Immune modulation associated with vascular endothelial growth factor (VEGF) blockade in patients with glioblastoma

BACKGROUND

Vascular endothelial growth factor (VEGF), in addition to being pro-angiogenic, is an immunomodulatory cytokine systemically and in the tumor microenvironment. We previously reported the immunomodulatory effects of radiation and temozolomide (TMZ) in newly diagnosed glioblastoma. This study aimed to assess changes in peripheral blood mononuclear cell (PBMC) populations, plasma cytokines, and growth factor concentrations following treatment with radiation, TMZ, and bevacizumab (BEV).

METHODS

Eleven patients with newly diagnosed glioblastoma were treated with radiation, TMZ, and BEV, following surgery. We measured immune-related PBMC subsets using multi-parameter flow cytometry and plasma cytokine and growth factor concentrations using electrochemiluminescence-based multiplex analysis at baseline and after 6 weeks of treatment.

RESULTS

The absolute number of peripheral blood regulatory T cells (Tregs) decreased significantly following treatment. The lower number of peripheral Tregs was associated with a CD4+ lymphopenia, and thus, the ratio of Tregs to PBMCs was unchanged. The addition of bevacizumab to standard radiation and temozolomide led to the decrease in the number of circulating Tregs when compared with our prior study. There was a significant decrease in CD8+ cytotoxic and CD4+ recent thymic emigrant T cells, but no change in the number of myeloid-derived suppressor cells. Significant increases in plasma VEGF and placental growth factor (PlGF) concentrations were observed.

CONCLUSIONS

Treatment with radiation, TMZ, and BEV decreased the number but not the proportion of peripheral Tregs and increased the concentration of circulating VEGF. This shift in the peripheral immune cell profile may modulate the tumor environment and have implications for combining immunotherapy with anti-angiogenic therapy.

Effective quality management practices in routine clinical next-generation sequencing

BACKGROUND

Molecular technologies have allowed laboratories to detect and establish the profiles of human cancers by identifying a variety of somatic variants. In order to improve personalized patient care, we have established a next-generation sequencing (NGS) test to screen for somatic variants in primary or advanced cancers. In this study, we describe the laboratory quality management program for NGS testing, and also provide an overview of the somatic variants identified in over 1000 patient samples as well as their implications in clinical practice.

METHODS

Over the past one-and-a-half years, our laboratory received a total of 1028 formalin-fixed, paraffin-embedded (FFPE) tumor tissues, which consisted of non-small-cell lung carcinomas (NSCLCs), colon adenocarcinomas, glioma/glioblastomas, melanomas, breast carcinomas, and other tumor types. During this time period, we implemented a series of quality control (QC) checks that included (1) pre-DNA extraction, (2) DNA quantification, (3) DNA quality, (4) library quantification, (5) post-emulsification PCR, and (6) post-sequencing metrics. At least 10 ng of genomic DNA (gDNA) were used to prepare barcoded libraries using the AmpliSeq CHPv2. Samples were multiplexed and sequenced on Ion Torrent 318 chips using the Ion PGM System. Variants were identified using the Variant Caller Plugin, and annotation and functional predictions were performed using the Golden Helix SVS.

RESULTS

A total of 1005 samples passed QC1-3, and following additional library preparation QC checkpoints, 877 samples were sequenced. Samples were classified into two categories: wild-type (127) and positive for somatic variants (750). Somatic variants were classified into clinically actionable (60%) and non-actionable (40%).

CONCLUSIONS

The use of NGS in routine clinical laboratory practice allowed for the detection of tumor profiles that are essential for the selection of targeted therapies and identification of applicable clinical trials, contributing to the improvement of personalized patient care in oncology.

