Alternative RNA Splicing Defects in Pediatric Cancers: New Insights in Tumorigenesis and Potential Therapeutic Vulnerabilities

BACKGROUND

Compared to adult cancers, pediatric cancers are uniquely characterized by a genomically stable landscape and lower tumor mutational burden. However, alternative splicing, a global cellular process that produces different mRNA/protein isoforms from a single mRNA transcript, has been increasingly implicated in the development of pediatric cancers.

DESIGN

We review the current literature on the role of alternative splicing in adult cancer, cancer predisposition syndromes, and pediatric cancers. We also describe multiple splice variants identified in adult cancers and confirmed through comprehensive genomic profiling in our institutional cohort of rare, refractory and relapsed pediatric and adolescent young adult cancer patients. Finally, we summarize the contributions of alternative splicing events to neoantigens and chemoresistance and prospects for splicing-based therapies.

RESULTS

Published dysregulated splicing events can be categorized as exon inclusion, exon exclusion, splicing factor upregulation, or splice site alterations. We observe these phenomena in cancer predisposition syndromes (Lynch syndrome, Li-Fraumeni syndrome, CHEK2) and pediatric leukemia (B-ALL), sarcomas (Ewing sarcoma, rhabdomyosarcoma, osteosarcoma), retinoblastoma, Wilms tumor, and neuroblastoma. Within our institutional cohort, we demonstrate splice variants in key regulatory genes (CHEK2, TP53, PIK3R1, MDM2, KDM6A, NF1) that resulted in exon exclusion or splice site alterations, which were predicted to impact functional protein expression and promote tumorigenesis. Differentially spliced isoforms and splicing proteins also impact neoantigen creation and treatment resistance, such as imatinib or glucocorticoid regimens. Additionally, splice-altering strategies with the potential to change the therapeutic landscape of pediatric cancers include antisense oligonucleotides, adeno-associated virus gene transfers, and small molecule inhibitors.

CONCLUSIONS

Alternative splicing plays a critical role in the formation and growth of pediatric cancers, and our institutional cohort confirms and highlights the broad spectrum of affected genes in a variety of cancers. Further studies that elucidate the mechanisms of disease-inducing splicing events will contribute toward the development of novel therapeutics.

Genomic characterization of HER2-positive breast cancer and response to neoadjuvant trastuzumab and chemotherapy-results from the ACOSOG Z1041 (Alliance) trial

Background

HER2 (ERBB2) gene amplification and its corresponding overexpression are present in 15-30% of invasive breast cancers. While HER2-targeted agents are effective treatments, resistance remains a major cause of death. The American College of Surgeons Oncology Group Z1041 trial (NCT00513292) was designed to compare the pathologic complete response (pCR) rate of distinct regimens of neoadjuvant chemotherapy and trastuzumab, but ultimately identified no difference.

Patients and methods

In supplement to tissues from 37 Z1041 cases, 11 similarly treated cases were obtained from a single institution study (NCT00353483). We have extracted genomic DNA from both pre-treatment tumor biopsies and blood of these 48 cases, and performed whole genome (WGS) and exome sequencing. Coincident with these efforts, we have generated RNA-seq profiles from 42 of the tumor biopsies. Among patients in this cohort, 24 (50%) achieved a pCR.

Results

We have characterized the genomic landscape of HER2-positive breast cancer and investigated associations between genomic features and pCR. Cases assigned to the HER2-enriched subtype by RNA-seq analysis were more likely to achieve a pCR compared to the luminal, basal-like, or normal-like subtypes (19/27 versus 3/15; P = 0.0032). Mutational events led to the generation of putatively active neoantigens, but were overall not associated with pCR. ERBB2 and GRB7 were the genes most commonly observed in fusion events, and genomic copy number analysis of the ERBB2 locus indicated that cases with either no observable or low-level ERBB2 amplification were less likely to achieve a pCR (7/8 versus 17/40; P = 0.048). Moreover, among cases that achieved a pCR, tumors consistently expressed immune signatures that may contribute to therapeutic response.

Conclusion

The identification of these features suggests that it may be possible to predict, at the time of diagnosis, those HER2-positive breast cancer patients who will not respond to treatment with chemotherapy and trastuzumab.

ClinicalTrials.gov identifiers

NCT00513292, NCT00353483.

Abstract GS2-01: Discovery and characterization of an estrogen bound LncRNA in late-Stage breast cancer

Breast cancer is the second most common newly diagnosed cancer and the second leading cause of cancer death among women in the United States. Despite the proven benefits of adjuvant endocrine therapy in women with hormone receptor positive breast cancer, relapses still occur over 5 years after initial treatment with endocrine therapy, referred to as late-stage relapse. Currently, the mechanisms of driving late-stage relapse are poorly characterized. To date, breast cancer research has primarily focused on protein-coding genes thereby missing the emerging class of long intergenic non-coding RNAs (lncRNAs) that may serve as critical regulators of relapse. Furthermore, the current understanding of lncRNA function is still in its infancy representing a critical gap for translating lncRNA discoveries into real-world applications to benefit patient care. Several well-described examples indicate that lncRNAs may be master epigenetic regulators in cancer biology through their interactions with proteins regulating target gene expression. Therefore, we hypothesize that lncRNAs may interact with estrogen receptor alpha 1 (ESR1) to regulate genes promoting late-stage relapse. To address this, we performed a transcriptome analysis of tumors from a unique cohort of 24 patients that had late-stage relapse to discover a novel set of lncRNAs, most of which have not yet been characterized. Next, we used RNA Immunoprecipitation coupled with transcriptome sequencing (RIP-Seq) to identify transcripts bound to ESR1 in T47D cells. We discovered 217 lncRNAs bound to ESR1 of which 50 were up-regulated in late-stage breast cancer. We chose to focus the most up-regulated lncRNA in late-stage relapse. Since it is an unannotated lncRNA we will refer to it as 'LAte-Stage relapse ESR1-Bound lncRNA 1', or LASER-1. To further understand the interplay between LASER-1 and ESR1, cells endogenously expressing LASER-1 were subjected to partial digestion to preserve lncRNA and protein interactions. Protected RNA fragments were subsequently immunoprecipitated with ESR1 and quantified by qPCR to reveal specific ESR1 interaction sites within LASER-1. Next, we observed increased expression of LASER-1 in ER+ breast cancer cell lines. Notably, LASER-1 expression was elevated in MCF7 long-term estrogen deprived (MCF7 LTED) cells -- that have amplified ESR1 -- relative to parental MCF7 cells. To demonstrate that LASER-1 promotes oncogenic phenotypes we transiently silenced LASER-1 in two cell lines with high endogenous expression of LASER-1 (including MCF LTED) and observed a decrease in cellular proliferation and invasion. Subsequent gene expression analysis after silencing LASER-1 altered mRNA and protein levels of critical cell cycle genes (i.e., p27). Overall, this is the first study to discover ESR1 bound lncRNAs that may be contributing to late-stage relapse in breast cancer. In the short-term, our ongoing research may lead to significant breakthroughs establishing the importance of LASER-1 as a master regulator in late-stage relapse. In the longer-term, we envision this research may lead to the development of novel therapeutics targeting LASER-1 with the potential for rapid clinical translation.

Citation Format: Maher CA, Silva-Fisher J, Eteleeb A, Tang C, Perou C, Reis-Filho JS, Mardis ER, Ellis MJ. Discovery and characterization of an estrogen bound LncRNA in late-Stage breast cancer [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 GS2-01.

