervention strategies.

Methods and results

Blood was withdrawn and echocardiography assessment was performed on a total of 43 patients that were enrolled, within 24 hours of the incidence of MI. Patients were divided in three main groups, based on the ejection fraction measurement from echocardiography: control (n = 14), MI with normal EF (MI+NEF, n = 13) and MI with low EF (MI+LEF, n = 16). Our results showed that TGFβ-1, TNF-α, IL-6 and MMP-9 were upregulated significantly in MI+NEF group and more so in MI+LEF group, as compared to control group (p<0.01). The circulating levels of miR-34a, miR-208b and miR-126 were positively correlated and showed elevated levels in the MI+NEF group, even higher in MI+LEF group, while levels of miR-24 and miR-29a were reduced in MI+NEF, and much lower in MI+LEF, as compared to the control group (p<0.01). Our results also demonstrated a direct correlation of IL-10 with the ejection fraction in patients with MI: IL-10 was elevated in MI+NEF group, however, the levels were significantly low in MI+LEF group suggesting an important role of IL-10 in predicting heart failure. Importantly, our study confirmed the correlation of IL-10 with EF by our follow-up echocardiography assessment that was performed 2 months after the incidence of MI.

Conclusion

Our results support the clinical application of these serum biomarkers to develop a panel for appropriate prognosis and management of adverse cardiac remodeling and development of heart failure post-myocardial infarction.

The ASOS Surgical Risk Calculator: development and validation of a tool for identifying African surgical patients at risk of severe postoperative complications

BACKGROUND

The African Surgical Outcomes Study (ASOS) showed that surgical patients in Africa have a mortality twice the global average. Existing risk assessment tools are not valid for use in this population because the pattern of risk for poor outcomes differs from high-income countries. The objective of this study was to derive and validate a simple, preoperative risk stratification tool to identify African surgical patients at risk for in-hospital postoperative mortality and severe complications.

METHODS

ASOS was a 7-day prospective cohort study of adult patients undergoing surgery in Africa. The ASOS Surgical Risk Calculator was constructed with a multivariable logistic regression model for the outcome of in-hospital mortality and severe postoperative complications. The following preoperative risk factors were entered into the model; age, sex, smoking status, ASA physical status, preoperative chronic comorbid conditions, indication for surgery, urgency, severity, and type of surgery.

RESULTS

The model was derived from 8799 patients from 168 African hospitals. The composite outcome of severe postoperative complications and death occurred in 423/8799 (4.8%) patients. The ASOS Surgical Risk Calculator includes the following risk factors: age, ASA physical status, indication for surgery, urgency, severity, and type of surgery. The model showed good discrimination with an area under the receiver operating characteristic curve of 0.805 and good calibration with c-statistic corrected for optimism of 0.784.

CONCLUSIONS

This simple preoperative risk calculator could be used to identify high-risk surgical patients in African hospitals and facilitate increased postoperative surveillance.

CLINICAL TRIAL REGISTRATION

NCT03044899.

Tissue kallikreins: new players in normal and abnormal cell growth?

Serine proteases are proteolytic enzymes with an active serine residue in their catalytic site. Kallikreins are a subgroup of the serine protease family and are known to have diverse physiological functions. The human tissue kallikrein gene family has now been fully characterized and includes 15 members, clustered in a 300 kb region on chromosome 19q13.4. In this review, we discuss the common structural features of kallik-reins at the DNA, mRNA and protein levels. Kallikreins are secreted as inactive zymogens and are activated by cleavage of an N-terminal peptide. Some kallikreins can undergo autoactivation while others may be activated by other kallikreins or other proteases. Most kallikreins are predicted to have trypsin-like enzymatic activity except for three members which may have chymotrypsin-like activity. Circumstantial evidence suggests that at least some kallikreins may be part of an enzymatic cascade pathway which is activated in aggressive forms of ovarian and probably other cancers. Accumulating evidence suggests potential diagnostic and/or prognostic roles of kallikreins in diverse malignancies. In addition to PSA, many other kallik-reins show differential expression in malignancy. For example, hK6, 10 and 11 are promising serological markers for ovarian cancer diagnosis. KLK10 may act as a tumor suppressor. In addition to their diagnostic and prognostic values, kallikreins may also be good therapeutic targets.

