Phase Ib Trial of the Combination of Imatinib and Binimetinib in Patients with Advanced Gastrointestinal Stromal Tumors

PURPOSE

This phase Ib trial was designed to evaluate the safety and early efficacy signal of the combination of imatinib and binimetinib in patients with imatinib-resistant advanced gastrointestinal stromal tumors (GISTs).

PATIENTS AND METHODS

This trial used a standard 3 + 3 design to determine the recommended phase II dose (RP2D). Additional patients were enrolled on an expansion cohort at the RP2D enriching for succinate dehydrogenase (SDH)-deficient GISTs to explore potential efficacy.

RESULTS

The trial enrolled nine patients in the dose-escalation cohort and 14 in the dose-expansion cohort including six with SDH-deficient GISTs. Imatinib 400 mg daily with binimetinib 45 mg twice daily was established as the RP2D. Dose-limiting toxicity (DLT) was asymptomatic grade 4 creatinine phosphokinase (CPK) elevation. The most common non-DLT grade 3/4 toxicity was asymptomatic CPK elevation (69.6%). Other common ≥grade 2 toxicities included peripheral edema (17.4%), acneiform rash (21.7%), anemia (30.4%), hypophosphatemia (39.1%), and aspartate aminotransferase (AST) increase (17.4%). Two serious adverse events occurred (grade 2 dropped head syndrome and grade 3 central retinal vein occlusion). No unexpected toxicities were observed. Limited clinical activity was observed in KIT-mutant GIST. For SDH-deficient GISTs, one of five had confirmed RECIST1.1 partial response (PR). The median progression-free survival (mPFS) in patients with SDH-deficient GIST was 45.1 months [95% confidence interval (CI), 15.8-not estimable (NE)]; the median overall survival (mOS) was not reached (95% CI, 31.6 months-NE). One patient with a refractory metastatic SDH-deficient GIST had an exceptional pathologic response and durable clinical benefit.

CONCLUSIONS

The combination of imatinib and binimetinib is safe with manageable toxicity and has encouraging activity in SDH-deficient but not imatinib-refractory KIT/PDGFRA-mutant GISTs. The observed clinical benefits provide a motivation for a larger trial of the combination strategy in SDH-deficient GISTs.

Massive digestive bleeding as a result of gastric heterotopy: a case report

INTRODUCTION

Gastric heterotopy is a rare entity in the pediatric population. It occurs in the gastrointestinal tract, leading to digestive bleeding.

CLINICAL CASE

This is the case of a 10-year-old boy with gastric tissue in the proximal jejunum, which caused two massive digestive bleeding episodes. Diagnostic techniques included endoscopic capsule, enteroscopy, and biopsy. The patient was scheduled for laparotomy and resection. After one year of follow-up, he remained asymptomatic.

DISCUSSION

Gastric heterotopy approach represents a diagnostic challenge. Owing to how rare it is, there is no global consensus in terms of treatment. However, surgery is the definitive therapy. In this case, decision was made not to perform intestinal resection and anastomosis, but resection of the compromised intestinal wall. No malignity was reported in the literature reviewed.

The contribution of germline DNA damage response mutations on prostate cancer risk and prognosis: A UK Biobank whole-exome analysis

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Background: Germline mutations in DNA Damage Response (DDR) genes such as BRCA2 and ATM have been associated with prostate cancer risk and aggressiveness. These associations are largely based on studies that ascertain for cancer diagnosis and family history and provide risk estimates with limited population-level accuracy. Here we evaluate the clinical significance of germline pathogenic variants in 20 DDR genes and a high-risk susceptibility coding variant in HOXB13 using whole exome sequences from (1) the UK Biobank (UKBB), a population-based cohort (300,000 participants) and (2) patients recruited in AZ clinical trials. Methods: Whole exomes from 6,987 prostate cancer patients (5,921 UKBB and 1,066 AZ) and 88,499 cancer-free males were analysed. Known and novel pathogenic variants were identified and associations with disease risk, age of onset, family history, response to hormonal therapy and overall survival were estimated (multiplicity corrected P value < 0.005). Results: HOXB13 G48E (1.36%), ATM (1.03%) and BRCA2 (0.99%) were the largest contributors to prostate cancer risk, each conferring an increase of ~4-fold, followed by CHEK2 with a moderate contribution (0.46%). No significant contributions to prostate cancer risk were observed for any of the other genes analysed. Family history of prostate cancer was not significantly enriched in any of the gene subpopulations of prostate cancer carriers and compared with non-carriers, there was no significant difference in the median age of disease onset. Analysis of clinical outcomes showed that BRCA2 carriers had a 4-fold increased risk of death (Cox PH HR p = 4.11E-12) and poorer overall survival (Log-Rank p = 4.60E-14), with 88% dying from prostate cancer compared to 49% of non- BRCA2 carriers (UKBB analysis). BRCA2 pathogenic mutations were also associated with early failure to hormonal therapy (Cox PH HR 2.38; p = 9.48E-04; AZ cohort analysis). HOXB13, ATM and CHEK2 mutations were not significantly associated with clinical outcomes. Conclusions: This is the largest study to date providing population-based estimates of prostate cancer risk and prognosis, highlighting BRCA2 carriers as a population in clinical need of early identification and targeted intervention. Updated analyses with data from the full 450,000 UKBB participants (9,000 prostate cancers) will be presented.

Abstract 3522: Population estimates of prostate cancer risk and prognosis for carriers of germline pathogenic variants in disease implicated genes, using 200,000 UK Biobank whole exomes

Germline deleterious variants in DNA Damage Response (DDR) genes such as BRCA2 and ATM have been associated with high risk of disease, poor prognosis and the development of metastatic prostate cancer. These associations have been reported in studies of individuals selected for family history or cancer diagnosis and, therefore, with limited potential to estimate accurate population disease risk. Here we evaluate the clinical significance of germline deleterious variants in 20 DDR genes and four known prostate cancer susceptibility coding variants in POUF51B, HOXB13 and KLK3 using germline whole exome sequencing (WES) data from (1) the UK Biobank (UKBB), a population-based cohort (200,000 with WES) and (2) prostate cancer patients recruited in AZ clinical trials.