Abstract P2-05-01: Whole genome sequencing reveals enrichment of mutations in mucin gene family in breast cancer diagnosed during pregnancy

Background

Pregnancy is known to modulate breast cancer (BC) risk. Different reproductive behaviors have been shown to impact not only the risk of developing BC but also the phenotypes of these tumors. Breast cancer diagnosed during pregnancy (BCP) is a rare disease but could serve as a good model to understand how pregnancy modulates BC biology. In this project, we aim to interrogate the effect of pregnancy on the biology of BC by performing whole genome sequencing (WGS) using a unique series of BC patients diagnosed during pregnancy (BCP).

Method

Whole genome sequencing was performed for 35 BCP and 20 non-pregnant controls matched for age and stage with available clinic-pathological data. DNA extracted from primary tumor and matched adjacent normal FFPE tissues was assessed using WGS on Illumina HiSeqXTen platform targeting 60x and 30x coverage for tumor and normal DNA respectively. Briefly, 2x150bp paired end sequence data were generated, cleaned, trimmed and aligned to the reference genome (hg19) using bwa-mem. Somatic mutations were detected using Strelka and annotated using SnpEff. Mutational signatures were extracted using deconstructSigs. Differences on mutational profiles between BCP and case controls were assessed using Wilcoxon test for continuous variables and Fisher exact test for categorical variables.

Result

No difference in clinic-pathological features was observed between BCP and control patients. A median of 10084 and 13829 SNVs and of 26 and 21 indels were identified in the BCP and controls respectively, no significant difference between the two groups being observed (p = 0.703 and p = 0.851). Of interest, a significantly higher number of mutations was found in the BCP as compared to the control group when considering only mutations associated with a deleterious effect (median: 20 vs. 12, p = 0.027). As expected, TP53 and PIK3CA were the most frequently mutated genes both in BCP and control cases without any significant difference between the groups (34.3% vs. 22.2%, p = 0.53 and 20.0% vs. 16.7%, p = 1, respectively). Interestingly, there was a significant enrichment of non-silent mutations in the mucin genes family (MUC2, MUC4, MUC12, MUC16, MUC17, MUC20) in the BCP group: 45.7% of BCP vs. 11.1% of control cases had at least one such mutation (p = 0.015). A similar significant result (45.7% vs. 23.1%, p = 0.034) was found when comparing BCP with BC control cases from the TCGA dataset (selected to have similar age, ER and PR distribution, N = 56). When comparing the distribution of the twelve BC mutational signatures, a borderline significant enrichment with a signature depicting mismatch-repair deficiency (signature 20) was observed in the BCP patients (p = 0.059).

Conclusion

This is the first study reporting the mutational landscape of breast cancer diagnosed during pregnancy using WGS. We found that BCP are associated with a higher number of putative driver mutations including mutations in mucin genes, shown to be implicated in tumorigenesis. Furthermore, BCP were enriched with a mismatch-repair deficiency signature. These results could open new avenues for the development of targeted therapeutic approaches for patients diagnosed with breast cancer during pregnancy.

Citation Format: Nguyen B, Venet D, Desmedt C, Pruneri G, Peccatori F, Mardis ER, Azim HA, Rothé F, Sotiriou C. Whole genome sequencing reveals enrichment of mutations in mucin gene family in breast cancer diagnosed during pregnancy [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 P2-05-01.

CTCF genetic alterations in endometrial carcinoma are pro-tumorigenic

CTCF is a haploinsufficient tumour suppressor gene with diverse normal functions in genome structure and gene regulation. However the mechanism by which CTCF haploinsufficiency contributes to cancer development is not well understood. CTCF is frequently mutated in endometrial cancer. Here we show that most CTCF mutations effectively result in CTCF haploinsufficiency through nonsense-mediated decay of mutant transcripts, or loss-of-function missense mutation. Conversely, we identified a recurrent CTCF mutation K365T, which alters a DNA binding residue, and acts as a gain-of-function mutation enhancing cell survival. CTCF genetic deletion occurs predominantly in poor prognosis serous subtype tumours, and this genetic deletion is associated with poor overall survival. In addition, we have shown that CTCF haploinsufficiency also occurs in poor prognosis endometrial clear cell carcinomas and has some association with endometrial cancer relapse and metastasis. Using shRNA targeting CTCF to recapitulate CTCF haploinsufficiency, we have identified a novel role for CTCF in the regulation of cellular polarity of endometrial glandular epithelium. Overall, we have identified two novel pro-tumorigenic roles (promoting cell survival and altering cell polarity) for genetic alterations of CTCF in endometrial cancer.

Abstract P1-05-30: Genomic and microenvironmental intra-tumor heterogeneity in DCIS

Intra-tumor heterogeneity drives neoplastic progression by supplying the fuel for natural selection among neoplastic cells. It also complicates screening and treatment of neoplasms. We hypothesize that the degree of intra-tumor heterogeneity in DCIS should predict which tumors are likely to become invasive and metastatic. We initiated a pilot project to test this hypothesis by comparing 9 cases of pure DCIS to 9 cases of DCIS with adjacent invasive disease. For each case, we sequenced the exome from two spatially distinct regions of DCIS as well as normal tissue taken from a lymph node with no tumor involvement. This required the development of new methods to extract high quality sequencing data from small amounts of DNA extracted from FFPE samples. We calculated the genetic divergence between the two tumor regions, defined as percent of the sequenced regions of the genome showing differences between the two samples that had sufficient sequencing coverage and quality scores for confident scoring. We also employed automated imaging analysis to score microenvironmental differences between the two tumor regions. These microenvironmental measures are based on ecological methods for measuring organismal interactions and habitats. We will present initial data on differences in phenotypic and genotypic intra-tumor heterogeneity comparing pure DCIS to DCIS associated with invasive breast cancer. Our methods can be readily translated to large tissue banks of FFPE samples from DCIS.

Citation Format: Fortunato A, King L, Mallo D, Kovacheva V, Yuan Y, Boddy A, Graham T, Aktipis A, Mardis ER, Hall A, Marks JR, Hwang S, Maley CC. Genomic and microenvironmental intra-tumor heterogeneity in DCIS [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 P1-05-30.

Abstract S3-05: Integrated analysis of multidimensional genomic data on CALGB 40601 (Alliance), a randomized neoadjuvant phase III trial of weekly paclitaxel (T) and trastuzumab (H) with or without lapatinib (L) for HER2-positive breast cancer

Background: RNA profiling and mutational analyses in CALGB 40601 (NCT00770809) found significant impact on pathologic complete response (pCR) rates from tumor (intrinsic subtype, p53 mutation) and microenvironmental (immune cell) features. Integrated analysis across platforms is needed to better understand the roles of these different factors with respect to response to HER2-targeted therapies.

Methods: We performed a comprehensive genomic analyses on pCR, defined as no invasive tumor in the breast, by integrating clinicopathological information with somatic mutation status, 422 segment-level DNA Copy Number Alterations (CNAs), and 510 gene expression signatures using mRNAseq and DNA exome sequencing from 213 pre-treatment tumors. Excluding 48 samples in the TL arm that was closed early due to futility, and 4 Normal-like tumors, the dataset consisted of 161 patients from TH and THL arms including 47 HER2-enriched (HER2E), 8 Basal-like, 54 Luminal A, and 52 Luminal B, all of whom received H. The main analysis was performed using the Elastic Net on multivariate logistic regression models for predicting pCR. The samples were divided into a training and a test set, then models were built to predict pCR by 10-fold cross-validation in the training set, then applying the best model onto the test set to construct ROC curves and evaluate prediction accuracy by calculating area under ROC (AUC). We also used the DawnRank, a network-based bioinformatics tool that integrates DNA and RNA data to identify driver genes, to find predictors of resistance to H-containing therapies.

