Abstract P1-08-16: Deep sequencing of breast tumor biopsies reveals an association between pathologic complete response and reduction of TP53 clonal abundance upon brief exposure to therapy

Background: Next generation deep sequencing has revealed the existence of intra-tumor heterogeneity within subsets of breast tumors. The clinical implications of intra-tumor heterogeneity are not fully understood, however subclonal heterogeneity likely plays a role in treatment resistance. We quantify the clonal abundance of somatic mutations in breast tumor biopsies using deep targeted amplicon sequencing and assess their changes over the course of preoperative therapy (PT). We also evaluate the association of changes in clonal abundance upon brief exposure (BE) to therapy with clinical outcome.

Methods: DNA from 69 breast tumor samples obtained from BE preoperative clinical trials BrUOG 211A/211B were sequenced. Patients received a run-in dose of bevacizumab(B), nab-paclitaxel(N) or trastuzumab (T), followed by combination biologic/chemotherapy (HER2- with B/carboplatin/N; HER2+ with T/carboplatin/N). We sequenced biopsy pairs obtained pre/post 10 day exposure to run-in targeted therapy and germline and surgical tumor DNA for a subset of patients upon completion of PT. A TruSeqCustom Amplicon (Illumina) for targeted enrichment sequencing that included 1183 amplicons covering either hotspot regions or whole exonic regions from 35 commoly mutated genes in breast cancer (TCGA, Stephens, 2012; Shah); a total of 101,484 bp of the genome was represented. Sequencing was performed using IlluminaMiSeq platform and analyzed for variant calls using IlluminaBasespace. High confidence somatic mutations were identified in samples with matched germline data using VarScan2. In the absence of matched normal DNA, germline variants were eliminated using dbSNP and the 1000 Genomes Project. Minor allele frequencies (MAF) of somatic aberrations were estimated as the percentage of reads matching the variant.

Results: Approximately 5 mutations on average were found baseline and post-exposure, with a maximum mutational burden of 15 mutations in one basal breast cancer. Recurrent somatic aberrations were observed in TP53 (42%), PIK3CA (16%) and FAT4 (13%), whereas sporadic aberrations were also seen in COL1A1, PTEN, CDH1. More than 85% of samples harboring TP53 mutations exhibited MAF≥40%. Similar high clonal abundance (MAF >50%) was observed for FAT4 mutations whereas PIK3CA mutations exhibited only subclonal frequencies (MAF≤30%). We evaluated changes in clonal architecture upon BE to therapy by scoring for a change in MAF of at least 10% from baseline to post-exposure sample. We scored a total of 16 cases for clonal abundance changes in TP53 mutations upon exposure to therapy. We found 6 cases that exhibited ≥10% reduction in MAF, of which 4 achieved pCR (p = 0.03) and the remaining 2 achieved RCB I. This association was independent of therapy arm and BE regimen.

Conclusions: We found that a reduction in TP53 clonal abundance upon BE to PT is associated with clinical outcome. We are currently integrating whole genome copy-number profiles with the deep sequencing data to more accurately assess clonal architecture and changes upon exposure to therapy. Clonal changes upon BE to therapy may provide early readouts of therapy benefit and provide biological insights into mechanisms of action.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P1-08-16.

Abstract PD05-05: RNA-seq identifies unique transcriptomic changes after brief exposure to preoperative nab-paclitaxel (N), bevacizumab (B) or trastuzumab (T) and reveals down-regulation of TGF-β signaling associated with response to bevacizumab

Background: Identification of differentially expressed transcripts upon brief exposure to preoperative therapy can help determine likely response markers. We quantify and compare differential transcript expression using RNA-seq on patient samples before and after one dose of T or B or N. We also evaluate correlation of brief-exposure transcriptomic changes with response to B.

