Evaluation of Cytologic Sample Preparations for Compatibility With Nucleic Acid Analysis

Objectives

In this study, the influence of several key elements of the cytologic sample workflow on DNA and RNA content was evaluated.

Methods

The A549 cell line, patient-derived organoids, and pleural effusions were used to investigate the effect of (1) several collection media and delayed time to processing; (2) cytology specimens; (3) cytologic staining; and (4) formalin-fixed, paraffin-embedded (FFPE) cell block processing on nucleic acid quality and quantity as determined by fragment analyzer, Qubit analysis (Thermo Fisher Scientific), and quantitative polymerase chain reaction–based analysis on the Idylla platform (Biocartis).

Results

Alcohol-based collection media (CytoRich Red [Thermo Fisher Scientific] and EtOH95%) displayed high DNA and RNA preservation capacity, while phosphate-buffered saline and, to a lesser extent, formalin were associated with high RNA quality. Cytospin and smear cytology specimens were subject to DNA and RNA loss. Cytologic staining had no further impact on sample quality, hence destaining is not necessary. Both H&E-stained and unstained FFPE sections are compatible with nucleic acid analysis, despite a strong decrease in DNA and RNA quality.

Conclusions

Although several key elements of the cytologic sample workflow have an influence on DNA and RNA quality and quantity, the selection of these elements is also dependent on the downstream (ancillary) testing methods.

OP0240 A MULTIMODAL MASS SPECTROMETRY APPROACH REVEALS SPECIFIC CARTILAGE MOLECULAR PROFILES ASSOCIATED TO TYPE 2 DIABETIC PATIENTS

Background:

Osteoarthritis (OA) is mainly characterized by the progressive deterioration of articular cartilage. Recent studies support that type 2 diabetes (TD2) is a risk factor to develop OA [1, 2]. However, the molecular cartilage profile of patients combining these two diseases remains unclear, and a better understanding of the different OA phenotypes should be considered for the development of personalized medicine.

Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) is used to investigate the bimolecular distribution of proteins, lipids or metabolites through thein-situanalysis of tissue sections. Bottom-up proteomics focuses on the relative quantification of proteins. The combination of both technologies could be considered to reveal specific molecular profiles and help for patient classification.

Objectives:

The main goal of this study is to apply a multimodal mass spectrometry approach on cartilage to reveal specific lipidomic and proteomic profiles associated to TD2 patients.

Methods:

Human cartilages from OA (na=10) and OA/TD2 human patients (nb=10) were obtained from donors undergoing total knee joint replacement. Cartilage punches of 8*8mm were sectioned at 12 µm thickness for MALDI-MSI and bottom-up proteomics.

For MALDI-MSI experiments (na=6; nb=6), norharmane matrix was sprayed over the samples for the detection of lipids. Experiments were then performed in positive ion polarity at 50 µm of lateral resolution using a RapifleX MALDI Tissue-typer instrument. LipostarMSI and in-house ChemomeTricks toolbox for MATLAB software were used for data processing and analysis.

For bottom-up proteomics experiment (na=10; nb=10), proteins were extracted, separated using SDS-PAGE and digested prior to liquid chromatography separation coupled to an orbitrap MS Q-Exactive HF mass spectrometer. Proteome Discoverer, enrichR and Reactome software were used for data processing and analysis.

Results:

MALDI-MSI showed overall differences between OA and OA/TD2 patients based on their specific lipidomic profiles. In particular, sphingomyelin and phosphatidylcholine species were significantly more abundant in OA patients whereas lysolipids such as lysophosphatidylcholine species were mainly present in OA/TD2 patients, providing therefore phenotype-specific OA molecular panels. Additionally, we observed that phosphatidylcholine and sphingomyelin species were more present in the superficial layer of the cartilage whereas lysophosphatidylcholine species were more abundant in the deep layer (Fig. 1A, B).

Proteomics experiments applied on cartilage enables the quantification of 114 proteins. Among those, 73 were overexpressed in OA samples whereas 41 were overexpressed in OA/TD2 patients. Among the differentially regulated proteins (Fig. 1C), phospholipase A2 was increased in the diabetic cohort, in line with the elevated level of lysolipids found in the imaging data. Our results also involved the fatty acid omega oxidation and the fatty acid biosynthesis pathways as relevant to explain this deregulation of the lipid metabolism.

Conclusion:

MALDI–MSI combined with proteomics experiments showed different profiles between OA and OA/TD2 patients and could be employed for patient classification.

References:

[1]Louati, K., et al., Association between diabetes mellitus and osteoarthritis: systematic literature review and meta-analysis. RMD Open, 2015.1(1): p. e000077.

[2]Williams, M.F., et al.,Type 2 diabetes and osteoarthritis: a systematic review and meta-analysis.J Diabetes Complications, 2016.30(5): p. 944-50.

Acknowledgments:

The Dutch Province of Limburg and MUMC institutional grant.

Disclosure of Interests:

Maxime Eveque: None declared, Pieter Emans Shareholder of: Shareholder and cofounder start-up company Chondropeptix, Grant/research support from: Institution received grants from STW, ReumaNederland, InSciTE, Consultant of: Consultancy to Kiomed, Speakers bureau: Payment for lectures by Kiomed, Episurf, Britt Claes: None declared, Freek Bouwman: None declared, Ron M A Heeren: None declared, Berta Cillero-Pastor: None declared

Clinical Impact of Circulating Tumor RAS and BRAF Mutation Dynamics in Patients With Metastatic Colorectal Cancer Treated With First-Line Chemotherapy Plus Anti-Epidermal Growth Factor Receptor Therapy

PURPOSE

RAS and BRAF mutations can be detected as a mechanism of acquired resistance in circulating tumor (ct) DNA in patients with metastatic colorectal cancer treated with anti-epidermal growth factor receptor therapy.

METHODS

RAS and BRAF mutational status was assessed in ctDNA in a baseline plasma sample and a serum sample collected at the time of the last available determination (named secondary extraction) from patients with KRAS exon 2 wild-type metastatic colorectal cancer treated in two first-line prospective biomarker-designed clinical trials (PULSE, ClinicalTrials.gov identifier: NCT01288339; and POSIBA, ClincialTrials.gov identifier: NCT01276379).

RESULTS

Analysis of extended RAS and BRAF in tissue and plasma from 178 patients with KRAS exon 2 wild-type metastatic colorectal cancer showed a sensitivity of 64.1% and a specificity of 90%. The median overall survival (OS) of baseline patients with RAS and BRAF mutations in ctDNA was 22.3 months (95% CI, 15.6 to 29 months) and 8.9 months (95% CI, 6.3 to 11.4 months), respectively, which was significantly inferior to the median OS of 40.4 months (95% CI, 35.9 to 44.9 months) in two patients with wild-type disease (P < .001). Acquisition of RAS/BRAF mutations occurred in nine of 63 patients (14%) with progressive disease (PD; ie, blood draw within 1 month before PD or after PD) compared with six of 73 patients (8%) with no PD or blood extraction for ctDNA analysis before 1 month of PD (P = .47). Median OS in patients with RAS/BRAF acquisition was 23.9 months (95% CI, 19.7 to 27.9 months) compared with 40.6 months (95% CI, not reached to not reached) in patients who remained free of mutations (P = .016).

CONCLUSION

Our results confirm that baseline RAS and BRAF testing in ctDNA discriminates survival. The emergence of RAS/BRAF mutations has limited relevance for the time to progression to anti-epidermal growth factor receptor therapy.

Abstract 940: Analytical and clinical validation of the Idylla™ ctKRAS and ctNRAS-BRAF liquid biopsy tests identifies mCRC patient groups with high and low ctDNA shedding

Background: Ras mutation analysis is required for the administration of anti-EGFR therapies to mCRC patients. Incorporating ctDNA testing in routine diagnostics allows rapid detection of baseline RAS mutation status from a single blood draw. We validated ctDNA analysis of 21 KRAS, 18 NRAS and 4 BRAF ctDNA mutations using 2 ml of plasma on the Idylla™ platform. The tests were performed using the Idylla™ ctKRAS and ctNRAS-BRAF Mutation Tests, comprising all required reagents for fully automated and integrated ctDNA analysis from plasma with a turnaround time of approximately 2hrs.

Methods: Analytical validation was performed using EDTA plasma samples containing fragmented DNA containing mutant sequences of interest. For both assays the LOD was calculated using regression models. Reproducibility studies were conducted using the Acrometrix™ Idylla™ ctRAS Verification Panel consisting of 4 KRAS mutations, 4 NRAS mutations and 1 BRAF mutation. During between-laboratory reproducibility studies, the panel of reference samples was tested at three different sites using two different Idylla™ instruments. Between-lot reproducibility was assessed on three different lots. For clinical validation, pre-treatment plasma samples from 203 mCRC patients enrolled in the prospective multicenter RASANC study (NCT02502656) were retrospectively assessed. Proper informed consent and statistical analysis were included. As a comparator test, NGS analysis was performed on ctDNA according to Pécuchet et al. (2016). In addition, tissue RAS/BRAF results were available from standard of care testing.