WES data from 4,975 prostate cancer patients (3,954 UKBB and 1,021 AZ) and 44,818 controls (cancer-free UKBB male participants) was analysed. We identified 218 carriers with deleterious variants in DDR genes. Of these, 190 carried known pathogenic variants (ClinVar, BIC and ENIGMA consortium) and 28 had novel, pathogenic protein truncating variants. Population disease risk, risk of metastatic disease and overall survival (UKBB patients only) were estimated (multiplicity corrected P value &lt;0.005).

Analysis of deleterious variants revealed significant associations with prostate cancer risk for ATM (OR 4.14, 95% CI 2.97-5.72, p=1.77E-15) and BRCA2 (OR 3.47, 95% CI 2.49-4.77, p=1.70E-12), each contributing to a similar number of cases (1.15% vs 1.11%, respectively). Damaging variants within the remaining DDR genes were less frequent with none reaching significance. A trend for increased disease risk was observed in CHEK2 carriers (OR 2.03, 95% CI 1.18-3.33, p=9.30E-03). Coding variant analysis confirmed associations between variants in POU5F1B, HOXB13 and KLK3 and prostate cancer risk. HOXB13 G84E carriers (1.29%) were at comparable risk to BRCA2 and ATM carriers (OR 3.88, 95% CI 2.85-5.24, p=4.29E-16).

Assesment of patient outcomes showed that BRCA2 carriers were more likely to develop metastatic disease (OR 3.32, 95% CI 1.74-6.45, p=9.94E-05) and had poorer overall survival (Log Rank p=1.33E-08; 85% of patients dying from prostate cancer vs 53% of non BRCA2 carriers). No other gene reached significance. A trend towards poorer survival was observed for PALB2 carriers (Log Rank p=7.91E-03) suggesting that PALB2 could act as a modifier gene once the disease has developed.

This is the largest study to date providing population based estimates of prostate cancer risk, metastasis and survival highlighting mutations in BRCA2, ATM and HOXB13 G48E as the largest contributors to disease risk and confirming the poor prognosis of BRCA2 carriers. Analyses will be updated with data from the full 500,000 UKBB participants (expected January 2020; total of 11,000 prostate cancer cases).

Citation Format: Niedzica Camacho, Liqin Dong, Athena Matakidou. Population estimates of prostate cancer risk and prognosis for carriers of germline pathogenic variants in disease implicated genes, using 200,000 UK Biobank whole exomes [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3522.

Genetic alterations in the 3q26.31-32 locus confer an aggressive prostate cancer phenotype

Large-scale genetic aberrations that underpin prostate cancer development and progression, such as copy-number alterations (CNAs), have been described but the consequences of specific changes in many identified loci is limited. Germline SNPs in the 3q26.31 locus are associated with aggressive prostate cancer, and is the location of NAALADL2, a gene overexpressed in aggressive disease. The closest gene to NAALADL2 is TBL1XR1, which is implicated in tumour development and progression. Using publicly-available cancer genomic data we report that NAALADL2 and TBL1XR1 gains/amplifications are more prevalent in aggressive sub-types of prostate cancer when compared to primary cohorts. In primary disease, gains/amplifications occurred in 15.99% (95% CI: 13.02–18.95) and 14.96% (95% CI: 12.08–17.84%) for NAALADL2 and TBL1XR1 respectively, increasing in frequency in higher Gleason grade and stage tumours. Gains/amplifications result in transcriptional changes and the development of a pro-proliferative and aggressive phenotype. These results support a pivotal role for copy-number gains in this genetic region.

Benjamin Simpson et al. use publicly available cancer genomic data to investigate copy number changes at the 3q26.31–32 locus, which has been associated with aggressive prostate cancer based on single-nucleotide polymorphisms. They find that gains of NAALADL2 and TBL1XR1 in this locus are associated with more aggressive subtypes of prostate cancer and the transcription of pro-proliferative signalling processes.

Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1-3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10-18.

Development of Genome-Derived Tumor Type Prediction to Inform Clinical Cancer Care

IMPORTANCE

Diagnosing the site of origin for cancer is a pillar of disease classification that has directed clinical care for more than a century. Even in an era of precision oncologic practice, in which treatment is increasingly informed by the presence or absence of mutant genes responsible for cancer growth and progression, tumor origin remains a critical factor in tumor biologic characteristics and therapeutic sensitivity.

OBJECTIVE

To evaluate whether data derived from routine clinical DNA sequencing of tumors could complement conventional approaches to enable improved diagnostic accuracy.

DESIGN, SETTING, AND PARTICIPANTS

A machine learning approach was developed to predict tumor type from targeted panel DNA sequence data obtained at the point of care, incorporating both discrete molecular alterations and inferred features such as mutational signatures. This algorithm was trained on 7791 tumors representing 22 cancer types selected from a prospectively sequenced cohort of patients with advanced cancer.

RESULTS

The correct tumor type was predicted for 5748 of the 7791 patients (73.8%) in the training set as well as 8623 of 11 644 patients (74.1%) in an independent cohort. Predictions were assigned probabilities that reflected empirical accuracy, with 3388 cases (43.5%) representing high-confidence predictions (>95% probability). Informative molecular features and feature categories varied widely by tumor type. Genomic analysis of plasma cell-free DNA yielded accurate predictions in 45 of 60 cases (75.0%), suggesting that this approach may be applied in diverse clinical settings including as an adjunct to cancer screening. Likely tissues of origin were predicted from targeted tumor sequencing in 95 of 141 patients (67.4%) with cancers of unknown primary site. Applying this method prospectively to patients under active care enabled genome-directed reassessment of diagnosis in 2 patients initially presumed to have metastatic breast cancer, leading to the selection of more appropriate treatments, which elicited clinical responses.

