2022 White Paper on Recent Issues in Bioanalysis: FDA Draft Guidance on Immunogenicity Information in Prescription Drug Labeling, LNP & Viral Vectors Therapeutics/Vaccines Immunogenicity, Prolongation Effect, ADA Affinity, Risk-based Approaches, NGS, qPCR, ddPCR Assays (Part 3 - Recommendations on Gene Therapy, Cell Therapy, Vaccines Immunogenicity & Technologies; Immunogenicity & Risk Assessment of Biotherapeutics and Novel Modalities; NAb Assays Integrated Approach)

The 2022 16th Workshop on Recent Issues in Bioanalysis (WRIB) took place in Atlanta, GA, USA on September 26-30, 2022. Over 1000 professionals representing pharma/biotech companies, CROs, and multiple regulatory agencies convened to actively discuss the most current topics of interest in bioanalysis. The 16th WRIB included 3 Main Workshops and 7 Specialized Workshops that together spanned 1 week in order to allow exhaustive and thorough coverage of all major issues in bioanalysis, biomarkers, immunogenicity, gene therapy, cell therapy and vaccines. Moreover, in-depth workshops on ICH M10 BMV final guideline (focused on this guideline training, interpretation, adoption and transition); mass spectrometry innovation (focused on novel technologies, novel modalities, and novel challenges); and flow cytometry bioanalysis (rising of the 3rd most common/important technology in bioanalytical labs) were the special features of the 16th edition. As in previous years, WRIB continued to gather a wide diversity of international, industry opinion leaders and regulatory authority experts working on both small and large molecules as well as gene, cell therapies and vaccines to facilitate sharing and discussions focused on improving quality, increasing regulatory compliance, and achieving scientific excellence on bioanalytical issues. This 2022 White Paper encompasses recommendations emerging from the extensive discussions held during the workshop and is aimed to provide the bioanalytical community with key information and practical solutions on topics and issues addressed, in an effort to enable advances in scientific excellence, improved quality and better regulatory compliance. Due to its length, the 2022 edition of this comprehensive White Paper has been divided into three parts for editorial reasons. This publication (Part 3) covers the recommendations on Gene Therapy, Cell therapy, Vaccines and Biotherapeutics Immunogenicity. Part 1 (Mass Spectrometry and ICH M10) and Part 2 (LBA, Biomarkers/CDx and Cytometry) are published in volume 15 of Bioanalysis, issues 16 and 15 (2023), respectively.

Colchicine, Aspirin, and Montelukast - A Case of Successful Combined Pharmacotherapy for Adult Multisystem Inflammatory Syndrome in COVID-19

Since the beginning of the COVID-19 pandemic, many therapeutic strategies have been tried, with mixed results, to prevent and treat adult multisystem inflammatory syndrome in COVID-19 (AMIS-COVID-19). The reason behind this may the complex web of highly intertwined pathophysiologic mechanisms involved in the SARS-CoV-2 infection and the corresponding human systemic response, leading to end-organ damage, disability, and death. Colchicine, high-dose aspirin, and montelukast are being investigated currently as potential modulators of AMIS-COVID-19 in patients who fail to improve with traditional therapeutic approaches. Here, we present a patient who presented with high fevers, extreme fatigue and dyspnea, and ongoing deterioration. As part of our clinical approach, we used the simultaneous combination of the three agents listed above, capitalizing on their different respective mechanisms of action against AMIS-COVID-19. Following the initiation of therapy, the patient showed symptomatic improvement within 24 h, with the ability to return to daily activities after 72 h of continued triple-agent approach. Based on this experience, we have reviewed the immunomodulatory basis of this regimen, including potential avenues in which it may prevent the development of cytokine release syndrome (CRS) and its clinical manifestation, AMIS-COVID-19. By blocking the early stages of an inflammatory response, via diverse mechanistic pathways, the regimen in question may prove effective in halting the escalation of CRS and AMIS-COVID-19 in acutely symptomatic, nonimproving COVID-19 patients.

Abstract 4986: Utilizing image analysis to characterize an 8-plex immunofluorescence immune checkpoint biomarker panel within the tumor tissue microenvironment

Multiplex staining and image analysis are being increasingly deployed for immuno-oncology (I/O) evaluations to investigate and understand the complexity of immune cell / tumor cell interactions in the tumor microenvironment (TME) and in discovering novel predictive biomarkers for targeted immunotherapy. Immune checkpoint inhibitor treatment, guided by immunohistochemically labelled tissue expression of PD-L1 and PD-1, have already been shown to improve outcomes, in the metastatic setting, for non-small cell lung carcinoma (NSCLC) and colorectal cancer (CRC) patients. The purpose of the current study was to phenotype and compare checkpoint and immune cell interactions within NSCLC and CRC tumor types. The study included samples from NSCLC, CRC, and normal tonsil tissues. Sections were stained using InSituPlex® multiplex immunofluorescence (mIF), for studying PD-L1/PD-1 checkpoint expression including immune cell markers for CD3, CD4, CD8, CD68, FoxP3, and pan-CK as an epithelial tumor indicator. Slides were scanned at 20X magnification on the ZEISS Axio Scan.Z1 platform, with individual .tiff format files being generated per marker. Image analysis was performed using the Visiopharm® Oncotopix® platform. Individual marker image layers were aligned, tumor/stroma regions of interest (ROI) classified, and cell formations detected. Quantification of markers was determined across the image layers to evaluate positive cell staining within both cancer indications. Quantitative image analysis data generated included total positive and negative cell counts per marker, per mm2 ROI. Co-localization analysis provided relevant immune cell phenotypes (T-cytotoxic, T-helper, T-regs, and macrophages) and immune cell functional status. Cell spatial analysis relationships were generated, including CD8+/PD-1− and CD8+/PD-1+ to CK+/PD-L1+ tumor cells. This study highlighted the benefits of utilizing an 8-plex staining protocol and detailed image analysis approach for the comprehensive assessment of the immune cell types and interactions within the TME. The ability to carry out multiparameter cellular analysis facilitates the delivery of key phenotypic data, thereby leading to greater understanding of tumor biology.

Citation Format: Alison L. Bigley, Lorcan A. Sherry, Nicole Stillie, Douglas Wood, Sean Downing. Utilizing image analysis to characterize an 8-plex immunofluorescence immune checkpoint biomarker panel within the tumor tissue microenvironment [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 4986.

Abstract 4989: Introduction of a robust workflow for the whole-side acquisition and co-registration of multiplex immunofluorescence tissue images for analysis of a 9-color, 8-marker immunophenotyping assay

Background: Profiling multiple cell types in tissue samples requires more markers than can be supported by conventional approaches to immunohistochemistry. InSituPlex® multiplex immunofluorescence (mIF) technology enables biomarker multiplexing in tissue samples with an automated workflow to support discovery of immune cell signatures in the tumor immune microenvironment (TiME). Here we have designed and tested an 8-plex immunophenotyping panel using the InSituPlex approach to detect and classify T cells, macrophages, and tumor cells in non-small cell lung cancer (NSCLC) and colorectal cancer (CRC) FFPE tissue.

Methods: An 8-plex UltiMapper™ immunofluorescence was developed to stain FFPE tissue, including colorectal cancer, human tonsil, and non-small cell lung cancer. Each sample was stained for the following 8 markers: CD3, CD4, CD8, CD68, FoxP3, PD-1, PD-L1, and pan-CK. Whole-slide imaging was performed in two imaging rounds on the RareCyte CyteFinder II HT slide scanner, and same-slide image alignment and phenotypic analysis was performed using the HALO Highplex FL module from Indica Labs.

Results: Co-registration of two 4-plex imaging rounds and fusing into a single image file allowed for the seamless cell phenotyping of markers across imaging rounds. The 8-plex assay and workflow is compatible across multiple tumor sample types. The samples were characterized based on binned expression and co-expression of biomarkers. The following major cell phenotypes were detected: PD-L1 checkpoint expression, T cells (CD3+), cytotoxic T cells (CD3+/CD8+), T-helper cells (CD3+/CD4+), regulatory T-cells (CD3+/CD4+/FoxP3+), exhausted T cells (CD3+/PD-1+), macrophages (CD68+), and tumor cells (pan-CK+).

