Abstract P4-02-06: Intratumoral and peritumoral MRI signatures of HER2-enriched subtype also predict pathological response to neoadjuvant chemotherapy in HER2+ breast cancers

Background: Applying the PAM50 classifier to targeted RNA-Sequencing data allows HER2+ tumors to be sub-categorized into intrinsic breast cancer subtypes. HER2+ breast cancers belonging to the HER2-enriched [HER2-E] subtype exhibit the highest rate of response to neoadjuvant therapy with combination of HER2-blockade and chemotherapy, as well as dual-HER2 blockade alone. A non-invasive predictor of PAM50 subtype from clinical dynamic contrast-enhanced MRI [DCE-MRI] could provide valuable clinical guidance in the treatment of HER2+ breast cancer. In this work, we identify a set of computer-extracted heterogeneity features computed within the lesion and its surrounding peritumoral region capable of distinguishing HER2-E from other HER2+ breast cancers [Non-HER2-E]. We then demonstrate that this imaging signature of HER2-E is also predictive of pathological complete response [pCR] in an independent HER2+ testing set, consistent with the HER2-E subtype's elevated response to HER2-targeted therapy.

Methods: The training set consisted of 42 HER2+ patients with both 1.5 or 3 T DCE-MRI and targeted RNA sequencing collected prior to neoadjuvant treatment from a multicenter trial [BrUOG 211B, n=35] and The Cancer Genome Atlas-Breast Cancer project [TCGA-BRCA, n=7]. Intrinsic subtypes were assigned by unsupervised hierarchical clustering of the PAM50 gene set. 19 patients were determined to belong to the HER2-E subtype, while the remaining 23 represented non-HER2-E subtypes [19 HER2-Luminal, 4 HER2-basal]. Lesion boundaries were annotated by an expertly trained radiologist and expanded to 5 annular peritumoral regions in 3 mm increments out to a maximum radius of 15 mm. Computer-extracted heterogeneity features were computed voxelwise within intratumoral and peritumoral regions by first order statistics. A top HER2-E-associated feature from each region was identified by Wilcoxon feature selection and used to train a diagonal linear discriminant analysis [DLDA] classifier to predict HER2-E in a 3-fold cross-validation setting. This classifier was then applied to pCR prediction from DCE-MRI in a testing set of 28 HER2+ patients with available post neoadjuvant chemotherapy surgical specimens at one institution. 16 patients achieved pCR (ypT0/is), while the remainder had partial or no response (non-pCR).

Results: A combination of heterogeneity features within the intratumoral region and annular peritumoral regions out to 12 mm from the tumor yielded optimal results within the training set, with an average HER2-E prediction AUC of .77 +/- .03. When applied to response prediction in an independent testing set, this HER2-E classifier was predictive of pCR (AUC = .72).

Conclusions: Computer-extracted heterogeneity features calculated within the tumor and the surrounding peritumoral environment on DCE-MRI were able to distinguish the HER2-E PAM50 intrinsic subtype from other HER2+ breast cancers. HER2-E was characterized by elevated expression of intratumoral and peritumoral heterogeneity features, indicating a more disordered imaging phenotype within and around the tumor. Additional independent validation of these findings is needed.

Citation Format: Braman N, Prasanna P, Singh S, Beig N, Gilmore H, Etesami M, Bates D, Gallagher K, Bloch BN, Somlo G, Sikov W, Harris L, Plecha D, Varadan V, Madabhushi A. Intratumoral and peritumoral MRI signatures of HER2-enriched subtype also predict pathological response to neoadjuvant chemotherapy in HER2+ breast cancers [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P4-02-06.

Abstract P2-05-06: Not presented

This abstract was not presented at the symposium.

Abstract P1-05-09: Association of co-amplicons with immune infiltration in subtypes of HER2-Positive breast cancer

Background: HER2+ breast cancers are heterogeneous at both clinical and molecular levels. We and others have determined that the HER2-Enriched subtype exhibits the highest rate of pathologic complete response (pCR) to neoadjuvant chemotherapy and trastuzumab (T), while the HER2-Basal subtype is resistant to anti-HER2 therapy (Carey et al, JCO 2015;Varadan et al, CCR 2016). Additionally, we reported that signatures of immune cell infiltration and immune cell subsets evaluated after one dose of T can predict pCR to preoperative T and chemotherapy (Varadan et al, CCR 2016). Given recent evidence for improved immune response with increasing mutational load, we chose to characterize the association of somatic mutations and copy-number alterations with subtypes of HER2+ breast cancer and immune modulation after one dose of T.

