Thomas A. Thomson

Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors.

BackgroundAdenocarcinomas of the tongue are rare and represent the minority (20 to 25%) of salivary gland tumors affecting the tongue. We investigated the utility of massively parallel sequencing to characterize an adenocarcinoma of the tongue, before and after treatment.ResultsIn the pre-treatment tumor we identified 7,629 genes within regions of copy number gain. There were 1,078 genes that exhibited increased expression relative to the blood and unrelated tumors and four genes contained somatic protein-coding mutations. Our analysis suggested the tumor cells were driven by the RET oncogene. Genes whose protein products are targeted by the RET inhibitors sunitinib and sorafenib correlated with being amplified and or highly expressed. Consistent with our observations, administration of sunitinib was associated with stable disease lasting 4 months, after which the lung lesions began to grow. Administration of sorafenib and sulindac provided disease stabilization for an additional 3 months after which the cancer progressed and new lesions appeared. A recurring metastasis possessed 7,288 genes within copy number amplicons, 385 genes exhibiting increased expression relative to other tumors and 9 new somatic protein coding mutations. The observed mutations and amplifications were consistent with therapeutic resistance arising through activation of the MAPK and AKT pathways.ConclusionsWe conclude that complete genomic characterization of a rare tumor has the potential to aid in clinical decision making and identifying therapeutic approaches where no established treatment protocols exist. These results also provide direct in vivo genomic evidence for mutational evolution within a tumor under drug selection and potential mechanisms of drug resistance accrual.

Tissue Microarray for Routine Analysis of Breast Biomarkers in the Clinical Laboratory

Tissue microarray analysis (TMA) allows multiple analyses on multiple patients on sections from a single paraffin block. Although it is widely used in research and in quality assurance settings, there are few references to its use in clinical practice. This study evaluated TMA assessment of breast biomarkers using immunohistochemical analysis in a clinical histopathology laboratory. Performance parameters, interobserver variability, and concordance between TMA and whole section results were assessed. The arrays had few lost or noninformative cores. A loss of stain intensity occurred in the arrays compared with the whole sections with some but not all antibodies, highlighting the need to validate the staining protocol for each antibody used on TMA sections. With recommended guidelines for specimen selection and reporting, TMA was found to be an economical replacement for whole section analysis for breast biomarkers.

Fine-needle aspiration of renal and extrarenal rhabdoid tumors: the experience of the Institut Curie regarding 20 tumors in 13 patients.

Rhabdoid tumors (RT) are rare, renal or extrarenal, high‐grade malignancies. The cytologic diagnosis may be confirmed if combined with genomic results. In the current study, the authors present the cytologic and ancillary techniques used to diagnose RT in their series of 20 tumors in 13 patients.

Assessment of ERCC1 and XPF Protein Expression Using Quantitative Immunohistochemistry in Nasopharyngeal Carcinoma Patients Undergoing Curative Intent Treatment

PURPOSE We sought to evaluate the prognostic/predictive value of ERCC1 and XPF in patients with nonmetastatic nasopharyngeal carcinoma (NPC) treated with curative intent. METHODS AND MATERIALS ERCC1 and XPF protein expression was evaluated by immunofluorescence combined with automated quantitative analysis (AQUA) using the FL297 and 3F2 antibodies, respectively. ERCC1 and XPF protein expression levels were correlated with clinical outcomes. RESULTS Patient characteristics were as follows: mean age 52 years (range, 18-85 years), 67% male, 72% Karnofsky performance status (KPS) ≥ 90%, World Health Organization (WHO) type 1/2/3 = 12%/28%/60%, stage III/IV 65%. With a median follow-up time of 50 months (range, 2.9 to 120 months), the 5-year overall survival (OS) was 70.8%. Median standardized nuclear AQUA scores were used as cutpoints for ERCC1 (n=138) and XPF (n=130) protein expression. Agreement between dichotomized ERCC1 and XPF scores was high at 79.4% (kappa = 0.587, P<.001). Neither biomarker predicted locoregional recurrence, DFS, or OS after adjustment for age and KPS, irrespective of stratification by stage, WHO type, or treatment. CONCLUSIONS Neither ERCC1 nor XPF, analyzed by quantitative immunohistochemistry using the FL297 and 3F2 antibodies, was prognostic or predictive in this cohort of NPC patients.