Conclusions: The 8-plex assay workflow involving InSituPlex mIF, CyteFinder HT scanner, and HALO analysis supports the ability to measure biomarkers in situ in streamlined and scalable approach.

Citation Format: Anne E. Hellebust, Kyla Teplitz, Katir K. Patel, Karan Sharma, Amanda Bares, Mael Manesse, Mark Burton, Bonnie Phillips, Sean Downing, Kate Lillard. Introduction of a robust workflow for the whole-side acquisition and co-registration of multiplex immunofluorescence tissue images for analysis of a 9-color, 8-marker immunophenotyping assay [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 4989.

Abstract 1677: Understanding the TME: Advanced analysis and visualization of multiplexed fluorescence images

Background: Multiplexed immunofluorescence (mIF) has the potential to revolutionize immuno-oncology and pathology research as it enables the identification of complex cell phenotypes and their potential interactions in the tumor microenvironment (TME). But for a whole slide image with millions of cells, as we increase the number of biomarkers imaged for every cell, the complexity of the data analysis and visualization task increases exponentially. For n markers, a total of 2n phenotypes are possible (e.g. 10 markers have 1024 potential phenotypes). To address this problem and reveal the biologically relevant information embedded in the data, we have developed software tools to reduce the complexity, visualize, and quantify spatial distributions of cells across the full spectrum of possible phenotypes.

Methods: Here we present results using two different methods. The first is an image processing technique called Phenotypic Surface Density Mapping (PSDM), that produces not only true surface density images of each phenotype (cells/µm2), but also surface density images that quantify a variety of other statistics such as the level of expression (intensity) of key markers, inter-phenotype nearest neighbor distance maps, and maps of cell size/morphology. Some important features of these surface density maps are that they are quantitatively robust, have real physical units (e.g. cells/µm2 or intensity/µm2), and they are generated in an unbiased fashion to reveal information about every possible phenotype. The second analysis method, dimensionality reduction, exploits a new technique called Uniform Manifold Approximation and Projection (UMAP), reducing dozens or even hundreds of dimensions for millions of cells to a simple 2D scatter plot. We have developed interactive software that displays the UMAP for a slide and allows the user to select a given cell or region of cells to view closeup images of each cell and statistics about the collection.

Results: Examples of the surface density maps provide insights into mapping the complexity of the TME. We assess the results on deidentified samples by comparison with both human generated labels (pathology review) for individual cells and with automatically generated labels (software review). We show how these tools can be used to both identify tumors and quantify the level of activity in different tumor regions. We demonstrate how increasing the level of multiplexing allows one to differentiate subtle variability and separate subclasses of cells from each other.

Conclusions: Multiplexed data brings valuable information about the TME but much of this information is inaccessible by simply viewing the captured images or performing simple cell counting alone. To address this problem, we demonstrate two new software tools, PSDM and UMAP that preserve and quantify the spatial information of the underlying biology and provide this analysis for all possible phenotypes.

Citation Format: Douglas Wood, Bonnie Phillips, Courtney Hebert, Aditi Sharma, Jamie Buell, Sean Downing. Understanding the TME: Advanced analysis and visualization of multiplexed fluorescence images [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 1677.

Abstract 4569: Intra- and inter-run assessment of reproducibility and quantification of UltiMapper™ I/O APC and T-act kits for tissue multiplexing

Background: The field of immuno-oncology research has enthusiastically adopted multiplex immunohistochemistry (IHC) techniques to establish the spatial relationships between various immune cell populations in a tumor biology in context. Multiplexing enables researchers to gain a deeper understanding and insight into the tumor microenvironment. Unfortunately, many multiplexing technologies face several challenges, specifically in generating highly robust, reproducible, and easily quantifiable data sets. Ultivue’s UltiMapper I/O APC and T-act kits utilize InSituPlex® technology, a new method of multiplexed IHC that utilizes a streamlined workflow with single antigen retrieval, staining, amplification, and detection steps, allowing for the completion of the assay in 5 hours. Here we assess these kits for intra- and inter-run reproducibility and quantification.

Methods: Intra-run reproducibility and quantification was accomplished by manually staining 5 serial sections from three tissue types (deidentified samples of tonsil, melanoma, NSCLC) with one set for each of the UltiMapper I/O APC (CD11c, CD20, CD68/CD163, and MHC Class II) and T-act (CD3, Granzyme B, Ki67, and pan-Cytokeratin/SOX10) kits. Inter-run assessment was determined by staining each slide from a set of five serial sections of each tissue type independently. Images were acquired using the ZEISS® Axio Scan.Z1, without the need for linear unmixing allowing for direct whole slide imaging. Analysis was accomplished using Indica Labs HALO® software. Coefficients of variation (CVs) were calculated based on resulting data.

Results: Analysis of intra-run serial section images revealed that cell counts from section to section had CVs of <10% across all markers, in all tissues, for both the UltiMapper I/O APC and T-act kits. This included total cell counts and average signal intensity. Similar results were seen for inter-run comparisons for both kits (<10% CV).

Conclusions: The results presented here indicate that InSituPlex technology is potentially much more reproducible than other tissue multiplexing techniques currently available. Histological standards for coefficients of variation in IHC based assays are typically <15%. Data presented here falls well within that standard indicating the potential for future translational applications. In conclusion, InSituPlex is a highly reproducible and quantifiable multiplexing technology that is able to produce these results across a variety of tissue types and markers.

Note: This abstract was not presented at the meeting.

Citation Format: Bonnie Phillips, Katir Patel, Courtney Hebert, Aditi Sharma, Jamie Buell, Sean Downing. Intra- and inter-run assessment of reproducibility and quantification of UltiMapper™ I/O APC and T-act kits for tissue multiplexing [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 4569.

Development of a PD-L1 multiplex immunofluorescence assay with advanced visual analysis for understanding the tumor microenvironment

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Background: Current PD-L1 Immunohistochemistry (IHC) assays utilizing conventional brightfield, chromogenic 3,3′-Diaminobenzidine (DAB) staining modalities are the norm in both translational and clinical research. With the rise of immuno-oncology, multiplexed immunofluorescence (mIF) has the potential to revolutionize pathology research as it enables the identification of complex cell phenotypes and their potential interactions in the tumor microenvironment (TME). Ultivue has developed a mIF assay for profiling PD-L1, CD8, CD68, pan-Cytokeratin, and Sox10 enabling whole-slide imaging and data analysis in a single workday. Methods: With an expanding number of biomarkers being interrogated, the complexity of the data analysis and visualization tasks increase exponentially. For N markers, a total of 2N phenotypes are possible. To address this problem and reveal the biologically relevant information embedded in the data, we have developed software tools to reduce the complexity, visualize, and quantify spatial distributions of cells across the full spectrum of possible phenotypes. In this study we demonstrate the utility, robustness, and ability to derive meaningful biological insights by validating the accuracy, precision, sensitivity, and specificity of the PD-L1 multiplex immunofluorescence assay. Results: Here we present results that identify all distinct binary phenotypes within cohorts of lung cancer and melanoma samples using qualitative pathology review and an image processing technique called Phenotypic Surface Density Mapping (PSDM). Important features of this quantitative technique are robustness, use of real physical units (e.g. cells/µm2 or intensity/µm2), and data generation in an unbiased fashion to reveal information about every possible phenotype. Conclusions: Applying the pathology review and PSDM to the cohorts of samples confirmed a high level of concordance demonstrating sensitivity and specificity with high degrees of confidence above 85%. Analysis of intra-run, inter-run, and inter-technician runs revealed that cell counts were within a CV less than 15% across all markers. Data presented here indicates the potential for use in a high throughput testing laboratory to aid in collection and interpretation of meaningful biological insights.