Methods: Fresh tumor core biopsies were taken at baseline and 2 weeks after one dose of either T or nab-paclitaxel (N) from 60 patients with stage II-III HER2+ cancers enrolled on a multicenter trial (BrUOG 211B). All patients then received 18 weeks of T+N+carboplatin. PAM50 subtyping was performed using gene expression data from patient tumor biopsies and tumors were classified into HER2-Enriched, HER2-Luminal and HER2-Basal subtypes. Whole-exome sequencing (WES) was performed on a total of 86 samples (49 baseline, 37 brief-exposure), sequenced at an average depth of 90X. Somatic mutations were detected by applying multiple mutation-detection algorithms on the WES data, followed by stringent quality control using public and in-house variant databases, and mutation data curated from 11,000 tumors sequenced by the TCGA. Somatic copy-number alterations were estimated using a published algorithm, ENVE (Varadan et al, Genome Med 2015) that robustly detects somatic copy-number alterations in WES tumor profiles. We employed previously defined gene-expression signatures (Varadan et al, CCR 2016) of total immune infiltration and immune cell subsets, to assess for association with genomic aberrations.

Results: HER2-Basal tumors exhibited lower average copy number for HER2 and were less likely to have high-level amplifications of co-amplicons (e.g. 11q13, 20q13) with the exception of the MYC amplicon (8q24). They also exhibited a non-significant (P=0.33) trend towards higher mutational burden (Avg=85) compared to HER2-Luminals (Avg=79). A majority of somatic mutations (62%, 2282/3666) persisted after a single-dose of either T or N, while 17% (624/3666) were not detectable after brief-exposure. There was no association between immune infiltration and mutational burden in any HER2 subtype. Tumors harboring FGFR1 (8p11) amplifications exhibited higher gene-signature levels for macrophages (P=0.0073) and T-cells (P=0.0493) but not B-cells (P=0.213).

Conclusions: The HER2-Basal subtype is less likely to respond to trastuzumab-based neoadjuvant therapy and exhibits lower numbers of common amplicons. The disappearance of mutations after brief-exposure to therapy may be due to either tumor heterogeneity/sampling or clonal selection. The association of 8p11 amplifications with increased T-cell infiltration suggests that this amplicon may play an immunogenic role in HER2+ breast cancer. These results warrant further investigation in larger cohorts.

Citation Format: Singh S, Gilmore H, Somlo G, Abu-Khalaf M, Sikov W, Harris L, Varadan V. Association of co-amplicons with immune infiltration in subtypes of HER2-Positive breast cancer [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P1-05-09.

Abstract P6-03-08: Novel recurrent lncRNA fusions detected in breast cancer using RNA-Seq technology in a neoadjuvant setting

Background: Recent discoveries of recurrent and targetable gene fusions in breast cancer suggest the need to characterize the functional significance of such genomic aberrations within larger cohorts. We quantified fusion transcript expression in patient samples using RNASeq to identify recurrent gene fusion events in breast cancer as well as study the fusions post-brief exposure to mono-therapy.

Methods: We sequenced transcriptomes of core biopsy RNA from 130 breast tumors obtained from brief-exposure preoperative clinical trials BrUOG 211A/211B. HER2- patients were treated with brief exposure to bevacizumab (B) or nab-paclitaxel (nP) followed by treatment with B/nP/carboplatin while HER2+ patients received brief exposure to trastuzumab (T) or nP followed by T/nP/carboplatin. Paired-end sequencing on 75 baseline biopsies and 55 post-exposure biopsies using amplified total RNA yielded 55 million reads on average perlsample. Fusion transcript abundance was evaluated using 2 pipelines, TopHat-Fusion and deFuse, due to their complementary strategies in fusion detection. We eliminated gene-pseuodogene fusion pairs as likely false positives arising due to alignment artifacts. Fusions that met 1 or more of the following 3 criteria were considered high confidence:

i) Called by both deFuse and TopHat. ii) Called by deFuse with probability >95% iii) Called by TopHat with > 15 reads supporting the fusion.