Results: The between-lab reproducibility for the 4 mutations evaluated with the Idylla™ ctKRAS Mutation Test is with 95% confidence at least 98.7% Idylla™ and is with 95% confidence above 98.7% for the 5 mutations evaluated with the Idylla™ ctNRAS-BRAF Mutation Test. The between-lot reproducibility for the evaluated mutations is with 95% confidence at least 98.9% for the ctKRAS Test and 98.5% for the ctNRAS-BRAF Test. In the clinical study, overall RAS agreement between Idylla™ and NGS on plasma was 90.0% with a sensitivity of 89.5% and specificity of 90.4%. RAS concordance between FFPE tissue and plasma was 78.9% in the whole study population. Low amounts of cfDNA in the sample, absence of liver metastases and primary tumor resection were associated with discordant results. In the population with liver metastases showing sufficient cfDNA, overall RAS agreement between plasma and tissue RAS status was 92.5% with a sensitivity of 93.2% and specificity of 90.9%.

Conclusions: The Idylla™ ctKRAS and ctNRAS-BRAF Mutation Tests provide a sensitive, reliable and fast solution for RAS-BRAF ctDNA testing. Results confirm that RAS-BRAF mutation status can be adequately determined using plasma from metastatic colorectal cancer patients with liver metastases.

Citation Format: Bart Jacobs, Bart Claes, Valentina Pomella, Sabine Tejpar, Jean-Baptiste Bachet, Pierre Laurent-Puig, Geert Maertens, Erwin Sablon. Analytical and clinical validation of the Idylla™ ctKRAS and ctNRAS-BRAF liquid biopsy tests identifies mCRC patient groups with high and low ctDNA shedding [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 940.

Key differences between 13 KRAS mutation detection technologies and their relevance for clinical practice

Introduction

This study assessed KRAS mutation detection and functional characteristics across 13 distinct technologies and assays available in clinical practice, in a blinded manner.

Methods

Five distinct KRAS-mutant cell lines were used to study five clinically relevant KRAS mutations: p.G12C, p.G12D, p.G12V, p.G13D and p.Q61H. 50 cell line admixtures with low (50 and 100) mutant KRAS allele copies at 20%, 10%, 5%, 1% and 0.5% frequency were processed using quantitative PCR (qPCR) (n=3), matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF) (n=2), next-generation sequencing (NGS) (n=6), digital PCR (n=1) and Sanger capillary sequencing (n=1) assays. Important performance differences were revealed, particularly assay sensitivity and turnaround time.

Results

Overall 406/728 data points across all 13 technologies were identified correctly. Successful genotyping of admixtures ranged from 0% (Sanger sequencing) to 100% (NGS). 5/6 NGS platforms reported similar allelic frequency for each sample. One NGS assay detected mutations down to a frequency of 0.5% and correctly identified all 56 samples (Oncomine Focus Assay, Thermo Fisher Scientific). One qPCR (Idylla, Biocartis) and MALDI-TOF (UltraSEEK, Agena Bioscience) assay identified 96% (all 100 copies and 23/25 at 50 copies input) and 92% (23/25 at 100 copies and 23/25 at 50 copies input) of samples, respectively. The digital PCR assay (KRAS PrimePCR ddPCR, Bio-Rad Laboratories) identified 60% (100 copies) and 52% (50 copies) of samples correctly. Turnaround time from sample to results ranged from ~2 hours (Idylla CE-IVD) to 2 days (TruSight Tumor 15 and Sentosa CE-IVD), to 2 weeks for certain NGS assays; the level of required expertise ranged from minimal (Idylla CE-IVD) to high for some technologies.

Discussion

This comprehensive parallel assessment used high molecular weight cell line DNA as a model system to address key questions for a laboratory when implementing routine KRAS testing. As most of the technologies are available for additional molecular biomarkers, this study may be informative for other applications.

Evaluation of a fully automated extended RAS-BRAF test on prospectively collected plasma samples from patients with metastatic colorectal cancer

e15127

Background: Extended analysis of RAS genes in metastatic colorectal cancer (mCRC) is not available in many settings and the need for an easy plasma test is high. Methods: Pre-treatment plasma samples from 198 mCRC patients enrolled in the prospective multicenter RASANC study (NCT02502656) were retrospectively assessed for the presence of ctDNA mutations in KRAS, NRAS and BRAF by the fully automated Idylla platform.Proper informed consent and statistical analysis were included. The study is ongoing. We used Idylla platform which allows analysis of 21 KRAS, 18 NRAS and 4 BRAF ctDNA mutations from mCRC using 2 ml of plasma. The tests were performed using prototype versions of the Idylla ctKRAS and ctNRAS-BRAF-EGFR S492R Mutation Assays (RUO), which contain all reagents for integrated sample preparation and multiplex real time PCR detection. The tests each require 1 ml of plasma, less than 1 minute hands-on time, and have a turnaround time of less than 130 minutes.As a comparator test, NGS analysis with a sensitivity of 0.2% was performed on extracted plasma ctDNA according to Pécuchet et al. (2016). Results: The Idylla ctDNA assays identified 84 KRAS mutated (42.4%), 6 NRAS mutated (3%) and 13 BRAF mutated (6.6%) cases. The Idylla assays detected 62 KRAS codon 12 (31%), 16 codon 13 (6.5%), 3 codon 61 (1.5%), and 8 codon 146 (4%), and 1 NRAS codon 13 (0.5%) and 5 (2.5%) codon 61 mutated samples. All BRAF mutations detected were V600E. Overall agreement between Idylla and NGS for KRAS, NRAS, and BRAF was 96%, 100%, and 99.5% respectively. Overall RASconcordance with the NGS reference method was 96.5% with a positive agreement of 98% and a negative agreement of 95% (Table 1). Discordancy analysis by means of ddPCR on plasma and/or tissue will be presented. Conclusions: Plasma-based analysis of 41 extended RAS and BRAF mutations in ctDNA on the Idylla platform enables rapid and reliable genotyping in patients with advanced colorectal cancers. Clinical trial information: NCT02502656. [Table: see text]

BRAF mutation testing with a rapid, fully integrated molecular diagnostics system

Fast and accurate diagnostic systems are needed for further implementation of precision therapy of BRAF-mutant and other cancers. The novel Idylla^TMBRAF Mutation Test has high sensitivity and shorter turnaround times compared to other methods. We used Idylla to detect BRAF V600 mutations in archived formalin-fixed paraffin-embedded (FFPE) tumor samples and compared these results with those obtained using the cobas 4800 BRAF V600 Mutation Test or MiSeq deep sequencing system and with those obtained by a Clinical Laboratory Improvement Amendments (CLIA)-certified laboratory employing polymerase chain reaction–based sequencing, mass spectrometric detection, or next-generation sequencing. In one set of 60 FFPE tumor samples (15 with BRAF mutations per Idylla), the Idylla and cobas results had an agreement of 97%. Idylla detected BRAF V600 mutations in two additional samples. The Idylla and MiSeq results had 100% concordance. In a separate set of 100 FFPE tumor samples (64 with BRAF mutation per Idylla), the Idylla and CLIA-certified laboratory results demonstrated an agreement of 96% even though the tests were not performed simultaneously and different FFPE blocks had to be used for 9 cases. The Idylla^TMBRAF Mutation Test produced results quickly (sample to results time was about 90 minutes with about 2 minutes of hands on time) and the closed nature of the cartridge eliminates the risk of PCR contamination. In conclusion, our observations demonstrate that the Idylla test is rapid and has high concordance with other routinely used but more complex BRAF mutation–detecting tests.

BRAF Mutation Testing in Cell-Free DNA from the Plasma of Patients with Advanced Cancers Using a Rapid, Automated Molecular Diagnostics System

Cell-free (cf) DNA from plasma offers an easily obtainable material for BRAF mutation analysis for diagnostics and response monitoring. In this study, plasma-derived cfDNA samples from patients with progressing advanced cancers or malignant histiocytosis with known BRAF(V600) status from formalin-fixed paraffin-embedded (FFPE) tumors were tested using a prototype version of the Idylla BRAF Mutation Test, a fully integrated real-time PCR-based test with turnaround time about 90 minutes. Of 160 patients, BRAF(V600) mutations were detected in 62 (39%) archival FFPE tumor samples and 47 (29%) plasma cfDNA samples. The two methods had overall agreement in 141 patients [88%; κ, 0.74; SE, 0.06; 95% confidence interval (CI), 0.63-0.85]. Idylla had a sensitivity of 73% (95% CI, 0.60-0.83) and specificity of 98% (95% CI, 0.93-1.00). A higher percentage, but not concentration, of BRAF(V600) cfDNA in the wild-type background (>2% vs. ≤ 2%) was associated with shorter overall survival (OS; P = 0.005) and in patients with BRAF mutations in the tissue, who were receiving BRAF/MEK inhibitors, shorter time to treatment failure (TTF; P = 0.001). Longitudinal monitoring demonstrated that decreasing levels of BRAF(V600) cfDNA were associated with longer TTF (P = 0.045). In conclusion, testing for BRAF(V600) mutations in plasma cfDNA using the Idylla BRAF Mutation Test has acceptable concordance with standard testing of tumor tissue. A higher percentage of mutant BRAF(V600) in cfDNA corresponded with shorter OS and in patients receiving BRAF/MEK inhibitors also with shorter TTF. Mol Cancer Ther; 15(6); 1397-404. ©2016 AACR.

