A Pan-Canadian Validation Study for the Detection of EGFR T790M Mutation Using Circulating Tumor DNA From Peripheral Blood.

INTRODUCTION: Genotyping circulating tumor DNA (ctDNA) is a promising noninvasive clinical tool to identify the EGFR T790M resistance mutation in patients with advanced NSCLC with resistance to EGFR inhibitors. To facilitate standardization and clinical adoption of ctDNA testing across Canada, we developed a 2-phase multicenter study to standardize T790M mutation detection using plasma ctDNA testing. METHODS: In phase 1, commercial reference standards were distributed to participating clinical laboratories, to use their existing platforms for mutation detection. Baseline performance characteristics were established using known and blinded engineered plasma samples spiked with predetermined concentrations of T790M, L858R, and exon 19 deletion variants. In phase II, peripheral blood collected from local patients with known EGFR activating mutations and progressing on treatment were assayed for the presence of EGFR variants and concordance with a clinically validated test at the reference laboratory. RESULTS: All laboratories in phase 1 detected the variants at 0.5 % and 5.0 % allele frequencies, with no false positives. In phase 2, the concordance with the reference laboratory for detection of both the primary and resistance mutation was high, with next-generation sequencing and droplet digital polymerase chain reaction exhibiting the best overall concordance. Data also suggested that the ability to detect mutations at clinically relevant limits of detection is generally not platform-specific, but rather impacted by laboratory-specific practices. CONCLUSIONS: Discrepancies among sending laboratories using the same assay suggest that laboratory-specific practices may impact performance. In addition, a negative or inconclusive ctDNA test should be followed by tumor testing when possible.

MCF: a tool to find multi-scale community profiles in biological networks.

Recent developments of complex graph clustering methods have implicated the practical applications with biological networks in different settings. Multi-scale Community Finder (MCF) is a tool to profile network communities (i.e., clusters of nodes) with the control of community sizes. The controlling parameter is referred to as the scale of the network community profile. MCF is able to find communities in all major types of networks including directed, signed, bipartite, and multi-slice networks. The fast computation promotes the practicability of the tool for large-scaled analysis (e.g., protein-protein interaction and gene co-expression networks). MCF is distributed as an open-source C++ package for academic use with both command line and user interface options, and can be downloaded at http://bsdxd.cpsc.ucalgary.ca/MCF. Detailed user manual and sample data sets are also available at the project website.

Primary squamous cell carcinoma of the endometrium: clinicopathologic and molecular characteristics.

Molecular alterations leading to cell cycle dysregulation in primary squamous cell carcinoma of the endometrium (PSCCE) and correlation with clinical outcome are incompletely described. Molecular variables of 5 cases of PSCCE were compared with 8 controls of endometrial endometrioid adenocarcinoma and correlated with overall survival. Immunohistochemical expression of pRB, p18, p19, CDK4, CDK6, Cyclin D1, p16, HPVE7, pTEN, ER, PR, and p53 was independently scored (intensity: 0-3 and proportion: 0-5) twice by 2 reviewers. Scores were averaged and expression was categorized as positive or negative. Human papillomavirus (HPV) DNA amplification and Braf and Kras mutations were assessed by polymerase chain reaction. Distribution differences between cases and controls were tested for significance using χ/Fisher exact tests. Differences in overall survival and correlation with variables were calculated using Kaplan-Meier and tested for significance using log rank tests. All cases and controls were mostly positive for pRB, p19, CDK6, and Cyclin D1 and mostly negative for p16, p18, CDK4, HPVE7, pTEN, and p53. Cases were mostly negative for ER and PR, whereas controls were mostly positive. All were negative for HPV DNA amplification and Braf mutations. One case and 2 controls had a Kras mutation. Only the ER and PR distribution difference was significant (P=0.03 and 0.02, respectively) and differences in overall survival did not correlate with any variable. PSCCE has molecular alterations involving the pRB-Cyclin D1-CDK4/6-p16 pathway, and pTEN. In contrast to the type I EACC, PSCCE is not hormonally sensitive, suggesting a unique pathogenesis.

Oligodendroglioma cell lines containing t(1;19)(q10;p10).

Investigating the biology of oligodendroglioma and its characteristic combined deletion of chromosomal arms 1p and 19q, mediated by an unbalanced translocation, t(1;19)(q10;p10), has been hampered by the lack of cell lines that harbor these traits. We grew cells from 2 anaplastic oligodendrogliomas in serum-free conditions. Serial propagation and expansion led to the establishment of permanent cell lines that maintained the genetic signature of the parent oligodendrogliomas and displayed features of brain tumor stem cells in vitro. One line was established from a treatment-naïve tumor and the other from a temozolomide resistant recurrent tumor. These lines may be important tools for understanding the biology of oligodendrogliomas and the function of their defining genetic traits.

Spontaneous autoimmunity sufficiently potent to induce diabetes mellitus is insufficient to protect against insulinoma.

Intact tolerogenic mechanisms preclude effective immunity against tumors, as most tumor Ags differ little from normal host Ags. In contrast, when tolerance fails, the immune system becomes inappropriately activated against an autoantigen. We postulated that CD8(+) T cells activated during autoimmunity are capable of protecting against tumors that express the targeted autoantigen. To test this hypothesis, double-transgenic 8.3-NOD-RIPTAg mice were developed (where NOD is nonobese diabetic, RIP is rat insulin promoter, and TAg is large T Ag). In this model, individuals with the RIPTAg transgene develop insulinoma; those expressing a transgenic TCR (8.3-TCR) recognizing the islet-specific glucose 6 phosphatase catalytic subunit-related protein (IGRP) harbor a peripheral immune system dominated by diabetogenic CD8(+) T cells. Although tumor emergence was significantly slower in 8.3-NOD-RIPTAg mice compared with NOD-RIPTAg mice, all 8.3-NOD-RIPTAg mice eventually developed insulinoma. Tumor emergence was not secondary to clonal deletion or anergy. Ag loss and MHC down-regulation were not apparent. Endogenous 8.3-TCR CD8(+) T cells were recruited to the tumor site and proliferated upon arrival to the tumor, although they were notably absent from the central parts of more advanced tumors. These results demonstrate that a breakdown of tolerance capable of causing autoimmune disease is insufficient for effective tumor immunity. Alterations in the tumor microenvironment may inhibit efficient and comprehensive delivery of CD8(+) T cells to all regions of the tumor. These data suggest that any immunotherapeutic strategy for cancer must involve enhancement of a proinflammatory tumor microenvironment in addition to inhibition of tolerogenic mechanisms.

Protein elongation factor EEF1A2 is a putative oncogene in ovarian cancer.

We have found that EEF1A2, the gene encoding protein elongation factor EEF1A2 (also known as eEF-1 alpha 2), is amplified in 25% of primary ovarian tumors and is highly expressed in approximately 30% of ovarian tumors and established cell lines. We have also demonstrated that EEF1A2 has oncogenic properties: it enhances focus formation, allows anchorage-independent growth and decreases the doubling time of rodent fibroblasts. In addition, EEF1A2 expression made NIH3T3 fibroblasts tumorigenic and increased the growth rate of ES-2 ovarian carcinoma cells xenografted in nude mice. Thus, EEF1A2 and the process of protein elongation are likely to be critical in the development of ovarian cancer.