Chromosomal instability by mutations in the novel minor spliceosome component CENATAC

Aneuploidy is the leading cause of miscarriage and congenital birth defects, and a hallmark of cancer. Despite this strong association with human disease, the genetic causes of aneuploidy remain largely unknown. Through exome sequencing of patients with constitutional mosaic aneuploidy, we identified biallelic truncating mutations in CENATAC (CCDC84). We show that CENATAC is a novel component of the minor (U12-dependent) spliceosome that promotes splicing of a specific, rare minor intron subtype. This subtype is characterized by AT-AN splice sites and relatively high basal levels of intron retention. CENATAC depletion or expression of disease mutants resulted in excessive retention of AT-AN minor introns in ˜ 100 genes enriched for nucleocytoplasmic transport and cell cycle regulators, and caused chromosome segregation errors. Our findings reveal selectivity in minor intron splicing and suggest a link between minor spliceosome defects and constitutional aneuploidy in humans.

Prolonged use of pegylated liposomal doxorubicin in gynecologic malignancies

Pegylated liposomal doxorubicin (PLD) is a palliative treatment option for patients with recurrent gynecologic malignancies. It has an appealing toxicity profile and responses can be prolonged. There is no consensus as to the level of cardiac toxicity. Current label warnings, National Comprehensive Cancer Network (NCCN) guidelines, and extrapolation of prescribing guidelines from doxorubicin, may limit PLD's use in patients with baseline cardiac comorbidities, limit the lifetime dosing of an effective palliative treatment, or lead to over-use of unnecessary cardiac testing. This case series describes the experience of 18 patients using prolonged courses of PLD for gynecologic malignancies with no cardiac toxicity.

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Prognosis is poor, and treatment options limited for patients with recurrent advanced gynecologic cancers.

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The true level of cardiac risk of prolonged pegylated liposomal doxorubicin (PLD) is not clear.

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There is no consensus about cardiac monitoring before, during, and after treatment with PLD.

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Prolonged use of PLD resulted in no symptomatic cardiac toxicity in 18 patients.

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Prolonged treatment with PLD has clinical benefit for patients undergoing palliative treatment.

Evaluation of Cancer-Based Criteria for Use in Mainstream BRCA1 and BRCA2 Genetic Testing in Patients With Breast Cancer

IMPORTANCE

Increasing BRCA1 and BRCA2 (collectively termed herein as BRCA) gene testing is required to improve cancer management and prevent BRCA-related cancers.

OBJECTIVE

To evaluate mainstream genetic testing using cancer-based criteria in patients with cancer.

DESIGN, SETTING, AND PARTICIPANTS

A quality improvement study and cost-effectiveness analysis of different BRCA testing selection criteria and access procedures to evaluate feasibility, acceptability, and mutation detection performance was conducted at the Royal Marsden National Health Service Foundation Trust as part of the Mainstreaming Cancer Genetics (MCG) Programme. Participants included 1184 patients with cancer who were undergoing genetic testing between September 1, 2013, and February 28, 2017.

MAIN OUTCOMES AND MEASURES

Mutation rates, quality-adjusted life-years (QALYs), and incremental cost-effectiveness ratios were the primary outcomes.

RESULTS

Of the 1184 patients (1158 women [97.8%]) meeting simple cancer-based criteria, 117 had a BRCA mutation (9.9%). The mutation rate was similar in retrospective United Kingdom (10.2% [235 of 2294]) and prospective Malaysian (9.7% [103 of 1061]) breast cancer studies. If traditional family history criteria had been used, more than 50% of the mutation-positive individuals would have been missed. Of the 117 mutation-positive individuals, 115 people (98.3%) attended their genetics appointment and cascade to relatives is underway in all appropriate families (85 of 85). Combining with the equivalent ovarian cancer study provides 5 simple cancer-based criteria for BRCA testing with a 10% mutation rate: (1) ovarian cancer; (2) breast cancer diagnosed when patients are 45 years or younger; (3) 2 primary breast cancers, both diagnosed when patients are 60 years or younger; (4) triple-negative breast cancer; and (5) male breast cancer. A sixth criterion-breast cancer plus a parent, sibling, or child with any of the other criteria-can be added to address family history. Criteria 1 through 5 are considered the MCG criteria, and criteria 1 through 6 are considered the MCGplus criteria. Testing using MCG or MCGplus criteria is cost-effective with cost-effectiveness ratios of $1330 per discounted QALYs and $1225 per discounted QALYs, respectively, and appears to lead to cancer and mortality reductions (MCG: 804 cancers, 161 deaths; MCGplus: 1020 cancers, 204 deaths per year over 50 years). Use of MCG or MCGplus criteria might allow detection of all BRCA mutations in patients with breast cancer in the United Kingdom through testing one-third of patients. Feedback questionnaires from 259 patients and 23 cancer team members (12 oncologists, 8 surgeons, and 3 nurse specialists) showed acceptability of the process with 100% of patients pleased they had genetic testing and 100% of cancer team members confident to approve patients for genetic testing. Use of MCGplus criteria also appeared to be time and resource efficient, requiring 95% fewer genetic consultations than the traditional process.

CONCLUSIONS AND RELEVANCE

This study suggests that mainstream testing using simple, cancer-based criteria might be able to efficiently deliver consistent, cost-effective, patient-centered BRCA testing.

Identification of new Wilms tumour predisposition genes: an exome sequencing study

BACKGROUND

Wilms tumour is the most common childhood renal cancer and is genetically heterogeneous. While several Wilms tumour predisposition genes have been identified, there is strong evidence that further predisposition genes are likely to exist. Our study aim was to identify new predisposition genes for Wilms tumour.

METHODS

In this exome sequencing study, we analysed lymphocyte DNA from 890 individuals with Wilms tumour, including 91 affected individuals from 49 familial Wilms tumour pedigrees. We used the protein-truncating variant prioritisation method to prioritise potential disease-associated genes for further assessment. We evaluated new predisposition genes in exome sequencing data that we generated in 334 individuals with 27 other childhood cancers and in exome data from The Cancer Genome Atlas obtained from 7632 individuals with 28 adult cancers.

FINDINGS

We identified constitutional cancer-predisposing mutations in 33 individuals with childhood cancer. The three identified genes with the strongest signal in the protein-truncating variant prioritisation analyses were TRIM28, FBXW7, and NYNRIN. 21 of 33 individuals had a mutation in TRIM28; there was a strong parent-of-origin effect, with all ten inherited mutations being maternally transmitted (p=0·00098). We also found a strong association with the rare epithelial subtype of Wilms tumour, with 14 of 16 tumours being epithelial or epithelial predominant. There were no TRIM28 mutations in individuals with other childhood or adult cancers. We identified truncating FBXW7 mutations in four individuals with Wilms tumour and a de-novo non-synonymous FBXW7 mutation in a child with a rhabdoid tumour. Biallelic truncating mutations in NYNRIN were identified in three individuals with Wilms tumour, which is highly unlikely to have occurred by chance (p<0·0001). Finally, we identified two de-novo KDM3B mutations, supporting the role of KDM3B as a childhood cancer predisposition gene.

INTERPRETATION

The four new Wilms tumour predisposition genes identified-TRIM28, FBXW7, NYNRIN, and KDM3B-are involved in diverse biological processes and, together with the other 17 known Wilms tumour predisposition genes, account for about 10% of Wilms tumour cases. The overlap between these 21 constitutionally mutated predisposition genes and 20 genes somatically mutated in Wilms tumour is limited, consisting of only four genes. We recommend that all individuals with Wilms tumour should be offered genetic testing and particularly, those with epithelial Wilms tumour should be offered TRIM28 genetic testing. Only a third of the familial Wilms tumour clusters we analysed were attributable to known genes, indicating that further Wilms tumour predisposition factors await discovery.

FUNDING

Wellcome Trust.

Insights into BRCA Cancer Predisposition from Integrated Germline and Somatic Analyses in 7632 Cancers

Background

It is often assumed any cancer in a germline BRCA1 or BRCA2 (collectively termed BRCA) mutation carrier was caused by that mutation. It is also often assumed the occurrence of breast or ovarian cancer in an individual with a variant of uncertain significance (VUS) suggests the VUS is pathogenic. These assumptions have profound management implications for cancer patients and healthy individuals.

Methods

We compared the frequency of BRCA mutations, allele loss, and Signature 3 in 7632 individuals with 28 cancers and 1000 population controls. Because only increased frequency was the focus of the study, all statistical tests were one-sided.