HS3ST1 genotype regulates antithrombin's inflammomodulatory tone and associates with atherosclerosis

The HS3ST1 gene controls endothelial cell production of HS^AT+ - a form of heparan sulfate containing a specific pentasaccharide motif that binds the anticoagulant protein antithrombin (AT). HS^AT+ has long been thought to act as an endogenous anticoagulant; however, coagulation was normal in Hs3st1^-/- mice that have greatly reduced HS^AT+ (HajMohammadi et al., 2003). This finding indicates that HS^AT+ is not essential for AT's anticoagulant activity. To determine if HS^AT+ is involved in AT's poorly understood inflammomodulatory activities, Hs3st1^-/- and Hs3st1^+/+ mice were subjected to a model of acute septic shock. Compared with Hs3st1^+/+ mice, Hs3st1^-/- mice were more susceptible to LPS-induced death due to an increased sensitivity to TNF. For Hs3st1^+/+ mice, AT treatment reduced LPS-lethality, reduced leukocyte firm adhesion to endothelial cells, and dilated isolated coronary arterioles. Conversely, for Hs3st1^-/- mice, AT induced the opposite effects. Thus, in the context of acute inflammation, HS^AT+ selectively mediates AT's anti-inflammatory activity; in the absence of HS^AT+, AT's pro-inflammatory effects predominate. To explore if the anti-inflammatory action of HS^AT+ also protects against a chronic vascular-inflammatory disease, atherosclerosis, we conducted a human candidate-gene association study on >2000 coronary catheterization patients. Bioinformatic analysis of the HS3ST1 gene identified an intronic SNP, rs16881446, in a putative transcriptional regulatory region. The rs16881446^G/G genotype independently associated with the severity of coronary artery disease and atherosclerotic cardiovascular events. In primary endothelial cells, the rs16881446^G allele associated with reduced HS3ST1 expression. Together with the mouse data, this leads us to conclude that the HS3ST1 gene is required for AT's anti-inflammatory activity that appears to protect against acute and chronic inflammatory disorders.

A Phase II Trial of Dovitinib in BCG-Unresponsive Urothelial Carcinoma with FGFR3 Mutations or Overexpression: Hoosier Cancer Research Network Trial HCRN 12-157

Purpose: To assess the clinical and pharmacodynamic activity of dovitinib in a treatment-resistant, molecularly enriched non-muscle-invasive urothelial carcinoma of the bladder (NMIUC) population.Experimental Design: A multi-site pilot phase II trial was conducted. Key eligibility criteria included the following: Bacillus Calmette-Guerin (BCG)-unresponsive NMIUC (>2 prior intravesical regimens) with increased phosphorylated FGFR3 (pFGFR3) expression by centrally analyzed immunohistochemistry (IHC+) or FGFR3 mutations (Mut+) assessed in a CLIA-licensed laboratory. Patients received oral dovitinib 500 mg daily (5 days on/2 days off). The primary endpoint was 6-month TURBT-confirmed complete response (CR) rate.Results: Between 11/2013 and 10/2014, 13 patients enrolled (10 IHC+ Mut-, 3 IHC+ Mut+). Accrual ended prematurely due to cessation of dovitinib clinical development. Demographics included the following: median age 70 years; 85% male; carcinoma in situ (CIS; 3 patients), Ta/T1 (8 patients), and Ta/T1 + CIS (2 patients); median prior regimens 3. Toxicity was frequent with all patients experiencing at least one grade 3-4 event. Six-month CR rate was 8% (0% in IHC+ Mut-; 33% in IHC+ Mut+). The primary endpoint was not met. Pharmacodynamically active (94-5,812 nmol/L) dovitinib concentrations in urothelial tissue were observed in all evaluable patients. Reductions in pFGFR3 IHC staining were observed post-dovitinib treatment.Conclusions: Dovitinib consistently achieved biologically active concentrations within the urothelium and demonstrated pharmacodynamic pFGFR3 inhibition. These results support systemic administration as a viable approach to clinical trials in patients with NMIUC. Long-term dovitinib administration was not feasible due to frequent toxicity. Absent clinical activity suggests that patient selection by pFGFR3 IHC alone does not enrich for response to FGFR3 kinase inhibitors in urothelial carcinoma. Clin Cancer Res; 23(12); 3003-11. ©2016 AACR.