Results: We identified high confidence gene fusions, detected by both TopHat and deFuse, in 73 of the 75 baseline biopsies with 16 fusions on average per sample. We looked for modulation of gene fusions upon brief exposure to therapy in 55 patients that had post exposure biopsy data and found that out of the 545 high confidence fusions detected across these patients, 62 (11.37%) of the fusions were found to be still present after the therapy exposure. For the recurrent fusion analyses, we considered the 75 baseline samples. We found a total of 1158 unique candidate fusions. Out of these, 116 (10%) were recurrent in more than 1 patient. After further filtering, we were able to narrow down to 9 (0.77%) fusions that were reliable since they were predicted by both the algorithms in different patients. 2 of these 9 fusions involved GAS5 as a partner gene. GAS5 have been studied to have a role in apoptosis and its down-regulation has been associated with cell proliferation, which makes it a very interesting fusion candidate.

Conclusions: We find that gene fusions in breast cancer are highly heterogeneous but are enriched with cancer-related pathway genes. This is the first study to report 2 novel gene-lincRNA fusion transcripts: MDN1-GAS5 and GABRB3-GAS5. Both these fusions are called in the baseline & post-therapy for atleast 1 patient (different patients each). GAS5 has been found as participating in a fusion in B-cell lymphoma. We are currently in the process of validating the fusion calls using qRT-PCR. The heterogeneity of detected fusions suggests that multiple mechanisms could underlie the selective advantage of tumor cells expressing fusion transcripts. The brief-exposure preoperative paradigm provides a unique opportunity to evaluate modulation of fusion transcripts that can shed light on their functional importance.

Citation Format: Agrawal V, Varadan V, Banerjee N, Miskimen K, Vadodkar A, Abu-Khalaf M, Sikov W, Harris L, Dimitrova N. Novel recurrent lncRNA fusions detected in breast cancer using RNA-Seq technology in a neoadjuvant setting. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P6-03-08.

Abstract P4-04-07: Heterogeneous gene fusions detected by RNASeq show enrichment of insulin signaling pathway genes in breast cancer

Background: Recent discoveries of recurrent and targetable gene fusions in breast cancer suggest the need to characterize the functional significance of such genomic aberrations within larger cohorts. We quantify fusion transcript expression in patient samples using RNASeq and evaluate their functional significance using biological pathway enrichment analysis.

Methods: We sequenced transcriptomes of core biopsy RNA from 97 breast tumors obtained from brief-exposure preoperative clinical trials BrUOG 211A/211B. HER2- patients were treated with brief exposure to bevacizumab (B) or nab-paclitaxel (nP) followed by treatment with B/nP/carboplatin while HER2+ patients received brief exposure to trastuzumab (T) or nP followed by T/nP/carboplatin. Paired-end sequencing on 55 baseline biopsies and 42 post-exposure biopsies using amplified total RNA yielded 55 million reads on average per sample. We assigned RNASeq-based PAM50 subtypes for each of the samples using standard methodology. Fusion transcript abundance was evaluated using two independent pipelines, TopHat and deFuse, due to their complementary strategies in fusion detection. We eliminated fusions of genes with their respective pseudogenes as likely false positives arising due to alignment artifacts. TopHat fusion calls with total supporting reads ≥10 and deFuse calls with probability of fusion ≥0.7 were considered reliable.

Results: We identified high confidence gene fusions, detected by both TopHat and deFuse, in 30 of the 55 baseline biopsies (54.4%), with 3.3 fusions on average per sample and a maximum of 10. Fusions were predominantly associated with chromosomal aberrations (75%), with putative deletions responsible for 32% of fusions and translocations responsible for 43%. We find a high level of fusion transcript heterogeneity within breast cancers, detecting a total of 80 fusions across the 30 samples with only three fusions recurrent in two samples with high expression in each: MDN1-GAS5 in two basal breast cancers, KRAS-GRIP1 and ITPR2-CCDC91 in two LumB cancers. Several cancer-related genes were found to be fusion partners: AKT3-SMYD3, CREB1-PPP1R1C, FLOT2-TOP2A and FOXC1-ARID1B. Pathway analysis of the fusion genes at baseline revealed enrichment of proteasome (p = 0.000752), tight junction (p = 0.027), insulin signaling (p = 0.0284) and melanogenesis (p = 0.05) pathways after multiple testing correction (FDR≤0.25). We looked for modulation of gene fusions upon brief exposure to therapy in 18 patients and found a majority of the baseline fusion transcripts to be present post-brief exposure in 44% of the patients, irrespective of therapy regimen.

Conclusions: We find that gene fusions in breast cancer are highly heterogeneous but are enriched with cancer-related pathway genes. This is the first study to report a novel gene-lincRNA fusion transcript (MDN1-GAS5). We are currently validating the fusion calls using qRT-PCR. The heterogeneity of detected fusions suggests that multiple mechanisms could underlie the selective advantage of tumor cells expressing fusion transcripts. The brief-exposure preoperative paradigm provides a unique opportunity to evaluate modulation of fusion transcripts that can shed light on their functional importance.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P4-04-07.