Results

Individuals with breast or ovarian cancer had increased germline BRCA pathogenic mutation frequencies compared to controls (P = 1.0x10⁻¹⁰ and P = 1.4x10⁻³⁴, respectively). There was no increase in other cancer types. Wild-type allele loss and Signature 3 were statistically significantly higher in breast and ovarian cancers with BRCA mutations compared with other cancers with BRCA mutations (P = 5.1x10⁻¹⁰ and P = 3.7x10⁻⁹) and cancers without BRCA mutations (P = 2.8x10⁻⁵³ and P = 1.0x10⁻¹³⁴). There was no difference between non-breast and non-ovarian cancers with BRCA mutations and cancers without BRCA mutations. Allele loss and Signature 3 were statistically significantly higher in breast and ovarian cancers in individuals with BRCA pathogenic mutations compared to those with VUS (P = 3.8x10⁻¹⁷ and P = 1.6x10⁻⁸) or benign variants (P = 1.2x10⁻²⁸ and P = 2.2x10⁻¹⁰). There was no difference between individuals with BRCA VUS and those with benign variants.

Conclusions

These data show that non-breast and non-ovarian cancers in individuals with germline BRCA pathogenic mutations are often not causally related to the mutation and that BRCA VUS are highly unlikely to be pathogenic. These results should reduce inappropriate management of germline BRCA information.

Abstract P6-18-18: Phase I trial of eribulin and everolimus in patients with metastatic triple negative breast cancer

Background: Alteration of PI3K/Akt/mTOR pathway is the most common genomic abnormality detected in triple negative breast cancer (TNBC). Everolimus acts synergistically with eribulin in inducing apoptosis in TNBC cell lines and xenografts in our preclinical study. This phase I trial was designed to test the safety and tolerability of combining eribulin and everolimus in patients (pts) with metastatic TNBC.

Methods: The overall objective of this study was to describe the safety and toxicities of the combination. The secondary objective was to assess activity based on response rate (RR) and progression free survival (PFS). Eligibility criteria included pts with metastatic TNBC, ECOG 0-2, 0-3 lines of prior chemotherapy in metastatic setting, and prior treatment with anthracycline and/or taxane therapy. The study utilized the toxicity equivalence range (TEQR) design with a target equivalence range for dose-limiting toxicities (DLTs) of 0.20-0.35. The recommended phase 2 dose (RP2D) will be the dose closest to the target of 0.25 below 0.51 based on isotonic regression.Three dosing levels of the combinations were tested: level A1 (everolimus 5mg daily; eribulin 1.4 mg/m2 days 1, 8 every 3 weeks), level A2 (everolimus 7.5mg daily; eribulin 1.4 mg/m2, days 1, 8 every 3 weeks), level B1(everolimus 5mg daily; eribulin 1.1 mg/m2 days 1, 8 every 3 weeks). Nanostring RNA analysis and genomic mutation analysis were conducted in 16 pts with available tumor tissue.

Results: A total of 27 pts were enrolled. Median age was 55 years (range 36-76). Two pts were ineligible due to HER2+ on repeat biopsy and were only included in the toxicity analysis. Dose level B1 (everolimus 5mg daily and eribulin 1.1 mg/m2 days 1, 8 every 3 weeks) was determined to be the RP2D doses. The DLTs were neutropenia, stomatitis and hyperglycemia. Across all cycles, 59% (16/27) had a ≥ Gr3 toxicity attributed to treatment at the possible or above level. 44% (12/27) had Gr3 heme-toxicities. The most common toxicities were ≥ Gr3 neutropenia (10 pts), Gr3 lymphopenia (6 pts) and ≥ Gr3 leukopenia (7 pts). 33% (9/27) had Gr3 non-heme toxicities. The most common were Gr3 stomatitis (3 pts), Gr3 hyperglycemia (3 pts) and Gr3 fatigue (5 pts). The median number of cycles completed was 4 (0-8). 68% (17/25) had a dose modification or hold, 14 of 25 (56%) were for eribulin and 15 of 25 (60%) were for everolimus. Of 25 eligible pts, 8 (32%) achieved a best response as partial response, 11 (44%) had stable disease and 6 (24%) had progression. 80% (20/25) experienced progression by RECIST or showed clinical progression, and the median time to progression was 2.7 mo (95% CI (2.2, 4.6)). At the time of this analysis, 16 participants had died, median OS was 6.3 mo (95% CI (5.3, undefined)). Two pts are still being followed on treatment. PI3K-Akt-mTOR pathway genes and mutations profiles were studied.

Conclusion: Eribulin 1.1 mg/m2 days 1, 8 and everolimus 5mg daily was defined as the RP2D. Genomic analysis is currently underway to understand the molecular mechanisms of resistance.

Citation Format: Yuan Y, Yost S, Blanchard S, Yin H, Li M, Robinson K, Tang A, Martinez N, Leong L, Somlo G, Tank Patel N, Waisman J, Portnow J, Hurria A, Luu T-H, Mortimer J. Phase I trial of eribulin and everolimus in patients with metastatic triple negative breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P6-18-18.

Clinical Annotation Reference Templates: a resource for consistent variant annotation

Annotating the impact of a variant on a gene is a vital component of genetic medicine and genetic research. Different gene annotations for the same genomic variant are possible, because different structures and sequences for the same gene are available. The clinical community typically use RefSeq NMs to annotate gene variation, which do not always match the reference genome. The scientific community typically use Ensembl ENSTs to annotate gene variation. These match the reference genome, but often do not match the equivalent NM. Often the transcripts used to annotate gene variation are not provided, impeding interoperability and consistency. Here we introduce the concept of the Clinical Annotation Reference Template (CART). CARTs are analogous to the reference genome; they provide a universal standard template so reference genomic coordinates are consistently annotated at the protein level. Naturally, there are many situations where annotations using a specific transcript, or multiple transcripts are useful. The aim of the CARTs is not to impede this practice. Rather, the CART annotation serves as an anchor to ensure interoperability between different annotation systems and variant frequency accuracy. Annotations using other explicitly-named transcripts should also be provided, wherever useful. We have integrated transcript data to generate CARTs for over 18,000 genes, for both GRCh37 and GRCh38, based on the associated NM and ENST identified through the CART selection process. Each CART has a unique ID and can be used individually or as a stable set of templates; CART37A for GRCh37 and CART38A for GRCh38. We have made the CARTs available on the UCSC browser and in different file formats on the Open Science Framework: https://osf.io/tcvbq/. We have also made the CARTtools software we used to generate the CARTs available on GitHub. We hope the CARTs will be useful in helping to drive transparent, stable, consistent, interoperable variant annotation.

ICR142 Benchmarker: evaluating, optimising and benchmarking variant calling performance using the ICR142 NGS validation series

Evaluating, optimising and benchmarking of next generation sequencing (NGS) variant calling performance are essential requirements for clinical, commercial and academic NGS pipelines. Such assessments should be performed in a consistent, transparent and reproducible fashion, using independently, orthogonally generated data. Here we present ICR142 Benchmarker, a tool to generate outputs for assessing germline base substitution and indel calling performance using the ICR142 NGS validation series, a dataset of Illumina platform-based exome sequence data from 142 samples together with Sanger sequence data at 704 sites. ICR142 Benchmarker provides summary and detailed information on the sensitivity, specificity and false detection rates of variant callers. ICR142 Benchmarker also automatically generates a single page report highlighting key performance metrics and how performance compares to widely-used open-source tools. We used ICR142 Benchmarker with VCF files outputted by GATK, OpEx and DeepVariant to create a benchmark for variant calling performance. This evaluation revealed pipeline-specific differences and shared challenges in variant calling, for example in detecting indels in short repeating sequence motifs. We next used ICR142 Benchmarker to perform regression testing with DeepVariant versions 0.5.2 and 0.6.1. This showed that v0.6.1 improves variant calling performance, but there was evidence of minor changes in indel calling behaviour that may benefit from attention. The data also allowed us to evaluate filters to optimise DeepVariant calling, and we recommend using 30 as the QUAL threshold for base substitution calls when using DeepVariant v0.6.1. Finally, we used ICR142 Benchmarker with VCF files from two commercial variant calling providers to facilitate optimisation of their in-house pipelines and to provide transparent benchmarking of their performance. ICR142 Benchmarker consistently and transparently analyses variant calling performance based on the ICR142 NGS validation series, using the standard VCF input and outputting informative metrics to enable user understanding of pipeline performance. ICR142 Benchmarker is freely available at https://github.com/RahmanTeamDevelopment/ICR142_Benchmarker/releases.