CONCLUSIONS AND RELEVANCE

These results suggest that the application of artificial intelligence to predict tissue of origin in oncologic practice can act as a useful complement to conventional histologic review to provide integrated pathologic diagnoses, often with important therapeutic implications.

Genomic and Transcriptomic Characterization of Papillary Microcarcinomas With Lateral Neck Lymph Node Metastases

CONTEXT

Most papillary microcarcinomas (PMCs) are indolent and subclinical. However, as many as 10% can present with clinically significant nodal metastases.

OBJECTIVE AND DESIGN

Characterization of the genomic and transcriptomic landscape of PMCs presenting with or without clinically important lymph node metastases.

SUBJECTS AND SAMPLES

Formalin-fixed paraffin-embedded PMC samples from 40 patients with lateral neck nodal metastases (pN1b) and 71 patients with PMC with documented absence of nodal disease (pN0).

OUTCOME MEASURES

To interrogate DNA alterations in 410 genes commonly mutated in cancer and test for differential gene expression using a custom NanoString panel of 248 genes selected primarily based on their association with tumor size and nodal disease in the papillary thyroid cancer TCGA project.

RESULTS

The genomic landscapes of PMC with or without pN1b were similar. Mutations in TERT promoter (3%) and TP53 (1%) were exclusive to N1b cases. Transcriptomic analysis revealed differential expression of 43 genes in PMCs with pN1b compared with pN0. A random forest machine learning-based molecular classifier developed to predict regional lymph node metastasis demonstrated a negative predictive value of 0.98 and a positive predictive value of 0.72 at a prevalence of 10% pN1b disease.

CONCLUSIONS

The genomic landscape of tumors with pN1b and pN0 disease was similar, whereas 43 genes selected primarily by mining the TCGA RNAseq data were differentially expressed. This bioinformatics-driven approach to the development of a custom transcriptomic assay provides a basis for a molecular classifier for pN1b risk stratification in PMC.

Abstract 1672: Clinical validation of a genomics-based classifier to predict tissue of origin from targeted tumor sequencing

Introduction

Various classes of genomic alterations can now be robustly detected from targeted Next Generation Sequencing (NGS)-based tumor profiling assays. Despite recent advances in genome-directed cancer therapies and lineage-agnostic basket clinical trials, tissue of origin remains a critical determinant of tumor biology and therapeutic sensitivity. Therefore, efficiently harnessing the mutational information to predict tissue of origin from NGS data can further aid diagnosis and treatment.

Methods

We have developed a novel random forest machine learning classifier that infers tissue of origin from the mutational features of each tumor NGS profile. We trained and validated the model using prospective sequencing data from &gt;30,000 patients profiled by MSK-IMPACT, a custom FDA-authorized clinical sequencing assay. An initial version of this classifier trained on a smaller cohort, presented previously, has been further optimized to incorporate additional tumor types, genomic features, mutational signatures, and accessibility features for clinicians. Altogether, the model evaluates a comprehensive range of mutational features to generate predictions. In addition, we developed a framework for the prospective clinical implementation of our method that allows for extension to the expanding MSK-IMPACT cohort and utilization at the point of care.

Results

Overall, we predicted the correct cancer type in 74% of cases, with nearly half of cases predicted with high confidence (&gt;95%). In order to make this tool accessible to pathologists for real-time diagnostic and treatment decisions, we also have implemented APIs that transmit our classifier predictions to the cBioPortal for Cancer Genomics and the MPath console from MSK Molecular Diagnostics Service. With the additional samples and genomic features, our model predictions have been improved and are considered during clinical review and sign-out. This practice has brought about critical diagnostic changes and orthogonal validation in several cases. In one case, a patient referred to MSK with a misdiagnosis of metastatic breast cancer to the bladder underwent MSK-IMPACT sequencing for her primary breast tumor and bladder lesion. The model predictions, confirmed by orthogonal testing, classified two lesions as independent primaries of breast and bladder origins, leading to significant changes in treatment regimens.

Conclusion

Our work delineates the framework of utilizing and optimizing machine learning models on NGS-based sequencing data to aid diagnosis and treatment. The same framework can be applied to cell-free DNA sequencing, which will capture tumor spatial heterogeneity and improve classifier performance. These results indicate that leveraging machine learning to

predict tissue of origin complements conventional histologic review to provide integrated diagnoses, often with critical therapeutic implications.

Citation Format: Youyun Zheng, Alexander V. Penson, Niedzica Camacho, Evan Biederstedt, Ahmet Zehir, Cyriac Kandoth, Aijazuddin Syed, Anna M. Varghese, Hikmat A. Al-Ahmadie, Nikolaus Schultz, Marc Ladanyi, David B. Solit, David S. Klimstra, David Hyman, Barry Taylor, Michael F. Berger. Clinical validation of a genomics-based classifier to predict tissue of origin from targeted tumor sequencing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1672.

Abstract 3024: Genomic characterization of organ-specific metastasis from prospective clinical sequencing of 20,000 cancer patients

We investigated genomic differences in sequenced biopsies of patients with metastatic cancer to identify associations between somatic alterations and anatomic site of metastasis.

