c-MYC expression and maturity phenotypes are associated with outcome benefit from addition of ixazomib to lenalidomide-dexamethasone in myeloma

OBJECTIVES

In the TOURMALINE-MM1 phase 3 trial in relapsed/refractory multiple myeloma, ixazomib-lenalidomide-dexamethasone (IRd) showed different magnitudes of progression-free survival (PFS) benefit vs placebo-Rd according to number and type of prior therapies, with greater benefit seen in patients with >1 prior line of therapy or 1 prior line of therapy without stem cell transplantation (SCT).

METHODS

RNA sequencing data were used to investigate the basis of these differences.

RESULTS

The PFS benefit of IRd vs placebo-Rd was greater in patients with tumors expressing high c-MYC levels (median not reached vs 11.3 months; hazard ratio [HR] 0.42; 95% CI, 0.26, 0.66; P < .001) compared with in those expressing low c-MYC levels (median 20.6 vs 16.6 months; HR 0.75; 95% CI, 0.42, 1.2). Expression of c-MYC in tumors varied based on the number and type of prior therapy received, with the lowest levels observed in tumors of patients who had received 1 prior line of therapy including SCT. These tumors also had higher expression levels of CD19 and CD81.

CONCLUSIONS

PFS analyses suggest that lenalidomide and ixazomib target tumors with different levels of c-MYC, CD19, and CD81 expression, thus providing a potential rationale for the differential benefits observed in the TOURMALINE-MM1 study. This trial was registered at www.clinicaltrials.gov as: NCT01564537.

Randomized Phase II Study of Paclitaxel plus Alisertib versus Paclitaxel plus Placebo as Second-Line Therapy for SCLC: Primary and Correlative Biomarker Analyses

INTRODUCTION

We assessed the Aurora A kinase inhibitor, alisertib, plus paclitaxel (henceforth referred to as alisertib/paclitaxel) as second-line treatment for SCLC.

METHODS

In this double-blind study, patients with relapsed or refractory SCLC were stratified by relapse type (sensitive versus resistant or refractory) and brain metastases and randomized 1:1 to alisertib/paclitaxel or placebo plus paclitaxel (henceforth referred to as placebo/paclitaxel) in 28-day cycles. The primary end point was progression-free survival (PFS). Associations of c-Myc expression in tumor tissue (prespecified) and genetic alterations in circulating tumor DNA (retrospective) with clinical outcome were evaluated.

RESULTS

A total of 178 patients were enrolled (89 in each arm). The median PFS was 3.32 months with alisertib/paclitaxel versus 2.17 months with placebo/paclitaxel (hazard ratio [HR] = 0.77, 95% confidence limit [CI]: 0.557-1.067, p = 0.113 in the intent-to-treat population versus HR = 0.71, 95% CI: 0.509-0.985, p = 0.038 with corrected analysis applied). Among 140 patients with genetic alternations, patients with cell cycle regulator mutations (cyclin-dependent kinase 6 gene [CDK6], retinoblastoma-like 1 gene [RBL1], retinoblastoma-like 2 gene [RBL2], and retinoblastoma 1 gene [RB1]) had significantly improved PFS with alisertib/paclitaxel versus with placebo/paclitaxel (3.68 versus 1.80 months, respectively [HR = 0.395, 95% CI: 0.239-0.654, p = 0.0003]), and overall survival (7.20 versus 4.47 months, respectively [HR = 0.427, 95% CI: 0.259-0.704, p = 0.00085]). A subset of patients with c-Myc expression showed significantly improved PFS with alisertib/paclitaxel. The incidence of grade 3 or higher drug-related adverse events was 67% (58 patients) with alisertib/paclitaxel versus 22% (25 patients) with placebo/paclitaxel. Twelve patients (14%) versus 11 (12%) died on study, including four versus zero treatment-related deaths.

CONCLUSIONS

Efficacy signals were seen with alisertib/paclitaxel in relapsed or refractory SCLC. c-Myc expression and mutations in cell cycle regulators may be potential predictive biomarkers of alisertib efficacy; further prospective validations are warranted.

Abstract CT164: Circulating tumor DNA analysis for predictive and prognostic factors in patients with metastatic colorectal cancer: An exploratory analysis from the phase III PARADIGM study

Introduction Circulating tumor DNA (ctDNA) is an emerging biomarker used to track disease progression and treatment response. To investigate mechanisms of resistance to panitumumab and bevacizumab, we performed an exploratory analysis of ctDNA from patients (pts) with metastatic colorectal cancer (mCRC) in the ongoing phase III PARADIGM study (NCT02394834). We present an initial feasibility report of this analysis using a next generation sequencing-based platform.