ICR142 Benchmarker: evaluating, optimising and benchmarking variant calling using the ICR142 NGS validation series

Evaluating, optimising and benchmarking of next generation sequencing (NGS) variant calling performance are essential requirements for clinical, commercial and academic NGS pipelines. Such assessments should be performed in a consistent, transparent and reproducible fashion, using independently, orthogonally generated data. Here we present ICR142 Benchmarker, a tool to generate outputs for assessing variant calling performance using the ICR142 NGS validation series, a dataset of exome sequence data from 142 samples together with Sanger sequence data at 704 sites. ICR142 Benchmarker provides summary and detailed information on the sensitivity, specificity and false detection rates of variant callers. ICR142 Benchmarker also automatically generates a single page report highlighting key performance metrics and how performance compares to widely-used open-source tools. We used ICR142 Benchmarker with VCF files outputted by GATK, OpEx and DeepVariant to create a benchmark for variant calling performance. This evaluation revealed pipeline-specific differences and shared challenges in variant calling, for example in detecting indels in short repeating sequence motifs. We next used ICR142 Benchmarker to perform regression testing with versions 0.5.2 and 0.6.1 of DeepVariant. This showed that v0.6.1 improves variant calling performance, but there was evidence of some minor changes in indel calling behaviour that may benefit from attention in future updates. The data also allowed us to evaluate filters to optimise DeepVariant calling, and we recommend using 30 as the QUAL threshold for base substitution calls when using DeepVariant v0.6.1. Finally, we used ICR142 Benchmarker with VCF files from two commercial variant calling providers to facilitate optimisation of their in-house pipelines and to provide transparent benchmarking of their performance. ICR142 Benchmarker consistently and transparently analyses variant calling performance based on the ICR142 NGS validation series, using the standard VCF input and outputting informative metrics to enable user understanding of pipeline performance. ICR142 Benchmarker is freely available at https://github.com/RahmanTeamDevelopment/ICR142_Benchmarker/releases.

The Quality Sequencing Minimum (QSM): providing comprehensive, consistent, transparent next generation sequencing data quality assurance

Next generation sequencing (NGS) is routinely used in clinical genetic testing. Quality management of NGS testing is essential to ensure performance is consistently and rigorously evaluated.

Three primary metrics are used in NGS quality evaluation: depth of coverage, base quality and mapping quality. To provide consistency and transparency in the utilisation of these metrics we present the Quality Sequencing Minimum (QSM).

The QSM defines the minimum quality requirement a laboratory has selected for depth of coverage (C), base quality (B) and mapping quality (M) and can be applied per base, exon, gene or other genomic region, as appropriate. The QSM format is CX_BY(P _Y)_MZ(P _Z). X is the parameter threshold for C, Y the parameter threshold for B, P _Y the percentage of reads that must reach Y, Z the parameter threshold for M, P _Z the percentage of reads that must reach Z. The data underlying the QSM is in the BAM file, so a QSM can be easily and automatically calculated in any NGS pipeline.

We used the QSM to optimise cancer predisposition gene testing using the TruSight Cancer Panel (TSCP). We set the QSM as C50_B10(85)_M20(95). Test regions falling below the QSM were automatically flagged for review, with 100/1471 test regions QSM-flagged in multiple individuals. Supplementing these regions with 132 additional probes improved performance in 85/100. We also used the QSM to optimise testing of genes with pseudogenes such as PTEN and PMS2. In TSCP data from 960 individuals the median number of regions that passed QSM per sample was 1429 (97%).  Importantly, the QSM can be used at an individual report level to provide succinct, comprehensive quality assurance information about individual test performance.

We believe many laboratories would find the QSM useful. Furthermore, widespread adoption of the QSM would facilitate consistent, transparent reporting of genetic test performance by different laboratories.

CoverView: a sequence quality evaluation tool for next generation sequencing data

Quality assurance and quality control are essential for robust next generation sequencing (NGS). Here we present CoverView, a fast, flexible, user-friendly quality evaluation tool for NGS data. CoverView processes mapped sequencing reads and user-specified regions to report depth of coverage, base and mapping quality metrics with increasing levels of detail from a chromosome-level summary to per-base profiles. CoverView can flag regions that do not fulfil user-specified quality requirements, allowing suboptimal data to be systematically and automatically presented for review. It also provides an interactive graphical user interface (GUI) that can be opened in a web browser and allows intuitive exploration of results.

We have integrated CoverView into our accredited clinical cancer predisposition gene testing laboratory that uses the TruSight Cancer Panel (TSCP). CoverView has been invaluable for optimisation and quality control of our testing pipeline, providing transparent, consistent quality metric information and automatic flagging of regions that fall below quality thresholds. We demonstrate this utility with TSCP data from the Genome in a Bottle reference sample, which CoverView analysed in 13 seconds.

CoverView uses data routinely generated by NGS pipelines, reads standard input formats, and rapidly creates easy-to-parse output text (.txt) files that are customised by a simple configuration file. CoverView can therefore be easily integrated into any NGS pipeline. CoverView and detailed documentation for its use are freely available at github.com/RahmanTeamDevelopment/CoverView/releases and www.icr.ac.uk/CoverView

Abstract P3-05-02: Immune profiling of paired primary and recurrent triple negative breast cancer

Background: Triple negative breast cancer (TNBC) is a heterogeneous disease with several molecular subtypes: basal-like1 (BL-1), basal-like 2 (BL-2), mesenchymal (M), and luminal androgen receptor (LAR). Molecular evolution of TNBC through chemotherapy selection pressure is well recognized but poorly understood. In addition, approximately 20% of TNBCs respond to PD-1 or PD-L1 inhibitors. It has been observed that heavily pre-treated patients may not respond well to immunotherapy. This study was carried out to perform immune profiling of paired primary and recurrent TNBC. Here we report the result of the first 10 paired tissue pilot analysis.

Methods: Twenty specimens were identified through an IRB-approved protocol via the City of Hope Biospecimen Repository (2002-2015). Two brain and one bone metastasis specimens were not included due to technical difficulty. Formalin-fixed paraffin embedded (FFPE) sample blocks were cut into 5-mm thick slides and labeled with the following antibodies: CD4, CD8, CD3, FOXP3, CD20, CD33, Pan-CK, and PD-1 using the multiplex IHC opal method. Image acquisition and cell counting were carried out using PerkinElmer Vectra automated quantitative pathology imaging system and inForm software analysis (PerkinElmer, Waltham, MA). mRNA expression profiling was performed using Affymetrix Human Genechip 2.0. Raw data were normalized and processed using Expression Console. Using Vanderbilt TNBC sub-classification tool, we have sub-classified the 20 primary and recurrent TNBC specimens. Tumor mutation burden (TMB) was generated through FoundationOne® platform.

Result: A total of 17 samples were analyzed (M, 5; LAR, 3; BL-1, 4; BL-2, 5). M-subtype had a significantly lower tumor-infiltrating CD3+ T cells (p=0.005), CD8+ T cells (p=0.024), CD4+ T cells (p=0.065) and CD4+FOXP3+ Treg cells (p=0.054), irrespective of the site of metastasis. CD20+ B cells were particularly enriched in BL-1 subtype (p=0.0013, 23.5% of 17 samples). Of 17 samples, 8 had TMB. Seven had low TMB (&lt;10 mut/Mb) and one had intermediate TMB (11 mut/Mb, LAR subtype). The tumor with intermediate TMB had the highest quantity of tumor-infiltrating CD3+ T cells, CD8+ T cells, CD8+PD1+ T cells, and CD4+FOXP3+PD1+ Treg cells compared to the 7 tumors with low TMB. Compared with recurrent tumors, primary tumors had a significantly higher percentage of tumor-infiltrating T cells (TIL). To validate multiplexed IHC results, these samples were evaluated by a licensed pathologist at City of Hope using the International TILs Working Group 2014 guidelines, and there was a good correlation between percent of TILs and CD3+ T cells by IHC approach.

Conclusion: To our knowledge, this is the first study linking tumor immune cell profiles with the TNBC 4 subtypes. Distinctive immune cell patterns were observed among 4 TNBC subtypes. M subtype had significantly lower TILs, which may indicate poor response to checkpoint inhibitors. Further analysis of a total of 50 paired TNBCs is currently underway.

Contact information: Yuan Yuan MD PhD, Email: yuyuan@coh.org

Citation Format: He T-F, Yost S, Schmolze D, Wang R, Rosario A, Tu T, Chu P, Lee P, Yuan Y. Immune profiling of paired primary and recurrent triple negative breast cancer [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P3-05-02.