Abstract 5657: Use of a novel immunofluorescence multiplexing technology, InSituPlex™, for the simultaneous detection of immune cells in multiple cancer types

Introduction: The field of immuno-oncology has enthusiastically adopted multiplexed

immunohistochemistry (IHC) techniques to establish the spatial relationships between various

immune cells in tumor biology. Multiplexing enables researchers to gain a deeper understanding

and insight into the tumor microenvironment. Unfortunately, many of the multiplexing

technologies currently utilized in the immuno-oncology field face a number of challenges. These

challenges include complicated and difficult assay optimizations for high-level multiplexing and

the need of specialized imaging instrumentation. In addition, harsh stripping methods and

irreversible staining techniques compromise the integrity of precious tissue samples that ultimately

can no longer be used for additional forms of testing. InSituPlex™ is a new method of multiplexed

IHC that relies on the detection of a unique DNA barcode conjugated to primary antibodies. This

technology removes the need to perform multiple, harsh stripping methods to perform multiplexed

IHC and allows for higher order of multiplexing in less time than currently available multiplexing

techniques, all the while maintaining tissue integrity for use in downstream analyses.

Methods: InSituPlex was used to perform a multiplexed IHC assay on 5 samples from 4 tumor

types (breast, lung, colon, and melanoma). The assay consisted of the following markers: CD4,

CD8, CD20, CD68, PD1, Ki67, FoxP3, and a tumor marker; pan-cytokeratin (CK) for breast,

colon, and lung carcinomas and Sox10 for melanoma. Staining was performed using the Leica

BOND RX autostainer, imaging was performed on various platforms including the Leica VERSA

whole slide scanner, and image analysis was performed using HALO from Indica Labs.

Data: All markers were detected utilizing the InSituPlex technology across all tumor types. Data

indicates a range of phenotypes for infiltrating immune cells in tumor types from highly inflamed

to “immune deserts”. The panel provided for analysis of many phenotypic subtypes, (e.g.,

CD4+/PD1+, CD8+/Ki67+, and Ki67+/CK+), cell densities, proliferative indexes, and spatial

analysis (e.g., CD8+ to tumor cells).

Conclusion: InSituPlex technology is proficient in maintaining tissue integrity and detecting a

range of immune cell phenotypes in multiple tumor types. InSituPlex can be implemented by any

lab possessing a standard fluorescent microscope and does not rely on the purchase of, nor access

to, more expensive platforms.

Citation Format: Sean Downing, Katir Patel, Jamie Buell, Courtney Hebert. Use of a novel immunofluorescence multiplexing technology, InSituPlex™, for the simultaneous detection of immune cells in multiple cancer types [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 5657.

Abstract 5652: Validation of novel InSituPlex™ technology utilizing standard chromogenic IHC and multiplexed tyramide-based immunofluorescence

Introduction: The demands of today's immuno-oncology research has driven the development of

more robust tools to interrogate the tumor microenvironment, specifically using multiplex

immunofluorescence (mIF). Multiplex immunofluorescence allows investigators to visualize

multiple biomarkers in tissue sections while preserving spatial context. The current gold standard

of immunohistochemistry is “brown” staining using DAB with a hematoxylin counterstain. In

recent years, multiplex immunofluorescence has been accepted in the field using tyramide

molecules (TSA) that permanently fix fluorescent dyes to the tissue. Consequently, tissue integrity

is compromised and cannot be utilized in additional forms of analysis. In addition, high-level

plexing using TSA requires the use of highly specialized and costly imaging equipment. Here we

validate a novel technology, InSituPlex™, utilizing DNA barcoding of antibodies and the detection

of markers using simple DNA hybridization techniques. InSituPlex allows for high-leveling of

multiplexing, preservation of tissue integrity for additional analyses, and implementation on a

variety of commonly used imaging platforms.

Methods: Performance of the InSituPlex technology was assessed using 15 immuno-oncology

relevant markers (CD3, CD4, CD8, CD20, CD25, CD68, CD163, FoxP3, Granzyme B, Ki67, PD1,

PD-L1, pan-cytokeratin, Sox10, and TTF1). Each marker was benchmarked by performing a

single-plex DAB chromogenic IHC and an immunofluorescence assay. Antibodies to be used for

InSituPlex testing were first conjugated to unique DNA barcodes and the resulting conjugates were

assessed utilizing the previously described assays to ensure equivalent performance of the

InSituPlex conjugate to unconjugated antibodies. The performance of the complete InSituPlex

assay was evaluated using InSituPlex HRP labelled imaging strands and the newly barcoded

antibodies. InSituPlex vs. DAB/TSA performance was compared across platforms. All staining

was performed manually and on the Leica BOND RX autostainer. Images were acquired across

multiple imaging platforms, including the Leica VERSA whole slide scanner, and image analysis

was performed using HALO from Indica Labs.

Results: All antibodies performed equally well across all the staining methodologies as assessed

qualitatively. Quantitatively, cell counts were performed on serial sections. Statistical analysis

comparing InSituPlex to standard chromogenic and immunofluorescent assays across all 15

antibodies did not yield any significance (p-value > 0.1).

Conclusions: Detection of relevant immune and cancer related markers utilizing InSituPlex

technology is equivalent to standard chromogenic IHC and immunofluorescent assays.

Citation Format: Katir Patel, Courtney Hebert, Jamie Buell, Sean Downing. Validation of novel InSituPlex™ technology utilizing standard chromogenic IHC and multiplexed tyramide-based immunofluorescence [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 5652.

Preliminary correlative analysis of PD-L1 expression from the SUNRISE study

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Background: SUNRISE, a global, double-bind, Phase III trial of docetaxel (D) plus bavituximab (B) or D plus placebo (P) in previously treated non-squamous non-small cell lung cancer, demonstrated similar overall survival (OS) in both treatment arms. Biomarkers including pre-treatment PD-L1 expression are being retrospectively assessed in on-going exploratory analyses. Methods: Archival tissue obtained at the time of diagnosis was requested but not required in the SUNRISE trial. FFPE slides were stained with a panel of lymphoid cell markers: CD3+, CD8+, FoxP3+, PD-L1+, CD163+, CK+ and DAPI using a 6-plex quantitative immunohistochemistry (IHC) assay (OPAL, PerkinElmer, Hopkinton, MA, USA). Baseline PD-L1 expression was retrospectively scored on tumor cells (TC) as a percentage of PD-L1 expressing tumor cells: TC3≥50%, TC2≥5% and < 50%, TC1≥1% and < 5%, and TC0 < 1%. Cox regression models for PD-L1 IHC subgroup populations were used for correlation with OS. Results: In the subset of patients with available diagnostic biopsies (110 out of 597 randomized patients), the prevalence of PD-L1 expression was 5% for TC3, 18% for TC2/3, 35% for TC1/2/3, 65% for TC0. Median OS (mOS) of the D+B arm is 11.5 months (TC0, < 1%) and 6.0 months (TC1/2/3, ≥1%) with HR 0.38 (95% CI, 0.19-0.76); p-value = 0.004. mOS of the D+P arm is 11.1 months (TC0, < 1%) and 10.4 months (TC1/2/3, ≥1%) with HR 0.93 (95% CI, 0.47-1.87); p value = 0.844. Conclusions: Baseline PD-L1 expression in a subset of SUNRISE patients demonstrated that PD-L1 expression (TC0) was associated with a significantly prolonged OS compared to positive PD-L1 expression (TC1/2/3) in patients receiving D+B. No difference in OS was observed in the D+P group by PD-L1 expression. These observations are consistent with the hypothesis that bavituximab may demonstrate more effect in PD-L1 negative or low expressing “immune cold” tumors. Clinical trial information: NCT01999673.