Methods Pts with chemotherapy-naïve RAS wild-type mCRC were randomized 1:1 to receive mFOLFOX6 plus either panitumumab or bevacizumab. Plasma samples were taken pre- and post-treatment. Samples with a DNA yield of &gt;10ng/mL and &gt;10nM (assessed using an Agilent 2100 Bioanalyzer) were sequenced using an mCRC-focused ctDNA sequencing panel (PlasmaSELECTTM-R 91, PGDx) to detect mutations, amplifications, and rearrangements for 90, 26, and 3 genes, respectively, and microsatellite instability with 250kb targeted regions. Selected genes covered known pathways and functions related to CRC and sensitivity/resistance to anti-EGFR/VEGF therapies. Sequenced DNA required &gt;12,500x average coverage, &gt;15% mapping to regions of interest, and &gt;75x average high quality distinct coverage; analytical validity of the panel was established using standard samples. Pre-treatment archival tissue samples were collected and analyzed by the Broad Institute Solid Tumor panel, which covers 1,072 genes with 7.3Mb targeted regions.

Results Between May 29th 2015 and June 8th 2017, 823 pts were enrolled at 197 sites. Pre-treatment plasma samples and tissue samples were collected from 756 pts (92%); &gt;99.9% of plasma samples met the pre-specified quality criteria (QC). At the time of this feasibility analysis, 337 pre-treatment plasma samples that fulfilled the QC had been sequenced. In sensitivity validation, 92% of mutations were detected at the 0.1% mutant allele fraction (MAF) and 100% were detected at the &gt;0.5% MAF with &gt;99.9% specificity. In total, 25 tissue- and plasma-matched samples and 5 plasma samples without matched tissue samples were analyzed. Using individual mutations in tissue DNA as the denominator, genetic concordance was 100% (3/3) with BRAF and 70% (7/10) with TP53 between plasma and tissue samples for common TCGA mutations. Mechanisms of resistance to each therapy will be assessed by sub-clone analysis of pre- and post-treatment samples using the validated ultra-deep ctDNA sequencing panel. Collection of post-treatment samples is ongoing.

Conclusion Initial data confirms the analytical feasibility of this method and supports the use of ctDNA to track clonal evolution. Further analyses are warranted in all pts to explore the underlying mechanisms of response to treatment with anti-EGFR/VEGF therapies.

Citation Format: Katsuya Tsuchihara, Kei Muro, Takayuki Yoshino, Kohei Shitara, Kentaro Yamazaki, Mitsuyoshi Ota, Eiji Oki, Takeo Sato, Takeshi Naitoh, Yoshito Komatsu, Takeshi Kato, Kazunori Yamanaka, Ikuo Mori, Masamitsu Hihara, Jumpei Soeda, Sunita Badola, Hyunjin Shin, Takeharu Yamanaka, Kiwamu Akagi, Atsushi Ochiai, Hiroyuki Uetake. Circulating tumor DNA analysis for predictive and prognostic factors in patients with metastatic colorectal cancer: An exploratory analysis from the phase III PARADIGM study [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 CT164.

Abstract LB-226: Exosomal liquid biopsy reveals mRNA and lincRNA biomarkers in early stage breast cancer patient plasma

Introduction

Breast cancer is the most prevalent cancer in women, with approximately 250,000 diagnoses per year in the US. Non-invasive detection of breast cancer is of critical importance but has proven challenging due to the rate of false-positive diagnoses with current tests. Liquid biopsies including circulating tumor cells (CTCs) or cell-free DNA (cfDNA) have struggled with the detection of early stage disease. For example, a recent multi-analyte (cfDNA+protein) analysis, ‘cancerSEEK', achieved a sensitivity of just 33% in breast cancer, highlighting the challenges facing the development of more sensitive and specific diagnostics for this disease.

Exosome-based liquid biopsy is a promising approach for minimally-invasive and highly sensitive diagnostics and it has been demonstrated that combining exosomal RNA and cfDNA greatly enhances mutation detection compared to profiling cfDNA alone. While most liquid biopsies profile mutations, studying RNA abundance in exosomes adds a new dimension to these non-invasive diagnostics. To date, much of the focus on exosomal RNA expression profiling has been on the small-RNA fraction. Here we demonstrate that whole-transcriptome profiling of mRNAs and lincRNAs greatly expands the landscape of potential biomarkers to clinically actionable genes.