We analyzed data from 20,000 patients treated at Memorial Sloan Kettering Cancer Center, covering &gt;50 cancer types and &gt;20 metastatic sites. Tumors were sequenced using MSK-IMPACT, a targeted sequencing assay that identifies somatic mutations, copy number changes and structural rearrangements in 468 cancer genes using tumor and matched normal DNA. We identified tumor types such as prostate cancer, lung adenocarcinoma, uterine endometrioid carcinoma, head and neck cancer and gastrointestinal stromal tumors, for which the primary biopsies differed significantly from the metastatic biopsies at the genomic level, suggesting a need for sample stratification in clinical studies. We also identified site-specific enrichment of individual somatic alterations for tumors from the same cancer type, including therapeutically relevant targets. For example, when evaluating patients with esophagogastric cancer, we found an enrichment of HER2 amplified tumors, which are candidates for trastuzumab therapy, in sequenced lung metastases as opposed to biopsies sequenced at other metastatic sites (8/16, 50% vs. 20/145, 14%; p&lt;0.001). Looking at sequenced metastases of lung adenocarcinoma (n=468), we found that brain metastases (n=34) exhibit increased aneuploidy (median fraction of genome altered 0.55 vs. 0.44; p&lt;0.001, purity-controlled results) and adrenal gland metastases (n=21) exhibit increased mutational burden (13.3 mut/Mb vs. 6.1 mut/Mb; p&lt;0.001) when compared to metastases sequenced at other anatomic sites. Other examples of novel findings include enrichment of amplifications in the MITF-ETV1 pathway in melanoma patients with brain metastatic disease (13/63, 21% vs. 10/234, 4%; p&lt;0.001) and enrichment of 20q chromosomal amplifications in patients with microsatellite stable colorectal tumors that exhibit oligo-metastatic (as opposed to poly-metastatic) patterns at first time of metastasis diagnosis (158/223, 71% vs. 28/58, 48%; p=0.002).

We provide a detailed analysis of associations between genomic features and metastatic patterns within a clinical sequencing setting. Our work has the potential to directly influence the management of patients with metastatic cancer by enabling clinicians to (a) estimate the risk of future metastasis based on the genomic profile of early stage tumors, (b) choose the appropriate site for biopsy in cases where mutation identification will influence the selection of targeted therapy, (c) optimize the use and frequency of imaging modalities for metastasis surveillance and (d) investigate and functionally characterize novel genomic alterations that have a role in metastasis and can lead to improved therapies.

Citation Format: Francisco Sanchez-Vega, Walid K. Chatila, Karuna Ganesh, Alexander Penson, Niedzica Camacho, Philip Jonsson, Ed Reznik, Jianjiong Gao, Rona Yaeger, Michael F. Berger, Barry S. Taylor, Nikolaus Schultz. Genomic characterization of organ-specific metastasis from prospective clinical sequencing of 20,000 cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3024.

Clinical and molecular characterization of patients with cancer of unknown primary in the modern era

Background

On the basis of historical data, patients with cancer of unknown primary (CUP) are generally assumed to have a dismal prognosis with overall survival of less than 1 year. Treatment is typically cytotoxic chemotherapy guided by histologic features and the pattern of metastatic spread. The purpose of this study was to provide a clinical and pathologic description of patients with CUP in the modern era, to define the frequency of clinically actionable molecular alterations in this population, to determine how molecular testing can alter therapeutic decisions, and to investigate novel uses of next-generation sequencing in the evaluation and treatment of patients with CUP.

Patients and methods

Under Institutional Review Board approval, we identified all CUP patients evaluated at our institution over a recent 2-year period. We documented demographic information, clinical outcomes, pathologic evaluations, next-generation sequencing of available tumor tissue, use of targeted therapies, and clinical trial enrollment.

Results

We identified 333 patients with a diagnosis of CUP evaluated at our institution from 1 January 2014 through 30 June 2016. Of these patients, 150 had targeted next-generation sequencing carried out on available tissue. Median overall survival in this cohort was 13 months. Forty-five of 150 (30%) patients had potentially targetable genomic alterations identified by tumor molecular profiling, and 15 of 150 (10%) received targeted therapies. Dominant mutation signatures were identified in 21 of 150 (14%), largely implicating exogenous mutagen exposures such as ultraviolet radiation and tobacco.

Conclusions

Patients with CUP represent a heterogeneous population, harboring a variety of potentially targetable alterations. Next-generation sequencing may provide an opportunity for CUP patients to benefit from novel personalized therapies.

Sequencing of prostate cancers identifies new cancer genes, routes of progression and drug targets

Prostate cancer represents a substantial clinical challenge because it is difficult to predict outcome and advanced disease is often fatal. We sequenced the whole genomes of 112 primary and metastatic prostate cancer samples. From joint analysis of these cancers with those from previous studies (930 cancers in total), we found evidence for 22 previously unidentified putative driver genes harboring coding mutations, as well as evidence for NEAT1 and FOXA1 acting as drivers through noncoding mutations. Through the temporal dissection of aberrations, we identified driver mutations specifically associated with steps in the progression of prostate cancer, establishing, for example, loss of CHD1 and BRCA2 as early events in cancer development of ETS fusion-negative cancers. Computational chemogenomic (canSAR) analysis of prostate cancer mutations identified 11 targets of approved drugs, 7 targets of investigational drugs, and 62 targets of compounds that may be active and should be considered candidates for future clinical trials.