Abstract 4699: Analytical validation of solid tumor fusion gene detection in a comprehensive NGS-based clinical cancer genomic test

Background: As the number of clinically actionable cancer genes grows and the size of most diagnostic biopsies decreases, next-generation sequencing (NGS) becomes increasingly attractive as a diagnostic tool, as it can detect all classes of genomic alterations in all cancer genes in a single test. However, for NGS to achieve its full utility in the clinic, robust analytical validation and performance comparisons against established detection methodologies are required for each class of targetable genomic alteration.

Methods: Previously, we reported on the development and validation of an NGS-based diagnostic test for accurate detection of clinically-relevant genomic alterations across all exons of 287 cancer genes in routine FFPE specimens (Frampton, et. al, Nat. Biotech. Oct 2013). Here, we present systematic validation of fusion gene detection in the test, enabled by hybrid-selection and deep sequencing of commonly rearranged introns in 19 (or, in an alternative version, 31) genes. We created reference samples reflecting key determinants of detection accuracy for gene fusions, including extent of stromal admixture and variety of partner genes: We obtained 5 solid tumor fusion-bearing cell-lines (2 ALK, 1 RET, 1 ROS1, 1 TMPRSS2) and mixed these into 23 variably sized pools, such that each fusion was represented at 100%, 50%, 33%, 25%, and 20% simulated cellular fraction at least once. Gene fusions were called if a well-mapped cluster of 5 chimeric reads or greater was observed in a targeted intron. We then verified that the observed performance translated to FFPE clinical samples by examining test concordance in 43 tumors (20+/23-) characterized for ALK rearrangement by FISH. Finally, we evaluated the test broadly by assessing detection prevalence of the three most common gene fusions (ALK, ROS1, RET) in 724 lung adenocarcinoma FFPE patient samples, including needle biopsies.

Results: Of 32 tested gene fusion instances in the 28 cell-lines samples, all were successfully detected (sensitivity 100%, 95% CI 89%-100%), with no false positive calls. Robust performance translated to FFPE: of the 20 ALK FISH+ specimens, 18 were unequivocally (+) by NGS, with remaining 2 specimens showing sub-threshold evidence of the events. 22/23 FISH- specimens were NGS-, with the remaining specimen an apparent false (-) by FISH. Clinical lung adenocarcinoma samples showed 5% ALK, 3% RET, and 2% ROS1 rearrangement rate respectively, in line with published data.

Conclusions: We present rigorous validation and performance benchmarks for efficient targeted fusion gene detection for solid tumors in an NGS-based test for use in clinical oncology. Given the ability of NGS to detect a much broader range of genomic alterations than currently available technologies, particularly on limited tissue, this type of testing can be a direct component of patient care and potentially expand targeted treatment options.

Citation Format: Roman Yelensky, Amy Donahue, Geoff Otto, Michelle Nahas, Jie He, Frank Juhn, Sean Downing, Garrett M. Frampton, Juliann Chmielecki, Jeffrey S. Ross, Maureen Zakowski, Marc Ladanyi, Vincent A. Miller, Philip J. Stephens, Doron Lipson. Analytical validation of solid tumor fusion gene detection in a comprehensive NGS-based clinical cancer genomic test. [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 4699. doi:10.1158/1538-7445.AM2014-4699

Use of next-generation sequencing (NGS) to identify actionable genomic alterations (GA) in diverse solid tumor types: The Foundation Medicine (FMI) experience with 2,200+ clinical samples

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Background: ST oncology has been transformed by the linkage of GA with targeted therapeutics. Unfortunately, most STs still have no target detected by clinically available assays. More comprehensive testing platforms are needed to determine GA in ST and thus broaden treatment options. We developed a ST NGS diagnostic assay, optimized for routine clinical FFPE specimens including core and fine needle biopsies and malignant effusions, and analyzed > 2,200 patients’ tumors in a CLIA-certified lab (Foundation Medicine). Methods: Hybridization capture of 3,320 exons from 182 cancer-related genes and 37 introns of 14 genes commonly rearranged in cancer was applied to ≥ 50ng of DNA extracted from 2,200+ consecutive FFPE tumor specimens and sequenced to high unique coverage. GA (base substitutions, small indels, rearrangements, copy number alterations) were categorized as “actionable” if directly linked to a clinically available targeted treatment option or a mechanism-driven clinical trial. Results: 2,112/2,221 (95%) of specimens (most common 1° sites: lung 18%, breast 14%, colon 7%, other 34%) were successfully profiled (mean coverage 1134X). Alterations were reported in 155/182 (85%) of genes. Seventy-six percent of cases harbored ≥1 actionable GA, mean 1.6 (range 0-16); sixty-two percent harbored at least one actionable GA not assayed by available tumor-type specific tests or hotspot panels. This approach has led to novel insights into advanced cancer including: 13 novel, potentially druggable kinase gene fusions; alterations in known drug targets (e.g. ALK, EGFR, ERRB2, KIT, MET, PDGFR α and β, RAF1 and RET) in novel tumor types and new mechanisms of resistance to approved targeted therapies. Several patients demonstrated dramatic responses to treatment with targeted therapies directed against these alterations. Conclusions: Comprehensive NGS genomic profiling was successful in profiling >2,200 unselected clinical cases, identified actionable alterations in 76% of cases and provided additional treatment options for 62% of patients targeting alterations in genes not assayed by available hotspot panels.

Use of the FoundationOne next-generation sequencing (NGS) assay to detect actionable alterations leading to clinical benefit of targeted therapies for relapsed and refractory breast cancer

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Background: Genomically-informed cancer therapy linking therapeutics targeting the molecular alterations driving the malignancy has the potential to transform the care of patients with metastatic breast cancer (MBC). Methods: DNA was isolated from 4 FFPE sections cut at 10 microns from 177 consecutive MBC that had relapsed after surgery, conventional hormonal/chemo and anti-HER2 targeted therapies received by our CLIA lab (Foundation Medicine). DNA sequencing was performed for 3,320 exons of 182 cancer-related genes to average depth of 1017X. Actionable Genomic alterations (GA) were defined as those linked to targeted anti-cancer therapies approved or being evaluated in active registered clinical trials. Results: Genomic profiles were generated from 169/177 (95%) BCs identifying 565 GA, averaging 3.34 GAs per tumor (range 0 to 10). 152 (90%) tumors harbored an actionable alteration mean 1.88 per tumor (range 0 to 6). In 124 (73%) tumors, ≥1.0 actionable GA was detected that would be missed by current “hotspot assays”. Notable GA involved PIK3CA (37%), ERBB2 (14%), FGFR1/2 (14%), PTEN (10%), MDM2 (7%), CCND1/CCNE1/CDK4 (7%), BRCA1 and BRCA2 (6% each) and ESR1 and EGFR (3% each). Of 23 ERBB2 GA, 74% were amplifications and 26% were mutation/gene fusion. The frequency of ERBB2 mutation/fusion was significantly enriched in CDH1 mutated ILC (~9% of total BC) with a frequency of 19.0% (4/21) compared to other histological types of BCs 1.4% (2/148) [p=0.002]. Significant clinical efficacy included patients with HER2 IHC/FISH negative tumors featuring HER2 and EGFR activating mutations benefitting from lapatinib/trastuzumab and erlotinib respectively. Conclusions: Comprehensive genomic profiling with a NGS assay identified actionable GAs in the majority of MBC patients including ERBB2 and EGFR mutations that initiated use of targeted therapies resulting in significant clinical benefit. These data provide a framework for the GAs expected in advanced BC and should facilitate the implementation of molecularly targeted trials supporting the efforts for a modern approach to precision medicine for the disease.

Abstract 2279: Bringing next generation sequencing (NGS) to the clinic: Analytical validation of a comprehensive NGS-based cancer gene test

Background: As the number of clinically relevant cancer genes grows and the amount of tissue available for analysis decreases, next-generation sequencing (NGS) becomes increasingly attractive as a diagnostic tool, as it can detect all classes of genomic alterations in all cancer genes in a single test. However, for NGS to demonstrate its full utility in the clinic, robust analytical validation approaches and performance benchmarks against gold standard methodologies are required.