Methods: We sequenced transcriptomes of core biopsy RNA from 50 pairs of breast tumors obtained from neoadjuvant clinical trials BrUOG 211A/211B. Patients were given a run-in dose of B or N or T, followed by combination biologic/chemotherapy (HER2− with B/carboplatin/N; HER2+ with T/carboplatin/N). We sequenced biopsy pairs obtained pre/post 10 day exposure to run-in monotherapy. Paired-end sequencing was done on Illumina GAII platform using amplified total RNA with 74bp read length, yielding expression data for 22,302 genes and 35,768 transcripts. We evaluated transcriptomic changes upon brief exposure to monotherapy assuming Poisson-distributed read-counts, followed by multiple testing correction and enrichment analysis of 185 KEGG pathways. We investigated association of transcriptomic changes upon brief exposure and pathologic complete response (pCR) in the B arm. Differential expression of previously published signatures of tumor vasculature, TGF-β, β-catenin, MYC, E2F3 and RAF-MEK pathway activities were evaluated to identify associations with pCR.

Results: PAM50-based clustering showed individual samples cluster together, demonstrating that tumor subtypes do not change over the 10-day treatment. We identified unique transcripts that were significantly differentially expressed in each therapy arm (p < 0.05;FDR<0.1). Significant down-regulation of tumor vasculature-related genes was seen in B samples (p = 0.05). We found 1024 genes whose significant differential expression correlated with pCR in the B arm (Mann-Whitney p-val<0.05; abs log2-fold change≥0.5). Only 4 KEGG pathways, TGF-β signaling, Cell Cycle, DNA Replication and Steroid Biosynthesis were found to be enriched (p ≤ 0.05) in the pCR-associated gene list, and displayed significant down-regulation of member genes within the pCR group. To further evaluate the enrichment results, we used several published pathway activity gene signatures. Interestingly, clustering of the B-treated samples using a TGF-β response signature strongly clustered pCR cases due to down-regulation of TGF-β activity in that group (p = 0.004). We found that the TGF-β signature was most informative of pCR when compared to E2F3, RAF-MEK, β-catenin and MYC signatures in the B arm.

Conclusions: This is the first study to compare differential gene expression upon brief exposure across therapies using RNA-seq technology. The association of TGF-β activity with pCR in B arm was identified using both a bottom-up statistical approach and with a previously published TGF-β activity signature. The unique aspects of transcriptional response to each treatment and the association of transcriptional changes with response underscore the value of the brief-exposure paradigm to identify markers of neo-adjuvant therapeutic response.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr PD05-05.

P3-06-04: Sno/miRNA Expression Via Next Generation Sequencing: Variation in Patients before and after Treatment

Background

Aberrant expression of small RNA molecules has been shown in breast cancer. It is yet unclear if variation exists in small RNA molecule expression in response to treatment. Since next generation sequencing offers more globally sensitive detection of sno and miRNAs, we performed an RNA-seq study to explore patients pre- and post- brief exposure to treatment.

Methods: We sequenced transcriptomes of frozen biopsy samples from 8 breast cancer patients enrolled in a clinical trial for neoadjuvant therapy using trastuzumab (HER2 positive) or bevacizumab (HER2 negative) with chemotherapy. Tumor core biopsies were taken before and after 10 days of either biologic or nab-paclitaxel treatment and stored in OCT compound. Total RNA was extracted and libraries were constructed for the 16 samples using TruSeq (Illumina). We performed 74bp paired-end sequencing with the Illumina GAII platform. Sequences were aligned to the sno/miRNA track (containing 928 miRNAs and 413 snoRNAs) in UCSC and read counts were determined using Bowtie. We performed differential miRNA and snoRNA expression analysis pair-wise in all pre- and post-therapy samples. Given that miRNA deregulation relies on their protein-coding gene targets, we analyzed the predicted targets of the significantly varying miRNAs for functional enrichment.

Results: Each sample had on average 46 million paired-end reads, of which on average 70% were mapped to the human genome. Overall, we detected 138 miRNAs in at least one sample, with each sample expressing 33 miRNAs on average. We detected a total of 11 miRNAs (7%) that showed significant differential expression with treatment. Interestingly, 6 of these miRNAs varied in all patients. The predicted targets of these miRNAs were enriched in DNA-dependent transcription, gene expression, cell proliferation and cell communication. Similarly, we detected 202 snoRNAs in at least one sample, with each sample expressing 87 snoRNAs on average. Of these, we found 21 snoRNAs (10%) to vary significantly upon treatment and 6 of these snoRNAs showed expression changes in all patients.