Abstract P4-04-02: RNA-seq reveals functional lncRNAs associated with estrogen-receptor status in breast cancer

Background: Long non-coding RNAs (lncRNAs) are pervasively transcribed in the genome yet their role in human disease is not well understood. LncRNAs can have regulatory effects on coding mRNAs through a number of mechanisms, including repressing their sense-strand protein-coding partners. There is also emerging evidence that estrogen signaling affects the expression of a wide variety of non-coding functional RNA transcripts in addition to protein-coding transcripts. We performed an RNA-seq study to characterize changes in lncRNA expression and evaluate their association to estrogen receptor (ER) status and estrogen signaling.

Methods: We sequenced transcriptomes of core biopsy RNA from 45 breast tumors obtained from neoadjuvant clinical trials BrUOG 211A/211B. RNA was derived from biopsy samples obtained before exposure to run-in monotherapy with either nab-paclitaxel, bevacizumab or trastuzumab. Paired-end sequencing was performed using amplified total RNA with 74bp read length, yielding genome-wide transcriptomic data. Transcriptomic abundance and differential expression were estimated assuming Poisson-distributed read-counts. Paired-end sequence data was aligned to a lncRNA database containing 14,572 unique lncRNAs. Changes in relative abundance of lncRNA transcripts were tested for association with estrogen receptor status using the Wilcoxon rank-sum test. Expression levels of the ER-associated lncRNAs were investigated in RNA-seq data from ER-positive MCF7 cells in response to treatment with E2 and tamoxifen (3hr, 12 hr and a non-treated control). ER-responsive binding sites on or near the ER-associated lncRNAs were investigated in a ChIP-seq study in MCF7 cells following estrogen treatment. MCF7 cell-line RNA-seq and ChIP-seq data were obtained from publicly available Short Read Archive (ERX030990 and SRX113365) at NCBI.

Results: On average, in each patient 5000 lncRNAs were detectable. Expression of 22 lncRNAs were associated ER status (p<0.05) in breast tumors. 17 of the 22 ER-associated lncRNAs were detectable in ER-positive MCF7 breast cancer cells and were all responsive to E2 (estradiol) treatment. Interestingly, all 17 lncRNAs showed significant downregulation (> = 2 fold) upon tamoxifen treatment. To further evaluate the regulatory relationship between ER and the 22 lncRNAs, we identified the binding sites of ER in estrogen-treated MCF7 cells using ChIP-seq. We found that >50% of the ER-associated lncRNAs had ER binding site either overlapping or neighboring the lncRNA.

Discussion: We have shown that lncRNA expression levels are associated with ER status in breast tumors. We have further established that they are estrogen-responsive with a majority being direct targets of ER using cell-line data. Further functional validation studies are ongoing. We are also exploring lncRNA-mRNA expression for coding partners of lncRNAs to identify coding/noncoding gene regulatory networks important in estrogen response. Understanding the regulatory effects of lncRNA expression opens up new opportunities for stratification and management of breast cancers.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P4-04-02.

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 P6-07-34: Disease-related outcomes with adjuvant chemotherapy in HER2 positive or triple negative T1a/bN0 breast cancers

Background: Previous studies reported higher relapse rates in T1a/bN0 breast cancers characterized by high-risk biology (HER2 positive or triple negative). The benefits of adjuvant chemotherapy in this group have not been evaluated. The purpose of our study was to determine potential impact of chemotherapy on incidence of relapses and to define the population appropriate for treatment based on observational data.

Methods: We pooled data from two multi-institutional databases spanning the period of 1996–2008 (Beth Israel Medical Center) and 2000–2010 (Brown University). We fitted a propensity score model to adjust for unbalanced confounders between the groups treated or untreated with adjuvant chemotherapy and, in case of HER2+ disease, with trastuzumab. Competing risk analysis was employed to study the effect of chemotherapy on cancer relapses in the matched population.