Methods: We have developed a comprehensive NGS-based diagnostic test to enable accurate detection of clinically-relevant genomic alterations across 4604 exons of 289 cancer genes (∼1.5 Mb) in routine FFPE specimens, including needle biopsies. To validate the test, we created synthetic reference standards spanning key determinants of detection accuracy for somatic alterations, such as a range of stromal admixture, indel length, and amplitude of copy change: For base substitutions, we mixed 2 pools of 10 normal cell-lines, thereby testing 1035 different variants in a broad 10%-100% allele frequency range. For indels, 28 tumor cell lines with 44 alterations (1-40bp) were mixed into 41 variably sized pools, creating a validation set of 163 events. For copy alterations, 7 matched tumor/normal cell-lines bearing a total of 12 amplifications (copy number 8-15) and 7 homozygous deletions were mixed in 5 tumor content ratios 20%-75%. The test was applied blinded to all pools and alteration calls compared to expectation based on constituents in each mix. We then verified that observed performance translated to FFPE by examining test concordance on 185 tumors characterized clinically for mutations in 8 genes including KRAS, BRAF, and EGFR (Sanger, Sequenom, and PCR) and 131 specimens characterized for CNAs in ERBB2, PTEN, AR and CCND1 (IHC and FISH).

Results: On synthetic standards, performance reached &gt;99% sensitivity for substitutions (1,035/1,035) and &gt;98% for indels (161/163) at ≥10% allele-frequency with PPV&gt;99%. Sensitivity for CNAs was &gt;95% for focal amplifications (46/48) and &gt;99% for homozygous deletions (28/28) at ≥30% tumor fraction, with PPV&gt;99%. Robust performance translated to FFPE: concordance was 98% for both substitutions and indels (164/168) and CNAs (41/42) relative to prior calls.

Conclusions: We present a rigorous validation approach and performance benchmarks for a comprehensive NGS-based test for use in clinical oncology. Given the ability of NGS to detect a much broader range of genomic alterations than currently available technologies, particularly on limited tissue, we suggest that this type of testing can be a direct component of patient care and potentially expand targeted treatment options.

Citation Format: Roman Yelensky, Garrett M. Frampton, Alex Fichtenholtz, Sean Downing, Jie He, Frank Juhn, Kristina Brennan, Kai Wang, Geoff Otto, Mirna Jarosz, Alex Parker, Jeffrey S. Ross, John Curran, Maureen T. Cronin, Philip J. Stephens, Doron Lipson. Bringing next generation sequencing (NGS) to the clinic: Analytical validation of a comprehensive NGS-based cancer gene test. [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 2279. doi:10.1158/1538-7445.AM2013-2279

Ageing and long-term CD4 cell count trends in HIV-positive patients with 5 years or more combination antiretroviral therapy experience

OBJECTIVES

The aim of this study was to describe the long-term changes in CD4 cell counts beyond 5 years of combination antiretroviral therapy (cART). If natural ageing leads to a long-term decline in the immune system via low-grade chronic immune activation/inflammation, then one might expect to see a greater or earlier decline in CD4 counts in older HIV-positive patients with increasing duration of cART.

METHODS

Retrospective and prospective data were examined from long-term virologically stable HIV-positive adults from the Australian HIV Observational Database. We estimated mean CD4 cell count changes following the completion of 5 years of cART using linear mixed models.

RESULTS

A total of 37 916 CD4 measurements were observed for 892 patients over a combined total of 9753 patient-years. Older patients (> 50 years old) at cART initiation had estimated mean (95% confidence interval) changes in CD4 counts by year-5 CD4 count strata (< 500, 500-750 and > 750 cells/μL) of 14 (7 to 21), 3 (-5 to 11) and -6 (-17 to 4) cells/μL/year. Of the CD4 cell count rates of change estimated, none were indicative of long-term declines in CD4 cell counts.

CONCLUSIONS

Our results suggest that duration of cART and increasing age do not result in decreasing mean changes in CD4 cell counts for long-term virologically suppressed patients, indicating that the level of immune recovery achieved during the first 5 years of treatment is sustained through long-term cART.

Use of next-generation sequencing (NGS) to detect a novel ALK fusion and a high frequency of other actionable alterations in colorectal cancer (CRC)

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Background: We hypothesized that NGS could identify genomic alterations that guide selection of targeted therapies and discover novel drug targets for primary and metastatic CRC. Methods: DNA was extracted and sequenced from 4 X 10 μ FFPE sections from 40 (32 primary and 8 metastatic) CRCs obtained from 2004-10 (52% male; 48% female; mean age 60 years; 10% Stages I/II; 40% Stage III; 40% Stage IV; 10% Stage unknown) using a targeted NGS assay in a CLIA laboratory (Foundation Medicine). 2574 exons of 145 cancer-related genes plus 37 introns from 14 genes often rearranged in cancer were fully sequenced for point mutations, insertions/deletions, copy number alterations (CNAs) and select gene fusions. Results: NGS revealed 125 genomic alterations in 39/40 tumors (mean 3.1, range1-7) in 21 genes, including 80 base substitutions (64%), 39 insertions/deletions (31%), 4 CNAs (3%) and 2 gene fusions (1.6%). TP53 and APC were altered in 80% (32/40) and 67.5% (27/40) of CRCs respectively, with both mutated more frequently than reported in COSMIC. Alterations associated with potential sensitivity to targeted therapies were identified in 21 (52.5%) of CRCs including: 10 KRAS (TK/MEK inhibitors), 6 BRAF (BRAF inhibitors), 5 FBXW7 (mTOR inhibitors); 2 PIK3CA (PI3K/mTOR inhibitors); 2 BRCA2 (PARP inhibitors); 2 GNAS (MEK/ERK inhibitors) and 1 CDK8 (CDK inhibitors). In 1 CRC, a 5.2 Mb tandem duplication generated a novel C2orf44-ALK gene fusion starting at the canonical exon 20 recombination site previously reported for the majority of ALK gene fusions. cDNA sequencing identified an 90-fold increase in 3’ ALK expression, suggesting the C2orf44-ALK fusion results in ALK kinase domain overexpression and contains the same intracellular domain as other ALK fusions including the ALK inhibitor sensitive EML4-ALK. Conclusions: NGS of broad, cancer-related gene content from FFPE CRC samples uncovered an unexpectedly high frequency of genomic alterations, many of which may be clinically actionable by informing treatment decisions, including a novel ALK gene fusion. This previously unrecognized subset of CRC patients may be candidates for clinical trials of crizotinib or other ALK inhibitors.

Targeted next-generation sequencing (NGS) of advanced prostate cancer (PCA) using formalin-fixed tissue

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Background: The genomic landscape of advanced PCA is not well characterized, partly due to limited availability of frozen metastatic tissue. This has created a gap in our knowledge of treatment related and potentially targetable genomic alterations. The purpose of this study was to demonstrate feasibility of performing NGS to molecularly characterize advanced PCA using formalin-fixed paraffin embedded (FFPE) tissue. Methods: 25 metastatic CRPC, 4 metastatic hormone naïve PCA, 3 primary localized PCA, and 18 benign matched prostates were evaluated (40mm FFPE tissue per case). High-density foci were captured and sequenced for 3230 exons of 182 cancer-related genes and 37 introns of 14 genes often rearranged in cancer to an average depth of >800x in a CLIA lab (Foundation Medicine). Recurrent mutations, copy number alterations, and fusions were validated using PCR and FISH. Results: In >90% of samples, there was sufficient DNA (≥50 ng) for analysis. Recurrent high confidence cancer alterations in CRPC included: TMPRSS2-ERG fusion (44%), PTEN loss (44%), TP53 mutation (40%), AR mutation (24%), AR gain (24%), RB mutation (28%), MYC gain (12%), and BRCA2 loss (12%). Overall 48% of CRPC harbored AR gene alterations. Additionally, there were mutations in CTNNB1 (12%), ATM (8%) and PIK3CA (4%). Copy number alterations not previously described in PCA included CCND1, CDK4/6 gains and CDKN2A/CDKN2B deletions. Hormone naïve metastatic and high risk localized PCA demonstrated similar frequency of TMPRSS2-ERG gene fusion, BRCA2 deletion, and TP53 mutations as CRPC, but AR alterations and MYC gain were not seen. Conclusions: This study demonstrates feasibility of in-depth, NGS based DNA analysis using FFPE tissue, even biopsy material. Frequent AR alterations in CRPC, mutations associated with disease progression, and potential drug targets were identified. Focused NGS has clinical potential to identify actionable genomic alterations in advanced PCA that can impact patient participation in trials as well as treatment and outcome. Treatment options include PARP inhibitors for patients with BRCA2 and ATM alterations (20% of cases) and PI3K/AKT inhibitors for PIK3CA mutations.