Abstract OT1-05-02: A phase II clinical trial of the combination of pembrolizumab and selective androgen receptor modulator GTx-024 in patients with advanced androgen receptor positive triple negative breast cancer

Background: Androgen receptor (AR) targeted therapy and immunotherapy represent one of the most promising strategies for metastatic triple negative breast cancer (mTNBC), which accounts for 15-20% of all breast cancers. As a nonsteroidal selective androgen receptor modulator (SARM), GTx-024 demonstrated preclinical activity in AR+ TNBC PDX model. Pembrolizumab is a highly selective humanized monoclonal antibody of the programmed cell death 1 receptor (PD-1). The complementary modes of action and low potential for overlapping toxicity make the combination promising in patients with AR+ mTNBC.

Trial Design: This is an open-label Phase 2 study for AR+ mTNBC. Eligible participants receive pembrolizumab 200mg IV every 3 weeks in combination with GTx-024 18mg po daily.

Eligibility Criteria: Eligible patients must have AR+ (&gt;10%, 1+ by IHC) TNBC; failed up to 2 lines of therapy in metastatic setting; and have measurable disease per RECIST1.1. Patients are excluded if they have had prior checkpoint inhibitors or AR targeted agents. Patients with current or prior use of testosterone, testosterone-like agents, androgenic compounds, or anti-androgens (including systemic steroids and immunosuppressive medications)are excluded, as well as current or prior history of noninfectious pneumonitis requiring systemic steroid therapy.

Specific Aims: The primary objective is to evaluate the safety/tolerability of GTx-024 and pembrolizumab and determine the response rate (CR or PR via RECIST 1.1) in patients with advanced AR+ TNBC. We will use clinical benefit rate (CBR), duration of response (DOR), PFS, and OS to test the efficacy of this novel drug combination.

Statistical Design: A Simon's MiniMax two-stage Phase 2 design will be utilized. Based on the previously reported response rate associated with single agent pembrolizumab (19%), we consider a response rate of 19% for the combination as discouraging, and a 39% response rate as encouraging. As a result, we will initially accrue 15 patients (including 6 patients from safety lead-in treated at the tolerable dose). If 2 or fewer patients respond, we will stop accrual for futility. Otherwise, the study will accrue an additional 14 patients for a total of 29 patients. With 29 patients, if only 8 or fewer respond (≤27.6%), the study will be considered discouraging unless secondary evidence of clinical benefit is substantial. With more than 8 patients responding out of the 29 patients, the combination would be considered promising. This design has 85% power to declare a true response rate of 39% as promising (power), and a 10% probability of declaring a true 19% response rate as encouraging (type I error). The probability of early termination if the true response rate is 19% is 44%.

Target Accrual: 29

Study Contact: Yuan Yuan MD PhD, City of Hope Comprehensive Cancer Center; Duarte, CA 91030; Email: yuyuan@coh.org

Citation Format: Yuan Y, Frankel P, Synold T, Lee P, Yost S, Martinez N, Tang A, Mendez B, Schmolze D, Apple S, Hurria A, Waisman J, Somlo G, Tank N, Sedrak M, Mortimer J. A phase II clinical trial of the combination of pembrolizumab and selective androgen receptor modulator GTx-024 in patients with advanced androgen receptor positive triple negative breast cancer [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr OT1-05-02.

Abstract PD8-02: Mechanisms of recurrence: Paired analysis of primary and metastatic triple negative breast cancer

Background: Triple negative breast cancer (TNBC) is the most aggressive subtype of invasive breast cancer that lacks ER, PR, and HER2 expression. It is a heterogeneous disease with several molecular subtypes: basal-like1 (BL-1), basal-like 2 (BL-2), mesenchymal (M), and luminal androgen receptor (LAR). Treatment for TNBC is normally limited to chemotherapy, and relapse is common. Here we report molecular alterations associated with TNBC metastasis by analyzing the genomic profiles of paired primary and metastatic TNBCs.

Methods:50 paired TNBCs were identified through an IRB-approved protocol via the City of Hope (COH) Biospecimen Repository. DNA mutation and mRNA expression profiles of 10 paired primary and metastatic TNBCs were analyzed. DNA mutations were identified using exome sequencing by FoundationOne®. Affymetrix Human Genechip 2.0 was used for mRNA expression profiling. Raw data were normalized and processed using Expression Console, and linear regression was performed using Limma to identify the differentially expressed genes between primary and metastatic TNBCs.

Results: DNA mutation profiling showed that multiple mutations occurred within genes covering pathways of PI3K/AKT/mTOR, DNA repair, RAS/MAPK, cell cycle, and growth factor receptor signaling, reconfirming genomic heterogeneity of TNBCs. Gene expression profiles were analyzed for Lehmann's TNBC molecular subtypes (BL-1, BL-2, M, and LAR). Six of ten TNBCs showed phenotype shift between the primary and metastatic TNBCs. Several unique gene expression patterns were identified by comparing the paired TNBCs. CCNE1 and TPX2 were co-overexpressed in metastatic TNBCs compared to paired primaries. This mirrored prior studies in ovarian cancer, where co-overexpression of CCNE1 and TPX2 were found related to clonal resistance against chemotherapy. Splicing factors TRA2B and SRSF7 were also over-expressed in metastatic TNBCs compared with primaries. The analysis studying the association of CCNE1 and TPX2 with overall survival is ongoing using TCGA.

Conclusion: Overall, these results show the comparative changes between primary and relapsed TNBCs and indicate the heterogeneity of molecular mechanisms of recurrence. CNNE1 and TPX2 may represent important genes involved in TNBC metastasis. Further analyses including a total of 50 paired TNBCs are currently underway.

Study Contact: Yuan Yuan MD PhD, City of Hope Comprehensive Cancer Center; Duarte, CA 91030; Email: yuyuan@coh.org

Citation Format: Zhao Z-M, Yost S, Yuan Y-C, Warden C, Chuang J, Yuan Y. Mechanisms of recurrence: Paired analysis of primary and metastatic triple negative breast cancer [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr PD8-02.

Epithelioid angiosarcoma of the vulva: A case report

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Vulvar angiosarcoma in a patient with pelvic radiation and chronic lymphedema

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Epithelioid histologic staining positive for vimentin, ERG, CD31

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Gross appearance of violaceous hyperpigmentation of the mons pubis

The ICR96 exon CNV validation series: a resource for orthogonal assessment of exon CNV calling in NGS data

Detection of deletions and duplications of whole exons (exon CNVs) is a key requirement of genetic testing. Accurate detection of this variant type has proved very challenging in targeted next-generation sequencing (NGS) data, particularly if only a single exon is involved. Many different NGS exon CNV calling methods have been developed over the last five years. Such methods are usually evaluated using simulated and/or in-house data due to a lack of publicly-available datasets with orthogonally generated results. This hinders tool comparisons, transparency and reproducibility. To provide a community resource for assessment of exon CNV calling methods in targeted NGS data, we here present the ICR96 exon CNV validation series. The dataset includes high-quality sequencing data from a targeted NGS assay (the TruSight Cancer Panel) together with Multiplex Ligation-dependent Probe Amplification (MLPA) results for 96 independent samples. 66 samples contain at least one validated exon CNV and 30 samples have validated negative results for exon CNVs in 26 genes. The dataset includes 46 exon CNVs in BRCA1, BRCA2, TP53, MLH1, MSH2, MSH6, PMS2, EPCAM or PTEN, giving excellent representation of the cancer predisposition genes most frequently tested in clinical practice. Moreover, the validated exon CNVs include 25 single exon CNVs, the most difficult type of exon CNV to detect. The FASTQ files for the ICR96 exon CNV validation series can be accessed through the European-Genome phenome Archive (EGA) under the accession number EGAS00001002428.

Mutations in Epigenetic Regulation Genes Are a Major Cause of Overgrowth with Intellectual Disability

To explore the genetic architecture of human overgrowth syndromes and human growth control, we performed experimental and bioinformatic analyses of 710 individuals with overgrowth (height and/or head circumference ≥+2 SD) and intellectual disability (OGID). We identified a causal mutation in 1 of 14 genes in 50% (353/710). This includes HIST1H1E, encoding histone H1.4, which has not been associated with a developmental disorder previously. The pathogenic HIST1H1E mutations are predicted to result in a product that is less effective in neutralizing negatively charged linker DNA because it has a reduced net charge, and in DNA binding and protein-protein interactions because key residues are truncated. Functional network analyses demonstrated that epigenetic regulation is a prominent biological process dysregulated in individuals with OGID. Mutations in six epigenetic regulation genes—NSD1, EZH2, DNMT3A, CHD8, HIST1H1E, and EED—accounted for 44% of individuals (311/710). There was significant overlap between the 14 genes involved in OGID and 611 genes in regions identified in GWASs to be associated with height (p = 6.84 × 10⁻⁸), suggesting that a common variation impacting function of genes involved in OGID influences height at a population level. Increased cellular growth is a hallmark of cancer and there was striking overlap between the genes involved in OGID and 260 somatically mutated cancer driver genes (p = 1.75 × 10⁻¹⁴). However, the mutation spectra of genes involved in OGID and cancer differ, suggesting complex genotype-phenotype relationships. These data reveal insights into the genetic control of human growth and demonstrate that exome sequencing in OGID has a high diagnostic yield.