Results

We have developed a novel platform designed to perform long-RNA sequencing on transcripts obtained from exosomes. We used this platform to compare expression profiles of total plasma exosomes versus subpopulations enriched for breast cancer-derived exosomes (CDE) versus depleted of non-cancer exosomes (NCE). The NCE-depleted and CDE-enriched exosomes equally outperformed total plasma exosomes, each detecting significantly more genes exhibiting breast cancer vs. healthy expression differences.

We performed NCE-depletion on 1.5 mL of input plasma from 15 stage I & II ER+/Her2- breast cancer patients and 12 healthy women matched for age & menopausal-status. RNA-seq data from these samples detected over 10,000 mRNAs and over 1,000 lincRNAs. Of these, we observed significantly increased abundance in over 100 mRNAs and lincRNAs in these early stage breast cancer patients. These mRNAs are enriched for gene-sets including those previously implicated in ‘breast cancer', ‘chromatin remodeling', and ‘immune response'.

We also performed RNA-seq on formalin-fixed paraffin-embedded (FFPE) samples from healthy and matched breast cancer tissue. The &gt;100 genes found to be more abundant in breast cancer plasma exosomes significantly (p&lt;0.05) separate the FFPE samples into two clusters corresponding to breast cancer patients and normal individuals, lending confidence to the exosomal signature.

Conclusions

This preliminary analysis highlights the exciting potential of exosomal long RNA based liquid biopsy for non-invasive early-stage detection of breast cancer. The platform is readily applicable to other disease areas and other biofluids such as urine or CSF.

Citation Format: Sudipto K. Chakrabortty, Robert R. Kitchen, Christine M. Coticchia, Vasisht R. Tadigotla, Erez Eitan, Elena Castellanos-Rizaldos, Lisa Bedford, Sunita Badola, Michael D. Valentino, Nicholas Colafemina, Hidefumi Uchiyama, Mario Morken, Miguel Williams, Sylvie Vincent, Hadi Danaee, Seth Yu, Johan Skog. Exosomal liquid biopsy reveals mRNA and lincRNA biomarkers in early stage breast cancer patient plasma [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 LB-226.

Abstract 5686: Long RNA sequencing of human plasma exosomes reveals full coverage of diverse protein coding and long non coding RNA

Growing research in oncology implicates exosomes in cell-to-cell communication and various cancer patho-physiologies. Vesicle-mediated signaling is thought to occur via both protein and RNA transport. However, there is a fundamental lack of understanding regarding the long RNA cargo within exosomes. Previous RNASeq studies on exosomes have largely focused on the small RNA fraction, although the clinical biomarker space remains dominated by mRNA. These studies have reported a relatively small proportion and poor transcript coverage of long RNA which has led many to conclude that exosomes only carry short fragments of mRNA and ncRNA.

To address this, we have developed a novel platform specifically designed to perform RNASeq on long RNA from exosomes to efficiently interrogate these as RNA biomarkers. Paired-end sequencing revealed the presence of a wider diversity of annotated mRNA and ncRNAs than previously recognized in exosomes. Employing our whole transcriptome unique molecular indexing strategy, we were able to accurately quantify the number of unique RNA molecules. We detected a total of over 1.4 million unique RNA molecules in our libraries, with 271,308 mapped to protein-coding regions from as little as 2 ml of plasma. We observed that even at a shallow sequencing depth (15 million read pairs), we could detect more than 10,000 genes, composed of 40,000 mRNA and 37,000 ncRNA annotated transcripts. ERCC spike-in analysis indicates that our RNASeq platform is highly sensitive, detecting as few as 8 copies of RNA. Long non-coding RNAs dominated the ncRNA classes and accounted for over 95% of all uniquely detected ncRNAs. We also observed a bimodal distribution of transcript coverage, similar to cellular and tissue derived RNA. In excess of 15,000 transcripts were detected with ≥80% coverage and of these high-coverage transcripts, more than 25% were over 1kb in length, the longest being 17.6kb. Taken together, these findings suggest exosomes harbor more than just small RNA transcripts and short fragments of mRNAs as was previously thought and is a treasure trove of RNA biomarkers.

Current research in the liquid biopsy space has been limited to variant detection in cell-free DNA and circulating tumor cells but transcriptional dysregulation is also an important feature of cancer. Our results shed new light on the biology of exosomes and indicate that, in addition to well-recognized small RNA cargo, plasma exosomes carry an abundance of long RNAs that can be interrogated by our optimized workflow. As exosomes provide a rich and protected source of RNA in biofluids, sequencing both long and small RNA from exosomes has the potential to identify biomarkers without the need for invasive tissue biopsies and allow us to have a more complete picture of how the RNA transcriptome in plasma changes in health and disease.