Abstract 967: Massively parallel sequencing of clinical FFPE cancer specimens enables comprehensive genomic assessment of patient eligibility for targeted therapy

Molecular diagnostics are growing in importance to clinical oncology as an increasing number of therapies targeting specific molecular alterations become available. This trend has led to a proliferation of focused biomarker tests delivered using a variety of technologies, which are generally restricted in their breadth of mutational status assessment and constrained by scarce tissue material. We deployed massively parallel sequencing (or “NGS”) technology to develop a pan-cancer, comprehensive genomic profiling assay interrogating 189 relevant cancer genes, using minimal DNA from fixed surgical or biopsy specimens. With this assay we identify all classes of DNA alterations (base substitutions, insertions and deletions, copy number alterations and rearrangements at specific loci) in a single test with high sensitivity and specificity. To assess the potential for comprehensive genomic profiling to inform clinical decisions, we sequenced 58 archival FFPE tumor specimens, including 16 breast, 16 colon, 14 lung, and 12 renal cell cancers to an average of depth of 850x and considered the resultant mutation profiles in the context of current treatment guidelines and clinical trial information. In total, 121 mutations and 30 copy number alterations were identified, of which less than one third could be identified by traditional “hotspot” analysis. The observed mutation frequencies were consistent with published studies for these tissue types: 56% of breast cancers carried TP53 mutations, 38% had PIK3CA mutations, and 13% harbored HER2 amplifications. In colon cancers, 75% and 63% carried APC and TP53 mutations, while 38%, 31%, and 25% harbored KRAS, BRAF, and PIK3CA mutations respectively. Finally, 57% and 42% of NSCLCs carried mutations in TP53 and KRAS, while 17% of RCCs had mutations in VHL. Nearly 70% of the 58 cases carried one or more mutations that could plausibly confer sensitivity or resistance to approved or experimental targeted therapies. Of these potentially clinically actionable mutations, 57% occurred at known sites of oncogene activation, 27% involved gene amplification or deletion, 14% resulted in tumor suppressor loss, and one resulted in the EML4-ALK fusion gene. Our results demonstrate technical feasibility of comprehensive cancer gene characterization through massively parallel sequencing in clinical FFPE specimens. The prevalence and diversity of potentially actionable mutations we observed highlights the benefits of adopting this approach. As massively-parallel sequencing is the only practical means to detect all classes of somatic mutation in a small, clinically relevant sample, we suggest that this type of testing will be an essential ingredient in bringing targeted therapies to cancer patient care.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 967. doi:1538-7445.AM2012-967

Abstract 5074: Massively parallel DNA-sequencing of aggressive prostate cancer reveals disease heterogeneity and identifies targetable mutations

Background: Recent advances in our understanding of the mutational landscape of prostate cancer (PCa) have occurred through sequencing of primary prostate tumors. Highly aggressive PCa most often does not come to surgery preventing access to frozen sample for high-throughput studies. The purpose of this study is to determine the spectrum of mutations in a subgroup of highly aggressive PCa and to evaluate for targetable molecular alterations using a novel mutation analysis platform from archival formalin-fixed paraffin embedded (FFPE) samples. Methods: 21 PCa (of which 9 were Gleason 5, 8 metastatic), 18 Neuroendocrine PCa (NEPC), and 18 benign FFPE prostate samples from 35 unique cases were evaluated and 77 high-density foci were selected for DNA extraction and sequencing library construction. Hybridization-based capture of 3230 exons and 37 intronic intervals of 189 cancer-related genes was performed, followed by deep, massively-parallel sequencing. Sequence data were analyzed for single nucleotide variants (sub), small insertions and deletions (indels), significant copy number changes, and selected re-arrangements/fusion genes. Results: 5/8 biopsies and 62/65 (overall 93%) of prostate or metastatic foci yielded sufficient DNA (≥50 ng) for analysis from 40μ of FFPE tissue. Average uniquely-mapping sequence coverage was 885x. 133 mutations were identified in 30 genes with 58/67 samples containing at least one mutation. TMPRSS2-ERG fusion was present in 31% of cases. Recurrent high confidence cancer alterations included: gain of MYC (9%), gain or sub/indel of AR (43%), deletion or sub/indel of PTEN (23%), RB1 (20%), BRCA2 (11%), and sub/indel of TP53 (40%), CTNNB1 (11%), PIK3CA (6%), ATM (6%). Several novel mutations were identified, including in BRAF and BRCA2. AR alterations were more common in PCa compared to NEPC, and were present even in clinically localized PCa. There was high concordance between NEPC and PCa foci in mixed tumors, as well as between primary tumor and metastases. Conclusions: This study demonstrates feasibility of in-depth DNA analysis using FFPE tissue, and even biopsy material. The spectrum of driver mutations observed highlights potential value of comprehensive genomic profiling for targeted therapy selection in clinical care. These analyses have laid the foundation for ongoing comparison with indolent PCa, and have identified potential new drug targets (e.g., PARP inhibitors for ATM and BRCA2 mutations), with a goal towards better defining biomarkers that distinguish aggressive and indolent PCa and designing more effective treatment approaches for patients with lethal PCa.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5074. doi:1538-7445.AM2012-5074

Abstract C22: Massively parallel DNA-sequencing of aggressive prostate cancer reveals disease heterogeneity and identifies targetable mutations

Background: Recent advances in our understanding of the mutational landscape of prostate cancer (PCa) have occurred through sequencing of primary prostate tumors. Highly aggressive PCa most often does not come to surgery preventing access to frozen sample for high-throughput studies. The purpose of this study is to determine the spectrum of mutations in a subgroup of highly aggressive PCa and to evaluate for targetable molecular alterations using a novel mutation analysis platform from archival formalin-fixed paraffin embedded (FFPE) samples.

Methods: 21 PCa (of which 9 were Gleason 5, 8 metastatic), 18 neuroendocrine PCa (NEPC), and 18 benign FFPE prostate samples from 35 unique cases were evaluated and 77 high-density foci were selected for DNA extraction and sequencing library construction. Hybridization-based capture of 3230 exons and 37 intronic intervals of 189 cancer-related genes was performed, followed by deep, massively-parallel sequencing. Sequence data were analyzed for single nucleotide variants (sub), small insertions and deletions (indels), significant copy number changes, and selected re-arrangements/fusion genes.

Results: 5/8 biopsies and 62/65 (overall 93%) of prostate or metastatic foci yielded sufficient DNA (≥50 ng) for analysis from 40μ of FFPE tissue. Average uniquely-mapping sequence coverage was 885×. 133 mutations were identified in 30 genes with 58/67 samples containing at least one mutation. TMPRSS2-ERG fusion was present in 31% of cases. Recurrent high confidence cancer alterations included: gain of MYC (9%), gain or sub/indel of AR (43%), deletion or sub/indel of PTEN (23%), RB1 (20%), BRCA2 (11%), and sub/indel of TP53 (40%), CTNNB1 (11%), PIK3CA (6%), ATM (6%). Several novel mutations were identified, including in BRAF and BRCA2. AR alterations were more common in PCa compared to NEPC, and were present even in clinically localized PCa. There was high concordance between NEPC and PCa foci in mixed tumors, as well as between primary tumor and metastases.