Appraising the relevance of DNA copy number loss and gain in prostate cancer using whole genome DNA sequence data

A variety of models have been proposed to explain regions of recurrent somatic copy number alteration (SCNA) in human cancer. Our study employs Whole Genome DNA Sequence (WGS) data from tumor samples (n = 103) to comprehensively assess the role of the Knudson two hit genetic model in SCNA generation in prostate cancer. 64 recurrent regions of loss and gain were detected, of which 28 were novel, including regions of loss with more than 15% frequency at Chr4p15.2-p15.1 (15.53%), Chr6q27 (16.50%) and Chr18q12.3 (17.48%). Comprehensive mutation screens of genes, lincRNA encoding sequences, control regions and conserved domains within SCNAs demonstrated that a two-hit genetic model was supported in only a minor proportion of recurrent SCNA losses examined (15/40). We found that recurrent breakpoints and regions of inversion often occur within Knudson model SCNAs, leading to the identification of ZNF292 as a target gene for the deletion at 6q14.3-q15 and NKX3.1 as a two-hit target at 8p21.3-p21.2. The importance of alterations of lincRNA sequences was illustrated by the identification of a novel mutational hotspot at the KCCAT42, FENDRR, CAT1886 and STCAT2 loci at the 16q23.1-q24.3 loss. Our data confirm that the burden of SCNAs is predictive of biochemical recurrence, define nine individual regions that are associated with relapse, and highlight the possible importance of ion channel and G-protein coupled-receptor (GPCR) pathways in cancer development. We concluded that a two-hit genetic model accounts for about one third of SCNA indicating that mechanisms, such haploinsufficiency and epigenetic inactivation, account for the remaining SCNA losses.

Abstract 971: Genome directed diagnosis informs clinical cancer care

Cancer treatment is primarily guided by the organ of origin, which despite extensive histopathological and clinical evaluation, remains ambiguous in many cases and may be inaccurate in cases of occult primary. We determine the extent to which routine prospective tumour sequencing, combined with conventional histopathology, can be used to infer the tumor type and thereby direct clinical decisions.

Characteristic patterns of somatic mutations, broad and focal copy number alterations, structural rearrangements, mutational signatures, and other facets acquired from prospective tumor sequencing can inform the tissue of origin classification of patient disease. Such prospective sequencing of active cancer patients presents an opportunity to guide diagnosis and therapy beyond the identification of individual biomarkers of treatment response. Probabilistic classification allows for systematic combination of genome-directed diagnosis with conventional histopathology and clinical history in the course of disease management.

Using more than 10,000 tumors collected from advanced cancer patients at our institution and sequenced using a comprehensive cancer panel (MSK-IMPACT) encompassing 341 genes, we have developed a probabilistic classifier that infers the tumor type from nine broad categories of genomic aberrations. Scores from a RandomForest classifier are calibrated to correspond to the probability for each of the 22 interrogated tumor types. In 18% of all cases, a prediction is made with very high confidence (greater than 99%), of which just over 99% agree with the existing diagnosis. The classifier has been used to guide clinical decision making, including re-diagnoses that distinguish between a recurrence and a new primary, spare or encourage surgery, facilitate access to FDA-approved molecularly targeted drugs and prompt germline genetic testing.

We demonstrate that genome-directed diagnosis, based on alterations routinely identified from prospective sequencing, can inform clinical cancer care with the potential to improve patient outcomes.

Citation Format: Alexander Penson, Niedzica Camacho, Anna M. Varghese, Adam Abeshouse, Pedram Razavi, Aijazuddin Syed, Ahmet Zehir, Nikolaus Schultz, David B. Solit, David Hyman, Barry S. Taylor, Michael F. Berger. Genome directed diagnosis informs clinical cancer care [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 971. doi:10.1158/1538-7445.AM2017-971

Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients

Tumor molecular profiling is a fundamental component of precision oncology, enabling the identification of genomic alterations in genes and pathways that can be targeted therapeutically. The existence of recurrent targetable alterations across distinct histologically defined tumor types, coupled with an expanding portfolio of molecularly targeted therapies, demands flexible and comprehensive approaches to profile clinically relevant genes across the full spectrum of cancers. We established a large-scale, prospective clinical sequencing initiative using a comprehensive assay, MSK-IMPACT, through which we have compiled tumor and matched normal sequence data from a unique cohort of more than 10,000 patients with advanced cancer and available pathological and clinical annotations. Using these data, we identified clinically relevant somatic mutations, novel noncoding alterations, and mutational signatures that were shared by common and rare tumor types. Patients were enrolled on genomically matched clinical trials at a rate of 11%. To enable discovery of novel biomarkers and deeper investigation into rare alterations and tumor types, all results are publicly accessible.

KRAS and Combined KRAS/TP53 Mutations in Locally Advanced Rectal Cancer are Independently Associated with Decreased Response to Neoadjuvant Therapy

BACKGROUND

The response of rectal cancers to neoadjuvant chemoradiation (CRT) is variable, but tools to predict response remain lacking. We evaluated whether KRAS and TP53 mutations are associated with pathologic complete response (pCR) and lymph node metastasis after adjusting for neoadjuvant regimen.

METHODS

Retrospective analysis of 229 pretreatment biopsies from patients with stage II/III rectal cancer was performed. All patients received CRT. Patients received 0-8 cycles of FOLFOX either before or after CRT, but prior to surgical excision. A subset was analyzed to assess concordance between mutation calls by Sanger Sequencing and a next-generation assay.

RESULTS

A total of 96 tumors (42 %) had KRAS mutation, 150 had TP53 mutation (66 %), and 59 (26 %) had both. Following neoadjuvant therapy, 59 patients (26 %) achieved pCR. Of 133 KRAS wild-type tumors, 45 (34 %) had pCR, compared with 14 of 96 (15 %) KRAS mutant tumors (p = .001). KRAS mutation remained independently associated with a lower pCR rate on multivariable analysis after adjusting for clinical stage, CRT-to-surgery interval and cycles of FOLFOX (OR 0.34; 95 % CI 0.17-0.66, p < .01). Of 29 patients with KRAS G12V or G13D, only 2 (7 %) achieved pCR. Tumors with both KRAS and TP53 mutation were associated with lymph node metastasis. The concordance between platforms was high for KRAS (40 of 43, 93 %).