Results: Among clinicopathological factors, clinical estrogen/progesterone receptor (ER/PgR) status and intrinsic subtype by PAM50 were statistically associated with pCR, but treatment arm (TH vs THL) and stage were not. In the Elastic Net analysis, the models incorporating either gene signatures (AUC: 0.724) or CNAs (AUC: 0.777) were more predictive of response than mutation status model (AUC: 0.635). Gene signatures and CNAs were further combined with either mutation status (AUC: 0.773), clinical ER/PgR status (AUC: 0.787) or ER/PgR status plus intrinsic subtype (AUC: 0.784). The combination with the highest AUC comprised gene signatures, CNAs, and ER/PgR status, and demonstrated that CNAs at Chromosome (Chr.) 6p, 10q22, or 11q23, the signature of Correlation to HER2E, and a T-cell signature, positively predicted pCR and that Luminal and PgR gene signatures were negative predictors. The CN gain of Chr.6p, which contains the HLA genes, predicted for pCR and was associated with higher expression of HLA genes and B cell / IgG signatures. The CN loss of Chr.11q23 including CD3D, CD3E, and CD3G was also identified by DawnRank as a region associated with resistance.

Conclusions: Tumor genetics (CNAs), tumor RNA subtype (HER2E, Luminal), and the microenvironment (immune cells) were independently predictive of response to H-containing therapies and biologically and clinically important for HER2-positive breast cancer, supporting integrated RNA- and DNA-based tumor assessments to clarify response to HER2-targeting.

Support: U10CA031946/033601/180821/180882/180888.

Citation Format: Tanioka M, Fan C, Carey LA, Hyslop T, Pitcher BN, Parker JA, Hoadley KA, Henry NL, Tolaney S, Dang C, Krop IE, Harris L, Berry DA, Mardis E, Perou CM, Winer EP, Hudis CA. Integrated analysis of multidimensional genomic data on CALGB 40601 (Alliance), a randomized neoadjuvant phase III trial of weekly paclitaxel (T) and trastuzumab (H) with or without lapatinib (L) for 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 S3-05.

Abstract P1-07-11: Tumor genomic profiling of triple negative breast cancer during neoadjuvant chemotherapy: Results from a prospective trial of carboplatin and docetaxel

Background-The clonal evolution and effect of neoadjuvant chemotherapy on the mutational landscape of triple negative breast cancer (TNBC) is unknown. Inability to eradicate TNBC may be due to clonal progression and selection of cells fundamentally resistant to chemotherapy.In this study, we sought to decipher the genomic architecture of TNBC serially during neoadjuvant chemotherapy to distinguish pre- versus post-chemotherapy genotypes.

Methods-Tumor specimens were obtained from patients with stages II and III TNBC enrolled on an ongoing prospective neoadjuvant co-clinical trial (NCT02124902). Patients have a research biopsy at baseline, cycle 1 day 3 (optional), and at definitive surgery for those with residual disease. Patients are treated with docetaxel 75mg/m2 and carboplatin AUC6 cycled every 3 weeks X six cycles. Definitive surgery is 3-5 weeks after chemotherapy. The primary endpoint is pathologic complete response rate. Correlative studies include development of patient derived xenografts, evaluation of genomic signatures of resistance and response, and comparison of chemotherapy responses between xenografts and host patients. Five patients' serial tumor samples and germline DNA were studied by exome and transcriptome sequencing. Three of these patients had an additional on-treatment sample at cycle 1 day 3. Two patients lacked residual disease samples- one was not banked and the other could not be accurately genotyped due to low cellularity. The median sequencing depth was 90.13x. Sequencing was performed on either fresh frozen or formalin-fixed paraffin-embedded samples with high cellularity (≥50%). After identifying somatic mutations in each tumor series, we evaluated whether each mutation was persistent, emergent, or cleared by comparing pre- and post-treatment (and when possible, on-treatment) samples.

Results-All five patients had response to neoadjuvant chemotherapy based on caliper-based and pathologic (residual cancer burden I or II) measurements. All residual disease remained TNBC by standard immunohistochemistry and all samples were basal-like from PAM50 gene expression analysis. We identified 908 somatic mutations, including the expected variants in TP53 which persisted in all post-treatment samples. Non-silent somatic variants were identified in other breast cancer-related genes, including GATA1, FBXO11, PIK3R1, AXIN2, ARID1B, BRCA2, and RBCC1. In spite of the clinico-pathologic evidence of response, we observed little change in clonal architecture, as derived from the purity-corrected variant allele fractions between baseline, cycle 1 day 3, and post-chemotherapy samples. Copy number alterations were likewise stable and transcriptional-based assessment indicated that patterns of mutant allele expression in driver genes were retained throughout the course of treatment.

Conclusion-In TNBC patients undergoing neoadjuvant platinum-based chemotherapy, there were no apparent shifts in the prevalence of known breast cancer specific somatic variants during or after chemotherapy. Despite pathologic response, core genomic features appear to be preserved in TNBC patients with residual disease following chemotherapy, likely accounting for high rates of relapse in these patients.

Citation Format: Ademuyiwa FO, Miller CA, Li T, Sanati S, Ma CX, Weilbaecher K, Ellis MJ, Mardis ER. Tumor genomic profiling of triple negative breast cancer during neoadjuvant chemotherapy: Results from a prospective trial of carboplatin and docetaxel [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 P1-07-11.

Consensus on precision medicine for metastatic cancers: a report from the MAP conference

Recent advances in biotechnologies have led to the development of multiplex genomic and proteomic analyses for clinical use. Nevertheless, guidelines are currently lacking to determine which molecular assays should be implemented in metastatic cancers. The first MAP conference was dedicated to exploring the use of genomics to better select therapies in the treatment of metastatic cancers. Sixteen consensus items were covered. There was a consensus that new technologies like next-generation sequencing of tumors and ddPCR on circulating free DNA have convincing analytical validity. Further work needs to be undertaken to establish the clinical utility of liquid biopsies and the added clinical value of expanding from individual gene tests into large gene panels. Experts agreed that standardized bioinformatics methods for biological interpretation of genomic data are needed and that precision medicine trials should be stratified based on the level of evidence available for the genomic alterations identified.

A genomic case study of mixed fibrolamellar hepatocellular carcinoma

We report the first comprehensive genomic analysis of a case of mixed conventional and fibrolamellar HCC (mFL-HCC). This study confirms the expression of DNAJB1:PRKACA, a fusion previously associated with pure FL-HCC but not conventional HCC, in mFL-HCC. These results indicate the DNAJB1:PRKACA fusion has diagnostic utility for both pure and mixed FL-HCC.

Background

Mixed fibrolamellar hepatocellular carcinoma (mFL-HCC) is a rare liver tumor defined by the presence of both pure FL-HCC and conventional HCC components, represents up to 25% of cases of FL-HCC, and has been associated with worse prognosis. Recent genomic characterization of pure FL-HCC identified a highly recurrent transcript fusion (DNAJB1:PRKACA) not found in conventional HCC.

Patients and Methods

We performed exome and transcriptome sequencing of a case of mFL-HCC. A novel BAC-capture approach was developed to identify a 400 kb deletion as the underlying genomic mechanism for a DNAJB1:PRKACA fusion in this case. A sensitive Nanostring Elements assay was used to screen for this transcript fusion in a second case of mFL-HCC, 112 additional HCC samples and 44 adjacent non-tumor liver samples.