Citation Format: Sudipto K. Chakrabortty, Lisa Bedford, Hidefumi Uchiyama, Vasisht Tadigotla, Michael D. Valentino, Dominik Grimm, Dalin Chan, Sunita Badola, Graham Brock, Johan Skog. Long RNA sequencing of human plasma exosomes reveals full coverage of diverse protein coding and long non coding RNA [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5686. doi:10.1158/1538-7445.AM2017-5686

Characterization of Circulating Tumor DNA for Genetic Assessment of solid Tumors

Personalized cancer therapy requires characterization of the current status of an individual's cancer, necessitating invasive tumor tissue biopsies at diagnosis, during treatment and at progression. Serial acquisition of solid tumor biopsies during treatment to characterize mutations related to acquired resistance may not be medically feasible. Circulating tumor DNA (ctDNA) in plasma offers a possible noninvasive "real time" tool for tumor characterization, providing accessible genetic biomarkers for cancer diagnosis, prognosis, and response to therapy.

Abstract B38: Evaluation of the OnTarget™ system for highly sensitive mutation detection

Background: Effective non-invasive methods for patient characterization and monitoring during treatment are desired. Cell-free circulating tumor DNA in plasma is elevated in cancer patients, and can be a valuable tool for evaluating mutation profile over time. Low mutant allele fraction in a limited amount of low quality DNA makes it very challenging to accurately characterize plasma samples. Therefore, a highly sensitive and robust testing method is required for genetic characterization of circulating tumor DNA.

The goals of this study were to:

• Evaluate assay performance and limit of detection of the Boreal Genomics OnTarget™ system 18-mutation panel using human germline DNA

• Assess the relative sensitivity of the OnTarget™ system for KRAS G13D and PIK3CA H1047R mutation detection using cell line derived DNA

• Compare assay performance and sensitivity with multiple DNA input amounts

Materials and methods: DNA was extracted from normal healthy human blood and HCT116 (KRAS G13D and PIK3CA H1047R heterozygous mutant) cell line pellets. The cell line DNA was diluted with the human blood DNA to produce samples with known ratios of mutant and wild-type alleles. Samples were run with the OnTarget™ mutation detection technology platform 18-mutation panel. The platform utilizes oligo probes and a gel based system to enrich targeted mutant fragments from a DNA sample, followed by PCR amplification and next generation sequencing with the Illumina MiSeq™ platform. The 18-plex panel tests mutant allele percentage of 18 common cancer mutations in the BRAF, EGFR, KRAS, and PIK3CA genes.

Results: Repeat testing of germline DNA from multiple human donors was conducted to determine the background variability (noise) of the 18-plex assay. The mean mutant allele percentage for 10 of the 18 mutations assessed was under 0.001%. 7 of the mutations were under 0.01%, with one other mutation was just over 0.01%. Comparing mutant allele percentages of the titrated cell line DNA samples assessed limit of detection of two of the assays at the 300ng input level. The PIK3CA H104R assay detected mutant DNA over the background levels at the 0.01 and 0.001% input amount of mutant DNA. The KRAS G13D assay signal was over background at the 0.01% input, but within the assay noise at the 0.001% input. When testing the same samples at 30ng of DNA input, all mutation detection was similar, except the PIK3CA mutation was not detected at the 0.001% input amount.

Summary: The OnTarget™ mutation enrichment system followed by NGS provides high sensitivity mutation profiling of DNA with high multiplexing capabilities. The low DNA input requirement and limit of detection make it a useful platform for testing of cell-free circulating plasma DNA.

Citation Information: Mol Cancer Ther 2013;12(11 Suppl):B38.

Citation Format: Russell M. Walker, Sara Dunaj, Dalin Chan, Sunita Badola. Evaluation of the OnTarget™ system for highly sensitive mutation detection. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr B38.

Abstract A45: Biomarker assay performance: The impact of the fixation method

Recent advances in genomic technologies dramatically illustrated the complexity of cancer genomes. These discoveries provide new opportunities for drug development and ultimately better patient care by informing treatment choice decisions in addition to the insights into the mechanisms of response or relapse to therapy. Formalin fixed paraffin embedded (FFPE) tumor tissue specimens routinely collected in Oncology diagnostic practice present a number of challenges for performing molecular biomarker assays. These problems include chemical cross-linking RNA/DNA and protein, nucleic acid fragmentation, and reduced amount of extractable material. We evaluated a new fixative agent (PAXgene, Qiagen) to assess whether an alternative fixation method could alleviate problems presented by the FFPE specimens.