CONCLUSIONS

KRAS mutation is independently associated with a lower pCR rate in locally advanced rectal cancer after adjusting for variations in neoadjuvant regimen. Genomic data can potentially be used to select patients for "watch and wait" strategies.

Analysis of the genetic phylogeny of multifocal prostate cancer identifies multiple independent clonal expansions in neoplastic and morphologically normal prostate tissue

Genome-wide DNA sequencing was used to decrypt the phylogeny of multiple samples from distinct areas of cancer and morphologically normal tissue taken from the prostates of three men. Mutations were present at high levels in morphologically normal tissue distant from the cancer, reflecting clonal expansions, and the underlying mutational processes at work in morphologically normal tissue were also at work in cancer. Our observations demonstrate the existence of ongoing abnormal mutational processes, consistent with field effects, underlying carcinogenesis. This mechanism gives rise to extensive branching evolution and cancer clone mixing, as exemplified by the coexistence of multiple cancer lineages harboring distinct ERG fusions within a single cancer nodule. Subsets of mutations were shared either by morphologically normal and malignant tissues or between different ERG lineages, indicating earlier or separate clonal cell expansions. Our observations inform on the origin of multifocal disease and have implications for prostate cancer therapy in individual cases.

Insights into the preclinical treatment of blood-stage malaria by the antibiotic borrelidin

BACKGROUND AND PURPOSE

Blood-stage Plasmodium parasites cause morbidity and mortality from malaria. Parasite resistance to drugs makes development of new chemotherapies an urgency. Aminoacyl-tRNA synthetases have been validated as antimalarial drug targets. We explored long-term effects of borrelidin and mupirocin in lethal P. yoelii murine malaria.

EXPERIMENTAL APPROACH

Long-term (up to 340 days) immunological responses to borrelidin or mupirocin were measured after an initial 4 day suppressive test. Prophylaxis and cure were evaluated and the inhibitory effect on the parasites analysed.

KEY RESULTS

Borrelidin protected against lethal malaria at 0.25 mg·kg⁻¹·day⁻¹. Antimalarial activity of borrelidin correlated with accumulation of trophozoites in peripheral blood. All infected mice treated with borrelidin survived and subsequently developed immunity protecting them from re-infection on further challenges, 75 and 340 days after the initial infection. This long-term immunity in borrelidin-treated mice resulted in negligible parasitaemia after re-infections and marked increases in total serum levels of antiparasite IgGs with augmented avidity. Long-term memory IgGs mainly reacted against high and low molecular weight parasite antigens. Immunofluorescence microscopy showed that circulating IgGs bound predominantly to late intracellular stage parasites, mainly schizonts.

CONCLUSIONS AND IMPLICATIONS

Low borrelidin doses protected mice from lethal malaria infections and induced protective immune responses after treatment. Development of combination therapies with borrelidin and selective modifications of the borrelidin molecule to specifically inhibit plasmodial threonyl tRNA synthetase should improve therapeutic strategies for malaria.

Prognostic value of PTEN loss in men with conservatively managed localised prostate cancer

Background:

The natural history of prostate cancer is highly variable and difficult to predict. We report on the prognostic value of phosphatase and tensin homologue (PTEN) loss in a cohort of 675 men with conservatively managed prostate cancer diagnosed by transurethral resection of the prostate.

Methods:

The PTEN status was assayed by immunohistochemistry (PTEN IHC) and fluorescent in situ hybridisation (PTEN FISH). The primary end point was death from prostate cancer.

Results:

The PTEN IHC loss was observed in 18% cases. This was significantly associated with prostate cancer death in univariate analysis (hazard ratio (HR)=3.51; 95% CI 2.60–4.73; P=3.1 × 10⁻¹⁴). It was highly predictive of prostate cancer death in the 50% of patients with a low risk score based on Gleason score, PSA, Ki-67 and extent of disease (HR=7.4; 95% CI 2.2–24.6; P=0.012) ), but had no prognostic value in the higher risk patients. The PTEN FISH loss was only weakly associated with PTEN IHC loss (κ=0.5). Both PTEN FISH loss and amplification were univariately predictive of death from prostate cancer, but this was not maintained in the multivariate analyses.

Conclusion:

In low-risk patients, PTEN IHC loss adds prognostic value to Gleason score, PSA, Ki-67 and extent of disease.

Influence of content and particle size of waste pet bottles on concrete behavior at different w/c ratios

The goal of this work was to study the mechanical behavior of concrete with recycled Polyethylene Therephtalate (PET), varying the water/cement ratio (0.50 and 0.60), PET content (10 and 20 vol%) and the particle size. Also, the influence of the thermal degradation of PET in the concrete was studied, when the blends were exposed to different temperatures (200, 400, 600 degrees C). Results indicate that PET-filled concrete, when volume proportion and particle size of PET increased, showed a decrease in compressive strength, splitting tensile strength, modulus of elasticity and ultrasonic pulse velocity; however, the water absorption increased. On the other hand, the flexural strength of concrete-PET when exposed to a heat source was strongly dependent on the temperature, water/cement ratio, as well as on the PET content and particle size. Moreover, the activation energy was affected by the temperature, PET particles location on the slabs and water/cement ratio.

Adiponectin multimers in maternal plasma

OBJECTIVE

Adiponectin is an anti-diabetic, anti-atherogenic, anti-inflammatory, and angiogenic adipokine that circulates in oligomeric complexes including: low molecular weight (LMW) trimers, medium molecular weight (MMW) hexamers, and high molecular weight (HMW) isoforms. The aim of this study was to determine whether there are changes in adiponectin multimers in pregnancy and as a function of maternal weight.