Part of this paper was originally presented at the joint meetings of the 16th International Congress of the International Society of Fibrinolysis and Proteolysis (ISFP) and the 17th International Fibrinogen Workshop of the International Fibrinogen Research Society (IFRS) held in Munich, Germany, September, 2002.

Abstract 2464: Papillary renal cell carcinoma, proposal of a new classification system based on integrated molecular, histological and clinical analysis

Background:

Papillary Renal Cell Carcinoma (PRCC) is divided into histological subtypes 1 and 2. Type 2 is known to have worse clinical behavior. A number of PRCC cases (~ 50%), fail to meet all reported morphological criteria for either type, hence are best characterized as PRCC not otherwise specified (NOS). There are yet no reliable markers to resolve the PRCC NOS category. That in turn reflects the clinical dilemma of how to manage these patients.

Experimental Design:

PRCC patient cohort of 115 cases was selected for the study. Cases were subtyped histologically into PRCC types 1, 2 and NOS. Potentially distinguishing markers ABCC2, CA9, SAll4, and BCL2 selected from our previous genomic analysis, were assessed by immunohistochemistry (IHC). A total of 24 cases were further selected for molecular analysis using miRNA expression and copy number variation (CNV). Univariate and multivariate survival analysis were performed using Log rank test and cox proportionate hazards.

Results:

Markers ABCC2, CA9 exhibited distinct staining patterns between the two classic PRCC subtypes; and successfully classified many of the PRCC NOS (45%) cases. Moreover, immunomarkers revealed a third distinct subtype of PRCC (35% of the PRCC cohort). Molecular

testing using miRNA expression and CNV analysis confirmed the presence of three distinct molecular signatures corresponding to the 3 subtypes. On univariate analysis DFS was significantly enhanced in the type1 versus 2& 3 (p value 0.047). PRCC subtyping retained

significance on multivariate analysis (p value 0.025, HR:6, 95% CI 1.25 to 32.2) .

Conclusion:

We propose a new classification system of PRCC integrating morphological, immunophenotypical, and molecular analysis. Our classification reveals a 3rd PRCC subtype that was not previously described. This subtype has overlapping morphology of with PRCC types 1 and 2, hence would be subtyped as PRCC NOS in the current classification. Molecularly PRCC type 3 has a distinct signature and clinically it behaves similar to PRCC type 2. The new classification stratifies PRCC patients into clinically relevant subgroups and has significant future implications on the management of PRCC.

Citation Format: Rola Saleeb, Mina Farag, Fadi Brimo, Fabio Rotondo, Pamela Plant, George Yousef. Papillary renal cell carcinoma, proposal of a new classification system based on integrated molecular, histological and clinical analysis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2464. doi:10.1158/1538-7445.AM2017-2464

Abstract 811: Histological heterogeneity contributes to sunitinib resistance in clear cell renal cell carcinoma

Introduction: The receptor tyrosine kinase (RTK) inhibitor sunitinib is the first line treatment for advanced clear cell renal cell carcinoma (ccRCC). Sunitinib inhibits angiogenesis via blocking signaling through VEGFR. About 80% of patients develop resistance after a drug-sensitive period. Molecular changes early in treatment may impact drug resistance, but are poorly understood.

Experimental Procedures: ACHN, 786-O and Renca cell lines were treated with 1 µM sunitinib. NSG mice were s.c. xenografted with the model cell lines and were treated with sunitinib at 40 mg/kg/day dose. mRNA expression was screened using Illumina HT-12 bead chip array and miRNA expression was assessed by Nanostring nCounter assay. R statistical packages were used for data processing. Reactome and miRPath softwares were used for downstream analysis.