Improving Adequacy of Small Biopsy and Fine-Needle Aspiration Specimens for Molecular Testing by Next-Generation Sequencing in Patients With Lung Cancer: A Quality Improvement Study at Dartmouth-Hitchcock Medical Center

Context.—

At our medical center, cytopathologists perform rapid on-site evaluation for specimen adequacy of fine-needle aspiration and touch imprint of needle core biopsy lung cancer samples. Two years ago the molecular diagnostics laboratory at our institution changed to next-generation sequencing using the Ion Torrent PGM and the 50-gene AmpliSeq Cancer Hotspot Panel v2 for analyzing mutations in a 50-gene cancer hot spot panel. This was associated with a dramatic fall in adequacy rate (68%).

Objective.—

To improve the adequacy rate to at least 90% for molecular testing using next-generation sequencing for all specimens collected by rapid on-site evaluation by the cytology laboratory.

Design.—

After baseline data on adequacy rate of cytology specimens with rapid on-site evaluation for molecular testing had been collected, 2 changes were implemented. Change 1 concentrated all the material in one block but did not produce desired results; change 2, in addition, faced the block only once with unstained slides cut up front for molecular testing. Data were collected in an Excel spreadsheet and adequacy rate was assessed.

Results.—

Following process changes 1 and 2 we reached our goal of at least 90% adequacy rate for molecular testing by next-generation sequencing on samples collected by rapid on-site evaluation including computed tomography–guided needle core biopsies (94%; 17 of 18) and fine-needle aspiration samples (94%; 30 of 32).

Conclusion.—

This study focused on factors that are controllable in a pathology department and on maximizing use of scant tissue. Optimizing the adequacy of the specimen available for molecular tests avoids the need for a second procedure to obtain additional tissue.

Detection of CALR Mutation in Clonal and Nonclonal Hematologic Diseases Using Fragment Analysis and Next-Generation Sequencing

OBJECTIVES

To describe three methods used to screen for frameshift mutations in exon 9 of the CALR gene.

METHODS

Genomic DNA from 47 patients was extracted from peripheral blood and bone marrow using the EZ1 DNA Blood Kit (Qiagen, Valencia, CA) and quantified by the Quant-iT PicoGreen dsDNA Assay Kit (Invitrogen, San Diego, CA). After clinical history, cytogenetics, and molecular tests, patients were diagnosed with either clonal or nonclonal hematologic diseases. CALR screening was primarily performed using fragment analysis polymerase chain reaction, then next-generation sequencing and Sanger sequencing.

RESULTS

Among the 18 patients diagnosed with clonal diseases, one had acute myeloid leukemia (positive for trisomy 8), and 17 had myeloproliferative neoplasms (MPNs), including chronic myeloid leukemia (CML), essential thrombocythemia (ET), primary myelofibrosis (PMF), and polycythemia vera (PV). Patients with CML were positive for the BCR-ABL1 fusion. Ten patients were positive for JAK2 (PMF, n = 1; ET, n = 2; PV, n = 7), and three were CALR positive (ET, n = 1; PMF, n = 2). Patients diagnosed with a nonclonal disease were negative for JAK2, BCR-ABL, and CALR mutations.

CONCLUSIONS

Screening for CALR mutations is essential in BCR-ABL-negative MPNs since it not only provides valuable diagnostic and prognostic information but also identifies potential treatment targets. Since this study describes the importance of screening for known and novel biomarkers, we described in detail three methods that could be easily integrated into a clinical laboratory.

Clinical Genotyping of Non-Small Cell Lung Cancers Using Targeted Next-Generation Sequencing: Utility of Identifying Rare and Co-mutations in Oncogenic Driver Genes