STUDY DESIGN

In this cross-sectional study, plasma concentrations of total, HMW, MMW, and LMW adiponectin were determined in women included in three groups: (1) normal pregnant women of normal body mass index (BMI) (n = 466), (2) overweight pregnant women (BMI >or=25; n = 257), and (3) non-pregnant women of normal weight (n = 40). Blood samples were collected once from each woman between 11 and 42 weeks of gestation. Plasma adiponectin multimer concentrations were determined by enzyme-linked immunosorbent assay (ELISA). Non-parametric statistics were used for analysis.

RESULTS

(1) The median HMW adiponectin concentration and the median HMW/total adiponectin ratio were significantly higher, and the median LMW adiponectin concentration was significantly lower in pregnant women than in non-pregnant women. (2) Among pregnant women, the median plasma concentration of total, HMW, and MMW adiponectin was significantly higher in normal weight women than in overweight patients. (3) Maternal HMW was the most prevalent adiponectin multimer regardless of gestational age or BMI status. (4) There were no significant differences in the median concentration of total, MMW, and LMW adiponectin and their relative distribution with advancing gestation.

CONCLUSION

Human pregnancy is characterized by quantitative and qualitative changes in adiponectin multimers, especially the most active isoform, HMW adiponectin.

Cell differentiation and infectivity ofLeishmania mexicanaare inhibited in a strain resistant to an ABC-transporter blocker

We analysed whether markers of cell differentiation and infectivity differed when compared to the parental sensitive strain [NR(Gs)] in anin vitroselectedLeishmaniastrain [NR(Gr)] resistant to Glibenclamide®, an ATP-binding-cassette (ABC)-transporter blocker. The data show that the cell body area was larger in NR(Gr) compared to NR(Gs) and that functional characters associated with an infective metacyclic phenotype, such as resistance to the lytic effect of the alternative complement pathway and expression of the Meta-1 protein, were reduced. The infectivity of NR(Gr) to J774.1 macrophages was also significantly reduced. These results suggest that resistance inLeishmaniaagainst Glibenclamide®, a general blocker of P-glycoproteins, could produce functional modifications that may be relevant forLeishmaniadifferentiation, infectivity and survival.

Maternal and fetal inflammatory responses in unexplained fetal death

OBJECTIVE

The role of intra-amniotic infection in the etiology of fetal death has been proposed. This study was conducted to determine the prevalence of microbial invasion of the amniotic cavity (MIAC) and the frequency of maternal and/or fetal inflammation in patients presenting with a fetal death.

METHODS

A prospective study was conducted in patients with a fetal death. Amniocenteses were performed for clinical indications (karyotype), as well as to assess the microbiological and cytological state of the amniotic cavity. Fluid was cultured for aerobic and anaerobic bacteria and genital mycoplasmas. An amniotic fluid white blood cell count and glucose determinations were also performed. Histological examination of the placenta was conducted to identify a maternal inflammatory response (acute chorioamnionitis) or a fetal inflammatory response (funisitis).

RESULTS

This study included 44 patients with intrauterine fetal death. The median gestational age at diagnosis was 30.1 weeks (range 16.3-40.4 weeks). One patient had documented MIAC (1/44). Acute histological chorioamnionitis was found in 20.9% (9/43), but a fetal inflammatory response was observed in only 2.3% (1/43) of cases. One patient had a positive amniotic fluid culture for Streptococcus agalactiae (group B streptococcus).

CONCLUSION

Histological chorioamnionitis was present in 20.9% of cases, but MIAC could be demonstrated with conventional microbiological techniques in only one case. A fetal inflammatory response was nine times less frequent than a maternal inflammatory response (maternal 20.9% vs. fetal 2.3%, p = 0.008) in cases of fetal death.

Differences in the fetal interleukin-6 response to microbial invasion of the amniotic cavity between term and preterm gestation

BACKGROUND/OBJECTIVE

Fetal inflammatory response has been implicated as a mechanism of multi-system organ injury in preterm and term neonates. Microbial invasion of the amniotic cavity (MIAC) is frequently associated with a fetal inflammatory response. However, there are no studies comparing the fetal response to MIAC in term and preterm gestations. The purpose of this study was to compare the umbilical cord plasma interleukin-6 (IL-6) concentrations in term and preterm neonates in the presence or absence of MIAC.

STUDY DESIGN

Umbilical cord blood was obtained at birth from 252 neonates whose mothers had an amniocentesis within 48 h of delivery (preterm delivery, n = 62; term delivery, n = 190). MIAC was defined as a positive amniotic fluid culture for bacteria or genital mycoplasmas. IL-6 was measured by a sensitive and specific immunoassay.

RESULTS

The median IL-6 concentration in umbilical cord plasma was significantly higher in preterm neonates than in term neonates (median 13.4 pg/ml, range 0.1-676 pg/ml vs. median 3.2 pg/ml, range 0.1-408 pg/ml; p < 0.0001). In the context of MIAC, the median umbilical cord plasma IL-6 concentration was significantly higher in preterm than in term neonates (median 31.6 pg/ml, range 1.4-676 pg/ml vs. median 11.7 pg/ml, range 1.3-82 pg/ml, respectively; p < 0.05). Neonates born to mothers with a positive amniotic fluid culture had a significantly higher median IL-6 concentration than neonates born to mothers with a negative amniotic fluid culture (preterm: median 31.6, range 1.4-676 pg/ml vs. median 8.0, range 0.1-656 pg/ml; p < 0.05 and term: median 11.7, range 1.3-82 pg/ml vs. median 3.1, range 0.1-408 pg/ml; p < 0.01, respectively).

CONCLUSIONS

The preterm fetus is capable of mounting a systemic cytokine response as measured by IL-6 in its peripheral blood. In the setting of MIAC, a fetal IL-6 response is higher in preterm than in term gestation.