Results

We report the first comprehensive genomic analysis of a case of mFL-HCC. No common HCC-associated mutations were identified. The very low mutation rate of this case, large number of mostly single-copy, long-range copy number variants, and high expression of ERBB2 were more consistent with previous reports of pure FL-HCC than conventional HCC. In particular, the DNAJB1:PRKACA fusion transcript specifically associated with pure FL-HCC was detected at very high expression levels. Subsequent analysis revealed the presence of this fusion in all primary and metastatic samples, including those with mixed or conventional HCC pathology. A second case of mFL-HCC confirmed our finding that the fusion was detectable in conventional components. An expanded screen identified a third case of fusion-positive HCC, which upon review, also had both conventional and fibrolamellar features. This screen confirmed the absence of the fusion in all conventional HCC and adjacent non-tumor liver samples.

Conclusion

These results indicate that mFL-HCC is similar to pure FL-HCC at the genomic level and the DNAJB1:PRKACA fusion can be used as a diagnostic tool for both pure and mFL-HCC.

Abstract S6-05: A phase II trial of neoadjuvant palbociclib, a cyclin-dependent kinase (CDK) 4/6 inhibitor, in combination with anastrozole for clinical stage 2 or 3 estrogen receptor positive HER2 negative (ER+HER2-) breast cancer (BC)

Background

ER+ BC is associated with activated CDK4/6. The CDK4/6 inhibitor palbociclib (P) markedly improves time to progression in advanced ER+HER2- BC. We conducted a neoadjuvant phase II trial to determine the activity of P in primary breast cancer as a prelude to adjuvant studies.

Methods

To assess molecular changes induced by anastrozole (A) or P+A, patients (pts) were treated initially with A alone (1mg PO daily) for 28 days in cycle 0 (C0) before the addition of P (125mg PO daily on D1-21 each cycle) on C1D1. P+A was administered for 4 28-day cycles followed by C5 with A alone for 2-4 weeks (wks) before surgery. P was added in C5 for 10-12 days immediately prior to surgery in the last 20 pts enrolled to assess molecular changes induced by A, either alone or in combination with P immediately prior to surgery, in resected tumor. Goserelin was added in premenopausal pts.

Research tumor biopsies were obtained at baseline, C1D1, and C1D15. Central Ki67 analysis was performed at all timepoints, those with Ki67 >10% at C1D15 went off study treatment.

The primary endpoint was complete cell cycle arrest (CCA), defined as Ki67 <2.7%, at C1D15. Patient stratification was based on PIK3CA mutation status with an initial focus on PIK3CA wild type (WT) disease. Pts with PIK3CA mutant (Mut) tumors enrolled to a separate cohort. A sample size of 33 pts in the PIK3CA WT cohort was chosen based on the Fleming's single-stage phase II design to test the hypothesis that P+A leads to > 50% improvement over A in CCA rate on C1D15 biopsy (44% with A alone based on historical data, vs 66% with P+A, power = 0.8, alpha=0.05). The primary endpoint is met if >20 pts achieved CCA in this cohort.

Correlative endpoints included assessment of markers of proliferation, apoptosis, senescence, Rb, gene expression microarray, intrinsic subtype, and next generation sequencing of 83-gene panels, which will be reported at the meeting.

Results

Between 4/23/2013 and 4/24/2015, 50 pts (33 PIK3CA WT, 11 PIK3CA Mut, 2 pending, 4 tissue quantity or quality not sufficient for sequencing (QNS)) were enrolled to the study. Median age was 57.5 (range: 34.1–79.6) years. Four pts, all with WT PIK3CA, went off study due to Ki67 >10% on C1D15 biopsy, 26 pts completed treatment and surgery, 1 refused surgery, 3 withdrew study treatment in C1, and 16 continued to receive study drug (2 in C0, 3 in C1, 4 in C2, 5 in C3, 1 in C4, and 1 in C5). Among the 40 pts currently evaluable for the primary endpoint (C1D15 Ki67), CCA occurred in 34 (85%) pts, including 9 of 9 (100%) PIK3CA Mut, 22 of 28 (78.5%) WT, and 3 of 3 QNS pts. Preliminary analysis of available data indicated a significantly lower Ki67 value after 2 wks of P+A (C1D15) compared to that on A alone (C1D1) (p=0.034, n=18).

Conclusion

This study met the primary endpoint demonstrating that P+A is a highly effective anti-proliferative combination. The sequential biopsy design clearly demonstrated that P+A increased cell cycle control over A alone. P+A was effective regardless of PIK3CA mutation status and these results support the evaluation of this combination in the adjuvant setting for ER+HER2- BC.

Citation Format: Ma CX, Gao F, Northfelt D, Goetz M, Forero A, Naughton M, Ademuyiwa F, Suresh R, Anderson KS, Margenthaler J, Aft R, Hobday T, Moynihan T, Gillanders W, Cyr A, Eberlein TJ, Hieken T, Krontiras H, Hoog J, Han J, Guo Z, Vij K, Mardis E, Al-Kateb H, Sanati S, Ellis MJ. A phase II trial of neoadjuvant palbociclib, a cyclin-dependent kinase (CDK) 4/6 inhibitor, in combination with anastrozole for clinical stage 2 or 3 estrogen receptor positive HER2 negative (ER+HER2-) breast cancer (BC). [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 S6-05.

Abstract PD6-02: The genomics of response to neoadjuvant trastuzumab and chemotherapy in HER2-positive breast cancer – Results from the ACOSOG Z1041 (Alliance) trial

Support: Alliance U10CA180821; Alliance Statistical Center grant U10CA180882; ACOSOG grant U10CA76001

HER2 gene amplification and its corresponding overexpression are present in approximately 12% of invasive breast cancers. While HER2-targeted agents (e.g. trastuzumab, pertuzumab, and lapatinib) are effective treatments, resistance remains a major cause of death from HER2-positive breast cancer. Mechanisms of resistance are poorly understood. Without a molecular understanding of these mechanisms, therapeutic advances will be delayed. We have generated molecular profiles of primary HER2-positive breast cancers treated on a neoadjuvant clinical trial, and compared features associated with response to treatment.

The American College of Surgeons Oncology Group (ACOSOG) Z1041 trial in HER2-positive breast cancer was designed to compare the pathologic complete response (pCR) rate of a regimen of paclitaxel and trastuzumab, followed by trastuzumab administered with fluorouracil, epirubicin, and cyclophosphamide (FEC-75) to a regimen of FEC-75 alone followed by paclitaxel and trastuzumab. The trial identified no difference in pCR rates between the regimens (Buzdar et al., The Lancet Oncology 2013). In supplement to the tissues obtained from 37 of the patients enrolled in the Z1041 trial, an additional 11 cases were obtained from a single institution study (201101961) of patients treated with neoadjuvant trastuzumab that had pre-treatment core biopsies suitable for genomic studies.

We have extracted genomic DNA from both pretreatment tumor biopsies and blood samples of these 48 patients and performed whole genome (WGS) and exome sequencing. Coincident with these efforts, we have extracted high quality RNA from 42 of the 48 biopsies, and have processed RNA-seq profiles of the tumors. Among patients in this cohort, 24 (50%) achieved a pCR. Because no difference was observed between arms of the Z1041 trial, patients with or without a pCR were directly compared without adjusting for treatment regimen.

On average, each tumor and normal sample pair were sequenced to a depth of 49.4x and 32.5x by WGS respectively. In total, 15,027 candidate somatic variants were identified in known genes, including 11,606 missense, 860 nonsense, and 418 frameshift insertions or deletions. Preliminary results identified mutations in HER2 that were associated with the failure to achieve pCR in several cases. Furthermore, tumors assigned to the HER2-enriched subtype by RNA-seq analysis were more likely to achieve a pCR (19 compared to 8) than tumors with genomic features indicative of either the luminal or basal-like subtypes (3 compared to 12); a significant difference in the proportion of cases that achieve pCR (Fisher's exact test p-value = 0.0032). The identification of these features suggests that it may be possible to predict, at the time of diagnosis, those patients who will not respond to the current standard of care for HER2-positive breast cancer.