Results: The study included 321 patients (160 from Beth Israel and 161 from Brown) with a median age of 57 years (range 28–88). 111 (35%) cases were triple negative (TN) and 210 (65%) were HER2+ (of which 64% were ER+). 41% patients received adjuvant chemotherapy and 22% of HER2+ cases received trastuzumab. The treated group differed from untreated with regards to distribution of age, menopausal status, year of diagnosis, histological subtype and grade, tumor size, rates of mastectomy, and adjuvant endocrine therapy. All confounders were successfully balanced with the propensity score analysis. With a median follow-up of 56 months, 20 relapses (12 locoregional and 8 distant) and 10 unrelated deaths occurred. The cumulative incidence of relapse at 5 years was 7.3% (95% CI, 4.3–11.4) and relapse-free survival was 90.2% (95% CI, 85.2–93.6). Age less then 35 years (46.4% vs. 6.1%, p = 0.0004) and TN status (12.9% for TN versus 4.8% for HER2+, p = 0.03) were associated with higher risk of relapse. No significant differences with regards to tumor size (T1a or T1b), surgery type and other variables were observed. There was no significant effect of chemotherapy on incidence of relapse (Hazard ratio 1.2, 95% CI 0.34–4.23, p = 0.78), relapse-free survival or distant recurrence-free interval after propensity score adjustment. Additionally in the HER2+ patients, no benefit of trastuzumab was detected (hazard ratio 0.78, 95% CI 0.06–9.85, p = 0.85). Adjuvant endocrine therapy was associated with lower risk of relapse in the ER+ subgroup (p = 0.04).

Conclusion: Survival outcomes in very early stage breast cancer are excellent with current therapy even in biologically aggressive subtypes. Triple negative status and very young age correlate with higher incidence of relapse. While adjuvant endocrine therapy may be effective in ER positive subset, the risk/benefit ratio of chemotherapy with or without trastuzumab remains uncertain.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P6-07-34.

Abstract P4-01-02: Association of DCE-MRI texture features with molecular phenotypes and neoadjuvant therapy response in breast cancer

Purpose: MRI imaging phenotype features such as volume and morphology are used to characterize tumor heterogeneity and tumor response. Texture-based imaging features are important in lesion characterization but their relationship to molecular phenotypes and response is unclear. Molecular stratification of breast cancer into luminal, basal, ERBB2, and normal-like can be made based on gene expression profiles. We investigate how texture-based imaging features relate to tumor biology, genetic subtypes and neoadjuvant therapy response using MRI, histopathological and RNA-sequencing data.

Materials and Methods: Data from 74 Stage IIA to IIIB breast cancer patients enrolled in neo-adjuvant clinical trials NCT00617942 and NCT00723125 were retrospectively reviewed. We evaluated 37 gray-level co-occurrence matrix features (GLCM) on post-contrast T1 fat-suppressed images of 38 HER2− tumors and 35 HER2+ tumors. The texture features included angular second moment, contrast, correlation, first diagonal moment, entropy, regularity, roughness, line likeness and other statistical summaries. We also performed RNA-sequencing on 23 tumors and compared RNAseq-based PAM50 clustering with texture-based clustering. Patients with pCR and RCB class=I were determined to be responders and the rest were labeled non-responders. Wilcoxon signed rank test was used to compare luminal vs. basal, ER+ vs. ER− and PR+ vs. PR- tumors and determine the discriminative power of the texture features. We then performed hierarchical clustering on our patient data set based on the significant texture features and evaluated their association with subtypes, hormone receptor status and response. Statistical significance of clusters was determined by hypergeometric test.

Results: We found five MRI texture features to be significantly associated with tumor subtypes: first diagonal moment, contrast range, correlation range and entropy range (p < 0.05). These five features together differentiated basal and luminal PAM50 subtypes with p = 0.001. Our analysis also showed an association between texture features and tumor hormone status. ER− tumors clustered strongly (13 of 20 ER− cases clustered, p = 0.009) with the 23 significant ER-associated texture features. Similarly, the PR- tumors formed tight grouping (15 of 24 PR- cases clustered, p = 0.006) with 26 significant PR-associated texture features in HER2− patients. Interestingly, only two texture features, entropy range and regularity, distinguished between responders and non-responders (p = 0.04). These features will be further evaluated with DCE-MRI data capturing post brief exposure dynamics.

Conclusion: Our results indicate that certain texture features from DCE-MRI images do capture biological heterogeneity in tumors and can potentially complement standard clinical evaluations. Texture features have previously been assessed for diagnostic settings but to our knowledge this is the first study that shows association of texture features with breast cancer subtyping and neoadjuvant therapy response. We speculate that this could potentially impact clinical management decisions and therapy selection.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P4-01-02.

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.