Abstract 1502: A rapid and fully automated multiplex assay for KRAS-BRAF mutations with high mutation sensitivity using novel selective amplification and detection technologies

Introduction

The MAPK/ERK pathway is a complex signaling cascade involved in many cancer types. KRAS and BRAF gene mutations are present in a number of cancers, including colon, lung and pancreas, and identification of mutations in these genes is of great importance in clinical diagnostics. Moreover, there is a growing demand for performing multiple tests simultaneously on a single sample and there is an increased need to provide these answers to oncologists in a short timeframe.

Methods

IdyllaTM is a fully integrated and automated molecular diagnostics platform (1) that combines speed and ease of use with high sensitivity and high multiplexing capabilities. Moreover, it overcomes the current time-consuming step of processing formalin-fixed paraffin-embedded tissue (FFPE) samples. After insertion of a single FFPE slice into the cartridge, the complete process of sample preparation, real-time PCR and reporting is fully automated and takes less than 2 hours. We present here a KRAS-BRAF mutations prototype assay that allows the sensitive detection of 13 KRAS mutations and 5 BRAF mutations in one single assay. The assay discriminates the individual mutations at codons 12, 13 and 61 of KRAS and codon 600 of BRAF using novel “Primer Assisted Sequence Switching” (PASS) primers along with “Multi-component Nucleic Acid enzyme” (MNAzyme) detection. These technologies confer advantages for multiplex mutation analysis; PASS primers selectively amplify the target sequences of interest resulting in enhanced specificity between wild type (WT) and mutant, and between mutants, and MNAzymes allow for efficient detection and discrimination of multiple mutations simultaneously.

Results

Several performance characteristics of the IdyllaTM KRAS-BRAF prototype assay were examined: specificity, cross-reactivity, sensitivity and performance on clinical samples. Specificity of mutant versus WT as well as cross-reactivity between individual mutations at each codon was evaluated. Results demonstrated excellent specificity and cross-reactivity for all individual targets, with delta Cq values of &gt;7 between mutants and &gt;12 between mutant and WT. Sensitivity was assessed using cell lines embedded in FFPE containing defined ratios of mutants and dilutions of these in FFPE WT background. The results indicated sensitivities of &lt;1% of mutant allele. The performance of the IdyllaTM KRAS-BRAF prototype assay was evaluated on a set of colon cancer and melanoma FFPE samples characterized by Sequenom MassARRAY, Illumina MiSeq, or Biocartis IdyllaTM BRAF-only assay which demonstrated a &gt;96 % concordance.

Conclusion

The new and fully integrated IdyllaTM KRAS-BRAF prototype assay combines extended multiplexing capabilities with excellent specificity, high sensitivity, ease of use, and short turnaround time for mutation analysis on FFPE samples.

(1) For research use only

Citation Format: Ina Vandenbroucke, Katrien Vermeiren, Elisa Mokany, Lit Yeen Tan, Nicole Lima, Samantha Walker, Geneviève Vandercruyssen, Bart Claes, Inky De Baere, Pascale Holemans, Evelien Rondelez, Alison Todd, Geert Maertens, Erwin Sablon. A rapid and fully automated multiplex assay for KRAS-BRAF mutations with high mutation sensitivity using novel selective amplification and detection technologies. [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 1502. doi:10.1158/1538-7445.AM2014-1502

VEGFR1 single nucleotide polymorphisms associated with outcome in patients with metastatic renal cell carcinoma treated with sunitinib - a multicentric retrospective analysis

BACKGROUND

There are no validated markers that predict outcome in metastatic renal cell cancer (mRCC) patients treated with sunitinib. Recently, single nucleotide polymorphism (SNP) rs9582036 in VEGFR1 has been proposed as a predictor of progression-free survival (PFS) and overall survival (OS) to bevacizumab in patients with pancreatic cancer and rs7993418 in VEGFR1 as predictor for PFS in mRCC-patients treated with bevacizumab. Here, we aim to study the impact of these SNPs in mRCC patients treated with sunitinib.

METHODS

We included patients with mRCC treated in 15 institutions in France and Belgium. Patients received sunitinib as first-line targeted therapy. We assessed response, time-to-tumor progression (TTP), OS, and clinical and biochemical parameters associated with outcome. We genotyped rs9582036 and rs7993418 as well as three other surrounding SNPs in VEGFR1: rs9554320, rs9554316 and rs9513070. Association between SNPs and treatment outcome were studied by univariate analysis and by multivariate Cox regression using relevant clinical factors associated with TTP and OS as covariates.

FINDINGS

Ninety-one patients were included. We found that mRCC patients with the CC-variant in rs9582036 in VEGFR1 have a poorer response rate (RR) (0% vs. 46%, p = 0.028), a poorer PFS (10 vs. 18 months, p = 0.033 on univariate and 0.06 on multivariate analysis) and a poorer OS (14 vs. 31 months, p = 0.019 on univariate and 0.008 on multivariate analysis) compared to patients with the AC- and AA-genotypes. mRCC patients with the AA-variant in rs9554320 in VEGFR1 have a poorer PFS (12 vs. 21 months, p = 0.0066 on univariate and 0.005 on multivariate analysis) and a poorer OS (22 vs. 34 months, p = 0.019 on univariate and 0.067 on multivariate analysis) compared to patients with the AC- and CC-genotypes. Interpretation. mRCC patients with the CC-genotype in VEGFR1 SNP rs9582036 have a poorer response rate, PFS and OS when treated with sunitinib. These findings are in agreement with the association of rs9582036 and outcome observed in bevacizumab treated pancreatic cancer patients. Prospective validation of this SNP is warranted.

Somatic profiling of the epidermal growth factor receptor pathway in tumors from patients with advanced colorectal cancer treated with chemotherapy ± cetuximab

PURPOSE

To study the somatic molecular profile of the EGF receptor (EGFR) pathway in advanced colorectal cancer, its relationship to prognosis, the site of the primary and metastases, and response to cetuximab.

EXPERIMENTAL DESIGN

We used Sequenom and Pyrosequencing for high-throughput somatic profiling of the EGFR pathway in 1,976 tumors from patients with advanced colorectal cancer from the COIN trial (oxaliplatin and fluoropyrimidine chemotherapy ± cetuximab). Correlations between mutations, clinicopathologic, response, and survival data were carried out.

RESULTS

Sequenom and Pyrosequencing had 99.0% (9,961/10,063) genotype concordance. We identified 13 different KRAS mutations in 42.3% of advanced colorectal cancers, 2 BRAF mutations in 9.0%, 4 NRAS mutations in 3.6%, and 5 PIK3CA mutations in 12.7%. 4.2% of advanced colorectal cancers had microsatellite instability (MSI). KRAS and PIK3CA exon 9, but not exon 20, mutations cooccurred (P = 8.9 × 10(-4)) as did MSI and BRAF mutations (P = 5.3 × 10(-10)). KRAS mutations were associated with right colon cancers (P = 5.2 × 10(-5)) and BRAF mutations with right (P = 7.2 × 10(-5)) and transverse colon (P = 9.8 × 10(-6)) cancers. KRAS mutations were associated with lung-only metastases (P = 2.3 × 10(-4)), BRAF mutations with peritoneal (P = 9.2 × 10(-4)) and nodal-only (P = 3.7 × 10(-5)) metastases, and MSI (BRAF(WT)) with nodal-only metastases (P = 2.9 × 10(-4)). MSI (BRAF(WT)) was associated with worse survival (HR = 1.89, 95% CI 1.30-2.76, P = 8.5 × 10(-4)). No mutations, subsets of mutations, or MSI status were associated with response to cetuximab.

CONCLUSIONS

Our data support a functional cooperation between KRAS and PIK3CA in colorectal tumorigenesis and link somatic profiles to the sites of metastases. MSI was associated with poor prognosis in advanced disease, and no individual somatic profile was associated with response to cetuximab in COIN.

Somatic mutation profiling and associations with prognosis and trastuzumab benefit in early breast cancer

Background

Certain somatic alterations in breast cancer can define prognosis and response to therapy. This study investigated the frequencies, prognostic effects, and predictive effects of known cancer somatic mutations using a randomized, adjuvant, phase III clinical trial dataset.

Methods

The FinHER trial was a phase III, randomized adjuvant breast cancer trial involving 1010 women. Patients with human epidermal growth factor receptor 2 (HER2)–positive breast cancer were further randomized to 9 weeks of trastuzumab or no trastuzumab. Seven hundred five of 1010 tumors had sufficient DNA for genotyping of 70 somatic hotspot mutations in 20 genes using mass spectrometry. Distant disease-free survival (DDFS), overall survival (OS), and interactions with trastuzumab were explored with Kaplan-Meier and Cox regression analyses. All statistical tests were two-sided.