Conclusions: These results suggest that variation in sno/miRNA expression may play a role in response to treatment. The consistent variation of sno/miRNAs in response to treatment suggests shared small RNA-mediated mechanisms. If validated, these results suggest that next generation sequencing technologies will allow lead to improved methods of stratifying, subclassifying and managing breast cancer.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P3-06-04.

P3-06-01: Next Generation RNA Sequencing Reveals Changes in Gene Expression and Alternative Splicing upon Brief Exposure to Therapy in Early Breast Cancer

Background

The use of next generation RNA sequencing (RNA-seq) allows for the characterization of the transcriptome at levels of detail unachievable by array-based technologies. RNA-seq analysis can quantify expression of novel transcripts and alternatively spliced isoforms in addition to known genes. Alternative splicing allows for flexibility in production of protein isoforms and is frequently dysregulated in cancer. As splice variants may play a role in response to therapy (Solier, et al, Cancer Res., 2010), we studied differential gene and isoform expression in breast cancers after one dose of treatment, prior to a course of preoperative therapy.

Methods: We sequenced transcriptomes of core biopsy samples from 8 breast cancer patients enrolled in a preoperative clinical trial using trastuzumab (HER2 positive) or bevacizumab (HER2 negative) with chemotherapy. Tumor core biopsies were taken before and after 10 days of either biologic or nab-paclitaxel treatment and stored in OCT compound. Total RNA was extracted, amplified and libraries were constructed for the 16 samples using TruSeq (Illumina). Paired-end sequencing was performed on the Illumina GAII platform with read length of 74bp. Sequence data was mapped using TopHat and transcript abundance in FPKM units (Fragments per kilo-base of mRNA per million reads) estimated for a total of 22,160 unique genes and 34,449 unique transcripts from RefSeq. Differential expression of transcripts between baseline and 10-day samples was estimated using t-statistics with read-counts modeled as a Poisson distribution. Differentially expressed transcripts were selected at a significance level of 0.05 after multiple testing correction.

Results: Each sample had on average 46 million paired-end reads, of which on average 70% were mappable to the human reference genome (UCSC, hg19). A median of 138 (range 68–948) transcripts varied with treatment. GO analysis showed enrichment of cell-adhesion, apoptosis, differentiation and cell proliferation pathways. Interestingly, the isoforms of several known cancer genes such as TP53 were seen in all treatment types. Certain isoforms were only seen to change upon brief exposure to chemotherapy such as BCL2 whereas TNF ligand and PCDH isoforms showed significant change only with biologic agents.

Conclusions: These results suggest that recurrent changes in both canonical genes and splice variants occur over the course of treatment in early breast cancer. This underscores the value of RNA-seq to provide novel information that may be clinically useful. Brief exposure to monotherapy prior to combination treatment may provide important mechanistic insights and produce predictive biomarkers. Biologic treatments may produce unique changes that can only be discovered with novel next generation sequencing techniques.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P3-06-01.

P1-06-23: Changes in Gene Expression after One Dose of Trastuzumab (T) in HER2+ Breast Cancer Cell Lines Predict Novel Pathways of Response in HER2 Positive Early Stage Breast Cancer

Introduction: Trastuzumab is a targeted therapy against the HER2 cell surface receptor and has greatly improved prognosis for HER2+ breast cancer patients. Despite decades of research, the mechanism of action of T remains unclear and mechanisms of resistance have not been adequately defined. We sought to determine if models of response and resistance in vitro could identify biomarkers in vivo in HER2+ early breast cancer.

Methods: BT474 and UACC812 cell lines were treated with 10ug/ml T for 0 and 24 hours. Fresh tumor core biopsies were taken at a 2 week timepoint after a single dose of T (8mg/m2) from 80 HER2−overexpressing, early breast cancer patients enrolled on a clinical trial of T>T+C. Nucleic acids were extracted using Qiagen AllPrep and were analyzed with Illumina HT12v3 Beadchip arrays. All arrays were processed at the Yale Center for Genome Analysis (West Haven, CT). Clinical response at surgery was defined as pathologic complete response (pCR), objective response (CR+PR=OR) and non-response (SD+PD=NOR) by RECIST criteria. Gene expression was analyzed in Bioconductor using LIMMA analysis. Pathway analysis was performed using the DAVID bioinformatics resource.

