Assessment of TROP2, CEACAM5 and DLL3 in metastatic prostate cancer: Expression landscape and molecular correlates

Therapeutic approaches targeting proteins on the surface of cancer cells have emerged as an important strategy for precision oncology. To capitalize on the potential impact of drugs targeting surface proteins, detailed knowledge about the expression patterns of the target proteins in tumor tissues is required. In castration-resistant prostate cancer (CRPC), agents targeting prostate-specific membrane antigen (PSMA) have demonstrated clinical activity. However, PSMA expression is lost in a significant number of CRPC tumors. The identification of additional cell surface targets is necessary to develop new therapeutic approaches. Here, we performed a comprehensive analysis of the expression heterogeneity and co-expression patterns of trophoblast cell-surface antigen 2 (TROP2), delta-like ligand 3 (DLL3), and carcinoembryonic antigen-related cell adhesion molecule 5 (CEACAM5) in CRPC samples from a rapid autopsy cohort. We show that DLL3 and CEACAM5 exhibit the highest expression in neuroendocrine prostate cancer (NEPC), while TROP2 is expressed across different CRPC molecular subtypes, except for NEPC. We further demonstrated that AR alterations were associated with higher expression of PSMA and TROP2. Conversely, PSMA and TROP2 expression was lower in RB1-altered tumors. In addition to genomic alterations, we show a tight correlation between epigenetic states, particularly histone H3 lysine 27 methylation (H3K27me3) at the transcriptional start site and gene body of TACSTD2 (encoding TROP2), DLL3, and CEACAM5, and their respective protein expression in CRPC patient-derived xenografts. Collectively, these findings provide insights into patterns and determinants of expression of TROP2, DLL3, and CEACAM5 with implications for the clinical development of cell surface targeting agents in CRPC.

Abstract B48: Cross sectional analysis of copy loss in Barrett’s Esophagus

B48

Introduction

Barrett’s Esophagus (BE) is a pre-malignant neoplasm that increases the risk of developing esophageal adenocarcinoma (EA) (Paulson et. al. Cancer Cell 2004;6(1):11-6). To identify groups of BE patients at high risk of cancer progression, we sought to identify common chromosomal aberrations across the full risk spectrum of the condition. We implemented a meta-analysis of three studies from the Seattle Barrett’s Esophagus Project. The goal of this analysis was to combine SNP and array-CGH datasets of chromosomal loss from BE and EA samples to pinpoint regions of common loss across patients.

Methods

The three datasets included Illumina 33k SNP arrays on whole biopsies (34 patients) and surgical resections specimens (8 patients), an Illumina 317K SNP array on 12 flow purified biopsies (1 patient) and a 4,500 spot bacterial artificial chromosome (BAC) hybridization array on 157 flow purified samples (72 patients). When there were multiple samples from a patient, we included the union of all detected lesions across those samples but only counted a lesion once per patient for the purposes of analysis. All SNP arrays were run on both BE and normal (gastric or lymphocyte) samples from the same patients for comparison. All BAC arrays were run on BE samples and compared against a common reference sample.

Illumina’s BeadStudio software was used to call genotypes and produce signal intensity data in log2(Rsub/Rref) format that represents the difference in copy number of BE versus normal samples, where we assume normal samples have no aberrations. We then processed the SNP data to call regions of copy number loss using GLAD (Hupe et. al. Bioinformatics 2004;20(18):3413-22) setting logR ratio thresholds of -0.2 for single and -1.5 for double copy loss. BAC data was processed by a wavelet method (Hsu et. al. Biostatistics 2005;6(2):211-26) to call copy loss, copy gain or no aberration for every BAC. Regions of copy number loss, for the combination of both SNP and BAC datasets, were analyzed using STAC (Diskin et. al. Genome Res. 2006;16(9):1149-58) to identify statistically significant areas of loss across samples. The STAC analysis was performed at 0.5Mb resolution using 500 permutations.

Results

The combined STAC analysis identified 78 regions that were significant at the 95% confidence level, after multiple testing correction, including some previously known losses at chr. 3: 59-61MB (FHIT, FRA3B), chr.16: 77-77.5Mb (WWOX, FRA16D), chr. 9p: 21-32Mb (p16/CDKN2A/INK4a), and some newly discovered losses at chr. X: 31.5-32Mb (DMD), chr. 22: 22.5-23Mb (SMARCB1, DERL3, SLC2A11, MIF, GSTT1, GSTT2, DDT, CABIN1, SUSD2, GGT5) and chr. 18: 57-57.5Mb (CDH20).

Conclusions

Combining copy number data across studies in STAC increases sample size that may increase power to detect statistically significant regions of copy number loss across samples. We are currently working to extend the same analysis to loss of heterozygosity and copy gain in the SNP array data.

Citation Information: Cancer Prev Res 2008;1(7 Suppl):B48.

Chromosomal instability in Barrett's esophagus is related to telomere shortening

Barrett's esophagus is a useful model for the study of carcinogenesis, as the metaplastic columnar epithelium that replaces squamous esophageal epithelium is at elevated risk for development of adenocarcinoma. We examined telomere length and chromosomal instability (CIN) in Barrett's esophagus biopsies using fluorescence in situ hybridization. To study CIN, we selected centromere and locus-specific arm probes to chromosomes 17/17p (p53), 11/11q (cyclin D1), and 9/9p (p16 INK4A), loci reported to be involved in early stages of Barrett's esophagus neoplasia. Telomere shortening was observed in Barrett's esophagus epithelium at all histologic grades, whereas CIN was highest in biopsies with dysplastic changes; there was, however, considerable heterogeneity between patients in each variable. Alterations on chromosome 17 were strongly correlated with telomere length (r = 0.55; P < 0.0001) and loss of the 17p arm signal was the most common event. CIN on chromosome 11 was also associated with telomere shortening (r =0.3; P = 0.05), although 11q arm gains were most common. On chromosome 9p, arm losses were the most common finding, but chromosome 9 CIN was not strongly correlated with telomere length. We conclude that CIN is related to telomere shortening in Barrett's esophagus but varies by chromosome. Whether instability is manifested as loss or gain seems to be influenced by the chromosomal loci involved. Because telomere shortening and CIN are early events in Barrett's esophagus neoplastic progression and are highly variable among patients, it will be important to determine whether they identify a subset of patients that is at risk for more rapid neoplastic evolution.