Citation Format: Lesurf R, Griffith O, Griffith M, Watson MA, Hoog J, Ellis MJ, Ota D, Suman VJ, Meric-Bernstam F, Leitch AM, Boughey JC, Unzeitig G, Buzdar AU, Hunt KK, Mardis ER. The genomics of response to neoadjuvant trastuzumab and chemotherapy in HER2-positive breast cancer – Results from the ACOSOG Z1041 (Alliance) trial. [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 PD6-02.

Abstract P6-05-03: Genomic diversity of ductal carcinoma in situ (DCIS) as a driver of invasion and metastasis

Background: Recent evidence indicates that breast cancers may have high levels of heterogeneity. Based on principles of tumor evolution, we are investigating whether DCIS with higher levels of intra-tumoral genetic heterogeneity are more likely to progress to invasive and/or metastatic disease.

Methods: Cases (DCIS with co-existing invasive or metastatic cancer) and controls (pure DCIS) are identified from Duke Pathology archives. From cases and controls, we are analyzing two areas of DCIS separated by >1cm with germ line DNA from the same subject to measure allele frequencies of somatic mutations and copy number variation (CNV). Small amounts of FFPE derived DNA are made into NGS libraries for full exome sequencing and hybridization to a 4.2 million element SNP array. Comparison of allele frequencies and CNV is made between specimens from the same cancer to assess heterogeneity.

Results: We identified a series of pure DCIS (controls for this study) and generated high coverage sequencing data from 20ng of FFPE DNA from 12 samples (4 subjects, germline + 2 DCIS containing areas from each subject) as proof of principle. We compared the occurrence of deletions, insertions and SNP's after a 20X coverage filtration. From these data, we identified between 50 to greater than 600 sequence changes in these DCIS compared to normal DNA. Present/absent calls and allele frequencies indicate both significant and variable degrees of heterogeneity even in these pure DCIS samples. Additional data is now being gathered and analyzed based on this established technical approach.

Conclusion: We have demonstrated the feasibility of acquiring high quality NGS data from archival DCIS specimens allowing us to test the hypothesis that genetic heterogeneity is a driving force in breast cancer progression. The degree and nature of this heterogeneity will be assessed in a panel of pure DCIS and DCIS co-existing with invasive and/or metastatic cancer. We are now generating and analyzing these data for Symposium presentation.

Citation Format: King LM, Marks JR, Hall AH, Temko D, Graham TA, Mardis ER, Maley CC, Hwang E. Genomic diversity of ductal carcinoma in situ (DCIS) as a driver of invasion and metastasis. [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 P6-05-03.

Abstract P5-13-04: A phase II neoadjuvant trial of MK-2206, an AKT inhibitor, in combination with anastrozole for clinical stage 2 or 3 PIK3CA mutant estrogen receptor positive HER2 negative (ER+HER2-) breast cancer (BC)

Background

Activating mutations in PIK3CA occur in approximately 40% ER+BC. MK-2206 (M), a pan-AKT inhibitor, induced apoptosis of ER+ BC under estrogen deprivation in preclinical studies. We conducted this neoadjuvant trial to determine the pathologic complete response (pCR) rate of M plus anastrozole (A) for PIK3CA mutant (Mut) ER+ BC.

Methods

This single arm open label study of M+A used a 2-stage Simon phase II design (stage 1, n=16; stage 2, n=13, alpha=0.10, power=0.90) to test whether pCR rate <1% (based on historical data with A alone), against the alternative that pCR rate ≥15% in PIK3CA Mut ER+ BC. At least 1 pCR in stage 1 was required to proceed to stage 2.

Eligible patients (pts) with clinical stage II or III ER+HER2- BC were pre-registered and proceeded to a research tumor biopsy for PIK3CA sequencing, followed by treatment with daily A monotherapy for 28 days (cycle 0). Pts with PIK3CA Mut BC were subsequently registered, underwent a second biopsy, and started M (150mg PO weekly) with daily A on cycle 1 day 1 (C1D1) for a maximum of four 28-day cycles followed by surgery. Goserelin was added for premenopausal pts. A tumor biopsy on C1D17, 17 days post the start of M, was performed. Those with C1D17 Ki67 >10% discontinued study treatment. pCR was defined as no invasive cancer in the breast and the lymph nodes. Tumor specimens collected at all timepoints are being analyzed for markers of proliferation, apoptosis, and PI3K pathway activity, gene expression microarray, intrinsic subtypes, and next generation sequencing of 83 genes.

Results

Of the 51 pts pre-registered, 35 pts did not register due to no PIK3CA mutation (n=22), inadequate specimen for testing (n=6), physician/pt decision (n=7). The remaining 16 pts (median age: 58, range: 40-77 years) received combination therapy. Three pts did not complete 4 cycles due to C1D17 Ki67 >10% (n=2) and intolerability (grade (Gr) 4 transaminase elevation in C1, n=1). Other severe toxicities possibly related to M included Gr 3 rash (25%) and pruritus (12.5%). Of the 13 pts completed study therapy and underwent surgery, all had residual disease in the breast and 7 also had positive nodes. Table 1 summarized changes in Ki67 during treatment.

ComparisonsnAbsolute changes in Ki67 median (range)Wilcoxon signed rank p-valueC1D1 relative to pre-registration11-17.0% (-49.8 to 4.1%)0.0020C1D17 relative to pre-registration14-16.4% (-51.4 to 4.1%)0.0004C1D17 relative to C1D112-1.5% (-18.6 to 15.8%)0.9697C1D1, biopsy post 28 days of A alone; C1D17 biopsy post 17 days on combination therapy

Although Ki67 levels post A monotherapy (C1D1) or M+A (C1D17) were significantly lower than that of pre-registration samples, Ki67 did not differ between C1D17 and C1D1 samples. Other correlative studies are ongoing and results will be presented.

Conclusion

Despite the small sample size, biomarker analysis on serial biopsy specimens demonstrated that M+A is unlikely to be more effective than A alone in PIK3CA Mut ER+ BC. This trial demonstrated the feasibility of genomic sequencing for pt selection and the value of a small, well-designed proof-of-principle neoadjuvant trial for the evaluation of targeted agents.

Citation Format: Ma CX, Suman VJ, Goetz M, Northfelt D, Burkard M, Ademuyiwa F, Naughton M, Margenthaler J, Aft R, Gray R, Tavaarwerk A, Wilke L, Haddad T, Moynihan T, Loprinzi C, Hieken T, Hoog J, Guo Z, Han J, Vij K, Mardis E, Sanati S, Al-Kateb H, Doyle L, Erlichman C, Ellis MJ. A phase II neoadjuvant trial of MK-2206, an AKT inhibitor, in combination with anastrozole for clinical stage 2 or 3 PIK3CA mutant estrogen receptor positive HER2 negative (ER+HER2-) breast cancer (BC). [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 P5-13-04.

Prioritizing targets for precision cancer medicine

The implementation of cancer genomic testing into the clinical setting has brought major opportunities. However, as our understanding of cancer initiation, maintenance and progression improves through detailed cancer genomic studies, the challenges associated with driver identification and target classification in the clinical setting become clearer. Here, we review recent insights into cancer genomic testing in the clinical setting, and suggest a target classification approach that considers the levels of evidence supporting the prioritization of tumour drivers for therapeutic targeting in light of complex cancer clonal and sub-clonal structures and clinical successes and failures in the field. We argue that such classification approaches, together with transparent reporting of both positive and negative clinical data and continued research to identify the sub-clonal dynamics of driver events during the disease course, will facilitate inter-trial comparisons, optimize patient informed consent and provide a critically balanced evaluation of genomic testing in clinical practice.