Results: We identified gene expression signatures of T response and resistance in HER2+ breast cancer cell lines across 24-hour exposure to trastuzumab. 180-genes changed significantly in a T-sensitive HER2+ cell line (BT474) and 58 genes changed significantly across treatment in a T-resistant HER2+ cell line (UACC812). We applied these signatures to gene expression profiles from early stage HER2+ breast tumors treated with a single dose of T. The BT474 T-responsive signature was enriched among the changes in expression across treatment for responsive patients. The expression change for the BT474 signature genes was also able to partially cluster responsive and resistant breast tumors by outcome. A subset of the UACC812 T-resistance signature was also enriched in the differential between responsive and resistant tumors prior to T treatment.

Pathway analysis based on the direction of change of genes in pCR and sensitive (BT474) cell lines found gland development/differentiation (enrichment score=4.5), DNA synthesis (ES=4.0), chaperone (ES=2.8) and transcriptional machinery (ES=2.2) to be coordinately downregulated in both sensitive cell lines and tumors. This suggests that the downregulation of differentiation pathways seen in our ‘pCR signature’ (Harris etal: AACR 2011) is not an epiphenomenon of cell loss. There were no significant pathways upregulated in both sensitive tumors and cell lines, however discordant genes were enriched in chromatin regulation pathways (ES=4.1). Of note, our previous findings of amplicon gene downregulation in pCR tumors, yet upregulation in cell lines points to a novel mechanism of chromatin modulation heretofor undiscovered in response to T.

Conclusions: These results demonstrate the value of iterative study of in vitro and in vivo response mechanisms in HER2 cell lines and tumors, and the importance of brief exposure studies in understanding the mechanism of response to T, and other targeted therapies.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P1-06-23.

Evaluation of ER/PR and HER2 status by RNA sequencing in tissue core biopsies from preoperative clinical trial specimens

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Background: Next-generation sequencing for measuring RNA (RNASeq) offer increased sensitivity, dynamic range and provide unbiased detection of all transcripts. To evaluate the clinical utility of such methods, we sequenced entire transcriptomes from fresh-frozen biopsies in a cohort of 120 patients enrolled on a preoperative therapy trial receiving carboplatin, nab paclitaxel and either bevacizumab (HER2-) or trastuzumab (HER2+).

Methods: Total RNA was extracted and amplified from frozen breast core biopsies and libraries constructed using TruSeq (Illumina). Sequencing was performed on the Illumina GAII platform. 75bp reads were mapped using Tophat and transcript abundance in FPKM units (Fragments per kilo-base of mRNA per million reads) calculated using Cufflinks. CLIA approved assays were performed for ER, PR, HER2 (IHC+/- FISH) on patient tumors. Four tumors from each subtype (ER +ve/HER2 -ve; HER2 +ve; ER/HER2 -ve) were analyzed for correlation with clinical status. PAM50 classification will be provided for verification of molecular subtypes.

Results: RNA-Seq library construction/sequencing were successful in 12/12 samples with 50-90% reads mapped. ER +ve tumors ranged in FPKM values from 1.76-22.67 and ER -ve tumors ranged from 0.00-0.79. i.e. ER RNASeq measurements can separate clinical ER status. HER2 +ve tumors ranged in FPKM values from 2.62-21.71 and HER2 -ve tumors from 0.21-1.79. Of note, 7/8 HER2 -ve tumors ranged from 0.21-0.87 with one ‘outlier’ at 1.79±0.3. This outlier was HER2 IHC 2+, FISH ratio 1.1 with 45% of tumor cells with polysomy chromosome 17. Correspondence of ER/PR and HER2 status with molecular subtyping by PAM50 analysis will be presented.

Conclusions: RNASeq has potential to provide in depth analysis of the breast cancer transcriptome and a single analysis test for standard markers. In addition, RNASeq may uncover unexpected expression patterns in conventionally-defined HER2 -ve tumors. If reproducible in larger datasets, this technology may provide both standard and novel information previously unavailable to oncologists and their patients.