Conclusions: This study demonstrates feasibility of in-depth DNA analysis using FFPE tissue, and even biopsy material. The spectrum of driver mutations observed highlights potential value of comprehensive genomic profiling for targeted therapy selection in clinical care. These analyses have laid the foundation for ongoing comparison with indolent PCa, and have identified potential new drug targets (e.g., PARP inhibitors for ATM and BRCA2 mutations), with a goal towards better defining biomarkers that distinguish aggressive and indolent PCa and designing more effective treatment approaches for patients with lethal PCa.

Citation Format: Himisha Beltran, Philip J. Stephens, Juan Miguel Mosquera, Maureen T. Cronin, Mark A. Rubin, Roman Yelensky, Garrett Frampton, Kyung Park, Sean Downing, Theresa Y. MacDonald, Doron Lipson, Scott T. Tagawa, David M. Nanus. Massively parallel DNA-sequencing of aggressive prostate cancer reveals disease heterogeneity and identifies targetable mutations [abstract]. In: Proceedings of the AACR Special Conference on Advances in Prostate Cancer Research; 2012 Feb 6-9; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2012;72(4 Suppl):Abstract nr C22.

Evaluation of the XRCC1 gene as a phenotypic modifier in BRCA1/2 mutation carriers. Results from the consortium of investigators of modifiers of BRCA1/BRCA2

BACKGROUND

Single-nucleotide polymorphisms (SNPs) in genes involved in DNA repair are good candidates to be tested as phenotypic modifiers for carriers of mutations in the high-risk susceptibility genes BRCA1 and BRCA2. The base excision repair (BER) pathway could be particularly interesting given the relation of synthetic lethality that exists between one of the components of the pathway, PARP1, and both BRCA1 and BRCA2. In this study, we have evaluated the XRCC1 gene that participates in the BER pathway, as phenotypic modifier of BRCA1 and BRCA2.

METHODS

Three common SNPs in the gene, c.-77C>T (rs3213245) p.Arg280His (rs25489) and p.Gln399Arg (rs25487) were analysed in a series of 701 BRCA1 and 576 BRCA2 mutation carriers.

RESULTS

An association was observed between p.Arg280His-rs25489 and breast cancer risk for BRCA2 mutation carriers, with rare homozygotes at increased risk relative to common homozygotes (hazard ratio: 22.3, 95% confidence interval: 14.3-34, P<0.001). This association was further tested in a second series of 4480 BRCA1 and 3016 BRCA2 mutation carriers from the Consortium of Investigators of Modifiers of BRCA1 and BRCA2.

CONCLUSIONS AND INTERPRETATION

No evidence of association was found when the larger series was analysed which lead us to conclude that none of the three SNPs are significant modifiers of breast cancer risk for mutation carriers.

Distinguishing the cyanobacterial neurotoxin β-N-methylamino-L-alanine (BMAA) from other diamino acids

β-N-methylamino-L-alanine (BMAA) is produced by diverse taxa of cyanobacteria, and has been detected by many investigators who have searched for it in cyanobacterial blooms, cultures and collections. Although BMAA is distinguishable from proteinogenic amino acids and its isomer 2,4-DAB using standard chromatographic and mass spectroscopy techniques routinely used for the analysis of amino acids, we studied whether BMAA could be reliably distinguished from other diamino acids, particularly 2,6-diaminopimelic acid which has been isolated from the cell walls of many bacterial species. We used HPLC-FD, UHPLC-UV, UHPLC-MS, and triple quadrupole tandem mass spectrometry (UHPLC-MS/MS) to differentiate BMAA from the diamino acids 2,6-diaminopimelic acid, N-2(amino)ethylglycine, lysine, ornithine, 2,4-diaminosuccinic acid, homocystine, cystine, tryptophan, as well as other amino acids including asparagine, glutamine, and methionine methylsulfonium.

Elevated levels of prostate-specific antigen (PSA) in prostate cancer cells expressing mutant p53 is associated with tumor metastasis

The underlying basis for rising levels of prostate-specific antigen (PSA) in prostate cancer is not fully understood, but attention has turned to the possibility that loss of normal p53 function might be directly involved. We have investigated the relationship between p53 function and PSA expression using in vitro and in vivo approaches. Three prostate cancer-derived p53 mutants (F134L, M237L, R273H) were introduced into LNCaP prostate cancer cells and stable transfectants established. Expression of mutant p53 was demonstrated by Western blot analysis, inactivation of wtp53 function, and a loss of p53-dependent responses to DNA damage induced by UV-irradiation and cisplatin. Levels of PSA mRNA and secreted protein were determined by RT-PCR and Western blotting, respectively. Serine protease activity was assessed using an esterase assay. In vivo effects of mutant p53 expression were examined after orthotopic implantation into prostates of nude mice. Expression of all p53 mutants was associated with elevated PSA mRNA and secreted PSA protein. In a representative line, mutant p53 was also associated with increased PSA protease-like activity compared with a control line expressing wildtype p53. Overall PSA levels, and PSA levels in serum from mice bearing tumors derived from cells expressing mutant p53, were increased compared with levels in mice bearing tumors derived from control cells. In addition, the tumors derived from cells with mutant p53 had increased vascularization and induced lymph node metastases. These data provide in vitro and in vivo support for the notion that p53 mutations directly contribute to increased levels of serum PSA, and are associated with more aggressive tumors.

Fostering hope in the clinical setting

Investigators agree that hope is an important coping skill for patients. Hope is stronger than optimism and influences one's physical well being. Suggestions and strategies that can be used in the clinical setting to increase hope begin with an admission of its important role.

Identification of monozygotic twins that are concordant for preeclampsia

Preeclampsia is thought to be discordant in monozygotic twins. While recruiting for a genetic study into preeclampsia, we identified 4 sets of twins and a triplet gestation; all were monozygous on deoxyribonucleic acid "fingerprinting." Two twins were concordant for preeclampsia, and 2 of the triplets had pregnancy-induced hypertension, although only 1 of them had proteinuria. Hence we confirm the existence of monozygotic twins that are concordant for preeclampsia.

Factor V Leiden and thermolabile methylenetetrahydrofolate reductase gene variants in an East Anglian preeclampsia cohort

Preeclampsia is a heritable condition that develops as a result of widespread vascular endothelial dysfunction. The thrombotic tendency in this condition has suggested a number of candidate genes, and there have been recent reports of positive association with the Leiden variant of factor V and the thermolabile variant of methylenetetrahydrofolate reductase. We attempted to reproduce these results in a large cohort of well-characterized women with preeclampsia, recruited prospectively within the East Anglian region of the United Kingdom. Women in the preeclampsia cohort (n=283) were genotyped for both the Leiden variant (G1691A) of factor V and the thermolabile variant (C677T) of methylenetetrahydrofolate reductase. Genotype and allele frequencies were compared with those of 2 control groups, one consisting of women recruited prospectively (n=100) from the same maternity hospital as the subjects and another consisting of normotensive women (n=100) from East Anglia. No significant differences were detected. Specifically, the carrier rate for the Leiden variant was 5.3% in the preeclampsia group and 5. 5% in the combined control group. T677 homozygotes for methylenetetrahydrofolate reductase were 11% and 11.5% in the 2 groups, respectively. We conclude that there is no evidence of association of preeclampsia with either of these 2 polymorphisms in our study population.

Biaryl acids: novel non-nucleoside inhibitors of HIV reverse transcriptase types 1 and 2

A series of biaryl acids has been found to show micromolar inhibition of the HIV reverse transcriptase (RT) from types 1 and 2 with IC50S in the micromolar range. The series was discovered by consideration of the polymerase active site and sub-structure searching of the company compound collection. Synthesis of analogues to investigate the SAR is described. Two of these compounds have shown inhibition of HIV-2 RT only.