PAXgene preservation method was compared to FFPE and frozen tissue utilizing tumor material from xenograft and primary tumor mouse models. We compared the performance of the following techniques across three types of specimens: allele-discrimination PCR, gene expression profiling by QPCR, CNV (copy number variation) analysis, and IHC. DNA and RNA based assay performance including allele-specific PCR, gene expression profiling and CNV demonstrated similar results between frozen and PAXgene tumor specimens. Comparison of transcriptional profiling data between all there type of specimens demonstrated artifacts likely related to the formalin fixation process. Additionally, DNA extracted from PAXgene specimens had higher amount of amplifiable templates compared to DNA extracted from the FFPE specimens. Tissue sections from PAXgene fixed specimens exhibited preserved tissue morphology of acceptable quality. We carried out pAKT and PTEN IHC assays in PAXgene and FFPE tissue sections. The results demonstrated superior performance for pAKT in the PAXgene format. In the case of PTEN IHC assay, the standard FFPE based IHC assay protocol required substantial modifications.

Collecting tumor biopsies in the PAXgene format provides an opportunity of conducting both molecular and tissue based biomarker assays from a single tumor specimen.

Citation Information: Mol Cancer Ther 2013;12(11 Suppl):A45.

Citation Format: Sunita Badola. Biomarker assay performance: The impact of the fixation method. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr A45.

Putative predictive biomarkers of survival in patients with metastatic pancreatic adenocarcinoma treated with gemcitabine and ganitumab, an IGF1R inhibitor

PURPOSE

This planned exploratory analysis assessed the predictive nature of baseline circulating factors of the insulin-like growth factor (IGF) axis on the treatment effect of ganitumab (monoclonal antibody inhibitor of IGF-1 receptor) plus gemcitabine in a randomized phase II study in metastatic pancreatic adenocarcinoma.

EXPERIMENTAL DESIGN

Baseline levels of IGFs/IGF binding proteins (IGFBP) were analyzed in serum or plasma. Mutations and gene expression were analyzed in archival samples. Treatment effects between biomarker subgroups were compared for overall survival (OS). Associations of tumor markers with OS were evaluated.

RESULTS

For patients with evaluable samples, ganitumab was associated with improved OS versus placebo (HR, 0.49; 95% CI: 0.28-0.87). The treatment effect on improved OS was strong in the patient subset with higher levels of IGF-1, IGF-2, or IGFBP-3, or lower levels of IGFBP-2, but not so on the other corresponding subset. Median OS of ganitumab versus placebo in patients with higher levels of IGF-1, IGF-2, and IGFBP-3 was 16 versus 6.8 months (HR, 0.25; 95% CI: 0.09-0.67), 16 versus 5.9 months (HR, 0.24; 95% CI: 0.09-0.68), and 16 versus 6.8 months (HR, 0.28; 95% CI: 0.11-0.73), and in patients with lower IGFBP-2 levels was 12.7 versus 6.6 months (HR, 0.19; 95% CI: 0.07-0.55). Interaction between treatment and IGFs/IGFBPs in multivariate analyses suggested predictive potential for IGF-2 (P = 0.002) and IGFBP-2 (P = 0.02). KRAS mutation status and PTEN expression were not associated with OS.

CONCLUSIONS

Baseline circulating factors of the IGF axis may predict OS benefit from ganitumab plus gemcitabine in metastatic pancreatic adenocarcinoma.

Phase II study of ganitumab, a fully human anti-type-1 insulin-like growth factor receptor antibody, in patients with metastatic Ewing family tumors or desmoplastic small round cell tumors

PURPOSE

Ganitumab is a fully human monoclonal antibody against type-1 insulin-like growth factor receptor (IGF1R). An open-label phase II study was conducted to evaluate the efficacy and safety of ganitumab monotherapy in patients with metastatic Ewing family tumors (EFT) or desmoplastic small round cell tumors (DSRCT).

PATIENTS AND METHODS

Patients ≥16 years of age with relapsed or refractory EFT or DSRCT received 12 mg/kg of ganitumab every 2 weeks. Objective response rate (ORR) was the primary end point. Secondary end points included clinical benefit rate (CBR = complete + partial responses + stable disease [SD] ≥ 24 weeks) and safety and pharmacokinetic profiles of ganitumab. The relationship between tumor response and EWS gene translocation status and IGF-1 levels was evaluated.