Abstract OT2-01-03: Phase II Trial of the addition of pembrolizumab to letrozole and palbociclib in patients with metastatic estrogen receptor positive breast cancer who have stable disease on letrozole and palbociclib

Background: The combination of palbociclib and letrozole has become the standard of care for patients with newly diagnosed estrogen receptor positive (ER+) metastatic breast cancer (MBC), with promising prolongation of progression free survival (PFS). However, nearly half of all patients achieved stable disease only after the first 6 months of therapy. Check-point inhibitor pembrolizumab was effective in ER+ MBC with a response rate of 13-17%, this study will evaluate the efficacy of adding pembrolizumab for patients with ER+ MBC who have achieved stable disease (SD) on letrozole and palbociclib.

Trial Design:This is an open-label single institutional study. Patient will receive letrozole (2.5 mg) once a day and palbociclib (125 mg, 100 mg, or 75 mg as established tolerated dose) once a day for 3 weeks on and 1 week off. Pembrolizumab will be given at 200 mg IV every 3 weeks.

Eligibility Criteria: Eligible patients must be postmenopausal women with ER+ MBC with measurable disease by RECIST1.1, ECOG performance status 0-1; must have received letrozole and palbociclib for at least 6 months, and have documented SD per RECIST 1.1. Up to3 lines of previous systemic therapy including endocrine therapy and/or chemotherapy are allowed. Patients are excluded if they had prior treatment with anti--PD1 or anti-PD-L1therapy, immunodeficiency; currently using systemic steroids active tuberculosis infection; major surgery within 28 days; active or untreated CNS metastases; history of interstitial lung disease; active infection requiring systemic therapy; or active cardiac disease.

Specific Aims: The primary objective is to evaluate the objective response rate(ORR). The secondary objective is to determine the safety and tolerability of pembrolizumab plus the letrozole/palbociclib combination. We will use clinical benefit rate (CBR), duration of response (DOR), PFS, and OS to test the efficacy of this novel drug combination.

Statistical Design: We will employ a three-at-risk design (modified rolling design) for the initial cohort of this Phase II study to insure the triplet is well-tolerated. This design permits only 3 patients to be a risk for DLT at any one time during the “safety lead-in” .When the first 6 patients have completed the observation period and treatment with ≤1 DLT, the safety lead-in for the triplet will be considered successful, and accrual will proceed to a total of 18 patients. Response (CR or PR by RECIST version 1.1) in patients who have demonstrated only SD on letrozole and palbociclib can be reasonably attributed to the addition of pembrolizumab. As a result, we set the probability of a response occurring without the addition of pembrolizumab as 3% or less. With 18 patients, a true response rate of 20% would result in at least 2 responders with 90% power and a type I error of 10%. With 18 patients, the response can be estimated with a 95% CI half-width of 23%.

Target Accrual: 18.

Citation Format: Yuan Y, Frankel P, Synold T, Yost S, Lee P, Waisman J, Somlo G, Hurria A, Mortimer J. Phase II Trial of the addition of pembrolizumab to letrozole and palbociclib in patients with metastatic estrogen receptor positive breast cancer who have stable disease on letrozole and palbociclib [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr OT2-01-03.

Abstract P1-05-26: Genomic analysis of molecular discordance of paired primary and recurrent triple negative breast cancer

Background: Triple negative breast cancer (TNBC) is a heterogeneous disease with several molecular subtypes: basal-like1 (BL1), basal-like 2 (BL-2), mesenchymal(M), mesenchymal-stem-like(MSL), immune-modulatory(IM) and unclassified (UNC) Molecular evolution of TNBC through chemotherapy selection pressure is well recognized but poorly understood. This study was carried out to perform paired genomic analysis of TNBC comparing primary breast cancer with recurrent/refractory disease. Here we report the result of the first10 paired tissue analysis.

Methods: 49 paired specimens were identified through an IRB-approved protocol via COH biorepository search (2002- 2015). miRNA and mRNA profiling of 22 samples were performed. The miRNA libraries were prepared and sequenced on Hiseq2500. Sequences were aligned to hg19 genome and miRNA expression levels were counted by in house built R scripts. Go and pathway annotation was performed using DAVID online tool. Affymetrix human Genechip 2.0st was used for mRNA expression profiling. Raw data were normalized and processed using Expression Console, and linear regression was performed using Limma to identify the differentially expressed genes between primary and recurrent/refractory TNBCs.

Result: Through mRNA profiling, we identified several unique gene expression patterns comparing the paired TNBC. Significant mRNA expression alterations were observed in: cell cycle, DNA repair and adhesion. Using Vanderbilt TNBC sub-classification tool, we have identified “phenotype shift” between primary and recurrent TNBCs. Of the 8 paired specimen analyzed, 3 paired tissue remain in the same subclass (2 in IM, 1 in M). Phenotype shift observed in: 1 from BL1 to BL2, 1 from BL2 to BL1, 1 UNC to IM; 1 MSL to UNC; 1 from M to UNC. 15 up regulated and 13 down regulated miRNAs were identified. Most significantly differentially expressed miRNA (with more than 4 fold expression changes, P-value &lt; 0.001) included: miR-206, miR-203, miR-144, miR-16-2, miR-15b, and miR-20b (un-regulated) and miR-10b, miR-125b and let-7c(down-regulated). These miRNA genes are involved in regulation of hormonal receptor signaling, cell cycle, proliferation and metastases. Statistically significant differentially expressed miRNAs identified from our TNBC patient cohort will be further validated using RT-PCR.

Conclusion: A number of mRNA gene pathways and miRNAs showed differential expression between paired recurrent and primary TNBC tumor specimen. The underlying biology driven the phenotype shift is being studied. Further analysis to include a total of 49 paired TNBCs is currently underway.

Contact information: Yuan Yuan MD PhD, Email: yuyuan@coh.org.

Citation Format: Yuan Y, Li A, Yost S, Yuan Y-C, Chu P, Warden C, Wang J, Liu Z, Liang Y, Goldstein L, Wu X. Genomic analysis of molecular discordance of paired primary and recurrent triple negative breast cancer [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P1-05-26.

Abstract OT1-02-05: Phase II clinical trial of neratinib in patients 60 and older with HER2 over-expressed or mutated breast cancer: Trial design considerations for older adults

Background: This study addresses a key knowledge gap identified by the Institute of Medicine report on quality cancer care. Although there has been a growth in the number of targeted agents approved for the treatment of breast cancer, there are limited data regarding the efficacy, toxicity, and management of side effects in older adults. Neratinib is a potent oral small molecule tyrosine kinase inhibitor. Early clinical data have demonstrated the activity of neratinib in patients who have already progressed through HER2 targeted therapies. This study is designed to evaluate the tolerability and toxicity profile of neratinib in older adults with metastatic breast cancer (MBC) incorporating geriatric oncology design considerations.

Trial Design: This is an open label, single arm, phase II study of single agent neratinib in patients with HER2 positive MBC. Neratinib is given at 240mg orally in 28 day cycles. Unique factors of this geriatric oncology trial design include: 1) pre-treatment and on-treatment geriatric assessment; 2) additional nurse toxicity visits; 3) an algorithm for aggressive management of diarrhea; 4) measurements of the pharmacokinetics (PK) of neratinib; 5) inclusion of biomarkers of aging; 6) measurement of patient adherence; and 7) evaluation of quality of life.

Eligibility Criteria: Patients must be age≥60 with histologically-proven HER2 positive MBC or MBC with HER2 receptor activating mutations. There is no limitation on the number of previous lines of therapy, but patients must have adequate organ and bone marrow functions, and a baseline LVEF ≥ 50%. Exclusion Criteria include: prior treatment with neratinib; major surgery within 28 days; uncontrolled cardiac disease; concurrent use of digoxin; or chronic diarrhea.

Specific Aims: The primary objective of this study is to identify the rate of grade 2 or higher toxicities attributed to neratinib in adult age ≥60 with HER2 over-expressing breast cancer. The secondary objectives are to describe the full toxicity profile (including all grades of gastrointestinal toxicities); to estimate the rate of dose reduction, holds and hospitalizations; to describe the PK parameters; to estimate the adherence rate to neratinib; and to estimate the overall response, clinical benefit rate, progression-free and overall survival. Furthermore, we will explore the role of a cancer-specific geriatric assessment and serum biomarkers of aging (IL-6, CRP, and D-dimer) in predicting treatment toxicities and PK parameters.