Factors determining the specificity of signal transduction by guanine nucleotide-binding protein-coupled receptors. I. Coupling of alpha 2-adrenergic receptor subtypes to distinct G-proteins

alpha 2-Adrenergic receptor (alpha 2-AR) subtypes couple to pertussis toxin (PT)-sensitive G-proteins to elicit both stimulatory and inhibitory cell responses. Signal specificity may be generated by the ability of the receptor subtypes to "recognize" distinct G-proteins with different affinity. To address this issue we stably expressed three alpha 2-AR subtypes, RNG alpha 2 (alpha 2B-AR), RG10 (alpha 2C-AR), and RG20 (alpha 2D-AR), in NIH-3T3 fibroblasts, which express two PT-sensitive G-proteins (Gi alpha 2, Gi alpha 3), and analyzed receptor/G-protein interactions by determining: 1) functional coupling to adenylylcyclase and 2) the ability of the receptors to exist in a high affinity state for agonist. In alpha 2D-AR transfectants expressing 200 or 2,200 fmol of receptor/mg of protein, epinephrine (10 microM) inhibited forskolin-induced elevation of cellular cAMP by 26 +/- 4.8% and 72 +/- 6.2%, respectively. Similar results were obtained in alpha 2B-AR transfectants. However, in alpha 2C-AR transfectants (200 fmol/mg) the forskolin-induced elevation of cellular cAMP was not altered by agonist treatment. In alpha 2C-AR transfectants expressing higher receptor densities (650-1,200 fmol/mg), epinephrine inhibited the effect of forskolin by 30 +/- 3.2%. This difference in functional coupling among the alpha 2-AR subtypes is reflected at the receptor/G-protein interface. In membrane preparations of alpha 2B and alpha 2D-AR but not alpha 2C-AR transfectants, agonist competition curves were biphasic, indicating high and low affinity states of the receptor for agonist. The high affinity state was guanyl-5'-yl imidodiphosphate- and PT-sensitive, indicative of receptor/G-protein coupling. These data suggest that the alpha 2C-AR differs from the alpha 2B and alpha 2D-AR subtypes in its ability to recognize PT-sensitive G-proteins expressed in NIH-3T3 fibroblasts. The alpha 2C-AR may couple preferentially to PT-sensitive G-proteins (Gi1, Go1,2) not expressed in NIH-3T3 fibroblasts and thereby elicit different cellular responses.

Isolation of rat genomic clones encoding subtypes of the alpha 2-adrenergic receptor. Identification of a unique receptor subtype

alpha 2-Adrenergic receptors (alpha 2-AR) exist as subtypes that are expressed in a tissue-specific manner and differ in 1) their ligand recognition properties, 2) their extent of receptor protein glycosylation, and possible 3) their mechanism of signal transduction. Genomic or cDNA clones encoding three receptor subtypes have been characterized; however, both functional and radioligand binding studies in rodents suggest the existence of a fourth receptor subtype. To isolate the rat genes encoding receptor subtypes we screened a rat genomic library with an oligonucleotide probe encompassing the third membrane span of the human C-4 alpha 2-AR. Two intronless rat genes were isolated that encode distinct receptor subtypes (RG10, RG20). RG10 and RG20 encode proteins of 458 and 450 amino acids, respectively, that are 56% homologous and possess the structural features expected of this class of membrane-bound receptors. RG10 identifies a mRNA species of approximately 2500 nucleotides that is found primarily in brain, whereas RG20 identifies a larger mRNA species (approximately 4000 nucleotides) that is found in several tissues including brain, kidney, and salivary gland. RG10 is 88% homologous to the human C-4 alpha 2-AR and exhibits similar binding properties ( [3H]rauwolscine KD = 0.7 +/- 0.3 nM) as determined following transient expression of the receptor in COS-1 cells. RG20 exhibits ligand binding properties distinct from the three receptor subtypes identified by molecular cloning. Saturation binding studies indicate an affinity constant of 15 +/- 1.2 nM for the alpha 2-AR antagonist [3H]rauwolscine, a value 6-20 times higher than that observed for the three cloned receptor subtypes. In competition binding studies the potency order of competing ligands for RG20 is phentolamine greater than idazoxan greater than yohimbine greater than rauwolscine greater than prazosin. Of the three previously cloned alpha 2-AR, RG20 is most closely related to the human C-10 alpha 2-AR (89% homology) and is also capable of mediating adenylylcyclase inhibition as determined following its stable expression in NIH-3T3 fibroblasts. However, in contrast to RG20, [3H] rauwolscine exhibits a KD of 2 nM for the C-10 receptor, and the potency order for competing ligands is rauwolscine greater than or equal to yohimbine greater than idazoxan greater than phentolamine greater than prazosin. RG20 and C-10 are also distinguished by their affinity for SKF-10478 (RG20 Ki = 531 nM, C-10 Ki = 101 nM), a compound that may functionally distinguish pre- and postsynaptic alpha 2-AR. These data suggest that RG20 represents a fourth alpha 2-AR subtype distinct from the known alpha 2A-C receptor subtypes.

Neurologic complications of the tryptophan-associated eosinophilia-myalgia syndrome

A case of tryptophan-associated eosinophilia, central nervous system complications, and multiple white matter lesions by magnetic resonance imaging is presented. Eosinophilia regardless of its cause should be included within the differential of patients exhibiting periventricular white matter lesions.

Metastatic cancer. A relative contraindication to vena cava filter placement

From October 1979 to November 1984, 41 patients underwent placement of vena cava filters for prevention of pulmonary emboli. After filter placement, no pulmonary emboli were documented. No patient died due to filter placement. However, 20 of these 41 patients are dead. Eighteen deaths were caused by cancer. Ten (24%) patients died within 2 months of filter placement. Five (12%) patients died prior to hospital discharge. All ten of these patients had known, widely metastatic cancer. Among the ten patients who died more than 2 months after filter placement, six had well-differentiated, slow growing tumors. Only three of these patients had brain metastases. Among the 21 survivors only two suffered from cancer. Strict adherence to accepted indications for vena cava filter placement required operative procedures on a small but significant number of patients who demonstrated no significant improvement in quality of life or time out of hospital. Filter placement in patients with aggressive cancers and proven metastases should be performed only after analysis of predicted survival and after detailed discussions with patients and referring physicians. Filter placement in patients with aggressive metastatic cancer may cause discomfort, risk, and expense with little hope for improvement of hospital course, longevity, or quality of life.

Valvular obstruction of blood flow through saphenous veins

To measure effects of vein valves upon blood flow through venous bypass conduits, 15 human saphenous veins (mean length 40.6 cm, 5.3 valves/vein) were perfused with normal saline at constant pressure (100 mm Hg). Flow through vein was measured before and after valve bisection. Vein valves were bisected using Leather's techniques. After valve bisection, flow in antegrade and retrograde directions was measured in seven veins. These data were analyzed using paired t tests. Antegrade flow through seven veins with intact valves averaged 317.1 cc/min. With valve bisection this increased significantly (P less than 0.001) to 474.3 cc/min. Retrograde flow through veins with valves bisected increased significantly (P less than 0.0001) to 428.3 cc/min. Eleven veins (mean length 42.2 cm, 5.6 valves/vein) perfused simulated capillary beds with banked blood using pulsatile flow (mean pressure 92 mm Hg). Flow, again, was measured before and after valve bisection. Data were analyzed using the paired t test. Antegrade flow increased from 124.4 cc/min in veins with valves intact to 142.5 cc/min once valves were bisected (P = 0.02). These data demonstrate that saphenous vein valves cause significant obstruction to blood flow under conditions similar to those in the arterial system. Bisection of vein valves significantly increases flow through vein. Improved patency of vein grafts using valve bisection techniques may be explained by increased blood flow alone.

Cystinuria: biochemical evidence for three genetically distinct diseases

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