RESULTS

Thirty-eight patients (22 with EFT; 16 with DSRCT) received one or more doses of ganitumab. Twenty-four patients (63%) experienced ganitumab-related adverse events. Grade 3 related events included hyperglycemia (n = 2), thrombocytopenia (n = 5), neutropenia (n = 2), leukopenia (n = 1), and transient ischemic attack (n = 1). There were no grade 4 or 5 treatment-related events. Of 35 patients assessed for response, two had partial responses (ORR, 6%) and 17 (49%) had SD. Four patients had SD ≥ 24 weeks, contributing to a CBR of 17%. The pharmacokinetic profile of ganitumab was similar to that observed in the first-in-human trial. Elevation of IGF-1 levels was observed postdose. EWS-Fli1 translocations were analyzed by RNA sequencing and fluorescent in situ hybridization, and novel translocations were observed in EFT and DSCRT. No apparent relationship between tumor response and IGF-1 levels or EWS gene translocations was observed.

CONCLUSION

Ganitumab was well tolerated and demonstrated antitumor activity in patients with advanced recurrent EFT or DSRCT.

Meta-analysis of genome-wide association studies in >80 000 subjects identifies multiple loci for C-reactive protein levels

BACKGROUND

C-reactive protein (CRP) is a heritable marker of chronic inflammation that is strongly associated with cardiovascular disease. We sought to identify genetic variants that are associated with CRP levels.

METHODS AND RESULTS

We performed a genome-wide association analysis of CRP in 66 185 participants from 15 population-based studies. We sought replication for the genome-wide significant and suggestive loci in a replication panel comprising 16 540 individuals from 10 independent studies. We found 18 genome-wide significant loci, and we provided evidence of replication for 8 of them. Our results confirm 7 previously known loci and introduce 11 novel loci that are implicated in pathways related to the metabolic syndrome (APOC1, HNF1A, LEPR, GCKR, HNF4A, and PTPN2) or the immune system (CRP, IL6R, NLRP3, IL1F10, and IRF1) or that reside in regions previously not known to play a role in chronic inflammation (PPP1R3B, SALL1, PABPC4, ASCL1, RORA, and BCL7B). We found a significant interaction of body mass index with LEPR (P<2.9×10(-6)). A weighted genetic risk score that was developed to summarize the effect of risk alleles was strongly associated with CRP levels and explained ≈5% of the trait variance; however, there was no evidence for these genetic variants explaining the association of CRP with coronary heart disease.

CONCLUSIONS

We identified 18 loci that were associated with CRP levels. Our study highlights immune response and metabolic regulatory pathways involved in the regulation of chronic inflammation.

New loci associated with kidney function and chronic kidney disease

Chronic kidney disease (CKD) is a significant public health problem, and recent genetic studies have identified common CKD susceptibility variants. The CKDGen consortium performed a meta-analysis of genome-wide association data in 67,093 individuals of European ancestry from 20 predominantly population-based studies in order to identify new susceptibility loci for reduced renal function as estimated by serum creatinine (eGFRcrea), serum cystatin c (eGFRcys) and CKD (eGFRcrea < 60 ml/min/1.73 m(2); n = 5,807 individuals with CKD (cases)). Follow-up of the 23 new genome-wide-significant loci (P < 5 x 10(-8)) in 22,982 replication samples identified 13 new loci affecting renal function and CKD (in or near LASS2, GCKR, ALMS1, TFDP2, DAB2, SLC34A1, VEGFA, PRKAG2, PIP5K1B, ATXN2, DACH1, UBE2Q2 and SLC7A9) and 7 loci suspected to affect creatinine production and secretion (CPS1, SLC22A2, TMEM60, WDR37, SLC6A13, WDR72 and BCAS3). These results further our understanding of the biologic mechanisms of kidney function by identifying loci that potentially influence nephrogenesis, podocyte function, angiogenesis, solute transport and metabolic functions of the kidney.