Results

Median follow-up was 62 months. Of 705 tumors, 687 were successfully genotyped. PIK3CA mutations (exons 1, 2, 4, 9, 13, 18, and 20) were present in 25.3% (174 of 687) and TP53 mutations in 10.2% (70 of 687). Few other mutations were found: three ERBB2 and single cases of KRAS, ALK, STK11/LKB1, and AKT2. PIK3CA mutations were associated with estrogen receptor positivity (P < .001) and the luminal-A phenotype (P = .04) but were not statistically significantly associated with prognosis (DDFS: hazard ratio [HR] = 0.88, 95% confidence [CI] = 0.58 to 1.34, P = .56; OS: HR = 0.603, 95% CI = .32 to 1.13, P = .11), although a statistically significant nonproportional prognostic effect was observed for DDFS (P = .002). PIK3CA mutations were not statistically significantly associated with trastuzumab benefit (P_interaction: DDFS P = .14; OS P = .24).

Conclusions

In this dataset, targeted genotyping revealed only two alterations at a frequency greater than 10%, with other mutations observed infrequently. PIK3CA mutations were associated with a better outcome, however this effect disappeared after 3 years. There were no statistically significant associations with trastuzumab benefit.

High-throughput interrogation of PIK3CA, PTEN, KRAS, FBXW7 and TP53 mutations in primary endometrial carcinoma

OBJECTIVE

Endometrial cancer patients may benefit from systemic adjuvant chemotherapy, alone or in combination with targeted therapies. Prognostic and predictive markers are needed, however, to identify patients amenable for these therapies.

METHODS

Primary endometrial tumors were genotyped for >100 hot spot mutations in genes potentially acting as prognostic or predictive markers. Mutations were correlated with tumor characteristics in a discovery cohort, replicated in independent cohorts and finally, confirmed in the overall population (n=1063).

RESULTS

PIK3CA, PTEN and KRAS mutations were most frequently detected, respectively in 172 (16.2%), 164 (15.4%) and 161 (15.1%) tumors. Binary logistic regression revealed that PIK3CA mutations were more common in high-grade tumors (OR=2.03; P=0.001 for grade 2 and OR=1.89; P=0.012 for grade 3 compared to grade 1), whereas a positive TP53 status correlated with type II tumors (OR=11.92; P<0.001) and PTEN mutations with type I tumors (OR=19.58; P=0.003). Conversely, FBXW7 mutations correlated with positive lymph nodes (OR=3.38; P=0.045). When assessing the effects of individual hot spot mutations, the H1047R mutation in PIK3CA correlated with high tumor grade and reduced relapse-free survival (HR=2.18; P=0.028).

CONCLUSIONS

Mutations in PIK3CA, TP53, PTEN and FBXW7 correlate with high tumor grade, endometrial cancer type and lymph node status, whereas PIK3CA H1047R mutations serve as prognostic markers for relapse-free survival in endometrial cancer patients.

Tumor PIK3CA mutations, lymphocyte infiltration, and recurrence-free survival (RFS) in early breast cancer (BC): Results from the FinHER trial

507

Background: Tumor PIK3CA mutations (mts) and lymphocyte infiltration (LI) are prognostic in BC, but their importance is unknown in HER2-positive (HER2+) BC treated with adjuvant trastuzumab (T). Methods: The FinHER trial randomized 1010 patients (pts) with pN+ or high-risk pN- BC to 3 cycles of docetaxel (D) or vinorelbine, followed by 3 cycles of FEC. Pts with HER2+ BC were further randomized to 9 weeks of T or no T (n=232). Pts treated with D and T had superior outcome in prior analyses. BC samples were subjected to somatic hotspot mt profiling (Sequenom) and quantification of percentage tumor LI using full-face H&E sections. RFS and interactions with T were explored with Kaplan-Meier and Cox regression analyses. Results: The median FU time was 62 months. 935 (92.6%) and 687 (68.1%) tumors underwent LI and mt analysis, respectively. Correlation of LI assessment between 2 pathologists was 0.78 (p<0.001). 54 mts detected in 13 genes were evaluated. PIK3CA mts (exons 1,2,9,13,18,20) was present in 25.3% (n=174) and ERBB2 mt in 4.5% (n=31) BCs. Only 1 AKT mt was found and none in KRAS, BRAF, NRAS or PTEN. In ER+/HER2-, HER2+ and ER-/HER2- subtypes the prevalence of PIK3CA mts was 30.2%, 19.5% and 9.2%; ERBB2 mt 6.3%, 1.9% and 2.6%, respectively (both p<0.05). Neither PIK3CA nor ERBB2 mts were associated with RFS overall or within BC subgroups. No interaction was found for the benefit with T and presence of PIK3CA mt in HER2+ BC (interaction p=0.17 T vs no T). Increasing LI was associated with favorable RFS in ER-/HER2- BC (continuous score adjusted p=0.032); 3-y RFS was 90% with extensive LI (>30% infiltrated) vs 66% with non-extensive LI (p=0.007). In HER2+ BC, whilst there was no association with prognosis overall, there was a significant interaction with the benefit from T vs. no T and increasing LI (continuous score interaction p=0.042) with 3-yr RFS 96% vs 78% for extensive and non-extensive LI treated with T respectively (p=0.014). Conclusions: We report 3 clinically relevant findings from this large clinical trial dataset: 1) PIK3CA mts were not prognostic; 2) LI is a strong prognostic factor in ER-/HER2- BC and 3) for the first time that extensive LI predicts benefit from adjuvant T.

VEGF pathway genetic variants as biomarkers of treatment outcome with bevacizumab: an analysis of data from the AViTA and AVOREN randomised trials

BACKGROUND

No biomarkers that could guide patient selection for treatment with the anti-VEGF monoclonal antibody bevacizumab have been identified. We assessed whether genetic variants in the VEGF pathway could act as biomarkers for bevacizumab treatment outcome.

METHODS

We investigated DNA from white patients from two phase 3 randomised studies. In AViTA, patients with metastatic pancreatic adenocarcinoma were randomly assigned to receive gemcitabine and erlotinib plus either bevacizumab or placebo. In AVOREN, patients with metastatic renal-cell carcinoma were randomly assigned to receive interferon alfa-2a plus either bevacizumab or placebo. We assessed the correlation of 138 SNPs in the VEGF pathway with progression-free survival and overall survival in a subpopulation of patients from AViTA. Significant findings were confirmed in a subpopulation of patients from AVOREN and functionally studied at the molecular level.

FINDINGS

We investigated DNA of 154 patients from AViTA, of whom 77 received bevacizumab, and 110 patients from AVOREN, of whom 59 received bevacizumab. Only rs9582036, a SNP in VEGF receptor 1 (VEGFR1 or FLT1), was significantly associated with overall survival in the bevacizumab group of AViTA after correction for multiplicity (per-allele hazard ratio [HR] 2·1, 95% CI 1·45-3·06, p=0·00014). This SNP was also associated with progression-free survival (per-allele HR 1·89, 1·31-2·71, p=0·00081) in bevacizumab-treated patients from AViTA. AC and CC carriers of this SNP exhibited HRs for overall survival of 2·0 (1·19-3·36; p=0·0091) and 4·72 (2·08-10·68; p=0·0002) relative to AA carriers. No effects were seen in placebo-treated patients and a significant genotype by treatment interaction (p=0·041) was recorded, indicating that the VEGFR1 locus containing this SNP serves as a predictive marker for bevacizumab treatment outcome in AViTA. Fine-mapping experiments of this locus identified rs7993418, a synonymous SNP affecting tyrosine 1213 in the VEGFR1 tyrosine-kinase domain, as the functional variant underlying the association. This SNP causes a shift in codon usage, leading to increased VEGFR1 expression and downstream VEGFR1 signalling. This VEGFR1 locus correlated significantly with progression-free survival (HR 1·81, 1·08-3·05; p=0·033) but not overall survival (HR 0·91, 0·45-1·82, p=0·78) in the bevacizumab group in AVOREN.

INTERPRETATION

A locus in VEGFR1 correlates with increased VEGFR1 expression and poor outcome of bevacizumab treatment. Prospective assessment is underway to validate the predictive value of this novel biomarker.

FUNDING

F Hoffmann-La Roche.

A pharmacogenomic scoring system predicting median time to progression (mTTP) on sunitinib (SUN) as first-line treatment in patients (pts) with metastatic renal cell carcinoma (mRCC)

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Background: There are no established biomarkers predicting outcome of SUN treatment in mRCC.

Methods: We assessed 30 single nucleotide polymorphisms (SNPs) in 10 genes on fresh frozen clear cell RCC nephrectomy specimens originating from pts who developed metastatic disease.