Genomic analysis of a rare human tumor

Genomic analysis of a rare human tumor Steven JM Jones, Janessa Laskin, Yvonne Y Li, Obi L Griffith, Jianghong An, Mikhail Bilenky, Yaron S Butterfield, Timothee Cezard, Eric Chuah, Richard Corbett, Anthony Fejes, Malachi Griffith, John Yee, Montgomery Martin, Michael Mayo, Nataliya Melnyk, Ryan D Morin, Trevor J Pugh, Tesa Severson, Sohrab P Shah, Margaret Sutcliffe, Angela Tam, Jefferson Terry, Nina Thiessen, Thomas Thomson, Richard Varhol, Thomas Zeng, Yongjun Zhao, Richard A Moore, David G Huntsman, Inanc Birol, Martin Hirst, Robert A Holt, Marco A Marra

Tissue microarray for routine clinical breast biomarker analysis. The British Columbia Cancer Agency 2008 experience.

Clinical use of tissue microarrays for immunohistochemical analysis of breast biomarkers, namely estrogen receptor, progesterone receptor, and HER2, was instituted in our laboratory in 2008. The method has proved reliable and cost-effective. We report the results of the initial year of testing with this method.

Diagnosis of Ovarian Carcinoma Histotype Based on Limited Sampling: A Prospective Study Comparing Cytology, Frozen Section, and Core Biopsies to Full Pathologic Examination.

Growing insights into the biological features and molecular underpinnings of ovarian cancer has prompted a shift toward histotype-specific treatments and clinical trials. As a result, the preoperative diagnosis of ovarian carcinomas based on small tissue sampling is rapidly gaining importance. The data on the accuracy of ovarian carcinoma histotype-specific diagnosis based on small tissue samples, however, remains very limited in the literature. Herein, we describe a prospective series of 30 ovarian tumors diagnosed using cytology, frozen section, core needle biopsy, and immunohistochemistry (p53, p16, WT1, HNF-1&bgr;, ARID1A, TFF3, vimentin, and PR). The accuracy of histotype diagnosis using each of these modalities was 52%, 81%, 85%, and 84% respectively, using the final pathology report as the reference standard. The accuracy of histotype diagnosis using the Calculator for Ovarian Subtype Prediction (COSP), which evaluates immunohistochemical stains independent of histopathologic features, was 85%. Diagnostic accuracy varied across histotype and was lowest for endometrioid carcinoma across all diagnostic modalities (54%). High-grade serous carcinomas were the most overdiagnosed on core needle biopsy (accounting for 45% of misdiagnoses) and clear cell carcinomas the most overdiagnosed on frozen section (accounting for 36% of misdiagnoses). On core needle biopsy, 2/30 (7%) cases had a higher grade lesion missed due to sampling limitations. In this study, we identify several challenges in the diagnosis of ovarian tumors based on limited tissue sampling. Recognition of these scenarios can help improve diagnostic accuracy as we move forward with histotype-specific therapeutic strategies.

ATM, THMS, and RRM1 protein expression in nasopharyngeal carcinomas treated with curative intent

In advanced nasopharyngeal carcinoma (NPC), biomarkers may help predict survival.

Pericellular lacunae in the diagnosis of metastatic carcinoma in effusions: Is this a useful sign?