Statistical Design: We plan to enroll 40 patients age ≥60 (at least 5 patients age 75 years or older, and no more than 15 patients 60-70) in order to assure that our sample is representative of the entire age range of older adults. Given a sample size of 40 subjects, the widest half-width of the 95% confidence limits for the rate of grade 2 or higher toxicities will be less than or equal to 0.16. An interim analysis will be performed after 20 subjects have been on study for at least one cycle.

Accrual goal: 40

Contact information: Yuan Yuan MD PhD, Email: yuyuan@coh.org.

Citation Format: Yuan Y, Blanchard S, Li D, Mortimer J, Waisman J, Somlo G, Yost S, Katheria V, Hurria A. Phase II clinical trial of neratinib in patients 60 and older with HER2 over-expressed or mutated breast cancer: Trial design considerations for older adults [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr OT1-02-05.

Abstract P6-16-08: The impact of genomic mutation on metastatic breast cancer treatment: A retrospective clinical trial

Background: Next-Generation Sequencing (NGS) has made genomic mutation-driven cancer medicine feasible. Recognizing the importance of pathway and biomarker-driven personalized therapy for patients with metastatic breast cancer (MBC), we frequently submit tumor tissue for FoundationOne® genomic sequencing. Here we report the results and clinical impact of this test in 44 patients with MBC.

Patients and Methods: An institution IRB protocol was established for this retrospective clinical trial performed at the City of Hope Comprehensive Cancer Center from January 2014 to May 2016 with available tumor genomic DNA mutation results through FoundationOne® testing. Patients' clinical characteristics including age, race, treatment history, clinical outcome and genomic mutation profiles were reviewed.

Results: We identified 44 patients with MBC submitted for FoundationOne® genomic profiling: 24 triple negative breast cancer (TNBC), 16 estrogen receptor positive (ER+) and 4 human epidermal growth factor receptor 2 positive (HER2+). A total of 23 patients received over 3 lines of chemotherapies prior to FoundationOne® testing. Actionable mutations were identified in 42 of the 44 patients and 23 patients (52%) initiated mutation-driven targeted therapies. Of these 23 patients treated, a total of 17 had accessible responses and 6 patients did not have accessible responses due to short exposure (&lt;2 weeks) and transition to hospice. The remaining 19 patients failed to initiate targeted therapy: 7 transitioned to palliative care/hospice, 5 were placed on other chemotherapy by treating physician, 4 had exhausted all of the targeted therapies recommended, and 3 chose not to start on treatment. Of the 7 responders, 2 received pazopanib and 5 received everolimus containing regimen. Durable response was observed in 3 cases: two patients carried PIK3CA alterations and were treated with everolimus, and the other responder had FGFR1 amplification and was treated with pazopanib. Comparing the genomic mutation profiling with The Cancer Genome Atlas (TCGA) database which contains primary breast cancer, the heavily pretreated TNBC tumors carried higher percentage of PIK3CA mutations (29% vs. 8%, p&lt;0.01).

Conclusion: Targeted genomic sequencing through FoundationOne® can identify effective therapy that has not generally been used based on pathology type. NGS should be performed early in patients with good performance status. This approach should be utilized in a setting where genomic mutation driven therapeutic trials are available.

Contact information: Yuan Yuan MD PhD, Department of Medical Oncology & Molecular Therapeutics; City of Hope Comprehensive Cancer Center; Duarte, CA 91030; Email: yuyuan@coh.org.

Citation Format: Yuan Y, Yost S, Yuan Y-C, Liu Z, Frankel P, Nicola S, Mortimer J. The impact of genomic mutation on metastatic breast cancer treatment: A retrospective clinical trial [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P6-16-08.

Mutational Profiling Can Establish Clonal or Independent Origin in Synchronous Bilateral Breast and Other Tumors

Background

Synchronous tumors can be independent primary tumors or a primary-metastatic (clonal) pair, which may have clinical implications. Mutational profiling of tumor DNA is increasingly common in the clinic. We investigated whether mutational profiling can distinguish independent from clonal tumors in breast and other cancers, using a carefully defined test based on the Clonal Likelihood Score (CLS = 100 x # shared high confidence (HC) mutations/ # total HC mutations).

Methods

Statistical properties of a formal test using the CLS were investigated. A high CLS is evidence in favor of clonality; the test is implemented as a one-sided binomial test of proportions. Test parameters were empirically determined using 16,422 independent breast tumor pairs and 15 primary-metastatic tumor pairs from 10 cancer types using The Cancer Genome Atlas.

Results

We validated performance of the test with its established parameters, using five published data sets comprising 15,758 known independent tumor pairs (maximum CLS = 4.1%, minimum p-value = 0.48) and 283 known tumor clonal pairs (minimum CLS 13%, maximum p-value <0.01), across renal cell, testicular, and colorectal cancer. The CLS test correctly classified all validation samples but one, which it appears may have been incorrectly classified in the published data. As proof-of-concept we then applied the CLS test to two new cases of invasive synchronous bilateral breast cancer at our institution, each with one hormone receptor positive (ER+/PR+/HER2-) lobular and one triple negative ductal carcinoma. High confidence mutations were identified by exome sequencing and results were validated using deep targeted sequencing. The first tumor pair had CLS of 81% (p-value < 10–15), supporting clonality. In the second pair, no common mutations of 184 variants were validated (p-value >0.99), supporting independence. A plausible molecular mechanism for the shift from hormone receptor positive to triple negative was identified in the clonal pair.

Conclusion

We have developed the statistical properties of a carefully defined Clonal Likelihood Score test from mutational profiling of tumor DNA. Under identified conditions, the test appears to reliably distinguish between synchronous tumors of clonal and of independent origin in several cancer types. This approach may have scientific and clinical utility.

Mutations in the transcriptional repressor REST predispose to Wilms tumor

Wilms tumor is the most common childhood renal cancer. To identify mutations that predispose to Wilms tumor, we are conducting exome sequencing studies. Here we describe 11 different inactivating mutations in the REST gene (encoding RE1-silencing transcription factor) in four familial Wilms tumor pedigrees and nine non-familial cases. Notably, no similar mutations were identified in the ICR1000 control series (13/558 versus 0/993; P < 0.0001) or in the ExAC series (13/558 versus 0/61,312; P < 0.0001). We identified a second mutational event in two tumors, suggesting that REST may act as a tumor-suppressor gene in Wilms tumor pathogenesis. REST is a zinc-finger transcription factor that functions in cellular differentiation and embryonic development. Notably, ten of 11 mutations clustered within the portion of REST encoding the DNA-binding domain, and functional analyses showed that these mutations compromise REST transcriptional repression. These data establish REST as a Wilms tumor predisposition gene accounting for ∼2% of Wilms tumor.

Abstract 4803: BAP1 mutation is a frequent somatic event in peritoneal malignant mesothelioma

Malignant mesothelioma (MM) arises from mesothelial cells that line the pleural, peritoneal and pericardial surfaces. The majority of MMs are pleural and have been associated with asbestos exposure. Previously, pleural MMs have been genetically characterized by the loss of BAP1 (40-60%) as well as loss of NF2 (75%) and CDKN2A (60%). The rare peritoneal form of MM occurs in ∼10% cases. With only ∼300 cases diagnosed in the US per year, its link to asbestos exposure is not clear and its mutational landscape unknown. We analyzed the somatic mutational landscape of 12 peritoneal MM of epitheloid subtype using copy number analysis (N = 9), whole exome sequencing (N = 7) and targeted sequencing (N = 12). Peritoneal MM display few copy number alterations, with most samples having less than 10 Mbp total changes, mostly through deletions and no high copy number amplification. Chromosome band 3p21 encoding BAP1 is the most recurrently deleted region (5/9), while, in contrast to pleural MM, NF2 and CDKN2A are not affected. We further identified 87 non-silent mutations across 7 sequenced tumors, with a median of 8 mutated genes per tumor, resulting in a very low mutation rate (median 1.3 10-6). BAP1 was the only recurrently mutated gene (N = 3/7). In one additional case, loss of the entire chromosome 3 leaves a non-functional copy of BAP1 carrying a rare nonsense germline variant, thus suggesting a potential genetic predisposition in this patient. Finally, with targeted sequencing of BAP1 in 3 additional cases, we conclude that BAP1 is frequently altered through copy number losses (N = 3/12), mutations (N = 3/12) or both (N = 2/12) sometimes at a sub-clonal level. Our findings suggest a major role for BAP1 in peritoneal MM susceptibility and oncogenesis and indicate important molecular differences to pleural MM as well as potential strategies for therapy and prevention.