Predicting response and survival in chemotherapy-treated triple-negative breast cancer

BACKGROUND

In this study, we evaluated the ability of gene expression profiles to predict chemotherapy response and survival in triple-negative breast cancer (TNBC).

METHODS

Gene expression and clinical-pathological data were evaluated in five independent cohorts, including three randomised clinical trials for a total of 1055 patients with TNBC, basal-like disease (BLBC) or both. Previously defined intrinsic molecular subtype and a proliferation signature were determined and tested. Each signature was tested using multivariable logistic regression models (for pCR (pathological complete response)) and Cox models (for survival). Within TNBC, interactions between each signature and the basal-like subtype (vs other subtypes) for predicting either pCR or survival were investigated.

RESULTS

Within TNBC, all intrinsic subtypes were identified but BLBC predominated (55-81%). Significant associations between genomic signatures and response and survival after chemotherapy were only identified within BLBC and not within TNBC as a whole. In particular, high expression of a previously identified proliferation signature, or low expression of the luminal A signature, was found independently associated with pCR and improved survival following chemotherapy across different cohorts. Significant interaction tests were only obtained between each signature and the BLBC subtype for prediction of chemotherapy response or survival.

CONCLUSIONS

The proliferation signature predicts response and improved survival after chemotherapy, but only within BLBC. This highlights the clinical implications of TNBC heterogeneity, and suggests that future clinical trials focused on this phenotypic subtype should consider stratifying patients as having BLBC or not.

Clonal diversity of recurrently mutated genes in myelodysplastic syndromes

Recent studies suggest that most cases of myelodysplastic syndrome (MDS) are clonally heterogeneous, with a founding clone and multiple subclones. It is not known whether specific gene mutations typically occur in founding clones or subclones. We screened a panel of 94 candidate genes in a cohort of 157 patients with MDS or secondary acute myeloid leukemia (sAML). This included 150 cases with samples obtained at MDS diagnosis and 15 cases with samples obtained at sAML transformation (8 were also analyzed at the MDS stage). We performed whole-genome sequencing (WGS) to define the clonal architecture in eight sAML genomes and identified the range of variant allele frequencies (VAFs) for founding clone mutations. At least one mutation or cytogenetic abnormality was detected in 83% of the 150 MDS patients and 17 genes were significantly mutated (false discovery rate ≤0.05). Individual genes and patient samples displayed a wide range of VAFs for recurrently mutated genes, indicating that no single gene is exclusively mutated in the founding clone. The VAFs of recurrently mutated genes did not fully recapitulate the clonal architecture defined by WGS, suggesting that comprehensive sequencing may be required to accurately assess the clonal status of recurrently mutated genes in MDS.

Abstract P6-07-10: Luminal A vs. Basal-like Breast Cancer: time dependent changes in the risk of relapse in the absence of treatment

Background: Numerous retrospective analyses of prospective randomized clinical trials of patients treated with adjuvant tamoxifen and chemotherapy have demonstrated that the breast cancer intrinsic subtype Luminal A tumors generally have favorable early initial outcomes, while basal-like tumors are associated with a marked risk of early relapse. To determine the extended natural history of the intrinsic subtypes across two decades of follow up the PAM50 “non-commercial open source bioinformatics” qPCR assay was conducted on node negative tumors accrued through the Cooperative Breast Cancer Tissue Registry (CBCTR) from patients who did not receive systemic therapy.

Methods: Intrinsic subtype calls were obtained from 331 CBCTR cases treated with local interventions only. Tumors were classified into Luminal A (LumA), Luminal B (LumB), HER2-enriched (HER2-E) and Basal-like (BLBC), and correlated relapse-free (RFS). Patient survival and hazard rate were estimated using Kaplan-Meier plots and log-rank test. Multivariable Cox regression analyses were used to determine the significance of the intrinsic subtypes, adjusted with standard clinicopathological variables including tumor size, age at diagnosis, grade, radiation therapy treatment, centralized reviewed estrogen receptor, progesterone receptor and human epidermal growth factor 2 status measured by immunohistochemistry. Patients were diagnosed from 1978 to 1992, with a mean follow-up time of 13 years (range 0.5–31).

Results: Of the 331 tumors tested, 51% of cases were classified as LumA, 18% as LumB, 11% as HER2-E and 20% as BLBC. Although LumA was associated with the best outcome for the first 10-year of follow-up, the final number of RFS events were eventually comparable with those observed for BLBC with prolonged follow up (Table 1). In the multivariable Cox model, only BLBC tumors were associated with worse prognosis than LumA with borderline significance (Hazard ratio: 2.0 (95% CI 0.9–5), p = 0.07). BLBC had the highest hazard rates for the first 5 years (7% at first year to 5% at 5 yr), consistent with previous observations. Interestingly, in the absence of treatment, the slow growing LumA subtype had a gradual increase of hazard for an RFS event from 3% at 5 yrs to 4% at 10 yrs to 7% at 20 yrs. The hazard rates of LumA cross with those of BLBC at 10 years.

Abstract S5-6: Activating HER2 mutations in HER2 gene amplification negative breast cancers

Background: Breast cancer genome sequencing projects, performed by the genome sequencing centers in the U.S., Canada, and the U.K., are elucidating the somatic mutations and other genomic alterations that occur in human breast cancer. These studies recently identified somatic HER2 mutations in breast cancers lacking HER2 gene amplification.

Results: Compilation of data from seven sequencing studies documented 22 patients with somatic HER2 mutations. These mutations clustered in three regions. The first cluster was at amino acid (aa) 309–310 (exon 8), located in the extracellular domain. These aa residues form part of the HER2 dimerization interface. The second cluster was at aa 755–781, located in the kinase domain (exons 19–20). This was the most common location for HER2 mutations, with 17 out of 22 patients having somatic mutations here. The third region was at aa 835–896, also in the kinase domain (exons 21–22). Using multiple experimental approaches (cell line experiments, in vitro kinase assays, protein structure modeling, and xenograft experiments), we tested seven of these HER2 mutations and showed that 4 of them are activating mutations that are sensitive to lapatinib and trastuzumab. Another 2 mutations were found to be lapatinib resistant and we determined their sensitivity to neratinib, canertinib, and gefitinib.

Conclusions: These findings biologically validate somatic HER2 mutations as good targets for breast cancer treatment, but the appropriate choice of targeted drug is dependent on the precise mutation present. This study is among the first to functionally characterize mutations identified by breast cancer genome sequencing. A prospective, multi-institutional clinical trial has been launched to screen for HER2 mutation positive patients and determine the clinical outcome of treatment with HER2 targeted drugs.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr S5-6.