Neoadjuvant bevacizumab, oxaliplatin, 5-fluorouracil, and radiation in clinical stage II-III rectal cancer

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Background: This study evaluates induction bevacizumab and FOLFOX followed by concurrent chemoradiotherapy (CRT) with bevacizumab, weekly oxaliplatin, and continuous infusion 5-FU prior to surgical resection of newly-diagnosed Stage II or III rectal cancer. Methods: Eligible patients received one month of induction, biweekly bevacizumab (5mg/kg) and modified FOLFOX6. Patients then received 50.4Gy of radiation and concurrent bevacizumab (5 mg/kg on days 1, 15, and 29), oxaliplatin (50 mg/m2/week for 6 weeks), and 5-FU (200mg/m2/day) as a continuous IV infusion throughout radiation. Due to gastrointestinal toxicity, the oxaliplatin dose was reduced to 40 mg/m2/week. Resection was performed 4 to 8 weeks after the completion of CRT. Adjuvant chemotherapy was started after 4 but less than 12 weeks following surgical resection and consisted of 6 biweekly treatments of modified FOLFOX6 and bevacizumab. Results: Twenty-six eligible patients were treated. The median age was 50. One patient developed a grade 4 arrhythmia during induction chemotherapy and was removed from the study. Of the remaining 25 patients, there were no other grade 3 or 4 toxicities during induction FOLFOX/bevacizumab. Toxicity was more significant during chemoradiation. Any grade 3 toxicity was experienced by 19 of 25 (76%) patients. Grade 3 toxicities included diarrhea (40%), neutropenia (16%), pain (16%), fatigue (8%), nausea (8%), and radiation dermatitis (8%) and bleeding with menstruation (4%). Grade 4 toxicities included neutropenia (4%), sepsis (4%) and nausea/diarrhea (4%). Six of 25 resected patients (24%) had a complete pathologic response. Eight of 25 patients (32%) developed post-operative wound complications including infection/abscess (n=4), fistula (n=2), ischemic colonic reservoir (n=1) and sterile fluid collection (n=1). Nine of 25 (36%) patients developed postoperative wound complications including infection (n=4), delayed healing (n=3), leak/abscess (n=2), sterile fluid collection (n=2), ischemic colonic reservoir (n=1), and fistula (n=1). Conclusions: Concurrent oxaliplatin, bevacizumab, continuous infusion 5-FU and radiation causes significant gastrointestinal toxicity. The pathologic complete response rate of this regimen to similar to other fluorouracil based chemoradiaton regimens. The high incidence of post-operative wound complications is concerning and consistent with other reports utilizing bevacizumab prior to major surgical resections.

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ASCO Conflict of Interest Policy and Exceptions

In compliance with the guidelines established by the ASCO Conflict of Interest Policy (J Clin Oncol. 2006 Jan 20;24[3]:519–521) and the Accreditation Council for Continuing Medical Education (ACCME), ASCO strives to promote balance, independence, objectivity, and scientific rigor through disclosure of financial and other interests, and identification and management of potential conflicts. According to the ASCO Conflict of Interest Policy, the following financial and other relationships must be disclosed: employment or leadership position, consultant or advisory role, stock ownership, honoraria, research funding, expert testimony, and other remuneration (J Clin Oncol. 2006 Jan 20;24[3]:520). The ASCO Conflict of Interest Policy disclosure requirements apply to all authors who submit abstracts to the Annual Meeting.

For clinical trials that began accrual on or after April 29, 2004, ASCO's Policy places some restrictions on the financial relationships of principal investigators (J Clin Oncol. 2006 Jan 20;24[3]:521). If a principal investigator holds any restricted relationships, his or her abstract will be ineligible for placement in the 2009 Annual Meeting unless the ASCO Ethics Committee grants an exception. Among the circumstances that might justify an exception are that the principal investigator (1) is a widely acknowledged expert in a particular therapeutic area; (2) is the inventor of a unique technology or treatment being evaluated in the clinical trial; or (3) is involved in international clinical oncology research and has acted consistently with recognized international standards of ethics in the conduct of clinical research. NIH-sponsored trials are exempt from the Policy restrictions. Abstracts for which authors requested and have been granted an exception in accordance with ASCO's Policy are designated with a caret symbol (^) in the Annual Meeting Proceedings.

For more information about the ASCO Conflict of Interest Policy and the exceptions process, please visit www.asco.org/conflictofinterest .

Fluorescent in situ hybridization for identifying cytogenetic abnormalities in inadequate and suboptimal specimens

Conventional cytogenetic analysis is often hampered by its dependency on the evaluation of dividing cells. When the mitotic index is low, or the cytogenetic preparation suboptimal, an accurate diagnosis often cannot be achieved using standard GTG banding. Molecular cytogenetics using fluorescent in situ hybridization (FISH) can be extremely useful in such a situation because it can be performed on nondividing interphase nuclei, and can usually be carried out on existing slides without requiring an additional specimen. The present paper presents two case histories to illustrate the utility of FISH in the clinical setting.