Abstract B45: Epigenetic signature of human breast cancer subtypes

Gene expression profiling has been used to extend classification of human breast cancers into five main sub-types having distinct clinical outcomes. The established prognostic markers ER, PR and HER-2 remain prominent components of this refined scheme that delineates luminal (luminal A, luminal B and HER-2) from non-luminal (basal/BRCA1 mutant and normal-like) breast cancers. Gene expression combined with immunohistochemical localization of various tumor markers in the normal mammary gland support the hypothesis that luminal and non-luminal breast tumors originate from different cell types. In the current study we explore epigenetic determinants of the different breast cancer sub-types using the genome-wide DNA methylation patterns (Illumina Infinium) of fifty human breast cancer cell lines. Principal component analysis of baseline gene expression profiles (Agilent) showed a clear separation between the luminal and non-luminal sub-types in agreement with previously published studies using a largely overlapping panel of breast cell lines. Comparative marker selection analysis using the GenePattern analysis package was then performed independently on the DNA methylation and gene expression datasets. When the results of these two analyses were compared, a statistically significant reciprocal overlap of the selected markers was observed. These results strongly suggest that a large fraction of the most robust luminal gene expression classifiers are silenced by promoter methylation in non-luminal cells, and conversely that many of the best non-luminal classifiers are silenced in luminal cells. The classifier genes indentified in the breast cancer cell line panel include the most highly referenced luminal (KRT8, ESR1, AR, TFF1, TFF3, TOB1 and XBP-1) and non-luminal markers (DSC3, VIM, SFRP1, KRT5, KRT16, KRT17, and RUNX3 that have been used to classify primary breast cancers. These striking differences in DNA methylation patterns strengthen the hypotheses that luminal and non-luminal sub-types arise from different precursor cells and that their transcriptional programs may be largely established during the process of cell specification in the mammary epithelial bi-layer. Since CpG island methylation is stable and robustly preserved in archival tissues, it is likely that a methylation signature comprised of a few key genes could be used to, for example, identify poor-prognosis, basal-type breast cancers. It is also possible that such a test would be more quantitative, accurate and reproducible than the “triple-negative” diagnosis currently based on the absence of immumohistochemical staining for ER, PR and HER-2.

Citation Information: Cancer Res 2009;69(23 Suppl):B45.

Novel association of ABO histo-blood group antigen with soluble ICAM-1: results of a genome-wide association study of 6,578 women

While circulating levels of soluble Intercellular Adhesion Molecule 1 (sICAM-1) have been associated with diverse conditions including myocardial infarction, stroke, malaria, and diabetes, comprehensive analysis of the common genetic determinants of sICAM-1 is not available. In a genome-wide association study conducted among 6,578 participants in the Women's Genome Health Study, we find that three SNPs at the ICAM1 (19p13.2) locus (rs1799969, rs5498 and rs281437) are non-redundantly associated with plasma sICAM-1 concentrations at a genome-wide significance level (P<5×10⁻⁸), thus extending prior results from linkage and candidate gene studies. We also find that a single SNP (rs507666, P = 5.1×10⁻²⁹) at the ABO (9q34.2) locus is highly correlated with sICAM-1 concentrations. The novel association at the ABO locus provides evidence for a previously unknown regulatory role of histo-blood group antigens in inflammatory adhesion processes.

Soluble Intercellular Adhesion Molecule 1 (sICAM-1) is an inflammatory marker that has been associated with several common diseases such as diabetes, heart disease, stroke, and malaria. While it is known that blood concentrations of sICAM-1 are at least partially genetically determined, our current knowledge of which genes mediate this effect is limited. Taking advantage of new technologies allowing us to interrogate genetic variation on a whole genome basis, we found that a variation in the ABO gene is an important determinant of sICAM-1 blood concentrations. Since the ABO gene is responsible for the ABO blood groups, this discovery sheds light on a new role for blood groups and offers novel mechanisms to explain the association between sICAM-1 blood concentrations and various common diseases.

Peripheral blood expression of nuclear factor-kappab-regulated genes is associated with rheumatoid arthritis disease activity and responds differentially to anti-tumor necrosis factor-alpha versus methotrexate

OBJECTIVE

To evaluate peripheral blood expression of genes regulated by nuclear factor-kappaB (NF-kappaB), a key mediator of tumor necrosis factor-alpha (TNF-alpha) signaling, in patients with rheumatoid arthritis (RA) before and during treatment with anti-TNF-alpha or methotrexate (MTX). We analyzed association of gene expression with disease activity, rheumatoid factor (RF), age, sex, disease duration, treatment modality, and clinical response.

METHODS

Sixty patients consented for RNA analysis at baseline and after 2 and 6 weeks of treatment. Disease activity was quantified using Disease Activity Score (DAS28) and C-reactive protein (CRP). Expression of 67 TNF-alpha-responsive, NF-kappaB-regulated genes was measured using Affymetrix arrays and RT-PCR.