Results: We processed 79 samples. In 49 pts, normal kidney tissue adjacent to the tumor was used, in 30 pts only tumoral tissue was available. After nephrectomy and in presence of synchronous or metachronous metastasis, all pts received SUN as 1st line treatment. We observed associations between several SNPs and mTTP: In the promotor region of the gene encoding for IL-8 (proangiogenic growth factor): rs4073: TT or TA versus (vs) AA variant: mTTP 12 mo vs not reached (NR) (p=0.02). In ABCB1 (involved in drug transport): rs2032582: TA or TT vs GT/GA or GG: 9 vs 16 mo (p=0.03). rs1128503: TT vs CT or CC: 9 vs 16 mo (p=0.02). In VEGFR3 (a target of SUN): rs307826 : GA vs AA: 9.3 vs 18 mo (p=0.01). rs307821 : GT vs GG: 10 vs 16 mo (p=0.08). rs448012 : CC/CG vs GG: 12 mo vs NR (p=0.02). In NR1/2 (promotor leading to increased CYP3A4 expression): rs3814055: TT vs CC/CT: 13 vs 18 mo (p=0.02). rs1054190: CC vs CT: 14 vs 20 mo (p=0.14). In PDGFR-alpha (another SUN target): rs1800812: TT vs GG/GT: 3.5 vs 16 mo (p<0.0001). A scoring system combining 7 non-overlapping SNPs was build and pts were classified in a favorable, intermediate and unfavorable SNP profile group. A link with mTTP and response rate was found, but not with established clinical prognostic scores (MSKCC).

Conclusions: SNPs in genes linked to the pharmacokinetics and -dynamics of SUN can probably predict outcome of SUN treatment in mRCC. Our results confirm in part previous observations made by other groups in pazopanib or SUN (in IL-8, VEGFR3 and NR1/2) and highlight the potential role of other SNPs (in ABCB1, NR1/2 and PDGFR). Extension of the series and univariate/multivariate validation are ongoing.

[Table: see text]

Low penetrance breast cancer susceptibility loci are associated with specific breast tumor subtypes: findings from the Breast Cancer Association Consortium

Breast cancers demonstrate substantial biological, clinical and etiological heterogeneity. We investigated breast cancer risk associations of eight susceptibility loci identified in GWAS and two putative susceptibility loci in candidate genes in relation to specific breast tumor subtypes. Subtypes were defined by five markers (ER, PR, HER2, CK5/6, EGFR) and other pathological and clinical features. Analyses included up to 30 040 invasive breast cancer cases and 53 692 controls from 31 studies within the Breast Cancer Association Consortium. We confirmed previous reports of stronger associations with ER+ than ER- tumors for six of the eight loci identified in GWAS: rs2981582 (10q26) (P-heterogeneity = 6.1 × 10(-18)), rs3803662 (16q12) (P = 3.7 × 10(-5)), rs13281615 (8q24) (P = 0.002), rs13387042 (2q35) (P = 0.006), rs4973768 (3p24) (P = 0.003) and rs6504950 (17q23) (P = 0.002). The two candidate loci, CASP8 (rs1045485, rs17468277) and TGFB1 (rs1982073), were most strongly related with the risk of PR negative tumors (P = 5.1 × 10(-6) and P = 4.1 × 10(-4), respectively), as previously suggested. Four of the eight loci identified in GWAS were associated with triple negative tumors (P ≤ 0.016): rs3803662 (16q12), rs889312 (5q11), rs3817198 (11p15) and rs13387042 (2q35); however, only two of them (16q12 and 2q35) were associated with tumors with the core basal phenotype (P ≤ 0.002). These analyses are consistent with different biological origins of breast cancers, and indicate that tumor stratification might help in the identification and characterization of novel risk factors for breast cancer subtypes. This may eventually result in further improvements in prevention, early detection and treatment.

Addition of cetuximab to oxaliplatin-based first-line combination chemotherapy for treatment of advanced colorectal cancer: results of the randomised phase 3 MRC COIN trial

BACKGROUND

In the Medical Research Council (MRC) COIN trial, the epidermal growth factor receptor (EGFR)-targeted antibody cetuximab was added to standard chemotherapy in first-line treatment of advanced colorectal cancer with the aim of assessing effect on overall survival.

METHODS

In this randomised controlled trial, patients who were fit for but had not received previous chemotherapy for advanced colorectal cancer were randomly assigned to oxaliplatin and fluoropyrimidine chemotherapy (arm A), the same combination plus cetuximab (arm B), or intermittent chemotherapy (arm C). The choice of fluoropyrimidine therapy (capecitabine or infused fluouroracil plus leucovorin) was decided before randomisation. Randomisation was done centrally (via telephone) by the MRC Clinical Trials Unit using minimisation. Treatment allocation was not masked. The comparison of arms A and C is described in a companion paper. Here, we present the comparison of arm A and B, for which the primary outcome was overall survival in patients with KRAS wild-type tumours. Analysis was by intention to treat. Further analyses with respect to NRAS, BRAF, and EGFR status were done. The trial is registered, ISRCTN27286448.

FINDINGS

1630 patients were randomly assigned to treatment groups (815 to standard therapy and 815 to addition of cetuximab). Tumour samples from 1316 (81%) patients were used for somatic molecular analyses; 565 (43%) had KRAS mutations. In patients with KRAS wild-type tumours (arm A, n=367; arm B, n=362), overall survival did not differ between treatment groups (median survival 17·9 months [IQR 10·3-29·2] in the control group vs 17·0 months [9·4-30·1] in the cetuximab group; HR 1·04, 95% CI 0·87-1·23, p=0·67). Similarly, there was no effect on progression-free survival (8·6 months [IQR 5·0-12·5] in the control group vs 8·6 months [5·1-13·8] in the cetuximab group; HR 0·96, 0·82-1·12, p=0·60). Overall response rate increased from 57% (n=209) with chemotherapy alone to 64% (n=232) with addition of cetuximab (p=0·049). Grade 3 and higher skin and gastrointestinal toxic effects were increased with cetuximab (14 vs 114 and 67 vs 97 patients in the control group vs the cetuximab group with KRAS wild-type tumours, respectively). Overall survival differs by somatic mutation status irrespective of treatment received: BRAF mutant, 8·8 months (IQR 4·5-27·4); KRAS mutant, 14·4 months (8·5-24·0); all wild-type, 20·1 months (11·5-31·7).

INTERPRETATION

This trial has not confirmed a benefit of addition of cetuximab to oxaliplatin-based chemotherapy in first-line treatment of patients with advanced colorectal cancer. Cetuximab increases response rate, with no evidence of benefit in progression-free or overall survival in KRAS wild-type patients or even in patients selected by additional mutational analysis of their tumours. The use of cetuximab in combination with oxaliplatin and capecitabine in first-line chemotherapy in patients with widespread metastases cannot be recommended.

FUNDING

Cancer Research UK, Cancer Research Wales, UK Medical Research Council, Merck KGgA.

Prediction of lymph node involvement in breast cancer from primary tumor tissue using gene expression profiling and miRNAs

The aim of this study was to investigate whether lymph node involvement in breast cancer is influenced by gene or miRNA expression of the primary tumor. For this purpose, we selected a very homogeneous patient population to minimize heterogeneity in other tumor and patient characteristics. First, we compared gene expression profiles of primary tumor tissue from a group of 96 breast cancer patients balanced for lymph node involvement using Affymetrix Human U133 Plus 2.0 microarray chip. A model was built by weighted Least-Squares Support Vector Machines and validated on an internal and external dataset. Next, miRNA profiling was performed on a subset of 82 tumors using Human MiRNA-microarray chips (Illumina). Finally, for each miRNA the number of significant inverse correlated targets was determined and compared with 1000 sets of randomly chosen targets. A model based on 241 genes was built (AUC 0.66). The AUC for the internal dataset was 0.646 and 0. 651 for the external datasets. The model includes multiple kinases, apoptosis-related, and zinc ion-binding genes. Integration of the microarray and miRNA data reveals ten miRNAs suppressing lymph node invasion and one miRNA promoting lymph node invasion. Our results provide evidence that measurable differences in gene and miRNA expression exist between node negative and node positive patients and thus that lymph node involvement is not a genetically random process. Moreover, our data suggest a general deregulation of the miRNA machinery that is potentially responsible for lymph node invasion.

Effects of KRAS, BRAF, NRAS, and PIK3CA mutations on the efficacy of cetuximab plus chemotherapy in chemotherapy-refractory metastatic colorectal cancer: a retrospective consortium analysis

BACKGROUND

Following the discovery that mutant KRAS is associated with resistance to anti-epidermal growth factor receptor (EGFR) antibodies, the tumours of patients with metastatic colorectal cancer are now profiled for seven KRAS mutations before receiving cetuximab or panitumumab. However, most patients with KRAS wild-type tumours still do not respond. We studied the effect of other downstream mutations on the efficacy of cetuximab in, to our knowledge, the largest cohort to date of patients with chemotherapy-refractory metastatic colorectal cancer treated with cetuximab plus chemotherapy in the pre-KRAS selection era.