Detection of somatic mutations in non-small cell lung cancers (NSCLCs), especially adenocarcinomas, is important for directing patient care when targeted therapy is available. Here, we present our experience with genotyping NSCLC using the Ion Torrent Personal Genome Machine (PGM) and the AmpliSeq Cancer Hotspot Panel v2. We tested 453 NSCLC samples from 407 individual patients using the 50 gene AmpliSeq Cancer Hotspot Panel v2 from May 2013 to July 2015. Using 10 ng of DNA, up to 11 samples were simultaneously sequenced on the Ion Torrent PGM (316 and 318 chips). We identified variants with the Ion Torrent Variant Caller Plugin, and Golden Helix's SVS software was used for annotation and prediction of the significance of the variants. Three hundred ninety-eight samples were successfully sequenced (12.1% failure rate). In all, 633 variants in 41 genes were detected with a median of 2 (range of 0 to 7) variants per sample. Mutations detected in BRAF, EGFR, ERBB2, KRAS, NRAS, and PIK3CA were considered potentially actionable and were identified in 237 samples, most commonly in KRAS (37.9%), EGFR (11.1%), BRAF (4.8%), and PIK3CA (4.3%). In our patient population, all mutations in EGFR, KRAS, and BRAF were mutually exclusive. The Ion Torrent Ampliseq technology can be utilized on small biopsy and cytology specimens, requires very little input DNA, and can be applied in clinical laboratories for genotyping of NSCLC. This targeted next-generation sequencing approach allows for detection of common and also rare mutations that are clinically actionable in multiple patients simultaneously.

Abstract 4503: Actionable mutations and mutational burden in renal cell carcinoma

Clear cell renal cell carcinoma (CCRCC), the most common subtype of renal cell carcinoma, is a heterogeneous cancer with variable outcomes and molecular aberrations. Further elucidation of mutational profiles and actionable mutations may improve patient outcomes in CCRCC. Somatic mutational profiling via next-generation sequencing was conducted on 30 CCRCC whole section FFPE patient samples to determine the mutational burden as compared to other solid tumor types. The sequencing failure rate for these samples was 20% (6/30). A 358-gene panel was also run on an additional 57 non-CCRCC solid tumor FFPE patient samples (81 samples in total). FASTQ files generated from Illumina's CASAVA software were submitted to the JAX Clinical Genome Analytics (CGA) data analysis pipeline to perform automated read quality assessment, alignment, and variant calling. Identified variants were then submitted for clinical curation using the JAX Clinical Knowledgebase (CKB) for actionable mutational analysis and overall mutational burden. Of the CCRCC sample set, 33% had one or more actionable mutations. This was low compared to actionable mutations in colon (16/16, 100% actionable), TNBC (18/20, 90% actionable), squamous lung (8/9, 89% actionable), and pancreatic (8/12, 67% actionable). Furthermore, the CCRCC set had a low overall mutational burden with 22 ± 6.7 nonsynonymous SNV's as compared to colon (29 ± 11), squamous lung (43 ± 17), and TNBC (31.5 ± 12). However, the pancreatic set had even lower SNV's at 12.7 ± 3.4. The number of indels was comparable across the five sets, except for colon, which averaged 6.9 ± 8.3. Significant copy number variations (CNV’s; amplification validated at greater than or equal to 6 copies) also had a wide range with squamous lung at the highest (11 ± 11), followed by TNBC (5.6 ± 5.0), and then colon (2.3 ± 3.0). Both the CCRCC and pancreatic sets had few CNV's at 0.8 ± 1.5 and 0.17 ± 0.40, respectively. Common mutations identified in the CCRCC set included EPHB6 duplications near S166, which were identified in 25% of samples. Gene specific mutations in CCRCC were also identified in VHL (54%) and SETD2 (21%). These three genes, EPHB6, VHL, and SETD2 have been previously implicated in CCRCC pathogenesis. Six variants identified in VHL were C77*, P86R, Q132fs, A149D, R177fs, and L184fs. Due to the low mutational burden and/or actionable mutations in CCRCC, even large NGS panels may not be adequate to profile somatic mutations and whole exome or whole genome may be more conducive for molecular subtyping of renal cell carcinoma.

Citation Format: Susan M. Mockus, Sara E. Patterson, Jason R. Pettus, Gregory J. Tsongalis. Actionable mutations and mutational burden in renal cell carcinoma. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4503.

Abstract 3630: Validation of the Archer FusionPlex solid tumor panel in the JAX cancer treatment profileTM

Introduction: A comprehensive somatic tumor profile with associated treatment selection options requires the detection of gene fusions. After evaluating the clinical utility of multiple methods of gene fusion detection, it was determined that the Archer FusionPlex Solid Tumor Panel (AFPSTP) best compliments the JAX Cancer Treatment ProfileTM (JAX-CTPTM) clinical test in terms of workflow, specimen requirements and turnaround time. Here we describe our analytical validation process for the AFPSTP assay.