A multimodal approach in the diagnosis of patients with hematopoietic disorders

Myelodysplastic syndromes (MDS) are a group of relatively ill-defined hematopoietic disorders in which both qualitative and quantitative defects of the hematopoietic cells cause bone marrow dysfunction. With an incidence estimated to be approximately 1 per 100,000 persons per year, MDS mainly affects the elderly. Myelodysplastic syndromes share many features with acute nonlymphocytic leukemia; in fact, a proportion of patients with MDS eventually develop acute myeloid leukemia. To illustrate a multimodal approach in the diagnosis of patients with hematopoietic disorders, we describe a 66-year-old patient with a question of myelodysplastic syndrome, leukemia, and two translocations involving chromosome 10:t(5;10) and t(7;10). These structural rearrangements effectively gave rise to monosomy for part of the long arm of chromosome 5 and for the long arm of chromosome 7. Findings of del(5q) and del(7) in MDS have been reported in the literature. The results of chromosome morphometry, which was conducted to compare the lengths of all relevant chromosome segments, are consistent with the hypothesized chromosomal abnormalities. The investigational technique of fluorescence in situ hybridization (FISH), using both painting and alpha-satellite probes, was used as an adjunct to conventional cytogenetics to further delineate the nature of the chromosome abnormalities observed in the GTG-banded studies. Confirmatory studies utilizing the new technique of spectral karyotyping (SKY) were also carried out. Thus, the multimodal approach of hematopathology, GTG-banding, chromosome morphometry, FISH, and SKY can be very useful for delineating complex cytogenetic cases.

Weekly paclitaxel in patients with advanced lung cancer: preliminary data from a phase II trial

We conducted a phase II trial in chemotherapy-naive patients with advanced non-small cell lung cancer to determine the efficacy of paclitaxel (Taxol; Bristol-Myers Squibb Company, Princeton, NJ) delivered at a maximum tolerated dose of 175 mg/m2 on an extended weekly schedule. Patients with stage IIIB/IV non-small cell lung cancer were eligible if they had an Eastern Cooperative Oncology Group performance status of 0 to 2, had received no previous chemotherapy, demonstrated normal hematologic and hepatic function, and could provide informed consent. Paclitaxel 175 mg/m2 was administered as an intravenous infusion weekly over 3 hours with standard premedication, for 6 weeks of an 8-week cycle. Doses were modified for absolute neutrophil count less than 1.5 x 10(9)/L or neuropathy greater than grade I on the day of therapy. Patients without progressive disease received subsequent cycles at the same dose. To date, 30 patients have been enrolled; data are available for 25. The median age was 65 years (range, 38 to 78 years), 23 patients were performance status 0 or 1, and 14 had received prior radiation. Sites of disease included the lung (23 patients), central nervous system (11), bone (seven), liver (one), kidney (one), and soft tissue (eight). Eighty-three percent, 75%, 58%, and 50% of intended doses were delivered during cycles 1 though 4, respectively. Grade 2/3 neuropathy occurred in nine patients, but improved in all nine following dose reduction. Grade 3/4 neutropenia occurred in 10 patients. Partial responses occurred in 14 of 25 patients (56%; 95% confidence interval, 46% to 66%). Median duration of response was 6.5 months, and the 1-year survival rate was 53%. The extended weekly paclitaxel schedule results in enhanced dose intensity, marked activity, and acceptable toxicity. Paclitaxel given weekly at maximum dose intensity may be more effective than conventional paclitaxel administration schedules.

Paclitaxel and concurrent radiation for locally advanced pancreatic and gastric cancer: a phase I study

PURPOSE

To determine the maximum-tolerated dose (MTD), dose-limiting toxicities, and potential antitumor activity of weekly paclitaxel with concurrent radiation (RT) for locally advanced pancreatic and gastric cancer.

PATIENTS AND METHODS

Thirty-four patients with locally advanced adenocarcinoma of the pancreas or stomach were studied. The initial dose of paclitaxel was 30 mg/m2 by 3-hour intravenous (I.V.) infusion repeated every week for 6 weeks with 50 Gy RT. Doses were escalated at 10-mg/m2 increments in successive cohorts of three new patients until dose-limiting toxicity was observed.