The presence of pericellular lacunae has been cited as a useful criterion in distinguishing between benign and malignant effusions from body cavities. This study assessed the presence of pericellular lacunae in 75 specimens of malignant and 38 specimens of benign effusions. In a large number of cases, lacunae could not be assessed reliably because of technical and artifactual reasons. Pericellular lacunae were detected around the majority of the cell clusters in only 4 of the malignant and 2 of the benign cases. In our material, peri‐cellular lacunae were not a useful criterion for the diagnosis of malignancy in body cavity fluids. Diagn Cytopathol 1996;15:193–196.

Abstract PR02: Integrated genomic analysis of a recurrent ghost cell odontogenic carcinoma

Introduction: The Personalized OncoGenomics (POG) project launched at the British Columbia Cancer Agency uses genome analyses to support cancer treatment decision making. The POG project enrolls patients with incurable cancers for which standard chemotherapy regimens fail or do not exist. Here we report the first genomic sequence of a ghost cell odontogenic carcinoma (GCOC) patient enrolled in the POG program. GCOC is a very rare cancer of the maxillofacial apparatus and only 35 GCOC cases have been reported in the literature. The etiology of GCOC is largely unknown and genomic profiling of this rare cancer-type has not been previously reported. Methods: We performed whole genome sequencing (WGS; ~100X coverage) and transcriptome sequencing (RNA-seq) of a fresh tumor biopsy sample and WGS (~50X coverage) of DNA purified from peripheral blood. Bioinformatics approaches were used to identify genes with somatic single nucleotide variants (SNVs), copy number variants (CNVs), structural variants (SVs), and expression changes. All variants were integrated to build an individual somatic molecular profile, followed by intensive pathway analysis and literature searches to identify the candidate biological processes that are deregulated. Based on the integration of these results, therapeutic options were explored. Results: The tumor genome was highly aneuploid with extensive regions of loss of heterozygosity. Homozygous deletion of RB1 and heterozygous loss of PTEN , RASSF4 and FHIT tumor suppressors was observed. Oncogenes belonging to the sonic hedgehog pathway ( GLI1 and SHH ) as well as a variety of other oncogenes including AURKA , AKT1 , GSK3B , MYCN also showed gains in copy number. Among the genes with predicted protein altering SNVs were APC , HLF , TWIST1 and UBR5 . The only translocation resulting in an expressed RNA product, a reciprocal t(3;18), resulted in a novel fusion involving the TCF4 and PTPRG genes. The predicted fusion product lacks all the functional domains of the PTPRG gene including the phosphatase domain, possibly leading to the loss of tumor suppressor activity. Oncogenes involved in tyrosine kinase signaling ( EGFR , KIT , FGFR1 ), various members of the PI3-kinase-mTOR pathway including PIK3R2 , PIK3CA and MYCN , members of the NOTCH signaling pathway ( NOTCH1 , NOTCH3 , JAG1 , DTX4 , HES2 and HEY1 ), the hedgehog pathway ( PTCH1 , GLI1 , TWIST1 and TWIST2 ), and the WNT pathway ( WNT4 , WNT5A , FZD2 , FZD10 , DVL3 and GSK3B ) were highly expressed in the GCOC sample. Conclusions: This study represents the first integrated genomic and transcriptomic analysis of a GCOC genome. Based on alterations in tyrosine kinase, PI3-kinase-mTOR, hedgehog and NOTCH pathways, inhibitors to these pathways were identified as therapeutic options. This abstract is also presented as Poster 06. Citation Format: Pinaki Bose, Erin Pleasance, Martin Jones, Yaoqing Shen, Carolyn Ch9ng, Caralyn Reisle, Jacqueline E. Schein, Andrew Mungall, Richard Moore, Yussanne Ma, Brandon S. Sheffield, Thomas Thomson, Steven Rasmussen, Christopher Lee, Stephen Yip, Marco A. Marra, Janessa Laskin, Cheryl Ho, Steven J. M. Jones. Integrated genomic analysis of a recurrent ghost cell odontogenic carcinoma. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Integrating Clinical Genomics and Cancer Therapy; Jun 13-16, 2015; Salt Lake City, UT. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(1_Suppl):Abstract nr PR02.