Results: Sunitinib treatment of ccRCC xenografts led to several early changes in tumor histology, such as the emergence of live tumor areas within the necrotic spaces. These areas showed membranous staining for E-cadherin, and β-catenin, while the rest of the tumor and vehicle-treated tumors were negative. In vitro model cell lines developed cancer spheroids when treated with sunitinib. Cancer spheroids were highly tumorigenic and metastatic, and expressed several established cancer stem cell markers. ccRCC cancer spheres, but not the 2D adherent cells, showed membranous staining for E-cadherin and β-catenin; similarly to the live tumor areas observed in

in vivo sunitinib treatment. In vitro inhibition of E-cadherin by EGTA or by siRNA, interfered with viability of sunitinib treated ccRCC cell lines.

Conclusions: Sunitinib treatment causes early phenotypic changes of the tumor in vivo and in vitro. The formation of highly metastatic and tumorigenic cancer spheres in model cell lines is the most prominent effect in vitro. We provide preliminary evidence that sunitinib induced in vitro cancer spheres and the live tumor areas that survive within necrotic patches of the sunitinib-treated xenografts, are related. Finally, membranous expression of E-cadherin enhances the survival of ccRCC cell lines under sunitinib treatment.

Citation Format: Zsuzsanna Lichner, Rola Saleeb, Henriett Butz, Roy Nofech-Mozes, Sara Riad, Mina Farag, Andras Kapus, George Yousef. Histological heterogeneity contributes to sunitinib resistance in clear cell renal cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 811. doi:10.1158/1538-7445.AM2017-811

Abstract 5447: A microRNA signature for the classification of renal cell carcinoma subtypes

Introduction: Renal cell carcinoma (RCC) accounts for 90% of all kidney cancers. It comprises a heterogeneous group of renal tumors with distinct genetic and molecular characteristics including

clear cell RCC (ccRCC), papillary RCC (pRCC) and chromophobe RCC (chRCC). The differential diagnosis of RCC subtypes relies on distinct morphology which is not always accurate. Accurate classification of RCC subtypes is critical since each exhibits different clinical behaviour, prognosis and response to therapy. The purpose of this study is to determine whether a limited number of

miRNAs can classify RCC subtypes with high accuracy.

Experimental Design: We extracted RNA from 90 formalin-fixed paraffin-embedded (FFPE) tissues including 27 clear cell RCC, 29 papillary RCC, 19 chromophobe RCC, 4 unclassified RCC tumors and 11 oncocytomas. We measured the absolute expression of six miRNAs by qRT-PCR. Receiver operator characteristic curves were constructed and the area under the curve (AUC) was calculated to assess diagnostic performance. We also tested miRNA expression by in situ hybridization (ISH) in an independent set of ninety-eight FFPE renal tumors.

Results: We developed a two-step miRNA classifier. In the first step, expressions of selected miRNAs were found to discriminate clear cell RCC and papillary RCC from chromophobe RCC and renal oncocytoma. Two miRNAs were able to discriminate clear cell RCC and papillary RCC from chromophobe RCC and oncocytoma. miR-221 was significantly overexpressed in chromophobe RCC and oncocytoma compared to clear cell RCC and papillary RCC (4.49-fold change, p= 6.398e-010) and was able to discriminate between the two groups (AUC: 0.9637, 95% CI: 0.9132 to 1.014, p&lt;0.0001). In the second step, the absolute expression of two miRNAs could distinguish clear cell RCC from papillary RCC (10.4-fold change, p = 1.243e-013). Moreover, an additional two miRNAs could differentiate chromophobe RCC from renal oncocytoma (3.30- fold change, p = 1.751e-006). In situ hybridization revealed that miRNAs display a nuclear staining pattern that was able to distinguish clear cell RCC from papillary RCC (p&lt;0.001) and chromophobe RCC from renal oncocytoma (p =0.009).

Conclusion: miRNA expressions were able to distinguish between RCC subtypes and renal oncocytoma. miRNA assessment by in situ hybridization is a clinically useful diagnostic tool that can complement current methods for RCC classification.