METHODS

1022 tumour DNA samples (73 from fresh-frozen and 949 from formalin-fixed, paraffin-embedded tissue) from patients treated with cetuximab between 2001 and 2008 were gathered from 11 centres in seven European countries. 773 primary tumour samples had sufficient quality DNA and were included in mutation frequency analyses; mass spectrometry genotyping of tumour samples for KRAS, BRAF, NRAS, and PIK3CA was done centrally. We analysed objective response, progression-free survival (PFS), and overall survival in molecularly defined subgroups of the 649 chemotherapy-refractory patients treated with cetuximab plus chemotherapy.

FINDINGS

40.0% (299/747) of the tumours harboured a KRAS mutation, 14.5% (108/743) harboured a PIK3CA mutation (of which 68.5% [74/108] were located in exon 9 and 20.4% [22/108] in exon 20), 4.7% (36/761) harboured a BRAF mutation, and 2.6% (17/644) harboured an NRAS mutation. KRAS mutants did not derive benefit compared with wild types, with a response rate of 6.7% (17/253) versus 35.8% (126/352; odds ratio [OR] 0.13, 95% CI 0.07-0.22; p<0.0001), a median PFS of 12 weeks versus 24 weeks (hazard ratio [HR] 1.98, 1.66-2.36; p<0.0001), and a median overall survival of 32 weeks versus 50 weeks (1.75, 1.47-2.09; p<0.0001). In KRAS wild types, carriers of BRAF and NRAS mutations had a significantly lower response rate than did BRAF and NRAS wild types, with a response rate of 8.3% (2/24) in carriers of BRAF mutations versus 38.0% in BRAF wild types (124/326; OR 0.15, 95% CI 0.02-0.51; p=0.0012); and 7.7% (1/13) in carriers of NRAS mutations versus 38.1% in NRAS wild types (110/289; OR 0.14, 0.007-0.70; p=0.013). PIK3CA exon 9 mutations had no effect, whereas exon 20 mutations were associated with a worse outcome compared with wild types, with a response rate of 0.0% (0/9) versus 36.8% (121/329; OR 0.00, 0.00-0.89; p=0.029), a median PFS of 11.5 weeks versus 24 weeks (HR 2.52, 1.33-4.78; p=0.013), and a median overall survival of 34 weeks versus 51 weeks (3.29, 1.60-6.74; p=0.0057). Multivariate analysis and conditional inference trees confirmed that, if KRAS is not mutated, assessing BRAF, NRAS, and PIK3CA exon 20 mutations (in that order) gives additional information about outcome. Objective response rates in our series were 24.4% in the unselected population, 36.3% in the KRAS wild-type selected population, and 41.2% in the KRAS, BRAF, NRAS, and PIK3CA exon 20 wild-type population.

INTERPRETATION

While confirming the negative effect of KRAS mutations on outcome after cetuximab, we show that BRAF, NRAS, and PIK3CA exon 20 mutations are significantly associated with a low response rate. Objective response rates could be improved by additional genotyping of BRAF, NRAS, and PIK3CA exon 20 mutations in a KRAS wild-type population.

FUNDING

Belgian Federation against Cancer (Stichting tegen Kanker).

Vitamin D deficiency is highly prevalent in COPD and correlates with variants in the vitamin D-binding gene

INTRODUCTION

Vitamin D deficiency has been associated with many chronic illnesses, but little is known about its relationship with chronic obstructive pulmonary disease (COPD).

OBJECTIVES

Serum 25-hydroxyvitamin D (25-OHD) levels were measured in 414 (ex)-smokers older than 50 years and the link between vitamin D status and presence of COPD was assessed. The rs7041 and rs4588 variants in the vitamin D-binding gene (GC) were genotyped and their effects on 25-OHD levels were tested.

RESULTS

In patients with COPD, 25-OHD levels correlated significantly with forced expiratory volume in 1 s (FEV(1)) (r=0.28, p<0.0001). Compared with 31% of the smokers with normal lung function, as many as 60% and 77% of patients with GOLD (Global Initiative for Obstructive Lung Disease) stage 3 and 4 exhibited deficient 25-OHD levels <20 ng/ml (p<0.0001). Additionally, 25-OHD levels were reduced by 25% in homozygous carriers of the rs7041 at-risk T allele (p<0.0001). This correlation was found to be independent of COPD severity, smoking history, age, gender, body mass index, corticosteroid intake, seasonal variation and rs4588 (p<0.0001). Notably, 76% and 100% of patients with GOLD stage 3 and 4 homozygous for the rs7041 T allele exhibited 25-OHD levels <20 ng/ml. Logistic regression corrected for age, gender and smoking history further revealed that homozygous carriers of the rs7041 T allele exhibited an increased risk for COPD (OR 2.11; 95% CI 1.20 to 3.71; p=0.009).

CONCLUSION

Vitamin D deficiency occurs frequently in COPD and correlates with severity of COPD. The data warrant vitamin D supplementation in patients with severe COPD, especially in those carrying at-risk rs7041 variants.

Thrombomodulin mutations in atypical hemolytic-uremic syndrome

BACKGROUND

The hemolytic-uremic syndrome consists of the triad of microangiopathic hemolytic anemia, thrombocytopenia, and renal failure. The common form of the syndrome is triggered by infection with Shiga toxin-producing bacteria and has a favorable outcome. The less common form of the syndrome, called atypical hemolytic-uremic syndrome, accounts for about 10% of cases, and patients with this form of the syndrome have a poor prognosis. Approximately half of the patients with atypical hemolytic-uremic syndrome have mutations in genes that regulate the complement system. Genetic factors in the remaining cases are unknown. We studied the role of thrombomodulin, an endothelial glycoprotein with anticoagulant, antiinflammatory, and cytoprotective properties, in atypical hemolytic-uremic syndrome.

METHODS

We sequenced the entire thrombomodulin gene (THBD) in 152 patients with atypical hemolytic-uremic syndrome and in 380 controls. Using purified proteins and cell-expression systems, we investigated whether thrombomodulin regulates the complement system, and we characterized the mechanisms. We evaluated the effects of thrombomodulin missense mutations associated with atypical hemolytic-uremic syndrome on complement activation by expressing thrombomodulin variants in cultured cells.

RESULTS

Of 152 patients with atypical hemolytic-uremic syndrome, 7 unrelated patients had six different heterozygous missense THBD mutations. In vitro, thrombomodulin binds to C3b and factor H (CFH) and negatively regulates complement by accelerating factor I-mediated inactivation of C3b in the presence of cofactors, CFH or C4b binding protein. By promoting activation of the plasma procarboxypeptidase B, thrombomodulin also accelerates the inactivation of anaphylatoxins C3a and C5a. Cultured cells expressing thrombomodulin variants associated with atypical hemolytic-uremic syndrome had diminished capacity to inactivate C3b and to activate procarboxypeptidase B and were thus less protected from activated complement.

CONCLUSIONS

Mutations that impair the function of thrombomodulin occur in about 5% of patients with atypical hemolytic-uremic syndrome.

Prevalent breast cancer patients with a homozygous mutant status for CYP2D6*4: response and biomarkers in tamoxifen users

Retrospective studies suggest that single nucleotide polymorphisms in the cytochrome P450 2D6 (CYP2D6) gene predict reduced tamoxifen metabolism, better tolerance and worse treatment outcome. We hypothesized that women with this genotype lack tamoxifen-induced endometrial and biochemical changes in follicle-stimulating hormone (FSH) and sex hormone-binding globulin (SHBG). We identified 56 breast cancer patients attending the follow-up clinic with a homozygous mutant (HM) status for the CYP2D6*4 null variant. Here, we report a detailed assessment of tamoxifen activity in 19 CYP2D6 HM women, while they were using tamoxifen either for metastatic (n = 5) or for early disease (n = 14). We assessed response to tamoxifen in metastatic disease. Endometrial appearances and serum levels of FSH and SHBG were assessed from retrospective and prospective testing. Our findings do suggest that the presence of two CYP2D6*4 alleles does not exclude a durable response of tamoxifen in metastatic breast cancer. The transvaginal ultrasonographic appearance of the endometrium in CYP2D6*4/*4 patients on tamoxifen is similar as seen in the normal population of tamoxifen users. The endometrium is increased in thickness with subepithelial cysts and endometrial polyps. Serum levels of FSH and SHBG in CYP2D6*4 HM tamoxifen users were in the range of what would be expected during tamoxifen treatment in the general population. Our findings do show CYP2D6*4/*4 carriers to have activity of tamoxifen on breast cancer, endometrium and serum levels of FSH and SHBG. They support clinical trials prospectively testing the effect of CYP2D6 genetic variability in response to tamoxifen before denying this drug to breast cancer patients only based on their CYP2D6*4 status.