MS1-3: Tumor Heterogeneity and Metastasis

Massively parallel sequencing using Next Gen sequencing approaches have opened a new window into our understanding of the molecular architecture of breast cancer. A significant advantage of these technologies are that they are digital in nature because the measurement technology begins with single DNA molecules attached to a substrate. As a result, not only do these technologies provide an efficient means to identify somatic mutations, information is also provided on the frequency with which any given mutation is observed within the population of DNA molecules in the sample under analysis. The first and most striking feature of Next Gen analysis of breast cancer is the large numbers of somatic mutations that have been identified. Genome wide, thousands of mutations can be present in a single tumor. While this finding generates immense complexity from the perspective of defining biological drivers versus passengers, it does open up a new opportunity to study variations in mutation frequency. In a perfectly monoclonal tumor with a diploid genome and no contaminating normal cell DNA the mutation frequencies generated by digital sequencing will be 50% for a heterozygous mutation or 100% for homozygous mutations. Very few breast cancers subjected to whole genome sequencing exhibit this pattern, rather mutations occur with a wide variation of frequencies from the detection limit, around 5%, through to 100%. Furthermore mutation frequency clustering often occurs, a phenomenon best explained by the presence of a repertoire of mutations present in a founder clone that are present in all tumors, combined with additional less common mutations that represent a subdominant or minority population of cells that have arisen through additional clonal outgrowth. In a multiclonal model one of the most critical questions is “which clone determines the prognosis?”. One way to begin to answer this question is to sequence tumors before and after therapy and to compare primary tumors versus metastases. In our initial experience of a patient with a basal-like breast cancer in which a whole cancer genome was generated from her primary, her subsequent brain metastasis and a mouse xenograft generated from the breast primary, there was clear evidence of a shift in mutation frequency primary to metastasis, suggesting the brain metastasis arose from a minor sub-clone. The mutational profile of the xenograft more closely resembled the metastasis rather than the primary, suggesting the grafting process captured the metastatic clone (1).

In this invited lecture we will present an extension of our sequencing experiences with further human progenitor-mouse xenograft comparisons, comparisons between human primaries and paired metastases and also examples of ER+ breast cancer genomes obtained before and after neoadjuvant endocrine therapy. In all these experiments multiclonality appears to be the rule rather than the exception. The clinical and biological implications of these findings will be discussed.

1. Ding L, Ellis MJ, Li S, Larson DE, Chen K, Wallis JW, et al. Genome remodelling in a basal-like breast cancer metastasis and xenograft. Nature. 2010;464(7291):999–1005. PMCID: 2872544.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr MS1-3.

SR2-1: The Genomic Mutation Landscape of Breast Cancer: A TCGA Report

An important goal, that of characterizing the breadth and complexity of mutations in breast cancer, is being approached by The Cancer Genome Atlas in its next-generation sequencing and analysis of the exome and whole genome content of breast cancer samples. At present, we have produced, analyzed, and validated mutations by exome capture of matched tumor and normal genomic DNA across all breast cancer subtypes, using over 500 samples as our primary discovery set. The resulting information has been further analyzed by integration with other data types being generated in the project, including RNA-seq, methylation and SNP array data. We have further initiated a study using whole genome sequencing of 21 basal subtype cases. My presentation will provide an overview of the methods of data generation, analysis and integration. I will further provide information about our discoveries to-date and future plans.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr SR2-1.

Abstract ES7-1: Next Generation Sequencing for the Clinician: A Breast Cancer Study

The ability to study genome-wide sequence alterations in cancer genomes has transformed our understanding of the intricacies of this disease. We have applied whole genome sequencing and analysis to tease apart the genomic predictors of aromatase inhibitor (AI) response, by selecting luminal breast cancer cases obtained within a clinical trial of aromatase inhibitor treatment (ACOSOG Z1031). Our study compared the constitutional genome to the cancer genome for patients that exhibit either a response or a resistance phenotype, based on their Ki67 IHC score following 4 month AI treatment and resection. My talk will highlight the process by which these genomes are sequenced and analyzed, and will provide our most recent insights into how the combination of the constitutional and somatic genomes determine whether a patient will respond to AI treatment.

Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr ES7-1.

Undergraduate research. Genomics Education Partnership

The Genomics Education Partnership offers an inclusive model for undergraduate research experiences incorporated into the academic year science curriculum, with students pooling their work to contribute to international data bases.

Undergraduate research. Genomics Education Partnership

The Genomics Education Partnership offers an inclusive model for undergraduate research experiences incorporated into the academic year science curriculum, with students pooling their work to contribute to international data bases.

Ki-67 is a Luminal B marker that identifies a high-risk subgroup in hormone receptor positive and node negative breast cancer

10521

Background: Gene expression profiling studies have revealed prognostically significant intrinsic breast cancer subtypes, designated Luminal A, Luminal B, Basal and Her2. Expression of ER and associated genes characterizes the luminal breast cancers. The Lum B subgroup is associated with poor outcome, but we lack immunohistochemical (IHC) markers to distinguish Lum A and Lum B subgroups. MKI67 is one gene known to be highly expressed in Lum B tumors, encoding the Ki-67 protein, a robust marker of cell proliferation. In this study, we perform IHC analysis of Ki-67 in a large breast cancer tissue microarray. Methods: Our patient cohort consists of 2222 consecutive cases of invasive breast cancer referred to the BC Cancer Agency from 1986 to 1992. Archival paraffin tissue blocks were used to construct a tissue microarray that was then stained for Ki-67 using a commercially available mouse monoclonal antibody. Ki-67 staining was scored quantitatively by automated image analysis and a tumor was positive if the percent positive nuclei was >30%’ Results: Of the 2,222 patients, there are 1,437 Luminal tumors as defined by IHC (ER or PR positive). As Her2 positive status is an established marker of poor prognosis, we excluded these tumors from our analysis. Of the remaining tumors, 9% were Ki-67 positive when using a ki-67 cut off of 30% positive nuclei. In survival analysis of patients ER/PR positive and Her2 negative, we found that Ki-67 identifies a population with poor prognosis (10-yr BCSS 60% vs. 80%). In a multivariate Cox regression we found that Ki-67 is independently prognostic. We repeated Cox regression analysis including only node negative patients and again found that Ki-67 is an independent predictor of poor outcome. Conclusions: Ki-67 has prognostic significance on multivariate survival analysis. Hormone receptor positive and node negative status is typically associated with a favorable outcome for breast cancer. However, Ki-67 is able to identify a small, but clinically significant subgroup with a particularly poor outcome. Defining the Luminal B subtype as (ER or PR) positive and (HER2 or Ki-67) positive, results in a subgroup that contains 18% of hormone receptor positive breast cancers with 10-yr BCSS of 61%.

No significant financial relationships to disclose.

A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms

We describe a map of 1.42 million single nucleotide polymorphisms (SNPs) distributed throughout the human genome, providing an average density on available sequence of one SNP every 1.9 kilobases. These SNPs were primarily discovered by two projects: The SNP Consortium and the analysis of clone overlaps by the International Human Genome Sequencing Consortium. The map integrates all publicly available SNPs with described genes and other genomic features. We estimate that 60,000 SNPs fall within exon (coding and untranslated regions), and 85% of exons are within 5 kb of the nearest SNP. Nucleotide diversity varies greatly across the genome, in a manner broadly consistent with a standard population genetic model of human history. This high-density SNP map provides a public resource for defining haplotype variation across the genome, and should help to identify biomedically important genes for diagnosis and therapy.

Initial sequencing and analysis of the human genome

The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.

A physical map of the human genome

The human genome is by far the largest genome to be sequenced, and its size and complexity present many challenges for sequence assembly. The International Human Genome Sequencing Consortium constructed a map of the whole genome to enable the selection of clones for sequencing and for the accurate assembly of the genome sequence. Here we report the construction of the whole-genome bacterial artificial chromosome (BAC) map and its integration with previous landmark maps and information from mapping efforts focused on specific chromosomal regions. We also describe the integration of sequence data with the map.

Association between DQB1 and cervical cancer in patients with human papillomavirus and family controls

OBJECTIVE

The role of human leukocyte antigen (HLA) DQB1 alleles and human papillomavirus (HPV) as contributing factors to invasive cervical cancer was investigated. To overcome problems of misleading causal inferences common in traditional case-control studies, a family-based test, the transmission/disequilibrium test, was used.