Citation Format: Ashley Di Meo, Mereet Hanna, Rola Saleeb, Samantha Wala, Adriana Krizova, Manal Gabril, Haiyan Zhai, Maria Pasic, Andrew Evans, Fadi Brimo, George Yousef. A microRNA signature for the classification of renal cell carcinoma subtypes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5447. doi:10.1158/1538-7445.AM2017-5447

Direct Comparison of Metastasis-Related miRNAs Expression Levels in Circulating Tumor Cells, Corresponding Plasma, and Primary Tumors of Breast Cancer Patients

BACKGROUND

Circulating tumor cells (CTCs) and microRNAs (miRNAs) are important in liquid biopsies in which peripheral blood is used to characterize the evolution of solid tumors. We evaluated the expression levels of miR-21, miR-146a, miR-200c, and miR-210 in CTCs of breast cancer patients with verified metastasis and compared their expression levels in corresponding plasma and primary tumors.

METHODS

Expression levels of the miRNAs were quantified by quantitative reverse transcription PCR (RT-qPCR) in (a) 89 primary breast tumors and 30 noncancerous breast tissues and (b) CTCs and corresponding plasma of 55 patients with metastatic breast cancer and 20 healthy donors. For 30 of these patients, CTCs, corresponding plasma, and primary tumor tissues were available.

RESULTS

In formalin-fixed, paraffin-embedded tissues, these miRNAs were differentially expressed between primary breast tumors and noncancerous breast tissues. miR-21 (P &lt; 0.001) and miR-146a (P = 0.001) were overexpressed, whereas miR-200c (P = 0.004) and miR-210 (P = 0.002) were underexpressed. In multivariate analysis, miR-146a overexpression was significantly [hazard ratio 2.969 (1.231–7.157), P = 0.015] associated with progression-free survival. In peripheral blood, all miRNAs studied were overexpressed in both CTC and corresponding plasma. There was a significant association between miR-21 expression levels in CTCs and plasma for 36 of 55 samples (P = 0.008). In plasma, ROC curve analysis revealed that miR-21, miR-146a, and miR-210 could discriminate patients from healthy individuals.

CONCLUSIONS

Metastasis-related miRNAs are overexpressed in CTCs and corresponding plasma; miR-21 expression levels highly correlate in CTCs and plasma; and miR-21, miR-146a, and miR-210 are valuable plasma biomarkers for discriminating patients from healthy individuals.

Giant fibroepithelial polyp of the glans penis not associated with condom-catheter use: A case report and literature review

Fibroepithelial polyps are rare benign tumours of the glans penis; there are only a few reported cases. The pathogenesis is unknown. However, they have been linked with chronic condom catheter use or prior penile surgery. We report a case of a 62-year-old man with a large fibroepithelial polyp of the glans penis of 11 years duration, which was not associated with condom catheter use or prior surgery. The mass was large, measuring 7 × 5 × 3 cm. Fibroepithelial polyps have been reported in a range of genito-urinary sites in males and females, adults and children, and in rare cases may be associated with malignant transformation. They should be considered in the differential diagnosis of both cutaneous and mucosal genitourinary lesions.

Subungual Metastasis from a Rectal Primary: Case Report and Review of the Literature

BACKGROUND

Subungual metastases from colorectal cancer are unusual and have mainly been reported in patients with lung, genitourinary, and breast cancer.

OBJECTIVE

We present the case of a 72-year-old man with rectal adenocarcinoma and a subungual metastasis to the left thumb 5 years later.

METHODS

A case report and a brief review of the literature of subungual metastases are given.

RESULTS

The thumb was amputated and the patient died 6 months later with extensive metastatic disease.

CONCLUSION

Metastatic carcinoma should be considered in the differential diagnosis of persistent subungual masses, particularly in patients with a history of cancer. The prognosis with such lesions is generally poor.