Abstract PD07-08: Integrated Genomic Analysis before and after Brief Exposure to Trastuzumab (T): The11q13 and 17q12 Amplicons Are Associated with Response to T+Chemotherapy in Early Stage HER2 Positive Breast Cancer

Background: The receptor tyrosine kinase HER2 is overexpressed in 18-20% of breast cancers and is the target of the highly effective therapy, trastuzumab. Coamplicons are frequent in HER2 amplified tumors, yet their role in response to T is not defined. To identify amplicons which might predict response to T in patients we performed gene expression and copy number analysis in tumor tissue from a preoperative trial with brief exposure to T, followed by T+C.

Methods: Fresh tumor core biopsies were taken before at a 2 week timepoint after a single dose of T (8mg/m2) from 80 HER2-overpressing, early breast cancer patients enrolled on a clinical trial of T>T+C. Nucleic acids were extracted using Qiagen AllPrep and were analyzed with Illumina Ref8 and Illumina QUAD 610 SNP arrays. Eight commonly amplified regions (11q13, 14q32, 17q12, 20q13, 21q22, 8p22, 8q24) were identified by FISH probe coordinates and copy number calculated using the GPHMM algorithm. Amplification was defined as 4 or more copies of the amplicon. Gene expression was analyzed in Bioconductor using LIMMA analysis. Genomic biomarkers were compared pathologic complete response (pCR) vs objective response (CR+PR) and non-response (SD+PD) by RECIST criteria at the surgical timepoint.

Results: There were 50 tumor pairs with adequate RNA for gene expression and 40 baseline tumors for copy number analysis with 28 paired samples. In the 40 baseline biopsies, the 11q13 amplicon was present in 14/40 (35%) of tumors but never seen in tumors with a pCR (t-test; p=0.004975). Of note, in the tumors with amplification of 11q13 there was no evidence of change in copy number after exposure to T, however numbers were small (7 pairs). Gene expression of the 11q13 region showed no significant change in common amplicon genes after one dose of T. The 17q12 amplicon, which harbors the HER2 locus, was amplified in 35/40 (87.5%) of cases - copy number was not associated with response, however, HER2 and GRB7 gene expression levels significantly declined in pCR tumors compared with <pCR (p=0.003).

Conclusions: Integrated genomic analysis after brief exposure to T may provide useful predictors for response to T+C in early stage, HER2 positive breast cancer.

Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr PD07-08.

Abstract P6-15-09: Insulin-Like Growth Factor Receptor I (IGF1R) Inhibitors May Be Synergistic with Chemotherapy in Basal Breast Cancer

Background: Preclinical and clinical data show associations between basal breast cancer (BBC) and obesity, insulin resistance and metabolic syndrome suggesting a role for the insulin-like growth factor (IGF) pathway in this disease. We hypothesized that IGF1R targeted therapy will be active in BBC and would enhance the activity of chemotherapeutic agents. We evaluated AG1024, a kinase inhibitor of IGF1R, and Figitumumab, a human anti-IGF1R antibody, in BBC cell lines as monotherapy and in combination with conventional chemotherapeutic agents, doxorubicin or paclitaxel.

Materials and Methods: To evaluate the effect of AG1024, Figitumumab, doxorubicin and paclitaxel, growth assays were conducted using four BBC cell lines (MDA-MB-231, MDA-MB-468, SUM149 and BT20) and the ER positive control cell line, MCF7. Cells were harvested, resuspended in OptiMEM and plated in triplicate at optimal cell densities (50-70% confluent). AG1024 (0-µM), Figitumumab (0-0.585μM), doxorubicin (0-0µM) and paclitaxel (0-20nM) were added after 24-hour incubation. On Day 5, at 70-90% confluence, the cell proliferation Reagent WST-1 (Roche) was added, cells incubated and OD measured as directed by the manufacturer. The percent of surviving cells in each test well was calculated as follows: OD drug-treated well/untreated mean x 100. Each drug combination was assessed in triplicate. Using CalcuSyn (BioSoft), the Median Effects method described by T-C Chou and P. Talaly was used to determine whether or not drug combinations were synergistic or additive. A combination index (CI) <0.90 = synergism, between 0.90 and 1.10 = additive and >1.10 = antagonism. The CI values reported were observed in two or more experiments.

Results: AG1024 produced dose-dependent growth inhibition in all BBC cell lines.

Cytotoxicity of AG1024 (40uM) after a five day incubation.