Citation Format: Olivier Harismendy, Hakan Alakus, Shawn Yost, Brian Woo, Randall French, Grace Y. Lin, Kristen Jepsen, Kelly A. Frazer, Andrew M. Lowy. BAP1 mutation is a frequent somatic event in peritoneal malignant mesothelioma. [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 4803. doi:10.1158/1538-7445.AM2015-4803

Whole-exome sequencing reveals the mutational spectrum of testicular germ cell tumours

Testicular germ cell tumours (TGCTs) are the most common cancer in young men. Here we perform whole-exome sequencing (WES) of 42 TGCTs to comprehensively study the cancer's mutational profile. The mutation rate is uniformly low in all of the tumours (mean 0.5 mutations per Mb) as compared with common cancers, consistent with the embryological origin of TGCT. In addition to expected copy number gain of chromosome 12p and mutation of KIT, we identify recurrent mutations in the tumour suppressor gene CDC27 (11.9%). Copy number analysis reveals recurring amplification of the spermatocyte development gene FSIP2 (15.3%) and a 0.4 Mb region at Xq28 (15.3%). Two treatment-refractory patients are shown to harbour XRCC2 mutations, a gene strongly implicated in defining cisplatin resistance. Our findings provide further insights into genes involved in the development and progression of TGCT.

Abstract 5191: Genome-wide mutational analysis reveals core signaling pathways in mucinous neoplasms of the appendix

Mucinous Neoplasm of the Appendix (MNA) is a rare malignancy often diagnosed after metastasis to the peritoneal surfaces resulting in Mucinous Carcinomatosis Peritonei (MCP). Genetic alterations in MNA are poorly characterized due to its low incidence, the hypo-cellularity of MCPs and a lack of relevant pre-clinical models. As such, application of targeted therapies to this disease is limited to those developed for colorectal cancer (CRC) and not based on molecular rationale. We sequenced the whole exomes of 10 MCPs to identify genome-wide somatic mutations and copy number aberrations and validated significant findings in 19 additional cases using deep sequencing and microdroplet PCR. These studies demonstrate that MNA has a different molecular makeup than CRC. Most tumors have co-existing oncogenic mutations in KRAS (26/29) and GNAS (21/29) and are characterized by cAMP-PKA pathway activation. High-grade tumors are GNAS wild-type (5/6), suggesting they do not progress from low-grade tumors. MNAs do share some genetic alterations with CRC including gain of 1q (5/10), Wnt and TGFβ pathway alteration. In contrast, mutations in TP53 (1/10) and APC (0/10), common in CRC, are rare in MNA. Coincident activation of the Ras-Raf-MEK-ERK and cAMP-PKA signaling pathways appears to be shared with pancreatic intraductal papillary mucinous neoplasm. Thus, MNA genome-wide mutational analysis reveals genetic alterations distinct from CRC, in support its unique pathophysiology and suggests MEK and PKA inhibition as new therapeutic opportunities.

Citation Format: Hakan Alakus, Michele Babicky, Pradipta Ghosh, Shawn Yost, Kristen Jepsen, Yang Dai, Angelo Arias, Michael Samuels, Evangeline Mose, Michael Peterson, Andrew Lowy, Kelly Frazer, Olivier Harismendy. Genome-wide mutational analysis reveals core signaling pathways in mucinous neoplasms of the appendix. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5191. doi:10.1158/1538-7445.AM2014-5191

Genome-wide mutational landscape of mucinous carcinomatosis peritonei of appendiceal origin

BACKGROUND

Mucinous neoplasms of the appendix (MNA) are rare tumors which may progress from benign to malignant disease with an aggressive biological behavior. MNA is often diagnosed after metastasis to the peritoneal surfaces resulting in mucinous carcinomatosis peritonei (MCP). Genetic alterations in MNA are poorly characterized due to its low incidence, the hypo-cellularity of MCPs, and a lack of relevant pre-clinical models. As such, application of targeted therapies to this disease is limited to those developed for colorectal cancer and not based on molecular rationale.

METHODS

We sequenced the whole exomes of 10 MCPs of appendiceal origin to identify genome-wide somatic mutations and copy number aberrations and validated significant findings in 19 additional cases.

RESULTS

Our study demonstrates that MNA has a different molecular makeup than colorectal cancer. Most tumors have co-existing oncogenic mutations in KRAS (26/29) and GNAS (20/29) and are characterized by downstream PKA activation. High-grade tumors are GNAS wild-type (5/6), suggesting they do not progress from low-grade tumors. MNAs do share some genetic alterations with colorectal cancer including gain of 1q (5/10), Wnt, and TGFβ pathway alterations. In contrast, mutations in TP53 (1/10) and APC (0/10), common in colorectal cancer, are rare in MNA. Concurrent activation of the KRAS and GNAS mediated signaling pathways appears to be shared with pancreatic intraductal papillary mucinous neoplasm.

CONCLUSIONS

MNA genome-wide mutational analysis reveals genetic alterations distinct from colorectal cancer, in support of its unique pathophysiology and suggests new targeted therapeutic opportunities.

Abstract 219: Splicing inhibitors reduce human AML CD34+ cell survival and self-renewal during MDS/AML evolution in a leukemia stem cell supportive niche assay

Introduction. Myelodysplastic syndromes (MDS) are relatively common neoplasms of hematopoietic stem cells, which commonly evolve to acute myeloid leukemia (AML). Recent results suggest that MDS evolution is controlled by mutations in splicing related genes and epigenetic modifiers of gene expression. Alternative splicing driven by these mutations has been implicated in the evolution of MDS to AML. However, little is known about the cell type and context specific functional effects of these mutations on leukemia stem cells (LSC) that promote AML therapeutic resistance. Therefore, we investigated 1) the effect of splicing inhibitors on LSC survival and self-renewal during the MSD/AML progression in a bone-marrow stromal co-cultures that recapitulates key aspects of the human LSC niche and 2) the genomic mutations in LSC and non-LSC populations during disease progression. Methods. Whole exome sequencing on CD34+ and CD34- cells before and after MDS/AML progression . Mouse bone marrow cell lines transfected to produce human SCF, IL3 and G-CSF, were used as a stromal monolayer. Human CD34+ cells were selected from MDS and AML primary samples (n=6). As a normal control, cord blood CD34+ cells (CB, n=3) were utilized. Two SF3B1-targeted splicing inhibitors: FD 895 and a FD-analog were added at the initiation of co-culture at concentrations ranging from 0.1 to10 uM. Results. Whole exome DNA sequencing analysis revealed that a loss of chr21 was observed at different frequencies in CD34- and CD34+ cells. We identified a RUNX1 missense mutation with increasing prevalence in CD34+ during progression. Notably, loss of heterozygosity and a missense mutation in the histone methyltransferase EZH2 gene, implicated in MDS progression, was detected only in CD34+ post-progression to AML. After 2 weeks of stromal co-culture, survival of the cells was investigated by colony forming assay in methylcellulose. While the splicing inhibitors demonstrated no cytotoxicity towards normal CB, MDS and AML samples showed a dose-dependent inhibition of colony formation. To analyze the effect of splicing inhibitors on LSC self-renewal, replating assays were performed. While compounds at high doses mediated only a slight decrease in colony formation in CB samples, MDS and AML samples exhibited a dose dependent inhibition of LSC survival (38.2+/-8.1% p&lt;0.001) for FD895 and (13.8+/-3.6% p&lt;0.001) for FD analog. Notably, the more potent FD-analog demonstrated considerably higher ability to eradicate LSC compared to FD895. Conclusions. These data demonstrate that molecular evolution of MDS to AML may be driven by specific mutations in epigenetic modifiers, such as EZH2, and alternative splicing in CD34+ cells which gain the capacity to survive and self-renew in LSC supportive niches. These properties can be inhibited using novel splicing inhibitors with minimal toxicity toward normal progenitors.