Human tissue kallikreins and testicular cancer

Human tissue kallikreins are fifteen homologous genes encoding for secreted serine proteases and residing tandemly on chromosome 19q13.4. These enzymes are highly expressed in a variety of tissues and participate in diverse physiological processes. Human tissue kallikreins were found to be associated with several malignancies, especially endocrine-related cancers, including prostate, ovarian, breast and testicular cancer. In testicular germ cell tumors, some tissue kallikrein genes, including KLK5, KLK10, KLK13 and KLK14, were found to be significantly down-regulated. Tissue-specific splice variant forms of some kallikreins have been identified in the testis. In this paper, the expression of KLK5, KLK10, KLK13 and KLK14 in testicular cancer and their possible roles during testicular cancer development, as well as their clinical applications are briefly reviewed.

A preliminary report: a new scale to identify the pseudodementia syndrome

BACKGROUND

The literature was reviewed to abstract items which were claimed to distinguish organic dementia from pseudodementia. Their discriminating powers were tested in a prospective study. Eighteen of these items were selected to create a questionnaire which should distinguish organic dementia from pseudodementia. The gold standard was the final diagnosis given by a consultant psychiatrist 12-14 months later.

METHOD

One hundred and twenty-eight patients referred to our service with a differential diagnosis of depressive pseudodementia were screened using a checklist of 44 characteristic features (in the form of questions with 'yes' or 'no' answers) which were claimed in the literature of differentiate between organic dementia and depressive pseudodementia. This checklist covers the areas of history, clinical data, insight and performance.

RESULTS

Forty points (questions) out of the 44 in the checklist showed significant discriminating power to differentiate dementia from depressive pseudodementia (p < 0.01). A principal component and factor analysis was performed from which 18 questions were extracted. The shortened questionnaire was able to classify (43/44 cases) 98% of dementia cases and (60/63) 95% of depression correctly. A new definition has been introduced for 'pseudodementia' as a syndrome of reversible subjective or objective cognitive problems caused by non-organic disorder. Thus depressive pseudodementia may be classified into two subtypes. Type I is a group of patients who have depressive symptoms with subject complaint of dysmnesia without measurable intellectual deficits. Type II is a group of patients who have depressive symptoms and show poor cognitive performance based on poor concentration not due to organic disorder.

Khat chewing as a cause of psychosis

It is well established that psychosis may arise in the context of abuse of certain illicit drugs (e.g. amphetamine). This article reviews the effects of chewing the plant khat and outlines the pharmacological aspects, the dependence issue and a comparative study between previously reported cases and four cases reported here to highlight the epidemiology, clinical features and prognosis of khat-induced psychosis.

Persistence of hepatitis A virus in fulminant hepatitis and after liver transplantation

A peroxidase-labelled, specific mouse monoclonal antibody to hepatitis A virus (HAV) and an in situ hybridization technique (streptavidin-biotin-horseradish peroxidase reaction) with an HAV-specific cDNA probe (recombinant plasmid pAWHA comprising 1.8 kb of the HAV-specific cDNA, located toward the 3' end of the genome) were used to detect HAV in liver tissues in two patients with fulminant viral hepatitis type A treated by liver transplantation after a protracted (day 40: case 1) and relapsing (day 60: case 2) clinical course. HAV antigens and HAV-specific genomic sequences were detected in the hepatectomy tissues and in serial biopsies of the liver grafts through to final follow-up at 2 months (case 2) or death at 7 months after re-grafting for chronic rejection (case 1). In the fulminant liver parenchyma, numerous degenerating and some surviving hepatocytes were positive and randomly scattered. The immunoperoxidase staining was predominantly cytoplasmic and often granular. The localization of the cDNA probe was predominantly nuclear/perinuclear but was occasionally cytoplasmic. High-titre IgM-anti-HAV antibodies persisted until death (case 1) or resolution (5 months) of an acute hepatitis (case 2), which occurred at 2 months, accompanied by HAV antigen (ELISA), in stool. Intact replicating virus particles must have been present in one or more sites in each case, including extrahepatic locations, with a viraemia as the most likely explanation for subsequent reinfection of the grafts.