The hormone-receptor positive MCF7 cell line was the least sensitive to AG1024. Figitumumab had no activity as monotherapy on BBC and control cell lines. Combination therapy with AG1024 and chemotherapy produced synergistic or additive effects in all BBC cell lines. For instance, combining 01µM doxorubicin with 1µM AG1024 produced a synergistic effect in all BBC cell lines except MDA-MB-468.

Combination Indices (CI) of combination therapy experiments.

Similarly, Figitumumab and chemotherapy produced additive or synergistic growth inhibition. Further data on IGF1R levels and phosphotyrosine activity will be presented

Conclusions: AG1024 causes a dose-dependent decrease in cell viability in BBC cell lines produced synergistic cytotoxicity with paclitaxel and doxorubicin. Figitumumab alone failed to have cytotoxic effects on BBC cell lines, however additive or synergistic effects were seen with paclitaxel or doxorubicin in combination with Figitumumab. The combination of IGF1R inhibitors with chemotherapy in BBC should be further explored.

Abstract PD01-06: Activation of the Insulin-Like Growth Factor Pathway Distinguishes African American from European American Patients with Triple-Negative Breast Cancer by Gene Expression Profiling

Background: Triple-negative breast cancer (TNBC) is characterized by high histologic grade, high rates of distant recurrence and a poor overall prognosis. Treatment options are limited due to the lack of specific targets such as hormone receptors or HER2 which drive other breast cancer subtypes. Epidemiological studies show a markedly higher prevalence of TNBC in young women of African ancestry. In this study we sought to identify transcriptional modules that are differentially regulated between African American (AA) and European American (EA) women. Methods: A hospital-based cohort of 130 breast cancer patients diagnosed between 1985 and 2007 was selected by an institutional pathology database (CoPath) search for invasive, triple-negative breast cancer and enriched for patients of African American ethnicity. Racial distribution 47% AA, 33% EA, 8% Hispanic and 12% other or unknown. Clinical data was extracted from the Yale and Bridgeport Hospitals Tumor Registry following IRB approval. Invasive disease was identified on H&E sections and an average of 3 tissue cores from FFPE blocks were subjected to RNA extraction using the RecoverAll Total Nucleic Acid Isolation kit (Applied Biosystems) following the manufacturer's protocol. The extracted material was hybridized to Whole Genome-DASL assays (Illumina). Statistical analysis of gene expression data was carried out using Bioconductor/R software. A set of relevant signatures was selected by enrichment analysis of modules identified by principal component analysis. Signature scores were computed as Pearson correlation between the signature vector of gene contributions and each sample's expression profile for these genes. Results: African American patients show a significantly higher activation score for a 273-gene Insulin-like Growth Factor 1 signature compared with European American patients (stage-adjusted p=0.0006). Similarly, samples from AA patients show higher scores in a BRCA 1 mutant signature defined by van ‘t Veer and colleagues in 2002 (p=0.001) and in a luminal progenitor (CD49f+EpCAM+) signature from Lim et al. (2009) (p=0.01). The Genomic Grade Index (GGI, Sotiriou et al. 2006) in samples from AA patients was also found to be significantly elevated (p=0.0007). Conclusions: Our findings indicate significant activation of the IGF pathway in AA compared to EA patients with TNBC. The 273-gene IGF signature was associated with poor differentiation and high proliferation in an independent cohort, which is in agreement with the high GGI score observed in AA patients. BRCA1 mutant-like and luminal progenitor-like properties in AA tumor samples further support this hypothesis as they both are related to basal-like histology which constitutes an aggressive subgroup of triple-negative tumors. These data suggest that African American patients may benefit from IGF pathway inhibiting drugs.

Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr PD01-06.