The role of KRAS, BRAF, NRAS, and PIK3CA mutations as markers of resistance to cetuximab in chemorefractory metastatic colorectal cancer

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Background: KRAS mutations (MUT) negatively affect outcome after cetuximab (CTX) in metastatic colorectal cancer (mCRC). As only 40% of KRAS wild-type (WT) respond it is possible that other MUT, constitutively activating the Ras/Erk or PI3K/Akt pathways, are present in the non-responding KRAS WT. We analyzed the KRAS, BRAF, NRAS & PIK3CA MUT status in 276 chemorefractory CRC treated with CTX +- irinotecan and correlated the MUT status with outcome. Methods: KRAS codon 12,13, 61&146, BRAF V600E, NRAS codon 12&13, PIK3CA E542K, E545K, A, G, V (exon 9), H1047Y, R, L (exon 20), N345K, R88Q and Q546K MUT were evaluated on FFPE primary CRC using the Sequenom MALDI TOF MassArray system. A two- sided Fisher's exact test was used to evaluate the association between PIK3CA, KRAS, BRAF & NRAS MUT and objective response (OR). Progression-free (PFS) and overall survival (OS) were estimated by the Kaplan-Meier method. Results: 116/276 (42%) CRC had a KRAS MUT, 96% of which occurred in codon 12 or 13. KRAS WT was associated with OR (p<.0001), longer median PFS (p<.0001) and OS (p<.0001). 15/153 (9.8%) KRAS WT had a BRAF MUT. BRAF WT was associated with OR (p=.01), longer PFS (p<.0001) and OS (p=.007). 5/98 (5%) KRAS WT had an NRAS MUT and none of these showed OR. KRAS, BRAF and NRAS MUT were mutually exclusive. The combined KRAS/BRAF/NRAS WT state was associated with OR (p<.0001), longer PFS (p<.0001) and OS (p<.0001). 23/200 (12%) CRC carried a PIK3CA mutation: 5/39 (13%) of responders and 18/160 (11%) of non-responders (p=.781). Median PFS and OS were not associated with PIK3CA MUT state (p=.760 & p=.698) overall, nor in the KRAS/BRAF/NRAS WT subgroup (p=.946 & p=.509). 5/13 (38.5%) PIK3CA MUT KRAS/BRAF/NRAS WT CRC showed an OR. 13/107 (12%) of KRAS/BRAF/NRAS WT and 10/93 (11%) of KRAS/BRAF/NRAS MUT tumors harbored a PIK3CA MUT (p=.826). Conclusions: KRAS, BRAF & NRAS MUT are mutually exclusive and occur in at least 47% of CRC. Like KRAS WT, BRAF WT state of the primary is significantly associated with outcome in mCRC treated with CTX. The combined KRAS/BRAF/NRAS WT state is significantly associated with outcome. PIK3CA MUT occur independently of the KRAS/BRAF/NRAS MUT status. We cannot provide any evidence for a strong role of PIK3CA MUT as a marker in determining outcome to CTX.

[Table: see text]

PIK3CA mutations are not a major determinant of resistance to the epidermal growth factor receptor inhibitor cetuximab in metastatic colorectal cancer

PURPOSE

It has been reported that activating KRAS mutations negatively affect response to anti-epidermal growth factor receptor (EGFR) monoclonal antibodies in metastatic colorectal cancer. The mutation status of signaling molecules downstream of the EGFR target is thus crucial to predict clinical benefit to EGFR-targeted therapies. Other mechanisms of resistance to EGFR inhibitors could involve activating mutations of the other main EGFR effector pathway, i.e., the PI3K/PTEN/AKT pathway.

EXPERIMENTAL DESIGN

We analyzed the PIK3CA and KRAS mutation status in a large group (n = 200) of chemorefractory metastatic colorectal cancers treated with cetuximab (Erbitux) in monotherapy or in combination with irinotecan, and correlated the mutation status with outcome.

RESULTS

Twenty-three (12%) of the 200 samples carried 1 of the PIK3CA mutations included in our assay. We found no correlation between the presence of a PIK3CA mutation and impaired response to cetuximab.

CONCLUSIONS

Our findings do not provide any evidence for a strong role of PIK3CA mutations as a single marker in determining response to cetuximab in chemorefractory metastatic colorectal cancer.

Critical Care Nurses’ Knowledge of Evidence-Based Guidelines for Preventing Infections Associated With Central Venous Catheters: An Evaluation Questionnaire

Background Lack of adherence to recommended evidence-based guidelines for preventing infections associated with use of central venous catheters may be due to nurses’ lack of knowledge of the guidelines.

Objective To develop a reliable and valid questionnaire for evaluating critical care nurses’ knowledge of evidence-based guidelines for preventing infections associated with central venous catheters.

Methods A total of 10 nursing-related strategies were identified from current evidence-based guidelines for preventing infections associated with use of central venous catheters. Face and content validation were determined for selected interventions and multiple-choice questions (1 question per intervention). The test results of 762 critical care nurses were evaluated for item difficulty, item discrimination, and quality of the response alternatives or options for answers (possible responses).

Results All 10 items had face and content validity. Values for item difficulty ranged from 0.1 to 0.9. Values for item discrimination ranged from 0.05 to 0.41. The quality of the response alternatives (0.0–0.8) indicated widespread misconceptions among the critical care nurses in the sample.

Conclusion The questionnaire is reliable and has face and content validity. Findings from surveys in which this questionnaire is used can lead to better educational programs for critical care nurses on infections associated with use of central venous catheters.

Critical care nurses' knowledge of evidence-based guidelines for preventing infections associated with central venous catheters: an evaluation questionnaire

BACKGROUND

Lack of adherence to recommended evidence-based guidelines for preventing infections associated with use of central venous catheters may be due to nurses' lack of knowledge of the guidelines.

OBJECTIVE

To develop a reliable and valid questionnaire for evaluating critical care nurses' knowledge of evidence-based guidelines for preventing infections associated with central venous catheters.

METHODS

A total of 10 nursing-related strategies were identified from current evidence-based guidelines for preventing infections associated with use of central venous catheters. Face and content validation were determined for selected interventions and multiple-choice questions (1 question per intervention). The test results of 762 critical care nurses were evaluated for item difficulty, item discrimination, and quality of the response alternatives or options for answers (possible responses).

RESULTS

All 10 items had face and content validity. Values for item difficulty ranged from 0.1 to 0.9. Values for item discrimination ranged from 0.05 to 0.41. The quality of the response alternatives (0.0-0.8) indicated widespread misconceptions among the critical care nurses in the sample.

CONCLUSION

The questionnaire is reliable and has face and content validity. Findings from surveys in which this questionnaire is used can lead to better educational programs for critical care nurses on infections associated with use of central venous catheters.

Critical Care Nurses’ Knowledge of Evidence-Based Guidelines for Preventing Ventilator-Associated Pneumonia: An Evaluation Questionnaire

Background Nurses’ lack of knowledge may be a barrier to adherence to evidence-based guidelines for preventing ventilator-associated pneumonia.

Objective To develop a reliable and valid questionnaire for evaluating critical care nurses’ knowledge of evidence-based guidelines for preventing ventilator-associated pneumonia.

Methods Ten nursing-related interventions were identified from a review of evidence-based guidelines for preventing ventilator-associated pneumonia. Selected interventions and multiple-choice questions (1 question per intervention) were subjected to face and content validation. Item difficulty, item discrimination, and the quality of the response alternatives or options for answers (possible responses) were evaluated on the test results of 638 critical care nurses.

Results Face and content validity were achieved for 9 items. Values for item difficulty ranged from 0.1 to 0.9. Values for item discrimination ranged from 0.10 to 0.65. The quality of the response alternatives led to the detection of widespread misconceptions among critical care nurses.

Conclusion The questionnaire is reliable and has face and content validity. Results of surveys with this questionnaire can be used to focus educational programs on preventing ventilator-associated pneumonia.

Critical care nurses' knowledge of evidence-based guidelines for preventing ventilator-associated pneumonia: an evaluation questionnaire

BACKGROUND

Nurses' lack of knowledge may be a barrier to adherence to evidence-based guidelines for preventing ventilator-associated pneumonia.

OBJECTIVE

To develop a reliable and valid questionnaire for evaluating critical care nurses' knowledge of evidence-based guidelines for preventing ventilator-associated pneumonia.

METHODS

Ten nursing-related interventions were identified from a review of evidence-based guidelines for preventing ventilator-associated pneumonia. Selected interventions and multiple-choice questions (1 question per intervention) were subjected to face and content validation. Item difficulty, item discrimination, and the quality of the response alternatives or options for answers (possible responses) were evaluated on the test results of 638 critical care nurses.

RESULTS

Face and content validity were achieved for 9 items. Values for item difficulty ranged from 0.1 to 0.9. Values for item discrimination ranged from 0.10 to 0.65. The quality of the response alternatives led to the detection of widespread misconceptions among critical care nurses.

CONCLUSION

The questionnaire is reliable and has face and content validity. Results of surveys with this questionnaire can be used to focus educational programs on preventing ventilator-associated pneumonia.