RESULTS

Expression of 34 genes was associated with DAS28-CRP, notably S100A12/calgranulin C, IL7R, and aquaporin 3. No association was observed with age, sex, RF, or disease duration. Expression of 16 genes changed in a manner that differed significantly between treatment groups. Eleven were reduced in anti-TNF-alpha-treated patients relative to MTX, while 5 were increased. The majority of these observations were confirmed using RT-PCR. Gene expression was not associated significantly with change in disease activity.

CONCLUSION

NF-kappaB-dependent gene expression in peripheral leukocytes is highly correlated with RA activity as measured by DAS28-CRP. Expression of many genes responds differentially to anti-TNF-alpha versus MTX, suggesting fundamentally different effects on the NF-kappaB pathway. This peripheral blood expression signature provides candidate markers that could lead to development of a simple, minimally invasive pharmacodynamic assay for RA treatments directed at the NF-kappaB pathway. Combination of gene expression data with clinical scores and serum markers may provide more sensitive and predictive measures of RA disease activity.

The JAMM motif of human deubiquitinase Poh1 is essential for cell viability

Poh1 deubiquitinase activity is required for proteolytic processing of polyubiquitinated substrates by the 26S proteasome, linking deubiquitination to complete substrate degradation. Poh1 RNA interference (RNAi) in HeLa cells resulted in a reduction in cell viability and an increase in polyubiquitinated protein levels, supporting the link between Poh1 and the ubiquitin proteasome pathway. To more specifically test for any requirement of the zinc metalloproteinase motif of Poh1 to support cell viability and proteasome function, we developed a RNAi complementation strategy. Effects on cell viability and proteasome activity were assessed in cells with RNAi of endogenous Poh1 and induced expression of wild-type Poh1 or a mutant form of Poh1, in which two conserved histidines of the proposed catalytic site were replaced with alanines. We show that an intact zinc metalloproteinase motif is essential for cell viability and 26S proteasome function. As a required enzymatic component of the proteasome, Poh1 is an intriguing therapeutic drug target for cancer.

CCR8 expression identifies CD4 memory T cells enriched for FOXP3+ regulatory and Th2 effector lymphocytes

CD4+ Th2 cells are important regulators of allergic inflammation. CCR8 is thought to play a role in Th2-mediated responses, however, expression of CCR8 in peripheral blood has not been fully characterized. Using a fluorescent form of the ligand selective for CCR8 (F-CCL1), we identified the leukocytes expressing CCR8 in human, monkey, and mouse peripheral blood. CCR8 expression is primarily restricted to a subset of human CD4 memory T lymphocytes (15%). Approximately 40% of CCR8+CD4+ T cells express Th2 cytokines IL-4 or IL-13 while 13% express the Th1 cytokine IFN-gamma. In fact, 50% of all Th2, but only 5% of Th1, cells express CCR8. Upon anti-CD3/anti-CD28 mAb-mediated activation, CCR8+CD4+ T cells secrete 3- to 7-fold higher levels of IL-4, IL-5, IL-9, and IL-13 and 10- to 20-fold lower levels of IFN-gamma or IL-17, compared with CCR8-CD4+ memory T cells. Two-thirds of CCR8+CD4 T cells express cutaneous lymphocyte-associated Ag while the majority lack gut-homing receptors. CCR8+CD4+ cells express CCR7 and CD62L and are present in spleen and lymph nodes of mice. Approximately 25% of CCR8+CD4 T cells express CD25high while 20% of CCR8+CD4+ express the T regulatory cell transcription factor FOXP3 accounting for 60% of all FOXP3-expressing CD4+ T cells. In conclusion, CCR8 marks a diverse subset of CD4 memory T cells enriched for T regulatory and Th2 cells which have the potential for recruitment into sites of allergic inflammation where they could participate in the induction and regulation of the allergic response.

Correlation of serpin–protease expression by comparative analysis of real-time PCR profiling data

Imbalanced protease activity has long been recognized in the progression of disease states such as cancer and inflammation. Serpins, the largest family of endogenous protease inhibitors, target a wide variety of serine and cysteine proteases and play a role in a number of physiological and pathological states. The expression profiles of 20 serpins and 105 serine and cysteine proteases were determined across a panel of normal and diseased human tissues. In general, expression of serpins was highly restricted in both normal and diseased tissues, suggesting defined physiological roles for these protease inhibitors. A high correlation in expression for a particular serpin-protease pair in healthy tissues was often predictive of a biological interaction. The most striking finding was the dramatic change observed in the regulation of expression between proteases and their cognate inhibitors in diseased tissues. The loss of regulated serpin-protease matched expression may underlie the imbalanced protease activity observed in pathological states.