Methods: AFPSTP was validated using 24 samples: 5 JAX Patient Derived Xenograft (PDX) cases, 4 translocation positive controls, 2 FFPE cancer samples, 1 normal tissue sample, and 12 cell lines. Nine of the cell lines were previously identified as positive for fusion transcripts and 3 lacked detectable fusion events. The validation was executed in 5 phases: (1) confirm that AFPSTP was able to detect known fusion or lack of fusion events in characterized specimens; (2) determine inter-assay concordance; (3) determine intra-assay concordance; (4) LOD and (5) sensitivity.

Results: The fusion detection results for this validation are listed in Table 1. All but one of these fusion events was previously identified. The one novel fusion was confirmed using TaqMan RT-PCR. In addition to the expected fusions, 4 false positive events were detected, 2 due to mispriming and 2 determined to be WT read through transcripts. The fusion detection inter and intra-assay concordance was found to be 100% and the sensitivity was calculated to be 91.67% at a LOD of 5%.

Conclusion: This analysis outlines the clinical validation of the incorporation of AFPSTP into the JAX-CTPTM test system. Once incorporated, the AFPSTP assay will accomplish the goal of making JAX-CTPTM a more comprehensive somatic tumor profiling assay without affecting the current acceptable turnaround time or required input material. List of 15 samples that were found to be fusion positive and the corresponding detected fusion.HorizonDx EML4/ALK PositiveEML4 → ALK variant 1HorizonDx RET PositiveCCDC6 → RETHorizonDx ROS PositiveSLC34A2 → ROS1HorizonDx Triple PositiveEML4 → ALK variant 3bHorizonDx Triple PositiveSLC34A2 → ROS1HorizonDx Triple PositiveCCDC6 → RETA673 Cell LineEWSR1 → FLI1VCaP Cell LineTMPRSS2 → ERGKM-12 Cell LineTPM3 → NTRK1RPMI-2650 Cell LineBRD4 → NUTM1NCI-H716 Cell LineFGFR2 → COL14A1OCI-AML2 Cell LineMBNL1 → RAF1REH Cell LineETV6 → RUNX1MDA-MB-175-VII Cell LineTENM4 → NRG1ASPS-1 Cell LineTFE3 → ASPSCR1ASPS-1 Cell LineASPSCR1 → TFE3PDX1EML4 → ALK 3bPDX2SYN2 → PPARG

Citation Format: Samantha Helm, Aleksandra Ras, Vanessa Spotlow, Kevin Kelly, Susan Mockus, Cara Statz, Guruprasad Ananda, Joan Malcolm, Gregory J. Tsongalis. Validation of the Archer FusionPlex solid tumor panel in the JAX cancer treatment profileTM. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3630.

Partnering for Success: Expanding Breast and Cancer Screening in Rural Honduras One Clinic at a Time

Abstract 36

Background:

Women in rural Honduras have limited access to cancer education, screening, and care. With village leaders, we piloted breast and cervical cancer screening in El Rosario, Honduras. Our objectives were to improve awareness and access, mitigate barriers, connect community and Honduran providers, and link patients with abnormal findings to cancer treatment. In 2013, health professionals and staff from Norris Cotton Cancer Center at Dartmouth- Hitchcock joined Honduran clinicians and medical students from La Liga Contra el Cáncer for two days of rural cancer screening. Peer educators taught 475 participants from 31 rural communities how to conduct self-breast exams. Of these participants, 238 chose clinical breast exams; 5% were clinically abnormal and 2.9% were referred for services at La Liga with 100% compliance. 34% reported barriers to cervical cancer screening due to distance and lack of transportation. 14.5% tested positive for HPV and 8% were positive for high risk HPV genotypes including 11 of 13 known high risk types. This group has been retested periodically by Pap. The collaborators will return in April 2016 to repeat the study, adding oral and thyroid screening. Genotyping for hrHPV will be onsite with a novel assay for PCR developed at Dartmouth-Hitchcock. Reflex testing with Pap will follow as needed. Follow up will be at La Liga where care is offered for free or at a reduced cost. A similar project for 400 urban factory-workers will also take place in April 2016.