RESULTS

The dose-limiting toxicities at 60 mg/m2/wk were abdominal pain within the RT field, nausea, and anorexia. Of 23 patients with assessable disease, 11 (seven with gastric, four with pancreatic cancer) had objective responses for an overall response rate of 48%.

CONCLUSION

Concurrent paclitaxel with upper abdominal RT is well tolerated at dosages that have substantial activity. A phase II trial of neoadjuvant paclitaxel and RT at the MTD of 50 mg/m2/wk is underway.

Phase II study of 5-fluoruracil leucovorin and azidothymidine in patients with metastatic colorectal cancer

The primary objective of this study was to determine the response rate of patients with metastatic colorectal cancer to combined therapy with 5-fluorouracil (5-FU), leucovorin, and intravenous azidothymidine (AZT), a thymidine nucleoside analog. By itself, AZT has limited antineoplastic efficacy. However, experimental studies indicate that 5-FU enhances the antitumor activity of AZT by inhibiting synthesis of normal thymidine nucleotides with which AZT competes for incorporation into nucleic acids. A phase I study defined the maximum tolerated dose of AZT as 7 g/m2 with hypotension during the infusion being the dose-limiting toxicity. A phase II study was performed with oral leucovorin (100 mg p.o. hourly for 4 h prior to 5-FU and 4 h and 8 h after 5-FU), bolus 5-FU (400 mg/m2) followed 1 h later by a 2-h infusion of AZT (7 g/m2). Treatment was given weekly for 4 weeks followed by a 1-week break, which constituted a cycle of therapy. Responses were evaluated after every two cycles. Patients continued on therapy as long as they tolerated treatment and did not have progressive disease. Of 15 evaluable patients who had received no chemotherapy there was 1 complete response and 4 partial responses (a 33% response rate), whereas only 1 of 6 patients who had received prior adjuvant chemotherapy had a partial response (17%). An additional 10 patients had stable disease lasting 2-14 months. Therapy was well tolerated with the only one instance each of grade 3 nausea and vomiting, diarrhea, anemia, and hypotension. Approximately 50% of treatments were accompanied by mild hypotension, which was easily corrected by increasing the rate of normal saline infusion. There was no difficulty administering this regimen in the outpatient setting. While the overall response rate (29%) is comparable to that seen with combinations of 5-FU and leucovorin alone, in most reported series a considerably higher dose of 5-FU was utilized than in this study. Since patients in the present study experienced relatively little 5-FU toxicity, increasing the dose of 5-FU in this regimen would appear to be feasible and might result in a higher response rate.

Fluorescent in situ hybridization for assessing the proportion of cells with trisomy 4 in a patient with acute non-lymphoblastic leukemia

A case of acute non-lymphoblastic leukemia is described in which fluorescent in situ hybridization (FISH) helped to resolve initially conflicting conventional cytogenetic results. Identification and assessment of the proportion of cells exhibiting trisomy of chromosome 4 in the patient's bone marrow were made using a probe which hybridizes to the centromeric region of chromosome 4. These FISH results were consistent with our retrospective GTG-banded analysis but differed from another study conducted elsewhere. Factors such as culture conditions and duration of culture which may have influenced the proportion of leukemic to nonleukemic cells are discussed. Fluorescent in situ hybridization is a powerful adjunct to conventional cytogenetic analysis and may prove to be a useful tool for monitoring minimal residual disease in this patient.

A phase II trial of continuous infusion cisplatin and 5-fluorouracil with oral calcium leucovorin in colorectal carcinoma

Twenty previously untreated patients with advanced colorectal adenocarcinoma were entered on a Phase II trial of 3-day continuous infusion cisplatin (25 mg/m2/day) and 5-fluorouracil (800 mg/M2/day) with oral calcium leucovorin (30 mg/dose) every 6 hours. There were four partial responses (20%) and two complete responses (10%) for a total response rate of 30% (95% confidence limits +/- 20%). Patients received a median of 4.5 cycles of therapy (range 2-9 cycles). Three patients experienced neutropenia; one had a life-threatening infection. One developed neuropathy at 375 mg/M2 cumulative dose. Four patients developed mucositis. Treatment was stopped for one patient with stable disease after 5 cycles because of anorexia and nausea and vomiting; treatment was stopped for four patients because of excessive fatigue. The median duration of responses was 4 months (range 3-6 months). Although this regimen is active, the response rate, cumulative nature of the toxicity, and the requirement for hospitalization led us to conclude that this regimen does not warrant Phase III testing but might be a basis for further Phase II therapeutic trials.