The expression of the salt-responsive gene salT from rice is regulated by hormonal and developmental cues

The expression pattern of the salT gene was analyzed in different cell types and organs of rice (Oryza sativa L.) in response to saline and hormonal treatments to obtain detailed information on the physiological cues controlling gene expression. Gel blot analysis of RNA and in-situ hybridization performed on seedlings grown for 10 ds in the presence of 1% NaCl revealed that salT was expressed mainly in the younger tissues of the plant. In contrast, 6-week-old plants exhibited maximal salT mRNA accumulation in sheaths of older leaves. In addition, salT was normally expressed in rapidly dividing suspension-cultured cells, but not in quiescent ones. Altogether, these results may indicate that salT expression in each region of the plant is dependent on the metabolic activity of the cells as well as on whether or not they are stressed. The effects of two growth regulators, abscisic acid (ABA) and gibberellic acid, were investigated in combination with the effects of NaCl. Gibberellic acid had a synergistic effect on the induction of the salT gene when combined with 0.5% NaCl, but did not induce salT on its own. At 10 microM, ABA induced salT both in the absence of NaCl and in its presence. Whereas 1 microM ABA acted additively with NaCl to induce gene expression, 5 microM ABA with NaCl was only as effective as NaCl alone. This may indicate that the two stimuli act independently and possibly through antagonistic signal transduction pathways.

Clonidine added to bupivacaine-epinephrine-sufentanil improves epidural analgesia during childbirth

BACKGROUND AND OBJECTIVES

A double-blind study was conducted to assess the efficacy and the side effects of a low dose of clonidine added to an epidural injection of bupivacaine and epinephrine, with or without sufentanil.

METHODS

One hundred healthy parturients (ASA 1) were randomly allocated into four groups according to the type of epidural analgesia administered. The bupivacaine/epinephrine (BE) group received a 10-mL standard injection of bupivacaine (B) 1.25 mg/mL and epinephrine (E) 1.25 microg/mL. In the bupivacaine/epinephrine/sufentanil (BES) group, 7.5 microg sufentanil (S) was added to the BE mixture. For the bupivacaine/ epinephrine/clonidine (BEC) group, 50 microg clonidine (C) was added to the BE mixture, whereas for the bupivacaine/epinephrine/sufentanil/clonidine (BESC) group, both sufentanil and clonidine were added to BE. Fetal heart rate was monitored by continuous cardiotocography. Duration of analgesia, method of delivery, and neonatal outcome (measured using APGAR score, peripheral oxygen saturation, and neurologic adaptive capacity score) and side effects of clonidine were observed. The parturients were routinely asked for their global appreciation of the epidural analgesia technique by visual analog score, 2 hours postpartum.

RESULTS

The overall quality and duration of analgesia were superior in the BESC group compared with the other groups, as was the global appreciation by the parturient. The frequency of side effects in the clonidine groups was comparable, with the exception of hypotension and sedation. Hypotension was easily treated by fluids or ephedrine and caused no fetal distress. The level of sedation was mild, and all parturients aroused immediately after verbal commands.

CONCLUSION

The addition of a low dose of clonidine to an epidural injection of bupivacaine with epinephrine and sufentanil provides better analgesia during labor, while keeping the side effects minimal and of minor clinical importance.

Heat-inducible rice hsp82 and hsp70 are not always co-regulated

We have characterized several heat-shock-induced genes in rice (Oryza sativa L.) and compared their expression under a variety of conditions. Three of these genes, which are analogs of the hsp82/90 family, lie within a cloned 18-kilobase (kb) region of the genome. The middle member of this cluster, designated hsp82B, has been fully sequenced. The gene uses a promoter containing six putative heat-shock elements as well as several unusual sequence motifs including a stretch of 11 thymidines alternating with 11 adenosines. The mRNA for this gene reaches its highest relative level of expression within 120 min after plants are shifted to 42 degrees C; no other conditions induce this gene. By contrast, we found that during heat stress the expression of hsp70 correlates well with increases in internal ion concentrations, and can also be induced by excess salt or ethanol at normal growth temperatures. These results appear to indicate that whereas hsp70 is induced by all stresses that lead to protein denaturation-including heat stress-HSP82 mRNA accumulates only upon heat stress.

Organ-dependent regulation of a plant promoter isolated from rice by 'promoter-trapping' in tobacco

A vector containing a transcriptionally inactive neomycin phosphotransferase II gene was used to select promoter sequences from a pool of random genomic DNA fragments. This paper describes how one such sequence (P4.7) isolated from Oryza sativa acts as a hormonally regulated promoter in Nicotiana tabacum. Relative expression ratios in leaf, root, midrib, callus, and stem tissue of tobacco plants are 1:5:4:10:17. Histochemical assays show that P4.7 activates the uidA reporter gene throughout the phloem and cortex of tobacco stems. Transcription from the P4.7 fragment is inducible in leaf tissue by low levels of alpha-naphthalene acetic acid or 6-benzyl-aminopurine, even when cell proliferation is inhibited by colchicine or hydroxyurea. Conversely, 1% DMSO was found to inhibit activation of P4.7 without interfering with callus formation. The fragment contains TATA and CAAT sequences normally found at the 5' end of many plant genes, and an additional region homologous to sequences located in similar positions in a variety of similarly regulated promoters. Promoter deletion and fusion experiments have indicated the location of a stem enhancer element in P4.7. The promoter trap system we have described may potentially be used to characterize transcriptional factors common to monocot and dicot species.

Flavomycin effects on performance of beef bulls and nutrient digestibility in wethers

For 28 weeks a feeding experiment was conducted to determine the effects of dietary flavomycin on performance of beef bulls. In the first and second half of the trial, 40 animals (average initial weight 352 kg) had free access to corn silage or beet pulp, respectively, both supplemented with an appropriate concentrate containing 0 or 10 mg/kg of the antibiotic. Daily flavomycin intake was 39 to 46 mg when the animals were on the corn silage diet and 51 to 54 mg when they were fed the beet pulp diet. The animals fed the corn silage-based diet supplemented with flavomycin showed a non-significant improvement of daily gain (1.4%) and feed conversion (2.3%). When the beet pulp-based diet was fed, flavomycin significantly increased daily gain (15.2%, P less than 0.002) and feed conversion efficiency (9.1%, P less than 0.03). For the overall feeding experiment the positive effect of flavomycin feeding was 6.7% on body weight gain (P less than 0.09) and 5.2% on feed conversion (P less than 0.13). Flavomycin did not affect carcass yield of beef bulls. Also the effect of flavomycin on diet digestibility was studied in wethers fed a mixture of beet pulp and concentrate, containing 0 or 10 ppm flavomycin. No significant effect from the antibiotic on digestion of dry matter, crude protein, fibre, fat, ash and N-free extract was observed.

Transient Gene Expression in Intact and Organized Rice Tissues

Regulated gene expression of chimeric genes has been studied extensively in electroporated protoplasts. The applicability of these assays is limited, however, because protoplasts are not always physiologically identical to the cells from which they are derived. We have developed a procedure to electroporate DNA into intact and organized leaf structures of rice. Optimization of the new gene delivery system mainly involved eliminating explant-released nucleases, prolonging the DNA/explant incubation time, and expanding the pulse time. Using a [beta]-glucuronidase gene under the control of constitutive promoters, we demonstrated that all cell types within a leaf base were susceptible to electroporation-mediated DNA uptake. Although the technique was initially developed for leaf bases of young etiolated rice seedlings, we proved that it was equally applicable both to other monocotyledons, including wheat, maize, and barley, and to other explants, such as etiolated and green sheath and lamina tissues from rice. Transient gene expression assays with electroporated leaf bases showed that the promoter from a pea light-harvesting chlorophyll a/b-binding protein gene displayed both light- and chloroplast-dependent expression in rice, and that the promoter from the Arabidopsis S-adenosylmethionine synthetase gene was, as in transgenic Arabidopsis and tobacco, preferentially expressed in cells surrounding the vascular bundles.

Transient Gene Expression in Intact and Organized Rice Tissues

Regulated gene expression of chimeric genes has been studied extensively in electroporated protoplasts. The applicability of these assays is limited, however, because protoplasts are not always physiologically identical to the cells from which they are derived. We have developed a procedure to electroporate DNA into intact and organized leaf structures of rice. Optimization of the new gene delivery system mainly involved eliminating explant-released nucleases, prolonging the DNA/explant incubation time, and expanding the pulse time. Using a [beta]-glucuronidase gene under the control of constitutive promoters, we demonstrated that all cell types within a leaf base were susceptible to electroporation-mediated DNA uptake. Although the technique was initially developed for leaf bases of young etiolated rice seedlings, we proved that it was equally applicable both to other monocotyledons, including wheat, maize, and barley, and to other explants, such as etiolated and green sheath and lamina tissues from rice. Transient gene expression assays with electroporated leaf bases showed that the promoter from a pea light-harvesting chlorophyll a/b-binding protein gene displayed both light- and chloroplast-dependent expression in rice, and that the promoter from the Arabidopsis S-adenosylmethionine synthetase gene was, as in transgenic Arabidopsis and tobacco, preferentially expressed in cells surrounding the vascular bundles.