Methods:

2-day, multi-modal education and screening outreach run brigade-style combining low-tech primary screening with onsite molecular pathology.

Conclusions:

Partnerships between local leaders and clinicians are predicted to be essential to project implementation. Targeting populations with education and screening plus building connections to follow up care will provide earlier detection of breast and cervical cancer. We predict that community leadership will be critical to preventing loss to follow-up.

AUTHORS' DISCLOSURES OF POTENTIAL CONFLICTS OF INTEREST:

Derek S. Stenquist No relationship to disclose Suyapa Bejarano No relationship to disclose Linda S. Kennedy No relationship to disclose Silvia Portillo No relationship to disclose Ana Barrientos No relationship to disclose Suzanne P. Burgos No relationship to disclose Roberto Armando Elvir Zelaya No relationship to disclose Christine Averill No relationship to disclose Emmeline Liu No relationship to disclose Francine de Abreau No relationship to disclose Paul Burchard No relationship to disclose Torrey Gallagher No relationship to disclose Martha Goodrich No relationship to disclose Scottie Eliassen No relationship to disclose Julie Weiss No relationship to disclose Camilo Mandujano No relationship to disclose Jennifer Alford-Teaster No relationship to disclose Gregory J. Tsongalis Research Funding: Illumina, Qiagen, Thermofisher Tracy Onega No relationship to disclose Mary D. Chamberlin No relationship to disclose

The potential utility of re-mining results of somatic mutation testing: KRAS status in lung adenocarcinoma

KRAS mutant non-small cell lung cancers (NSCLCs) vary in clinical outcome depending on which specific KRAS mutation is present. Shorter progression free survival has been associated with KRAS variants G12C and G12V. Cell lines with these variants depend to a greater extent on the RAS/RAF/MEK/ERK signaling pathway and become more susceptible to MEK inhibition. Because different KRAS mutations may lead to altered drug sensitivity, we aimed to determine specific KRAS mutation status in a NSCLC patient cohort at our institution. A total of 502 NSCLC samples were screened for somatic mutations using the 50 gene AmpliSeq™ Cancer Hotspot Panel v2 (CHPv2). However only samples positive for variants in the KRAS gene were included in this study. Variants identified in the KRAS genes were curated using publicly available databases. The overall mutation rate in the KRAS gene was 32.7% (164/502). The most common KRAS mutations were G12C (41%), G12V (19%), and G12D (14%) along with less frequent variants. After re-mining our sequencing data, we found that more than a half of our KRAS mutant NSCLC patients could potentially benefit from the addition of a MEK inhibitor such as selumetinib to standard chemotherapeutic agents. Due to mutated KRAS, these patients will likely fail traditional anti-EGFR therapies but be eligible for newer combination therapies.

An analysis of human papillomavirus testing and endocervical component on pap tests: A pilot study using the Roche Cobas(®) assay

INTRODUCTION

HPV is known to have a predilection for infecting the transformation zone (TZ). Endocervical cells (EC) on a Pap test (PT) indicate that the cervical TZ has been sampled. Earlier repeat testing of women lacking EC is of little value in further detecting disease, thus a sample without EC is not necessarily inadequate. Both HPV testing and PT can be performed using a single sample; however, few studies have investigated the relationship between HPV results and TZ sampling.

MATERIALS AND METHODS

Specimens were collected following the ThinPrep(®) liquid-based PT protocol. The Roche Cobas(®) HPV test was performed on post-aliquot samples. Data was collected retrospectively on 500 patients: 250 consecutive cases of EC- and 250 of EC+ on PT. To maintain uniformity, we included only cases diagnosed as negative (NILM). We compared HPV test results within each category. As a positive control, five consecutive cases each of LSIL and HSIL were also reviewed.