METHODS

Ninety-six patients with pathologically confirmed invasive cervical cancer were ascertained. Human papillomavirus types were determined in 80 patients, of whom 81.25% were HPV-positive, and 18.75% were HPV-negative. Deoxyribonucleic acid was extracted from samples, taken from patients and their parents, and sequenced to determine DQB1 genotypes. Nuclear family data were used to test whether the DQB1 locus is associated with invasive cervical cancer while controlling for high-risk HPV-positive patients. The transmission/disequilibrium test evaluates whether the frequency of transmission of parental marker alleles to their affected offspring deviates from the expected Mendelian frequency of 50%.

RESULTS

The HLA DQB1 locus showed evidence for allelic association with invasive cervical cancer in high-risk HPV-positive patients (P = .006). The transmission/disequilibrium test showed that the DQB1*0303 allele was transmitted to high-risk HPV patients more often than expected by chance, chi2(1) = 8.0, P = .005 (P = .035 when correcting for multiple tests). Tests of association were negative when applied to all 96 patients, irrespective of HPV status. No significant differences were found in the distribution of the DQB1 alleles among HPV-positive patients compared with those who were HPV-negative, indicating that HLA alleles are not associated with susceptibility to HPV infection.

CONCLUSION

These results suggest that the DQB1*0303 allele increases the risk for invasive cervical cancer in women who are HPV-positive.

Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana

The higher plant Arabidopsis thaliana (Arabidopsis) is an important model for identifying plant genes and determining their function. To assist biological investigations and to define chromosome structure, a coordinated effort to sequence the Arabidopsis genome was initiated in late 1996. Here we report one of the first milestones of this project, the sequence of chromosome 4. Analysis of 17.38 megabases of unique sequence, representing about 17% of the genome, reveals 3,744 protein coding genes, 81 transfer RNAs and numerous repeat elements. Heterochromatic regions surrounding the putative centromere, which has not yet been completely sequenced, are characterized by an increased frequency of a variety of repeats, new repeats, reduced recombination, lowered gene density and lowered gene expression. Roughly 60% of the predicted protein-coding genes have been functionally characterized on the basis of their homology to known genes. Many genes encode predicted proteins that are homologous to human and Caenorhabditis elegans proteins.

Capillary electrophoresis platforms for DNA sequence analysis

Commercial availability of multicapillary DNA sequencing instruments can significantly impact the existing paradigm in high-throughput DNA sequencing facilities, shifting the rate-limiting step away from the electrophoresis and detection step. These instruments, although novel and poorly understood, represent a significant capital investment.This review informs the reader about the state-of-the-art instruments, although capillary sequencers are in a state of almost constant flux, with improvements emerging rapidly.

An encyclopedia of mouse genes

The laboratory mouse is the premier model system for studies of mammalian development due to the powerful classical genetic analysis possible (see also the Jackson Laboratory web site, http://www.jax.org/) and the ever-expanding collection of molecular tools. To enhance the utility of the mouse system, we initiated a program to generate a large database of expressed sequence tags (ESTs) that can provide rapid access to genes. Of particular significance was the possibility that cDNA libraries could be prepared from very early stages of development, a situation unrealized in human EST projects. We report here the development of a comprehensive database of ESTs for the mouse. The project, initiated in March 1996, has focused on 5' end sequences from directionally cloned, oligo-dT primed cDNA libraries. As of 23 October 1998, 352,040 sequences had been generated, annotated and deposited in dbEST, where they comprised 93% of the total ESTs available for mouse. EST data are versatile and have been applied to gene identification, comparative sequence analysis, comparative gene mapping and candidate disease gene identification, genome sequence annotation, microarray development and the development of gene-based map resources.

A pneumatic device for rapid loading of DNA sequencing gels

This work describes the design and construction of a device that facilitates the loading of DNA samples onto polyacrylamide gels for detection in the Perkin Elmer/Applied Biosystems (PE/ABI) 373 and 377 DNA sequencing instruments. The device is mounted onto the existing gel cassettes and makes the process of loading high-density gels less cumbersome while the associated time and errors are reduced. The principle of operation includes the simultaneous transfer of the entire batch of samples, in which a spring-loaded air cylinder generates positive pressure and flexible silica capillaries transfer the samples. A retractable capillary array carrier allows the delivery ends of the capillaries to be held up clear of the gel during loader attachment on the gel plates, while enabling their insertion in the gel wells once the device is securely mounted. Gel-loading devices capable of simultaneously transferring 72 samples onto the PE/ABI 373 and 377 are currently being used in our production sequencing groups while a 96-sample transfer prototype undergoes testing.

End sequence determination from large insert clones using energy transfer fluorescent primers

Genome mapping strategies depend heavily on confirmatory data of several types to establish overlaps between contiguous stretches of cloned DNA derived from genomic regions. One type of ancillary data that can contribute to establishing these overlaps is DNA sequence data derived from the ends of large (> 30 kb) inserts in genomic clones. This type of data can be difficult to obtain routinely, because large clones are often unstable and microgram quantities of highly purified DNA are required in each sequencing reaction to obtain sufficient signal for accurate base calling and maximum read length. Recently, we have been experimenting with methods to consistently obtain up to 800 bases of high-quality sequence data from the ends of large insert clones using ThermoSequenase DNA polymerase and Energy Transfer fluorescent primers. Our experimental approach and results, described in this paper, indicate that routinely obtaining high-quality sequence data from the ends of large insert genomic clones is feasible. Such data can contribute to the assessment of common regions between large insert clones, to the establishment of conservation of synteny between closely related species, and to the detection of additional contiguous clones.

Generation and analysis of 280,000 human expressed sequence tags

We report the generation of 319,311 single-pass sequencing reactions (known as expressed sequence tags, or ESTs) obtained from the 5' and 3' ends of 194,031 human cDNA clones. Our goal has been to obtain tag sequences from many different genes and to deposit these in the publicly accessible Data Base for Expressed Sequence Tags. Highly efficient automatic screening of the data allows deposition of the annotated sequences without delay. Sequences have been generated from 26 oligo(dT) primed directionally cloned libraries, of which 18 were normalized. The libraries were constructed using mRNA isolated from 17 different tissues representing three developmental states. Comparisons of a subset of our data with nonredundant human mRNA and protein data bases show that the ESTs represent many known sequences and contain many that are novel. Analysis of protein families using Hidden Markov Models confirms this observation and supports the contention that although normalization reduces significantly the relative abundance of redundant cDNA clones, it does not result in the complete removal of members of gene families.

An infrared fluorescent dATP for labeling DNA

Near-infrared fluorescence provides a nonradioactive method of detection with high sensitivity and low background. An infrared fluorophore has been attached covalently to the nucleotide deoxyadenosine triphosphate (dATP) to provide a reagent for enzymatic labeling of various types of DNA molecules and for facilitating their detection with an automated DNA sequencing and analysis system. DNA sequencing reaction products can be labeled internally by performing limited polymerization utilizing infrared-labeled dATP (IR-dATP) as the sole source of adenine deoxynucleotide prior to a dideoxy-specific termination reaction. PCR products can be labeled fluorescently by the addition of limited quantities of IR-dATP to the amplification reaction. This latter strategy has been utilized for detection of short tandem repeat polymorphisms (STRPs) which are useful for gene mapping, genetic diagnostics, forensic analysis, and paternity testing. Restriction fragments can be labeled also by fill-in reactions of appropriate 5' overhangs. Diminutive amounts of such fluorescently labeled DNA molecules can be visualized rapidly and conveniently using infrared detection technology.