CALGB 150002: Correlation of HER2 and chromosome 17 (ch17) copy number with trastuzumab (T) efficacy in CALGB 9840, paclitaxel (P) with or without T in HER2+ and HER2- metastatic breast cancer (MBC)

1009

Background: Accurate assessment of HER-2 is critical in MBC and predicts benefit from T. We have previously shown low level amplification of HER-2 associated with ch17 polysomy is common in IHC 2+ cases that are FISH(-). However, the clinical relevance of this is unknown. Methods: CALGB 150002, a correlative companion to 9840, was designed to assess the predictive role of HER-2 in MBC pts treated with weekly vs q 3W P ± T. Pts HER-2(-) locally were randomized to ±T. 585 pts were enrolled in 9840; 304 blocks were available for central analysis with DAKO HercepTest (IHC) and Pathvysion (FISH). Logistic regression was used to test HER-2:ch17 ratio and HER-2 copy # as predictor of response rate (RR) to T in HER-2(+) pts. 1-sided Fisher’s Exact Test was used to compare RR of P vs P+T in pts with ch17 polysomy on central testing (>2.2 copies ch17/cell), but defined as HER-2(-) locally and randomized to T. Results: In pts HER-2(+) locally, FISH is a significant predictor of RR to P+T. A higher HER-2:ch17 ratio is associated with a higher RR by logistic regression (p=0.033, n=95). No interaction is seen between HER-2 and P schedule, p=0.71. On central testing of cases IHC(-) locally, 16/140 (11%) were IHC 3+ and 5/133 (4%) HER-2 amplified. In 21 HER-2(-) cases reclassified as HER-2 3+ or FISH (+) centrally, we do not find a difference in RR to P vs P+T. However among 133 cases HER-2(-) locally and central FISH(-) we find 32 with ch17 polysomy (copy # ch17 = 2.2); 12 treated with P alone, and 19 with P+T (see table for RR). Conclusions: These data suggest a higher RR to P+T in HER-2(+) pts with a higher HER-2:ch17 ratio, consistent with a relationship between RR to T and HER-2 copy #. In FISH(-) cases we note an increased RR to P+T vs P in cases with ch17 polysomy, typically reported clinically as HER-2(-). This analysis suggests that T might be effective in a subpopulation of breast cancer conventionally defined as HER-2(-), but in fact displaying low level HER-2 amplification.

[Table: see text]

[Table: see text]

Deletions of PURA, at 5q31, and PURB, at 7p13, in myelodysplastic syndrome and progression to acute myelogenous leukemia

Deletions or monosomy of chromosomes 5 and 7 are frequently observed in myelodysplastic syndromes (MDS) and acute myelogenous leukemia (AML). In this study two genes, PURA and PURB, encoding functionally cooperative proteins in the Pur family, are localized to chromosome bands 5q31.1 and 7p13, respectively. One or both of these loci are shown to be hemizygously deleted in 60 MDS or AML patients using fluorescence in situ hybridization (FISH). High-resolution mapping of PURA localizes it approximately 1.1 Mb telomeric to the EGR-1 gene. Frequency of PURA deletion and segregation with EGR-1 indicate that PURA is within the most commonly deleted segment in myeloid disorders characterized by del(5)(q31). No mutations have been detected within the coding sequence of PURA. Concurrent deletions of PURA and PURB occur in MDS at a rate nearly 1.5-fold higher than statistically expected and in AML at a rate > 5-fold higher. This novel simultaneous deletion of two closely related gene family members may thus have consequences related to progression to AML. Pur alpha, an Rb-binding protein, has been implicated in cell cycle control and differentiation, and Pur alpha and Pur beta are reported to function as heterodimers. Alterations in these genes could affect a delicate balance critical in myeloid development.

Chrysotile asbestos fibers mediate homologous recombination in Rat2 lambda fibroblasts: implications for carcinogenesis

Asbestos fibers are widespread environmental carcinogens whose mutagenicity is now established. Nonetheless, the molecular nature of these mutations and the mechanisms by which they accelerate carcinogenesis remain poorly understood. We have assessed the ability of asbestos fibers to promote homologous recombination, a potent mechanism for generating intrachromosomal rearrangements, such as deletions, and mitotic recombination. For this, we have developed a new assay which determines the extent to which a marker gene present in DNA introduced by asbestos can recombine with homologous genes residing in a transfected cell. We have demonstrated that Calidria chrysotile fibers are mutagenic and are able to mediate transfection of molecularly marked mutant lacI genes in a manner that results in their preferential recombination with homologous wild-type genes in the transfected cell. Asbestos induced recombination events may play a significant role in asbestos mutagenesis and carcinogenesis, and promotion of recombination may underlie the well-recognized synergy of asbestos with other carcinogens.