RESULTS

Of NILM cases, 11 of 250 EC+ cases and 14 of 250 EC- cases were positive for hrHPV. HPV 16 was present in 5 of 11 EC + cases and in 1 of 14 EC- cases. Of LSIL cases, 1 of 5 EC+ cases was positive for hrHPV, and 2 of 5 EC- cases were positive for hrHPV. Of HSIL cases, 5 of 5 EC+ cases were hrHPV+. In the time period studied, only one case of EC- HSIL was found, which was positive for hrHPV.

DISCUSSION

Although our study did not prove a significant correlation between HPV testing results and EC on PT, more EC+ PTs were positive for HPV16 compared to EC- PTs. The absence of EC on PT does not appear to warrant re-testing for HPV infection, though larger studies are required to determine the significance of low HPV 16 in PT without EC. Diagn. Cytopathol. 2016;44:280-282. © 2016 Wiley Periodicals, Inc.

Molecular Genetic Analysis of Ovarian Brenner Tumors and Associated Mucinous Epithelial Neoplasms: High Variant Concordance and Identification of Mutually Exclusive RAS Driver Mutations and MYC Amplification

Benign ovarian Brenner tumors often are associated with mucinous cystic neoplasms, which are hypothesized to share a histogenic origin and progression, however, supporting molecular characterization is limited. Our goal was to identify molecular mechanisms linking these tumors. DNA from six Brenner tumors with paired mucinous tumors, two Brenner tumors not associated with a mucinous neoplasm, and two atypical proliferative (borderline) Brenner tumors was extracted from formalin-fixed, paraffin-embedded tumor samples and sequenced using a 358-gene next-generation sequencing assay. Variant calls were compared within tumor groups to assess somatic mutation profiles. There was high concordance of the variants between paired samples (40% to 75%; P < 0.0001). Four of the six tumor pairs showed KRAS hotspot driver mutations specifically in the mucinous tumor. In the two paired samples that lacked KRAS mutations, MYC amplification was detected in both of the mucinous and the Brenner components; MYC amplification also was detected in a third Brenner tumor. Five of the Brenner tumors had no reportable potential driver alterations. The two atypical proliferative (borderline) Brenner tumors both had RAS mutations. The high degree of coordinate variants between paired Brenner and mucinous tumors supports a shared origin or progression. Differences observed in affected genes and pathways, particularly involving RAS and MYC, may point to molecular drivers of a divergent phenotype and progression of these tumors.

Clinical Trials in Precision Oncology

BACKGROUND

Availability of genomic information used in the management of cancer treatment has outpaced both regulatory and reimbursement efforts. Many types of clinical trials are underway to validate the utility of emerging genome-based biomarkers for diagnostic, prognostic, and predictive applications. Clinical trials are a key source of evidence required for US Food and Drug Administration approval of therapies and companion diagnostics and for establishing the acceptance criteria for reimbursement.

CONTENT

Determining the eligibility of patients for molecular-based clinical trials and the interpretation of data emerging from clinical trials is significantly hampered by 2 primary factors: the lack of specific reporting standards for biomarkers in clinical trials and the lack of adherence to official gene and variant naming standards. Clinical trial registries need specifics on the mutation required for enrollment as opposed to allowing a generic mutation entry such as, "EGFR mutation." The use of clinical trials data in bioinformatics analysis and reporting is also gated by the lack of robust, state of the art programmatic access support. An initiative is needed to develop community standards for clinical trial descriptions and outcome reporting that are modeled after similar efforts in the genomics research community.

SUMMARY

Systematic implementation of reporting standards is needed to insure consistency and specificity of biomarker data, which will in turn enable better comparison and assessment of clinical trial outcomes across multiple studies. Reporting standards will facilitate improved identification of relevant clinical trials, aggregation and comparison of information across independent trials, and programmatic access to clinical trials databases.