Citation Format: Larisa Balaian, Michael Burkart, Shawn Yost, Sophie Rozenhak, Edward D. Ball, Kelly Frazer, Olivier Harismendy, Catriona Jamieson. Splicing inhibitors reduce human AML CD34+ cell survival and self-renewal during MDS/AML evolution in a leukemia stem cell supportive niche assay. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 219. doi:10.1158/1538-7445.AM2013-219

A common origin for cosmic explosions inferred from calorimetry of GRB030329

Past studies have suggested that long-duration gamma-ray bursts have a 'standard' energy of E(gamma) approximately 10(51) erg in the ultra-relativistic ejecta, after correcting for asymmetries in the explosion ('jets'). But a group of sub-energetic bursts, including the peculiar GRB980425 associated with the supernova SN1998bw (E(gamma) approximately 10(48) erg), has recently been identified. Here we report radio observations of GRB030329 that allow us to undertake calorimetry of the explosion. Our data require a two-component explosion: a narrow (5 degrees opening angle) ultra-relativistic component responsible for the gamma-rays and early afterglow, and a wide, mildly relativistic component that produces the radio and optical afterglow more than 1.5 days after the explosion. The total energy release, which is dominated by the wide component, is similar to that of other gamma-ray bursts, but the contribution of the gamma-rays is energetically minor. Given the firm link of GRB030329 with SN2003dh, our result indicates a common origin for cosmic explosions in which, for reasons not yet understood, the energy in the highest-velocity ejecta is extremely variable.

Early optical emission from the gamma-ray burst of 4 October 2002

Observations of the long-lived emission--or 'afterglow'--of long-duration gamma-ray bursts place them at cosmological distances, but the origin of these energetic explosions remains a mystery. Observations of optical emission contemporaneous with the burst of gamma-rays should provide insight into the details of the explosion, as well as into the structure of the surrounding environment. One bright optical flash was detected during a burst, but other efforts have produced negative results. Here we report the discovery of the optical counterpart of GRB021004 only 193 seconds after the event. The initial decline is unexpectedly slow and requires varying energy content in the gamma-ray burst blastwave over the course of the first hour. Further analysis of the X-ray and optical afterglow suggests additional energy variations over the first few days.

Air emission flux from contaminated dredged materials stored in a pilot-scale confined disposal facility

A pilot-scale field simulation was conducted to estimate the air emissions from contaminated dredged material stored in a confined disposal facility (CDF). Contaminated dredged material with a variety of organic chemicals, obtained from Indiana Harbor Canal, was used in the study. It was placed in an outdoor CDF simulator (i.e., a lysimeter of dimensions 4 ft x 4 ft x 2 ft). A portable, dynamic flux chamber was used to periodically measure emissions of various polynuclear aromatic hydrocarbons (PAHs). A weather station was set up to monitor and record the meteorological conditions during the experiment. The fluxes of several PAHs were monitored over time for 6 1/2 months. Initial 6-hr average fluxes varied from 2 to 20 ng/cm2/hr for six different PAHs. The flux values declined rapidly for all compounds soon after placement of the dredged material in the CDE Chemical concentrations derived from flux values were generally of low magnitude compared with ambient standards. Data obtained from the experiment were compared against those predicted using models for air emissions. Model simulations showed that initially the flux was largely from exposed pore water from saturated (wet) sediment, whereas the long-term flux was controlled by diffusion through the pore air of the unsaturated sediment. Model predictions generally overestimated the measured emissions. A rainfall event was simulated, and the dredged material was reworked to simulate that typical of a CDF operation. Increased flux was observed upon reworking the dredged material.

Aneurysms of the pancreaticoduodenal arteries: a change in management

Since the first report of an aneurysm involving the pancreaticoduodenal arteries a century ago, only 83 cases have been reported in our collective review of the English literature. Their presentation varies from indistinct abdominal pain to hemorrhagic shock, often making the diagnosis onerous. The mortality rate in this patient group has been significant, and in cases reported since 1980, the mortality rate remains at 17% (7 deaths/42 reported cases). Surgery has been, and continues to be, the cornerstone of therapy, with an incumbent mortality rate of 19% (5 deaths/26 patients treated surgically since 1980). This case report and 100-year review of the literature describes the causes, natural history, and historic management of pancreaticoduodenal artery aneurysms. Most importantly, it demonstrates the use of angiographic embolization in the definitive management of these aneurysms with no mortality.

Randomized clinical trial of antithymocyte globulin induction in renal transplantation comparing a fixed daily dose with dose adjustment according to T cell monitoring

Antithymocyte globulin (ATG) has been used successfully for induction therapy as well as for treatment of established allograft rejection. However, this therapy has often been associated with problems of overimmunosuppression and increased costs. In a randomized clinical trial, we compared the immunosuppressive benefits, complication rates, and treatment costs when ATG is given as a fixed daily dose or when the dose is adjusted daily according to its biologic effects on T cells. Forty-five recipients of cadaver renal allografts were randomized into two groups. In group 1 (n = 23), ATG (ATGAM) was administered in variable doses to maintain the absolute number of peripheral CD3 T cells at 50-100/microliters. In group 2 (n = 22), ATG was given at a fixed dose of 15 mg/kg/day. All patients received azathioprine and prednisone. ATG was discontinued at 7-14 days when cyclosporine was introduced. In both groups, CD2, CD3, CD4, CD8, and CD19 cells were measured by flow cytometry and the levels of cytokines IL-1 beta, IL-2R, ICAM-1, IL-6, IL-7, and levels of cytokines IL-1 beta, IL-2R, ICAM-1, IL-6, IL-7, and levels of cytokines IL-1 beta, IL-2R, ICAM-1, IL-6, Il-7, and IL-10 were measured by ELISA. In group 2, the levels of all T cell subsets were profoundly suppressed. In group 1, the number of CD3 and other T cells was maintained at about 100 cells/microliters, while the CD19 T cells remained unsuppressed. Cytokine levels were greatly suppressed in group 2 compared with group 1, except for IL-10 levels, which remained elevated in the latter group. Patient survival, graft function, and the incidence of acute and recurrent rejections were similar in the two groups. Bone marrow suppression and infective complications were greater in group 2 than in group 1. The mean daily dose and the total quantity of ATG used in group 1 were significantly smaller than in group 2, resulting in a savings of $2,398.00 per patient per treatment. It is concluded that monitoring of ATG by its biologic effects on T cells is a rational and safe method of regulating the dose of this important agent; in this way, it is possible to reduce the total amount of the drug given to patients with consequent reduction in undesirable complications as well as in the cost of treatment without loss of immunosuppressive benefits.

Flanking and intragenic sequences regulating the expression of the rabbit alpha-globin gene

Despite their descent from a common ancestral gene and the requirement for coordinated, tissue-specific regulation, the alpha- and beta-globin genes in many mammals are regulated in distinctly different ways. Unlike the beta-globin gene, the rabbit alpha-globin gene is transiently expressed at a high level without an added enhancer in transfected erythroid and non-erythroid cells. By examining a series of alpha/beta fusion genes, we show that internal sequences of the rabbit alpha-globin gene (within the first two exons and introns) are required along with the 5' flank for this enhancer-independent expression. Furthermore, deletion of the introns of the alpha-globin gene, or replacement by introns of the beta-globin gene, results in severely decreased expression of the transfecting genes. Hybrid constructs between segments of the alpha-globin gene and a luciferase gene confirm that internal alpha-globin sequences are needed for high level production of RNA in transfected cells. The flanking and internal sequences implicated in regulation of the rabbit alpha-globin gene coincide with a prominent CpG-rich island and may comprise an extended promoter (including both flanking and intragenic sequences) that is active in transfected cells without an enhancer.

Activation of brain acetylcholine receptors by neuromuscular blocking drugs. A possible mechanism of neurotoxicity

BACKGROUND

Neuromuscular blocking drugs cause excitement and seizures when introduced into the central nervous system. We examined the possibility that these drugs produce paradoxical activation of acetylcholine or glutamate receptors, the chief types of brain receptors involved in excitatory neurotransmission.

METHODS

Because activation of central glutamate or acetylcholine receptors causes calcium influx into postsynaptic neurons, we measured intracellular calcium concentration ([Ca2+]i) as an index of receptor activation. Changes in [Ca2+]i were compared in brain slices exposed to neuromuscular blocking drugs or acetylcholine and glutamate receptor agonists. [Ca2+]i was measured with the fluorescent dye fura-2.

RESULTS

Pancuronium and vecuronium caused sustained increases in [Ca2+]i in approximately the same potency ratio as for seizure activity in vivo (concentrations at which the increase in [Ca2+]i was 95% of maximal: 100 and 400 microM, respectively). Atracurium and laudanosine did not increase [Ca2+]i in cortical slices. Increases in [Ca2+]i caused by both pancuronium and vecuronium were prevented by the non-subtype-specific nicotinic acetylcholine receptor antagonist D-tubocurarine and were reduced 44-73% by atropine. Blockade of glutamate receptors or voltage-gated calcium or sodium channels had no effect on calcium influx.

CONCLUSIONS

The results suggest that the acute excitement and seizures caused by introduction of pancuronium and vecuronium into the central nervous system is due to accumulation of cytosolic calcium caused by sustained activation of acetylcholine receptor ion channels.