Antimicrobial peptides in amniotic fluid: defensins, calprotectin and bacterial/permeability-increasing protein in patients with microbial invasion of the amniotic cavity, intra-amniotic inflammation, preterm labor and premature rupture of membranes

OBJECTIVE

Neutrophil defensins (HNP 1-3), bactericidal/permeability-increasing protein (BPI) and calprotectin (MRP8/14) are antimicrobial peptides stored in leukocytes that act as effector molecules of the innate immune response. The purpose of this study was to determine whether parturition, premature rupture of the membranes (PROM) and microbial invasion of the amniotic cavity (MIAC) are associated with changes in amniotic fluid concentrations of these antimicrobial peptides.

STUDY DESIGN

Amniotic fluid was retrieved by amniocentesis from 333 patients in the following groups: group 1, mid-trimester with a subsequent normal pregnancy outcome (n = 84); group 2, preterm labor and intact membranes without MIAC who delivered at term (n = 36), or prematurely (n = 52) and preterm labor with MIAC (n = 26); group 3, preterm PROM with (n = 26) and without (n = 26) MIAC; and group 4, term with intact membranes in the absence of MIAC, in labor (n = 52) and not in labor (n = 31). The concentrations of HNP 1-3, BPI and calprotectin in amniotic fluid were determined by specific and sensitive immunoassays. Placentae of patients in both preterm labor with intact membranes and preterm PROM groups who delivered within 72 h of amniocentesis were examined. Non-parametric statistics, receiver-operating characteristic (ROC) curves and Cox regression models were used for analysis. A p value of < 0.05 was considered statistically significant.

RESULTS

Intra-amniotic infection was associated with a significant increase in amniotic fluid concentrations of immunoreactive HNP 1-3, BPI and calprotectin in both women with preterm labor and intact membranes, and women with preterm PROM. Preterm PROM was associated with a significant increase in amniotic fluid concentrations of immunoreactive HNP 1-3, BPI and calprotectin. Preterm parturition was associated with a significant increase in amniotic fluid concentrations of immunoreactive HNP 1-3, BPI and calprotectin, while parturition at term was associated with a significant increase in amniotic fluid concentrations of immunoreactive HNP 1-3. Among patients with preterm labor and intact membranes, elevation of amniotic fluid HNP 1-3, BPI and calprotectin concentrations was associated with intra-amniotic inflammation, histological chorioamnionitis and a shorter interval to delivery.

CONCLUSION

MIAC, preterm parturition and preterm PROM are associated with increased amniotic fluid concentrations of immunoreactive HNP 1-3, BPI and calprotectin. Moreover, elevated amniotic fluid concentrations of BPI, immunoreactive HNP 1-3 and calprotectin are associated with intra-amniotic inflammation, histological chorioamnionitis and shorter amniocentesis-to-delivery interval in patients presenting with preterm labor with intact membranes.

Human osteoarthritic cartilage matrix vesicles generate both calcium pyrophosphate dihydrate and apatite in vitro

Calcium crystals in osteoarthritic (OA) joints promote enzymatic degradation of articular tissues. Matrix vesicles provide a nidus for calcium crystal formation in chick epiphyseal and mature porcine articular cartilage. In order to examine a potential role for matrix vesicles from OA cartilage in generating pathologic crystals, we sought to determine whether vesicles derived from human OA cartilage (OAMV) could mineralize; and we characterized the resultant mineral species. OAMV were isolated and examined for alkaline phosphatase (AP) and nucleoside triphosphate pyrophosphohydrolase (NTPPPH) activity. OAMV ATP-dependent and independent mineralization were measured in a radiometric biomineralization assay, and newly formed OAMV crystals were examined using Fourier transform infrared spectroscopy (FTIR) and compensated polarized light microscopy. The mean specific activity of OAMV AP was approximately 6 times higher and NTPPPH activity 11 times lower than that of previously characterized, mature, porcine, articular cartilage vesicles. OAMV progressively precipitated 45Ca over time both in the presence and absence of ATP. The FTIR spectra of mineral formed in ATP-dependent assays most closely resembled the standard spectrum for calcium pyrophosphate dihydrate (CPPD). The FTIR spectra of OAMV mineral formed in the absence of ATP closely resembled apatite. These data support the hypothesis that OAMV may form mineral phases of two key crystals found in degenerating cartilage and provide further evidence for the role of matrix vesicles in pathologic articular cartilage biomineralization.

Irreversible antagonism of 5HT2c receptors by N-ethoxycarbonyl-2-ethoxy-1,2-dihydroquinoline (EEDQ)

To determine if N-ethoxycarbonyl-2-ethoxy-1,2-dihydroquinoline (EEDQ), a carboxyl group activating agent, can inactivate 5HT2c receptors, we have examined the effects of EEDQ on 5HT2c receptor-mediated responses to 5-hydroxytryptamine (5HT) in Xenopus oocytes, and on the binding of [3H]5HT to 5HT2c receptors in transfected HeLa cells. In oocytes expressing rat 5HT2c receptors, EEDQ inhibited the 5HT2c receptor-mediated Cl- currents; and the response did not recover more than 24 h after removal of the EEDQ. To see if this effect of EEDQ was on the receptor itself, the binding of 5HT to 5HT2c receptors was studied in transfected HeLa cells. EEDQ decreased the specific binding of [3H]5HT to 5HT2c receptors. At approximately 22 degrees C, incubating the membranes with 2 x 10(-4) M EEDQ for 1 h caused a 40% decrease in the Bmax, without changing the K(d). At 37 degrees C, the same treatment with EEDQ blocked [3H]5HT binding completely. Half-maximal inhibition occurred at 5 microM EEDQ at both temperatures, and washing for 1.5 h did not restore the binding, suggesting that the inactivation of 5HT2c receptor binding was practically irreversible. Results from both systems showed clearly that EEDQ is an irreversible antagonist of 5HT2c receptors and therefore can be used for many studies of this receptor.