Abstract 5354: The guilty bystander model for electrochemotherapy of cancer: Verification in vitro

Electroporation (EPR) is the induction of pores in cellular membranes in cells by application of a short application of a high voltage, low amperage electric current. If the cells are immersed in a solution containing a large molecule which is normally impervious to this membrane, it may be introduced into the cells in this manner. Electrochemotherapy (ECT) is a clinical procedure in which a drug, such as bleomicin or cisplatin, is introduced into the blood of or intratumorally into an animal or human subject by intravenous injection followed by application of a short high dose, low amperage electric current into a neoplasm after a delay enabling the drug to reach the neoplasm through the bloodstream or by other means. ECT is normally used for palliative care in human subjects, however there are now a number of reports, numbering well over 10, of unexpected complete clearance of neoplasms following ECT. Many of these reports have come from university centers in Europe and elsewhere. Although ECT is not yet approved in the USA, we believe that these reports can no longer be ignored. We and others have used EPR in culture to introduce large molecules into cells for experimental purposes for decades. Even under the controlled experimental conditions we have employed, however, the proportion of cells into which these molecules have been introduced has been well below 100 per cent. To account for the clearance of some tumors by ECT, in which the proportion of cells in which drug is introduced would be expected to be lower than for EPR, we have proposed a “Guilty Bystander Model”, in which cells adjacent to neoplastic cells into which drug has been introduced are also cleared. To test this model in vitro, we optimized conditions for EPR but were unable to produce more than 88 per cent introduction of labeled large molecules into lymphoblastoid cells (GM 1989A, derived from a healthy 33 year old Caucasian male, and GM 3999, derived from a healthy 8 year old Caucasian female), even under conditions which reduced cell viability from 99 per cent to 79 per cent. Increasing voltage produced a marked loss of viability. We conclude that EPR does not produce 100 per cent introduction of large molecules into human cells, even under optimized conditions in vitro, and that there must remain neoplastic cells in tumors treated by ECT that are eliminated by means other than introduction of the drug.

Citation Format: W Clark Lambert, Gregory J. Tsongalis, Claude E. Gagna, Muriel W. Lambert. The guilty bystander model for electrochemotherapy of cancer: Verification in vitro. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 5354. doi:10.1158/1538-7445.AM2015-5354

Implementation of a Molecular Tumor Board: The Impact on Treatment Decisions for 35 Patients Evaluated at Dartmouth-Hitchcock Medical Center

BACKGROUND

Although genetic profiling of tumors is a potentially powerful tool to predict drug sensitivity and resistance, its routine use has been limited because clinicians are often unfamiliar with interpretation and incorporation of the information into practice. We established a Molecular Tumor Board (MTB) to interpret individual patients' tumor genetic profiles and provide treatment recommendations.

PATIENTS AND METHODS

DNA from tumor specimens was sequenced in a Clinical Laboratory Improvement Amendments-certified laboratory to identify coding mutations in a 50-gene panel (n = 34) or a 255-gene panel (n = 1). Cases were evaluated by a multidisciplinary MTB that included pathologists, oncologists, hematologists, basic scientists, and genetic counselors.

RESULTS

During the first year, 35 cases were evaluated by the MTB, with 32 presented for recommendations on targeted therapies, and 3 referred for potential germline mutations. In 56.3% of cases, MTB recommended treatment with a targeted agent based on evaluation of tumor genetic profile and treatment history. Four patients (12.5%) were subsequently treated with a MTB-recommended targeted therapy; 3 of the 4 patients remain on therapy, 2 of whom experienced clinical benefit lasting >10 months.

CONCLUSION

For the majority of cases evaluated, the MTB was able to provide treatment recommendations based on targetable genetic alterations. The most common reasons that MTB-recommended therapy was not administered stemmed from patient preferences and genetic profiling at either very early or very late stages of disease; lack of drug access was rarely encountered. Increasing awareness of molecular profiling and targeted therapies by both clinicians and patients will improve acceptance and adherence to treatments that could significantly improve outcomes.

IMPLICATIONS FOR PRACTICE

Case evaluation by a multidisciplinary Molecular Tumor Board (MTB) is critical to benefit from individualized genetic data and maximize clinical impact. MTB recommendations shaped treatment options for the majority of cases evaluated. In the few patients treated with MTB-recommended therapy, disease outcomes were positive and support genetically informed treatment.